Starting phenix.real_space_refine on Tue Sep 24 11:48:46 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6gmh_0031/09_2024/6gmh_0031_neut.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6gmh_0031/09_2024/6gmh_0031.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6gmh_0031/09_2024/6gmh_0031.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6gmh_0031/09_2024/6gmh_0031.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6gmh_0031/09_2024/6gmh_0031_neut.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6gmh_0031/09_2024/6gmh_0031_neut.cif" } resolution = 3.1 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= 0.001 sd= 0.004 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: 7 Type Number sf(0) Gaussians Zn 9 6.06 5 P 108 5.49 5 Mg 1 5.21 5 S 235 5.16 5 C 30458 2.51 5 N 9346 2.21 5 O 10082 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 38 residue(s): 0.09s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 50239 Number of models: 1 Model: "" Number of chains: 31 Chain: "A" Number of atoms: 11371 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1441, 11371 Classifications: {'peptide': 1441} Link IDs: {'PCIS': 1, 'PTRANS': 72, 'TRANS': 1367} Chain breaks: 6 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'TPO:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "B" Number of atoms: 9052 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1132, 9052 Classifications: {'peptide': 1132} Link IDs: {'PTRANS': 53, 'TRANS': 1078} Chain breaks: 4 Chain: "C" Number of atoms: 2115 Number of conformers: 1 Conformer: "" Number of residues, atoms: 263, 2115 Classifications: {'peptide': 263} Link IDs: {'PTRANS': 15, 'TRANS': 247} Chain breaks: 1 Chain: "D" Number of atoms: 1004 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 1004 Classifications: {'peptide': 126} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 3, 'TRANS': 122} Unresolved non-hydrogen bonds: 26 Unresolved non-hydrogen angles: 32 Unresolved non-hydrogen dihedrals: 20 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 3, 'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 22 Chain: "E" Number of atoms: 1720 Number of conformers: 1 Conformer: "" Number of residues, atoms: 209, 1720 Classifications: {'peptide': 209} Link IDs: {'PTRANS': 11, 'TRANS': 197} Chain: "F" Number of atoms: 657 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 657 Classifications: {'peptide': 82} Link IDs: {'PTRANS': 5, 'TRANS': 76} Chain: "G" Number of atoms: 1333 Number of conformers: 1 Conformer: "" Number of residues, atoms: 171, 1333 Classifications: {'peptide': 171} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 10, 'TRANS': 160} Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 21 Unresolved non-hydrogen dihedrals: 15 Planarities with less than four sites: {'GLU:plan': 1, 'ASN:plan1': 2} Unresolved non-hydrogen planarities: 10 Chain: "H" Number of atoms: 1186 Number of conformers: 1 Conformer: "" Number of residues, atoms: 148, 1186 Classifications: {'peptide': 148} Link IDs: {'PTRANS': 4, 'TRANS': 143} Chain: "I" Number of atoms: 949 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 949 Classifications: {'peptide': 117} Link IDs: {'PTRANS': 5, 'TRANS': 111} Chain: "J" Number of atoms: 533 Number of conformers: 1 Conformer: "" Number of residues, atoms: 67, 533 Classifications: {'peptide': 67} Link IDs: {'PTRANS': 2, 'TRANS': 64} Chain: "K" Number of atoms: 920 Number of conformers: 1 Conformer: "" Number of residues, atoms: 115, 920 Classifications: {'peptide': 115} Link IDs: {'PTRANS': 8, 'TRANS': 106} Chain: "L" Number of atoms: 388 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 388 Classifications: {'peptide': 46} Link IDs: {'PTRANS': 2, 'TRANS': 43} Chain: "M" Number of atoms: 3281 Number of conformers: 1 Conformer: "" Number of residues, atoms: 823, 3281 Classifications: {'peptide': 823} Incomplete info: {'backbone_only': 780, 'n_c_alpha_c_only': 11} Link IDs: {'PTRANS': 33, 'TRANS': 789} Chain breaks: 9 Unresolved chain link angles: 44 Unresolved non-hydrogen bonds: 3605 Unresolved non-hydrogen angles: 5159 Unresolved non-hydrogen dihedrals: 2333 Unresolved non-hydrogen chiralities: 1013 Planarities with less than four sites: {'GLN:plan1': 42, 'HIS:plan': 19, 'TYR:plan': 32, 'ASN:plan1': 30, 'TRP:plan': 8, 'ASP:plan': 52, 'PHE:plan': 35, 'GLU:plan': 82, 'ARG:plan': 58} Unresolved non-hydrogen planarities: 1809 Chain: "M" Number of atoms: 1456 Number of conformers: 1 Conformer: "" Number of residues, atoms: 179, 1456 Classifications: {'peptide': 179} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 10, 'TRANS': 168} Chain breaks: 2 Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'UNK:plan-1': 8} Unresolved non-hydrogen planarities: 8 Chain: "N" Number of atoms: 773 Number of conformers: 1 Conformer: "" Number of residues, atoms: 37, 773 Classifications: {'DNA': 37} Link IDs: {'rna3p': 36} Chain breaks: 1 Chain: "P" Number of atoms: 452 Number of conformers: 1 Conformer: "" Number of residues, atoms: 21, 452 Classifications: {'RNA': 21} Modifications used: {'rna2p_pur': 4, 'rna2p_pyr': 2, 'rna3p_pur': 9, 'rna3p_pyr': 6} Link IDs: {'rna2p': 6, 'rna3p': 14} Chain: "Q" Number of atoms: 4116 Number of conformers: 1 Conformer: "" Number of residues, atoms: 884, 4116 Classifications: {'peptide': 884} Incomplete info: {'backbone_only': 730} Link IDs: {'PTRANS': 11, 'TRANS': 872} Chain breaks: 1 Unresolved chain link angles: 11 Unresolved non-hydrogen bonds: 2853 Unresolved non-hydrogen angles: 4312 Unresolved non-hydrogen dihedrals: 1601 Unresolved non-hydrogen chiralities: 830 Planarities with less than four sites: {'GLN:plan1': 33, 'ASN:plan1': 20, 'ASP:plan': 24, 'TYR:plan': 30, 'UNK:plan-1': 300, 'TRP:plan': 6, 'HIS:plan': 15, 'PHE:plan': 17, 'GLU:plan': 35, 'ARG:plan': 22} Unresolved non-hydrogen planarities: 1367 Chain: "T" Number of atoms: 974 Number of conformers: 1 Conformer: "" Number of residues, atoms: 48, 974 Classifications: {'DNA': 48} Link IDs: {'rna3p': 47} Chain: "U" Number of atoms: 440 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 440 Classifications: {'peptide': 110} Incomplete info: {'backbone_only': 110} Link IDs: {'TRANS': 109} Chain breaks: 3 Unresolved non-hydrogen bonds: 330 Unresolved non-hydrogen angles: 550 Unresolved non-hydrogen dihedrals: 110 Unresolved non-hydrogen chiralities: 110 Planarities with less than four sites: {'UNK:plan-1': 110} Unresolved non-hydrogen planarities: 110 Chain: "V" Number of atoms: 324 Number of conformers: 1 Conformer: "" Number of residues, atoms: 81, 324 Classifications: {'peptide': 81} Incomplete info: {'backbone_only': 81} Link IDs: {'TRANS': 80} Chain breaks: 3 Unresolved non-hydrogen bonds: 243 Unresolved non-hydrogen angles: 405 Unresolved non-hydrogen dihedrals: 81 Unresolved non-hydrogen chiralities: 81 Planarities with less than four sites: {'UNK:plan-1': 81} Unresolved non-hydrogen planarities: 81 Chain: "W" Number of atoms: 2333 Number of conformers: 1 Conformer: "" Number of residues, atoms: 300, 2333 Classifications: {'peptide': 300} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 291} Chain: "X" Number of atoms: 63 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 63 Classifications: {'peptide': 16} Incomplete info: {'backbone_only': 15, 'n_c_alpha_c_only': 1} Link IDs: {'TRANS': 15} Unresolved non-hydrogen bonds: 49 Unresolved non-hydrogen angles: 81 Unresolved non-hydrogen dihedrals: 16 Unresolved non-hydrogen chiralities: 16 Planarities with less than four sites: {'UNK:plan-1': 16} Unresolved non-hydrogen planarities: 17 Chain: "Y" Number of atoms: 911 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 911 Classifications: {'peptide': 116} Link IDs: {'PTRANS': 4, 'TRANS': 111} Chain: "Z" Number of atoms: 3878 Number of conformers: 1 Conformer: "" Number of residues, atoms: 486, 3878 Classifications: {'peptide': 486} Link IDs: {'PTRANS': 17, 'TRANS': 468} Chain breaks: 4 Chain: "A" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' MG': 1, ' ZN': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "I" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "J" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "L" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "Y" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 464 SG CYS A 71 93.770 77.827 171.174 1.00117.25 S ATOM 486 SG CYS A 74 94.040 81.833 171.340 1.00111.80 S ATOM 768 SG CYS A 111 137.912 73.247 190.959 1.00155.94 S ATOM 796 SG CYS A 114 136.157 73.338 194.021 1.00149.48 S ATOM 19993 SG CYS B1119 104.682 90.581 180.326 1.00107.14 S ATOM 20015 SG CYS B1122 107.724 87.632 180.162 1.00107.48 S ATOM 20130 SG CYS B1137 103.803 86.665 179.870 1.00124.23 S ATOM 21117 SG CYS C 88 69.721 93.066 107.346 1.00101.13 S ATOM 21130 SG CYS C 90 69.558 90.041 109.295 1.00103.04 S ATOM 21165 SG CYS C 94 68.876 89.726 105.847 1.00 91.83 S ATOM 21187 SG CYS C 97 72.191 88.940 107.004 1.00 92.65 S ATOM 28507 SG CYS I 17 174.209 36.643 148.392 1.00119.90 S ATOM 28531 SG CYS I 20 171.135 36.270 150.349 1.00124.94 S ATOM 28692 SG CYS I 39 172.468 39.299 151.765 1.00131.91 S ATOM 28717 SG CYS I 42 174.419 35.554 151.775 1.00130.15 S ATOM 29069 SG CYS I 86 171.718 54.991 107.256 1.00110.24 S ATOM 29093 SG CYS I 89 171.056 52.005 104.728 1.00112.38 S ATOM 29297 SG CYS I 114 167.939 54.246 106.945 1.00105.02 S ATOM 29332 SG CYS I 119 170.429 51.758 108.326 1.00107.70 S ATOM 29442 SG CYS J 7 102.229 82.680 98.765 1.00 66.18 S ATOM 29730 SG CYS J 44 104.567 85.076 96.312 1.00 71.21 S ATOM 29736 SG CYS J 45 101.894 82.821 94.464 1.00 71.33 S ATOM 30898 SG CYS L 19 86.032 47.990 120.947 1.00100.50 S ATOM 30917 SG CYS L 22 84.158 46.070 118.583 1.00100.52 S ATOM 31034 SG CYS L 36 82.721 46.279 121.901 1.00106.90 S ATOM 31060 SG CYS L 39 86.884 44.067 120.290 1.00112.55 S ATOM 45559 SG CYS Y 16 108.538 22.292 193.958 1.00364.03 S ATOM 45581 SG CYS Y 19 112.573 22.248 192.996 1.00367.84 S ATOM 45693 SG CYS Y 33 110.802 19.310 192.101 1.00370.66 S ATOM 45715 SG CYS Y 36 112.436 19.828 196.043 1.00371.23 S Residues with excluded nonbonded symmetry interactions: 94 residue: pdb=" N ASN M1145 " occ=0.00 ... (2 atoms not shown) pdb=" O ASN M1145 " occ=0.00 residue: pdb=" N THR M1146 " occ=0.00 ... (2 atoms not shown) pdb=" O THR M1146 " occ=0.00 residue: pdb=" N GLU M1147 " occ=0.00 ... (2 atoms not shown) pdb=" O GLU M1147 " occ=0.00 residue: pdb=" N GLU M1148 " occ=0.00 ... (2 atoms not shown) pdb=" O GLU M1148 " occ=0.00 residue: pdb=" N ILE M1149 " occ=0.00 ... (2 atoms not shown) pdb=" O ILE M1149 " occ=0.00 residue: pdb=" N PHE M1150 " occ=0.00 ... (2 atoms not shown) pdb=" O PHE M1150 " occ=0.00 residue: pdb=" N ASN M1151 " occ=0.00 ... (2 atoms not shown) pdb=" O ASN M1151 " occ=0.00 residue: pdb=" N MET M1152 " occ=0.00 ... (2 atoms not shown) pdb=" O MET M1152 " occ=0.00 residue: pdb=" N LEU M1153 " occ=0.00 ... (2 atoms not shown) pdb=" O LEU M1153 " occ=0.00 residue: pdb=" N THR M1154 " occ=0.00 ... (2 atoms not shown) pdb=" O THR M1154 " occ=0.00 residue: pdb=" N LYS M1155 " occ=0.00 ... (2 atoms not shown) pdb=" O LYS M1155 " occ=0.00 residue: pdb=" N GLU M1156 " occ=0.00 ... (2 atoms not shown) pdb=" O GLU M1156 " occ=0.00 ... (remaining 82 not shown) Time building chain proxies: 21.23, per 1000 atoms: 0.42 Number of scatterers: 50239 At special positions: 0 Unit cell: (207.702, 190.918, 247.564, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 9 29.99 S 235 16.00 P 108 15.00 Mg 1 11.99 O 10082 8.00 N 9346 7.00 C 30458 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Atom "HETATM11330 OG SEP A1547 .*. O " rejected from bonding due to valence issues. Number of custom bonds: simple=2, symmetry=0 Number of additional bonds: simple=2, symmetry=0 Coordination: Other bonds: Time building additional restraints: 9.24 Conformation dependent library (CDL) restraints added in 4.9 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A2001 " pdb="ZN ZN A2001 " - pdb=" NE2 HIS A 84 " pdb="ZN ZN A2001 " - pdb=" SG CYS A 74 " pdb="ZN ZN A2001 " - pdb=" SG CYS A 71 " pdb=" ZN A2002 " pdb="ZN ZN A2002 " - pdb=" SG CYS A 114 " pdb="ZN ZN A2002 " - pdb=" SG CYS A 111 " pdb=" ZN B1201 " pdb="ZN ZN B1201 " - pdb=" SG CYS B1122 " pdb="ZN ZN B1201 " - pdb=" SG CYS B1137 " pdb="ZN ZN B1201 " - pdb=" SG CYS B1119 " pdb=" ZN C 301 " pdb="ZN ZN C 301 " - pdb=" SG CYS C 90 " pdb="ZN ZN C 301 " - pdb=" SG CYS C 88 " pdb="ZN ZN C 301 " - pdb=" SG CYS C 94 " pdb="ZN ZN C 301 " - pdb=" SG CYS C 97 " pdb=" ZN I 201 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 17 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 39 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 20 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 42 " pdb=" ZN I 202 " pdb="ZN ZN I 202 " - pdb=" SG CYS I 114 " pdb="ZN ZN I 202 " - pdb=" SG CYS I 89 " pdb="ZN ZN I 202 " - pdb=" SG CYS I 119 " pdb="ZN ZN I 202 " - pdb=" SG CYS I 86 " pdb=" ZN J 101 " pdb="ZN ZN J 101 " - pdb=" SG CYS J 45 " pdb="ZN ZN J 101 " - pdb=" SG CYS J 44 " pdb="ZN ZN J 101 " - pdb=" SG CYS J 7 " pdb=" ZN L 101 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 22 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 39 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 19 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 36 " pdb=" ZN Y 201 " pdb="ZN ZN Y 201 " - pdb=" SG CYS Y 33 " pdb="ZN ZN Y 201 " - pdb=" SG CYS Y 19 " pdb="ZN ZN Y 201 " - pdb=" SG CYS Y 36 " pdb="ZN ZN Y 201 " - pdb=" SG CYS Y 16 " Number of angles added : 30 12606 Ramachandran restraints generated. 6303 Oldfield, 0 Emsley, 6303 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 9640 Finding SS restraints... Secondary structure from input PDB file: 237 helices and 69 sheets defined 44.2% alpha, 17.6% beta 46 base pairs and 80 stacking pairs defined. Time for finding SS restraints: 13.83 Creating SS restraints... Processing helix chain 'A' and resid 27 through 35 Processing helix chain 'A' and resid 99 through 110 Processing helix chain 'A' and resid 123 through 133 Processing helix chain 'A' and resid 136 through 150 removed outlier: 4.353A pdb=" N GLY A 150 " --> pdb=" O ASP A 146 " (cutoff:3.500A) Processing helix chain 'A' and resid 217 through 227 Processing helix chain 'A' and resid 229 through 237 Processing helix chain 'A' and resid 244 through 248 Processing helix chain 'A' and resid 274 through 297 removed outlier: 3.737A pdb=" N LYS A 279 " --> pdb=" O ASP A 275 " (cutoff:3.500A) Processing helix chain 'A' and resid 301 through 319 removed outlier: 3.657A pdb=" N GLU A 305 " --> pdb=" O HIS A 301 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N VAL A 318 " --> pdb=" O VAL A 314 " (cutoff:3.500A) Processing helix chain 'A' and resid 338 through 343 Processing helix chain 'A' and resid 349 through 354 Processing helix chain 'A' and resid 381 through 386 Processing helix chain 'A' and resid 398 through 409 Processing helix chain 'A' and resid 488 through 493 removed outlier: 3.560A pdb=" N TYR A 492 " --> pdb=" O VAL A 488 " (cutoff:3.500A) Processing helix chain 'A' and resid 508 through 519 Processing helix chain 'A' and resid 520 through 525 removed outlier: 3.841A pdb=" N ILE A 525 " --> pdb=" O PRO A 522 " (cutoff:3.500A) Processing helix chain 'A' and resid 540 through 549 Processing helix chain 'A' and resid 556 through 565 Processing helix chain 'A' and resid 588 through 596 removed outlier: 3.751A pdb=" N LEU A 594 " --> pdb=" O GLN A 590 " (cutoff:3.500A) Processing helix chain 'A' and resid 611 through 616 removed outlier: 4.459A pdb=" N SER A 615 " --> pdb=" O ASP A 611 " (cutoff:3.500A) Processing helix chain 'A' and resid 641 through 646 Processing helix chain 'A' and resid 651 through 660 Processing helix chain 'A' and resid 661 through 684 removed outlier: 3.962A pdb=" N LEU A 681 " --> pdb=" O ASN A 677 " (cutoff:3.500A) removed outlier: 4.628A pdb=" N ILE A 682 " --> pdb=" O ASN A 678 " (cutoff:3.500A) Processing helix chain 'A' and resid 696 through 722 removed outlier: 3.862A pdb=" N GLN A 700 " --> pdb=" O SER A 696 " (cutoff:3.500A) Processing helix chain 'A' and resid 732 through 760 Processing helix chain 'A' and resid 764 through 773 removed outlier: 3.745A pdb=" N MET A 769 " --> pdb=" O ASN A 765 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N SER A 772 " --> pdb=" O SER A 768 " (cutoff:3.500A) Processing helix chain 'A' and resid 777 through 786 removed outlier: 3.656A pdb=" N ILE A 781 " --> pdb=" O SER A 777 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N SER A 782 " --> pdb=" O LYS A 778 " (cutoff:3.500A) Processing helix chain 'A' and resid 832 through 869 removed outlier: 3.855A pdb=" N GLU A 845 " --> pdb=" O MET A 841 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N GLY A 846 " --> pdb=" O GLY A 842 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N ALA A 851 " --> pdb=" O LEU A 847 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N THR A 854 " --> pdb=" O THR A 850 " (cutoff:3.500A) removed outlier: 4.558A pdb=" N ALA A 855 " --> pdb=" O ALA A 851 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N GLU A 856 " --> pdb=" O VAL A 852 " (cutoff:3.500A) removed outlier: 4.212A pdb=" N TYR A 859 " --> pdb=" O ALA A 855 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N SER A 867 " --> pdb=" O ARG A 863 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N MET A 868 " --> pdb=" O LEU A 864 " (cutoff:3.500A) Processing helix chain 'A' and resid 890 through 894 Processing helix chain 'A' and resid 897 through 901 removed outlier: 3.769A pdb=" N SER A 900 " --> pdb=" O ALA A 897 " (cutoff:3.500A) removed outlier: 4.132A pdb=" N VAL A 901 " --> pdb=" O GLY A 898 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 897 through 901' Processing helix chain 'A' and resid 913 through 921 removed outlier: 3.684A pdb=" N GLU A 917 " --> pdb=" O ASN A 913 " (cutoff:3.500A) Processing helix chain 'A' and resid 926 through 934 removed outlier: 3.533A pdb=" N LEU A 930 " --> pdb=" O ASN A 926 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N THR A 933 " --> pdb=" O ALA A 929 " (cutoff:3.500A) Processing helix chain 'A' and resid 935 through 945 removed outlier: 3.944A pdb=" N LYS A 940 " --> pdb=" O GLU A 936 " (cutoff:3.500A) removed outlier: 4.562A pdb=" N ASP A 941 " --> pdb=" O ASP A 937 " (cutoff:3.500A) Processing helix chain 'A' and resid 945 through 970 removed outlier: 3.523A pdb=" N GLN A 949 " --> pdb=" O ASN A 945 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N GLU A 964 " --> pdb=" O ARG A 960 