Starting phenix.real_space_refine on Wed Aug 7 20:18:53 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mjo_23880/08_2024/7mjo_23880_neut.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mjo_23880/08_2024/7mjo_23880.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mjo_23880/08_2024/7mjo_23880.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mjo_23880/08_2024/7mjo_23880.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mjo_23880/08_2024/7mjo_23880_neut.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mjo_23880/08_2024/7mjo_23880_neut.cif" } resolution = 4.0 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 ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 1.000 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians K 2 8.98 5 P 28 5.49 5 S 76 5.16 5 Cl 1 4.86 5 C 12656 2.51 5 N 3556 2.21 5 O 3658 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 226": "NH1" <-> "NH2" Residue "A ARG 274": "NH1" <-> "NH2" Residue "A GLU 301": "OE1" <-> "OE2" Residue "A ARG 347": "NH1" <-> "NH2" Residue "B ARG 187": "NH1" <-> "NH2" Residue "B ARG 226": "NH1" <-> "NH2" Residue "B GLU 239": "OE1" <-> "OE2" Residue "B ARG 274": "NH1" <-> "NH2" Residue "B ARG 310": "NH1" <-> "NH2" Residue "B ARG 347": "NH1" <-> "NH2" Residue "B ARG 352": "NH1" <-> "NH2" Residue "C ARG 70": "NH1" <-> "NH2" Residue "C ARG 187": "NH1" <-> "NH2" Residue "C ARG 216": "NH1" <-> "NH2" Residue "C ARG 226": "NH1" <-> "NH2" Residue "C ARG 274": "NH1" <-> "NH2" Residue "C ARG 347": "NH1" <-> "NH2" Residue "C ARG 352": "NH1" <-> "NH2" Residue "D ARG 51": "NH1" <-> "NH2" Residue "D ARG 70": "NH1" <-> "NH2" Residue "D ARG 187": "NH1" <-> "NH2" Residue "D ARG 216": "NH1" <-> "NH2" Residue "D ARG 226": "NH1" <-> "NH2" Residue "D ARG 310": "NH1" <-> "NH2" Residue "D ARG 347": "NH1" <-> "NH2" Residue "D ARG 352": "NH1" <-> "NH2" Residue "E ARG 97": "NH1" <-> "NH2" Residue "E ARG 166": "NH1" <-> "NH2" Residue "E ARG 189": "NH1" <-> "NH2" Residue "E ARG 304": "NH1" <-> "NH2" Residue "E ARG 776": "NH1" <-> "NH2" Residue "E ARG 815": "NH1" <-> "NH2" Residue "E ARG 1091": "NH1" <-> "NH2" Residue "E ARG 1112": "NH1" <-> "NH2" Residue "E ARG 1316": "NH1" <-> "NH2" Residue "E ARG 1382": "NH1" <-> "NH2" Residue "E ARG 1450": "NH1" <-> "NH2" Residue "G ARG 97": "NH1" <-> "NH2" Residue "G ARG 189": "NH1" <-> "NH2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/chem_data/mon_lib" Total number of atoms: 19977 Number of models: 1 Model: "" Number of chains: 13 Chain: "A" Number of atoms: 2448 Number of conformers: 1 Conformer: "" Number of residues, atoms: 345, 2448 Classifications: {'peptide': 345} Incomplete info: {'truncation_to_alanine': 89} Link IDs: {'PTRANS': 11, 'TRANS': 333} Unresolved non-hydrogen bonds: 278 Unresolved non-hydrogen angles: 346 Unresolved non-hydrogen dihedrals: 212 Unresolved non-hydrogen chiralities: 35 Planarities with less than four sites: {'GLN:plan1': 5, 'GLU:plan': 15, 'ARG:plan': 6, 'PHE:plan': 1, 'ASP:plan': 5} Unresolved non-hydrogen planarities: 131 Chain: "B" Number of atoms: 2426 Number of conformers: 1 Conformer: "" Number of residues, atoms: 337, 2426 Classifications: {'peptide': 337} Incomplete info: {'truncation_to_alanine': 78} Link IDs: {'PTRANS': 10, 'TRANS': 326} Unresolved non-hydrogen bonds: 230 Unresolved non-hydrogen angles: 293 Unresolved non-hydrogen dihedrals: 169 Unresolved non-hydrogen chiralities: 39 Planarities with less than four sites: {'GLN:plan1': 2, 'ASP:plan': 5, 'ASN:plan1': 2, 'HIS:plan': 1, 'GLU:plan': 10, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 89 Chain: "C" Number of atoms: 2407 Number of conformers: 1 Conformer: "" Number of residues, atoms: 337, 2407 Classifications: {'peptide': 337} Incomplete info: {'truncation_to_alanine': 76} Link IDs: {'PTRANS': 10, 'TRANS': 326} Unresolved non-hydrogen bonds: 248 Unresolved non-hydrogen angles: 310 Unresolved non-hydrogen dihedrals: 190 Unresolved non-hydrogen chiralities: 28 Planarities with less than four sites: {'GLN:plan1': 2, 'ASP:plan': 7, 'HIS:plan': 1, 'PHE:plan': 1, 'GLU:plan': 17, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 128 Chain: "D" Number of atoms: 2423 Number of conformers: 1 Conformer: "" Number of residues, atoms: 337, 2423 Classifications: {'peptide': 337} Incomplete info: {'truncation_to_alanine': 76} Link IDs: {'PTRANS': 10, 'TRANS': 326} Unresolved non-hydrogen bonds: 234 Unresolved non-hydrogen angles: 296 Unresolved non-hydrogen dihedrals: 176 Unresolved non-hydrogen chiralities: 33 Planarities with less than four sites: {'GLN:plan1': 2, 'ASP:plan': 4, 'ASN:plan1': 2, 'HIS:plan': 2, 'GLU:plan': 13, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 108 Chain: "E" Number of atoms: 8338 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1420, 8338 Classifications: {'peptide': 1420} Incomplete info: {'truncation_to_alanine': 861} Link IDs: {'PTRANS': 44, 'TRANS': 1375} Chain breaks: 5 Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 3014 Unresolved non-hydrogen angles: 3849 Unresolved non-hydrogen dihedrals: 2447 Unresolved non-hydrogen chiralities: 346 Planarities with less than four sites: {'GLN:plan1': 37, 'ARG:plan': 44, 'TYR:plan': 21, 'ASN:plan1': 49, 'TRP:plan': 11, 'HIS:plan': 19, 'PHE:plan': 44, 'GLU:plan': 62, 'ASP:plan': 51} Unresolved non-hydrogen planarities: 1521 Chain: "G" Number of atoms: 1261 Number of conformers: 1 Conformer: "" Number of residues, atoms: 205, 1261 Classifications: {'peptide': 205} Incomplete info: {'truncation_to_alanine': 114} Link IDs: {'PTRANS': 9, 'TRANS': 195} Unresolved non-hydrogen bonds: 433 Unresolved non-hydrogen angles: 563 Unresolved non-hydrogen dihedrals: 369 Unresolved non-hydrogen chiralities: 48 Planarities with less than four sites: {'GLN:plan1': 6, 'ARG:plan': 4, 'TYR:plan': 4, 'ASN:plan1': 8, 'TRP:plan': 4, 'ASP:plan': 2, 'PHE:plan': 8, 'GLU:plan': 4, 'HIS:plan': 5} Unresolved non-hydrogen planarities: 227 Chain: "N" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 161 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 161 Unusual residues: {' K': 2, 'ATP': 1, 'PTY': 4} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 72 Unresolved non-hydrogen angles: 72 Unresolved non-hydrogen dihedrals: 72 Chain: "B" Number of atoms: 98 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 98 Unusual residues: {'ATP': 2, 'POV': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 16 Planarities with less than four sites: {'POV:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "C" Number of atoms: 131 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 131 Unusual residues: {'ATP': 1, 'POV': 1, 'PTY': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 52 Unresolved non-hydrogen angles: 52 Unresolved non-hydrogen dihedrals: 52 Planarities with less than four sites: {'POV:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "D" Number of atoms: 68 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 68 Unusual residues: {'POV': 1, 'PTY': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 34 Unresolved non-hydrogen angles: 34 Unresolved non-hydrogen dihedrals: 34 Planarities with less than four sites: {'POV:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "E" Number of atoms: 160 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 160 Unusual residues: {'ATP': 1, 'GBM': 1, 'PTY': 3} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 54 Unresolved non-hydrogen angles: 54 Unresolved non-hydrogen dihedrals: 54 Time building chain proxies: 11.89, per 1000 atoms: 0.60 Number of scatterers: 19977 At special positions: 0 Unit cell: (110.751, 157.035, 148.77, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) K 2 19.00 Cl 1 17.00 S 76 16.00 P 28 15.00 O 3658 8.00 N 3556 7.00 C 12656 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=7, symmetry=0 Simple disulfide: pdb=" SG CYS A 120 " - pdb=" SG CYS A 152 " distance=2.03 Simple disulfide: pdb=" SG CYS B 120 " - pdb=" SG CYS B 152 " distance=1.84 Simple disulfide: pdb=" SG CYS C 120 " - pdb=" SG CYS C 152 " distance=2.03 Simple disulfide: pdb=" SG CYS D 120 " - pdb=" SG CYS D 152 " distance=2.03 Simple disulfide: pdb=" SG CYS E 6 " - pdb=" SG CYS E 24 " distance=2.03 Simple disulfide: pdb=" SG CYS E1407 " - pdb=" SG CYS E1409 " distance=2.04 Simple disulfide: pdb=" SG CYS G 6 " - pdb=" SG CYS G 24 " distance=2.04 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 Links applied BETA1-4 " NAG F 1 " - " NAG F 2 " " NAG N 1 " - " NAG N 2 " NAG-ASN " NAG F 1 " - " ASN G 9 " " NAG N 1 " - " ASN E 9 " Time building additional restraints: 8.91 Conformation dependent library (CDL) restraints added in 4.1 seconds 5918 Ramachandran restraints generated. 2959 Oldfield, 0 Emsley, 2959 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5638 Finding SS restraints... Secondary structure from input PDB file: 101 helices and 20 sheets defined 50.4% alpha, 6.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.11 Creating SS restraints... Processing helix chain 'A' and resid 25 through 31 removed outlier: 3.898A pdb=" N ASP A 29 " --> pdb=" O PRO A 25 " (cutoff:3.500A) Processing helix chain 'A' and resid 58 through 66 Processing helix chain 'A' and resid 68 through 98 Processing helix chain 'A' and resid 100 through 106 Processing helix chain 'A' and resid 126 through 139 Processing helix chain 'A' and resid 152 through 183 removed outlier: 3.563A pdb=" N ILE A 156 " --> pdb=" O CYS A 152 " (cutoff:3.500A) Processing helix chain 'A' and resid 282 through 287 removed outlier: 3.694A pdb=" N LEU A 285 " --> pdb=" O ALA A 282 " (cutoff:3.500A) removed outlier: 4.285A pdb=" N VAL A 286 " --> pdb=" O THR A 283 " (cutoff:3.500A) Processing helix chain 'A' and resid 314 through 318 removed outlier: 3.584A pdb=" N ILE A 318 " --> pdb=" O ALA A 315 " (cutoff:3.500A) Processing helix chain 'A' and resid 353 through 358 removed outlier: 3.901A pdb=" N GLU A 357 " --> pdb=" O CYS A 353 " (cutoff:3.500A) Processing helix chain 'B' and resid 56 through 66 removed outlier: 3.612A pdb=" N ILE B 60 " --> pdb=" O PHE B 56 " (cutoff:3.500A) Processing helix chain 'B' and resid 68 through 98 removed outlier: 4.684A pdb=" N VAL B 74 " --> pdb=" O ARG B 70 " (cutoff:3.500A) removed outlier: 4.473A pdb=" N THR B 77 " --> pdb=" O LEU B 73 " (cutoff:3.500A) Processing helix chain 'B' and resid 100 through 105 Processing helix chain 'B' and resid 111 through 116 Processing helix chain 'B' and resid 126 through 139 removed outlier: 4.037A pdb=" N VAL B 139 " --> pdb=" O ILE B 135 " (cutoff:3.500A) Processing helix chain 'B' and resid 152 through 184 Processing helix chain 'B' and resid 281 through 286 removed outlier: 4.148A pdb=" N VAL B 286 " --> pdb=" O ALA B 282 " (cutoff:3.500A) Processing helix chain 'B' and resid 314 through 316 No H-bonds generated for 'chain 'B' and resid 314 through 316' Processing helix chain 'B' and resid 355 through 361 Processing helix chain 'C' and resid 57 through 66 removed outlier: 4.321A pdb=" N PHE C 61 " --> pdb=" O LEU C 57 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N ASP C 66 " --> pdb=" O THR C 62 " (cutoff:3.500A) Processing helix chain 'C' and resid 68 