Starting phenix.real_space_refine on Tue Sep 15 05:29:18 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6c66_7347/09_2026/6c66_7347.cif Found real_map, /net/cci-nas-00/data/ceres_data/6c66_7347/09_2026/6c66_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/cci-nas-00/data/ceres_data/6c66_7347/09_2026/6c66_7347.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6c66_7347/09_2026/6c66_7347.map" model { file = "/net/cci-nas-00/data/ceres_data/6c66_7347/09_2026/6c66_7347.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6c66_7347/09_2026/6c66_7347.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/6c66_7347/09_2026/6c66_7347.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6c66_7347/09_2026/6c66_7347.cif" } resolution = 3.66 write_initial_geo_file = False refinement { macro_cycles = 10 } 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. Time to flip 58 residue(s): 0.06s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/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: {'ARG:plan': 1, 'GLN:plan1': 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: {'ARG:plan': 7, 'GLU:plan': 2, 'ASP:plan': 5, 'ASN:plan1': 1} 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: {'RNAv2': 59} Modifications used: {'rna2p_pur': 9, 'rna2p_pyr': 12, 'rna3p_pur': 25, 'rna3p_pyr': 13} Link IDs: {'rna2p': 21, 'rna3p': 37} Chain breaks: 1 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 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: 7.94, per 1000 atoms: 0.22 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 - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.31 Conformation dependent library (CDL) restraints added in 1.5 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: 4.20 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: 8.50 Time building geometry restraints manager: 4.30 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=" C3' DC L 22 " pdb=" C2' DC L 22 " ideal model delta sigma weight residual 1.516 1.548 -0.032 8.00e-03 1.56e+04 1.62e+01 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=" C1' DC L 22 " pdb=" N1 DC L 22 " ideal model delta sigma weight residual 1.468 1.518 -0.050 1.40e-02 5.10e+03 1.29e+01 bond pdb=" C3' DA N 32 " pdb=" O3' DA N 32 " ideal model delta sigma weight residual 1.435 1.388 0.047 1.30e-02 5.92e+03 1.28e+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 ... (remaining 37318 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.79: 49615 2.79 - 5.59: 1580 5.59 - 8.38: 147 8.38 - 11.17: 23 11.17 - 13.96: 9 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=" N3 DT N 19 " pdb=" C4 DT N 19 " pdb=" O4 DT N 19 " ideal model delta sigma weight residual 119.90 123.48 -3.58 6.00e-01 2.78e+00 3.56e+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 ... (remaining 51369 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 31.11: 21187 31.11 - 62.23: 800 62.23 - 93.34: 67 93.34 - 124.45: 0 124.45 - 155.57: 2 Dihedral angle restraints: 22056 sinusoidal: 9695 harmonic: 12361 Sorted by residual: dihedral pdb=" C4' G J 31 " pdb=" C3' G J 31 " pdb=" C2' G J 31 " pdb=" C1' G J 31 " ideal model delta sinusoidal sigma weight residual 36.35 -37.36 73.71 1 3.10e+00 1.04e-01 7.19e+02 dihedral pdb=" C4' A J 44 " pdb=" C3' A J 44 " pdb=" C2' A J 44 " pdb=" C1' A J 44 " ideal model delta sinusoidal sigma weight residual 36.34 -36.36 72.70 1 3.10e+00 1.04e-01 7.02e+02 dihedral pdb=" C4' U J 2 " pdb=" C3' U J 2 " pdb=" C2' U J 2 " pdb=" C1' U J 2 " ideal model delta sinusoidal sigma weight residual 36.35 -36.07 72.41 1 3.10e+00 1.04e-01 6.97e+02 ... (remaining 22053 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.117: 5429 0.117 - 0.235: 330 0.235 - 0.352: 54 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=" C2' C J 7 " pdb=" C3' C J 7 " pdb=" O2' C J 7 " pdb=" C1' C J 7 " both_signs ideal model delta sigma weight residual False -2.79 -2.49 -0.30 2.00e-01 2.50e+01 2.27e+00 chirality pdb=" C2' U J 25 " pdb=" C3' U J 25 " pdb=" O2' U J 25 " pdb=" C1' U J 25 " both_signs ideal model delta sigma weight residual False -2.79 -2.49 -0.30 2.00e-01 2.50e+01 2.26e+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 Time spend for trying shortcut: 0.00 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: 1.130 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.580 Check model and map are aligned: 0.120 Set scattering table: 0.090 Process input model: 37.240 Find NCS groups from input model: 0.730 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.360 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 41.350 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7605 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= 0.393 Angle : 1.139 13.964 51374 Z= 0.663 Chirality : 0.065 0.586 5814 Planarity : 0.007 0.080 6199 Dihedral : 14.891 155.568 14056 Min Nonbonded Distance : 1.812 Molprobity Statistics. All-atom Clashscore : 21.34 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. 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 ARG 0.023 0.001 ARG A 417 TYR 0.040 0.003 TYR K 82 PHE 0.032 0.003 PHE A 379 TRP 0.062 0.004 TRP I 202 HIS 0.012 0.002 HIS G 620 Details of bonding type rmsd/Z covalent geometry : bond 0.00785 / 0.39 (37323) covalent geometry : angle 1.13888 / 0.66 (51374) hydrogen bonds : bond 0.12949 / 8.55 ( 1647) hydrogen bonds : angle 9.29917 / 6.60 ( 4477) *********************** 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 to be fit. rotamer outliers: 53 poor density : 694 time to evaluate : 1.313 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: symmetry clash REVERT: G 28 ARG cc_start: 0.5918 (mpp80) cc_final: 0.4890 (ttp80) REVERT: G 465 GLU cc_start: 0.7023 (OUTLIER) cc_final: 0.6530 (tt0) REVERT: G 510 GLU cc_start: 0.7034 (OUTLIER) cc_final: 0.5588 (mm-30) REVERT: G 717 GLN cc_start: 0.4067 (tt0) cc_final: 0.2728 (mm-40) REVERT: G 852 GLU cc_start: 0.6654 (mt-10) cc_final: 0.6215 (pt0) REVERT: G 870 MET cc_start: 0.5321 (mmt) cc_final: 0.4764 (tpt) REVERT: G 885 MET cc_start: 0.3149 (tpp) cc_final: 0.2917 (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: 0.8022 (m110) REVERT: A 308 GLU cc_start: 0.7869 (tp30) cc_final: 0.7539 (tp30) REVERT: B 48 ARG cc_start: 0.9061 (OUTLIER) cc_final: 0.8834 (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: 0.4488 (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: 0.8152 (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: 0.7451 (m-40) REVERT: D 20 ASP cc_start: 0.7996 (t0) cc_final: 0.7785 (p0) REVERT: D 317 GLU cc_start: 0.8442 (tm-30) cc_final: 0.8193 (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: 0.7175 (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: 0.8083 (mttm) 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: 0.8147 (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: 0.8327 (mt) REVERT: I 205 THR cc_start: 0.5605 (t) cc_final: 0.5320 (t) REVERT: K 78 GLU cc_start: 0.6733 (tm-30) cc_final: 0.6511 (tm-30) REVERT: K 191 ASP cc_start: 0.7093 (m-30) cc_final: 0.6784 (m-30) REVERT: K 222 GLU cc_start: 0.7743 (tm-30) cc_final: 0.7363 (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: 0.5679 (mmp-170) REVERT: O 5 THR cc_start: 0.0422 (t) cc_final: -0.0169 (t) outliers start: 53 outliers final: 26 residues processed: 744 average time/residue: 0.2576 time to fit residues: 297.5935 Evaluate side-chains 365 residues out of total 3474 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 332 time to evaluate : 1.297 ------------------------------------------------------------------------------- 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 432 optimal weight: 7.9990 chunk 197 optimal weight: 0.7980 chunk 388 optimal weight: 4.9990 chunk 215 optimal weight: 2.9990 chunk 20 optimal weight: 9.9990 chunk 132 optimal weight: 3.9990 chunk 261 optimal weight: 1.9990 chunk 248 optimal weight: 0.1980 chunk 207 optimal weight: 0.9980 chunk 401 optimal weight: 10.0000 chunk 424 optimal weight: 20.0000 overall best weight: 1.3984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** G 281 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 290 HIS G 435 HIS G 581 GLN G 664 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 366 GLN ** A 412 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 445 ASN A 532 HIS B 7 HIS B 10 GLN ** B 168 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 187 GLN B 195 HIS B 214 ASN B 236 ASN B 285 HIS C 7 HIS ** C 18 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 49 HIS C 195 HIS C 220 HIS C 272 GLN D 7 HIS ** D 18 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 49 HIS ** D 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 195 HIS ** D 220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 238 ASN D 285 HIS E 7 HIS E 49 HIS E 89 GLN E 134 HIS E 195 HIS ** E 285 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 7 HIS ** F 18 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 49 HIS F 195 HIS F 285 HIS H 7 HIS H 49 HIS H 89 GLN H 134 HIS H 195 HIS H 285 HIS ** H 319 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 8 GLN I 173 HIS ** K 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 175 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 201 ASN ** O 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 48 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3844 r_free = 0.3844 target = 0.128055 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3330 r_free = 0.3330 target = 0.096328 restraints weight = 83306.855| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.098726 restraints weight = 41621.152| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.098767 restraints weight = 25137.261| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.099202 restraints weight = 21970.421| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.099295 restraints weight = 20020.044| |-----------------------------------------------------------------------------| r_work (final): 0.3366 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8130 moved from start: 0.2098 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 37323 Z= 0.199 Angle : 1.001 21.165 51374 Z= 0.473 Chirality : 0.069 1.053 5814 Planarity : 0.007 0.075 6199 Dihedral : 16.202 154.817 6433 Min Nonbonded Distance : 1.996 Molprobity Statistics. All-atom Clashscore : 15.01 Ramachandran Plot: Outliers : 0.19 % Allowed : 6.47 % Favored : 93.34 % Rotamer: Outliers : 2.74 % Allowed : 10.10 % Favored : 87.