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N VAL A 965 " --> pdb=" O GLU A 961 " (cutoff:3.500A) Processing helix chain 'A' and resid 982 through 994 removed outlier: 3.573A pdb=" N LYS A 992 " --> pdb=" O TRP A 988 " (cutoff:3.500A) Processing helix chain 'A' and resid 1005 through 1020 removed outlier: 3.725A pdb=" N VAL A1009 " --> pdb=" O HIS A1005 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N VAL A1010 " --> pdb=" O PRO A1006 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N GLU A1015 " --> pdb=" O GLU A1011 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N LYS A1018 " --> pdb=" O LYS A1014 " (cutoff:3.500A) Processing helix chain 'A' and resid 1027 through 1038 removed outlier: 3.544A pdb=" N ALA A1033 " --> pdb=" O LEU A1029 " (cutoff:3.500A) Processing helix chain 'A' and resid 1038 through 1049 Processing helix chain 'A' and resid 1050 through 1057 Processing helix chain 'A' and resid 1061 through 1078 removed outlier: 3.767A pdb=" N GLU A1073 " --> pdb=" O LEU A1069 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N SER A1074 " --> pdb=" O GLY A1070 " (cutoff:3.500A) Processing helix chain 'A' and resid 1086 through 1097 Processing helix chain 'A' and resid 1098 through 1101 Processing helix chain 'A' and resid 1120 through 1129 Processing helix chain 'A' and resid 1145 through 1150 removed outlier: 3.602A pdb=" N ARG A1149 " --> pdb=" O GLY A1145 " (cutoff:3.500A) Processing helix chain 'A' and resid 1150 through 1162 removed outlier: 3.625A pdb=" N ALA A1154 " --> pdb=" O ASP A1150 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N ARG A1160 " --> pdb=" O ASP A1156 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N LEU A1161 " --> pdb=" O ILE A1157 " (cutoff:3.500A) Processing helix chain 'A' and resid 1165 through 1169 removed outlier: 4.185A pdb=" N VAL A1169 " --> pdb=" O THR A1165 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1165 through 1169' Processing helix chain 'A' and resid 1188 through 1195 removed outlier: 3.664A pdb=" N TRP A1192 " --> pdb=" O GLU A1188 " (cutoff:3.500A) Processing helix chain 'A' and resid 1217 through 1225 removed outlier: 3.588A pdb=" N MET A1221 " --> pdb=" O ASP A1217 " (cutoff:3.500A) Processing helix chain 'A' and resid 1227 through 1239 Processing helix chain 'A' and resid 1282 through 1295 removed outlier: 3.640A pdb=" N ASP A1295 " --> pdb=" O ASN A1291 " (cutoff:3.500A) Processing helix chain 'A' and resid 1361 through 1369 Processing helix chain 'A' and resid 1370 through 1388 removed outlier: 3.569A pdb=" N LYS A1376 " --> pdb=" O GLU A1372 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N VAL A1385 " --> pdb=" O GLU A1381 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N ILE A1386 " --> pdb=" O LEU A1382 " (cutoff:3.500A) Processing helix chain 'A' and resid 1394 through 1405 removed outlier: 3.785A pdb=" N LEU A1398 " --> pdb=" O ASN A1394 " (cutoff:3.500A) Processing helix chain 'A' and resid 1415 through 1420 removed outlier: 3.691A pdb=" N ASN A1420 " --> pdb=" O ARG A1416 " (cutoff:3.500A) Processing helix chain 'A' and resid 1425 through 1430 Processing helix chain 'A' and resid 1436 through 1446 Processing helix chain 'A' and resid 1453 through 1458 removed outlier: 4.291A pdb=" N ASN A1457 " --> pdb=" O GLY A1453 " (cutoff:3.500A) Processing helix chain 'A' and resid 1478 through 1482 Processing helix chain 'B' and resid 21 through 37 removed outlier: 4.758A pdb=" N TRP B 27 " --> pdb=" O GLN B 23 " (cutoff:3.500A) Processing helix chain 'B' and resid 40 through 62 removed outlier: 5.355A pdb=" N VAL B 55 " --> pdb=" O ILE B 51 " (cutoff:3.500A) removed outlier: 5.213A pdb=" N GLN B 56 " --> pdb=" O GLN B 52 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N ALA B 62 " --> pdb=" O ILE B 58 " (cutoff:3.500A) Processing helix chain 'B' and resid 109 through 117 Processing helix chain 'B' and resid 167 through 174 Processing helix chain 'B' and resid 269 through 277 Processing helix chain 'B' and resid 281 through 286 Processing helix chain 'B' and resid 294 through 306 removed outlier: 3.670A pdb=" N MET B 298 " --> pdb=" O ASP B 294 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N MET B 300 " --> pdb=" O GLU B 296 " (cutoff:3.500A) Proline residue: B 303 - end of helix Processing helix chain 'B' and resid 313 through 324 removed outlier: 3.759A pdb=" N ALA B 317 " --> pdb=" O GLU B 313 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N ARG B 324 " --> pdb=" O PHE B 320 " (cutoff:3.500A) Processing helix chain 'B' and resid 331 through 346 removed outlier: 3.570A pdb=" N ARG B 335 " --> pdb=" O THR B 331 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N LYS B 337 " --> pdb=" O GLU B 333 " (cutoff:3.500A) Processing helix chain 'B' and resid 357 through 377 removed outlier: 3.543A pdb=" N ALA B 375 " --> pdb=" O ARG B 371 " (cutoff:3.500A) Processing helix chain 'B' and resid 395 through 426 removed outlier: 3.811A pdb=" N GLY B 406 " --> pdb=" O PHE B 402 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N GLU B 414 " --> pdb=" O ASN B 410 " (cutoff:3.500A) removed outlier: 4.363A pdb=" N ILE B 417 " --> pdb=" O LYS B 413 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N ARG B 425 " --> pdb=" O LYS B 421 " (cutoff:3.500A) Processing helix chain 'B' and resid 430 through 435 Processing helix chain 'B' and resid 437 through 451 removed outlier: 3.833A pdb=" N SER B 441 " --> pdb=" O THR B 437 " (cutoff:3.500A) Processing helix chain 'B' and resid 474 through 483 Processing helix chain 'B' and resid 502 through 506 removed outlier: 3.768A pdb=" N TRP B 506 " --> pdb=" O ASN B 503 " (cutoff:3.500A) Processing helix chain 'B' and resid 538 through 546 Processing helix chain 'B' and resid 583 through 592 Processing helix chain 'B' and resid 636 through 645 removed outlier: 3.607A pdb=" N GLU B 645 " --> pdb=" O ASP B 641 " (cutoff:3.500A) Processing helix chain 'B' and resid 652 through 659 Processing helix chain 'B' and resid 667 through 672 removed outlier: 3.984A pdb=" N THR B 672 " --> pdb=" O LEU B 668 " (cutoff:3.500A) Processing helix chain 'B' and resid 678 through 683 Processing helix chain 'B' and resid 699 through 704 removed outlier: 3.536A pdb=" N LEU B 704 " --> pdb=" O SER B 701 " (cutoff:3.500A) Processing helix chain 'B' and resid 706 through 711 removed outlier: 3.788A pdb=" N ILE B 710 " --> pdb=" O CYS B 707 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N ILE B 711 " --> pdb=" O ALA B 708 " (cutoff:3.500A) Processing helix chain 'B' and resid 713 through 717 Processing helix chain 'B' and resid 718 through 729 removed outlier: 3.738A pdb=" N ASN B 722 " --> pdb=" O GLN B 718 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N TYR B 724 " --> pdb=" O PRO B 720 " (cutoff:3.500A) Processing helix chain 'B' and resid 798 through 804 Processing helix chain 'B' and resid 969 through 972 Processing helix chain 'B' and resid 977 through 994 removed outlier: 4.007A pdb=" N LEU B 981 " --> pdb=" O THR B 977 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N LYS B 988 " --> pdb=" O CYS B 984 " (cutoff:3.500A) Processing helix chain 'B' and resid 1007 through 1016 Processing helix chain 'B' and resid 1017 through 1019 No H-bonds generated for 'chain 'B' and resid 1017 through 1019' Processing helix chain 'B' and resid 1087 through 1098 removed outlier: 3.631A pdb=" N ASP B1092 " --> pdb=" O GLU B1088 " (cutoff:3.500A) Processing helix chain 'B' and resid 1099 through 1108 Processing helix chain 'B' and resid 1152 through 1165 Processing helix chain 'C' and resid 27 through 41 removed outlier: 3.695A pdb=" N ILE C 39 " --> pdb=" O ARG C 35 " (cutoff:3.500A) Processing helix chain 'C' and resid 60 through 70 Processing helix chain 'C' and resid 77 through 82 removed outlier: 3.780A pdb=" N LYS C 81 " --> pdb=" O ASP C 77 " (cutoff:3.500A) Processing helix chain 'C' and resid 118 through 120 No H-bonds generated for 'chain 'C' and resid 118 through 120' Processing helix chain 'C' and resid 173 through 177 Processing helix chain 'C' and resid 199 through 203 Processing helix chain 'C' and resid 240 through 271 removed outlier: 3.874A pdb=" N VAL C 245 " --> pdb=" O PRO C 241 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N LEU C 246 " --> pdb=" O GLU C 242 " (cutoff:3.500A) Processing helix chain 'D' and resid 33 through 50 removed outlier: 3.569A pdb=" N SER D 50 " --> pdb=" O GLN D 46 " (cutoff:3.500A) Processing helix chain 'D' and resid 58 through 71 Processing helix chain 'D' and resid 76 through 90 removed outlier: 3.674A pdb=" N ILE D 80 " --> pdb=" O ASN D 76 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N ALA D 81 " --> pdb=" O ARG D 77 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N LYS D 90 " --> pdb=" O LEU D 86 " (cutoff:3.500A) Processing helix chain 'D' and resid 95 through 104 removed outlier: 4.108A pdb=" N CYS D 99 " --> pdb=" O PHE D 95 " (cutoff:3.500A) Processing helix chain 'D' and resid 107 through 115 Processing helix chain 'D' and resid 116 through 119 Processing helix chain 'D' and resid 123 through 137 Processing helix chain 'E' and resid 3 through 25 Processing helix chain 'E' and resid 29 through 34 Processing helix chain 'E' and resid 36 through 45 removed outlier: 3.836A pdb=" N PHE E 40 " --> pdb=" O THR E 36 " (cutoff:3.500A) Processing helix chain 'E' and resid 87 through 97 Processing helix chain 'E' and resid 111 through 121 Processing helix chain 'E' and resid 133 through 136 removed outlier: 3.902A pdb=" N LEU E 136 " --> pdb=" O GLN E 133 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 133 through 136' Processing helix chain 'E' and resid 138 through 142 Processing helix chain 'E' and resid 152 through 164 Processing helix chain 'E' and resid 177 through 184 Processing helix chain 'F' and resid 58 through 75 removed outlier: 3.710A pdb=" N LEU F 66 " --> pdb=" O ARG F 62 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N GLN F 72 " --> pdb=" O THR F 68 " (cutoff:3.500A) Processing helix chain 'F' and resid 88 through 100 Processing helix chain 'F' and resid 121 through 123 No H-bonds generated for 'chain 'F' and resid 121 through 123' Processing helix chain 'G' and resid 14 through 19 removed outlier: 3.833A pdb=" N GLY G 19 " --> pdb=" O ARG G 16 " (cutoff:3.500A) Processing helix chain 'G' and resid 21 through 35 removed outlier: 3.717A pdb=" N THR G 25 " --> pdb=" O ASN G 21 " (cutoff:3.500A) Processing helix chain 'H' and resid 84 through 88 removed outlier: 3.592A pdb=" N GLN H 87 " --> pdb=" O ARG H 84 " (cutoff:3.500A) Processing helix chain 'I' and resid 63 through 67 removed outlier: 3.509A pdb=" N THR I 66 " --> pdb=" O ASP I 63 " (cutoff:3.500A) Processing helix chain 'I' and resid 69 through 75 removed outlier: 3.511A pdb=" N VAL I 72 " --> pdb=" O ILE I 69 " (cutoff:3.500A) Processing helix chain 'J' and resid 17 through 26 Processing helix chain 'J' and resid 30 through 38 removed outlier: 4.301A pdb=" N ASP J 36 " --> pdb=" O GLY J 32 " (cutoff:3.500A) Processing helix chain 'J' and resid 42 through 51 removed outlier: 3.854A pdb=" N MET J 48 " --> pdb=" O CYS J 44 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N LEU J 49 " --> pdb=" O CYS J 45 " (cutoff:3.500A) Processing helix chain 'J' and resid 55 through 60 Processing helix chain 'K' and resid 5 through 10 removed outlier: 3.725A pdb=" N SER K 9 " --> pdb=" O ALA K 6 " (cutoff:3.500A) Processing helix chain 'K' and resid 39 through 51 removed outlier: 4.372A pdb=" N ILE K 45 " --> pdb=" O THR K 41 " (cutoff:3.500A) Processing helix chain 'K' and resid 82 through 113 removed outlier: 3.730A pdb=" N SER K 96 " --> pdb=" O THR K 92 " (cutoff:3.500A) Processing helix chain 'M' and resid 286 through 291 Processing helix chain 'M' and resid 295 through 300 Processing helix chain 'M' and resid 310 through 324 removed outlier: 4.220A pdb=" N GLU M 314 " --> pdb=" O ASP M 310 " (cutoff:3.500A) removed outlier: 4.605A pdb=" N GLU M 315 " --> pdb=" O ASP M 311 " (cutoff:3.500A) Processing helix chain 'M' and resid 351 through 367 Processing helix chain 'M' and resid 372 through 379 Processing helix chain 'M' and resid 391 through 430 Processing helix chain 'M' and resid 445 through 453 removed outlier: 3.846A pdb=" N GLU M 449 " --> pdb=" O THR M 445 " (cutoff:3.500A) Processing helix chain 'M' and resid 456 through 471 WARNING: missing atoms! Processing helix chain 'M' and resid 542 through 548 Processing helix chain 'M' and resid 588 through 598 Processing helix chain 'M' and resid 599 through 607 removed outlier: 4.105A pdb=" N ARG M 603 " --> pdb=" O GLU M 599 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N GLN M 604 " --> pdb=" O PRO M 600 " (cutoff:3.500A) Processing helix chain 'M' and resid 644 through 650 Processing helix chain 'M' and resid 652 through 663 Processing helix chain 'M' and resid 686 through 692 removed outlier: 3.561A pdb=" N GLN M 691 " --> pdb=" O GLU M 687 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N PHE M 692 " --> pdb=" O GLU M 688 " (cutoff:3.500A) Processing helix chain 'M' and resid 702 through 721 Processing helix chain 'M' and resid 723 through 753 Processing helix chain 'M' and resid 759 through 763 removed outlier: 3.531A pdb=" N GLN M 762 " --> pdb=" O ARG M 759 " (cutoff:3.500A) Processing helix chain 'M' and resid 830 through 841 Processing helix chain 'M' and resid 854 through 870 Processing helix chain 'M' and resid 907 through 922 removed outlier: 3.640A pdb=" N ARG M 911 " --> pdb=" O PRO M 907 " (cutoff:3.500A) Processing helix chain 'M' and resid 922 through 928 removed outlier: 3.685A pdb=" N GLU M 926 " --> pdb=" O ASP M 922 " (cutoff:3.500A) Processing helix chain 'M' and resid 936 through 940 Processing helix chain 'M' and resid 951 through 970 Processing helix chain 'M' and resid 985 through 989 removed outlier: 3.872A pdb=" N TYR M 988 " --> pdb=" O LEU M 985 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N VAL M 989 " --> pdb=" O ILE M 986 " (cutoff:3.500A) No H-bonds generated for 'chain 'M' and resid 985 through 989' Processing helix chain 'M' and resid 993 through 1007 Processing helix chain 'M' and resid 1015 through 1020 removed outlier: 3.547A pdb=" N MET M1020 " --> pdb=" O GLN M1016 " (cutoff:3.500A) Processing helix chain 'M' and resid 1024 through 1031 Processing helix chain 'M' and resid 1051 through 1055 removed outlier: 3.837A pdb=" N ASP M1054 " --> pdb=" O GLU M1051 " (cutoff:3.500A) removed outlier: 4.316A pdb=" N GLY M1055 " --> pdb=" O VAL M1052 " (cutoff:3.500A) No H-bonds generated for 'chain 'M' and resid 1051 through 1055' Processing helix chain 'M' and resid 1062 through 1073 removed outlier: 3.896A pdb=" N LYS M1068 " --> pdb=" O GLU M1064 " (cutoff:3.500A) Processing helix chain 'M' and resid 1085 through 1095 removed outlier: 3.629A pdb=" N GLU M1091 " --> pdb=" O GLY M1087 " (cutoff:3.500A) removed outlier: 4.182A pdb=" N ILE M1092 " --> pdb=" O ALA M1088 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N LEU M1093 " --> pdb=" O LEU M1089 " (cutoff:3.500A) Processing helix chain 'M' and resid 1103 through 1112 Processing helix chain 'M' and resid 1121 through 1132 removed outlier: 3.596A pdb=" N ASP M1125 " --> pdb=" O ILE M1121 " (cutoff:3.500A) Processing helix chain 'M' and resid 1146 through 1155 Processing helix chain 'M' and resid 1241 through 1246 Processing helix chain 'M' and resid 1252 through 1256 removed outlier: 4.406A pdb=" N GLU M1255 " --> pdb=" O ARG M1252 " (cutoff:3.500A) Processing helix chain 'M' and resid 1272 through 1275 Processing helix chain 'M' and resid 1282 through 1286 Processing helix chain 'M' and resid 1339 through 1350 removed outlier: 3.838A pdb=" N THR M1349 " --> pdb=" O LYS M1345 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N MET M1350 " --> pdb=" O MET M1346 " (cutoff:3.500A) Processing helix chain 'M' and resid 1402 through 1406 removed outlier: 3.566A pdb=" N PHE M1405 " --> pdb=" O SER M1402 " (cutoff:3.500A) Processing helix chain 'M' and resid 1407 through 1428 removed outlier: 3.563A pdb=" N ILE M1411 " --> pdb=" O ASP M1407 " (cutoff:3.500A) removed outlier: 4.857A pdb=" N GLN M1417 " --> pdb=" O ALA M1413 " (cutoff:3.500A) Proline residue: M1418 - end of helix Processing helix chain 'M' and resid 1434 through 1439 Processing helix chain 'M' and resid 1439 through 1454 Processing helix chain 'M' and resid 1503 through 1515 Processing helix chain 'Q' and resid 23 through 37 removed outlier: 3.549A pdb=" N UNK Q 27 " --> pdb=" O UNK Q 23 " (cutoff:3.500A) Processing helix chain 'Q' and resid 40 through 55 removed outlier: 3.669A pdb=" N UNK Q 44 " --> pdb=" O UNK Q 40 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N UNK Q 50 " --> pdb=" O UNK Q 46 " (cutoff:3.500A) Processing helix chain 'Q' and resid 56 through 70 Processing helix chain 'Q' and resid 79 through 97 Processing helix chain 'Q' and resid 105 through 125 removed outlier: 3.587A pdb=" N UNK Q 125 " --> pdb=" O UNK Q 121 " (cutoff:3.500A) Processing helix chain 'Q' and resid 127 through 141 removed outlier: 3.811A pdb=" N UNK Q 141 " --> pdb=" O UNK Q 137 " (cutoff:3.500A) Processing helix chain 'Q' and resid 144 through 157 removed outlier: 3.833A pdb=" N UNK Q 148 " --> pdb=" O UNK Q 144 " (cutoff:3.500A) Processing helix chain 'Q' and resid 162 through 177 Processing helix chain 'Q' and resid 178 through 192 Processing helix chain 'Q' and resid 200 through 211 removed outlier: 3.697A pdb=" N UNK Q 206 " --> pdb=" O UNK Q 202 " (cutoff:3.500A) Processing helix chain 'Q' and resid 213 through 228 Processing helix chain 'Q' and resid 232 through 246 removed outlier: 3.528A pdb=" N UNK Q 246 " --> pdb=" O UNK Q 242 " (cutoff:3.500A) Processing helix chain 'Q' and resid 250 through 265 Processing helix chain 'Q' and resid 268 through 283 Processing helix chain 'Q' and resid 284 through 298 Processing helix chain 'Q' and resid 306 through 319 Processing helix chain 'Q' and resid 321 through 336 Processing helix chain 'Q' and resid 337 through 339 No H-bonds generated for 'chain 'Q' and resid 337 through 339' Processing helix chain 'Q' and resid 340 through 355 removed outlier: 3.642A pdb=" N PHE Q 345 " --> pdb=" O VAL Q 341 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N GLY Q 346 " --> pdb=" O LEU Q 342 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N GLN Q 349 " --> pdb=" O PHE Q 345 " (cutoff:3.500A) Processing helix chain 'Q' and resid 356 through 371 Processing helix chain 'Q' and resid 374 through 389 Processing helix chain 'Q' and resid 390 through 