Starting phenix.real_space_refine on Sun Apr 14 07:33:17 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8qcf_18329/04_2024/8qcf_18329_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8qcf_18329/04_2024/8qcf_18329.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.55 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8qcf_18329/04_2024/8qcf_18329.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8qcf_18329/04_2024/8qcf_18329.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8qcf_18329/04_2024/8qcf_18329_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8qcf_18329/04_2024/8qcf_18329_updated.pdb" } resolution = 2.55 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= 0.008 sd= 0.156 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: 5 Type Number sf(0) Gaussians P 37 5.49 5 S 150 5.16 5 C 19380 2.51 5 N 5220 2.21 5 O 5964 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "G PHE 203": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K GLU 480": "OE1" <-> "OE2" Residue "M PHE 443": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M PHE 956": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.10s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 30751 Number of models: 1 Model: "" Number of chains: 14 Chain: "B" Number of atoms: 2261 Number of conformers: 1 Conformer: "" Number of residues, atoms: 297, 2261 Classifications: {'peptide': 297} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PTRANS': 10, 'TRANS': 286} Unresolved non-hydrogen bonds: 51 Unresolved non-hydrogen angles: 62 Unresolved non-hydrogen dihedrals: 42 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 4, 'HIS:plan': 1, 'ARG:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 38 Chain: "C" Number of atoms: 1881 Number of conformers: 1 Conformer: "" Number of residues, atoms: 241, 1881 Classifications: {'peptide': 241} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 233} Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 13 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "D" Number of atoms: 2358 Number of conformers: 1 Conformer: "" Number of residues, atoms: 305, 2358 Classifications: {'peptide': 305} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 13, 'TRANS': 291} Chain breaks: 5 Unresolved non-hydrogen bonds: 22 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 13 Chain: "E" Number of atoms: 1691 Number of conformers: 1 Conformer: "" Number of residues, atoms: 221, 1691 Classifications: {'peptide': 221} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 211} Chain: "F" Number of atoms: 1998 Number of conformers: 1 Conformer: "" Number of residues, atoms: 263, 1998 Classifications: {'peptide': 263} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 248} Unresolved non-hydrogen bonds: 33 Unresolved non-hydrogen angles: 39 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 3, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 18 Chain: "G" Number of atoms: 1581 Number of conformers: 1 Conformer: "" Number of residues, atoms: 209, 1581 Classifications: {'peptide': 209} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 203} Chain breaks: 2 Unresolved non-hydrogen bonds: 36 Unresolved non-hydrogen angles: 45 Unresolved non-hydrogen dihedrals: 29 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 2, 'ARG:plan': 1, 'ASP:plan': 3, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 27 Chain: "H" Number of atoms: 1765 Number of conformers: 1 Conformer: "" Number of residues, atoms: 228, 1765 Classifications: {'peptide': 228} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 11, 'TRANS': 216} Chain breaks: 1 Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 13 Unresolved non-hydrogen chiralities: 1 Chain: "I" Number of atoms: 2084 Number of conformers: 1 Conformer: "" Number of residues, atoms: 268, 2084 Classifications: {'peptide': 268} Link IDs: {'PTRANS': 8, 'TRANS': 259} Chain breaks: 2 Chain: "J" Number of atoms: 1689 Number of conformers: 1 Conformer: "" Number of residues, atoms: 227, 1689 Classifications: {'peptide': 227} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 214} Chain breaks: 3 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "K" Number of atoms: 7231 Number of conformers: 1 Conformer: "" Number of residues, atoms: 915, 7231 Classifications: {'peptide': 915} Incomplete info: {'truncation_to_alanine': 26} Link IDs: {'PCIS': 1, 'PTRANS': 46, 'TRANS': 867} Chain breaks: 6 Unresolved non-hydrogen bonds: 105 Unresolved non-hydrogen angles: 119 Unresolved non-hydrogen dihedrals: 91 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 4, 'ARG:plan': 4, 'ASN:plan1': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 49 Chain: "L" Number of atoms: 618 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 618 Classifications: {'peptide': 79} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 4, 'TRANS': 74} Chain breaks: 2 Unresolved non-hydrogen bonds: 29 Unresolved non-hydrogen angles: 30 Unresolved non-hydrogen dihedrals: 28 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "M" Number of atoms: 5050 Number of conformers: 1 Conformer: "" Number of residues, atoms: 657, 5050 Classifications: {'peptide': 657} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 79} Link IDs: {'PTRANS': 27, 'TRANS': 629} Chain breaks: 3 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 283 Unresolved non-hydrogen angles: 341 Unresolved non-hydrogen dihedrals: 231 Unresolved non-hydrogen chiralities: 19 Planarities with less than four sites: {'GLN:plan1': 6, 'ASP:plan': 6, 'TYR:plan': 1, 'ASN:plan1': 4, 'HIS:plan': 1, 'GLU:plan': 10, 'ARG:plan': 7} Unresolved non-hydrogen planarities: 141 Chain: "N" Number of atoms: 513 Number of conformers: 1 Conformer: "" Number of residues, atoms: 34, 513 Classifications: {'RNA': 34} Modifications used: {'rna2p_pyr': 2, 'rna3p_pyr': 32} Link IDs: {'rna2p': 2, 'rna3p': 31} Unresolved non-hydrogen bonds: 188 Unresolved non-hydrogen angles: 292 Unresolved non-hydrogen dihedrals: 168 Unresolved non-hydrogen chiralities: 20 Planarities with less than four sites: {' U%rna3p_pyr:plan': 21} Unresolved non-hydrogen planarities: 167 Chain: "M" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 15.92, per 1000 atoms: 0.52 Number of scatterers: 30751 At special positions: 0 Unit cell: (145.555, 131.936, 196.627, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 150 16.00 P 37 15.00 O 5964 8.00 N 5220 7.00 C 19380 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 11.06 Conformation dependent library (CDL) restraints added in 5.0 seconds 7676 Ramachandran restraints generated. 3838 Oldfield, 0 Emsley, 3838 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7390 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 125 helices and 47 sheets defined 31.5% alpha, 19.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 6.34 Creating SS restraints... Processing helix chain 'B' and resid 9 through 20 Processing helix chain 'B' and resid 85 through 87 No H-bonds generated for 'chain 'B' and resid 85 through 87' Processing helix chain 'B' and resid 99 through 112 Processing helix chain 'B' and resid 121 through 123 No H-bonds generated for 'chain 'B' and resid 121 through 123' Processing helix chain 'B' and resid 147 through 161 Processing helix chain 'B' and resid 179 through 182 No H-bonds generated for 'chain 'B' and resid 179 through 182' Processing helix chain 'B' and resid 206 through 211 Processing helix chain 'B' and resid 225 through 228 No H-bonds generated for 'chain 'B' and resid 225 through 228' Processing helix chain 'B' and resid 258 through 296 removed outlier: 3.960A pdb=" N TYR B 269 " --> pdb=" O CYS B 265 " (cutoff:3.500A) removed outlier: 4.395A pdb=" N SER B 270 " --> pdb=" O HIS B 266 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N ILE B 271 " --> pdb=" O GLU B 267 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N LYS B 274 " --> pdb=" O SER B 270 " (cutoff:3.500A) Processing helix chain 'C' and resid 95 through 109 Processing helix chain 'C' and resid 114 through 116 No H-bonds generated for 'chain 'C' and resid 114 through 116' Processing helix chain 'C' and resid 135 through 149 Processing helix chain 'C' and resid 176 through 179 No H-bonds generated for 'chain 'C' and resid 176 through 179' Processing helix chain 'C' and resid 207 through 242 removed outlier: 3.965A pdb=" N LEU C 210 " --> pdb=" O LEU C 207 " (cutoff:3.500A) removed outlier: 6.062A pdb=" N GLU C 211 " --> pdb=" O ASP C 208 " (cutoff:3.500A) removed outlier: 4.461A pdb=" N ASN C 212 " --> pdb=" O ARG C 209 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N SER C 241 " --> pdb=" O LYS C 238 " (cutoff:3.500A) removed outlier: 4.093A pdb=" N ASN C 242 " --> pdb=" O ARG C 239 " (cutoff:3.500A) Processing helix chain 'D' and resid 19 through 25 Processing helix chain 'D' and resid 27 through 37 removed outlier: 3.888A pdb=" N LEU D 37 " --> pdb=" O ARG D 33 " (cutoff:3.500A) Processing helix chain 'D' and resid 124 through 126 No H-bonds generated for 'chain 'D' and resid 124 through 126' Processing helix chain 'D' and resid 146 through 161 Processing helix chain 'D' and resid 167 through 170 Processing helix chain 'D' and resid 227 through 240 removed outlier: 3.714A pdb=" N GLN D 239 " --> pdb=" O MET D 235 " (cutoff:3.500A) removed outlier: 4.335A pdb=" N SER D 240 " --> pdb=" O TYR D 236 " (cutoff:3.500A) Processing helix chain 'D' and resid 288 through 290 No H-bonds generated for 'chain 'D' and resid 288 through 290' Processing helix chain 'D' and resid 304 through 306 No H-bonds generated for 'chain 'D' and resid 304 through 306' Processing helix chain 'D' and resid 336 through 342 Processing helix chain 'D' and resid 371 through 389 Processing helix chain 'E' and resid 38 through 40 No H-bonds generated for 'chain 'E' and resid 38 through 40' Processing helix chain 'E' and resid 61 through 77 removed outlier: 3.644A pdb=" N VAL E 65 " --> pdb=" O THR E 61 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N LEU E 66 " --> pdb=" O ARG E 62 " (cutoff:3.500A) Proline residue: E 76 - end of helix Processing helix chain 'E' and resid 80 through 82 No H-bonds generated for 'chain 'E' and resid 80 through 82' Processing helix chain 'E' and resid 106 through 123 Processing helix chain 'E' and resid 151 through 156 removed outlier: 3.675A pdb=" N LYS E 155 " --> pdb=" O ALA E 151 " (cutoff:3.500A) removed outlier: 4.042A pdb=" N ILE E 156 " --> pdb=" O GLU E 152 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 151 through 156' Processing helix chain 'E' and resid 188 through 220 removed outlier: 3.594A pdb=" N GLU E 196 " --> pdb=" O PHE E 192 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N GLN E 200 " --> pdb=" O GLU E 196 " (cutoff:3.500A) Proline residue: E 219 - end of helix Processing helix chain 'F' and resid 5 through 15 Processing helix chain 'F' and resid 90 through 102 Processing helix chain 'F' and resid 111 through 114 Processing helix chain 'F' and resid 138 through 151 removed outlier: 3.583A pdb=" N ASN F 150 " --> pdb=" O TYR F 146 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N SER F 151 " --> pdb=" O SER F 147 " (cutoff:3.500A) Processing helix chain 'F' and resid 203 through 206 No H-bonds generated for 'chain 'F' and resid 203 through 206' Processing helix chain 'F' and resid 241 through 262 removed outlier: 3.716A pdb=" N LYS F 245 " --> pdb=" O HIS F 242 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N GLN F 246 " --> pdb=" O LEU F 243 " (cutoff:3.500A) removed outlier: 4.242A pdb=" N ALA F 255 " --> pdb=" O GLU F 252 " (cutoff:3.500A) Proline residue: F 256 - end of helix Processing helix chain 'G' and resid 107 through 121 Processing helix chain 'G' and resid 127 through 129 