Starting phenix.real_space_refine on Sun Mar 24 23:31:01 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7e8h_31019/03_2024/7e8h_31019.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7e8h_31019/03_2024/7e8h_31019.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7e8h_31019/03_2024/7e8h_31019.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7e8h_31019/03_2024/7e8h_31019.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7e8h_31019/03_2024/7e8h_31019.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7e8h_31019/03_2024/7e8h_31019.pdb" } resolution = 4.5 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 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: 4 Type Number sf(0) Gaussians S 216 5.16 5 C 28726 2.51 5 N 7612 2.21 5 O 8340 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "J TYR 399": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 57": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 82": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 168": "OE1" <-> "OE2" Residue "F GLU 197": "OE1" <-> "OE2" Residue "B PHE 92": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 117": "OE1" <-> "OE2" Residue "B PHE 298": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 409": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 85": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 399": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 57": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 82": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 168": "OE1" <-> "OE2" Residue "H GLU 197": "OE1" <-> "OE2" Residue "D PHE 92": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 117": "OE1" <-> "OE2" Residue "D PHE 298": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 409": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 85": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.13s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 44894 Number of models: 1 Model: "" Number of chains: 12 Chain: "J" Number of atoms: 6071 Number of conformers: 1 Conformer: "" Number of residues, atoms: 756, 6071 Classifications: {'peptide': 756} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 33, 'TRANS': 721} Chain breaks: 1 Chain: "I" Number of atoms: 6093 Number of conformers: 1 Conformer: "" Number of residues, atoms: 760, 6093 Classifications: {'peptide': 760} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 34, 'TRANS': 724} Chain: "F" Number of atoms: 1459 Number of conformers: 1 Conformer: "" Number of residues, atoms: 176, 1459 Classifications: {'peptide': 176} Link IDs: {'PTRANS': 4, 'TRANS': 171} Chain breaks: 1 Chain: "B" Number of atoms: 3675 Number of conformers: 1 Conformer: "" Number of residues, atoms: 459, 3675 Classifications: {'peptide': 459} Link IDs: {'PTRANS': 20, 'TRANS': 438} Chain breaks: 3 Chain: "E" Number of atoms: 1466 Number of conformers: 1 Conformer: "" Number of residues, atoms: 177, 1466 Classifications: {'peptide': 177} Link IDs: {'PTRANS': 4, 'TRANS': 172} Chain breaks: 1 Chain: "A" Number of atoms: 3683 Number of conformers: 1 Conformer: "" Number of residues, atoms: 460, 3683 Classifications: {'peptide': 460} Link IDs: {'PTRANS': 20, 'TRANS': 439} Chain breaks: 3 Chain: "L" Number of atoms: 6071 Number of conformers: 1 Conformer: "" Number of residues, atoms: 756, 6071 Classifications: {'peptide': 756} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 33, 'TRANS': 721} Chain breaks: 1 Chain: "K" Number of atoms: 6093 Number of conformers: 1 Conformer: "" Number of residues, atoms: 760, 6093 Classifications: {'peptide': 760} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 34, 'TRANS': 724} Chain: "H" Number of atoms: 1459 Number of conformers: 1 Conformer: "" Number of residues, atoms: 176, 1459 Classifications: {'peptide': 176} Link IDs: {'PTRANS': 4, 'TRANS': 171} Chain breaks: 1 Chain: "D" Number of atoms: 3675 Number of conformers: 1 Conformer: "" Number of residues, atoms: 459, 3675 Classifications: {'peptide': 459} Link IDs: {'PTRANS': 20, 'TRANS': 438} Chain breaks: 3 Chain: "G" Number of atoms: 1466 Number of conformers: 1 Conformer: "" Number of residues, atoms: 177, 1466 Classifications: {'peptide': 177} Link IDs: {'PTRANS': 4, 'TRANS': 172} Chain breaks: 1 Chain: "C" Number of atoms: 3683 Number of conformers: 1 Conformer: "" Number of residues, atoms: 460, 3683 Classifications: {'peptide': 460} Link IDs: {'PTRANS': 20, 'TRANS': 439} Chain breaks: 3 Time building chain proxies: 22.11, per 1000 atoms: 0.49 Number of scatterers: 44894 At special positions: 0 Unit cell: (159.426, 215.576, 206.552, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 216 16.00 O 8340 8.00 N 7612 7.00 C 28726 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=16, symmetry=0 Simple disulfide: pdb=" SG CYS J 349 " - pdb=" SG CYS J 356 " distance=2.03 Simple disulfide: pdb=" SG CYS J 465 " - pdb=" SG CYS J 468 " distance=2.03 Simple disulfide: pdb=" SG CYS J 474 " - pdb=" SG CYS J 492 " distance=2.03 Simple disulfide: pdb=" SG CYS J 673 " - pdb=" SG CYS J 784 " distance=2.03 Simple disulfide: pdb=" SG CYS I 349 " - pdb=" SG CYS I 356 " distance=2.03 Simple disulfide: pdb=" SG CYS I 465 " - pdb=" SG CYS I 468 " distance=2.04 Simple disulfide: pdb=" SG CYS I 474 " - pdb=" SG CYS I 492 " distance=2.03 Simple disulfide: pdb=" SG CYS I 673 " - pdb=" SG CYS I 784 " distance=2.03 Simple disulfide: pdb=" SG CYS L 349 " - pdb=" SG CYS L 356 " distance=2.03 Simple disulfide: pdb=" SG CYS L 465 " - pdb=" SG CYS L 468 " distance=2.03 Simple disulfide: pdb=" SG CYS L 474 " - pdb=" SG CYS L 492 " distance=2.03 Simple disulfide: pdb=" SG CYS L 673 " - pdb=" SG CYS L 784 " distance=2.03 Simple disulfide: pdb=" SG CYS K 349 " - pdb=" SG CYS K 356 " distance=2.03 Simple disulfide: pdb=" SG CYS K 465 " - pdb=" SG CYS K 468 " distance=2.03 Simple disulfide: pdb=" SG CYS K 474 " - pdb=" SG CYS K 492 " distance=2.03 Simple disulfide: pdb=" SG CYS K 673 " - pdb=" SG CYS K 784 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 18.25 Conformation dependent library (CDL) restraints added in 8.1 seconds 11032 Ramachandran restraints generated. 5516 Oldfield, 0 Emsley, 5516 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 10552 Finding SS restraints... Secondary structure from input PDB file: 186 helices and 54 sheets defined 43.6% alpha, 13.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 5.04 Creating SS restraints... Processing helix chain 'J' and resid 31 through 56 Processing helix chain 'J' and resid 70 through 76 Processing helix chain 'J' and resid 77 through 80 Processing helix chain 'J' and resid 118 through 124 removed outlier: 3.636A pdb=" N LYS J 121 " --> pdb=" O GLU J 118 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N SER J 124 " --> pdb=" O LYS J 121 " (cutoff:3.500A) Processing helix chain 'J' and resid 228 through 234 Processing helix chain 'J' and resid 517 through 526 Processing helix chain 'J' and resid 582 through 592 Processing helix chain 'J' and resid 607 through 614 removed outlier: 3.601A pdb=" N LEU J 611 " --> pdb=" O GLY J 607 " (cutoff:3.500A) removed outlier: 4.343A pdb=" N VAL J 614 " --> pdb=" O LEU J 610 " (cutoff:3.500A) Processing helix chain 'J' and resid 621 through 635 Processing helix chain 'J' and resid 650 through 659 Processing helix chain 'J' and resid 682 through 686 Processing helix chain 'J' and resid 687 through 696 removed outlier: 4.083A pdb=" N ARG J 693 " --> pdb=" O ALA J 689 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N TYR J 694 " --> pdb=" O PHE J 690 " (cutoff:3.500A) Processing helix chain 'J' and resid 704 through 708 removed outlier: 3.997A pdb=" N MET J 707 " --> pdb=" O ALA J 704 " (cutoff:3.500A) Processing helix chain 'J' and resid 711 through 715 removed outlier: 3.515A pdb=" N VAL J 714 " --> pdb=" O ALA J 711 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N SER J 715 " --> pdb=" O HIS J 712 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 711 through 715' Processing helix chain 'J' and resid 734 through 749 removed outlier: 4.131A pdb=" N THR J 738 " --> pdb=" O HIS J 734 " (cutoff:3.500A) Processing helix chain 'J' and resid 766 through 784 removed outlier: 3.863A pdb=" N GLU J 783 " --> pdb=" O ASN J 779 " (cutoff:3.500A) Processing helix chain 'I' and resid 29 through 54 removed outlier: 3.632A pdb=" N CYS I 45 " --> pdb=" O ILE I 41 " (cutoff:3.500A) Processing helix chain 'I' and resid 70 through 76 Processing helix chain 'I' and resid 118 through 124 removed outlier: 3.609A pdb=" N LYS I 121 " --> pdb=" O GLU I 118 " (cutoff:3.500A) Processing helix chain 'I' and resid 228 through 234 Processing helix chain 'I' and resid 517 through 527 Processing helix chain 'I' and resid 582 through 590 Processing helix chain 'I' and resid 607 through 613 Processing helix chain 'I' and resid 620 through 635 Processing helix chain 'I' and resid 650 through 659 Processing helix chain 'I' and resid 682 through 686 Processing helix chain 'I' and resid 687 through 696 removed outlier: 3.790A pdb=" N ARG I 693 " --> pdb=" O ALA I 689 " (cutoff:3.500A) Processing helix chain 'I' and resid 712 through 716 removed outlier: 3.558A pdb=" N SER I 715 " --> pdb=" O HIS I 712 " (cutoff:3.500A) removed outlier: 4.295A pdb=" N ALA I 716 " --> pdb=" O ARG I 713 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 712 through 716' Processing helix chain 'I' and resid 734 through 749 removed outlier: 4.353A pdb=" N THR I 738 " --> pdb=" O HIS I 734 " (cutoff:3.500A) Processing helix chain 'I' and resid 766 through 786 Processing helix chain 'F' and resid 49 through 64 Processing helix chain 'F' and resid 70 through 82 Processing helix chain 'F' and resid 88 through 99 Processing helix chain 'F' and resid 100 through 103 Processing helix chain 'F' and resid 107 through 120 removed outlier: 3.536A pdb=" N PHE F 111 " --> pdb=" O LYS F 107 " (cutoff:3.500A) Processing helix chain 'F' and resid 122 through 135 Processing helix chain 'F' and resid 143 through 156 removed outlier: 3.545A pdb=" N MET F 147 " --> pdb=" O ASN F 143 " (cutoff:3.500A) Processing helix chain 'F' and resid 168 through 182 removed outlier: 3.701A pdb=" N ARG F 172 " --> pdb=" O GLU F 168 " (cutoff:3.500A) Processing helix chain 'F' and resid 192 through 202 Processing helix chain 'F' and resid 202 through 208 removed outlier: 3.734A pdb=" N MET F 206 " --> pdb=" O ASP F 202 " (cutoff:3.500A) Processing helix chain 'F' and resid 209 through 214 removed outlier: 3.923A pdb=" N GLN F 213 " --> pdb=" O LEU F 209 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N ASN F 214 " --> pdb=" O GLN F 210 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 209 through 214' Processing helix chain 'B' and resid 5 through 7 No H-bonds generated for 'chain 'B' and resid 5 through 7' Processing helix chain 'B' and resid 8 through 20 removed outlier: 3.535A pdb=" N ALA B 16 " --> pdb=" O ALA B 12 " (cutoff:3.500A) removed outlier: 4.200A pdb=" N ILE B 17 " --> pdb=" O ARG B 13 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N GLY B 18 " --> pdb=" O ALA B 14 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N TRP B 19 " --> pdb=" O ALA B 15 " (cutoff:3.500A) Processing helix chain 'B' and resid 56 through 61 Processing helix chain 'B' and resid 70 through 74 Processing helix chain 'B' and resid 90 through 102 removed outlier: 3.506A pdb=" N HIS B 94 " --> pdb=" O ASP B 90 " (cutoff:3.500A) Processing helix chain 'B' and resid 111 through 122 Processing helix chain 'B' and resid 125 through 129 removed outlier: 3.716A pdb=" N ILE B 128 " --> pdb=" O ILE B 125 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N ILE B 129 " --> pdb=" O PRO B 126 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 125 through 129' Processing helix chain 'B' and resid 130 through 152 removed outlier: 