408 removed outlier: 4.733A pdb=" N ILE Q 396 " --> pdb=" O GLU Q 392 " (cutoff:3.500A) Processing helix chain 'Q' and resid 411 through 425 Processing helix chain 'Q' and resid 429 through 448 removed outlier: 4.302A pdb=" N ALA Q 433 " --> pdb=" O GLY Q 429 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N ILE Q 440 " --> pdb=" O THR Q 436 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N GLU Q 443 " --> pdb=" O ARG Q 439 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N ALA Q 447 " --> pdb=" O GLU Q 443 " (cutoff:3.500A) Processing helix chain 'Q' and resid 450 through 465 removed outlier: 3.637A pdb=" N LEU Q 454 " --> pdb=" O PRO Q 450 " (cutoff:3.500A) Processing helix chain 'Q' and resid 466 through 480 removed outlier: 3.557A pdb=" N LEU Q 478 " --> pdb=" O PHE Q 474 " (cutoff:3.500A) Processing helix chain 'Q' and resid 490 through 492 No H-bonds generated for 'chain 'Q' and resid 490 through 492' Processing helix chain 'Q' and resid 493 through 510 removed outlier: 3.722A pdb=" N THR Q 498 " --> pdb=" O ALA Q 494 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N THR Q 499 " --> pdb=" O ILE Q 495 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N ALA Q 504 " --> pdb=" O SER Q 500 " (cutoff:3.500A) Processing helix chain 'Q' and resid 512 through 527 Processing helix chain 'Q' and resid 530 through 544 removed outlier: 4.092A pdb=" N TYR Q 534 " --> pdb=" O TYR Q 530 " (cutoff:3.500A) Processing helix chain 'Q' and resid 546 through 561 Processing helix chain 'Q' and resid 564 through 578 Processing helix chain 'Q' and resid 580 through 592 Processing helix chain 'Q' and resid 600 through 616 removed outlier: 3.624A pdb=" N THR Q 614 " --> pdb=" O VAL Q 610 " (cutoff:3.500A) Processing helix chain 'Q' and resid 619 through 627 Processing helix chain 'Q' and resid 627 through 641 removed outlier: 3.666A pdb=" N ARG Q 631 " --> pdb=" O ARG Q 627 " (cutoff:3.500A) Processing helix chain 'Q' and resid 646 through 660 removed outlier: 4.148A pdb=" N ALA Q 650 " --> pdb=" O ASN Q 646 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N LYS Q 660 " --> pdb=" O VAL Q 656 " (cutoff:3.500A) Processing helix chain 'Q' and resid 662 through 676 removed outlier: 4.451A pdb=" N ASP Q 668 " --> pdb=" O ARG Q 664 " (cutoff:3.500A) Processing helix chain 'Q' and resid 680 through 694 removed outlier: 3.947A pdb=" N TRP Q 684 " --> pdb=" O ILE Q 680 " (cutoff:3.500A) Processing helix chain 'Q' and resid 696 through 712 Processing helix chain 'Q' and resid 718 through 726 removed outlier: 3.772A pdb=" N ALA Q 726 " --> pdb=" O TYR Q 722 " (cutoff:3.500A) Processing helix chain 'Q' and resid 738 through 744 removed outlier: 3.959A pdb=" N ARG Q 744 " --> pdb=" O LEU Q 740 " (cutoff:3.500A) Processing helix chain 'Q' and resid 755 through 773 removed outlier: 4.098A pdb=" N ALA Q 765 " --> pdb=" O LEU Q 761 " (cutoff:3.500A) removed outlier: 4.292A pdb=" N ASP Q 771 " --> pdb=" O SER Q 767 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N GLU Q 772 " --> pdb=" O VAL Q 768 " (cutoff:3.500A) Processing helix chain 'Q' and resid 778 through 797 removed outlier: 3.817A pdb=" N TYR Q 795 " --> pdb=" O ARG Q 791 " (cutoff:3.500A) Processing helix chain 'Q' and resid 808 through 891 removed outlier: 3.710A pdb=" N ARG Q 815 " --> pdb=" O ALA Q 811 " (cutoff:3.500A) removed outlier: 4.283A pdb=" N SER Q 818 " --> pdb=" O ALA Q 814 " (cutoff:3.500A) removed outlier: 4.173A pdb=" N TYR Q 826 " --> pdb=" O SER Q 822 " (cutoff:3.500A) removed outlier: 4.549A pdb=" N ALA Q 829 " --> pdb=" O GLN Q 825 " (cutoff:3.500A) removed outlier: 4.347A pdb=" N PHE Q 891 " --> pdb=" O ASN Q 887 " (cutoff:3.500A) Processing helix chain 'U' and resid 380 through 396 Processing helix chain 'U' and resid 499 through 515 Processing helix chain 'V' and resid 210 through 214 Processing helix chain 'X' and resid 248 through 260 Processing helix chain 'Y' and resid 2 through 6 Processing helix chain 'Y' and resid 25 through 32 Processing helix chain 'Y' and resid 36 through 41 Processing helix chain 'Y' and resid 45 through 52 Processing helix chain 'Y' and resid 65 through 68 Processing helix chain 'Y' and resid 69 through 75 Processing helix chain 'Y' and resid 94 through 104 Processing helix chain 'Z' and resid 188 through 204 Processing helix chain 'Z' and resid 231 through 239 removed outlier: 3.545A pdb=" N VAL Z 235 " --> pdb=" O LYS Z 231 " (cutoff:3.500A) Processing helix chain 'Z' and resid 245 through 249 removed outlier: 3.648A pdb=" N TYR Z 249 " --> pdb=" O ARG Z 246 " (cutoff:3.500A) Processing helix chain 'Z' and resid 256 through 260 Processing helix chain 'Z' and resid 341 through 349 Processing helix chain 'Z' and resid 389 through 396 Processing helix chain 'Z' and resid 464 through 466 No H-bonds generated for 'chain 'Z' and resid 464 through 466' Processing helix chain 'Z' and resid 514 through 516 No H-bonds generated for 'chain 'Z' and resid 514 through 516' Processing helix chain 'Z' and resid 630 through 633 removed outlier: 3.728A pdb=" N GLY Z 633 " --> pdb=" O VAL Z 630 " (cutoff:3.500A) No H-bonds generated for 'chain 'Z' and resid 630 through 633' Processing sheet with id=AA1, first strand: chain 'A' and resid 15 through 16 removed outlier: 4.693A pdb=" N ARG B1150 " --> pdb=" O ARG A 16 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 1448 through 1449 Processing sheet with id=AA3, first strand: chain 'A' and resid 86 through 94 removed outlier: 10.492A pdb=" N LEU A 90 " --> pdb=" O PRO A 254 " (cutoff:3.500A) removed outlier: 10.705A pdb=" N LYS A 92 " --> pdb=" O VAL A 252 " (cutoff:3.500A) removed outlier: 7.241A pdb=" N VAL A 252 " --> pdb=" O LYS A 92 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 190 through 194 Processing sheet with id=AA5, first strand: chain 'A' and resid 357 through 358 Processing sheet with id=AA6, first strand: chain 'B' and resid 1060 through 1062 removed outlier: 3.517A pdb=" N PHE A 458 " --> pdb=" O MET A 470 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N MET A 470 " --> pdb=" O PHE A 458 " (cutoff:3.500A) removed outlier: 5.506A pdb=" N VAL A 378 " --> pdb=" O ARG A 475 " (cutoff:3.500A) removed outlier: 7.916A pdb=" N PHE A 482 " --> pdb=" O ARG A 364 " (cutoff:3.500A) removed outlier: 6.192A pdb=" N VAL A 366 " --> pdb=" O PHE A 482 " (cutoff:3.500A) removed outlier: 7.717A pdb=" N LEU A 484 " --> pdb=" O VAL A 366 " (cutoff:3.500A) removed outlier: 6.327A pdb=" N THR A 368 " --> pdb=" O LEU A 484 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 389 through 393 removed outlier: 3.912A pdb=" N TYR A 418 " --> pdb=" O GLU A 447 " (cutoff:3.500A) removed outlier: 6.375A pdb=" N HIS A 449 " --> pdb=" O ALA A 416 " (cutoff:3.500A) removed outlier: 7.332A pdb=" N ALA A 416 " --> pdb=" O HIS A 449 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 554 through 555 Processing sheet with id=AA9, first strand: chain 'A' and resid 579 through 581 removed outlier: 5.680A pdb=" N ILE A 579 " --> pdb=" O TYR H 93 " (cutoff:3.500A) removed outlier: 6.851A pdb=" N TYR H 93 " --> pdb=" O ILE A 579 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N LYS A 581 " --> pdb=" O VAL H 91 " (cutoff:3.500A) removed outlier: 5.585A pdb=" N VAL H 96 " --> pdb=" O SER H 117 " (cutoff:3.500A) removed outlier: 6.613A pdb=" N SER H 117 " --> pdb=" O VAL H 96 " (cutoff:3.500A) removed outlier: 5.024A pdb=" N LEU H 122 " --> pdb=" O ASP H 42 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N VAL H 43 " --> pdb=" O SER H 26 " (cutoff:3.500A) removed outlier: 6.711A pdb=" N GLU H 31 " --> pdb=" O VAL H 12 " (cutoff:3.500A) removed outlier: 5.916A pdb=" N VAL H 12 " --> pdb=" O GLU H 31 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 579 through 581 removed outlier: 5.680A pdb=" N ILE A 579 " --> pdb=" O TYR H 93 " (cutoff:3.500A) removed outlier: 6.851A pdb=" N TYR H 93 " --> pdb=" O ILE A 579 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N LYS A 581 " --> pdb=" O VAL H 91 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 602 through 603 removed outlier: 3.769A pdb=" N MET A 637 " --> pdb=" O VAL A 629 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 789 through 790 Processing sheet with id=AB4, first strand: chain 'A' and resid 872 through 873 removed outlier: 6.786A pdb=" N VAL A 879 " --> pdb=" O VAL A 887 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 902 through 905 Processing sheet with id=AB6, first strand: chain 'A' and resid 1140 through 1142 Processing sheet with id=AB7, first strand: chain 'A' and resid 1245 through 1247 removed outlier: 6.819A pdb=" N LEU A1211 " --> pdb=" O ILE A1175 " (cutoff:3.500A) removed outlier: 4.769A pdb=" N ILE A1175 " --> pdb=" O LEU A1211 " (cutoff:3.500A) removed outlier: 6.850A pdb=" N ARG A1213 " --> pdb=" O THR A1173 " (cutoff:3.500A) removed outlier: 4.635A pdb=" N THR A1173 " --> pdb=" O ARG A1213 " (cutoff:3.500A) removed outlier: 6.682A pdb=" N GLU A1215 " --> pdb=" O ALA A1171 " (cutoff:3.500A) removed outlier: 4.167A pdb=" N TYR I 54 " --> pdb=" O ILE A1175 " (cutoff:3.500A) removed outlier: 7.520A pdb=" N TYR A1177 " --> pdb=" O CYS I 52 " (cutoff:3.500A) removed outlier: 7.260A pdb=" N CYS I 52 " --> pdb=" O TYR A1177 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 1319 through 1320 Processing sheet with id=AB9, first strand: chain 'A' and resid 1408 through 1409 removed outlier: 7.728A pdb=" N ARG E 172 " --> pdb=" O GLY A1409 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'A' and resid 1472 through 1475 Processing sheet with id=AC2, first strand: chain 'B' and resid 87 through 93 removed outlier: 4.927A pdb=" N PHE B 88 " --> pdb=" O THR B 129 " (cutoff:3.500A) removed outlier: 6.722A pdb=" N THR B 129 " --> pdb=" O PHE B 88 " (cutoff:3.500A) removed outlier: 5.028A pdb=" N GLN B 90 " --> pdb=" O ASP B 127 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N ASP B 127 " --> pdb=" O GLN B 90 " (cutoff:3.500A) removed outlier: 6.666A pdb=" N ALA B 122 " --> pdb=" O GLY B 150 " (cutoff:3.500A) removed outlier: 7.003A pdb=" N GLY B 150 " --> pdb=" O ALA B 122 " (cutoff:3.500A) removed outlier: 7.858A pdb=" N LEU B 124 " --> pdb=" O PHE B 148 " (cutoff:3.500A) removed outlier: 5.198A pdb=" N PHE B 148 " --> pdb=" O LEU B 124 " (cutoff:3.500A) removed outlier: 5.828A pdb=" N VAL B 126 " --> pdb=" O LYS B 146 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N LYS B 146 " --> pdb=" O VAL B 126 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 97 through 98 Processing sheet with id=AC4, first strand: chain 'B' and resid 185 through 186 Processing sheet with id=AC5, first strand: chain 'B' and resid 391 through 394 Processing sheet with id=AC6, first strand: chain 'B' and resid 206 through 208 removed outlier: 3.593A pdb=" N TYR B 217 " --> pdb=" O MET B 239 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N ILE B 235 " --> pdb=" O CYS B 221 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 531 through 534 removed outlier: 4.612A pdb=" N ARG B 620 " --> pdb=" O SER B 533 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 632 through 633 Processing sheet with id=AC9, first strand: chain 'B' and resid 551 through 552 removed outlier: 5.532A pdb=" N TRP B 573 " --> pdb=" O VAL B 569 " (cutoff:3.500A) removed outlier: 6.826A pdb=" N VAL B 569 " --> pdb=" O TRP B 573 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N GLY B 575 " --> pdb=" O ILE B 567 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N ILE B 567 " --> pdb=" O GLY B 575 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 748 through 751 removed outlier: 6.702A pdb=" N PHE B 918 " --> pdb=" O VAL B 909 " (cutoff:3.500A) removed outlier: 4.431A pdb=" N VAL B 909 " --> pdb=" O PHE B 918 " (cutoff:3.500A) removed outlier: 6.721A pdb=" N LYS B 920 " --> pdb=" O VAL B 907 " (cutoff:3.500A) removed outlier: 4.586A pdb=" N VAL B 907 " --> pdb=" O LYS B 920 " (cutoff:3.500A) removed outlier: 6.636A pdb=" N ARG B 922 " --> pdb=" O ASP B 905 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 759 through 760 Processing sheet with id=AD3, first strand: chain 'B' and resid 1025 through 1026 removed outlier: 7.240A pdb=" N VAL B 794 " --> pdb=" O GLY B 946 " (cutoff:3.500A) removed outlier: 6.352A pdb=" N GLN B 948 " --> pdb=" O VAL B 794 " (cutoff:3.500A) removed outlier: 6.508A pdb=" N MET B 796 " --> pdb=" O GLN B 948 " (cutoff:3.500A) removed outlier: 8.836A pdb=" N ILE B 965 " --> pdb=" O ASN B 777 " (cutoff:3.500A) removed outlier: 6.204A pdb=" N ILE B 779 " --> pdb=" O ILE B 965 " (cutoff:3.500A) removed outlier: 7.622A pdb=" N ILE B 967 " --> pdb=" O ILE B 779 " (cutoff:3.500A) removed outlier: 6.327A pdb=" N ALA B 781 " --> pdb=" O ILE B 967 " (cutoff:3.500A) removed outlier: 4.402A pdb=" N PHE B1042 " --> pdb=" O ILE B 782 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 827 through 829 Processing sheet with id=AD5, first strand: chain 'B' and resid 865 through 867 removed outlier: 6.957A pdb=" N THR B 894 " --> pdb=" O ILE B 866 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'B' and resid 1127 through 1129 Processing sheet with id=AD7, first strand: chain 'C' and resid 8 through 14 removed outlier: 6.513A pdb=" N LYS C 20 " --> pdb=" O THR C 12 " (cutoff:3.500A) removed outlier: 4.687A pdb=" N LEU C 14 " --> pdb=" O ASN C 18 " (cutoff:3.500A) removed outlier: 6.806A pdb=" N ASN C 18 " --> pdb=" O LEU C 14 " (cutoff:3.500A) removed outlier: 6.658A pdb=" N TYR C 230 " --> pdb=" O PHE C 184 " (cutoff:3.500A) removed outlier: 4.197A pdb=" N PHE C 184 " --> pdb=" O TYR C 230 " (cutoff:3.500A) removed outlier: 6.047A pdb=" N ASN C 232 " --> pdb=" O VAL C 182 " (cutoff:3.500A) removed outlier: 4.092A pdb=" N VAL C 182 " --> pdb=" O ASN C 232 " (cutoff:3.500A) removed outlier: 6.566A pdb=" N GLU C 234 " --> pdb=" O ALA C 180 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 121 through 122 removed outlier: 6.896A pdb=" N GLU C 158 " --> pdb=" O ALA C 54 " (cutoff:3.500A) removed outlier: 6.584A pdb=" N ALA C 54 " --> pdb=" O GLU C 158 " (cutoff:3.500A) removed outlier: 7.233A pdb=" N ARG C 160 " --> pdb=" O ILE C 52 " (cutoff:3.500A) removed outlier: 4.926A pdb=" N ILE C 52 " --> pdb=" O ARG C 160 " (cutoff:3.500A) removed outlier: 6.755A pdb=" N ARG C 162 " --> pdb=" O VAL C 50 " (cutoff:3.500A) removed outlier: 4.661A pdb=" N VAL C 50 " --> pdb=" O ARG C 162 " (cutoff:3.500A) removed outlier: 6.586A pdb=" N TYR C 164 " --> pdb=" O ASP C 48 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 113 through 116 removed outlier: 6.406A pdb=" N ARG C 113 " --> pdb=" O LYS C 152 " (cutoff:3.500A) removed outlier: 4.515A pdb=" N LYS C 152 " --> pdb=" O ARG C 113 " (cutoff:3.500A) removed outlier: 6.990A pdb=" N VAL C 115 " --> pdb=" O ILE C 150 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'D' and resid 30 through 31 removed outlier: 4.060A pdb=" N GLU D 30 " --> pdb=" O HIS G 4 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N ILE G 11 " --> pdb=" O TYR G 68 " (cutoff:3.500A) removed outlier: 11.488A pdb=" N LEU G 67 " --> pdb=" O ILE G 54 " (cutoff:3.500A) removed outlier: 10.476A pdb=" N ILE G 54 " --> pdb=" O LEU G 67 " (cutoff:3.500A) removed outlier: 8.825A pdb=" N ASP G 52 " --> pdb=" O PRO G 69 " (cutoff:3.500A) removed outlier: 7.707A pdb=" N LYS G 71 " --> pdb=" O THR G 50 " (cutoff:3.500A) removed outlier: 7.681A pdb=" N THR G 50 " --> pdb=" O LYS G 71 " (cutoff:3.500A) removed outlier: 7.491A pdb=" N LYS G 73 " --> pdb=" O VAL G 48 " (cutoff:3.500A) removed outlier: 5.265A pdb=" N VAL G 48 " --> pdb=" O LYS G 73 " (cutoff:3.500A) removed outlier: 6.922A pdb=" N ILE G 75 " --> pdb=" O ILE G 46 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N THR G 39 " --> pdb=" O GLY G 43 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'D' and resid 30 through 31 removed outlier: 4.060A pdb=" N GLU D 30 " --> pdb=" O HIS G 4 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N ILE G 11 " --> pdb=" O TYR G 68 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'E' and resid 26 through 27 removed outlier: 4.536A pdb=" N ALA E 63 " --> pdb=" O LEU E 27 " (cutoff:3.500A) removed outlier: 4.151A pdb=" N ARG E 101 " --> pdb=" O GLN E 71 " (cutoff:3.500A) removed outlier: 6.205A pdb=" N ALA E 102 " --> pdb=" O GLU E 128 " (cutoff:3.500A) removed outlier: 7.818A pdb=" N PHE E 130 " --> pdb=" O ALA E 102 " (cutoff:3.500A) removed outlier: 6.036A pdb=" N ILE E 104 " --> pdb=" O PHE E 130 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'G' and resid 83 through 92 removed outlier: 3.546A pdb=" N VAL G 88 " --> pdb=" O GLU G 100 " (cutoff:3.500A) removed outlier: 6.607A pdb=" N PHE G 98 " --> pdb=" O THR G 90 " (cutoff:3.500A) removed outlier: 4.862A pdb=" N VAL G 92 " --> pdb=" O GLY G 96 " (cutoff:3.500A) removed outlier: 6.517A pdb=" N GLY G 96 " --> pdb=" O VAL G 92 " (cutoff:3.500A) removed outlier: 6.527A pdb=" N SER G 105 " --> pdb=" O ALA G 159 " (cutoff:3.500A) removed outlier: 7.846A pdb=" N GLY G 161 " --> pdb=" O SER G 105 " (cutoff:3.500A) removed outlier: 6.112A pdb=" N PHE G 107 " --> pdb=" O GLY G 161 " (cutoff:3.500A) removed outlier: 6.326A pdb=" N SER G 162 " --> pdb=" O ILE G 147 " (cutoff:3.500A) removed outlier: 5.434A pdb=" N ILE G 147 " --> pdb=" O SER G 162 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N GLU G 83 " --> pdb=" O ILE G 147 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'G' and resid 118 through 120 Processing sheet with id=AE6, first strand: chain 'I' and resid 25 through 29 Processing sheet with id=AE7, first strand: chain 'I' and resid 80 through 81 Processing sheet with id=AE8, first strand: chain 'K' and resid 19 through 23 Processing sheet with id=AE9, first strand: chain 'M' and resid 804 through 809 removed outlier: 4.137A pdb=" N GLU M 804 " --> pdb=" O ASN M 800 " (cutoff:3.500A) removed outlier: 6.693A pdb=" N LEU M 798 " --> pdb=" O THR M 806 " (cutoff:3.500A) removed outlier: 4.310A pdb=" N PHE M 808 " --> pdb=" O CYS M 796 " (cutoff:3.500A) removed outlier: 6.638A pdb=" N CYS M 796 " --> pdb=" O PHE M 808 " (cutoff:3.500A) removed outlier: 6.076A pdb=" N VAL M 848 " --> pdb=" O GLU M 883 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'M' and resid 1238 through 1240 removed outlier: 7.059A pdb=" N LYS M1229 " --> pdb=" O THR M1172 " (cutoff:3.500A) removed outlier: 6.636A pdb=" N ILE M1267 " --> pdb=" O THR M1280 " (cutoff:3.500A) removed outlier: 6.506A pdb=" N THR M1280 " --> pdb=" O ILE M1267 " (cutoff:3.500A) removed outlier: 4.136A pdb=" N LYS M1269 " --> pdb=" O ASP M1278 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N ASP M1278 " --> pdb=" O LYS M1269 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ASP M1271 " --> pdb=" O SER M1276 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'M' and resid 1330 through 1332 removed outlier: 3.664A pdb=" N LEU M1367 " --> pdb=" O VAL M1383 " (cutoff:3.500A) removed outlier: 6.908A pdb=" N ILE M1377 " --> pdb=" O VAL M1373 " (cutoff:3.500A) removed outlier: 7.785A pdb=" N LEU M1398 " --> pdb=" O HIS M1380 " (cutoff:3.500A) removed outlier: 6.405A pdb=" N ASP M1382 " --> pdb=" O LEU M1398 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'M' and resid 1460 through 1464 Processing sheet with id=AF4, first strand: chain 'Q' and resid 8 through 9 removed outlier: 3.762A pdb=" N UNK Q 8 " --> pdb=" O UNK Q 17 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'U' and resid 422 through 423 removed outlier: 4.241A pdb=" N UNK U 488 " --> pdb=" O UNK U 462 " (cutoff:3.500A) removed outlier: 6.389A pdb=" N UNK U 471 " --> pdb=" O UNK U 482 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N UNK U 472 " --> pdb=" O UNK V 201 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N UNK V 201 " --> pdb=" O UNK U 472 " (cutoff:3.500A) removed outlier: 6.887A pdb=" N UNK V 200 " --> pdb=" O UNK V 328 " (cutoff:3.500A) removed outlier: 7.860A pdb=" N UNK V 330 " --> pdb=" O UNK V 200 " (cutoff:3.500A) removed outlier: 5.686A pdb=" N UNK V 202 " --> pdb=" O UNK V 330 " (cutoff:3.500A) removed outlier: 6.663A pdb=" N UNK V 332 " --> pdb=" O UNK V 202 " (cutoff:3.500A) removed outlier: 6.100A pdb=" N UNK V 204 " --> pdb=" O UNK V 332 " (cutoff:3.500A) removed outlier: 7.648A pdb=" N UNK V 334 " --> pdb=" O UNK V 204 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N UNK V 222 " --> pdb=" O UNK V 257 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'U' and resid 422 through 423 removed outlier: 4.241A pdb=" N UNK U 488 " --> pdb=" O UNK U 462 " (cutoff:3.500A) removed outlier: 7.165A pdb=" N UNK U 373 " --> pdb=" O UNK U 487 " (cutoff:3.500A) removed outlier: 8.685A pdb=" N UNK U 489 " --> pdb=" O UNK U 373 " (cutoff:3.500A) removed outlier: 6.933A pdb=" N UNK U 375 " --> pdb=" O UNK U 489 " (cutoff:3.500A) removed outlier: 8.002A pdb=" N UNK U 491 " --> pdb=" O UNK U 375 " (cutoff:3.500A) removed outlier: 7.015A pdb=" N UNK U 377 " --> pdb=" O UNK U 491 " (cutoff:3.500A) removed outlier: 9.828A pdb=" N UNK U 372 " --> pdb=" O UNK V 316 " (cutoff:3.500A) removed outlier: 6.404A pdb=" N UNK V 316 " --> pdb=" O UNK U 372 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N UNK U 374 " --> pdb=" O UNK V 314 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'W' and resid 6 through 11 removed outlier: 6.126A pdb=" N ILE W 7 " --> pdb=" O ASP W 302 " (cutoff:3.500A) removed outlier: 5.835A pdb=" N ASP W 302 " --> pdb=" O ILE W 7 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'W' and resid 19 through 23 removed outlier: 6.767A pdb=" N GLY W 38 " --> pdb=" O TRP W 20 " (cutoff:3.500A) removed outlier: 4.438A pdb=" N VAL W 22 " --> pdb=" O VAL W 36 " (cutoff:3.500A) removed outlier: 6.817A pdb=" N VAL W 36 " --> pdb=" O VAL W 22 " (cutoff:3.500A) removed outlier: 6.516A pdb=" N VAL W 44 " --> pdb=" O SER W 59 " (cutoff:3.500A) removed outlier: 4.762A pdb=" N SER W 59 " --> pdb=" O VAL W 44 " (cutoff:3.500A) removed outlier: 6.661A pdb=" N VAL W 46 " --> pdb=" O GLN W 57 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'W' and resid 67 through 72 removed outlier: 3.866A pdb=" N SER W 83 " --> pdb=" O HIS W 87 " (cutoff:3.500A) removed outlier: 4.274A pdb=" N HIS W 87 " --> pdb=" O SER W 83 " (cutoff:3.500A) removed outlier: 6.352A pdb=" N ILE W 88 " --> pdb=" O SER W 101 " (cutoff:3.500A) removed outlier: 4.299A pdb=" N SER W 101 " --> pdb=" O ILE W 88 " (cutoff:3.500A) removed outlier: 6.660A pdb=" N LEU W 90 " --> pdb=" O ILE W 99 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'W' and resid 112 through 114 removed outlier: 6.094A pdb=" N GLY W 134 " --> pdb=" O LYS W 140 " (cutoff:3.500A) removed outlier: 6.169A pdb=" N LYS W 140 " --> pdb=" O GLY W 134 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'W' and resid 151 through 156 removed outlier: 6.539A pdb=" N ILE W 172 " --> pdb=" O THR W 185 " (cutoff:3.500A) removed outlier: 4.338A pdb=" N THR W 185 " --> pdb=" O ILE W 172 " (cutoff:3.500A) removed outlier: 6.490A pdb=" N ILE W 174 " --> pdb=" O LEU W 183 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'W' and resid 193 through 198 removed outlier: 6.014A pdb=" N ASP W 218 " --> pdb=" O LEU W 224 " (cutoff:3.500A) removed outlier: 6.071A pdb=" N LEU W 224 " --> pdb=" O ASP W 218 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'W' and resid 235 through 240 removed outlier: 6.830A pdb=" N SER W 250 " --> pdb=" O LEU W 236 " (cutoff:3.500A) removed outlier: 4.451A pdb=" N VAL W 238 " --> pdb=" O VAL W 248 " (cutoff:3.500A) removed outlier: 6.807A pdb=" N VAL W 248 " --> pdb=" O VAL W 238 " (cutoff:3.500A) removed outlier: 5.388A pdb=" N PHE W 240 " --> pdb=" O HIS W 246 " (cutoff:3.500A) removed outlier: 7.672A pdb=" N HIS W 246 " --> pdb=" O PHE W 240 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N SER W 255 " --> pdb=" O SER W 251 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N HIS W 268 " --> pdb=" O VAL W 258 " (cutoff:3.500A) removed outlier: 6.516A pdb=" N ASP W 260 " --> pdb=" O CYS W 266 " (cutoff:3.500A) removed outlier: 5.573A pdb=" N CYS W 266 " --> pdb=" O ASP W 260 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'Y' and resid 22 through 24 Processing sheet with id=AG6, first strand: chain 'Y' and resid 57 through 58 Processing sheet with id=AG7, first strand: chain 'Y' and resid 83 through 85 removed outlier: 3.662A pdb=" N SER Z 214 " --> pdb=" O GLU Z 228 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'Y' and resid 115 through 116 removed outlier: 6.862A pdb=" N ILE Y 115 " --> pdb=" O LYS Z 268 " (cutoff:3.500A) No H-bonds generated for sheet with id=AG8 Processing sheet with id=AG9, first strand: chain 'Z' and resid 352 through 355 removed outlier: 3.995A pdb=" N PHE Z 358 " --> pdb=" O ASP Z 355 " (cutoff:3.500A) removed outlier: 4.797A pdb=" N TYR Z 366 " --> pdb=" O PHE Z 373 " (cutoff:3.500A) removed outlier: 8.018A pdb=" N THR Z 302 " --> pdb=" O VAL Z 296 " (cutoff:3.500A) removed outlier: 5.821A pdb=" N VAL Z 296 " --> pdb=" O THR Z 302 " (cutoff:3.500A) removed outlier: 6.527A pdb=" N SER Z 304 " --> pdb=" O ASP Z 294 " (cutoff:3.500A) Processing sheet with id=AH1, first strand: chain 'Z' and resid 453 through 454 Processing sheet with id=AH2, first strand: chain 'Z' and resid 510 through 513 removed outlier: 7.176A pdb=" N ILE Z 501 " --> pdb=" O VAL Z 493 " (cutoff:3.500A) Processing sheet with id=AH3, first strand: chain 'Z' and resid 567 through 571 removed outlier: 6.972A pdb=" N THR Z 557 " --> pdb=" O LEU Z 553 " (cutoff:3.500A) removed outlier: 5.224A pdb=" N LEU Z 553 " --> pdb=" O THR Z 557 " (cutoff:3.500A) removed outlier: 6.613A pdb=" N GLN Z 559 " --> pdb=" O VAL Z 551 " (cutoff:3.500A) Processing sheet with id=AH4, first strand: chain 'Z' and resid 585 through 587 Processing sheet with id=AH5, first strand: chain 'Z' and resid 635 through 639 removed outlier: 7.044A pdb=" N PHE Z 621 " --> pdb=" O LEU Z 617 " (cutoff:3.500A) removed outlier: 4.979A pdb=" N LEU Z 617 " --> pdb=" O PHE Z 621 " (cutoff:3.500A) removed outlier: 6.872A pdb=" N PHE Z 623 " --> pdb=" O ARG Z 615 " (cutoff:3.500A) Processing sheet with id=AH6, first strand: chain 'Z' and resid 742 through 746 removed outlier: 6.954A pdb=" N THR Z 731 " --> pdb=" O ALA Z 727 " (cutoff:3.500A) removed outlier: 4.999A pdb=" N ALA Z 727 " --> pdb=" O THR Z 731 " (cutoff:3.500A) removed outlier: 6.661A pdb=" N ARG Z 733 " --> pdb=" O LYS Z 725 " (cutoff:3.500A) 2367 hydrogen bonds defined for protein. 6690 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 122 hydrogen bonds 236 hydrogen bond angles 0 basepair planarities 46 basepair parallelities 80 stacking parallelities Total time for adding SS restraints: 26.54 Time building geometry restraints manager: 11.19 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 15182 1.33 - 1.46: 9753 1.46 - 1.58: 25735 1.58 - 1.70: 215 1.70 - 1.82: 371 Bond restraints: 51256 Sorted by residual: bond pdb=" OG1 TPO A1525 " pdb=" P TPO A1525 " ideal model delta sigma weight residual 1.717 1.601 0.116 2.00e-02 2.50e+03 3.34e+01 bond pdb=" O1P TPO A1525 " pdb=" P TPO A1525 " ideal model delta sigma weight residual 1.525 1.606 -0.081 2.00e-02 2.50e+03 1.62e+01 bond pdb=" O3P TPO A1525 " pdb=" P TPO A1525 " ideal model delta sigma weight residual 1.528 1.608 -0.080 2.00e-02 2.50e+03 1.61e+01 bond pdb=" C CYS D 104 " pdb=" N PRO D 105 " ideal model delta sigma weight residual 1.332 1.371 -0.039 1.26e-02 6.30e+03 9.77e+00 bond pdb=" CA GLU B 70 " pdb=" CB GLU B 70 " ideal model delta sigma weight residual 1.523 1.561 -0.038 1.27e-02 6.20e+03 8.89e+00 ... (remaining 51251 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.96: 67695 2.96 - 5.92: 1057 5.92 - 8.87: 167 8.87 - 11.83: 27 11.83 - 14.79: 5 Bond angle restraints: 68951 Sorted by residual: angle pdb=" C THR E 56 " pdb=" N ASP E 57 " pdb=" CA ASP E 57 " ideal model delta sigma weight residual 121.54 133.40 -11.86 1.91e+00 2.74e-01 3.85e+01 angle pdb=" C PHE A 112 " pdb=" N PHE A 113 " pdb=" CA PHE A 113 " ideal model delta sigma weight residual 121.54 132.79 -11.25 1.91e+00 2.74e-01 3.47e+01 angle pdb=" N ASP M1082 " pdb=" CA ASP M1082 " pdb=" C ASP M1082 " ideal model delta sigma weight residual 113.18 105.43 7.75 1.33e+00 5.65e-01 3.40e+01 angle pdb=" CA ASP Z 543 " pdb=" C ASP Z 543 " pdb=" N PRO Z 544 " ideal model delta sigma weight residual 117.68 121.76 -4.08 7.10e-01 1.98e+00 3.30e+01 angle pdb=" C ALA I 104 " pdb=" N GLU I 105 " pdb=" CA GLU I 105 " ideal model delta sigma weight residual 120.82 129.10 -8.28 1.50e+00 4.44e-01 3.05e+01 ... (remaining 68946 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.27: 27791 35.27 - 70.54: 626 70.54 - 105.81: 35 105.81 - 141.08: 0 141.08 - 176.34: 5 Dihedral angle restraints: 28457 sinusoidal: 11792 harmonic: 16665 Sorted by residual: dihedral pdb=" CA HIS B 98 " pdb=" C HIS B 98 " pdb=" N TRP B 99 " pdb=" CA TRP B 99 " ideal model delta harmonic sigma weight residual 180.00 135.34 44.66 0 5.00e+00 4.00e-02 7.98e+01 dihedral pdb=" CA GLU B 629 " pdb=" C GLU B 629 " pdb=" N LYS B 630 " pdb=" CA LYS B 630 " ideal model delta harmonic sigma weight residual -180.00 -135.60 -44.40 0 5.00e+00 4.00e-02 7.89e+01 dihedral pdb=" CA GLU C 91 " pdb=" C GLU C 91 " pdb=" N GLU C 92 " pdb=" CA GLU C 92 " ideal model delta harmonic sigma weight residual -180.00 -139.09 -40.91 0 5.00e+00 4.00e-02 6.69e+01 ... (remaining 28454 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.094: 5938 0.094 - 0.189: 734 0.189 - 0.283: 40 0.283 - 0.377: 8 0.377 - 0.471: 3 Chirality restraints: 6723 Sorted by residual: chirality pdb=" CB ILE A 65 " pdb=" CA ILE A 65 " pdb=" CG1 ILE A 65 " pdb=" CG2 ILE A 65 " both_signs ideal model delta sigma weight residual False 2.64 2.17 0.47 2.00e-01 2.50e+01 5.56e+00 chirality pdb=" CB ILE A 621 " pdb=" CA ILE A 621 " pdb=" CG1 ILE A 621 " pdb=" CG2 ILE A 621 " both_signs ideal model delta sigma weight residual False 2.64 2.21 0.43 2.00e-01 2.50e+01 4.64e+00 chirality pdb=" CG LEU A 760 " pdb=" CB LEU A 760 " pdb=" CD1 LEU A 760 " pdb=" CD2 LEU A 760 " both_signs ideal model delta sigma weight residual False -2.59 -2.19 -0.40 2.00e-01 2.50e+01 4.04e+00 ... (remaining 6720 not shown) Planarity restraints: 9154 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR M1515 " -0.006 2.00e-02 2.50e+03 3.65e-02 2.67e+01 pdb=" CG TYR M1515 " 0.073 2.00e-02 2.50e+03 pdb=" CD1 TYR M1515 " -0.035 2.00e-02 2.50e+03 pdb=" CD2 TYR M1515 " -0.003 2.00e-02 2.50e+03 pdb=" CE1 TYR M1515 " -0.015 2.00e-02 2.50e+03 pdb=" CE2 TYR M1515 " -0.042 2.00e-02 2.50e+03 pdb=" CZ TYR M1515 " -0.016 2.00e-02 2.50e+03 pdb=" OH TYR M1515 " 0.044 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C THR A1540 " 0.062 5.00e-02 4.00e+02 9.45e-02 1.43e+01 pdb=" N PRO A1541 " -0.164 5.00e-02 4.00e+02 pdb=" CA PRO A1541 " 0.050 5.00e-02 4.00e+02 pdb=" CD PRO A1541 " 0.051 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TRP B 573 " 0.018 2.00e-02 2.50e+03 2.10e-02 1.10e+01 pdb=" CG TRP B 573 " -0.053 2.00e-02 2.50e+03 pdb=" CD1 TRP B 573 " 0.029 2.00e-02 2.50e+03 pdb=" CD2 TRP B 573 " 0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP B 573 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP B 573 " 0.002 2.00e-02 2.50e+03 pdb=" CE3 TRP B 573 " -0.002 2.00e-02 2.50e+03 pdb=" CZ2 TRP B 573 " -0.014 2.00e-02 2.50e+03 pdb=" CZ3 TRP B 573 " 0.009 2.00e-02 2.50e+03 pdb=" CH2 TRP B 573 " 0.010 2.00e-02 2.50e+03 ... (remaining 9151 not shown) Histogram of nonbonded interaction distances: 1.92 - 2.52: 181 2.52 - 3.11: 35141 3.11 - 3.71: 74913 3.71 - 4.30: 106351 4.30 - 4.90: 173218 Nonbonded interactions: 389804 Sorted by model distance: nonbonded pdb=" NZ LYS E 85 " pdb=" OP2 DC N 41 " model vdw 1.921 3.120 nonbonded pdb=" OE2 GLU B 816 " pdb=" NZ LYS B 869 " model vdw 2.002 3.120 nonbonded pdb=" O LEU I 65 " pdb=" NH1 ARG I 122 " model vdw 2.062 3.120 nonbonded pdb=" O3' U P 46 " pdb="MG MG A2003 " model vdw 2.084 2.170 nonbonded pdb=" OD1 ASP A 497 " pdb="MG MG A2003 " model vdw 2.110 2.170 ... (remaining 389799 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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=0.00 max=1.00 mean=0.99 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.680 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: 1.450 Check model and map are aligned: 0.280 Set scattering table: 0.370 Process input model: 111.350 Find NCS groups from input model: 0.750 Set up NCS constraints: 0.180 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: 0.020 Load rotamer database and sin/cos tables:2.770 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 118.900 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7957 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 : 0.006 0.116 51256 Z= 0.425 Angle : 0.973 14.789 68951 Z= 0.540 Chirality : 0.061 0.471 6723 Planarity : 0.006 0.095 9154 Dihedral : 13.097 176.344 18817 Min Nonbonded Distance : 1.921 Molprobity Statistics. All-atom Clashscore : 5.48 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.84 % Favored : 95.07 % Rotamer: Outliers : 0.53 % Allowed : 4.71 % Favored : 94.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.74 % Cis-general : 0.00 % Twisted Proline : 0.74 % Twisted General : 0.16 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.86 (0.09), residues: 6303 helix: -1.97 (0.08), residues: 2289 sheet: -1.20 (0.17), residues: 817 loop : -1.99 (0.10), residues: 3197 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.053 0.004 TRP B 573 HIS 0.014 0.002 HIS A 809 PHE 0.049 0.004 PHE G 44 TYR 0.073 0.003 TYR M1515 ARG 0.013 0.001 ARG B1131 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12606 Ramachandran restraints generated. 6303 Oldfield, 0 Emsley, 6303 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12606 Ramachandran restraints generated. 6303 Oldfield, 0 Emsley, 6303 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 766 residues out of total 5627 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 742 time to evaluate : 4.193 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 301 HIS cc_start: 0.7711 (t-170) cc_final: 0.7510 (t-90) REVERT: A 309 LEU cc_start: 0.9402 (OUTLIER) cc_final: 0.9127 (tm) REVERT: A 327 ARG cc_start: 0.8883 (mpt90) cc_final: 0.8631 (mmt-90) REVERT: A 425 ASP cc_start: 0.8091 (m-30) cc_final: 0.7649 (m-30) REVERT: A 467 MET cc_start: 0.8647 (mpt) cc_final: 0.8256 (mpp) REVERT: A 495 ASP cc_start: 0.7390 (t0) cc_final: 0.5899 (t0) REVERT: A 655 ILE cc_start: 0.9674 (OUTLIER) cc_final: 0.9471 (mp) REVERT: A 750 ASP cc_start: 0.8310 (m-30) cc_final: 0.8040 (m-30) REVERT: A 1359 SER cc_start: 0.8847 (p) cc_final: 0.8569 (t) REVERT: B 792 ASP cc_start: 0.7914 (m-30) cc_final: 0.7553 (m-30) REVERT: B 1081 ASP cc_start: 0.8486 (t70) cc_final: 0.8088 (t0) REVERT: D 16 ASP cc_start: 0.8254 (t0) cc_final: 0.8036 (t70) REVERT: D 38 HIS cc_start: 0.9487 (t70) cc_final: 0.9195 (t-90) REVERT: D 44 ARG cc_start: 0.8807 (ttt-90) cc_final: 0.8521 (tpt90) REVERT: D 62 MET cc_start: 0.8894 (mmp) cc_final: 0.8665 (mmp) REVERT: D 70 ARG cc_start: 0.7998 (mtp180) cc_final: 0.7459 (ptm160) REVERT: F 57 MET cc_start: 0.9145 (ttp) cc_final: 0.8899 (ttp) REVERT: G 2 PHE cc_start: 0.7916 (m-80) cc_final: 0.7657 (m-10) REVERT: G 4 HIS cc_start: 0.8027 (t-170) cc_final: 0.7592 (t70) REVERT: G 24 ASN cc_start: 0.8964 (t0) cc_final: 0.8573 (t0) REVERT: G 28 GLN cc_start: 0.8604 (mp10) cc_final: 0.7899 (mp10) REVERT: G 48 VAL cc_start: 0.8936 (OUTLIER) cc_final: 0.8595 (m) REVERT: G 98 PHE cc_start: 0.8535 (m-10) cc_final: 0.8297 (m-80) REVERT: G 104 MET cc_start: 0.7245 (ttp) cc_final: 0.6762 (tmm) REVERT: G 142 GLU cc_start: 0.8311 (mt-10) cc_final: 0.7276 (mm-30) REVERT: H 13 LYS cc_start: 0.8959 (mmmt) cc_final: 0.8734 (mmmt) REVERT: H 118 TYR cc_start: 0.9064 (m-80) cc_final: 0.8450 (m-80) REVERT: H 128 ASP cc_start: 0.8103 (p0) cc_final: 0.7781 (p0) REVERT: K 38 GLU cc_start: 0.8249 (mm-30) cc_final: 0.7994 (mm-30) REVERT: K 80 ASP cc_start: 0.8229 (p0) cc_final: 0.8018 (p0) REVERT: Q 762 GLN cc_start: 0.5640 (mt0) cc_final: 0.5214 (mm-40) REVERT: Q 823 GLN cc_start: 0.3462 (mt0) cc_final: 0.3198 (tm-30) REVERT: Q 871 GLN cc_start: 0.9376 (mm-40) cc_final: 0.9131 (pp30) REVERT: Q 872 LYS cc_start: 0.8938 (tptt) cc_final: 0.8474 (ptmm) REVERT: Q 878 ARG cc_start: 0.7784 (tpt170) cc_final: 0.7098 (tpt-90) REVERT: Z 254 MET cc_start: 0.8818 (ttp) cc_final: 0.8561 (tpp) REVERT: Z 378 MET cc_start: -0.2982 (mtt) cc_final: -0.3463 (mtp) REVERT: Z 597 LYS cc_start: 0.6333 (mttt) cc_final: 0.6063 (mtmt) outliers start: 24 outliers final: 7 residues processed: 764 average time/residue: 0.5596 time to fit residues: 686.2047 Evaluate side-chains 449 residues out of total 5627 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 439 time to evaluate : 4.232 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 309 LEU Chi-restraints excluded: chain A residue 655 ILE Chi-restraints excluded: chain B residue 612 ILE Chi-restraints excluded: chain B residue 896 LEU Chi-restraints excluded: chain F residue 123 LEU Chi-restraints excluded: chain G residue 48 VAL Chi-restraints excluded: chain G residue 108 ILE Chi-restraints excluded: chain H residue 96 VAL Chi-restraints excluded: chain M residue 1515 TYR Chi-restraints excluded: chain Q residue 776 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 603 random chunks: chunk 509 optimal weight: 50.0000 chunk 457 optimal weight: 8.9990 chunk 253 optimal weight: 6.9990 chunk 156 optimal weight: 1.9990 chunk 308 optimal weight: 2.9990 chunk 244 optimal weight: 1.9990 chunk 472 optimal weight: 50.0000 chunk 182 optimal weight: 0.9980 chunk 287 optimal weight: 20.0000 chunk 351 optimal weight: 0.8980 chunk 547 optimal weight: 9.9990 overall best weight: 1.