Starting phenix.real_space_refine on Sun Feb 18 06:18:03 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6c1g_7330/02_2024/6c1g_7330_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6c1g_7330/02_2024/6c1g_7330.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6c1g_7330/02_2024/6c1g_7330.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6c1g_7330/02_2024/6c1g_7330.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6c1g_7330/02_2024/6c1g_7330_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6c1g_7330/02_2024/6c1g_7330_updated.pdb" } resolution = 3.8 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.003 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 12 5.49 5 Mg 6 5.21 5 S 126 5.16 5 C 13115 2.51 5 N 3630 2.21 5 O 4105 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "P ARG 38": "NH1" <-> "NH2" Residue "P TYR 209": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P TYR 389": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P PHE 394": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P ARG 498": "NH1" <-> "NH2" Residue "P TYR 535": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P ARG 536": "NH1" <-> "NH2" Residue "P ARG 566": "NH1" <-> "NH2" Residue "P ARG 635": "NH1" <-> "NH2" Residue "A ARG 62": "NH1" <-> "NH2" Residue "A PHE 255": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 335": "NH1" <-> "NH2" Residue "A ARG 372": "NH1" <-> "NH2" Residue "B ARG 62": "NH1" <-> "NH2" Residue "B PHE 255": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 335": "NH1" <-> "NH2" Residue "B ARG 372": "NH1" <-> "NH2" Residue "C ARG 62": "NH1" <-> "NH2" Residue "C PHE 255": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 335": "NH1" <-> "NH2" Residue "C ARG 372": "NH1" <-> "NH2" Residue "D ARG 62": "NH1" <-> "NH2" Residue "D PHE 255": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 335": "NH1" <-> "NH2" Residue "D ARG 372": "NH1" <-> "NH2" Residue "E ARG 62": "NH1" <-> "NH2" Residue "E PHE 255": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 335": "NH1" <-> "NH2" Residue "E ARG 372": "NH1" <-> "NH2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 20994 Number of models: 1 Model: "" Number of chains: 13 Chain: "P" Number of atoms: 5570 Number of conformers: 1 Conformer: "" Number of residues, atoms: 729, 5570 Classifications: {'peptide': 729} Incomplete info: {'backbone_only': 71, 'n_c_alpha_c_only': 1} Link IDs: {'CIS': 5, 'PCIS': 2, 'PTRANS': 21, 'TRANS': 700} Unresolved chain link angles: 4 Unresolved non-hydrogen bonds: 367 Unresolved non-hydrogen angles: 521 Unresolved non-hydrogen dihedrals: 259 Unresolved non-hydrogen chiralities: 92 Planarities with less than four sites: {'GLN:plan1': 3, 'ASP:plan': 2, 'TYR:plan': 4, 'ASN:plan1': 2, 'TRP:plan': 3, 'HIS:plan': 2, 'PHE:plan': 3, 'GLU:plan': 8, 'ARG:plan': 6} Unresolved non-hydrogen planarities: 185 Chain: "R" Number of atoms: 591 Number of conformers: 1 Conformer: "" Number of residues, atoms: 148, 591 Classifications: {'peptide': 148} Incomplete info: {'backbone_only': 136, 'n_c_alpha_c_only': 1} Link IDs: {'CIS': 2, 'PTRANS': 2, 'TRANS': 143} Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 587 Unresolved non-hydrogen angles: 842 Unresolved non-hydrogen dihedrals: 357 Unresolved non-hydrogen chiralities: 173 Planarities with less than four sites: {'GLN:plan1': 6, 'HIS:plan': 1, 'TYR:plan': 2, 'ASN:plan1': 6, 'ASP:plan': 17, 'PHE:plan': 8, 'GLU:plan': 21, 'ARG:plan': 6} Unresolved non-hydrogen planarities: 308 Chain: "A" Number of atoms: 2933 Number of conformers: 1 Conformer: "" Number of residues, atoms: 375, 2933 Classifications: {'peptide': 375} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 355} Chain: "B" Number of atoms: 2933 Number of conformers: 1 Conformer: "" Number of residues, atoms: 375, 2933 Classifications: {'peptide': 375} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 355} Chain: "C" Number of atoms: 2933 Number of conformers: 1 Conformer: "" Number of residues, atoms: 375, 2933 Classifications: {'peptide': 375} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 355} Chain: "D" Number of atoms: 2933 Number of conformers: 1 Conformer: "" Number of residues, atoms: 375, 2933 Classifications: {'peptide': 375} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 355} Chain: "E" Number of atoms: 2933 Number of conformers: 1 Conformer: "" Number of residues, atoms: 375, 2933 Classifications: {'peptide': 375} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 355} Chain: "P" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "A" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 11.23, per 1000 atoms: 0.53 Number of scatterers: 20994 At special positions: 0 Unit cell: (201.5, 106.6, 193.7, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 126 16.00 P 12 15.00 Mg 6 11.99 O 4105 8.00 N 3630 7.00 C 13115 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 8.18 Conformation dependent library (CDL) restraints added in 3.8 seconds 5476 Ramachandran restraints generated. 2738 Oldfield, 0 Emsley, 2738 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4714 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 122 helices and 26 sheets defined 43.1% alpha, 11.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.56 Creating SS restraints... Processing helix chain 'P' and resid 29 through 40 Processing helix chain 'P' and resid 62 through 64 No H-bonds generated for 'chain 'P' and resid 62 through 64' Processing helix chain 'P' and resid 66 through 72 removed outlier: 3.532A pdb=" N TYR P 72 " --> pdb=" O LYS P 68 " (cutoff:3.500A) Processing helix chain 'P' and resid 84 through 96 removed outlier: 3.537A pdb=" N SER P 88 " --> pdb=" O ILE P 84 " (cutoff:3.500A) Processing helix chain 'P' and resid 115 through 129 Processing helix chain 'P' and resid 132 through 152 removed outlier: 4.295A pdb=" N GLN P 137 " --> pdb=" O GLU P 134 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N LYS P 139 " --> pdb=" O ASN P 136 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N GLU P 140 " --> pdb=" O GLN P 137 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N LEU P 143 " --> pdb=" O GLU P 140 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N GLN P 144 " --> pdb=" O GLN P 141 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N THR P 146 " --> pdb=" O LEU P 143 " (cutoff:3.500A) Proline residue: P 147 - end of helix removed outlier: 3.755A pdb=" N GLU P 150 " --> pdb=" O PRO P 147 " (cutoff:3.500A) Processing helix chain 'P' and resid 192 through 196 Processing helix chain 'P' and resid 206 through 214 Processing helix chain 'P' and resid 217 through 222 Processing helix chain 'P' and resid 237 through 239 No H-bonds generated for 'chain 'P' and resid 237 through 239' Processing helix chain 'P' and resid 247 through 260 removed outlier: 4.133A pdb=" N GLN P 259 " --> pdb=" O ARG P 255 " (cutoff:3.500A) removed outlier: 4.279A pdb=" N ILE P 260 " --> pdb=" O ASN P 256 " (cutoff:3.500A) Processing helix chain 'P' and resid 265 through 283 removed outlier: 3.960A pdb=" N GLU P 269 " --> pdb=" O ASP P 265 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N VAL P 274 " --> pdb=" O SER P 270 " (cutoff:3.500A) removed outlier: 4.441A pdb=" N GLY P 282 " --> pdb=" O VAL P 278 " (cutoff:3.500A) removed outlier: 4.824A pdb=" N ASN P 283 " --> pdb=" O LEU P 279 " (cutoff:3.500A) Processing helix chain 'P' and resid 304 through 312 Processing helix chain 'P' and resid 317 through 325 removed outlier: 4.108A pdb=" N SER P 325 " --> pdb=" O GLU P 321 " (cutoff:3.500A) Processing helix chain 'P' and resid 342 through 372 removed outlier: 4.433A pdb=" N SER P 371 " --> pdb=" O ARG P 367 " (cutoff:3.500A) removed outlier: 4.483A pdb=" N ILE P 372 " --> pdb=" O ILE P 368 " (cutoff:3.500A) Processing helix chain 'P' and resid 399 through 429 Processing helix chain 'P' and resid 443 through 450 removed outlier: 3.526A pdb=" N ASP P 447 " --> pdb=" O ALA P 443 " (cutoff:3.500A) Processing helix chain 'P' and resid 456 through 465 Processing helix chain 'P' and resid 472 through 482 Processing helix chain 'P' and resid 526 through 530 Processing helix chain 'P' and resid 536 through 543 Processing helix chain 'P' and resid 548 through 553 Processing helix chain 'P' and resid 555 through 557 No H-bonds generated for 'chain 'P' and resid 555 through 557' Processing helix chain 'P' and resid 570 through 585 Processing helix chain 'P' and resid 609 through 619 Processing helix chain 'P' and resid 621 through 628 removed outlier: 3.713A pdb=" N ARG P 626 " --> pdb=" O LEU P 622 " (cutoff:3.500A) removed outlier: 4.380A pdb=" N VAL P 627 " --> pdb=" O GLU P 623 " (cutoff:3.500A) removed outlier: 4.420A pdb=" N ARG P 