Starting phenix.real_space_refine on Wed Mar 20 17:01:09 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5xtb_6771/03_2024/5xtb_6771_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5xtb_6771/03_2024/5xtb_6771.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5xtb_6771/03_2024/5xtb_6771_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5xtb_6771/03_2024/5xtb_6771_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5xtb_6771/03_2024/5xtb_6771_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5xtb_6771/03_2024/5xtb_6771.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5xtb_6771/03_2024/5xtb_6771.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5xtb_6771/03_2024/5xtb_6771_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5xtb_6771/03_2024/5xtb_6771_updated.pdb" } resolution = 3.4 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= 0.005 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians Fe 28 7.16 5 P 5 5.49 5 S 186 5.16 5 C 17726 2.51 5 N 4892 2.21 5 O 5125 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 52": "NH1" <-> "NH2" Residue "A ARG 59": "NH1" <-> "NH2" Residue "A ARG 109": "NH1" <-> "NH2" Residue "A ARG 199": "NH1" <-> "NH2" Residue "A ARG 256": "NH1" <-> "NH2" Residue "A ARG 257": "NH1" <-> "NH2" Residue "A ARG 386": "NH1" <-> "NH2" Residue "A ARG 449": "NH1" <-> "NH2" Residue "B ARG 54": "NH1" <-> "NH2" Residue "B ARG 77": "NH1" <-> "NH2" Residue "B ARG 102": "NH1" <-> "NH2" Residue "B ARG 110": "NH1" <-> "NH2" Residue "B ARG 133": "NH1" <-> "NH2" Residue "B ARG 139": "NH1" <-> "NH2" Residue "B ARG 210": "NH1" <-> "NH2" Residue "C ARG 59": "NH1" <-> "NH2" Residue "C ARG 75": "NH1" <-> "NH2" Residue "C ARG 100": "NH1" <-> "NH2" Residue "C ARG 105": "NH1" <-> "NH2" Residue "C ARG 111": "NH1" <-> "NH2" Residue "C ARG 135": "NH1" <-> "NH2" Residue "C ARG 145": "NH1" <-> "NH2" Residue "C ARG 168": "NH1" <-> "NH2" Residue "C ARG 203": "NH1" <-> "NH2" Residue "C ARG 212": "NH1" <-> "NH2" Residue "E ARG 30": "NH1" <-> "NH2" Residue "E ARG 77": "NH1" <-> "NH2" Residue "E ARG 105": "NH1" <-> "NH2" Residue "F ARG 20": "NH1" <-> "NH2" Residue "F ARG 26": "NH1" <-> "NH2" Residue "G TYR 155": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ARG 23": "NH1" <-> "NH2" Residue "I ARG 10": "NH1" <-> "NH2" Residue "I ARG 60": "NH1" <-> "NH2" Residue "J ARG 48": "NH1" <-> "NH2" Residue "J ARG 67": "NH1" <-> "NH2" Residue "J ARG 75": "NH1" <-> "NH2" Residue "J ARG 95": "NH1" <-> "NH2" Residue "J ARG 117": "NH1" <-> "NH2" Residue "J ARG 299": "NH1" <-> "NH2" Residue "J ARG 303": "NH1" <-> "NH2" Residue "J ARG 316": "NH1" <-> "NH2" Residue "J ARG 360": "NH1" <-> "NH2" Residue "L ARG 75": "NH1" <-> "NH2" Residue "L ARG 78": "NH1" <-> "NH2" Residue "L ARG 84": "NH1" <-> "NH2" Residue "L ARG 106": "NH1" <-> "NH2" Residue "L ARG 169": "NH1" <-> "NH2" Residue "M ARG 68": "NH1" <-> "NH2" Residue "M ARG 150": "NH1" <-> "NH2" Residue "M ARG 175": "NH1" <-> "NH2" Residue "M ARG 308": "NH1" <-> "NH2" Residue "M ARG 325": "NH1" <-> "NH2" Residue "M ARG 360": "NH1" <-> "NH2" Residue "M ARG 382": "NH1" <-> "NH2" Residue "M ARG 417": "NH1" <-> "NH2" Residue "M ARG 557": "NH1" <-> "NH2" Residue "M ARG 645": "NH1" <-> "NH2" Residue "O ARG 111": "NH1" <-> "NH2" Residue "O ARG 143": "NH1" <-> "NH2" Residue "P ARG 48": "NH1" <-> "NH2" Residue "P ARG 142": "NH1" <-> "NH2" Residue "P ARG 168": "NH1" <-> "NH2" Residue "P ARG 186": "NH1" <-> "NH2" Residue "P ARG 211": "NH1" <-> "NH2" Residue "Q ARG 96": "NH1" <-> "NH2" Residue "Q PHE 200": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q ARG 207": "NH1" <-> "NH2" Residue "Q ARG 221": "NH1" <-> "NH2" Residue "Q ARG 342": "NH1" <-> "NH2" Residue "Q ARG 368": "NH1" <-> "NH2" Residue "Q ARG 421": "NH1" <-> "NH2" Residue "T ARG 120": "NH1" <-> "NH2" Time to flip residues: 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 27962 Number of models: 1 Model: "" Number of chains: 25 Chain: "A" Number of atoms: 3322 Number of conformers: 1 Conformer: "" Number of residues, atoms: 431, 3322 Classifications: {'peptide': 431} Link IDs: {'PTRANS': 21, 'TRANS': 409} Chain: "B" Number of atoms: 1420 Number of conformers: 1 Conformer: "" Number of residues, atoms: 176, 1420 Classifications: {'peptide': 176} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 165} Chain: "C" Number of atoms: 1249 Number of conformers: 1 Conformer: "" Number of residues, atoms: 156, 1249 Classifications: {'peptide': 156} Link IDs: {'PCIS': 2, 'PTRANS': 8, 'TRANS': 145} Chain: "E" Number of atoms: 968 Number of conformers: 1 Conformer: "" Number of residues, atoms: 113, 968 Classifications: {'peptide': 113} Link IDs: {'PTRANS': 6, 'TRANS': 106} Chain: "F" Number of atoms: 670 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 670 Classifications: {'peptide': 83} Link IDs: {'PTRANS': 5, 'TRANS': 77} Chain: "G" Number of atoms: 672 Number of conformers: 1 Conformer: "" Number of residues, atoms: 85, 672 Classifications: {'peptide': 85} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 4} Link IDs: {'PTRANS': 4, 'TRANS': 80} Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 19 Unresolved non-hydrogen dihedrals: 13 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASP:plan': 2} Unresolved non-hydrogen planarities: 6 Chain: "H" Number of atoms: 922 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 922 Classifications: {'peptide': 112} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 104} Chain: "I" Number of atoms: 769 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 769 Classifications: {'peptide': 95} Link IDs: {'PTRANS': 11, 'TRANS': 83} Chain breaks: 1 Chain: "J" Number of atoms: 2712 Number of conformers: 1 Conformer: "" Number of residues, atoms: 337, 2712 Classifications: {'peptide': 337} Link IDs: {'PTRANS': 20, 'TRANS': 316} Chain: "K" Number of atoms: 274 Number of conformers: 1 Conformer: "" Number of residues, atoms: 33, 274 Classifications: {'peptide': 33} Link IDs: {'PTRANS': 3, 'TRANS': 29} Chain: "L" Number of atoms: 964 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 964 Classifications: {'peptide': 118} Link IDs: {'PTRANS': 6, 'TRANS': 111} Chain: "M" Number of atoms: 5274 Number of conformers: 1 Conformer: "" Number of residues, atoms: 687, 5274 Classifications: {'peptide': 687} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 2, 'PTRANS': 30, 'TRANS': 654} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Chain: "N" Number of atoms: 1195 Number of conformers: 1 Conformer: "" Number of residues, atoms: 143, 1195 Classifications: {'peptide': 143} Link IDs: {'PTRANS': 10, 'TRANS': 132} Chain: "O" Number of atoms: 1643 Number of conformers: 1 Conformer: "" Number of residues, atoms: 212, 1643 Classifications: {'peptide': 212} Link IDs: {'PTRANS': 20, 'TRANS': 191} Chain: "P" Number of atoms: 1730 Number of conformers: 1 Conformer: "" Number of residues, atoms: 208, 1730 Classifications: {'peptide': 208} Link IDs: {'PTRANS': 15, 'TRANS': 192} Chain: "Q" Number of atoms: 3087 Number of conformers: 1 Conformer: "" Number of residues, atoms: 385, 3087 Classifications: {'peptide': 385} Link IDs: {'PCIS': 1, 'PTRANS': 20, 'TRANS': 363} Chain: "T" Number of atoms: 742 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 742 Classifications: {'peptide': 95} Link IDs: {'PTRANS': 3, 'TRANS': 91} Chain: "W" Number of atoms: 179 Number of conformers: 1 Conformer: "" Number of residues, atoms: 22, 179 Classifications: {'peptide': 22} Link IDs: {'PTRANS': 5, 'TRANS': 16} Chain: "A" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 39 Unusual residues: {'FMN': 1, 'SF4': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 16 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 16 Unusual residues: {'SF4': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 8 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 8 Unusual residues: {'SF4': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 35 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 35 Unusual residues: {'8Q1': 1} Classifications: {'undetermined': 1} Chain: "J" Number of atoms: 48 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 48 Unusual residues: {'NDP': 1} Classifications: {'undetermined': 1} Chain: "M" Number of atoms: 20 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 20 Unusual residues: {'FES': 1, 'SF4': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "O" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 4 Unusual residues: {'FES': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 2695 SG CYS A 379 42.240 49.324 105.118 1.00 32.72 S ATOM 3979 SG CYS B 114 41.739 62.723 69.877 1.00 12.09 S ATOM 4030 SG CYS B 121 48.356 69.171 59.911 1.00 12.49 S ATOM 4256 SG CYS B 150 46.686 67.243 54.199 1.00 10.16 S ATOM 4282 SG CYS B 153 51.395 63.904 57.905 1.00 12.44 S ATOM 5725 SG CYS C 183 53.673 67.028 50.736 1.00 12.72 S ATOM 4996 SG CYS C 89 55.022 70.262 43.946 1.00 26.32 S ATOM 4990 SG CYS C 88 58.840 66.831 46.571 1.00 28.78 S ATOM 5494 SG CYS C 153 56.066 73.123 49.754 1.00 14.63 S ATOM 14700 SG CYS M 128 44.919 58.072 79.079 1.00 16.07 S ATOM 14760 SG CYS M 137 46.377 62.343 85.746 1.00 15.29 S ATOM 15071 SG CYS M 176 40.034 60.764 93.963 1.00 19.64 S ATOM 15094 SG CYS M 179 44.841 60.845 94.861 1.00 23.25 S ATOM 15448 SG CYS M 226 41.277 64.926 90.818 1.00 20.74 S ATOM 15118 SG CYS M 182 41.059 66.027 95.884 1.00 25.87 S ATOM 15071 SG CYS M 176 40.034 60.764 93.963 1.00 19.64 S ATOM 21531 SG CYS O 176 37.428 32.675 111.106 1.00 61.11 S ATOM 21554 SG CYS O 180 38.589 29.695 112.055 1.00 70.08 S Time building chain proxies: 14.61, per 1000 atoms: 0.52 Number of scatterers: 27962 At special positions: 0 Unit cell: (125.628, 145.122, 158.118, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Fe 28 26.01 S 186 16.00 P 5 15.00 O 5125 8.00 N 4892 7.00 C 17726 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 10.85 Conformation dependent library (CDL) restraints added in 4.7 seconds Dynamic metal coordination Iron sulfur cluster coordination pdb=" FES M 803 " pdb="FE1 FES M 803 " - pdb=" SG CYS M 78 " pdb="FE2 FES M 803 " - pdb=" SG CYS M 64 " pdb="FE2 FES M 803 " - pdb=" SG CYS M 92 " pdb=" FES O 301 " pdb="FE2 FES O 301 " - pdb=" SG CYS O 176 " pdb="FE2 FES O 301 " - pdb=" SG CYS O 180 " pdb="FE1 FES O 301 " - pdb=" SG CYS O 140 " pdb=" SF4 A 501 " pdb="FE4 SF4 A 501 " - pdb=" SG CYS A 379 " pdb="FE1 SF4 A 501 " - pdb=" SG CYS A 382 " pdb="FE3 SF4 A 501 " - pdb=" SG CYS A 385 " pdb=" SF4 B 301 " pdb="FE4 SF4 B 301 " - pdb=" SG CYS B 160 " pdb="FE1 SF4 B 301 " - pdb=" SG CYS B 111 " pdb="FE4 SF4 B 301 " - pdb=" SG CYS B 117 " pdb=" SF4 B 302 " pdb="FE2 SF4 B 302 " - pdb=" SG CYS B 150 " pdb="FE4 SF4 B 302 " - pdb=" SG CYS B 153 " pdb="FE1 SF4 B 302 " - pdb=" SG CYS B 121 " pdb="FE3 SF4 B 302 " - pdb=" SG CYS B 156 " pdb="FE3 SF4 B 302 " - pdb=" NE2 HIS B 99 " pdb=" SF4 C 301 " pdb="FE2 SF4 C 301 " - pdb=" SG CYS C 89 " pdb="FE3 SF4 C 301 " - pdb=" SG CYS C 88 " pdb="FE4 SF4 C 301 " - pdb=" SG CYS C 153 " pdb="FE1 SF4 C 301 " - pdb=" SG CYS C 183 " pdb=" SF4 M 801 " pdb="FE3 SF4 M 801 " - pdb=" NE2 HIS M 124 " pdb="FE4 SF4 M 801 " - pdb=" SG CYS M 137 " pdb="FE2 SF4 M 801 " - pdb=" SG CYS M 128 " pdb=" SF4 M 802 " pdb="FE4 SF4 M 802 " - pdb=" SG CYS M 176 " pdb="FE3 SF4 M 802 " - pdb=" SG CYS M 182 " pdb="FE2 SF4 M 802 " - pdb=" SG CYS M 226 " pdb="FE1 SF4 M 802 " - pdb=" SG CYS M 179 " Number of angles added : 68 6906 Ramachandran restraints generated. 3453 Oldfield, 0 Emsley, 3453 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6488 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 137 helices and 22 sheets defined 36.1% alpha, 5.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 5.94 Creating SS restraints... Processing helix chain 'A' and resid 53 through 58 Processing helix chain 'A' and resid 75 through 81 Processing helix chain 'A' and resid 95 through 103 removed outlier: 3.752A pdb=" N PHE A 101 " --> pdb=" O LEU A 97 " (cutoff:3.500A) removed outlier: 5.122A pdb=" N MET A 102 " --> pdb=" O LYS A 98 " (cutoff:3.500A) removed outlier: 4.652A pdb=" N ASN A 103 " --> pdb=" O TRP A 99 " (cutoff:3.500A) Processing helix chain 'A' and resid 126 through 133 removed outlier: 4.000A pdb=" N ILE A 130 " --> pdb=" O LYS A 126 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N LEU A 131 " --> pdb=" O ASP A 127 " (cutoff:3.500A) Processing helix chain 'A' and resid 135 through 148 Processing helix chain 'A' and resid 164 through 178 Processing helix chain 'A' and resid 204 through 207 Processing helix chain 'A' and resid 209 through 216 Processing helix chain 'A' and resid 235 through 237 No H-bonds generated for 'chain 'A' and resid 235 through 237' Processing helix chain 'A' and resid 245 through 256 Proline residue: A 252 - end of helix Processing helix chain 'A' and resid 259 through 263 Processing helix chain 'A' and resid 296 through 301 removed outlier: 3.836A pdb=" N ILE A 300 " --> pdb=" O LEU A 296 " (cutoff:3.500A) Processing helix chain 'A' and resid 311 through 313 No H-bonds generated for 'chain 'A' and resid 311 through 313' Processing helix chain 'A' and resid 329 through 332 No H-bonds generated for 'chain 'A' and resid 329 through 332' Processing helix chain 'A' and resid 339 through 344 Processing helix chain 'A' and resid 350 through 352 No H-bonds generated for 'chain 'A' and resid 350 through 352' Processing helix chain 'A' and resid 364 through 376 Processing helix chain 'A' and resid 383 through 401 removed outlier: 3.886A pdb=" N LYS A 394 " --> pdb=" O ASP A 390 " (cutoff:3.500A) Processing helix chain 'A' and resid 406 through 419 removed outlier: 3.688A pdb=" N ILE A 409 " --> pdb=" O PRO A 406 " (cutoff:3.500A) Processing helix chain 'A' and resid 427 through 456 Proline residue: A 434 - end of helix Proline residue: A 444 - end of helix removed outlier: 3.688A pdb=" N ARG A 452 " --> pdb=" O GLU A 448 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N PHE A 453 " --> pdb=" O ARG A 449 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N GLN A 456 " --> pdb=" O ARG A 452 " (cutoff:3.500A) Processing helix chain 'B' and resid 48 through 60 Processing helix chain 'B' and resid 63 through 76 removed outlier: 3.621A pdb=" N THR B 71 " --> pdb=" O GLY B 67 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N LEU B 72 " --> pdb=" O LEU B 68 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N SER B 73 " --> pdb=" O GLY B 69 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N TYR B 74 " --> pdb=" O MET B 70 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N LEU B 75 " --> pdb=" O THR B 71 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N PHE B 76 " --> pdb=" O LEU B 72 " (cutoff:3.500A) Processing helix