Starting phenix.real_space_refine on Tue Aug 26 04:54:56 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ij1_35461/08_2025/8ij1_35461.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ij1_35461/08_2025/8ij1_35461.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8ij1_35461/08_2025/8ij1_35461.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ij1_35461/08_2025/8ij1_35461.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8ij1_35461/08_2025/8ij1_35461.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ij1_35461/08_2025/8ij1_35461.map" } resolution = 4.2 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.008 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 10514 atoms to isotropic. 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 Zn 5 6.06 5 S 179 5.16 5 C 15931 2.51 5 N 4321 2.21 5 O 4717 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 30 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 25153 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 6085 Number of conformers: 1 Conformer: "" Number of residues, atoms: 743, 6085 Classifications: {'peptide': 743} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 18, 'TRANS': 724} Chain breaks: 1 Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "R" Number of atoms: 568 Number of conformers: 1 Conformer: "" Number of residues, atoms: 70, 568 Classifications: {'peptide': 70} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 1, 'TRANS': 68} Chain breaks: 1 Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 21 Unresolved non-hydrogen dihedrals: 16 Planarities with less than four sites: {'GLN:plan1': 1, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 13 Chain: "B" Number of atoms: 718 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 93, 716 Classifications: {'peptide': 93} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 4} Link IDs: {'PTRANS': 7, 'TRANS': 85} Chain breaks: 1 Unresolved non-hydrogen bonds: 22 Unresolved non-hydrogen angles: 29 Unresolved non-hydrogen dihedrals: 17 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ASP:plan': 2, 'ARG:plan': 1, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 18 Conformer: "B" Number of residues, atoms: 93, 716 Classifications: {'peptide': 93} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 4} Link IDs: {'PTRANS': 7, 'TRANS': 85} Chain breaks: 1 Unresolved non-hydrogen bonds: 22 Unresolved non-hydrogen angles: 29 Unresolved non-hydrogen dihedrals: 17 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ASP:plan': 2, 'ARG:plan': 1, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 18 bond proxies already assigned to first conformer: 726 Chain: "C" Number of atoms: 721 Number of conformers: 1 Conformer: "" Number of residues, atoms: 92, 721 Classifications: {'peptide': 92} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 5, 'TRANS': 86} Chain breaks: 1 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "D" Number of atoms: 4853 Number of conformers: 1 Conformer: "" Number of residues, atoms: 627, 4853 Classifications: {'peptide': 627} Incomplete info: {'truncation_to_alanine': 20} Link IDs: {'PTRANS': 15, 'TRANS': 611} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 81 Unresolved non-hydrogen angles: 100 Unresolved non-hydrogen dihedrals: 66 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'ASN:plan1': 5, 'GLN:plan1': 2, 'ARG:plan': 4, 'ASP:plan': 1, 'GLU:plan': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 52 Chain: "F" Number of atoms: 5892 Number of conformers: 1 Conformer: "" Number of residues, atoms: 721, 5892 Classifications: {'peptide': 721} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 19, 'TRANS': 701} Chain breaks: 1 Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 19 Unresolved non-hydrogen dihedrals: 13 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PHE:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 11 Chain: "G" Number of atoms: 718 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 93, 716 Classifications: {'peptide': 93} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 4} Link IDs: {'PTRANS': 7, 'TRANS': 85} Chain breaks: 1 Unresolved non-hydrogen bonds: 22 Unresolved non-hydrogen angles: 29 Unresolved non-hydrogen dihedrals: 17 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ASP:plan': 2, 'ARG:plan': 1, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 18 Conformer: "B" Number of residues, atoms: 93, 716 Classifications: {'peptide': 93} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 4} Link IDs: {'PTRANS': 7, 'TRANS': 85} Chain breaks: 1 Unresolved non-hydrogen bonds: 22 Unresolved non-hydrogen angles: 29 Unresolved non-hydrogen dihedrals: 17 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ASP:plan': 2, 'ARG:plan': 1, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 18 bond proxies already assigned to first conformer: 726 Chain: "H" Number of atoms: 752 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 96, 751 Classifications: {'peptide': 96} Modifications used: {'COO': 1} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 1} Link IDs: {'PTRANS': 5, 'TRANS': 90} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Conformer: "B" Number of residues, atoms: 96, 751 Classifications: {'peptide': 96} Modifications used: {'COO': 1} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 1} Link IDs: {'PTRANS': 5, 'TRANS': 90} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 bond proxies already assigned to first conformer: 766 Chain: "I" Number of atoms: 4841 Number of conformers: 1 Conformer: "" Number of residues, atoms: 627, 4841 Classifications: {'peptide': 627} Incomplete info: {'truncation_to_alanine': 22} Link IDs: {'PTRANS': 15, 'TRANS': 611} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 93 Unresolved non-hydrogen angles: 115 Unresolved non-hydrogen dihedrals: 75 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'ASN:plan1': 5, 'GLN:plan1': 3, 'ARG:plan': 5, 'ASP:plan': 2, 'GLU:plan': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 63 Chain: "R" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' ZN': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "D" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "I" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 6251 SG CYS R 42 116.557 113.575 126.376 1.00511.47 S ATOM 6270 SG CYS R 45 115.456 110.075 125.438 1.00515.92 S ATOM 6492 SG CYS R 83 118.885 110.941 124.553 1.00688.36 S ATOM 6337 SG CYS R 53 120.706 108.485 127.817 1.00581.86 S ATOM 6360 SG CYS R 56 122.985 105.967 128.879 1.00588.97 S ATOM 6371 SG CYS R 68 122.542 109.327 131.481 1.00707.25 S ATOM 6421 SG CYS R 75 121.496 122.708 121.461 1.00656.48 S ATOM 12716 SG CYS D 599 65.387 48.567 159.218 1.00107.23 S ATOM 24919 SG CYS I 599 45.251 96.118 63.385 1.00 48.66 S Time building chain proxies: 6.98, per 1000 atoms: 0.28 Number of scatterers: 25153 At special positions: 0 Unit cell: (144.44, 186.76, 218.96, 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) Zn 5 29.99 S 179 16.00 O 4717 8.00 N 4321 7.00 C 15931 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.47 Conformation dependent library (CDL) restraints added in 1.3 seconds Enol-peptide restraints added in 953.7 nanoseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN D 701 " pdb="ZN ZN D 701 " - pdb=" NE2 HIS D 627 " pdb="ZN ZN D 701 " - pdb=" NE2 HIS D 565 " pdb="ZN ZN D 701 " - pdb=" SG CYS D 599 " pdb=" ZN I 701 " pdb="ZN ZN I 701 " - pdb=" NE2 HIS I 627 " pdb="ZN ZN I 701 " - pdb=" NE2 HIS I 565 " pdb="ZN ZN I 701 " - pdb=" SG CYS I 599 " pdb=" ZN R 201 " pdb="ZN ZN R 201 " - pdb=" ND1 HIS R 80 " pdb="ZN ZN R 201 " - pdb=" SG CYS R 45 " pdb="ZN ZN R 201 " - pdb=" SG CYS R 83 " pdb="ZN ZN R 201 " - pdb=" SG CYS R 42 " pdb=" ZN R 202 " pdb="ZN ZN R 202 " - pdb=" SG CYS R 68 " pdb="ZN ZN R 202 " - pdb=" ND1 HIS R 82 " pdb="ZN ZN R 202 " - pdb=" SG CYS R 53 " pdb="ZN ZN R 202 " - pdb=" SG CYS R 56 " pdb=" ZN R 203 " pdb="ZN ZN R 203 " - pdb=" SG CYS R 75 " Number of angles added : 6 6270 Ramachandran restraints generated. 3135 Oldfield, 0 Emsley, 3135 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6064 Finding SS restraints... Secondary structure from input PDB file: 149 helices and 14 sheets defined 64.9% alpha, 4.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.95 Creating SS restraints... Processing helix chain 'A' and resid 9 through 26 removed outlier: 3.718A pdb=" N THR A 19 " --> pdb=" O ASN A 15 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N THR A 20 " --> pdb=" O LYS A 16 " (cutoff:3.500A) Processing helix chain 'A' and resid 31 through 47 removed outlier: 3.900A pdb=" N SER A 40 " --> pdb=" O ASN A 36 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N ASP A 41 " --> pdb=" O ASP A 37 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N ILE A 42 " --> pdb=" O ARG A 38 " (cutoff:3.500A) removed outlier: 4.343A pdb=" N TYR A 43 " --> pdb=" O PHE A 39 " (cutoff:3.500A) Processing helix chain 'A' and resid 53 through 79 removed outlier: 3.520A pdb=" N SER A 79 " --> pdb=" O ARG A 75 " (cutoff:3.500A) Processing helix chain 'A' and resid 82 through 105 removed outlier: 3.830A pdb=" N HIS A 88 " --> pdb=" O LEU A 84 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N ARG A 89 " --> pdb=" O VAL A 85 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N TYR A 90 " --> pdb=" O MET A 86 " (cutoff:3.500A) Processing helix chain 'A' and resid 105 through 112 Processing helix chain 'A' and resid 112 through 117 removed outlier: 3.916A pdb=" N ASN A 116 " --> pdb=" O PHE A 112 " (cutoff:3.500A) Processing helix chain 'A' and resid 119 through 125 Processing helix chain 'A' and resid 138 through 151 Processing helix chain 'A' and resid 156 through 172 Processing helix chain 'A' and resid 177 through 192 removed outlier: 3.581A pdb=" N ILE A 181 " --> pdb=" O ASN A 177 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N PHE A 188 " --> pdb=" O VAL A 184 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N VAL A 189 " --> pdb=" O ILE A 185 " (cutoff:3.500A) removed outlier: 4.214A pdb=" N GLU A 192 " --> pdb=" O PHE A 188 " (cutoff:3.500A) Processing helix chain 'A' and resid 200 through 207 Processing helix chain 'A' and resid 207 through 230 removed outlier: 3.633A pdb=" N GLN A 228 " --> pdb=" O SER A 224 " (cutoff:3.500A) Processing helix chain 'A' and resid 231 through 254 Processing helix chain 'A' and resid 255 through 257 No H-bonds generated for 'chain 'A' and resid 255 through 257' Processing helix chain 'A' and resid 258 through 273 removed outlier: 3.803A pdb=" N VAL A 262 " --> pdb=" O SER A 258 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N ILE A 263 " --> pdb=" O TYR A 259 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N ARG A 269 " --> pdb=" O GLU A 265 " (cutoff:3.500A) removed outlier: 4.127A pdb=" N MET A 270 " --> pdb=" O CYS A 266 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N ASP A 273 " --> pdb=" O ARG A 269 " (cutoff:3.500A) Processing helix chain 'A' and resid 275 through 288 removed outlier: 4.215A pdb=" N ASN A 284 " --> pdb=" O ALA A 280 " (cutoff:3.500A) removed