No H-bonds generated for 'chain 'G' and resid 127 through 129' Processing helix chain 'G' and resid 166 through 183 Proline residue: G 170 - end of helix Processing helix chain 'G' and resid 224 through 247 removed outlier: 3.724A pdb=" N ARG G 236 " --> pdb=" O GLU G 232 " (cutoff:3.500A) Processing helix chain 'H' and resid 160 through 168 Processing helix chain 'H' and resid 174 through 179 Processing helix chain 'H' and resid 201 through 216 Processing helix chain 'H' and resid 220 through 233 removed outlier: 3.848A pdb=" N PHE H 223 " --> pdb=" O THR H 220 " (cutoff:3.500A) removed outlier: 4.750A pdb=" N LYS H 224 " --> pdb=" O ALA H 221 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N ASP H 225 " --> pdb=" O ALA H 222 " (cutoff:3.500A) Processing helix chain 'I' and resid 138 through 140 No H-bonds generated for 'chain 'I' and resid 138 through 140' Processing helix chain 'I' and resid 159 through 161 No H-bonds generated for 'chain 'I' and resid 159 through 161' Processing helix chain 'I' and resid 204 through 206 No H-bonds generated for 'chain 'I' and resid 204 through 206' Processing helix chain 'I' and resid 238 through 243 Processing helix chain 'I' and resid 278 through 281 removed outlier: 4.175A pdb=" N TYR I 281 " --> pdb=" O TRP I 278 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 278 through 281' Processing helix chain 'I' and resid 291 through 309 Processing helix chain 'I' and resid 316 through 328 removed outlier: 4.014A pdb=" N MET I 327 " --> pdb=" O TYR I 323 " (cutoff:3.500A) removed outlier: 5.340A pdb=" N VAL I 328 " --> pdb=" O GLU I 324 " (cutoff:3.500A) Processing helix chain 'I' and resid 332 through 336 removed outlier: 3.806A pdb=" N ILE I 336 " --> pdb=" O GLY I 333 " (cutoff:3.500A) Processing helix chain 'I' and resid 338 through 353 Processing helix chain 'J' and resid 184 through 186 No H-bonds generated for 'chain 'J' and resid 184 through 186' Processing helix chain 'J' and resid 190 through 192 No H-bonds generated for 'chain 'J' and resid 190 through 192' Processing helix chain 'J' and resid 207 through 209 No H-bonds generated for 'chain 'J' and resid 207 through 209' Processing helix chain 'J' and resid 220 through 222 No H-bonds generated for 'chain 'J' and resid 220 through 222' Processing helix chain 'K' and resid 55 through 57 No H-bonds generated for 'chain 'K' and resid 55 through 57' Processing helix chain 'K' and resid 92 through 97 Processing helix chain 'K' and resid 115 through 124 Processing helix chain 'K' and resid 126 through 137 Processing helix chain 'K' and resid 166 through 184 Processing helix chain 'K' and resid 186 through 188 No H-bonds generated for 'chain 'K' and resid 186 through 188' Processing helix chain 'K' and resid 218 through 224 removed outlier: 3.631A pdb=" N LEU K 224 " --> pdb=" O GLN K 220 " (cutoff:3.500A) Processing helix chain 'K' and resid 228 through 234 removed outlier: 5.686A pdb=" N ASP K 233 " --> pdb=" O ASP K 229 " (cutoff:3.500A) removed outlier: 6.395A pdb=" N SER K 234 " --> pdb=" O ASP K 230 " (cutoff:3.500A) Processing helix chain 'K' and resid 261 through 270 Processing helix chain 'K' and resid 323 through 325 No H-bonds generated for 'chain 'K' and resid 323 through 325' Processing helix chain 'K' and resid 367 through 380 Processing helix chain 'K' and resid 483 through 487 Processing helix chain 'K' and resid 497 through 501 Processing helix chain 'K' and resid 507 through 509 No H-bonds generated for 'chain 'K' and resid 507 through 509' Processing helix chain 'K' and resid 519 through 524 Processing helix chain 'K' and resid 573 through 575 No H-bonds generated for 'chain 'K' and resid 573 through 575' Processing helix chain 'K' and resid 582 through 589 Processing helix chain 'K' and resid 606 through 609 No H-bonds generated for 'chain 'K' and resid 606 through 609' Processing helix chain 'K' and resid 654 through 662 Processing helix chain 'K' and resid 669 through 691 Processing helix chain 'K' and resid 724 through 745 removed outlier: 3.882A pdb=" N GLU K 728 " --> pdb=" O ASN K 724 " (cutoff:3.500A) removed outlier: 4.165A pdb=" N GLU K 729 " --> pdb=" O SER K 725 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N PHE K 730 " --> pdb=" O LEU K 726 " (cutoff:3.500A) Processing helix chain 'K' and resid 761 through 772 removed outlier: 3.716A pdb=" N LEU K 766 " --> pdb=" O ASN K 762 " (cutoff:3.500A) Processing helix chain 'K' and resid 783 through 792 Processing helix chain 'K' and resid 799 through 811 removed outlier: 3.644A pdb=" N ILE K 807 " --> pdb=" O LEU K 804 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N MET K 808 " --> pdb=" O VAL K 805 " (cutoff:3.500A) Processing helix chain 'K' and resid 826 through 829 Processing helix chain 'K' and resid 849 through 860 Processing helix chain 'K' and resid 870 through 872 No H-bonds generated for 'chain 'K' and resid 870 through 872' Processing helix chain 'K' and resid 874 through 909 Processing helix chain 'K' and resid 941 through 944 No H-bonds generated for 'chain 'K' and resid 941 through 944' Processing helix chain 'K' and resid 948 through 950 No H-bonds generated for 'chain 'K' and resid 948 through 950' Processing helix chain 'L' and resid 121 through 131 Processing helix chain 'L' and resid 150 through 155 Processing helix chain 'L' and resid 178 through 182 Processing helix chain 'L' and resid 197 through 208 removed outlier: 3.756A pdb=" N PHE L 207 " --> pdb=" O ALA L 203 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N ASN L 208 " --> pdb=" O ILE L 204 " (cutoff:3.500A) Processing helix chain 'L' and resid 212 through 223 removed outlier: 3.565A pdb=" N ILE L 216 " --> pdb=" O PRO L 212 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N LEU L 221 " --> pdb=" O GLN L 217 " (cutoff:3.500A) removed outlier: 4.833A pdb=" N ASN L 222 " --> pdb=" O SER L 218 " (cutoff:3.500A) removed outlier: 4.360A pdb=" N ALA L 223 " --> pdb=" O ALA L 219 " (cutoff:3.500A) Processing helix chain 'M' and resid 315 through 318 No H-bonds generated for 'chain 'M' and resid 315 through 318' Processing helix chain 'M' and resid 332 through 341 Processing helix chain 'M' and resid 357 through 371 Processing helix chain 'M' and resid 382 through 395 removed outlier: 4.139A pdb=" N ASN M 386 " --> pdb=" O LYS M 382 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N GLN M 387 " --> pdb=" O ALA M 383 " (cutoff:3.500A) Processing helix chain 'M' and resid 421 through 430 Processing helix chain 'M' and resid 433 through 437 Processing helix chain 'M' and resid 446 through 448 No H-bonds generated for 'chain 'M' and resid 446 through 448' Processing helix chain 'M' and resid 453 through 464 removed outlier: 4.476A pdb=" N VAL M 457 " --> pdb=" O ASP M 453 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N TRP M 458 " --> pdb=" O ARG M 454 " (cutoff:3.500A) Processing helix chain 'M' and resid 482 through 491 Processing helix chain 'M' and resid 530 through 539 Processing helix chain 'M' and resid 614 through 618 Processing helix chain 'M' and resid 620 through 623 No H-bonds generated for 'chain 'M' and resid 620 through 623' Processing helix chain 'M' and resid 636 through 645 removed outlier: 3.980A pdb=" N GLU M 640 " --> pdb=" O LYS M 636 " (cutoff:3.500A) Processing helix chain 'M' and resid 656 through 670 removed outlier: 3.766A pdb=" N THR M 669 " --> pdb=" O GLU M 665 " (cutoff:3.500A) removed outlier: 4.929A pdb=" N ARG M 670 " --> pdb=" O LYS M 666 " (cutoff:3.500A) Processing helix chain 'M' and resid 673 through 675 No H-bonds generated for 'chain 'M' and resid 673 through 675' Processing helix chain 'M' and resid 679 through 690 removed outlier: 4.291A pdb=" N ARG M 690 " --> pdb=" O SER M 686 " (cutoff:3.500A) Processing helix chain 'M' and resid 701 through 712 Processing helix chain 'M' and resid 723 through 725 No H-bonds generated for 'chain 'M' and resid 723 through 725' Processing helix chain 'M' and resid 754 through 761 Processing helix chain 'M' and resid 786 through 793 Processing helix chain 'M' and resid 808 through 816 removed outlier: 3.771A pdb=" N ARG M 816 " --> pdb=" O LEU M 812 " (cutoff:3.500A) Processing helix chain 'M' and resid 823 through 826 No H-bonds generated for 'chain 'M' and resid 823 through 826' Processing helix chain 'M' and resid 842 through 854 removed outlier: 3.635A pdb=" N LYS M 847 " --> pdb=" O PRO M 843 " (cutoff:3.500A) Processing helix chain 'M' and resid 866 through 873 removed outlier: 3.800A pdb=" N GLU M 873 " --> pdb=" O ARG M 869 " (cutoff:3.500A) Processing helix chain 'M' and resid 879 through 888 Processing helix chain 'M' and resid 896 through 906 removed outlier: 3.608A pdb=" N SER M 904 " --> pdb=" O VAL M 900 " (cutoff:3.500A) removed outlier: 4.993A pdb=" N VAL M 905 " --> pdb=" O ALA M 901 " (cutoff:3.500A) removed outlier: 5.269A pdb=" N PHE M 906 " --> pdb=" O LEU M 902 " (cutoff:3.500A) Processing helix chain 'M' and resid 926 through 944 Processing helix chain 'M' and resid 951 through 954 No H-bonds generated for 'chain 'M' and resid 951 through 954' Processing helix chain 'M' and resid 965 through 973 Processing helix chain 'M' and resid 977 through 982 removed outlier: 3.655A pdb=" N GLU M 982 " --> pdb=" O LYS M 978 " (cutoff:3.500A) Processing helix chain 'M' and resid 988 through 1012 removed outlier: 3.547A pdb=" N ASP M 999 " --> pdb=" O ILE M 995 " (cutoff:3.500A) removed outlier: 4.335A pdb=" N GLU M1000 " --> pdb=" O THR M 996 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N ILE M1001 " --> pdb=" O TRP M 997 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N ILE M1010 " --> pdb=" O LYS M1006 " (cutoff:3.500A) Processing helix chain 'M' and resid 1015 through 1028 removed outlier: 3.631A pdb=" N GLU M1026 " --> pdb=" O SER M1022 " (cutoff:3.500A) Processing helix chain 'M' and resid 1032 through 1034 No H-bonds generated for 'chain 'M' and resid 1032 through 1034' Processing sheet with id= A, first strand: chain 'B' and resid 37 through 40 removed outlier: 3.552A pdb=" N ASP B 142 " --> pdb=" O LYS B 55 " (cutoff:3.500A) removed outlier: 7.028A pdb=" N HIS B 57 " --> pdb=" O PHE B 140 " (cutoff:3.500A) removed outlier: 5.261A pdb=" N PHE B 140 " --> pdb=" O HIS B 57 " (cutoff:3.500A) removed outlier: 7.348A pdb=" N ARG B 59 " --> pdb=" O VAL B 138 " (cutoff:3.500A) removed outlier: 5.612A pdb=" N VAL B 138 " --> pdb=" O ARG B 59 " (cutoff:3.500A) removed outlier: 7.631A pdb=" N SER B 61 " --> pdb=" O ALA B 136 " (cutoff:3.500A) removed outlier: 5.550A pdb=" N ALA B 136 " --> pdb=" O SER B 61 " (cutoff:3.500A) removed outlier: 7.377A pdb=" N GLN B 63 " --> pdb=" O VAL B 134 " (cutoff:3.500A) removed outlier: 5.441A pdb=" N VAL B 134 " --> pdb=" O GLN B 63 " (cutoff:3.500A) removed outlier: 5.883A pdb=" N ALA B 65 " --> pdb=" O TRP B 132 " (cutoff:3.500A) removed outlier: 5.385A pdb=" N TRP B 132 " --> pdb=" O ALA B 65 " (cutoff:3.500A) removed outlier: 6.497A pdb=" N LEU B 76 " --> pdb=" O VAL B 134 " (cutoff:3.500A) removed outlier: 8.226A pdb=" N ALA B 136 " --> pdb=" O LEU B 76 " (cutoff:3.500A) removed outlier: 6.851A pdb=" N VAL B 78 " --> pdb=" O ALA B 136 " (cutoff:3.500A) removed outlier: 8.264A pdb=" N VAL B 138 " --> pdb=" O VAL B 78 " (cutoff:3.500A) removed outlier: 6.942A pdb=" N SER B 80 " --> pdb=" O VAL B 138 " (cutoff:3.500A) removed outlier: 8.122A pdb=" N PHE B 140 " --> pdb=" O SER B 80 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'B' and resid 167 through 170 Processing sheet with id= C, first strand: chain 'B' and resid 218 through 221 removed outlier: 3.676A pdb=" N GLN B 247 " --> pdb=" O THR B 238 " (cutoff:3.500A) removed outlier: 7.181A pdb=" N ASN B 240 " --> pdb=" O VAL B 245 " (cutoff:3.500A) removed