Starting phenix.real_space_refine on Fri Feb 23 00:24:08 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8aa2_15291/02_2024/8aa2_15291_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8aa2_15291/02_2024/8aa2_15291.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8aa2_15291/02_2024/8aa2_15291.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8aa2_15291/02_2024/8aa2_15291.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8aa2_15291/02_2024/8aa2_15291_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8aa2_15291/02_2024/8aa2_15291_updated.pdb" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.007 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians Mg 4 5.21 5 S 136 5.16 5 C 22700 2.51 5 N 5948 2.21 5 O 7154 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "E TYR 84": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 181": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 227": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M TYR 84": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M TYR 181": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M PHE 227": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 438": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 463": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 801": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 976": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 438": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 463": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 801": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 976": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.10s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 35942 Number of models: 1 Model: "" Number of chains: 19 Chain: "E" Number of atoms: 3979 Number of conformers: 1 Conformer: "" Number of residues, atoms: 497, 3979 Classifications: {'peptide': 497} Link IDs: {'PTRANS': 18, 'TRANS': 478} Chain: "T" Number of atoms: 721 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 721 Classifications: {'peptide': 93} Link IDs: {'PTRANS': 2, 'TRANS': 90} Chain: "G" Number of atoms: 3351 Number of conformers: 1 Conformer: "" Number of residues, atoms: 435, 3351 Classifications: {'peptide': 435} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 16, 'TRANS': 418} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 4 Planarities with less than four sites: {'ASP:plan': 2} Unresolved non-hydrogen planarities: 6 Chain: "M" Number of atoms: 3979 Number of conformers: 1 Conformer: "" Number of residues, atoms: 497, 3979 Classifications: {'peptide': 497} Link IDs: {'PTRANS': 18, 'TRANS': 478} Chain: "B" Number of atoms: 4436 Number of conformers: 1 Conformer: "" Number of residues, atoms: 551, 4436 Classifications: {'peptide': 551} Link IDs: {'PTRANS': 18, 'TRANS': 532} Chain: "A" Number of atoms: 7267 Number of conformers: 1 Conformer: "" Number of residues, atoms: 924, 7267 Classifications: {'peptide': 924} Link IDs: {'PTRANS': 32, 'TRANS': 891} Chain: "J" Number of atoms: 4436 Number of conformers: 1 Conformer: "" Number of residues, atoms: 551, 4436 Classifications: {'peptide': 551} Link IDs: {'PTRANS': 18, 'TRANS': 532} Chain: "I" Number of atoms: 7267 Number of conformers: 1 Conformer: "" Number of residues, atoms: 924, 7267 Classifications: {'peptide': 924} Link IDs: {'PTRANS': 32, 'TRANS': 891} Chain: "H" Number of atoms: 144 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 144 Unusual residues: {'FRU': 13} Classifications: {'undetermined': 13} Link IDs: {None: 12} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 36 Unresolved non-hydrogen dihedrals: 48 Unresolved non-hydrogen chiralities: 12 Chain: "F" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 56 Unusual residues: {'FRU': 5} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 16 Unresolved non-hydrogen chiralities: 4 Chain: "N" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 56 Unusual residues: {'FRU': 5} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 16 Unresolved non-hydrogen chiralities: 4 Chain: "C" Number of atoms: 78 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 78 Unusual residues: {'FRU': 7} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 6 Chain: "D" Number of atoms: 45 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 45 Unusual residues: {'FRU': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 3 Chain: "K" Number of atoms: 78 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 78 Unusual residues: {'FRU': 7} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 6 Chain: "L" Number of atoms: 45 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 45 Unusual residues: {'FRU': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 3 Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "J" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "I" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Time building chain proxies: 17.77, per 1000 atoms: 0.49 Number of scatterers: 35942 At special positions: 0 Unit cell: (116.085, 189.57, 195.96, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 136 16.00 Mg 4 11.99 O 7154 8.00 N 5948 7.00 C 22700 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS B 387 " - pdb=" SG CYS B 389 " distance=2.03 Simple disulfide: pdb=" SG CYS J 387 " - pdb=" SG CYS J 389 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied ALPHA2-1 " FRU C 2 " - " FRU C 7 " ~> Even though FRU is a beta isomer, an alpha linkage is required... " FRU H 6 " - " FRU H 13 " " FRU K 2 " - " FRU K 7 " ALPHA2-6 " FRU C 1 " - " FRU C 2 " " FRU C 2 " - " FRU C 3 " " FRU C 3 " - " FRU C 4 " " FRU C 4 " - " FRU C 5 " " FRU C 5 " - " FRU C 6 " " FRU D 1 " - " FRU D 2 " " FRU D 2 " - " FRU D 3 " " FRU D 3 " - " FRU D 4 " " FRU F 1 " - " FRU F 2 " " FRU F 2 " - " FRU F 3 " " FRU F 3 " - " FRU F 4 " " FRU F 4 " - " FRU F 5 " " FRU H 1 " - " FRU H 2 " " FRU H 2 " - " FRU H 3 " " FRU H 3 " - " FRU H 4 " " FRU H 4 " - " FRU H 5 " " FRU H 5 " - " FRU H 6 " " FRU H 6 " - " FRU H 7 " " FRU H 7 " - " FRU H 8 " " FRU H 8 " - " FRU H 9 " " FRU H 9 " - " FRU H 10 " " FRU H 10 " - " FRU H 11 " " FRU H 11 " - " FRU H 12 " " FRU K 1 " - " FRU K 2 " " FRU K 2 " - " FRU K 3 " " FRU K 3 " - " FRU K 4 " " FRU K 4 " - " FRU K 5 " " FRU K 5 " - " FRU K 6 " " FRU L 1 " - " FRU L 2 " " FRU L 2 " - " FRU L 3 " " FRU L 3 " - " FRU L 4 " " FRU N 1 " - " FRU N 2 " " FRU N 2 " - " FRU N 3 " " FRU N 3 " - " FRU N 4 " " FRU N 4 " - " FRU N 5 " Time building additional restraints: 17.82 Conformation dependent library (CDL) restraints added in 8.1 seconds 8912 Ramachandran restraints generated. 4456 Oldfield, 0 Emsley, 4456 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8152 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 100 helices and 46 sheets defined 18.1% alpha, 26.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 7.94 Creating SS restraints... Processing helix chain 'E' and resid 158 through 161 Processing helix chain 'E' and resid 255 through 260 Processing helix chain 'E' and resid 304 through 306 No H-bonds generated for 'chain 'E' and resid 304 through 306' Processing helix chain 'E' and resid 341 through 346 Processing helix chain 'G' and resid 199 through 211 Processing helix chain 'G' and resid 220 through 225 Processing helix chain 'G' and resid 230 through 232 No H-bonds generated for 'chain 'G' and resid 230 through 232' Processing helix chain 'G' and resid 252 through 267 removed outlier: 4.534A pdb=" N GLU G 259 " --> pdb=" O LYS G 255 " (cutoff:3.500A) removed outlier: 4.873A pdb=" N LYS G 260 " --> pdb=" O ALA G 256 " (cutoff:3.500A) Processing helix chain 'G' and resid 279 through 284 Processing helix chain 'G' and resid 301 through 303 No H-bonds generated for 'chain 'G' and resid 301 through 303' Processing helix chain 'G' and resid 365 through 372 Processing helix chain 'G' and resid 422 through 437 Processing helix chain 'M' and resid 158 through 161 Processing helix chain 'M' and resid 255 through 260 Processing helix chain 'M' and resid 304 through 306 No H-bonds generated for 'chain 'M' and resid 304 through 306' Processing helix chain 'M' and resid 341 through 346 Processing helix chain 'B' and resid 16 through 19 No H-bonds generated for 'chain 'B' and resid 16 through 19' Processing helix chain 'B' and resid 22 through 38 removed outlier: 3.653A pdb=" N VAL B 25 " --> pdb=" O PRO B 22 " (cutoff:3.500A) removed outlier: 4.759A pdb=" N ASP B 26 " --> pdb=" O GLU B 23 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N ILE B 35 " --> pdb=" O ALA B 32 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N THR B 38 " --> pdb=" O ILE B 35 " (cutoff:3.500A) Processing helix chain 'B' and resid 69 through 76 Processing helix chain 'B' and resid 85 through 110 removed outlier: 3.826A pdb=" N GLN B 110 " --> pdb=" O GLN B 106 " (cutoff:3.500A) Processing helix chain 'B' and resid 117 through 140 removed outlier: 4.552A pdb=" N ASN B 120 " --> pdb=" O PRO B 117 " (cutoff:3.500A) Processing helix chain 'B' and resid 154 through 159 removed outlier: 3.857A pdb=" N ASN B 158 " --> pdb=" O ASP B 155 " (cutoff:3.500A) Processing helix chain 'B' and resid 167 through 184 removed outlier: 3.878A pdb=" N ASP B 177 " --> pdb=" O LYS B 173 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N PHE B 178 " --> pdb=" O ILE B 174 " (cutoff:3.500A) Processing helix chain 'B' and resid 197 through 212 Processing helix chain 'B' and resid 227 through 237 Processing helix chain 'B' and resid 239 through 245 Processing helix chain 'B' and resid 254 through 256 No H-bonds generated for 'chain 'B' and resid 254 through 256' Processing helix chain 'B' and resid 259 through 261 No H-bonds generated for 'chain 'B' and resid 