through 98 removed outlier: 3.994A pdb=" N LEU C 73 " --> pdb=" O TRP C 69 " (cutoff:3.500A) removed outlier: 5.498A pdb=" N VAL C 74 " --> pdb=" O ARG C 70 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N HIS C 98 " --> pdb=" O VAL C 94 " (cutoff:3.500A) Processing helix chain 'C' and resid 100 through 107 Processing helix chain 'C' and resid 127 through 139 Processing helix chain 'C' and resid 152 through 182 removed outlier: 3.870A pdb=" N ILE C 156 " --> pdb=" O CYS C 152 " (cutoff:3.500A) Processing helix chain 'C' and resid 275 through 280 removed outlier: 4.289A pdb=" N ASP C 279 " --> pdb=" O PRO C 276 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N ILE C 280 " --> pdb=" O LEU C 277 " (cutoff:3.500A) Processing helix chain 'C' and resid 314 through 318 Processing helix chain 'C' and resid 356 through 361 removed outlier: 4.260A pdb=" N LYS C 361 " --> pdb=" O GLU C 357 " (cutoff:3.500A) Processing helix chain 'D' and resid 58 through 66 removed outlier: 3.548A pdb=" N THR D 62 " --> pdb=" O GLN D 58 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N ASP D 66 " --> pdb=" O THR D 62 " (cutoff:3.500A) Processing helix chain 'D' and resid 70 through 73 removed outlier: 3.841A pdb=" N LEU D 73 " --> pdb=" O ARG D 70 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 70 through 73' Processing helix chain 'D' and resid 74 through 98 removed outlier: 3.664A pdb=" N HIS D 98 " --> pdb=" O VAL D 94 " (cutoff:3.500A) Processing helix chain 'D' and resid 99 through 106 Processing helix chain 'D' and resid 126 through 139 removed outlier: 3.929A pdb=" N GLU D 136 " --> pdb=" O LEU D 132 " (cutoff:3.500A) Processing helix chain 'D' and resid 152 through 183 removed outlier: 3.546A pdb=" N ILE D 156 " --> pdb=" O CYS D 152 " (cutoff:3.500A) Processing helix chain 'D' and resid 275 through 280 removed outlier: 3.523A pdb=" N TYR D 278 " --> pdb=" O SER D 275 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N ASP D 279 " --> pdb=" O PRO D 276 " (cutoff:3.500A) Processing helix chain 'D' and resid 283 through 288 removed outlier: 3.962A pdb=" N GLN D 288 " --> pdb=" O LEU D 285 " (cutoff:3.500A) Processing helix chain 'D' and resid 316 through 318 No H-bonds generated for 'chain 'D' and resid 316 through 318' Processing helix chain 'D' and resid 340 through 342 No H-bonds generated for 'chain 'D' and resid 340 through 342' Processing helix chain 'D' and resid 354 through 359 Processing helix chain 'D' and resid 361 through 366 Processing helix chain 'E' and resid 22 through 48 Proline residue: E 33 - end of helix removed outlier: 4.581A pdb=" N ILE E 40 " --> pdb=" O PHE E 36 " (cutoff:3.500A) Proline residue: E 43 - end of helix Processing helix chain 'E' and resid 56 through 61 removed outlier: 3.726A pdb=" N HIS E 60 " --> pdb=" O VAL E 56 " (cutoff:3.500A) Processing helix chain 'E' and resid 62 through 64 No H-bonds generated for 'chain 'E' and resid 62 through 64' Processing helix chain 'E' and resid 68 through 97 removed outlier: 3.693A pdb=" N GLN E 96 " --> pdb=" O VAL E 92 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N ARG E 97 " --> pdb=" O SER E 93 " (cutoff:3.500A) Processing helix chain 'E' and resid 101 through 104 removed outlier: 3.507A pdb=" N LEU E 104 " --> pdb=" O HIS E 101 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 101 through 104' Processing helix chain 'E' and resid 105 through 128 removed outlier: 3.592A pdb=" N VAL E 113 " --> pdb=" O VAL E 109 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N SER E 128 " --> pdb=" O ASN E 124 " (cutoff:3.500A) Processing helix chain 'E' and resid 130 through 133 Processing helix chain 'E' and resid 134 through 157 removed outlier: 3.684A pdb=" N PHE E 138 " --> pdb=" O LEU E 134 " (cutoff:3.500A) Processing helix chain 'E' and resid 164 through 196 removed outlier: 4.506A pdb=" N VAL E 190 " --> pdb=" O ASN E 186 " (cutoff:3.500A) removed outlier: 4.153A pdb=" N ARG E 191 " --> pdb=" O VAL E 187 " (cutoff:3.500A) Processing helix chain 'E' and resid 218 through 225 Processing helix chain 'E' and resid 228 through 237 removed outlier: 4.076A pdb=" N THR E 233 " --> pdb=" O TRP E 229 " (cutoff:3.500A) removed outlier: 5.255A pdb=" N LEU E 234 " --> pdb=" O TRP E 230 " (cutoff:3.500A) Processing helix chain 'E' and resid 251 through 256 removed outlier: 3.840A pdb=" N MET E 255 " --> pdb=" O LEU E 251 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N ARG E 256 " --> pdb=" O PRO E 252 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 251 through 256' Processing helix chain 'E' and resid 257 through 276 removed outlier: 4.046A pdb=" N GLU E 266 " --> pdb=" O VAL E 262 " (cutoff:3.500A) Processing helix chain 'E' and resid 297 through 324 Proline residue: E 315 - end of helix removed outlier: 3.873A pdb=" N ARG E 324 " --> pdb=" O GLY E 320 " (cutoff:3.500A) Processing helix chain 'E' and resid 347 through 394 removed outlier: 3.584A pdb=" N LEU E 351 " --> pdb=" O ASN E 347 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N ASN E 379 " --> pdb=" O GLU E 375 " (cutoff:3.500A) removed outlier: 4.234A pdb=" N ARG E 394 " --> pdb=" O ASN E 390 " (cutoff:3.500A) Processing helix chain 'E' and resid 400 through 405 removed outlier: 3.673A pdb=" N GLY E 403 " --> pdb=" O LEU E 400 " (cutoff:3.500A) Processing helix chain 'E' and resid 408 through 413 Processing helix chain 'E' and resid 417 through 434 Proline residue: E 429 - end of helix Processing helix chain 'E' and resid 434 through 450 removed outlier: 4.064A pdb=" N MET E 440 " --> pdb=" O VAL E 436 " (cutoff:3.500A) Processing helix chain 'E' and resid 453 through 497 removed outlier: 4.416A pdb=" N VAL E 459 " --> pdb=" O VAL E 455 " (cutoff:3.500A) removed outlier: 5.604A pdb=" N ILE E 460 " --> pdb=" O GLY E 456 " (cutoff:3.500A) removed outlier: 4.475A pdb=" N VAL E 461 " --> pdb=" O ALA E 457 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N LEU E 462 " --> pdb=" O ALA E 458 " (cutoff:3.500A) Proline residue: E 465 - end of helix removed outlier: 4.434A pdb=" N THR E 472 " --> pdb=" O TYR E 468 " (cutoff:3.500A) removed outlier: 4.168A pdb=" N LYS E 473 " --> pdb=" O PHE E 469 " (cutoff:3.500A) Processing helix chain 'E' and resid 498 through 503 Processing helix chain 'E' and resid 509 through 511 No H-bonds generated for 'chain 'E' and resid 509 through 511' Processing helix chain 'E' and resid 512 through 556 removed outlier: 3.761A pdb=" N SER E 525 " --> pdb=" O LYS E 521 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N TYR E 532 " --> pdb=" O THR E 528 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N ILE E 543 " --> pdb=" O MET E 539 " (cutoff:3.500A) Proline residue: E 544 - end of helix removed outlier: 3.776A pdb=" N ALA E 556 " --> pdb=" O PHE E 552 " (cutoff:3.500A) Processing helix chain 'E' and resid 564 through 579 removed outlier: 3.551A pdb=" N ALA E 568 " --> pdb=" O LYS E 564 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N PHE E 569 " --> pdb=" O PRO E 565 " (cutoff:3.500A) removed outlier: 5.370A pdb=" N ALA E 570 " --> pdb=" O ALA E 566 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N SER E 571 " --> pdb=" O GLU E 567 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N VAL E 579 " --> pdb=" O PHE E 575 " (cutoff:3.500A) Processing helix chain 'E' and resid 580 through 607 removed outlier: 4.177A pdb=" N LEU E 584 " --> pdb=" O THR E 580 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N ARG E 590 " --> pdb=" O SER E 586 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N VAL E 593 " --> pdb=" O VAL E 589 " (cutoff:3.500A) Processing helix chain 'E' and resid 706 through 715 removed outlier: 4.189A pdb=" N LEU E 715 " --> pdb=" O LEU E 711 " (cutoff:3.500A) Processing helix chain 'E' and resid 761 through 768 removed outlier: 4.337A pdb=" N PHE E 768 " --> pdb=" O GLU E 764 " (cutoff:3.500A) Processing helix chain 'E' and resid 773 through 784 removed outlier: 3.680A pdb=" N TYR E 777 " --> pdb=" O ASN E 773 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N CYS E 784 " --> pdb=" O VAL E 780 " (cutoff:3.500A) Processing helix chain 'E' and resid 786 through 793 Processing helix chain 'E' and resid 795 through 799 removed outlier: 3.788A pdb=" N GLN E 798 " --> pdb=" O PHE E 795 " (cutoff:3.500A) Processing helix chain 'E' and resid 809 through 823 Processing helix chain 'E' and resid 843 through 855 Processing helix chain 'E' and resid 893 through 899 removed outlier: 3.520A pdb=" N LYS E 898 " --> pdb=" O ASP E 894 " (cutoff:3.500A) Processing helix chain 'E' and resid 900 through 910 removed outlier: 4.486A pdb=" N GLU E 904 " --> pdb=" O VAL E 900 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N TRP E 906 " --> pdb=" O LEU E 902 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N LYS E 907 " --> pdb=" O TYR E 903 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N THR E 908 " --> pdb=" O GLU E 904 " (cutoff:3.500A) Processing helix chain 'E' and resid 962 through 966 Processing helix chain 'E' and resid 974 through 985 removed outlier: 3.547A pdb=" N SER E 984 " --> pdb=" O TRP E 980 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N GLY E 985 " --> pdb=" O TYR E 981 " (cutoff:3.500A) Processing helix chain 'E' and resid 992 through 1015 removed outlier: 3.556A pdb=" N THR E1015 " --> pdb=" O LEU E1011 " (cutoff:3.500A) Processing helix chain 'E' and resid 1029 through 1034 removed outlier: 3.686A pdb=" N VAL E1032 " --> pdb=" O THR E1029 " (cutoff:3.500A) removed outlier: 4.081A pdb=" N ALA E1033 " --> pdb=" O PHE E1030 " (cutoff:3.500A) Processing helix chain 'E' and resid 1035 through 1037 No H-bonds generated for 'chain 'E' and resid 1035 through 1037' Processing helix chain 'E' and resid 1038 through 1072 removed outlier: 4.358A pdb=" N CYS E1046 " --> pdb=" O GLY E1042 " (cutoff:3.500A) removed outlier: 4.367A pdb=" N LEU E1047 " --> pdb=" O ILE E1043 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N LEU E1051 " --> pdb=" O LEU E1047 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N VAL E1053 " --> pdb=" O THR E1049 " (cutoff:3.500A) removed outlier: 5.127A pdb=" N GLU E1054 " --> pdb=" O SER E1050 " (cutoff:3.500A) Processing helix chain 'E' and resid 1076 through 1083 removed outlier: 3.777A pdb=" N PHE E1080 " --> pdb=" O PRO E1076 " (cutoff:3.500A) Processing helix chain 'E' and resid 1084 through 1102 removed outlier: 3.979A pdb=" N ILE E1088 " --> pdb=" O PRO E1084 " (cutoff:3.500A) removed outlier: 4.148A pdb=" N ASP E1095 " --> pdb=" O ARG E1091 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N THR E1096 " --> pdb=" O PHE E1092 " (cutoff:3.500A) Processing helix chain 'E' and resid 1102 through 1128 removed outlier: 3.858A pdb=" N THR E1128 " --> pdb=" O ILE E1124 " (cutoff:3.500A) Processing helix chain 'E' and resid 1128 through 1135 removed outlier: 3.911A pdb=" N LEU E1132 " --> pdb=" O THR E1128 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N ILE E1133 " --> pdb=" O PRO E1129 " (cutoff:3.500A) Processing helix chain 'E' and resid 1136 through 1164 removed outlier: 3.518A pdb=" N PHE E1144 " --> pdb=" O VAL E1140 