outlier: 6.420A pdb=" N VAL B 245 " --> pdb=" O ASN B 240 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'C' and resid 25 through 29 removed outlier: 3.527A pdb=" N GLU C 130 " --> pdb=" O LYS C 48 " (cutoff:3.500A) removed outlier: 7.185A pdb=" N ILE C 50 " --> pdb=" O VAL C 128 " (cutoff:3.500A) removed outlier: 5.415A pdb=" N VAL C 128 " --> pdb=" O ILE C 50 " (cutoff:3.500A) removed outlier: 7.325A pdb=" N LEU C 52 " --> pdb=" O ILE C 126 " (cutoff:3.500A) removed outlier: 5.484A pdb=" N ILE C 126 " --> pdb=" O LEU C 52 " (cutoff:3.500A) removed outlier: 7.264A pdb=" N LYS C 54 " --> pdb=" O ILE C 124 " (cutoff:3.500A) removed outlier: 5.349A pdb=" N ILE C 124 " --> pdb=" O LYS C 54 " (cutoff:3.500A) removed outlier: 6.431A pdb=" N LEU C 71 " --> pdb=" O ILE C 122 " (cutoff:3.500A) removed outlier: 7.870A pdb=" N ILE C 124 " --> pdb=" O LEU C 71 " (cutoff:3.500A) removed outlier: 6.601A pdb=" N ASN C 73 " --> pdb=" O ILE C 124 " (cutoff:3.500A) removed outlier: 8.156A pdb=" N ILE C 126 " --> pdb=" O ASN C 73 " (cutoff:3.500A) removed outlier: 6.718A pdb=" N SER C 75 " --> pdb=" O ILE C 126 " (cutoff:3.500A) removed outlier: 7.984A pdb=" N VAL C 128 " --> pdb=" O SER C 75 " (cutoff:3.500A) removed outlier: 7.051A pdb=" N ASN C 77 " --> pdb=" O VAL C 128 " (cutoff:3.500A) removed outlier: 8.161A pdb=" N GLU C 130 " --> pdb=" O ASN C 77 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'C' and resid 169 through 172 removed outlier: 4.224A pdb=" N SER C 183 " --> pdb=" O LEU C 165 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N LEU C 198 " --> pdb=" O GLY C 188 " (cutoff:3.500A) removed outlier: 6.680A pdb=" N VAL C 190 " --> pdb=" O LEU C 196 " (cutoff:3.500A) removed outlier: 6.847A pdb=" N LEU C 196 " --> pdb=" O VAL C 190 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'D' and resid 52 through 56 removed outlier: 3.689A pdb=" N GLY D 76 " --> pdb=" O ILE D 91 " (cutoff:3.500A) removed outlier: 6.387A pdb=" N TYR D 131 " --> pdb=" O ALA D 215 " (cutoff:3.500A) removed outlier: 7.951A pdb=" N ILE D 217 " --> pdb=" O TYR D 131 " (cutoff:3.500A) removed outlier: 6.431A pdb=" N VAL D 133 " --> pdb=" O ILE D 217 " (cutoff:3.500A) removed outlier: 7.950A pdb=" N VAL D 219 " --> pdb=" O VAL D 133 " (cutoff:3.500A) removed outlier: 6.837A pdb=" N GLU D 135 " --> pdb=" O VAL D 219 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'D' and resid 176 through 178 removed outlier: 3.518A pdb=" N VAL D 176 " --> pdb=" O LEU D 188 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'D' and resid 242 through 244 Processing sheet with id= I, first strand: chain 'D' and resid 246 through 248 Processing sheet with id= J, first strand: chain 'D' and resid 328 through 332 removed outlier: 4.637A pdb=" N SER D 345 " --> pdb=" O ILE D 299 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N GLN D 359 " --> pdb=" O LEU D 350 " (cutoff:3.500A) removed outlier: 6.549A pdb=" N ALA D 352 " --> pdb=" O TYR D 357 " (cutoff:3.500A) removed outlier: 5.956A pdb=" N TYR D 357 " --> pdb=" O ALA D 352 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'E' and resid 3 through 7 removed outlier: 6.880A pdb=" N ILE E 27 " --> pdb=" O ILE E 94 " (cutoff:3.500A) removed outlier: 5.327A pdb=" N ILE E 94 " --> pdb=" O ILE E 27 " (cutoff:3.500A) removed outlier: 7.504A pdb=" N SER E 29 " --> pdb=" O CYS E 92 " (cutoff:3.500A) removed outlier: 5.665A pdb=" N CYS E 92 " --> pdb=" O SER E 29 " (cutoff:3.500A) removed outlier: 7.681A pdb=" N THR E 31 " --> pdb=" O ILE E 90 " (cutoff:3.500A) removed outlier: 5.617A pdb=" N ILE E 90 " --> pdb=" O THR E 31 " (cutoff:3.500A) removed outlier: 6.643A pdb=" N ALA E 47 " --> pdb=" O CYS E 88 " (cutoff:3.500A) removed outlier: 7.813A pdb=" N ILE E 90 " --> pdb=" O ALA E 47 " (cutoff:3.500A) removed outlier: 6.201A pdb=" N GLU E 49 " --> pdb=" O ILE E 90 " (cutoff:3.500A) removed outlier: 7.810A pdb=" N CYS E 92 " --> pdb=" O GLU E 49 " (cutoff:3.500A) removed outlier: 6.510A pdb=" N ILE E 51 " --> pdb=" O CYS E 92 " (cutoff:3.500A) removed outlier: 7.866A pdb=" N ILE E 94 " --> pdb=" O ILE E 51 " (cutoff:3.500A) removed outlier: 6.948A pdb=" N ARG E 53 " --> pdb=" O ILE E 94 " (cutoff:3.500A) removed outlier: 7.993A pdb=" N GLU E 96 " --> pdb=" O ARG E 53 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'E' and resid 145 through 147 removed outlier: 3.799A pdb=" N SER E 159 " --> pdb=" O ILE E 138 " (cutoff:3.500A) removed outlier: 6.957A pdb=" N GLU E 166 " --> pdb=" O VAL E 177 " (cutoff:3.500A) removed outlier: 6.333A pdb=" N VAL E 177 " --> pdb=" O GLU E 166 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'F' and resid 34 through 38 removed outlier: 3.567A pdb=" N GLY F 46 " --> pdb=" O ILE F 62 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N SER F 132 " --> pdb=" O GLU F 57 " (cutoff:3.500A) removed outlier: 7.200A pdb=" N ILE F 59 " --> pdb=" O VAL F 130 " (cutoff:3.500A) removed outlier: 5.389A pdb=" N VAL F 130 " --> pdb=" O ILE F 59 " (cutoff:3.500A) removed outlier: 7.464A pdb=" N SER F 61 " --> pdb=" O VAL F 128 " (cutoff:3.500A) removed outlier: 5.690A pdb=" N VAL F 128 " --> pdb=" O SER F 61 " (cutoff:3.500A) removed outlier: 7.602A pdb=" N LYS F 63 " --> pdb=" O VAL F 126 " (cutoff:3.500A) removed outlier: 5.316A pdb=" N VAL F 126 " --> pdb=" O LYS F 63 " (cutoff:3.500A) removed outlier: 7.167A pdb=" N LYS F 65 " --> pdb=" O ILE F 124 " (cutoff:3.500A) removed outlier: 5.488A pdb=" N ILE F 124 " --> pdb=" O LYS F 65 " (cutoff:3.500A) removed outlier: 6.273A pdb=" N VAL F 67 " --> pdb=" O PHE F 122 " (cutoff:3.500A) removed outlier: 5.420A pdb=" N PHE F 122 " --> pdb=" O VAL F 67 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'F' and resid 153 through 155 Processing sheet with id= O, first strand: chain 'F' and resid 196 through 199 Processing sheet with id= P, first strand: chain 'F' and resid 216 through 218 removed outlier: 4.463A pdb=" N SER F 216 " --> pdb=" O THR F 223 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'G' and resid 45 through 50 removed outlier: 3.533A pdb=" N GLY G 58 " --> pdb=" O VAL G 77 " (cutoff:3.500A) removed outlier: 7.474A pdb=" N ILE G 74 " --> pdb=" O LEU G 141 " (cutoff:3.500A) removed outlier: 5.435A pdb=" N LEU G 141 " --> pdb=" O ILE G 74 " (cutoff:3.500A) removed outlier: 7.343A pdb=" N ALA G 76 " --> pdb=" O VAL G 139 " (cutoff:3.500A) removed outlier: 5.477A pdb=" N VAL G 139 " --> pdb=" O ALA G 76 " (cutoff:3.500A) removed outlier: 7.191A pdb=" N TYR G 78 " --> pdb=" O ILE G 137 " (cutoff:3.500A) removed outlier: 5.385A pdb=" N ILE G 137 " --> pdb=" O TYR G 78 " (cutoff:3.500A) removed outlier: 6.414A pdb=" N THR G 92 " --> pdb=" O ILE G 135 " (cutoff:3.500A) removed outlier: 7.865A pdb=" N ILE G 137 " --> pdb=" O THR G 92 " (cutoff:3.500A) removed outlier: 6.526A pdb=" N SER G 94 " --> pdb=" O ILE G 137 " (cutoff:3.500A) removed outlier: 8.042A pdb=" N VAL G 139 " --> pdb=" O SER G 94 " (cutoff:3.500A) removed outlier: 6.707A pdb=" N GLN G 96 " --> pdb=" O VAL G 139 " (cutoff:3.500A) removed outlier: 7.882A pdb=" N LEU G 141 " --> pdb=" O GLN G 96 " (cutoff:3.500A) removed outlier: 7.637A pdb=" N LYS G 98 " --> pdb=" O LEU G 141 " (cutoff:3.500A) removed outlier: 8.321A pdb=" N TYR G 143 " --> pdb=" O LYS G 98 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'G' and resid 192 through 196 removed outlier: 3.832A pdb=" N GLY G 212 " --> pdb=" O SER G 202 " (cutoff:3.500A) removed outlier: 6.448A pdb=" N ILE G 204 " --> pdb=" O ILE G 210 " (cutoff:3.500A) removed outlier: 5.486A pdb=" N ILE G 210 " --> pdb=" O ILE G 204 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'H' and resid 3 through 5 removed outlier: 3.849A pdb=" N THR H 3 " --> pdb=" O LEU H 42 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'H' and resid 25 through 27 Processing sheet with id= U, first strand: chain 'H' and resid 148 through 150 removed outlier: 4.623A pdb=" N LEU H 118 " --> pdb=" O LEU H 150 " (cutoff:3.500A) removed outlier: 6.520A pdb=" N LYS H 85 " --> pdb=" O ILE H 77 " (cutoff:3.500A) removed outlier: 5.187A pdb=" N THR H 79 " --> pdb=" O SER H 83 " (cutoff:3.500A) removed outlier: 7.092A pdb=" N SER H 83 " --> pdb=" O THR H 79 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'H' and resid 154 through 157 removed outlier: 3.519A pdb=" N LYS H 193 " --> pdb=" O GLY H 189 " (cutoff:3.500A) Processing sheet with id= W, first strand: chain 'H' and resid 122 through 125 removed outlier: 6.729A pdb=" N GLU H 133 " --> pdb=" O CYS H 124 " (cutoff:3.500A) Processing sheet with id= X, first strand: chain 'I' and resid 73 through 76 Processing sheet with id= Y, first strand: chain 'I' and resid 86 through 91 Processing sheet with id= Z, first strand: chain 'I' and resid 134 through 137 removed outlier: 6.084A pdb=" N ASP I 127 " --> pdb=" O ILE I 116 " (cutoff:3.500A) removed outlier: 5.868A pdb=" N ILE I 116 " --> pdb=" O ASP I 127 " (cutoff:3.500A) removed outlier: 6.792A pdb=" N SER I 183 " --> pdb=" O GLN I 174 " (cutoff:3.500A) Processing sheet with id= AA, first strand: chain 'I' and resid 197 through 201 removed outlier: 3.569A pdb=" N ILE I 221 " --> pdb=" O LEU I 217 " (cutoff:3.500A) Processing sheet with id= AB, first strand: chain 'J' and resid 34 through 37 removed outlier: 4.058A pdb=" N ASN J 105 " --> pdb=" O GLU J 69 " (cutoff:3.500A) Processing sheet with id= AC, first strand: chain 'J' and resid 41 through 48 removed outlier: 3.705A pdb=" N ALA J 55 " --> pdb=" O ILE J 44 " (cutoff:3.500A) Processing sheet with id= AD, first strand: chain 'J' and resid 233 through 236 removed outlier: 6.795A pdb=" N TYR J 244 " --> pdb=" O LEU J 235 " (cutoff:3.500A) removed outlier: 7.243A pdb=" N ARG J 202 " --> pdb=" O TYR J 243 " (cutoff:3.500A) removed outlier: 7.794A pdb=" N LEU J 245 " --> pdb=" O ARG J 202 " (cutoff:3.500A) removed outlier: 6.369A pdb=" N ILE J 204 " --> pdb=" O LEU J 245 " (cutoff:3.500A) removed outlier: 6.712A pdb=" N LEU J 140 " --> pdb=" O LEU J 156 " (cutoff:3.500A) removed outlier: 5.152A pdb=" N VAL J 158 " --> pdb=" O ILE J 138 " (cutoff:3.500A) removed outlier: 7.300A pdb=" N ILE J 138 " --> pdb=" O VAL J 158 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N PHE J 256 " --> pdb=" O ILE J 229 " (cutoff:3.500A) removed outlier: 6.413A pdb=" N ARG J 231 " --> pdb=" O VAL J 254 " (cutoff:3.500A) removed outlier: 5.772A pdb=" N VAL J 254 " --> pdb=" O ARG J 231 " (cutoff:3.500A) Processing sheet with id= AE, first strand: chain 'J' and resid 267 through 271 removed outlier: 6.588A pdb=" N MET J 274 " --> pdb=" O THR J 270 " (cutoff:3.500A) Processing sheet with id= AF, first strand: chain 'K' and resid 18 through 27 Processing sheet with id= AG, first strand: chain 'K' and resid 86 through 89 removed outlier: 6.647A pdb=" N ASN K 191 " --> pdb=" O TYR K 87 " (cutoff:3.500A) removed outlier: 7.755A pdb=" N VAL K 89 " --> pdb=" O ASN K 191 " (cutoff:3.500A) removed outlier: 6.457A pdb=" N VAL K 193 " --> pdb=" O VAL K 89 " (cutoff:3.500A) removed outlier: 6.586A pdb=" N ILE K 214 " --> pdb=" O LEU K 194 " (cutoff:3.500A) No H-bonds generated for sheet with id= AG Processing sheet with id= AH, first strand: chain 'K' and resid 110 through 114 removed outlier: 6.669A pdb=" N ARG K 144 " --> pdb=" O VAL K 111 " (cutoff:3.500A) removed outlier: 7.805A pdb=" N VAL K 113 " --> pdb=" O ARG K 144 " (cutoff:3.500A) removed outlier: 6.481A pdb=" N ILE K 146 " --> pdb=" O VAL K 113 " (cutoff:3.500A) No H-bonds generated for sheet with id= AH Processing sheet with id= AI, first strand: chain 'K' and resid 274 through 277 Processing sheet with id= AJ, first strand: chain 'K' and resid 287 through 290 Processing sheet with id= AK, first strand: chain 'K' and resid 451 through 455 removed outlier: 