259 through 261' Processing helix chain 'B' and resid 286 through 291 removed outlier: 4.382A pdb=" N LEU B 290 " --> pdb=" O GLY B 287 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 296 No H-bonds generated for 'chain 'B' and resid 294 through 296' Processing helix chain 'B' and resid 306 through 312 Processing helix chain 'B' and resid 339 through 344 Processing helix chain 'B' and resid 407 through 421 Processing helix chain 'B' and resid 426 through 442 Processing helix chain 'B' and resid 448 through 454 removed outlier: 3.527A pdb=" N LYS B 451 " --> pdb=" O PHE B 448 " (cutoff:3.500A) removed outlier: 4.438A pdb=" N TYR B 454 " --> pdb=" O LYS B 451 " (cutoff:3.500A) Processing helix chain 'B' and resid 470 through 484 Processing helix chain 'B' and resid 491 through 498 Processing helix chain 'B' and resid 501 through 512 Processing helix chain 'B' and resid 518 through 520 No H-bonds generated for 'chain 'B' and resid 518 through 520' Processing helix chain 'B' and resid 536 through 541 Processing helix chain 'A' and resid 106 through 112 removed outlier: 3.668A pdb=" N GLN A 112 " --> pdb=" O GLU A 108 " (cutoff:3.500A) Processing helix chain 'A' and resid 117 through 120 No H-bonds generated for 'chain 'A' and resid 117 through 120' Processing helix chain 'A' and resid 168 through 170 No H-bonds generated for 'chain 'A' and resid 168 through 170' Processing helix chain 'A' and resid 185 through 191 removed outlier: 4.866A pdb=" N ILE A 190 " --> pdb=" O ALA A 186 " (cutoff:3.500A) removed outlier: 5.165A pdb=" N TYR A 191 " --> pdb=" O SER A 187 " (cutoff:3.500A) Processing helix chain 'A' and resid 234 through 248 Processing helix chain 'A' and resid 252 through 255 Processing helix chain 'A' and resid 295 through 299 Processing helix chain 'A' and resid 377 through 383 Processing helix chain 'A' and resid 410 through 419 removed outlier: 4.893A pdb=" N ASP A 419 " --> pdb=" O GLU A 415 " (cutoff:3.500A) Processing helix chain 'A' and resid 601 through 603 No H-bonds generated for 'chain 'A' and resid 601 through 603' Processing helix chain 'A' and resid 605 through 607 No H-bonds generated for 'chain 'A' and resid 605 through 607' Processing helix chain 'A' and resid 780 through 785 Processing helix chain 'A' and resid 816 through 821 Processing helix chain 'A' and resid 889 through 894 removed outlier: 3.959A pdb=" N LYS A 893 " --> pdb=" O ASP A 889 " (cutoff:3.500A) Processing helix chain 'A' and resid 909 through 913 Processing helix chain 'A' and resid 940 through 942 No H-bonds generated for 'chain 'A' and resid 940 through 942' Processing helix chain 'A' and resid 962 through 967 Processing helix chain 'A' and resid 995 through 997 No H-bonds generated for 'chain 'A' and resid 995 through 997' Processing helix chain 'J' and resid 16 through 19 No H-bonds generated for 'chain 'J' and resid 16 through 19' Processing helix chain 'J' and resid 22 through 38 removed outlier: 3.652A pdb=" N VAL J 25 " --> pdb=" O PRO J 22 " (cutoff:3.500A) removed outlier: 4.761A pdb=" N ASP J 26 " --> pdb=" O GLU J 23 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N ILE J 35 " --> pdb=" O ALA J 32 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N THR J 38 " --> pdb=" O ILE J 35 " (cutoff:3.500A) Processing helix chain 'J' and resid 69 through 76 Processing helix chain 'J' and resid 85 through 110 removed outlier: 3.825A pdb=" N GLN J 110 " --> pdb=" O GLN J 106 " (cutoff:3.500A) Processing helix chain 'J' and resid 117 through 140 removed outlier: 4.553A pdb=" N ASN J 120 " --> pdb=" O PRO J 117 " (cutoff:3.500A) Processing helix chain 'J' and resid 154 through 159 removed outlier: 3.856A pdb=" N ASN J 158 " --> pdb=" O ASP J 155 " (cutoff:3.500A) Processing helix chain 'J' and resid 167 through 184 removed outlier: 3.878A pdb=" N ASP J 177 " --> pdb=" O LYS J 173 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N PHE J 178 " --> pdb=" O ILE J 174 " (cutoff:3.500A) Processing helix chain 'J' and resid 197 through 212 Processing helix chain 'J' and resid 227 through 237 Processing helix chain 'J' and resid 239 through 245 Processing helix chain 'J' and resid 254 through 256 No H-bonds generated for 'chain 'J' and resid 254 through 256' Processing helix chain 'J' and resid 259 through 261 No H-bonds generated for 'chain 'J' and resid 259 through 261' Processing helix chain 'J' and resid 286 through 291 removed outlier: 4.381A pdb=" N LEU J 290 " --> pdb=" O GLY J 287 " (cutoff:3.500A) Processing helix chain 'J' and resid 294 through 296 No H-bonds generated for 'chain 'J' and resid 294 through 296' Processing helix chain 'J' and resid 306 through 312 Processing helix chain 'J' and resid 339 through 344 Processing helix chain 'J' and resid 407 through 421 Processing helix chain 'J' and resid 426 through 442 Processing helix chain 'J' and resid 448 through 454 removed outlier: 3.527A pdb=" N LYS J 451 " --> pdb=" O PHE J 448 " (cutoff:3.500A) removed outlier: 4.438A pdb=" N TYR J 454 " --> pdb=" O LYS J 451 " (cutoff:3.500A) Processing helix chain 'J' and resid 470 through 484 Processing helix chain 'J' and resid 491 through 498 Processing helix chain 'J' and resid 501 through 512 Processing helix chain 'J' and resid 518 through 520 No H-bonds generated for 'chain 'J' and resid 518 through 520' Processing helix chain 'J' and resid 536 through 541 Processing helix chain 'I' and resid 106 through 112 removed outlier: 3.668A pdb=" N GLN I 112 " --> pdb=" O GLU I 108 " (cutoff:3.500A) Processing helix chain 'I' and resid 117 through 120 No H-bonds generated for 'chain 'I' and resid 117 through 120' Processing helix chain 'I' and resid 168 through 170 No H-bonds generated for 'chain 'I' and resid 168 through 170' Processing helix chain 'I' and resid 185 through 191 removed outlier: 4.865A pdb=" N ILE I 190 " --> pdb=" O ALA I 186 " (cutoff:3.500A) removed outlier: 5.165A pdb=" N TYR I 191 " --> pdb=" O SER I 187 " (cutoff:3.500A) Processing helix chain 'I' and resid 234 through 248 Processing helix chain 'I' and resid 252 through 255 Processing helix chain 'I' and resid 295 through 299 Processing helix chain 'I' and resid 377 through 383 Processing helix chain 'I' and resid 410 through 419 removed outlier: 4.893A pdb=" N ASP I 419 " --> pdb=" O GLU I 415 " (cutoff:3.500A) Processing helix chain 'I' and resid 601 through 603 No H-bonds generated for 'chain 'I' and resid 601 through 603' Processing helix chain 'I' and resid 605 through 607 No H-bonds generated for 'chain 'I' and resid 605 through 607' Processing helix chain 'I' and resid 780 through 785 Processing helix chain 'I' and resid 816 through 821 Processing helix chain 'I' and resid 889 through 894 removed outlier: 3.959A pdb=" N LYS I 893 " --> pdb=" O ASP I 889 " (cutoff:3.500A) Processing helix chain 'I' and resid 909 through 913 Processing helix chain 'I' and resid 940 through 942 No H-bonds generated for 'chain 'I' and resid 940 through 942' Processing helix chain 'I' and resid 962 through 967 Processing helix chain 'I' and resid 995 through 997 No H-bonds generated for 'chain 'I' and resid 995 through 997' Processing sheet with id= A, first strand: chain 'E' and resid 39 through 41 removed outlier: 6.202A pdb=" N GLY E 75 " --> pdb=" O GLU E 89 " (cutoff:3.500A) removed outlier: 6.295A pdb=" N GLU E 89 " --> pdb=" O GLY E 75 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'E' and resid 102 through 104 removed outlier: 4.051A pdb=" N THR E 122 " --> pdb=" O GLY E 104 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'E' and resid 107 through 111 Processing sheet with id= D, first strand: chain 'E' and resid 172 through 175 removed outlier: 5.771A pdb=" N GLU E 197 " --> pdb=" O THR E 211 " (cutoff:3.500A) removed outlier: 5.603A pdb=" N THR E 211 " --> pdb=" O GLU E 197 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'E' and resid 225 through 229 removed outlier: 3.727A pdb=" N TRP E 232 " --> pdb=" O MET E 229 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'E' and resid 286 through 289 removed outlier: 5.095A pdb=" N ARG E 294 " --> pdb=" O LEU E 327 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'E' and resid 349 through 351 removed outlier: 4.241A pdb=" N VAL E 500 " --> pdb=" O GLN E 351 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'E' and resid 369 through 371 Processing sheet with id= I, first strand: chain 'E' and resid 376 through 378 removed outlier: 3.708A pdb=" N PHE E 401 " --> pdb=" O VAL E 419 " (cutoff:3.500A) removed outlier: 6.334A pdb=" N LYS E 430 " --> pdb=" O TYR E 437 " (cutoff:3.500A) removed outlier: 5.130A pdb=" N TYR E 437 " --> pdb=" O LYS E 430 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'T' and resid 27 through 30 removed outlier: 8.482A pdb=" N ILE T 36 " --> pdb=" O SER T 88 " (cutoff:3.500A) removed outlier: 6.441A pdb=" N THR T 90 " --> pdb=" O ILE T 36 " (cutoff:3.500A) removed outlier: 7.803A pdb=" N VAL T 38 " --> pdb=" O THR T 90 " (cutoff:3.500A) removed outlier: 6.594A pdb=" N THR T 92 " --> pdb=" O VAL T 38 " (cutoff:3.500A) removed outlier: 7.777A pdb=" N VAL T 40 " --> pdb=" O THR T 92 " (cutoff:3.500A) removed outlier: 6.129A pdb=" N LYS T 94 " --> pdb=" O VAL T 40 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'G' and resid 27 through 30 removed outlier: 8.270A pdb=" N ILE G 36 " --> pdb=" O SER G 88 " (cutoff:3.500A) removed outlier: 6.244A pdb=" N THR G 90 " --> pdb=" O ILE G 36 " (cutoff:3.500A) removed outlier: 7.687A pdb=" N VAL G 38 " --> pdb=" O THR G 90 " (cutoff:3.500A) removed outlier: 6.573A pdb=" N THR G 92 " --> pdb=" O VAL G 38 " (cutoff:3.500A) removed outlier: 7.563A pdb=" N VAL G 40 " --> pdb=" O THR G 92 " (cutoff:3.500A) removed outlier: 6.341A