628 " --> pdb=" O ASN P 624 " (cutoff:3.500A) Processing helix chain 'P' and resid 638 through 645 Processing helix chain 'P' and resid 660 through 670 Processing helix chain 'P' and resid 690 through 728 removed outlier: 3.706A pdb=" N GLU P 705 " --> pdb=" O LYS P 701 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N ILE P 714 " --> pdb=" O LEU P 710 " (cutoff:3.500A) Processing helix chain 'R' and resid 6 through 18 removed outlier: 3.755A pdb=" N GLU R 14 " --> pdb=" O ALA R 10 " (cutoff:3.500A) removed outlier: 4.234A pdb=" N ALA R 15 " --> pdb=" O GLU R 11 " (cutoff:3.500A) Processing helix chain 'R' and resid 32 through 38 removed outlier: 4.031A pdb=" N MET R 36 " --> pdb=" O LEU R 32 " (cutoff:3.500A) Processing helix chain 'R' and resid 45 through 55 removed outlier: 3.875A pdb=" N VAL R 55 " --> pdb=" O MET R 51 " (cutoff:3.500A) Processing helix chain 'R' and resid 65 through 74 Processing helix chain 'R' and resid 82 through 90 Processing helix chain 'R' and resid 102 through 109 Processing helix chain 'R' and resid 118 through 128 removed outlier: 3.558A pdb=" N ARG R 126 " --> pdb=" O ASP R 122 " (cutoff:3.500A) Processing helix chain 'R' and resid 139 through 145 removed outlier: 3.892A pdb=" N GLN R 143 " --> pdb=" O GLU R 139 " (cutoff:3.500A) Processing helix chain 'A' and resid 56 through 60 Processing helix chain 'A' and resid 62 through 64 No H-bonds generated for 'chain 'A' and resid 62 through 64' Processing helix chain 'A' and resid 79 through 91 Processing helix chain 'A' and resid 113 through 125 Processing helix chain 'A' and resid 137 through 144 Processing helix chain 'A' and resid 172 through 174 No H-bonds generated for 'chain 'A' and resid 172 through 174' Processing helix chain 'A' and resid 182 through 196 Processing helix chain 'A' and resid 203 through 216 Processing helix chain 'A' and resid 223 through 232 Processing helix chain 'A' and resid 252 through 262 removed outlier: 3.629A pdb=" N ARG A 256 " --> pdb=" O GLU A 253 " (cutoff:3.500A) removed outlier: 4.457A pdb=" N CYS A 257 " --> pdb=" O ARG A 254 " (cutoff:3.500A) Proline residue: A 258 - end of helix Processing helix chain 'A' and resid 274 through 283 Processing helix chain 'A' and resid 287 through 296 removed outlier: 5.403A pdb=" N LYS A 291 " --> pdb=" O ASP A 288 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N ALA A 295 " --> pdb=" O ASP A 292 " (cutoff:3.500A) Processing helix chain 'A' and resid 309 through 320 Processing helix chain 'A' and resid 338 through 347 Processing helix chain 'A' and resid 351 through 354 removed outlier: 3.994A pdb=" N GLN A 354 " --> pdb=" O THR A 351 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 351 through 354' Processing helix chain 'A' and resid 362 through 365 No H-bonds generated for 'chain 'A' and resid 362 through 365' Processing helix chain 'A' and resid 367 through 373 removed outlier: 4.114A pdb=" N VAL A 370 " --> pdb=" O PRO A 367 " (cutoff:3.500A) Processing helix chain 'B' and resid 56 through 60 Processing helix chain 'B' and resid 62 through 64 No H-bonds generated for 'chain 'B' and resid 62 through 64' Processing helix chain 'B' and resid 79 through 91 Processing helix chain 'B' and resid 113 through 125 Processing helix chain 'B' and resid 137 through 144 Processing helix chain 'B' and resid 172 through 174 No H-bonds generated for 'chain 'B' and resid 172 through 174' Processing helix chain 'B' and resid 182 through 196 Processing helix chain 'B' and resid 203 through 216 Processing helix chain 'B' and resid 223 through 232 Processing helix chain 'B' and resid 252 through 262 removed outlier: 3.629A pdb=" N ARG B 256 " --> pdb=" O GLU B 253 " (cutoff:3.500A) removed outlier: 4.458A pdb=" N CYS B 257 " --> pdb=" O ARG B 254 " (cutoff:3.500A) Proline residue: B 258 - end of helix Processing helix chain 'B' and resid 274 through 283 Processing helix chain 'B' and resid 287 through 296 removed outlier: 5.403A pdb=" N LYS B 291 " --> pdb=" O ASP B 288 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N ALA B 295 " --> pdb=" O ASP B 292 " (cutoff:3.500A) Processing helix chain 'B' and resid 309 through 320 Processing helix chain 'B' and resid 338 through 347 Processing helix chain 'B' and resid 351 through 354 removed outlier: 3.995A pdb=" N GLN B 354 " --> pdb=" O THR B 351 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 351 through 354' Processing helix chain 'B' and resid 362 through 365 No H-bonds generated for 'chain 'B' and resid 362 through 365' Processing helix chain 'B' and resid 367 through 373 removed outlier: 4.115A pdb=" N VAL B 370 " --> pdb=" O PRO B 367 " (cutoff:3.500A) Processing helix chain 'C' and resid 56 through 60 Processing helix chain 'C' and resid 62 through 64 No H-bonds generated for 'chain 'C' and resid 62 through 64' Processing helix chain 'C' and resid 79 through 91 Processing helix chain 'C' and resid 113 through 125 Processing helix chain 'C' and resid 137 through 144 Processing helix chain 'C' and resid 172 through 174 No H-bonds generated for 'chain 'C' and resid 172 through 174' Processing helix chain 'C' and resid 182 through 196 Processing helix chain 'C' and resid 203 through 216 Processing helix chain 'C' and resid 223 through 232 Processing helix chain 'C' and resid 252 through 262 removed outlier: 3.629A pdb=" N ARG C 256 " --> pdb=" O GLU C 253 " (cutoff:3.500A) removed outlier: 4.457A pdb=" N CYS C 257 " --> pdb=" O ARG C 254 " (cutoff:3.500A) Proline residue: C 258 - end of helix Processing helix chain 'C' and resid 274 through 283 Processing helix chain 'C' and resid 287 through 296 removed outlier: 5.403A pdb=" N LYS C 291 " --> pdb=" O ASP C 288 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N ALA C 295 " --> pdb=" O ASP C 292 " (cutoff:3.500A) Processing helix chain 'C' and resid 309 through 320 Processing helix chain 'C' and resid 338 through 347 Processing helix chain 'C' and resid 351 through 354 removed outlier: 3.993A pdb=" N GLN C 354 " --> pdb=" O THR C 351 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 351 through 354' Processing helix chain 'C' and resid 362 through 365 No H-bonds generated for 'chain 'C' and resid 362 through 365' Processing helix chain 'C' and resid 367 through 373 removed outlier: 4.114A pdb=" N VAL C 370 " --> pdb=" O PRO C 367 " (cutoff:3.500A) Processing helix chain 'D' and resid 56 through 60 Processing helix chain 'D' and resid 62 through 64 No H-bonds generated for 'chain 'D' and resid 62 through 64' Processing helix chain 'D' and resid 79 through 91 Processing helix chain 'D' and resid 113 through 125 Processing helix chain 'D' and resid 137 through 144 Processing helix chain 'D' and resid 172 through 174 No H-bonds generated for 'chain 'D' and resid 172 through 174' Processing helix chain 'D' and resid 182 through 196 Processing helix chain 'D' and resid 203 through 216 Processing helix chain 'D' and resid 223 through 232 Processing helix chain 'D' and resid 252 through 262 removed outlier: 3.628A pdb=" N ARG D 256 " --> pdb=" O GLU D 253 " (cutoff:3.500A) removed outlier: 4.457A pdb=" N CYS D 257 " --> pdb=" O ARG D 254 " (cutoff:3.500A) Proline residue: D 258 - end of helix Processing helix chain 'D' and resid 274 through 283 Processing helix chain 'D' and resid 287 through 296 removed outlier: 5.403A pdb=" N LYS D 291 " --> pdb=" O ASP D 288 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N ALA D 295 " --> pdb=" O ASP D 292 " (cutoff:3.500A) Processing helix chain 'D' and resid 309 through 320 Processing helix chain 'D' and resid 338 through 347 Processing helix chain 'D' and resid 351 through 354 removed outlier: 3.994A pdb=" N GLN D 354 " --> pdb=" O THR D 351 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 351 through 354' Processing helix chain 'D' and resid 362 through 365 No H-bonds generated for 'chain 'D' and resid 362 through 365' Processing helix chain 'D' and resid 367 through 373 removed outlier: 4.115A pdb=" N VAL D 370 " --> pdb=" O PRO D 367 " (cutoff:3.500A) Processing helix chain 'E' and resid 56 through 60 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 79 through 91 Processing helix chain 'E' and resid 113 through 125 Processing helix chain 'E' and resid 137 through 144 Processing helix chain 'E' and resid 172 through 174 No H-bonds generated for 'chain 'E' and resid 172 through 174' Processing helix chain 'E' and resid 182 through 196 Processing helix chain 'E' and resid 203 through 216 Processing helix chain 'E' and resid 223 through 232 Processing helix chain 'E' and resid 252 through 262 removed outlier: 3.629A pdb=" N ARG E 256 " --> pdb=" O GLU E 253 " (cutoff:3.500A) removed outlier: 4.457A pdb=" N CYS E 257 " --> pdb=" O