6.965A pdb=" N LEU K 464 " --> pdb=" O ASP K 454 " (cutoff:3.500A) removed outlier: 4.595A pdb=" N ARG K 437 " --> pdb=" O GLY K 465 " (cutoff:3.500A) removed outlier: 5.419A pdb=" N PHE K 467 " --> pdb=" O ARG K 437 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N VAL K 434 " --> pdb=" O VAL K 424 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N GLY K 472 " --> pdb=" O ARG K 448 " (cutoff:3.500A) removed outlier: 6.696A pdb=" N VAL K 450 " --> pdb=" O ASP K 470 " (cutoff:3.500A) removed outlier: 5.715A pdb=" N ASP K 470 " --> pdb=" O VAL K 450 " (cutoff:3.500A) Processing sheet with id= AL, first strand: chain 'K' and resid 540 through 542 removed outlier: 6.771A pdb=" N GLU K 650 " --> pdb=" O SER K 541 " (cutoff:3.500A) No H-bonds generated for sheet with id= AL Processing sheet with id= AM, first strand: chain 'K' and resid 552 through 558 removed outlier: 3.919A pdb=" N HIS K 555 " --> pdb=" O GLY K 567 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N GLY K 567 " --> pdb=" O HIS K 555 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N LYS K 557 " --> pdb=" O GLU K 565 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N ILE K 646 " --> pdb=" O ARG K 621 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N ALA K 623 " --> pdb=" O SER K 644 " (cutoff:3.500A) Processing sheet with id= AN, first strand: chain 'K' and resid 751 through 754 Processing sheet with id= AO, first strand: chain 'K' and resid 936 through 940 removed outlier: 3.873A pdb=" N LYS K 920 " --> pdb=" O VAL K 927 " (cutoff:3.500A) removed outlier: 6.379A pdb=" N LEU K 929 " --> pdb=" O VAL K 918 " (cutoff:3.500A) removed outlier: 5.055A pdb=" N VAL K 918 " --> pdb=" O LEU K 929 " (cutoff:3.500A) Processing sheet with id= AP, first strand: chain 'K' and resid 952 through 954 Processing sheet with id= AQ, first strand: chain 'K' and resid 981 through 983 removed outlier: 3.508A pdb=" N GLN K 982 " --> pdb=" O LEU K 999 " (cutoff:3.500A) Processing sheet with id= AR, first strand: chain 'K' and resid 315 through 317 removed outlier: 6.614A pdb=" N ILE K 317 " --> pdb=" O ILE K 395 " (cutoff:3.500A) removed outlier: 6.008A pdb=" N ILE K 395 " --> pdb=" O ILE K 317 " (cutoff:3.500A) Processing sheet with id= AS, first strand: chain 'M' and resid 303 through 306 removed outlier: 6.444A pdb=" N ILE M 496 " --> pdb=" O HIS M 304 " (cutoff:3.500A) removed outlier: 7.506A pdb=" N VAL M 306 " --> pdb=" O ILE M 496 " (cutoff:3.500A) removed outlier: 6.012A pdb=" N VAL M 498 " --> pdb=" O VAL M 306 " (cutoff:3.500A) removed outlier: 7.215A pdb=" N SER M 346 " --> pdb=" O TYR M 497 " (cutoff:3.500A) removed outlier: 8.178A pdb=" N ILE M 499 " --> pdb=" O SER M 346 " (cutoff:3.500A) removed outlier: 6.423A pdb=" N PHE M 348 " --> pdb=" O ILE M 499 " (cutoff:3.500A) removed outlier: 7.425A pdb=" N LYS M 374 " --> pdb=" O GLU M 439 " (cutoff:3.500A) removed outlier: 6.104A pdb=" N VAL M 441 " --> pdb=" O LYS M 374 " (cutoff:3.500A) removed outlier: 6.672A pdb=" N ILE M 376 " --> pdb=" O VAL M 441 " (cutoff:3.500A) removed outlier: 5.642A pdb=" N PHE M 443 " --> pdb=" O ILE M 376 " (cutoff:3.500A) removed outlier: 6.941A pdb=" N THR M 378 " --> pdb=" O PHE M 443 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N SER M 379 " --> pdb=" O MET M 419 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N THR M 420 " --> pdb=" O ILE M 404 " (cutoff:3.500A) Processing sheet with id= AT, first strand: chain 'M' and resid 692 through 695 removed outlier: 6.592A pdb=" N VAL M 718 " --> pdb=" O ALA M 693 " (cutoff:3.500A) removed outlier: 8.082A pdb=" N HIS M 695 " --> pdb=" O VAL M 718 " (cutoff:3.500A) removed outlier: 6.597A pdb=" N PHE M 720 " --> pdb=" O HIS M 695 " (cutoff:3.500A) removed outlier: 6.802A pdb=" N MET M 629 " --> pdb=" O LEU M 719 " (cutoff:3.500A) removed outlier: 7.644A pdb=" N ALA M 721 " --> pdb=" O MET M 629 " (cutoff:3.500A) removed outlier: 6.037A pdb=" N VAL M 631 " --> pdb=" O ALA M 721 " (cutoff:3.500A) removed outlier: 6.541A pdb=" N THR M 735 " --> pdb=" O VAL M 630 " (cutoff:3.500A) removed outlier: 7.829A pdb=" N PHE M 632 " --> pdb=" O THR M 735 " (cutoff:3.500A) removed outlier: 7.152A pdb=" N ILE M 737 " --> pdb=" O PHE M 632 " (cutoff:3.500A) removed outlier: 8.949A pdb=" N VAL M 736 " --> pdb=" O THR M 772 " (cutoff:3.500A) removed outlier: 6.782A pdb=" N THR M 774 " --> pdb=" O VAL M 736 " (cutoff:3.500A) removed outlier: 8.295A pdb=" N PHE M 738 " --> pdb=" O THR M 774 " (cutoff:3.500A) removed outlier: 6.962A pdb=" N ILE M 776 " --> pdb=" O PHE M 738 " (cutoff:3.500A) removed outlier: 8.033A pdb=" N VAL M 775 " --> pdb=" O PRO M 507 " (cutoff:3.500A) removed outlier: 6.552A pdb=" N GLU M 509 " --> pdb=" O VAL M 775 " (cutoff:3.500A) removed outlier: 7.836A pdb=" N VAL M 777 " --> pdb=" O GLU M 509 " (cutoff:3.500A) removed outlier: 6.807A pdb=" N ASN M 511 " --> pdb=" O VAL M 777 " (cutoff:3.500A) removed outlier: 6.501A pdb=" N ILE M 512 " --> pdb=" O PRO M 520 " (cutoff:3.500A) Processing sheet with id= AU, first strand: chain 'M' and resid 742 through 744 1089 hydrogen bonds defined for protein. 2856 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 12.93 Time building geometry restraints manager: 12.11 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 9654 1.34 - 1.45: 3928 1.45 - 1.57: 17432 1.57 - 1.69: 73 1.69 - 1.81: 234 Bond restraints: 31321 Sorted by residual: bond pdb=" C1' ATP M1101 " pdb=" C2' ATP M1101 " ideal model delta sigma weight residual 1.531 1.304 0.227 1.20e-02 6.94e+03 3.57e+02 bond pdb=" C1' ATP M1101 " pdb=" O4' ATP M1101 " ideal model delta sigma weight residual 1.416 1.620 -0.204 1.30e-02 5.92e+03 2.47e+02 bond pdb=" C4' ATP M1101 " pdb=" O4' ATP M1101 " ideal model delta sigma weight residual 1.444 1.272 0.172 1.10e-02 8.26e+03 2.44e+02 bond pdb=" C6 ATP M1101 " pdb=" N6 ATP M1101 " ideal model delta sigma weight residual 1.337 1.450 -0.113 1.10e-02 8.26e+03 1.06e+02 bond pdb=" C2' ATP M1101 " pdb=" O2' ATP M1101 " ideal model delta sigma weight residual 1.423 1.508 -0.085 1.30e-02 5.92e+03 4.23e+01 ... (remaining 31316 not shown) Histogram of bond angle deviations from ideal: 99.74 - 106.71: 969 106.71 - 113.69: 17788 113.69 - 120.66: 12527 120.66 - 127.64: 11072 127.64 - 134.61: 218 Bond angle restraints: 42574 Sorted by residual: angle pdb=" PB ATP M1101 " pdb=" O3B ATP M1101 " pdb=" PG ATP M1101 " ideal model delta sigma weight residual 139.87 124.42 15.45 1.00e+00 1.00e+00 2.39e+02 angle pdb=" PA ATP M1101 " pdb=" O3A ATP M1101 " pdb=" PB ATP M1101 " ideal model delta sigma weight residual 136.83 124.03 12.80 1.00e+00 1.00e+00 1.64e+02 angle pdb=" C5 ATP M1101 " pdb=" C4 ATP M1101 " pdb=" N3 ATP M1101 " ideal model delta sigma weight residual 126.80 119.26 7.54 1.00e+00 1.00e+00 5.69e+01 angle pdb=" N1 ATP M1101 " pdb=" C2 ATP M1101 " pdb=" N3 ATP M1101 " ideal model delta sigma weight residual 128.69 121.26 7.43 1.00e+00 1.00e+00 5.53e+01 angle pdb=" N3 ATP M1101 " pdb=" C4 ATP M1101 " pdb=" N9 ATP M1101 " ideal model delta sigma weight residual 127.04 134.61 -7.57 1.15e+00 7.59e-01 4.35e+01 ... (remaining 42569 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.71: 18814 33.71 - 67.42: 361 67.42 - 101.14: 31 101.14 - 134.85: 0 134.85 - 168.56: 1 Dihedral angle restraints: 19207 sinusoidal: 7833 harmonic: 11374 Sorted by residual: dihedral pdb=" O4' U N 10 " pdb=" C1' U N 10 " pdb=" N1 U N 10 " pdb=" C2 U N 10 " ideal model delta sinusoidal sigma weight residual 232.00 63.44 168.56 1 1.70e+01 3.46e-03 6.58e+01 dihedral pdb=" CA ARG B 182 " pdb=" C ARG B 182 " pdb=" N GLU B 183 " pdb=" CA GLU B 183 " ideal model delta harmonic sigma weight residual 180.00 156.77 23.23 0 5.00e+00 4.00e-02 2.16e+01 dihedral pdb=" CA PHE K 842 " pdb=" C PHE K 842 " pdb=" N THR K 843 " pdb=" CA THR K 843 " ideal model delta harmonic sigma weight residual -180.00 -158.83 -21.17 0 5.00e+00 4.00e-02 1.79e+01 ... (remaining 19204 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.061: 4324 0.061 - 0.121: 673 0.121 - 0.182: 29 0.182 - 0.243: 0 0.243 - 0.304: 1 Chirality restraints: 5027 Sorted by residual: chirality pdb=" C2' ATP M1101 " pdb=" C1' ATP M1101 " pdb=" C3' ATP M1101 " pdb=" O2' ATP M1101 " both_signs ideal model delta sigma weight residual False -2.68 -2.38 -0.30 2.00e-01 2.50e+01 2.30e+00 chirality pdb=" CA ASP K 189 " pdb=" N ASP K 189 " pdb=" C ASP K 189 " pdb=" CB ASP K 189 " both_signs ideal model delta sigma weight residual False 2.51 2.34 0.17 2.00e-01 2.50e+01 6.93e-01 chirality pdb=" CA ARG E 85 " pdb=" N ARG E 85 " pdb=" C ARG E 85 " pdb=" CB ARG E 85 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.16 2.00e-01 2.50e+01 6.54e-01 ... (remaining 5024 not shown) Planarity restraints: 5384 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLU M 895 " 0.037 5.00e-02 4.00e+02 5.68e-02 5.16e+00 pdb=" N PRO M 896 " -0.098 5.00e-02 4.00e+02 pdb=" CA PRO M 896 " 0.029 5.00e-02 4.00e+02 pdb=" CD PRO M 896 " 0.032 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TYR K 826 " -0.032 5.00e-02 4.00e+02 4.84e-02 3.74e+00 pdb=" N PRO K 827 " 0.084 5.00e-02 4.00e+02 pdb=" CA PRO K 827 " -0.025 5.00e-02 4.00e+02 pdb=" CD PRO K 827 " -0.027 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TRP M 614 " -0.027 5.00e-02 4.00e+02 4.08e-02 2.66e+00 pdb=" N PRO M 615 " 0.071 5.00e-02 4.00e+02 pdb=" CA PRO M 615 " -0.020 5.00e-02 4.00e+02 pdb=" CD PRO M 615 " -0.023 5.00e-02 4.00e+02 ... (remaining 5381 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.76: 3726 2.76 - 3.29: 27425 3.29 - 3.83: 47778 3.83 - 4.36: 57178 4.36 - 4.90: 99611 Nonbonded interactions: 235718 Sorted by model distance: nonbonded pdb=" NH2 ARG I 123 " pdb=" O2' U N 8 " model vdw 2.221 2.520 nonbonded pdb=" OE1 GLN K 275 " pdb=" NE2 GLN K 315 " model vdw 2.226 2.520 nonbonded pdb=" OD1 ASP D 51 " pdb=" NH2 ARG D 391 " model vdw 2.242 2.520 nonbonded pdb=" OE2 GLU K 120 " pdb=" ND2 ASN K 170 " model vdw 2.250 2.520 nonbonded pdb=" O ARG K 309 " pdb=" NH2 ARG K 398 " model vdw 2.262 2.520 ... (remaining 235713 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== 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=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.170 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: 0.040 Extract box with map and model: 11.630 Check model and map are aligned: 0.470 Set scattering table: 0.310 Process input model: 79.790 Find NCS groups from input model: 1.230 Set up NCS constraints: 0.120 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:12.440 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 109.210 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8774 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 : 0.003 0.227 31321 Z= 0.238 Angle : 0.497 15.447 42574 Z= 0.285 Chirality : 0.043 0.304 5027 Planarity : 0.004 0.057 5384 Dihedral : 13.523 168.559 11817 Min Nonbonded Distance : 2.221 Molprobity Statistics. All-atom Clashscore : 2.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.36 % Favored : 96.64 % Rotamer: Outliers : 0.00 % Allowed : 0.12 % Favored : 99.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.59 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.71 (0.13), residues: 3838 helix: 1.89 (0.16), residues: 1210 sheet: 0.93 (0.18), residues: 795 loop : -0.72 (0.14), residues: 1833 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP F 217 HIS 0.005 0.001 HIS K 888 PHE 0.021 0.001 PHE F 122 TYR 0.013 0.001 TYR C 157 ARG 0.005 0.000 ARG D 138 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7676 Ramachandran restraints generated. 3838 Oldfield, 0 Emsley, 3838 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7676 Ramachandran restraints generated. 