pdb=" N LYS G 94 " --> pdb=" O VAL G 40 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'G' and resid 112 through 114 removed outlier: 8.465A pdb=" N ILE G 120 " --> pdb=" O PRO G 171 " (cutoff:3.500A) removed outlier: 6.442A pdb=" N VAL G 173 " --> pdb=" O ILE G 120 " (cutoff:3.500A) removed outlier: 7.916A pdb=" N VAL G 122 " --> pdb=" O VAL G 173 " (cutoff:3.500A) removed outlier: 6.641A pdb=" N THR G 175 " --> pdb=" O VAL G 122 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'G' and resid 133 through 135 removed outlier: 3.539A pdb=" N LEU G 133 " --> pdb=" O GLN G 153 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N GLY G 135 " --> pdb=" O SER G 151 " (cutoff:3.500A) removed outlier: 4.210A pdb=" N SER G 151 " --> pdb=" O GLY G 135 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'G' and resid 215 through 219 removed outlier: 6.367A pdb=" N THR G 184 " --> pdb=" O GLU G 216 " (cutoff:3.500A) removed outlier: 7.518A pdb=" N ILE G 218 " --> pdb=" O THR G 184 " (cutoff:3.500A) removed outlier: 5.798A pdb=" N PHE G 186 " --> pdb=" O ILE G 218 " (cutoff:3.500A) removed outlier: 6.429A pdb=" N ALA G 235 " --> pdb=" O ALA G 185 " (cutoff:3.500A) removed outlier: 7.634A pdb=" N VAL G 187 " --> pdb=" O ALA G 235 " (cutoff:3.500A) removed outlier: 6.690A pdb=" N TRP G 237 " --> pdb=" O VAL G 187 " (cutoff:3.500A) removed outlier: 6.647A pdb=" N ASN G 270 " --> pdb=" O ILE G 236 " (cutoff:3.500A) removed outlier: 7.936A pdb=" N TRP G 238 " --> pdb=" O ASN G 270 " (cutoff:3.500A) removed outlier: 6.302A pdb=" N LEU G 272 " --> pdb=" O TRP G 238 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N ILE G 387 " --> pdb=" O ALA G 378 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N ALA G 378 " --> pdb=" O ILE G 387 " (cutoff:3.500A) removed outlier: 6.954A pdb=" N GLU G 389 " --> pdb=" O ASP G 376 " (cutoff:3.500A) removed outlier: 5.601A pdb=" N ASP G 376 " --> pdb=" O GLU G 389 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'G' and resid 312 through 314 Processing sheet with id= P, first strand: chain 'G' and resid 17 through 21 removed outlier: 7.111A pdb=" N ASN G 55 " --> pdb=" O ASN G 18 " (cutoff:3.500A) removed outlier: 4.854A pdb=" N ILE G 20 " --> pdb=" O GLU G 53 " (cutoff:3.500A) removed outlier: 6.873A pdb=" N GLU G 53 " --> pdb=" O ILE G 20 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'G' and resid 100 through 104 removed outlier: 6.442A pdb=" N THR G 138 " --> pdb=" O LEU G 101 " (cutoff:3.500A) removed outlier: 4.580A pdb=" N PHE G 103 " --> pdb=" O THR G 136 " (cutoff:3.500A) removed outlier: 6.841A pdb=" N THR G 136 " --> pdb=" O PHE G 103 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'M' and resid 39 through 41 removed outlier: 6.202A pdb=" N GLY M 75 " --> pdb=" O GLU M 89 " (cutoff:3.500A) removed outlier: 6.295A pdb=" N GLU M 89 " --> pdb=" O GLY M 75 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'M' and resid 102 through 104 removed outlier: 4.051A pdb=" N THR M 122 " --> pdb=" O GLY M 104 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'M' and resid 107 through 111 Processing sheet with id= U, first strand: chain 'M' and resid 172 through 175 removed outlier: 5.771A pdb=" N GLU M 197 " --> pdb=" O THR M 211 " (cutoff:3.500A) removed outlier: 5.603A pdb=" N THR M 211 " --> pdb=" O GLU M 197 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'M' and resid 225 through 229 removed outlier: 3.727A pdb=" N TRP M 232 " --> pdb=" O MET M 229 " (cutoff:3.500A) Processing sheet with id= W, first strand: chain 'M' and resid 286 through 289 removed outlier: 5.095A pdb=" N ARG M 294 " --> pdb=" O LEU M 327 " (cutoff:3.500A) Processing sheet with id= X, first strand: chain 'M' and resid 349 through 351 removed outlier: 4.241A pdb=" N VAL M 500 " --> pdb=" O GLN M 351 " (cutoff:3.500A) Processing sheet with id= Y, first strand: chain 'M' and resid 369 through 371 Processing sheet with id= Z, first strand: chain 'M' and resid 376 through 378 removed outlier: 3.708A pdb=" N PHE M 401 " --> pdb=" O VAL M 419 " (cutoff:3.500A) removed outlier: 6.334A pdb=" N LYS M 430 " --> pdb=" O TYR M 437 " (cutoff:3.500A) removed outlier: 5.131A pdb=" N TYR M 437 " --> pdb=" O LYS M 430 " (cutoff:3.500A) Processing sheet with id= AA, first strand: chain 'B' and resid 390 through 392 Processing sheet with id= AB, first strand: chain 'A' and resid 101 through 104 removed outlier: 4.135A pdb=" N ILE A 179 " --> pdb=" O VAL A 104 " (cutoff:3.500A) removed outlier: 6.582A pdb=" N THR A 203 " --> pdb=" O GLU A 177 " (cutoff:3.500A) removed outlier: 4.303A pdb=" N ILE A 179 " --> pdb=" O ILE A 201 " (cutoff:3.500A) removed outlier: 6.668A pdb=" N ILE A 201 " --> pdb=" O ILE A 179 " (cutoff:3.500A) removed outlier: 4.562A pdb=" N VAL A 181 " --> pdb=" O VAL A 199 " (cutoff:3.500A) removed outlier: 6.650A pdb=" N VAL A 199 " --> pdb=" O VAL A 181 " (cutoff:3.500A) removed outlier: 6.545A pdb=" N LEU A 156 " --> pdb=" O ILE A 200 " (cutoff:3.500A) removed outlier: 7.483A pdb=" N ILE A 202 " --> pdb=" O LEU A 156 " (cutoff:3.500A) removed outlier: 6.484A pdb=" N ILE A 158 " --> pdb=" O ILE A 202 " (cutoff:3.500A) removed outlier: 7.504A pdb=" N THR A 204 " --> pdb=" O ILE A 158 " (cutoff:3.500A) Processing sheet with id= AC, first strand: chain 'A' and resid 128 through 131 Processing sheet with id= AD, first strand: chain 'A' and resid 303 through 314 removed outlier: 6.671A pdb=" N PHE A 877 " --> pdb=" O ARG A 952 " (cutoff:3.500A) removed outlier: 4.295A pdb=" N ILE A 954 " --> pdb=" O THR A 875 " (cutoff:3.500A) removed outlier: 6.611A pdb=" N THR A 875 " --> pdb=" O ILE A 954 " (cutoff:3.500A) removed outlier: 4.407A pdb=" N LEU A 956 " --> pdb=" O ASP A 873 " (cutoff:3.500A) removed outlier: 6.694A pdb=" N ASP A 873 " --> pdb=" O LEU A 956 " (cutoff:3.500A) removed outlier: 6.342A pdb=" N ALA A 740 " --> pdb=" O LEU A 776 " (cutoff:3.500A) removed outlier: 7.348A pdb=" N GLY A 626 " --> pdb=" O THR A 591 " (cutoff:3.500A) removed outlier: 9.986A pdb=" N THR A 591 " --> pdb=" O GLY A 626 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N ARG A 457 " --> pdb=" O ARG A 421 " (cutoff:3.500A) removed outlier: 4.457A pdb=" N ARG A 421 " --> pdb=" O ARG A 457 " (cutoff:3.500A) Processing sheet with id= AE, first strand: chain 'A' and resid 719 through 722 Processing sheet with id= AF, first strand: chain 'A' and resid 885 through 887 Processing sheet with id= AG, first strand: chain 'A' and resid 948 through 951 removed outlier: 4.443A pdb=" N LEU A 983 " --> pdb=" O LEU A 951 " (cutoff:3.500A) Processing sheet with id= AH, first strand: chain 'A' and resid 259 through 265 removed outlier: 6.817A pdb=" N GLY A 264 " --> pdb=" O LEU A 273 " (cutoff:3.500A) removed outlier: 5.272A pdb=" N LEU A 273 " --> pdb=" O GLY A 264 " (cutoff:3.500A) Processing sheet with id= AI, first strand: chain 'A' and resid 638 through 640 removed outlier: 3.829A pdb=" N GLN A 677 " --> pdb=" O ILE A 638 " (cutoff:3.500A) removed outlier: 6.501A pdb=" N ALA A 640 " --> pdb=" O ARG A 675 " (cutoff:3.500A) removed outlier: 5.453A pdb=" N ARG A 675 " --> pdb=" O ALA A 640 " (cutoff:3.500A) Processing sheet with id= AJ, first strand: chain 'A' and resid 804 through 806 removed outlier: 6.417A pdb=" N GLY A 806 " --> pdb=" O TRP A 851 " (cutoff:3.500A) removed outlier: 5.188A pdb=" N TRP A 851 " --> pdb=" O GLY A 806 " (cutoff:3.500A) Processing sheet with id= AK, first strand: chain 'J' and resid 390 through 392 Processing sheet with id= AL, first strand: chain 'I' and resid 101 through 104 removed outlier: 4.137A pdb=" N ILE I 179 " --> pdb=" O VAL I 104 " (cutoff:3.500A) removed outlier: 6.582A pdb=" N THR I 203 " --> pdb=" O GLU I 177 " (cutoff:3.500A) removed outlier: 4.302A pdb=" N ILE I 179 " --> pdb=" O ILE I 201 " (cutoff:3.500A) removed outlier: 6.669A pdb=" N ILE I 201 " --> pdb=" O ILE I 179 " (cutoff:3.500A) removed outlier: 4.561A pdb=" N VAL I 181 " --> pdb=" O VAL I 199 " (cutoff:3.500A) removed outlier: 6.649A pdb=" N VAL I 199 " --> pdb=" O VAL I 181 " (cutoff:3.500A) removed outlier: 6.544A pdb=" N LEU I 156 " --> pdb=" O ILE I 200 " (cutoff:3.500A) removed outlier: 7.483A pdb=" N ILE I 202 " --> pdb=" O LEU I 156 " (cutoff:3.500A) removed outlier: 6.483A pdb=" N ILE I 158 " --> pdb=" O ILE I 202 " (cutoff:3.500A) removed outlier: 7.504A pdb=" N THR I 204 " --> pdb=" O ILE I 158 " (cutoff:3.500A) Processing sheet with id= AM, first strand: chain 'I' and resid 128 through 131 Processing sheet with id= AN, first strand: chain 'I' and resid 303 through 314 removed outlier: 6.670A pdb=" N PHE I 877 " --> pdb=" O ARG I 952 " (cutoff:3.500A) removed outlier: 4.295A pdb=" N ILE I 954 " --> pdb=" O THR I 875 " (cutoff:3.500A) removed outlier: 6.611A pdb=" N THR I 875 " --> pdb=" O ILE I 954 " (cutoff:3.500A) removed outlier: 4.407A pdb=" N LEU I 956 " --> pdb=" O ASP I 873 " (cutoff:3.500A) removed outlier: 6.694A pdb=" N ASP I 873 " --> pdb=" O LEU I 956 " (cutoff:3.500A) removed outlier: 6.342A pdb=" N ALA I 740 " --> pdb=" O LEU I 776 " (cutoff:3.500A) removed outlier: 7.348A pdb=" N GLY I 626 " --> pdb=" O THR I 591 " (cutoff:3.500A) removed outlier: 9.986A pdb=" N THR I 591 " --> pdb=" O GLY I 626 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N ARG I 457 " --> pdb=" O ARG I 421 " (cutoff:3.500A) removed outlier: 4.458A pdb=" N ARG I 421 " --> pdb=" O ARG I 457 " (cutoff:3.500A) Processing sheet with id= AO, first strand: chain 'I' and resid 719 through 722 Processing sheet with id= AP, first strand: chain 'I' and resid 885 through 887 Processing sheet with id= AQ, first strand: chain 'I' and resid 948 through 951 removed outlier: 4.442A pdb=" N LEU I 983 " --> pdb=" O LEU I 951 " (cutoff:3.500A) Processing sheet with id= AR, first strand: chain 'I' and resid 259 through 265 removed outlier: 6.816A pdb=" N GLY I 264 " --> pdb=" O LEU I 273 " (cutoff:3.500A) removed outlier: 5.273A pdb=" N LEU I 273 " --> pdb=" O GLY I 264 " (cutoff:3.500A) Processing sheet with id= AS, first strand: chain 'I' and resid 638 through 640 removed outlier: 3.830A pdb=" N GLN I 677 " --> pdb=" O ILE I 638 " (cutoff:3.500A) removed outlier: 6.501A pdb=" N ALA I 640 " --> pdb=" O ARG I 675 " (cutoff:3.500A) removed outlier: 5.453A pdb=" N ARG I 675 " --> pdb=" O ALA I 640 " (cutoff:3.500A) Processing sheet with id= AT, first strand: chain 'I' and resid 804 through 806 removed outlier: 6.417A pdb=" N GLY I 806 " --> pdb=" O TRP I 851 " (cutoff:3.500A) removed outlier: 5.188A pdb=" N TRP I 851 " --> pdb=" O GLY I 806 " (cutoff:3.500A) 1339 hydrogen bonds defined for protein. 