ARG E 254 " (cutoff:3.500A) Proline residue: E 258 - end of helix Processing helix chain 'E' and resid 274 through 283 Processing helix chain 'E' and resid 287 through 296 removed outlier: 5.403A pdb=" N LYS E 291 " --> pdb=" O ASP E 288 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N ALA E 295 " --> pdb=" O ASP E 292 " (cutoff:3.500A) Processing helix chain 'E' and resid 309 through 320 Processing helix chain 'E' and resid 338 through 347 Processing helix chain 'E' and resid 351 through 354 removed outlier: 3.995A pdb=" N GLN E 354 " --> pdb=" O THR E 351 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 351 through 354' Processing helix chain 'E' and resid 362 through 365 No H-bonds generated for 'chain 'E' and resid 362 through 365' Processing helix chain 'E' and resid 367 through 373 removed outlier: 4.115A pdb=" N VAL E 370 " --> pdb=" O PRO E 367 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'P' and resid 45 through 48 removed outlier: 9.036A pdb=" N VAL P 52 " --> pdb=" O PRO P 590 " (cutoff:3.500A) removed outlier: 6.671A pdb=" N TYR P 592 " --> pdb=" O VAL P 52 " (cutoff:3.500A) removed outlier: 7.703A pdb=" N SER P 54 " --> pdb=" O TYR P 592 " (cutoff:3.500A) removed outlier: 6.224A pdb=" N ARG P 594 " --> pdb=" O SER P 54 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'P' and resid 286 through 288 Processing sheet with id= C, first strand: chain 'P' and resid 326 through 330 Processing sheet with id= D, first strand: chain 'P' and resid 509 through 513 Processing sheet with id= E, first strand: chain 'P' and resid 634 through 637 Processing sheet with id= F, first strand: chain 'R' and resid 99 through 101 Processing sheet with id= G, first strand: chain 'A' and resid 132 through 136 removed outlier: 6.776A pdb=" N THR A 103 " --> pdb=" O TYR A 133 " (cutoff:3.500A) removed outlier: 7.848A pdb=" N ALA A 135 " --> pdb=" O THR A 103 " (cutoff:3.500A) removed outlier: 6.651A pdb=" N LEU A 105 " --> pdb=" O ALA A 135 " (cutoff:3.500A) removed outlier: 7.289A pdb=" N LEU A 8 " --> pdb=" O LEU A 104 " (cutoff:3.500A) removed outlier: 8.540A pdb=" N THR A 106 " --> pdb=" O LEU A 8 " (cutoff:3.500A) removed outlier: 8.289A pdb=" N CYS A 10 " --> pdb=" O THR A 106 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'A' and resid 52 through 54 Processing sheet with id= I, first strand: chain 'A' and resid 297 through 299 removed outlier: 6.039A pdb=" N ILE A 151 " --> pdb=" O VAL A 298 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'A' and resid 238 through 241 Processing sheet with id= K, first strand: chain 'B' and resid 132 through 136 removed outlier: 6.776A pdb=" N THR B 103 " --> pdb=" O TYR B 133 " (cutoff:3.500A) removed outlier: 7.847A pdb=" N ALA B 135 " --> pdb=" O THR B 103 " (cutoff:3.500A) removed outlier: 6.651A pdb=" N LEU B 105 " --> pdb=" O ALA B 135 " (cutoff:3.500A) removed outlier: 7.289A pdb=" N LEU B 8 " --> pdb=" O LEU B 104 " (cutoff:3.500A) removed outlier: 8.540A pdb=" N THR B 106 " --> pdb=" O LEU B 8 " (cutoff:3.500A) removed outlier: 8.290A pdb=" N CYS B 10 " --> pdb=" O THR B 106 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'B' and resid 52 through 54 Processing sheet with id= M, first strand: chain 'B' and resid 297 through 299 removed outlier: 6.039A pdb=" N ILE B 151 " --> pdb=" O VAL B 298 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'B' and resid 238 through 241 Processing sheet with id= O, first strand: chain 'C' and resid 132 through 136 removed outlier: 6.776A pdb=" N THR C 103 " --> pdb=" O TYR C 133 " (cutoff:3.500A) removed outlier: 7.847A pdb=" N ALA C 135 " --> pdb=" O THR C 103 " (cutoff:3.500A) removed outlier: 6.650A pdb=" N LEU C 105 " --> pdb=" O ALA C 135 " (cutoff:3.500A) removed outlier: 7.289A pdb=" N LEU C 8 " --> pdb=" O LEU C 104 " (cutoff:3.500A) removed outlier: 8.540A pdb=" N THR C 106 " --> pdb=" O LEU C 8 " (cutoff:3.500A) removed outlier: 8.289A pdb=" N CYS C 10 " --> pdb=" O THR C 106 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'C' and resid 52 through 54 Processing sheet with id= Q, first strand: chain 'C' and resid 297 through 299 removed outlier: 6.040A pdb=" N ILE C 151 " --> pdb=" O VAL C 298 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'C' and resid 238 through 241 Processing sheet with id= S, first strand: chain 'D' and resid 132 through 136 removed outlier: 6.776A pdb=" N THR D 103 " --> pdb=" O TYR D 133 " (cutoff:3.500A) removed outlier: 7.848A pdb=" N ALA D 135 " --> pdb=" O THR D 103 " (cutoff:3.500A) removed outlier: 6.651A pdb=" N LEU D 105 " --> pdb=" O ALA D 135 " (cutoff:3.500A) removed outlier: 7.289A pdb=" N LEU D 8 " --> pdb=" O LEU D 104 " (cutoff:3.500A) removed outlier: 8.540A pdb=" N THR D 106 " --> pdb=" O LEU D 8 " (cutoff:3.500A) removed outlier: 8.290A pdb=" N CYS D 10 " --> pdb=" O THR D 106 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'D' and resid 52 through 54 Processing sheet with id= U, first strand: chain 'D' and resid 297 through 299 removed outlier: 6.040A pdb=" N ILE D 151 " --> pdb=" O VAL D 298 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'D' and resid 238 through 241 Processing sheet with id= W, first strand: chain 'E' and resid 132 through 136 removed outlier: 6.776A pdb=" N THR E 103 " --> pdb=" O TYR E 133 " (cutoff:3.500A) removed outlier: 7.847A pdb=" N ALA E 135 " --> pdb=" O THR E 103 " (cutoff:3.500A) removed outlier: 6.651A pdb=" N LEU E 105 " --> pdb=" O ALA E 135 " (cutoff:3.500A) removed outlier: 7.288A pdb=" N LEU E 8 " --> pdb=" O LEU E 104 " (cutoff:3.500A) removed outlier: 8.539A pdb=" N THR E 106 " --> pdb=" O LEU E 8 " (cutoff:3.500A) removed outlier: 8.290A pdb=" N CYS E 10 " --> pdb=" O THR E 106 " (cutoff:3.500A) Processing sheet with id= X, first strand: chain 'E' and resid 52 through 54 Processing sheet with id= Y, first strand: chain 'E' and resid 297 through 299 removed outlier: 6.040A pdb=" N ILE E 151 " --> pdb=" O VAL E 298 " (cutoff:3.500A) Processing sheet with id= Z, first strand: chain 'E' and resid 238 through 241 835 hydrogen bonds defined for protein. 2205 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: 6.95 Time building geometry restraints manager: 8.80 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 6996 1.34 - 1.46: 4393 1.46 - 1.58: 9789 1.58 - 1.70: 17 1.70 - 1.82: 216 Bond restraints: 21411 Sorted by residual: bond pdb=" O3A ADP B 401 " pdb=" PA ADP B 401 " ideal model delta sigma weight residual 1.610 1.469 0.141 2.00e-02 2.50e+03 4.96e+01 bond pdb=" C4 ADP B 401 " pdb=" C5 ADP B 401 " ideal model delta sigma weight residual 1.490 1.381 0.109 2.00e-02 2.50e+03 2.97e+01 bond pdb=" C5 ADP B 401 " pdb=" C6 ADP B 401 " ideal model delta sigma weight residual 1.490 1.405 0.085 2.00e-02 2.50e+03 1.82e+01 bond pdb=" O1A ADP B 401 " pdb=" PA ADP B 401 " ideal model delta sigma weight residual 1.510 1.427 0.083 2.00e-02 2.50e+03 1.71e+01 bond pdb=" C5 ADP B 401 " pdb=" N7 ADP B 401 " ideal model delta sigma weight residual 1.350 1.414 -0.064 2.00e-02 2.50e+03 1.03e+01 ... (remaining 21406 not shown) Histogram of bond angle deviations from ideal: 98.31 - 107.80: 973 107.80 - 117.30: 14124 117.30 - 126.79: 13571 126.79 - 136.28: 251 136.28 - 145.78: 1 Bond angle restraints: 28920 Sorted by residual: angle pdb=" CG ARG D 95 " pdb=" CD ARG D 95 " pdb=" NE ARG D 95 " ideal model delta sigma weight residual 112.00 145.78 -33.78 2.20e+00 2.07e-01 2.36e+02 angle pdb=" O1B ADP B 401 " pdb=" PB ADP B 401 " pdb=" O3B ADP B 401 " ideal model delta sigma weight residual 119.90 98.31 21.59 3.00e+00 1.11e-01 5.18e+01 angle pdb=" C ASP R 2 " pdb=" N GLN R 3 " pdb=" CA GLN R 3 " ideal model delta sigma weight residual 121.70 132.32 -10.62 1.80e+00 3.09e-01 3.48e+01 angle pdb=" C GLN R 3 " pdb=" N LEU R 4 " pdb=" CA LEU R 4 " ideal model delta sigma weight residual 121.31 129.38 -8.07 1.49e+00 4.50e-01 2.93e+01 angle pdb=" C GLY E 302 " pdb=" N THR E 303 " pdb=" CA THR E 303 " ideal model delta sigma weight residual 120.38 127.55 -7.17 1.46e+00 4.69e-01 2.41e+01 ... (remaining 28915 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.00: 12287 21.00 - 42.01: 277 42.01 - 63.01: 40 63.01 - 84.02: 10 84.02 - 105.02: 4 Dihedral angle restraints: 12618 sinusoidal: 5053 harmonic: 7565 Sorted by residual: dihedral pdb=" CA GLU P 24 " pdb=" C GLU P 24 " pdb=" N PRO P 25 " pdb=" CA PRO P 25 " ideal model delta harmonic sigma weight residual 180.00 -107.06 -72.94 0 5.00e+00 4.00e-02 2.13e+02 dihedral pdb=" CA GLU A 361 " pdb=" C GLU A 361 " pdb=" N TYR A 362 " pdb=" CA TYR A 362 " ideal model delta harmonic sigma weight residual 180.00 144.72 35.28 0 5.00e+00 4.00e-02 4.98e+01 dihedral pdb=" CA GLU C 361 " pdb=" C GLU C 361 " pdb=" N TYR