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N SER E1153 " --> pdb=" O PHE E1149 " (cutoff:3.500A) removed outlier: 5.772A pdb=" N LYS E1154 " --> pdb=" O ARG E1150 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N GLN E1164 " --> pdb=" O ASP E1160 " (cutoff:3.500A) Processing helix chain 'E' and resid 1164 through 1177 removed outlier: 3.925A pdb=" N LEU E1168 " --> pdb=" O GLN E1164 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N CYS E1169 " --> pdb=" O LEU E1165 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N PHE E1171 " --> pdb=" O LEU E1167 " (cutoff:3.500A) removed outlier: 4.175A pdb=" N ALA E1175 " --> pdb=" O PHE E1171 " (cutoff:3.500A) Processing helix chain 'E' and resid 1189 through 1238 removed outlier: 4.180A pdb=" N ARG E1193 " --> pdb=" O ARG E1189 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N MET E1194 " --> pdb=" O PHE E1190 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N GLU E1196 " --> pdb=" O GLN E1192 " (cutoff:3.500A) removed outlier: 4.308A pdb=" N ASP E1199 " --> pdb=" O LEU E1195 " (cutoff:3.500A) removed outlier: 4.339A pdb=" N ALA E1204 " --> pdb=" O THR E1200 " (cutoff:3.500A) Processing helix chain 'E' and resid 1240 through 1280 removed outlier: 4.390A pdb=" N ASN E1256 " --> pdb=" O LEU E1252 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N TYR E1257 " --> pdb=" O THR E1253 " (cutoff:3.500A) removed outlier: 4.150A pdb=" N LEU E1258 " --> pdb=" O ILE E1254 " (cutoff:3.500A) removed outlier: 5.617A pdb=" N ASN E1259 " --> pdb=" O THR E1255 " (cutoff:3.500A) removed outlier: 4.130A pdb=" N TRP E1260 " --> pdb=" O ASN E1256 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N LYS E1277 " --> pdb=" O GLY E1273 " (cutoff:3.500A) removed outlier: 4.415A pdb=" N VAL E1278 " --> pdb=" O ALA E1274 " (cutoff:3.500A) Processing helix chain 'E' and resid 1343 through 1354 removed outlier: 4.286A pdb=" N LYS E1348 " --> pdb=" O THR E1344 " (cutoff:3.500A) removed outlier: 5.386A pdb=" N SER E1349 " --> pdb=" O GLY E1345 " (cutoff:3.500A) Processing helix chain 'E' and resid 1380 through 1385 removed outlier: 3.584A pdb=" N LEU E1385 " --> pdb=" O ARG E1382 " (cutoff:3.500A) Processing helix chain 'E' and resid 1423 through 1428 Processing helix chain 'E' and resid 1453 through 1458 Processing helix chain 'E' and resid 1475 through 1491 Processing helix chain 'E' and resid 1502 through 1507 Processing helix chain 'E' and resid 1526 through 1533 Processing helix chain 'E' and resid 1536 through 1541 Processing helix chain 'G' and resid 22 through 47 removed outlier: 3.753A pdb=" N VAL G 26 " --> pdb=" O ASN G 22 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N ASP G 27 " --> pdb=" O PRO G 23 " (cutoff:3.500A) Proline residue: G 33 - end of helix removed outlier: 4.354A pdb=" N PHE G 39 " --> pdb=" O VAL G 35 " (cutoff:3.500A) Proline residue: G 43 - end of helix Processing helix chain 'G' and resid 68 through 95 removed outlier: 3.973A pdb=" N ARG G 72 " --> pdb=" O GLY G 68 " (cutoff:3.500A) removed outlier: 4.076A pdb=" N TRP G 73 " --> pdb=" O HIS G 69 " (cutoff:3.500A) removed outlier: 4.504A pdb=" N ILE G 74 " --> pdb=" O ASN G 70 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N SER G 95 " --> pdb=" O ILE G 91 " (cutoff:3.500A) Processing helix chain 'G' and resid 101 through 104 Processing helix chain 'G' and resid 105 through 127 Processing helix chain 'G' and resid 130 through 133 removed outlier: 3.645A pdb=" N LEU G 133 " --> pdb=" O PHE G 130 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 130 through 133' Processing helix chain 'G' and resid 134 through 159 removed outlier: 3.674A pdb=" N PHE G 138 " --> pdb=" O LEU G 134 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N LEU G 139 " --> pdb=" O LEU G 135 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N TYR G 140 " --> pdb=" O ALA G 136 " (cutoff:3.500A) removed outlier: 4.262A pdb=" N LYS G 154 " --> pdb=" O ILE G 150 " (cutoff:3.500A) Processing helix chain 'G' and resid 164 through 187 removed outlier: 4.151A pdb=" N VAL G 172 " --> pdb=" O CYS G 168 " (cutoff:3.500A) removed outlier: 4.817A pdb=" N MET G 173 " --> pdb=" O ILE G 169 " (cutoff:3.500A) removed outlier: 4.539A pdb=" N VAL G 174 " --> pdb=" O THR G 170 " (cutoff:3.500A) removed outlier: 4.269A pdb=" N ILE G 175 " --> pdb=" O GLY G 171 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N VAL G 187 " --> pdb=" O VAL G 183 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 191 through 193 Processing sheet with id=AA2, first strand: chain 'A' and resid 198 through 202 removed outlier: 3.678A pdb=" N VAL A 198 " --> pdb=" O MET A 209 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 244 through 248 removed outlier: 4.594A pdb=" N ILE A 227 " --> pdb=" O ILE A 248 " (cutoff:3.500A) removed outlier: 5.349A pdb=" N SER A 222 " --> pdb=" O VAL A 299 " (cutoff:3.500A) removed outlier: 5.091A pdb=" N VAL A 299 " --> pdb=" O SER A 222 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 323 through 324 Processing sheet with id=AA5, first strand: chain 'A' and resid 328 through 330 removed outlier: 3.915A pdb=" N ALA D 46 " --> pdb=" O TYR A 335 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N VAL A 337 " --> pdb=" O ALA D 46 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 265 through 270 removed outlier: 4.013A pdb=" N PHE B 210 " --> pdb=" O ILE B 267 " (cutoff:3.500A) removed outlier: 6.611A pdb=" N ALA B 197 " --> pdb=" O GLN B 319 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 246 through 248 removed outlier: 3.545A pdb=" N VAL B 229 " --> pdb=" O GLN B 246 " (cutoff:3.500A) removed outlier: 4.271A pdb=" N ILE B 227 " --> pdb=" O ILE B 248 " (cutoff:3.500A) removed outlier: 5.791A pdb=" N SER B 222 " --> pdb=" O VAL B 299 " (cutoff:3.500A) removed outlier: 5.669A pdb=" N VAL B 299 " --> pdb=" O SER B 222 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 233 through 235 removed outlier: 3.501A pdb=" N THR B 233 " --> pdb=" O VAL B 241 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 47 through 48 removed outlier: 7.146A pdb=" N LYS C 48 " --> pdb=" O TYR D 335 " (cutoff:3.500A) removed outlier: 6.224A pdb=" N VAL D 337 " --> pdb=" O LYS C 48 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 210 through 212 Processing sheet with id=AB2, first strand: chain 'C' and resid 245 through 248 removed outlier: 4.496A pdb=" N ILE C 227 " --> pdb=" O ILE C 248 " (cutoff:3.500A) removed outlier: 5.274A pdb=" N SER C 222 " --> pdb=" O VAL C 299 " (cutoff:3.500A) removed outlier: 5.132A pdb=" N VAL C 299 " --> pdb=" O SER C 222 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 233 through 234 Processing sheet with id=AB4, first strand: chain 'C' and resid 322 through 323 Processing sheet with id=AB5, first strand: chain 'D' and resid 37 through 38 Processing sheet with id=AB6, first strand: chain 'D' and resid 201 through 202 Processing sheet with id=AB7, first strand: chain 'D' and resid 240 through 248 removed outlier: 5.083A pdb=" N THR D 233 " --> pdb=" O PRO D 242 " (cutoff:3.500A) removed outlier: 4.285A pdb=" N ILE D 227 " --> pdb=" O ILE D 248 " (cutoff:3.500A) removed outlier: 5.634A pdb=" N SER D 222 " --> pdb=" O VAL D 299 " (cutoff:3.500A) removed outlier: 5.341A pdb=" N VAL D 299 " --> pdb=" O SER D 222 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N VAL D 292 " --> pdb=" O TYR D 313 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'D' and resid 323 through 324 Processing sheet with id=AB9, first strand: chain 'E' and resid 669 through 670 Processing sheet with id=AC1, first strand: chain 'E' and resid 748 through 750 removed outlier: 5.655A pdb=" N ALA E 749 " --> pdb=" O PHE E 830 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC1 Processing sheet with id=AC2, first strand: chain 'E' and resid 1513 through 1516 removed outlier: 6.806A pdb=" N VAL E1514 " --> pdb=" O LEU E1521 " (cutoff:3.500A) 1090 hydrogen bonds defined for protein. 3147 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: 6.63 Time building geometry restraints manager: 9.60 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 3252 1.31 - 1.44: 5346 1.44 - 1.57: 11572 1.57 - 1.71: 54 1.71 - 1.84: 116 Bond restraints: 20340 Sorted by residual: bond pdb=" C29 POV B 503 " pdb="C210 POV B 503 " ideal model delta sigma weight residual 1.333 1.544 -0.211 2.00e-02 2.50e+03 1.11e+02 bond pdb=" C29 POV D 801 " pdb="C210 POV D 801 " ideal model delta sigma weight residual 1.333 1.544 -0.211 2.00e-02 2.50e+03 1.11e+02 bond pdb=" C29 POV C 504 " pdb="C210 POV C 504 " ideal model delta sigma weight residual 1.333 1.544 -0.211 2.00e-02 2.50e+03 1.11e+02 bond pdb=" O5 GBM E1602 " pdb=" S2 GBM E1602 " ideal model delta sigma weight residual 1.448 1.650 -0.202 2.00e-02 2.50e+03 1.02e+02 bond pdb=" O4 GBM E1602 " pdb=" S2 GBM E1602 " ideal model delta sigma weight residual 1.453 1.651 -0.198 2.00e-02 2.50e+03 9.83e+01 ... (remaining 20335 not shown) Histogram of bond angle deviations from ideal: 98.58 - 106.09: 449 106.09 - 113.59: 11766 113.59 - 121.10: 10056 121.10 - 128.61: 5498 128.61 - 136.11: 163 Bond angle restraints: 27932 Sorted by residual: angle pdb=" PB ATP E1601 " pdb=" O3B ATP E1601 " pdb=" PG ATP E1601 " ideal model delta sigma weight residual 139.87 118.66 21.21 1.00e+00 1.00e+00 4.50e+02 angle pdb=" PB ATP C 501 " pdb=" O3B ATP C 501 " pdb=" PG ATP C 501 " ideal model delta sigma weight residual 139.87 118.76 21.11 1.00e+00 1.00e+00 4.45e+02 angle pdb=" PB ATP B 502 " pdb=" O3B ATP B 502 " pdb=" PG ATP B 502 " ideal model delta sigma weight residual 139.87 120.42 19.45 1.00e+00 1.00e+00 3.78e+02 angle pdb=" PB ATP B 501 " pdb=" O3B ATP B 501 " pdb=" PG ATP B 501 " ideal model delta sigma weight residual 139.87 121.04 18.83 1.00e+00 1.00e+00 3.55e+02 angle pdb=" PA ATP B 501 " pdb=" O3A ATP B 501 " pdb=" PB ATP B 501 " ideal model delta sigma weight residual 136.83 118.05 18.78 1.00e+00 1.00e+00 3.53e+02 ... (remaining 27927 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.78: 11737 34.78 - 69.57: 269 69.57 - 104.35: 35 104.35 - 139.13: 10 139.13 - 173.91: 3 Dihedral angle restraints: 12054 sinusoidal: 3396 harmonic: 8658 Sorted by residual: dihedral pdb=" CB CYS E1407 " pdb=" SG CYS E1407 " pdb=" SG CYS E1409 " pdb=" CB CYS E1409 " ideal model delta sinusoidal sigma weight residual -86.00 -139.09 53.09 1 1.00e+01 1.00e-02 3.83e+01 dihedral pdb=" N1 PTY A 504 " pdb=" C2 PTY A 504 " pdb=" C3 PTY A 504 " pdb=" O11 PTY A 504 " ideal model delta sinusoidal sigma weight residual 65.33 -120.76 -173.91 1 3.00e+01 1.11e-03 2.13e+01 dihedral pdb=" CA PHE A 56 " pdb=" C PHE A 56 " pdb=" N LEU A 57 " pdb=" CA LEU A 57 " ideal model delta harmonic sigma weight residual -180.00 -157.01 -22.99 0 5.00e+00 4.00e-02 2.11e+01 ... (remaining 12051 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.070: 2942 0.070 - 0.141: 412 0.141 - 0.211: 25 0.211 - 0.281: 7 0.281 - 0.352: 4 Chirality restraints: 3390 Sorted by residual: chirality pdb=" CA TRP E 230 " pdb=" N TRP E 230 " pdb=" C TRP E 230 " pdb=" CB TRP E 230 " both_signs ideal model delta sigma weight residual False 2.51 2.16 0.35 2.00e-01 