3.631A pdb=" N GLU B 135 " --> pdb=" O ASP B 131 " (cutoff:3.500A) removed outlier: 4.892A pdb=" N GLU B 136 " --> pdb=" O CYS B 132 " (cutoff:3.500A) Processing helix chain 'B' and resid 169 through 177 removed outlier: 3.819A pdb=" N ARG B 173 " --> pdb=" O GLN B 169 " (cutoff:3.500A) Processing helix chain 'B' and resid 181 through 207 Processing helix chain 'B' and resid 207 through 212 Processing helix chain 'B' and resid 228 through 250 removed outlier: 3.513A pdb=" N LEU B 232 " --> pdb=" O ALA B 228 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N ASP B 233 " --> pdb=" O PHE B 229 " (cutoff:3.500A) removed outlier: 4.256A pdb=" N THR B 234 " --> pdb=" O PHE B 230 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N GLU B 243 " --> pdb=" O ILE B 239 " (cutoff:3.500A) Processing helix chain 'B' and resid 255 through 260 Processing helix chain 'B' and resid 260 through 283 Proline residue: B 272 - end of helix Processing helix chain 'B' and resid 288 through 296 Processing helix chain 'B' and resid 298 through 303 Processing helix chain 'B' and resid 307 through 320 removed outlier: 4.206A pdb=" N ARG B 311 " --> pdb=" O SER B 307 " (cutoff:3.500A) removed outlier: 4.175A pdb=" N ILE B 312 " --> pdb=" O GLN B 308 " (cutoff:3.500A) Processing helix chain 'B' and resid 320 through 347 Processing helix chain 'B' and resid 356 through 369 removed outlier: 3.565A pdb=" N TRP B 362 " --> pdb=" O PRO B 358 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N TYR B 363 " --> pdb=" O ALA B 359 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N THR B 369 " --> pdb=" O ILE B 365 " (cutoff:3.500A) Processing helix chain 'B' and resid 380 through 400 removed outlier: 3.531A pdb=" N ILE B 385 " --> pdb=" O ILE B 381 " (cutoff:3.500A) Processing helix chain 'B' and resid 401 through 450 Processing helix chain 'B' and resid 473 through 490 removed outlier: 3.793A pdb=" N GLN B 477 " --> pdb=" O SER B 473 " (cutoff:3.500A) Processing helix chain 'E' and resid 49 through 64 removed outlier: 3.785A pdb=" N GLU E 63 " --> pdb=" O GLY E 59 " (cutoff:3.500A) Processing helix chain 'E' and resid 71 through 80 Processing helix chain 'E' and resid 87 through 99 Processing helix chain 'E' and resid 100 through 103 removed outlier: 3.615A pdb=" N THR E 103 " --> pdb=" O THR E 100 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 100 through 103' Processing helix chain 'E' and resid 108 through 121 Processing helix chain 'E' and resid 122 through 135 removed outlier: 4.605A pdb=" N LEU E 127 " --> pdb=" O VAL E 123 " (cutoff:3.500A) removed outlier: 4.716A pdb=" N ARG E 128 " --> pdb=" O HIS E 124 " (cutoff:3.500A) removed outlier: 4.516A pdb=" N TRP E 129 " --> pdb=" O GLU E 125 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N THR E 130 " --> pdb=" O LYS E 126 " (cutoff:3.500A) Processing helix chain 'E' and resid 147 through 156 Processing helix chain 'E' and resid 157 through 159 No H-bonds generated for 'chain 'E' and resid 157 through 159' Processing helix chain 'E' and resid 169 through 182 removed outlier: 4.031A pdb=" N LYS E 181 " --> pdb=" O VAL E 177 " (cutoff:3.500A) Processing helix chain 'E' and resid 192 through 200 removed outlier: 4.457A pdb=" N GLN E 200 " --> pdb=" O LEU E 196 " (cutoff:3.500A) Processing helix chain 'E' and resid 202 through 214 removed outlier: 3.918A pdb=" N MET E 206 " --> pdb=" O ASP E 202 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N GLN E 210 " --> pdb=" O MET E 206 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N LEU E 211 " --> pdb=" O ARG E 207 " (cutoff:3.500A) removed outlier: 4.308A pdb=" N PHE E 212 " --> pdb=" O SER E 208 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N ASN E 214 " --> pdb=" O GLN E 210 " (cutoff:3.500A) Processing helix chain 'A' and resid 5 through 7 No H-bonds generated for 'chain 'A' and resid 5 through 7' Processing helix chain 'A' and resid 8 through 18 removed outlier: 3.593A pdb=" N GLY A 18 " --> pdb=" O ALA A 14 " (cutoff:3.500A) Processing helix chain 'A' and resid 56 through 60 Processing helix chain 'A' and resid 88 through 102 removed outlier: 3.607A pdb=" N HIS A 94 " --> pdb=" O ASP A 90 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N ILE A 95 " --> pdb=" O ILE A 91 " (cutoff:3.500A) Processing helix chain 'A' and resid 111 through 122 Processing helix chain 'A' and resid 133 through 152 Processing helix chain 'A' and resid 168 through 177 removed outlier: 3.531A pdb=" N ARG A 173 " --> pdb=" O GLN A 169 " (cutoff:3.500A) Processing helix chain 'A' and resid 181 through 205 removed outlier: 3.792A pdb=" N LEU A 185 " --> pdb=" O SER A 181 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N VAL A 186 " --> pdb=" O THR A 182 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N THR A 191 " --> pdb=" O PHE A 187 " (cutoff:3.500A) Processing helix chain 'A' and resid 228 through 251 Processing helix chain 'A' and resid 253 through 259 removed outlier: 3.570A pdb=" N ARG A 259 " --> pdb=" O TYR A 255 " (cutoff:3.500A) Processing helix chain 'A' and resid 260 through 281 Proline residue: A 272 - end of helix removed outlier: 3.924A pdb=" N ASP A 281 " --> pdb=" O LEU A 277 " (cutoff:3.500A) Processing helix chain 'A' and resid 288 through 296 removed outlier: 3.521A pdb=" N LEU A 292 " --> pdb=" O ALA A 288 " (cutoff:3.500A) Processing helix chain 'A' and resid 297 through 305 removed outlier: 3.573A pdb=" N ARG A 305 " --> pdb=" O LYS A 302 " (cutoff:3.500A) Processing helix chain 'A' and resid 307 through 320 removed outlier: 3.984A pdb=" N ARG A 311 " --> pdb=" O SER A 307 " (cutoff:3.500A) Processing helix chain 'A' and resid 321 through 346 Processing helix chain 'A' and resid 356 through 369 removed outlier: 3.755A pdb=" N TRP A 362 " --> pdb=" O PRO A 358 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N TYR A 363 " --> pdb=" O ALA A 359 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N THR A 367 " --> pdb=" O TYR A 363 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N THR A 369 " --> pdb=" O ILE A 365 " (cutoff:3.500A) Processing helix chain 'A' and resid 380 through 400 Processing helix chain 'A' and resid 401 through 450 Processing helix chain 'A' and resid 473 through 489 Processing helix chain 'L' and resid 32 through 56 Processing helix chain 'L' and resid 70 through 76 Processing helix chain 'L' and resid 77 through 80 Processing helix chain 'L' and resid 118 through 124 removed outlier: 3.636A pdb=" N LYS L 121 " --> pdb=" O GLU L 118 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N SER L 124 " --> pdb=" O LYS L 121 " (cutoff:3.500A) Processing helix chain 'L' and resid 228 through 234 Processing helix chain 'L' and resid 517 through 526 Processing helix chain 'L' and resid 582 through 592 Processing helix chain 'L' and resid 607 through 614 removed outlier: 3.601A pdb=" N LEU L 611 " --> pdb=" O GLY L 607 " (cutoff:3.500A) removed outlier: 4.343A pdb=" N VAL L 614 " --> pdb=" O LEU L 610 " (cutoff:3.500A) Processing helix chain 'L' and resid 621 through 635 Processing helix chain 'L' and resid 650 through 659 Processing helix chain 'L' and resid 682 through 686 Processing helix chain 'L' and resid 687 through 696 removed outlier: 4.084A pdb=" N ARG L 693 " --> pdb=" O ALA L 689 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N TYR L 694 " --> pdb=" O PHE L 690 " (cutoff:3.500A) Processing helix chain 'L' and resid 704 through 708 removed outlier: 3.997A pdb=" N MET L 707 " --> pdb=" O ALA L 704 " (cutoff:3.500A) Processing helix chain 'L' and resid 711 through 715 removed outlier: 3.514A pdb=" N VAL L 714 " --> pdb=" O ALA L 711 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N SER L 715 " --> pdb=" O HIS L 712 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 711 through 715' Processing helix chain 'L' and resid 734 through 749 removed outlier: 4.130A pdb=" N THR L 738 " --> pdb=" O HIS L 734 " (cutoff:3.500A) Processing helix chain 'L' and resid 766 through 784 removed outlier: 3.863A pdb=" N GLU L 783 " --> pdb=" O ASN L 779 " (cutoff:3.500A) Processing helix chain 'K' and resid 29 through 54 removed outlier: 3.632A pdb=" N CYS K 45 " --> pdb=" O ILE K 41 " (cutoff:3.500A) Processing helix chain 'K' and resid 70 through 76 Processing helix chain 'K' and resid 118 through 124 removed outlier: 3.609A pdb=" N LYS K 121 " --> pdb=" O GLU K 118 " (cutoff:3.500A) Processing helix chain 'K' and resid 228 through 234 Processing helix chain 'K' and resid 517 through 527 Processing helix chain 'K' and resid 582 through 590 Processing helix chain 'K' and resid 607 through 613 Processing helix chain 'K' and resid 620 through 635 Processing helix chain 'K' and resid 650 through 659 Processing helix chain 'K' and resid 682 through 686 Processing helix chain 'K' and resid 687 through 696 removed outlier: 3.791A pdb=" N ARG K 693 " --> pdb=" O ALA K 689 " (cutoff:3.500A) Processing helix chain 'K' and resid 712 through 716 removed outlier: 3.558A pdb=" N SER K 715 " --> pdb=" O HIS K 712 " (cutoff:3.500A) removed outlier: 4.296A pdb=" N ALA K 716 " --> pdb=" O ARG K 713 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 712 through 716' Processing helix chain 'K' and resid 734 through 749 removed outlier: 4.355A pdb=" N THR K 738 " --> pdb=" O HIS K 734 " (cutoff:3.500A) Processing helix chain 'K' and resid 766 through 786 Processing helix chain 'H' and resid 49 through 64 Processing helix chain 'H' and resid 70 through 82 Processing helix chain 'H' and resid 88 through 99 Processing helix chain 'H' and resid 100 through 103 Processing helix chain 'H' and resid 107 through 120 removed outlier: 3.537A pdb=" N PHE H 111 " --> pdb=" O LYS H 107 " (cutoff:3.500A) Processing helix chain 'H' and resid 122 through 135 Processing helix chain 'H' and resid 143 through 156 removed outlier: 3.545A pdb=" N MET H 147 " --> pdb=" O ASN H 143 " (cutoff:3.500A) Processing helix chain 'H' and resid 168 through 182 removed outlier: 3.702A pdb=" N ARG H 172 " --> pdb=" O GLU H 168 " (cutoff:3.500A) Processing helix chain 'H' and resid 192 through 202 Processing helix chain 'H' and resid 202 through 208 removed outlier: 3.733A pdb=" N MET H 206 " --> pdb=" O ASP H 202 " (cutoff:3.500A) Processing helix chain 'H' and resid 209 through 214 removed outlier: 3.923A pdb=" N GLN H 213 " --> pdb=" O LEU H 209 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N ASN H 214 " --> pdb=" O GLN H 210 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 209 through 214' Processing helix chain 'D' and resid 5 through 7 No H-bonds generated for 'chain 'D' and resid 5 through 7' Processing helix chain 'D' and resid 8 through 20 removed outlier: 3.539A pdb=" N ALA D 16 " --> pdb=" O ALA D 12 " (cutoff:3.500A) removed outlier: 4.197A pdb=" N ILE D 17 " --> pdb=" O ARG D 13 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N GLY D 18 " --> pdb=" O ALA D 14 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N TRP D 19 " --> pdb=" O ALA D 15 " (cutoff:3.500A) Processing helix chain 'D' and resid 56 through 61 Processing helix chain 'D' and resid 70 through 74 Processing helix chain 'D' and resid 90 through 102 removed outlier: 3.505A pdb=" N HIS D 94 " --> pdb=" O ASP D 90 " (cutoff:3.500A) Processing helix chain 'D' and resid 111 through 122 Processing helix chain 'D' and resid 125 through 129 removed outlier: 3.715A pdb=" N ILE D 128 " --> pdb=" O ILE D 125 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N ILE D 129 " --> pdb=" O PRO D 126 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 125 through 129' Processing helix chain 'D' and resid 130 through 152 removed outlier: 3.630A pdb=" N GLU D 135 " --> pdb=" O ASP D 131 " (cutoff:3.500A) removed outlier: 4.891A pdb=" N GLU D 136 " --> pdb=" O CYS D 132 " (cutoff:3.500A) Processing helix chain 'D' and