C 362 " pdb=" CA TYR C 362 " ideal model delta harmonic sigma weight residual 180.00 144.75 35.25 0 5.00e+00 4.00e-02 4.97e+01 ... (remaining 12615 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.053: 2214 0.053 - 0.105: 644 0.105 - 0.158: 182 0.158 - 0.211: 27 0.211 - 0.263: 10 Chirality restraints: 3077 Sorted by residual: chirality pdb=" CB ILE E 71 " pdb=" CA ILE E 71 " pdb=" CG1 ILE E 71 " pdb=" CG2 ILE E 71 " both_signs ideal model delta sigma weight residual False 2.64 2.38 0.26 2.00e-01 2.50e+01 1.73e+00 chirality pdb=" CB ILE C 71 " pdb=" CA ILE C 71 " pdb=" CG1 ILE C 71 " pdb=" CG2 ILE C 71 " both_signs ideal model delta sigma weight residual False 2.64 2.38 0.26 2.00e-01 2.50e+01 1.70e+00 chirality pdb=" CB ILE D 71 " pdb=" CA ILE D 71 " pdb=" CG1 ILE D 71 " pdb=" CG2 ILE D 71 " both_signs ideal model delta sigma weight residual False 2.64 2.39 0.26 2.00e-01 2.50e+01 1.69e+00 ... (remaining 3074 not shown) Planarity restraints: 3803 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' ADP B 401 " 0.052 2.00e-02 2.50e+03 7.82e-02 1.68e+02 pdb=" C2 ADP B 401 " -0.021 2.00e-02 2.50e+03 pdb=" C4 ADP B 401 " 0.019 2.00e-02 2.50e+03 pdb=" C5 ADP B 401 " 0.001 2.00e-02 2.50e+03 pdb=" C6 ADP B 401 " -0.010 2.00e-02 2.50e+03 pdb=" C8 ADP B 401 " -0.105 2.00e-02 2.50e+03 pdb=" N1 ADP B 401 " -0.155 2.00e-02 2.50e+03 pdb=" N3 ADP B 401 " 0.079 2.00e-02 2.50e+03 pdb=" N6 ADP B 401 " 0.146 2.00e-02 2.50e+03 pdb=" N7 ADP B 401 " -0.024 2.00e-02 2.50e+03 pdb=" N9 ADP B 401 " 0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLU P 24 " 0.068 5.00e-02 4.00e+02 1.04e-01 1.73e+01 pdb=" N PRO P 25 " -0.180 5.00e-02 4.00e+02 pdb=" CA PRO P 25 " 0.055 5.00e-02 4.00e+02 pdb=" CD PRO P 25 " 0.057 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA LYS B 359 " 0.020 2.00e-02 2.50e+03 3.97e-02 1.57e+01 pdb=" C LYS B 359 " -0.069 2.00e-02 2.50e+03 pdb=" O LYS B 359 " 0.026 2.00e-02 2.50e+03 pdb=" N GLN B 360 " 0.023 2.00e-02 2.50e+03 ... (remaining 3800 not shown) Histogram of nonbonded interaction distances: 1.77 - 2.40: 78 2.40 - 3.02: 10843 3.02 - 3.65: 31939 3.65 - 4.27: 49693 4.27 - 4.90: 82504 Nonbonded interactions: 175057 Sorted by model distance: nonbonded pdb=" O3B ADP B 401 " pdb="MG MG B 402 " model vdw 1.770 2.170 nonbonded pdb=" O1B ADP B 401 " pdb="MG MG B 402 " model vdw 1.872 2.170 nonbonded pdb=" CD2 LEU P 142 " pdb=" SD MET P 170 " model vdw 2.011 3.820 nonbonded pdb=" O3B ADP A 401 " pdb="MG MG A 402 " model vdw 2.091 2.170 nonbonded pdb="MG MG P 801 " pdb=" O2B ADP P 802 " model vdw 2.102 2.170 ... (remaining 175052 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' } 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: 3.940 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: 15.070 Check model and map are aligned: 0.280 Set scattering table: 0.170 Process input model: 56.310 Find NCS groups from input model: 1.170 Set up NCS constraints: 0.150 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:2.870 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 79.980 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7057 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.141 21411 Z= 0.389 Angle : 0.979 33.777 28920 Z= 0.552 Chirality : 0.056 0.263 3077 Planarity : 0.007 0.104 3803 Dihedral : 10.059 105.020 7904 Min Nonbonded Distance : 1.770 Molprobity Statistics. All-atom Clashscore : 6.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.70 % Favored : 94.30 % Rotamer: Outliers : 0.51 % Allowed : 2.21 % Favored : 97.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.67 % Cis-general : 0.27 % Twisted Proline : 0.83 % Twisted General : 0.38 % 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: -3.41 (0.13), residues: 2738 helix: -2.71 (0.10), residues: 1197 sheet: -1.33 (0.25), residues: 389 loop : -1.88 (0.16), residues: 1152 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.004 TRP A 340 HIS 0.008 0.002 HIS D 40 PHE 0.024 0.003 PHE C 124 TYR 0.030 0.003 TYR C 294 ARG 0.011 0.001 ARG P 511 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5476 Ramachandran restraints generated. 2738 Oldfield, 0 Emsley, 2738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5476 Ramachandran restraints generated. 2738 Oldfield, 0 Emsley, 2738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 455 residues out of total 2367 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 444 time to evaluate : 2.506 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: P 485 THR cc_start: 0.7512 (p) cc_final: 0.7149 (t) REVERT: B 305 MET cc_start: 0.7389 (mmm) cc_final: 0.6433 (mmt) REVERT: C 44 MET cc_start: 0.8008 (mmm) cc_final: 0.7720 (mmm) outliers start: 11 outliers final: 0 residues processed: 454 average time/residue: 0.4015 time to fit residues: 262.5064 Evaluate side-chains 194 residues out of total 2367 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 194 time to evaluate : 2.616 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 271 random chunks: chunk 228 optimal weight: 3.9990 chunk 205 optimal weight: 4.9990 chunk 113 optimal weight: 0.6980 chunk 70 optimal weight: 6.9990 chunk 138 optimal weight: 2.9990 chunk 109 optimal weight: 9.9990 chunk 212 optimal weight: 9.9990 chunk 82 optimal weight: 30.0000 chunk 129 optimal weight: 3.9990 chunk 158 optimal weight: 0.9980 chunk 246 optimal weight: 8.9990 overall best weight: 2.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: P 41 HIS P 74 ASN ** P 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 141 GLN P 293 ASN P 304 ASN P 563 ASN ** P 589 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 591 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 624 ASN A 59 GLN A 162 ASN ** A 225 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 360 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 137 GLN B 162 ASN ** B 225 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 360 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 371 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 162 ASN ** C 225 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 297 ASN ** C 360 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 371 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 41 GLN D 162 ASN D 173 HIS ** D 225 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 314 GLN ** D 360 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 371 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 115 ASN E 121 GLN E 162 ASN ** E 225 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 297 ASN ** E 360 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7321 moved from start: 0.2697 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.082 21411 Z= 0.276 Angle : 0.673 8.482 28920 Z= 0.343 Chirality : 0.045 0.169 3077 Planarity : 0.005 0.095 3803 Dihedral : 7.294 93.632 3050 Min Nonbonded Distance : 1.890 Molprobity Statistics. All-atom Clashscore : 13.75 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.24 % Favored : 95.73 % Rotamer: Outliers : 1.66 % Allowed : 10.18 % Favored : 88.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.67 % Cis-general : 0.27 % Twisted Proline : 0.83 % 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: -1.66 (0.15), residues: 2738 helix: -0.72 (0.14), residues: 1232 sheet: -0.95 (0.25), residues: 416 loop : -1.45 (0.18), residues: 1090 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A 340 HIS 0.009 0.001 HIS A 73 PHE 0.024 0.002 PHE D 124 TYR 0.018 0.002 TYR B 143 ARG 0.015 0.001 ARG P 231 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5476 Ramachandran restraints generated. 2738 Oldfield, 0 Emsley, 2738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5476 Ramachandran restraints generated. 