outlier: 4.178A pdb=" N ARG A 287 " --> pdb=" O HIS A 283 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N GLN A 288 " --> pdb=" O ASN A 284 " (cutoff:3.500A) Processing helix chain 'A' and resid 290 through 304 Processing helix chain 'A' and resid 307 through 329 removed outlier: 3.988A pdb=" N MET A 311 " --> pdb=" O GLY A 307 " (cutoff:3.500A) Processing helix chain 'A' and resid 336 through 357 removed outlier: 3.796A pdb=" N VAL A 340 " --> pdb=" O PRO A 336 " (cutoff:3.500A) removed outlier: 4.169A pdb=" N VAL A 343 " --> pdb=" O PHE A 339 " (cutoff:3.500A) Processing helix chain 'A' and resid 361 through 377 removed outlier: 3.773A pdb=" N SER A 374 " --> pdb=" O LYS A 370 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N VAL A 375 " --> pdb=" O ALA A 371 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N VAL A 376 " --> pdb=" O LEU A 372 " (cutoff:3.500A) Processing helix chain 'A' and resid 386 through 400 Processing helix chain 'A' and resid 407 through 423 Processing helix chain 'A' and resid 427 through 445 removed outlier: 3.837A pdb=" N PHE A 431 " --> pdb=" O ASP A 427 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N HIS A 445 " --> pdb=" O LYS A 441 " (cutoff:3.500A) Processing helix chain 'A' and resid 450 through 466 removed outlier: 3.519A pdb=" N GLU A 454 " --> pdb=" O SER A 450 " (cutoff:3.500A) Processing helix chain 'A' and resid 467 through 496 removed outlier: 4.773A pdb=" N LYS A 472 " --> pdb=" O GLU A 468 " (cutoff:3.500A) removed outlier: 5.613A pdb=" N LEU A 473 " --> pdb=" O PHE A 469 " (cutoff:3.500A) removed outlier: 4.224A pdb=" N ALA A 484 " --> pdb=" O MET A 480 " (cutoff:3.500A) removed outlier: 4.297A pdb=" N ASP A 485 " --> pdb=" O SER A 481 " (cutoff:3.500A) Processing helix chain 'A' and resid 530 through 548 removed outlier: 3.545A pdb=" N GLU A 534 " --> pdb=" O PRO A 530 " (cutoff:3.500A) removed outlier: 4.197A pdb=" N LYS A 535 " --> pdb=" O GLN A 531 " (cutoff:3.500A) removed outlier: 4.752A pdb=" N SER A 536 " --> pdb=" O GLU A 532 " (cutoff:3.500A) Processing helix chain 'A' and resid 579 through 587 Processing helix chain 'A' and resid 596 through 604 Processing helix chain 'A' and resid 606 through 621 removed outlier: 3.559A pdb=" N VAL A 620 " --> pdb=" O SER A 616 " (cutoff:3.500A) Processing helix chain 'A' and resid 661 through 692 removed outlier: 3.626A pdb=" N MET A 665 " --> pdb=" O THR A 661 " (cutoff:3.500A) Processing helix chain 'A' and resid 696 through 708 Processing helix chain 'A' and resid 714 through 728 Processing helix chain 'R' and resid 36 through 40 Processing helix chain 'R' and resid 81 through 90 Processing helix chain 'B' and resid 23 through 36 Processing helix chain 'B' and resid 56 through 61 removed outlier: 4.015A pdb=" N GLY B 61 " --> pdb=" O LEU B 57 " (cutoff:3.500A) Processing helix chain 'C' and resid 33 through 37 Processing helix chain 'C' and resid 39 through 47 Processing helix chain 'C' and resid 66 through 83 Processing helix chain 'C' and resid 98 through 111 removed outlier: 4.573A pdb=" N GLU C 102 " --> pdb=" O GLU C 98 " (cutoff:3.500A) removed outlier: 4.143A pdb=" N ASN C 108 " --> pdb=" O LEU C 104 " (cutoff:3.500A) removed outlier: 4.208A pdb=" N PHE C 109 " --> pdb=" O MET C 105 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N LEU C 110 " --> pdb=" O ALA C 106 " (cutoff:3.500A) Processing helix chain 'D' and resid 2 through 15 Processing helix chain 'D' and resid 16 through 24 Processing helix chain 'D' and resid 28 through 38 removed outlier: 3.624A pdb=" N TYR D 38 " --> pdb=" O TYR D 34 " (cutoff:3.500A) Processing helix chain 'D' and resid 48 through 57 Processing helix chain 'D' and resid 58 through 68 removed outlier: 4.168A pdb=" N HIS D 68 " --> pdb=" O LEU D 64 " (cutoff:3.500A) Processing helix chain 'D' and resid 90 through 99 Processing helix chain 'D' and resid 100 through 110 Processing helix chain 'D' and resid 123 through 132 Processing helix chain 'D' and resid 133 through 143 Processing helix chain 'D' and resid 156 through 165 Processing helix chain 'D' and resid 166 through 176 Processing helix chain 'D' and resid 189 through 198 removed outlier: 3.631A pdb=" N PHE D 193 " --> pdb=" O THR D 189 " (cutoff:3.500A) Processing helix chain 'D' and resid 199 through 209 Processing helix chain 'D' and resid 221 through 229 Processing helix chain 'D' and resid 231 through 242 Processing helix chain 'D' and resid 245 through 263 removed outlier: 3.536A pdb=" N ARG D 249 " --> pdb=" O ASP D 245 " (cutoff:3.500A) Processing helix chain 'D' and resid 268 through 284 Processing helix chain 'D' and resid 299 through 303 Processing helix chain 'D' and resid 310 through 318 Processing helix chain 'D' and resid 320 through 337 Processing helix chain 'D' and resid 340 through 342 No H-bonds generated for 'chain 'D' and resid 340 through 342' Processing helix chain 'D' and resid 343 through 358 removed outlier: 4.426A pdb=" N ILE D 347 " --> pdb=" O VAL D 343 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N TYR D 349 " --> pdb=" O HIS D 345 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N ASN D 357 " --> pdb=" O VAL D 353 " (cutoff:3.500A) Processing helix chain 'D' and resid 360 through 376 removed outlier: 3.610A pdb=" N LYS D 365 " --> pdb=" O GLU D 361 " (cutoff:3.500A) Processing helix chain 'D' and resid 381 through 398 Processing helix chain 'D' and resid 404 through 429 removed outlier: 4.096A pdb=" N GLU D 408 " --> pdb=" O ALA D 404 " (cutoff:3.500A) Processing helix chain 'D' and resid 433 through 457 Processing helix chain 'D' and resid 460 through 477 removed outlier: 3.719A pdb=" N LEU D 477 " --> pdb=" O ASN D 473 " (cutoff:3.500A) Processing helix chain 'D' and resid 486 through 493 Processing helix chain 'D' and resid 512 through 522 Processing helix chain 'D' and resid 536 through 541 removed outlier: 3.553A pdb=" N VAL D 540 " --> pdb=" O LEU D 536 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N GLN D 541 " --> pdb=" O HIS D 537 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 536 through 541' Processing helix chain 'D' and resid 548 through 561 Processing helix chain 'D' and resid 575 through 580 Processing helix chain 'D' and resid 583 through 591 removed outlier: 3.539A pdb=" N ILE D 587 " --> pdb=" O GLY D 583 " (cutoff:3.500A) Processing helix chain 'D' and resid 596 through 608 removed outlier: 3.540A pdb=" N ASN D 608 " --> pdb=" O ALA D 604 " (cutoff:3.500A) Processing helix chain 'D' and resid 617 through 627 removed outlier: 3.683A pdb=" N GLU D 621 " --> pdb=" O PRO D 617 " (cutoff:3.500A) removed outlier: 4.064A pdb=" N GLU D 622 " --> pdb=" O ARG D 618 " (cutoff:3.500A) Processing helix chain 'F' and resid 9 through 25 removed outlier: 3.836A pdb=" N THR F 13 " --> pdb=" O ASP F 9 " (cutoff:3.500A) Processing helix chain 'F' and resid 26 through 28 No H-bonds generated for 'chain 'F' and resid 26 through 28' Processing helix chain 'F' and resid 31 through 47 removed outlier: 3.978A pdb=" N PHE F 39 " --> pdb=" O TRP F 35 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N SER F 40 " --> pdb=" O ASN F 36 " (cutoff:3.500A) Processing helix chain 'F' and resid 53 through 79 removed outlier: 3.860A pdb=" N SER F 79 " --> pdb=" O ARG F 75 " (cutoff:3.500A) Processing helix chain 'F' and resid 82 through 103 removed outlier: 3.759A pdb=" N LYS F 96 " --> pdb=" O GLU F 92 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N CYS F 103 " --> pdb=" O ASP F 99 " (cutoff:3.500A) Processing helix chain 'F' and resid 105 through 112 Processing helix chain 'F' and resid 112 through 117 removed outlier: 3.791A pdb=" N ASN F 116 " --> pdb=" O PHE F 112 " (cutoff:3.500A) Processing helix chain 'F' and resid 119 through 125 Processing helix chain 'F' and resid 138 through 151 Processing helix chain 'F' and resid 155 through 161 removed outlier: 3.942A pdb=" N ILE F 160 " --> pdb=" O GLN F 156 " (cutoff:3.500A) Processing helix chain 'F' and resid 163 through 171 Processing helix chain 'F' and resid 177 through 192 removed outlier: 3.810A pdb=" N ILE F 181 " --> pdb=" O ASN F 177 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N HIS F 182 " --> pdb=" O GLN F 178 " (cutoff:3.500A) removed outlier: 4.433A pdb=" N GLU F 192 " --> pdb=" O PHE F 188 " (cutoff:3.500A) Processing helix chain 'F' and resid 200 through 207 Processing helix chain 'F' and resid 207 through 230 removed outlier: 3.629A pdb=" N GLU F 229 " --> pdb=" O ASN F 225 " (cutoff:3.500A) Processing helix chain 'F' and resid 231 through 254 removed outlier: 3.623A pdb=" N GLU F 247 " --> pdb=" O LEU F 243 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N ILE F 248 " --> pdb=" O LYS F 244 " (cutoff:3.500A) Processing helix chain 'F' and resid 255 through 257 No H-bonds generated for 'chain 'F' and resid 255 through 257' Processing helix chain 'F' and resid 258 through 274 removed outlier: 3.626A pdb=" N VAL F 271 " --> pdb=" O GLN F 267 " (cutoff:3.500A) removed outlier: 4.389A pdb=" N ALA F 272 " --> pdb=" O GLN F 268 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N ASP F 273 " --> pdb=" O ARG F 269 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N HIS F 274 " --> pdb=" O MET F 270 " (cutoff:3.500A) Processing helix chain 'F' and resid 274 through 288 removed outlier: 4.161A pdb=" N HIS F 283 " --> pdb=" O HIS F 279 " (cutoff:3.500A) removed outlier: 5.159A pdb=" N ASN F 284 " --> pdb=" O ALA F 280 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ILE F 285 " --> pdb=" O GLU F 281 " (cutoff:3.500A) Processing helix chain 'F' and resid 290 through 304 removed outlier: 3.685A pdb=" N MET F 297 " --> pdb=" O ASP F 293 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N TYR F 298 " --> pdb=" O MET F 294 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N VAL F 299 " --> pdb=" O ALA F 295 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N ALA F 303 " --> pdb=" O VAL F 299 " (cutoff:3.500A) removed outlier: 4.141A pdb=" N VAL F 304 " --> pdb=" O LEU F 300 " (cutoff:3.500A) Processing helix chain 'F' and resid 307 through 329 removed outlier: 4.208A pdb=" N MET F 311 " --> pdb=" O GLY F 307 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N ILE F 312 " --> pdb=" O LEU F 308 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N GLN F 313 " --> pdb=" O PRO F 309 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N GLN F 316 " --> pdb=" O ILE F 312 " (cutoff:3.500A) Processing helix chain 'F' and resid 334 through 358 removed outlier: 4.032A pdb=" N LEU F 338 " --> pdb=" O ASN F 334 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N PHE F 339 " --> pdb=" O MET F 335 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N VAL F 340 " --> pdb=" O PRO F 336 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N GLU F 341 " --> pdb=" O THR F 337 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N LEU F 344 " --> pdb=" O VAL F 340 " (cutoff:3.500A) Processing helix chain 'F' and resid 361 through 377 removed outlier: 3.564A pdb=" N MET F 365 " --> pdb=" O ASP F 361 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N ASN F 