3435 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: 14.89 Time building geometry restraints manager: 18.81 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: 11716 1.34 - 1.46: 8739 1.46 - 1.58: 15974 1.58 - 1.70: 135 1.70 - 1.81: 240 Bond restraints: 36804 Sorted by residual: bond pdb=" C2 FRU F 4 " pdb=" O5 FRU F 4 " ideal model delta sigma weight residual 1.412 1.642 -0.230 2.00e-02 2.50e+03 1.32e+02 bond pdb=" C2 FRU H 6 " pdb=" O5 FRU H 6 " ideal model delta sigma weight residual 1.412 1.642 -0.230 2.00e-02 2.50e+03 1.32e+02 bond pdb=" C2 FRU H 2 " pdb=" O5 FRU H 2 " ideal model delta sigma weight residual 1.412 1.641 -0.229 2.00e-02 2.50e+03 1.31e+02 bond pdb=" C2 FRU K 4 " pdb=" O5 FRU K 4 " ideal model delta sigma weight residual 1.412 1.641 -0.229 2.00e-02 2.50e+03 1.31e+02 bond pdb=" C2 FRU N 4 " pdb=" O5 FRU N 4 " ideal model delta sigma weight residual 1.412 1.641 -0.229 2.00e-02 2.50e+03 1.31e+02 ... (remaining 36799 not shown) Histogram of bond angle deviations from ideal: 87.84 - 97.09: 2 97.09 - 106.33: 970 106.33 - 115.58: 22149 115.58 - 124.83: 26202 124.83 - 134.07: 633 Bond angle restraints: 49956 Sorted by residual: angle pdb=" C1 FRU H 13 " pdb=" C2 FRU H 13 " pdb=" C3 FRU H 13 " ideal model delta sigma weight residual 113.36 91.65 21.71 3.00e+00 1.11e-01 5.24e+01 angle pdb=" C1 FRU H 13 " pdb=" C2 FRU H 13 " pdb=" O5 FRU H 13 " ideal model delta sigma weight residual 109.29 87.84 21.45 3.00e+00 1.11e-01 5.11e+01 angle pdb=" C2 FRU H 5 " pdb=" O5 FRU H 5 " pdb=" C5 FRU H 5 " ideal model delta sigma weight residual 112.00 100.68 11.32 3.00e+00 1.11e-01 1.42e+01 angle pdb=" C3 FRU H 13 " pdb=" C2 FRU H 13 " pdb=" O5 FRU H 13 " ideal model delta sigma weight residual 104.71 115.26 -10.55 3.00e+00 1.11e-01 1.24e+01 angle pdb=" C ASP T 45 " pdb=" N ILE T 46 " pdb=" CA ILE T 46 " ideal model delta sigma weight residual 121.97 127.74 -5.77 1.80e+00 3.09e-01 1.03e+01 ... (remaining 49951 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 26.44: 20934 26.44 - 52.89: 1004 52.89 - 79.33: 183 79.33 - 105.77: 25 105.77 - 132.21: 3 Dihedral angle restraints: 22149 sinusoidal: 9254 harmonic: 12895 Sorted by residual: dihedral pdb=" C1 FRU H 13 " pdb=" C2 FRU H 13 " pdb=" O5 FRU H 13 " pdb=" C5 FRU H 13 " ideal model delta sinusoidal sigma weight residual 127.64 -100.15 -132.21 1 3.00e+01 1.11e-03 1.78e+01 dihedral pdb=" C1 FRU H 13 " pdb=" C2 FRU H 13 " pdb=" C3 FRU H 13 " pdb=" C4 FRU H 13 " ideal model delta sinusoidal sigma weight residual 213.28 83.35 129.93 1 3.00e+01 1.11e-03 1.75e+01 dihedral pdb=" C1 FRU H 13 " pdb=" C2 FRU H 13 " pdb=" C3 FRU H 13 " pdb=" O3 FRU H 13 " ideal model delta sinusoidal sigma weight residual 89.04 -38.08 127.12 1 3.00e+01 1.11e-03 1.71e+01 ... (remaining 22146 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 1.178: 5348 1.178 - 2.355: 0 2.355 - 3.533: 0 3.533 - 4.710: 0 4.710 - 5.888: 1 Chirality restraints: 5349 Sorted by residual: chirality pdb=" C2 FRU H 13 " pdb=" O1 FRU H 6 " pdb=" C1 FRU H 13 " pdb=" O5 FRU H 13 " both_signs ideal model delta sigma weight residual False 2.60 -3.29 5.89 2.00e-02 2.50e+03 8.67e+04 chirality pdb=" C2 FRU H 6 " pdb=" O6 FRU H 5 " pdb=" C1 FRU H 6 " pdb=" O5 FRU H 6 " both_signs ideal model delta sigma weight residual False 2.60 2.75 -0.15 2.00e-02 2.50e+03 5.98e+01 chirality pdb=" C2 FRU K 7 " pdb=" O1 FRU K 2 " pdb=" C1 FRU K 7 " pdb=" O5 FRU K 7 " both_signs ideal model delta sigma weight residual False 2.60 2.71 -0.11 2.00e-02 2.50e+03 3.18e+01 ... (remaining 5346 not shown) Planarity restraints: 6448 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASN M 111 " -0.036 5.00e-02 4.00e+02 5.45e-02 4.76e+00 pdb=" N PRO M 112 " 0.094 5.00e-02 4.00e+02 pdb=" CA PRO M 112 " -0.028 5.00e-02 4.00e+02 pdb=" CD PRO M 112 " -0.030 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASN E 111 " -0.036 5.00e-02 4.00e+02 5.44e-02 4.73e+00 pdb=" N PRO E 112 " 0.094 5.00e-02 4.00e+02 pdb=" CA PRO E 112 " -0.028 5.00e-02 4.00e+02 pdb=" CD PRO E 112 " -0.030 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TRP G 359 " 0.013 2.00e-02 2.50e+03 9.54e-03 2.28e+00 pdb=" CG TRP G 359 " -0.026 2.00e-02 2.50e+03 pdb=" CD1 TRP G 359 " 0.008 2.00e-02 2.50e+03 pdb=" CD2 TRP G 359 " -0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP G 359 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP G 359 " -0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP G 359 " 0.003 2.00e-02 2.50e+03 pdb=" CZ2 TRP G 359 " 0.003 2.00e-02 2.50e+03 pdb=" CZ3 TRP G 359 " -0.001 2.00e-02 2.50e+03 pdb=" CH2 TRP G 359 " 0.000 2.00e-02 2.50e+03 ... (remaining 6445 not shown) Histogram of nonbonded interaction distances: 1.96 - 2.55: 351 2.55 - 3.13: 27821 3.13 - 3.72: 56859 3.72 - 4.31: 83504 4.31 - 4.90: 140812 Nonbonded interactions: 309347 Sorted by model distance: nonbonded pdb=" OD1 ASN A 841 " pdb="MG MG A1101 " model vdw 1.958 2.170 nonbonded pdb=" OD1 ASN I 841 " pdb="MG MG I1101 " model vdw 1.959 2.170 nonbonded pdb=" OD2 ASP A 848 " pdb="MG MG A1101 " model vdw 1.972 2.170 nonbonded pdb=" OD2 ASP I 848 " pdb="MG MG I1101 " model vdw 1.972 2.170 nonbonded pdb=" OD1 ASN A 664 " pdb="MG MG B 601 " model vdw 1.998 2.170 ... (remaining 309342 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 'I' } ncs_group { reference = chain 'B' selection = chain 'J' } ncs_group { reference = chain 'C' selection = chain 'K' } ncs_group { reference = chain 'D' selection = chain 'L' } ncs_group { reference = chain 'E' selection = chain 'M' } ncs_group { reference = chain 'F' selection = chain 'N' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.010 Normalize map: mean=0, sd=1: 3.820 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.030 Extract box with map and model: 8.070 Check model and map are aligned: 0.600 Set scattering table: 0.370 Process input model: 103.650 Find NCS groups from input model: 2.150 Set up NCS constraints: 0.340 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.010 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.770 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 121.840 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8452 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 : 0.012 0.230 36804 Z= 0.787 Angle : 0.600 21.712 49956 Z= 0.281 Chirality : 0.092 5.888 5349 Planarity : 0.003 0.055 6448 Dihedral : 15.445 132.215 13991 Min Nonbonded Distance : 1.958 Molprobity Statistics. All-atom Clashscore : 7.56 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.34 % Favored : 96.59 % Rotamer: Outliers : 0.00 % Allowed : 0.19 % Favored : 99.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.59 (0.13), residues: 4456 helix: 1.75 (0.19), residues: 806 sheet: 0.78 (0.14), residues: 1298 loop : -0.26 (0.13), residues: 2352 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP G 359 HIS 0.006 0.001 HIS B 302 PHE 0.011 0.001 PHE I 758 TYR 0.016 0.001 TYR A 350 ARG 0.007 0.000 ARG B 100 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8912 Ramachandran restraints generated. 4456 Oldfield, 0 Emsley, 4456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8912 Ramachandran restraints generated. 4456 Oldfield, 0 Emsley, 4456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 234 residues out of total 3766 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 234 time to evaluate : 4.142 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: E 216 MET cc_start: 0.7665 (tpt) cc_final: 0.7188 (tpt) REVERT: T 31 TYR cc_start: 0.8616 (m-80) cc_final: 0.8155 (m-80) REVERT: M 44 MET cc_start: 0.8891 (mtt) cc_final: 0.8647 (mtp) REVERT: M 216 MET cc_start: 0.6552 (tpt) cc_final: 0.6073 (tpt) REVERT: J 7 ARG cc_start: 0.7758 (ttm170) cc_final: 0.7201 (ttt90) REVERT: I 506 MET cc_start: 0.8753 (ttm) cc_final: 0.8468 (ttp) outliers start: 0 outliers final: 0 residues processed: 234 average time/residue: 0.5330 time to fit residues: 199.7005 Evaluate side-chains 151 residues out of total 3766 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 151 time to evaluate : 3.923 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 444 random chunks: chunk 374 optimal weight: 9.9990 chunk 336 optimal weight: 0.9990 chunk 186 optimal weight: 0.8980 chunk 114 optimal weight: 4.9990 chunk 227 optimal weight: 10.0000 chunk 179 optimal weight: 4.9990 chunk 348 optimal weight: 9.9990 chunk 134 optimal weight: 1.9990 chunk 211 optimal weight: 0.0870 chunk 259 optimal weight: 6.9990 chunk 403 optimal weight: 8.9990 overall best weight: 1.7964 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 133 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 467 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 133 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 467 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 211 GLN ** A 482 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 482 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8490 moved from start: 0.0673 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.075 36804 Z= 0.215 Angle : 0.511 25.561 49956 Z= 0.260 Chirality : 0.043 0.237 5349 Planarity : 0.003 0.039 6448 Dihedral : 10.209 159.965 5850 Min Nonbonded Distance : 1.864 Molprobity Statistics. All-atom Clashscore : 6.51 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.30 % Favored : 96.61 % Rotamer: Outliers : 0.43 % Allowed : 3.53 % Favored : 96.