2738 Oldfield, 0 Emsley, 2738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 237 residues out of total 2367 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 201 time to evaluate : 2.697 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: P 122 MET cc_start: 0.7537 (mmt) cc_final: 0.7315 (mmt) REVERT: P 485 THR cc_start: 0.7562 (p) cc_final: 0.7135 (t) REVERT: P 520 LEU cc_start: 0.7280 (OUTLIER) cc_final: 0.7069 (tp) REVERT: A 313 MET cc_start: 0.7610 (tpt) cc_final: 0.7408 (tpp) REVERT: B 305 MET cc_start: 0.7548 (mmm) cc_final: 0.6747 (mmt) REVERT: D 346 LEU cc_start: 0.8658 (tp) cc_final: 0.8438 (tt) outliers start: 36 outliers final: 21 residues processed: 224 average time/residue: 0.3486 time to fit residues: 120.7891 Evaluate side-chains 188 residues out of total 2367 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 166 time to evaluate : 2.443 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 70 GLU Chi-restraints excluded: chain P residue 105 LEU Chi-restraints excluded: chain P residue 260 ILE Chi-restraints excluded: chain P residue 292 MET Chi-restraints excluded: chain P residue 370 GLU Chi-restraints excluded: chain P residue 498 ARG Chi-restraints excluded: chain P residue 520 LEU Chi-restraints excluded: chain P residue 585 LEU Chi-restraints excluded: chain A residue 80 ASP Chi-restraints excluded: chain A residue 278 THR Chi-restraints excluded: chain A residue 286 ASP Chi-restraints excluded: chain B residue 100 GLU Chi-restraints excluded: chain B residue 194 THR Chi-restraints excluded: chain B residue 250 ILE Chi-restraints excluded: chain C residue 41 GLN Chi-restraints excluded: chain C residue 155 SER Chi-restraints excluded: chain C residue 292 ASP Chi-restraints excluded: chain C residue 351 THR Chi-restraints excluded: chain D residue 155 SER Chi-restraints excluded: chain E residue 56 ASP Chi-restraints excluded: chain E residue 89 THR Chi-restraints excluded: chain E residue 194 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 271 random chunks: chunk 136 optimal weight: 1.9990 chunk 76 optimal weight: 0.8980 chunk 204 optimal weight: 9.9990 chunk 167 optimal weight: 7.9990 chunk 67 optimal weight: 30.0000 chunk 246 optimal weight: 10.0000 chunk 266 optimal weight: 5.9990 chunk 219 optimal weight: 0.9980 chunk 244 optimal weight: 20.0000 chunk 84 optimal weight: 0.9980 chunk 197 optimal weight: 30.0000 overall best weight: 2.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: P 76 ASN ** P 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 141 GLN ** P 206 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 481 GLN ** P 589 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 591 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 689 ASN A 40 HIS ** A 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 225 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 360 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 371 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 115 ASN ** C 225 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 360 GLN ** C 371 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 225 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 360 GLN ** D 371 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 225 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7376 moved from start: 0.3380 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.106 21411 Z= 0.237 Angle : 0.629 8.844 28920 Z= 0.315 Chirality : 0.043 0.162 3077 Planarity : 0.004 0.081 3803 Dihedral : 6.810 91.240 3050 Min Nonbonded Distance : 1.884 Molprobity Statistics. All-atom Clashscore : 13.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.67 % Favored : 95.33 % Rotamer: Outliers : 1.80 % Allowed : 10.50 % Favored : 87.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.67 % Cis-general : 0.27 % Twisted Proline : 0.83 % 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: -0.79 (0.16), residues: 2738 helix: 0.17 (0.15), residues: 1250 sheet: -0.56 (0.25), residues: 407 loop : -1.21 (0.19), residues: 1081 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A 340 HIS 0.005 0.001 HIS A 73 PHE 0.015 0.001 PHE C 90 TYR 0.013 0.001 TYR B 143 ARG 0.004 0.000 ARG P 231 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5476 Ramachandran restraints generated. 2738 Oldfield, 0 Emsley, 2738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5476 Ramachandran restraints generated. 2738 Oldfield, 0 Emsley, 2738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 212 residues out of total 2367 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 173 time to evaluate : 2.453 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 305 MET cc_start: 0.7587 (mmm) cc_final: 0.6795 (mmt) REVERT: C 41 GLN cc_start: 0.6673 (OUTLIER) cc_final: 0.6453 (mm-40) outliers start: 39 outliers final: 19 residues processed: 201 average time/residue: 0.2974 time to fit residues: 96.6684 Evaluate side-chains 177 residues out of total 2367 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 157 time to evaluate : 2.278 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 105 LEU Chi-restraints excluded: chain P residue 137 GLN Chi-restraints excluded: chain P residue 243 ASN Chi-restraints excluded: chain P residue 370 GLU Chi-restraints excluded: chain P residue 498 ARG Chi-restraints excluded: chain A residue 12 ASN Chi-restraints excluded: chain A residue 80 ASP Chi-restraints excluded: chain A residue 227 MET Chi-restraints excluded: chain A residue 278 THR Chi-restraints excluded: chain A residue 286 ASP Chi-restraints excluded: chain B residue 100 GLU Chi-restraints excluded: chain B residue 194 THR Chi-restraints excluded: chain B residue 261 LEU Chi-restraints excluded: chain C residue 41 GLN Chi-restraints excluded: chain C residue 155 SER Chi-restraints excluded: chain C residue 351 THR Chi-restraints excluded: chain D residue 155 SER Chi-restraints excluded: chain D residue 292 ASP Chi-restraints excluded: chain E residue 56 ASP Chi-restraints excluded: chain E residue 194 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 271 random chunks: chunk 243 optimal weight: 1.9990 chunk 185 optimal weight: 0.9990 chunk 127 optimal weight: 0.0050 chunk 27 optimal weight: 4.9990 chunk 117 optimal weight: 3.9990 chunk 165 optimal weight: 1.9990 chunk 247 optimal weight: 6.9990 chunk 261 optimal weight: 0.8980 chunk 129 optimal weight: 3.9990 chunk 234 optimal weight: 20.0000 chunk 70 optimal weight: 9.9990 overall best weight: 1.1800 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** P 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 206 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 481 GLN ** P 589 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 591 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 297 ASN ** C 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 225 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 371 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 371 HIS ** E 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7358 moved from start: 0.3705 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 21411 Z= 0.166 Angle : 0.593 9.482 28920 Z= 0.290 Chirality : 0.043 0.157 3077 Planarity : 0.004 0.076 3803 Dihedral : 6.421 84.140 3050 Min Nonbonded Distance : 1.901 Molprobity Statistics. All-atom Clashscore : 12.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.49 % Favored : 95.51 % Rotamer: Outliers : 1.11 % Allowed : 11.70 % Favored : 87.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.67 % Cis-general : 0.27 % Twisted Proline : 0.83 % 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: -0.21 (0.16), residues: 2738 helix: 0.78 (0.15), residues: 1224 sheet: -0.44 (0.25), residues: 405 loop : -0.99 (0.19), residues: 1109 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 356 HIS 0.006 0.001 HIS B 371 PHE 0.012 0.001 PHE C 90 TYR 0.010 0.001 TYR B 143 ARG 0.002 0.000 ARG A 28 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5476 Ramachandran restraints generated. 2738 Oldfield, 0 Emsley, 2738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5476 Ramachandran restraints generated. 2738 Oldfield, 0 Emsley, 2738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 2367 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 169 time to evaluate : 2.434 Fit side-chains revert: symmetry clash REVERT: P 459 MET cc_start: 0.7307 (mmm) cc_final: 0.7032 (mmp) REVERT: B 305 MET cc_start: 0.7607 (mmm) cc_final: 0.6816 (mmt) outliers start: 24 outliers final: 12 residues processed: 185 average time/residue: 0.2817 time to fit residues: 87.4679 Evaluate side-chains 163 residues out of total 2367 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 151 time to evaluate : 2.438 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 211 LEU Chi-restraints excluded: chain P residue 243 ASN Chi-restraints excluded: chain P residue 370 GLU Chi-restraints excluded: chain P residue 498 ARG Chi-restraints excluded: chain A residue 80 ASP Chi-restraints excluded: chain A residue 303 THR Chi-restraints excluded: chain B residue 141 SER Chi-restraints excluded: chain B residue 194 THR Chi-restraints excluded: chain C residue 155 SER Chi-restraints excluded: chain C residue 351 THR Chi-restraints excluded: chain D residue 155 SER Chi-restraints excluded: chain E residue 56 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 271 random chunks: chunk 218 optimal weight: 0.9990 chunk 148 optimal weight: 2.9990 chunk 3 optimal weight: 9.9990 chunk 195 optimal weight: 0.7980 chunk 108 optimal weight: 5.9990 chunk 223 optimal weight: 0.5980 chunk 181 optimal weight: 0.9990 chunk 0 optimal weight: 30.0000 chunk 133 optimal weight: 6.9990 chunk 235 optimal weight: 9.9990 chunk 66 optimal weight: 1.9990 overall best weight: 1.0786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** P 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 206 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 589 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 115 ASN A 297 ASN ** C 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 371 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7357 moved from start: 0.3967 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.046 21411 Z= 0.156 Angle : 0.578 8.362 28920 Z= 0.282 Chirality : 0.042 0.156 3077 Planarity : 0.004 0.072 3803 Dihedral : 6.107 77.492 3050 Min Nonbonded Distance : 1.916 Molprobity Statistics. All-atom Clashscore : 11.