chain 'B' and resid 155 through 159 Processing helix chain 'B' and resid 178 through 181 Processing helix chain 'B' and resid 185 through 194 Processing helix chain 'B' and resid 196 through 209 removed outlier: 6.281A pdb=" N LEU B 208 " --> pdb=" O GLN B 204 " (cutoff:3.500A) removed outlier: 6.486A pdb=" N TYR B 209 " --> pdb=" O ALA B 205 " (cutoff:3.500A) Processing helix chain 'C' and resid 60 through 76 removed outlier: 3.952A pdb=" N VAL C 64 " --> pdb=" O GLY C 60 " (cutoff:3.500A) Processing helix chain 'C' and resid 90 through 96 removed outlier: 4.009A pdb=" N HIS C 95 " --> pdb=" O VAL C 91 " (cutoff:3.500A) Processing helix chain 'C' and resid 103 through 106 Processing helix chain 'C' and resid 131 through 140 Processing helix chain 'C' and resid 151 through 156 Processing helix chain 'C' and resid 158 through 160 No H-bonds generated for 'chain 'C' and resid 158 through 160' Processing helix chain 'C' and resid 170 through 172 No H-bonds generated for 'chain 'C' and resid 170 through 172' Processing helix chain 'C' and resid 187 through 202 Processing helix chain 'C' and resid 206 through 211 Processing helix chain 'E' and resid 25 through 40 removed outlier: 3.983A pdb=" N ARG E 31 " --> pdb=" O GLU E 27 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N ARG E 33 " --> pdb=" O LYS E 29 " (cutoff:3.500A) Processing helix chain 'E' and resid 43 through 49 Processing helix chain 'E' and resid 56 through 66 Processing helix chain 'E' and resid 76 through 94 Processing helix chain 'E' and resid 100 through 106 removed outlier: 4.325A pdb=" N PHE E 106 " --> pdb=" O HIS E 102 " (cutoff:3.500A) Processing helix chain 'E' and resid 118 through 124 Processing helix chain 'F' and resid 28 through 47 removed outlier: 4.446A pdb=" N GLY F 32 " --> pdb=" O PRO F 28 " (cutoff:3.500A) removed outlier: 5.306A pdb=" N VAL F 33 " --> pdb=" O GLY F 29 " (cutoff:3.500A) removed outlier: 4.197A pdb=" N TYR F 41 " --> pdb=" O ILE F 37 " (cutoff:3.500A) removed outlier: 6.345A pdb=" N VAL F 42 " --> pdb=" O GLU F 38 " (cutoff:3.500A) removed outlier: 4.790A pdb=" N GLU F 43 " --> pdb=" O LYS F 39 " (cutoff:3.500A) Processing helix chain 'F' and resid 70 through 72 No H-bonds generated for 'chain 'F' and resid 70 through 72' Processing helix chain 'F' and resid 84 through 93 removed outlier: 3.961A pdb=" N ASN F 93 " --> pdb=" O ARG F 89 " (cutoff:3.500A) Processing helix chain 'G' and resid 76 through 89 Processing helix chain 'G' and resid 112 through 126 Processing helix chain 'G' and resid 132 through 137 Processing helix chain 'G' and resid 141 through 151 Processing helix chain 'H' and resid 20 through 35 Processing helix chain 'H' and resid 43 through 61 removed outlier: 4.227A pdb=" N TYR H 47 " --> pdb=" O ALA H 43 " (cutoff:3.500A) Processing helix chain 'H' and resid 65 through 71 removed outlier: 3.815A pdb=" N GLU H 69 " --> pdb=" O VAL H 65 " (cutoff:3.500A) removed outlier: 4.478A pdb=" N ASP H 70 " --> pdb=" O LYS H 66 " (cutoff:3.500A) Processing helix chain 'H' and resid 80 through 94 Processing helix chain 'I' and resid 6 through 16 Processing helix chain 'I' and resid 54 through 57 No H-bonds generated for 'chain 'I' and resid 54 through 57' Processing helix chain 'I' and resid 60 through 62 No H-bonds generated for 'chain 'I' and resid 60 through 62' Processing helix chain 'I' and resid 108 through 110 No H-bonds generated for 'chain 'I' and resid 108 through 110' Processing helix chain 'J' and resid 64 through 75 removed outlier: 4.107A pdb=" N TYR J 68 " --> pdb=" O PHE J 64 " (cutoff:3.500A) Processing helix chain 'J' and resid 89 through 97 removed outlier: 4.919A pdb=" N HIS J 93 " --> pdb=" O ASP J 90 " (cutoff:3.500A) Proline residue: J 96 - end of helix Processing helix chain 'J' and resid 100 through 102 No H-bonds generated for 'chain 'J' and resid 100 through 102' Processing helix chain 'J' and resid 114 through 119 Processing helix chain 'J' and resid 141 through 145 removed outlier: 3.778A pdb=" N PHE J 145 " --> pdb=" O PHE J 141 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 141 through 145' Processing helix chain 'J' and resid 147 through 159 Processing helix chain 'J' and resid 179 through 194 removed outlier: 3.865A pdb=" N ALA J 185 " --> pdb=" O LEU J 181 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N VAL J 186 " --> pdb=" O ARG J 182 " (cutoff:3.500A) Processing helix chain 'J' and resid 212 through 223 removed outlier: 3.863A pdb=" N PHE J 217 " --> pdb=" O PHE J 213 " (cutoff:3.500A) removed outlier: 4.852A pdb=" N HIS J 221 " --> pdb=" O PHE J 217 " (cutoff:3.500A) removed outlier: 5.272A pdb=" N ARG J 222 " --> pdb=" O ALA J 218 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N PHE J 223 " --> pdb=" O SER J 219 " (cutoff:3.500A) Processing helix chain 'J' and resid 242 through 254 Processing helix chain 'J' and resid 273 through 284 Processing helix chain 'J' and resid 295 through 305 Processing helix chain 'J' and resid 316 through 323 removed outlier: 3.888A pdb=" N GLU J 320 " --> pdb=" O ARG J 316 " (cutoff:3.500A) Processing helix chain 'J' and resid 335 through 337 No H-bonds generated for 'chain 'J' and resid 335 through 337' Processing helix chain 'J' and resid 345 through 347 No H-bonds generated for 'chain 'J' and resid 345 through 347' Processing helix chain 'J' and resid 349 through 353 Processing helix chain 'J' and resid 359 through 362 No H-bonds generated for 'chain 'J' and resid 359 through 362' Processing helix chain 'J' and resid 367 through 369 No H-bonds generated for 'chain 'J' and resid 367 through 369' Processing helix chain 'K' and resid 83 through 94 removed outlier: 3.648A pdb=" N LEU K 91 " --> pdb=" O LEU K 87 " (cutoff:3.500A) removed outlier: 4.573A pdb=" N LYS K 93 " --> pdb=" O LEU K 89 " (cutoff:3.500A) removed outlier: 5.173A pdb=" N PHE K 94 " --> pdb=" O GLU K 90 " (cutoff:3.500A) Processing helix chain 'L' and resid 69 through 73 Processing helix chain 'L' and resid 120 through 123 removed outlier: 4.450A pdb=" N ASN L 123 " --> pdb=" O PRO L 120 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 120 through 123' Processing helix chain 'L' and resid 131 through 141 Processing helix chain 'L' and resid 161 through 163 No H-bonds generated for 'chain 'L' and resid 161 through 163' Processing helix chain 'M' and resid 49 through 56 removed outlier: 3.820A pdb=" N VAL M 56 " --> pdb=" O ALA M 52 " (cutoff:3.500A) Processing helix chain 'M' and resid 107 through 122 removed outlier: 3.724A pdb=" N PHE M 119 " --> pdb=" O GLY M 115 " (cutoff:3.500A) Processing helix chain 'M' and resid 138 through 145 Processing helix chain 'M' and resid 181 through 186 Processing helix chain 'M' and resid 220 through 225 Processing helix chain 'M' and resid 242 through 244 No H-bonds generated for 'chain 'M' and resid 242 through 244' Processing helix chain 'M' and resid 288 through 291 No H-bonds generated for 'chain 'M' and resid 288 through 291' Processing helix chain 'M' and resid 293 through 298 Processing helix chain 'M' and resid 319 through 330 Processing helix chain 'M' and resid 348 through 360 Processing helix chain 'M' and resid 394 through 396 No H-bonds generated for 'chain 'M' and resid 394 through 396' Processing helix chain 'M' and resid 407 through 409 No H-bonds generated for 'chain 'M' and resid 407 through 409' Processing helix chain 'M' and resid 412 through 423 Processing helix chain 'M' and resid 448 through 456 removed outlier: 4.248A pdb=" N GLN M 453 " --> pdb=" O PRO M 449 " (cutoff:3.500A) Processing helix chain 'M' and resid 461 through 468 Processing helix chain 'M' and resid 478 through 481 Processing helix chain 'M' and resid 486 through 503 Processing helix chain 'M' and resid 522 through 527 Processing helix chain 'M' and resid 535 through 537 No H-bonds generated for 'chain 'M' and resid 535 through 537' Processing helix chain 'M' and resid 576 through 579 No H-bonds generated for 'chain 'M' and resid 576 through 579' Processing helix chain 'M' and resid 619 through 629 removed outlier: 4.045A pdb=" N ILE M 623 " --> pdb=" O ASP M 619 " (cutoff:3.500A) Processing helix chain 'M' and resid 639 through 648 removed outlier: 3.565A pdb=" N GLU M 647 " --> pdb=" O ARG M 643 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N GLU M 648 " --> pdb=" O ASN M 644 " (cutoff:3.500A) Processing helix chain 'M' and resid 652 through 654 No H-bonds generated for 'chain 'M' and resid 652 through 654' Processing helix chain 'M' and resid 666 through 673 removed outlier: 3.731A pdb=" N LEU M 671 " --> pdb=" O GLN M 667 " (cutoff:3.500A) removed outlier: 4.528A pdb=" N SER M 672 " --> pdb=" O ALA M 668 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N LYS M 673 " --> pdb=" O ASN M 669 " (cutoff:3.500A) Processing helix chain 'M' and resid 691 through 695 removed outlier: 4.143A pdb=" N TYR M 695 " --> pdb=" O LYS M 692 " (cutoff:3.500A) Processing helix chain 'M' and resid 699 through 703 Processing helix chain 'M' and resid 705 through 715 Processing helix chain 'N' and resid 3 through 15 Processing helix chain 'N' and resid 21 through 29 removed outlier: 3.753A pdb=" N ARG N 25 " --> pdb=" O ARG N 21 " (cutoff:3.500A) Processing helix chain 'N' and resid 68 through 70 No H-bonds generated for 'chain 'N' and resid 68 through 70' Processing helix chain 'N' and resid 84 through 90 Processing helix chain 'O' and resid 57 through 69 Processing helix chain 'O' and resid 75 through 88 removed outlier: 4.324A pdb=" N LEU O 80 " --> pdb=" O ALA O 77 " (cutoff:3.500A) Proline residue: O 81 - end of helix removed outlier: 3.511A pdb=" N ALA O 86 " --> pdb=" O LEU O 83 " (cutoff:3.500A) Processing helix chain 'O' and resid 95 through 104 Processing helix chain 'O' and resid 109 through 118 Processing helix chain 'O' and resid 138 through 141 No H-bonds generated for 'chain 'O' and resid 138 through 141' Processing helix chain 'O' and resid 145 through 156 Processing helix chain 'O' and resid 198 through 208 Processing helix chain 'P' and resid 52 through 68 Processing helix chain 'P' and resid 90 through 101 removed outlier: 5.397A pdb=" N ILE P 94 " --> pdb=" O ASP P 91 " (cutoff:3.500A) Proline residue: P 95 - end of helix removed outlier: 4.002A pdb=" N THR P 98 " --> pdb=" O PRO P 95 " (cutoff:3.500A) Processing helix chain 'P' and resid 162 through 172 removed outlier: 4.034A pdb=" N TRP P 165 " --> pdb=" O ALA P 162 " (cutoff:3.500A) removed outlier: 4.625A pdb=" N TYR P 166 " --> pdb=" O ALA P 163 " (cutoff:3.500A) removed outlier: 4.658A pdb=" N GLU P 167 " --> pdb=" O ASN P 164 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N GLU P 169 " --> pdb=" O TYR P 166 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N TRP P 171 " --> pdb=" O ARG P 168 " (cutoff:3.500A) Processing helix chain 'Q' and resid 120 through 125 removed outlier: 3.763A pdb=" N GLU Q 125 " --> pdb=" O GLU Q 121 " (cutoff:3.500A) Processing helix chain 'Q' and resid 133 through 137 Processing helix chain 'Q' and resid 145 through 158 removed outlier: 3.915A pdb=" N ALA Q 154 " --> pdb=" O ALA Q 150 " (cutoff:3.500A) removed outlier: 4.086A pdb=" N LEU Q 158 " --> pdb=" O ALA Q 154 " (cutoff:3.500A) Processing helix chain 'Q' and resid 165 through 193 Processing helix chain 'Q' and resid 198 through 218 removed outlier: 4.236A pdb=" N GLU Q 205 " --> pdb=" O PHE Q 201 " (cutoff:3.500A) removed outlier: 4.889A pdb=" N GLU Q 206 " --> pdb=" O TRP Q 202 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N LYS Q 209 " --> pdb=" O GLU Q 205 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N PHE Q 213 " --> pdb=" O LYS Q 209 " (cutoff:3.500A) Processing helix chain 'Q' and resid 238 through 248 removed outlier: 3.884A pdb=" N MET Q 241 " --> pdb=" O LEU Q 238 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N ASP Q 242 " --> pdb=" O GLY Q 239 " (cutoff:3.500A) removed outlier: 4.595A pdb=" N ILE Q 244 " --> pdb=" O MET Q 241 " (cutoff:3.500A) Processing helix chain 'Q' and resid 251 through 259 removed outlier: 3.656A pdb=" N LEU Q 258 " --> pdb=" O ARG Q 254 " (cutoff:3.500A) Processing helix chain 'Q' and resid 266 through 272 removed outlier: 3.593A pdb=" N ASN Q 270 " --> pdb=" O ARG Q 266 " (cutoff:3.500A) Processing helix chain 'Q' and resid 280 through 286 Processing helix chain 'Q' and resid 290 through 294 Processing helix chain 'Q' and resid 310 through 312 No H-bonds generated for 'chain 'Q' and resid 310 through 312' Processing helix chain 'Q' and resid 326 through 348 removed outlier: 3.972A pdb=" N ALA Q 345 " --> pdb=" O LEU Q 341 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N GLN Q 346 " --> pdb=" O ARG Q 342 " (cutoff:3.500A) Processing helix chain 'Q' and resid 368 through 371 No H-bonds generated for 'chain 'Q' and resid 368 through 371' Processing helix chain 'Q' and resid 375 through 384 Processing helix chain 'Q' and resid 427 through 439 removed outlier: 3.806A pdb=" N HIS Q 431 " --> pdb=" O PRO Q 427 " (cutoff:3.500A) removed outlier: 4.673A pdb=" N ASP Q 436 " --> pdb=" O LEU Q 432 " (cutoff:3.500A) removed outlier: 5.240A pdb=" N LYS Q 437 " --> pdb=" O ALA Q 433 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N MET Q 438 " --> pdb=" O GLY Q 434 " (cutoff:3.500A) Processing helix chain 'Q' and resid 444 through 454 removed outlier: 3.939A pdb=" N GLY Q 452 " --> pdb=" O VAL Q 448 " (cutoff:3.500A) Processing helix chain 'T' and resid 51 through 56 Processing helix chain 'T' and resid 68 through 74 removed outlier: 3.802A pdb=" N ALA T 73 " --> pdb=" O ILE T 69 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 114 through 116 Processing sheet with id= B, first strand: chain 'A' and resid 153 through 158 removed outlier: 7.301A pdb=" N ASP A 194 " --> pdb=" O ALA A 154 " (cutoff:3.500A) removed outlier: 7.927A pdb=" N ILE A 156 " --> pdb=" O ASP A 194 " (cutoff:3.500A) removed outlier: 6.521A pdb=" N PHE A 196 " --> pdb=" O ILE A 156 " (cutoff:3.500A) removed outlier: 7.549A pdb=" N ILE A 158 " --> pdb=" O PHE A 196 " (cutoff:3.500A) removed outlier: 6.587A pdb=" N VAL A 198 " --> pdb=" O ILE A 158 " (cutoff:3.500A) No H-bonds generated for sheet with id= B Processing sheet with id= C, first strand: chain 'A' and resid 286 through 291 removed outlier: 3.937A pdb=" N ALA A 316 " --> pdb=" O MET A 357 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 99 through 101 Processing sheet with id= E, first strand: chain 'B' and resid 130 through 132 Processing sheet with id= F, first strand: chain 'B' and resid 144 through 146 Processing sheet with id= G, first strand: chain 'F' and resid 52 through 56 removed outlier: 4.265A pdb=" N GLU F 18 " --> pdb=" O ARG F 68 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'J' and