377 " --> pdb=" O THR F 373 " (cutoff:3.500A) Processing helix chain 'F' and resid 385 through 400 removed outlier: 3.689A pdb=" N ALA F 392 " --> pdb=" O PRO F 388 " (cutoff:3.500A) Processing helix chain 'F' and resid 407 through 425 removed outlier: 3.831A pdb=" N THR F 420 " --> pdb=" O THR F 416 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N VAL F 421 " --> pdb=" O SER F 417 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N TYR F 424 " --> pdb=" O THR F 420 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N ILE F 425 " --> pdb=" O VAL F 421 " (cutoff:3.500A) Processing helix chain 'F' and resid 427 through 445 removed outlier: 3.772A pdb=" N PHE F 431 " --> pdb=" O ASP F 427 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N ARG F 437 " --> pdb=" O LYS F 433 " (cutoff:3.500A) Processing helix chain 'F' and resid 450 through 465 removed outlier: 3.636A pdb=" N GLU F 454 " --> pdb=" O SER F 450 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N GLN F 463 " --> pdb=" O ASN F 459 " (cutoff:3.500A) Processing helix chain 'F' and resid 467 through 489 removed outlier: 3.875A pdb=" N LYS F 472 " --> pdb=" O GLU F 468 " (cutoff:3.500A) removed outlier: 4.634A pdb=" N LEU F 473 " --> pdb=" O PHE F 469 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N TYR F 477 " --> pdb=" O LEU F 473 " (cutoff:3.500A) removed outlier: 4.092A pdb=" N MET F 480 " --> pdb=" O MET F 476 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N SER F 481 " --> pdb=" O TYR F 477 " (cutoff:3.500A) Processing helix chain 'F' and resid 530 through 548 removed outlier: 3.926A pdb=" N LYS F 535 " --> pdb=" O GLN F 531 " (cutoff:3.500A) removed outlier: 4.727A pdb=" N SER F 536 " --> pdb=" O GLU F 532 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N PHE F 543 " --> pdb=" O MET F 539 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N TYR F 544 " --> pdb=" O PHE F 540 " (cutoff:3.500A) removed outlier: 4.473A pdb=" N SER F 545 " --> pdb=" O GLU F 541 " (cutoff:3.500A) removed outlier: 5.287A pdb=" N GLN F 546 " --> pdb=" O LEU F 542 " (cutoff:3.500A) removed outlier: 4.094A pdb=" N HIS F 547 " --> pdb=" O PHE F 543 " (cutoff:3.500A) Processing helix chain 'F' and resid 579 through 587 removed outlier: 3.654A pdb=" N VAL F 584 " --> pdb=" O TYR F 580 " (cutoff:3.500A) Processing helix chain 'F' and resid 596 through 604 Processing helix chain 'F' and resid 606 through 620 removed outlier: 3.520A pdb=" N VAL F 620 " --> pdb=" O SER F 616 " (cutoff:3.500A) Processing helix chain 'F' and resid 661 through 688 removed outlier: 3.839A pdb=" N MET F 665 " --> pdb=" O THR F 661 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N GLU F 666 " --> pdb=" O PRO F 662 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N THR F 668 " --> pdb=" O GLU F 664 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N GLN F 681 " --> pdb=" O LYS F 677 " (cutoff:3.500A) Processing helix chain 'F' and resid 701 through 708 removed outlier: 3.650A pdb=" N SER F 705 " --> pdb=" O GLN F 701 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N GLN F 706 " --> pdb=" O GLU F 702 " (cutoff:3.500A) Processing helix chain 'F' and resid 714 through 728 removed outlier: 3.548A pdb=" N ILE F 722 " --> pdb=" O ILE F 718 " (cutoff:3.500A) Processing helix chain 'G' and resid 23 through 36 Processing helix chain 'G' and resid 56 through 61 removed outlier: 3.967A pdb=" N CYS G 60 " --> pdb=" O THR G 56 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N GLY G 61 " --> pdb=" O LEU G 57 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 56 through 61' Processing helix chain 'H' and resid 33 through 37 Processing helix chain 'H' and resid 39 through 47 Processing helix chain 'H' and resid 66 through 83 removed outlier: 3.716A pdb=" N LEU H 70 " --> pdb=" O PRO H 66 " (cutoff:3.500A) Processing helix chain 'H' and resid 98 through 111 removed outlier: 4.540A pdb=" N GLU H 102 " --> pdb=" O GLU H 98 " (cutoff:3.500A) Processing helix chain 'I' and resid 2 through 15 Processing helix chain 'I' and resid 16 through 25 Processing helix chain 'I' and resid 28 through 38 Processing helix chain 'I' and resid 48 through 57 Processing helix chain 'I' and resid 58 through 69 Processing helix chain 'I' and resid 91 through 99 removed outlier: 3.559A pdb=" N GLY I 99 " --> pdb=" O ALA I 95 " (cutoff:3.500A) Processing helix chain 'I' and resid 100 through 110 Processing helix chain 'I' and resid 123 through 132 Processing helix chain 'I' and resid 133 through 143 Processing helix chain 'I' and resid 156 through 165 Processing helix chain 'I' and resid 166 through 176 Processing helix chain 'I' and resid 189 through 198 Processing helix chain 'I' and resid 199 through 209 Processing helix chain 'I' and resid 221 through 229 Processing helix chain 'I' and resid 231 through 242 Processing helix chain 'I' and resid 245 through 263 Processing helix chain 'I' and resid 268 through 285 removed outlier: 3.636A pdb=" N THR I 272 " --> pdb=" O ASP I 268 " (cutoff:3.500A) Processing helix chain 'I' and resid 310 through 316 Processing helix chain 'I' and resid 320 through 337 Processing helix chain 'I' and resid 343 through 355 removed outlier: 3.905A pdb=" N ILE I 347 " --> pdb=" O VAL I 343 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N ILE I 348 " --> pdb=" O SER I 344 " (cutoff:3.500A) Processing helix chain 'I' and resid 360 through 377 Processing helix chain 'I' and resid 381 through 399 Processing helix chain 'I' and resid 404 through 429 removed outlier: 3.889A pdb=" N GLU I 408 " --> pdb=" O ALA I 404 " (cutoff:3.500A) Processing helix chain 'I' and resid 433 through 457 Processing helix chain 'I' and resid 460 through 477 removed outlier: 3.915A pdb=" N LEU I 477 " --> pdb=" O ASN I 473 " (cutoff:3.500A) Processing helix chain 'I' and resid 486 through 493 Processing helix chain 'I' and resid 512 through 522 Processing helix chain 'I' and resid 529 through 533 removed outlier: 4.079A pdb=" N ASN I 533 " --> pdb=" O ASN I 530 " (cutoff:3.500A) Processing helix chain 'I' and resid 535 through 539 Processing helix chain 'I' and resid 548 through 561 removed outlier: 3.831A pdb=" N GLU I 561 " --> pdb=" O ILE I 557 " (cutoff:3.500A) Processing helix chain 'I' and resid 575 through 580 removed outlier: 3.514A pdb=" N SER I 580 " --> pdb=" O PRO I 576 " (cutoff:3.500A) Processing helix chain 'I' and resid 584 through 593 removed outlier: 4.131A pdb=" N LEU I 588 " --> pdb=" O VAL I 584 " (cutoff:3.500A) Processing helix chain 'I' and resid 596 through 608 removed outlier: 3.611A pdb=" N LEU I 600 " --> pdb=" O SER I 596 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N ASN I 608 " --> pdb=" O ALA I 604 " (cutoff:3.500A) Processing helix chain 'I' and resid 617 through 627 removed outlier: 3.771A pdb=" N GLU I 621 " --> pdb=" O PRO I 617 " (cutoff:3.500A) removed outlier: 4.426A pdb=" N GLU I 622 " --> pdb=" O ARG I 618 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N PHE I 623 " --> pdb=" O THR I 619 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 506 through 513 Processing sheet with id=AA2, first strand: chain 'A' and resid 506 through 513 removed outlier: 3.601A pdb=" N LYS R 26 " --> pdb=" O GLU A 563 " (cutoff:3.500A) removed outlier: 6.555A pdb=" N VAL A 574 " --> pdb=" O PHE A 651 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 593 through 595 Processing sheet with id=AA4, first strand: chain 'A' and resid 693 through 695 Processing sheet with id=AA5, first strand: chain 'R' and resid 70 through 72 removed outlier: 3.888A pdb=" N ALA R 71 " --> pdb=" O PHE R 79 " (cutoff:3.500A) removed outlier: 4.248A pdb=" N PHE R 79 " --> pdb=" O ALA R 71 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'R' and resid 93 through 94 Processing sheet with id=AA7, first strand: chain 'B' and resid 43 through 44 removed outlier: 4.059A pdb=" N LEU B 77 " --> pdb=" O ARG B 8 " (cutoff:3.500A) removed outlier: 6.885A pdb=" N THR B 13 " --> pdb=" O ILE C 30 " (cutoff:3.500A) removed outlier: 8.822A pdb=" N LYS C 32 " --> pdb=" O THR B 13 " (cutoff:3.500A) removed outlier: 9.532A pdb=" N PHE B 15 " --> pdb=" O LYS C 32 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 80 through 81 Processing sheet with id=AA9, first strand: chain 'F' and resid 561 through 566 Processing sheet with id=AB1, first strand: chain 'F' and resid 593 through 595 Processing sheet with id=AB2, first strand: chain 'G' and resid 73 through 75 removed outlier: 3.578A pdb=" N ARG G 8 " --> pdb=" O VAL G 75 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N PHE G 15 " --> pdb=" O ILE H 30 " (cutoff:3.500A) removed outlier: 5.776A pdb=" N LYS H 32 " --> pdb=" O PHE G 15 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'G' and resid 44 through 45 removed outlier: 4.678A pdb=" N LEU G 44 " --> pdb=" O LEU G 51 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'I' and resid 76 through 77 Processing sheet with id=AB5, first strand: chain 'I' and resid 80 through 81 1402 hydrogen bonds defined for protein. 4146 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: 4.80 Time building geometry restraints manager: 3.21 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 5898 1.33 - 1.45: 5101 1.45 - 1.58: 14339 1.58 - 1.70: 0 1.70 - 1.82: 286 Bond restraints: 25624 Sorted by residual: bond pdb=" N PHE A 198 " pdb=" CA PHE A 198 " ideal model delta sigma weight residual 1.458 1.488 -0.031 7.40e-03 1.83e+04 1.72e+01 bond pdb=" N VAL A 577 " pdb=" CA VAL A 577 " ideal model delta sigma weight residual 1.456 1.496 -0.041 1.15e-02 7.56e+03 1.24e+01 bond pdb=" N ILE C 90 " pdb=" CA ILE C 90 " ideal model delta sigma weight residual 1.461 1.493 -0.032 9.10e-03 1.21e+04 1.23e+01 bond pdb=" N ASP A 131 " pdb=" CA ASP A 131 " ideal model delta sigma weight residual 1.454 1.497 -0.043 1.34e-02 5.57e+03 1.04e+01 bond pdb=" N VAL I 498 " pdb=" CA VAL I 498 " ideal model delta sigma weight residual 1.456 1.495 -0.038 1.19e-02 7.06e+03 1.03e+01 ... (remaining 25619 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.77: 33471 1.77 - 3.55: 1016 3.55 - 5.32: 130 5.32 - 7.09: 22 7.09 - 8.87: 5 Bond angle restraints: 34644 Sorted by residual: angle pdb=" N PRO I 510 " pdb=" CA PRO I 510 " pdb=" CB PRO I 510 " ideal model delta sigma weight residual 103.25 111.44 -8.19 1.05e+00 9.07e-01 6.09e+01 angle pdb=" N PRO D 510 " pdb=" CA PRO D 510 " pdb=" CB PRO D 510 " ideal model delta sigma weight residual 103.25 111.31 -8.06 1.05e+00 9.07e-01 5.89e+01 angle pdb=" N ILE D 471 " pdb=" CA ILE D 471 " pdb=" C ILE D 471 " ideal model delta sigma weight residual 110.62 103.00 7.62 1.02e+00 9.61e-01 5.59e+01 angle pdb=" N GLN D 464 " pdb=" CA GLN D 464 " pdb=" C GLN D 464 " ideal model delta sigma weight residual 111.71 104.93 6.78 1.15e+00 7.56e-01 3.48e+01 angle pdb=" N ILE D 467 " pdb=" CA ILE D 467 " pdb=" C ILE D 467 " ideal model delta sigma weight residual 110.42 105.16 5.26 9.60e-01 1.09e+00 3.00e+01 ... (remaining 34639 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.49: 14263 17.49 - 34.97: 1088 34.97 - 52.46: 195 52.46 - 69.94: 24 69.94 - 87.43: 17 Dihedral