3838 Oldfield, 0 Emsley, 3838 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 367 residues out of total 3449 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 367 time to evaluate : 3.730 Fit side-chains REVERT: C 237 GLN cc_start: 0.7583 (tp40) cc_final: 0.7311 (tp40) REVERT: D 28 GLU cc_start: 0.8083 (mp0) cc_final: 0.7835 (mp0) REVERT: F 72 GLU cc_start: 0.7916 (mm-30) cc_final: 0.7699 (mm-30) REVERT: G 164 GLN cc_start: 0.7266 (pm20) cc_final: 0.6835 (tp40) REVERT: K 386 ILE cc_start: 0.6414 (mp) cc_final: 0.6208 (pt) REVERT: K 413 ASP cc_start: 0.5987 (t0) cc_final: 0.5654 (t0) REVERT: K 705 MET cc_start: 0.4075 (tpt) cc_final: 0.2621 (tmt) REVERT: K 869 LEU cc_start: 0.7567 (tp) cc_final: 0.7057 (pt) REVERT: K 905 GLN cc_start: 0.6538 (tp40) cc_final: 0.5994 (tm-30) REVERT: M 306 VAL cc_start: 0.7311 (p) cc_final: 0.7048 (m) REVERT: M 790 LYS cc_start: 0.6962 (mtmm) cc_final: 0.6707 (mtmm) REVERT: M 965 MET cc_start: 0.8027 (mtm) cc_final: 0.7728 (mtp) REVERT: M 1023 ARG cc_start: 0.7678 (mmm160) cc_final: 0.7336 (mtp-110) outliers start: 0 outliers final: 0 residues processed: 367 average time/residue: 1.6830 time to fit residues: 703.6782 Evaluate side-chains 263 residues out of total 3449 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 263 time to evaluate : 2.501 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 387 random chunks: chunk 326 optimal weight: 2.9990 chunk 293 optimal weight: 3.9990 chunk 162 optimal weight: 0.9980 chunk 100 optimal weight: 4.9990 chunk 197 optimal weight: 2.9990 chunk 156 optimal weight: 0.9980 chunk 303 optimal weight: 9.9990 chunk 117 optimal weight: 7.9990 chunk 184 optimal weight: 6.9990 chunk 225 optimal weight: 10.0000 chunk 351 optimal weight: 10.0000 overall best weight: 2.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 66 GLN D 56 ASN E 200 GLN F 115 GLN H 114 GLN J 105 ASN ** K 275 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 315 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 184 ASN ** M 387 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8792 moved from start: 0.0753 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 31321 Z= 0.220 Angle : 0.539 7.646 42574 Z= 0.290 Chirality : 0.045 0.172 5027 Planarity : 0.005 0.055 5384 Dihedral : 8.927 168.024 4702 Min Nonbonded Distance : 2.219 Molprobity Statistics. All-atom Clashscore : 2.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.54 % Favored : 96.46 % Rotamer: Outliers : 1.22 % Allowed : 6.44 % Favored : 92.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.59 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.56 (0.13), residues: 3838 helix: 1.70 (0.15), residues: 1215 sheet: 0.96 (0.18), residues: 798 loop : -0.83 (0.13), residues: 1825 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP G 214 HIS 0.011 0.001 HIS K 888 PHE 0.018 0.001 PHE M 977 TYR 0.015 0.001 TYR C 157 ARG 0.005 0.000 ARG K 806 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7676 Ramachandran restraints generated. 3838 Oldfield, 0 Emsley, 3838 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7676 Ramachandran restraints generated. 3838 Oldfield, 0 Emsley, 3838 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 318 residues out of total 3449 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 278 time to evaluate : 3.392 Fit side-chains REVERT: B 147 PHE cc_start: 0.8746 (OUTLIER) cc_final: 0.8349 (m-10) REVERT: D 20 GLU cc_start: 0.8321 (OUTLIER) cc_final: 0.7909 (mp0) REVERT: D 28 GLU cc_start: 0.8110 (mp0) cc_final: 0.7839 (mp0) REVERT: G 164 GLN cc_start: 0.7238 (pm20) cc_final: 0.6800 (tp40) REVERT: I 317 GLN cc_start: 0.8085 (OUTLIER) cc_final: 0.7451 (tm-30) REVERT: I 327 MET cc_start: 0.9307 (mmt) cc_final: 0.9073 (mmt) REVERT: J 45 GLN cc_start: 0.7333 (mm110) cc_final: 0.6902 (mm110) REVERT: J 54 GLU cc_start: 0.7491 (mm-30) cc_final: 0.7013 (tp30) REVERT: J 192 GLN cc_start: 0.8438 (OUTLIER) cc_final: 0.8196 (mt0) REVERT: K 413 ASP cc_start: 0.6032 (t0) cc_final: 0.5698 (t0) REVERT: K 563 ASN cc_start: 0.4382 (OUTLIER) cc_final: 0.3895 (t0) REVERT: K 575 HIS cc_start: 0.5904 (t-90) cc_final: 0.5691 (t-90) REVERT: K 672 MET cc_start: 0.4290 (OUTLIER) cc_final: 0.4066 (mpm) REVERT: K 705 MET cc_start: 0.4094 (tpt) cc_final: 0.2640 (tmt) REVERT: K 905 GLN cc_start: 0.6447 (tp40) cc_final: 0.5878 (tm-30) REVERT: M 790 LYS cc_start: 0.6876 (mtmm) cc_final: 0.6571 (mtmm) REVERT: M 824 GLU cc_start: 0.7258 (OUTLIER) cc_final: 0.6582 (mp0) REVERT: M 965 MET cc_start: 0.8078 (mtm) cc_final: 0.7810 (mtp) REVERT: M 1023 ARG cc_start: 0.7525 (mmm160) cc_final: 0.7126 (mtp-110) outliers start: 40 outliers final: 11 residues processed: 296 average time/residue: 1.8488 time to fit residues: 626.0288 Evaluate side-chains 281 residues out of total 3449 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 263 time to evaluate : 3.478 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 147 PHE Chi-restraints excluded: chain B residue 284 LYS Chi-restraints excluded: chain C residue 42 MET Chi-restraints excluded: chain C residue 232 LEU Chi-restraints excluded: chain D residue 20 GLU Chi-restraints excluded: chain D residue 55 GLU Chi-restraints excluded: chain D residue 273 GLU Chi-restraints excluded: chain E residue 144 ASP Chi-restraints excluded: chain I residue 317 GLN Chi-restraints excluded: chain J residue 192 GLN Chi-restraints excluded: chain J residue 214 ASP Chi-restraints excluded: chain K residue 300 LEU Chi-restraints excluded: chain K residue 563 ASN Chi-restraints excluded: chain K residue 672 MET Chi-restraints excluded: chain K residue 703 VAL Chi-restraints excluded: chain L residue 198 THR Chi-restraints excluded: chain M residue 451 ASP Chi-restraints excluded: chain M residue 824 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 387 random chunks: chunk 195 optimal weight: 0.9980 chunk 109 optimal weight: 5.9990 chunk 292 optimal weight: 8.9990 chunk 239 optimal weight: 6.9990 chunk 96 optimal weight: 0.4980 chunk 352 optimal weight: 3.9990 chunk 380 optimal weight: 2.9990 chunk 313 optimal weight: 9.9990 chunk 349 optimal weight: 2.9990 chunk 120 optimal weight: 0.0980 chunk 282 optimal weight: 4.9990 overall best weight: 1.5184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 66 GLN B 242 ASN D 56 ASN E 200 GLN H 114 GLN I 158 GLN J 105 ASN ** K 275 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 315 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 184 ASN ** M 387 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8774 moved from start: 0.0842 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 31321 Z= 0.161 Angle : 0.481 7.065 42574 Z= 0.259 Chirality : 0.043 0.174 5027 Planarity : 0.004 0.053 5384 Dihedral : 8.728 168.918 4702 Min Nonbonded Distance : 2.208 Molprobity Statistics. All-atom Clashscore : 2.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer: Outliers : 1.00 % Allowed : 8.51 % Favored : 90.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.59 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.63 (0.13), residues: 3838 helix: 1.71 (0.15), residues: 1219 sheet: 1.00 (0.18), residues: 817 loop : -0.78 (0.14), residues: 1802 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP G 214 HIS 0.010 0.001 HIS K 888 PHE 0.014 0.001 PHE F 122 TYR 0.013 0.001 TYR C 157 ARG 0.005 0.000 ARG K 675 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7676 Ramachandran restraints generated. 3838 Oldfield, 0 Emsley, 3838 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7676 Ramachandran restraints generated. 3838 Oldfield, 0 Emsley, 3838 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 307 residues out of total 3449 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 274 time to evaluate : 3.709 Fit side-chains REVERT: B 4 ASP cc_start: 0.7987 (m-30) cc_final: 0.7767 (m-30) REVERT: B 147 PHE cc_start: 0.8729 (OUTLIER) cc_final: 0.8337 (m-10) REVERT: D 20 GLU cc_start: 0.8282 (OUTLIER) cc_final: 0.7896 (mp0) REVERT: D 28 GLU cc_start: 0.8129 (mp0) cc_final: 0.7819 (mp0) REVERT: F 197 MET cc_start: 0.8917 (OUTLIER) cc_final: 0.8704 (mmm) REVERT: G 164 GLN cc_start: 0.7202 (pm20) cc_final: 0.6788 (tp40) REVERT: I 278 TRP cc_start: 0.7105 (OUTLIER) cc_final: 0.6818 (t60) REVERT: I 327 MET cc_start: 0.9328 (mmt) cc_final: 0.9059 (mmt) REVERT: J 45 GLN cc_start: 0.7327 (mm110) cc_final: 0.6853 (mm110) REVERT: J 54 GLU cc_start: 0.7554 (mm-30) cc_final: 0.6976 (tp30) REVERT: K 413 ASP cc_start: 0.6053 (t0) cc_final: 0.5704 (t0) REVERT: K 575 HIS cc_start: 0.5872 (t-90) cc_final: 0.5648 (t-90) REVERT: K 687 LYS cc_start: 0.6039 (tmmt) cc_final: 0.5830 (mtpp) REVERT: K 705 MET cc_start: 0.3966 (tpt) cc_final: 0.2541 (tmt) REVERT: K 905 GLN cc_start: 0.6507 (tp40) cc_final: 0.5944 (tm-30) REVERT: K 938 LEU cc_start: 0.3203 (tm) cc_final: 0.2821 (tp) REVERT: M 541 ASN cc_start: 0.6302 (t0) cc_final: 0.5790 (m110) REVERT: M 621 LEU cc_start: 0.8210 (mp) cc_final: 0.7958 (mp) REVERT: M 790 LYS cc_start: 0.6904 (mtmm) cc_final: 0.6570 (mttp) REVERT: M 824 GLU cc_start: 0.7155 (OUTLIER) cc_final: 0.6503 (mp0) REVERT: M 965 MET cc_start: 0.8075 (mtm) cc_final: 0.7796 (mtp) outliers start: 33 outliers final: 8 residues processed: 291 average time/residue: 1.8117 time to fit residues: 605.5373 Evaluate side-chains 276 residues out of total 3449 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 263 time to evaluate : 3.525 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 147 PHE Chi-restraints excluded: chain D residue 20 GLU Chi-restraints excluded: chain D residue 216 LYS Chi-restraints excluded: chain D residue 273 GLU Chi-restraints excluded: chain E residue 144 ASP Chi-restraints excluded: chain F residue 197 MET Chi-restraints excluded: chain I residue 278 TRP Chi-restraints excluded: chain K residue 296 SER Chi-restraints excluded: chain K residue 300 LEU Chi-restraints excluded: chain K residue 703 VAL Chi-restraints excluded: chain L residue 198 THR Chi-restraints excluded: chain M residue 306 VAL Chi-restraints excluded: chain M residue 824 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 387 random chunks: chunk 347 optimal weight: 7.9990 chunk 264 optimal weight: 7.9990 chunk 182 optimal weight: 9.9990 chunk 38 optimal weight: 5.9990 chunk 168 optimal weight: 5.9990 chunk 236 optimal weight: 10.0000 chunk 353 optimal weight: 0.2980 chunk 374 optimal weight: 4.9990 chunk 184 optimal weight: 3.9990 chunk 334 optimal weight: 1.9990 chunk 100 optimal weight: 1.9990 overall best weight: 2.6588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 66 GLN E 200 GLN F 73 ASN H 114 GLN I 158 GLN J 105 ASN ** K 275 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 315 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 387 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 400 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8801 moved from start: 0.0995 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 31321 Z= 0.232 Angle : 0.539 8.701 42574 Z= 0.289 Chirality : 0.045 0.180 5027 Planarity : 0.004 0.052 5384 Dihedral : 8.780 167.473 4702 Min Nonbonded Distance : 2.199 Molprobity Statistics. All-atom Clashscore : 2.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.88 % Favored : 96.12 % Rotamer: Outliers : 1.40 % Allowed : 9.18 % Favored : 89.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.59 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.49 (0.13), residues: 3838 helix: 1.59 (0.15), residues: 1219 sheet: 0.90 (0.18), residues: 812 loop : -0.85 (0.13), residues: 1807 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP G 214 HIS 0.009 0.001 HIS K 888 PHE 0.018 0.002 PHE D 227 TYR 0.016 0.002 TYR K 181 ARG 0.005 0.000 ARG K 806 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7676 Ramachandran restraints generated. 