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.49 % Favored : 95.51 % Rotamer: Outliers : 1.61 % Allowed : 11.47 % Favored : 86.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.67 % Cis-general : 0.27 % Twisted Proline : 0.83 % 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: 0.04 (0.16), residues: 2738 helix: 0.93 (0.15), residues: 1249 sheet: -0.35 (0.26), residues: 405 loop : -0.80 (0.19), residues: 1084 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 356 HIS 0.005 0.001 HIS B 371 PHE 0.011 0.001 PHE C 90 TYR 0.011 0.001 TYR B 143 ARG 0.003 0.000 ARG E 206 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5476 Ramachandran restraints generated. 2738 Oldfield, 0 Emsley, 2738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5476 Ramachandran restraints generated. 2738 Oldfield, 0 Emsley, 2738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 2367 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 159 time to evaluate : 2.439 Fit side-chains revert: symmetry clash REVERT: P 258 MET cc_start: 0.7034 (ppp) cc_final: 0.6444 (ppp) REVERT: B 305 MET cc_start: 0.7591 (mmm) cc_final: 0.6837 (mmt) REVERT: D 283 MET cc_start: 0.7689 (mmp) cc_final: 0.7464 (mmp) REVERT: E 47 MET cc_start: 0.5833 (ptm) cc_final: 0.5431 (ptm) outliers start: 35 outliers final: 21 residues processed: 181 average time/residue: 0.2762 time to fit residues: 83.3643 Evaluate side-chains 167 residues out of total 2367 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 146 time to evaluate : 2.589 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 137 GLN Chi-restraints excluded: chain P residue 211 LEU Chi-restraints excluded: chain P residue 243 ASN Chi-restraints excluded: chain P residue 260 ILE Chi-restraints excluded: chain P residue 324 PHE Chi-restraints excluded: chain P residue 329 VAL Chi-restraints excluded: chain P residue 356 LEU Chi-restraints excluded: chain P residue 370 GLU Chi-restraints excluded: chain P residue 498 ARG Chi-restraints excluded: chain P residue 585 LEU Chi-restraints excluded: chain A residue 80 ASP Chi-restraints excluded: chain A residue 155 SER Chi-restraints excluded: chain B residue 141 SER Chi-restraints excluded: chain B residue 155 SER Chi-restraints excluded: chain B residue 194 THR Chi-restraints excluded: chain C residue 155 SER Chi-restraints excluded: chain C residue 351 THR Chi-restraints excluded: chain D residue 132 MET Chi-restraints excluded: chain D residue 155 SER Chi-restraints excluded: chain D residue 292 ASP Chi-restraints excluded: chain E residue 56 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 271 random chunks: chunk 88 optimal weight: 0.7980 chunk 235 optimal weight: 10.0000 chunk 51 optimal weight: 10.0000 chunk 153 optimal weight: 1.9990 chunk 64 optimal weight: 6.9990 chunk 262 optimal weight: 8.9990 chunk 217 optimal weight: 2.9990 chunk 121 optimal weight: 5.9990 chunk 21 optimal weight: 6.9990 chunk 86 optimal weight: 10.0000 chunk 137 optimal weight: 5.9990 overall best weight: 3.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** P 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 198 GLN ** P 206 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 317 GLN ** P 589 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 360 GLN ** C 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 225 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 371 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 40 HIS ** E 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7503 moved from start: 0.4482 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.087 21411 Z= 0.319 Angle : 0.662 8.598 28920 Z= 0.329 Chirality : 0.044 0.160 3077 Planarity : 0.004 0.072 3803 Dihedral : 6.386 84.305 3050 Min Nonbonded Distance : 1.942 Molprobity Statistics. All-atom Clashscore : 16.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.97 % Favored : 95.03 % Rotamer: Outliers : 2.12 % Allowed : 11.33 % Favored : 86.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.67 % Cis-general : 0.27 % Twisted Proline : 0.83 % 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: 0.11 (0.16), residues: 2738 helix: 0.91 (0.15), residues: 1256 sheet: -0.44 (0.25), residues: 415 loop : -0.61 (0.20), residues: 1067 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP E 79 HIS 0.006 0.001 HIS B 371 PHE 0.013 0.002 PHE P 526 TYR 0.014 0.002 TYR B 143 ARG 0.005 0.001 ARG P 511 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5476 Ramachandran restraints generated. 2738 Oldfield, 0 Emsley, 2738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5476 Ramachandran restraints generated. 2738 Oldfield, 0 Emsley, 2738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 2367 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 143 time to evaluate : 2.461 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: P 258 MET cc_start: 0.7093 (ppp) cc_final: 0.6698 (ppp) REVERT: B 105 LEU cc_start: 0.9073 (OUTLIER) cc_final: 0.8849 (mm) REVERT: B 227 MET cc_start: 0.7807 (tpt) cc_final: 0.7591 (tpt) REVERT: B 305 MET cc_start: 0.7576 (mmm) cc_final: 0.6744 (mmt) REVERT: D 84 LYS cc_start: 0.8558 (OUTLIER) cc_final: 0.8284 (ttpt) REVERT: D 305 MET cc_start: 0.7990 (pmm) cc_final: 0.7235 (mtm) REVERT: E 47 MET cc_start: 0.5740 (ptm) cc_final: 0.5190 (ptm) outliers start: 46 outliers final: 30 residues processed: 180 average time/residue: 0.2937 time to fit residues: 86.9488 Evaluate side-chains 169 residues out of total 2367 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 137 time to evaluate : 2.377 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 105 LEU Chi-restraints excluded: chain P residue 137 GLN Chi-restraints excluded: chain P residue 211 LEU Chi-restraints excluded: chain P residue 243 ASN Chi-restraints excluded: chain P residue 329 VAL Chi-restraints excluded: chain P residue 356 LEU Chi-restraints excluded: chain P residue 370 GLU Chi-restraints excluded: chain P residue 447 ASP Chi-restraints excluded: chain P residue 498 ARG Chi-restraints excluded: chain A residue 12 ASN Chi-restraints excluded: chain A residue 80 ASP Chi-restraints excluded: chain A residue 227 MET Chi-restraints excluded: chain A residue 303 THR Chi-restraints excluded: chain B residue 105 LEU Chi-restraints excluded: chain B residue 141 SER Chi-restraints excluded: chain B residue 194 THR Chi-restraints excluded: chain B residue 261 LEU Chi-restraints excluded: chain C residue 41 GLN Chi-restraints excluded: chain C residue 71 ILE Chi-restraints excluded: chain C residue 155 SER Chi-restraints excluded: chain C residue 274 ILE Chi-restraints excluded: chain C residue 351 THR Chi-restraints excluded: chain D residue 84 LYS Chi-restraints excluded: chain D residue 105 LEU Chi-restraints excluded: chain D residue 132 MET Chi-restraints excluded: chain D residue 155 SER Chi-restraints excluded: chain D residue 274 ILE Chi-restraints excluded: chain D residue 292 ASP Chi-restraints excluded: chain E residue 56 ASP Chi-restraints excluded: chain E residue 194 THR Chi-restraints excluded: chain E residue 303 THR Chi-restraints excluded: chain E residue 360 GLN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 271 random chunks: chunk 252 optimal weight: 7.9990 chunk 29 optimal weight: 6.9990 chunk 149 optimal weight: 2.9990 chunk 191 optimal weight: 2.9990 chunk 148 optimal weight: 0.9980 chunk 220 optimal weight: 0.8980 chunk 146 optimal weight: 4.9990 chunk 261 optimal weight: 4.9990 chunk 163 optimal weight: 1.9990 chunk 159 optimal weight: 6.9990 chunk 120 optimal weight: 0.9990 overall best weight: 1.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** P 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 206 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 589 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 41 GLN ** B 360 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 371 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7441 moved from start: 0.4580 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 21411 Z= 0.185 Angle : 0.598 9.148 28920 Z= 0.290 Chirality : 0.043 0.158 3077 Planarity : 0.004 0.069 3803 Dihedral : 6.101 81.522 3050 Min Nonbonded Distance : 1.945 Molprobity Statistics. All-atom Clashscore : 13.