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.87 % Cis-general : 0.35 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.86 (0.11), residues: 4206 helix: -1.26 (0.11), residues: 1745 sheet: -1.67 (0.19), residues: 573 loop : -2.55 (0.13), residues: 1888 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG I 207 TYR 0.030 0.002 TYR K 82 PHE 0.021 0.002 PHE M 4 TRP 0.031 0.002 TRP O 148 HIS 0.011 0.002 HIS G 695 Details of bonding type rmsd/Z covalent geometry : bond 0.00414 / 0.20 (37323) covalent geometry : angle 1.00105 / 0.47 (51374) hydrogen bonds : bond 0.05141 / 3.47 ( 1647) hydrogen bonds : angle 6.09708 / 4.34 ( 4477) *********************** 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 513 residues out of total 3474 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 419 time to evaluate : 1.282 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: G 198 MET cc_start: 0.6358 (ppp) cc_final: 0.6147 (tmm) REVERT: G 717 GLN cc_start: 0.3900 (tt0) cc_final: 0.2561 (mm-40) REVERT: G 870 MET cc_start: 0.5218 (mmt) cc_final: 0.4792 (tpt) REVERT: G 906 PHE cc_start: 0.5553 (p90) cc_final: 0.3781 (t80) REVERT: A 235 ASN cc_start: 0.8281 (m110) cc_final: 0.7920 (m110) REVERT: B 21 ASP cc_start: 0.8536 (t0) cc_final: 0.8335 (t0) REVERT: B 61 ARG cc_start: 0.5109 (OUTLIER) cc_final: 0.4033 (mmt-90) REVERT: B 161 LYS cc_start: 0.6523 (OUTLIER) cc_final: 0.5852 (mmtt) REVERT: B 172 ARG cc_start: 0.9125 (OUTLIER) cc_final: 0.8884 (ppt170) REVERT: B 212 LYS cc_start: 0.8432 (pttt) cc_final: 0.8101 (pttp) REVERT: C 236 ASN cc_start: 0.8310 (m-40) cc_final: 0.7729 (m-40) REVERT: D 5 ASP cc_start: 0.7705 (m-30) cc_final: 0.7498 (m-30) REVERT: D 173 MET cc_start: 0.8928 (ttt) cc_final: 0.8575 (ttt) REVERT: D 317 GLU cc_start: 0.8042 (tm-30) cc_final: 0.7779 (tm-30) REVERT: E 20 ASP cc_start: 0.8010 (t0) cc_final: 0.7774 (t0) REVERT: E 225 GLN cc_start: 0.8805 (mp10) cc_final: 0.8549 (mp10) REVERT: E 356 TYR cc_start: 0.8709 (m-10) cc_final: 0.8505 (m-10) REVERT: F 148 LYS cc_start: 0.8560 (ptpt) cc_final: 0.8191 (mttm) REVERT: F 187 GLN cc_start: 0.8908 (mt0) cc_final: 0.8707 (mt0) REVERT: F 209 ASP cc_start: 0.8332 (m-30) cc_final: 0.8056 (m-30) REVERT: F 221 MET cc_start: 0.8158 (ptp) cc_final: 0.7914 (ptp) REVERT: F 363 MET cc_start: 0.9049 (mmt) cc_final: 0.8709 (mmp) REVERT: H 97 LYS cc_start: 0.8031 (mmtm) cc_final: 0.7597 (ptpp) REVERT: H 286 ILE cc_start: 0.9014 (OUTLIER) cc_final: 0.8750 (mp) REVERT: I 23 ASN cc_start: 0.8295 (t0) cc_final: 0.7998 (t0) REVERT: I 88 MET cc_start: 0.8741 (mtm) cc_final: 0.8467 (mtp) REVERT: I 196 ILE cc_start: 0.8980 (OUTLIER) cc_final: 0.8312 (mt) REVERT: I 212 GLU cc_start: 0.8460 (OUTLIER) cc_final: 0.8246 (pt0) REVERT: K 78 GLU cc_start: 0.6800 (tm-30) cc_final: 0.6417 (tm-30) REVERT: K 187 GLN cc_start: 0.8838 (mp10) cc_final: 0.8303 (mp10) REVERT: K 222 GLU cc_start: 0.7671 (tm-30) cc_final: 0.7236 (tm-30) REVERT: M 172 ARG cc_start: 0.6341 (mmt180) cc_final: 0.6091 (mmp-170) REVERT: O 5 THR cc_start: -0.0701 (t) cc_final: -0.1047 (t) REVERT: O 7 ILE cc_start: 0.6729 (pt) cc_final: 0.6474 (mm) REVERT: O 62 LEU cc_start: 0.3470 (OUTLIER) cc_final: 0.3171 (mt) REVERT: O 63 TYR cc_start: 0.6942 (m-80) cc_final: 0.6432 (m-80) outliers start: 94 outliers final: 57 residues processed: 485 average time/residue: 0.2342 time to fit residues: 183.9204 Evaluate side-chains 360 residues out of total 3474 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 296 time to evaluate : 1.269 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 137 LEU Chi-restraints excluded: chain G residue 145 MET 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 778 LEU Chi-restraints excluded: chain A residue 151 LEU Chi-restraints excluded: chain A residue 169 HIS Chi-restraints excluded: chain A residue 280 VAL Chi-restraints excluded: chain A residue 304 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 43 TRP 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 160 LEU Chi-restraints excluded: chain B residue 161 LYS Chi-restraints excluded: chain B residue 172 ARG Chi-restraints excluded: chain B residue 239 LEU Chi-restraints excluded: chain B residue 242 LEU Chi-restraints excluded: chain B residue 302 THR Chi-restraints excluded: chain C residue 200 GLU Chi-restraints excluded: chain C residue 239 LEU 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 H residue 198 THR Chi-restraints excluded: chain H residue 286 ILE Chi-restraints excluded: chain I residue 5 TYR Chi-restraints excluded: chain I residue 8 GLN Chi-restraints excluded: chain I residue 196 ILE Chi-restraints excluded: chain I residue 212 GLU Chi-restraints excluded: chain K residue 15 LYS Chi-restraints excluded: chain K residue 143 LEU 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 Chi-restraints excluded: chain M residue 103 THR Chi-restraints excluded: chain M residue 144 VAL Chi-restraints excluded: chain O residue 62 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 434 random chunks: chunk 205 optimal weight: 3.9990 chunk 178 optimal weight: 10.0000 chunk 353 optimal weight: 4.9990 chunk 112 optimal weight: 5.9990 chunk 352 optimal weight: 0.8980 chunk 8 optimal weight: 9.9990 chunk 21 optimal weight: 6.9990 chunk 342 optimal weight: 10.0000 chunk 114 optimal weight: 7.9990 chunk 246 optimal weight: 9.9990 chunk 433 optimal weight: 10.0000 overall best weight: 4.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** G 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 149 HIS G 160 GLN G 184 HIS ** G 281 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 695 HIS A 95 GLN ** A 174 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 349 ASN ** A 412 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 505 ASN ** B 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 168 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 18 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 272 GLN ** D 18 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 89 GLN D 187 GLN ** D 220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 272 GLN ** E 18 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 222 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 285 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 18 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 89 GLN ** F 273 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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** M 239 GLN O 25 ASN ** O 27 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3773 r_free = 0.3773 target = 0.123164 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3242 r_free = 0.3242 target = 0.091239 restraints weight = 83603.259| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3278 r_free = 0.3278 target = 0.093126 restraints weight = 43754.949| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3281 r_free = 0.3281 target = 0.093232 restraints weight = 27358.649| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3290 r_free = 0.3290 target = 0.093704 restraints weight = 24150.580| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.093721 restraints weight = 20837.696| |-----------------------------------------------------------------------------| r_work (final): 0.3267 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8251 moved from start: 0.2593 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.120 37323 Z= 0.275 Angle : 0.899 13.287 51374 Z= 0.442 Chirality : 0.062 1.002 5814 Planarity : 0.006 0.110 6199 Dihedral : 16.099 154.487 6396 Min Nonbonded Distance : 1.927 Molprobity Statistics. All-atom Clashscore : 14.37 Ramachandran Plot: Outliers : 0.17 % Allowed : 6.51 % Favored : 93.32 % Rotamer: Outliers : 3.27 % Allowed : 13.13 % Favored : 83.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.87 % Cis-general : 0.35 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.16 (0.12), residues: 4206 helix: -0.60 (0.12), residues: 1760 sheet: -1.35 (0.19), residues: 567 loop : -2.24 (0.13), residues: 1879 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG E 233 TYR 0.028 0.002 TYR K 82 PHE 0.022 0.002 PHE G 223 TRP 0.037 0.003 TRP F 43 HIS 0.012 0.002 HIS G 695 Details of bonding type rmsd/Z covalent geometry : bond 0.00625 / 0.28 (37323) covalent geometry : angle 0.89947 / 0.44 (51374) hydrogen bonds : bond 0.05013 / 3.37 ( 1647) hydrogen bonds : angle 5.68741 / 4.04 ( 4477) *********************** 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 427 residues out of total 3474 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 112 poor density : 315 time to evaluate : 1.544 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 717 GLN cc_start: 0.4162 (tt0) cc_final: 0.2783 (mm-40) REVERT: G 744 TYR cc_start: 0.6323 (t80) cc_final: 0.6019 (t80) REVERT: G 785 MET cc_start: 0.7738 (ptm) cc_final: 0.7173 (ptp) REVERT: G 870 MET cc_start: 0.5180 (mmt) cc_final: 0.4626 (tpt) REVERT: G 906 PHE cc_start: 0.5591 (p90) cc_final: 0.3801 (t80) REVERT: G 937 ASP cc_start: 0.4946 (t70) cc_final: 0.3824 (p0) REVERT: A 235 ASN cc_start: 0.8476 (m110) cc_final: 0.8084 (m110) REVERT: A 443 GLU cc_start: 0.8208 (tp30) cc_final: 0.7996 (tt0) REVERT: B 61 ARG cc_start: 0.5119 (OUTLIER) cc_final: 0.3797 (mmp-170) REVERT: B 172 ARG cc_start: 0.9227 (OUTLIER) cc_final: 0.8960 (ppt170) REVERT: B 212 LYS cc_start: 0.8473 (pttt) cc_final: 0.8113 (pttp) REVERT: D 173 MET cc_start: 0.9192 (ttt) cc_final: 0.8117 (ttt) REVERT: D 317 GLU cc_start: 0.8124 (tm-30) cc_final: 0.7773 (tm-30) REVERT: E 20 ASP cc_start: 0.8082 (t0) cc_final: 0.7879 (t0) REVERT: E 225 GLN cc_start: 0.8985 (mp10) cc_final: 0.8704 (mp10) REVERT: F 148 LYS cc_start: 0.8696 (ptpt) cc_final: 0.8215 (mttt) REVERT: F 187 GLN cc_start: 0.9016 (mt0) cc_final: 0.8771 (mt0) REVERT: H 97 LYS cc_start: 0.7962 (mmtm) cc_final: 0.7599 (ptpp) REVERT: H 286 ILE cc_start: 0.9108 (OUTLIER) cc_final: 0.8812 (mp) REVERT: I 23 ASN cc_start: 0.8334 (t0) cc_final: 0.8006 (t0) REVERT: I 88 MET cc_start: 0.8827 (mtm) cc_final: 0.8595 (mtp) REVERT: I 196 ILE cc_start: 0.9106 (OUTLIER) cc_final: 0.8493 (mt) REVERT: I 207 ARG cc_start: 0.6923 (ppt170) cc_final: 0.6462 (pmt-80) REVERT: K 78 GLU cc_start: 0.6982 (tm-30) cc_final: 0.6553 (tm-30) REVERT: K 186 ASP cc_start: 0.7907 (m-30) cc_final: 0.7626 (m-30) REVERT: K 187 GLN cc_start: 0.8849 (mp10) cc_final: 0.8314 (mp10) REVERT: M 172 ARG cc_start: 0.6586 (mmt180) cc_final: 0.6127 (mmp-170) REVERT: O 62 LEU cc_start: 0.3711 (mt) cc_final: 0.3467 (mt) REVERT: O 63 TYR cc_start: 0.6789 (m-80) cc_final: 0.6104 (m-80) REVERT: O 86 MET cc_start: 0.2775 (mmt) cc_final: 0.2472 (mmm) outliers start: 112 outliers final: 69 residues processed: 399 average time/residue: 0.2198 time to fit residues: 146.8054 Evaluate side-chains 340 residues out of total 3474 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 267 time to evaluate : 1.406 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 137 LEU Chi-restraints excluded: chain G residue 145 MET 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 434 LYS 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 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 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 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 172 ARG Chi-restraints excluded: chain B residue 242 LEU Chi-restraints excluded: chain B residue 340 VAL Chi-restraints excluded: chain C residue 94 VAL Chi-restraints excluded: chain C residue 157 THR Chi-restraints excluded: chain C residue 200 GLU Chi-restraints excluded: chain C residue 230 THR Chi-restraints excluded: chain C residue 275 THR Chi-restraints excluded: chain D residue 113 THR Chi-restraints excluded: chain D residue 186 VAL Chi-restraints excluded: chain D residue 280 LEU Chi-restraints excluded: chain D residue 328 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 124 ILE Chi-restraints excluded: chain E residue 240 ASP 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 186 VAL 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 I residue 196 ILE Chi-restraints excluded: chain K residue 15 LYS Chi-restraints excluded: chain K residue 143 LEU 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 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 75 THR 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 Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 434 random chunks: chunk 141 optimal weight: 10.0000 chunk 147 optimal weight: 5.9990 chunk 306 optimal weight: 0.8980 chunk 419 optimal weight: 3.9990 chunk 254 optimal weight: 7.9990 chunk 129 optimal weight: 0.9980 chunk 178 optimal weight: 6.9990 chunk 334 optimal weight: 1.9990 chunk 258 optimal weight: 0.0570 chunk 94 optimal weight: 0.9990 chunk 173 optimal weight: 3.9990 overall best weight: 0.9902 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** G 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 154 HIS ** G 281 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 174 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 412 ASN A 505 ASN ** B 168 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 236 ASN ** C 18 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 236 ASN ** E 285 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 18 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 222 ASN ** 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 175 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 27 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3812 r_free = 0.3812 target = 0.125761 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3324 r_free = 0.3324 target = 0.095261 restraints weight = 82860.835| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3313 r_free = 0.3313 target = 0.094942 restraints weight = 50350.171| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.096194 restraints weight = 32693.518| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3347 r_free = 0.3347 target = 0.096922 restraints weight = 24449.377| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.097057 restraints weight = 22201.551| |-----------------------------------------------------------------------------| r_work (final): 0.3336 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8154 moved from start: 0.2857 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.098 37323 Z= 0.157 Angle : 0.794 12.957 51374 Z= 0.387 Chirality : 0.055 0.924 5814 Planarity : 0.005 0.063 6199 Dihedral : 15.929 152.382 6385 Min Nonbonded Distance : 2.024 Molprobity Statistics. All-atom Clashscore : 12.94 Ramachandran Plot: Outliers : 0.14 % Allowed : 5.97 % Favored : 93.89 % Rotamer: Outliers : 3.18 % Allowed : 15.00 % Favored : 81.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.87 % Cis-general : 0.35 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.75 (0.12), residues: 4206 helix: -0.24 (0.12), residues: 1775 sheet: -1.15 (0.20), residues: 563 loop : -2.05 (0.14), residues: 1868 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG F 233 TYR 0.022 0.001 TYR K 82 PHE 0.018 0.001 PHE G 244 TRP 0.032 0.002 TRP E 43 HIS 0.008 0.001 HIS B 220 Details of bonding type rmsd/Z covalent geometry : bond 0.00337 / 0.16 (37323) covalent geometry : angle 0.79420 / 0.39 (51374) hydrogen bonds : bond 0.04421 / 2.96 ( 1647) hydrogen bonds : angle 5.32688 / 3.79 ( 4477) *********************** 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 434 residues out of total 3474 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 109 poor density : 325 time to evaluate : 1.324 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 717 GLN cc_start: 0.4263 (tt0) cc_final: 0.2775 (mm-40) REVERT: G 744 TYR cc_start: 0.6431 (t80) cc_final: 0.5926 (t80) REVERT: G 870 MET cc_start: 0.4992 (mmt) cc_final: 0.4494 (mmt) REVERT: G 906 PHE cc_start: 0.5110 (p90) cc_final: 0.3742 (t80) REVERT: G 937 ASP cc_start: 0.5326 (t70) cc_final: 0.4115 (p0) REVERT: A 235 ASN cc_start: 0.8278 (m110) cc_final: 0.7889 (m110) REVERT: B 61 ARG cc_start: 0.5053 (OUTLIER) cc_final: 0.3620 (mmp-170) REVERT: B 172 ARG cc_start: 0.9116 (OUTLIER) cc_final: 0.7663 (ppt170) REVERT: B 212 LYS cc_start: 0.8468 (pttt) cc_final: 0.8120 (pttp) REVERT: D 5 ASP cc_start: 0.7623 (m-30) cc_final: 0.7311 (m-30) REVERT: D 173 MET cc_start: 0.9064 (ttt) cc_final: 0.7899 (ttt) REVERT: D 225 GLN cc_start: 0.9153 (mp10) cc_final: 0.8292 (mt0) REVERT: D 317 GLU cc_start: 0.7961 (tm-30) cc_final: 0.7359 (tm-30) REVERT: E 20 ASP cc_start: 0.8058 (t0) cc_final: 0.7819 (t70) REVERT: E 202 ASP cc_start: 0.8521 (t70) cc_final: 0.8223 (t70) REVERT: E 225 GLN cc_start: 0.8893 (mp10) cc_final: 0.8546 (mp10) REVERT: F 20 ASP cc_start: 0.8489 (t0) cc_final: 0.8270 (t0) REVERT: F 43 TRP cc_start: 0.8932 (OUTLIER) cc_final: 0.8380 (t-100) REVERT: F 148 LYS cc_start: 0.8651 (ptpt) cc_final: 0.8278 (mttm) REVERT: F 187 GLN cc_start: 0.9000 (mt0) cc_final: 0.8797 (mt0) REVERT: H 97 LYS cc_start: 0.7989 (mmtm) cc_final: 0.7618 (ptpp) REVERT: I 23 ASN cc_start: 0.8274 (t0) cc_final: 0.7977 (t0) REVERT: I 88 MET cc_start: 0.8748 (mtm) cc_final: 0.8436 (mtp) REVERT: I 196 ILE cc_start: 0.9071 (OUTLIER) cc_final: 0.8464 (mt) REVERT: K 78 GLU cc_start: 0.6817 (tm-30) cc_final: 0.6570 (tm-30) REVERT: K 82 TYR cc_start: 0.5706 (p90) cc_final: 0.5104 (p90) REVERT: K 186 ASP cc_start: 0.7839 (m-30) cc_final: 0.7590 (m-30) REVERT: K 187 GLN cc_start: 0.8790 (mp10) cc_final: 0.8247 (mp10) REVERT: M 172 ARG cc_start: 0.6609 (mmt180) cc_final: 0.6099 (mmp-170) REVERT: O 63 TYR cc_start: 0.6419 (m-80) cc_final: 0.5840 (m-80) REVERT: O 86 MET cc_start: 0.2351 (mmt) cc_final: 0.1828 (mmm) outliers start: 109 outliers final: 65 residues processed: 406 average time/residue: 0.2109 time to fit residues: 144.3442 Evaluate side-chains 352 residues out of total 3474 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 283 time to evaluate : 1.547 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 21 TRP 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 710 LEU Chi-restraints excluded: chain G residue 778 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 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 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 121 VAL 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 C residue 94 VAL Chi-restraints excluded: chain C residue 200 GLU Chi-restraints excluded: chain C residue 332 ASP Chi-restraints excluded: chain D residue 43 TRP Chi-restraints excluded: chain D residue 221 MET Chi-restraints excluded: chain D residue 328 VAL Chi-restraints excluded: chain E residue 43 TRP 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 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 186 VAL Chi-restraints excluded: chain F residue 239 LEU 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 340 VAL Chi-restraints excluded: chain I residue 139 LEU Chi-restraints excluded: chain I residue 196 ILE 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 205 THR Chi-restraints excluded: chain K residue 208 HIS 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 75 THR Chi-restraints excluded: chain M residue 86 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 Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 434 random chunks: chunk 411 optimal weight: 40.0000 chunk 374 optimal weight: 3.9990 chunk 295 optimal weight: 4.9990 chunk 308 optimal weight: 0.9980 chunk 92 optimal weight: 3.9990 chunk 422 optimal weight: 9.9990 chunk 369 optimal weight: 1.9990 chunk 228 optimal weight: 4.9990 chunk 70 optimal weight: 10.0000 chunk 87 optimal weight: 0.8980 chunk 22 optimal weight: 10.0000 overall best weight: 2.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** G 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 281 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 454 HIS A 87 ASN ** A 174 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 505 ASN B 168 ASN B 236 ASN ** C 18 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 18 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 134 HIS ** D 220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 272 GLN ** E 285 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 18 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 222 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 16 ASN ** H 319 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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** M 239 GLN O 27 HIS ** O 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 150 HIS Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3796 r_free = 0.3796 target = 0.124695 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3262 r_free = 0.3262 target = 0.091785 restraints weight = 83167.786| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 63)----------------| | r_work = 0.3300 r_free = 0.3300 target = 0.093842 restraints weight = 41600.390| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 55)----------------| | r_work = 0.3323 r_free = 0.3323 target = 0.095116 restraints weight = 26766.578| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 68)----------------| | r_work = 0.3336 r_free = 0.3336 target = 0.095882 restraints weight = 20616.694| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3342 r_free = 0.3342 target = 0.096252 restraints weight = 17781.178| |-----------------------------------------------------------------------------| r_work (final): 0.3325 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8184 moved from start: 0.3102 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.074 37323 Z= 0.178 Angle : 0.783 13.180 51374 Z= 0.382 Chirality : 0.054 0.904 5814 Planarity : 0.005 0.074 6199 Dihedral : 15.876 152.719 6379 Min Nonbonded Distance : 2.000 Molprobity Statistics. All-atom Clashscore : 12.39 Ramachandran Plot: Outliers : 0.14 % Allowed : 6.23 % Favored : 93.63 % Rotamer: Outliers : 4.03 % Allowed : 15.41 % Favored : 80.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.87 % Cis-general : 0.35 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.55 (0.13), residues: 4206 helix: -0.11 (0.12), residues: 1793 sheet: -1.00 (0.20), residues: 557 loop : -1.94 (0.14), residues: 1856 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG E 233 TYR 0.022 0.002 TYR K 82 PHE 0.016 0.001 PHE M 4 TRP 0.038 0.002 TRP C 43 HIS 0.014 0.001 HIS O 150 Details of bonding type rmsd/Z covalent geometry : bond 0.00397 / 0.18 (37323) covalent geometry : angle 0.78341 / 0.38 (51374) hydrogen bonds : bond 0.04328 / 2.90 ( 1647) hydrogen bonds : angle 5.12939 / 3.64 ( 4477) *********************** 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 442 residues out of total 3474 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 138 poor density : 304 time to evaluate : 1.344 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 497 TYR cc_start: 0.7768 (t80) cc_final: 0.7505 (t80) REVERT: G 717 GLN cc_start: 0.3810 (tt0) cc_final: 0.2449 (mm-40) REVERT: G 744 TYR cc_start: 0.6383 (t80) cc_final: 0.6127 (t80) REVERT: G 782 MET cc_start: 0.7554 (mtt) cc_final: 0.7280 (mmm) REVERT: G 870 MET cc_start: 0.4831 (mmt) cc_final: 0.4260 (mmt) REVERT: G 906 PHE cc_start: 0.5201 (p90) cc_final: 0.3772 (t80) REVERT: G 937 ASP cc_start: 0.4950 (t70) cc_final: 0.3867 (p0) REVERT: A 235 ASN cc_start: 0.8340 (m110) cc_final: 0.7981 (m110) REVERT: B 61 ARG cc_start: 0.4958 (OUTLIER) cc_final: 0.3407 (mmp-170) REVERT: B 172 ARG cc_start: 0.9076 (OUTLIER) cc_final: 0.7655 (ppt170) REVERT: B 212 LYS cc_start: 0.8418 (pttt) cc_final: 0.8061 (pttp) REVERT: B 250 GLN cc_start: 0.8115 (pp30) cc_final: 0.7617 (pp30) REVERT: B 317 GLU cc_start: 0.7007 (tm-30) cc_final: 0.6787 (tm-30) REVERT: C 5 ASP cc_start: 0.7768 (m-30) cc_final: 0.7404 (t0) REVERT: D 5 ASP cc_start: 0.7632 (m-30) cc_final: 0.7307 (m-30) REVERT: D 173 MET cc_start: 0.9124 (ttt) cc_final: 0.7939 (ttt) REVERT: D 225 GLN cc_start: 0.9184 (mp10) cc_final: 0.8383 (mt0) REVERT: D 317 GLU cc_start: 0.7989 (tm-30) cc_final: 0.7379 (tm-30) REVERT: E 20 ASP cc_start: 0.8034 (t0) cc_final: 0.7756 (t70) REVERT: E 109 GLU cc_start: 0.6142 (OUTLIER) cc_final: 0.5932 (pt0) REVERT: E 173 MET cc_start: 0.8054 (OUTLIER) cc_final: 0.7766 (mmm) REVERT: F 20 ASP cc_start: 0.8486 (t0) cc_final: 0.8244 (t0) REVERT: F 43 TRP cc_start: 0.9048 (OUTLIER) cc_final: 0.8458 (t-100) REVERT: F 148 LYS cc_start: 0.8614 (ptpt) cc_final: 0.8262 (mttm) REVERT: H 97 LYS cc_start: 0.7920 (mmtm) cc_final: 0.7614 (ptpp) REVERT: H 286 ILE cc_start: 0.8980 (OUTLIER) cc_final: 0.8715 (mp) REVERT: I 16 ARG cc_start: 0.8129 (OUTLIER) cc_final: 0.7889 (ttt180) REVERT: I 23 ASN cc_start: 0.8269 (t0) cc_final: 0.7981 (t0) REVERT: I 88 MET cc_start: 0.8770 (mtm) cc_final: 0.8488 (mtp) REVERT: I 196 ILE cc_start: 0.9125 (OUTLIER) cc_final: 0.8547 (mt) REVERT: K 78 GLU cc_start: 0.7229 (tm-30) cc_final: 0.6832 (tm-30) REVERT: K 82 TYR cc_start: 0.5639 (p90) cc_final: 0.5130 (p90) REVERT: K 186 ASP cc_start: 0.7904 (m-30) cc_final: 0.7647 (m-30) REVERT: K 187 GLN cc_start: 0.8831 (mp10) cc_final: 0.8259 (mp10) REVERT: M 7 ARG cc_start: 0.8881 (ttt-90) cc_final: 0.8149 (ttt90) REVERT: M 238 TYR cc_start: 0.8657 (t80) cc_final: 0.8367 (t80) REVERT: O 7 ILE cc_start: 0.5925 (pt) cc_final: 0.5703 (mm) REVERT: O 63 TYR cc_start: 0.6574 (m-80) cc_final: 0.6248 (m-80) REVERT: O 86 MET cc_start: 0.2756 (mmt) cc_final: 0.2413 (mmm) outliers start: 138 outliers final: 90 residues processed: 409 average time/residue: 0.2197 time to fit residues: 150.6774 Evaluate side-chains 378 residues out of total 3474 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 280 time to evaluate : 1.257 ------------------------------------------------------------------------------- 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 141 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 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 498 LEU 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 151 LEU Chi-restraints excluded: chain A residue 185 LEU 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 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 43 TRP 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 121 VAL Chi-restraints excluded: chain B residue 130 ILE 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 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 94 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 332 ASP 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 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 109 GLU Chi-restraints excluded: chain E residue 121 VAL Chi-restraints excluded: chain E residue 173 MET Chi-restraints excluded: chain E residue 193 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 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 305 TYR Chi-restraints excluded: chain F residue 316 GLN Chi-restraints excluded: chain H residue 43 TRP Chi-restraints excluded: chain H residue 65 ILE 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 340 VAL Chi-restraints excluded: chain I residue 16 ARG Chi-restraints excluded: chain I residue 139 LEU Chi-restraints excluded: chain I residue 196 ILE Chi-restraints excluded: chain K residue 15 LYS 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 26 THR 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 61 VAL Chi-restraints excluded: chain M residue 71 VAL Chi-restraints excluded: chain M residue 75 THR 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 O residue 199 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 434 random chunks: chunk 216 optimal weight: 5.9990 chunk 213 optimal weight: 2.9990 chunk 329 optimal weight: 5.9990 chunk 310 optimal weight: 5.9990 chunk 355 optimal weight: 2.9990 chunk 309 optimal weight: 10.0000 chunk 118 optimal weight: 10.0000 chunk 404 optimal weight: 10.0000 chunk 296 optimal weight: 20.0000 chunk 319 optimal weight: 0.8980 chunk 128 optimal weight: 5.9990 overall best weight: 3.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** G 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 281 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 174 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 235 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 18 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 236 ASN ** D 18 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 285 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 18 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 222 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 319 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3767 r_free = 0.3767 target = 0.122802 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3241 r_free = 0.3241 target = 0.090949 restraints weight = 83355.196| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3275 r_free = 0.3275 target = 0.093042 restraints weight = 42597.363| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3277 r_free = 0.3277 target = 0.093167 restraints weight = 25626.451| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3284 r_free = 0.3284 target = 0.093414 restraints weight = 24691.962| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3283 r_free = 0.3283 target = 0.093421 restraints weight = 21182.187| |-----------------------------------------------------------------------------| r_work (final): 0.3262 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8254 moved from start: 0.3322 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.089 37323 Z= 0.224 Angle : 0.802 13.215 51374 Z= 0.393 Chirality : 0.054 0.908 5814 Planarity : 0.005 0.063 6199 Dihedral : 15.905 153.647 6375 Min Nonbonded Distance : 1.979 Molprobity Statistics. All-atom Clashscore : 12.42 Ramachandran Plot: Outliers : 0.14 % Allowed : 6.28 % Favored : 93.58 % Rotamer: Outliers : 4.38 % Allowed : 16.14 % Favored : 79.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.87 % Cis-general : 0.35 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.46 (0.13), residues: 4206 helix: -0.07 (0.12), residues: 1789 sheet: -0.87 (0.21), residues: 543 loop : -1.88 (0.14), residues: 1874 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG C 233 TYR 0.025 0.002 TYR K 82 PHE 0.018 0.002 PHE G 244 TRP 0.038 0.002 TRP E 43 HIS 0.009 0.001 HIS I 204 Details of bonding type rmsd/Z covalent geometry : bond 0.00509 / 0.22 (37323) covalent geometry : angle 0.80226 / 0.39 (51374) hydrogen bonds : bond 0.04438 / 2.97 ( 1647) hydrogen bonds : angle 5.11689 / 3.63 ( 4477) *********************** 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 442 residues out of total 3474 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 150 poor density : 292 time to evaluate : 1.239 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 717 GLN cc_start: 0.3928 (tt0) cc_final: 0.2648 (mm-40) REVERT: G 782 MET cc_start: 0.7342 (mtt) cc_final: 0.7088 (mmm) REVERT: G 870 MET cc_start: 0.4948 (mmt) cc_final: 0.4391 (mmt) REVERT: G 906 PHE cc_start: 0.5202 (p90) cc_final: 0.3780 (t80) REVERT: G 937 ASP cc_start: 0.5094 (t70) cc_final: 0.3974 (p0) REVERT: A 235 ASN cc_start: 0.8414 (m110) cc_final: 0.8096 (m110) REVERT: A 331 GLU cc_start: 0.7886 (OUTLIER) cc_final: 0.7659 (mt-10) REVERT: A 334 ILE cc_start: 0.9019 (OUTLIER) cc_final: 0.8665 (tp) REVERT: B 57 ASP cc_start: 0.7228 (t0) cc_final: 0.7007 (t0) REVERT: B 61 ARG cc_start: 0.4977 (OUTLIER) cc_final: 0.3348 (mmp-170) REVERT: B 172 ARG cc_start: 0.9157 (OUTLIER) cc_final: 0.7741 (ppt170) REVERT: B 212 LYS cc_start: 0.8457 (pttt) cc_final: 0.8006 (pttp) REVERT: B 250 GLN cc_start: 0.8212 (pp30) cc_final: 0.7718 (pp30) REVERT: D 5 ASP cc_start: 0.7759 (m-30) cc_final: 0.7453 (m-30) REVERT: D 173 MET cc_start: 0.9128 (ttt) cc_final: 0.7900 (ttt) REVERT: D 317 GLU cc_start: 0.8101 (tm-30) cc_final: 0.7335 (tm-30) REVERT: E 20 ASP cc_start: 0.8056 (t0) cc_final: 0.7778 (t70) REVERT: E 107 ASP cc_start: 0.8127 (OUTLIER) cc_final: 0.7856 (p0) REVERT: F 20 ASP cc_start: 0.8423 (t0) cc_final: 0.8164 (t0) REVERT: F 43 TRP cc_start: 0.9150 (OUTLIER) cc_final: 0.8597 (t-100) REVERT: F 301 GLU cc_start: 0.8320 (OUTLIER) cc_final: 0.8063 (tt0) REVERT: H 97 LYS cc_start: 0.8075 (mmtm) cc_final: 0.7740 (ptpp) REVERT: H 286 ILE cc_start: 0.9057 (OUTLIER) cc_final: 0.8844 (mt) REVERT: I 16 ARG cc_start: 0.8070 (OUTLIER) cc_final: 0.7747 (ttt180) REVERT: I 23 ASN cc_start: 0.8294 (t0) cc_final: 0.7993 (t0) REVERT: I 88 MET cc_start: 0.8808 (mtm) cc_final: 0.8535 (mtp) REVERT: K 78 GLU cc_start: 0.7410 (tm-30) cc_final: 0.6738 (tm-30) REVERT: K 186 ASP cc_start: 0.7914 (m-30) cc_final: 0.7648 (m-30) REVERT: K 187 GLN cc_start: 0.8821 (mp10) cc_final: 0.8279 (mp10) REVERT: M 7 ARG cc_start: 0.8886 (ttt-90) cc_final: 0.8268 (ttt90) REVERT: M 238 TYR cc_start: 0.8696 (t80) cc_final: 0.8257 (t80) REVERT: O 63 TYR cc_start: 0.6698 (m-80) cc_final: 0.6345 (m-80) REVERT: O 86 MET cc_start: 0.2486 (mmt) cc_final: 0.2029 (mmm) outliers start: 150 outliers final: 104 residues processed: 410 average time/residue: 0.2154 time to fit residues: 149.1668 Evaluate side-chains 382 residues out of total 3474 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 113 poor density : 269 time to evaluate : 1.342 ------------------------------------------------------------------------------- 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 141 LEU Chi-restraints excluded: chain G residue 145 MET 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 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 498 LEU 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 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 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 43 TRP 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 121 VAL Chi-restraints excluded: chain B residue 130 ILE 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 199 VAL 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 94 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 267 VAL Chi-restraints excluded: chain D residue 43 TRP Chi-restraints excluded: chain D residue 55 LEU Chi-restraints excluded: chain D residue 121 VAL Chi-restraints excluded: chain D residue 182 VAL 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 107 ASP 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 240 ASP Chi-restraints excluded: chain E residue 328 VAL 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 186 VAL Chi-restraints excluded: chain F residue 239 LEU Chi-restraints excluded: chain F residue 264 LEU Chi-restraints excluded: chain F residue 301 GLU 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 65 ILE Chi-restraints excluded: chain H residue 198 THR Chi-restraints excluded: chain H residue 230 THR Chi-restraints excluded: chain H residue 264 LEU Chi-restraints excluded: chain H residue 267 VAL Chi-restraints excluded: chain H residue 286 ILE Chi-restraints excluded: chain H residue 340 VAL Chi-restraints excluded: chain I residue 16 ARG Chi-restraints excluded: chain K residue 6 ILE Chi-restraints excluded: chain K residue 15 LYS Chi-restraints excluded: chain K residue 163 LEU Chi-restraints excluded: chain K residue 170 ASP 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 6 LEU Chi-restraints excluded: chain M residue 26 THR 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 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 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 199 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 434 random chunks: chunk 252 optimal weight: 9.9990 chunk 369 optimal weight: 7.9990 chunk 111 optimal weight: 6.9990 chunk 55 optimal weight: 40.0000 chunk 122 optimal weight: 6.9990 chunk 335 optimal weight: 10.0000 chunk 177 optimal weight: 6.9990 chunk 375 optimal weight: 8.9990 chunk 212 optimal weight: 8.9990 chunk 163 optimal weight: 2.9990 chunk 400 optimal weight: 6.9990 overall best weight: 6.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** G 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 281 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 167 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 174 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 235 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 7 HIS ** B 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 10 GLN ** C 18 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 18 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 285 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 236 ASN ** E 285 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 18 ASN ** F 222 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 319 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 218 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 9 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 153 ASN ** K 175 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 170 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 208 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3716 r_free = 0.3716 target = 0.119518 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3167 r_free = 0.3167 target = 0.087342 restraints weight = 83517.403| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3204 r_free = 0.3204 target = 0.089007 restraints weight = 44718.698| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3210 r_free = 0.3210 target = 0.089448 restraints weight = 26744.450| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3217 r_free = 0.3217 target = 0.089774 restraints weight = 24738.819| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3220 r_free = 0.3220 target = 0.089893 restraints weight = 21463.055| |-----------------------------------------------------------------------------| r_work (final): 0.3199 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8320 moved from start: 0.3607 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.107 37323 Z= 0.324 Angle : 0.894 14.985 51374 Z= 0.441 Chirality : 0.058 0.974 5814 Planarity : 0.006 0.062 6199 Dihedral : 16.021 157.146 6375 Min Nonbonded Distance : 1.932 Molprobity Statistics. All-atom Clashscore : 14.26 Ramachandran Plot: Outliers : 0.14 % Allowed : 6.68 % Favored : 93.18 % Rotamer: Outliers : 4.96 % Allowed : 16.37 % Favored : 78.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.87 % Cis-general : 0.35 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.62 (0.13), residues: 4206 helix: -0.20 (0.12), residues: 1771 sheet: -0.90 (0.21), residues: 535 loop : -1.96 (0.14), residues: 1900 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG G 249 TYR 0.032 0.003 TYR K 82 PHE 0.030 0.003 PHE C 263 TRP 0.042 0.003 TRP E 43 HIS 0.011 0.002 HIS D 195 Details of bonding type rmsd/Z covalent geometry : bond 0.00743 / 0.32 (37323) covalent geometry : angle 0.89354 / 0.44 (51374) hydrogen bonds : bond 0.04945 / 3.32 ( 1647) hydrogen bonds : angle 5.32219 / 3.78 ( 4477) *********************** 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 440 residues out of total 3474 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 170 poor density : 270 time to evaluate : 1.317 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 528 ARG cc_start: 0.7826 (OUTLIER) cc_final: 0.7334 (mtm-85) REVERT: G 717 GLN cc_start: 0.3869 (tt0) cc_final: 0.2567 (mm-40) REVERT: G 870 MET cc_start: 0.5049 (mmt) cc_final: 0.4475 (mmt) REVERT: G 906 PHE cc_start: 0.5446 (p90) cc_final: 0.3779 (t80) REVERT: G 937 ASP cc_start: 0.5280 (t70) cc_final: 0.4095 (p0) REVERT: A 133 LEU cc_start: 0.8549 (OUTLIER) cc_final: 0.8172 (pp) REVERT: A 138 LEU cc_start: 0.9190 (OUTLIER) cc_final: 0.8939 (tt) REVERT: A 235 ASN cc_start: 0.8521 (m110) cc_final: 0.8245 (m110) REVERT: A 331 GLU cc_start: 0.8138 (OUTLIER) cc_final: 0.7898 (mt-10) REVERT: A 334 ILE cc_start: 0.9184 (OUTLIER) cc_final: 0.8843 (tp) REVERT: B 57 ASP cc_start: 0.7176 (t0) cc_final: 0.6948 (t0) REVERT: B 61 ARG cc_start: 0.5265 (OUTLIER) cc_final: 0.3507 (mmp-170) REVERT: B 78 TRP cc_start: 0.3314 (OUTLIER) cc_final: 0.1682 (m100) REVERT: B 212 LYS cc_start: 0.8527 (pttt) cc_final: 0.8090 (pttp) REVERT: B 250 GLN cc_start: 0.8367 (pp30) cc_final: 0.7894 (pp30) REVERT: B 285 HIS cc_start: 0.8790 (OUTLIER) cc_final: 0.8015 (t-90) REVERT: D 173 MET cc_start: 0.9222 (ttt) cc_final: 0.8053 (ttt) REVERT: E 107 ASP cc_start: 0.8105 (OUTLIER) cc_final: 0.7838 (p0) REVERT: E 173 MET cc_start: 0.8366 (OUTLIER) cc_final: 0.7987 (ttm) REVERT: F 20 ASP cc_start: 0.8511 (t0) cc_final: 0.8273 (t0) REVERT: F 43 TRP cc_start: 0.9291 (OUTLIER) cc_final: 0.8725 (t-100) REVERT: H 19 ARG cc_start: 0.7829 (ptp-170) cc_final: 0.7402 (ptp90) REVERT: H 97 LYS cc_start: 0.8065 (mmtm) cc_final: 0.7721 (ptpp) REVERT: H 286 ILE cc_start: 0.9109 (OUTLIER) cc_final: 0.8833 (mp) REVERT: I 16 ARG cc_start: 0.8234 (OUTLIER) cc_final: 0.7862 (ttt180) REVERT: I 23 ASN cc_start: 0.8336 (t0) cc_final: 0.8034 (t0) REVERT: I 84 VAL cc_start: 0.9353 (OUTLIER) cc_final: 0.9145 (t) REVERT: I 88 MET cc_start: 0.8791 (mtm) cc_final: 0.8588 (mtp) REVERT: I 196 ILE cc_start: 0.9187 (OUTLIER) cc_final: 0.8516 (mt) REVERT: I 216 ASP cc_start: 0.8295 (m-30) cc_final: 0.8023 (m-30) REVERT: K 78 GLU cc_start: 0.7452 (tm-30) cc_final: 0.6805 (tm-30) REVERT: K 187 GLN cc_start: 0.8868 (mp10) cc_final: 0.8323 (mp10) REVERT: M 7 ARG cc_start: 0.8911 (ttt-90) cc_final: 0.8524 (ttt90) REVERT: M 238 TYR cc_start: 0.8850 (t80) cc_final: 0.8281 (t80) REVERT: O 63 TYR cc_start: 0.6694 (m-80) cc_final: 0.6274 (m-80) REVERT: O 86 MET cc_start: 0.2295 (mmt) cc_final: 0.1765 (mmm) outliers start: 170 outliers final: 111 residues processed: 414 average time/residue: 0.2186 time to fit residues: 152.1685 Evaluate side-chains 375 residues out of total 3474 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 126 poor density : 249 time to evaluate : 1.347 ------------------------------------------------------------------------------- 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 141 LEU Chi-restraints excluded: chain G residue 145 MET Chi-restraints excluded: chain G residue 222 ASP Chi-restraints excluded: chain G residue 260 LEU 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 463 LEU Chi-restraints excluded: chain G residue 478 VAL Chi-restraints excluded: chain G residue 487 HIS Chi-restraints excluded: chain G residue 528 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 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 41 GLN 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 65 ILE 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 130 ILE 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 199 VAL 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 285 HIS Chi-restraints excluded: chain B residue 340 VAL Chi-restraints excluded: chain B residue 345 ASP Chi-restraints excluded: chain C residue 41 GLN 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 D residue 43 TRP Chi-restraints excluded: chain D residue 55 LEU Chi-restraints excluded: chain D residue 113 THR 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 267 VAL 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 107 ASP Chi-restraints excluded: chain E residue 109 GLU Chi-restraints excluded: chain E residue 121 VAL Chi-restraints excluded: chain E residue 136 ASP Chi-restraints excluded: chain E residue 173 MET 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 60 VAL 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 186 VAL Chi-restraints excluded: chain F residue 239 LEU Chi-restraints excluded: chain F residue 254 THR 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 198 THR Chi-restraints excluded: chain H residue 230 THR Chi-restraints excluded: chain H residue 264 LEU 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 16 ARG Chi-restraints excluded: chain I residue 84 VAL Chi-restraints excluded: chain I residue 196 ILE Chi-restraints excluded: chain I residue 223 THR Chi-restraints excluded: chain K residue 6 ILE Chi-restraints excluded: chain K residue 15 LYS Chi-restraints excluded: chain K residue 163 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 6 LEU Chi-restraints excluded: chain M residue 26 THR Chi-restraints excluded: chain M residue 29 TYR Chi-restraints excluded: chain M residue 35 LEU 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 129 LEU 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 199 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 434 random chunks: chunk 430 optimal weight: 20.0000 chunk 245 optimal weight: 3.9990 chunk 211 optimal weight: 4.9990 chunk 201 optimal weight: 0.3980 chunk 15 optimal weight: 5.9990 chunk 301 optimal weight: 10.0000 chunk 431 optimal weight: 8.9990 chunk 150 optimal weight: 4.9990 chunk 85 optimal weight: 4.9990 chunk 113 optimal weight: 0.7980 chunk 289 optimal weight: 4.9990 overall best weight: 3.0386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** G 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 281 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 167 HIS ** A 174 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 235 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 18 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 18 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 285 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 236 ASN ** E 285 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 18 ASN ** F 222 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 218 HIS ** K 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 153 ASN ** K 175 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 170 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3752 r_free = 0.3752 target = 0.121855 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3224 r_free = 0.3224 target = 0.090171 restraints weight = 82572.144| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3254 r_free = 0.3254 target = 0.092079 restraints weight = 42186.026| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3257 r_free = 0.3257 target = 0.092174 restraints weight = 25937.687| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3265 r_free = 0.3265 target = 0.092498 restraints weight = 23998.804| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3264 r_free = 0.3264 target = 0.092438 restraints weight = 21211.791| |-----------------------------------------------------------------------------| r_work (final): 0.3242 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8275 moved from start: 0.3738 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.083 37323 Z= 0.200 Angle : 0.808 13.871 51374 Z= 0.394 Chirality : 0.054 0.910 5814 Planarity : 0.005 0.061 6199 Dihedral : 15.919 156.422 6367 Min Nonbonded Distance : 1.988 Molprobity Statistics. All-atom Clashscore : 13.08 Ramachandran Plot: Outliers : 0.14 % Allowed : 6.04 % Favored : 93.82 % Rotamer: Outliers : 4.09 % Allowed : 17.43 % Favored : 78.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.87 % Cis-general : 0.35 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.42 (0.13), residues: 4206 helix: -0.03 (0.12), residues: 1794 sheet: -0.78 (0.21), residues: 537 loop : -1.87 (0.14), residues: 1875 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.001 ARG C 233 TYR 0.025 0.002 TYR K 82 PHE 0.024 0.002 PHE M 59 TRP 0.041 0.002 TRP H 43 HIS 0.011 0.001 HIS O 185 Details of bonding type rmsd/Z covalent geometry : bond 0.00452 / 0.20 (37323) covalent geometry : angle 0.80752 / 0.39 (51374) hydrogen bonds : bond 0.04398 / 2.94 ( 1647) hydrogen bonds : angle 5.06236 / 3.59 ( 4477) *********************** 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 431 residues out of total 3474 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 140 poor density : 291 time to evaluate : 1.363 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 717 GLN cc_start: 0.3909 (tt0) cc_final: 0.2622 (mm-40) REVERT: G 870 MET cc_start: 0.5165 (mmt) cc_final: 0.4546 (mmt) REVERT: G 906 PHE cc_start: 0.5393 (p90) cc_final: 0.3762 (t80) REVERT: G 937 ASP cc_start: 0.5085 (t70) cc_final: 0.3931 (p0) REVERT: A 133 LEU cc_start: 0.8466 (OUTLIER) cc_final: 0.8162 (pp) REVERT: A 138 LEU cc_start: 0.9163 (OUTLIER) cc_final: 0.8925 (tt) REVERT: A 235 ASN cc_start: 0.8389 (m110) cc_final: 0.8113 (m110) REVERT: A 239 PRO cc_start: 0.8939 (Cg_endo) cc_final: 0.8695 (Cg_exo) REVERT: B 57 ASP cc_start: 0.7212 (t0) cc_final: 0.6993 (t0) REVERT: B 61 ARG cc_start: 0.5194 (OUTLIER) cc_final: 0.3427 (mmp-170) REVERT: B 78 TRP cc_start: 0.3238 (OUTLIER) cc_final: 0.1600 (m100) REVERT: B 202 ASP cc_start: 0.8970 (t0) cc_final: 0.8653 (t70) REVERT: B 212 LYS cc_start: 0.8483 (pttt) cc_final: 0.8016 (pttp) REVERT: B 250 GLN cc_start: 0.8291 (pp30) cc_final: 0.7827 (pp30) REVERT: C 200 GLU cc_start: 0.8138 (OUTLIER) cc_final: 0.7893 (pt0) REVERT: C 275 THR cc_start: 0.8916 (OUTLIER) cc_final: 0.8636 (p) REVERT: D 5 ASP cc_start: 0.7963 (m-30) cc_final: 0.7713 (m-30) REVERT: D 173 MET cc_start: 0.9050 (ttt) cc_final: 0.8015 (ttt) REVERT: E 107 ASP cc_start: 0.8137 (OUTLIER) cc_final: 0.7930 (p0) REVERT: E 173 MET cc_start: 0.8527 (OUTLIER) cc_final: 0.8315 (tpp) REVERT: E 182 VAL cc_start: 0.9176 (OUTLIER) cc_final: 0.8920 (t) REVERT: F 20 ASP cc_start: 0.8413 (t0) cc_final: 0.8200 (t0) REVERT: F 43 TRP cc_start: 0.9189 (OUTLIER) cc_final: 0.8470 (t-100) REVERT: H 19 ARG cc_start: 0.7775 (ptp-170) cc_final: 0.7286 (ptp90) REVERT: H 97 LYS cc_start: 0.8022 (mmtm) cc_final: 0.7785 (ptpp) REVERT: H 286 ILE cc_start: 0.9073 (OUTLIER) cc_final: 0.8850 (mt) REVERT: I 16 ARG cc_start: 0.8100 (OUTLIER) cc_final: 0.7793 (ttt180) REVERT: I 23 ASN cc_start: 0.8279 (t0) cc_final: 0.7956 (t0) REVERT: I 88 MET cc_start: 0.8702 (mtm) cc_final: 0.8416 (mtp) REVERT: K 78 GLU cc_start: 0.7388 (tm-30) cc_final: 0.6733 (tm-30) REVERT: K 187 GLN cc_start: 0.8831 (mp10) cc_final: 0.8264 (mp10) REVERT: M 7 ARG cc_start: 0.8807 (ttt-90) cc_final: 0.8259 (ttt90) REVERT: M 203 VAL cc_start: 0.9432 (m) cc_final: 0.9184 (p) REVERT: M 238 TYR cc_start: 0.8798 (t80) cc_final: 0.8338 (t80) REVERT: O 63 TYR cc_start: 0.6712 (m-80) cc_final: 0.6237 (m-80) REVERT: O 77 LEU cc_start: 0.3312 (OUTLIER) cc_final: 0.2731 (mm) REVERT: O 86 MET cc_start: 0.2480 (mmt) cc_final: 0.2138 (mmm) outliers start: 140 outliers final: 98 residues processed: 399 average time/residue: 0.2124 time to fit residues: 144.6531 Evaluate side-chains 383 residues out of total 3474 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 111 poor density : 272 time to evaluate : 1.350 ------------------------------------------------------------------------------- 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 139 THR Chi-restraints excluded: chain G residue 141 LEU Chi-restraints excluded: chain G residue 167 GLU Chi-restraints excluded: chain G residue 222 ASP Chi-restraints excluded: chain G residue 300 LEU 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 464 LEU Chi-restraints excluded: chain G residue 478 VAL Chi-restraints excluded: chain G residue 487 HIS Chi-restraints excluded: chain G residue 663 GLU Chi-restraints excluded: chain G residue 673 MET Chi-restraints excluded: chain G residue 710 LEU 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 150 LYS 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 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 43 TRP Chi-restraints excluded: chain B residue 54 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 179 SER Chi-restraints excluded: chain B residue 188 PHE Chi-restraints excluded: chain B residue 199 VAL 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 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 267 VAL Chi-restraints excluded: chain C residue 275 THR 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 D residue 328 VAL Chi-restraints excluded: chain E residue 43 TRP Chi-restraints excluded: chain E residue 107 ASP Chi-restraints excluded: chain E residue 109 GLU Chi-restraints excluded: chain E residue 121 VAL Chi-restraints excluded: chain E residue 136 ASP Chi-restraints excluded: chain E residue 173 MET 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 60 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 186 VAL Chi-restraints excluded: chain F residue 239 LEU 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 198 THR Chi-restraints excluded: chain H residue 230 THR Chi-restraints excluded: chain H residue 264 LEU Chi-restraints excluded: chain H residue 267 VAL 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 K residue 6 ILE Chi-restraints excluded: chain K residue 15 LYS Chi-restraints excluded: chain K residue 139 LEU Chi-restraints excluded: chain K residue 153 ASN Chi-restraints excluded: chain K residue 205 THR Chi-restraints excluded: chain K residue 208 HIS Chi-restraints excluded: chain M residue 26 THR 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 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 7 ILE Chi-restraints excluded: chain O residue 77 LEU 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 165 optimal weight: 0.0670 chunk 388 optimal weight: 3.9990 chunk 139 optimal weight: 0.3980 chunk 344 optimal weight: 3.9990 chunk 96 optimal weight: 0.8980 chunk 42 optimal weight: 6.9990 chunk 72 optimal weight: 30.0000 chunk 270 optimal weight: 6.9990 chunk 101 optimal weight: 10.0000 chunk 353 optimal weight: 6.9990 chunk 3 optimal weight: 20.0000 overall best weight: 1.8722 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** G 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 281 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 87 ASN ** A 174 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 235 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 18 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 272 GLN ** D 18 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 164 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 285 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 285 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 18 ASN ** F 222 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 319 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 175 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3769 r_free = 0.3769 target = 0.122936 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3261 r_free = 0.3261 target = 0.092005 restraints weight = 82925.344| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3262 r_free = 0.3262 target = 0.092199 restraints weight = 45359.593| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3276 r_free = 0.3276 target = 0.093058 restraints weight = 31850.091| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3285 r_free = 0.3285 target = 0.093499 restraints weight = 25022.599| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3284 r_free = 0.3284 target = 0.093441 restraints weight = 22994.490| |-----------------------------------------------------------------------------| r_work (final): 0.3261 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8253 moved from start: 0.3826 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 37323 Z= 0.166 Angle : 0.787 13.986 51374 Z= 0.382 Chirality : 0.052 0.884 5814 Planarity : 0.005 0.065 6199 Dihedral : 15.870 156.101 6367 Min Nonbonded Distance : 1.997 Molprobity Statistics. All-atom Clashscore : 12.89 Ramachandran Plot: Outliers : 0.12 % Allowed : 6.18 % Favored : 93.70 % Rotamer: Outliers : 3.82 % Allowed : 17.60 % Favored : 78.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.87 % Cis-general : 0.35 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.27 (0.13), residues: 4206 helix: 0.09 (0.12), residues: 1785 sheet: -0.69 (0.22), residues: 530 loop : -1.79 (0.14), residues: 1891 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG C 233 TYR 0.024 0.002 TYR B 234 PHE 0.022 0.002 PHE M 59 TRP 0.041 0.002 TRP H 43 HIS 0.008 0.001 HIS B 220 Details of bonding type rmsd/Z covalent geometry : bond 0.00370 / 0.17 (37323) covalent geometry : angle 0.78664 / 0.38 (51374) hydrogen bonds : bond 0.04218 / 2.83 ( 1647) hydrogen bonds : angle 4.96296 / 3.52 ( 4477) *********************** 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 428 residues out of total 3474 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 131 poor density : 297 time to evaluate : 1.155 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 528 ARG cc_start: 0.7793 (OUTLIER) cc_final: 0.7303 (mtm-85) REVERT: G 717 GLN cc_start: 0.3651 (tt0) cc_final: 0.2215 (mm-40) REVERT: G 744 TYR cc_start: 0.6553 (t80) cc_final: 0.6250 (t80) REVERT: G 870 MET cc_start: 0.5086 (mmt) cc_final: 0.4499 (mmt) REVERT: G 906 PHE cc_start: 0.5137 (p90) cc_final: 0.3753 (t80) REVERT: G 937 ASP cc_start: 0.5165 (t70) cc_final: 0.3986 (p0) REVERT: A 133 LEU cc_start: 0.8325 (OUTLIER) cc_final: 0.8124 (pp) REVERT: A 138 LEU cc_start: 0.9137 (OUTLIER) cc_final: 0.8915 (tt) REVERT: A 189 LEU cc_start: 0.9399 (tt) cc_final: 0.9175 (tt) REVERT: A 235 ASN cc_start: 0.8316 (m110) cc_final: 0.8028 (m110) REVERT: A 239 PRO cc_start: 0.8951 (Cg_endo) cc_final: 0.8728 (Cg_exo) REVERT: A 334 ILE cc_start: 0.9024 (OUTLIER) cc_final: 0.8661 (tp) REVERT: B 61 ARG cc_start: 0.4802 (OUTLIER) cc_final: 0.2950 (mmp-170) REVERT: B 78 TRP cc_start: 0.3178 (OUTLIER) cc_final: 0.1554 (m100) REVERT: B 202 ASP cc_start: 0.8914 (t0) cc_final: 0.8611 (t70) REVERT: B 212 LYS cc_start: 0.8463 (pttt) cc_final: 0.8010 (pttp) REVERT: B 250 GLN cc_start: 0.8261 (pp30) cc_final: 0.7812 (pp30) REVERT: C 275 THR cc_start: 0.8972 (OUTLIER) cc_final: 0.8644 (p) REVERT: D 5 ASP cc_start: 0.7917 (m-30) cc_final: 0.7676 (m-30) REVERT: D 173 MET cc_start: 0.9133 (ttt) cc_final: 0.8108 (ttt) REVERT: E 107 ASP cc_start: 0.8149 (OUTLIER) cc_final: 0.7824 (p0) REVERT: E 109 GLU cc_start: 0.6369 (OUTLIER) cc_final: 0.6068 (pt0) REVERT: E 182 VAL cc_start: 0.9158 (OUTLIER) cc_final: 0.8889 (t) REVERT: F 20 ASP cc_start: 0.8376 (t0) cc_final: 0.8158 (t0) REVERT: F 43 TRP cc_start: 0.9131 (OUTLIER) cc_final: 0.8418 (t-100) REVERT: H 19 ARG cc_start: 0.7758 (ptp-170) cc_final: 0.7281 (ptp90) REVERT: H 97 LYS cc_start: 0.7955 (mmtm) cc_final: 0.7749 (ptpp) REVERT: H 286 ILE cc_start: 0.9006 (OUTLIER) cc_final: 0.8787 (mt) REVERT: I 16 ARG cc_start: 0.8106 (OUTLIER) cc_final: 0.7819 (ttt180) REVERT: I 23 ASN cc_start: 0.8340 (t0) cc_final: 0.8064 (t0) REVERT: I 88 MET cc_start: 0.8685 (mtm) cc_final: 0.8397 (mtp) REVERT: K 78 GLU cc_start: 0.7211 (tm-30) cc_final: 0.6519 (tm-30) REVERT: K 187 GLN cc_start: 0.8828 (mp10) cc_final: 0.8243 (mp10) REVERT: M 6 LEU cc_start: 0.8761 (OUTLIER) cc_final: 0.8516 (mt) REVERT: M 7 ARG cc_start: 0.8794 (ttt-90) cc_final: 0.8300 (ttt90) REVERT: M 203 VAL cc_start: 0.9414 (m) cc_final: 0.9158 (p) REVERT: M 238 TYR cc_start: 0.8795 (t80) cc_final: 0.8045 (t80) REVERT: O 77 LEU cc_start: 0.3293 (OUTLIER) cc_final: 0.2681 (mm) REVERT: O 86 MET cc_start: 0.2332 (mmt) cc_final: 0.1982 (mmm) outliers start: 131 outliers final: 97 residues processed: 398 average time/residue: 0.2042 time to fit residues: 139.1948 Evaluate side-chains 391 residues out of total 3474 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 112 poor density : 279 time to evaluate : 1.261 ------------------------------------------------------------------------------- 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 139 THR Chi-restraints excluded: chain G residue 167 GLU Chi-restraints excluded: chain G residue 222 ASP 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 478 VAL Chi-restraints excluded: chain G residue 487 HIS Chi-restraints excluded: chain G residue 528 ARG Chi-restraints excluded: chain G residue 663 GLU Chi-restraints excluded: chain G residue 673 MET Chi-restraints excluded: chain G residue 683 LEU Chi-restraints excluded: chain G residue 710 LEU Chi-restraints excluded: chain G residue 778 LEU Chi-restraints excluded: chain G residue 807 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 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 399 LEU Chi-restraints excluded: chain A residue 497 MET Chi-restraints excluded: chain A residue 504 PHE Chi-restraints excluded: chain B residue 43 TRP Chi-restraints excluded: chain B residue 61 ARG Chi-restraints excluded: chain B residue 65 ILE 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 179 SER Chi-restraints excluded: chain B residue 199 VAL 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 94 VAL Chi-restraints excluded: chain C residue 165 VAL Chi-restraints excluded: chain C residue 183 ASP 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 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 D residue 194 VAL Chi-restraints excluded: chain D residue 267 VAL Chi-restraints excluded: chain D residue 328 VAL Chi-restraints excluded: chain E residue 11 THR Chi-restraints excluded: chain E residue 43 TRP Chi-restraints excluded: chain E residue 107 ASP Chi-restraints excluded: chain E residue 109 GLU Chi-restraints excluded: chain E residue 121 VAL Chi-restraints excluded: chain E residue 136 ASP 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 60 VAL 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 186 VAL 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 43 TRP 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 286 ILE Chi-restraints excluded: chain H residue 340 VAL Chi-restraints excluded: chain H residue 359 LEU Chi-restraints excluded: chain I residue 16 ARG Chi-restraints excluded: chain I residue 37 LEU Chi-restraints excluded: chain K residue 6 ILE Chi-restraints excluded: chain K residue 15 LYS Chi-restraints excluded: chain K residue 205 THR Chi-restraints excluded: chain K residue 208 HIS Chi-restraints excluded: chain M residue 6 LEU Chi-restraints excluded: chain M residue 26 THR 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 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 7 ILE Chi-restraints excluded: chain O residue 77 LEU 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 131 optimal weight: 4.9990 chunk 76 optimal weight: 20.0000 chunk 263 optimal weight: 2.9990 chunk 340 optimal weight: 6.9990 chunk 258 optimal weight: 4.9990 chunk 182 optimal weight: 1.9990 chunk 54 optimal weight: 0.0470 chunk 261 optimal weight: 7.9990 chunk 308 optimal weight: 10.0000 chunk 89 optimal weight: 8.9990 chunk 209 optimal weight: 0.9980 overall best weight: 2.2084 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** G 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 281 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 174 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 235 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 18 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 18 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 164 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 285 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 285 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 18 ASN ** F 222 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 319 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 9 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 153 ASN ** K 175 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3771 r_free = 0.3771 target = 0.123028 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3249 r_free = 0.3249 target = 0.091478 restraints weight = 83141.427| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3277 r_free = 0.3277 target = 0.092991 restraints weight = 41682.427| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3284 r_free = 0.3284 target = 0.093431 restraints weight = 27376.582| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3292 r_free = 0.3292 target = 0.093783 restraints weight = 23650.925| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3293 r_free = 0.3293 target = 0.093843 restraints weight = 21218.831| |-----------------------------------------------------------------------------| r_work (final): 0.3271 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8250 moved from start: 0.3928 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.068 37323 Z= 0.171 Angle : 0.785 15.595 51374 Z= 0.381 Chirality : 0.052 0.879 5814 Planarity : 0.005 0.066 6199 Dihedral : 15.854 158.087 6363 Min Nonbonded Distance : 1.994 Molprobity Statistics. All-atom Clashscore : 12.80 Ramachandran Plot: Outliers : 0.12 % Allowed : 6.02 % Favored : 93.87 % Rotamer: Outliers : 3.50 % Allowed : 18.21 % Favored : 78.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.87 % Cis-general : 0.35 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.19 (0.13), residues: 4206 helix: 0.14 (0.12), residues: 1789 sheet: -0.57 (0.22), residues: 525 loop : -1.74 (0.14), residues: 1892 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG C 233 TYR 0.026 0.002 TYR B 234 PHE 0.019 0.001 PHE M 73 TRP 0.041 0.002 TRP H 43 HIS 0.008 0.001 HIS B 220 Details of bonding type rmsd/Z covalent geometry : bond 0.00385 / 0.17 (37323) covalent geometry : angle 0.78544 / 0.38 (51374) hydrogen bonds : bond 0.04146 / 2.78 ( 1647) hydrogen bonds : angle 4.90579 / 3.47 ( 4477) ********************** 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 414 residues out of total 3474 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 120 poor density : 294 time to evaluate : 1.386 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 333 LEU cc_start: 0.7034 (pt) cc_final: 0.6697 (pp) REVERT: G 528 ARG cc_start: 0.7771 (OUTLIER) cc_final: 0.7327 (mtm-85) REVERT: G 717 GLN cc_start: 0.3617 (tt0) cc_final: 0.2371 (mm-40) REVERT: G 744 TYR cc_start: 0.6541 (t80) cc_final: 0.6245 (t80) REVERT: G 870 MET cc_start: 0.5134 (mmt) cc_final: 0.4508 (mmt) REVERT: G 906 PHE cc_start: 0.5133 (p90) cc_final: 0.3738 (t80) REVERT: G 937 ASP cc_start: 0.5111 (t70) cc_final: 0.3940 (p0) REVERT: A 138 LEU cc_start: 0.9108 (OUTLIER) cc_final: 0.8893 (tt) REVERT: A 235 ASN cc_start: 0.8313 (m110) cc_final: 0.8034 (m110) REVERT: A 239 PRO cc_start: 0.8906 (Cg_endo) cc_final: 0.8678 (Cg_exo) REVERT: A 334 ILE cc_start: 0.9012 (OUTLIER) cc_final: 0.8665 (tp) REVERT: B 61 ARG cc_start: 0.4693 (OUTLIER) cc_final: 0.2834 (mmp-170) REVERT: B 78 TRP cc_start: 0.3164 (OUTLIER) cc_final: 0.1532 (m100) REVERT: B 202 ASP cc_start: 0.8906 (t0) cc_final: 0.8594 (t70) REVERT: B 212 LYS cc_start: 0.8446 (pttt) cc_final: 0.8015 (pttp) REVERT: B 250 GLN cc_start: 0.8244 (pp30) cc_final: 0.7795 (pp30) REVERT: C 20 ASP cc_start: 0.8284 (t0) cc_final: 0.8035 (p0) REVERT: D 5 ASP cc_start: 0.7930 (m-30) cc_final: 0.7729 (m-30) REVERT: D 173 MET cc_start: 0.9141 (ttt) cc_final: 0.8088 (ttt) REVERT: E 107 ASP cc_start: 0.8159 (OUTLIER) cc_final: 0.7824 (p0) REVERT: E 109 GLU cc_start: 0.6445 (OUTLIER) cc_final: 0.6120 (pt0) REVERT: E 173 MET cc_start: 0.8537 (tpp) cc_final: 0.8221 (tpp) REVERT: E 182 VAL cc_start: 0.9169 (OUTLIER) cc_final: 0.8879 (t) REVERT: E 316 GLN cc_start: 0.8452 (pt0) cc_final: 0.8235 (pt0) REVERT: F 20 ASP cc_start: 0.8378 (t0) cc_final: 0.8142 (t0) REVERT: F 43 TRP cc_start: 0.9126 (OUTLIER) cc_final: 0.8472 (t-100) REVERT: H 19 ARG cc_start: 0.7727 (ptp-170) cc_final: 0.7241 (ptp90) REVERT: H 286 ILE cc_start: 0.9055 (OUTLIER) cc_final: 0.8835 (mt) REVERT: I 16 ARG cc_start: 0.8093 (OUTLIER) cc_final: 0.7815 (ttt180) REVERT: I 23 ASN cc_start: 0.8322 (t0) cc_final: 0.8059 (t0) REVERT: I 88 MET cc_start: 0.8668 (mtm) cc_final: 0.8402 (mtp) REVERT: K 78 GLU cc_start: 0.7213 (tm-30) cc_final: 0.6500 (tm-30) REVERT: K 187 GLN cc_start: 0.8824 (mp10) cc_final: 0.8233 (mp10) REVERT: M 7 ARG cc_start: 0.8663 (ttt-90) cc_final: 0.8130 (ttt90) REVERT: M 203 VAL cc_start: 0.9385 (m) cc_final: 0.9150 (p) REVERT: M 238 TYR cc_start: 0.8732 (t80) cc_final: 0.8347 (t80) REVERT: O 63 TYR cc_start: 0.6678 (m-80) cc_final: 0.6322 (m-80) REVERT: O 77 LEU cc_start: 0.3639 (OUTLIER) cc_final: 0.3070 (mm) REVERT: O 86 MET cc_start: 0.2274 (mmt) cc_final: 0.1827 (mmm) outliers start: 120 outliers final: 94 residues processed: 388 average time/residue: 0.2021 time to fit residues: 133.7969 Evaluate side-chains 386 residues out of total 3474 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 106 poor density : 280 time to evaluate : 1.318 ------------------------------------------------------------------------------- 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 139 THR Chi-restraints excluded: chain G residue 167 GLU 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 478 VAL Chi-restraints excluded: chain G residue 487 HIS Chi-restraints excluded: chain G residue 528 ARG Chi-restraints excluded: chain G residue 663 GLU Chi-restraints excluded: chain G residue 673 MET Chi-restraints excluded: chain G residue 710 LEU Chi-restraints excluded: chain G residue 778 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 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 399 LEU Chi-restraints excluded: chain A residue 497 MET Chi-restraints excluded: chain A residue 504 PHE Chi-restraints excluded: chain B residue 43 TRP Chi-restraints excluded: chain B residue 61 ARG Chi-restraints excluded: chain B residue 65 ILE 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 179 SER Chi-restraints excluded: chain B residue 199 VAL 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 B residue 345 ASP Chi-restraints excluded: chain C residue 94 VAL Chi-restraints excluded: chain C residue 165 VAL Chi-restraints excluded: chain C residue 183 ASP 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 D residue 11 THR 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 D residue 328 VAL Chi-restraints excluded: chain E residue 11 THR Chi-restraints excluded: chain E residue 43 TRP Chi-restraints excluded: chain E residue 107 ASP Chi-restraints excluded: chain E residue 109 GLU Chi-restraints excluded: chain E residue 121 VAL Chi-restraints excluded: chain E residue 136 ASP 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 182 VAL Chi-restraints excluded: chain F residue 183 ASP Chi-restraints excluded: chain F residue 186 VAL 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 43 TRP Chi-restraints excluded: chain H residue 198 THR Chi-restraints excluded: chain H residue 230 THR Chi-restraints excluded: chain H residue 264 LEU Chi-restraints excluded: chain H residue 267 VAL Chi-restraints excluded: chain H residue 286 ILE Chi-restraints excluded: chain H residue 340 VAL Chi-restraints excluded: chain H residue 359 LEU Chi-restraints excluded: chain I residue 16 ARG Chi-restraints excluded: chain I residue 37 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 26 THR 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 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 7 ILE Chi-restraints excluded: chain O residue 77 LEU 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 256 optimal weight: 8.9990 chunk 236 optimal weight: 7.9990 chunk 327 optimal weight: 7.9990 chunk 276 optimal weight: 2.9990 chunk 302 optimal weight: 0.5980 chunk 118 optimal weight: 4.9990 chunk 337 optimal weight: 6.9990 chunk 261 optimal weight: 7.9990 chunk 64 optimal weight: 7.9990 chunk 399 optimal weight: 8.9990 chunk 201 optimal weight: 0.0270 overall best weight: 3.1244 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** G 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 174 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 235 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 18 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 18 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 164 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 285 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 18 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 285 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 18 ASN ** F 222 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 319 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 9 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 175 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 170 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3757 r_free = 0.3757 target = 0.122163 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3231 r_free = 0.3231 target = 0.090647 restraints weight = 82965.398| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3255 r_free = 0.3255 target = 0.092014 restraints weight = 43574.545| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3261 r_free = 0.3261 target = 0.092367 restraints weight = 27843.422| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.092756 restraints weight = 24712.527| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.092712 restraints weight = 21516.590| |-----------------------------------------------------------------------------| r_work (final): 0.3247 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8274 moved from start: 0.4032 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.069 37323 Z= 0.201 Angle : 0.802 15.655 51374 Z= 0.391 Chirality : 0.053 0.887 5814 Planarity : 0.005 0.060 6199 Dihedral : 15.877 161.921 6361 Min Nonbonded Distance : 1.977 Molprobity Statistics. All-atom Clashscore : 13.03 Ramachandran Plot: Outliers : 0.14 % Allowed : 6.30 % Favored : 93.56 % Rotamer: Outliers : 3.65 % Allowed : 18.36 % Favored : 77.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.87 % Cis-general : 0.35 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.16 (0.13), residues: 4206 helix: 0.16 (0.12), residues: 1776 sheet: -0.52 (0.22), residues: 530 loop : -1.73 (0.14), residues: 1900 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG C 233 TYR 0.025 0.002 TYR B 234 PHE 0.020 0.002 PHE M 59 TRP 0.042 0.002 TRP H 43 HIS 0.008 0.001 HIS B 220 Details of bonding type rmsd/Z covalent geometry : bond 0.00457 / 0.20 (37323) covalent geometry : angle 0.80243 / 0.39 (51374) hydrogen bonds : bond 0.04238 / 2.84 ( 1647) hydrogen bonds : angle 4.92797 / 3.49 ( 4477) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6206.84 seconds wall clock time: 108 minutes 15.19 seconds (6495.19 seconds total)