3838 Oldfield, 0 Emsley, 3838 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7676 Ramachandran restraints generated. 3838 Oldfield, 0 Emsley, 3838 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 312 residues out of total 3449 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 266 time to evaluate : 3.680 Fit side-chains revert: symmetry clash REVERT: B 147 PHE cc_start: 0.8787 (OUTLIER) cc_final: 0.8384 (m-10) REVERT: C 65 MET cc_start: 0.8616 (tmm) cc_final: 0.8220 (tmm) REVERT: D 28 GLU cc_start: 0.8160 (mp0) cc_final: 0.7864 (mp0) REVERT: G 164 GLN cc_start: 0.7240 (pm20) cc_final: 0.6835 (tp40) REVERT: I 156 GLU cc_start: 0.7613 (tt0) cc_final: 0.7371 (tt0) REVERT: I 278 TRP cc_start: 0.7118 (OUTLIER) cc_final: 0.6853 (t60) REVERT: I 317 GLN cc_start: 0.8102 (OUTLIER) cc_final: 0.7447 (tm-30) REVERT: I 327 MET cc_start: 0.9327 (mmt) cc_final: 0.9117 (mmt) REVERT: J 160 ASP cc_start: 0.7838 (p0) cc_final: 0.7589 (p0) REVERT: J 192 GLN cc_start: 0.8459 (OUTLIER) cc_final: 0.8187 (mt0) REVERT: K 413 ASP cc_start: 0.6102 (t0) cc_final: 0.5736 (t0) REVERT: K 563 ASN cc_start: 0.4490 (OUTLIER) cc_final: 0.3938 (t0) REVERT: K 575 HIS cc_start: 0.5852 (t-90) cc_final: 0.5617 (t-90) REVERT: K 705 MET cc_start: 0.4005 (tpt) cc_final: 0.2558 (tmt) REVERT: M 370 ARG cc_start: 0.7186 (OUTLIER) cc_final: 0.6428 (ttm170) REVERT: M 790 LYS cc_start: 0.6970 (mtmm) cc_final: 0.6615 (mttp) REVERT: M 824 GLU cc_start: 0.7125 (OUTLIER) cc_final: 0.6526 (mp0) REVERT: M 983 MET cc_start: 0.7288 (OUTLIER) cc_final: 0.6771 (ptt) outliers start: 46 outliers final: 17 residues processed: 292 average time/residue: 1.7582 time to fit residues: 591.2480 Evaluate side-chains 280 residues out of total 3449 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 255 time to evaluate : 3.452 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 147 PHE Chi-restraints excluded: chain C residue 232 LEU Chi-restraints excluded: chain D residue 20 GLU Chi-restraints excluded: chain D residue 55 GLU Chi-restraints excluded: chain D residue 216 LYS Chi-restraints excluded: chain D residue 273 GLU Chi-restraints excluded: chain E residue 144 ASP Chi-restraints excluded: chain F residue 257 ASP Chi-restraints excluded: chain H residue 20 LYS Chi-restraints excluded: chain I residue 278 TRP Chi-restraints excluded: chain I residue 317 GLN Chi-restraints excluded: chain J residue 192 GLN Chi-restraints excluded: chain J residue 214 ASP Chi-restraints excluded: chain K residue 296 SER Chi-restraints excluded: chain K residue 300 LEU Chi-restraints excluded: chain K residue 323 GLN Chi-restraints excluded: chain K residue 563 ASN Chi-restraints excluded: chain K residue 903 VAL Chi-restraints excluded: chain L residue 198 THR Chi-restraints excluded: chain M residue 306 VAL Chi-restraints excluded: chain M residue 370 ARG Chi-restraints excluded: chain M residue 451 ASP Chi-restraints excluded: chain M residue 753 THR Chi-restraints excluded: chain M residue 824 GLU Chi-restraints excluded: chain M residue 983 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 387 random chunks: chunk 311 optimal weight: 9.9990 chunk 212 optimal weight: 0.0870 chunk 5 optimal weight: 3.9990 chunk 278 optimal weight: 20.0000 chunk 154 optimal weight: 3.9990 chunk 319 optimal weight: 20.0000 chunk 258 optimal weight: 5.9990 chunk 0 optimal weight: 10.0000 chunk 191 optimal weight: 2.9990 chunk 335 optimal weight: 5.9990 chunk 94 optimal weight: 3.9990 overall best weight: 3.0166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 66 GLN E 200 GLN H 114 GLN I 158 GLN J 105 ASN ** K 275 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 315 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 184 ASN ** M 387 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 400 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8810 moved from start: 0.1091 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 31321 Z= 0.258 Angle : 0.561 8.141 42574 Z= 0.301 Chirality : 0.046 0.182 5027 Planarity : 0.005 0.054 5384 Dihedral : 8.844 165.875 4702 Min Nonbonded Distance : 2.193 Molprobity Statistics. All-atom Clashscore : 2.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.91 % Favored : 96.09 % Rotamer: Outliers : 1.46 % Allowed : 10.06 % Favored : 88.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.59 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.40 (0.13), residues: 3838 helix: 1.53 (0.15), residues: 1215 sheet: 0.82 (0.18), residues: 823 loop : -0.90 (0.13), residues: 1800 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP G 214 HIS 0.008 0.001 HIS K 888 PHE 0.019 0.002 PHE D 227 TYR 0.017 0.002 TYR K 181 ARG 0.006 0.000 ARG K 806 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7676 Ramachandran restraints generated. 3838 Oldfield, 0 Emsley, 3838 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7676 Ramachandran restraints generated. 3838 Oldfield, 0 Emsley, 3838 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 308 residues out of total 3449 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 260 time to evaluate : 3.701 Fit side-chains REVERT: B 147 PHE cc_start: 0.8821 (OUTLIER) cc_final: 0.8432 (m-10) REVERT: C 65 MET cc_start: 0.8639 (tmm) cc_final: 0.8220 (tmm) REVERT: D 28 GLU cc_start: 0.8166 (mp0) cc_final: 0.7841 (mp0) REVERT: G 164 GLN cc_start: 0.7246 (pm20) cc_final: 0.6833 (tp40) REVERT: I 156 GLU cc_start: 0.7591 (tt0) cc_final: 0.7333 (tt0) REVERT: I 278 TRP cc_start: 0.7067 (OUTLIER) cc_final: 0.6751 (t60) REVERT: I 317 GLN cc_start: 0.8099 (OUTLIER) cc_final: 0.7445 (tm-30) REVERT: J 45 GLN cc_start: 0.7494 (mm110) cc_final: 0.6957 (mm110) REVERT: J 160 ASP cc_start: 0.7864 (p0) cc_final: 0.7659 (p0) REVERT: J 192 GLN cc_start: 0.8491 (OUTLIER) cc_final: 0.8230 (mt0) REVERT: K 413 ASP cc_start: 0.6132 (t0) cc_final: 0.5766 (t0) REVERT: K 563 ASN cc_start: 0.4477 (OUTLIER) cc_final: 0.3921 (t0) REVERT: K 575 HIS cc_start: 0.5837 (t-90) cc_final: 0.5598 (t-90) REVERT: K 705 MET cc_start: 0.3983 (tpt) cc_final: 0.2537 (tmt) REVERT: M 790 LYS cc_start: 0.7020 (mtmm) cc_final: 0.6645 (mttp) REVERT: M 824 GLU cc_start: 0.7146 (OUTLIER) cc_final: 0.6552 (mp0) REVERT: M 983 MET cc_start: 0.7252 (OUTLIER) cc_final: 0.6747 (ptt) REVERT: M 1023 ARG cc_start: 0.7594 (mmm160) cc_final: 0.7129 (mtp-110) outliers start: 48 outliers final: 21 residues processed: 287 average time/residue: 1.8622 time to fit residues: 624.9380 Evaluate side-chains 280 residues out of total 3449 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 252 time to evaluate : 3.522 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 147 PHE Chi-restraints excluded: chain C residue 232 LEU Chi-restraints excluded: chain D residue 20 GLU Chi-restraints excluded: chain D residue 55 GLU Chi-restraints excluded: chain D residue 216 LYS Chi-restraints excluded: chain D residue 273 GLU Chi-restraints excluded: chain E residue 144 ASP Chi-restraints excluded: chain F residue 182 ILE Chi-restraints excluded: chain F residue 223 THR Chi-restraints excluded: chain F residue 257 ASP Chi-restraints excluded: chain H residue 20 LYS Chi-restraints excluded: chain I residue 187 ARG Chi-restraints excluded: chain I residue 278 TRP Chi-restraints excluded: chain I residue 317 GLN Chi-restraints excluded: chain J residue 192 GLN Chi-restraints excluded: chain J residue 214 ASP Chi-restraints excluded: chain K residue 296 SER Chi-restraints excluded: chain K residue 300 LEU Chi-restraints excluded: chain K residue 323 GLN Chi-restraints excluded: chain K residue 563 ASN Chi-restraints excluded: chain K residue 805 VAL Chi-restraints excluded: chain K residue 903 VAL Chi-restraints excluded: chain L residue 198 THR Chi-restraints excluded: chain M residue 306 VAL Chi-restraints excluded: chain M residue 451 ASP Chi-restraints excluded: chain M residue 753 THR Chi-restraints excluded: chain M residue 824 GLU Chi-restraints excluded: chain M residue 983 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 387 random chunks: chunk 125 optimal weight: 8.9990 chunk 336 optimal weight: 0.0770 chunk 73 optimal weight: 3.9990 chunk 219 optimal weight: 3.9990 chunk 92 optimal weight: 5.9990 chunk 374 optimal weight: 3.9990 chunk 310 optimal weight: 9.9990 chunk 173 optimal weight: 5.9990 chunk 31 optimal weight: 4.9990 chunk 123 optimal weight: 10.0000 chunk 196 optimal weight: 5.9990 overall best weight: 3.4146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 66 GLN E 200 GLN H 114 GLN I 158 GLN J 105 ASN ** K 275 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 315 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 184 ASN ** M 387 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8818 moved from start: 0.1194 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 31321 Z= 0.286 Angle : 0.587 11.768 42574 Z= 0.313 Chirality : 0.047 0.214 5027 Planarity : 0.005 0.055 5384 Dihedral : 8.920 164.420 4702 Min Nonbonded Distance : 2.182 Molprobity Statistics. All-atom Clashscore : 3.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.09 % Favored : 95.91 % Rotamer: Outliers : 1.70 % Allowed : 10.76 % Favored : 87.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.59 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.33 (0.13), residues: 3838 helix: 1.46 (0.15), residues: 1215 sheet: 0.85 (0.18), residues: 813 loop : -0.96 (0.13), residues: 1810 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP G 214 HIS 0.008 0.001 HIS K 888 PHE 0.019 0.002 PHE D 227 TYR 0.016 0.002 TYR C 157 ARG 0.012 0.000 ARG K 493 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7676 Ramachandran restraints generated. 3838 Oldfield, 0 Emsley, 3838 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7676 Ramachandran restraints generated. 3838 Oldfield, 0 Emsley, 3838 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 318 residues out of total 3449 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 262 time to evaluate : 3.837 Fit side-chains revert: symmetry clash REVERT: B 4 ASP cc_start: 0.8108 (m-30) cc_final: 0.7870 (m-30) REVERT: B 109 GLU cc_start: 0.8940 (OUTLIER) cc_final: 0.8621 (tt0) REVERT: B 147 PHE cc_start: 0.8825 (OUTLIER) cc_final: 0.8425 (m-10) REVERT: C 65 MET cc_start: 0.8601 (tmm) cc_final: 0.8161 (tmm) REVERT: D 28 GLU cc_start: 0.8171 (mp0) cc_final: 0.7832 (mp0) REVERT: G 164 GLN cc_start: 0.7262 (pm20) cc_final: 0.6827 (tp40) REVERT: I 156 GLU cc_start: 0.7669 (tt0) cc_final: 0.7454 (tt0) REVERT: I 278 TRP cc_start: 0.7099 (OUTLIER) cc_final: 0.6776 (t60) REVERT: I 317 GLN cc_start: 0.8104 (OUTLIER) cc_final: 0.7450 (tm-30) REVERT: J 192 GLN cc_start: 0.8500 (OUTLIER) cc_final: 0.8244 (mt0) REVERT: K 413 ASP cc_start: 0.6153 (t0) cc_final: 0.5796 (t0) REVERT: K 563 ASN cc_start: 0.4451 (OUTLIER) cc_final: 0.3861 (t0) REVERT: K 575 HIS cc_start: 0.5904 (t-90) cc_final: 0.5671 (t-90) REVERT: K 672 MET cc_start: 0.4407 (OUTLIER) cc_final: 0.4206 (mpm) REVERT: K 705 MET cc_start: 0.3965 (tpt) cc_final: 0.2520 (tmt) REVERT: M 790 LYS cc_start: 0.7031 (mtmm) cc_final: 0.6640 (mtmm) REVERT: M 824 GLU cc_start: 0.7145 (OUTLIER) cc_final: 0.6556 (mp0) REVERT: M 983 MET cc_start: 0.7239 (OUTLIER) cc_final: 0.6713 (ptt) outliers start: 56 outliers final: 25 residues processed: 296 average time/residue: 1.7604 time to fit residues: 599.1777 Evaluate side-chains 289 residues out of total 3449 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 255 time to evaluate : 3.551 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 109 GLU Chi-restraints excluded: chain B residue 147 PHE Chi-restraints excluded: chain C residue 232 LEU Chi-restraints excluded: chain D residue 20 GLU Chi-restraints excluded: chain D residue 55 GLU Chi-restraints excluded: chain D residue 216 LYS Chi-restraints excluded: chain D residue 273 GLU Chi-restraints excluded: chain E residue 144 ASP Chi-restraints excluded: chain E residue 197 LEU Chi-restraints excluded: chain F residue 182 ILE Chi-restraints excluded: chain F residue 223 THR Chi-restraints excluded: chain F residue 257 ASP Chi-restraints excluded: chain G residue 197 ASN Chi-restraints excluded: chain H residue 20 LYS Chi-restraints excluded: chain I residue 187 ARG Chi-restraints excluded: chain I residue 278 TRP Chi-restraints excluded: chain I residue 317 GLN Chi-restraints excluded: chain J residue 45 GLN Chi-restraints excluded: chain J residue 192 GLN Chi-restraints excluded: chain J residue 214 ASP Chi-restraints excluded: chain K residue 296 SER Chi-restraints excluded: chain K residue 300 LEU Chi-restraints excluded: chain K residue 323 GLN Chi-restraints excluded: chain K residue 563 ASN Chi-restraints excluded: chain K residue 672 MET Chi-restraints excluded: chain K residue 805 VAL Chi-restraints excluded: chain K residue 903 VAL Chi-restraints excluded: chain L residue 198 THR Chi-restraints excluded: chain M residue 306 VAL Chi-restraints excluded: chain M residue 451 ASP Chi-restraints excluded: chain M residue 506 VAL Chi-restraints excluded: chain M residue 753 THR Chi-restraints excluded: chain M residue 824 GLU Chi-restraints excluded: chain M residue 983 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 387 random chunks: chunk 361 optimal weight: 20.0000 chunk 42 optimal weight: 4.9990 chunk 213 optimal weight: 7.9990 chunk 273 optimal weight: 9.9990 chunk 211 optimal weight: 9.9990 chunk 315 optimal weight: 0.9990 chunk 209 optimal weight: 3.9990 chunk 373 optimal weight: 5.9990 chunk 233 optimal weight: 4.9990 chunk 227 optimal weight: 5.9990 chunk 172 optimal weight: 2.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 66 GLN E 200 GLN H 114 GLN I 158 GLN J 105 ASN ** K 275 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 315 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 184 ASN ** M 387 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 400 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8821 moved from start: 0.1263 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.067 31321 Z= 0.299 Angle : 0.599 10.555 42574 Z= 0.320 Chirality : 0.047 0.186 5027 Planarity : 0.005 0.055 5384 Dihedral : 8.969 162.981 4702 Min Nonbonded Distance : 2.174 Molprobity Statistics. All-atom Clashscore : 3.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.06 % Favored : 95.94 % Rotamer: Outliers : 1.64 % Allowed : 11.37 % Favored : 86.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.59 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.26 (0.13), residues: 3838 helix: 1.41 (0.15), residues: 1213 sheet: 0.83 (0.18), residues: 819 loop : -1.02 (0.13), residues: 1806 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP G 214 HIS 0.007 0.001 HIS K 888 PHE 0.020 0.002 PHE D 227 TYR 0.016 0.002 TYR C 157 ARG 0.011 0.000 ARG K 493 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7676 Ramachandran restraints generated. 3838 Oldfield, 0 Emsley, 3838 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7676 Ramachandran restraints generated. 3838 Oldfield, 0 Emsley, 3838 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 310 residues out of total 3449 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 256 time to evaluate : 3.608 Fit side-chains REVERT: B 4 ASP cc_start: 0.8139 (m-30) cc_final: 0.7916 (m-30) REVERT: B 109 GLU cc_start: 0.8939 (OUTLIER) cc_final: 0.8615 (tt0) REVERT: B 147 PHE cc_start: 0.8831 (OUTLIER) cc_final: 0.8447 (m-10) REVERT: C 65 MET cc_start: 0.8609 (tmm) cc_final: 0.8136 (tmm) REVERT: D 28 GLU cc_start: 0.8208 (mp0) cc_final: 0.7841 (mp0) REVERT: G 164 GLN cc_start: 0.7264 (pm20) cc_final: 0.6827 (tp40) REVERT: I 156 GLU cc_start: 0.7670 (tt0) cc_final: 0.7446 (tt0) REVERT: I 278 TRP cc_start: 0.7141 (OUTLIER) cc_final: 0.6680 (t60) REVERT: I 317 GLN cc_start: 0.8107 (OUTLIER) cc_final: 0.7447 (tm-30) REVERT: J 192 GLN cc_start: 0.8507 (OUTLIER) cc_final: 0.8252 (mt0) REVERT: K 413 ASP cc_start: 0.6171 (t0) cc_final: 0.5798 (t0) REVERT: K 563 ASN cc_start: 0.4353 (OUTLIER) cc_final: 0.3749 (t0) REVERT: K 575 HIS cc_start: 0.5908 (t-90) cc_final: 0.5678 (t-90) REVERT: K 672 MET cc_start: 0.4331 (OUTLIER) cc_final: 0.4116 (mpm) REVERT: K 705 MET cc_start: 0.3912 (tpt) cc_final: 0.2514 (tmt) REVERT: K 808 MET cc_start: 0.6455 (tpt) cc_final: 0.5849 (tmm) REVERT: M 790 LYS cc_start: 0.7029 (mtmm) cc_final: 0.6705 (mttp) REVERT: M 824 GLU cc_start: 0.7168 (OUTLIER) cc_final: 0.6586 (mp0) outliers start: 54 outliers final: 31 residues processed: 292 average time/residue: 1.6965 time to fit residues: 572.9462 Evaluate side-chains 291 residues out of total 3449 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 252 time to evaluate : 3.729 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 109 GLU Chi-restraints excluded: chain B residue 147 PHE Chi-restraints excluded: chain C residue 232 LEU Chi-restraints excluded: chain D residue 20 GLU Chi-restraints excluded: chain D residue 55 GLU Chi-restraints excluded: chain D residue 216 LYS Chi-restraints excluded: chain D residue 273 GLU Chi-restraints excluded: chain E residue 144 ASP Chi-restraints excluded: chain E residue 197 LEU Chi-restraints excluded: chain E residue 206 VAL Chi-restraints excluded: chain F residue 109 VAL Chi-restraints excluded: chain F residue 182 ILE Chi-restraints excluded: chain F residue 223 THR Chi-restraints excluded: chain F residue 257 ASP Chi-restraints excluded: chain G residue 88 THR Chi-restraints excluded: chain G residue 197 ASN Chi-restraints excluded: chain H residue 20 LYS Chi-restraints excluded: chain I residue 187 ARG Chi-restraints excluded: chain I residue 278 TRP Chi-restraints excluded: chain I residue 317 GLN Chi-restraints excluded: chain J residue 192 GLN Chi-restraints excluded: chain J residue 214 ASP Chi-restraints excluded: chain K residue 296 SER Chi-restraints excluded: chain K residue 300 LEU Chi-restraints excluded: chain K residue 323 GLN Chi-restraints excluded: chain K residue 563 ASN Chi-restraints excluded: chain K residue 592 THR Chi-restraints excluded: chain K residue 672 MET Chi-restraints excluded: chain K residue 805 VAL Chi-restraints excluded: chain K residue 903 VAL Chi-restraints excluded: chain L residue 198 THR Chi-restraints excluded: chain M residue 306 VAL Chi-restraints excluded: chain M residue 451 ASP Chi-restraints excluded: chain M residue 506 VAL Chi-restraints excluded: chain M residue 741 ILE Chi-restraints excluded: chain M residue 753 THR Chi-restraints excluded: chain M residue 784 LEU Chi-restraints excluded: chain M residue 824 GLU Chi-restraints excluded: chain M residue 983 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 387 random chunks: chunk 230 optimal weight: 7.9990 chunk 148 optimal weight: 3.9990 chunk 222 optimal weight: 4.9990 chunk 112 optimal weight: 4.9990 chunk 73 optimal weight: 0.0070 chunk 72 optimal weight: 1.9990 chunk 237 optimal weight: 10.0000 chunk 254 optimal weight: 0.4980 chunk 184 optimal weight: 1.9990 chunk 34 optimal weight: 1.9990 chunk 293 optimal weight: 5.9990 overall best weight: 1.3004 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 66 GLN E 200 GLN H 114 GLN I 158 GLN J 105 ASN ** K 275 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 315 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 831 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 184 ASN ** M 387 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8775 moved from start: 0.1188 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 31321 Z= 0.152 Angle : 0.485 10.741 42574 Z= 0.258 Chirality : 0.043 0.164 5027 Planarity : 0.004 0.056 5384 Dihedral : 8.696 167.060 4702 Min Nonbonded Distance : 2.176 Molprobity Statistics. All-atom Clashscore : 2.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.20 % Favored : 96.80 % Rotamer: Outliers : 1.03 % Allowed : 12.16 % Favored : 86.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.59 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.51 (0.13), residues: 3838 helix: 1.65 (0.16), residues: 1209 sheet: 0.90 (0.18), residues: 841 loop : -0.88 (0.14), residues: 1788 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP G 214 HIS 0.007 0.001 HIS K 888 PHE 0.012 0.001 PHE F 122 TYR 0.012 0.001 TYR C 157 ARG 0.011 0.000 ARG K 493 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7676 Ramachandran restraints generated. 3838 Oldfield, 0 Emsley, 3838 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7676 Ramachandran restraints generated. 3838 Oldfield, 0 Emsley, 3838 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 297 residues out of total 3449 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 263 time to evaluate : 3.775 Fit side-chains REVERT: B 4 ASP cc_start: 0.7977 (m-30) cc_final: 0.7713 (m-30) REVERT: B 147 PHE cc_start: 0.8709 (OUTLIER) cc_final: 0.8322 (m-10) REVERT: C 65 MET cc_start: 0.8580 (tmm) cc_final: 0.8135 (tmm) REVERT: D 20 GLU cc_start: 0.8301 (OUTLIER) cc_final: 0.7896 (mp0) REVERT: D 28 GLU cc_start: 0.8147 (mp0) cc_final: 0.7822 (mp0) REVERT: G 164 GLN cc_start: 0.7256 (pm20) cc_final: 0.6799 (tp40) REVERT: I 278 TRP cc_start: 0.7126 (OUTLIER) cc_final: 0.6781 (t60) REVERT: I 317 GLN cc_start: 0.8065 (OUTLIER) cc_final: 0.7410 (tm-30) REVERT: J 45 GLN cc_start: 0.7263 (mm-40) cc_final: 0.6878 (mm-40) REVERT: J 192 GLN cc_start: 0.8456 (OUTLIER) cc_final: 0.8176 (mt0) REVERT: K 413 ASP cc_start: 0.6144 (t0) cc_final: 0.5779 (t0) REVERT: K 563 ASN cc_start: 0.4374 (OUTLIER) cc_final: 0.3790 (t0) REVERT: K 672 MET cc_start: 0.4416 (OUTLIER) cc_final: 0.4211 (mpm) REVERT: K 705 MET cc_start: 0.3884 (tpt) cc_final: 0.2456 (tmt) REVERT: K 808 MET cc_start: 0.6514 (tpt) cc_final: 0.5934 (tmm) REVERT: M 541 ASN cc_start: 0.6274 (t0) cc_final: 0.5739 (m110) REVERT: M 621 LEU cc_start: 0.8249 (mp) cc_final: 0.7986 (mp) REVERT: M 790 LYS cc_start: 0.7022 (mtmm) cc_final: 0.6641 (mttm) REVERT: M 824 GLU cc_start: 0.7174 (OUTLIER) cc_final: 0.6559 (mp0) outliers start: 34 outliers final: 16 residues processed: 284 average time/residue: 1.7657 time to fit residues: 576.5851 Evaluate side-chains 277 residues out of total 3449 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 253 time to evaluate : 3.552 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 147 PHE Chi-restraints excluded: chain D residue 20 GLU Chi-restraints excluded: chain D residue 216 LYS Chi-restraints excluded: chain D residue 273 GLU Chi-restraints excluded: chain E residue 144 ASP Chi-restraints excluded: chain E residue 206 VAL Chi-restraints excluded: chain F residue 109 VAL Chi-restraints excluded: chain F residue 182 ILE Chi-restraints excluded: chain G residue 88 THR Chi-restraints excluded: chain G residue 197 ASN Chi-restraints excluded: chain I residue 278 TRP Chi-restraints excluded: chain I residue 317 GLN Chi-restraints excluded: chain J residue 192 GLN Chi-restraints excluded: chain J residue 214 ASP Chi-restraints excluded: chain K residue 296 SER Chi-restraints excluded: chain K residue 300 LEU Chi-restraints excluded: chain K residue 563 ASN Chi-restraints excluded: chain K residue 592 THR Chi-restraints excluded: chain K residue 672 MET Chi-restraints excluded: chain K residue 805 VAL Chi-restraints excluded: chain L residue 198 THR Chi-restraints excluded: chain M residue 306 VAL Chi-restraints excluded: chain M residue 784 LEU Chi-restraints excluded: chain M residue 824 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 387 random chunks: chunk 339 optimal weight: 0.5980 chunk 357 optimal weight: 0.9980 chunk 326 optimal weight: 7.9990 chunk 347 optimal weight: 8.9990 chunk 209 optimal weight: 9.9990 chunk 151 optimal weight: 2.9990 chunk 272 optimal weight: 5.9990 chunk 106 optimal weight: 0.9980 chunk 314 optimal weight: 8.9990 chunk 328 optimal weight: 0.6980 chunk 346 optimal weight: 9.9990 overall best weight: 1.2582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 66 GLN E 200 GLN I 158 GLN J 105 ASN ** K 275 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 315 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 831 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 387 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8772 moved from start: 0.1196 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 31321 Z= 0.149 Angle : 0.487 11.098 42574 Z= 0.256 Chirality : 0.043 0.167 5027 Planarity : 0.004 0.056 5384 Dihedral : 8.570 167.681 4702 Min Nonbonded Distance : 2.177 Molprobity Statistics. All-atom Clashscore : 2.