Starting phenix.real_space_refine on Sat Jun 28 21:04:21 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ij1_35461/06_2025/8ij1_35461.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ij1_35461/06_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8ij1_35461/06_2025/8ij1_35461.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ij1_35461/06_2025/8ij1_35461.map" model { file = "/net/cci-nas-00/data/ceres_data/8ij1_35461/06_2025/8ij1_35461.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ij1_35461/06_2025/8ij1_35461.cif" } resolution = 4.2 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.008 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): 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: {'PHE:plan': 1, 'ARG:plan': 1, 'ASP:plan': 2} 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: {'PHE:plan': 1, 'ARG:plan': 1, 'ASP:plan': 2} 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: {'GLN:plan1': 2, 'ARG:plan': 4, 'ASN:plan1': 5, 'HIS:plan': 1, 'GLU:plan': 1, 'ASP: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: {'PHE:plan': 1, 'ARG:plan': 1, 'ASP:plan': 2} 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: {'PHE:plan': 1, 'ARG:plan': 1, 'ASP:plan': 2} 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: {'GLN:plan1': 3, 'ARG:plan': 5, 'ASN:plan1': 5, 'HIS:plan': 1, 'GLU:plan': 1, 'ASP:plan': 2} 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: 14.99, per 1000 atoms: 0.60 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: 6.11 Conformation dependent library (CDL) restraints added in 3.6 seconds 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: 2.90 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: 9.39 Time building geometry restraints manager: 7.26 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 627 or resid 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: 3.770 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.210 Construct map_model_manager: 0.020 Extract box with map and model: 1.080 Check model and map are aligned: 0.180 Set scattering table: 0.220 Process input model: 62.860 Find NCS groups from input model: 1.110 Set up NCS constraints: 0.130 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:3.350 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 72.940 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.97 (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 TRP 0.017 0.002 TRP D 209 HIS 0.004 0.001 HIS A 68 PHE 0.036 0.001 PHE D 392 TYR 0.031 0.001 TYR A 43 ARG 0.010 0.000 ARG A 686 Details of bonding type rmsd hydrogen bonds : bond 0.18526 ( 1395) hydrogen bonds : angle 6.00791 ( 4146) metal coordination : bond 0.17239 ( 15) metal coordination : angle 14.47639 ( 6) covalent geometry : bond 0.00379 (25624) covalent geometry : angle 0.67898 (34644) *********************** 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 : 2.928 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 86 MET cc_start: 0.9107 (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: 0.9205 (ptp) REVERT: C 85 ASN cc_start: 0.9197 (m-40) cc_final: 0.8565 (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: 0.8212 (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: 0.8549 (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: 0.3844 time to fit residues: 133.0407 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 : 2.933 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 313 random chunks: chunk 264 optimal weight: 30.0000 chunk 237 optimal weight: 1.9990 chunk 131 optimal weight: 6.9990 chunk 81 optimal weight: 10.0000 chunk 160 optimal weight: 1.9990 chunk 126 optimal weight: 2.9990 chunk 245 optimal weight: 2.9990 chunk 94 optimal weight: 4.9990 chunk 149 optimal weight: 9.9990 chunk 182 optimal weight: 0.7980 chunk 284 optimal weight: 30.0000 overall best weight: 2.1588 ------------------------------------------------------------------------------- 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 199 HIS D 468 ASN D 592 GLN F 274 HIS ** F 681 GLN ** 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** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3807 r_free = 0.3807 target = 0.066815 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3138 r_free = 0.3138 target = 0.045060 restraints weight = 237366.958| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3199 r_free = 0.3199 target = 0.046190 restraints weight = 141343.591| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3209 r_free = 0.3209 target = 0.046725 restraints weight = 88517.209| |-----------------------------------------------------------------------------| r_work (final): 0.3109 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3110 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3110 r_free = 0.3110 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 = 0.3110 r_free = 0.3110 target_work(ls_wunit_k1) = 0.043 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3110 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8124 moved from start: 0.1052 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 25639 Z= 0.153 Angle : 0.572 19.333 34650 Z= 0.309 Chirality : 0.039 0.176 3923 Planarity : 0.004 0.043 4448 Dihedral : 4.498 42.623 3429 Min Nonbonded Distance : 2.109 Molprobity Statistics. All-atom Clashscore : 10.56 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.13 % Favored : 96.81 % Rotamer: Outliers : 0.04 % Allowed : 3.08 % Favored : 96.