resid 169 through 177 removed outlier: 3.819A pdb=" N ARG D 173 " --> pdb=" O GLN D 169 " (cutoff:3.500A) Processing helix chain 'D' and resid 181 through 207 Processing helix chain 'D' and resid 207 through 212 Processing helix chain 'D' and resid 228 through 250 removed outlier: 3.514A pdb=" N LEU D 232 " --> pdb=" O ALA D 228 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N ASP D 233 " --> pdb=" O PHE D 229 " (cutoff:3.500A) removed outlier: 4.256A pdb=" N THR D 234 " --> pdb=" O PHE D 230 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N GLU D 243 " --> pdb=" O ILE D 239 " (cutoff:3.500A) Processing helix chain 'D' and resid 255 through 260 Processing helix chain 'D' and resid 260 through 283 Proline residue: D 272 - end of helix Processing helix chain 'D' and resid 288 through 296 Processing helix chain 'D' and resid 298 through 303 Processing helix chain 'D' and resid 307 through 320 removed outlier: 4.206A pdb=" N ARG D 311 " --> pdb=" O SER D 307 " (cutoff:3.500A) removed outlier: 4.176A pdb=" N ILE D 312 " --> pdb=" O GLN D 308 " (cutoff:3.500A) Processing helix chain 'D' and resid 320 through 347 Processing helix chain 'D' and resid 356 through 369 removed outlier: 3.565A pdb=" N TRP D 362 " --> pdb=" O PRO D 358 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N TYR D 363 " --> pdb=" O ALA D 359 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N THR D 369 " --> pdb=" O ILE D 365 " (cutoff:3.500A) Processing helix chain 'D' and resid 380 through 400 removed outlier: 3.532A pdb=" N ILE D 385 " --> pdb=" O ILE D 381 " (cutoff:3.500A) Processing helix chain 'D' and resid 401 through 450 Processing helix chain 'D' and resid 473 through 490 removed outlier: 3.793A pdb=" N GLN D 477 " --> pdb=" O SER D 473 " (cutoff:3.500A) Processing helix chain 'G' and resid 49 through 64 removed outlier: 3.785A pdb=" N GLU G 63 " --> pdb=" O GLY G 59 " (cutoff:3.500A) Processing helix chain 'G' and resid 71 through 80 Processing helix chain 'G' and resid 87 through 99 Processing helix chain 'G' and resid 100 through 103 removed outlier: 3.617A pdb=" N THR G 103 " --> pdb=" O THR G 100 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 100 through 103' Processing helix chain 'G' and resid 108 through 121 Processing helix chain 'G' and resid 122 through 135 removed outlier: 4.604A pdb=" N LEU G 127 " --> pdb=" O VAL G 123 " (cutoff:3.500A) removed outlier: 4.715A pdb=" N ARG G 128 " --> pdb=" O HIS G 124 " (cutoff:3.500A) removed outlier: 4.515A pdb=" N TRP G 129 " --> pdb=" O GLU G 125 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N THR G 130 " --> pdb=" O LYS G 126 " (cutoff:3.500A) Processing helix chain 'G' and resid 147 through 156 Processing helix chain 'G' and resid 157 through 159 No H-bonds generated for 'chain 'G' and resid 157 through 159' Processing helix chain 'G' and resid 169 through 182 removed outlier: 4.014A pdb=" N LYS G 181 " --> pdb=" O VAL G 177 " (cutoff:3.500A) Processing helix chain 'G' and resid 192 through 200 removed outlier: 4.457A pdb=" N GLN G 200 " --> pdb=" O LEU G 196 " (cutoff:3.500A) Processing helix chain 'G' and resid 202 through 214 removed outlier: 3.920A pdb=" N MET G 206 " --> pdb=" O ASP G 202 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N GLN G 210 " --> pdb=" O MET G 206 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N LEU G 211 " --> pdb=" O ARG G 207 " (cutoff:3.500A) removed outlier: 4.302A pdb=" N PHE G 212 " --> pdb=" O SER G 208 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N ASN G 214 " --> pdb=" O GLN G 210 " (cutoff:3.500A) Processing helix chain 'C' and resid 5 through 7 No H-bonds generated for 'chain 'C' and resid 5 through 7' Processing helix chain 'C' and resid 8 through 18 removed outlier: 3.593A pdb=" N GLY C 18 " --> pdb=" O ALA C 14 " (cutoff:3.500A) Processing helix chain 'C' and resid 56 through 60 Processing helix chain 'C' and resid 88 through 102 removed outlier: 3.607A pdb=" N HIS C 94 " --> pdb=" O ASP C 90 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N ILE C 95 " --> pdb=" O ILE C 91 " (cutoff:3.500A) Processing helix chain 'C' and resid 111 through 122 Processing helix chain 'C' and resid 133 through 152 Processing helix chain 'C' and resid 168 through 177 removed outlier: 3.532A pdb=" N ARG C 173 " --> pdb=" O GLN C 169 " (cutoff:3.500A) Processing helix chain 'C' and resid 181 through 205 removed outlier: 3.792A pdb=" N LEU C 185 " --> pdb=" O SER C 181 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N VAL C 186 " --> pdb=" O THR C 182 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N THR C 191 " --> pdb=" O PHE C 187 " (cutoff:3.500A) Processing helix chain 'C' and resid 228 through 251 Processing helix chain 'C' and resid 253 through 259 removed outlier: 3.571A pdb=" N ARG C 259 " --> pdb=" O TYR C 255 " (cutoff:3.500A) Processing helix chain 'C' and resid 260 through 281 Proline residue: C 272 - end of helix removed outlier: 3.924A pdb=" N ASP C 281 " --> pdb=" O LEU C 277 " (cutoff:3.500A) Processing helix chain 'C' and resid 288 through 296 removed outlier: 3.522A pdb=" N LEU C 292 " --> pdb=" O ALA C 288 " (cutoff:3.500A) Processing helix chain 'C' and resid 297 through 305 removed outlier: 3.573A pdb=" N ARG C 305 " --> pdb=" O LYS C 302 " (cutoff:3.500A) Processing helix chain 'C' and resid 307 through 320 removed outlier: 3.984A pdb=" N ARG C 311 " --> pdb=" O SER C 307 " (cutoff:3.500A) Processing helix chain 'C' and resid 321 through 346 Processing helix chain 'C' and resid 356 through 369 removed outlier: 3.756A pdb=" N TRP C 362 " --> pdb=" O PRO C 358 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N TYR C 363 " --> pdb=" O ALA C 359 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N THR C 367 " --> pdb=" O TYR C 363 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N THR C 369 " --> pdb=" O ILE C 365 " (cutoff:3.500A) Processing helix chain 'C' and resid 380 through 400 Processing helix chain 'C' and resid 401 through 450 Processing helix chain 'C' and resid 473 through 489 Processing sheet with id=AA1, first strand: chain 'J' and resid 103 through 107 removed outlier: 6.836A pdb=" N VAL J 103 " --> pdb=" O LEU J 116 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N LEU J 116 " --> pdb=" O VAL J 103 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'J' and resid 129 through 132 removed outlier: 3.943A pdb=" N ARG J 129 " --> pdb=" O SER J 142 " (cutoff:3.500A) removed outlier: 4.358A pdb=" N VAL J 145 " --> pdb=" O THR J 154 " (cutoff:3.500A) removed outlier: 6.524A pdb=" N THR J 154 " --> pdb=" O VAL J 145 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'J' and resid 192 through 195 Processing sheet with id=AA4, first strand: chain 'J' and resid 305 through 307 removed outlier: 3.681A pdb=" N ALA J 254 " --> pdb=" O ALA J 241 " (cutoff:3.500A) removed outlier: 7.382A pdb=" N ALA J 241 " --> pdb=" O ALA J 254 " (cutoff:3.500A) removed outlier: 4.188A pdb=" N GLY J 225 " --> pdb=" O ALA J 241 " (cutoff:3.500A) removed outlier: 11.758A pdb=" N TRP J 243 " --> pdb=" O TYR J 223 " (cutoff:3.500A) removed outlier: 16.362A pdb=" N TYR J 223 " --> pdb=" O TRP J 243 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N GLY J 225 " --> pdb=" O ALA J 254 " (cutoff:3.500A) removed outlier: 6.908A pdb=" N ALA J 254 " --> pdb=" O GLY J 225 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'J' and resid 263 through 266 Processing sheet with id=AA6, first strand: chain 'J' and resid 319 through 325 removed outlier: 5.589A pdb=" N ILE J 321 " --> pdb=" O LEU J 337 " (cutoff:3.500A) removed outlier: 6.916A pdb=" N LEU J 337 " --> pdb=" O ILE J 321 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N MET J 323 " --> pdb=" O THR J 335 " (cutoff:3.500A) removed outlier: 5.631A pdb=" N VAL J 343 " --> pdb=" O ASN J 338 " (cutoff:3.500A) removed outlier: 6.742A pdb=" N SER J 344 " --> pdb=" O GLU J 361 " (cutoff:3.500A) removed outlier: 4.477A pdb=" N GLU J 361 " --> pdb=" O SER J 344 " (cutoff:3.500A) removed outlier: 6.710A pdb=" N LEU J 346 " --> pdb=" O LYS J 359 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'J' and resid 384 through 390 Processing sheet with id=AA8, first strand: chain 'J' and resid 425 through 432 removed outlier: 5.834A pdb=" N ILE J 428 " --> pdb=" O LEU J 441 " (cutoff:3.500A) removed outlier: 6.522A pdb=" N LEU J 441 " --> pdb=" O ILE J 428 " (cutoff:3.500A) removed outlier: 4.159A pdb=" N LYS J 437 " --> pdb=" O ASP J 432 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'J' and resid 478 through 481 removed outlier: 6.199A pdb=" N VAL J 502 " --> pdb=" O ASP J 513 " (cutoff:3.500A) removed outlier: 5.928A pdb=" N ASP J 513 " --> pdb=" O VAL J 502 " (cutoff:3.500A) removed outlier: 9.879A pdb=" N ASN J 504 " --> pdb=" O MET J 511 " (cutoff:3.500A) removed outlier: 8.498A pdb=" N MET J 511 " --> pdb=" O ASN J 504 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'J' and resid 531 through 534 removed outlier: 3.613A pdb=" N LEU J 549 " --> pdb=" O VAL J 595 " (cutoff:3.500A) removed outlier: 4.565A pdb=" N VAL J 595 " --> pdb=" O LEU J 549 " (cutoff:3.500A) removed outlier: 4.611A pdb=" N CYS J 598 " --> pdb=" O VAL J 565 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N CYS J 673 " --> pdb=" O VAL J 644 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N VAL J 646 " --> pdb=" O CYS J 673 " (cutoff:3.500A) removed outlier: 4.218A pdb=" N GLY J 648 " --> pdb=" O SER J 675 " (cutoff:3.500A) removed outlier: 8.269A pdb=" N GLN J 755 " --> pdb=" O PHE J 722 " (cutoff:3.500A) removed outlier: 6.615A pdb=" N ILE J 724 " --> pdb=" O GLN J 755 " (cutoff:3.500A) removed outlier: 8.103A pdb=" N TYR J 757 " --> pdb=" O ILE J 724 " (cutoff:3.500A) removed outlier: 7.166A pdb=" N HIS J 726 " --> pdb=" O TYR J 757 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'J' and resid 537 through 539 Processing sheet with id=AB3, first strand: chain 'I' and resid 104 through 107 Processing sheet with id=AB4, first strand: chain 'I' and resid 129 through 132 Processing sheet with id=AB5, first strand: chain 'I' and resid 192 through 195 removed outlier: 3.791A pdb=" N VAL I 214 " --> pdb=" O ILE I 200 " (cutoff:3.500A) removed outlier: 7.456A pdb=" N TYR I 202 " --> pdb=" O ARG I 212 " (cutoff:3.500A) removed outlier: 6.273A pdb=" N ARG I 212 " --> pdb=" O TYR I 202 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'I' and resid 222 through 224 Processing sheet with id=AB7, first strand: chain 'I' and resid 222 through 224 removed outlier: 4.709A pdb=" N LEU I 294 " --> pdb=" O MET I 308 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'I' and resid 263 through 266 Processing sheet with id=AB9, first strand: chain 'I' and resid 319 through 326 removed outlier: 5.653A pdb=" N ILE I 321 " --> pdb=" O LEU I 337 " (cutoff:3.500A) removed outlier: 7.334A pdb=" N LEU I 337 " --> pdb=" O ILE I 321 " (cutoff:3.500A) removed outlier: 5.082A pdb=" N MET I 323 " --> pdb=" O THR I 335 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N THR I 335 " --> pdb=" O MET I 323 " (cutoff:3.500A) removed outlier: 5.710A pdb=" N VAL I 343 " --> pdb=" O ASN I 338 " (cutoff:3.500A) removed outlier: 7.076A pdb=" N SER I 344 " --> pdb=" O GLU I 361 " (cutoff:3.500A) removed outlier: 4.851A pdb=" N GLU I 361 " --> pdb=" O SER I 344 " (cutoff:3.500A) removed outlier: 6.541A pdb=" N LEU I 346 " --> pdb=" O LYS I 359 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'I' and resid 384 through 390 Processing sheet with id=AC2, first strand: chain 'I' and resid 427 through 432 removed outlier: 6.571A pdb=" N TYR I 439 " --> pdb=" O LEU I 429 " (cutoff:3.500A) removed outlier: 4.328A pdb=" N TYR I 431 " --> pdb=" O LYS I 437 " (cutoff:3.500A) removed outlier: 6.917A pdb=" N LYS I 437 " --> pdb=" O TYR I 431 " (cutoff:3.500A) removed