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.44 % Favored : 96.56 % Rotamer: Outliers : 1.06 % Allowed : 12.37 % Favored : 86.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.59 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.61 (0.14), residues: 3838 helix: 1.69 (0.16), residues: 1216 sheet: 0.99 (0.18), residues: 836 loop : -0.80 (0.14), residues: 1786 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP F 217 HIS 0.007 0.001 HIS K 888 PHE 0.011 0.001 PHE F 122 TYR 0.016 0.001 TYR K 832 ARG 0.011 0.000 ARG K 493 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7676 Ramachandran restraints generated. 3838 Oldfield, 0 Emsley, 3838 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7676 Ramachandran restraints generated. 3838 Oldfield, 0 Emsley, 3838 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 300 residues out of total 3449 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 265 time to evaluate : 3.534 Fit side-chains REVERT: B 4 ASP cc_start: 0.7955 (m-30) cc_final: 0.7705 (m-30) REVERT: B 147 PHE cc_start: 0.8696 (OUTLIER) cc_final: 0.8307 (m-10) REVERT: C 65 MET cc_start: 0.8592 (tmm) cc_final: 0.8139 (tmm) REVERT: D 20 GLU cc_start: 0.8267 (OUTLIER) cc_final: 0.7859 (mp0) REVERT: D 28 GLU cc_start: 0.8170 (mp0) cc_final: 0.7820 (mp0) REVERT: G 164 GLN cc_start: 0.7259 (pm20) cc_final: 0.6804 (tp40) REVERT: I 278 TRP cc_start: 0.7120 (OUTLIER) cc_final: 0.6623 (t60) REVERT: I 317 GLN cc_start: 0.8063 (OUTLIER) cc_final: 0.7407 (tm-30) REVERT: J 192 GLN cc_start: 0.8449 (OUTLIER) cc_final: 0.8168 (mt0) REVERT: K 563 ASN cc_start: 0.4367 (OUTLIER) cc_final: 0.3783 (t0) REVERT: K 672 MET cc_start: 0.4419 (OUTLIER) cc_final: 0.4201 (mpm) REVERT: K 705 MET cc_start: 0.3917 (tpt) cc_final: 0.2472 (tmt) REVERT: K 808 MET cc_start: 0.6492 (tpt) cc_final: 0.5910 (tmm) REVERT: K 938 LEU cc_start: 0.3162 (tm) cc_final: 0.2666 (mt) REVERT: M 541 ASN cc_start: 0.6287 (t0) cc_final: 0.5752 (m110) REVERT: M 621 LEU cc_start: 0.8240 (mp) cc_final: 0.7982 (mp) REVERT: M 790 LYS cc_start: 0.7012 (mtmm) cc_final: 0.6774 (mttp) REVERT: M 983 MET cc_start: 0.6937 (OUTLIER) cc_final: 0.5896 (ptt) outliers start: 35 outliers final: 18 residues processed: 285 average time/residue: 1.7855 time to fit residues: 590.7148 Evaluate side-chains 280 residues out of total 3449 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 254 time to evaluate : 3.539 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 147 PHE Chi-restraints excluded: chain C residue 232 LEU Chi-restraints excluded: chain D residue 20 GLU Chi-restraints excluded: chain D residue 176 VAL Chi-restraints excluded: chain D residue 216 LYS Chi-restraints excluded: chain D residue 273 GLU Chi-restraints excluded: chain E residue 206 VAL Chi-restraints excluded: chain F residue 109 VAL Chi-restraints excluded: chain F residue 182 ILE Chi-restraints excluded: chain G residue 88 THR Chi-restraints excluded: chain I residue 278 TRP Chi-restraints excluded: chain I residue 317 GLN Chi-restraints excluded: chain J residue 192 GLN Chi-restraints excluded: chain J residue 214 ASP Chi-restraints excluded: chain K residue 296 SER Chi-restraints excluded: chain K residue 300 LEU Chi-restraints excluded: chain K residue 563 ASN Chi-restraints excluded: chain K residue 592 THR Chi-restraints excluded: chain K residue 672 MET Chi-restraints excluded: chain K residue 805 VAL Chi-restraints excluded: chain K residue 944 LEU Chi-restraints excluded: chain L residue 198 THR Chi-restraints excluded: chain M residue 306 VAL Chi-restraints excluded: chain M residue 784 LEU Chi-restraints excluded: chain M residue 824 GLU Chi-restraints excluded: chain M residue 983 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 387 random chunks: chunk 228 optimal weight: 0.0980 chunk 367 optimal weight: 0.9990 chunk 224 optimal weight: 2.9990 chunk 174 optimal weight: 10.0000 chunk 255 optimal weight: 7.9990 chunk 385 optimal weight: 30.0000 chunk 354 optimal weight: 10.0000 chunk 307 optimal weight: 3.9990 chunk 31 optimal weight: 0.5980 chunk 237 optimal weight: 10.0000 chunk 188 optimal weight: 10.0000 overall best weight: 1.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 66 GLN E 200 GLN I 158 GLN J 105 ASN ** K 275 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 315 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 831 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 184 ASN ** M 387 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8784 moved from start: 0.1196 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 31321 Z= 0.174 Angle : 0.505 11.284 42574 Z= 0.267 Chirality : 0.043 0.163 5027 Planarity : 0.004 0.055 5384 Dihedral : 8.570 167.074 4702 Min Nonbonded Distance : 2.119 Molprobity Statistics. All-atom Clashscore : 2.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.41 % Favored : 96.59 % Rotamer: Outliers : 0.91 % Allowed : 12.67 % Favored : 86.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.59 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.58 (0.14), residues: 3838 helix: 1.66 (0.15), residues: 1218 sheet: 0.98 (0.18), residues: 834 loop : -0.82 (0.14), residues: 1786 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP G 214 HIS 0.007 0.001 HIS K 888 PHE 0.050 0.001 PHE K 842 TYR 0.013 0.001 TYR C 157 ARG 0.011 0.000 ARG K 493 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7676 Ramachandran restraints generated. 3838 Oldfield, 0 Emsley, 3838 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7676 Ramachandran restraints generated. 3838 Oldfield, 0 Emsley, 3838 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 287 residues out of total 3449 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 257 time to evaluate : 3.762 Fit side-chains REVERT: B 4 ASP cc_start: 0.7960 (m-30) cc_final: 0.7705 (m-30) REVERT: B 147 PHE cc_start: 0.8720 (OUTLIER) cc_final: 0.8324 (m-10) REVERT: C 65 MET cc_start: 0.8589 (tmm) cc_final: 0.8126 (tmm) REVERT: D 20 GLU cc_start: 0.8290 (OUTLIER) cc_final: 0.7880 (mp0) REVERT: D 28 GLU cc_start: 0.8187 (mp0) cc_final: 0.7833 (mp0) REVERT: G 129 ARG cc_start: 0.8835 (mtp85) cc_final: 0.8579 (mmm160) REVERT: G 164 GLN cc_start: 0.7249 (pm20) cc_final: 0.6838 (tp40) REVERT: I 278 TRP cc_start: 0.7128 (OUTLIER) cc_final: 0.6629 (t60) REVERT: I 317 GLN cc_start: 0.8069 (OUTLIER) cc_final: 0.7418 (tm-30) REVERT: J 192 GLN cc_start: 0.8455 (OUTLIER) cc_final: 0.8183 (mt0) REVERT: K 493 ARG cc_start: 0.7384 (mtm110) cc_final: 0.6927 (ptp-110) REVERT: K 563 ASN cc_start: 0.4347 (OUTLIER) cc_final: 0.3769 (t0) REVERT: K 672 MET cc_start: 0.4415 (OUTLIER) cc_final: 0.4212 (mpm) REVERT: K 705 MET cc_start: 0.3961 (tpt) cc_final: 0.2512 (tmt) REVERT: K 808 MET cc_start: 0.6433 (tpt) cc_final: 0.5926 (tmm) REVERT: K 879 MET cc_start: 0.4640 (mmt) cc_final: 0.4384 (mtm) REVERT: K 938 LEU cc_start: 0.3154 (tm) cc_final: 0.2617 (mt) REVERT: M 541 ASN cc_start: 0.6296 (t0) cc_final: 0.5756 (m110) REVERT: M 790 LYS cc_start: 0.7025 (mtmm) cc_final: 0.6785 (mttp) REVERT: M 983 MET cc_start: 0.7001 (OUTLIER) cc_final: 0.5976 (ptt) outliers start: 30 outliers final: 18 residues processed: 277 average time/residue: 1.7682 time to fit residues: 564.9607 Evaluate side-chains 279 residues out of total 3449 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 253 time to evaluate : 3.999 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 147 PHE Chi-restraints excluded: chain C residue 232 LEU Chi-restraints excluded: chain D residue 20 GLU Chi-restraints excluded: chain D residue 176 VAL Chi-restraints excluded: chain D residue 216 LYS Chi-restraints excluded: chain D residue 273 GLU Chi-restraints excluded: chain E residue 206 VAL Chi-restraints excluded: chain F residue 109 VAL Chi-restraints excluded: chain F residue 182 ILE Chi-restraints excluded: chain G residue 88 THR Chi-restraints excluded: chain I residue 278 TRP Chi-restraints excluded: chain I residue 317 GLN Chi-restraints excluded: chain J residue 192 GLN Chi-restraints excluded: chain J residue 214 ASP Chi-restraints excluded: chain K residue 296 SER Chi-restraints excluded: chain K residue 300 LEU Chi-restraints excluded: chain K residue 563 ASN Chi-restraints excluded: chain K residue 592 THR Chi-restraints excluded: chain K residue 672 MET Chi-restraints excluded: chain K residue 805 VAL Chi-restraints excluded: chain K residue 944 LEU Chi-restraints excluded: chain L residue 198 THR Chi-restraints excluded: chain M residue 306 VAL Chi-restraints excluded: chain M residue 784 LEU Chi-restraints excluded: chain M residue 824 GLU Chi-restraints excluded: chain M residue 983 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 387 random chunks: chunk 243 optimal weight: 3.9990 chunk 327 optimal weight: 2.9990 chunk 94 optimal weight: 2.9990 chunk 283 optimal weight: 6.9990 chunk 45 optimal weight: 0.0770 chunk 85 optimal weight: 2.9990 chunk 307 optimal weight: 1.9990 chunk 128 optimal weight: 2.9990 chunk 315 optimal weight: 4.9990 chunk 38 optimal weight: 0.8980 chunk 56 optimal weight: 0.1980 overall best weight: 1.2342 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 66 GLN E 200 GLN I 158 GLN J 105 ASN ** K 275 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 315 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 831 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 184 ASN ** M 387 GLN ** 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 = 0.3956 r_free = 0.3956 target = 0.162822 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.109308 restraints weight = 36225.524| |-----------------------------------------------------------------------------| r_work (start): 0.3222 rms_B_bonded: 1.90 r_work: 0.3029 rms_B_bonded: 2.11 restraints_weight: 0.5000 r_work: 0.2923 rms_B_bonded: 3.35 restraints_weight: 0.2500 r_work (final): 0.2923 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8794 moved from start: 0.1224 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 31321 Z= 0.146 Angle : 0.480 12.140 42574 Z= 0.253 Chirality : 0.043 0.161 5027 Planarity : 0.004 0.056 5384 Dihedral : 8.469 168.258 4702 Min Nonbonded Distance : 2.178 Molprobity Statistics. All-atom Clashscore : 2.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % Rotamer: Outliers : 0.94 % Allowed : 12.77 % Favored : 86.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.59 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.66 (0.14), residues: 3838 helix: 1.74 (0.16), residues: 1216 sheet: 1.02 (0.18), residues: 836 loop : -0.77 (0.14), residues: 1786 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP F 217 HIS 0.011 0.001 HIS K 888 PHE 0.055 0.001 PHE K 842 TYR 0.015 0.001 TYR K 832 ARG 0.011 0.000 ARG K 493 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10577.46 seconds wall clock time: 203 minutes 4.84 seconds (12184.84 seconds total)