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.06 (0.15), residues: 3135 helix: 1.53 (0.12), residues: 1925 sheet: 0.24 (0.52), residues: 99 loop : -0.68 (0.19), residues: 1111 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP D 209 HIS 0.005 0.001 HIS D 565 PHE 0.018 0.001 PHE D 392 TYR 0.029 0.001 TYR D 472 ARG 0.009 0.000 ARG A 686 Details of bonding type rmsd hydrogen bonds : bond 0.04846 ( 1395) hydrogen bonds : angle 4.72838 ( 4146) metal coordination : bond 0.02071 ( 15) metal coordination : angle 8.80141 ( 6) covalent geometry : bond 0.00304 (25624) covalent geometry : angle 0.56054 (34644) *********************** 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 185 residues out of total 2801 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 184 time to evaluate : 3.174 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 86 MET cc_start: 0.8915 (mmp) cc_final: 0.8165 (mmm) REVERT: A 90 TYR cc_start: 0.7570 (p90) cc_final: 0.7050 (p90) REVERT: A 151 MET cc_start: 0.8493 (tmm) cc_final: 0.7665 (tmm) REVERT: A 365 MET cc_start: 0.9417 (mmt) cc_final: 0.9080 (mmt) REVERT: A 576 MET cc_start: 0.9198 (mmp) cc_final: 0.8985 (mmm) REVERT: A 582 MET cc_start: 0.8379 (mtm) cc_final: 0.7938 (mpp) REVERT: A 622 MET cc_start: 0.9308 (mtm) cc_final: 0.9095 (mtm) REVERT: A 642 MET cc_start: 0.9285 (mpp) cc_final: 0.9082 (tpt) REVERT: A 717 MET cc_start: 0.8930 (ttt) cc_final: 0.8153 (tpp) REVERT: R 50 MET cc_start: 0.8715 (tpt) cc_final: 0.8202 (ptt) REVERT: C 17 MET cc_start: 0.7391 (ttt) cc_final: 0.7050 (ttt) REVERT: C 85 ASN cc_start: 0.8664 (m-40) cc_final: 0.8328 (t0) REVERT: D 199 HIS cc_start: 0.8637 (m90) cc_final: 0.8432 (m-70) REVERT: D 422 MET cc_start: 0.8930 (ppp) cc_final: 0.8603 (ppp) REVERT: F 101 MET cc_start: 0.9267 (tmm) cc_final: 0.9039 (tmm) REVERT: F 162 MET cc_start: 0.8711 (ttm) cc_final: 0.8414 (ttm) REVERT: F 294 MET cc_start: 0.8384 (ppp) cc_final: 0.7948 (tmm) REVERT: F 424 TYR cc_start: 0.9135 (m-80) cc_final: 0.8422 (m-80) REVERT: F 476 MET cc_start: 0.9051 (mmp) cc_final: 0.8769 (mmm) REVERT: I 358 MET cc_start: 0.7380 (ppp) cc_final: 0.6162 (ppp) REVERT: I 360 PHE cc_start: 0.8894 (m-10) cc_final: 0.8483 (m-10) outliers start: 1 outliers final: 0 residues processed: 185 average time/residue: 0.3299 time to fit residues: 102.6014 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 : 2.765 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 313 random chunks: chunk 221 optimal weight: 20.0000 chunk 65 optimal weight: 0.5980 chunk 158 optimal weight: 6.9990 chunk 196 optimal weight: 0.9980 chunk 287 optimal weight: 0.5980 chunk 51 optimal weight: 3.9990 chunk 209 optimal weight: 10.0000 chunk 27 optimal weight: 20.0000 chunk 32 optimal weight: 0.8980 chunk 146 optimal weight: 0.7980 chunk 31 optimal weight: 1.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 41 ASN ** D 565 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 627 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 320 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 347 HIS ** F 681 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.3824 r_free = 0.3824 target = 0.067452 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3177 r_free = 0.3177 target = 0.046003 restraints weight = 218978.335| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3239 r_free = 0.3239 target = 0.047074 restraints weight = 133549.148| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3251 r_free = 0.3251 target = 0.047776 restraints weight = 83430.341| |-----------------------------------------------------------------------------| r_work (final): 0.3153 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3155 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3155 r_free = 0.3155 target_work(ls_wunit_k1) = 0.044 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3155 r_free = 0.3155 target_work(ls_wunit_k1) = 0.044 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3155 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8069 moved from start: 0.1352 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= 0.115 Angle : 0.525 13.366 34650 Z= 0.280 Chirality : 0.039 0.200 3923 Planarity : 0.003 0.044 4448 Dihedral : 4.377 39.389 3429 Min Nonbonded Distance : 2.175 Molprobity Statistics. All-atom Clashscore : 9.34 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.29 % Favored : 96.65 % Rotamer: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.14 (0.15), residues: 3135 helix: 1.60 (0.12), residues: 1919 sheet: 0.34 (0.51), residues: 99 loop : -0.65 (0.19), residues: 1117 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP D 209 HIS 0.006 0.001 HIS D 218 PHE 0.036 0.001 PHE I 260 TYR 0.023 0.001 TYR A 105 ARG 0.008 0.000 ARG D 379 Details of bonding type rmsd hydrogen bonds : bond 0.04307 ( 1395) hydrogen bonds : angle 4.49748 ( 4146) metal coordination : bond 0.01166 ( 15) metal coordination : angle 6.07321 ( 6) covalent geometry : bond 0.00232 (25624) covalent geometry : angle 0.51912 (34644) *********************** 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 185 residues out of total 2801 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 185 time to evaluate : 2.805 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: 0.8791 (mmp) cc_final: 0.8041 (mmm) REVERT: A 90 TYR cc_start: 0.7501 (p90) cc_final: 0.6961 (p90) REVERT: A 151 MET cc_start: 0.8627 (tmm) cc_final: 0.7611 (tmm) REVERT: A 365 MET cc_start: 0.9416 (mmt) cc_final: 0.9094 (mmt) REVERT: A 622 MET cc_start: 0.9261 (mtm) cc_final: 0.9051 (mtm) REVERT: A 717 MET cc_start: 0.8939 (ttt) cc_final: 0.8178 (tpp) REVERT: R 50 MET cc_start: 0.8732 (tpt) cc_final: 0.8157 (ptt) REVERT: C 17 MET cc_start: 0.7507 (ttt) cc_final: 0.7226 (ttt) REVERT: C 85 ASN cc_start: 0.8591 (m-40) cc_final: 0.8336 (t0) REVERT: D 422 MET cc_start: 0.8875 (ppp) cc_final: 0.8582 (ppp) REVERT: F 101 MET cc_start: 0.9359 (tmm) cc_final: 0.9114 (tmm) REVERT: F 162 MET cc_start: 0.8240 (ttm) cc_final: 0.7906 (ttm) REVERT: F 424 TYR cc_start: 0.9073 (m-80) cc_final: 0.8361 (m-80) REVERT: F 476 MET cc_start: 0.9002 (mmp) cc_final: 0.8740 (mmm) REVERT: I 241 HIS cc_start: 0.7960 (m90) cc_final: 0.7451 (p-80) REVERT: I 358 MET cc_start: 0.6787 (ppp) cc_final: 0.6490 (ppp) REVERT: I 360 PHE cc_start: 0.8755 (m-10) cc_final: 0.8334 (m-10) outliers start: 0 outliers final: 0 residues processed: 185 average time/residue: 0.3090 time to fit residues: 96.7044 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 : 2.648 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 313 random chunks: chunk 130 optimal weight: 8.9990 chunk 56 optimal weight: 0.0980 chunk 139 optimal weight: 5.9990 chunk 35 optimal weight: 5.9990 chunk 141 optimal weight: 3.9990 chunk 216 optimal weight: 20.0000 chunk 283 optimal weight: 8.9990 chunk 226 optimal weight: 10.0000 chunk 0 optimal weight: 10.0000 chunk 251 optimal weight: 0.6980 chunk 264 optimal weight: 30.0000 overall best weight: 3.3586 ------------------------------------------------------------------------------- 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 143 ASN D 502 HIS ** D 570 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 68 HIS ** F 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 320 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 377 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 681 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 439 ASN ** 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 = 0.3782 r_free = 0.3782 target = 0.066054 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3104 r_free = 0.3104 target = 0.043869 restraints weight = 237549.088| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3159 r_free = 0.3159 target = 0.045370 restraints weight = 146248.718| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3158 r_free = 0.3158 target = 0.045209 restraints weight = 83255.193| |-----------------------------------------------------------------------------| r_work (final): 0.3045 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3045 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3045 r_free = 0.3045 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 = 0.3045 r_free = 0.3045 target_work(ls_wunit_k1) = 0.041 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3045 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8186 moved from start: 0.1672 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 25639 Z= 0.181 Angle : 0.571 10.632 34650 Z= 0.305 Chirality : 0.039 0.175 3923 Planarity : 0.004 0.064 4448 Dihedral : 4.455 41.896 3429 Min Nonbonded Distance : 1.936 Molprobity Statistics. All-atom Clashscore : 11.28 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.58 % Favored : 96.36 % Rotamer: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.08 (0.15), residues: 3135 helix: 1.56 (0.12), residues: 1921 sheet: 0.02 (0.50), residues: 99 loop : -0.67 (0.19), residues: 1115 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP D 209 HIS 0.009 0.001 HIS C 68 PHE 0.040 0.002 PHE G 4 TYR 0.019 0.001 TYR D 440 ARG 0.010 0.000 ARG H 82 Details of bonding type rmsd hydrogen bonds : bond 0.04216 ( 1395) hydrogen bonds : angle 4.52249 ( 4146) metal coordination : bond 0.00978 ( 15) metal coordination : angle 5.00686 ( 6) covalent geometry : bond 0.00381 (25624) covalent geometry : angle 0.56740 (34644) *********************** 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 181 residues out of total 2801 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 181 time to evaluate : 2.875 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 86 MET cc_start: 0.8863 (mmp) cc_final: 0.8048 (mmm) REVERT: A 90 TYR cc_start: 0.7606 (p90) cc_final: 0.7058 (p90) REVERT: A 151 MET cc_start: 0.8101 (tmm) cc_final: 0.7538 (tmm) REVERT: A 365 MET cc_start: 0.9456 (mmt) cc_final: 0.9135 (mmt) REVERT: A 476 MET cc_start: 0.9415 (mmp) cc_final: 0.9128 (mmt) REVERT: A 582 MET cc_start: 0.8412 (mtm) cc_final: 0.7975 (mpp) REVERT: A 717 MET cc_start: 0.9048 (ttt) cc_final: 0.8275 (tpp) REVERT: R 50 MET cc_start: 0.8729 (tpt) cc_final: 0.8179 (ptt) REVERT: C 17 MET cc_start: 0.7397 (ttt) cc_final: 0.7197 (ttt) REVERT: C 85 ASN cc_start: 0.8784 (m-40) cc_final: 0.8440 (t0) REVERT: D 159 MET cc_start: 0.8277 (mpp) cc_final: 0.8070 (mpp) REVERT: D 199 HIS cc_start: 0.8625 (m-70) cc_final: 0.8404 (m-70) REVERT: D 326 MET cc_start: 0.8883 (mmp) cc_final: 0.8680 (mmp) REVERT: D 422 MET cc_start: 0.9028 (ppp) cc_final: 0.8778 (ppp) REVERT: F 101 MET cc_start: 0.9389 (tmm) cc_final: 0.9116 (tmm) REVERT: F 162 MET cc_start: 0.8551 (ttm) cc_final: 0.8265 (ttm) REVERT: F 294 MET cc_start: 0.8354 (tmm) cc_final: 0.8004 (tmm) REVERT: F 424 TYR cc_start: 0.9097 (m-80) cc_final: 0.8465 (m-80) REVERT: F 476 MET cc_start: 0.8943 (mmp) cc_final: 0.8614 (mmm) REVERT: F 566 MET cc_start: -0.2781 (tpp) cc_final: -0.3119 (tmm) REVERT: F 605 MET cc_start: -0.1272 (ttt) cc_final: -0.1679 (ttt) REVERT: F 642 MET cc_start: 0.9066 (mmt) cc_final: 0.8778 (mmp) REVERT: I 241 HIS cc_start: 0.8020 (m90) cc_final: 0.7436 (p-80) REVERT: I 371 LEU cc_start: 0.9639 (tp) cc_final: 0.9417 (mt) REVERT: I 388 PHE cc_start: 0.8548 (m-10) cc_final: 0.8137 (m-80) outliers start: 0 outliers final: 0 residues processed: 181 average time/residue: 0.3318 time to fit residues: 100.5750 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 : 2.832 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 313 random chunks: chunk 270 optimal weight: 40.0000 chunk 120 optimal weight: 0.6980 chunk 190 optimal weight: 2.9990 chunk 40 optimal weight: 20.0000 chunk 298 optimal weight: 8.9990 chunk 273 optimal weight: 20.0000 chunk 309 optimal weight: 0.9990 chunk 91 optimal weight: 1.9990 chunk 119 optimal weight: 0.9990 chunk 64 optimal weight: 6.9990 chunk 180 optimal weight: 3.9990 overall best weight: 1.