resid 103 through 107 removed outlier: 8.272A pdb=" N LEU J 104 " --> pdb=" O SER J 78 " (cutoff:3.500A) removed outlier: 6.809A pdb=" N VAL J 80 " --> pdb=" O LEU J 104 " (cutoff:3.500A) removed outlier: 7.982A pdb=" N LEU J 106 " --> pdb=" O VAL J 80 " (cutoff:3.500A) removed outlier: 6.580A pdb=" N ILE J 82 " --> pdb=" O LEU J 106 " (cutoff:3.500A) removed outlier: 7.879A pdb=" N SER J 52 " --> pdb=" O GLN J 79 " (cutoff:3.500A) removed outlier: 10.579A pdb=" N ILE J 81 " --> pdb=" O SER J 52 " (cutoff:3.500A) removed outlier: 11.466A pdb=" N ILE J 54 " --> pdb=" O ILE J 81 " (cutoff:3.500A) removed outlier: 11.955A pdb=" N ALA J 56 " --> pdb=" O PRO J 83 " (cutoff:3.500A) No H-bonds generated for sheet with id= H Processing sheet with id= I, first strand: chain 'J' and resid 165 through 167 removed outlier: 5.920A pdb=" N ILE J 199 " --> pdb=" O HIS J 166 " (cutoff:3.500A) No H-bonds generated for sheet with id= I Processing sheet with id= J, first strand: chain 'J' and resid 226 through 229 Processing sheet with id= K, first strand: chain 'L' and resid 77 through 80 Processing sheet with id= L, first strand: chain 'L' and resid 106 through 108 removed outlier: 3.637A pdb=" N TRP L 107 " --> pdb=" O SER L 116 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'M' and resid 32 through 35 Processing sheet with id= N, first strand: chain 'M' and resid 246 through 251 removed outlier: 6.026A pdb=" N ARG M 266 " --> pdb=" O VAL M 270 " (cutoff:3.500A) removed outlier: 4.727A pdb=" N VAL M 270 " --> pdb=" O ARG M 266 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'M' and resid 305 through 308 Processing sheet with id= P, first strand: chain 'M' and resid 399 through 401 Processing sheet with id= Q, first strand: chain 'M' and resid 595 through 597 Processing sheet with id= R, first strand: chain 'P' and resid 76 through 79 removed outlier: 3.573A pdb=" N SER P 79 " --> pdb=" O GLU P 83 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N GLU P 83 " --> pdb=" O SER P 79 " (cutoff:3.500A) removed outlier: 4.364A pdb=" N LEU P 84 " --> pdb=" O ARG P 140 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N ASP P 113 " --> pdb=" O ASN P 131 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'P' and resid 209 through 213 Processing sheet with id= T, first strand: chain 'Q' and resid 80 through 82 removed outlier: 3.657A pdb=" N ARG Q 96 " --> pdb=" O HIS Q 112 " (cutoff:3.500A) removed outlier: 4.114A pdb=" N LYS Q 108 " --> pdb=" O GLU Q 100 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'Q' and resid 394 through 402 Processing sheet with id= V, first strand: chain 'T' and resid 85 through 87 755 hydrogen bonds defined for protein. 2076 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: 7.98 Time building geometry restraints manager: 11.47 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.38: 11214 1.38 - 1.59: 17077 1.59 - 1.79: 92 1.79 - 1.99: 169 1.99 - 2.20: 80 Bond restraints: 28632 Sorted by residual: bond pdb=" O2B NDP J 401 " pdb=" P2B NDP J 401 " ideal model delta sigma weight residual 1.833 1.608 0.225 3.80e-02 6.93e+02 3.51e+01 bond pdb=" S3 SF4 M 801 " pdb="FE4 SF4 M 801 " ideal model delta sigma weight residual 2.280 2.111 0.169 3.00e-02 1.11e+03 3.17e+01 bond pdb=" S1 SF4 M 801 " pdb="FE3 SF4 M 801 " ideal model delta sigma weight residual 2.280 2.115 0.165 3.00e-02 1.11e+03 3.04e+01 bond pdb=" S4 SF4 M 801 " pdb="FE3 SF4 M 801 " ideal model delta sigma weight residual 2.280 2.115 0.165 3.00e-02 1.11e+03 3.03e+01 bond pdb=" S2 SF4 M 801 " pdb="FE4 SF4 M 801 " ideal model delta sigma weight residual 2.280 2.115 0.165 3.00e-02 1.11e+03 3.03e+01 ... (remaining 28627 not shown) Histogram of bond angle deviations from ideal: 87.34 - 97.08: 152 97.08 - 106.82: 1150 106.82 - 116.56: 19385 116.56 - 126.30: 17714 126.30 - 136.03: 418 Bond angle restraints: 38819 Sorted by residual: angle pdb=" S1 FES M 803 " pdb="FE2 FES M 803 " pdb=" S2 FES M 803 " ideal model delta sigma weight residual 104.33 89.22 15.11 1.14e+00 7.69e-01 1.76e+02 angle pdb=" S1 FES M 803 " pdb="FE1 FES M 803 " pdb=" S2 FES M 803 " ideal model delta sigma weight residual 104.33 89.23 15.10 1.20e+00 6.94e-01 1.58e+02 angle pdb="FE2 SF4 M 801 " pdb=" S3 SF4 M 801 " pdb="FE4 SF4 M 801 " ideal model delta sigma weight residual 73.70 92.45 -18.75 1.50e+00 4.44e-01 1.56e+02 angle pdb="FE2 SF4 M 801 " pdb=" S1 SF4 M 801 " pdb="FE4 SF4 M 801 " ideal model delta sigma weight residual 73.70 92.39 -18.69 1.50e+00 4.44e-01 1.55e+02 angle pdb=" S1 FES O 301 " pdb="FE2 FES O 301 " pdb=" S2 FES O 301 " ideal model delta sigma weight residual 104.33 90.50 13.83 1.14e+00 7.69e-01 1.47e+02 ... (remaining 38814 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 19.35: 16799 19.35 - 38.71: 383 38.71 - 58.06: 61 58.06 - 77.42: 15 77.42 - 96.77: 13 Dihedral angle restraints: 17271 sinusoidal: 7186 harmonic: 10085 Sorted by residual: dihedral pdb=" CA LYS A 226 " pdb=" C LYS A 226 " pdb=" N PRO A 227 " pdb=" CA PRO A 227 " ideal model delta harmonic sigma weight residual 180.00 153.56 26.44 0 5.00e+00 4.00e-02 2.80e+01 dihedral pdb=" C5' FMN A 502 " pdb=" O5' FMN A 502 " pdb=" P FMN A 502 " pdb=" O1P FMN A 502 " ideal model delta sinusoidal sigma weight residual 75.26 172.03 -96.77 1 2.00e+01 2.50e-03 2.68e+01 dihedral pdb=" CA PHE P 202 " pdb=" C PHE P 202 " pdb=" N PRO P 203 " pdb=" CA PRO P 203 " ideal model delta harmonic sigma weight residual -180.00 -154.57 -25.43 0 5.00e+00 4.00e-02 2.59e+01 ... (remaining 17268 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.223: 4213 0.223 - 0.445: 4 0.445 - 0.668: 0 0.668 - 0.890: 0 0.890 - 1.113: 4 Chirality restraints: 4221 Sorted by residual: chirality pdb="FE4 SF4 M 801 " pdb=" S1 SF4 M 801 " pdb=" S2 SF4 M 801 " pdb=" S3 SF4 M 801 " both_signs ideal model delta sigma weight residual False 10.55 9.44 1.11 2.00e-01 2.50e+01 3.10e+01 chirality pdb="FE3 SF4 M 801 " pdb=" S1 SF4 M 801 " pdb=" S2 SF4 M 801 " pdb=" S4 SF4 M 801 " both_signs ideal model delta sigma weight residual False -10.55 -9.47 -1.09 2.00e-01 2.50e+01 2.95e+01 chirality pdb="FE1 SF4 M 801 " pdb=" S2 SF4 M 801 " pdb=" S3 SF4 M 801 " pdb=" S4 SF4 M 801 " both_signs ideal model delta sigma weight residual False -10.55 -9.52 -1.04 2.00e-01 2.50e+01 2.70e+01 ... (remaining 4218 not shown) Planarity restraints: 5009 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C MET W 10 " -0.065 5.00e-02 4.00e+02 9.95e-02 1.58e+01 pdb=" N PRO W 11 " 0.172 5.00e-02 4.00e+02 pdb=" CA PRO W 11 " -0.046 5.00e-02 4.00e+02 pdb=" CD PRO W 11 " -0.060 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ARG C 59 " -0.015 2.00e-02 2.50e+03 2.99e-02 8.96e+00 pdb=" C ARG C 59 " 0.052 2.00e-02 2.50e+03 pdb=" O ARG C 59 " -0.019 2.00e-02 2.50e+03 pdb=" N GLY C 60 " -0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C CYS M 128 " 0.048 5.00e-02 4.00e+02 7.35e-02 8.65e+00 pdb=" N PRO M 129 " -0.127 5.00e-02 4.00e+02 pdb=" CA PRO M 129 " 0.040 5.00e-02 4.00e+02 pdb=" CD PRO M 129 " 0.038 5.00e-02 4.00e+02 ... (remaining 5006 not shown) Histogram of nonbonded interaction distances: 1.48 - 2.17: 22 2.17 - 2.85: 10137 2.85 - 3.53: 42547 3.53 - 4.22: 68703 4.22 - 4.90: 113838 Nonbonded interactions: 235247 Sorted by model distance: nonbonded pdb=" O ILE M 177 " pdb=" N CYS M 179 " model vdw 1.482 2.520 nonbonded pdb=" O ILE J 206 " pdb=" OD2 ASP J 211 " model vdw 1.609 3.040 nonbonded pdb=" O ASN J 171 " pdb=" CD2 LEU J 181 " model vdw 1.923 3.460 nonbonded pdb=" OD1 ASN E 70 " pdb=" O4 8Q1 E 201 " model vdw 1.948 3.040 nonbonded pdb=" OE2 GLU C 204 " pdb=" NH1 ARG C 206 " model vdw 1.980 2.520 ... (remaining 235242 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 7.730 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 23.150 Check model and map are aligned: 0.440 Set scattering table: 0.220 Process input model: 76.180 Find NCS groups from input model: 0.790 Set up NCS constraints: 0.100 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:2.760 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 111.400 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7182 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 : 0.010 0.225 28632 Z= 0.640 Angle : 1.626 18.751 38819 Z= 1.109 Chirality : 0.065 1.113 4221 Planarity : 0.006 0.100 5009 Dihedral : 9.563 96.775 10783 Min Nonbonded Distance : 1.482 Molprobity Statistics. All-atom Clashscore : 28.48 Ramachandran Plot: Outliers : 3.01 % Allowed : 6.66 % Favored : 90.33 % Rotamer: Outliers : 0.33 % Allowed : 1.06 % Favored : 98.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.35 % 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: -1.70 (0.14), residues: 3453 helix: -2.50 (0.10), residues: 1215 sheet: -3.47 (0.22), residues: 338 loop : 0.55 (0.16), residues: 1900 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.003 TRP B 61 HIS 0.012 0.002 HIS Q 431 PHE 0.046 0.003 PHE C 106 TYR 0.037 0.003 TYR Q 151 ARG 0.011 0.001 ARG N 88 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6906 Ramachandran restraints generated. 3453 Oldfield, 0 Emsley, 3453 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6906 Ramachandran restraints generated. 3453 Oldfield, 0 Emsley, 3453 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1181 residues out of total 3012 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 1171 time to evaluate : 2.912 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 173 ILE cc_start: 0.8182 (mt) cc_final: 0.7963 (mt) REVERT: B 92 SER cc_start: 0.8707 (p) cc_final: 0.8052 (p) REVERT: G 101 ASN cc_start: 0.8330 (m110) cc_final: 0.8026 (p0) REVERT: H 48 THR cc_start: 0.7341 (t) cc_final: 0.7111 (t) REVERT: J 62 THR cc_start: 0.7151 (m) cc_final: 0.6820 (m) REVERT: J 146 VAL cc_start: 0.8442 (t) cc_final: 0.8082 (t) REVERT: J 212 ARG cc_start: 0.8211 (OUTLIER) cc_final: 0.7883 (mtp180) REVERT: J 223 PHE cc_start: 0.5773 (m-10) cc_final: 0.5447 (m-80) REVERT: J 347 LEU cc_start: 0.8442 (mp) cc_final: 0.8139 (tt) REVERT: L 61 ILE cc_start: 0.8518 (pt) cc_final: 0.8248 (pt) REVERT: L 79 ILE cc_start: 0.8832 (mt) cc_final: 0.8551 (mp) REVERT: M 271 MET cc_start: 0.7416 (mmt) cc_final: 0.7197 (mmt) REVERT: M 316 TYR cc_start: 0.6924 (m-10) cc_final: 0.6686 (m-10) REVERT: M 510 TRP cc_start: 0.6095 (t-100) cc_final: 0.5579 (t-100) REVERT: M 568 TYR cc_start: 0.7805 (t80) cc_final: 0.7571 (t80) REVERT: N 61 TRP cc_start: 0.8040 (p-90) cc_final: 0.6937 (p-90) REVERT: O 169 PHE cc_start: 0.7851 (m-80) cc_final: 0.7611 (m-10) REVERT: P 47 VAL cc_start: 0.7780 (t) cc_final: 0.7557 (t) REVERT: Q 264 ASN cc_start: 0.7824 (t0) cc_final: 0.7393 (t0) REVERT: Q 268 TRP cc_start: 0.8275 (OUTLIER) cc_final: 0.7010 (t60) outliers start: 10 outliers final: 4 residues processed: 1177 average time/residue: 0.4715 time to fit residues: 817.0119 Evaluate side-chains 637 residues out of total 3012 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 631 time to evaluate : 3.194 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 85 ARG Chi-restraints excluded: chain J residue 206 ILE Chi-restraints excluded: chain J residue 212 ARG Chi-restraints excluded: chain M residue 130 ILE Chi-restraints excluded: chain Q residue 268 TRP Chi-restraints excluded: chain Q residue 273 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 341 random chunks: chunk 287 optimal weight: 0.3980 chunk 258 optimal weight: 1.9990 chunk 143 optimal weight: 0.5980 chunk 88 optimal weight: 0.7980 chunk 174 optimal weight: 0.3980 chunk 138 optimal weight: 0.7980 chunk 267 optimal weight: 2.9990 chunk 103 optimal weight: 0.9990 chunk 162 optimal weight: 0.3980 chunk 198 optimal weight: 0.5980 chunk 309 optimal weight: 0.5980 overall best weight: 0.4780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 44 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 164 ASN A 393 ASN A 441 HIS C 95 HIS E 48 HIS E 70 ASN E 72 HIS ** E 102 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 126 HIS F 62 GLN ** F 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 86 GLN G 80 GLN G 101 ASN ** H 50 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 73 GLN H 83 GLN H 89 ASN H 111 GLN I 21 GLN I 36 GLN J 122 HIS J 171 ASN J 275 HIS J 285 HIS ** K 77 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 205 GLN ** M 425 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 444 HIS M 498 GLN M 514 ASN M 688 GLN ** N 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 69 ASN O 133 GLN ** O 182 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 187 GLN O 189 ASN P 105 ASN P 180 ASN Q 79 ASN ** Q 147 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 182 ASN Q 183 HIS Q 234 GLN Q 339 GLN ** Q 431 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** T 41 HIS T 64 ASN Total number of N/Q/H flips: 40 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7613 moved from start: 0.4036 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.070 28632 Z= 0.271 Angle : 0.791 10.720 38819 Z= 0.409 Chirality : 0.048 0.200 4221 Planarity : 0.006 0.072 5009 Dihedral : 7.213 100.338 3897 Min Nonbonded Distance : 2.010 Molprobity Statistics. All-atom Clashscore : 18.08 Ramachandran Plot: Outliers : 0.93 % Allowed : 5.85 % Favored : 93.22 % Rotamer: Outliers : 3.36 % Allowed : 11.88 % Favored : 84.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.35 % Cis-general : 0.00 % Twisted Proline : 1.44 % Twisted General : 0.03 % 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: -1.54 (0.14), residues: 3453 helix: -0.94 (0.13), residues: 1238 sheet: -2.94 (0.21), residues: 395 loop : -0.46 (0.15), residues: 1820 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP J 108 HIS 0.014 0.002 HIS E 126 PHE 0.036 0.002 PHE P 137 TYR 0.024 0.002 TYR Q 226 ARG 0.012 0.001 ARG M 624 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6906 Ramachandran restraints generated. 3453 Oldfield, 0 Emsley, 3453 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6906 Ramachandran restraints generated. 