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.71 % Favored : 95.29 % Rotamer: Outliers : 1.61 % Allowed : 12.16 % Favored : 86.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.67 % Cis-general : 0.27 % Twisted Proline : 0.83 % 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: 0.34 (0.17), residues: 2738 helix: 1.20 (0.15), residues: 1223 sheet: -0.33 (0.26), residues: 405 loop : -0.57 (0.20), residues: 1110 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 356 HIS 0.005 0.001 HIS C 371 PHE 0.008 0.001 PHE P 694 TYR 0.015 0.001 TYR B 143 ARG 0.002 0.000 ARG P 165 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5476 Ramachandran restraints generated. 2738 Oldfield, 0 Emsley, 2738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5476 Ramachandran restraints generated. 2738 Oldfield, 0 Emsley, 2738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 2367 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 153 time to evaluate : 2.553 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: P 258 MET cc_start: 0.7010 (ppp) cc_final: 0.6524 (ppp) REVERT: B 305 MET cc_start: 0.7631 (mmm) cc_final: 0.6893 (mmt) REVERT: D 305 MET cc_start: 0.8085 (pmm) cc_final: 0.7068 (mtm) REVERT: E 47 MET cc_start: 0.5749 (ptm) cc_final: 0.5266 (ptm) outliers start: 35 outliers final: 25 residues processed: 179 average time/residue: 0.2875 time to fit residues: 85.1276 Evaluate side-chains 172 residues out of total 2367 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 147 time to evaluate : 2.487 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 105 LEU Chi-restraints excluded: chain P residue 211 LEU Chi-restraints excluded: chain P residue 243 ASN Chi-restraints excluded: chain P residue 260 ILE Chi-restraints excluded: chain P residue 329 VAL Chi-restraints excluded: chain P residue 356 LEU Chi-restraints excluded: chain P residue 370 GLU Chi-restraints excluded: chain P residue 447 ASP Chi-restraints excluded: chain P residue 498 ARG Chi-restraints excluded: chain A residue 227 MET Chi-restraints excluded: chain A residue 303 THR Chi-restraints excluded: chain B residue 141 SER Chi-restraints excluded: chain B residue 194 THR Chi-restraints excluded: chain B residue 261 LEU Chi-restraints excluded: chain C residue 71 ILE Chi-restraints excluded: chain C residue 155 SER Chi-restraints excluded: chain C residue 274 ILE Chi-restraints excluded: chain C residue 351 THR Chi-restraints excluded: chain D residue 132 MET Chi-restraints excluded: chain D residue 155 SER Chi-restraints excluded: chain D residue 202 THR Chi-restraints excluded: chain D residue 244 ASP Chi-restraints excluded: chain D residue 292 ASP Chi-restraints excluded: chain E residue 56 ASP Chi-restraints excluded: chain E residue 303 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 271 random chunks: chunk 161 optimal weight: 3.9990 chunk 104 optimal weight: 2.9990 chunk 156 optimal weight: 5.9990 chunk 78 optimal weight: 5.9990 chunk 51 optimal weight: 0.8980 chunk 50 optimal weight: 10.0000 chunk 166 optimal weight: 7.9990 chunk 177 optimal weight: 0.8980 chunk 129 optimal weight: 0.9990 chunk 24 optimal weight: 9.9990 chunk 205 optimal weight: 1.9990 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** P 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 206 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 589 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 360 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 371 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7440 moved from start: 0.4714 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 21411 Z= 0.188 Angle : 0.616 11.296 28920 Z= 0.298 Chirality : 0.043 0.178 3077 Planarity : 0.003 0.065 3803 Dihedral : 5.908 77.809 3050 Min Nonbonded Distance : 1.951 Molprobity Statistics. All-atom Clashscore : 13.99 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.75 % Favored : 95.22 % Rotamer: Outliers : 1.52 % Allowed : 12.62 % Favored : 85.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.67 % Cis-general : 0.27 % Twisted Proline : 0.83 % 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 (0.17), residues: 2738 helix: 1.33 (0.15), residues: 1215 sheet: -0.36 (0.26), residues: 409 loop : -0.49 (0.20), residues: 1114 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP P 363 HIS 0.005 0.001 HIS C 371 PHE 0.008 0.001 PHE C 90 TYR 0.015 0.001 TYR A 169 ARG 0.002 0.000 ARG A 28 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5476 Ramachandran restraints generated. 2738 Oldfield, 0 Emsley, 2738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5476 Ramachandran restraints generated. 2738 Oldfield, 0 Emsley, 2738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 2367 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 152 time to evaluate : 2.629 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: P 258 MET cc_start: 0.6852 (ppp) cc_final: 0.6445 (ppp) REVERT: B 305 MET cc_start: 0.7623 (mmm) cc_final: 0.6908 (mmt) REVERT: D 305 MET cc_start: 0.8059 (pmm) cc_final: 0.7282 (mtm) outliers start: 33 outliers final: 29 residues processed: 174 average time/residue: 0.2893 time to fit residues: 83.9223 Evaluate side-chains 177 residues out of total 2367 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 148 time to evaluate : 2.372 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 105 LEU Chi-restraints excluded: chain P residue 211 LEU Chi-restraints excluded: chain P residue 243 ASN Chi-restraints excluded: chain P residue 260 ILE Chi-restraints excluded: chain P residue 329 VAL Chi-restraints excluded: chain P residue 356 LEU Chi-restraints excluded: chain P residue 370 GLU Chi-restraints excluded: chain P residue 447 ASP Chi-restraints excluded: chain P residue 498 ARG Chi-restraints excluded: chain A residue 34 ILE Chi-restraints excluded: chain A residue 155 SER Chi-restraints excluded: chain A residue 227 MET Chi-restraints excluded: chain A residue 261 LEU Chi-restraints excluded: chain A residue 303 THR Chi-restraints excluded: chain B residue 141 SER Chi-restraints excluded: chain B residue 194 THR Chi-restraints excluded: chain B residue 261 LEU Chi-restraints excluded: chain C residue 71 ILE Chi-restraints excluded: chain C residue 155 SER Chi-restraints excluded: chain C residue 244 ASP Chi-restraints excluded: chain C residue 274 ILE Chi-restraints excluded: chain C residue 351 THR Chi-restraints excluded: chain D residue 132 MET Chi-restraints excluded: chain D residue 155 SER Chi-restraints excluded: chain D residue 202 THR Chi-restraints excluded: chain D residue 244 ASP Chi-restraints excluded: chain D residue 274 ILE Chi-restraints excluded: chain D residue 292 ASP Chi-restraints excluded: chain E residue 56 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 271 random chunks: chunk 237 optimal weight: 1.9990 chunk 250 optimal weight: 10.0000 chunk 228 optimal weight: 3.9990 chunk 243 optimal weight: 0.0980 chunk 146 optimal weight: 9.9990 chunk 106 optimal weight: 2.9990 chunk 191 optimal weight: 3.9990 chunk 74 optimal weight: 50.0000 chunk 219 optimal weight: 0.9980 chunk 230 optimal weight: 4.9990 chunk 242 optimal weight: 1.9990 overall best weight: 1.6186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** P 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 206 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 589 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 360 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7441 moved from start: 0.4861 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 21411 Z= 0.192 Angle : 0.621 13.282 28920 Z= 0.298 Chirality : 0.043 0.157 3077 Planarity : 0.003 0.063 3803 Dihedral : 5.768 74.043 3050 Min Nonbonded Distance : 1.951 Molprobity Statistics. All-atom Clashscore : 14.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.89 % Favored : 95.11 % Rotamer: Outliers : 1.61 % Allowed : 12.76 % Favored : 85.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.67 % Cis-general : 0.27 % Twisted Proline : 0.83 % 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: 0.52 (0.17), residues: 2738 helix: 1.35 (0.15), residues: 1225 sheet: -0.35 (0.26), residues: 409 loop : -0.44 (0.20), residues: 1104 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP P 363 HIS 0.004 0.001 HIS C 371 PHE 0.009 0.001 PHE C 90 TYR 0.012 0.001 TYR B 143 ARG 0.003 0.000 ARG D 177 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5476 Ramachandran restraints generated. 