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.48 (0.13), residues: 4456 helix: 1.45 (0.19), residues: 770 sheet: 0.74 (0.14), residues: 1297 loop : -0.25 (0.13), residues: 2389 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP G 359 HIS 0.004 0.001 HIS B 302 PHE 0.011 0.001 PHE J 342 TYR 0.013 0.001 TYR A 422 ARG 0.004 0.000 ARG J 100 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8912 Ramachandran restraints generated. 4456 Oldfield, 0 Emsley, 4456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8912 Ramachandran restraints generated. 4456 Oldfield, 0 Emsley, 4456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 3766 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 152 time to evaluate : 4.223 Fit side-chains revert: symmetry clash REVERT: E 216 MET cc_start: 0.7787 (tpt) cc_final: 0.7327 (tpt) REVERT: T 30 ASP cc_start: 0.7927 (t0) cc_final: 0.7689 (t70) REVERT: T 31 TYR cc_start: 0.8543 (m-80) cc_final: 0.8245 (m-80) REVERT: M 216 MET cc_start: 0.6588 (tpt) cc_final: 0.6215 (tpt) REVERT: M 244 MET cc_start: 0.8750 (tpp) cc_final: 0.8483 (tpp) REVERT: B 111 MET cc_start: 0.8019 (mtp) cc_final: 0.7813 (mtp) REVERT: B 229 ASP cc_start: 0.8956 (m-30) cc_final: 0.8653 (m-30) REVERT: J 7 ARG cc_start: 0.7808 (ttm170) cc_final: 0.7252 (ttt90) REVERT: I 346 MET cc_start: 0.9102 (mtm) cc_final: 0.8779 (mtt) REVERT: I 506 MET cc_start: 0.8752 (ttm) cc_final: 0.8471 (ttp) REVERT: I 608 LYS cc_start: 0.8377 (mmmt) cc_final: 0.8167 (tppt) outliers start: 16 outliers final: 12 residues processed: 161 average time/residue: 0.4705 time to fit residues: 128.2112 Evaluate side-chains 158 residues out of total 3766 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 146 time to evaluate : 3.968 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain T residue 46 ILE Chi-restraints excluded: chain T residue 84 ASP Chi-restraints excluded: chain G residue 252 ASP Chi-restraints excluded: chain B residue 347 MET Chi-restraints excluded: chain A residue 224 MET Chi-restraints excluded: chain A residue 354 ASP Chi-restraints excluded: chain A residue 498 VAL Chi-restraints excluded: chain J residue 314 THR Chi-restraints excluded: chain J residue 465 LEU Chi-restraints excluded: chain I residue 430 ASP Chi-restraints excluded: chain I residue 487 MET Chi-restraints excluded: chain I residue 918 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 444 random chunks: chunk 224 optimal weight: 6.9990 chunk 125 optimal weight: 4.9990 chunk 335 optimal weight: 3.9990 chunk 274 optimal weight: 8.9990 chunk 111 optimal weight: 9.9990 chunk 403 optimal weight: 5.9990 chunk 436 optimal weight: 4.9990 chunk 359 optimal weight: 0.8980 chunk 400 optimal weight: 6.9990 chunk 137 optimal weight: 20.0000 chunk 324 optimal weight: 7.9990 overall best weight: 4.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 133 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 351 GLN ** E 467 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 241 HIS ** M 133 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 467 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 283 ASN A 211 GLN A 362 HIS A 366 ASN A 816 GLN ** J 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 361 GLN I 362 HIS I 512 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8575 moved from start: 0.1576 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.060 36804 Z= 0.422 Angle : 0.583 23.457 49956 Z= 0.303 Chirality : 0.045 0.168 5349 Planarity : 0.004 0.037 6448 Dihedral : 7.875 139.257 5850 Min Nonbonded Distance : 1.858 Molprobity Statistics. All-atom Clashscore : 7.27 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.99 % Favored : 95.94 % Rotamer: Outliers : 0.77 % Allowed : 5.37 % Favored : 93.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.07 (0.12), residues: 4456 helix: 0.61 (0.18), residues: 791 sheet: 0.59 (0.14), residues: 1317 loop : -0.41 (0.13), residues: 2348 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP G 359 HIS 0.007 0.001 HIS J 132 PHE 0.018 0.002 PHE B 485 TYR 0.026 0.002 TYR I 350 ARG 0.010 0.001 ARG J 100 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8912 Ramachandran restraints generated. 4456 Oldfield, 0 Emsley, 4456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8912 Ramachandran restraints generated. 4456 Oldfield, 0 Emsley, 4456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 3766 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 147 time to evaluate : 3.837 Fit side-chains revert: symmetry clash REVERT: T 30 ASP cc_start: 0.8003 (t0) cc_final: 0.7753 (t70) REVERT: T 87 MET cc_start: 0.8285 (tpp) cc_final: 0.7866 (ttt) REVERT: M 213 MET cc_start: 0.8055 (ttm) cc_final: 0.7491 (mtp) REVERT: M 216 MET cc_start: 0.6822 (tpt) cc_final: 0.6498 (tpt) REVERT: B 229 ASP cc_start: 0.9010 (m-30) cc_final: 0.8767 (m-30) REVERT: J 7 ARG cc_start: 0.7869 (ttm170) cc_final: 0.7357 (ttt90) REVERT: I 506 MET cc_start: 0.8761 (ttm) cc_final: 0.8532 (ttp) outliers start: 29 outliers final: 23 residues processed: 166 average time/residue: 0.4716 time to fit residues: 132.5610 Evaluate side-chains 167 residues out of total 3766 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 144 time to evaluate : 4.653 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 479 MET Chi-restraints excluded: chain T residue 33 ASN Chi-restraints excluded: chain T residue 46 ILE Chi-restraints excluded: chain T residue 77 SER Chi-restraints excluded: chain T residue 84 ASP Chi-restraints excluded: chain T residue 94 LYS Chi-restraints excluded: chain G residue 252 ASP Chi-restraints excluded: chain M residue 8 ILE Chi-restraints excluded: chain M residue 314 VAL Chi-restraints excluded: chain M residue 341 ASP Chi-restraints excluded: chain A residue 121 LEU Chi-restraints excluded: chain A residue 354 ASP Chi-restraints excluded: chain A residue 498 VAL Chi-restraints excluded: chain A residue 607 MET Chi-restraints excluded: chain J residue 99 THR Chi-restraints excluded: chain J residue 314 THR Chi-restraints excluded: chain J residue 460 VAL Chi-restraints excluded: chain J residue 465 LEU Chi-restraints excluded: chain I residue 121 LEU Chi-restraints excluded: chain I residue 268 ASP Chi-restraints excluded: chain I residue 361 GLN Chi-restraints excluded: chain I residue 487 MET Chi-restraints excluded: chain I residue 918 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 444 random chunks: chunk 399 optimal weight: 1.9990 chunk 303 optimal weight: 8.9990 chunk 209 optimal weight: 8.9990 chunk 44 optimal weight: 7.9990 chunk 192 optimal weight: 5.9990 chunk 271 optimal weight: 6.9990 chunk 405 optimal weight: 0.9990 chunk 429 optimal weight: 8.9990 chunk 211 optimal weight: 0.4980 chunk 384 optimal weight: 3.9990 chunk 115 optimal weight: 0.0070 overall best weight: 1.5004 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 133 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 467 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 133 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 467 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8544 moved from start: 0.1543 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 36804 Z= 0.192 Angle : 0.490 23.931 49956 Z= 0.256 Chirality : 0.042 0.142 5349 Planarity : 0.003 0.036 6448 Dihedral : 7.305 138.889 5850 Min Nonbonded Distance : 1.888 Molprobity Statistics. All-atom Clashscore : 6.96 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.01 % Favored : 96.93 % Rotamer: Outliers : 0.56 % Allowed : 6.70 % Favored : 92.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.05 (0.13), residues: 4456 helix: 0.50 (0.18), residues: 801 sheet: 0.56 (0.14), residues: 1333 loop : -0.38 (0.13), residues: 2322 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP G 359 HIS 0.003 0.001 HIS G 241 PHE 0.012 0.001 PHE J 342 TYR 0.014 0.001 TYR B 203 ARG 0.004 0.000 ARG J 100 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8912 Ramachandran restraints generated. 4456 Oldfield, 0 Emsley, 4456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8912 Ramachandran restraints generated. 