3453 Oldfield, 0 Emsley, 3453 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 828 residues out of total 3012 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 101 poor density : 727 time to evaluate : 3.170 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 164 ASN cc_start: 0.5294 (m110) cc_final: 0.4703 (m-40) REVERT: A 177 TYR cc_start: 0.7378 (m-80) cc_final: 0.7025 (m-80) REVERT: A 276 PHE cc_start: 0.6421 (m-10) cc_final: 0.6183 (m-80) REVERT: E 96 VAL cc_start: 0.8030 (t) cc_final: 0.7627 (t) REVERT: F 19 ILE cc_start: 0.8211 (OUTLIER) cc_final: 0.7892 (pt) REVERT: F 45 LYS cc_start: 0.9248 (tppt) cc_final: 0.8812 (tppt) REVERT: G 101 ASN cc_start: 0.8546 (m-40) cc_final: 0.7979 (p0) REVERT: G 118 ILE cc_start: 0.8556 (mt) cc_final: 0.8321 (mt) REVERT: J 291 PHE cc_start: 0.8026 (p90) cc_final: 0.7744 (p90) REVERT: K 78 ASP cc_start: 0.5437 (OUTLIER) cc_final: 0.4863 (p0) REVERT: K 86 ASP cc_start: 0.7848 (t0) cc_final: 0.7415 (t0) REVERT: K 96 MET cc_start: 0.7078 (mpp) cc_final: 0.6847 (mpp) REVERT: L 87 MET cc_start: 0.7831 (mmm) cc_final: 0.7477 (mmm) REVERT: L 146 ASP cc_start: 0.7575 (p0) cc_final: 0.7308 (p0) REVERT: N 21 ARG cc_start: 0.6101 (ttt-90) cc_final: 0.3784 (tpt170) REVERT: N 61 TRP cc_start: 0.8114 (p-90) cc_final: 0.6610 (p-90) REVERT: N 76 ASP cc_start: 0.7929 (t0) cc_final: 0.7687 (t0) REVERT: O 191 ASN cc_start: 0.7527 (m-40) cc_final: 0.7080 (t0) REVERT: P 204 LEU cc_start: 0.8908 (OUTLIER) cc_final: 0.8674 (tp) REVERT: Q 194 LEU cc_start: 0.7773 (mt) cc_final: 0.6853 (mp) REVERT: Q 264 ASN cc_start: 0.7748 (t0) cc_final: 0.7415 (t0) REVERT: Q 279 THR cc_start: 0.7897 (p) cc_final: 0.7401 (t) REVERT: W 20 ASP cc_start: 0.7711 (p0) cc_final: 0.7510 (p0) outliers start: 101 outliers final: 42 residues processed: 782 average time/residue: 0.4002 time to fit residues: 489.0907 Evaluate side-chains 622 residues out of total 3012 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 577 time to evaluate : 3.031 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 251 SER Chi-restraints excluded: chain A residue 299 LEU Chi-restraints excluded: chain A residue 307 VAL Chi-restraints excluded: chain A residue 308 THR Chi-restraints excluded: chain A residue 385 CYS Chi-restraints excluded: chain B residue 117 CYS Chi-restraints excluded: chain C residue 127 THR Chi-restraints excluded: chain C residue 147 VAL Chi-restraints excluded: chain F residue 19 ILE Chi-restraints excluded: chain F residue 58 CYS Chi-restraints excluded: chain F residue 76 ASN Chi-restraints excluded: chain F residue 92 GLU Chi-restraints excluded: chain H residue 53 ASN Chi-restraints excluded: chain I residue 71 SER Chi-restraints excluded: chain J residue 69 VAL Chi-restraints excluded: chain J residue 296 PHE Chi-restraints excluded: chain J residue 325 THR Chi-restraints excluded: chain J residue 358 THR Chi-restraints excluded: chain K residue 78 ASP Chi-restraints excluded: chain L residue 67 VAL Chi-restraints excluded: chain M residue 31 LEU Chi-restraints excluded: chain M residue 168 LEU Chi-restraints excluded: chain M residue 182 CYS Chi-restraints excluded: chain M residue 265 THR Chi-restraints excluded: chain M residue 314 LEU Chi-restraints excluded: chain M residue 368 THR Chi-restraints excluded: chain M residue 465 VAL Chi-restraints excluded: chain M residue 564 CYS Chi-restraints excluded: chain M residue 627 SER Chi-restraints excluded: chain O residue 121 MET Chi-restraints excluded: chain O residue 141 MET Chi-restraints excluded: chain P residue 43 THR Chi-restraints excluded: chain P residue 69 LEU Chi-restraints excluded: chain P residue 114 LEU Chi-restraints excluded: chain P residue 147 THR Chi-restraints excluded: chain P residue 148 ASP Chi-restraints excluded: chain P residue 180 ASN Chi-restraints excluded: chain P residue 204 LEU Chi-restraints excluded: chain Q residue 158 LEU Chi-restraints excluded: chain Q residue 208 GLU Chi-restraints excluded: chain Q residue 273 ILE Chi-restraints excluded: chain Q residue 313 GLN Chi-restraints excluded: chain Q residue 386 THR Chi-restraints excluded: chain T residue 84 VAL Chi-restraints excluded: chain T residue 99 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 341 random chunks: chunk 172 optimal weight: 0.9990 chunk 96 optimal weight: 0.0870 chunk 257 optimal weight: 1.9990 chunk 210 optimal weight: 3.9990 chunk 85 optimal weight: 1.9990 chunk 310 optimal weight: 0.4980 chunk 335 optimal weight: 4.9990 chunk 276 optimal weight: 0.5980 chunk 307 optimal weight: 0.9990 chunk 105 optimal weight: 0.0870 chunk 248 optimal weight: 4.9990 overall best weight: 0.4538 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 44 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 220 GLN A 313 ASN ** A 393 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 72 HIS E 102 HIS F 81 ASN F 86 GLN F 93 ASN G 80 GLN H 50 GLN ** H 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 111 GLN J 183 ASN K 77 HIS L 167 ASN ** M 278 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 425 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 514 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 522 GLN N 69 ASN N 72 ASN N 91 HIS N 113 HIS O 69 ASN O 133 GLN ** O 182 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 187 GLN P 82 ASN P 180 ASN P 247 GLN Q 79 ASN ** Q 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 88 HIS Q 147 ASN Q 431 HIS T 41 HIS ** T 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 8 GLN Total number of N/Q/H flips: 30 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7758 moved from start: 0.4967 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 28632 Z= 0.226 Angle : 0.687 9.244 38819 Z= 0.351 Chirality : 0.045 0.231 4221 Planarity : 0.005 0.072 5009 Dihedral : 6.458 89.008 3883 Min Nonbonded Distance : 2.105 Molprobity Statistics. All-atom Clashscore : 15.86 Ramachandran Plot: Outliers : 0.84 % Allowed : 6.52 % Favored : 92.64 % Rotamer: Outliers : 3.33 % Allowed : 14.64 % Favored : 82.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.35 % Cis-general : 0.00 % Twisted Proline : 0.48 % 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 (0.14), residues: 3453 helix: -0.15 (0.14), residues: 1242 sheet: -2.52 (0.22), residues: 397 loop : -0.71 (0.15), residues: 1814 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP I 14 HIS 0.009 0.001 HIS T 41 PHE 0.029 0.002 PHE M 414 TYR 0.020 0.002 TYR N 124 ARG 0.013 0.001 ARG F 40 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6906 Ramachandran restraints generated. 3453 Oldfield, 0 Emsley, 3453 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6906 Ramachandran restraints generated. 3453 Oldfield, 0 Emsley, 3453 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 733 residues out of total 3012 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 100 poor density : 633 time to evaluate : 3.302 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 70 MET cc_start: 0.7790 (tpp) cc_final: 0.7456 (tpp) REVERT: B 81 THR cc_start: 0.8069 (p) cc_final: 0.7861 (p) REVERT: C 96 MET cc_start: 0.7694 (tmm) cc_final: 0.7265 (tmm) REVERT: C 103 MET cc_start: 0.7505 (ptm) cc_final: 0.6387 (ptp) REVERT: C 110 PHE cc_start: 0.6615 (OUTLIER) cc_final: 0.5647 (m-10) REVERT: E 49 GLN cc_start: 0.7409 (mt0) cc_final: 0.7091 (mt0) REVERT: E 65 GLU cc_start: 0.7677 (tm-30) cc_final: 0.7346 (tm-30) REVERT: F 19 ILE cc_start: 0.8421 (OUTLIER) cc_final: 0.8160 (pt) REVERT: H 94 MET cc_start: 0.7727 (mmm) cc_final: 0.7252 (mmm) REVERT: I 11 LEU cc_start: 0.7654 (tp) cc_final: 0.7118 (mt) REVERT: K 78 ASP cc_start: 0.5548 (OUTLIER) cc_final: 0.5230 (p0) REVERT: K 86 ASP cc_start: 0.7979 (t0) cc_final: 0.7235 (t0) REVERT: L 79 ILE cc_start: 0.8711 (mp) cc_final: 0.8420 (mp) REVERT: L 146 ASP cc_start: 0.7733 (p0) cc_final: 0.7428 (p0) REVERT: L 168 LYS cc_start: 0.8110 (mmmt) cc_final: 0.7731 (mmmt) REVERT: M 431 LEU cc_start: 0.8553 (OUTLIER) cc_final: 0.8344 (mp) REVERT: N 21 ARG cc_start: 0.5844 (ttt-90) cc_final: 0.3777 (tpt170) REVERT: N 61 TRP cc_start: 0.8181 (p-90) cc_final: 0.6631 (p-90) REVERT: Q 98 VAL cc_start: 0.8686 (OUTLIER) cc_final: 0.8434 (t) REVERT: Q 144 MET cc_start: 0.7971 (mpp) cc_final: 0.7375 (mpp) REVERT: Q 241 MET cc_start: 0.6068 (mmp) cc_final: 0.5841 (mmp) REVERT: Q 451 ILE cc_start: 0.7863 (OUTLIER) cc_final: 0.7229 (tp) REVERT: W 20 ASP cc_start: 0.7589 (p0) cc_final: 0.7382 (p0) outliers start: 100 outliers final: 50 residues processed: 697 average time/residue: 0.3995 time to fit residues: 436.4861 Evaluate side-chains 603 residues out of total 3012 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 547 time to evaluate : 2.974 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 167 SER Chi-restraints excluded: chain A residue 212 LEU Chi-restraints excluded: chain A residue 251 SER Chi-restraints excluded: chain A residue 299 LEU Chi-restraints excluded: chain A residue 307 VAL Chi-restraints excluded: chain A residue 308 THR Chi-restraints excluded: chain A residue 337 MET Chi-restraints excluded: chain B residue 129 GLU Chi-restraints excluded: chain B residue 145 ILE Chi-restraints excluded: chain B residue 172 GLU Chi-restraints excluded: chain C residue 69 ASP Chi-restraints excluded: chain C residue 110 PHE Chi-restraints excluded: chain C residue 127 THR Chi-restraints excluded: chain C residue 194 ILE Chi-restraints excluded: chain F residue 19 ILE Chi-restraints excluded: chain F residue 76 ASN Chi-restraints excluded: chain F residue 92 GLU Chi-restraints excluded: chain G residue 83 VAL Chi-restraints excluded: chain G residue 100 VAL Chi-restraints excluded: chain G residue 105 MET Chi-restraints excluded: chain G residue 108 LEU Chi-restraints excluded: chain G residue 145 VAL Chi-restraints excluded: chain J residue 315 THR Chi-restraints excluded: chain J residue 325 THR Chi-restraints excluded: chain J residue 343 THR Chi-restraints excluded: chain K residue 78 ASP Chi-restraints excluded: chain L residue 67 VAL Chi-restraints excluded: chain L residue 125 VAL Chi-restraints excluded: chain M residue 31 LEU Chi-restraints excluded: chain M residue 34 VAL Chi-restraints excluded: chain M residue 182 CYS Chi-restraints excluded: chain M residue 210 ILE Chi-restraints excluded: chain M residue 265 THR Chi-restraints excluded: chain M residue 314 LEU Chi-restraints excluded: chain M residue 368 THR Chi-restraints excluded: chain M residue 431 LEU Chi-restraints excluded: chain M residue 438 LEU Chi-restraints excluded: chain M residue 465 VAL Chi-restraints excluded: chain M residue 564 CYS Chi-restraints excluded: chain M residue 627 SER Chi-restraints excluded: chain M residue 650 SER Chi-restraints excluded: chain N residue 129 THR Chi-restraints excluded: chain O residue 38 LEU Chi-restraints excluded: chain O residue 141 MET Chi-restraints excluded: chain P residue 43 THR Chi-restraints excluded: chain P residue 69 LEU Chi-restraints excluded: chain P residue 244 VAL Chi-restraints excluded: chain Q residue 79 ASN Chi-restraints excluded: chain Q residue 83 ASN Chi-restraints excluded: chain Q residue 98 VAL Chi-restraints excluded: chain Q residue 158 LEU Chi-restraints excluded: chain Q residue 208 GLU Chi-restraints excluded: chain Q residue 386 THR Chi-restraints excluded: chain Q residue 451 ILE Chi-restraints excluded: chain T residue 84 VAL Chi-restraints excluded: chain T residue 99 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 341 random chunks: chunk 306 optimal weight: 1.9990 chunk 233 optimal weight: 1.9990 chunk 161 optimal weight: 1.9990 chunk 34 optimal weight: 1.9990 chunk 148 optimal weight: 4.9990 chunk 208 optimal weight: 3.9990 chunk 311 optimal weight: 2.9990 chunk 329 optimal weight: 0.3980 chunk 162 optimal weight: 1.9990 chunk 295 optimal weight: 1.9990 chunk 88 optimal weight: 0.8980 overall best weight: 1.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 220 GLN A 303 HIS A 376 HIS ** A 393 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 72 HIS F 22 HIS F 86 GLN H 53 ASN ** H 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 43 HIS J 79 GLN J 154 GLN J 166 HIS ** L 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 167 ASN M 59 GLN ** M 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 142 GLN ** M 278 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 514 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 72 ASN O 187 GLN P 82 ASN P 124 ASN P 131 ASN Q 87 GLN Q 183 HIS T 64 ASN Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8091 moved from start: 0.6527 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.100 28632 Z= 0.463 Angle : 0.830 10.968 38819 Z= 0.425 Chirality : 0.051 0.287 4221 Planarity : 0.007 0.075 5009 Dihedral : 6.680 91.586 3881 Min Nonbonded Distance : 2.026 Molprobity Statistics. All-atom Clashscore : 17.10 Ramachandran Plot: Outliers : 0.87 % Allowed : 6.69 % Favored : 92.44 % Rotamer: Outliers : 4.26 % Allowed : 16.87 % Favored : 78.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.35 % Cis-general : 0.00 % Twisted Proline : 1.44 % Twisted General : 0.03 % 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: -1.28 (0.14), residues: 3453 helix: -0.02 (0.14), residues: 1236 sheet: -2.22 (0.23), residues: 396 loop : -1.05 (0.15), residues: 1821 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.003 TRP M 510 HIS 0.008 0.002 HIS P 196 PHE 0.040 0.003 PHE J 59 TYR 0.031 0.003 TYR M 530 ARG 0.020 0.001 ARG M 501 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6906 Ramachandran restraints generated. 3453 Oldfield, 0 Emsley, 3453 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6906 Ramachandran restraints generated. 