2738 Oldfield, 0 Emsley, 2738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5476 Ramachandran restraints generated. 2738 Oldfield, 0 Emsley, 2738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 2367 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 152 time to evaluate : 2.270 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: P 258 MET cc_start: 0.6655 (ppp) cc_final: 0.6300 (ppp) REVERT: A 283 MET cc_start: 0.7943 (mmm) cc_final: 0.7737 (mmp) REVERT: B 305 MET cc_start: 0.7572 (mmm) cc_final: 0.6919 (mmt) REVERT: D 305 MET cc_start: 0.8057 (pmm) cc_final: 0.7207 (mtm) REVERT: E 227 MET cc_start: 0.7427 (mmm) cc_final: 0.7226 (mmm) outliers start: 35 outliers final: 31 residues processed: 177 average time/residue: 0.2950 time to fit residues: 86.2326 Evaluate side-chains 178 residues out of total 2367 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 147 time to evaluate : 2.554 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 105 LEU Chi-restraints excluded: chain P residue 211 LEU Chi-restraints excluded: chain P residue 243 ASN Chi-restraints excluded: chain P residue 260 ILE Chi-restraints excluded: chain P residue 329 VAL Chi-restraints excluded: chain P residue 356 LEU Chi-restraints excluded: chain P residue 370 GLU Chi-restraints excluded: chain P residue 447 ASP Chi-restraints excluded: chain P residue 498 ARG Chi-restraints excluded: chain A residue 34 ILE Chi-restraints excluded: chain A residue 80 ASP Chi-restraints excluded: chain A residue 155 SER Chi-restraints excluded: chain A residue 227 MET Chi-restraints excluded: chain A residue 261 LEU Chi-restraints excluded: chain A residue 303 THR Chi-restraints excluded: chain B residue 141 SER Chi-restraints excluded: chain B residue 194 THR Chi-restraints excluded: chain B residue 261 LEU Chi-restraints excluded: chain C residue 71 ILE Chi-restraints excluded: chain C residue 155 SER Chi-restraints excluded: chain C residue 244 ASP Chi-restraints excluded: chain C residue 274 ILE Chi-restraints excluded: chain C residue 351 THR Chi-restraints excluded: chain D residue 71 ILE Chi-restraints excluded: chain D residue 132 MET Chi-restraints excluded: chain D residue 155 SER Chi-restraints excluded: chain D residue 202 THR Chi-restraints excluded: chain D residue 244 ASP Chi-restraints excluded: chain D residue 274 ILE Chi-restraints excluded: chain D residue 292 ASP Chi-restraints excluded: chain E residue 56 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 271 random chunks: chunk 159 optimal weight: 0.0570 chunk 257 optimal weight: 7.9990 chunk 157 optimal weight: 8.9990 chunk 122 optimal weight: 6.9990 chunk 178 optimal weight: 1.9990 chunk 269 optimal weight: 2.9990 chunk 248 optimal weight: 7.9990 chunk 214 optimal weight: 0.0980 chunk 22 optimal weight: 4.9990 chunk 166 optimal weight: 4.9990 chunk 131 optimal weight: 0.9990 overall best weight: 1.2304 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** P 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 206 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 589 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 360 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7419 moved from start: 0.4984 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 21411 Z= 0.169 Angle : 0.618 12.982 28920 Z= 0.295 Chirality : 0.043 0.159 3077 Planarity : 0.003 0.060 3803 Dihedral : 5.616 68.102 3050 Min Nonbonded Distance : 1.954 Molprobity Statistics. All-atom Clashscore : 13.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.64 % Favored : 95.36 % Rotamer: Outliers : 1.38 % Allowed : 12.94 % Favored : 85.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.67 % Cis-general : 0.27 % Twisted Proline : 0.83 % 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: 0.53 (0.17), residues: 2738 helix: 1.22 (0.15), residues: 1261 sheet: -0.33 (0.26), residues: 409 loop : -0.31 (0.20), residues: 1068 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP P 363 HIS 0.004 0.001 HIS D 275 PHE 0.011 0.001 PHE C 223 TYR 0.013 0.001 TYR B 279 ARG 0.002 0.000 ARG A 28 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5476 Ramachandran restraints generated. 2738 Oldfield, 0 Emsley, 2738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5476 Ramachandran restraints generated. 2738 Oldfield, 0 Emsley, 2738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 2367 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 155 time to evaluate : 2.593 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: P 258 MET cc_start: 0.6586 (ppp) cc_final: 0.6314 (ppp) REVERT: P 383 MET cc_start: 0.7025 (ppp) cc_final: 0.6809 (ppp) REVERT: A 283 MET cc_start: 0.7964 (mmm) cc_final: 0.7762 (mmp) REVERT: B 305 MET cc_start: 0.7594 (mmm) cc_final: 0.6946 (mmt) REVERT: D 305 MET cc_start: 0.8093 (pmm) cc_final: 0.7296 (mtm) outliers start: 30 outliers final: 25 residues processed: 178 average time/residue: 0.2961 time to fit residues: 86.4393 Evaluate side-chains 171 residues out of total 2367 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 146 time to evaluate : 2.478 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 105 LEU Chi-restraints excluded: chain P residue 211 LEU Chi-restraints excluded: chain P residue 243 ASN Chi-restraints excluded: chain P residue 260 ILE Chi-restraints excluded: chain P residue 329 VAL Chi-restraints excluded: chain P residue 356 LEU Chi-restraints excluded: chain P residue 370 GLU Chi-restraints excluded: chain P residue 447 ASP Chi-restraints excluded: chain P residue 498 ARG Chi-restraints excluded: chain P residue 585 LEU Chi-restraints excluded: chain A residue 303 THR Chi-restraints excluded: chain B residue 141 SER Chi-restraints excluded: chain C residue 71 ILE Chi-restraints excluded: chain C residue 155 SER Chi-restraints excluded: chain C residue 244 ASP Chi-restraints excluded: chain C residue 274 ILE Chi-restraints excluded: chain C residue 351 THR Chi-restraints excluded: chain D residue 71 ILE Chi-restraints excluded: chain D residue 132 MET Chi-restraints excluded: chain D residue 155 SER Chi-restraints excluded: chain D residue 202 THR Chi-restraints excluded: chain D residue 244 ASP Chi-restraints excluded: chain D residue 274 ILE Chi-restraints excluded: chain D residue 292 ASP Chi-restraints excluded: chain E residue 56 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 271 random chunks: chunk 170 optimal weight: 4.9990 chunk 229 optimal weight: 2.9990 chunk 65 optimal weight: 10.0000 chunk 198 optimal weight: 6.9990 chunk 31 optimal weight: 5.9990 chunk 59 optimal weight: 10.0000 chunk 215 optimal weight: 3.9990 chunk 90 optimal weight: 8.9990 chunk 221 optimal weight: 5.9990 chunk 27 optimal weight: 9.9990 chunk 39 optimal weight: 5.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** P 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 206 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 360 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 371 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.054803 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.2908 r_free = 0.2908 target = 0.040682 restraints weight = 120186.310| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 50)----------------| | r_work = 0.2948 r_free = 0.2948 target = 0.041954 restraints weight = 59042.870| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.2974 r_free = 0.2974 target = 0.042776 restraints weight = 35778.675| |-----------------------------------------------------------------------------| r_work (final): 0.2953 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8496 moved from start: 0.5315 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.111 21411 Z= 0.418 Angle : 0.753 13.539 28920 Z= 0.373 Chirality : 0.046 0.328 3077 Planarity : 0.004 0.061 3803 Dihedral : 6.312 81.270 3050 Min Nonbonded Distance : 1.801 Molprobity Statistics. All-atom Clashscore : 18.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.84 % Favored : 94.16 % Rotamer: Outliers : 1.38 % Allowed : 12.99 % Favored : 85.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.67 % Cis-general : 0.27 % Twisted Proline : 0.83 % 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: 0.30 (0.16), residues: 2738 helix: 1.03 (0.15), residues: 1224 sheet: -0.45 (0.26), residues: 417 loop : -0.36 (0.20), residues: 1097 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP E 79 HIS 0.008 0.002 HIS C 371 PHE 0.018 0.002 PHE P 526 TYR 0.018 0.002 TYR C 143 ARG 0.005 0.001 ARG P 165 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3579.38 seconds wall clock time: 67 minutes 2.45 seconds (4022.45 seconds total)