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 62 GLN A 96 HIS A 313 HIS ** A 410 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 606 HIS A 678 ASN A 757 GLN ** A 861 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 884 ASN ** A1005 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1082 HIS A1093 GLN A1108 HIS ** A1182 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1194 ASN A1220 HIS A1248 ASN ** A1303 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1332 GLN A1457 ASN A1462 GLN ** B 319 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 344 GLN B 525 ASN B 631 GLN B 649 ASN B 725 GLN B1120 ASN E 133 GLN G 93 ASN I 22 ASN I 60 HIS J 52 HIS L 26 ASN Q 775 ASN Q 834 GLN Q 877 GLN W 98 GLN W 189 HIS W 221 HIS W 273 HIS Y 12 HIS Total number of N/Q/H flips: 36 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8006 moved from start: 0.2017 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.075 51256 Z= 0.268 Angle : 0.639 13.172 68951 Z= 0.337 Chirality : 0.045 0.208 6723 Planarity : 0.005 0.087 9154 Dihedral : 13.606 173.183 8573 Min Nonbonded Distance : 1.958 Molprobity Statistics. All-atom Clashscore : 8.36 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.76 % Favored : 95.18 % Rotamer: Outliers : 1.71 % Allowed : 8.80 % Favored : 89.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.74 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.32 (0.10), residues: 6303 helix: 0.00 (0.10), residues: 2312 sheet: -0.89 (0.17), residues: 810 loop : -1.53 (0.10), residues: 3181 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP A 988 HIS 0.005 0.001 HIS B 387 PHE 0.036 0.002 PHE D 26 TYR 0.019 0.002 TYR M1515 ARG 0.010 0.001 ARG B 380 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12606 Ramachandran restraints generated. 6303 Oldfield, 0 Emsley, 6303 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12606 Ramachandran restraints generated. 6303 Oldfield, 0 Emsley, 6303 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 571 residues out of total 5627 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 77 poor density : 494 time to evaluate : 4.239 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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: A 301 HIS cc_start: 0.7716 (t-170) cc_final: 0.7507 (t-170) REVERT: A 309 LEU cc_start: 0.9527 (OUTLIER) cc_final: 0.9232 (tm) REVERT: A 404 GLU cc_start: 0.8308 (tm-30) cc_final: 0.8042 (tm-30) REVERT: A 495 ASP cc_start: 0.7320 (t0) cc_final: 0.6433 (t0) REVERT: A 655 ILE cc_start: 0.9752 (OUTLIER) cc_final: 0.9480 (mp) REVERT: A 750 ASP cc_start: 0.8330 (m-30) cc_final: 0.8114 (m-30) REVERT: A 868 MET cc_start: 0.8798 (mtp) cc_final: 0.8574 (mtp) REVERT: A 1359 SER cc_start: 0.8781 (p) cc_final: 0.8503 (t) REVERT: B 198 GLU cc_start: 0.7734 (pt0) cc_final: 0.6709 (pt0) REVERT: B 1081 ASP cc_start: 0.8649 (t70) cc_final: 0.8270 (t0) REVERT: B 1131 ARG cc_start: 0.9056 (ptp-110) cc_final: 0.8828 (ptp90) REVERT: D 16 ASP cc_start: 0.8359 (t0) cc_final: 0.7258 (t70) REVERT: D 34 ASN cc_start: 0.8428 (m-40) cc_final: 0.8020 (t0) REVERT: D 38 HIS cc_start: 0.9460 (t70) cc_final: 0.9158 (t70) REVERT: D 62 MET cc_start: 0.8928 (mmp) cc_final: 0.8491 (mmm) REVERT: D 122 PHE cc_start: 0.7557 (m-80) cc_final: 0.7350 (m-80) REVERT: D 128 GLN cc_start: 0.9150 (mm110) cc_final: 0.8934 (mm110) REVERT: F 86 GLU cc_start: 0.7859 (pm20) cc_final: 0.7507 (pm20) REVERT: F 88 ASP cc_start: 0.8520 (t0) cc_final: 0.8258 (t0) REVERT: G 2 PHE cc_start: 0.8026 (m-80) cc_final: 0.7002 (m-10) REVERT: G 44 PHE cc_start: 0.8888 (OUTLIER) cc_final: 0.8530 (m-80) REVERT: G 68 TYR cc_start: 0.8841 (m-80) cc_final: 0.8448 (m-80) REVERT: G 104 MET cc_start: 0.7387 (ttp) cc_final: 0.6559 (tmm) REVERT: G 110 ARG cc_start: 0.5862 (tpt170) cc_final: 0.5528 (tpt170) REVERT: G 118 GLU cc_start: 0.9181 (mm-30) cc_final: 0.8840 (mm-30) REVERT: G 144 ARG cc_start: 0.4133 (mtm180) cc_final: 0.3855 (mtm-85) REVERT: H 13 LYS cc_start: 0.9141 (mmmt) cc_final: 0.8799 (mmmm) REVERT: I 83 ASP cc_start: 0.8425 (p0) cc_final: 0.8147 (p0) REVERT: L 25 GLU cc_start: 0.8243 (mt-10) cc_final: 0.7969 (tt0) REVERT: W 98 GLN cc_start: 0.1423 (tt0) cc_final: 0.0974 (tp40) REVERT: Y 63 MET cc_start: 0.6039 (tmm) cc_final: 0.5714 (tmm) REVERT: Y 64 MET cc_start: 0.6964 (mtp) cc_final: 0.6256 (mtm) REVERT: Z 197 MET cc_start: 0.8566 (ttt) cc_final: 0.7602 (tpt) REVERT: Z 378 MET cc_start: -0.3001 (mtt) cc_final: -0.3451 (mtp) REVERT: Z 474 MET cc_start: 0.6713 (mpp) cc_final: 0.6308 (mmm) REVERT: Z 748 GLN cc_start: 0.8821 (mm-40) cc_final: 0.8556 (mm-40) outliers start: 77 outliers final: 31 residues processed: 554 average time/residue: 0.5052 time to fit residues: 465.4907 Evaluate side-chains 459 residues out of total 5627 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 425 time to evaluate : 4.174 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain A residue 148 CYS Chi-restraints excluded: chain A residue 309 LEU Chi-restraints excluded: chain A residue 423 ASN Chi-restraints excluded: chain A residue 439 HIS Chi-restraints excluded: chain A residue 514 GLU Chi-restraints excluded: chain A residue 545 VAL Chi-restraints excluded: chain A residue 655 ILE Chi-restraints excluded: chain A residue 732 THR Chi-restraints excluded: chain A residue 902 GLU Chi-restraints excluded: chain B residue 18 THR Chi-restraints excluded: chain B residue 84 TYR Chi-restraints excluded: chain B residue 440 ILE Chi-restraints excluded: chain B residue 612 ILE Chi-restraints excluded: chain B residue 896 LEU Chi-restraints excluded: chain B residue 1149 VAL Chi-restraints excluded: chain C residue 89 THR Chi-restraints excluded: chain C residue 259 LEU Chi-restraints excluded: chain D residue 95 PHE Chi-restraints excluded: chain E residue 185 ILE Chi-restraints excluded: chain F residue 90 LEU Chi-restraints excluded: chain F residue 123 LEU Chi-restraints excluded: chain G residue 44 PHE Chi-restraints excluded: chain G residue 108 ILE Chi-restraints excluded: chain G residue 158 PHE Chi-restraints excluded: chain H residue 34 SER Chi-restraints excluded: chain H residue 96 VAL Chi-restraints excluded: chain I residue 59 THR Chi-restraints excluded: chain I residue 115 THR Chi-restraints excluded: chain M residue 1355 VAL Chi-restraints excluded: chain M residue 1373 VAL Chi-restraints excluded: chain M residue 1515 TYR Chi-restraints excluded: chain Q residue 776 LEU Chi-restraints excluded: chain Z residue 601 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 603 random chunks: chunk 304 optimal weight: 0.1980 chunk 169 optimal weight: 4.9990 chunk 455 optimal weight: 50.0000 chunk 372 optimal weight: 5.9990 chunk 151 optimal weight: 0.9990 chunk 548 optimal weight: 40.0000 chunk 592 optimal weight: 30.0000 chunk 488 optimal weight: 50.0000 chunk 544 optimal weight: 40.0000 chunk 187 optimal weight: 0.7980 chunk 440 optimal weight: 0.0670 overall best weight: 1.4122 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 410 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 861 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 884 ASN ** A1005 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1182 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1303 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 144 HIS B 319 ASN B 649 ASN ** B1094 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 4 HIS ** G 9 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 130 ASN H 131 ASN I 60 HIS Q 854 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8011 moved from start: 0.2422 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 51256 Z= 0.223 Angle : 0.584 12.154 68951 Z= 0.306 Chirality : 0.044 0.219 6723 Planarity : 0.004 0.069 9154 Dihedral : 13.398 172.551 8572 Min Nonbonded Distance : 2.002 Molprobity Statistics. All-atom Clashscore : 7.94 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.74 % Favored : 95.22 % Rotamer: Outliers : 1.84 % Allowed : 9.71 % Favored : 88.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.74 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.69 (0.10), residues: 6303 helix: 0.82 (0.11), residues: 2307 sheet: -0.88 (0.17), residues: 840 loop : -1.31 (0.11), residues: 3156 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP A1210 HIS 0.006 0.001 HIS G 4 PHE 0.030 0.002 PHE D 26 TYR 0.017 0.001 TYR M1515 ARG 0.006 0.000 ARG I 40 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12606 Ramachandran restraints generated. 6303 Oldfield, 0 Emsley, 6303 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12606 Ramachandran restraints generated. 6303 Oldfield, 0 Emsley, 6303 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 535 residues out of total 5627 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 83 poor density : 452 time to evaluate : 4.211 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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: A 136 GLN cc_start: 0.8492 (mp10) cc_final: 0.8253 (mp10) REVERT: A 301 HIS cc_start: 0.7723 (t-170) cc_final: 0.7452 (t-170) REVERT: A 309 LEU cc_start: 0.9539 (OUTLIER) cc_final: 0.9266 (tm) REVERT: A 404 GLU cc_start: 0.8304 (tm-30) cc_final: 0.8019 (tm-30) REVERT: A 495 ASP cc_start: 0.7465 (t0) cc_final: 0.6744 (t0) REVERT: A 750 ASP cc_start: 0.8328 (m-30) cc_final: 0.8110 (m-30) REVERT: A 1359 SER cc_start: 0.8796 (p) cc_final: 0.8518 (t) REVERT: B 198 GLU cc_start: 0.7495 (pt0) cc_final: 0.6778 (pt0) REVERT: B 692 THR cc_start: 0.9292 (OUTLIER) cc_final: 0.8803 (p) REVERT: B 1081 ASP cc_start: 0.8707 (t70) cc_final: 0.8330 (t0) REVERT: B 1131 ARG cc_start: 0.9052 (ptp-110) cc_final: 0.8785 (ptp90) REVERT: D 34 ASN cc_start: 0.8412 (m-40) cc_final: 0.7927 (t0) REVERT: D 38 HIS cc_start: 0.9419 (t70) cc_final: 0.9100 (t70) REVERT: D 62 MET cc_start: 0.8912 (mmp) cc_final: 0.8474 (mmm) REVERT: D 70 ARG cc_start: 0.7848 (mtp-110) cc_final: 0.7350 (ptp-170) REVERT: D 122 PHE cc_start: 0.7530 (m-80) cc_final: 0.7324 (m-80) REVERT: D 128 GLN cc_start: 0.9146 (mm110) cc_final: 0.8940 (mm110) REVERT: E 121 MET cc_start: 0.8426 (pmm) cc_final: 0.8220 (pmm) REVERT: G 1 MET cc_start: 0.7528 (ptt) cc_final: 0.7058 (ptp) REVERT: G 2 PHE cc_start: 0.7906 (m-80) cc_final: 0.7449 (m-10) REVERT: G 44 PHE cc_start: 0.8925 (OUTLIER) cc_final: 0.8568 (m-80) REVERT: G 68 TYR cc_start: 0.8815 (m-80) cc_final: 0.8597 (m-80) REVERT: G 104 MET cc_start: 0.7458 (ttp) cc_final: 0.6738 (tmm) REVERT: G 118 GLU cc_start: 0.9220 (mm-30) cc_final: 0.8883 (mm-30) REVERT: G 142 GLU cc_start: 0.8361 (mt-10) cc_final: 0.7969 (mp0) REVERT: G 167 TYR cc_start: 0.7432 (m-10) cc_final: 0.7031 (m-10) REVERT: H 9 ILE cc_start: 0.9494 (mp) cc_final: 0.9250 (mp) REVERT: H 13 LYS cc_start: 0.9155 (mmmt) cc_final: 0.8851 (mmmm) REVERT: H 100 GLU cc_start: 0.7457 (mt-10) cc_final: 0.7246 (mt-10) REVERT: H 103 GLU cc_start: 0.8341 (pm20) cc_final: 0.8091 (pm20) REVERT: I 23 MET cc_start: 0.8285 (ttp) cc_final: 0.8056 (ttp) REVERT: L 47 LYS cc_start: 0.8418 (OUTLIER) cc_final: 0.8195 (mmmm) REVERT: M 1347 MET cc_start: -0.2866 (ptt) cc_final: -0.4639 (mtt) REVERT: W 98 GLN cc_start: 0.1508 (tt0) cc_final: 0.1032 (tp40) REVERT: Y 63 MET cc_start: 0.6322 (tmm) cc_final: 0.6060 (tmm) REVERT: Y 64 MET cc_start: 0.7169 (mtp) cc_final: 0.6339 (mtm) REVERT: Z 197 MET cc_start: 0.8561 (ttt) cc_final: 0.7589 (tpt) REVERT: Z 307 MET cc_start: 0.4745 (mtm) cc_final: 0.3058 (mmm) REVERT: Z 378 MET cc_start: -0.3174 (mtt) cc_final: -0.3474 (mtp) REVERT: Z 474 MET cc_start: 0.6816 (mpp) cc_final: 0.6505 (mmp) REVERT: Z 508 MET cc_start: 0.6036 (ttp) cc_final: 0.5547 (tpp) outliers start: 83 outliers final: 34 residues processed: 517 average time/residue: 0.5246 time to fit residues: 456.9537 Evaluate side-chains 455 residues out of total 5627 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 417 time to evaluate : 4.294 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 309 LEU Chi-restraints excluded: chain A residue 423 ASN Chi-restraints excluded: chain A residue 425 ASP Chi-restraints excluded: chain A residue 439 HIS Chi-restraints excluded: chain A residue 502 ASN Chi-restraints excluded: chain A residue 514 GLU Chi-restraints excluded: chain A residue 545 VAL Chi-restraints excluded: chain A residue 732 THR Chi-restraints excluded: chain A residue 902 GLU Chi-restraints excluded: chain A residue 1343 LEU Chi-restraints excluded: chain A residue 1436 VAL Chi-restraints excluded: chain B residue 18 THR Chi-restraints excluded: chain B residue 84 TYR Chi-restraints excluded: chain B residue 276 LEU Chi-restraints excluded: chain B residue 347 MET Chi-restraints excluded: chain B residue 440 ILE Chi-restraints excluded: chain B residue 612 ILE Chi-restraints excluded: chain B residue 692 THR Chi-restraints excluded: chain B residue 896 LEU Chi-restraints excluded: chain B residue 1149 VAL Chi-restraints excluded: chain C residue 259 LEU Chi-restraints excluded: chain D residue 95 PHE Chi-restraints excluded: chain D residue 107 THR Chi-restraints excluded: chain E residue 185 ILE Chi-restraints excluded: chain F residue 90 LEU Chi-restraints excluded: chain F residue 123 LEU Chi-restraints excluded: chain G residue 44 PHE Chi-restraints excluded: chain G residue 108 ILE Chi-restraints excluded: chain G residue 111 HIS Chi-restraints excluded: chain H residue 34 SER Chi-restraints excluded: chain H residue 96 VAL Chi-restraints excluded: chain I residue 59 THR Chi-restraints excluded: chain I residue 115 THR Chi-restraints excluded: chain L residue 47 LYS Chi-restraints excluded: chain M residue 1355 VAL Chi-restraints excluded: chain M residue 1373 VAL Chi-restraints excluded: chain M residue 1515 TYR Chi-restraints excluded: chain Q residue 776 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 603 random chunks: chunk 541 optimal weight: 50.0000 chunk 412 optimal weight: 40.0000 chunk 284 optimal weight: 7.9990 chunk 60 optimal weight: 2.9990 chunk 261 optimal weight: 2.9990 chunk 368 optimal weight: 0.2980 chunk 550 optimal weight: 7.9990 chunk 582 optimal weight: 10.0000 chunk 287 optimal weight: 3.9990 chunk 521 optimal weight: 50.0000 chunk 157 optimal weight: 0.8980 overall best weight: 2.2386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 273 GLN ** A 410 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 861 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1182 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1303 GLN B 452 ASN G 9 HIS ** G 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 84 HIS J 52 HIS L 23 HIS L 26 ASN ** Q 854 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 11 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8045 moved from start: 0.2736 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.064 51256 Z= 0.295 Angle : 0.593 14.421 68951 Z= 0.308 Chirality : 0.045 0.215 6723 Planarity : 0.004 0.060 9154 Dihedral : 13.289 173.518 8570 Min Nonbonded Distance : 1.973 Molprobity Statistics. All-atom Clashscore : 8.26 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.11 % Favored : 94.86 % Rotamer: Outliers : 2.11 % Allowed : 10.37 % Favored : 87.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.74 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.38 (0.11), residues: 6303 helix: 1.21 (0.11), residues: 2309 sheet: -0.88 (0.16), residues: 926 loop : -1.19 (0.11), residues: 3068 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.001 TRP B 99 HIS 0.007 0.001 HIS B 98 PHE 0.027 0.002 PHE D 26 TYR 0.016 0.001 TYR M1515 ARG 0.008 0.000 ARG L 31 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12606 Ramachandran restraints generated. 6303 Oldfield, 0 Emsley, 6303 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12606 Ramachandran restraints generated. 