3453 Oldfield, 0 Emsley, 3453 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 706 residues out of total 3012 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 128 poor density : 578 time to evaluate : 3.452 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 214 GLU cc_start: 0.7223 (mm-30) cc_final: 0.6974 (mm-30) REVERT: C 68 ASP cc_start: 0.7818 (t70) cc_final: 0.7504 (t0) REVERT: C 96 MET cc_start: 0.7941 (tmm) cc_final: 0.7736 (tmm) REVERT: E 49 GLN cc_start: 0.7675 (mt0) cc_final: 0.7418 (mt0) REVERT: E 65 GLU cc_start: 0.7746 (tm-30) cc_final: 0.7454 (tm-30) REVERT: F 81 ASN cc_start: 0.8034 (m110) cc_final: 0.7820 (m-40) REVERT: I 11 LEU cc_start: 0.7700 (tp) cc_final: 0.7149 (mt) REVERT: J 296 PHE cc_start: 0.6641 (OUTLIER) cc_final: 0.6400 (p90) REVERT: K 86 ASP cc_start: 0.8021 (t0) cc_final: 0.7709 (t0) REVERT: K 91 LEU cc_start: 0.8881 (tp) cc_final: 0.8540 (tp) REVERT: L 146 ASP cc_start: 0.7765 (p0) cc_final: 0.7565 (p0) REVERT: L 152 VAL cc_start: 0.7741 (OUTLIER) cc_final: 0.7458 (m) REVERT: L 168 LYS cc_start: 0.8299 (mmmt) cc_final: 0.7950 (mmtt) REVERT: M 431 LEU cc_start: 0.9117 (OUTLIER) cc_final: 0.8849 (mp) REVERT: M 462 PHE cc_start: 0.7871 (t80) cc_final: 0.7547 (t80) REVERT: N 21 ARG cc_start: 0.5926 (ttt-90) cc_final: 0.3923 (tpt170) REVERT: N 61 TRP cc_start: 0.8426 (p-90) cc_final: 0.6888 (p-90) REVERT: O 92 TRP cc_start: 0.7905 (t60) cc_final: 0.7698 (t60) REVERT: O 176 CYS cc_start: 0.7470 (OUTLIER) cc_final: 0.7245 (t) REVERT: O 191 ASN cc_start: 0.7542 (t0) cc_final: 0.6987 (t0) REVERT: P 114 LEU cc_start: 0.9230 (OUTLIER) cc_final: 0.8854 (tt) REVERT: Q 241 MET cc_start: 0.7236 (mmp) cc_final: 0.6906 (mmt) REVERT: Q 451 ILE cc_start: 0.8273 (OUTLIER) cc_final: 0.8072 (mm) REVERT: Q 458 PHE cc_start: 0.8087 (m-80) cc_final: 0.7824 (m-80) REVERT: T 62 GLU cc_start: 0.7321 (tt0) cc_final: 0.7103 (tt0) outliers start: 128 outliers final: 81 residues processed: 657 average time/residue: 0.4024 time to fit residues: 423.4070 Evaluate side-chains 591 residues out of total 3012 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 87 poor density : 504 time to evaluate : 3.188 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 125 CYS Chi-restraints excluded: chain A residue 130 ILE Chi-restraints excluded: chain A residue 212 LEU Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain A residue 251 SER Chi-restraints excluded: chain A residue 287 THR Chi-restraints excluded: chain A residue 299 LEU Chi-restraints excluded: chain A residue 307 VAL Chi-restraints excluded: chain A residue 409 ILE Chi-restraints excluded: chain A residue 435 VAL Chi-restraints excluded: chain B residue 71 THR Chi-restraints excluded: chain B residue 129 GLU Chi-restraints excluded: chain B residue 145 ILE Chi-restraints excluded: chain B residue 172 GLU Chi-restraints excluded: chain C residue 69 ASP Chi-restraints excluded: chain C residue 79 LEU Chi-restraints excluded: chain C residue 110 PHE Chi-restraints excluded: chain C residue 127 THR Chi-restraints excluded: chain C residue 194 ILE Chi-restraints excluded: chain E residue 54 ILE Chi-restraints excluded: chain E residue 103 VAL Chi-restraints excluded: chain F residue 42 VAL Chi-restraints excluded: chain F residue 76 ASN Chi-restraints excluded: chain F residue 92 GLU Chi-restraints excluded: chain G residue 83 VAL Chi-restraints excluded: chain G residue 86 VAL Chi-restraints excluded: chain G residue 100 VAL Chi-restraints excluded: chain G residue 108 LEU Chi-restraints excluded: chain G residue 126 PHE Chi-restraints excluded: chain G residue 134 ASP Chi-restraints excluded: chain G residue 145 VAL Chi-restraints excluded: chain H residue 8 THR Chi-restraints excluded: chain I residue 8 ILE Chi-restraints excluded: chain I residue 70 MET Chi-restraints excluded: chain J residue 129 LEU Chi-restraints excluded: chain J residue 138 ASN Chi-restraints excluded: chain J residue 190 VAL Chi-restraints excluded: chain J residue 296 PHE Chi-restraints excluded: chain J residue 325 THR Chi-restraints excluded: chain L residue 67 VAL Chi-restraints excluded: chain L residue 125 VAL Chi-restraints excluded: chain L residue 152 VAL Chi-restraints excluded: chain L residue 165 SER Chi-restraints excluded: chain M residue 31 LEU Chi-restraints excluded: chain M residue 32 ILE Chi-restraints excluded: chain M residue 78 CYS Chi-restraints excluded: chain M residue 97 MET Chi-restraints excluded: chain M residue 110 LYS Chi-restraints excluded: chain M residue 168 LEU Chi-restraints excluded: chain M residue 182 CYS Chi-restraints excluded: chain M residue 187 SER Chi-restraints excluded: chain M residue 210 ILE Chi-restraints excluded: chain M residue 225 ILE Chi-restraints excluded: chain M residue 265 THR Chi-restraints excluded: chain M residue 314 LEU Chi-restraints excluded: chain M residue 368 THR Chi-restraints excluded: chain M residue 431 LEU Chi-restraints excluded: chain M residue 451 ILE Chi-restraints excluded: chain M residue 490 LEU Chi-restraints excluded: chain M residue 540 ASN Chi-restraints excluded: chain M residue 564 CYS Chi-restraints excluded: chain M residue 590 THR Chi-restraints excluded: chain M residue 627 SER Chi-restraints excluded: chain M residue 649 VAL Chi-restraints excluded: chain M residue 650 SER Chi-restraints excluded: chain M residue 691 ILE Chi-restraints excluded: chain O residue 176 CYS Chi-restraints excluded: chain P residue 43 THR Chi-restraints excluded: chain P residue 47 VAL Chi-restraints excluded: chain P residue 69 LEU Chi-restraints excluded: chain P residue 114 LEU Chi-restraints excluded: chain P residue 134 SER Chi-restraints excluded: chain P residue 244 VAL Chi-restraints excluded: chain Q residue 98 VAL Chi-restraints excluded: chain Q residue 158 LEU Chi-restraints excluded: chain Q residue 189 THR Chi-restraints excluded: chain Q residue 232 VAL Chi-restraints excluded: chain Q residue 273 ILE Chi-restraints excluded: chain Q residue 322 SER Chi-restraints excluded: chain Q residue 386 THR Chi-restraints excluded: chain Q residue 400 ILE Chi-restraints excluded: chain Q residue 451 ILE Chi-restraints excluded: chain T residue 32 VAL Chi-restraints excluded: chain T residue 40 THR Chi-restraints excluded: chain T residue 78 SER Chi-restraints excluded: chain T residue 84 VAL Chi-restraints excluded: chain T residue 99 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 341 random chunks: chunk 274 optimal weight: 0.0980 chunk 187 optimal weight: 0.6980 chunk 4 optimal weight: 3.9990 chunk 245 optimal weight: 0.1980 chunk 135 optimal weight: 3.9990 chunk 281 optimal weight: 0.5980 chunk 227 optimal weight: 0.9990 chunk 0 optimal weight: 6.9990 chunk 168 optimal weight: 0.0000 chunk 295 optimal weight: 1.9990 chunk 83 optimal weight: 2.9990 overall best weight: 0.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 393 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 83 ASN C 196 GLN E 72 HIS F 31 GLN H 53 ASN ** H 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 72 HIS L 71 HIS L 167 ASN ** M 105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 359 ASN ** M 444 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 514 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 182 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 187 GLN P 82 ASN Q 112 HIS T 64 ASN T 66 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8011 moved from start: 0.6756 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 28632 Z= 0.196 Angle : 0.663 9.567 38819 Z= 0.335 Chirality : 0.043 0.183 4221 Planarity : 0.005 0.063 5009 Dihedral : 6.138 82.748 3881 Min Nonbonded Distance : 2.066 Molprobity Statistics. All-atom Clashscore : 14.33 Ramachandran Plot: Outliers : 0.84 % Allowed : 6.11 % Favored : 93.05 % Rotamer: Outliers : 3.26 % Allowed : 19.56 % Favored : 77.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.35 % Cis-general : 0.00 % Twisted Proline : 0.96 % 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: -0.93 (0.14), residues: 3453 helix: 0.46 (0.15), residues: 1225 sheet: -1.87 (0.23), residues: 400 loop : -1.03 (0.15), residues: 1828 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.001 TRP J 134 HIS 0.008 0.001 HIS P 181 PHE 0.031 0.002 PHE P 202 TYR 0.028 0.002 TYR E 40 ARG 0.006 0.001 ARG N 106 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6906 Ramachandran restraints generated. 3453 Oldfield, 0 Emsley, 3453 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6906 Ramachandran restraints generated. 3453 Oldfield, 0 Emsley, 3453 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 665 residues out of total 3012 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 98 poor density : 567 time to evaluate : 3.429 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 214 GLU cc_start: 0.7165 (mm-30) cc_final: 0.6926 (mm-30) REVERT: B 147 MET cc_start: 0.9058 (OUTLIER) cc_final: 0.8791 (mmm) REVERT: C 96 MET cc_start: 0.8048 (tmm) cc_final: 0.7781 (tmm) REVERT: E 40 TYR cc_start: 0.8047 (t80) cc_final: 0.7711 (t80) REVERT: E 65 GLU cc_start: 0.7762 (tm-30) cc_final: 0.7532 (tm-30) REVERT: F 18 GLU cc_start: 0.7553 (pm20) cc_final: 0.6434 (pm20) REVERT: F 81 ASN cc_start: 0.8081 (m110) cc_final: 0.7863 (m-40) REVERT: I 11 LEU cc_start: 0.7613 (tp) cc_final: 0.7079 (mt) REVERT: I 28 TYR cc_start: 0.7068 (OUTLIER) cc_final: 0.6498 (m-10) REVERT: J 296 PHE cc_start: 0.6586 (OUTLIER) cc_final: 0.6246 (p90) REVERT: J 315 THR cc_start: 0.7935 (t) cc_final: 0.7696 (t) REVERT: K 78 ASP cc_start: 0.6310 (p0) cc_final: 0.5906 (p0) REVERT: K 86 ASP cc_start: 0.7912 (t0) cc_final: 0.7648 (t0) REVERT: K 91 LEU cc_start: 0.8800 (tp) cc_final: 0.8579 (tp) REVERT: K 96 MET cc_start: 0.7743 (mpp) cc_final: 0.7230 (ptp) REVERT: L 146 ASP cc_start: 0.7754 (p0) cc_final: 0.7467 (p0) REVERT: L 152 VAL cc_start: 0.7720 (OUTLIER) cc_final: 0.7497 (m) REVERT: M 462 PHE cc_start: 0.7805 (t80) cc_final: 0.7582 (t80) REVERT: N 21 ARG cc_start: 0.5714 (ttt-90) cc_final: 0.3884 (tpt170) REVERT: N 61 TRP cc_start: 0.8309 (p-90) cc_final: 0.6850 (p-90) REVERT: O 141 MET cc_start: 0.7574 (OUTLIER) cc_final: 0.7350 (ttp) REVERT: P 114 LEU cc_start: 0.9205 (OUTLIER) cc_final: 0.8899 (tt) REVERT: Q 241 MET cc_start: 0.7046 (mmp) cc_final: 0.6778 (tpp) REVERT: Q 451 ILE cc_start: 0.8254 (OUTLIER) cc_final: 0.7759 (tp) REVERT: Q 458 PHE cc_start: 0.7956 (m-80) cc_final: 0.7736 (m-80) REVERT: T 52 ARG cc_start: 0.8610 (ptp-170) cc_final: 0.8298 (ptp90) outliers start: 98 outliers final: 52 residues processed: 625 average time/residue: 0.4048 time to fit residues: 395.2016 Evaluate side-chains 565 residues out of total 3012 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 506 time to evaluate : 3.243 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 212 LEU Chi-restraints excluded: chain A residue 251 SER Chi-restraints excluded: chain A residue 287 THR Chi-restraints excluded: chain A residue 307 VAL Chi-restraints excluded: chain A residue 448 GLU Chi-restraints excluded: chain B residue 147 MET Chi-restraints excluded: chain B residue 172 GLU Chi-restraints excluded: chain C residue 69 ASP Chi-restraints excluded: chain C residue 147 VAL Chi-restraints excluded: chain C residue 194 ILE Chi-restraints excluded: chain E residue 54 ILE Chi-restraints excluded: chain F residue 25 GLN Chi-restraints excluded: chain F residue 61 VAL Chi-restraints excluded: chain F residue 76 ASN Chi-restraints excluded: chain F residue 92 GLU Chi-restraints excluded: chain G residue 81 ASP Chi-restraints excluded: chain G residue 100 VAL Chi-restraints excluded: chain G residue 105 MET Chi-restraints excluded: chain G residue 108 LEU Chi-restraints excluded: chain G residue 126 PHE Chi-restraints excluded: chain G residue 145 VAL Chi-restraints excluded: chain I residue 8 ILE Chi-restraints excluded: chain I residue 28 TYR Chi-restraints excluded: chain I residue 63 SER Chi-restraints excluded: chain I residue 95 VAL Chi-restraints excluded: chain J residue 296 PHE Chi-restraints excluded: chain L residue 67 VAL Chi-restraints excluded: chain L residue 125 VAL Chi-restraints excluded: chain L residue 152 VAL Chi-restraints excluded: chain L residue 166 TRP Chi-restraints excluded: chain M residue 31 LEU Chi-restraints excluded: chain M residue 103 LEU Chi-restraints excluded: chain M residue 146 PHE Chi-restraints excluded: chain M residue 168 LEU Chi-restraints excluded: chain M residue 210 ILE Chi-restraints excluded: chain M residue 225 ILE Chi-restraints excluded: chain M residue 265 THR Chi-restraints excluded: chain M residue 314 LEU Chi-restraints excluded: chain M residue 368 THR Chi-restraints excluded: chain M residue 519 ILE Chi-restraints excluded: chain M residue 564 CYS Chi-restraints excluded: chain M residue 650 SER Chi-restraints excluded: chain M residue 674 LEU Chi-restraints excluded: chain M residue 691 ILE Chi-restraints excluded: chain N residue 15 THR Chi-restraints excluded: chain O residue 141 MET Chi-restraints excluded: chain P residue 69 LEU Chi-restraints excluded: chain P residue 114 LEU Chi-restraints excluded: chain P residue 209 GLU Chi-restraints excluded: chain P residue 244 VAL Chi-restraints excluded: chain Q residue 98 VAL Chi-restraints excluded: chain Q residue 158 LEU Chi-restraints excluded: chain Q residue 206 GLU Chi-restraints excluded: chain Q residue 386 THR Chi-restraints excluded: chain Q residue 400 ILE Chi-restraints excluded: chain Q residue 451 ILE Chi-restraints excluded: chain Q residue 457 VAL Chi-restraints excluded: chain T residue 40 THR Chi-restraints excluded: chain T residue 99 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 341 random chunks: chunk 110 optimal weight: 1.9990 chunk 296 optimal weight: 0.7980 chunk 65 optimal weight: 0.9990 chunk 193 optimal weight: 0.9980 chunk 81 optimal weight: 0.9980 chunk 329 optimal weight: 0.6980 chunk 273 optimal weight: 1.9990 chunk 152 optimal weight: 0.7980 chunk 27 optimal weight: 0.9980 chunk 109 optimal weight: 0.0870 chunk 173 optimal weight: 2.9990 overall best weight: 0.6758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 393 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 40 ASN E 72 HIS G 142 GLN H 53 ASN ** H 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 167 ASN ** M 444 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 514 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 667 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 187 GLN P 82 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8066 moved from start: 0.7076 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 28632 Z= 0.255 Angle : 0.665 9.336 38819 Z= 0.335 Chirality : 0.045 0.251 4221 Planarity : 0.005 0.077 5009 Dihedral : 5.993 78.271 3881 Min Nonbonded Distance : 2.080 Molprobity Statistics. All-atom Clashscore : 14.12 Ramachandran Plot: Outliers : 0.90 % Allowed : 6.69 % Favored : 92.41 % Rotamer: Outliers : 3.66 % Allowed : 19.66 % Favored : 76.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.35 % Cis-general : 0.00 % Twisted Proline : 0.96 % 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: -0.84 (0.14), residues: 3453 helix: 0.55 (0.15), residues: 1233 sheet: -1.60 (0.24), residues: 399 loop : -1.06 (0.15), residues: 1821 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.002 TRP J 134 HIS 0.007 0.001 HIS T 122 PHE 0.026 0.002 PHE P 202 TYR 0.025 0.002 TYR J 89 ARG 0.013 0.001 ARG H 95 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6906 Ramachandran restraints generated. 3453 Oldfield, 0 Emsley, 3453 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6906 Ramachandran restraints generated. 