4456 Oldfield, 0 Emsley, 4456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 3766 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 148 time to evaluate : 4.022 Fit side-chains revert: symmetry clash REVERT: T 30 ASP cc_start: 0.7970 (t0) cc_final: 0.7720 (t70) REVERT: T 87 MET cc_start: 0.8224 (tpp) cc_final: 0.7846 (ttt) REVERT: M 213 MET cc_start: 0.8023 (ttm) cc_final: 0.7439 (mtp) REVERT: M 216 MET cc_start: 0.6816 (tpt) cc_final: 0.6448 (tpt) REVERT: B 229 ASP cc_start: 0.8987 (m-30) cc_final: 0.8753 (m-30) REVERT: J 7 ARG cc_start: 0.7893 (ttm170) cc_final: 0.7432 (ttt90) REVERT: I 506 MET cc_start: 0.8730 (ttm) cc_final: 0.8462 (ttp) outliers start: 21 outliers final: 16 residues processed: 162 average time/residue: 0.5000 time to fit residues: 137.2690 Evaluate side-chains 160 residues out of total 3766 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 144 time to evaluate : 3.850 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 479 MET Chi-restraints excluded: chain T residue 46 ILE Chi-restraints excluded: chain T residue 84 ASP Chi-restraints excluded: chain T residue 94 LYS Chi-restraints excluded: chain G residue 122 VAL Chi-restraints excluded: chain G residue 252 ASP Chi-restraints excluded: chain B residue 203 TYR Chi-restraints excluded: chain B residue 347 MET Chi-restraints excluded: chain A residue 354 ASP Chi-restraints excluded: chain A residue 498 VAL Chi-restraints excluded: chain J residue 314 THR Chi-restraints excluded: chain J residue 465 LEU Chi-restraints excluded: chain I residue 121 LEU Chi-restraints excluded: chain I residue 268 ASP Chi-restraints excluded: chain I residue 487 MET Chi-restraints excluded: chain I residue 918 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 444 random chunks: chunk 357 optimal weight: 10.0000 chunk 243 optimal weight: 3.9990 chunk 6 optimal weight: 3.9990 chunk 319 optimal weight: 10.0000 chunk 177 optimal weight: 5.9990 chunk 366 optimal weight: 3.9990 chunk 296 optimal weight: 4.9990 chunk 0 optimal weight: 10.0000 chunk 219 optimal weight: 5.9990 chunk 385 optimal weight: 2.9990 chunk 108 optimal weight: 10.0000 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 133 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 467 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 300 ASN ** M 133 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 467 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 361 GLN J 283 ASN I 361 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8590 moved from start: 0.1886 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.057 36804 Z= 0.420 Angle : 0.562 24.242 49956 Z= 0.292 Chirality : 0.044 0.150 5349 Planarity : 0.004 0.037 6448 Dihedral : 7.231 138.480 5850 Min Nonbonded Distance : 1.852 Molprobity Statistics. All-atom Clashscore : 7.16 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.88 % Favored : 96.05 % Rotamer: Outliers : 1.12 % Allowed : 7.52 % Favored : 91.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.13 (0.12), residues: 4456 helix: 0.33 (0.18), residues: 799 sheet: 0.48 (0.14), residues: 1317 loop : -0.51 (0.13), residues: 2340 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP G 359 HIS 0.005 0.001 HIS J 132 PHE 0.017 0.002 PHE B 485 TYR 0.023 0.002 TYR B 203 ARG 0.008 0.000 ARG J 100 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8912 Ramachandran restraints generated. 4456 Oldfield, 0 Emsley, 4456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8912 Ramachandran restraints generated. 4456 Oldfield, 0 Emsley, 4456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 3766 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 150 time to evaluate : 4.110 Fit side-chains REVERT: T 30 ASP cc_start: 0.7993 (t0) cc_final: 0.7736 (t70) REVERT: T 87 MET cc_start: 0.8233 (tpp) cc_final: 0.7907 (ttt) REVERT: T 89 TYR cc_start: 0.8866 (m-80) cc_final: 0.8607 (m-80) REVERT: M 213 MET cc_start: 0.8068 (ttm) cc_final: 0.7519 (mtp) REVERT: B 229 ASP cc_start: 0.8963 (m-30) cc_final: 0.8749 (m-30) REVERT: J 7 ARG cc_start: 0.7925 (ttm170) cc_final: 0.7461 (ttt90) REVERT: I 346 MET cc_start: 0.9173 (mtm) cc_final: 0.8890 (mtt) REVERT: I 506 MET cc_start: 0.8821 (ttm) cc_final: 0.8579 (ttp) outliers start: 42 outliers final: 33 residues processed: 182 average time/residue: 0.4948 time to fit residues: 152.7497 Evaluate side-chains 177 residues out of total 3766 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 144 time to evaluate : 4.005 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 69 THR Chi-restraints excluded: chain E residue 145 PHE Chi-restraints excluded: chain E residue 479 MET Chi-restraints excluded: chain T residue 33 ASN Chi-restraints excluded: chain T residue 46 ILE Chi-restraints excluded: chain T residue 84 ASP Chi-restraints excluded: chain T residue 92 THR Chi-restraints excluded: chain T residue 94 LYS Chi-restraints excluded: chain G residue 122 VAL Chi-restraints excluded: chain G residue 140 THR Chi-restraints excluded: chain G residue 176 VAL Chi-restraints excluded: chain G residue 252 ASP Chi-restraints excluded: chain M residue 8 ILE Chi-restraints excluded: chain M residue 314 VAL Chi-restraints excluded: chain M residue 341 ASP Chi-restraints excluded: chain B residue 99 THR Chi-restraints excluded: chain B residue 203 TYR Chi-restraints excluded: chain A residue 121 LEU Chi-restraints excluded: chain A residue 354 ASP Chi-restraints excluded: chain A residue 498 VAL Chi-restraints excluded: chain A residue 607 MET Chi-restraints excluded: chain A residue 722 MET Chi-restraints excluded: chain J residue 99 THR Chi-restraints excluded: chain J residue 188 VAL Chi-restraints excluded: chain J residue 203 TYR Chi-restraints excluded: chain J residue 314 THR Chi-restraints excluded: chain J residue 460 VAL Chi-restraints excluded: chain J residue 465 LEU Chi-restraints excluded: chain I residue 121 LEU Chi-restraints excluded: chain I residue 268 ASP Chi-restraints excluded: chain I residue 498 VAL Chi-restraints excluded: chain I residue 876 MET Chi-restraints excluded: chain I residue 918 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 444 random chunks: chunk 144 optimal weight: 4.9990 chunk 386 optimal weight: 5.9990 chunk 84 optimal weight: 7.9990 chunk 251 optimal weight: 0.9990 chunk 105 optimal weight: 9.9990 chunk 429 optimal weight: 6.9990 chunk 356 optimal weight: 6.9990 chunk 198 optimal weight: 0.6980 chunk 35 optimal weight: 20.0000 chunk 142 optimal weight: 5.9990 chunk 225 optimal weight: 0.7980 overall best weight: 2.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 133 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 65 ASN ** M 133 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 361 GLN I 816 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8575 moved from start: 0.1951 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 36804 Z= 0.287 Angle : 0.508 24.321 49956 Z= 0.266 Chirality : 0.043 0.142 5349 Planarity : 0.003 0.036 6448 Dihedral : 6.980 138.633 5850 Min Nonbonded Distance : 1.869 Molprobity Statistics. All-atom Clashscore : 7.18 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.34 % Favored : 96.59 % Rotamer: Outliers : 1.09 % Allowed : 8.32 % Favored : 90.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.14 (0.12), residues: 4456 helix: 0.33 (0.18), residues: 797 sheet: 0.40 (0.14), residues: 1345 loop : -0.48 (0.13), residues: 2314 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP G 359 HIS 0.004 0.001 HIS J 132 PHE 0.014 0.001 PHE J 342 TYR 0.021 0.001 TYR B 203 ARG 0.013 0.000 ARG M 452 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8912 Ramachandran restraints generated. 4456 Oldfield, 0 Emsley, 4456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8912 Ramachandran restraints generated. 4456 Oldfield, 0 Emsley, 4456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 3766 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 147 time to evaluate : 4.251 Fit side-chains REVERT: T 30 ASP cc_start: 0.8036 (t0) cc_final: 0.7788 (t70) REVERT: T 43 ASP cc_start: 0.6152 (p0) cc_final: 0.5499 (p0) REVERT: T 87 MET cc_start: 0.8224 (tpp) cc_final: 0.7879 (ttt) REVERT: M 213 MET cc_start: 0.8035 (ttm) cc_final: 0.7545 (mtp) REVERT: M 216 MET cc_start: 0.6773 (tpt) cc_final: 0.6392 (tpt) REVERT: J 7 ARG cc_start: 0.7911 (ttm170) cc_final: 0.7445 (ttt90) REVERT: I 506 MET cc_start: 0.8796 (ttm) cc_final: 0.8536 (ttp) outliers start: 41 outliers final: 32 residues processed: 177 average time/residue: 0.4641 time to fit residues: 141.1679 Evaluate side-chains 176 residues out of total 3766 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 144 time to evaluate : 4.053 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 69 THR Chi-restraints excluded: chain E residue 145 PHE Chi-restraints excluded: chain E residue 479 MET Chi-restraints excluded: chain T residue 46 ILE Chi-restraints excluded: chain T residue 84 ASP Chi-restraints excluded: chain T residue 92 THR Chi-restraints excluded: chain G residue 122 VAL Chi-restraints excluded: chain G residue 140 THR Chi-restraints excluded: chain G residue 176 VAL Chi-restraints excluded: chain G residue 252 ASP Chi-restraints excluded: chain M residue 69 THR Chi-restraints excluded: chain M residue 314 VAL Chi-restraints excluded: chain M residue 341 ASP Chi-restraints excluded: chain B residue 99 THR Chi-restraints excluded: chain B residue 203 TYR Chi-restraints excluded: chain B residue 347 MET Chi-restraints excluded: chain A residue 121 LEU Chi-restraints excluded: chain A residue 312 VAL Chi-restraints excluded: chain A residue 354 ASP Chi-restraints excluded: chain A residue 498 VAL Chi-restraints excluded: chain A residue 722 MET Chi-restraints excluded: chain J residue 203 TYR Chi-restraints excluded: chain J residue 314 THR Chi-restraints excluded: chain J residue 460 VAL Chi-restraints excluded: chain J residue 465 LEU Chi-restraints excluded: chain I residue 121 LEU Chi-restraints excluded: chain I residue 268 ASP Chi-restraints excluded: chain I residue 312 VAL Chi-restraints excluded: chain I residue 361 GLN Chi-restraints excluded: chain I residue 487 MET Chi-restraints excluded: chain I residue 498 VAL Chi-restraints excluded: chain I residue 918 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 444 random chunks: chunk 414 optimal weight: 8.9990 chunk 48 optimal weight: 10.0000 chunk 244 optimal weight: 1.9990 chunk 313 optimal weight: 0.8980 chunk 243 optimal weight: 1.9990 chunk 361 optimal weight: 0.8980 chunk 239 optimal weight: 5.9990 chunk 427 optimal weight: 5.9990 chunk 267 optimal weight: 0.9990 chunk 260 optimal weight: 7.9990 chunk 197 optimal weight: 0.9990 overall best weight: 1.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 133 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 300 ASN ** M 133 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 226 ASN ** A 482 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 361 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8550 moved from start: 0.1909 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 36804 Z= 0.163 Angle : 0.473 24.428 49956 Z= 0.248 Chirality : 0.041 0.141 5349 Planarity : 0.003 0.036 6448 Dihedral : 6.701 138.576 5850 Min Nonbonded Distance : 1.904 Molprobity Statistics. All-atom Clashscore : 6.93 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.25 % Favored : 96.68 % Rotamer: Outliers : 1.12 % Allowed : 8.55 % Favored : 90.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.06 (0.13), residues: 4456 helix: 0.42 (0.18), residues: 793 sheet: 0.42 (0.14), residues: 1355 loop : -0.42 (0.13), residues: 2308 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP G 359 HIS 0.007 0.001 HIS I 362 PHE 0.011 0.001 PHE J 342 TYR 0.017 0.001 TYR B 203 ARG 0.008 0.000 ARG M 452 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8912 Ramachandran restraints generated. 4456 Oldfield, 0 Emsley, 4456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8912 Ramachandran restraints generated. 4456 Oldfield, 0 Emsley, 4456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 3766 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 148 time to evaluate : 4.217 Fit side-chains REVERT: T 30 ASP cc_start: 0.8118 (t0) cc_final: 0.7873 (t70) REVERT: T 43 ASP cc_start: 0.6215 (p0) cc_final: 0.5637 (p0) REVERT: T 87 MET cc_start: 0.8172 (tpp) cc_final: 0.7873 (ttt) REVERT: M 213 MET cc_start: 0.8023 (ttm) cc_final: 0.7549 (mtp) REVERT: M 216 MET cc_start: 0.6745 (tpt) cc_final: 0.5994 (tpt) REVERT: J 7 ARG cc_start: 0.7858 (ttm170) cc_final: 0.7406 (ttt90) REVERT: I 506 MET cc_start: 0.8776 (ttm) cc_final: 0.8552 (ttp) REVERT: I 923 ASP cc_start: 0.8315 (OUTLIER) cc_final: 0.8021 (t0) outliers start: 42 outliers final: 29 residues processed: 180 average time/residue: 0.4763 time to fit residues: 146.5010 Evaluate side-chains 173 residues out of total 3766 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 143 time to evaluate : 4.088 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 69 THR Chi-restraints excluded: chain E residue 145 PHE Chi-restraints excluded: chain E residue 479 MET Chi-restraints excluded: chain T residue 46 ILE Chi-restraints excluded: chain T residue 92 THR Chi-restraints excluded: chain G residue 122 VAL Chi-restraints excluded: chain G residue 140 THR Chi-restraints excluded: chain G residue 176 VAL Chi-restraints excluded: chain G residue 252 ASP Chi-restraints excluded: chain M residue 69 THR Chi-restraints excluded: chain M residue 314 VAL Chi-restraints excluded: chain B residue 99 THR Chi-restraints excluded: chain B residue 203 TYR Chi-restraints excluded: chain B residue 347 MET Chi-restraints excluded: chain A residue 312 VAL Chi-restraints excluded: chain A residue 354 ASP Chi-restraints excluded: chain A residue 498 VAL Chi-restraints excluded: chain J residue 114 LYS Chi-restraints excluded: chain J residue 203 TYR Chi-restraints excluded: chain J residue 314 THR Chi-restraints excluded: chain J residue 460 VAL Chi-restraints excluded: chain J residue 465 LEU Chi-restraints excluded: chain I residue 121 LEU Chi-restraints excluded: chain I residue 268 ASP Chi-restraints excluded: chain I residue 312 VAL Chi-restraints excluded: chain I residue 487 MET Chi-restraints excluded: chain I residue 498 VAL Chi-restraints excluded: chain I residue 876 MET Chi-restraints excluded: chain I residue 918 THR Chi-restraints excluded: chain I residue 923 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 444 random chunks: chunk 264 optimal weight: 7.9990 chunk 170 optimal weight: 5.9990 chunk 255 optimal weight: 5.9990 chunk 128 optimal weight: 10.0000 chunk 84 optimal weight: 6.9990 chunk 82 optimal weight: 0.7980 chunk 272 optimal weight: 6.9990 chunk 291 optimal weight: 8.9990 chunk 211 optimal weight: 3.9990 chunk 39 optimal weight: 10.0000 chunk 336 optimal weight: 5.9990 overall best weight: 4.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 133 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 300 ASN ** M 133 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 351 GLN ** I 361 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8606 moved from start: 0.2192 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.072 36804 Z= 0.470 Angle : 0.588 24.905 49956 Z= 0.304 Chirality : 0.045 0.143 5349 Planarity : 0.004 0.044 6448 Dihedral : 6.983 139.595 5850 Min Nonbonded Distance : 1.846 Molprobity Statistics. All-atom Clashscore : 7.51 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.13 % Favored : 95.80 % Rotamer: Outliers : 1.17 % Allowed : 8.85 % Favored : 89.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.26 (0.12), residues: 4456 helix: 0.24 (0.18), residues: 793 sheet: 0.28 (0.14), residues: 1361 loop : -0.53 (0.13), residues: 2302 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP I 851 HIS 0.005 0.001 HIS J 132 PHE 0.018 0.002 PHE J 71 TYR 0.024 0.002 TYR B 203 ARG 0.007 0.001 ARG J 100 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8912 Ramachandran restraints generated. 4456 Oldfield, 0 Emsley, 4456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8912 Ramachandran restraints generated. 4456 Oldfield, 0 Emsley, 4456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 3766 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 143 time to evaluate : 4.369 Fit side-chains REVERT: T 30 ASP cc_start: 0.8037 (t0) cc_final: 0.7774 (t70) REVERT: T 87 MET cc_start: 0.8287 (tpp) cc_final: 0.8007 (ttt) REVERT: M 213 MET cc_start: 0.8119 (ttm) cc_final: 0.7605 (mtp) REVERT: M 216 MET cc_start: 0.6910 (tpt) cc_final: 0.6255 (tpt) REVERT: J 7 ARG cc_start: 0.7984 (ttm170) cc_final: 0.7499 (ttt90) REVERT: I 346 MET cc_start: 0.9161 (mtm) cc_final: 0.8925 (mtt) REVERT: I 506 MET cc_start: 0.8761 (ttm) cc_final: 0.8510 (ttp) REVERT: I 923 ASP cc_start: 0.8360 (OUTLIER) cc_final: 0.8008 (t0) outliers start: 44 outliers final: 38 residues processed: 179 average time/residue: 0.4797 time to fit residues: 146.6323 Evaluate side-chains 180 residues out of total 3766 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 141 time to evaluate : 3.994 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 69 THR Chi-restraints excluded: chain E residue 145 PHE Chi-restraints excluded: chain E residue 479 MET Chi-restraints excluded: chain T residue 42 TYR Chi-restraints excluded: chain T residue 46 ILE Chi-restraints excluded: chain T residue 84 ASP Chi-restraints excluded: chain T residue 92 THR Chi-restraints excluded: chain G residue 122 VAL Chi-restraints excluded: chain G residue 140 THR Chi-restraints excluded: chain G residue 176 VAL Chi-restraints excluded: chain G residue 252 ASP Chi-restraints excluded: chain M residue 8 ILE Chi-restraints excluded: chain M residue 69 THR Chi-restraints excluded: chain M residue 105 THR Chi-restraints excluded: chain M residue 314 VAL Chi-restraints excluded: chain M residue 341 ASP Chi-restraints excluded: chain M residue 377 VAL Chi-restraints excluded: chain B residue 99 THR Chi-restraints excluded: chain B residue 203 TYR Chi-restraints excluded: chain A residue 121 LEU Chi-restraints excluded: chain A residue 312 VAL Chi-restraints excluded: chain A residue 354 ASP Chi-restraints excluded: chain A residue 498 VAL Chi-restraints excluded: chain J residue 99 THR Chi-restraints excluded: chain J residue 114 LYS Chi-restraints excluded: chain J residue 188 VAL Chi-restraints excluded: chain J residue 203 TYR Chi-restraints excluded: chain J residue 314 THR Chi-restraints excluded: chain J residue 460 VAL Chi-restraints excluded: chain J residue 465 LEU Chi-restraints excluded: chain I residue 121 LEU Chi-restraints excluded: chain I residue 268 ASP Chi-restraints excluded: chain I residue 312 VAL Chi-restraints excluded: chain I residue 498 VAL Chi-restraints excluded: chain I residue 607 MET Chi-restraints excluded: chain I residue 876 MET Chi-restraints excluded: chain I residue 918 THR Chi-restraints excluded: chain I residue 923 ASP Chi-restraints excluded: chain I residue 984 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 444 random chunks: chunk 389 optimal weight: 2.9990 chunk 409 optimal weight: 3.9990 chunk 374 optimal weight: 6.9990 chunk 398 optimal weight: 3.9990 chunk 240 optimal weight: 2.9990 chunk 173 optimal weight: 0.9980 chunk 313 optimal weight: 0.6980 chunk 122 optimal weight: 9.9990 chunk 360 optimal weight: 1.9990 chunk 377 optimal weight: 2.9990 chunk 397 optimal weight: 5.9990 overall best weight: 1.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 133 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 133 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 351 GLN ** I 361 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8573 moved from start: 0.2129 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 36804 Z= 0.233 Angle : 0.499 24.506 49956 Z= 0.261 Chirality : 0.042 0.148 5349 Planarity : 0.003 0.036 6448 Dihedral : 6.746 139.978 5850 Min Nonbonded Distance : 1.879 Molprobity Statistics. All-atom Clashscore : 7.34 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.34 % Favored : 96.59 % Rotamer: Outliers : 1.14 % Allowed : 9.09 % Favored : 89.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.20 (0.12), residues: 4456 helix: 0.30 (0.18), residues: 793 sheet: 0.31 (0.14), residues: 1355 loop : -0.49 (0.13), residues: 2308 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP I 486 HIS 0.003 0.001 HIS J 132 PHE 0.017 0.001 PHE A 758 TYR 0.020 0.001 TYR B 203 ARG 0.006 0.000 ARG M 452 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8912 Ramachandran restraints generated. 