6303 Oldfield, 0 Emsley, 6303 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 526 residues out of total 5627 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 95 poor density : 431 time to evaluate : 4.290 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 136 GLN cc_start: 0.8452 (mp10) cc_final: 0.8184 (mp10) REVERT: A 301 HIS cc_start: 0.7814 (t-170) cc_final: 0.7557 (t-170) REVERT: A 309 LEU cc_start: 0.9573 (OUTLIER) cc_final: 0.9295 (tm) REVERT: A 343 LEU cc_start: 0.9245 (OUTLIER) cc_final: 0.8988 (pp) REVERT: A 495 ASP cc_start: 0.7717 (t0) cc_final: 0.6923 (t0) REVERT: A 750 ASP cc_start: 0.8337 (m-30) cc_final: 0.8127 (m-30) REVERT: A 1359 SER cc_start: 0.8814 (p) cc_final: 0.8325 (t) REVERT: B 438 ARG cc_start: 0.8160 (tpp80) cc_final: 0.7830 (tpp80) REVERT: B 692 THR cc_start: 0.9366 (OUTLIER) cc_final: 0.8936 (p) REVERT: B 1081 ASP cc_start: 0.8734 (t70) cc_final: 0.8344 (t0) REVERT: B 1131 ARG cc_start: 0.9122 (ptp-110) cc_final: 0.8820 (ptp90) REVERT: D 34 ASN cc_start: 0.8427 (m-40) cc_final: 0.8086 (t0) REVERT: D 38 HIS cc_start: 0.9421 (t70) cc_final: 0.9158 (t70) REVERT: D 62 MET cc_start: 0.8949 (mmp) cc_final: 0.8486 (mmm) REVERT: D 70 ARG cc_start: 0.7920 (mtp-110) cc_final: 0.7486 (ptp-170) REVERT: D 122 PHE cc_start: 0.7620 (m-80) cc_final: 0.7387 (m-80) REVERT: D 128 GLN cc_start: 0.9203 (mm110) cc_final: 0.8989 (mm110) REVERT: G 2 PHE cc_start: 0.7814 (m-80) cc_final: 0.7423 (m-10) REVERT: G 28 GLN cc_start: 0.8725 (tm-30) cc_final: 0.8414 (tm-30) REVERT: G 44 PHE cc_start: 0.8945 (OUTLIER) cc_final: 0.8577 (m-80) REVERT: G 104 MET cc_start: 0.7454 (ttp) cc_final: 0.6711 (tmm) REVERT: G 116 GLU cc_start: 0.8609 (pt0) cc_final: 0.8218 (pm20) REVERT: G 118 GLU cc_start: 0.9232 (mm-30) cc_final: 0.8886 (mm-30) REVERT: G 142 GLU cc_start: 0.8354 (mt-10) cc_final: 0.7988 (mp0) REVERT: H 13 LYS cc_start: 0.9182 (mmmt) cc_final: 0.8848 (mmmm) REVERT: J 65 LEU cc_start: 0.9189 (tp) cc_final: 0.8959 (tp) REVERT: M 1347 MET cc_start: -0.2948 (ptt) cc_final: -0.4370 (mmm) REVERT: M 1350 MET cc_start: 0.3584 (OUTLIER) cc_final: 0.3057 (ppp) REVERT: Q 830 ARG cc_start: -0.1230 (ttt180) cc_final: -0.1474 (ptp-170) REVERT: W 98 GLN cc_start: 0.1682 (tt0) cc_final: 0.1210 (tp40) REVERT: Y 64 MET cc_start: 0.7273 (mtp) cc_final: 0.6832 (mtm) REVERT: Z 197 MET cc_start: 0.8583 (ttt) cc_final: 0.7583 (tpt) REVERT: Z 307 MET cc_start: 0.4699 (mtm) cc_final: 0.3085 (mmm) REVERT: Z 378 MET cc_start: -0.3199 (mtt) cc_final: -0.3578 (mtp) REVERT: Z 474 MET cc_start: 0.6778 (mpp) cc_final: 0.6453 (mmp) outliers start: 95 outliers final: 48 residues processed: 507 average time/residue: 0.5059 time to fit residues: 432.4041 Evaluate side-chains 446 residues out of total 5627 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 393 time to evaluate : 4.254 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain A residue 309 LEU Chi-restraints excluded: chain A residue 343 LEU Chi-restraints excluded: chain A residue 423 ASN Chi-restraints excluded: chain A residue 425 ASP Chi-restraints excluded: chain A residue 439 HIS Chi-restraints excluded: chain A residue 440 LEU Chi-restraints excluded: chain A residue 441 GLN Chi-restraints excluded: chain A residue 502 ASN Chi-restraints excluded: chain A residue 514 GLU Chi-restraints excluded: chain A residue 545 VAL Chi-restraints excluded: chain A residue 886 VAL Chi-restraints excluded: chain A residue 902 GLU Chi-restraints excluded: chain A residue 996 ILE Chi-restraints excluded: chain A residue 1343 LEU Chi-restraints excluded: chain A residue 1436 VAL Chi-restraints excluded: chain B residue 18 THR Chi-restraints excluded: chain B residue 84 TYR Chi-restraints excluded: chain B residue 218 THR Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain B residue 276 LEU Chi-restraints excluded: chain B residue 347 MET Chi-restraints excluded: chain B residue 440 ILE Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 603 MET Chi-restraints excluded: chain B residue 612 ILE Chi-restraints excluded: chain B residue 692 THR Chi-restraints excluded: chain B residue 896 LEU Chi-restraints excluded: chain B residue 1004 ASP Chi-restraints excluded: chain B residue 1149 VAL Chi-restraints excluded: chain C residue 89 THR Chi-restraints excluded: chain C residue 259 LEU Chi-restraints excluded: chain D residue 95 PHE Chi-restraints excluded: chain D residue 107 THR Chi-restraints excluded: chain E residue 99 ILE Chi-restraints excluded: chain E residue 185 ILE Chi-restraints excluded: chain E residue 190 VAL Chi-restraints excluded: chain F residue 90 LEU Chi-restraints excluded: chain F residue 123 LEU Chi-restraints excluded: chain G residue 44 PHE Chi-restraints excluded: chain G residue 66 VAL Chi-restraints excluded: chain G residue 108 ILE Chi-restraints excluded: chain G residue 111 HIS Chi-restraints excluded: chain H residue 34 SER Chi-restraints excluded: chain H residue 96 VAL Chi-restraints excluded: chain I residue 59 THR Chi-restraints excluded: chain I residue 115 THR Chi-restraints excluded: chain L residue 47 LYS Chi-restraints excluded: chain M residue 1350 MET Chi-restraints excluded: chain M residue 1355 VAL Chi-restraints excluded: chain M residue 1373 VAL Chi-restraints excluded: chain M residue 1515 TYR Chi-restraints excluded: chain Q residue 776 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 603 random chunks: chunk 485 optimal weight: 40.0000 chunk 330 optimal weight: 5.9990 chunk 8 optimal weight: 0.9980 chunk 433 optimal weight: 8.9990 chunk 240 optimal weight: 2.9990 chunk 497 optimal weight: 50.0000 chunk 402 optimal weight: 50.0000 chunk 0 optimal weight: 7.9990 chunk 297 optimal weight: 0.9980 chunk 523 optimal weight: 0.1980 chunk 147 optimal weight: 3.9990 overall best weight: 1.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 410 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 861 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1182 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1303 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 157 GLN ** G 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 60 HIS L 26 ASN W 276 GLN Z 625 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8044 moved from start: 0.3001 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 51256 Z= 0.253 Angle : 0.574 12.758 68951 Z= 0.298 Chirality : 0.044 0.215 6723 Planarity : 0.003 0.056 9154 Dihedral : 13.199 173.431 8570 Min Nonbonded Distance : 1.994 Molprobity Statistics. All-atom Clashscore : 8.07 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.89 % Favored : 95.08 % Rotamer: Outliers : 2.04 % Allowed : 11.22 % Favored : 86.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.74 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.14 (0.11), residues: 6303 helix: 1.43 (0.11), residues: 2316 sheet: -0.70 (0.17), residues: 902 loop : -1.09 (0.11), residues: 3085 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRP A1210 HIS 0.005 0.001 HIS A 620 PHE 0.024 0.001 PHE D 26 TYR 0.015 0.001 TYR M1515 ARG 0.007 0.000 ARG Q 763 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12606 Ramachandran restraints generated. 6303 Oldfield, 0 Emsley, 6303 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12606 Ramachandran restraints generated. 6303 Oldfield, 0 Emsley, 6303 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 521 residues out of total 5627 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 92 poor density : 429 time to evaluate : 4.228 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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: A 136 GLN cc_start: 0.8434 (mp10) cc_final: 0.8167 (mp10) REVERT: A 301 HIS cc_start: 0.7826 (t-170) cc_final: 0.7522 (t-170) REVERT: A 309 LEU cc_start: 0.9595 (OUTLIER) cc_final: 0.9323 (tm) REVERT: A 329 MET cc_start: 0.8810 (mtp) cc_final: 0.8567 (mtp) REVERT: A 343 LEU cc_start: 0.9222 (OUTLIER) cc_final: 0.8975 (pp) REVERT: A 495 ASP cc_start: 0.7747 (t0) cc_final: 0.7020 (t0) REVERT: A 750 ASP cc_start: 0.8324 (m-30) cc_final: 0.8123 (m-30) REVERT: B 230 ARG cc_start: 0.7239 (mmm160) cc_final: 0.6956 (mmp80) REVERT: B 438 ARG cc_start: 0.8128 (tpp80) cc_final: 0.7798 (tpp80) REVERT: B 692 THR cc_start: 0.9392 (OUTLIER) cc_final: 0.9012 (p) REVERT: B 1081 ASP cc_start: 0.8773 (t70) cc_final: 0.8382 (t0) REVERT: B 1131 ARG cc_start: 0.9114 (ptp-110) cc_final: 0.8793 (ptp90) REVERT: B 1161 GLU cc_start: 0.8794 (mm-30) cc_final: 0.8435 (mp0) REVERT: B 1172 MET cc_start: 0.8640 (mmm) cc_final: 0.8403 (mmm) REVERT: D 34 ASN cc_start: 0.8441 (m-40) cc_final: 0.8128 (t0) REVERT: D 38 HIS cc_start: 0.9420 (t70) cc_final: 0.9180 (t70) REVERT: D 44 ARG cc_start: 0.9210 (ttt180) cc_final: 0.9002 (tpp80) REVERT: D 62 MET cc_start: 0.8874 (mmp) cc_final: 0.8432 (mmm) REVERT: D 74 PHE cc_start: 0.5101 (OUTLIER) cc_final: 0.4555 (p90) REVERT: D 122 PHE cc_start: 0.7594 (m-80) cc_final: 0.7330 (m-80) REVERT: G 28 GLN cc_start: 0.8686 (tm-30) cc_final: 0.8386 (tm-30) REVERT: G 33 GLU cc_start: 0.8730 (tm-30) cc_final: 0.8435 (tm-30) REVERT: G 44 PHE cc_start: 0.8996 (OUTLIER) cc_final: 0.8580 (m-80) REVERT: G 63 ARG cc_start: 0.7982 (mtp85) cc_final: 0.7739 (mtp180) REVERT: G 80 PHE cc_start: 0.4457 (OUTLIER) cc_final: 0.3847 (m-80) REVERT: G 104 MET cc_start: 0.7389 (ttp) cc_final: 0.6676 (tmm) REVERT: G 116 GLU cc_start: 0.8788 (pt0) cc_final: 0.8511 (pm20) REVERT: G 117 MET cc_start: 0.7710 (mmm) cc_final: 0.7231 (mmm) REVERT: G 118 GLU cc_start: 0.9260 (mm-30) cc_final: 0.8909 (mm-30) REVERT: G 142 GLU cc_start: 0.8338 (mt-10) cc_final: 0.7989 (mp0) REVERT: H 13 LYS cc_start: 0.9209 (mmmt) cc_final: 0.8858 (mmmm) REVERT: H 103 GLU cc_start: 0.8527 (pm20) cc_final: 0.8275 (pm20) REVERT: H 118 TYR cc_start: 0.9139 (m-80) cc_final: 0.8521 (m-80) REVERT: J 65 LEU cc_start: 0.9099 (tp) cc_final: 0.8847 (tp) REVERT: L 44 MET cc_start: 0.8591 (mmt) cc_final: 0.8240 (mmt) REVERT: M 1347 MET cc_start: -0.3081 (ptt) cc_final: -0.4606 (mtt) REVERT: M 1350 MET cc_start: 0.3478 (OUTLIER) cc_final: 0.3103 (ppp) REVERT: Q 830 ARG cc_start: -0.1058 (ttt180) cc_final: -0.1332 (ptp-170) REVERT: Q 878 ARG cc_start: 0.7851 (tpt170) cc_final: 0.7400 (tpt-90) REVERT: W 98 GLN cc_start: 0.1698 (tt0) cc_final: 0.1213 (tp40) REVERT: Y 64 MET cc_start: 0.7296 (mtp) cc_final: 0.6703 (mtm) REVERT: Z 197 MET cc_start: 0.8591 (ttt) cc_final: 0.7604 (tpt) REVERT: Z 307 MET cc_start: 0.4865 (mtm) cc_final: 0.3250 (mmm) REVERT: Z 378 MET cc_start: -0.3190 (mtt) cc_final: -0.3590 (mtp) REVERT: Z 474 MET cc_start: 0.6945 (mpp) cc_final: 0.6586 (mmp) REVERT: Z 508 MET cc_start: 0.6791 (ttp) cc_final: 0.6224 (tpp) outliers start: 92 outliers final: 51 residues processed: 500 average time/residue: 0.4962 time to fit residues: 419.0984 Evaluate side-chains 464 residues out of total 5627 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 406 time to evaluate : 4.211 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain A residue 309 LEU Chi-restraints excluded: chain A residue 343 LEU Chi-restraints excluded: chain A residue 419 ILE Chi-restraints excluded: chain A residue 423 ASN Chi-restraints excluded: chain A residue 425 ASP Chi-restraints excluded: chain A residue 439 HIS Chi-restraints excluded: chain A residue 502 ASN Chi-restraints excluded: chain A residue 510 GLU Chi-restraints excluded: chain A residue 514 GLU Chi-restraints excluded: chain A residue 545 VAL Chi-restraints excluded: chain A residue 886 VAL Chi-restraints excluded: chain A residue 902 GLU Chi-restraints excluded: chain A residue 996 ILE Chi-restraints excluded: chain A residue 1343 LEU Chi-restraints excluded: chain A residue 1436 VAL Chi-restraints excluded: chain B residue 18 THR Chi-restraints excluded: chain B residue 59 VAL Chi-restraints excluded: chain B residue 84 TYR Chi-restraints excluded: chain B residue 93 LEU Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain B residue 276 LEU Chi-restraints excluded: chain B residue 347 MET Chi-restraints excluded: chain B residue 440 ILE Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 603 MET Chi-restraints excluded: chain B residue 612 ILE Chi-restraints excluded: chain B residue 692 THR Chi-restraints excluded: chain B residue 896 LEU Chi-restraints excluded: chain B residue 931 ILE Chi-restraints excluded: chain B residue 1004 ASP Chi-restraints excluded: chain B residue 1149 VAL Chi-restraints excluded: chain C residue 89 THR Chi-restraints excluded: chain C residue 259 LEU Chi-restraints excluded: chain D residue 21 ILE Chi-restraints excluded: chain D residue 74 PHE Chi-restraints excluded: chain D residue 95 PHE Chi-restraints excluded: chain D residue 107 THR Chi-restraints excluded: chain E residue 99 ILE Chi-restraints excluded: chain E residue 137 ILE Chi-restraints excluded: chain E residue 185 ILE Chi-restraints excluded: chain E residue 190 VAL Chi-restraints excluded: chain F residue 90 LEU Chi-restraints excluded: chain F residue 123 LEU Chi-restraints excluded: chain G residue 44 PHE Chi-restraints excluded: chain G residue 66 VAL Chi-restraints excluded: chain G residue 80 PHE Chi-restraints excluded: chain G residue 108 ILE Chi-restraints excluded: chain G residue 111 HIS Chi-restraints excluded: chain H residue 96 VAL Chi-restraints excluded: chain I residue 59 THR Chi-restraints excluded: chain M residue 1350 MET Chi-restraints excluded: chain M residue 1355 VAL Chi-restraints excluded: chain M residue 1373 VAL Chi-restraints excluded: chain M residue 1515 TYR Chi-restraints excluded: chain Q residue 776 LEU Chi-restraints excluded: chain Z residue 481 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 603 random chunks: chunk 196 optimal weight: 0.7980 chunk 524 optimal weight: 7.9990 chunk 115 optimal weight: 0.9990 chunk 342 optimal weight: 0.6980 chunk 143 optimal weight: 30.0000 chunk 583 optimal weight: 20.0000 chunk 484 optimal weight: 9.9990 chunk 270 optimal weight: 0.0570 chunk 48 optimal weight: 2.9990 chunk 192 optimal weight: 4.9990 chunk 306 optimal weight: 3.9990 overall best weight: 1.1102 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 410 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 861 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1182 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 503 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1094 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1115 GLN C 157 GLN ** G 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 26 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8026 moved from start: 0.3169 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.083 51256 Z= 0.190 Angle : 0.558 12.923 68951 Z= 0.288 Chirality : 0.043 0.215 6723 Planarity : 0.003 0.064 9154 Dihedral : 13.117 173.034 8570 Min Nonbonded Distance : 2.018 Molprobity Statistics. All-atom Clashscore : 7.90 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.87 % Favored : 95.10 % Rotamer: Outliers : 2.00 % Allowed : 11.82 % Favored : 86.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.74 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.04 (0.11), residues: 6303 helix: 1.61 (0.11), residues: 2316 sheet: -0.57 (0.17), residues: 891 loop : -1.03 (0.11), residues: 3096 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.001 TRP A1210 HIS 0.005 0.001 HIS A 620 PHE 0.043 0.001 PHE G 2 TYR 0.018 0.001 TYR H 118 ARG 0.014 0.000 ARG L 31 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12606 Ramachandran restraints generated. 6303 Oldfield, 0 Emsley, 6303 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12606 Ramachandran restraints generated. 6303 Oldfield, 0 Emsley, 6303 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 523 residues out of total 5627 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 90 poor density : 433 time to evaluate : 4.225 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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: A 136 GLN cc_start: 0.8389 (mp10) cc_final: 0.8091 (mp10) REVERT: A 301 HIS cc_start: 0.7831 (t-170) cc_final: 0.7503 (t-170) REVERT: A 309 LEU cc_start: 0.9602 (OUTLIER) cc_final: 0.9338 (tm) REVERT: A 343 LEU cc_start: 0.9143 (OUTLIER) cc_final: 0.8890 (pp) REVERT: A 495 ASP cc_start: 0.7764 (t0) cc_final: 0.6937 (t0) REVERT: A 655 ILE cc_start: 0.9763 (OUTLIER) cc_final: 0.9480 (mp) REVERT: A 769 MET cc_start: 0.8899 (OUTLIER) cc_final: 0.8505 (mtt) REVERT: B 230 ARG cc_start: 0.7263 (mmm160) cc_final: 0.6958 (mmp80) REVERT: B 692 THR cc_start: 0.9363 (OUTLIER) cc_final: 0.8945 (p) REVERT: B 1081 ASP cc_start: 0.8739 (t70) cc_final: 0.8365 (t0) REVERT: B 1131 ARG cc_start: 0.9101 (ptp-110) cc_final: 0.8759 (ptp90) REVERT: B 1172 MET cc_start: 0.8643 (mmm) cc_final: 0.8425 (mmm) REVERT: D 34 ASN cc_start: 0.8383 (m-40) cc_final: 0.8072 (t0) REVERT: D 44 ARG cc_start: 0.9268 (ttt180) cc_final: 0.8948 (tpp80) REVERT: D 62 MET cc_start: 0.8874 (mmp) cc_final: 0.8427 (mmm) REVERT: D 70 ARG cc_start: 0.8027 (mtp-110) cc_final: 0.7549 (ptp-170) REVERT: D 74 PHE cc_start: 0.5132 (OUTLIER) cc_final: 0.4528 (p90) REVERT: D 122 PHE cc_start: 0.7499 (m-80) cc_final: 0.7279 (m-80) REVERT: G 28 GLN cc_start: 0.8635 (tm-30) cc_final: 0.8346 (tm-30) REVERT: G 33 GLU cc_start: 0.8694 (tm-30) cc_final: 0.8420 (tm-30) REVERT: G 44 PHE cc_start: 0.8997 (OUTLIER) cc_final: 0.8518 (m-80) REVERT: G 63 ARG cc_start: 0.7901 (mtp85) cc_final: 0.7638 (mtp180) REVERT: G 104 MET cc_start: 0.7695 (ttp) cc_final: 0.6942 (tmm) REVERT: G 116 GLU cc_start: 0.8788 (pt0) cc_final: 0.8482 (pm20) REVERT: G 117 MET cc_start: 0.7547 (mmm) cc_final: 0.7169 (mmm) REVERT: G 118 GLU cc_start: 0.9276 (mm-30) cc_final: 0.8942 (mm-30) REVERT: G 142 GLU cc_start: 0.8291 (mt-10) cc_final: 0.7848 (mp0) REVERT: H 13 LYS cc_start: 0.9190 (mmmt) cc_final: 0.8836 (mmmm) REVERT: H 103 GLU cc_start: 0.8563 (pm20) cc_final: 0.8224 (pm20) REVERT: H 143 LEU cc_start: 0.8947 (OUTLIER) cc_final: 0.8655 (tm) REVERT: M 1347 MET cc_start: -0.3301 (ptt) cc_final: -0.4669 (mtt) REVERT: M 1350 MET cc_start: 0.3416 (OUTLIER) cc_final: 0.3041 (ppp) REVERT: Q 830 ARG cc_start: -0.1019 (ttt180) cc_final: -0.1289 (ptp-170) REVERT: W 98 GLN cc_start: 0.1845 (tt0) cc_final: 0.1296 (tp40) REVERT: Y 63 MET cc_start: 0.6405 (tmm) cc_final: 0.6129 (ppp) REVERT: Y 64 MET cc_start: 0.7415 (mtp) cc_final: 0.6519 (mtm) REVERT: Z 197 MET cc_start: 0.8604 (ttt) cc_final: 0.7622 (tpt) REVERT: Z 307 MET cc_start: 0.4883 (mtm) cc_final: 0.3250 (mmm) REVERT: Z 378 MET cc_start: -0.3216 (mtt) cc_final: -0.3656 (mtp) REVERT: Z 474 MET cc_start: 0.6977 (mpp) cc_final: 0.6614 (mmp) REVERT: Z 508 MET cc_start: 0.6844 (ttp) cc_final: 0.6290 (tpp) outliers start: 90 outliers final: 56 residues processed: 507 average time/residue: 0.4852 time to fit residues: 417.0493 Evaluate side-chains 473 residues out of total 5627 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 408 time to evaluate : 4.157 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain A residue 309 LEU Chi-restraints excluded: chain A residue 343 LEU Chi-restraints excluded: chain A residue 419 ILE Chi-restraints excluded: chain A residue 423 ASN Chi-restraints excluded: chain A residue 425 ASP Chi-restraints excluded: chain A residue 439 HIS Chi-restraints excluded: chain A residue 440 LEU Chi-restraints excluded: chain A residue 502 ASN Chi-restraints excluded: chain A residue 510 GLU Chi-restraints excluded: chain A residue 514 GLU Chi-restraints excluded: chain A residue 545 VAL Chi-restraints excluded: chain A residue 655 ILE Chi-restraints excluded: chain A residue 769 MET Chi-restraints excluded: chain A residue 886 VAL Chi-restraints excluded: chain A residue 902 GLU Chi-restraints excluded: chain A residue 996 ILE Chi-restraints excluded: chain A residue 1087 VAL Chi-restraints excluded: chain A residue 1175 ILE Chi-restraints excluded: chain A residue 1336 LEU Chi-restraints excluded: chain A residue 1343 LEU Chi-restraints excluded: chain A residue 1428 MET Chi-restraints excluded: chain A residue 1436 VAL Chi-restraints excluded: chain B residue 18 THR Chi-restraints excluded: chain B residue 59 VAL Chi-restraints excluded: chain B residue 84 TYR Chi-restraints excluded: chain B residue 93 LEU Chi-restraints excluded: chain B residue 215 TYR Chi-restraints excluded: chain B residue 235 ILE Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain B residue 276 LEU Chi-restraints excluded: chain B residue 347 MET Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 603 MET Chi-restraints excluded: chain B residue 612 ILE Chi-restraints excluded: chain B residue 692 THR Chi-restraints excluded: chain B residue 896 LEU Chi-restraints excluded: chain B residue 1149 VAL Chi-restraints excluded: chain C residue 89 THR Chi-restraints excluded: chain C residue 259 LEU Chi-restraints excluded: chain D residue 21 ILE Chi-restraints excluded: chain D residue 74 PHE Chi-restraints excluded: chain D residue 95 PHE Chi-restraints excluded: chain E residue 99 ILE Chi-restraints excluded: chain E residue 137 ILE Chi-restraints excluded: chain E residue 185 ILE Chi-restraints excluded: chain E residue 190 VAL Chi-restraints excluded: chain F residue 83 LEU Chi-restraints excluded: chain F residue 90 LEU Chi-restraints excluded: chain F residue 123 LEU Chi-restraints excluded: chain G residue 44 PHE Chi-restraints excluded: chain G residue 66 VAL Chi-restraints excluded: chain G residue 108 ILE Chi-restraints excluded: chain G residue 111 HIS Chi-restraints excluded: chain H residue 34 SER Chi-restraints excluded: chain H residue 58 LEU Chi-restraints excluded: chain H residue 96 VAL Chi-restraints excluded: chain H residue 143 LEU Chi-restraints excluded: chain I residue 30 LYS Chi-restraints excluded: chain M residue 1350 MET Chi-restraints excluded: chain M residue 1373 VAL Chi-restraints excluded: chain M residue 1515 TYR Chi-restraints excluded: chain Q residue 776 LEU Chi-restraints excluded: chain Z residue 481 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 603 random chunks: chunk 562 optimal weight: 30.0000 chunk 65 optimal weight: 4.9990 chunk 332 optimal weight: 9.9990 chunk 426 optimal weight: 8.9990 chunk 330 optimal weight: 2.9990 chunk 491 optimal weight: 10.0000 chunk 325 optimal weight: 0.0670 chunk 581 optimal weight: 50.0000 chunk 363 optimal weight: 7.9990 chunk 354 optimal weight: 7.9990 chunk 268 optimal weight: 1.9990 overall best weight: 3.6126 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 313 HIS ** A 410 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 465 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 861 GLN ** A1044 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1182 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 72 GLN ** B1094 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1115 GLN C 157 GLN ** G 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 100 HIS K 2 ASN ** L 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 272 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 572 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8099 moved from start: 0.3430 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.095 51256 Z= 0.439 Angle : 0.650 13.339 68951 Z= 0.335 Chirality : 0.046 0.214 6723 Planarity : 0.004 0.055 9154 Dihedral : 13.146 175.190 8570 Min Nonbonded Distance : 1.957 Molprobity Statistics. All-atom Clashscore : 8.71 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.43 % Favored : 94.54 % Rotamer: Outliers : 2.24 % Allowed : 12.24 % Favored : 85.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.74 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.04 (0.11), residues: 6303 helix: 1.60 (0.11), residues: 2325 sheet: -0.72 (0.17), residues: 893 loop : -0.97 (0.11), residues: 3085 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.001 TRP A1210 HIS 0.008 0.001 HIS D 38 PHE 0.023 0.002 PHE A 458 TYR 0.020 0.002 TYR H 115 ARG 0.014 0.001 ARG L 31 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12606 Ramachandran restraints generated. 6303 Oldfield, 0 Emsley, 6303 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12606 Ramachandran restraints generated. 6303 Oldfield, 0 Emsley, 6303 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 502 residues out of total 5627 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 101 poor density : 401 time to evaluate : 4.269 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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: A 67 ARG cc_start: 0.8435 (mpp80) cc_final: 0.7814 (mmm-85) REVERT: A 136 GLN cc_start: 0.8474 (mp10) cc_final: 0.8167 (mp10) REVERT: A 301 HIS cc_start: 0.7851 (t-170) cc_final: 0.7490 (t-170) REVERT: A 322 LEU cc_start: 0.9028 (OUTLIER) cc_final: 0.8804 (mm) REVERT: A 343 LEU cc_start: 0.9230 (OUTLIER) cc_final: 0.8883 (pp) REVERT: A 930 LEU cc_start: 0.9468 (OUTLIER) cc_final: 0.9216 (tt) REVERT: B 230 ARG cc_start: 0.7494 (mmm160) cc_final: 0.7174 (mmp80) REVERT: B 675 LEU cc_start: 0.9437 (OUTLIER) cc_final: 0.9219 (tp) REVERT: B 692 THR cc_start: 0.9463 (OUTLIER) cc_final: 0.9132 (p) REVERT: B 913 GLN cc_start: 0.8472 (pt0) cc_final: 0.8254 (tp-100) REVERT: B 1081 ASP cc_start: 0.8806 (t70) cc_final: 0.8409 (t0) REVERT: B 1131 ARG cc_start: 0.9127 (ptp-110) cc_final: 0.8769 (ptp90) REVERT: D 16 ASP cc_start: 0.7931 (t0) cc_final: 0.7644 (t70) REVERT: D 38 HIS cc_start: 0.9364 (t70) cc_final: 0.9081 (t70) REVERT: D 44 ARG cc_start: 0.9325 (ttt180) cc_final: 0.9095 (tpp80) REVERT: D 62 MET cc_start: 0.8851 (mmp) cc_final: 0.8379 (mmm) REVERT: D 70 ARG cc_start: 0.8176 (mtp-110) cc_final: 0.7780 (ptp-170) REVERT: D 74 PHE cc_start: 0.5387 (OUTLIER) cc_final: 0.4677 (p90) REVERT: E 18 MET cc_start: 0.9139 (mmm) cc_final: 0.8790 (mmm) REVERT: G 28 GLN cc_start: 0.8683 (tm-30) cc_final: 0.8403 (tm-30) REVERT: G 44 PHE cc_start: 0.9038 (OUTLIER) cc_final: 0.8585 (m-80) REVERT: G 63 ARG cc_start: 0.8127 (mtp85) cc_final: 0.7860 (mtm110) REVERT: G 104 MET cc_start: 0.7669 (ttp) cc_final: 0.6947 (tmm) REVERT: G 116 GLU cc_start: 0.8788 (pt0) cc_final: 0.8542 (pm20) REVERT: G 117 MET cc_start: 0.7463 (mmm) cc_final: 0.7191 (mmm) REVERT: G 118 GLU cc_start: 0.9308 (mm-30) cc_final: 0.8970 (mm-30) REVERT: H 13 LYS cc_start: 0.9202 (mmmt) cc_final: 0.8793 (mmmm) REVERT: H 143 LEU cc_start: 0.9095 (OUTLIER) cc_final: 0.8807 (tm) REVERT: M 1347 MET cc_start: -0.3317 (ptt) cc_final: -0.4755 (mtt) REVERT: M 1350 MET cc_start: 0.3085 (OUTLIER) cc_final: 0.2761 (ppp) REVERT: Q 830 ARG cc_start: -0.1039 (ttt180) cc_final: -0.1355 (ptp-170) REVERT: Q 878 ARG cc_start: 0.7771 (tpt170) cc_final: 0.7326 (tpt-90) REVERT: W 98 GLN cc_start: 0.1957 (tt0) cc_final: 0.1402 (tp40) REVERT: Y 64 MET cc_start: 0.7534 (mtp) cc_final: 0.6684 (mtm) REVERT: Z 197 MET cc_start: 0.8630 (ttt) cc_final: 0.7698 (tpt) REVERT: Z 307 MET cc_start: 0.4719 (mtm) cc_final: 0.3107 (mmm) REVERT: Z 378 MET cc_start: -0.3235 (mtt) cc_final: -0.3682 (mtp) REVERT: Z 474 MET cc_start: 0.6998 (mpp) cc_final: 0.6688 (mmp) REVERT: Z 489 THR cc_start: 0.8310 (OUTLIER) cc_final: 0.8086 (p) REVERT: Z 508 MET cc_start: 0.6880 (ttp) cc_final: 0.6427 (tpp) outliers start: 101 outliers final: 61 residues processed: 486 average time/residue: 0.4904 time to fit residues: 402.0507 Evaluate side-chains 466 residues out of total 5627 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 395 time to evaluate : 4.202 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain A residue 309 LEU Chi-restraints excluded: chain A residue 322 LEU Chi-restraints excluded: chain A residue 343 LEU Chi-restraints excluded: chain A residue 419 ILE Chi-restraints excluded: chain A residue 423 ASN Chi-restraints excluded: chain A residue 439 HIS Chi-restraints excluded: chain A residue 441 GLN Chi-restraints excluded: chain A residue 502 ASN Chi-restraints excluded: chain A residue 510 GLU Chi-restraints excluded: chain A residue 514 GLU Chi-restraints excluded: chain A residue 886 VAL Chi-restraints excluded: chain A residue 930 LEU Chi-restraints excluded: chain A residue 996 ILE Chi-restraints excluded: chain A residue 1175 ILE Chi-restraints excluded: chain A residue 1336 LEU Chi-restraints excluded: chain A residue 1343 LEU Chi-restraints excluded: chain A residue 1428 MET Chi-restraints excluded: chain A residue 1436 VAL Chi-restraints excluded: chain B residue 18 THR Chi-restraints excluded: chain B residue 59 VAL Chi-restraints excluded: chain B residue 84 TYR Chi-restraints excluded: chain B residue 93 LEU Chi-restraints excluded: chain B residue 218 THR Chi-restraints excluded: chain B residue 235 ILE Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain B residue 276 LEU Chi-restraints excluded: chain B residue 347 MET Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 603 MET Chi-restraints excluded: chain B residue 612 ILE Chi-restraints excluded: chain B residue 675 LEU Chi-restraints excluded: chain B residue 692 THR Chi-restraints excluded: chain B residue 896 LEU Chi-restraints excluded: chain B residue 931 ILE Chi-restraints excluded: chain B residue 1060 HIS Chi-restraints excluded: chain B residue 1149 VAL Chi-restraints excluded: chain C residue 89 THR Chi-restraints excluded: chain C residue 259 LEU Chi-restraints excluded: chain D residue 21 ILE Chi-restraints excluded: chain D residue 43 HIS Chi-restraints excluded: chain D residue 74 PHE Chi-restraints excluded: chain D residue 95 PHE Chi-restraints excluded: chain E residue 99 ILE Chi-restraints excluded: chain E residue 137 ILE Chi-restraints excluded: chain E residue 185 ILE Chi-restraints excluded: chain E residue 190 VAL Chi-restraints excluded: chain F residue 54 THR Chi-restraints excluded: chain F residue 83 LEU Chi-restraints excluded: chain F residue 90 LEU Chi-restraints excluded: chain F residue 110 LEU Chi-restraints excluded: chain F residue 123 LEU Chi-restraints excluded: chain G residue 44 PHE Chi-restraints excluded: chain G residue 66 VAL Chi-restraints excluded: chain G residue 108 ILE Chi-restraints excluded: chain G residue 111 HIS Chi-restraints excluded: chain H residue 58 LEU Chi-restraints excluded: chain H residue 96 VAL Chi-restraints excluded: chain H residue 116 VAL Chi-restraints excluded: chain H residue 143 LEU Chi-restraints excluded: chain I residue 30 LYS Chi-restraints excluded: chain J residue 33 ASP Chi-restraints excluded: chain M residue 1350 MET Chi-restraints excluded: chain M residue 1373 VAL Chi-restraints excluded: chain M residue 1412 VAL Chi-restraints excluded: chain M residue 1515 TYR Chi-restraints excluded: chain M residue 1519 VAL Chi-restraints excluded: chain Q residue 776 LEU Chi-restraints excluded: chain Z residue 481 ILE Chi-restraints excluded: chain Z residue 489 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 603 random chunks: chunk 359 optimal weight: 0.5980 chunk 232 optimal weight: 0.9990 chunk 347 optimal weight: 1.9990 chunk 175 optimal weight: 7.9990 chunk 114 optimal weight: 1.9990 chunk 112 optimal weight: 3.9990 chunk 369 optimal weight: 0.7980 chunk 395 optimal weight: 50.0000 chunk 287 optimal weight: 0.6980 chunk 54 optimal weight: 0.7980 chunk 456 optimal weight: 4.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 410 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1182 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 503 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 157 GLN ** D 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 276 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 272 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8030 moved from start: 0.3529 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 51256 Z= 0.176 Angle : 0.576 14.131 68951 Z= 0.296 Chirality : 0.043 0.214 6723 Planarity : 0.003 0.054 9154 Dihedral : 13.074 172.954 8570 Min Nonbonded Distance : 2.037 Molprobity Statistics. All-atom Clashscore : 7.86 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.82 % Favored : 95.15 % Rotamer: Outliers : 1.75 % Allowed : 12.84 % Favored : 85.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.74 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: 0.20 (0.11), residues: 6303 helix: 1.77 (0.11), residues: 2319 sheet: -0.53 (0.17), residues: 865 loop : -0.94 (0.11), residues: 3119 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.001 TRP A1210 HIS 0.005 0.001 HIS A 620 PHE 0.026 0.001 PHE B 356 TYR 0.044 0.001 TYR G 3 ARG 0.014 0.000 ARG L 31 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12606 Ramachandran restraints generated. 6303 Oldfield, 0 Emsley, 6303 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12606 Ramachandran restraints generated. 6303 Oldfield, 0 Emsley, 6303 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 502 residues out of total 5627 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 79 poor density : 423 time to evaluate : 4.246 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 136 GLN cc_start: 0.8479 (mp10) cc_final: 0.8155 (mp10) REVERT: A 301 HIS cc_start: 0.7808 (t-170) cc_final: 0.7445 (t-170) REVERT: A 343 LEU cc_start: 0.9042 (OUTLIER) cc_final: 0.8763 (pp) REVERT: A 1221 MET cc_start: 0.8364 (mmm) cc_final: 0.7965 (mmm) REVERT: A 1396 ARG cc_start: 0.8615 (mtt90) cc_final: 0.8369 (mmt-90) REVERT: B 230 ARG cc_start: 0.7248 (mmm160) cc_final: 0.6902 (mmp80) REVERT: B 692 THR cc_start: 0.9372 (OUTLIER) cc_final: 0.9001 (p) REVERT: B 1081 ASP cc_start: 0.8738 (t70) cc_final: 0.8353 (t0) REVERT: B 1131 ARG cc_start: 0.9092 (ptp-110) cc_final: 0.8717 (ptp90) REVERT: D 44 ARG cc_start: 0.9311 (ttt180) cc_final: 0.9063 (tpp80) REVERT: D 62 MET cc_start: 0.8838 (mmp) cc_final: 0.8363 (mmm) REVERT: D 74 PHE cc_start: 0.5476 (OUTLIER) cc_final: 0.4786 (p90) REVERT: E 18 MET cc_start: 0.9080 (mmm) cc_final: 0.8809 (mmm) REVERT: G 28 GLN cc_start: 0.8605 (tm-30) cc_final: 0.8319 (tm-30) REVERT: G 44 PHE cc_start: 0.8992 (OUTLIER) cc_final: 0.8781 (m-80) REVERT: G 63 ARG cc_start: 0.8092 (mtp85) cc_final: 0.7820 (mtm110) REVERT: G 104 MET cc_start: 0.7649 (ttp) cc_final: 0.6993 (tmm) REVERT: G 116 GLU cc_start: 0.8783 (pt0) cc_final: 0.8472 (pm20) REVERT: G 117 MET cc_start: 0.7314 (mmm) cc_final: 0.6944 (mmm) REVERT: G 118 GLU cc_start: 0.9310 (mm-30) cc_final: 0.8969 (mm-30) REVERT: G 120 ASP cc_start: 0.7270 (t0) cc_final: 0.6874 (t0) REVERT: G 142 GLU cc_start: 0.8172 (mt-10) cc_final: 0.7682 (mm-30) REVERT: G 165 ASP cc_start: 0.7680 (t0) cc_final: 0.7256 (t0) REVERT: H 13 LYS cc_start: 0.9199 (mmmt) cc_final: 0.8813 (mmmm) REVERT: H 118 TYR cc_start: 0.9143 (m-80) cc_final: 0.8508 (m-80) REVERT: H 140 ARG cc_start: 0.8928 (mmm160) cc_final: 0.8718 (mmt180) REVERT: H 143 LEU cc_start: 0.8926 (OUTLIER) cc_final: 0.8601 (tm) REVERT: M 1344 GLU cc_start: -0.1854 (OUTLIER) cc_final: -0.2098 (tm-30) REVERT: M 1347 MET cc_start: -0.3364 (ptt) cc_final: -0.4695 (mtt) REVERT: M 1350 MET cc_start: 0.3084 (OUTLIER) cc_final: 0.2669 (ppp) REVERT: Q 830 ARG cc_start: -0.0976 (ttt180) cc_final: -0.1240 (ptp-170) REVERT: Q 878 ARG cc_start: 0.7748 (tpt170) cc_final: 0.7411 (tpt-90) REVERT: W 98 GLN cc_start: 0.1890 (tt0) cc_final: 0.1349 (tp40) REVERT: Y 64 MET cc_start: 0.7492 (mtp) cc_final: 0.6502 (mtm) REVERT: Z 197 MET cc_start: 0.8625 (ttt) cc_final: 0.7712 (tpt) REVERT: Z 307 MET cc_start: 0.4793 (mtm) cc_final: 0.3171 (mmm) REVERT: Z 378 MET cc_start: -0.3259 (mtt) cc_final: -0.3697 (mtp) REVERT: Z 508 MET cc_start: 0.7089 (ttp) cc_final: 0.6654 (tpp) outliers start: 79 outliers final: 48 residues processed: 487 average time/residue: 0.4960 time to fit residues: 405.7214 Evaluate side-chains 451 residues out of total 5627 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 396 time to evaluate : 4.140 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain A residue 309 LEU Chi-restraints excluded: chain A residue 343 LEU Chi-restraints excluded: chain A residue 419 ILE Chi-restraints excluded: chain A residue 423 ASN Chi-restraints excluded: chain A residue 439 HIS Chi-restraints excluded: chain A residue 440 LEU Chi-restraints excluded: chain A residue 502 ASN Chi-restraints excluded: chain A residue 510 GLU Chi-restraints excluded: chain A residue 514 GLU Chi-restraints excluded: chain A residue 886 VAL Chi-restraints excluded: chain A residue 1343 LEU Chi-restraints excluded: chain A residue 1428 MET Chi-restraints excluded: chain A residue 1436 VAL Chi-restraints excluded: chain B residue 18 THR Chi-restraints excluded: chain B residue 59 VAL Chi-restraints excluded: chain B residue 84 TYR Chi-restraints excluded: chain B residue 93 LEU Chi-restraints excluded: chain B residue 218 THR Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain B residue 276 LEU Chi-restraints excluded: chain B residue 347 MET Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 612 ILE Chi-restraints excluded: chain B residue 692 THR Chi-restraints excluded: chain B residue 896 LEU Chi-restraints excluded: chain B residue 1149 VAL Chi-restraints excluded: chain C residue 89 THR Chi-restraints excluded: chain C residue 259 LEU Chi-restraints excluded: chain D residue 21 ILE Chi-restraints excluded: chain D residue 74 PHE Chi-restraints excluded: chain D residue 95 PHE Chi-restraints excluded: chain E residue 99 ILE Chi-restraints excluded: chain E residue 137 ILE Chi-restraints excluded: chain E residue 185 ILE Chi-restraints excluded: chain E residue 190 VAL Chi-restraints excluded: chain F residue 54 THR Chi-restraints excluded: chain F residue 123 LEU Chi-restraints excluded: chain G residue 44 PHE Chi-restraints excluded: chain G residue 66 VAL Chi-restraints excluded: chain G residue 108 ILE Chi-restraints excluded: chain H residue 34 SER Chi-restraints excluded: chain H residue 58 LEU Chi-restraints excluded: chain H residue 96 VAL Chi-restraints excluded: chain H residue 143 LEU Chi-restraints excluded: chain I residue 30 LYS Chi-restraints excluded: chain L residue 16 ILE Chi-restraints excluded: chain M residue 1344 GLU Chi-restraints excluded: chain M residue 1350 MET Chi-restraints excluded: chain M residue 1373 VAL Chi-restraints excluded: chain M residue 1412 VAL Chi-restraints excluded: chain M residue 1515 TYR Chi-restraints excluded: chain M residue 1519 VAL Chi-restraints excluded: chain Q residue 776 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 603 random chunks: chunk 528 optimal weight: 50.0000 chunk 556 optimal weight: 20.0000 chunk 508 optimal weight: 50.0000 chunk 541 optimal weight: 9.9990 chunk 325 optimal weight: 5.9990 chunk 235 optimal weight: 0.8980 chunk 425 optimal weight: 40.0000 chunk 166 optimal weight: 9.9990 chunk 489 optimal weight: 8.9990 chunk 512 optimal weight: 50.0000 chunk 539 optimal weight: 0.0870 overall best weight: 5.1964 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 410 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 432 HIS ** A 465 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1005 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1044 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1182 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 66 HIS C 157 GLN ** D 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 14 HIS I 91 HIS ** I 100 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 237 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 276 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 272 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8134 moved from start: 0.3820 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.113 51256 Z= 0.595 Angle : 0.733 14.198 68951 Z= 0.375 Chirality : 0.049 0.232 6723 Planarity : 0.004 0.073 9154 Dihedral : 13.178 176.523 8570 Min Nonbonded Distance : 1.954 Molprobity Statistics. All-atom Clashscore : 9.75 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.65 % Favored : 94.32 % Rotamer: Outliers : 1.78 % Allowed : 13.22 % Favored : 85.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.74 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.01 (0.11), residues: 6303 helix: 1.56 (0.11), residues: 2335 sheet: -0.76 (0.17), residues: 902 loop : -0.98 (0.11), residues: 3066 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP A1210 HIS 0.011 0.001 HIS D 38 PHE 0.032 0.002 PHE A 458 TYR 0.044 0.002 TYR G 3 ARG 0.014 0.001 ARG L 31 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12606 Ramachandran restraints generated. 6303 Oldfield, 0 Emsley, 6303 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12606 Ramachandran restraints generated. 6303 Oldfield, 0 Emsley, 6303 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 470 residues out of total 5627 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 80 poor density : 390 time to evaluate : 4.218 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 67 ARG cc_start: 0.8497 (mpp80) cc_final: 0.7891 (mmm-85) REVERT: A 136 GLN cc_start: 0.8526 (mp10) cc_final: 0.8191 (mp10) REVERT: A 301 HIS cc_start: 0.7901 (t-170) cc_final: 0.7589 (t-170) REVERT: A 322 LEU cc_start: 0.9072 (OUTLIER) cc_final: 0.8837 (mm) REVERT: A 343 LEU cc_start: 0.9348 (OUTLIER) cc_final: 0.8963 (pp) REVERT: A 861 GLN cc_start: 0.8672 (tp-100) cc_final: 0.8314 (tp-100) REVERT: A 865 ILE cc_start: 0.9485 (mt) cc_final: 0.9148 (mt) REVERT: A 930 LEU cc_start: 0.9481 (OUTLIER) cc_final: 0.9228 (tt) REVERT: B 230 ARG cc_start: 0.7531 (mmm160) cc_final: 0.7201 (mmp80) REVERT: B 692 THR cc_start: 0.9503 (OUTLIER) cc_final: 0.9159 (p) REVERT: B 1081 ASP cc_start: 0.8808 (t70) cc_final: 0.8393 (t0) REVERT: B 1131 ARG cc_start: 0.9137 (ptp-110) cc_final: 0.8930 (ptp90) REVERT: D 16 ASP cc_start: 0.8005 (t0) cc_final: 0.7732 (t70) REVERT: D 44 ARG cc_start: 0.9333 (ttt180) cc_final: 0.9107 (tpp80) REVERT: D 62 MET cc_start: 0.8816 (mmp) cc_final: 0.8325 (mmm) REVERT: D 70 ARG cc_start: 0.8216 (mtp-110) cc_final: 0.7888 (ptp-170) REVERT: D 74 PHE cc_start: 0.5545 (OUTLIER) cc_final: 0.4643 (p90) REVERT: E 18 MET cc_start: 0.9190 (mmm) cc_final: 0.8849 (mmm) REVERT: G 1 MET cc_start: 0.9192 (pmm) cc_final: 0.8774 (pmm) REVERT: G 28 GLN cc_start: 0.8672 (tm-30) cc_final: 0.8328 (tm-30) REVERT: G 63 ARG cc_start: 0.8234 (mtp85) cc_final: 0.7948 (mtp180) REVERT: G 104 MET cc_start: 0.7689 (ttp) cc_final: 0.7001 (tmm) REVERT: G 110 ARG cc_start: 0.5734 (tpt170) cc_final: 0.5418 (tpt170) REVERT: G 115 SER cc_start: 0.7869 (t) cc_final: 0.7614 (p) REVERT: G 116 GLU cc_start: 0.8721 (pt0) cc_final: 0.8421 (pm20) REVERT: G 117 MET cc_start: 0.7328 (mmm) cc_final: 0.7062 (mmm) REVERT: G 118 GLU cc_start: 0.9297 (mm-30) cc_final: 0.8958 (mm-30) REVERT: G 120 ASP cc_start: 0.7184 (t0) cc_final: 0.6790 (t0) REVERT: G 165 ASP cc_start: 0.7758 (t0) cc_final: 0.7295 (t0) REVERT: H 13 LYS cc_start: 0.9261 (mmmt) cc_final: 0.8817 (mmmm) REVERT: H 143 LEU cc_start: 0.9102 (OUTLIER) cc_final: 0.8800 (tm) REVERT: I 82 GLU cc_start: 0.8485 (mp0) cc_final: 0.8220 (mm-30) REVERT: M 1347 MET cc_start: -0.3127 (ptt) cc_final: -0.4529 (mtt) REVERT: M 1350 MET cc_start: 0.2831 (OUTLIER) cc_final: 0.2445 (ppp) REVERT: Q 830 ARG cc_start: -0.1017 (ttt180) cc_final: -0.1289 (ptp-170) REVERT: Q 878 ARG cc_start: 0.7856 (tpt170) cc_final: 0.7406 (tpt-90) REVERT: W 98 GLN cc_start: 0.1935 (tt0) cc_final: 0.1378 (tp40) REVERT: Y 63 MET cc_start: 0.5769 (ppp) cc_final: 0.4609 (ppp) REVERT: Y 64 MET cc_start: 0.7256 (mtp) cc_final: 0.6198 (mtm) REVERT: Z 197 MET cc_start: 0.8687 (ttt) cc_final: 0.7793 (tpt) REVERT: Z 307 MET cc_start: 0.4853 (mtm) cc_final: 0.3238 (mmm) REVERT: Z 378 MET cc_start: -0.3289 (mtt) cc_final: -0.3588 (mtm) REVERT: Z 508 MET cc_start: 0.6955 (ttp) cc_final: 0.6539 (tpp) outliers start: 80 outliers final: 55 residues processed: 459 average time/residue: 0.5087 time to fit residues: 391.8139 Evaluate side-chains 441 residues out of total 5627 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 379 time to evaluate : 4.158 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain A residue 309 LEU Chi-restraints excluded: chain A residue 322 LEU Chi-restraints excluded: chain A residue 343 LEU Chi-restraints excluded: chain A residue 419 ILE Chi-restraints excluded: chain A residue 423 ASN Chi-restraints excluded: chain A residue 425 ASP Chi-restraints excluded: chain A residue 439 HIS Chi-restraints excluded: chain A residue 441 GLN Chi-restraints excluded: chain A residue 514 GLU Chi-restraints excluded: chain A residue 886 VAL Chi-restraints excluded: chain A residue 930 LEU Chi-restraints excluded: chain A residue 977 VAL Chi-restraints excluded: chain A residue 996 ILE Chi-restraints excluded: chain A residue 1087 VAL Chi-restraints excluded: chain A residue 1175 ILE Chi-restraints excluded: chain A residue 1336 LEU Chi-restraints excluded: chain A residue 1343 LEU Chi-restraints excluded: chain A residue 1436 VAL Chi-restraints excluded: chain B residue 18 THR Chi-restraints excluded: chain B residue 59 VAL Chi-restraints excluded: chain B residue 84 TYR Chi-restraints excluded: chain B residue 218 THR Chi-restraints excluded: chain B residue 235 ILE Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain B residue 276 LEU Chi-restraints excluded: chain B residue 347 MET Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 612 ILE Chi-restraints excluded: chain B residue 692 THR Chi-restraints excluded: chain B residue 750 VAL Chi-restraints excluded: chain B residue 896 LEU Chi-restraints excluded: chain B residue 931 ILE Chi-restraints excluded: chain B residue 1060 HIS Chi-restraints excluded: chain B residue 1149 VAL Chi-restraints excluded: chain C residue 89 THR Chi-restraints excluded: chain C residue 259 LEU Chi-restraints excluded: chain D residue 21 ILE Chi-restraints excluded: chain D residue 74 PHE Chi-restraints excluded: chain D residue 95 PHE Chi-restraints excluded: chain E residue 99 ILE Chi-restraints excluded: chain E residue 185 ILE Chi-restraints excluded: chain E residue 190 VAL Chi-restraints excluded: chain F residue 54 THR Chi-restraints excluded: chain F residue 83 LEU Chi-restraints excluded: chain F residue 90 LEU Chi-restraints excluded: chain F residue 123 LEU Chi-restraints excluded: chain G residue 66 VAL Chi-restraints excluded: chain G residue 108 ILE Chi-restraints excluded: chain H residue 34 SER Chi-restraints excluded: chain H residue 58 LEU Chi-restraints excluded: chain H residue 96 VAL Chi-restraints excluded: chain H residue 143 LEU Chi-restraints excluded: chain I residue 30 LYS Chi-restraints excluded: chain J residue 33 ASP Chi-restraints excluded: chain M residue 1350 MET Chi-restraints excluded: chain M residue 1373 VAL Chi-restraints excluded: chain M residue 1412 VAL Chi-restraints excluded: chain M residue 1515 TYR Chi-restraints excluded: chain M residue 1519 VAL Chi-restraints excluded: chain Q residue 776 LEU Chi-restraints excluded: chain Z residue 481 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 603 random chunks: chunk 355 optimal weight: 2.9990 chunk 572 optimal weight: 5.9990 chunk 349 optimal weight: 2.9990 chunk 271 optimal weight: 2.9990 chunk 398 optimal weight: 30.0000 chunk 600 optimal weight: 10.0000 chunk 552 optimal weight: 7.9990 chunk 478 optimal weight: 8.9990 chunk 49 optimal weight: 0.8980 chunk 369 optimal weight: 0.4980 chunk 293 optimal weight: 20.0000 overall best weight: 2.0786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 410 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 465 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1182 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 157 GLN ** D 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 100 HIS ** L 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 237 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 276 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 272 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8079 moved from start: 0.3880 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.096 51256 Z= 0.284 Angle : 0.634 14.508 68951 Z= 0.324 Chirality : 0.045 0.213 6723 Planarity : 0.004 0.077 9154 Dihedral : 13.144 174.726 8570 Min Nonbonded Distance : 1.997 Molprobity Statistics. All-atom Clashscore : 8.83 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.19 % Favored : 94.78 % Rotamer: Outliers : 1.47 % Allowed : 13.51 % Favored : 85.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.74 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.13 (0.11), residues: 6303 helix: 1.74 (0.11), residues: 2319 sheet: -0.76 (0.17), residues: 914 loop : -0.93 (0.11), residues: 3070 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.060 0.002 TRP Y 70 HIS 0.006 0.001 HIS A1445 PHE 0.036 0.002 PHE A 458 TYR 0.016 0.001 TYR H 115 ARG 0.016 0.000 ARG L 31 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12606 Ramachandran restraints generated. 6303 Oldfield, 0 Emsley, 6303 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12606 Ramachandran restraints generated. 6303 Oldfield, 0 Emsley, 6303 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 464 residues out of total 5627 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 398 time to evaluate : 4.223 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 67 ARG cc_start: 0.8445 (mpp80) cc_final: 0.7796 (mmm-85) REVERT: A 136 GLN cc_start: 0.8527 (mp10) cc_final: 0.8202 (mp10) REVERT: A 301 HIS cc_start: 0.7838 (t-170) cc_final: 0.7556 (t-90) REVERT: A 322 LEU cc_start: 0.9055 (OUTLIER) cc_final: 0.8820 (mm) REVERT: A 343 LEU cc_start: 0.9185 (OUTLIER) cc_final: 0.8858 (pp) REVERT: A 930 LEU cc_start: 0.9417 (OUTLIER) cc_final: 0.9144 (tt) REVERT: B 230 ARG cc_start: 0.7394 (mmm160) cc_final: 0.7035 (mmp80) REVERT: B 692 THR cc_start: 0.9441 (OUTLIER) cc_final: 0.9099 (p) REVERT: B 1081 ASP cc_start: 0.8752 (t70) cc_final: 0.8373 (t0) REVERT: D 44 ARG cc_start: 0.9323 (ttt180) cc_final: 0.9085 (tpp80) REVERT: D 62 MET cc_start: 0.8798 (mmp) cc_final: 0.8295 (mmm) REVERT: D 74 PHE cc_start: 0.5465 (OUTLIER) cc_final: 0.4525 (p90) REVERT: E 18 MET cc_start: 0.9137 (mmm) cc_final: 0.8819 (mmm) REVERT: G 1 MET cc_start: 0.9171 (pmm) cc_final: 0.8912 (pmm) REVERT: G 8 GLU cc_start: 0.8440 (mm-30) cc_final: 0.8044 (mm-30) REVERT: G 28 GLN cc_start: 0.8547 (tm-30) cc_final: 0.8259 (tm-30) REVERT: G 63 ARG cc_start: 0.8182 (mtp85) cc_final: 0.7886 (mtm110) REVERT: G 104 MET cc_start: 0.7585 (ttp) cc_final: 0.6948 (tmm) REVERT: G 110 ARG cc_start: 0.5770 (tpt170) cc_final: 0.5451 (tpt170) REVERT: G 115 SER cc_start: 0.7920 (t) cc_final: 0.7677 (p) REVERT: G 116 GLU cc_start: 0.8696 (pt0) cc_final: 0.8339 (pm20) REVERT: G 117 MET cc_start: 0.7319 (mmm) cc_final: 0.6956 (mmm) REVERT: G 118 GLU cc_start: 0.9334 (mm-30) cc_final: 0.8995 (mm-30) REVERT: G 120 ASP cc_start: 0.7278 (t0) cc_final: 0.6898 (t0) REVERT: G 165 ASP cc_start: 0.7733 (t0) cc_final: 0.7307 (t0) REVERT: H 13 LYS cc_start: 0.9234 (mmmt) cc_final: 0.8804 (mmmm) REVERT: H 140 ARG cc_start: 0.8968 (mmm160) cc_final: 0.8737 (mmt180) REVERT: H 143 LEU cc_start: 0.9066 (OUTLIER) cc_final: 0.8732 (tm) REVERT: L 16 ILE cc_start: 0.9281 (pt) cc_final: 0.8994 (pt) REVERT: L 25 GLU cc_start: 0.8216 (tp30) cc_final: 0.7871 (tp30) REVERT: M 1344 GLU cc_start: -0.1979 (OUTLIER) cc_final: -0.2246 (tm-30) REVERT: M 1347 MET cc_start: -0.3183 (ptt) cc_final: -0.4537 (mtt) REVERT: M 1350 MET cc_start: 0.2837 (OUTLIER) cc_final: 0.2382 (ppp) REVERT: M 1492 GLU cc_start: 0.4510 (mp0) cc_final: 0.4255 (mp0) REVERT: Q 830 ARG cc_start: -0.1010 (ttt180) cc_final: -0.1277 (ptp-170) REVERT: Q 878 ARG cc_start: 0.7896 (tpt170) cc_final: 0.7484 (tpt-90) REVERT: W 11 GLN cc_start: 0.7191 (tp40) cc_final: 0.6662 (mp-120) REVERT: W 98 GLN cc_start: 0.2015 (tt0) cc_final: 0.1465 (tp40) REVERT: Y 63 MET cc_start: 0.5779 (ppp) cc_final: 0.4590 (ppp) REVERT: Y 64 MET cc_start: 0.7283 (mtp) cc_final: 0.6192 (mtm) REVERT: Z 197 MET cc_start: 0.8669 (ttt) cc_final: 0.7828 (tpt) REVERT: Z 307 MET cc_start: 0.4797 (mtm) cc_final: 0.3229 (mmm) REVERT: Z 508 MET cc_start: 0.7382 (ttp) cc_final: 0.7024 (tpp) outliers start: 66 outliers final: 52 residues processed: 453 average time/residue: 0.5069 time to fit residues: 385.5329 Evaluate side-chains 448 residues out of total 5627 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 388 time to evaluate : 4.196 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain A residue 309 LEU Chi-restraints excluded: chain A residue 322 LEU Chi-restraints excluded: chain A residue 343 LEU Chi-restraints excluded: chain A residue 419 ILE Chi-restraints excluded: chain A residue 423 ASN Chi-restraints excluded: chain A residue 425 ASP Chi-restraints excluded: chain A residue 439 HIS Chi-restraints excluded: chain A residue 440 LEU Chi-restraints excluded: chain A residue 514 GLU Chi-restraints excluded: chain A residue 886 VAL Chi-restraints excluded: chain A residue 930 LEU Chi-restraints excluded: chain A residue 996 ILE Chi-restraints excluded: chain A residue 1343 LEU Chi-restraints excluded: chain A residue 1428 MET Chi-restraints excluded: chain A residue 1436 VAL Chi-restraints excluded: chain B residue 18 THR Chi-restraints excluded: chain B residue 59 VAL Chi-restraints excluded: chain B residue 84 TYR Chi-restraints excluded: chain B residue 93 LEU Chi-restraints excluded: chain B residue 218 THR Chi-restraints excluded: chain B residue 235 ILE Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain B residue 276 LEU Chi-restraints excluded: chain B residue 347 MET Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 612 ILE Chi-restraints excluded: chain B residue 692 THR Chi-restraints excluded: chain B residue 896 LEU Chi-restraints excluded: chain B residue 931 ILE Chi-restraints excluded: chain B residue 1149 VAL Chi-restraints excluded: chain C residue 89 THR Chi-restraints excluded: chain C residue 259 LEU Chi-restraints excluded: chain D residue 21 ILE Chi-restraints excluded: chain D residue 74 PHE Chi-restraints excluded: chain D residue 95 PHE Chi-restraints excluded: chain E residue 99 ILE Chi-restraints excluded: chain E residue 185 ILE Chi-restraints excluded: chain E residue 190 VAL Chi-restraints excluded: chain F residue 54 THR Chi-restraints excluded: chain F residue 83 LEU Chi-restraints excluded: chain F residue 90 LEU Chi-restraints excluded: chain F residue 123 LEU Chi-restraints excluded: chain G residue 66 VAL Chi-restraints excluded: chain G residue 108 ILE Chi-restraints excluded: chain H residue 34 SER Chi-restraints excluded: chain H residue 47 ILE Chi-restraints excluded: chain H residue 58 LEU Chi-restraints excluded: chain H residue 96 VAL Chi-restraints excluded: chain H residue 143 LEU Chi-restraints excluded: chain I residue 30 LYS Chi-restraints excluded: chain I residue 100 HIS Chi-restraints excluded: chain M residue 1344 GLU Chi-restraints excluded: chain M residue 1350 MET Chi-restraints excluded: chain M residue 1373 VAL Chi-restraints excluded: chain M residue 1412 VAL Chi-restraints excluded: chain M residue 1515 TYR Chi-restraints excluded: chain M residue 1519 VAL Chi-restraints excluded: chain Q residue 776 LEU Chi-restraints excluded: chain Z residue 481 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 603 random chunks: chunk 379 optimal weight: 0.0980 chunk 509 optimal weight: 50.0000 chunk 146 optimal weight: 0.8980 chunk 441 optimal weight: 9.9990 chunk 70 optimal weight: 5.9990 chunk 132 optimal weight: 0.5980 chunk 479 optimal weight: 7.9990 chunk 200 optimal weight: 0.8980 chunk 491 optimal weight: 10.0000 chunk 60 optimal weight: 2.9990 chunk 88 optimal weight: 0.9980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 273 GLN ** A 410 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1182 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 145 GLN B 197 GLN ** B 503 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 60 HIS I 100 HIS ** W 237 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 276 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 272 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4281 r_free = 0.4281 target = 0.142372 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.086725 restraints weight = 130069.167| |-----------------------------------------------------------------------------| r_work (start): 0.3055 rms_B_bonded: 3.75 r_work: 0.2847 rms_B_bonded: 4.20 restraints_weight: 0.5000 r_work (final): 0.2847 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2831 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2831 r_free = 0.2831 target_work(ls_wunit_k1) = 0.064 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 465 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2831 r_free = 0.2831 target_work(ls_wunit_k1) = 0.064 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 468 | |-----------------------------------------------------------------------------| r_final: 0.2831 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8266 moved from start: 0.3972 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 51256 Z= 0.168 Angle : 0.600 14.177 68951 Z= 0.306 Chirality : 0.043 0.215 6723 Planarity : 0.003 0.067 9154 Dihedral : 13.029 172.771 8570 Min Nonbonded Distance : 2.053 Molprobity Statistics. All-atom Clashscore : 7.92 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.11 % Favored : 94.86 % Rotamer: Outliers : 1.42 % Allowed : 13.59 % Favored : 84.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.74 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: 0.28 (0.11), residues: 6303 helix: 1.85 (0.11), residues: 2320 sheet: -0.57 (0.17), residues: 890 loop : -0.88 (0.11), residues: 3093 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.047 0.001 TRP Y 70 HIS 0.038 0.001 HIS I 100 PHE 0.029 0.001 PHE A1388 TYR 0.012 0.001 TYR B 766 ARG 0.016 0.000 ARG L 31 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10697.05 seconds wall clock time: 185 minutes 45.54 seconds (11145.54 seconds total)