3453 Oldfield, 0 Emsley, 3453 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 634 residues out of total 3012 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 110 poor density : 524 time to evaluate : 3.082 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 214 GLU cc_start: 0.7169 (mm-30) cc_final: 0.6950 (mm-30) REVERT: A 390 ASP cc_start: 0.6760 (t0) cc_final: 0.6323 (t0) REVERT: A 429 ASP cc_start: 0.8914 (OUTLIER) cc_final: 0.8633 (m-30) REVERT: C 140 GLN cc_start: 0.8635 (mt0) cc_final: 0.8422 (mt0) REVERT: E 65 GLU cc_start: 0.7805 (tm-30) cc_final: 0.7575 (tm-30) REVERT: F 81 ASN cc_start: 0.8020 (m110) cc_final: 0.7788 (m-40) REVERT: I 11 LEU cc_start: 0.7710 (tp) cc_final: 0.7232 (mt) REVERT: I 28 TYR cc_start: 0.6906 (OUTLIER) cc_final: 0.6349 (m-10) REVERT: J 220 MET cc_start: 0.7833 (tpp) cc_final: 0.7543 (tpp) REVERT: J 296 PHE cc_start: 0.6550 (OUTLIER) cc_final: 0.6084 (p90) REVERT: K 78 ASP cc_start: 0.6605 (p0) cc_final: 0.6185 (p0) REVERT: K 86 ASP cc_start: 0.8075 (t70) cc_final: 0.7562 (t0) REVERT: K 96 MET cc_start: 0.7742 (mpp) cc_final: 0.7415 (ptp) REVERT: L 146 ASP cc_start: 0.7709 (p0) cc_final: 0.7437 (p0) REVERT: L 152 VAL cc_start: 0.7866 (OUTLIER) cc_final: 0.7558 (m) REVERT: M 145 MET cc_start: 0.8354 (mmt) cc_final: 0.7971 (mmt) REVERT: M 333 PHE cc_start: 0.8131 (m-10) cc_final: 0.7929 (m-10) REVERT: M 707 MET cc_start: 0.8600 (mmp) cc_final: 0.8314 (mmp) REVERT: N 21 ARG cc_start: 0.5791 (ttt-90) cc_final: 0.3967 (tpt170) REVERT: N 61 TRP cc_start: 0.8325 (p-90) cc_final: 0.6894 (p-90) REVERT: P 63 GLU cc_start: 0.7462 (OUTLIER) cc_final: 0.7147 (pm20) REVERT: P 114 LEU cc_start: 0.9195 (OUTLIER) cc_final: 0.8913 (tt) REVERT: Q 197 MET cc_start: 0.6897 (mtp) cc_final: 0.6607 (ttm) REVERT: Q 253 LEU cc_start: 0.8381 (OUTLIER) cc_final: 0.8138 (tp) REVERT: Q 458 PHE cc_start: 0.8119 (m-80) cc_final: 0.7837 (m-80) REVERT: T 52 ARG cc_start: 0.8708 (ptp-170) cc_final: 0.8374 (ptp90) REVERT: W 27 ARG cc_start: 0.5859 (tpt90) cc_final: 0.5459 (tpt90) outliers start: 110 outliers final: 71 residues processed: 595 average time/residue: 0.3775 time to fit residues: 357.6484 Evaluate side-chains 565 residues out of total 3012 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 78 poor density : 487 time to evaluate : 3.189 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 130 ILE Chi-restraints excluded: chain A residue 212 LEU Chi-restraints excluded: chain A residue 251 SER Chi-restraints excluded: chain A residue 273 THR Chi-restraints excluded: chain A residue 287 THR Chi-restraints excluded: chain A residue 307 VAL Chi-restraints excluded: chain A residue 409 ILE Chi-restraints excluded: chain A residue 429 ASP Chi-restraints excluded: chain A residue 448 GLU Chi-restraints excluded: chain B residue 37 LYS Chi-restraints excluded: chain B residue 145 ILE Chi-restraints excluded: chain B residue 167 GLU Chi-restraints excluded: chain B residue 172 GLU Chi-restraints excluded: chain C residue 69 ASP Chi-restraints excluded: chain C residue 110 PHE Chi-restraints excluded: chain C residue 194 ILE Chi-restraints excluded: chain E residue 54 ILE Chi-restraints excluded: chain E residue 81 LEU Chi-restraints excluded: chain F residue 42 VAL Chi-restraints excluded: chain F residue 51 LEU Chi-restraints excluded: chain F residue 58 CYS Chi-restraints excluded: chain F residue 61 VAL Chi-restraints excluded: chain F residue 76 ASN Chi-restraints excluded: chain F residue 92 GLU Chi-restraints excluded: chain G residue 100 VAL Chi-restraints excluded: chain G residue 105 MET Chi-restraints excluded: chain G residue 108 LEU Chi-restraints excluded: chain G residue 125 GLU Chi-restraints excluded: chain G residue 145 VAL Chi-restraints excluded: chain I residue 8 ILE Chi-restraints excluded: chain I residue 28 TYR Chi-restraints excluded: chain I residue 29 GLN Chi-restraints excluded: chain I residue 63 SER Chi-restraints excluded: chain J residue 296 PHE Chi-restraints excluded: chain J residue 325 THR Chi-restraints excluded: chain L residue 67 VAL Chi-restraints excluded: chain L residue 70 GLU Chi-restraints excluded: chain L residue 76 LYS Chi-restraints excluded: chain L residue 86 ASN Chi-restraints excluded: chain L residue 125 VAL Chi-restraints excluded: chain L residue 152 VAL Chi-restraints excluded: chain L residue 166 TRP Chi-restraints excluded: chain M residue 31 LEU Chi-restraints excluded: chain M residue 146 PHE Chi-restraints excluded: chain M residue 187 SER Chi-restraints excluded: chain M residue 210 ILE Chi-restraints excluded: chain M residue 260 ASN Chi-restraints excluded: chain M residue 265 THR Chi-restraints excluded: chain M residue 314 LEU Chi-restraints excluded: chain M residue 368 THR Chi-restraints excluded: chain M residue 371 VAL Chi-restraints excluded: chain M residue 519 ILE Chi-restraints excluded: chain M residue 564 CYS Chi-restraints excluded: chain M residue 627 SER Chi-restraints excluded: chain M residue 649 VAL Chi-restraints excluded: chain M residue 650 SER Chi-restraints excluded: chain M residue 674 LEU Chi-restraints excluded: chain M residue 691 ILE Chi-restraints excluded: chain N residue 15 THR Chi-restraints excluded: chain O residue 133 GLN Chi-restraints excluded: chain O residue 191 ASN Chi-restraints excluded: chain O residue 201 ILE Chi-restraints excluded: chain O residue 223 PHE Chi-restraints excluded: chain O residue 233 SER Chi-restraints excluded: chain P residue 63 GLU Chi-restraints excluded: chain P residue 69 LEU Chi-restraints excluded: chain P residue 94 ILE Chi-restraints excluded: chain P residue 114 LEU Chi-restraints excluded: chain P residue 244 VAL Chi-restraints excluded: chain Q residue 98 VAL Chi-restraints excluded: chain Q residue 158 LEU Chi-restraints excluded: chain Q residue 253 LEU Chi-restraints excluded: chain Q residue 273 ILE Chi-restraints excluded: chain Q residue 386 THR Chi-restraints excluded: chain Q residue 400 ILE Chi-restraints excluded: chain Q residue 457 VAL Chi-restraints excluded: chain T residue 40 THR Chi-restraints excluded: chain T residue 99 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 341 random chunks: chunk 318 optimal weight: 1.9990 chunk 37 optimal weight: 0.8980 chunk 187 optimal weight: 0.2980 chunk 240 optimal weight: 4.9990 chunk 186 optimal weight: 1.9990 chunk 277 optimal weight: 0.9990 chunk 184 optimal weight: 0.5980 chunk 328 optimal weight: 1.9990 chunk 205 optimal weight: 0.6980 chunk 200 optimal weight: 3.9990 chunk 151 optimal weight: 3.9990 overall best weight: 0.6982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 393 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 418 GLN A 436 GLN E 72 HIS G 142 GLN H 53 ASN ** H 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 29 GLN ** L 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 444 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 514 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 667 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 82 ASN Q 79 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8083 moved from start: 0.7364 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 28632 Z= 0.252 Angle : 0.663 9.384 38819 Z= 0.334 Chirality : 0.044 0.221 4221 Planarity : 0.005 0.070 5009 Dihedral : 5.879 77.179 3881 Min Nonbonded Distance : 2.092 Molprobity Statistics. All-atom Clashscore : 14.80 Ramachandran Plot: Outliers : 0.90 % Allowed : 6.37 % Favored : 92.73 % Rotamer: Outliers : 3.89 % Allowed : 19.73 % Favored : 76.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.35 % Cis-general : 0.00 % Twisted Proline : 0.96 % 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: -0.78 (0.14), residues: 3453 helix: 0.62 (0.15), residues: 1229 sheet: -1.50 (0.25), residues: 408 loop : -1.05 (0.15), residues: 1816 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.052 0.002 TRP M 510 HIS 0.006 0.001 HIS T 122 PHE 0.039 0.002 PHE M 462 TYR 0.035 0.002 TYR E 40 ARG 0.005 0.000 ARG Q 254 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6906 Ramachandran restraints generated. 3453 Oldfield, 0 Emsley, 3453 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6906 Ramachandran restraints generated. 3453 Oldfield, 0 Emsley, 3453 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 644 residues out of total 3012 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 117 poor density : 527 time to evaluate : 3.213 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 214 GLU cc_start: 0.7205 (mm-30) cc_final: 0.6996 (mm-30) REVERT: A 390 ASP cc_start: 0.6785 (t0) cc_final: 0.6346 (t0) REVERT: A 429 ASP cc_start: 0.8884 (OUTLIER) cc_final: 0.8657 (m-30) REVERT: B 147 MET cc_start: 0.9123 (OUTLIER) cc_final: 0.8870 (mmm) REVERT: C 96 MET cc_start: 0.7679 (tmm) cc_final: 0.7397 (ttp) REVERT: C 103 MET cc_start: 0.7084 (ptt) cc_final: 0.6090 (ptm) REVERT: C 110 PHE cc_start: 0.6691 (OUTLIER) cc_final: 0.5921 (m-10) REVERT: E 65 GLU cc_start: 0.7812 (tm-30) cc_final: 0.7549 (tm-30) REVERT: F 81 ASN cc_start: 0.8211 (m110) cc_final: 0.7948 (m-40) REVERT: G 132 ASP cc_start: 0.6771 (p0) cc_final: 0.6378 (m-30) REVERT: H 95 ARG cc_start: 0.7977 (mpt-90) cc_final: 0.7549 (mtt-85) REVERT: I 28 TYR cc_start: 0.6965 (OUTLIER) cc_final: 0.6529 (m-10) REVERT: I 30 GLU cc_start: 0.7895 (pm20) cc_final: 0.7693 (pm20) REVERT: I 63 SER cc_start: 0.8802 (OUTLIER) cc_final: 0.8574 (m) REVERT: J 296 PHE cc_start: 0.6547 (OUTLIER) cc_final: 0.6024 (p90) REVERT: K 82 TYR cc_start: 0.7844 (m-10) cc_final: 0.7633 (m-80) REVERT: K 86 ASP cc_start: 0.8118 (t70) cc_final: 0.7670 (t0) REVERT: K 96 MET cc_start: 0.7686 (mpp) cc_final: 0.7228 (ptp) REVERT: L 146 ASP cc_start: 0.7757 (p0) cc_final: 0.7421 (p0) REVERT: L 152 VAL cc_start: 0.7919 (OUTLIER) cc_final: 0.7618 (m) REVERT: M 314 LEU cc_start: 0.8371 (OUTLIER) cc_final: 0.7949 (pp) REVERT: M 431 LEU cc_start: 0.8870 (OUTLIER) cc_final: 0.8614 (mp) REVERT: M 543 LYS cc_start: 0.6870 (ptmm) cc_final: 0.6529 (ptmm) REVERT: M 707 MET cc_start: 0.8602 (mmp) cc_final: 0.8395 (mmp) REVERT: N 21 ARG cc_start: 0.5762 (ttt-90) cc_final: 0.3961 (tpt170) REVERT: N 61 TRP cc_start: 0.8330 (p-90) cc_final: 0.6885 (p-90) REVERT: N 134 ILE cc_start: 0.9105 (mm) cc_final: 0.8894 (mm) REVERT: P 63 GLU cc_start: 0.7504 (OUTLIER) cc_final: 0.7196 (pm20) REVERT: P 114 LEU cc_start: 0.9124 (OUTLIER) cc_final: 0.8832 (tt) REVERT: P 215 GLU cc_start: 0.7598 (pm20) cc_final: 0.6878 (pm20) REVERT: Q 197 MET cc_start: 0.6921 (mtp) cc_final: 0.6670 (ttm) REVERT: Q 241 MET cc_start: 0.7461 (mmp) cc_final: 0.7090 (mmt) REVERT: Q 253 LEU cc_start: 0.8393 (OUTLIER) cc_final: 0.8116 (tp) REVERT: Q 458 PHE cc_start: 0.8020 (m-80) cc_final: 0.7763 (m-80) REVERT: T 52 ARG cc_start: 0.8697 (ptp-170) cc_final: 0.8492 (ptp-170) REVERT: W 27 ARG cc_start: 0.5882 (tpt90) cc_final: 0.5621 (tpt90) outliers start: 117 outliers final: 72 residues processed: 599 average time/residue: 0.3811 time to fit residues: 363.8107 Evaluate side-chains 577 residues out of total 3012 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 84 poor density : 493 time to evaluate : 3.025 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 130 ILE Chi-restraints excluded: chain A residue 212 LEU Chi-restraints excluded: chain A residue 251 SER Chi-restraints excluded: chain A residue 287 THR Chi-restraints excluded: chain A residue 307 VAL Chi-restraints excluded: chain A residue 409 ILE Chi-restraints excluded: chain A residue 429 ASP Chi-restraints excluded: chain A residue 448 GLU Chi-restraints excluded: chain A residue 455 GLN Chi-restraints excluded: chain B residue 37 LYS Chi-restraints excluded: chain B residue 40 ASN Chi-restraints excluded: chain B residue 71 THR Chi-restraints excluded: chain B residue 145 ILE Chi-restraints excluded: chain B residue 147 MET Chi-restraints excluded: chain B residue 167 GLU Chi-restraints excluded: chain B residue 172 GLU Chi-restraints excluded: chain C residue 69 ASP Chi-restraints excluded: chain C residue 109 VAL Chi-restraints excluded: chain C residue 110 PHE Chi-restraints excluded: chain C residue 194 ILE Chi-restraints excluded: chain E residue 54 ILE Chi-restraints excluded: chain E residue 81 LEU Chi-restraints excluded: chain F residue 42 VAL Chi-restraints excluded: chain F residue 51 LEU Chi-restraints excluded: chain F residue 58 CYS Chi-restraints excluded: chain F residue 61 VAL Chi-restraints excluded: chain F residue 76 ASN Chi-restraints excluded: chain F residue 91 LEU Chi-restraints excluded: chain F residue 92 GLU Chi-restraints excluded: chain G residue 81 ASP Chi-restraints excluded: chain G residue 83 VAL Chi-restraints excluded: chain G residue 108 LEU Chi-restraints excluded: chain G residue 134 ASP Chi-restraints excluded: chain H residue 8 THR Chi-restraints excluded: chain I residue 8 ILE Chi-restraints excluded: chain I residue 28 TYR Chi-restraints excluded: chain I residue 29 GLN Chi-restraints excluded: chain I residue 63 SER Chi-restraints excluded: chain J residue 296 PHE Chi-restraints excluded: chain J residue 325 THR Chi-restraints excluded: chain L residue 67 VAL Chi-restraints excluded: chain L residue 70 GLU Chi-restraints excluded: chain L residue 86 ASN Chi-restraints excluded: chain L residue 94 THR Chi-restraints excluded: chain L residue 125 VAL Chi-restraints excluded: chain L residue 152 VAL Chi-restraints excluded: chain L residue 166 TRP Chi-restraints excluded: chain M residue 31 LEU Chi-restraints excluded: chain M residue 34 VAL Chi-restraints excluded: chain M residue 146 PHE Chi-restraints excluded: chain M residue 187 SER Chi-restraints excluded: chain M residue 210 ILE Chi-restraints excluded: chain M residue 265 THR Chi-restraints excluded: chain M residue 314 LEU Chi-restraints excluded: chain M residue 368 THR Chi-restraints excluded: chain M residue 371 VAL Chi-restraints excluded: chain M residue 431 LEU Chi-restraints excluded: chain M residue 519 ILE Chi-restraints excluded: chain M residue 627 SER Chi-restraints excluded: chain M residue 649 VAL Chi-restraints excluded: chain M residue 650 SER Chi-restraints excluded: chain M residue 674 LEU Chi-restraints excluded: chain M residue 691 ILE Chi-restraints excluded: chain N residue 15 THR Chi-restraints excluded: chain N residue 53 LYS Chi-restraints excluded: chain N residue 73 THR Chi-restraints excluded: chain O residue 191 ASN Chi-restraints excluded: chain O residue 223 PHE Chi-restraints excluded: chain O residue 233 SER Chi-restraints excluded: chain P residue 63 GLU Chi-restraints excluded: chain P residue 69 LEU Chi-restraints excluded: chain P residue 114 LEU Chi-restraints excluded: chain P residue 244 VAL Chi-restraints excluded: chain Q residue 97 LEU Chi-restraints excluded: chain Q residue 158 LEU Chi-restraints excluded: chain Q residue 189 THR Chi-restraints excluded: chain Q residue 253 LEU Chi-restraints excluded: chain Q residue 273 ILE Chi-restraints excluded: chain Q residue 386 THR Chi-restraints excluded: chain Q residue 400 ILE Chi-restraints excluded: chain Q residue 457 VAL Chi-restraints excluded: chain Q residue 462 ASP Chi-restraints excluded: chain T residue 40 THR Chi-restraints excluded: chain T residue 99 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 341 random chunks: chunk 203 optimal weight: 0.9990 chunk 131 optimal weight: 1.9990 chunk 196 optimal weight: 0.0670 chunk 99 optimal weight: 0.7980 chunk 64 optimal weight: 1.9990 chunk 63 optimal weight: 0.9980 chunk 208 optimal weight: 2.9990 chunk 223 optimal weight: 5.9990 chunk 162 optimal weight: 0.7980 chunk 30 optimal weight: 3.9990 chunk 258 optimal weight: 0.5980 overall best weight: 0.6518 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 393 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 53 ASN ** H 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 444 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 514 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 667 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 131 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 79 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8092 moved from start: 0.7542 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 28632 Z= 0.249 Angle : 0.667 10.307 38819 Z= 0.335 Chirality : 0.044 0.174 4221 Planarity : 0.005 0.079 5009 Dihedral : 5.726 71.211 3881 Min Nonbonded Distance : 2.105 Molprobity Statistics. All-atom Clashscore : 14.82 Ramachandran Plot: Outliers : 0.84 % Allowed : 6.89 % Favored : 92.27 % Rotamer: Outliers : 3.49 % Allowed : 20.29 % Favored : 76.