4456 Oldfield, 0 Emsley, 4456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8912 Ramachandran restraints generated. 4456 Oldfield, 0 Emsley, 4456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 3766 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 142 time to evaluate : 4.097 Fit side-chains revert: symmetry clash REVERT: T 30 ASP cc_start: 0.8103 (t0) cc_final: 0.7850 (t70) REVERT: T 87 MET cc_start: 0.8218 (tpp) cc_final: 0.7912 (ttt) REVERT: M 213 MET cc_start: 0.8068 (ttm) cc_final: 0.7591 (mtp) REVERT: M 216 MET cc_start: 0.6883 (tpt) cc_final: 0.6173 (tpt) REVERT: M 362 MET cc_start: 0.7559 (OUTLIER) cc_final: 0.7353 (tmm) REVERT: J 7 ARG cc_start: 0.7835 (ttm170) cc_final: 0.7606 (ttm170) REVERT: I 506 MET cc_start: 0.8792 (ttm) cc_final: 0.8573 (ttp) REVERT: I 923 ASP cc_start: 0.8308 (OUTLIER) cc_final: 0.8006 (t0) outliers start: 43 outliers final: 35 residues processed: 177 average time/residue: 0.4709 time to fit residues: 143.5974 Evaluate side-chains 179 residues out of total 3766 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 142 time to evaluate : 4.048 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 69 THR Chi-restraints excluded: chain E residue 479 MET Chi-restraints excluded: chain T residue 42 TYR Chi-restraints excluded: chain T residue 46 ILE Chi-restraints excluded: chain T residue 92 THR Chi-restraints excluded: chain G residue 122 VAL Chi-restraints excluded: chain G residue 140 THR Chi-restraints excluded: chain G residue 176 VAL Chi-restraints excluded: chain G residue 252 ASP Chi-restraints excluded: chain M residue 69 THR Chi-restraints excluded: chain M residue 105 THR Chi-restraints excluded: chain M residue 314 VAL Chi-restraints excluded: chain M residue 362 MET Chi-restraints excluded: chain M residue 377 VAL Chi-restraints excluded: chain B residue 99 THR Chi-restraints excluded: chain B residue 203 TYR Chi-restraints excluded: chain B residue 543 ASN Chi-restraints excluded: chain A residue 121 LEU Chi-restraints excluded: chain A residue 312 VAL Chi-restraints excluded: chain A residue 354 ASP Chi-restraints excluded: chain A residue 498 VAL Chi-restraints excluded: chain J residue 99 THR Chi-restraints excluded: chain J residue 114 LYS Chi-restraints excluded: chain J residue 188 VAL Chi-restraints excluded: chain J residue 203 TYR Chi-restraints excluded: chain J residue 314 THR Chi-restraints excluded: chain J residue 460 VAL Chi-restraints excluded: chain J residue 465 LEU Chi-restraints excluded: chain I residue 121 LEU Chi-restraints excluded: chain I residue 268 ASP Chi-restraints excluded: chain I residue 312 VAL Chi-restraints excluded: chain I residue 368 THR Chi-restraints excluded: chain I residue 487 MET Chi-restraints excluded: chain I residue 498 VAL Chi-restraints excluded: chain I residue 876 MET Chi-restraints excluded: chain I residue 918 THR Chi-restraints excluded: chain I residue 923 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 444 random chunks: chunk 261 optimal weight: 3.9990 chunk 421 optimal weight: 4.9990 chunk 257 optimal weight: 7.9990 chunk 200 optimal weight: 4.9990 chunk 293 optimal weight: 7.9990 chunk 442 optimal weight: 5.9990 chunk 407 optimal weight: 5.9990 chunk 352 optimal weight: 10.0000 chunk 36 optimal weight: 2.9990 chunk 272 optimal weight: 5.9990 chunk 215 optimal weight: 7.9990 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 133 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 240 GLN ** M 133 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 351 GLN I 361 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8611 moved from start: 0.2324 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.072 36804 Z= 0.473 Angle : 0.593 24.571 49956 Z= 0.307 Chirality : 0.045 0.145 5349 Planarity : 0.004 0.042 6448 Dihedral : 6.986 140.694 5850 Min Nonbonded Distance : 1.844 Molprobity Statistics. All-atom Clashscore : 7.54 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.31 % Favored : 95.62 % Rotamer: Outliers : 1.06 % Allowed : 9.30 % Favored : 89.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.37 (0.12), residues: 4456 helix: 0.16 (0.18), residues: 793 sheet: 0.19 (0.14), residues: 1361 loop : -0.59 (0.13), residues: 2302 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP I 851 HIS 0.005 0.001 HIS J 132 PHE 0.019 0.002 PHE A 758 TYR 0.025 0.002 TYR B 203 ARG 0.007 0.000 ARG J 100 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8912 Ramachandran restraints generated. 4456 Oldfield, 0 Emsley, 4456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8912 Ramachandran restraints generated. 4456 Oldfield, 0 Emsley, 4456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 3766 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 143 time to evaluate : 4.189 Fit side-chains revert: symmetry clash REVERT: T 30 ASP cc_start: 0.8035 (t0) cc_final: 0.7765 (t70) REVERT: T 87 MET cc_start: 0.8290 (tpp) cc_final: 0.8018 (ttt) REVERT: M 213 MET cc_start: 0.8113 (ttm) cc_final: 0.7645 (mtp) REVERT: M 216 MET cc_start: 0.7023 (tpt) cc_final: 0.6407 (tpt) REVERT: J 7 ARG cc_start: 0.7921 (ttm170) cc_final: 0.7334 (ttt90) REVERT: I 346 MET cc_start: 0.9165 (mtm) cc_final: 0.8930 (mtt) REVERT: I 506 MET cc_start: 0.8757 (ttm) cc_final: 0.8548 (ttp) REVERT: I 923 ASP cc_start: 0.8389 (OUTLIER) cc_final: 0.7995 (t0) outliers start: 40 outliers final: 36 residues processed: 177 average time/residue: 0.4579 time to fit residues: 138.9011 Evaluate side-chains 178 residues out of total 3766 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 141 time to evaluate : 4.341 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 69 THR Chi-restraints excluded: chain E residue 479 MET Chi-restraints excluded: chain T residue 42 TYR Chi-restraints excluded: chain T residue 46 ILE Chi-restraints excluded: chain T residue 92 THR Chi-restraints excluded: chain G residue 122 VAL Chi-restraints excluded: chain G residue 176 VAL Chi-restraints excluded: chain G residue 252 ASP Chi-restraints excluded: chain M residue 69 THR Chi-restraints excluded: chain M residue 105 THR Chi-restraints excluded: chain M residue 147 THR Chi-restraints excluded: chain M residue 314 VAL Chi-restraints excluded: chain M residue 377 VAL Chi-restraints excluded: chain B residue 99 THR Chi-restraints excluded: chain B residue 203 TYR Chi-restraints excluded: chain B residue 543 ASN Chi-restraints excluded: chain A residue 121 LEU Chi-restraints excluded: chain A residue 312 VAL Chi-restraints excluded: chain A residue 354 ASP Chi-restraints excluded: chain A residue 498 VAL Chi-restraints excluded: chain J residue 99 THR Chi-restraints excluded: chain J residue 114 LYS Chi-restraints excluded: chain J residue 188 VAL Chi-restraints excluded: chain J residue 203 TYR Chi-restraints excluded: chain J residue 314 THR Chi-restraints excluded: chain J residue 460 VAL Chi-restraints excluded: chain J residue 465 LEU Chi-restraints excluded: chain I residue 121 LEU Chi-restraints excluded: chain I residue 268 ASP Chi-restraints excluded: chain I residue 312 VAL Chi-restraints excluded: chain I residue 361 GLN Chi-restraints excluded: chain I residue 368 THR Chi-restraints excluded: chain I residue 498 VAL Chi-restraints excluded: chain I residue 876 MET Chi-restraints excluded: chain I residue 918 THR Chi-restraints excluded: chain I residue 923 ASP Chi-restraints excluded: chain I residue 984 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 444 random chunks: chunk 279 optimal weight: 0.0570 chunk 375 optimal weight: 0.9990 chunk 107 optimal weight: 5.9990 chunk 324 optimal weight: 0.7980 chunk 52 optimal weight: 0.8980 chunk 97 optimal weight: 9.9990 chunk 352 optimal weight: 10.0000 chunk 147 optimal weight: 4.9990 chunk 362 optimal weight: 0.9980 chunk 44 optimal weight: 9.9990 chunk 64 optimal weight: 6.9990 overall best weight: 0.7500 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 133 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 240 GLN ** M 133 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 351 GLN ** A 482 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 139 GLN ** I 482 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3243 r_free = 0.3243 target = 0.072027 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2810 r_free = 0.2810 target = 0.052681 restraints weight = 89397.222| |-----------------------------------------------------------------------------| r_work (start): 0.2789 rms_B_bonded: 2.16 r_work: 0.2682 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.2555 rms_B_bonded: 4.06 restraints_weight: 0.2500 r_work (final): 0.2555 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8808 moved from start: 0.2186 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.057 36804 Z= 0.148 Angle : 0.486 24.465 49956 Z= 0.255 Chirality : 0.041 0.142 5349 Planarity : 0.003 0.037 6448 Dihedral : 6.608 140.693 5850 Min Nonbonded Distance : 1.900 Molprobity Statistics. All-atom Clashscore : 7.10 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.07 % Favored : 96.86 % Rotamer: Outliers : 1.01 % Allowed : 9.33 % Favored : 89.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.20 (0.13), residues: 4456 helix: 0.29 (0.19), residues: 781 sheet: 0.29 (0.14), residues: 1355 loop : -0.46 (0.13), residues: 2320 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP I 486 HIS 0.004 0.001 HIS I 362 PHE 0.016 0.001 PHE A 758 TYR 0.017 0.001 TYR B 203 ARG 0.006 0.000 ARG M 452 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6117.05 seconds wall clock time: 114 minutes 23.05 seconds (6863.05 seconds total)