outlier: 5.059A pdb=" N GLU I 444 " --> pdb=" O ARG I 449 " (cutoff:3.500A) removed outlier: 8.422A pdb=" N ARG I 449 " --> pdb=" O GLU I 444 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'I' and resid 478 through 481 removed outlier: 6.544A pdb=" N VAL I 502 " --> pdb=" O ASP I 513 " (cutoff:3.500A) removed outlier: 6.345A pdb=" N ASP I 513 " --> pdb=" O VAL I 502 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'I' and resid 531 through 533 removed outlier: 3.992A pdb=" N VAL I 595 " --> pdb=" O LEU I 549 " (cutoff:3.500A) removed outlier: 4.585A pdb=" N CYS I 598 " --> pdb=" O VAL I 565 " (cutoff:3.500A) removed outlier: 6.385A pdb=" N TYR I 560 " --> pdb=" O ASP I 640 " (cutoff:3.500A) removed outlier: 7.529A pdb=" N THR I 642 " --> pdb=" O TYR I 560 " (cutoff:3.500A) removed outlier: 8.026A pdb=" N LEU I 562 " --> pdb=" O THR I 642 " (cutoff:3.500A) removed outlier: 4.242A pdb=" N VAL I 644 " --> pdb=" O LEU I 562 " (cutoff:3.500A) removed outlier: 7.427A pdb=" N LEU I 564 " --> pdb=" O VAL I 644 " (cutoff:3.500A) removed outlier: 4.444A pdb=" N VAL I 646 " --> pdb=" O LEU I 564 " (cutoff:3.500A) removed outlier: 7.297A pdb=" N VAL I 566 " --> pdb=" O VAL I 646 " (cutoff:3.500A) removed outlier: 4.497A pdb=" N GLY I 648 " --> pdb=" O VAL I 566 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N VAL I 646 " --> pdb=" O CYS I 673 " (cutoff:3.500A) removed outlier: 4.104A pdb=" N GLY I 648 " --> pdb=" O SER I 675 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'I' and resid 537 through 539 Processing sheet with id=AC6, first strand: chain 'B' and resid 51 through 55 removed outlier: 9.218A pdb=" N TYR B 83 " --> pdb=" O LEU B 42 " (cutoff:3.500A) removed outlier: 7.255A pdb=" N VAL B 44 " --> pdb=" O TYR B 83 " (cutoff:3.500A) removed outlier: 7.609A pdb=" N PHE B 85 " --> pdb=" O VAL B 44 " (cutoff:3.500A) removed outlier: 6.271A pdb=" N ASN B 46 " --> pdb=" O PHE B 85 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'E' and resid 68 through 70 Processing sheet with id=AC8, first strand: chain 'A' and resid 42 through 43 Processing sheet with id=AC9, first strand: chain 'A' and resid 50 through 51 Processing sheet with id=AD1, first strand: chain 'L' and resid 103 through 107 removed outlier: 6.836A pdb=" N VAL L 103 " --> pdb=" O LEU L 116 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N LEU L 116 " --> pdb=" O VAL L 103 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'L' and resid 129 through 132 removed outlier: 3.943A pdb=" N ARG L 129 " --> pdb=" O SER L 142 " (cutoff:3.500A) removed outlier: 4.357A pdb=" N VAL L 145 " --> pdb=" O THR L 154 " (cutoff:3.500A) removed outlier: 6.524A pdb=" N THR L 154 " --> pdb=" O VAL L 145 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'L' and resid 192 through 195 Processing sheet with id=AD4, first strand: chain 'L' and resid 305 through 307 removed outlier: 3.680A pdb=" N ALA L 254 " --> pdb=" O ALA L 241 " (cutoff:3.500A) removed outlier: 7.382A pdb=" N ALA L 241 " --> pdb=" O ALA L 254 " (cutoff:3.500A) removed outlier: 4.188A pdb=" N GLY L 225 " --> pdb=" O ALA L 241 " (cutoff:3.500A) removed outlier: 11.757A pdb=" N TRP L 243 " --> pdb=" O TYR L 223 " (cutoff:3.500A) removed outlier: 16.361A pdb=" N TYR L 223 " --> pdb=" O TRP L 243 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N GLY L 225 " --> pdb=" O ALA L 254 " (cutoff:3.500A) removed outlier: 6.908A pdb=" N ALA L 254 " --> pdb=" O GLY L 225 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'L' and resid 263 through 266 Processing sheet with id=AD6, first strand: chain 'L' and resid 319 through 325 removed outlier: 5.589A pdb=" N ILE L 321 " --> pdb=" O LEU L 337 " (cutoff:3.500A) removed outlier: 6.916A pdb=" N LEU L 337 " --> pdb=" O ILE L 321 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N MET L 323 " --> pdb=" O THR L 335 " (cutoff:3.500A) removed outlier: 5.631A pdb=" N VAL L 343 " --> pdb=" O ASN L 338 " (cutoff:3.500A) removed outlier: 6.741A pdb=" N SER L 344 " --> pdb=" O GLU L 361 " (cutoff:3.500A) removed outlier: 4.478A pdb=" N GLU L 361 " --> pdb=" O SER L 344 " (cutoff:3.500A) removed outlier: 6.710A pdb=" N LEU L 346 " --> pdb=" O LYS L 359 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'L' and resid 384 through 390 Processing sheet with id=AD8, first strand: chain 'L' and resid 425 through 432 removed outlier: 5.834A pdb=" N ILE L 428 " --> pdb=" O LEU L 441 " (cutoff:3.500A) removed outlier: 6.522A pdb=" N LEU L 441 " --> pdb=" O ILE L 428 " (cutoff:3.500A) removed outlier: 4.160A pdb=" N LYS L 437 " --> pdb=" O ASP L 432 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'L' and resid 478 through 481 removed outlier: 6.199A pdb=" N VAL L 502 " --> pdb=" O ASP L 513 " (cutoff:3.500A) removed outlier: 5.927A pdb=" N ASP L 513 " --> pdb=" O VAL L 502 " (cutoff:3.500A) removed outlier: 9.878A pdb=" N ASN L 504 " --> pdb=" O MET L 511 " (cutoff:3.500A) removed outlier: 8.499A pdb=" N MET L 511 " --> pdb=" O ASN L 504 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'L' and resid 531 through 534 removed outlier: 3.613A pdb=" N LEU L 549 " --> pdb=" O VAL L 595 " (cutoff:3.500A) removed outlier: 4.565A pdb=" N VAL L 595 " --> pdb=" O LEU L 549 " (cutoff:3.500A) removed outlier: 4.611A pdb=" N CYS L 598 " --> pdb=" O VAL L 565 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N CYS L 673 " --> pdb=" O VAL L 644 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N VAL L 646 " --> pdb=" O CYS L 673 " (cutoff:3.500A) removed outlier: 4.217A pdb=" N GLY L 648 " --> pdb=" O SER L 675 " (cutoff:3.500A) removed outlier: 8.269A pdb=" N GLN L 755 " --> pdb=" O PHE L 722 " (cutoff:3.500A) removed outlier: 6.617A pdb=" N ILE L 724 " --> pdb=" O GLN L 755 " (cutoff:3.500A) removed outlier: 8.103A pdb=" N TYR L 757 " --> pdb=" O ILE L 724 " (cutoff:3.500A) removed outlier: 7.167A pdb=" N HIS L 726 " --> pdb=" O TYR L 757 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'L' and resid 537 through 539 Processing sheet with id=AE3, first strand: chain 'K' and resid 104 through 107 Processing sheet with id=AE4, first strand: chain 'K' and resid 129 through 132 Processing sheet with id=AE5, first strand: chain 'K' and resid 192 through 195 removed outlier: 3.791A pdb=" N VAL K 214 " --> pdb=" O ILE K 200 " (cutoff:3.500A) removed outlier: 7.455A pdb=" N TYR K 202 " --> pdb=" O ARG K 212 " (cutoff:3.500A) removed outlier: 6.273A pdb=" N ARG K 212 " --> pdb=" O TYR K 202 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'K' and resid 222 through 224 Processing sheet with id=AE7, first strand: chain 'K' and resid 222 through 224 removed outlier: 4.710A pdb=" N LEU K 294 " --> pdb=" O MET K 308 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'K' and resid 263 through 266 Processing sheet with id=AE9, first strand: chain 'K' and resid 319 through 326 removed outlier: 5.655A pdb=" N ILE K 321 " --> pdb=" O LEU K 337 " (cutoff:3.500A) removed outlier: 7.329A pdb=" N LEU K 337 " --> pdb=" O ILE K 321 " (cutoff:3.500A) removed outlier: 5.022A pdb=" N MET K 323 " --> pdb=" O THR K 335 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N THR K 335 " --> pdb=" O MET K 323 " (cutoff:3.500A) removed outlier: 5.710A pdb=" N VAL K 343 " --> pdb=" O ASN K 338 " (cutoff:3.500A) removed outlier: 7.076A pdb=" N SER K 344 " --> pdb=" O GLU K 361 " (cutoff:3.500A) removed outlier: 4.851A pdb=" N GLU K 361 " --> pdb=" O SER K 344 " (cutoff:3.500A) removed outlier: 6.541A pdb=" N LEU K 346 " --> pdb=" O LYS K 359 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'K' and resid 384 through 390 Processing sheet with id=AF2, first strand: chain 'K' and resid 427 through 432 removed outlier: 6.571A pdb=" N TYR K 439 " --> pdb=" O LEU K 429 " (cutoff:3.500A) removed outlier: 4.328A pdb=" N TYR K 431 " --> pdb=" O LYS K 437 " (cutoff:3.500A) removed outlier: 6.917A pdb=" N LYS K 437 " --> pdb=" O TYR K 431 " (cutoff:3.500A) removed outlier: 5.059A pdb=" N GLU K 444 " --> pdb=" O ARG K 449 " (cutoff:3.500A) removed outlier: 8.422A pdb=" N ARG K 449 " --> pdb=" O GLU K 444 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'K' and resid 478 through 481 removed outlier: 6.544A pdb=" N VAL K 502 " --> pdb=" O ASP K 513 " (cutoff:3.500A) removed outlier: 6.345A pdb=" N ASP K 513 " --> pdb=" O VAL K 502 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'K' and resid 531 through 533 removed outlier: 3.993A pdb=" N VAL K 595 " --> pdb=" O LEU K 549 " (cutoff:3.500A) removed outlier: 4.586A pdb=" N CYS K 598 " --> pdb=" O VAL K 565 " (cutoff:3.500A) removed outlier: 6.385A pdb=" N TYR K 560 " --> pdb=" O ASP K 640 " (cutoff:3.500A) removed outlier: 7.529A pdb=" N THR K 642 " --> pdb=" O TYR K 560 " (cutoff:3.500A) removed outlier: 8.026A pdb=" N LEU K 562 " --> pdb=" O THR K 642 " (cutoff:3.500A) removed outlier: 4.241A pdb=" N VAL K 644 " --> pdb=" O LEU K 562 " (cutoff:3.500A) removed outlier: 7.428A pdb=" N LEU K 564 " --> pdb=" O VAL K 644 " (cutoff:3.500A) removed outlier: 4.443A pdb=" N VAL K 646 " --> pdb=" O LEU K 564 " (cutoff:3.500A) removed outlier: 7.297A pdb=" N VAL K 566 " --> pdb=" O VAL K 646 " (cutoff:3.500A) removed outlier: 4.496A pdb=" N GLY K 648 " --> pdb=" O VAL K 566 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N VAL K 646 " --> pdb=" O CYS K 673 " (cutoff:3.500A) removed outlier: 4.104A pdb=" N GLY K 648 " --> pdb=" O SER K 675 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'K' and resid 537 through 539 Processing sheet with id=AF6, first strand: chain 'D' and resid 51 through 55 removed outlier: 9.215A pdb=" N TYR D 83 " --> pdb=" O LEU D 42 " (cutoff:3.500A) removed outlier: 7.254A pdb=" N VAL D 44 " --> pdb=" O TYR D 83 " (cutoff:3.500A) removed outlier: 7.609A pdb=" N PHE D 85 " --> pdb=" O VAL D 44 " (cutoff:3.500A) removed outlier: 6.270A pdb=" N ASN D 46 " --> pdb=" O PHE D 85 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'G' and resid 68 through 70 Processing sheet with id=AF8, first strand: chain 'C' and resid 42 through 43 Processing sheet with id=AF9, first strand: chain 'C' and resid 50 through 51 2015 hydrogen bonds defined for protein. 