angle restraints: 15587 sinusoidal: 6243 harmonic: 9344 Sorted by residual: dihedral pdb=" C ASN D 473 " pdb=" N ASN D 473 " pdb=" CA ASN D 473 " pdb=" CB ASN D 473 " ideal model delta harmonic sigma weight residual -122.60 -137.29 14.69 0 2.50e+00 1.60e-01 3.45e+01 dihedral pdb=" N ASN D 473 " pdb=" C ASN D 473 " pdb=" CA ASN D 473 " pdb=" CB ASN D 473 " ideal model delta harmonic sigma weight residual 122.80 134.44 -11.64 0 2.50e+00 1.60e-01 2.17e+01 dihedral pdb=" C THR C 88 " pdb=" N THR C 88 " pdb=" CA THR C 88 " pdb=" CB THR C 88 " ideal model delta harmonic sigma weight residual -122.00 -133.12 11.12 0 2.50e+00 1.60e-01 1.98e+01 ... (remaining 15584 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.097: 3731 0.097 - 0.195: 177 0.195 - 0.292: 11 0.292 - 0.390: 3 0.390 - 0.487: 1 Chirality restraints: 3923 Sorted by residual: chirality pdb=" CA ASN D 473 " pdb=" N ASN D 473 " pdb=" C ASN D 473 " pdb=" CB ASN D 473 " both_signs ideal model delta sigma weight residual False 2.51 2.02 0.49 2.00e-01 2.50e+01 5.94e+00 chirality pdb=" CA THR C 88 " pdb=" N THR C 88 " pdb=" C THR C 88 " pdb=" CB THR C 88 " both_signs ideal model delta sigma weight residual False 2.53 2.18 0.35 2.00e-01 2.50e+01 3.01e+00 chirality pdb=" CA ASP D 478 " pdb=" N ASP D 478 " pdb=" C ASP D 478 " pdb=" CB ASP D 478 " both_signs ideal model delta sigma weight residual False 2.51 2.19 0.32 2.00e-01 2.50e+01 2.52e+00 ... (remaining 3920 not shown) Planarity restraints: 4448 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LEU A 123 " -0.025 2.00e-02 2.50e+03 5.05e-02 2.55e+01 pdb=" C LEU A 123 " 0.087 2.00e-02 2.50e+03 pdb=" O LEU A 123 " -0.033 2.00e-02 2.50e+03 pdb=" N GLN A 124 " -0.029 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA CYS D 459 " -0.022 2.00e-02 2.50e+03 4.33e-02 1.88e+01 pdb=" C CYS D 459 " 0.075 2.00e-02 2.50e+03 pdb=" O CYS D 459 " -0.028 2.00e-02 2.50e+03 pdb=" N SER D 460 " -0.025 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE D 392 " 0.022 2.00e-02 2.50e+03 1.63e-02 4.66e+00 pdb=" CG PHE D 392 " -0.036 2.00e-02 2.50e+03 pdb=" CD1 PHE D 392 " 0.003 2.00e-02 2.50e+03 pdb=" CD2 PHE D 392 " -0.001 2.00e-02 2.50e+03 pdb=" CE1 PHE D 392 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 PHE D 392 " 0.004 2.00e-02 2.50e+03 pdb=" CZ PHE D 392 " 0.008 2.00e-02 2.50e+03 ... (remaining 4445 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.76: 3463 2.76 - 3.29: 26622 3.29 - 3.83: 41373 3.83 - 4.36: 47020 4.36 - 4.90: 77088 Nonbonded interactions: 195566 Sorted by model distance: nonbonded pdb=" NH1 ARG F 475 " pdb=" O ALA F 516 " model vdw 2.220 3.120 nonbonded pdb=" O GLU A 31 " pdb=" OG1 THR A 34 " model vdw 2.230 3.040 nonbonded pdb=" OH TYR D 302 " pdb=" OE1 GLU D 333 " model vdw 2.233 3.040 nonbonded pdb=" OH TYR D 9 " pdb=" O SER D 47 " model vdw 2.237 3.040 nonbonded pdb=" OH TYR A 219 " pdb=" OE1 GLU A 246 " model vdw 2.240 3.040 ... (remaining 195561 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 1 through 421 or (resid 422 and (name N or name CA or name \ C or name O or name CB )) or resid 423 through 441 or (resid 442 and (name N or \ name CA or name C or name O or name CB )) or resid 443 through 495 or resid 503 \ through 728)) selection = (chain 'F' and (resid 1 through 522 or resid 525 through 728)) } ncs_group { reference = (chain 'B' and (resid 1 through 51 or resid 53 through 97)) selection = (chain 'G' and (resid 1 through 51 or resid 53 through 97)) } ncs_group { reference = (chain 'C' and (resid 17 through 87 or resid 89 through 112)) selection = (chain 'H' and (resid 17 through 53 or resid 58 through 87 or resid 89 through 1 \ 12)) } ncs_group { reference = (chain 'D' and (resid 1 through 317 or (resid 318 and (name N or name CA or name \ C or name O or name CB )) or (resid 319 and (name N or name CA or name C or nam \ e O or name CB or name CG )) or (resid 320 and (name N or name CA or name C or n \ ame O or name CB )) or resid 321 through 701)) selection = chain 'I' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.50 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.340 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.080 Construct map_model_manager: 0.020 Extract box with map and model: 0.570 Check model and map are aligned: 0.090 Set scattering table: 0.100 Process input model: 28.420 Find NCS groups from input model: 0.500 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.430 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.630 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8154 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.321 25639 Z= 0.296 Angle : 0.705 24.380 34650 Z= 0.447 Chirality : 0.046 0.487 3923 Planarity : 0.004 0.050 4448 Dihedral : 12.978 87.429 9523 Min Nonbonded Distance : 2.220 Molprobity Statistics. All-atom Clashscore : 11.42 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.26 % Favored : 96.68 % Rotamer: Outliers : 0.44 % Allowed : 0.88 % Favored : 98.68 % Cbeta Deviations : 0.10 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.97 (0.15), residues: 3135 helix: 1.54 (0.12), residues: 1852 sheet: 0.31 (0.52), residues: 99 loop : -0.73 (0.18), residues: 1184 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A 686 TYR 0.031 0.001 TYR A 43 PHE 0.036 0.001 PHE D 392 TRP 0.017 0.002 TRP D 209 HIS 0.004 0.001 HIS A 68 Details of bonding type rmsd covalent geometry : bond 0.00379 (25624) covalent geometry : angle 0.67898 (34644) hydrogen bonds : bond 0.18526 ( 1395) hydrogen bonds : angle 6.00791 ( 4146) metal coordination : bond 0.17239 ( 15) metal coordination : angle 14.47639 ( 6) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6270 Ramachandran restraints generated. 3135 Oldfield, 0 Emsley, 3135 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6270 Ramachandran restraints generated. 3135 Oldfield, 0 Emsley, 3135 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 210 residues out of total 2801 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 198 time to evaluate : 1.182 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 86 MET cc_start: 0.9107 (mmp) cc_final: 0.8217 (mmm) REVERT: A 90 TYR cc_start: 0.7573 (p90) cc_final: 0.7085 (p90) REVERT: A 151 MET cc_start: 0.7941 (tmm) cc_final: 0.7332 (tmm) REVERT: A 294 MET cc_start: 0.9473 (mmp) cc_final: 0.9164 (mmp) REVERT: A 365 MET cc_start: 0.9421 (mmt) cc_final: 0.9101 (mmt) REVERT: A 457 MET cc_start: 0.9461 (mmp) cc_final: 0.9225 (mmp) REVERT: A 678 MET cc_start: 0.9445 (tpt) cc_final: 0.9213 (ptp) REVERT: R 50 MET cc_start: 0.8711 (tpt) cc_final: 0.8308 (ptt) REVERT: C 85 ASN cc_start: 0.9197 (m-40) cc_final: 0.8558 (t0) REVERT: C 111 ASP cc_start: 0.8211 (t70) cc_final: 0.7975 (t0) REVERT: D 101 PHE cc_start: 0.9416 (m-10) cc_final: 0.9134 (t80) REVERT: D 280 MET cc_start: 0.8250 (ttt) cc_final: 0.7870 (tmm) REVERT: D 422 MET cc_start: 0.9144 (ppp) cc_final: 0.8858 (ppp) REVERT: D 502 HIS cc_start: 0.8498 (m-70) cc_final: 0.8233 (m-70) REVERT: D 521 CYS cc_start: 0.8955 (m) cc_final: 0.8745 (t) REVERT: D 567 ASP cc_start: 0.9286 (OUTLIER) cc_final: 0.8548 (p0) REVERT: F 26 MET cc_start: 0.9225 (mtp) cc_final: 0.8739 (mmm) REVERT: F 146 MET cc_start: 0.9260 (mmm) cc_final: 0.9037 (mmm) REVERT: F 162 MET cc_start: 0.9103 (ttm) cc_final: 0.8749 (ttm) REVERT: F 406 MET cc_start: 0.5814 (ptt) cc_final: 0.5143 (ptm) REVERT: F 424 TYR cc_start: 0.9207 (m-80) cc_final: 0.8459 (m-80) REVERT: F 438 MET cc_start: 0.9567 (mpp) cc_final: 0.9344 (mpp) REVERT: F 476 MET cc_start: 0.9333 (mmp) cc_final: 0.9130 (mmm) REVERT: G 79 PHE cc_start: 0.9302 (m-80) cc_final: 0.9007 (m-80) REVERT: I 395 MET cc_start: 0.9274 (ptt) cc_final: 0.9029 (ptt) outliers start: 12 outliers final: 3 residues processed: 209 average time/residue: 0.1722 time to fit residues: 59.0019 Evaluate side-chains 160 residues out of total 2801 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 156 time to evaluate : 1.198 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 313 random chunks: chunk 197 optimal weight: 1.9990 chunk 215 optimal weight: 10.0000 chunk 20 optimal weight: 4.9990 chunk 132 optimal weight: 0.0030 chunk 261 optimal weight: 7.9990 chunk 248 optimal weight: 0.9990 chunk 207 optimal weight: 10.0000 chunk 155 optimal weight: 2.9990 chunk 244 optimal weight: 0.9980 chunk 183 optimal weight: 0.0770 chunk 298 optimal weight: 6.9990 overall best weight: 0.8152 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 124 GLN A 487 ASN ** R 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 468 ASN D 592 GLN F 274 HIS F 681 GLN ** G 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3828 r_free = 0.3828 target = 0.067567 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3174 r_free = 0.3174 target = 0.045906 restraints weight = 238236.272| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3228 r_free = 0.3228 target = 0.046907 restraints weight = 146644.720| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3260 r_free = 0.3260 target = 0.048012 restraints weight = 87616.980| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3256 r_free = 0.3256 target = 0.047593 restraints weight = 68978.988| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3254 r_free = 0.3254 target = 0.047583 restraints weight = 66243.833| |-----------------------------------------------------------------------------| r_work (final): 0.3143 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3143 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3143 r_free = 0.3143 target_work(ls_wunit_k1) = 0.043 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3143 r_free = 0.3143 target_work(ls_wunit_k1) = 0.043 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3143 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8086 moved from start: 0.1042 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.069 25639 Z= 0.126 Angle : 0.561 21.545 34650 Z= 0.300 Chirality : 0.039 0.186 3923 Planarity : 0.004 0.041 4448 Dihedral : 4.419 39.990 3429 Min Nonbonded Distance : 2.235 Molprobity Statistics. All-atom Clashscore : 9.38 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.03 % Favored : 96.90 % Rotamer: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.13 (0.15), residues: 3135 helix: 1.60 (0.12), residues: 1921 sheet: 0.37 (0.52), residues: 99 loop : -0.68 (0.19), residues: 1115 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 710 TYR 0.027 0.001 TYR D 472 PHE 0.018 0.001 PHE D 392 TRP 0.017 0.001 TRP D 209 HIS 0.005 0.001 HIS D 218 Details of bonding type rmsd covalent geometry : bond 0.00244 (25624) covalent geometry : angle 0.54543 (34644) hydrogen bonds : bond 0.04927 ( 1395) hydrogen bonds : angle 4.64157 ( 4146) metal coordination : bond 0.02833 ( 15) metal coordination : angle 9.83440 ( 6) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6270 Ramachandran restraints generated. 3135 Oldfield, 0 Emsley, 3135 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6270 Ramachandran restraints generated. 3135 Oldfield, 0 Emsley, 3135 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 2801 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 189 time to evaluate : 1.223 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 86 MET cc_start: 0.8845 (mmp) cc_final: 0.8091 (mmm) REVERT: A 90 TYR cc_start: 0.7462 (p90) cc_final: 0.6942 (p90) REVERT: A 151 MET cc_start: 0.8465 (tmm) cc_final: 0.7605 (tmm) REVERT: A 365 MET cc_start: 0.9390 (mmt) cc_final: 0.9036 (mmt) REVERT: A 576 MET cc_start: 0.9171 (mmp) cc_final: 0.8969 (mmm) REVERT: A 622 MET cc_start: 0.9290 (mtm) cc_final: 0.9073 (mtm) REVERT: A 642 MET cc_start: 0.9298 (mpp) cc_final: 0.9092 (tpt) REVERT: A 678 MET cc_start: 0.9568 (tpt) cc_final: 0.9285 (ptp) REVERT: A 717 MET cc_start: 0.8916 (ttt) cc_final: 0.8151 (tpp) REVERT: R 50 MET cc_start: 0.8704 (tpt) cc_final: 0.8204 (ptt) REVERT: C 17 MET cc_start: 0.7367 (ttt) cc_final: 0.7050 (ttt) REVERT: C 85 ASN cc_start: 0.8675 (m-40) cc_final: 0.8332 (t0) REVERT: D 422 MET cc_start: 0.8831 (ppp) cc_final: 0.8490 (ppp) REVERT: F 101 MET cc_start: 0.9246 (tmm) cc_final: 0.9036 (tmm) REVERT: F 162 MET cc_start: 0.8645 (ttm) cc_final: 0.8388 (ttm) REVERT: F 294 MET cc_start: 0.8371 (ppp) cc_final: 0.7903 (tmm) REVERT: F 424 TYR cc_start: 0.9088 (m-80) cc_final: 0.8336 (m-80) REVERT: F 476 MET cc_start: 0.9047 (mmp) cc_final: 0.8786 (mmm) REVERT: I 358 MET cc_start: 0.7302 (ppp) cc_final: 0.6112 (ppp) REVERT: I 360 PHE cc_start: 0.8869 (m-10) cc_final: 0.8469 (m-10) outliers start: 0 outliers final: 0 residues processed: 189 average time/residue: 0.1595 time to fit residues: 50.6996 Evaluate side-chains 151 residues out of total 2801 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 151 time to evaluate : 0.980 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 313 random chunks: chunk 207 optimal weight: 8.9990 chunk 52 optimal weight: 0.2980 chunk 190 optimal weight: 5.9990 chunk 42 optimal weight: 5.9990 chunk 221 optimal weight: 10.0000 chunk 119 optimal weight: 3.9990 chunk 85 optimal weight: 2.9990 chunk 164 optimal weight: 0.4980 chunk 9 optimal weight: 8.9990 chunk 21 optimal weight: 6.9990 chunk 121 optimal weight: 5.9990 overall best weight: 2.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 362 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 41 ASN ** D 565 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 320 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 377 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 51 GLN ** I 241 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 541 GLN ** I 565 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 = 0.3797 r_free = 0.3797 target = 0.066468 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3136 r_free = 0.3136 target = 0.044973 restraints weight = 221868.860| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3186 r_free = 0.3186 target = 0.045750 restraints weight = 145075.191| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3171 r_free = 0.3171 target = 0.045696 restraints weight = 92332.070| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3178 r_free = 0.3178 target = 0.045821 restraints weight = 92166.891| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3179 r_free = 0.3179 target = 0.045778 restraints weight = 85109.244| |-----------------------------------------------------------------------------| r_work (final): 0.3058 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3058 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3058 r_free = 0.3058 target_work(ls_wunit_k1) = 0.041 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3058 r_free = 0.3058 target_work(ls_wunit_k1) = 0.041 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3058 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8184 moved from start: 0.1408 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 25639 Z= 0.160 Angle : 0.558 12.540 34650 Z= 0.298 Chirality : 0.039 0.199 3923 Planarity : 0.004 0.042 4448 Dihedral : 4.429 40.993 3429 Min Nonbonded Distance : 2.112 Molprobity Statistics. All-atom Clashscore : 10.98 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.38 % Favored : 96.55 % Rotamer: Outliers : 0.00 % Allowed : 2.71 % Favored : 97.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.10 (0.15), residues: 3135 helix: 1.56 (0.12), residues: 1924 sheet: 0.22 (0.51), residues: 99 loop : -0.65 (0.19), residues: 1112 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 686 TYR 0.021 0.001 TYR A 105 PHE 0.035 0.002 PHE I 260 TRP 0.016 0.001 TRP D 209 HIS 0.008 0.001 HIS C 68 Details of bonding type rmsd covalent geometry : bond 0.00337 (25624) covalent geometry : angle 0.55270 (34644) hydrogen bonds : bond 0.04433 ( 1395) hydrogen bonds : angle 4.58959 ( 4146) metal coordination : bond 0.01387 ( 15) metal coordination : angle 5.85468 ( 6) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6270 Ramachandran restraints generated. 3135 Oldfield, 0 Emsley, 3135 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6270 Ramachandran restraints generated. 3135 Oldfield, 0 Emsley, 3135 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 2801 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 182 time to evaluate : 1.070 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 86 MET cc_start: 0.8878 (mmp) cc_final: 0.8047 (mmm) REVERT: A 90 TYR cc_start: 0.7606 (p90) cc_final: 0.7082 (p90) REVERT: A 151 MET cc_start: 0.8681 (tmm) cc_final: 0.7710 (tmm) REVERT: A 365 MET cc_start: 0.9448 (mmt) cc_final: 0.9123 (mmt) REVERT: A 582 MET cc_start: 0.8548 (mtm) cc_final: 0.8140 (mpp) REVERT: A 622 MET cc_start: 0.9336 (mtm) cc_final: 0.9112 (mtm) REVERT: A 642 MET cc_start: 0.9342 (mpp) cc_final: 0.9136 (tpt) REVERT: A 678 MET cc_start: 0.9611 (tpt) cc_final: 0.9296 (ptp) REVERT: A 717 MET cc_start: 0.9006 (ttt) cc_final: 0.8266 (tpp) REVERT: R 50 MET cc_start: 0.8723 (tpt) cc_final: 0.8138 (ptt) REVERT: C 17 MET cc_start: 0.7392 (ttt) cc_final: 0.7192 (ttt) REVERT: C 85 ASN cc_start: 0.8835 (m-40) cc_final: 0.8449 (t0) REVERT: D 220 MET cc_start: 0.7653 (ppp) cc_final: 0.7446 (ppp) REVERT: D 326 MET cc_start: 0.8915 (mmp) cc_final: 0.8711 (mmp) REVERT: D 422 MET cc_start: 0.9030 (ppp) cc_final: 0.8731 (ppp) REVERT: D 502 HIS cc_start: 0.8147 (m-70) cc_final: 0.7911 (m90) REVERT: D 568 MET cc_start: 0.8705 (mmm) cc_final: 0.8453 (tpt) REVERT: F 101 MET cc_start: 0.9309 (tmm) cc_final: 0.8988 (tmm) REVERT: F 162 MET cc_start: 0.8494 (ttm) cc_final: 0.8245 (ttm) REVERT: F 424 TYR cc_start: 0.9122 (m-80) cc_final: 0.8413 (m-80) REVERT: F 476 MET cc_start: 0.9053 (mmp) cc_final: 0.8779 (mmm) REVERT: I 241 HIS cc_start: 0.8006 (m90) cc_final: 0.7480 (p-80) REVERT: I 358 MET cc_start: 0.7049 (ppp) cc_final: 0.6847 (ppp) outliers start: 0 outliers final: 0 residues processed: 182 average time/residue: 0.1555 time to fit residues: 47.9612 Evaluate side-chains 149 residues out of total 2801 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 149 time to evaluate : 1.035 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 313 random chunks: chunk 255 optimal weight: 9.9990 chunk 84 optimal weight: 9.9990 chunk 0 optimal weight: 10.0000 chunk 143 optimal weight: 5.9990 chunk 267 optimal weight: 7.9990 chunk 146 optimal weight: 0.8980 chunk 10 optimal weight: 2.9990 chunk 194 optimal weight: 0.8980 chunk 123 optimal weight: 3.9990 chunk 262 optimal weight: 0.7980 chunk 95 optimal weight: 10.0000 overall best weight: 1.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 565 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 68 HIS ** F 320 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 347 HIS ** F 377 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 565 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 627 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3803 r_free = 0.3803 target = 0.066836 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3140 r_free = 0.3140 target = 0.044896 restraints weight = 236677.127| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3187 r_free = 0.3187 target = 0.045951 restraints weight = 153109.239| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3185 r_free = 0.3185 target = 0.046014 restraints weight = 93257.636| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3188 r_free = 0.3188 target = 0.046098 restraints weight = 93174.399| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3193 r_free = 0.3193 target = 0.046181 restraints weight = 83781.340| |-----------------------------------------------------------------------------| r_work (final): 0.3076 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3076 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3076 r_free = 0.3076 target_work(ls_wunit_k1) = 0.042 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3076 r_free = 0.3076 target_work(ls_wunit_k1) = 0.042 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3076 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8162 moved from start: 0.1616 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 25639 Z= 0.126 Angle : 0.523 9.894 34650 Z= 0.280 Chirality : 0.038 0.183 3923 Planarity : 0.003 0.043 4448 Dihedral : 4.384 39.868 3429 Min Nonbonded Distance : 1.999 Molprobity Statistics. All-atom Clashscore : 9.98 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.38 % Favored : 96.52 % Rotamer: Outliers : 0.00 % Allowed : 2.31 % Favored : 97.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.18 (0.15), residues: 3135 helix: 1.65 (0.12), residues: 1917 sheet: 0.07 (0.50), residues: 99 loop : -0.65 (0.19), residues: 1119 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 686 TYR 0.019 0.001 TYR A 105 PHE 0.031 0.001 PHE D 388 TRP 0.013 0.001 TRP D 209 HIS 0.006 0.001 HIS D 218 Details of bonding type rmsd covalent geometry : bond 0.00264 (25624) covalent geometry : angle 0.51990 (34644) hydrogen bonds : bond 0.03962 ( 1395) hydrogen bonds : angle 4.41267 ( 4146) metal coordination : bond 0.00866 ( 15) metal coordination : angle 4.68058 ( 6) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6270 Ramachandran restraints generated. 3135 Oldfield, 0 Emsley, 3135 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6270 Ramachandran restraints generated. 