2.50e+01 3.09e+00 chirality pdb=" CA LEU E 902 " pdb=" N LEU E 902 " pdb=" C LEU E 902 " pdb=" CB LEU E 902 " both_signs ideal model delta sigma weight residual False 2.51 2.21 0.30 2.00e-01 2.50e+01 2.29e+00 chirality pdb=" CA TYR E 228 " pdb=" N TYR E 228 " pdb=" C TYR E 228 " pdb=" CB TYR E 228 " both_signs ideal model delta sigma weight residual False 2.51 2.21 0.30 2.00e-01 2.50e+01 2.24e+00 ... (remaining 3387 not shown) Planarity restraints: 3601 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA PHE E 145 " 0.016 2.00e-02 2.50e+03 3.21e-02 1.03e+01 pdb=" C PHE E 145 " -0.056 2.00e-02 2.50e+03 pdb=" O PHE E 145 " 0.021 2.00e-02 2.50e+03 pdb=" N ILE E 146 " 0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA MET E 143 " -0.013 2.00e-02 2.50e+03 2.68e-02 7.17e+00 pdb=" C MET E 143 " 0.046 2.00e-02 2.50e+03 pdb=" O MET E 143 " -0.017 2.00e-02 2.50e+03 pdb=" N ALA E 144 " -0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA E1061 " -0.013 2.00e-02 2.50e+03 2.58e-02 6.65e+00 pdb=" C ALA E1061 " 0.045 2.00e-02 2.50e+03 pdb=" O ALA E1061 " -0.017 2.00e-02 2.50e+03 pdb=" N LYS E1062 " -0.015 2.00e-02 2.50e+03 ... (remaining 3598 not shown) Histogram of nonbonded interaction distances: 1.86 - 2.51: 106 2.51 - 3.17: 18062 3.17 - 3.83: 35722 3.83 - 4.48: 41963 4.48 - 5.14: 68073 Nonbonded interactions: 163926 Sorted by model distance: nonbonded pdb=" NE2 HIS D 196 " pdb=" OE1 GLN D 319 " model vdw 1.857 3.120 nonbonded pdb=" CB ALA B 34 " pdb=" O GLY C 333 " model vdw 2.046 3.460 nonbonded pdb=" CD2 HIS D 196 " pdb=" OE1 GLN D 319 " model vdw 2.128 3.260 nonbonded pdb=" O LEU G 37 " pdb=" OG1 THR G 41 " model vdw 2.131 3.040 nonbonded pdb=" NH1 ARG E1213 " pdb=" O5 GBM E1602 " model vdw 2.215 3.120 ... (remaining 163921 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 31 through 32 or (resid 33 through 35 and (name N or name \ CA or name C or name O or name CB )) or resid 36 through 44 or (resid 45 through \ 46 and (name N or name CA or name C or name O or name CB )) or resid 47 through \ 49 or (resid 50 and (name N or name CA or name C or name O or name CB )) or res \ id 51 through 54 or (resid 55 and (name N or name CA or name C or name O or name \ CB )) or resid 56 through 58 or (resid 59 and (name N or name CA or name C or n \ ame O or name CB )) or resid 60 through 65 or (resid 66 and (name N or name CA o \ r name C or name O or name CB )) or resid 67 through 74 or (resid 75 and (name N \ or name CA or name C or name O or name CB )) or resid 76 through 80 or (resid 8 \ 1 and (name N or name CA or name C or name O or name CB )) or resid 82 through 9 \ 3 or (resid 94 through 95 and (name N or name CA or name C or name O or name CB \ )) or resid 96 through 100 or (resid 101 and (name N or name CA or name C or nam \ e O or name CB )) or resid 102 through 104 or (resid 105 through 107 and (name N \ or name CA or name C or name O or name CB )) or resid 108 through 124 or (resid \ 125 through 126 and (name N or name CA or name C or name O or name CB )) or res \ id 127 or (resid 128 through 130 and (name N or name CA or name C or name O or n \ ame CB )) or resid 131 or (resid 132 and (name N or name CA or name C or name O \ or name CB )) or resid 133 through 134 or (resid 135 through 137 and (name N or \ name CA or name C or name O or name CB )) or resid 138 or (resid 139 and (name N \ or name CA or name C or name O or name CB )) or resid 140 or (resid 141 and (na \ me N or name CA or name C or name O or name CB )) or resid 142 through 161 or (r \ esid 162 and (name N or name CA or name C or name O or name CB )) or resid 163 o \ r (resid 164 and (name N or name CA or name C or name O or name CB )) or resid 1 \ 65 through 167 or (resid 168 through 169 and (name N or name CA or name C or nam \ e O or name CB )) or resid 170 through 180 or (resid 181 through 185 and (name N \ or name CA or name C or name O or name CB )) or resid 186 through 189 or (resid \ 190 and (name N or name CA or name C or name O or name CB )) or resid 191 or (r \ esid 192 and (name N or name CA or name C or name O or name CB )) or resid 193 t \ hrough 198 or (resid 199 through 200 and (name N or name CA or name C or name O \ or name CB )) or resid 201 through 204 or (resid 205 and (name N or name CA or n \ ame C or name O or name CB )) or resid 206 or (resid 207 through 208 and (name N \ or name CA or name C or name O or name CB )) or resid 209 through 210 or (resid \ 211 through 212 and (name N or name CA or name C or name O or name CB )) or res \ id 213 or (resid 214 and (name N or name CA or name C or name O or name CB )) or \ resid 215 through 216 or (resid 217 through 225 and (name N or name CA or name \ C or name O or name CB )) or resid 226 through 229 or (resid 230 and (name N or \ name CA or name C or name O or name CB )) or resid 231 through 250 or (resid 251 \ and (name N or name CA or name C or name O or name CB )) or resid 252 through 2 \ 54 or (resid 255 through 258 and (name N or name CA or name C or name O or name \ CB )) or resid 259 through 260 or (resid 261 through 263 and (name N or name CA \ or name C or name O or name CB )) or resid 264 or (resid 265 through 275 and (na \ me N or name CA or name C or name O or name CB )) or resid 276 or (resid 277 and \ (name N or name CA or name C or name O or name CB )) or resid 278 or (resid 279 \ through 290 and (name N or name CA or name C or name O or name CB )) or resid 2 \ 91 or (resid 292 and (name N or name CA or name C or name O or name CB )) or res \ id 293 or (resid 294 through 295 and (name N or name CA or name C or name O or n \ ame CB )) or resid 296 or (resid 297 and (name N or name CA or name C or name O \ or name CB )) or resid 298 or (resid 299 and (name N or name CA or name C or nam \ e O or name CB )) or resid 300 or (resid 301 through 303 and (name N or name CA \ or name C or name O or name CB )) or resid 304 through 315 or (resid 316 through \ 317 and (name N or name CA or name C or name O or name CB )) or resid 318 throu \ gh 321 or (resid 322 and (name N or name CA or name C or name O or name CB )) or \ resid 323 through 324 or (resid 325 through 326 and (name N or name CA or name \ C or name O or name CB )) or resid 327 or (resid 328 through 332 and (name N or \ name CA or name C or name O or name CB )) or resid 333 through 336 or (resid 337 \ and (name N or name CA or name C or name O or name CB )) or resid 338 through 3 \ 39 or (resid 340 and (name N or name CA or name C or name O or name CB )) or res \ id 341 through 343 or (resid 344 and (name N or name CA or name C or name O or n \ ame CB )) or resid 345 through 366)) selection = (chain 'B' and (resid 31 through 34 or (resid 35 and (name N or name CA or name \ C or name O or name CB )) or resid 36 through 39 or (resid 40 and (name N or nam \ e CA or name C or name O or name CB )) or resid 41 through 47 or (resid 48 and ( \ name N or name CA or name C or name O or name CB )) or resid 49 through 51 or (r \ esid 52 through 53 and (name N or name CA or name C or name O or name CB )) or r \ esid 54 or (resid 55 and (name N or name CA or name C or name O or name CB )) or \ resid 56 through 57 or (resid 58 through 59 and (name N or name CA or name C or \ name O or name CB )) or resid 60 through 67 or (resid 68 and (name N or name CA \ or name C or name O or name CB )) or resid 69 or (resid 70 and (name N or name \ CA or name C or name O or name CB )) or resid 71 through 84 or (resid 85 and (na \ me N or name CA or name C or name O or name CB )) or resid 86 through 93 or (res \ id 94 through 95 and (name N or name CA or name C or name O or name CB )) or res \ id 96 through 104 or (resid 105 through 107 and (name N or name CA or name C or \ name O or name CB )) or (resid 108 through 119 and (name N or name CA or name C \ or name O or name CB )) or resid 120 through 121 or (resid 122 and (name N or na \ me CA or name C or name O or name CB )) or resid 123 through 124 or (resid 125 t \ hrough 126 and (name N or name CA or name C or name O or name CB )) or resid 127 \ or (resid 128 through 130 and (name N or name CA or name C or name O or name CB \ )) or resid 131 or (resid 132 and (name N or name CA or name C or name O or nam \ e CB )) or resid 133 or (resid 134 through 137 and (name N or name CA or name C \ or name O or name CB )) or resid 138 through 147 or (resid 148 through 151 and ( \ name N or name CA or name C or name O or name CB )) or resid 152 through 156 or \ (resid 157 and (name N or name CA or name C or name O or name CB )) or resid 158 \ through 163 or (resid 164 and (name N or name CA or name C or name O or name CB \ )) or resid 165 through 167 or (resid 168 through 169 and (name N or name CA or \ name C or name O or name CB )) or resid 170 through 171 or (resid 172 through 1 \ 73 and (name N or name CA or name C or name O or name CB )) or resid 174 through \ 176 or (resid 177 and (name N or name CA or name C or name O or name CB )) or r \ esid 178 through 179 or (resid 180 through 185 and (name N or name CA or name C \ or name O or name CB )) or resid 186 or (resid 187 through 190 and (name N or na \ me CA or name C or name O or name CB )) or resid 191 through 193 or (resid 194 a \ nd (name N or name CA or name C or name O or name CB )) or resid 195 through 198 \ or (resid 199 through 200 and (name N or name CA or name C or name O or name CB \ )) or resid 201 through 204 or (resid 205 and (name N or name CA or name C or n \ ame O or name CB )) or resid 206 or (resid 207 through 208 and (name N or name C \ A or name C or name O or name CB )) or resid 209 or (resid 210 through 212 and ( \ name N or name CA or name C or name O or name CB )) or resid 213 or (resid 214 a \ nd (name N or name CA or name C or name O or name CB )) or resid 215 through 221 \ or (resid 222 through 225 and (name N or name CA or name C or name O or name CB \ )) or resid 226 or (resid 227 and (name N or name CA or name C or name O or nam \ e CB )) or resid 228 through 236 or (resid 237 and (name N or name CA or name C \ or name O or name CB )) or resid 238 or (resid 239 and (name N or name CA or nam \ e C or name O or name CB )) or resid 240 or (resid 241 and (name N or name CA or \ name C or name O or name CB )) or resid 242 through 254 or (resid 255 through 2 \ 58 and (name N or name CA or name C or name O or name CB )) or resid 259 through \ 260 or (resid 261 through 263 and (name N or name CA or name C or name O or nam \ e CB )) or resid 264 through 268 or (resid 269 through 275 and (name N or name C \ A or name C or name O or name CB )) or resid 276 or (resid 277 and (name N or na \ me CA or name C or name O or name CB )) or resid 278 or (resid 279 through 290 a \ nd (name N or name CA or name C or name O or name CB )) or resid 291 or (resid 2 \ 92 and (name N or name CA or name C or name O or name CB )) or resid 293 or (res \ id 294 through 295 and (name N or name CA or name C or name O or name CB )) or r \ esid 296 through 298 or (resid 299 and (name N or name CA or name C or name O or \ name CB )) or resid 300 or (resid 301 through 303 and (name N or name CA or nam \ e C or name O or name CB )) or resid 304 