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.35 % Cis-general : 0.00 % Twisted Proline : 0.96 % 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: -0.73 (0.14), residues: 3453 helix: 0.68 (0.15), residues: 1229 sheet: -1.36 (0.25), residues: 408 loop : -1.07 (0.15), residues: 1816 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.001 TRP M 510 HIS 0.011 0.001 HIS T 122 PHE 0.027 0.002 PHE P 202 TYR 0.028 0.002 TYR E 40 ARG 0.010 0.000 ARG J 85 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6906 Ramachandran restraints generated. 3453 Oldfield, 0 Emsley, 3453 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6906 Ramachandran restraints generated. 3453 Oldfield, 0 Emsley, 3453 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 616 residues out of total 3012 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 105 poor density : 511 time to evaluate : 3.249 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 390 ASP cc_start: 0.6731 (t0) cc_final: 0.6342 (t0) REVERT: A 429 ASP cc_start: 0.8875 (OUTLIER) cc_final: 0.8633 (m-30) REVERT: C 96 MET cc_start: 0.7675 (tmm) cc_final: 0.7411 (ttp) REVERT: C 103 MET cc_start: 0.7177 (ptt) cc_final: 0.6186 (ptm) REVERT: C 110 PHE cc_start: 0.6665 (OUTLIER) cc_final: 0.5886 (m-10) REVERT: E 65 GLU cc_start: 0.7830 (tm-30) cc_final: 0.7504 (tm-30) REVERT: G 132 ASP cc_start: 0.7023 (p0) cc_final: 0.6570 (m-30) REVERT: H 95 ARG cc_start: 0.8052 (mpt-90) cc_final: 0.7652 (mtt-85) REVERT: I 11 LEU cc_start: 0.7837 (tp) cc_final: 0.7272 (mt) REVERT: I 28 TYR cc_start: 0.6836 (OUTLIER) cc_final: 0.6346 (m-10) REVERT: I 60 ARG cc_start: 0.8175 (ptm-80) cc_final: 0.7641 (mtm110) REVERT: J 296 PHE cc_start: 0.6499 (OUTLIER) cc_final: 0.6024 (p90) REVERT: J 315 THR cc_start: 0.7824 (t) cc_final: 0.7541 (t) REVERT: K 86 ASP cc_start: 0.8059 (t70) cc_final: 0.7615 (t0) REVERT: K 96 MET cc_start: 0.7679 (mpp) cc_final: 0.7146 (ptp) REVERT: L 146 ASP cc_start: 0.7763 (p0) cc_final: 0.7388 (p0) REVERT: L 152 VAL cc_start: 0.7945 (OUTLIER) cc_final: 0.7638 (m) REVERT: L 168 LYS cc_start: 0.8212 (mmmt) cc_final: 0.7519 (mttp) REVERT: M 314 LEU cc_start: 0.8385 (OUTLIER) cc_final: 0.7989 (pp) REVERT: M 431 LEU cc_start: 0.8798 (OUTLIER) cc_final: 0.8543 (mp) REVERT: M 638 THR cc_start: 0.8628 (p) cc_final: 0.8389 (p) REVERT: N 21 ARG cc_start: 0.5767 (ttt-90) cc_final: 0.3974 (tpt170) REVERT: N 61 TRP cc_start: 0.8319 (p-90) cc_final: 0.6898 (p-90) REVERT: N 134 ILE cc_start: 0.9128 (mm) cc_final: 0.8927 (mm) REVERT: N 144 TYR cc_start: 0.6645 (OUTLIER) cc_final: 0.6252 (m-80) REVERT: P 215 GLU cc_start: 0.7613 (pm20) cc_final: 0.6878 (pm20) REVERT: Q 144 MET cc_start: 0.8450 (mpp) cc_final: 0.7790 (mpp) REVERT: Q 197 MET cc_start: 0.6921 (mtp) cc_final: 0.6688 (ttm) REVERT: Q 241 MET cc_start: 0.7550 (mmp) cc_final: 0.7213 (mmt) REVERT: Q 418 ARG cc_start: 0.8536 (OUTLIER) cc_final: 0.8037 (mtt90) REVERT: Q 458 PHE cc_start: 0.8048 (m-80) cc_final: 0.7788 (m-80) REVERT: W 27 ARG cc_start: 0.5896 (tpt90) cc_final: 0.5643 (tpt90) outliers start: 105 outliers final: 84 residues processed: 580 average time/residue: 0.3790 time to fit residues: 353.5419 Evaluate side-chains 574 residues out of total 3012 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 93 poor density : 481 time to evaluate : 3.020 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 130 ILE Chi-restraints excluded: chain A residue 212 LEU Chi-restraints excluded: chain A residue 251 SER Chi-restraints excluded: chain A residue 273 THR Chi-restraints excluded: chain A residue 287 THR Chi-restraints excluded: chain A residue 307 VAL Chi-restraints excluded: chain A residue 409 ILE Chi-restraints excluded: chain A residue 429 ASP Chi-restraints excluded: chain A residue 448 GLU Chi-restraints excluded: chain A residue 455 GLN Chi-restraints excluded: chain B residue 37 LYS Chi-restraints excluded: chain B residue 40 ASN Chi-restraints excluded: chain B residue 145 ILE Chi-restraints excluded: chain B residue 167 GLU Chi-restraints excluded: chain B residue 172 GLU Chi-restraints excluded: chain C residue 69 ASP Chi-restraints excluded: chain C residue 109 VAL Chi-restraints excluded: chain C residue 110 PHE Chi-restraints excluded: chain C residue 147 VAL Chi-restraints excluded: chain C residue 194 ILE Chi-restraints excluded: chain E residue 54 ILE Chi-restraints excluded: chain E residue 81 LEU Chi-restraints excluded: chain F residue 42 VAL Chi-restraints excluded: chain F residue 51 LEU Chi-restraints excluded: chain F residue 61 VAL Chi-restraints excluded: chain F residue 76 ASN Chi-restraints excluded: chain F residue 91 LEU Chi-restraints excluded: chain F residue 92 GLU Chi-restraints excluded: chain G residue 83 VAL Chi-restraints excluded: chain G residue 100 VAL Chi-restraints excluded: chain G residue 105 MET Chi-restraints excluded: chain G residue 108 LEU Chi-restraints excluded: chain G residue 134 ASP Chi-restraints excluded: chain G residue 144 ILE Chi-restraints excluded: chain H residue 8 THR Chi-restraints excluded: chain I residue 8 ILE Chi-restraints excluded: chain I residue 28 TYR Chi-restraints excluded: chain I residue 63 SER Chi-restraints excluded: chain I residue 70 MET Chi-restraints excluded: chain J residue 69 VAL Chi-restraints excluded: chain J residue 129 LEU Chi-restraints excluded: chain J residue 245 VAL Chi-restraints excluded: chain J residue 296 PHE Chi-restraints excluded: chain J residue 322 MET Chi-restraints excluded: chain J residue 325 THR Chi-restraints excluded: chain L residue 67 VAL Chi-restraints excluded: chain L residue 70 GLU Chi-restraints excluded: chain L residue 76 LYS Chi-restraints excluded: chain L residue 86 ASN Chi-restraints excluded: chain L residue 89 SER Chi-restraints excluded: chain L residue 125 VAL Chi-restraints excluded: chain L residue 152 VAL Chi-restraints excluded: chain L residue 166 TRP Chi-restraints excluded: chain M residue 31 LEU Chi-restraints excluded: chain M residue 34 VAL Chi-restraints excluded: chain M residue 146 PHE Chi-restraints excluded: chain M residue 187 SER Chi-restraints excluded: chain M residue 210 ILE Chi-restraints excluded: chain M residue 265 THR Chi-restraints excluded: chain M residue 314 LEU Chi-restraints excluded: chain M residue 368 THR Chi-restraints excluded: chain M residue 371 VAL Chi-restraints excluded: chain M residue 431 LEU Chi-restraints excluded: chain M residue 519 ILE Chi-restraints excluded: chain M residue 564 CYS Chi-restraints excluded: chain M residue 627 SER Chi-restraints excluded: chain M residue 649 VAL Chi-restraints excluded: chain M residue 650 SER Chi-restraints excluded: chain M residue 674 LEU Chi-restraints excluded: chain M residue 691 ILE Chi-restraints excluded: chain N residue 15 THR Chi-restraints excluded: chain N residue 53 LYS Chi-restraints excluded: chain N residue 73 THR Chi-restraints excluded: chain N residue 144 TYR Chi-restraints excluded: chain O residue 191 ASN Chi-restraints excluded: chain O residue 223 PHE Chi-restraints excluded: chain O residue 233 SER Chi-restraints excluded: chain P residue 69 LEU Chi-restraints excluded: chain P residue 244 VAL Chi-restraints excluded: chain Q residue 79 ASN Chi-restraints excluded: chain Q residue 97 LEU Chi-restraints excluded: chain Q residue 142 VAL Chi-restraints excluded: chain Q residue 158 LEU Chi-restraints excluded: chain Q residue 189 THR Chi-restraints excluded: chain Q residue 232 VAL Chi-restraints excluded: chain Q residue 273 ILE Chi-restraints excluded: chain Q residue 386 THR Chi-restraints excluded: chain Q residue 400 ILE Chi-restraints excluded: chain Q residue 418 ARG Chi-restraints excluded: chain Q residue 457 VAL Chi-restraints excluded: chain Q residue 462 ASP Chi-restraints excluded: chain T residue 40 THR Chi-restraints excluded: chain T residue 99 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 341 random chunks: chunk 298 optimal weight: 1.9990 chunk 314 optimal weight: 0.4980 chunk 287 optimal weight: 0.0270 chunk 306 optimal weight: 1.9990 chunk 184 optimal weight: 0.5980 chunk 133 optimal weight: 0.7980 chunk 240 optimal weight: 6.9990 chunk 93 optimal weight: 2.9990 chunk 276 optimal weight: 0.9980 chunk 289 optimal weight: 0.9980 chunk 305 optimal weight: 0.6980 overall best weight: 0.5238 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 164 ASN A 381 GLN ** A 393 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 93 ASN ** H 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 105 ASN ** M 444 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 514 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 663 ASN ** M 667 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 131 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 191 ASN Q 79 ASN ** Q 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8081 moved from start: 0.7669 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 28632 Z= 0.224 Angle : 0.663 10.619 38819 Z= 0.333 Chirality : 0.043 0.162 4221 Planarity : 0.005 0.074 5009 Dihedral : 5.634 64.126 3881 Min Nonbonded Distance : 2.113 Molprobity Statistics. All-atom Clashscore : 14.73 Ramachandran Plot: Outliers : 0.84 % Allowed : 6.40 % Favored : 92.76 % Rotamer: Outliers : 3.56 % Allowed : 20.43 % Favored : 76.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.35 % Cis-general : 0.00 % Twisted Proline : 0.48 % 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: -0.66 (0.14), residues: 3453 helix: 0.69 (0.15), residues: 1240 sheet: -1.16 (0.26), residues: 399 loop : -1.05 (0.15), residues: 1814 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.001 TRP M 510 HIS 0.009 0.001 HIS T 122 PHE 0.047 0.002 PHE P 202 TYR 0.031 0.001 TYR E 40 ARG 0.008 0.000 ARG F 26 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6906 Ramachandran restraints generated. 3453 Oldfield, 0 Emsley, 3453 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6906 Ramachandran restraints generated. 3453 Oldfield, 0 Emsley, 3453 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 612 residues out of total 3012 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 107 poor density : 505 time to evaluate : 2.945 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 62 TRP cc_start: 0.7537 (m100) cc_final: 0.7094 (m100) REVERT: A 390 ASP cc_start: 0.6610 (t0) cc_final: 0.6292 (t0) REVERT: A 429 ASP cc_start: 0.8843 (OUTLIER) cc_final: 0.8620 (m-30) REVERT: B 147 MET cc_start: 0.9110 (OUTLIER) cc_final: 0.8888 (mmm) REVERT: C 96 MET cc_start: 0.7654 (tmm) cc_final: 0.7355 (ttp) REVERT: C 103 MET cc_start: 0.7090 (ptt) cc_final: 0.6105 (ptm) REVERT: C 110 PHE cc_start: 0.6565 (OUTLIER) cc_final: 0.5860 (m-10) REVERT: E 65 GLU cc_start: 0.7825 (tm-30) cc_final: 0.7560 (tm-30) REVERT: G 132 ASP cc_start: 0.6962 (p0) cc_final: 0.6584 (m-30) REVERT: H 95 ARG cc_start: 0.7951 (mpt-90) cc_final: 0.7593 (mtt-85) REVERT: I 11 LEU cc_start: 0.7834 (tp) cc_final: 0.7275 (mt) REVERT: I 28 TYR cc_start: 0.6791 (OUTLIER) cc_final: 0.6499 (m-10) REVERT: I 60 ARG cc_start: 0.8149 (ptm-80) cc_final: 0.7625 (mtm110) REVERT: I 63 SER cc_start: 0.8737 (OUTLIER) cc_final: 0.8513 (m) REVERT: J 296 PHE cc_start: 0.6530 (OUTLIER) cc_final: 0.6046 (p90) REVERT: J 315 THR cc_start: 0.7819 (t) cc_final: 0.7535 (t) REVERT: K 78 ASP cc_start: 0.6859 (p0) cc_final: 0.6643 (p0) REVERT: K 86 ASP cc_start: 0.8109 (t70) cc_final: 0.7838 (t0) REVERT: K 96 MET cc_start: 0.7645 (mpp) cc_final: 0.7150 (ptp) REVERT: L 146 ASP cc_start: 0.7801 (p0) cc_final: 0.7410 (p0) REVERT: L 152 VAL cc_start: 0.7971 (OUTLIER) cc_final: 0.7644 (m) REVERT: L 168 LYS cc_start: 0.8255 (mmmt) cc_final: 0.7566 (mttp) REVERT: M 314 LEU cc_start: 0.8421 (OUTLIER) cc_final: 0.7994 (pp) REVERT: M 431 LEU cc_start: 0.8763 (OUTLIER) cc_final: 0.8496 (mp) REVERT: N 21 ARG cc_start: 0.5715 (ttt-90) cc_final: 0.3968 (tpt170) REVERT: N 61 TRP cc_start: 0.8309 (p-90) cc_final: 0.6894 (p-90) REVERT: N 134 ILE cc_start: 0.9132 (mm) cc_final: 0.8923 (mm) REVERT: P 215 GLU cc_start: 0.7590 (pm20) cc_final: 0.6856 (pm20) REVERT: Q 144 MET cc_start: 0.8428 (mpp) cc_final: 0.7751 (mpp) REVERT: Q 197 MET cc_start: 0.6919 (mtp) cc_final: 0.6690 (ttm) REVERT: Q 241 MET cc_start: 0.7554 (mmp) cc_final: 0.7220 (mmt) REVERT: Q 282 GLU cc_start: 0.7730 (mt-10) cc_final: 0.7484 (mt-10) REVERT: Q 418 ARG cc_start: 0.8530 (OUTLIER) cc_final: 0.8032 (mtt90) REVERT: Q 458 PHE cc_start: 0.8003 (m-80) cc_final: 0.7749 (m-80) REVERT: T 81 GLU cc_start: 0.6105 (mm-30) cc_final: 0.5751 (tt0) REVERT: W 27 ARG cc_start: 0.5935 (tpt90) cc_final: 0.5667 (tpt90) outliers start: 107 outliers final: 73 residues processed: 575 average time/residue: 0.3904 time to fit residues: 357.6073 Evaluate side-chains 576 residues out of total 3012 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 83 poor density : 493 time to evaluate : 3.764 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 130 ILE Chi-restraints excluded: chain A residue 212 LEU Chi-restraints excluded: chain A residue 251 SER Chi-restraints excluded: chain A residue 273 THR Chi-restraints excluded: chain A residue 287 THR Chi-restraints excluded: chain A residue 307 VAL Chi-restraints excluded: chain A residue 409 ILE Chi-restraints excluded: chain A residue 429 ASP Chi-restraints excluded: chain A residue 448 GLU Chi-restraints excluded: chain A residue 455 GLN Chi-restraints excluded: chain B residue 40 ASN Chi-restraints excluded: chain B residue 145 ILE Chi-restraints excluded: chain B residue 147 MET Chi-restraints excluded: chain B residue 148 THR Chi-restraints excluded: chain B residue 172 GLU Chi-restraints excluded: chain B residue 208 LEU Chi-restraints