3135 Oldfield, 0 Emsley, 3135 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 2801 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 182 time to evaluate : 1.079 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 86 MET cc_start: 0.8786 (mmp) cc_final: 0.7956 (mmm) REVERT: A 90 TYR cc_start: 0.7508 (p90) cc_final: 0.7034 (p90) REVERT: A 365 MET cc_start: 0.9441 (mmt) cc_final: 0.9149 (mmt) REVERT: A 622 MET cc_start: 0.9273 (mtm) cc_final: 0.9067 (mtm) REVERT: A 678 MET cc_start: 0.9598 (tpt) cc_final: 0.9294 (ptp) REVERT: A 717 MET cc_start: 0.9032 (ttt) cc_final: 0.8281 (tpp) REVERT: R 50 MET cc_start: 0.8726 (tpt) cc_final: 0.8141 (ptt) REVERT: R 96 LEU cc_start: 0.4601 (tp) cc_final: 0.4320 (tp) REVERT: R 97 ASP cc_start: 0.7884 (m-30) cc_final: 0.7286 (p0) REVERT: C 85 ASN cc_start: 0.8778 (m-40) cc_final: 0.8440 (t0) REVERT: D 220 MET cc_start: 0.7691 (ppp) cc_final: 0.7391 (ppp) REVERT: D 326 MET cc_start: 0.8837 (mmp) cc_final: 0.8636 (mmp) REVERT: D 422 MET cc_start: 0.8979 (ppp) cc_final: 0.8741 (ppp) REVERT: F 101 MET cc_start: 0.9326 (tmm) cc_final: 0.9019 (tmm) REVERT: F 162 MET cc_start: 0.8446 (ttm) cc_final: 0.8196 (ttm) REVERT: F 294 MET cc_start: 0.8372 (tmm) cc_final: 0.8011 (tmm) REVERT: F 424 TYR cc_start: 0.9036 (m-80) cc_final: 0.8358 (m-80) REVERT: F 438 MET cc_start: 0.9511 (mmp) cc_final: 0.9251 (mmt) REVERT: F 476 MET cc_start: 0.8913 (mmp) cc_final: 0.8587 (mmm) REVERT: F 642 MET cc_start: 0.9033 (mmt) cc_final: 0.8743 (mmp) REVERT: I 241 HIS cc_start: 0.7966 (m90) cc_final: 0.7436 (p-80) outliers start: 0 outliers final: 0 residues processed: 182 average time/residue: 0.1573 time to fit residues: 48.1315 Evaluate side-chains 148 residues out of total 2801 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 148 time to evaluate : 1.074 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 313 random chunks: chunk 29 optimal weight: 3.9990 chunk 123 optimal weight: 5.9990 chunk 205 optimal weight: 9.9990 chunk 143 optimal weight: 5.9990 chunk 64 optimal weight: 30.0000 chunk 72 optimal weight: 7.9990 chunk 209 optimal weight: 10.0000 chunk 32 optimal weight: 0.9980 chunk 140 optimal weight: 2.9990 chunk 186 optimal weight: 5.9990 chunk 224 optimal weight: 40.0000 overall best weight: 3.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 362 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 427 ASN D 502 HIS ** D 570 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 320 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 377 ASN ** G 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 627 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 = 0.3760 r_free = 0.3760 target = 0.065226 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3085 r_free = 0.3085 target = 0.043581 restraints weight = 281047.841| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3125 r_free = 0.3125 target = 0.044509 restraints weight = 161767.529| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3155 r_free = 0.3155 target = 0.044959 restraints weight = 108306.011| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3148 r_free = 0.3148 target = 0.044817 restraints weight = 97408.727| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3147 r_free = 0.3147 target = 0.044821 restraints weight = 80121.907| |-----------------------------------------------------------------------------| r_work (final): 0.3042 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3042 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3042 r_free = 0.3042 target_work(ls_wunit_k1) = 0.041 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3042 r_free = 0.3042 target_work(ls_wunit_k1) = 0.041 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3042 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8195 moved from start: 0.2032 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 25639 Z= 0.213 Angle : 0.612 7.940 34650 Z= 0.326 Chirality : 0.040 0.193 3923 Planarity : 0.004 0.046 4448 Dihedral : 4.603 45.677 3429 Min Nonbonded Distance : 1.923 Molprobity Statistics. All-atom Clashscore : 12.60 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.96 % Favored : 95.98 % Rotamer: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.92 (0.15), residues: 3135 helix: 1.45 (0.12), residues: 1918 sheet: -0.24 (0.50), residues: 99 loop : -0.76 (0.19), residues: 1118 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG D 379 TYR 0.026 0.002 TYR D 440 PHE 0.021 0.002 PHE D 392 TRP 0.013 0.002 TRP D 209 HIS 0.007 0.001 HIS A 255 Details of bonding type rmsd covalent geometry : bond 0.00449 (25624) covalent geometry : angle 0.60935 (34644) hydrogen bonds : bond 0.04257 ( 1395) hydrogen bonds : angle 4.60455 ( 4146) metal coordination : bond 0.00830 ( 15) metal coordination : angle 4.66781 ( 6) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6270 Ramachandran restraints generated. 3135 Oldfield, 0 Emsley, 3135 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6270 Ramachandran restraints generated. 3135 Oldfield, 0 Emsley, 3135 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 2801 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 179 time to evaluate : 0.910 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 86 MET cc_start: 0.8822 (mmp) cc_final: 0.8089 (mmm) REVERT: A 90 TYR cc_start: 0.7676 (p90) cc_final: 0.7164 (p90) REVERT: A 151 MET cc_start: 0.8552 (tmm) cc_final: 0.7251 (tmm) REVERT: A 365 MET cc_start: 0.9501 (mmt) cc_final: 0.9196 (mmt) REVERT: A 622 MET cc_start: 0.9273 (mtm) cc_final: 0.8929 (tpt) REVERT: A 717 MET cc_start: 0.9100 (ttt) cc_final: 0.8350 (tpp) REVERT: R 50 MET cc_start: 0.8726 (tpt) cc_final: 0.8059 (ptt) REVERT: R 77 HIS cc_start: 0.8419 (m-70) cc_final: 0.8174 (m170) REVERT: C 85 ASN cc_start: 0.8705 (m-40) cc_final: 0.8440 (t0) REVERT: D 159 MET cc_start: 0.8310 (mpp) cc_final: 0.8086 (mpp) REVERT: D 199 HIS cc_start: 0.8510 (m-70) cc_final: 0.8305 (m-70) REVERT: D 220 MET cc_start: 0.7801 (ppp) cc_final: 0.7446 (ppp) REVERT: D 326 MET cc_start: 0.8950 (mmp) cc_final: 0.8748 (mmp) REVERT: D 568 MET cc_start: 0.8778 (mmt) cc_final: 0.8513 (tpt) REVERT: F 101 MET cc_start: 0.9376 (tmm) cc_final: 0.9057 (tmm) REVERT: F 162 MET cc_start: 0.8615 (ttm) cc_final: 0.8376 (ttm) REVERT: F 294 MET cc_start: 0.8372 (tmm) cc_final: 0.7914 (tmm) REVERT: F 424 TYR cc_start: 0.9087 (m-80) cc_final: 0.8390 (m-80) REVERT: F 438 MET cc_start: 0.9537 (mmp) cc_final: 0.9279 (mmt) REVERT: F 476 MET cc_start: 0.8962 (mmp) cc_final: 0.8520 (mmm) REVERT: F 642 MET cc_start: 0.9061 (mmt) cc_final: 0.8787 (mmp) REVERT: I 341 ILE cc_start: 0.9303 (pt) cc_final: 0.9016 (tp) REVERT: I 422 MET cc_start: 0.9518 (ptt) cc_final: 0.9280 (ptt) outliers start: 0 outliers final: 0 residues processed: 179 average time/residue: 0.1462 time to fit residues: 43.5924 Evaluate side-chains 146 residues out of total 2801 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 146 time to evaluate : 1.017 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 313 random chunks: chunk 284 optimal weight: 0.0030 chunk 298 optimal weight: 0.3980 chunk 294 optimal weight: 4.9990 chunk 188 optimal weight: 4.9990 chunk 18 optimal weight: 5.9990 chunk 158 optimal weight: 4.9990 chunk 105 optimal weight: 5.9990 chunk 246 optimal weight: 0.9990 chunk 82 optimal weight: 20.0000 chunk 288 optimal weight: 9.9990 chunk 245 optimal weight: 0.0670 overall best weight: 1.2932 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 320 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 627 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3794 r_free = 0.3794 target = 0.066427 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3136 r_free = 0.3136 target = 0.044807 restraints weight = 236291.396| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3201 r_free = 0.3201 target = 0.046094 restraints weight = 149296.443| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3176 r_free = 0.3176 target = 0.045733 restraints weight = 86286.535| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3186 r_free = 0.3186 target = 0.045945 restraints weight = 97156.727| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3188 r_free = 0.3188 target = 0.045941 restraints weight = 82877.512| |-----------------------------------------------------------------------------| r_work (final): 0.3068 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3068 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3068 r_free = 0.3068 target_work(ls_wunit_k1) = 0.041 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3068 r_free = 0.3068 target_work(ls_wunit_k1) = 0.041 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3068 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8173 moved from start: 0.2082 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 25639 Z= 0.111 Angle : 0.534 8.291 34650 Z= 0.283 Chirality : 0.039 0.197 3923 Planarity : 0.003 0.044 4448 Dihedral : 4.441 38.552 3429 Min Nonbonded Distance : 1.944 Molprobity Statistics. All-atom Clashscore : 10.34 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.51 % Favored : 96.42 % Rotamer: Outliers : 0.00 % Allowed : 1.10 % Favored : 98.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.15 (0.15), residues: 3135 helix: 1.62 (0.12), residues: 1926 sheet: 0.32 (0.53), residues: 89 loop : -0.68 (0.19), residues: 1120 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 412 TYR 0.017 0.001 TYR D 440 PHE 0.031 0.001 PHE D 388 TRP 0.013 0.001 TRP D 209 HIS 0.008 0.001 HIS C 68 Details of bonding type rmsd covalent geometry : bond 0.00233 (25624) covalent geometry : angle 0.53057 (34644) hydrogen bonds : bond 0.03759 ( 1395) hydrogen bonds : angle 4.31273 ( 4146) metal coordination : bond 0.00708 ( 15) metal coordination : angle 4.46217 ( 6) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6270 Ramachandran restraints generated. 3135 Oldfield, 0 Emsley, 3135 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6270 Ramachandran restraints generated. 3135 Oldfield, 0 Emsley, 3135 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 2801 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 174 time to evaluate : 1.123 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 86 MET cc_start: 0.8792 (mmp) cc_final: 0.7965 (mmm) REVERT: A 90 TYR cc_start: 0.7594 (p90) cc_final: 0.7237 (p90) REVERT: A 365 MET cc_start: 0.9512 (mmt) cc_final: 0.9190 (mmt) REVERT: A 622 MET cc_start: 0.9281 (mtm) cc_final: 0.9078 (mtm) REVERT: A 678 MET cc_start: 0.9668 (tpp) cc_final: 0.9379 (ptp) REVERT: A 717 MET cc_start: 0.9089 (ttt) cc_final: 0.8374 (tpp) REVERT: R 50 MET cc_start: 0.8736 (tpt) cc_final: 0.8114 (ptt) REVERT: C 17 MET cc_start: 0.7737 (ttt) cc_final: 0.7524 (ttt) REVERT: C 85 ASN cc_start: 0.8830 (m-40) cc_final: 0.8474 (t0) REVERT: D 159 MET cc_start: 0.8274 (mpp) cc_final: 0.8046 (mpp) REVERT: D 326 MET cc_start: 0.8889 (mmp) cc_final: 0.8677 (mmp) REVERT: D 422 MET cc_start: 0.8935 (ppp) cc_final: 0.8556 (ppp) REVERT: D 568 MET cc_start: 0.8742 (mmt) cc_final: 0.8473 (tpt) REVERT: F 294 MET cc_start: 0.8412 (tmm) cc_final: 0.8108 (tmm) REVERT: F 424 TYR cc_start: 0.9061 (m-80) cc_final: 0.8430 (m-80) REVERT: F 476 MET cc_start: 0.8846 (mmp) cc_final: 0.8375 (mmm) REVERT: F 642 MET cc_start: 0.9045 (mmt) cc_final: 0.8753 (mmp) outliers start: 0 outliers final: 0 residues processed: 174 average time/residue: 0.1531 time to fit residues: 44.9496 Evaluate side-chains 142 residues out of total 2801 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 142 time to evaluate : 0.960 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 313 random chunks: chunk 10 optimal weight: 0.9980 chunk 254 optimal weight: 40.0000 chunk 64 optimal weight: 8.9990 chunk 298 optimal weight: 0.9990 chunk 25 optimal weight: 0.3980 chunk 103 optimal weight: 50.0000 chunk 175 optimal weight: 0.3980 chunk 264 optimal weight: 20.0000 chunk 220 optimal weight: 6.9990 chunk 116 optimal weight: 9.9990 chunk 41 optimal weight: 2.9990 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 77 HIS ** F 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 320 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 627 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3803 r_free = 0.3803 target = 0.066685 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3149 r_free = 0.3149 target = 0.044844 restraints weight = 276819.427| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3194 r_free = 0.3194 target = 0.046050 restraints weight = 169213.131| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3187 r_free = 0.3187 target = 0.045917 restraints weight = 100830.191| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3191 r_free = 0.3191 target = 0.046084 restraints weight = 104695.788| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3198 r_free = 0.3198 target = 0.046173 restraints weight = 89758.435| |-----------------------------------------------------------------------------| r_work (final): 0.3079 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3079 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3079 r_free = 0.3079 target_work(ls_wunit_k1) = 0.042 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3079 r_free = 0.3079 target_work(ls_wunit_k1) = 0.042 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3079 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8161 moved from start: 0.2218 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 25639 Z= 0.105 Angle : 0.522 9.294 34650 Z= 0.275 Chirality : 0.039 0.202 3923 Planarity : 0.003 0.044 4448 Dihedral : 4.311 35.722 3429 Min Nonbonded Distance : 1.946 Molprobity Statistics. All-atom Clashscore : 9.52 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.61 % Favored : 96.33 % Rotamer: Outliers : 0.00 % Allowed : 1.14 % Favored : 98.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.20 (0.15), residues: 3135 helix: 1.68 (0.12), residues: 1926 sheet: 0.35 (0.53), residues: 89 loop : -0.71 (0.19), residues: 1120 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 686 TYR 0.015 0.001 TYR D 440 PHE 0.017 0.001 PHE D 388 TRP 0.015 0.001 TRP D 209 HIS 0.005 0.001 HIS H 35 Details of bonding type rmsd covalent geometry : bond 0.00220 (25624) covalent geometry : angle 0.51936 (34644) hydrogen bonds : bond 0.03522 ( 1395) hydrogen bonds : angle 4.19763 ( 4146) metal coordination : bond 0.00567 ( 15) metal coordination : angle 3.92482 ( 6) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6270 Ramachandran restraints generated. 3135 Oldfield, 0 Emsley, 3135 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6270 Ramachandran restraints generated. 3135 Oldfield, 0 Emsley, 3135 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 2801 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 174 time to evaluate : 0.835 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 86 MET cc_start: 0.8739 (mmp) cc_final: 0.7942 (mmm) REVERT: A 90 TYR cc_start: 0.7540 (p90) cc_final: 0.7042 (p90) REVERT: A 151 MET cc_start: 0.8415 (tmm) cc_final: 0.7508 (tmm) REVERT: A 365 MET cc_start: 0.9477 (mmt) cc_final: 0.9205 (mmt) REVERT: A 622 MET cc_start: 0.9268 (mtm) cc_final: 0.9063 (mtm) REVERT: A 678 MET cc_start: 0.9659 (tpp) cc_final: 0.9362 (ptp) REVERT: A 717 MET cc_start: 0.9100 (ttt) cc_final: 0.8372 (tpp) REVERT: R 50 MET cc_start: 0.8740 (tpt) cc_final: 0.8225 (ptt) REVERT: C 17 MET cc_start: 0.7655 (ttt) cc_final: 0.7435 (ttt) REVERT: C 85 ASN cc_start: 0.8854 (m-40) cc_final: 0.8511 (t0) REVERT: D 159 MET cc_start: 0.8307 (mpp) cc_final: 0.8097 (mpp) REVERT: D 326 MET cc_start: 0.8876 (mmp) cc_final: 0.8596 (mmp) REVERT: D 422 MET cc_start: 0.8872 (ppp) cc_final: 0.8502 (ppp) REVERT: D 568 MET cc_start: 0.8717 (mmt) cc_final: 0.8452 (tpt) REVERT: F 294 MET cc_start: 0.8445 (tmm) cc_final: 0.8136 (tmm) REVERT: F 424 TYR cc_start: 0.8995 (m-80) cc_final: 0.8307 (m-80) REVERT: F 476 MET cc_start: 0.8848 (mmp) cc_final: 0.8354 (mmm) REVERT: F 642 MET cc_start: 0.9007 (mmt) cc_final: 0.8735 (mmp) REVERT: I 358 MET cc_start: 0.7527 (ppp) cc_final: 0.7045 (ppp) outliers start: 0 outliers final: 0 residues processed: 174 average time/residue: 0.1386 time to fit residues: 40.6644 Evaluate side-chains 145 residues out of total 2801 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 145 time to evaluate : 0.863 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 313 random chunks: chunk 51 optimal weight: 0.0010 chunk 107 optimal weight: 7.9990 chunk 271 optimal weight: 7.9990 chunk 4 optimal weight: 0.9980 chunk 134 optimal weight: 0.9990 chunk 221 optimal weight: 6.9990 chunk 203 optimal weight: 3.9990 chunk 123 optimal weight: 9.9990 chunk 29 optimal weight: 4.9990 chunk 229 optimal weight: 9.9990 chunk 124 optimal weight: 4.9990 overall best weight: 2.1992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 362 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 262 ASN ** D 570 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 320 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3790 r_free = 0.3790 target = 0.066238 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3122 r_free = 0.3122 target = 0.044550 restraints weight = 233455.972| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3210 r_free = 0.3210 target = 0.045967 restraints weight = 143451.338| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3181 r_free = 0.3181 target = 0.045723 restraints weight = 84042.150| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3188 r_free = 0.3188 target = 0.045812 restraints weight = 79974.377| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3190 r_free = 0.3190 target = 0.045840 restraints weight = 73644.720| |-----------------------------------------------------------------------------| r_work (final): 0.3078 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3078 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3078 r_free = 0.3078 target_work(ls_wunit_k1) = 0.042 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3078 r_free = 0.3078 target_work(ls_wunit_k1) = 0.042 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3078 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8169 moved from start: 0.2342 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 25639 Z= 0.135 Angle : 0.541 10.578 34650 Z= 0.287 Chirality : 0.039 0.193 3923 Planarity : 0.003 0.046 4448 Dihedral : 4.347 36.009 3429 Min Nonbonded Distance : 1.932 Molprobity Statistics. All-atom Clashscore : 10.24 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.83 % Favored : 96.10 % Rotamer: Outliers : 0.00 % Allowed : 0.73 % Favored : 99.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.17 (0.15), residues: 3135 helix: 1.65 (0.12), residues: 1931 sheet: 0.33 (0.53), residues: 89 loop : -0.72 (0.19), residues: 1115 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 379 TYR 0.036 0.001 TYR F 219 PHE 0.030 0.001 PHE D 388 TRP 0.013 0.001 TRP D 209 HIS 0.006 0.001 HIS D 199 Details of bonding type rmsd covalent geometry : bond 0.00288 (25624) covalent geometry : angle 0.53891 (34644) hydrogen bonds : bond 0.03594 ( 1395) hydrogen bonds : angle 4.25387 ( 4146) metal coordination : bond 0.00633 ( 15) metal coordination : angle 3.61731 ( 6) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6270 Ramachandran restraints generated. 3135 Oldfield, 0 Emsley, 3135 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6270 Ramachandran restraints generated. 3135 Oldfield, 0 Emsley, 3135 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 2801 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 168 time to evaluate : 0.784 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 86 MET cc_start: 0.8746 (mmp) cc_final: 0.7983 (mmm) REVERT: A 90 TYR cc_start: 0.7538 (p90) cc_final: 0.7181 (p90) REVERT: A 365 MET cc_start: 0.9497 (mmt) cc_final: 0.9185 (mmt) REVERT: A 622 MET cc_start: 0.9276 (mtm) cc_final: 0.9072 (mtm) REVERT: A 678 MET cc_start: 0.9658 (tpp) cc_final: 0.9372 (ptp) REVERT: A 717 MET cc_start: 0.9086 (ttt) cc_final: 0.8362 (tpp) REVERT: R 50 MET cc_start: 0.8743 (tpt) cc_final: 0.8185 (ptt) REVERT: C 17 MET cc_start: 0.7658 (ttt) cc_final: 0.7446 (ttt) REVERT: C 85 ASN cc_start: 0.8718 (m-40) cc_final: 0.8465 (t0) REVERT: D 326 MET cc_start: 0.8969 (mmp) cc_final: 0.8694 (mmp) REVERT: D 422 MET cc_start: 0.8854 (ppp) cc_final: 0.8512 (ppp) REVERT: D 568 MET cc_start: 0.8679 (mmt) cc_final: 0.8451 (tpt) REVERT: F 162 MET cc_start: 0.8629 (ttm) cc_final: 0.8401 (ttm) REVERT: F 294 MET cc_start: 0.8441 (tmm) cc_final: 0.8077 (tmm) REVERT: F 424 TYR cc_start: 0.9042 (m-80) cc_final: 0.8339 (m-80) REVERT: F 438 MET cc_start: 0.9520 (mmp) cc_final: 0.9223 (mmt) REVERT: F 476 MET cc_start: 0.8871 (mmp) cc_final: 0.8352 (mmm) REVERT: F 642 MET cc_start: 0.9033 (mmt) cc_final: 0.8782 (mmp) REVERT: I 341 ILE cc_start: 0.9240 (pt) cc_final: 0.8951 (tp) REVERT: I 395 MET cc_start: 0.9326 (ptt) cc_final: 0.9039 (ptt) outliers start: 0 outliers final: 0 residues processed: 168 average time/residue: 0.1313 time to fit residues: 36.9451 Evaluate side-chains 144 residues out of total 2801 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 144 time to evaluate : 0.937 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 313 random chunks: chunk 293 optimal weight: 7.9990 chunk 294 optimal weight: 0.9980 chunk 124 optimal weight: 4.9990 chunk 66 optimal weight: 7.9990 chunk 156 optimal weight: 0.6980 chunk 101 optimal weight: 40.0000 chunk 249 optimal weight: 4.9990 chunk 168 optimal weight: 6.9990 chunk 108 optimal weight: 20.0000 chunk 286 optimal weight: 9.9990 chunk 202 optimal weight: 10.0000 overall best weight: 3.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 362 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 241 HIS D 319 GLN D 502 HIS ** D 570 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 320 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 489 HIS ** I 627 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3763 r_free = 0.3763 target = 0.065238 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3091 r_free = 0.3091 target = 0.043470 restraints weight = 241258.624| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3139 r_free = 0.3139 target = 0.044560 restraints weight = 163267.489| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3125 r_free = 0.3125 target = 0.044311 restraints weight = 101830.518| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3131 r_free = 0.3131 target = 0.044478 restraints weight = 103462.138| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3133 r_free = 0.3133 target = 0.044510 restraints weight = 91373.873| |-----------------------------------------------------------------------------| r_work (final): 0.3012 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3011 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3011 r_free = 0.3011 target_work(ls_wunit_k1) = 0.040 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3011 r_free = 0.3011 target_work(ls_wunit_k1) = 0.040 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3011 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8245 moved from start: 0.2526 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 25639 Z= 0.202 Angle : 0.611 11.471 34650 Z= 0.324 Chirality : 0.040 0.214 3923 Planarity : 0.004 0.047 4448 Dihedral : 4.531 40.719 3429 Min Nonbonded Distance : 1.913 Molprobity Statistics. All-atom Clashscore : 11.88 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.09 % Favored : 95.82 % Rotamer: Outliers : 0.00 % Allowed : 0.62 % Favored : 99.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.98 (0.15), residues: 3135 helix: 1.51 (0.12), residues: 1928 sheet: 0.13 (0.53), residues: 89 loop : -0.80 (0.19), residues: 1118 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG D 379 TYR 0.025 0.002 TYR D 440 PHE 0.020 0.002 PHE D 392 TRP 0.012 0.002 TRP A 14 HIS 0.006 0.001 HIS A 255 Details of bonding type rmsd covalent geometry : bond 0.00426 (25624) covalent geometry : angle 0.60897 (34644) hydrogen bonds : bond 0.03971 ( 1395) hydrogen bonds : angle 4.47943 ( 4146) metal coordination : bond 0.00786 ( 15) metal coordination : angle 3.64548 ( 6) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6270 Ramachandran restraints generated. 3135 Oldfield, 0 Emsley, 3135 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6270 Ramachandran restraints generated. 3135 Oldfield, 0 Emsley, 3135 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 2801 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 167 time to evaluate : 0.784 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 86 MET cc_start: 0.8837 (mmp) cc_final: 0.8105 (mmm) REVERT: A 90 TYR cc_start: 0.7729 (p90) cc_final: 0.7159 (p90) REVERT: A 151 MET cc_start: 0.8450 (tmm) cc_final: 0.7514 (tmm) REVERT: A 365 MET cc_start: 0.9536 (mmt) cc_final: 0.9208 (mmt) REVERT: A 622 MET cc_start: 0.9315 (mtm) cc_final: 0.8962 (tpt) REVERT: A 678 MET cc_start: 0.9697 (tpp) cc_final: 0.9401 (ptp) REVERT: A 717 MET cc_start: 0.9162 (ttt) cc_final: 0.8468 (tpp) REVERT: R 50 MET cc_start: 0.8773 (tpt) cc_final: 0.8211 (ptt) REVERT: C 85 ASN cc_start: 0.8878 (m-40) cc_final: 0.8536 (t0) REVERT: D 326 MET cc_start: 0.9008 (mmp) cc_final: 0.8686 (mmp) REVERT: D 422 MET cc_start: 0.8967 (ppp) cc_final: 0.8646 (ppp) REVERT: D 568 MET cc_start: 0.8737 (mmt) cc_final: 0.8450 (tpt) REVERT: F 294 MET cc_start: 0.8491 (tmm) cc_final: 0.8021 (tmm) REVERT: F 424 TYR cc_start: 0.9075 (m-80) cc_final: 0.8388 (m-80) REVERT: F 438 MET cc_start: 0.9521 (mmp) cc_final: 0.9221 (mmt) REVERT: F 476 MET cc_start: 0.8957 (mmp) cc_final: 0.8430 (mmm) REVERT: F 642 MET cc_start: 0.9071 (mmt) cc_final: 0.8820 (mmp) REVERT: F 678 MET cc_start: 0.8901 (tmm) cc_final: 0.8690 (ptt) REVERT: I 341 ILE cc_start: 0.9225 (pt) cc_final: 0.8944 (tp) REVERT: I 358 MET cc_start: 0.7583 (ppp) cc_final: 0.7059 (ppp) REVERT: I 395 MET cc_start: 0.9344 (ptt) cc_final: 0.9044 (ptt) outliers start: 0 outliers final: 0 residues processed: 167 average time/residue: 0.1436 time to fit residues: 39.9245 Evaluate side-chains 141 residues out of total 2801 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 141 time to evaluate : 0.781 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 313 random chunks: chunk 72 optimal weight: 10.0000 chunk 16 optimal weight: 5.9990 chunk 312 optimal weight: 0.0980 chunk 294 optimal weight: 5.9990 chunk 84 optimal weight: 0.6980 chunk 183 optimal weight: 1.9990 chunk 21 optimal weight: 0.8980 chunk 33 optimal weight: 10.0000 chunk 164 optimal weight: 3.9990 chunk 76 optimal weight: 1.9990 chunk 123 optimal weight: 0.0770 overall best weight: 0.7540 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 241 HIS ** F 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 320 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 432 GLN ** G 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 627 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3802 r_free = 0.3802 target = 0.066550 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3162 r_free = 0.3162 target = 0.044780 restraints weight = 234977.739| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3193 r_free = 0.3193 target = 0.046164 restraints weight = 148128.861| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3190 r_free = 0.3190 target = 0.045820 restraints weight = 96915.067| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3197 r_free = 0.3197 target = 0.046005 restraints weight = 93134.229| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3197 r_free = 0.3197 target = 0.046031 restraints weight = 86405.389| |-----------------------------------------------------------------------------| r_work (final): 0.3074 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3073 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3073 r_free = 0.3073 target_work(ls_wunit_k1) = 0.041 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3073 r_free = 0.3073 target_work(ls_wunit_k1) = 0.041 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3073 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8181 moved from start: 0.2537 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 25639 Z= 0.106 Angle : 0.548 12.106 34650 Z= 0.286 Chirality : 0.039 0.209 3923 Planarity : 0.003 0.045 4448 Dihedral : 4.395 37.609 3429 Min Nonbonded Distance : 1.938 Molprobity Statistics. All-atom Clashscore : 9.58 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.42 % Favored : 96.49 % Rotamer: Outliers : 0.00 % Allowed : 0.26 % Favored : 99.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.17 (0.15), residues: 3135 helix: 1.66 (0.12), residues: 1925 sheet: 0.12 (0.52), residues: 97 loop : -0.71 (0.19), residues: 1113 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG D 379 TYR 0.019 0.001 TYR F 219 PHE 0.023 0.001 PHE D 392 TRP 0.016 0.001 TRP D 209 HIS 0.006 0.001 HIS H 35 Details of bonding type rmsd covalent geometry : bond 0.00219 (25624) covalent geometry : angle 0.54588 (34644) hydrogen bonds : bond 0.03510 ( 1395) hydrogen bonds : angle 4.20143 ( 4146) metal coordination : bond 0.00513 ( 15) metal coordination : angle 3.35591 ( 6) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6270 Ramachandran restraints generated. 3135 Oldfield, 0 Emsley, 3135 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6270 Ramachandran restraints generated. 3135 Oldfield, 0 Emsley, 3135 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 2801 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 169 time to evaluate : 0.888 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 86 MET cc_start: 0.8772 (mmp) cc_final: 0.7986 (mmm) REVERT: A 90 TYR cc_start: 0.7568 (p90) cc_final: 0.7189 (p90) REVERT: A 365 MET cc_start: 0.9500 (mmt) cc_final: 0.9187 (mmt) REVERT: A 622 MET cc_start: 0.9325 (mtm) cc_final: 0.8982 (tpt) REVERT: A 678 MET cc_start: 0.9696 (tpp) cc_final: 0.9385 (ptp) REVERT: A 717 MET cc_start: 0.9121 (ttt) cc_final: 0.8427 (tpp) REVERT: R 50 MET cc_start: 0.8753 (tpt) cc_final: 0.8187 (ptt) REVERT: C 17 MET cc_start: 0.7532 (ttt) cc_final: 0.7290 (ttt) REVERT: C 75 MET cc_start: 0.9251 (ptp) cc_final: 0.9050 (ptp) REVERT: C 85 ASN cc_start: 0.8834 (m-40) cc_final: 0.8509 (t0) REVERT: D 326 MET cc_start: 0.8956 (mmp) cc_final: 0.8668 (mmp) REVERT: D 422 MET cc_start: 0.8913 (ppp) cc_final: 0.8608 (ppp) REVERT: D 568 MET cc_start: 0.8683 (mmt) cc_final: 0.8453 (tpt) REVERT: F 162 MET cc_start: 0.8584 (ttm) cc_final: 0.8373 (ttm) REVERT: F 294 MET cc_start: 0.8487 (tmm) cc_final: 0.8122 (tmm) REVERT: F 365 MET cc_start: 0.9116 (ptp) cc_final: 0.8753 (mpp) REVERT: F 424 TYR cc_start: 0.9007 (m-80) cc_final: 0.8241 (m-10) REVERT: F 438 MET cc_start: 0.9499 (mmp) cc_final: 0.9204 (mmt) REVERT: F 476 MET cc_start: 0.8881 (mmp) cc_final: 0.8362 (mmm) REVERT: F 642 MET cc_start: 0.9055 (mmt) cc_final: 0.8809 (mmp) REVERT: F 678 MET cc_start: 0.8917 (tmm) cc_final: 0.8712 (ptt) outliers start: 0 outliers final: 0 residues processed: 169 average time/residue: 0.1390 time to fit residues: 39.8219 Evaluate side-chains 141 residues out of total 2801 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 141 time to evaluate : 0.932 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 313 random chunks: chunk 230 optimal weight: 0.1980 chunk 312 optimal weight: 0.0670 chunk 232 optimal weight: 0.8980 chunk 40 optimal weight: 20.0000 chunk 50 optimal weight: 9.9990 chunk 277 optimal weight: 20.0000 chunk 17 optimal weight: 5.9990 chunk 84 optimal weight: 7.9990 chunk 164 optimal weight: 5.9990 chunk 31 optimal weight: 6.9990 chunk 252 optimal weight: 9.9990 overall best weight: 2.6322 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 255 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 362 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 241 HIS ** D 570 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 320 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 359 ASN ** G 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 627 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3781 r_free = 0.3781 target = 0.065806 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3099 r_free = 0.3099 target = 0.043726 restraints weight = 276824.182| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3189 r_free = 0.3189 target = 0.045536 restraints weight = 152913.195| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3164 r_free = 0.3164 target = 0.045111 restraints weight = 83616.228| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3173 r_free = 0.3173 target = 0.045271 restraints weight = 84455.710| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3175 r_free = 0.3175 target = 0.045306 restraints weight = 76448.572| |-----------------------------------------------------------------------------| r_work (final): 0.3055 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3055 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3055 r_free = 0.3055 target_work(ls_wunit_k1) = 0.041 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3055 r_free = 0.3055 target_work(ls_wunit_k1) = 0.041 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3055 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8204 moved from start: 0.2621 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.067 25639 Z= 0.151 Angle : 0.561 11.760 34650 Z= 0.296 Chirality : 0.039 0.185 3923 Planarity : 0.003 0.045 4448 Dihedral : 4.387 39.555 3429 Min Nonbonded Distance : 1.930 Molprobity Statistics. All-atom Clashscore : 10.76 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.09 % Favored : 95.82 % Rotamer: Outliers : 0.00 % Allowed : 0.15 % Favored : 99.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.14 (0.15), residues: 3135 helix: 1.63 (0.12), residues: 1936 sheet: 0.04 (0.52), residues: 95 loop : -0.73 (0.19), residues: 1104 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 379 TYR 0.019 0.001 TYR D 440 PHE 0.025 0.001 PHE D 392 TRP 0.012 0.001 TRP D 209 HIS 0.004 0.001 HIS D 241 Details of bonding type rmsd covalent geometry : bond 0.00324 (25624) covalent geometry : angle 0.55962 (34644) hydrogen bonds : bond 0.03608 ( 1395) hydrogen bonds : angle 4.28404 ( 4146) metal coordination : bond 0.00656 ( 15) metal coordination : angle 3.44559 ( 6) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5538.99 seconds wall clock time: 96 minutes 10.50 seconds (5770.50 seconds total)