through 305 or (resid 306 and (name N o \ r name CA or name C or name O or name CB )) or resid 307 through 311 or (resid 3 \ 12 and (name N or name CA or name C or name O or name CB )) or resid 313 through \ 315 or (resid 316 through 317 and (name N or name CA or name C or name O or nam \ e CB )) or resid 318 through 327 or (resid 328 through 332 and (name N or name C \ A or name C or name O or name CB )) or resid 333 through 335 or (resid 336 throu \ gh 337 and (name N or name CA or name C or name O or name CB )) or resid 338 thr \ ough 339 or (resid 340 and (name N or name CA or name C or name O or name CB )) \ or resid 341 through 343 or (resid 344 and (name N or name CA or name C or name \ O or name CB )) or resid 345 through 347 or (resid 348 through 350 and (name N o \ r name CA or name C or name O or name CB )) or resid 351 through 352 or (resid 3 \ 53 through 361 and (name N or name CA or name C or name O or name CB )) or resid \ 362 through 366)) selection = (chain 'C' and (resid 31 through 32 or (resid 33 through 35 and (name N or name \ CA or name C or name O or name CB )) or resid 36 through 39 or (resid 40 and (na \ me N or name CA or name C or name O or name CB )) or resid 41 through 44 or (res \ id 45 through 46 and (name N or name CA or name C or name O or name CB )) or res \ id 47 or (resid 48 and (name N or name CA or name C or name O or name CB )) or r \ esid 49 through 57 or (resid 58 through 59 and (name N or name CA or name C or n \ ame O or name CB )) or resid 60 through 67 or (resid 68 and (name N or name CA o \ r name C or name O or name CB )) or resid 69 or (resid 70 and (name N or name CA \ or name C or name O or name CB )) or resid 71 through 80 or (resid 81 and (name \ N or name CA or name C or name O or name CB )) or resid 82 through 84 or (resid \ 85 and (name N or name CA or name C or name O or name CB )) or resid 86 through \ 93 or (resid 94 through 95 and (name N or name CA or name C or name O or name C \ B )) or resid 96 through 100 or (resid 101 and (name N or name CA or name C or n \ ame O or name CB )) or resid 102 through 121 or (resid 122 and (name N or name C \ A or name C or name O or name CB )) or resid 123 through 125 or (resid 126 and ( \ name N or name CA or name C or name O or name CB )) or resid 127 through 128 or \ (resid 129 through 130 and (name N or name CA or name C or name O or name CB )) \ or resid 131 through 133 or (resid 134 through 137 and (name N or name CA or nam \ e C or name O or name CB )) or resid 138 or (resid 139 and (name N or name CA or \ name C or name O or name CB )) or resid 140 or (resid 141 and (name N or name C \ A or name C or name O or name CB )) or resid 142 through 147 or (resid 148 throu \ gh 151 and (name N or name CA or name C or name O or name CB )) or resid 152 thr \ ough 156 or (resid 157 and (name N or name CA or name C or name O or name CB )) \ or resid 158 through 161 or (resid 162 and (name N or name CA or name C or name \ O or name CB )) or resid 163 through 167 or (resid 168 through 169 and (name N o \ r name CA or name C or name O or name CB )) or resid 170 through 171 or (resid 1 \ 72 through 173 and (name N or name CA or name C or name O or name CB )) or resid \ 174 through 179 or (resid 180 through 185 and (name N or name CA or name C or n \ ame O or name CB )) or resid 186 or (resid 187 through 190 and (name N or name C \ A or name C or name O or name CB )) or resid 191 or (resid 192 and (name N or na \ me CA or name C or name O or name CB )) or resid 193 or (resid 194 and (name N o \ r name CA or name C or name O or name CB )) or resid 195 through 198 or (resid 1 \ 99 through 200 and (name N or name CA or name C or name O or name CB )) or resid \ 201 through 206 or (resid 207 through 208 and (name N or name CA or name C or n \ ame O or name CB )) or resid 209 or (resid 210 through 212 and (name N or name C \ A or name C or name O or name CB )) or resid 213 through 217 or (resid 218 throu \ gh 225 and (name N or name CA or name C or name O or name CB )) or resid 226 or \ (resid 227 and (name N or name CA or name C or name O or name CB )) or resid 228 \ through 229 or (resid 230 and (name N or name CA or name C or name O or name CB \ )) or resid 231 through 236 or (resid 237 and (name N or name CA or name C or n \ ame O or name CB )) or resid 238 through 240 or (resid 241 and (name N or name C \ A or name C or name O or name CB )) or resid 242 through 249 or (resid 250 throu \ gh 251 and (name N or name CA or name C or name O or name CB )) or resid 252 thr \ ough 255 or (resid 256 through 258 and (name N or name CA or name C or name O or \ name CB )) or resid 259 through 261 or (resid 262 through 263 and (name N or na \ me CA or name C or name O or name CB )) or resid 264 through 265 or (resid 266 t \ hrough 275 and (name N or name CA or name C or name O or name CB )) or resid 276 \ or (resid 277 and (name N or name CA or name C or name O or name CB )) or resid \ 278 through 279 or (resid 280 through 290 and (name N or name CA or name C or n \ ame O or name CB )) or resid 291 through 293 or (resid 294 through 295 and (name \ N or name CA or name C or name O or name CB )) or resid 296 or (resid 297 and ( \ name N or name CA or name C or name O or name CB )) or resid 298 through 301 or \ (resid 302 through 303 and (name N or name CA or name C or name O or name CB )) \ or resid 304 through 305 or (resid 306 and (name N or name CA or name C or name \ O or name CB )) or resid 307 through 310 or (resid 311 through 312 and (name N o \ r name CA or name C or name O or name CB )) or resid 313 through 321 or (resid 3 \ 22 and (name N or name CA or name C or name O or name CB )) or resid 323 through \ 324 or (resid 325 through 326 and (name N or name CA or name C or name O or nam \ e CB )) or resid 327 or (resid 328 through 332 and (name N or name CA or name C \ or name O or name CB )) or resid 333 through 335 or (resid 336 through 337 and ( \ name N or name CA or name C or name O or name CB )) or resid 338 through 343 or \ (resid 344 and (name N or name CA or name C or name O or name CB )) or resid 345 \ through 347 or (resid 348 through 350 and (name N or name CA or name C or name \ O or name CB )) or resid 351 through 352 or (resid 353 through 361 and (name N o \ r name CA or name C or name O or name CB )) or resid 362 through 366)) selection = (chain 'D' and (resid 31 through 32 or (resid 33 through 35 and (name N or name \ CA or name C or name O or name CB )) or resid 36 through 39 or (resid 40 and (na \ me N or name CA or name C or name O or name CB )) or resid 41 through 44 or (res \ id 45 through 46 and (name N or name CA or name C or name O or name CB )) or res \ id 47 or (resid 48 and (name N or name CA or name C or name O or name CB )) or r \ esid 49 or (resid 50 and (name N or name CA or name C or name O or name CB )) or \ resid 51 through 52 or (resid 53 and (name N or name CA or name C or name O or \ name CB )) or resid 54 through 65 or (resid 66 and (name N or name CA or name C \ or name O or name CB )) or resid 67 or (resid 68 and (name N or name CA or name \ C or name O or name CB )) or resid 69 or (resid 70 and (name N or name CA or nam \ e C or name O or name CB )) or resid 71 through 74 or (resid 75 and (name N or n \ ame CA or name C or name O or name CB )) or resid 76 through 80 or (resid 81 and \ (name N or name CA or name C or name O or name CB )) or resid 82 through 84 or \ (resid 85 and (name N or name CA or name C or name O or name CB )) or resid 86 t \ hrough 88 or (resid 89 and (name N or name CA or name C or name O or name CB )) \ or resid 90 through 118 or (resid 119 and (name N or name CA or name C or name O \ or name CB )) or resid 120 through 121 or (resid 122 and (name N or name CA or \ name C or name O or name CB )) or resid 123 through 124 or (resid 125 through 12 \ 6 and (name N or name CA or name C or name O or name CB )) or resid 127 or (resi \ d 128 through 130 and (name N or name CA or name C or name O or name CB )) or re \ sid 131 or (resid 132 and (name N or name CA or name C or name O or name CB )) o \ r resid 133 or (resid 134 through 137 and (name N or name CA or name C or name O \ or name CB )) or resid 138 or (resid 139 and (name N or name CA or name C or na \ me O or name CB )) or resid 140 or (resid 141 and (name N or name CA or name C o \ r name O or name CB )) or resid 142 through 147 or (resid 148 through 151 and (n \ ame N or name CA or name C or name O or name CB )) or resid 152 through 156 or ( \ resid 157 and (name N or name CA or name C or name O or name CB )) or resid 158 \ through 163 or (resid 164 and (name N or name CA or name C or name O or name CB \ )) or resid 165 through 171 or (resid 172 through 173 and (name N or name CA or \ name C or name O or name CB )) or resid 174 through 179 or (resid 180 through 18 \ 5 and (name N or name CA or name C or name O or name CB )) or resid 186 or (resi \ d 187 through 190 and (name N or name CA or name C or name O or name CB )) or re \ sid 191 or (resid 192 and (name N or name CA or name C or name O or name CB )) o \ r resid 193 or (resid 194 and (name N or name CA or name C or name O or name CB \ )) or resid 195 through 197 or (resid 198 through 200 and (name N or name CA or \ name C or name O or name CB )) or resid 201 through 204 or (resid 205 and (name \ N or name CA or name C or name O or name CB )) or resid 206 through 207 or (resi \ d 208 and (name N or name CA or name C or name O or name CB )) or resid 209 or ( \ resid 210 through 212 and (name N or name CA or name C or name O or name CB )) o \ r resid 213 or (resid 214 and (name N or name CA or name C or name O or name CB \ )) or resid 215 through 217 or (resid 218 through 225 and (name N or name CA or \ name C or name O or name CB )) or resid 226 or (resid 227 and (name N or name CA \ or name C or name O or name CB )) or resid 228 through 229 or (resid 230 and (n \ ame N or name CA or name C or name O or name CB )) or resid 231 through 236 or ( \ resid 237 and (name N or name CA or name C or name O or name CB )) or resid 238 \ through 247 or (resid 248 and (name N or name CA or name C or name O or name CB \ )) or resid 249 or (resid 250 through 251 and (name N or name CA or name C or na \ me O or name CB )) or resid 252 through 254 or (resid 255 through 258 and (name \ N or name CA or name C or name O or name CB )) or resid 259 through 260 or (resi \ d 261 through 263 and (name N or name CA or name C or name O or name CB )) or re \ sid 264 through 265 or (resid 266 through 275 and (name N or name CA or name C o \ r name O or name CB )) or resid 276 through 282 or (resid 283 through 290 and (n \ ame N or name CA or name C or name O or name CB )) or resid 291 or (resid 292 an \ d (name N or name CA or name C or name O or name CB )) or resid 293 through 294 \ or (resid 295 and (name N or name CA or name C or name O or name CB )) or resid \ 296 or (resid 297 and (name N or name CA or name C or name O or name CB )) or re \ sid 298 or (resid 299 and (name N or name CA or name C or name O or name CB )) o \ r resid 300 or (resid 301 through 303 and (name N or name CA or name C or name O \ or name CB )) or resid 304 through 310 or (resid 311 through 312 and (name N or \ name CA or name C or name O or name CB )) or resid 313 through 316 or (resid 31 \ 7 and (name N or name CA or name C or name O or name CB )) or resid 318 through \ 321 or (resid 322 and (name N or name CA or name C or name O or name CB )) or re \ sid 323 through 324 or (resid 325 through 326 and (name N or name CA or name C o \ r name O or name CB )) or resid 327 through 328 or (resid 329 through 332 and (n \ ame N or name CA or name C or name O or name CB )) or resid 333 through 335 or ( \ resid 336 through 337 and (name N or name CA or name C or name O or name CB )) o \ r resid 338 through 352 or (resid 353 through 361 and (name N or name CA or name \ C or name O or name CB )) or resid 362 through 366)) } ncs_group { reference = chain 'F' selection = chain 'N' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.020 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.780 Check model and map are aligned: 0.150 Set scattering table: 0.170 Process input model: 56.760 Find NCS groups from input model: 0.780 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.710 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 61.480 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7552 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.211 20340 Z= 0.555 Angle : 1.063 21.207 27932 Z= 0.640 Chirality : 0.050 0.352 3390 Planarity : 0.005 0.046 3599 Dihedral : 16.267 173.913 6395 Min Nonbonded Distance : 1.857 Molprobity Statistics. All-atom Clashscore : 8.