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 156 GLN ** F 320 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 377 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 681 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 51 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: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3802 r_free = 0.3802 target = 0.066752 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3147 r_free = 0.3147 target = 0.044859 restraints weight = 233315.229| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3195 r_free = 0.3195 target = 0.046162 restraints weight = 147844.706| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3189 r_free = 0.3189 target = 0.045942 restraints weight = 88549.646| |-----------------------------------------------------------------------------| r_work (final): 0.3069 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3069 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3069 r_free = 0.3069 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 = 0.3069 r_free = 0.3069 target_work(ls_wunit_k1) = 0.041 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3069 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8168 moved from start: 0.1830 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 25639 Z= 0.115 Angle : 0.515 7.660 34650 Z= 0.276 Chirality : 0.038 0.214 3923 Planarity : 0.003 0.044 4448 Dihedral : 4.371 40.374 3429 Min Nonbonded Distance : 1.960 Molprobity Statistics. All-atom Clashscore : 9.96 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.48 % Favored : 96.42 % Rotamer: Outliers : 0.04 % Allowed : 1.94 % Favored : 98.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.18 (0.15), residues: 3135 helix: 1.65 (0.12), residues: 1919 sheet: 0.15 (0.51), residues: 99 loop : -0.66 (0.19), residues: 1117 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP D 209 HIS 0.008 0.001 HIS H 35 PHE 0.033 0.001 PHE D 388 TYR 0.021 0.001 TYR D 440 ARG 0.009 0.000 ARG H 82 Details of bonding type rmsd hydrogen bonds : bond 0.03773 ( 1395) hydrogen bonds : angle 4.33641 ( 4146) metal coordination : bond 0.00722 ( 15) metal coordination : angle 4.54887 ( 6) covalent geometry : bond 0.00240 (25624) covalent geometry : angle 0.51181 (34644) *********************** 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 180 residues out of total 2801 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 179 time to evaluate : 2.705 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 86 MET cc_start: 0.8820 (mmp) cc_final: 0.7983 (mmm) REVERT: A 90 TYR cc_start: 0.7612 (p90) cc_final: 0.7116 (p90) REVERT: A 365 MET cc_start: 0.9465 (mmt) cc_final: 0.9178 (mmt) REVERT: A 449 MET cc_start: 0.7133 (mmp) cc_final: 0.6897 (mmt) REVERT: A 582 MET cc_start: 0.8598 (mtm) cc_final: 0.8131 (mpp) REVERT: A 717 MET cc_start: 0.9052 (ttt) cc_final: 0.8306 (tpp) REVERT: R 50 MET cc_start: 0.8703 (tpt) cc_final: 0.8105 (ptt) REVERT: C 17 MET cc_start: 0.7531 (ttt) cc_final: 0.7264 (ttt) REVERT: C 85 ASN cc_start: 0.8825 (m-40) cc_final: 0.8467 (t0) REVERT: D 159 MET cc_start: 0.8339 (mpp) cc_final: 0.8102 (mpp) REVERT: D 326 MET cc_start: 0.8868 (mmp) cc_final: 0.8668 (mmp) REVERT: D 422 MET cc_start: 0.9015 (ppp) cc_final: 0.8772 (ppp) REVERT: F 101 MET cc_start: 0.9354 (tmm) cc_final: 0.9045 (tmm) REVERT: F 156 GLN cc_start: 0.9240 (OUTLIER) cc_final: 0.8309 (tm-30) REVERT: F 162 MET cc_start: 0.8484 (ttm) cc_final: 0.8230 (ttm) REVERT: F 294 MET cc_start: 0.8412 (tmm) cc_final: 0.7982 (tmm) REVERT: F 424 TYR cc_start: 0.9026 (m-80) cc_final: 0.8300 (m-10) REVERT: F 476 MET cc_start: 0.8926 (mmp) cc_final: 0.8499 (mmm) REVERT: F 605 MET cc_start: -0.1367 (ttt) cc_final: -0.1715 (ttt) REVERT: F 642 MET cc_start: 0.9054 (mmt) cc_final: 0.8741 (mmp) REVERT: I 241 HIS cc_start: 0.8055 (m90) cc_final: 0.7485 (p-80) REVERT: I 371 LEU cc_start: 0.9640 (tp) cc_final: 0.9401 (mt) REVERT: I 388 PHE cc_start: 0.8468 (m-10) cc_final: 0.8028 (m-80) outliers start: 1 outliers final: 0 residues processed: 180 average time/residue: 0.3343 time to fit residues: 100.3503 Evaluate side-chains 149 residues out of total 2801 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 148 time to evaluate : 2.890 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 313 random chunks: chunk 61 optimal weight: 4.9990 chunk 204 optimal weight: 10.0000 chunk 101 optimal weight: 30.0000 chunk 222 optimal weight: 40.0000 chunk 149 optimal weight: 5.9990 chunk 173 optimal weight: 8.9990 chunk 207 optimal weight: 0.0870 chunk 190 optimal weight: 2.9990 chunk 244 optimal weight: 0.7980 chunk 162 optimal weight: 1.9990 chunk 140 optimal weight: 0.9980 overall best weight: 1.3762 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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** ** 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 = 0.3805 r_free = 0.3805 target = 0.066867 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3147 r_free = 0.3147 target = 0.044823 restraints weight = 276059.054| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3193 r_free = 0.3193 target = 0.046088 restraints weight = 164873.399| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3195 r_free = 0.3195 target = 0.046180 restraints weight = 96736.560| |-----------------------------------------------------------------------------| r_work (final): 0.3079 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3080 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3080 r_free = 0.3080 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 = 0.3080 r_free = 0.3080 target_work(ls_wunit_k1) = 0.042 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3080 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8154 moved from start: 0.1988 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= 0.110 Angle : 0.513 8.111 34650 Z= 0.272 Chirality : 0.038 0.198 3923 Planarity : 0.003 0.044 4448 Dihedral : 4.306 38.506 3429 Min Nonbonded Distance : 1.944 Molprobity Statistics. All-atom Clashscore : 9.72 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.48 % Favored : 96.46 % Rotamer: Outliers : 0.00 % Allowed : 1.06 % Favored : 98.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.24 (0.15), residues: 3135 helix: 1.69 (0.12), residues: 1928 sheet: 0.21 (0.51), residues: 99 loop : -0.64 (0.19), residues: 1108 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP D 209 HIS 0.008 0.001 HIS C 68 PHE 0.021 0.001 PHE D 388 TYR 0.018 0.001 TYR D 440 ARG 0.005 0.000 ARG D 379 Details of bonding type rmsd hydrogen bonds : bond 0.03614 ( 1395) hydrogen bonds : angle 4.24608 ( 4146) metal coordination : bond 0.00628 ( 15) metal coordination : angle 4.67356 ( 6) covalent geometry : bond 0.00231 (25624) covalent geometry : angle 0.50891 (34644) *********************** 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 182 residues out of total 2801 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 182 time to evaluate : 3.125 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: 0.8783 (mmp) cc_final: 0.7971 (mmm) REVERT: A 90 TYR cc_start: 0.7554 (p90) cc_final: 0.7064 (p90) REVERT: A 151 MET cc_start: 0.8471 (tmm) cc_final: 0.7208 (tmm) REVERT: A 365 MET cc_start: 0.9446 (mmt) cc_final: 0.9173 (mmt) REVERT: A 717 MET cc_start: 0.9051 (ttt) cc_final: 0.8306 (tpp) REVERT: R 50 MET cc_start: 0.8724 (tpt) cc_final: 0.8171 (ptt) REVERT: C 85 ASN cc_start: 0.8856 (m-40) cc_final: 0.8494 (t0) REVERT: D 422 MET cc_start: 0.9008 (ppp) cc_final: 0.8792 (ppp) REVERT: D 502 HIS cc_start: 0.8200 (m-70) cc_final: 0.7999 (m90) REVERT: F 101 MET cc_start: 0.9349 (tmm) cc_final: 0.9055 (tmm) REVERT: F 162 MET cc_start: 0.8455 (ttm) cc_final: 0.8230 (ttm) REVERT: F 294 MET cc_start: 0.8459 (tmm) cc_final: 0.8000 (tmm) REVERT: F 424 TYR cc_start: 0.8970 (m-80) cc_final: 0.8291 (m-10) REVERT: F 476 MET cc_start: 0.8926 (mmp) cc_final: 0.8495 (mmm) REVERT: F 566 MET cc_start: -0.2992 (tpp) cc_final: -0.3320 (tmm) REVERT: F 642 MET cc_start: 0.9006 (mmt) cc_final: 0.8699 (mmp) REVERT: I 241 HIS cc_start: 0.8028 (m90) cc_final: 0.7436 (p-80) REVERT: I 358 MET cc_start: 0.7334 (ppp) cc_final: 0.6798 (ppp) REVERT: I 371 LEU cc_start: 0.9642 (tp) cc_final: 0.9414 (mt) REVERT: I 388 PHE cc_start: 0.8351 (m-10) cc_final: 0.8032 (m-80) outliers start: 0 outliers final: 0 residues processed: 182 average time/residue: 0.3441 time to fit residues: 105.0792 Evaluate side-chains 152 residues out of total 2801 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 152 time to evaluate : 3.176 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 313 random chunks: chunk 102 optimal weight: 4.9990 chunk 245 optimal weight: 0.0870 chunk 56 optimal weight: 9.9990 chunk 164 optimal weight: 0.8980 chunk 191 optimal weight: 0.0470 chunk 251 optimal weight: 30.0000 chunk 31 optimal weight: 0.5980 chunk 180 optimal weight: 0.0030 chunk 296 optimal weight: 7.9990 chunk 231 optimal weight: 0.8980 chunk 267 optimal weight: 30.0000 overall best weight: 0.3266 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 565 HIS ** 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 = 0.3829 r_free = 0.3829 target = 0.067528 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3192 r_free = 0.3192 target = 0.046171 restraints weight = 222381.976| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3245 r_free = 0.3245 target = 0.047007 restraints weight = 141972.419| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3268 r_free = 0.3268 target = 0.048145 restraints weight = 90215.489| |-----------------------------------------------------------------------------| r_work (final): 0.3180 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3180 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3180 r_free = 0.3180 target_work(ls_wunit_k1) = 0.044 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3180 r_free = 0.3180 target_work(ls_wunit_k1) = 0.044 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3180 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8050 moved from start: 0.2166 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 25639 Z= 0.099 Angle : 0.507 7.350 34650 Z= 0.266 Chirality : 0.038 0.219 3923 Planarity : 0.003 0.044 4448 Dihedral : 4.200 33.706 3429 Min Nonbonded Distance : 1.968 Molprobity Statistics. All-atom Clashscore : 8.40 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.19 % Favored : 96.74 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.26 (0.15), residues: 3135 helix: 1.70 (0.12), residues: 1929 sheet: 0.11 (0.51), residues: 105 loop : -0.62 (0.19), residues: 1101 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP D 209 HIS 0.005 0.001 HIS H 35 PHE 0.031 0.001 PHE D 388 TYR 0.015 0.001 TYR F 394 ARG 0.006 0.000 ARG F 686 Details of bonding type rmsd hydrogen bonds : bond 0.03373 ( 1395) hydrogen bonds : angle 4.11351 ( 4146) metal coordination : bond 0.00505 ( 15) metal coordination : angle 3.73371 ( 6) covalent geometry : bond 0.00200 (25624) covalent geometry : angle 0.50478 (34644) *********************** 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 184 residues out of total 2801 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 184 time to evaluate : 4.102 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 86 MET cc_start: 0.8686 (mmp) cc_final: 0.8093 (mmm) REVERT: A 90 TYR cc_start: 0.7519 (p90) cc_final: 0.7221 (p90) REVERT: A 365 MET cc_start: 0.9454 (mmt) cc_final: 0.9189 (mmt) REVERT: A 576 MET cc_start: 0.9111 (mmp) cc_final: 0.8910 (mmm) REVERT: A 717 MET cc_start: 0.8979 (ttt) cc_final: 0.8225 (tpp) REVERT: R 50 MET cc_start: 0.8742 (tpt) cc_final: 0.8206 (ptt) REVERT: C 85 ASN cc_start: 0.8617 (m-40) cc_final: 0.8397 (t0) REVERT: D 326 MET cc_start: 0.8817 (mmp) cc_final: 0.8567 (mmp) REVERT: F 101 MET cc_start: 0.9334 (tmm) cc_final: 0.8921 (tmm) REVERT: F 162 MET cc_start: 0.8457 (ttm) cc_final: 0.8143 (ttm) REVERT: F 294 MET cc_start: 0.8443 (tmm) cc_final: 0.8130 (tmm) REVERT: F 424 TYR cc_start: 0.8937 (m-80) cc_final: 0.8199 (m-80) REVERT: F 476 MET cc_start: 0.8867 (mmp) cc_final: 0.8495 (mmm) REVERT: F 566 MET cc_start: -0.3385 (tpp) cc_final: -0.3702 (tmm) REVERT: F 605 MET cc_start: -0.1631 (ttt) cc_final: -0.1840 (ttt) REVERT: F 642 MET cc_start: 0.9011 (mmt) cc_final: 0.8721 (mmp) REVERT: F 678 MET cc_start: 0.8855 (tmm) cc_final: 0.8647 (ptt) REVERT: I 241 HIS cc_start: 0.8022 (m90) cc_final: 0.7472 (p-80) REVERT: I 371 LEU cc_start: 0.9622 (tp) cc_final: 0.9376 (mt) REVERT: I 388 PHE cc_start: 0.8467 (m-10) cc_final: 0.8114 (m-80) outliers start: 0 outliers final: 0 residues processed: 184 average time/residue: 0.4273 time to fit residues: 134.8945 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 : 2.761 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 313 random chunks: chunk 142 optimal weight: 0.9990 chunk 272 optimal weight: 20.0000 chunk 161 optimal weight: 10.0000 chunk 164 optimal weight: 0.8980 chunk 36 optimal weight: 8.9990 chunk 267 optimal weight: 30.0000 chunk 237 optimal weight: 4.9990 chunk 248 optimal weight: 2.9990 chunk 89 optimal weight: 20.0000 chunk 112 optimal weight: 6.9990 chunk 297 optimal weight: 3.9990 overall best weight: 2.7788 ------------------------------------------------------------------------------- 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 502 HIS ** D 570 ASN ** 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 110 HIS ** 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 = 0.3788 r_free = 0.3788 target = 0.066200 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3119 r_free = 0.3119 target = 0.044394 restraints weight = 236579.634| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3202 r_free = 0.3202 target = 0.045757 restraints weight = 148540.055| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3184 r_free = 0.3184 target = 0.045704 restraints weight = 90102.537| |-----------------------------------------------------------------------------| r_work (final): 0.3081 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3082 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3082 r_free = 0.3082 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 = 0.3082 r_free = 0.3082 target_work(ls_wunit_k1) = 0.042 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3082 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8164 moved from start: 0.2287 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 25639 Z= 0.159 Angle : 0.554 7.942 34650 Z= 0.294 Chirality : 0.039 0.195 3923 Planarity : 0.004 0.045 4448 Dihedral : 4.334 35.974 3429 Min Nonbonded Distance : 1.923 Molprobity Statistics. All-atom Clashscore : 10.44 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.70 % Favored : 96.23 % Rotamer: Outliers : 0.00 % Allowed : 0.84 % Favored : 99.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.23 (0.15), residues: 3135 helix: 1.68 (0.12), residues: 1930 sheet: 0.23 (0.51), residues: 99 loop : -0.64 (0.19), residues: 1106 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 14 HIS 0.007 0.001 HIS I 565 PHE 0.029 0.002 PHE D 392 TYR 0.019 0.001 TYR D 440 ARG 0.008 0.000 ARG D 379 Details of bonding type rmsd hydrogen bonds : bond 0.03705 ( 1395) hydrogen bonds : angle 4.27008 ( 4146) metal coordination : bond 0.00834 ( 15) metal coordination : angle 3.48633 ( 6) covalent geometry : bond 0.00339 (25624) covalent geometry : angle 0.55172 (34644) *********************** 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 173 residues out of total 2801 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 173 time to evaluate : 2.775 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 86 MET cc_start: 0.8757 (mmp) cc_final: 0.7897 (mmm) REVERT: A 90 TYR cc_start: 0.7681 (p90) cc_final: 0.7242 (p90) REVERT: A 151 MET cc_start: 0.8445 (tmm) cc_final: 0.7620 (tmm) REVERT: A 365 MET cc_start: 0.9489 (mmt) cc_final: 0.9206 (mmt) REVERT: A 642 MET cc_start: 0.8920 (mmp) cc_final: 0.8140 (pmm) REVERT: A 717 MET cc_start: 0.9071 (ttt) cc_final: 0.8329 (tpp) REVERT: R 50 MET cc_start: 0.8756 (tpt) cc_final: 0.8243 (ptt) REVERT: C 17 MET cc_start: 0.7686 (ttt) cc_final: 0.7470 (ttt) REVERT: D 220 MET cc_start: 0.7643 (ppp) cc_final: 0.7191 (ppp) REVERT: D 326 MET cc_start: 0.8971 (mmp) cc_final: 0.8713 (mmp) REVERT: D 422 MET cc_start: 0.8856 (ppp) cc_final: 0.8542 (ppp) REVERT: F 101 MET cc_start: 0.9406 (tmm) cc_final: 0.9020 (tmm) REVERT: F 162 MET cc_start: 0.8583 (ttm) cc_final: 0.8333 (ttm) REVERT: F 294 MET cc_start: 0.8513 (tmm) cc_final: 0.8054 (tmm) REVERT: F 424 TYR cc_start: 0.8955 (m-80) cc_final: 0.8193 (m-10) REVERT: F 438 MET cc_start: 0.9515 (mmp) cc_final: 0.9226 (mmt) REVERT: F 476 MET cc_start: 0.8847 (mmp) cc_final: 0.8351 (mmm) REVERT: F 605 MET cc_start: -0.1408 (ttt) cc_final: -0.1610 (ttt) REVERT: F 642 MET cc_start: 0.9039 (mmt) cc_final: 0.8791 (mmp) REVERT: F 678 MET cc_start: 0.8854 (tmm) cc_final: 0.8630 (ptt) REVERT: I 341 ILE cc_start: 0.9275 (pt) cc_final: 0.8986 (tp) REVERT: I 358 MET cc_start: 0.7384 (ppp) cc_final: 0.6801 (ppp) REVERT: I 371 LEU cc_start: 0.9647 (tp) cc_final: 0.9405 (mt) REVERT: I 388 PHE cc_start: 0.8356 (m-10) cc_final: 0.8036 (m-80) outliers start: 0 outliers final: 0 residues processed: 173 average time/residue: 0.3197 time to fit residues: 93.2873 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 : 2.728 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 313 random chunks: chunk 206 optimal weight: 20.0000 chunk 175 optimal weight: 0.9990 chunk 292 optimal weight: 0.9980 chunk 139 optimal weight: 1.9990 chunk 124 optimal weight: 4.9990 chunk 55 optimal weight: 20.0000 chunk 174 optimal weight: 6.9990 chunk 12 optimal weight: 9.9990 chunk 284 optimal weight: 7.9990 chunk 155 optimal weight: 10.0000 chunk 192 optimal weight: 7.9990 overall best weight: 3.1988 ------------------------------------------------------------------------------- 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 570 ASN ** 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 110 HIS ** 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 = 0.3780 r_free = 0.3780 target = 0.065869 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3138 r_free = 0.3138 target = 0.045068 restraints weight = 279433.485| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3177 r_free = 0.3177 target = 0.045514 restraints weight = 147925.698| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3152 r_free = 0.3152 target = 0.045161 restraints weight = 109428.267| |-----------------------------------------------------------------------------| r_work (final): 0.3033 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3033 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3033 r_free = 0.3033 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 = 0.3033 r_free = 0.3033 target_work(ls_wunit_k1) = 0.040 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3033 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8205 moved from start: 0.2406 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 25639 Z= 0.171 Angle : 0.575 9.997 34650 Z= 0.303 Chirality : 0.039 0.208 3923 Planarity : 0.004 0.045 4448 Dihedral : 4.437 33.662 3429 Min Nonbonded Distance : 1.906 Molprobity Statistics. All-atom Clashscore : 11.24 Ramachandran Plot: Outliers : 0.13 % Allowed : 3.90 % Favored : 95.98 % Rotamer: Outliers : 0.00 % Allowed : 0.48 % Favored : 99.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.14 (0.15), residues: 3135 helix: 1.60 (0.12), residues: 1931 sheet: 0.32 (0.53), residues: 89 loop : -0.67 (0.19), residues: 1115 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 147 HIS 0.008 0.001 HIS D 199 PHE 0.032 0.001 PHE D 392 TYR 0.025 0.001 TYR D 440 ARG 0.009 0.000 ARG D 379 Details of bonding type rmsd hydrogen bonds : bond 0.03752 ( 1395) hydrogen bonds : angle 4.35619 ( 4146) metal coordination : bond 0.00662 ( 15) metal coordination : angle 3.27856 ( 6) covalent geometry : bond 0.00364 (25624) covalent geometry : angle 0.57339 (34644) *********************** 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 170 residues out of total 2801 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 170 time to evaluate : 2.823 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 86 MET cc_start: 0.8878 (mmp) cc_final: 0.8054 (mmm) REVERT: A 90 TYR cc_start: 0.7768 (p90) cc_final: 0.7437 (p90) REVERT: A 137 MET cc_start: 0.8098 (ppp) cc_final: 0.7715 (ppp) REVERT: A 365 MET cc_start: 0.9544 (mmt) cc_final: 0.9227 (mmt) REVERT: A 642 MET cc_start: 0.9027 (mmp) cc_final: 0.8276 (pmm) REVERT: A 717 MET cc_start: 0.9103 (ttt) cc_final: 0.8401 (tpp) REVERT: R 50 MET cc_start: 0.8764 (tpt) cc_final: 0.8244 (ptt) REVERT: C 17 MET cc_start: 0.7707 (ttt) cc_final: 0.7491 (ttt) REVERT: D 326 MET cc_start: 0.9119 (mmp) cc_final: 0.8842 (mmp) REVERT: D 422 MET cc_start: 0.9045 (ppp) cc_final: 0.8698 (ppp) REVERT: D 502 HIS cc_start: 0.8405 (m-70) cc_final: 0.8136 (m90) REVERT: F 101 MET cc_start: 0.9224 (tmm) cc_final: 0.8739 (tmm) REVERT: F 162 MET cc_start: 0.8632 (ttm) cc_final: 0.8350 (ttm) REVERT: F 294 MET cc_start: 0.8547 (tmm) cc_final: 0.8084 (tmm) REVERT: F 424 TYR cc_start: 0.8992 (m-80) cc_final: 0.8240 (m-10) REVERT: F 438 MET cc_start: 0.9494 (mmp) cc_final: 0.9209 (mmt) REVERT: F 476 MET cc_start: 0.8906 (mmp) cc_final: 0.8372 (mmm) REVERT: F 605 MET cc_start: -0.1456 (ttt) cc_final: -0.1874 (ttt) REVERT: F 642 MET cc_start: 0.9027 (mmt) cc_final: 0.8763 (mmp) REVERT: I 341 ILE cc_start: 0.9235 (pt) cc_final: 0.8951 (tp) REVERT: I 371 LEU cc_start: 0.9657 (tp) cc_final: 0.9427 (mt) REVERT: I 388 PHE cc_start: 0.8388 (m-10) cc_final: 0.8152 (m-80) REVERT: I 395 MET cc_start: 0.9375 (ptt) cc_final: 0.9119 (ptt) outliers start: 0 outliers final: 0 residues processed: 170 average time/residue: 0.3342 time to fit residues: 96.2224 Evaluate side-chains 143 residues out of total 2801 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 143 time to evaluate : 2.846 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 313 random chunks: chunk 275 optimal weight: 30.0000 chunk 7 optimal weight: 3.9990 chunk 39 optimal weight: 9.9990 chunk 171 optimal weight: 2.9990 chunk 44 optimal weight: 2.9990 chunk 19 optimal weight: 0.7980 chunk 285 optimal weight: 20.0000 chunk 129 optimal weight: 0.9980 chunk 177 optimal weight: 3.9990 chunk 88 optimal weight: 20.0000 chunk 6 optimal weight: 0.9990 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 241 HIS ** D 570 ASN ** 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 110 HIS ** 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: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3794 r_free = 0.3794 target = 0.066342 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3133 r_free = 0.3133 target = 0.044692 restraints weight = 232748.176| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3193 r_free = 0.3193 target = 0.045869 restraints weight = 151347.211| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3178 r_free = 0.3178 target = 0.045834 restraints weight = 91218.818| |-----------------------------------------------------------------------------| r_work (final): 0.3066 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3066 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3066 r_free = 0.3066 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 = 0.3066 r_free = 0.3066 target_work(ls_wunit_k1) = 0.041 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3066 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8179 moved from start: 0.2472 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 25639 Z= 0.121 Angle : 0.542 11.564 34650 Z= 0.285 Chirality : 0.039 0.207 3923 Planarity : 0.003 0.043 4448 Dihedral : 4.380 33.063 3429 Min Nonbonded Distance : 1.917 Molprobity Statistics. All-atom Clashscore : 10.20 Ramachandran Plot: Outliers : 0.13 % Allowed : 3.54 % Favored : 96.33 % Rotamer: Outliers : 0.00 % Allowed : 0.18 % Favored : 99.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.21 (0.15), residues: 3135 helix: 1.67 (0.12), residues: 1930 sheet: 0.14 (0.52), residues: 95 loop : -0.66 (0.19), residues: 1110 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP D 209 HIS 0.009 0.001 HIS A 318 PHE 0.047 0.001 PHE D 392 TYR 0.018 0.001 TYR D 440 ARG 0.007 0.000 ARG D 379 Details of bonding type rmsd hydrogen bonds : bond 0.03553 ( 1395) hydrogen bonds : angle 4.22438 ( 4146) metal coordination : bond 0.00491 ( 15) metal coordination : angle 3.13306 ( 6) covalent geometry : bond 0.00260 (25624) covalent geometry : angle 0.54056 (34644) ********************** 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 : 3.971 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: 0.8811 (mmp) cc_final: 0.7984 (mmm) REVERT: A 90 TYR cc_start: 0.7732 (p90) cc_final: 0.7415 (p90) REVERT: A 137 MET cc_start: 0.7942 (ppp) cc_final: 0.7517 (ppp) REVERT: A 365 MET cc_start: 0.9513 (mmt) cc_final: 0.9205 (mmt) REVERT: A 642 MET cc_start: 0.8986 (mmp) cc_final: 0.8267 (pmm) REVERT: A 717 MET cc_start: 0.9078 (ttt) cc_final: 0.8335 (tpp) REVERT: R 50 MET cc_start: 0.8762 (tpt) cc_final: 0.8245 (ptt) REVERT: C 17 MET cc_start: 0.7662 (ttt) cc_final: 0.7453 (ttt) REVERT: D 326 MET cc_start: 0.8913 (mmp) cc_final: 0.8666 (mmp) REVERT: D 422 MET cc_start: 0.8918 (ppp) cc_final: 0.8543 (ppp) REVERT: D 568 MET cc_start: 0.8496 (tpp) cc_final: 0.8201 (mmt) REVERT: F 101 MET cc_start: 0.9383 (tmm) cc_final: 0.9141 (tmm) REVERT: F 162 MET cc_start: 0.8564 (ttm) cc_final: 0.8305 (ttm) REVERT: F 294 MET cc_start: 0.8535 (tmm) cc_final: 0.8321 (tmm) REVERT: F 365 MET cc_start: 0.9095 (ptp) cc_final: 0.8749 (mpp) REVERT: F 424 TYR cc_start: 0.8995 (m-80) cc_final: 0.8243 (m-10) REVERT: F 438 MET cc_start: 0.9503 (mmp) cc_final: 0.9215 (mmt) REVERT: F 476 MET cc_start: 0.8869 (mmp) cc_final: 0.8350 (mmm) REVERT: F 605 MET cc_start: -0.1540 (ttt) cc_final: -0.1959 (ttt) REVERT: F 642 MET cc_start: 0.9030 (mmt) cc_final: 0.8779 (mmp) REVERT: I 341 ILE cc_start: 0.9226 (pt) cc_final: 0.8940 (tp) REVERT: I 358 MET cc_start: 0.7466 (ppp) cc_final: 0.7133 (ppp) REVERT: I 371 LEU cc_start: 0.9662 (tp) cc_final: 0.9432 (mt) REVERT: I 388 PHE cc_start: 0.8347 (m-10) cc_final: 0.8041 (m-80) outliers start: 0 outliers final: 0 residues processed: 169 average time/residue: 0.3889 time to fit residues: 112.1143 Evaluate side-chains 140 residues out of total 2801 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 140 time to evaluate : 3.514 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 313 random chunks: chunk 215 optimal weight: 0.7980 chunk 177 optimal weight: 0.6980 chunk 300 optimal weight: 0.7980 chunk 189 optimal weight: 10.0000 chunk 108 optimal weight: 20.0000 chunk 41 optimal weight: 2.9990 chunk 308 optimal weight: 0.9990 chunk 91 optimal weight: 0.6980 chunk 274 optimal weight: 6.9990 chunk 258 optimal weight: 8.9990 chunk 63 optimal weight: 5.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 116 ASN D 241 HIS D 502 HIS ** F 320 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 110 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 439 ASN ** 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 = 0.3810 r_free = 0.3810 target = 0.066917 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3174 r_free = 0.3174 target = 0.045964 restraints weight = 278665.123| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3229 r_free = 0.3229 target = 0.046621 restraints weight = 148967.411| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3232 r_free = 0.3232 target = 0.047254 restraints weight = 96533.117| |-----------------------------------------------------------------------------| r_work (final): 0.3137 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3137 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3137 r_free = 0.3137 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 = 0.3137 r_free = 0.3137 target_work(ls_wunit_k1) = 0.043 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3137 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8091 moved from start: 0.2581 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 25639 Z= 0.101 Angle : 0.528 11.166 34650 Z= 0.276 Chirality : 0.039 0.195 3923 Planarity : 0.003 0.067 4448 Dihedral : 4.263 29.375 3429 Min Nonbonded Distance : 1.931 Molprobity Statistics. All-atom Clashscore : 9.02 Ramachandran Plot: Outliers : 0.13 % Allowed : 3.42 % Favored : 96.46 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.26 (0.15), residues: 3135 helix: 1.71 (0.12), residues: 1933 sheet: 0.20 (0.52), residues: 95 loop : -0.65 (0.19), residues: 1107 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP D 209 HIS 0.005 0.001 HIS H 35 PHE 0.043 0.001 PHE D 392 TYR 0.018 0.001 TYR D 349 ARG 0.006 0.000 ARG D 379 Details of bonding type rmsd hydrogen bonds : bond 0.03340 ( 1395) hydrogen bonds : angle 4.10761 ( 4146) metal coordination : bond 0.00416 ( 15) metal coordination : angle 3.01432 ( 6) covalent geometry : bond 0.00212 (25624) covalent geometry : angle 0.52684 (34644) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 11203.18 seconds wall clock time: 197 minutes 37.96 seconds (11857.96 seconds total)