5709 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 17.44 Time building geometry restraints manager: 19.69 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 14443 1.34 - 1.46: 10030 1.46 - 1.58: 21175 1.58 - 1.70: 0 1.70 - 1.82: 344 Bond restraints: 45992 Sorted by residual: bond pdb=" C LEU D 400 " pdb=" N PRO D 401 " ideal model delta sigma weight residual 1.336 1.355 -0.019 9.80e-03 1.04e+04 3.77e+00 bond pdb=" C LEU B 400 " pdb=" N PRO B 401 " ideal model delta sigma weight residual 1.336 1.354 -0.018 9.80e-03 1.04e+04 3.42e+00 bond pdb=" C ILE J 162 " pdb=" N PRO J 163 " ideal model delta sigma weight residual 1.334 1.366 -0.032 2.34e-02 1.83e+03 1.87e+00 bond pdb=" C ILE L 162 " pdb=" N PRO L 163 " ideal model delta sigma weight residual 1.334 1.365 -0.031 2.34e-02 1.83e+03 1.76e+00 bond pdb=" CG GLU L 307 " pdb=" CD GLU L 307 " ideal model delta sigma weight residual 1.516 1.483 0.033 2.50e-02 1.60e+03 1.72e+00 ... (remaining 45987 not shown) Histogram of bond angle deviations from ideal: 93.95 - 101.96: 118 101.96 - 109.98: 6147 109.98 - 117.99: 27792 117.99 - 126.01: 27581 126.01 - 134.02: 674 Bond angle restraints: 62312 Sorted by residual: angle pdb=" N VAL D 227 " pdb=" CA VAL D 227 " pdb=" C VAL D 227 " ideal model delta sigma weight residual 112.80 107.38 5.42 1.15e+00 7.56e-01 2.22e+01 angle pdb=" N VAL B 227 " pdb=" CA VAL B 227 " pdb=" C VAL B 227 " ideal model delta sigma weight residual 112.80 107.38 5.42 1.15e+00 7.56e-01 2.22e+01 angle pdb=" N GLU C 117 " pdb=" CA GLU C 117 " pdb=" CB GLU C 117 " ideal model delta sigma weight residual 110.28 116.45 -6.17 1.55e+00 4.16e-01 1.58e+01 angle pdb=" N GLU A 117 " pdb=" CA GLU A 117 " pdb=" CB GLU A 117 " ideal model delta sigma weight residual 110.28 116.43 -6.15 1.55e+00 4.16e-01 1.57e+01 angle pdb=" N THR K 249 " pdb=" CA THR K 249 " pdb=" C THR K 249 " ideal model delta sigma weight residual 114.56 109.88 4.68 1.27e+00 6.20e-01 1.36e+01 ... (remaining 62307 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.86: 24627 17.86 - 35.72: 2314 35.72 - 53.58: 398 53.58 - 71.44: 53 71.44 - 89.30: 46 Dihedral angle restraints: 27438 sinusoidal: 11064 harmonic: 16374 Sorted by residual: dihedral pdb=" CB CYS J 673 " pdb=" SG CYS J 673 " pdb=" SG CYS J 784 " pdb=" CB CYS J 784 " ideal model delta sinusoidal sigma weight residual 93.00 3.70 89.30 1 1.00e+01 1.00e-02 9.48e+01 dihedral pdb=" CB CYS L 673 " pdb=" SG CYS L 673 " pdb=" SG CYS L 784 " pdb=" CB CYS L 784 " ideal model delta sinusoidal sigma weight residual 93.00 3.73 89.27 1 1.00e+01 1.00e-02 9.48e+01 dihedral pdb=" CB CYS I 474 " pdb=" SG CYS I 474 " pdb=" SG CYS I 492 " pdb=" CB CYS I 492 " ideal model delta sinusoidal sigma weight residual 93.00 10.91 82.09 1 1.00e+01 1.00e-02 8.28e+01 ... (remaining 27435 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.048: 5233 0.048 - 0.096: 1260 0.096 - 0.143: 324 0.143 - 0.191: 7 0.191 - 0.239: 6 Chirality restraints: 6830 Sorted by residual: chirality pdb=" CB ILE I 548 " pdb=" CA ILE I 548 " pdb=" CG1 ILE I 548 " pdb=" CG2 ILE I 548 " both_signs ideal model delta sigma weight residual False 2.64 2.41 0.24 2.00e-01 2.50e+01 1.43e+00 chirality pdb=" CB ILE K 548 " pdb=" CA ILE K 548 " pdb=" CG1 ILE K 548 " pdb=" CG2 ILE K 548 " both_signs ideal model delta sigma weight residual False 2.64 2.41 0.24 2.00e-01 2.50e+01 1.38e+00 chirality pdb=" CB ILE I 438 " pdb=" CA ILE I 438 " pdb=" CG1 ILE I 438 " pdb=" CG2 ILE I 438 " both_signs ideal model delta sigma weight residual False 2.64 2.43 0.21 2.00e-01 2.50e+01 1.12e+00 ... (remaining 6827 not shown) Planarity restraints: 7980 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE A 329 " 0.014 2.00e-02 2.50e+03 1.72e-02 5.16e+00 pdb=" CG PHE A 329 " -0.040 2.00e-02 2.50e+03 pdb=" CD1 PHE A 329 " 0.013 2.00e-02 2.50e+03 pdb=" CD2 PHE A 329 " 0.009 2.00e-02 2.50e+03 pdb=" CE1 PHE A 329 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 PHE A 329 " 0.004 2.00e-02 2.50e+03 pdb=" CZ PHE A 329 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE C 329 " 0.014 2.00e-02 2.50e+03 1.70e-02 5.08e+00 pdb=" CG PHE C 329 " -0.039 2.00e-02 2.50e+03 pdb=" CD1 PHE C 329 " 0.014 2.00e-02 2.50e+03 pdb=" CD2 PHE C 329 " 0.009 2.00e-02 2.50e+03 pdb=" CE1 PHE C 329 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 PHE C 329 " 0.004 2.00e-02 2.50e+03 pdb=" CZ PHE C 329 " -0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LEU D 400 " 0.032 5.00e-02 4.00e+02 4.88e-02 3.81e+00 pdb=" N PRO D 401 " -0.084 5.00e-02 4.00e+02 pdb=" CA PRO D 401 " 0.024 5.00e-02 4.00e+02 pdb=" CD PRO D 401 " 0.028 5.00e-02 4.00e+02 ... (remaining 7977 not shown) Histogram of nonbonded interaction distances: 2.09 - 2.65: 925 2.65 - 3.21: 45865 3.21 - 3.78: 76174 3.78 - 4.34: 101611 4.34 - 4.90: 157717 Nonbonded interactions: 382292 Sorted by model distance: nonbonded pdb=" OH TYR K 654 " pdb=" O THR K 708 " model vdw 2.089 2.440 nonbonded pdb=" OH TYR I 654 " pdb=" O THR I 708 " model vdw 2.090 2.440 nonbonded pdb=" O HIS E 92 " pdb=" ND2 ASN E 96 " model vdw 2.097 2.520 nonbonded pdb=" O MET B 238 " pdb=" OG1 THR B 241 " model vdw 2.115 2.440 nonbonded pdb=" O MET D 238 " pdb=" OG1 THR D 241 " model vdw 2.115 2.440 ... (remaining 382287 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 2 through 218 or resid 224 through 495)) selection = chain 'B' selection = (chain 'C' and (resid 2 through 218 or resid 224 through 495)) selection = chain 'D' } ncs_group { reference = (chain 'E' and resid 37 through 216) selection = chain 'F' selection = (chain 'G' and resid 37 through 216) selection = chain 'H' } ncs_group { reference = (chain 'I' and (resid 31 through 301 or resid 303 through 787)) selection = chain 'J' selection = (chain 'K' and (resid 31 through 301 or resid 303 through 787)) selection = chain 'L' } 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: 1.730 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: 0.050 Extract box with map and model: 8.140 Check model and map are aligned: 0.670 Set scattering table: 0.370 Process input model: 114.970 Find NCS groups from input model: 3.040 Set up NCS constraints: 0.170 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: 0.000 Load rotamer database and sin/cos tables:2.670 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 131.810 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6331 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 45992 Z= 0.162 Angle : 0.618 8.590 62312 Z= 0.324 Chirality : 0.044 0.239 6830 Planarity : 0.004 0.049 7980 Dihedral : 14.211 86.941 16838 Min Nonbonded Distance : 2.089 Molprobity Statistics. All-atom Clashscore : 18.26 Ramachandran Plot: Outliers : 0.07 % Allowed : 6.89 % Favored : 93.04 % Rotamer: Outliers : 0.00 % Allowed : 0.45 % Favored : 99.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.71 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.78 (0.11), residues: 5516 helix: 0.57 (0.11), residues: 2150 sheet: -0.39 (0.19), residues: 756 loop : -1.50 (0.13), residues: 2610 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP G 129 HIS 0.004 0.001 HIS H 174 PHE 0.040 0.001 PHE A 329 TYR 0.023 0.001 TYR K 153 ARG 0.006 0.000 ARG D 141 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11032 Ramachandran restraints generated. 5516 Oldfield, 0 Emsley, 5516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11032 Ramachandran restraints generated. 5516 Oldfield, 0 Emsley, 5516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 418 residues out of total 4894 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 418 time to evaluate : 4.808 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: J 634 LEU cc_start: 0.7667 (tp) cc_final: 0.7405 (mt) REVERT: I 460 ASN cc_start: 0.5774 (p0) cc_final: 0.5450 (p0) REVERT: I 511 MET cc_start: 0.5517 (mpp) cc_final: 0.3716 (mtp) REVERT: I 763 TYR cc_start: 0.7376 (m-10) cc_final: 0.7110 (m-10) REVERT: B 329 PHE cc_start: 0.7172 (t80) cc_final: 0.6904 (t80) REVERT: E 76 GLN cc_start: 0.7248 (tp40) cc_final: 0.6861 (pp30) REVERT: E 129 TRP cc_start: 0.6199 (m-90) cc_final: 0.5223 (m-10) REVERT: E 182 MET cc_start: 0.5212 (tpp) cc_final: 0.3907 (mmm) REVERT: A 368 MET cc_start: 0.7244 (mpp) cc_final: 0.6351 (mpp) REVERT: L 634 LEU cc_start: 0.7655 (tp) cc_final: 0.7385 (mt) REVERT: K 460 ASN cc_start: 0.5743 (p0) cc_final: 0.5404 (p0) REVERT: K 511 MET cc_start: 0.5554 (mpp) cc_final: 0.3761 (mtp) REVERT: K 763 TYR cc_start: 0.7395 (m-10) cc_final: 0.7131 (m-10) REVERT: D 329 PHE cc_start: 0.7201 (t80) cc_final: 0.6900 (t80) REVERT: G 76 GLN cc_start: 0.7247 (tp40) cc_final: 0.6857 (pp30) REVERT: G 129 TRP cc_start: 0.6229 (m-90) cc_final: 0.5252 (m-10) REVERT: G 182 MET cc_start: 0.5226 (tpp) cc_final: 0.3906 (mmm) REVERT: C 368 MET cc_start: 0.7141 (mpp) cc_final: 0.6171 (mpp) outliers start: 0 outliers final: 0 residues processed: 418 average time/residue: 0.5486 time to fit residues: 395.2299 Evaluate side-chains 286 residues out of total 4894 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 286 time to evaluate : 5.186 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 552 random chunks: chunk 466 optimal weight: 9.9990 chunk 418 optimal weight: 30.0000 chunk 232 optimal weight: 6.9990 chunk 142 optimal weight: 30.0000 chunk 282 optimal weight: 30.0000 chunk 223 optimal weight: 10.0000 chunk 432 optimal weight: 8.9990 chunk 167 optimal weight: 10.0000 chunk 263 optimal weight: 9.9990 chunk 322 optimal weight: 4.9990 chunk 501 optimal weight: 7.9990 overall best weight: 7.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** J 517 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 612 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 191 GLN ** I 242 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 392 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 755 GLN ** F 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 144 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 80 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 132 ASN ** E 174 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 517 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 191 GLN ** K 242 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 392 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 755 GLN ** H 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 144 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 80 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 132 ASN ** G 174 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6477 moved from start: 0.1273 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 45992 Z= 0.296 Angle : 0.650 8.538 62312 Z= 0.346 Chirality : 0.045 0.190 6830 Planarity : 0.005 0.055 7980 Dihedral : 4.841 23.952 6130 Min Nonbonded Distance : 2.077 Molprobity Statistics. All-atom Clashscore : 25.02 Ramachandran Plot: Outliers : 0.04 % Allowed : 8.59 % Favored : 91.37 % Rotamer: Outliers : 0.27 % Allowed : 8.07 % Favored : 91.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.71 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.10 (0.11), residues: 5516 helix: 0.32 (0.11), residues: 2192 sheet: -0.70 (0.19), residues: 790 loop : -1.68 (0.13), residues: 2534 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP L 229 HIS 0.006 0.001 HIS E 92 PHE 0.026 0.002 PHE D 194 TYR 0.034 0.002 TYR E 93 ARG 0.005 0.001 ARG J 747 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11032 Ramachandran restraints generated. 5516 Oldfield, 0 Emsley, 5516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11032 Ramachandran restraints generated. 5516 Oldfield, 0 Emsley, 5516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 356 residues out of total 4894 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 343 time to evaluate : 5.306 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: J 511 MET cc_start: 0.3179 (ptt) cc_final: 0.2970 (ptt) REVERT: J 634 LEU cc_start: 0.7673 (tp) cc_final: 0.7465 (mt) REVERT: I 264 MET cc_start: 0.5668 (mmm) cc_final: 0.5382 (mmm) REVERT: I 511 MET cc_start: 0.5827 (mpp) cc_final: 0.4524 (mtt) REVERT: B 155 ASP cc_start: 0.7165 (m-30) cc_final: 0.6689 (t0) REVERT: E 129 TRP cc_start: 0.6257 (m-90) cc_final: 0.5425 (m-10) REVERT: E 182 MET cc_start: 0.4965 (tpp) cc_final: 0.3989 (mmm) REVERT: A 117 GLU cc_start: 0.8508 (OUTLIER) cc_final: 0.8056 (pp20) REVERT: A 368 MET cc_start: 0.7205 (mpp) cc_final: 0.6293 (mpp) REVERT: L 634 LEU cc_start: 0.7674 (tp) cc_final: 0.7460 (mt) REVERT: K 264 MET cc_start: 0.5662 (mmm) cc_final: 0.5364 (mmm) REVERT: K 511 MET cc_start: 0.5860 (mpp) cc_final: 0.4573 (mtt) REVERT: D 155 ASP cc_start: 0.7140 (m-30) cc_final: 0.6679 (t0) REVERT: G 129 TRP cc_start: 0.6291 (m-90) cc_final: 0.5444 (m-10) REVERT: G 182 MET cc_start: 0.4995 (tpp) cc_final: 0.4026 (mmm) REVERT: C 117 GLU cc_start: 0.8521 (OUTLIER) cc_final: 0.8081 (pp20) REVERT: C 368 MET cc_start: 0.7133 (mpp) cc_final: 0.5994 (mpp) outliers start: 13 outliers final: 4 residues processed: 353 average time/residue: 0.5201 time to fit residues: 320.0779 Evaluate side-chains 263 residues out of total 4894 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 257 time to evaluate : 4.779 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 552 random chunks: chunk 278 optimal weight: 0.3980 chunk 155 optimal weight: 40.0000 chunk 417 optimal weight: 20.0000 chunk 341 optimal weight: 20.0000 chunk 138 optimal weight: 2.9990 chunk 502 optimal weight: 7.9990 chunk 542 optimal weight: 3.9990 chunk 447 optimal weight: 5.9990 chunk 497 optimal weight: 50.0000 chunk 171 optimal weight: 40.0000 chunk 402 optimal weight: 20.0000 overall best weight: 4.2788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** I 190 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 191 GLN ** I 392 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 755 GLN F 47 ASN ** F 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 144 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 308 GLN ** B 477 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 80 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 174 HIS ** K 190 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 191 GLN K 392 GLN K 755 GLN H 47 ASN ** H 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 144 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 308 GLN ** D 477 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 80 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 174 HIS Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6423 moved from start: 0.1412 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 45992 Z= 0.207 Angle : 0.601 7.754 62312 Z= 0.313 Chirality : 0.044 0.184 6830 Planarity : 0.004 0.054 7980 Dihedral : 4.740 24.826 6130 Min Nonbonded Distance : 2.080 Molprobity Statistics. All-atom Clashscore : 20.95 Ramachandran Plot: Outliers : 0.04 % Allowed : 7.49 % Favored : 92.48 % Rotamer: Outliers : 0.06 % Allowed : 3.78 % Favored : 96.