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.99 % Favored : 91.01 % Rotamer: Outliers : 0.00 % Allowed : 16.41 % Favored : 83.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.30 (0.16), residues: 2959 helix: 0.78 (0.15), residues: 1298 sheet: -1.31 (0.36), residues: 219 loop : -2.45 (0.16), residues: 1442 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP D 92 HIS 0.013 0.001 HIS D 98 PHE 0.039 0.002 PHE B 178 TYR 0.035 0.002 TYR E 370 ARG 0.005 0.001 ARG C 226 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5918 Ramachandran restraints generated. 2959 Oldfield, 0 Emsley, 2959 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5918 Ramachandran restraints generated. 2959 Oldfield, 0 Emsley, 2959 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 577 residues out of total 2604 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 577 time to evaluate : 2.198 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 90 MET cc_start: 0.7366 (ttm) cc_final: 0.6972 (tpp) REVERT: A 102 TYR cc_start: 0.8871 (t80) cc_final: 0.8247 (t80) REVERT: A 121 VAL cc_start: 0.9264 (t) cc_final: 0.8921 (t) REVERT: A 124 VAL cc_start: 0.9331 (t) cc_final: 0.9004 (p) REVERT: A 214 ASP cc_start: 0.8677 (t0) cc_final: 0.8283 (t0) REVERT: A 220 ILE cc_start: 0.8911 (mm) cc_final: 0.8251 (mm) REVERT: A 256 SER cc_start: 0.9206 (t) cc_final: 0.8947 (t) REVERT: A 257 ASN cc_start: 0.8211 (p0) cc_final: 0.7579 (p0) REVERT: A 320 TRP cc_start: 0.9120 (t-100) cc_final: 0.8730 (t-100) REVERT: A 341 LYS cc_start: 0.8859 (mtpm) cc_final: 0.8626 (mtmt) REVERT: B 48 LYS cc_start: 0.9095 (mttm) cc_final: 0.8879 (mttt) REVERT: B 58 GLN cc_start: 0.9197 (tp40) cc_final: 0.8744 (tp40) REVERT: B 64 LEU cc_start: 0.9176 (tp) cc_final: 0.8834 (tp) REVERT: B 186 ARG cc_start: 0.6688 (ptp-170) cc_final: 0.6428 (ptp90) REVERT: B 232 LYS cc_start: 0.9229 (ttpp) cc_final: 0.9019 (tttt) REVERT: B 320 TRP cc_start: 0.8508 (t-100) cc_final: 0.8098 (t60) REVERT: B 336 SER cc_start: 0.9450 (t) cc_final: 0.9233 (t) REVERT: B 347 ARG cc_start: 0.8192 (ttm170) cc_final: 0.7944 (mtp85) REVERT: C 36 PHE cc_start: 0.9002 (t80) cc_final: 0.8788 (t80) REVERT: C 44 ASN cc_start: 0.8817 (p0) cc_final: 0.8543 (p0) REVERT: C 48 LYS cc_start: 0.8620 (tppt) cc_final: 0.8330 (ttmm) REVERT: C 92 TRP cc_start: 0.9220 (t60) cc_final: 0.9013 (t60) REVERT: C 161 LEU cc_start: 0.9331 (tp) cc_final: 0.9030 (tp) REVERT: C 183 GLN cc_start: 0.8172 (mm-40) cc_final: 0.7566 (mt0) REVERT: C 209 MET cc_start: 0.8758 (mtt) cc_final: 0.8472 (mtt) REVERT: C 231 LYS cc_start: 0.8972 (ptmm) cc_final: 0.8722 (ptmm) REVERT: D 178 PHE cc_start: 0.6500 (t80) cc_final: 0.5661 (t80) REVERT: D 244 HIS cc_start: 0.8535 (t-90) cc_final: 0.8200 (t70) REVERT: D 255 GLU cc_start: 0.8438 (mp0) cc_final: 0.8167 (mm-30) REVERT: D 284 ASP cc_start: 0.8902 (m-30) cc_final: 0.8612 (t70) REVERT: D 288 GLN cc_start: 0.8634 (tp40) cc_final: 0.7826 (tp40) REVERT: E 856 GLN cc_start: 0.4897 (tp40) cc_final: 0.4605 (mm-40) REVERT: E 1126 TYR cc_start: 0.7522 (t80) cc_final: 0.7269 (t80) REVERT: E 1250 TYR cc_start: 0.7260 (m-80) cc_final: 0.7052 (m-80) REVERT: E 1260 TRP cc_start: 0.8205 (m100) cc_final: 0.7768 (m100) REVERT: E 1263 ARG cc_start: 0.8668 (tpp80) cc_final: 0.8030 (tpp80) REVERT: G 1 MET cc_start: 0.4804 (mtp) cc_final: 0.4598 (mtm) REVERT: G 189 ARG cc_start: 0.6646 (ttp-170) cc_final: 0.5681 (mtm110) outliers start: 0 outliers final: 0 residues processed: 577 average time/residue: 0.2965 time to fit residues: 264.2176 Evaluate side-chains 503 residues out of total 2604 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 503 time to evaluate : 2.107 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 295 random chunks: chunk 249 optimal weight: 50.0000 chunk 223 optimal weight: 0.1980 chunk 124 optimal weight: 9.9990 chunk 76 optimal weight: 5.9990 chunk 150 optimal weight: 10.0000 chunk 119 optimal weight: 1.9990 chunk 231 optimal weight: 0.5980 chunk 89 optimal weight: 4.9990 chunk 140 optimal weight: 10.0000 chunk 172 optimal weight: 40.0000 chunk 267 optimal weight: 0.9990 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 244 HIS A 287 ASN ** A 319 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 83 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7491 moved from start: 0.1334 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 20340 Z= 0.184 Angle : 0.610 9.826 27932 Z= 0.316 Chirality : 0.045 0.201 3390 Planarity : 0.004 0.054 3599 Dihedral : 14.687 160.497 3699 Min Nonbonded Distance : 2.394 Molprobity Statistics. All-atom Clashscore : 5.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.22 % Favored : 93.78 % Rotamer: Outliers : 2.98 % Allowed : 20.99 % Favored : 76.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.46 (0.16), residues: 2959 helix: 1.58 (0.15), residues: 1331 sheet: -1.10 (0.36), residues: 219 loop : -2.17 (0.17), residues: 1409 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP D 69 HIS 0.004 0.001 HIS B 98 PHE 0.043 0.002 PHE D 178 TYR 0.028 0.001 TYR E 370 ARG 0.004 0.000 ARG C 274 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5918 Ramachandran restraints generated. 2959 Oldfield, 0 Emsley, 2959 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5918 Ramachandran restraints generated. 2959 Oldfield, 0 Emsley, 2959 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 573 residues out of total 2604 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 534 time to evaluate : 2.113 Fit side-chains REVERT: A 102 TYR cc_start: 0.8789 (t80) cc_final: 0.8299 (t80) REVERT: A 124 VAL cc_start: 0.9225 (t) cc_final: 0.8984 (p) REVERT: A 138 GLN cc_start: 0.9171 (tt0) cc_final: 0.8807 (tp40) REVERT: A 147 MET cc_start: 0.8623 (ptp) cc_final: 0.8395 (ptp) REVERT: A 168 ILE cc_start: 0.9300 (OUTLIER) cc_final: 0.9079 (mm) REVERT: A 190 THR cc_start: 0.8276 (p) cc_final: 0.7981 (t) REVERT: A 256 SER cc_start: 0.8983 (t) cc_final: 0.8695 (t) REVERT: A 257 ASN cc_start: 0.8004 (p0) cc_final: 0.7683 (p0) REVERT: A 296 LEU cc_start: 0.9147 (OUTLIER) cc_final: 0.8858 (pt) REVERT: A 320 TRP cc_start: 0.9075 (t-100) cc_final: 0.8805 (t-100) REVERT: A 322 HIS cc_start: 0.8525 (m90) cc_final: 0.8179 (m170) REVERT: B 58 GLN cc_start: 0.8968 (tp40) cc_final: 0.8398 (tp40) REVERT: B 64 LEU cc_start: 0.9030 (tp) cc_final: 0.8687 (tp) REVERT: B 179 MET cc_start: 0.8364 (tpt) cc_final: 0.7846 (tpp) REVERT: B 186 ARG cc_start: 0.6874 (ptp-170) cc_final: 0.6638 (ptp90) REVERT: B 232 LYS cc_start: 0.9186 (ttpp) cc_final: 0.8967 (tttp) REVERT: B 237 GLU cc_start: 0.8098 (tm-30) cc_final: 0.7651 (tm-30) REVERT: B 320 TRP cc_start: 0.8355 (t-100) cc_final: 0.7964 (t60) REVERT: C 44 ASN cc_start: 0.8687 (p0) cc_final: 0.8462 (p0) REVERT: C 48 LYS cc_start: 0.8777 (tppt) cc_final: 0.8545 (ttmm) REVERT: C 92 TRP cc_start: 0.9188 (t60) cc_final: 0.8978 (t60) REVERT: C 183 GLN cc_start: 0.7617 (mm-40) cc_final: 0.7308 (mt0) REVERT: C 209 MET cc_start: 0.8747 (mtt) cc_final: 0.8406 (mtt) REVERT: D 214 ASP cc_start: 0.7563 (t0) cc_final: 0.7282 (t0) REVERT: D 244 HIS cc_start: 0.8518 (t-90) cc_final: 0.8150 (t-90) REVERT: D 255 GLU cc_start: 0.8502 (mp0) cc_final: 0.8145 (mm-30) REVERT: D 284 ASP cc_start: 0.8941 (m-30) cc_final: 0.8653 (t70) REVERT: E 140 TYR cc_start: 0.9354 (t80) cc_final: 0.9092 (t80) REVERT: E 148 LYS cc_start: 0.8567 (mmtp) cc_final: 0.8100 (mmtp) REVERT: E 173 MET cc_start: 0.7629 (tpp) cc_final: 0.7153 (tpp) REVERT: E 507 TRP cc_start: 0.5877 (m100) cc_final: 0.5640 (m100) REVERT: E 856 GLN cc_start: 0.4307 (tp40) cc_final: 0.3850 (mm-40) REVERT: E 1197 LEU cc_start: 0.6550 (mt) cc_final: 0.5785 (mp) REVERT: E 1250 TYR cc_start: 0.7176 (m-80) cc_final: 0.6965 (m-80) REVERT: E 1260 TRP cc_start: 0.8123 (m100) cc_final: 0.7706 (m100) REVERT: E 1263 ARG cc_start: 0.8632 (tpp80) cc_final: 0.7997 (tpp80) REVERT: G 189 ARG cc_start: 0.5991 (ttp-170) cc_final: 0.5102 (mtm110) outliers start: 39 outliers final: 23 residues processed: 553 average time/residue: 0.2850 time to fit residues: 246.5494 Evaluate side-chains 533 residues out of total 2604 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 508 time to evaluate : 2.089 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 129 SER Chi-restraints excluded: chain A residue 137 VAL Chi-restraints excluded: chain A residue 164 ILE Chi-restraints excluded: chain A residue 165 VAL Chi-restraints excluded: chain A residue 168 ILE Chi-restraints excluded: chain A residue 296 LEU Chi-restraints excluded: chain A residue 338 ASP Chi-restraints excluded: chain B residue 68 LYS Chi-restraints excluded: chain B residue 78 MET Chi-restraints excluded: chain B residue 152 CYS Chi-restraints excluded: chain B residue 296 LEU Chi-restraints excluded: chain B residue 299 VAL Chi-restraints excluded: chain C residue 158 VAL Chi-restraints excluded: chain C residue 274 ARG Chi-restraints excluded: chain D residue 152 CYS Chi-restraints excluded: chain D residue 176 CYS Chi-restraints excluded: chain D residue 209 MET Chi-restraints excluded: chain D residue 308 GLN Chi-restraints excluded: chain E residue 120 VAL Chi-restraints excluded: chain E residue 537 ILE Chi-restraints excluded: chain E residue 578 LEU Chi-restraints excluded: chain E residue 588 VAL Chi-restraints excluded: chain E residue 1083 THR Chi-restraints excluded: chain E residue 1225 CYS Chi-restraints excluded: chain E residue 1371 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 295 random chunks: chunk 148 optimal weight: 20.0000 chunk 83 optimal weight: 8.9990 chunk 222 optimal weight: 30.0000 chunk 182 optimal weight: 30.0000 chunk 73 optimal weight: 9.9990 chunk 268 optimal weight: 2.9990 chunk 289 optimal weight: 5.9990 chunk 239 optimal weight: 0.0970 chunk 266 optimal weight: 40.0000 chunk 91 optimal weight: 5.9990 chunk 215 optimal weight: 50.0000 overall best weight: 4.8186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 269 HIS ** A 319 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 344 ASN ** C 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 196 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 228 GLN ** D 319 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 83 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7522 moved from start: 0.1594 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 20340 Z= 0.245 Angle : 0.603 9.447 27932 Z= 0.313 Chirality : 0.045 0.225 3390 Planarity : 0.004 0.056 3599 Dihedral : 13.921 160.144 3699 Min Nonbonded Distance : 2.402 Molprobity Statistics. All-atom Clashscore : 6.