excluded: chain C residue 69 ASP Chi-restraints excluded: chain C residue 109 VAL Chi-restraints excluded: chain C residue 110 PHE Chi-restraints excluded: chain C residue 147 VAL Chi-restraints excluded: chain C residue 194 ILE Chi-restraints excluded: chain E residue 54 ILE Chi-restraints excluded: chain E residue 81 LEU Chi-restraints excluded: chain F residue 42 VAL Chi-restraints excluded: chain F residue 51 LEU Chi-restraints excluded: chain F residue 58 CYS Chi-restraints excluded: chain F residue 61 VAL Chi-restraints excluded: chain F residue 91 LEU Chi-restraints excluded: chain F residue 92 GLU Chi-restraints excluded: chain G residue 83 VAL Chi-restraints excluded: chain G residue 100 VAL Chi-restraints excluded: chain G residue 108 LEU Chi-restraints excluded: chain G residue 134 ASP Chi-restraints excluded: chain G residue 144 ILE Chi-restraints excluded: chain H residue 8 THR Chi-restraints excluded: chain I residue 8 ILE Chi-restraints excluded: chain I residue 28 TYR Chi-restraints excluded: chain I residue 63 SER Chi-restraints excluded: chain I residue 70 MET Chi-restraints excluded: chain J residue 69 VAL Chi-restraints excluded: chain J residue 245 VAL Chi-restraints excluded: chain J residue 296 PHE Chi-restraints excluded: chain J residue 322 MET Chi-restraints excluded: chain L residue 67 VAL Chi-restraints excluded: chain L residue 70 GLU Chi-restraints excluded: chain L residue 76 LYS Chi-restraints excluded: chain L residue 86 ASN Chi-restraints excluded: chain L residue 89 SER Chi-restraints excluded: chain L residue 125 VAL Chi-restraints excluded: chain L residue 152 VAL Chi-restraints excluded: chain L residue 166 TRP Chi-restraints excluded: chain M residue 31 LEU Chi-restraints excluded: chain M residue 187 SER Chi-restraints excluded: chain M residue 210 ILE Chi-restraints excluded: chain M residue 265 THR Chi-restraints excluded: chain M residue 314 LEU Chi-restraints excluded: chain M residue 367 CYS Chi-restraints excluded: chain M residue 368 THR Chi-restraints excluded: chain M residue 371 VAL Chi-restraints excluded: chain M residue 431 LEU Chi-restraints excluded: chain M residue 519 ILE Chi-restraints excluded: chain M residue 564 CYS Chi-restraints excluded: chain M residue 627 SER Chi-restraints excluded: chain M residue 649 VAL Chi-restraints excluded: chain M residue 674 LEU Chi-restraints excluded: chain N residue 15 THR Chi-restraints excluded: chain N residue 53 LYS Chi-restraints excluded: chain N residue 73 THR Chi-restraints excluded: chain O residue 201 ILE Chi-restraints excluded: chain O residue 223 PHE Chi-restraints excluded: chain O residue 233 SER Chi-restraints excluded: chain P residue 69 LEU Chi-restraints excluded: chain P residue 244 VAL Chi-restraints excluded: chain Q residue 97 LEU Chi-restraints excluded: chain Q residue 189 THR Chi-restraints excluded: chain Q residue 232 VAL Chi-restraints excluded: chain Q residue 386 THR Chi-restraints excluded: chain Q residue 400 ILE Chi-restraints excluded: chain Q residue 418 ARG Chi-restraints excluded: chain Q residue 457 VAL Chi-restraints excluded: chain Q residue 462 ASP Chi-restraints excluded: chain T residue 40 THR Chi-restraints excluded: chain T residue 99 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 341 random chunks: chunk 201 optimal weight: 0.9980 chunk 323 optimal weight: 0.0020 chunk 197 optimal weight: 0.7980 chunk 153 optimal weight: 4.9990 chunk 225 optimal weight: 2.9990 chunk 339 optimal weight: 0.9980 chunk 312 optimal weight: 0.3980 chunk 270 optimal weight: 0.7980 chunk 28 optimal weight: 1.9990 chunk 208 optimal weight: 0.0050 chunk 165 optimal weight: 0.8980 overall best weight: 0.4002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 164 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 220 GLN ** A 393 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 196 GLN ** E 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 25 GLN ** H 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 444 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 514 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 667 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 131 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 180 ASN Q 79 ASN ** Q 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 182 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8066 moved from start: 0.7791 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 28632 Z= 0.208 Angle : 0.661 9.803 38819 Z= 0.331 Chirality : 0.043 0.167 4221 Planarity : 0.005 0.080 5009 Dihedral : 5.480 59.952 3881 Min Nonbonded Distance : 2.114 Molprobity Statistics. All-atom Clashscore : 14.69 Ramachandran Plot: Outliers : 0.81 % Allowed : 6.60 % Favored : 92.59 % Rotamer: Outliers : 3.03 % Allowed : 21.26 % Favored : 75.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.35 % 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: -0.58 (0.15), residues: 3453 helix: 0.76 (0.15), residues: 1238 sheet: -1.03 (0.26), residues: 399 loop : -1.03 (0.15), residues: 1816 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRP M 510 HIS 0.009 0.001 HIS T 122 PHE 0.045 0.002 PHE P 202 TYR 0.031 0.001 TYR B 84 ARG 0.008 0.000 ARG F 26 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6906 Ramachandran restraints generated. 3453 Oldfield, 0 Emsley, 3453 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6906 Ramachandran restraints generated. 3453 Oldfield, 0 Emsley, 3453 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 604 residues out of total 3012 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 91 poor density : 513 time to evaluate : 3.241 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 390 ASP cc_start: 0.6565 (t0) cc_final: 0.6252 (t0) REVERT: A 429 ASP cc_start: 0.8842 (OUTLIER) cc_final: 0.8623 (m-30) REVERT: B 66 ARG cc_start: 0.6762 (mtp180) cc_final: 0.6504 (mtt180) REVERT: B 147 MET cc_start: 0.9084 (OUTLIER) cc_final: 0.8837 (mmm) REVERT: C 96 MET cc_start: 0.7666 (tmm) cc_final: 0.7397 (ttp) REVERT: C 103 MET cc_start: 0.6981 (ptt) cc_final: 0.5984 (ptm) REVERT: C 110 PHE cc_start: 0.6607 (OUTLIER) cc_final: 0.5829 (m-10) REVERT: E 80 ASP cc_start: 0.7612 (p0) cc_final: 0.7276 (p0) REVERT: G 132 ASP cc_start: 0.6761 (p0) cc_final: 0.6466 (m-30) REVERT: H 76 GLN cc_start: 0.8442 (tt0) cc_final: 0.7895 (tt0) REVERT: H 95 ARG cc_start: 0.7895 (mpt-90) cc_final: 0.7595 (mtt-85) REVERT: I 11 LEU cc_start: 0.7805 (tp) cc_final: 0.7252 (mt) REVERT: I 60 ARG cc_start: 0.8122 (ptm-80) cc_final: 0.7657 (mtm110) REVERT: I 63 SER cc_start: 0.8751 (OUTLIER) cc_final: 0.8538 (m) REVERT: J 296 PHE cc_start: 0.6488 (OUTLIER) cc_final: 0.6264 (p90) REVERT: J 315 THR cc_start: 0.7823 (t) cc_final: 0.7465 (t) REVERT: K 86 ASP cc_start: 0.8065 (t70) cc_final: 0.7782 (t0) REVERT: K 96 MET cc_start: 0.7628 (mpp) cc_final: 0.7154 (ptp) REVERT: L 146 ASP cc_start: 0.7834 (p0) cc_final: 0.7461 (p0) REVERT: L 152 VAL cc_start: 0.7969 (OUTLIER) cc_final: 0.7598 (m) REVERT: L 168 LYS cc_start: 0.8216 (mmmt) cc_final: 0.7468 (mttp) REVERT: M 314 LEU cc_start: 0.8415 (OUTLIER) cc_final: 0.7942 (pp) REVERT: M 431 LEU cc_start: 0.8642 (OUTLIER) cc_final: 0.8374 (mp) REVERT: M 541 PRO cc_start: 0.8489 (Cg_endo) cc_final: 0.8183 (Cg_exo) REVERT: N 21 ARG cc_start: 0.5640 (ttt-90) cc_final: 0.3946 (tpt170) REVERT: N 49 TYR cc_start: 0.8429 (m-80) cc_final: 0.7639 (m-80) REVERT: N 61 TRP cc_start: 0.8287 (p-90) cc_final: 0.6772 (p-90) REVERT: P 215 GLU cc_start: 0.7590 (pm20) cc_final: 0.6855 (pm20) REVERT: Q 144 MET cc_start: 0.8388 (mpp) cc_final: 0.7728 (mpp) REVERT: Q 197 MET cc_start: 0.6904 (mtp) cc_final: 0.6690 (ttm) REVERT: Q 241 MET cc_start: 0.7521 (mmp) cc_final: 0.7223 (mmt) REVERT: Q 253 LEU cc_start: 0.8231 (tp) cc_final: 0.7908 (tp) REVERT: Q 418 ARG cc_start: 0.8528 (OUTLIER) cc_final: 0.8023 (mtt90) REVERT: Q 458 PHE cc_start: 0.7968 (m-80) cc_final: 0.7719 (m-80) REVERT: T 81 GLU cc_start: 0.6140 (mm-30) cc_final: 0.5822 (tt0) outliers start: 91 outliers final: 71 residues processed: 574 average time/residue: 0.4019 time to fit residues: 364.8154 Evaluate side-chains 569 residues out of total 3012 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 80 poor density : 489 time to evaluate : 3.243 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 130 ILE Chi-restraints excluded: chain A residue 167 SER Chi-restraints excluded: chain A residue 212 LEU Chi-restraints excluded: chain A residue 251 SER Chi-restraints excluded: chain A residue 273 THR Chi-restraints excluded: chain A residue 287 THR Chi-restraints excluded: chain A residue 307 VAL Chi-restraints excluded: chain A residue 409 ILE Chi-restraints excluded: chain A residue 412 LEU Chi-restraints excluded: chain A residue 429 ASP Chi-restraints excluded: chain A residue 455 GLN Chi-restraints excluded: chain B residue 40 ASN Chi-restraints excluded: chain B residue 145 ILE Chi-restraints excluded: chain B residue 147 MET Chi-restraints excluded: chain B residue 172 GLU Chi-restraints excluded: chain C residue 69 ASP Chi-restraints excluded: chain C residue 109 VAL Chi-restraints excluded: chain C residue 110 PHE Chi-restraints excluded: chain C residue 119 VAL Chi-restraints excluded: chain C residue 147 VAL Chi-restraints excluded: chain C residue 194 ILE Chi-restraints excluded: chain E residue 54 ILE Chi-restraints excluded: chain E residue 81 LEU Chi-restraints excluded: chain F residue 42 VAL Chi-restraints excluded: chain F residue 61 VAL Chi-restraints excluded: chain F residue 91 LEU Chi-restraints excluded: chain F residue 92 GLU Chi-restraints excluded: chain G residue 83 VAL Chi-restraints excluded: chain G residue 100 VAL Chi-restraints excluded: chain G residue 108 LEU Chi-restraints excluded: chain G residue 144 ILE Chi-restraints excluded: chain H residue 8 THR Chi-restraints excluded: chain I residue 8 ILE Chi-restraints excluded: chain I residue 63 SER Chi-restraints excluded: chain I residue 70 MET Chi-restraints excluded: chain J residue 69 VAL Chi-restraints excluded: chain J residue 129 LEU Chi-restraints excluded: chain J residue 245 VAL Chi-restraints excluded: chain J residue 296 PHE Chi-restraints excluded: chain L residue 67 VAL Chi-restraints excluded: chain L residue 70 GLU Chi-restraints excluded: chain L residue 76 LYS Chi-restraints excluded: chain L residue 86 ASN Chi-restraints excluded: chain L residue 89 SER Chi-restraints excluded: chain L residue 125 VAL Chi-restraints excluded: chain L residue 152 VAL Chi-restraints excluded: chain L residue 166 TRP Chi-restraints excluded: chain M residue 31 LEU Chi-restraints excluded: chain M residue 187 SER Chi-restraints excluded: chain M residue 210 ILE Chi-restraints excluded: chain M residue 265 THR Chi-restraints excluded: chain M residue 314 LEU Chi-restraints excluded: chain M residue 367 CYS Chi-restraints excluded: chain M residue 368 THR Chi-restraints excluded: chain M residue 371 VAL Chi-restraints excluded: chain M residue 431 LEU Chi-restraints excluded: chain M residue 519 ILE Chi-restraints excluded: chain M residue 564 CYS Chi-restraints excluded: chain M residue 649 VAL Chi-restraints excluded: chain M residue 674 LEU Chi-restraints excluded: chain M residue 691 ILE Chi-restraints excluded: chain N residue 15 THR Chi-restraints excluded: chain N residue 73 THR Chi-restraints excluded: chain O residue 133 GLN Chi-restraints excluded: chain O residue 201 ILE Chi-restraints excluded: chain O residue 223 PHE Chi-restraints excluded: chain O residue 233 SER Chi-restraints excluded: chain P residue 69 LEU Chi-restraints excluded: chain P residue 224 VAL Chi-restraints excluded: chain P residue 244 VAL Chi-restraints excluded: chain Q residue 97 LEU Chi-restraints excluded: chain Q residue 189 THR Chi-restraints excluded: chain Q residue 232 VAL Chi-restraints excluded: chain Q residue 386 THR Chi-restraints excluded: chain Q residue 400 ILE Chi-restraints excluded: chain Q residue 418 ARG Chi-restraints excluded: chain Q residue 457 VAL Chi-restraints excluded: chain Q residue 462 ASP Chi-restraints excluded: chain T residue 40 THR Chi-restraints excluded: chain T residue 99 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 341 random chunks: chunk 214 optimal weight: 4.9990 chunk 288 optimal weight: 0.7980 chunk 82 optimal weight: 0.6980 chunk 249 optimal weight: 0.5980 chunk 39 optimal weight: 1.9990 chunk 75 optimal weight: 0.7980 chunk 270 optimal weight: 0.7980 chunk 113 optimal weight: 4.9990 chunk 278 optimal weight: 1.9990 chunk 34 optimal weight: 0.9990 chunk 49 optimal weight: 2.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 164 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 220 GLN ** A 393 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 76 GLN ** H 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 183 ASN ** L 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 88 GLN ** M 444 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 514 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 667 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 131 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 79 ASN ** Q 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 182 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3678 r_free = 0.3678 target = 0.121832 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.098508 restraints weight = 50292.685| |-----------------------------------------------------------------------------| r_work (start): 0.3314 rms_B_bonded: 2.28 r_work: 0.3135 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work (final): 0.3135 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8323 moved from start: 0.7938 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 28632 Z= 0.270 Angle : 0.689 11.502 38819 Z= 0.346 Chirality : 0.044 0.177 4221 Planarity : 0.005 0.082 5009 Dihedral : 5.530 56.789 3881 Min Nonbonded Distance : 2.115 Molprobity Statistics. All-atom Clashscore : 15.37 Ramachandran Plot: Outliers : 0.81 % Allowed : 6.66 % Favored : 92.53 % Rotamer: Outliers : 3.09 % Allowed : 21.36 % Favored : 75.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.35 % Cis-general : 0.00 % Twisted Proline : 0.48 % 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: -0.65 (0.15), residues: 3453 helix: 0.71 (0.15), residues: 1253 sheet: -1.10 (0.26), residues: 404 loop : -1.07 (0.15), residues: 1796 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.002 TRP M 510 HIS 0.008 0.001 HIS T 122 PHE 0.039 0.002 PHE Q 84 TYR 0.030 0.002 TYR B 84 ARG 0.008 0.000 ARG F 26 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7888.87 seconds wall clock time: 142 minutes 45.20 seconds (8565.20 seconds total)