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.71 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.05 (0.11), residues: 5516 helix: 0.41 (0.11), residues: 2190 sheet: -0.73 (0.19), residues: 782 loop : -1.67 (0.13), residues: 2544 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP I 106 HIS 0.007 0.001 HIS A 491 PHE 0.020 0.001 PHE G 178 TYR 0.017 0.001 TYR I 153 ARG 0.004 0.000 ARG K 535 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11032 Ramachandran restraints generated. 5516 Oldfield, 0 Emsley, 5516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11032 Ramachandran restraints generated. 5516 Oldfield, 0 Emsley, 5516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 367 residues out of total 4894 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 364 time to evaluate : 5.358 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: I 460 ASN cc_start: 0.6310 (p0) cc_final: 0.5859 (p0) REVERT: B 155 ASP cc_start: 0.7153 (m-30) cc_final: 0.6699 (t0) REVERT: E 78 TYR cc_start: 0.6011 (t80) cc_final: 0.5335 (t80) REVERT: A 117 GLU cc_start: 0.8478 (OUTLIER) cc_final: 0.7994 (pp20) REVERT: A 342 MET cc_start: 0.8083 (mmt) cc_final: 0.7791 (mmm) REVERT: A 368 MET cc_start: 0.7056 (mpp) cc_final: 0.6111 (mpp) REVERT: L 511 MET cc_start: 0.3349 (ptt) cc_final: 0.3124 (ptt) REVERT: K 460 ASN cc_start: 0.6252 (p0) cc_final: 0.5793 (p0) REVERT: D 155 ASP cc_start: 0.7130 (m-30) cc_final: 0.6691 (t0) REVERT: G 78 TYR cc_start: 0.6155 (t80) cc_final: 0.5861 (t80) REVERT: G 129 TRP cc_start: 0.6242 (m-90) cc_final: 0.5369 (m-10) REVERT: C 117 GLU cc_start: 0.8493 (OUTLIER) cc_final: 0.8021 (pp20) REVERT: C 342 MET cc_start: 0.8033 (mmt) cc_final: 0.7733 (mmm) REVERT: C 368 MET cc_start: 0.6980 (mpp) cc_final: 0.5799 (mpp) outliers start: 3 outliers final: 0 residues processed: 364 average time/residue: 0.5234 time to fit residues: 326.2381 Evaluate side-chains 269 residues out of total 4894 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 267 time to evaluate : 5.064 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 552 random chunks: chunk 496 optimal weight: 7.9990 chunk 377 optimal weight: 50.0000 chunk 260 optimal weight: 0.3980 chunk 55 optimal weight: 6.9990 chunk 239 optimal weight: 9.9990 chunk 337 optimal weight: 20.0000 chunk 503 optimal weight: 0.0980 chunk 533 optimal weight: 8.9990 chunk 263 optimal weight: 10.0000 chunk 477 optimal weight: 9.9990 chunk 143 optimal weight: 0.7980 overall best weight: 3.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** J 190 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 669 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 190 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 191 GLN I 392 GLN ** I 547 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 144 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 80 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 478 HIS ** L 190 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 669 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 190 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 191 GLN ** K 547 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 144 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 80 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 478 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6402 moved from start: 0.1559 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 45992 Z= 0.186 Angle : 0.583 8.181 62312 Z= 0.303 Chirality : 0.043 0.333 6830 Planarity : 0.004 0.043 7980 Dihedral : 4.629 24.942 6130 Min Nonbonded Distance : 2.079 Molprobity Statistics. All-atom Clashscore : 20.11 Ramachandran Plot: Outliers : 0.04 % Allowed : 8.23 % Favored : 91.73 % Rotamer: Outliers : 0.02 % Allowed : 3.41 % Favored : 96.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.71 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.00 (0.11), residues: 5516 helix: 0.45 (0.11), residues: 2190 sheet: -0.64 (0.19), residues: 774 loop : -1.65 (0.13), residues: 2552 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP B 8 HIS 0.006 0.001 HIS A 491 PHE 0.043 0.001 PHE A 240 TYR 0.021 0.001 TYR K 153 ARG 0.004 0.000 ARG L 641 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11032 Ramachandran restraints generated. 5516 Oldfield, 0 Emsley, 5516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11032 Ramachandran restraints generated. 5516 Oldfield, 0 Emsley, 5516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 365 residues out of total 4894 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 364 time to evaluate : 5.429 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: J 511 MET cc_start: 0.3385 (ptt) cc_final: 0.3122 (ptt) REVERT: I 264 MET cc_start: 0.5739 (mmm) cc_final: 0.5328 (mmm) REVERT: I 460 ASN cc_start: 0.6411 (p0) cc_final: 0.5894 (p0) REVERT: B 155 ASP cc_start: 0.7364 (m-30) cc_final: 0.6907 (t0) REVERT: E 78 TYR cc_start: 0.6376 (t80) cc_final: 0.5824 (t80) REVERT: A 342 MET cc_start: 0.8031 (mmt) cc_final: 0.7770 (mmm) REVERT: A 368 MET cc_start: 0.7246 (mpp) cc_final: 0.6199 (mpp) REVERT: A 445 MET cc_start: 0.4147 (tmm) cc_final: 0.2151 (mmm) REVERT: L 511 MET cc_start: 0.3344 (ptt) cc_final: 0.3124 (ptt) REVERT: K 264 MET cc_start: 0.5730 (mmm) cc_final: 0.5313 (mmm) REVERT: K 460 ASN cc_start: 0.6353 (p0) cc_final: 0.5826 (p0) REVERT: D 155 ASP cc_start: 0.7341 (m-30) cc_final: 0.6899 (t0) REVERT: G 78 TYR cc_start: 0.6378 (t80) cc_final: 0.5827 (t80) REVERT: G 129 TRP cc_start: 0.6215 (m-90) cc_final: 0.5412 (m-10) REVERT: C 342 MET cc_start: 0.7981 (mmt) cc_final: 0.7735 (mmm) REVERT: C 368 MET cc_start: 0.7196 (mpp) cc_final: 0.5975 (mpp) REVERT: C 445 MET cc_start: 0.4171 (tmm) cc_final: 0.2169 (mmm) outliers start: 1 outliers final: 0 residues processed: 364 average time/residue: 0.5463 time to fit residues: 340.8571 Evaluate side-chains 260 residues out of total 4894 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 260 time to evaluate : 5.157 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 552 random chunks: chunk 444 optimal weight: 0.0370 chunk 302 optimal weight: 5.9990 chunk 7 optimal weight: 20.0000 chunk 397 optimal weight: 30.0000 chunk 220 optimal weight: 7.9990 chunk 455 optimal weight: 7.9990 chunk 368 optimal weight: 7.9990 chunk 0 optimal weight: 40.0000 chunk 272 optimal weight: 5.9990 chunk 478 optimal weight: 0.0970 chunk 134 optimal weight: 6.9990 overall best weight: 3.8262 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 65 GLN ** J 190 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 190 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 191 GLN ** I 547 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 144 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 80 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 132 ASN A 478 HIS L 65 GLN ** L 190 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 190 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 191 GLN ** K 547 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 144 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 80 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 478 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6408 moved from start: 0.1734 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 45992 Z= 0.195 Angle : 0.586 8.250 62312 Z= 0.305 Chirality : 0.044 0.263 6830 Planarity : 0.004 0.066 7980 Dihedral : 4.620 24.664 6130 Min Nonbonded Distance : 2.071 Molprobity Statistics. All-atom Clashscore : 20.79 Ramachandran Plot: Outliers : 0.04 % Allowed : 7.87 % Favored : 92.10 % Rotamer: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.71 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.04 (0.11), residues: 5516 helix: 0.44 (0.11), residues: 2192 sheet: -0.74 (0.18), residues: 800 loop : -1.69 (0.13), residues: 2524 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP D 8 HIS 0.005 0.001 HIS C 491 PHE 0.023 0.001 PHE A 240 TYR 0.021 0.001 TYR K 153 ARG 0.005 0.000 ARG B 247 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11032 Ramachandran restraints generated. 5516 Oldfield, 0 Emsley, 5516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11032 Ramachandran restraints generated. 5516 Oldfield, 0 Emsley, 5516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 349 residues out of total 4894 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 349 time to evaluate : 5.301 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: J 511 MET cc_start: 0.3303 (ptt) cc_final: 0.3054 (ptt) REVERT: I 460 ASN cc_start: 0.6358 (p0) cc_final: 0.5831 (p0) REVERT: I 511 MET cc_start: 0.5414 (mtm) cc_final: 0.4082 (mtp) REVERT: B 155 ASP cc_start: 0.7375 (m-30) cc_final: 0.6911 (t0) REVERT: E 76 GLN cc_start: 0.7872 (pp30) cc_final: 0.7499 (tp40) REVERT: E 78 TYR cc_start: 0.6201 (t80) cc_final: 0.5532 (t80) REVERT: A 342 MET cc_start: 0.8146 (mmt) cc_final: 0.7846 (mmm) REVERT: A 364 THR cc_start: 0.7125 (t) cc_final: 0.6801 (t) REVERT: A 368 MET cc_start: 0.7118 (mpp) cc_final: 0.6006 (mpp) REVERT: A 445 MET cc_start: 0.4089 (tmm) cc_final: 0.2177 (mmm) REVERT: L 511 MET cc_start: 0.3278 (ptt) cc_final: 0.3024 (ptt) REVERT: K 460 ASN cc_start: 0.6299 (p0) cc_final: 0.5767 (p0) REVERT: K 511 MET cc_start: 0.5446 (mtm) cc_final: 0.4122 (mtp) REVERT: D 155 ASP cc_start: 0.7350 (m-30) cc_final: 0.6903 (t0) REVERT: G 78 TYR cc_start: 0.6282 (t80) cc_final: 0.5641 (t80) REVERT: C 342 MET cc_start: 0.8076 (mmt) cc_final: 0.7795 (mmm) REVERT: C 364 THR cc_start: 0.7006 (t) cc_final: 0.6645 (t) REVERT: C 368 MET cc_start: 0.7102 (mpp) cc_final: 0.5721 (mpp) REVERT: C 445 MET cc_start: 0.4122 (tmm) cc_final: 0.2200 (mmm) outliers start: 0 outliers final: 0 residues processed: 349 average time/residue: 0.5264 time to fit residues: 317.9391 Evaluate side-chains 259 residues out of total 4894 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 259 time to evaluate : 4.973 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 552 random chunks: chunk 179 optimal weight: 8.9990 chunk 480 optimal weight: 3.9990 chunk 105 optimal weight: 9.9990 chunk 313 optimal weight: 20.0000 chunk 131 optimal weight: 5.9990 chunk 534 optimal weight: 0.0870 chunk 443 optimal weight: 4.9990 chunk 247 optimal weight: 0.9980 chunk 44 optimal weight: 4.9990 chunk 176 optimal weight: 10.0000 chunk 280 optimal weight: 5.9990 overall best weight: 3.0164 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** J 190 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 190 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 191 GLN ** I 547 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 144 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 417 GLN ** E 80 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 190 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 190 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 191 GLN ** K 547 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 144 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 80 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6389 moved from start: 0.1823 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 45992 Z= 0.177 Angle : 0.580 8.000 62312 Z= 0.300 Chirality : 0.044 0.293 6830 Planarity : 0.004 0.056 7980 Dihedral : 4.588 24.965 6130 Min Nonbonded Distance : 2.066 Molprobity Statistics. All-atom Clashscore : 19.10 Ramachandran Plot: Outliers : 0.04 % Allowed : 7.99 % Favored : 91.97 % Rotamer: Outliers : 0.00 % Allowed : 2.47 % Favored : 97.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.71 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.98 (0.11), residues: 5516 helix: 0.47 (0.11), residues: 2192 sheet: -0.67 (0.19), residues: 796 loop : -1.65 (0.13), residues: 2528 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 19 HIS 0.005 0.001 HIS C 491 PHE 0.019 0.001 PHE C 240 TYR 0.018 0.001 TYR E 93 ARG 0.005 0.000 ARG L 713 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11032 Ramachandran restraints generated. 5516 Oldfield, 0 Emsley, 5516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11032 Ramachandran restraints generated. 5516 Oldfield, 0 Emsley, 5516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 362 residues out of total 4894 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 362 time to evaluate : 4.968 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: J 511 MET cc_start: 0.3333 (ptt) cc_final: 0.3043 (ptt) REVERT: J 633 MET cc_start: 0.5929 (tpt) cc_final: 0.5193 (mmt) REVERT: I 264 MET cc_start: 0.5715 (mmm) cc_final: 0.5224 (mmm) REVERT: I 460 ASN cc_start: 0.6341 (p0) cc_final: 0.5808 (p0) REVERT: I 511 MET cc_start: 0.5623 (mtm) cc_final: 0.4333 (mtp) REVERT: B 155 ASP cc_start: 0.7394 (m-30) cc_final: 0.6942 (t0) REVERT: E 76 GLN cc_start: 0.7914 (pp30) cc_final: 0.7494 (tp40) REVERT: E 78 TYR cc_start: 0.6097 (t80) cc_final: 0.5332 (t80) REVERT: A 20 MET cc_start: 0.6422 (mpp) cc_final: 0.5563 (mtm) REVERT: A 203 VAL cc_start: 0.7979 (t) cc_final: 0.7778 (t) REVERT: A 364 THR cc_start: 0.7097 (t) cc_final: 0.6443 (t) REVERT: A 368 MET cc_start: 0.7193 (mpp) cc_final: 0.6143 (mpp) REVERT: A 445 MET cc_start: 0.4178 (tmm) cc_final: 0.2261 (mmm) REVERT: L 42 LEU cc_start: 0.8175 (pp) cc_final: 0.7965 (pp) REVERT: L 511 MET cc_start: 0.3148 (ptt) cc_final: 0.2866 (ptt) REVERT: L 633 MET cc_start: 0.5929 (tpt) cc_final: 0.5188 (mmt) REVERT: K 264 MET cc_start: 0.5695 (mmm) cc_final: 0.5194 (mmm) REVERT: K 460 ASN cc_start: 0.6284 (p0) cc_final: 0.5743 (p0) REVERT: K 511 MET cc_start: 0.5657 (mtm) cc_final: 0.4370 (mtp) REVERT: D 155 ASP cc_start: 0.7370 (m-30) cc_final: 0.6936 (t0) REVERT: G 78 TYR cc_start: 0.6179 (t80) cc_final: 0.5402 (t80) REVERT: C 20 MET cc_start: 0.6442 (mpp) cc_final: 0.5599 (mtm) REVERT: C 203 VAL cc_start: 0.7908 (t) cc_final: 0.7704 (t) REVERT: C 342 MET cc_start: 0.8037 (mmt) cc_final: 0.7831 (mmm) REVERT: C 364 THR cc_start: 0.7015 (t) cc_final: 0.6312 (t) REVERT: C 368 MET cc_start: 0.7162 (mpp) cc_final: 0.5886 (mpp) outliers start: 0 outliers final: 0 residues processed: 362 average time/residue: 0.5171 time to fit residues: 320.4638 Evaluate side-chains 264 residues out of total 4894 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 264 time to evaluate : 5.069 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 552 random chunks: chunk 514 optimal weight: 20.0000 chunk 60 optimal weight: 0.0870 chunk 304 optimal weight: 3.9990 chunk 390 optimal weight: 7.9990 chunk 302 optimal weight: 6.9990 chunk 449 optimal weight: 20.0000 chunk 298 optimal weight: 5.9990 chunk 532 optimal weight: 7.9990 chunk 332 optimal weight: 10.0000 chunk 324 optimal weight: 10.0000 chunk 245 optimal weight: 40.0000 overall best weight: 5.0166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** J 190 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 190 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 191 GLN ** F 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 144 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 80 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 478 HIS ** L 190 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 190 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 191 GLN ** H 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 144 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 417 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 80 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 132 ASN C 478 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6430 moved from start: 0.2032 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 45992 Z= 0.224 Angle : 0.605 7.985 62312 Z= 0.316 Chirality : 0.044 0.281 6830 Planarity : 0.004 0.047 7980 Dihedral : 4.699 24.912 6130 Min Nonbonded Distance : 2.088 Molprobity Statistics. All-atom Clashscore : 21.77 Ramachandran Plot: Outliers : 0.04 % Allowed : 8.36 % Favored : 91.61 % Rotamer: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.71 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.06 (0.11), residues: 5516 helix: 0.40 (0.11), residues: 2192 sheet: -0.62 (0.19), residues: 770 loop : -1.71 (0.13), residues: 2554 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP C 19 HIS 0.007 0.001 HIS A 491 PHE 0.032 0.002 PHE J 79 TYR 0.019 0.002 TYR B 413 ARG 0.009 0.000 ARG K 527 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11032 Ramachandran restraints generated. 5516 Oldfield, 0 Emsley, 5516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11032 Ramachandran restraints generated. 5516 Oldfield, 0 Emsley, 5516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 348 residues out of total 4894 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 348 time to evaluate : 5.691 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: J 511 MET cc_start: 0.3255 (ptt) cc_final: 0.2865 (ptt) REVERT: J 633 MET cc_start: 0.5943 (tpt) cc_final: 0.5398 (mmt) REVERT: I 460 ASN cc_start: 0.6543 (p0) cc_final: 0.5976 (p0) REVERT: I 511 MET cc_start: 0.5693 (mtm) cc_final: 0.4420 (mtp) REVERT: B 155 ASP cc_start: 0.7384 (m-30) cc_final: 0.6933 (t0) REVERT: E 76 GLN cc_start: 0.7962 (pp30) cc_final: 0.7445 (tp40) REVERT: E 78 TYR cc_start: 0.5920 (t80) cc_final: 0.5011 (t80) REVERT: L 42 LEU cc_start: 0.8135 (pp) cc_final: 0.7898 (pp) REVERT: L 511 MET cc_start: 0.3236 (ptt) cc_final: 0.2866 (ptt) REVERT: L 633 MET cc_start: 0.5938 (tpt) cc_final: 0.5392 (mmt) REVERT: K 460 ASN cc_start: 0.6498 (p0) cc_final: 0.5922 (p0) REVERT: K 511 MET cc_start: 0.5710 (mtm) cc_final: 0.4446 (mtp) REVERT: D 155 ASP cc_start: 0.7357 (m-30) cc_final: 0.6924 (t0) REVERT: G 78 TYR cc_start: 0.5986 (t80) cc_final: 0.5073 (t80) REVERT: C 27 MET cc_start: 0.1755 (tpt) cc_final: -0.0289 (ttp) REVERT: C 342 MET cc_start: 0.8148 (mmt) cc_final: 0.7886 (mmm) REVERT: C 445 MET cc_start: 0.4365 (tmm) cc_final: 0.2335 (mmm) outliers start: 0 outliers final: 0 residues processed: 348 average time/residue: 0.5363 time to fit residues: 320.4745 Evaluate side-chains 245 residues out of total 4894 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 245 time to evaluate : 5.861 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 552 random chunks: chunk 329 optimal weight: 7.9990 chunk 212 optimal weight: 7.9990 chunk 317 optimal weight: 6.9990 chunk 160 optimal weight: 8.9990 chunk 104 optimal weight: 9.9990 chunk 103 optimal weight: 0.0770 chunk 338 optimal weight: 6.9990 chunk 362 optimal weight: 9.9990 chunk 263 optimal weight: 5.9990 chunk 49 optimal weight: 20.0000 chunk 418 optimal weight: 9.9990 overall best weight: 5.6146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** J 190 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 190 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 191 GLN ** F 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 144 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 80 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 478 HIS ** L 190 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 626 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 190 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 191 GLN ** K 242 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 46 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 144 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 417 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 80 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 478 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6453 moved from start: 0.2255 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 45992 Z= 0.242 Angle : 0.634 8.749 62312 Z= 0.332 Chirality : 0.045 0.256 6830 Planarity : 0.004 0.045 7980 Dihedral : 4.819 24.332 6130 Min Nonbonded Distance : 2.098 Molprobity Statistics. All-atom Clashscore : 22.85 Ramachandran Plot: Outliers : 0.04 % Allowed : 8.74 % Favored : 91.23 % Rotamer: Outliers : 0.00 % Allowed : 1.63 % Favored : 98.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.71 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.19 (0.11), residues: 5516 helix: 0.30 (0.11), residues: 2188 sheet: -0.73 (0.19), residues: 776 loop : -1.78 (0.12), residues: 2552 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP C 19 HIS 0.006 0.001 HIS E 92 PHE 0.027 0.002 PHE B 361 TYR 0.058 0.002 TYR E 93 ARG 0.005 0.000 ARG L 713 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11032 Ramachandran restraints generated. 5516 Oldfield, 0 Emsley, 5516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11032 Ramachandran restraints generated. 5516 Oldfield, 0 Emsley, 5516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 349 residues out of total 4894 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 349 time to evaluate : 5.684 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: J 511 MET cc_start: 0.3242 (ptt) cc_final: 0.2921 (ptt) REVERT: J 546 MET cc_start: 0.5812 (tmm) cc_final: 0.5186 (tmm) REVERT: J 633 MET cc_start: 0.6009 (tpt) cc_final: 0.5290 (mmt) REVERT: I 264 MET cc_start: 0.5645 (mmm) cc_final: 0.5172 (mmm) REVERT: I 316 MET cc_start: -0.0680 (mtt) cc_final: -0.1033 (ttt) REVERT: I 460 ASN cc_start: 0.6165 (p0) cc_final: 0.5526 (p0) REVERT: I 511 MET cc_start: 0.5866 (mtm) cc_final: 0.4608 (mtp) REVERT: B 155 ASP cc_start: 0.7279 (m-30) cc_final: 0.6878 (t0) REVERT: E 78 TYR cc_start: 0.5765 (t80) cc_final: 0.4766 (t80) REVERT: A 27 MET cc_start: 0.1685 (tpt) cc_final: 0.1212 (tpt) REVERT: A 364 THR cc_start: 0.7431 (t) cc_final: 0.6902 (t) REVERT: A 368 MET cc_start: 0.7316 (mpp) cc_final: 0.6060 (mpp) REVERT: A 445 MET cc_start: 0.4407 (tmm) cc_final: 0.2297 (mmm) REVERT: L 42 LEU cc_start: 0.8077 (pp) cc_final: 0.7814 (pp) REVERT: L 511 MET cc_start: 0.3227 (ptt) cc_final: 0.2896 (ptt) REVERT: L 546 MET cc_start: 0.5844 (tmm) cc_final: 0.5215 (tmm) REVERT: L 633 MET cc_start: 0.6004 (tpt) cc_final: 0.5282 (mmt) REVERT: K 264 MET cc_start: 0.5644 (mmm) cc_final: 0.5155 (mmm) REVERT: K 316 MET cc_start: -0.0709 (mtt) cc_final: -0.1062 (ttt) REVERT: K 460 ASN cc_start: 0.6110 (p0) cc_final: 0.5464 (p0) REVERT: K 511 MET cc_start: 0.5895 (mtm) cc_final: 0.4639 (mtp) REVERT: D 155 ASP cc_start: 0.7257 (m-30) cc_final: 0.6872 (t0) REVERT: G 78 TYR cc_start: 0.5883 (t80) cc_final: 0.4811 (t80) REVERT: C 342 MET cc_start: 0.7954 (mmt) cc_final: 0.7698 (mmm) REVERT: C 364 THR cc_start: 0.7283 (t) cc_final: 0.6791 (t) REVERT: C 368 MET cc_start: 0.7278 (mpp) cc_final: 0.5698 (mpp) REVERT: C 445 MET cc_start: 0.4481 (tmm) cc_final: 0.2367 (mmm) outliers start: 0 outliers final: 0 residues processed: 349 average time/residue: 0.5330 time to fit residues: 321.3707 Evaluate side-chains 249 residues out of total 4894 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 249 time to evaluate : 5.263 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 552 random chunks: chunk 483 optimal weight: 6.9990 chunk 509 optimal weight: 30.0000 chunk 465 optimal weight: 6.9990 chunk 495 optimal weight: 50.0000 chunk 298 optimal weight: 30.0000 chunk 215 optimal weight: 30.0000 chunk 389 optimal weight: 50.0000 chunk 152 optimal weight: 8.9990 chunk 448 optimal weight: 20.0000 chunk 468 optimal weight: 5.9990 chunk 494 optimal weight: 8.9990 overall best weight: 7.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** J 612 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 626 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 190 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 191 GLN ** I 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 144 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 204 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 478 HIS ** L 190 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 612 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 626 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 190 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 191 GLN ** K 242 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 144 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 417 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 204 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 478 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6502 moved from start: 0.2561 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 45992 Z= 0.304 Angle : 0.691 9.057 62312 Z= 0.364 Chirality : 0.046 0.301 6830 Planarity : 0.005 0.047 7980 Dihedral : 5.085 24.075 6130 Min Nonbonded Distance : 2.070 Molprobity Statistics. All-atom Clashscore : 26.45 Ramachandran Plot: Outliers : 0.07 % Allowed : 8.85 % Favored : 91.08 % Rotamer: Outliers : 0.00 % Allowed : 1.00 % Favored : 99.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.71 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.41 (0.11), residues: 5516 helix: 0.11 (0.11), residues: 2184 sheet: -0.88 (0.19), residues: 768 loop : -1.88 (0.12), residues: 2564 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP I 88 HIS 0.007 0.001 HIS J 612 PHE 0.045 0.002 PHE B 194 TYR 0.035 0.002 TYR E 93 ARG 0.008 0.001 ARG J 713 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11032 Ramachandran restraints generated. 5516 Oldfield, 0 Emsley, 5516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11032 Ramachandran restraints generated. 5516 Oldfield, 0 Emsley, 5516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 331 residues out of total 4894 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 331 time to evaluate : 5.442 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: J 511 MET cc_start: 0.3289 (ptt) cc_final: 0.2889 (ptt) REVERT: J 633 MET cc_start: 0.6121 (tpt) cc_final: 0.5365 (mmt) REVERT: I 316 MET cc_start: -0.0330 (mtt) cc_final: -0.0830 (ttt) REVERT: I 460 ASN cc_start: 0.6202 (p0) cc_final: 0.5088 (p0) REVERT: I 511 MET cc_start: 0.6009 (mtm) cc_final: 0.4749 (mtp) REVERT: B 155 ASP cc_start: 0.7226 (m-30) cc_final: 0.6806 (t0) REVERT: E 78 TYR cc_start: 0.5698 (t80) cc_final: 0.4733 (t80) REVERT: A 27 MET cc_start: 0.1457 (tpt) cc_final: 0.1036 (tpt) REVERT: A 445 MET cc_start: 0.4396 (tmm) cc_final: 0.2281 (mmm) REVERT: L 42 LEU cc_start: 0.8125 (pp) cc_final: 0.7855 (pp) REVERT: L 511 MET cc_start: 0.3285 (ptt) cc_final: 0.2909 (ptt) REVERT: L 633 MET cc_start: 0.6119 (tpt) cc_final: 0.5355 (mmt) REVERT: K 316 MET cc_start: -0.0365 (mtt) cc_final: -0.0854 (ttt) REVERT: K 460 ASN cc_start: 0.6149 (p0) cc_final: 0.5017 (p0) REVERT: K 511 MET cc_start: 0.6032 (mtm) cc_final: 0.4780 (mtp) REVERT: D 155 ASP cc_start: 0.7207 (m-30) cc_final: 0.6785 (t0) REVERT: G 78 TYR cc_start: 0.5704 (t80) cc_final: 0.4644 (t80) REVERT: C 183 MET cc_start: 0.7247 (tmm) cc_final: 0.6887 (tmm) REVERT: C 342 MET cc_start: 0.7952 (mmt) cc_final: 0.7697 (mmm) REVERT: C 445 MET cc_start: 0.4380 (tmm) cc_final: 0.2324 (mmm) outliers start: 0 outliers final: 0 residues processed: 331 average time/residue: 0.5281 time to fit residues: 302.9934 Evaluate side-chains 239 residues out of total 4894 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 239 time to evaluate : 5.012 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 552 random chunks: chunk 325 optimal weight: 5.9990 chunk 524 optimal weight: 5.9990 chunk 319 optimal weight: 20.0000 chunk 248 optimal weight: 0.9990 chunk 364 optimal weight: 0.9980 chunk 549 optimal weight: 40.0000 chunk 506 optimal weight: 0.4980 chunk 437 optimal weight: 0.0070 chunk 45 optimal weight: 10.0000 chunk 338 optimal weight: 6.9990 chunk 268 optimal weight: 8.9990 overall best weight: 1.7002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** J 190 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 612 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 190 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 191 GLN ** F 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 144 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 80 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 190 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 612 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 190 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 191 GLN ** H 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 144 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 417 GLN C 478 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6396 moved from start: 0.2411 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 45992 Z= 0.172 Angle : 0.631 9.409 62312 Z= 0.323 Chirality : 0.045 0.303 6830 Planarity : 0.004 0.052 7980 Dihedral : 4.767 24.854 6130 Min Nonbonded Distance : 2.097 Molprobity Statistics. All-atom Clashscore : 19.81 Ramachandran Plot: Outliers : 0.04 % Allowed : 7.65 % Favored : 92.31 % Rotamer: Outliers : 0.00 % Allowed : 0.35 % Favored : 99.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.71 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.15 (0.11), residues: 5516 helix: 0.38 (0.11), residues: 2182 sheet: -0.77 (0.19), residues: 766 loop : -1.77 (0.12), residues: 2568 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP C 19 HIS 0.011 0.001 HIS L 151 PHE 0.020 0.001 PHE J 79 TYR 0.018 0.001 TYR C 444 ARG 0.007 0.000 ARG J 713 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11032 Ramachandran restraints generated. 5516 Oldfield, 0 Emsley, 5516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11032 Ramachandran restraints generated. 5516 Oldfield, 0 Emsley, 5516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 353 residues out of total 4894 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 353 time to evaluate : 5.661 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: J 511 MET cc_start: 0.3184 (ptt) cc_final: 0.2791 (ptt) REVERT: J 546 MET cc_start: 0.5617 (tmm) cc_final: 0.5166 (tmm) REVERT: J 633 MET cc_start: 0.6104 (tpt) cc_final: 0.5436 (mmt) REVERT: I 264 MET cc_start: 0.5700 (mmm) cc_final: 0.5275 (mmm) REVERT: I 316 MET cc_start: -0.0660 (mtt) cc_final: -0.1062 (ttt) REVERT: I 511 MET cc_start: 0.5519 (mtm) cc_final: 0.4229 (mtp) REVERT: B 155 ASP cc_start: 0.7267 (m-30) cc_final: 0.6823 (t0) REVERT: E 78 TYR cc_start: 0.5558 (t80) cc_final: 0.4526 (t80) REVERT: A 368 MET cc_start: 0.7116 (mpp) cc_final: 0.6021 (mpp) REVERT: A 445 MET cc_start: 0.4399 (tmm) cc_final: 0.2429 (mmm) REVERT: L 42 LEU cc_start: 0.8172 (pp) cc_final: 0.7901 (pp) REVERT: L 511 MET cc_start: 0.3231 (ptt) cc_final: 0.2875 (ptt) REVERT: L 546 MET cc_start: 0.5643 (tmm) cc_final: 0.5197 (tmm) REVERT: L 633 MET cc_start: 0.6094 (tpt) cc_final: 0.5423 (mmt) REVERT: K 264 MET cc_start: 0.5692 (mmm) cc_final: 0.5257 (mmm) REVERT: K 316 MET cc_start: -0.0612 (mtt) cc_final: -0.1041 (ttt) REVERT: K 511 MET cc_start: 0.5559 (mtm) cc_final: 0.4272 (mtp) REVERT: D 155 ASP cc_start: 0.7244 (m-30) cc_final: 0.6813 (t0) REVERT: G 78 TYR cc_start: 0.5538 (t80) cc_final: 0.4620 (t80) REVERT: C 368 MET cc_start: 0.7101 (mpp) cc_final: 0.5911 (mpp) REVERT: C 445 MET cc_start: 0.4368 (tmm) cc_final: 0.2470 (mmm) outliers start: 0 outliers final: 0 residues processed: 353 average time/residue: 0.5290 time to fit residues: 324.7422 Evaluate side-chains 260 residues out of total 4894 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 260 time to evaluate : 5.184 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 552 random chunks: chunk 347 optimal weight: 9.9990 chunk 466 optimal weight: 5.9990 chunk 134 optimal weight: 20.0000 chunk 403 optimal weight: 4.9990 chunk 64 optimal weight: 20.0000 chunk 121 optimal weight: 20.0000 chunk 438 optimal weight: 7.9990 chunk 183 optimal weight: 9.9990 chunk 450 optimal weight: 0.7980 chunk 55 optimal weight: 3.9990 chunk 80 optimal weight: 0.0070 overall best weight: 3.1604 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** J 190 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 612 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 626 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 190 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 191 GLN ** F 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 144 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 80 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 190 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 612 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 626 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 190 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 191 GLN ** H 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 144 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 80 GLN ** 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 = 0.3866 r_free = 0.3866 target = 0.073054 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3420 r_free = 0.3420 target = 0.056026 restraints weight = 439178.926| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3430 r_free = 0.3430 target = 0.056357 restraints weight = 306191.804| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.056600 restraints weight = 230049.617| |-----------------------------------------------------------------------------| r_work (final): 0.3341 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7343 moved from start: 0.2477 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 45992 Z= 0.190 Angle : 0.620 9.254 62312 Z= 0.320 Chirality : 0.044 0.289 6830 Planarity : 0.004 0.049 7980 Dihedral : 4.720 24.622 6130 Min Nonbonded Distance : 2.118 Molprobity Statistics. All-atom Clashscore : 20.63 Ramachandran Plot: Outliers : 0.04 % Allowed : 8.10 % Favored : 91.86 % Rotamer: Outliers : 0.00 % Allowed : 0.33 % Favored : 99.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.71 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.10 (0.11), residues: 5516 helix: 0.42 (0.11), residues: 2188 sheet: -0.71 (0.19), residues: 782 loop : -1.78 (0.12), residues: 2546 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP G 129 HIS 0.007 0.001 HIS J 612 PHE 0.023 0.001 PHE D 329 TYR 0.016 0.001 TYR D 413 ARG 0.009 0.000 ARG C 432 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7819.94 seconds wall clock time: 153 minutes 7.95 seconds (9187.95 seconds total)