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.30 % Favored : 92.70 % Rotamer: Outliers : 3.97 % Allowed : 22.98 % Favored : 73.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.36 (0.16), residues: 2959 helix: 1.64 (0.15), residues: 1355 sheet: -1.04 (0.36), residues: 216 loop : -2.14 (0.17), residues: 1388 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP E 230 HIS 0.005 0.001 HIS B 269 PHE 0.058 0.002 PHE D 178 TYR 0.028 0.002 TYR E 370 ARG 0.012 0.000 ARG A 51 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5918 Ramachandran restraints generated. 2959 Oldfield, 0 Emsley, 2959 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5918 Ramachandran restraints generated. 2959 Oldfield, 0 Emsley, 2959 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 562 residues out of total 2604 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 510 time to evaluate : 2.296 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 102 TYR cc_start: 0.8562 (t80) cc_final: 0.8165 (t80) REVERT: A 138 GLN cc_start: 0.9169 (tt0) cc_final: 0.8755 (tp40) REVERT: A 190 THR cc_start: 0.8341 (p) cc_final: 0.7863 (t) REVERT: A 209 MET cc_start: 0.7937 (mmm) cc_final: 0.7706 (mmm) REVERT: A 256 SER cc_start: 0.9093 (t) cc_final: 0.8888 (t) REVERT: A 257 ASN cc_start: 0.8049 (p0) cc_final: 0.7714 (p0) REVERT: A 296 LEU cc_start: 0.9132 (OUTLIER) cc_final: 0.8851 (pt) REVERT: A 320 TRP cc_start: 0.9108 (t-100) cc_final: 0.8755 (t-100) REVERT: A 322 HIS cc_start: 0.8581 (m90) cc_final: 0.8193 (m170) REVERT: B 58 GLN cc_start: 0.9033 (tp40) cc_final: 0.8427 (tp40) REVERT: B 64 LEU cc_start: 0.9107 (tp) cc_final: 0.8713 (tp) REVERT: B 186 ARG cc_start: 0.6975 (ptp-170) cc_final: 0.6723 (ptp90) REVERT: B 320 TRP cc_start: 0.8447 (t-100) cc_final: 0.8073 (t60) REVERT: C 44 ASN cc_start: 0.8650 (p0) cc_final: 0.8429 (p0) REVERT: C 48 LYS cc_start: 0.8841 (tppt) cc_final: 0.8609 (ttmm) REVERT: C 67 LEU cc_start: 0.7846 (mt) cc_final: 0.7622 (mt) REVERT: C 92 TRP cc_start: 0.9223 (t60) cc_final: 0.8919 (t60) REVERT: C 93 LEU cc_start: 0.9321 (mt) cc_final: 0.9106 (mt) REVERT: C 183 GLN cc_start: 0.7871 (mm-40) cc_final: 0.7504 (mt0) REVERT: D 178 PHE cc_start: 0.5937 (t80) cc_final: 0.5460 (t80) REVERT: D 214 ASP cc_start: 0.7619 (t0) cc_final: 0.7360 (t0) REVERT: D 226 ARG cc_start: 0.8633 (mtp180) cc_final: 0.8238 (mtm180) REVERT: D 244 HIS cc_start: 0.8580 (t-90) cc_final: 0.8180 (t-90) REVERT: D 255 GLU cc_start: 0.8504 (mp0) cc_final: 0.8155 (mm-30) REVERT: D 284 ASP cc_start: 0.8938 (m-30) cc_final: 0.8575 (t70) REVERT: E 130 PHE cc_start: 0.8558 (t80) cc_final: 0.8052 (t80) REVERT: E 173 MET cc_start: 0.7739 (OUTLIER) cc_final: 0.7499 (tpp) REVERT: E 494 GLU cc_start: 0.7841 (mt-10) cc_final: 0.7576 (tt0) REVERT: E 578 LEU cc_start: 0.8601 (OUTLIER) cc_final: 0.8302 (tt) REVERT: E 753 GLN cc_start: 0.5787 (tm-30) cc_final: 0.4516 (tt0) REVERT: E 856 GLN cc_start: 0.4433 (tp40) cc_final: 0.4220 (mm-40) REVERT: E 1197 LEU cc_start: 0.6526 (mt) cc_final: 0.5992 (mp) REVERT: E 1250 TYR cc_start: 0.7217 (m-80) cc_final: 0.7001 (m-80) REVERT: E 1260 TRP cc_start: 0.8186 (m100) cc_final: 0.7749 (m100) REVERT: E 1263 ARG cc_start: 0.8586 (tpp80) cc_final: 0.8023 (tpp80) REVERT: G 110 MET cc_start: 0.7595 (mmp) cc_final: 0.7387 (mmm) outliers start: 52 outliers final: 37 residues processed: 534 average time/residue: 0.3138 time to fit residues: 259.6022 Evaluate side-chains 533 residues out of total 2604 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 493 time to evaluate : 2.344 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 ILE Chi-restraints excluded: chain A residue 62 THR Chi-restraints excluded: chain A residue 129 SER Chi-restraints excluded: chain A residue 137 VAL Chi-restraints excluded: chain A residue 152 CYS Chi-restraints excluded: chain A residue 164 ILE Chi-restraints excluded: chain A residue 165 VAL Chi-restraints excluded: chain A residue 221 ILE Chi-restraints excluded: chain A residue 296 LEU Chi-restraints excluded: chain A residue 338 ASP Chi-restraints excluded: chain B residue 68 LYS Chi-restraints excluded: chain B residue 78 MET Chi-restraints excluded: chain B residue 152 CYS Chi-restraints excluded: chain B residue 191 LEU Chi-restraints excluded: chain B residue 299 VAL Chi-restraints excluded: chain B residue 305 ILE Chi-restraints excluded: chain B residue 336 SER Chi-restraints excluded: chain B residue 348 VAL Chi-restraints excluded: chain C residue 33 LYS Chi-restraints excluded: chain C residue 37 ILE Chi-restraints excluded: chain C residue 137 VAL Chi-restraints excluded: chain C residue 158 VAL Chi-restraints excluded: chain C residue 181 THR Chi-restraints excluded: chain C residue 280 ILE Chi-restraints excluded: chain D residue 64 LEU Chi-restraints excluded: chain D residue 152 CYS Chi-restraints excluded: chain D residue 176 CYS Chi-restraints excluded: chain D residue 209 MET Chi-restraints excluded: chain D residue 308 GLN Chi-restraints excluded: chain D residue 329 THR Chi-restraints excluded: chain E residue 120 VAL Chi-restraints excluded: chain E residue 142 VAL Chi-restraints excluded: chain E residue 173 MET Chi-restraints excluded: chain E residue 537 ILE Chi-restraints excluded: chain E residue 578 LEU Chi-restraints excluded: chain E residue 588 VAL Chi-restraints excluded: chain E residue 1083 THR Chi-restraints excluded: chain E residue 1225 CYS Chi-restraints excluded: chain E residue 1258 LEU Chi-restraints excluded: chain E residue 1371 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 295 random chunks: chunk 265 optimal weight: 50.0000 chunk 201 optimal weight: 0.6980 chunk 139 optimal weight: 1.9990 chunk 29 optimal weight: 10.0000 chunk 128 optimal weight: 4.9990 chunk 180 optimal weight: 8.9990 chunk 269 optimal weight: 6.9990 chunk 285 optimal weight: 20.0000 chunk 140 optimal weight: 8.9990 chunk 255 optimal weight: 50.0000 chunk 76 optimal weight: 9.9990 overall best weight: 4.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 47 HIS A 287 ASN ** A 319 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 228 GLN E 83 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7523 moved from start: 0.1845 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 20340 Z= 0.236 Angle : 0.596 9.415 27932 Z= 0.305 Chirality : 0.045 0.226 3390 Planarity : 0.004 0.055 3599 Dihedral : 13.271 158.655 3699 Min Nonbonded Distance : 2.387 Molprobity Statistics. All-atom Clashscore : 5.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.86 % Favored : 93.14 % Rotamer: Outliers : 4.66 % Allowed : 24.20 % Favored : 71.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.31 (0.16), residues: 2959 helix: 1.65 (0.15), residues: 1361 sheet: -0.98 (0.36), residues: 216 loop : -2.10 (0.17), residues: 1382 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 91 HIS 0.005 0.001 HIS B 269 PHE 0.055 0.002 PHE D 178 TYR 0.027 0.002 TYR E 370 ARG 0.004 0.000 ARG B 202 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5918 Ramachandran restraints generated. 2959 Oldfield, 0 Emsley, 2959 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5918 Ramachandran restraints generated. 2959 Oldfield, 0 Emsley, 2959 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 575 residues out of total 2604 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 514 time to evaluate : 2.259 Fit side-chains revert: symmetry clash REVERT: A 84 TRP cc_start: 0.9146 (m-10) cc_final: 0.8753 (m-10) REVERT: A 102 TYR cc_start: 0.8567 (t80) cc_final: 0.8163 (t80) REVERT: A 138 GLN cc_start: 0.9114 (tt0) cc_final: 0.8899 (tp40) REVERT: A 190 THR cc_start: 0.8308 (p) cc_final: 0.7841 (t) REVERT: A 257 ASN cc_start: 0.8046 (p0) cc_final: 0.7743 (p0) REVERT: A 285 LEU cc_start: 0.9373 (OUTLIER) cc_final: 0.8841 (tp) REVERT: A 296 LEU cc_start: 0.9135 (OUTLIER) cc_final: 0.8872 (pt) REVERT: A 320 TRP cc_start: 0.9101 (t-100) cc_final: 0.8792 (t-100) REVERT: A 322 HIS cc_start: 0.8517 (m90) cc_final: 0.8258 (m170) REVERT: B 58 GLN cc_start: 0.9027 (tp40) cc_final: 0.8444 (tp40) REVERT: B 64 LEU cc_start: 0.9067 (tp) cc_final: 0.8768 (tp) REVERT: B 147 MET cc_start: 0.8681 (ttm) cc_final: 0.8432 (ttm) REVERT: B 179 MET cc_start: 0.8281 (tpt) cc_final: 0.8060 (tpp) REVERT: B 232 LYS cc_start: 0.9217 (ttpp) cc_final: 0.8982 (tttm) REVERT: B 287 ASN cc_start: 0.8099 (t0) cc_final: 0.7608 (t0) REVERT: B 320 TRP cc_start: 0.8446 (t-100) cc_final: 0.8100 (t60) REVERT: C 44 ASN cc_start: 0.8646 (p0) cc_final: 0.8419 (p0) REVERT: C 48 LYS cc_start: 0.8865 (tppt) cc_final: 0.8628 (ttmm) REVERT: C 92 TRP cc_start: 0.9231 (t60) cc_final: 0.8898 (t60) REVERT: C 93 LEU cc_start: 0.9327 (mt) cc_final: 0.9124 (mt) REVERT: C 183 GLN cc_start: 0.7659 (mm-40) cc_final: 0.7280 (mt0) REVERT: C 278 TYR cc_start: 0.8844 (t80) cc_final: 0.8601 (t80) REVERT: C 322 HIS cc_start: 0.8256 (m90) cc_final: 0.7953 (m170) REVERT: D 178 PHE cc_start: 0.5875 (t80) cc_final: 0.5430 (t80) REVERT: D 214 ASP cc_start: 0.7615 (t0) cc_final: 0.7264 (t0) REVERT: D 226 ARG cc_start: 0.8632 (mtp180) cc_final: 0.8292 (mtm180) REVERT: D 244 HIS cc_start: 0.8569 (t-90) cc_final: 0.8233 (t-90) REVERT: D 255 GLU cc_start: 0.8504 (mp0) cc_final: 0.8156 (mm-30) REVERT: D 284 ASP cc_start: 0.8941 (m-30) cc_final: 0.8576 (t70) REVERT: E 112 PHE cc_start: 0.8115 (t80) cc_final: 0.7794 (t80) REVERT: E 130 PHE cc_start: 0.8442 (t80) cc_final: 0.8014 (t80) REVERT: E 132 LYS cc_start: 0.8373 (OUTLIER) cc_final: 0.8149 (mtpt) REVERT: E 494 GLU cc_start: 0.7839 (mt-10) cc_final: 0.7561 (tt0) REVERT: E 578 LEU cc_start: 0.8612 (OUTLIER) cc_final: 0.8306 (tt) REVERT: E 753 GLN cc_start: 0.6080 (tm-30) cc_final: 0.4804 (tp40) REVERT: E 1197 LEU cc_start: 0.6483 (mt) cc_final: 0.6023 (mp) REVERT: E 1250 TYR cc_start: 0.7177 (m-80) cc_final: 0.6968 (m-80) REVERT: E 1260 TRP cc_start: 0.8189 (m100) cc_final: 0.7757 (m100) REVERT: E 1263 ARG cc_start: 0.8576 (tpp80) cc_final: 0.8012 (tpp80) outliers start: 61 outliers final: 45 residues processed: 544 average time/residue: 0.3075 time to fit residues: 262.2550 Evaluate side-chains 549 residues out of total 2604 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 500 time to evaluate : 2.289 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 ILE Chi-restraints excluded: chain A residue 62 THR Chi-restraints excluded: chain A residue 129 SER Chi-restraints excluded: chain A residue 135 ILE Chi-restraints excluded: chain A residue 137 VAL Chi-restraints excluded: chain A residue 152 CYS Chi-restraints excluded: chain A residue 164 ILE Chi-restraints excluded: chain A residue 165 VAL Chi-restraints excluded: chain A residue 221 ILE Chi-restraints excluded: chain A residue 261 LEU Chi-restraints excluded: chain A residue 285 LEU Chi-restraints excluded: chain A residue 296 LEU Chi-restraints excluded: chain A residue 338 ASP Chi-restraints excluded: chain B residue 65 VAL Chi-restraints excluded: chain B residue 68 LYS Chi-restraints excluded: chain B residue 78 MET Chi-restraints excluded: chain B residue 152 CYS Chi-restraints excluded: chain B residue 296 LEU Chi-restraints excluded: chain B residue 299 VAL Chi-restraints excluded: chain B residue 305 ILE Chi-restraints excluded: chain B residue 336 SER Chi-restraints excluded: chain B residue 348 VAL Chi-restraints excluded: chain C residue 33 LYS Chi-restraints excluded: chain C residue 37 ILE Chi-restraints excluded: chain C residue 137 VAL Chi-restraints excluded: chain C residue 158 VAL Chi-restraints excluded: chain C residue 181 THR Chi-restraints excluded: chain C residue 231 LYS Chi-restraints excluded: chain D residue 64 LEU Chi-restraints excluded: chain D residue 146 ARG Chi-restraints excluded: chain D residue 152 CYS Chi-restraints excluded: chain D residue 172 VAL Chi-restraints excluded: chain D residue 176 CYS Chi-restraints excluded: chain D residue 209 MET Chi-restraints excluded: chain D residue 308 GLN Chi-restraints excluded: chain D residue 329 THR Chi-restraints excluded: chain E residue 76 THR Chi-restraints excluded: chain E residue 120 VAL Chi-restraints excluded: chain E residue 132 LYS Chi-restraints excluded: chain E residue 142 VAL Chi-restraints excluded: chain E residue 525 SER Chi-restraints excluded: chain E residue 578 LEU Chi-restraints excluded: chain E residue 588 VAL Chi-restraints excluded: chain E residue 1083 THR Chi-restraints excluded: chain E residue 1225 CYS Chi-restraints excluded: chain E residue 1258 LEU Chi-restraints excluded: chain E residue 1371 ILE Chi-restraints excluded: chain E residue 1489 THR Chi-restraints excluded: chain G residue 155 TYR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 295 random chunks: chunk 237 optimal weight: 20.0000 chunk 161 optimal weight: 0.9980 chunk 4 optimal weight: 4.9990 chunk 212 optimal weight: 50.0000 chunk 117 optimal weight: 8.9990 chunk 243 optimal weight: 30.0000 chunk 197 optimal weight: 20.0000 chunk 0 optimal weight: 50.0000 chunk 145 optimal weight: 10.0000 chunk 255 optimal weight: 30.0000 chunk 71 optimal weight: 9.9990 overall best weight: 6.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 47 HIS A 269 HIS ** A 319 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 228 GLN E 83 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7558 moved from start: 0.1935 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.058 20340 Z= 0.312 Angle : 0.628 9.370 27932 Z= 0.326 Chirality : 0.046 0.248 3390 Planarity : 0.004 0.055 3599 Dihedral : 12.936 158.054 3699 Min Nonbonded Distance : 2.334 Molprobity Statistics. All-atom Clashscore : 6.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.25 % Favored : 91.75 % Rotamer: Outliers : 5.73 % Allowed : 23.44 % Favored : 70.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.37 (0.16), residues: 2959 helix: 1.63 (0.14), residues: 1347 sheet: -0.88 (0.36), residues: 213 loop : -2.16 (0.17), residues: 1399 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP B 91 HIS 0.009 0.001 HIS B 269 PHE 0.054 0.002 PHE D 178 TYR 0.026 0.002 TYR E 370 ARG 0.005 0.000 ARG C 202 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5918 Ramachandran restraints generated. 2959 Oldfield, 0 Emsley, 2959 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5918 Ramachandran restraints generated. 2959 Oldfield, 0 Emsley, 2959 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 585 residues out of total 2604 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 75 poor density : 510 time to evaluate : 2.999 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 102 TYR cc_start: 0.8604 (t80) cc_final: 0.8215 (t80) REVERT: A 138 GLN cc_start: 0.9166 (tt0) cc_final: 0.8895 (tp40) REVERT: A 190 THR cc_start: 0.8344 (p) cc_final: 0.7887 (t) REVERT: A 257 ASN cc_start: 0.8194 (p0) cc_final: 0.7778 (p0) REVERT: A 269 HIS cc_start: 0.8721 (OUTLIER) cc_final: 0.7275 (t70) REVERT: A 285 LEU cc_start: 0.9387 (OUTLIER) cc_final: 0.8885 (tp) REVERT: A 296 LEU cc_start: 0.9156 (OUTLIER) cc_final: 0.8875 (pt) REVERT: A 320 TRP cc_start: 0.9074 (t-100) cc_final: 0.8700 (t-100) REVERT: B 58 GLN cc_start: 0.9113 (tp40) cc_final: 0.8590 (tp40) REVERT: B 64 LEU cc_start: 0.9122 (tp) cc_final: 0.8738 (tp) REVERT: B 147 MET cc_start: 0.8705 (ttm) cc_final: 0.8398 (ttm) REVERT: B 179 MET cc_start: 0.8481 (tpt) cc_final: 0.7951 (tpp) REVERT: B 232 LYS cc_start: 0.9199 (ttpp) cc_final: 0.8997 (tttp) REVERT: B 287 ASN cc_start: 0.8123 (t0) cc_final: 0.7643 (t0) REVERT: B 320 TRP cc_start: 0.8461 (t-100) cc_final: 0.8106 (t60) REVERT: C 36 PHE cc_start: 0.9105 (t80) cc_final: 0.8873 (t80) REVERT: C 44 ASN cc_start: 0.8687 (p0) cc_final: 0.8454 (p0) REVERT: C 48 LYS cc_start: 0.8900 (tppt) cc_final: 0.8696 (ttmm) REVERT: C 183 GLN cc_start: 0.7883 (mm-40) cc_final: 0.7506 (mt0) REVERT: C 322 HIS cc_start: 0.8318 (m90) cc_final: 0.7958 (m170) REVERT: D 178 PHE cc_start: 0.6232 (t80) cc_final: 0.5126 (t80) REVERT: D 226 ARG cc_start: 0.8620 (mtp180) cc_final: 0.8235 (mtm180) REVERT: D 244 HIS cc_start: 0.8576 (t-90) cc_final: 0.8268 (t-90) REVERT: D 255 GLU cc_start: 0.8505 (mp0) cc_final: 0.8161 (mm-30) REVERT: D 284 ASP cc_start: 0.9065 (m-30) cc_final: 0.8634 (t70) REVERT: E 112 PHE cc_start: 0.8063 (t80) cc_final: 0.7733 (t80) REVERT: E 130 PHE cc_start: 0.8405 (t80) cc_final: 0.7988 (t80) REVERT: E 132 LYS cc_start: 0.8369 (OUTLIER) cc_final: 0.8082 (mttt) REVERT: E 479 LYS cc_start: 0.6037 (tptt) cc_final: 0.5784 (tptt) REVERT: E 494 GLU cc_start: 0.7861 (mt-10) cc_final: 0.7582 (tt0) REVERT: E 578 LEU cc_start: 0.8564 (OUTLIER) cc_final: 0.8258 (tt) REVERT: E 753 GLN cc_start: 0.5975 (tm-30) cc_final: 0.4599 (tp40) REVERT: E 1107 LEU cc_start: 0.7616 (OUTLIER) cc_final: 0.7414 (mp) REVERT: E 1197 LEU cc_start: 0.6480 (mt) cc_final: 0.6051 (mp) REVERT: E 1250 TYR cc_start: 0.7213 (m-80) cc_final: 0.6982 (m-80) REVERT: E 1260 TRP cc_start: 0.8206 (m100) cc_final: 0.7721 (m100) REVERT: E 1263 ARG cc_start: 0.8625 (tpp80) cc_final: 0.8070 (tpp80) REVERT: E 1394 LEU cc_start: 0.4548 (OUTLIER) cc_final: 0.3863 (mp) REVERT: G 189 ARG cc_start: 0.6145 (ttp-170) cc_final: 0.5472 (mtm110) outliers start: 75 outliers final: 56 residues processed: 546 average time/residue: 0.2962 time to fit residues: 254.0365 Evaluate side-chains 565 residues out of total 2604 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 502 time to evaluate : 2.311 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 ILE Chi-restraints excluded: chain A residue 62 THR Chi-restraints excluded: chain A residue 129 SER Chi-restraints excluded: chain A residue 135 ILE Chi-restraints excluded: chain A residue 137 VAL Chi-restraints excluded: chain A residue 152 CYS Chi-restraints excluded: chain A residue 164 ILE Chi-restraints excluded: chain A residue 165 VAL Chi-restraints excluded: chain A residue 216 ARG Chi-restraints excluded: chain A residue 221 ILE Chi-restraints excluded: chain A residue 247 ASP Chi-restraints excluded: chain A residue 269 HIS Chi-restraints excluded: chain A residue 285 LEU Chi-restraints excluded: chain A residue 296 LEU Chi-restraints excluded: chain A residue 338 ASP Chi-restraints excluded: chain B residue 65 VAL Chi-restraints excluded: chain B residue 68 LYS Chi-restraints excluded: chain B residue 78 MET Chi-restraints excluded: chain B residue 152 CYS Chi-restraints excluded: chain B residue 262 VAL Chi-restraints excluded: chain B residue 296 LEU Chi-restraints excluded: chain B residue 299 VAL Chi-restraints excluded: chain B residue 305 ILE Chi-restraints excluded: chain B residue 336 SER Chi-restraints excluded: chain B residue 347 ARG Chi-restraints excluded: chain B residue 348 VAL Chi-restraints excluded: chain C residue 33 LYS Chi-restraints excluded: chain C residue 37 ILE Chi-restraints excluded: chain C residue 137 VAL Chi-restraints excluded: chain C residue 158 VAL Chi-restraints excluded: chain C residue 172 VAL Chi-restraints excluded: chain C residue 181 THR Chi-restraints excluded: chain C residue 227 ILE Chi-restraints excluded: chain C residue 231 LYS Chi-restraints excluded: chain C residue 280 ILE Chi-restraints excluded: chain D residue 40 SER Chi-restraints excluded: chain D residue 62 THR Chi-restraints excluded: chain D residue 64 LEU Chi-restraints excluded: chain D residue 172 VAL Chi-restraints excluded: chain D residue 176 CYS Chi-restraints excluded: chain D residue 209 MET Chi-restraints excluded: chain D residue 225 VAL Chi-restraints excluded: chain D residue 300 VAL Chi-restraints excluded: chain D residue 308 GLN Chi-restraints excluded: chain D residue 329 THR Chi-restraints excluded: chain E residue 76 THR Chi-restraints excluded: chain E residue 92 VAL Chi-restraints excluded: chain E residue 120 VAL Chi-restraints excluded: chain E residue 132 LYS Chi-restraints excluded: chain E residue 142 VAL Chi-restraints excluded: chain E residue 361 LEU Chi-restraints excluded: chain E residue 525 SER Chi-restraints excluded: chain E residue 578 LEU Chi-restraints excluded: chain E residue 588 VAL Chi-restraints excluded: chain E residue 1083 THR Chi-restraints excluded: chain E residue 1107 LEU Chi-restraints excluded: chain E residue 1225 CYS Chi-restraints excluded: chain E residue 1258 LEU Chi-restraints excluded: chain E residue 1371 ILE Chi-restraints excluded: chain E residue 1394 LEU Chi-restraints excluded: chain E residue 1489 THR Chi-restraints excluded: chain G residue 155 TYR Chi-restraints excluded: chain G residue 172 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 295 random chunks: chunk 95 optimal weight: 4.9990 chunk 256 optimal weight: 9.9990 chunk 56 optimal weight: 7.9990 chunk 167 optimal weight: 7.9990 chunk 70 optimal weight: 8.9990 chunk 285 optimal weight: 9.9990 chunk 236 optimal weight: 20.0000 chunk 132 optimal weight: 20.0000 chunk 23 optimal weight: 2.9990 chunk 94 optimal weight: 5.9990 chunk 149 optimal weight: 20.0000 overall best weight: 5.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 269 HIS A 287 ASN ** A 319 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 44 ASN B 71 HIS D 228 GLN E 323 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7547 moved from start: 0.2038 Sorry: Reduce crashed with command 'molprobity.reduce -quiet -trim -'. Dumping stdin to file 'reduce_fail.pdb'. Return code: -15 Dumping stderr: