Starting phenix.real_space_refine on Tue Feb 20 16:08:05 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rjb_24483/02_2024/7rjb_24483_trim_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rjb_24483/02_2024/7rjb_24483.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rjb_24483/02_2024/7rjb_24483.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rjb_24483/02_2024/7rjb_24483.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rjb_24483/02_2024/7rjb_24483_trim_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rjb_24483/02_2024/7rjb_24483_trim_updated.pdb" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.004 sd= 0.164 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 5 7.16 5 S 44 5.16 5 C 9471 2.51 5 N 2447 2.21 5 O 2742 1.98 5 H 13664 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 49": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 244": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 366": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A GLU 374": "OE1" <-> "OE2" Residue "K GLU 59": "OE1" <-> "OE2" Residue "K PHE 184": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D TYR 55": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D ARG 282": not complete - not flipped Residue "G TYR 38": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "G ASP 47": "OD1" <-> "OD2" Residue "G GLU 98": "OE1" <-> "OE2" Residue "G ASP 99": "OD1" <-> "OD2" Residue "G TYR 106": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F GLU 88": "OE1" <-> "OE2" Residue "B ASP 85": "OD1" <-> "OD2" Residue "B TYR 100": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 151": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B TYR 254": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B TYR 284": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B ASP 340": "OD1" <-> "OD2" Residue "B GLU 350": "OE1" <-> "OE2" Residue "B TYR 370": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B ASP 372": "OD1" <-> "OD2" Residue "M PHE 52": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "M PHE 79": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 28373 Number of models: 1 Model: "" Number of chains: 13 Chain: "A" Number of atoms: 6364 Number of conformers: 1 Conformer: "" Number of residues, atoms: 416, 6364 Classifications: {'peptide': 416} Link IDs: {'PTRANS': 8, 'TRANS': 407} Chain: "K" Number of atoms: 6146 Number of conformers: 1 Conformer: "" Number of residues, atoms: 383, 6146 Classifications: {'peptide': 383} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 23, 'TRANS': 359} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'PHE:plan': 1} Unresolved non-hydrogen planarities: 6 Chain: "D" Number of atoms: 3736 Number of conformers: 1 Conformer: "" Number of residues, atoms: 244, 3736 Classifications: {'peptide': 244} Link IDs: {'PTRANS': 21, 'TRANS': 222} Unresolved non-hydrogen bonds: 22 Unresolved non-hydrogen angles: 27 Unresolved non-hydrogen dihedrals: 17 Planarities with less than four sites: {'GLU:plan': 3, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 18 Chain: "G" Number of atoms: 1978 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 1978 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 7, 'TRANS': 114} Chain: "F" Number of atoms: 1399 Number of conformers: 1 Conformer: "" Number of residues, atoms: 85, 1399 Classifications: {'peptide': 85} Link IDs: {'PTRANS': 4, 'TRANS': 80} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 10 Planarities with less than four sites: {'TYR:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 10 Chain: "H" Number of atoms: 1148 Number of conformers: 1 Conformer: "" Number of residues, atoms: 72, 1148 Classifications: {'peptide': 72} Link IDs: {'PTRANS': 4, 'TRANS': 67} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "I" Number of atoms: 639 Number of conformers: 1 Conformer: "" Number of residues, atoms: 39, 639 Classifications: {'peptide': 39} Link IDs: {'TRANS': 38} Chain: "B" Number of atoms: 5392 Number of conformers: 1 Conformer: "" Number of residues, atoms: 364, 5392 Classifications: {'peptide': 364} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 18, 'TRANS': 345} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 13 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASN:plan1': 1} Unresolved non-hydrogen planarities: 3 Chain: "M" Number of atoms: 723 Number of conformers: 1 Conformer: "" Number of residues, atoms: 50, 723 Classifications: {'peptide': 50} Link IDs: {'PTRANS': 1, 'TRANS': 48} Chain: "E" Number of atoms: 664 Number of conformers: 1 Conformer: "" Number of residues, atoms: 132, 664 Classifications: {'peptide': 132} Incomplete info: {'truncation_to_alanine': 103} Link IDs: {'PTRANS': 9, 'TRANS': 122} Unresolved chain link angles: 9 Unresolved non-hydrogen bonds: 386 Unresolved non-hydrogen angles: 498 Unresolved non-hydrogen dihedrals: 326 Unresolved non-hydrogen chiralities: 33 Planarities with less than four sites: {'GLN:plan1': 3, 'ASP:plan': 10, 'TYR:plan': 2, 'ASN:plan1': 4, 'TRP:plan': 3, 'HIS:plan': 4, 'PHE:plan': 4, 'GLU:plan': 10, 'ARG:plan': 6} Unresolved non-hydrogen planarities: 209 Chain: "K" Number of atoms: 137 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 137 Unusual residues: {'HEM': 2, 'U10': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 75 Unresolved non-hydrogen angles: 90 Unresolved non-hydrogen dihedrals: 60 Planarities with less than four sites: {'U10:plan-8': 2, 'U10:plan-9': 2, 'U10:plan-4': 1, 'U10:plan-5': 2, 'U10:plan-6': 2, 'U10:plan-7': 2, 'U10:plan-10': 2, 'U10:plan-11': 2} Unresolved non-hydrogen planarities: 60 Chain: "D" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 43 Unusual residues: {'HEC': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 4 Unusual residues: {'FES': 1} Classifications: {'undetermined': 1} Time building chain proxies: 12.57, per 1000 atoms: 0.44 Number of scatterers: 28373 At special positions: 0 Unit cell: (117.42, 89.61, 159.65, 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 5 26.01 S 44 16.00 O 2742 8.00 N 2447 7.00 C 9471 6.00 H 13664 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS H 89 " - pdb=" SG CYS H 111 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=7, symmetry=0 Number of additional bonds: simple=7, symmetry=0 Coordination: Other bonds: Time building additional restraints: 23.15 Conformation dependent library (CDL) restraints added in 3.4 seconds 3774 Ramachandran restraints generated. 1887 Oldfield, 0 Emsley, 1887 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3578 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 80 helices and 8 sheets defined 51.5% alpha, 6.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.54 Creating SS restraints... Processing helix chain 'A' and resid 53 through 55 No H-bonds generated for 'chain 'A' and resid 53 through 55' Processing helix chain 'A' and resid 63 through 72 Processing helix chain 'A' and resid 98 through 113 removed outlier: 4.739A pdb=" N THR A 102 " --> pdb=" O ASP A 99 " (cutoff:3.500A) Processing helix chain 'A' and resid 115 through 120 Processing helix chain 'A' and resid 124 through 138 Processing helix chain 'A' and resid 142 through 154 Processing helix chain 'A' and resid 159 through 161 No H-bonds generated for 'chain 'A' and resid 159 through 161' Processing helix chain 'A' and resid 168 through 173 removed outlier: 3.817A pdb=" N GLU A 172 " --> pdb=" O THR A 168 " (cutoff:3.500A) removed outlier: 4.251A pdb=" N ASN A 173 " --> pdb=" O GLU A 169 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 168 through 173' Processing helix chain 'A' and resid 176 through 186 Processing helix chain 'A' and resid 189 through 191 No H-bonds generated for 'chain 'A' and resid 189 through 191' Processing helix chain 'A' and resid 202 through 210 Processing helix chain 'A' and resid 259 through 269 removed outlier: 4.032A pdb=" N TYR A 269 " --> pdb=" O ALA A 265 " (cutoff:3.500A) Processing helix chain 'A' and resid 277 through 280 removed outlier: 3.912A pdb=" N LYS A 280 " --> pdb=" O THR A 277 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 277 through 280' Processing helix chain 'A' and resid 285 through 290 Processing helix chain 'A' and resid 324 through 339 removed outlier: 3.537A pdb=" N LEU A 338 " --> pdb=" O GLU A 334 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N SER A 339 " --> pdb=" O TRP A 335 " (cutoff:3.500A) Processing helix chain 'A' and resid 344 through 361 Processing helix chain 'A' and resid 365 through 378 Processing helix chain 'A' and resid 385 through 393 Processing helix chain 'A' and resid 397 through 407 Processing helix chain 'A' and resid 427 through 434 removed outlier: 3.623A pdb=" N MET A 434 " --> pdb=" O ASN A 430 " (cutoff:3.500A) Processing helix chain 'K' and resid 3 through 6 No H-bonds generated for 'chain 'K' and resid 3 through 6' Processing helix chain 'K' and resid 8 through 17 Processing helix chain 'K' and resid 29 through 51 removed outlier: 3.956A pdb=" N GLY K 33 " --> pdb=" O TRP K 30 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N GLN K 43 " --> pdb=" O LEU K 40 " (cutoff:3.500A) removed outlier: 4.125A pdb=" N SER K 46 " --> pdb=" O GLN K 43 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N ALA K 51 " --> pdb=" O VAL K 48 " (cutoff:3.500A) Processing helix chain 'K' and resid 61 through 70 Processing helix chain 'K' and resid 75 through 102 removed outlier: 3.605A pdb=" N ALA K 86 " --> pdb=" O HIS K 82 " (cutoff:3.500A) Processing helix chain 'K' and resid 108 through 135 removed outlier: 5.445A pdb=" N MET K 112 " --> pdb=" O PRO K 109 " (cutoff:3.500A) Processing helix chain 'K' and resid 138 through 153 removed outlier: 4.073A pdb=" N ALA K 153 " --> pdb=" O ASN K 149 " (cutoff:3.500A) Processing helix chain 'K' and resid 157 through 166 removed outlier: 3.502A pdb=" N ILE K 161 " --> pdb=" O GLY K 158 " (cutoff:3.500A) removed outlier: 4.585A pdb=" N VAL K 162 " --> pdb=" O ASN K 159 " (cutoff:3.500A) Proline residue: K 163 - end of helix removed outlier: 3.511A pdb=" N TRP K 166 " --> pdb=" O PRO K 163 " (cutoff:3.500A) Processing helix chain 'K' and resid 173 through 204 Proline residue: K 187 - end of helix removed outlier: 4.144A pdb=" N HIS K 204 " --> pdb=" O ALA K 200 " (cutoff:3.500A) Processing helix chain 'K' and resid 226 through 244 Processing helix chain 'K' and resid 254 through 257 Processing helix chain 'K' and resid 273 through 284 Proline residue: K 277 - end of helix Processing helix chain 'K' and resid 288 through 308 removed outlier: 5.110A pdb=" N LEU K 302 " --> pdb=" O ALA K 298 " (cutoff:3.500A) removed outlier: 5.174A pdb=" N LEU K 303 " --> pdb=" O ILE K 299 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N SER K 304 " --> pdb=" O LEU K 300 " (cutoff:3.500A) Proline residue: K 306 - end of helix Processing helix chain 'K' and resid 320 through 341 removed outlier: 3.762A pdb=" N GLN K 341 " --> pdb=" O GLY K 337 " (cutoff:3.500A) Processing helix chain 'K' and resid 346 through 382 removed outlier: 4.149A pdb=" N GLN K 350 " --> pdb=" O VAL K 346 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N TYR K 363 " --> pdb=" O TYR K 359 " (cutoff:3.500A) removed outlier: 4.523A pdb=" N VAL K 367 " --> pdb=" O TYR K 363 " (cutoff:3.500A) Proline residue: K 368 - end of helix Processing helix chain 'D' and resid 45 through 48 No H-bonds generated for 'chain 'D' and resid 45 through 48' Processing helix chain 'D' and resid 68 through 80 Processing helix chain 'D' and resid 82 through 84 No H-bonds generated for 'chain 'D' and resid 82 through 84' Processing helix chain 'D' and resid 93 through 96 Processing helix chain 'D' and resid 103 through 111 Processing helix chain 'D' and resid 143 through 150 Processing helix chain 'D' and resid 169 through 176 Processing helix chain 'D' and resid 225 through 240 Processing helix chain 'D' and resid 244 through 277 Proline residue: D 275 - end of helix Processing helix chain 'G' and resid 5 through 16 Processing helix chain 'G' and resid 19 through 35 Proline residue: G 27 - end of helix Processing helix chain 'G' and resid 39 through 41 No H-bonds generated for 'chain 'G' and resid 39 through 41' Processing helix chain 'G' and resid 45 through 48 Processing helix chain 'G' and resid 54 through 62 Processing helix chain 'G' and resid 65 through 84 Processing helix chain 'G' and resid 104 through 121 Processing helix chain 'F' and resid 41 through 81 removed outlier: 3.646A pdb=" N VAL F 46 " --> pdb=" O ALA F 42 " (cutoff:3.500A) removed outlier: 4.207A pdb=" N THR F 49 " --> pdb=" O ALA F 45 " (cutoff:3.500A) removed outlier: 4.884A pdb=" N LEU F 58 " --> pdb=" O LYS F 54 " (cutoff:3.500A) removed outlier: 5.525A pdb=" N TYR F 59 " --> pdb=" O ASN F 55 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N VAL F 60 " --> pdb=" O GLN F 56 " (cutoff:3.500A) Proline residue: F 63 - end of helix Processing helix chain 'F' and resid 87 through 92 Processing helix chain 'H' and resid 65 through 74 Processing helix chain 'H' and resid 77 through 98 Proline residue: H 81 - end of helix Processing helix chain 'H' and resid 102 through 104 No H-bonds generated for 'chain 'H' and resid 102 through 104' Processing helix chain 'H' and resid 112 through 132 removed outlier: 3.890A pdb=" N CYS H 125 " --> pdb=" O CYS H 121 " (cutoff:3.500A) Proline residue: H 128 - end of helix removed outlier: 4.686A pdb=" N PHE H 131 " --> pdb=" O ALA H 127 " (cutoff:3.500A) removed outlier: 5.313A pdb=" N ASN H 132 " --> pdb=" O PRO H 128 " (cutoff:3.500A) Processing helix chain 'I' and resid 18 through 41 removed outlier: 3.712A pdb=" N PHE I 24 " --> pdb=" O PHE I 20 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N ALA I 25 " --> pdb=" O GLY I 21 " (cutoff:3.500A) removed outlier: 4.554A pdb=" N GLU I 39 " --> pdb=" O ASN I 35 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N GLU I 40 " --> pdb=" O LYS I 36 " (cutoff:3.500A) Processing helix chain 'I' and resid 47 through 54 removed outlier: 5.344A pdb=" N GLY I 52 " --> pdb=" O LYS I 48 " (cutoff:3.500A) removed outlier: 5.661A pdb=" N LYS I 53 " --> pdb=" O ASN I 49 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N PHE I 54 " --> pdb=" O VAL I 50 " (cutoff:3.500A) Processing helix chain 'B' and resid 47 through 54 Processing helix chain 'B' and resid 64 through 74 removed outlier: 3.741A pdb=" N ARG B 69 " --> pdb=" O LEU B 65 " (cutoff:3.500A) Processing helix chain 'B' and resid 95 through 109 removed outlier: 3.946A pdb=" N LEU B 98 " --> pdb=" O LYS B 95 " (cutoff:3.500A) Proline residue: B 99 - end of helix removed outlier: 4.283A pdb=" N VAL B 102 " --> pdb=" O PRO B 99 " (cutoff:3.500A) Processing helix chain 'B' and resid 116 through 121 Processing helix chain 'B' and resid 124 through 135 Processing helix chain 'B' and resid 138 through 150 Processing helix chain 'B' and resid 154 through 156 No H-bonds generated for 'chain 'B' and resid 154 through 156' Processing helix chain 'B' and resid 169 through 176 Processing helix chain 'B' and resid 182 through 184 No H-bonds generated for 'chain 'B' and resid 182 through 184' Processing helix chain 'B' and resid 194 through 203 Processing helix chain 'B' and resid 205 through 208 Processing helix chain 'B' and resid 248 through 261 removed outlier: 4.462A pdb=" N GLY B 252 " --> pdb=" O ALA B 249 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N TYR B 254 " --> pdb=" O PHE B 251 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N GLU B 255 " --> pdb=" O GLY B 252 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N SER B 258 " --> pdb=" O GLU B 255 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N ALA B 259 " --> pdb=" O VAL B 256 " (cutoff:3.500A) Processing helix chain 'B' and resid 273 through 275 No H-bonds generated for 'chain 'B' and resid 273 through 275' Processing helix chain 'B' and resid 300 through 314 removed outlier: 3.692A pdb=" N GLN B 305 " --> pdb=" O SER B 301 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N LYS B 308 " --> pdb=" O ALA B 304 " (cutoff:3.500A) Processing helix chain 'B' and resid 319 through 336 removed outlier: 4.666A pdb=" N LYS B 327 " --> pdb=" O SER B 323 " (cutoff:3.500A) removed outlier: 4.658A pdb=" N ALA B 328 " --> pdb=" O GLU B 324 " (cutoff:3.500A) Processing helix chain 'B' and resid 371 through 373 No H-bonds generated for 'chain 'B' and resid 371 through 373' Processing helix chain 'M' and resid 48 through 78 removed outlier: 3.705A pdb=" N SER M 78 " --> pdb=" O ALA M 74 " (cutoff:3.500A) Processing helix chain 'E' and resid 83 through 86 No H-bonds generated for 'chain 'E' and resid 83 through 86' Processing helix chain 'E' and resid 95 through 97 No H-bonds generated for 'chain 'E' and resid 95 through 97' Processing helix chain 'E' and resid 120 through 128 Processing helix chain 'E' and resid 140 through 143 No H-bonds generated for 'chain 'E' and resid 140 through 143' Processing sheet with id= A, first strand: chain 'A' and resid 23 through 25 removed outlier: 3.689A pdb=" N GLY A 198 " --> pdb=" O GLU A 35 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N VAL A 45 " --> pdb=" O ALA A 94 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 232 through 234 removed outlier: 6.262A pdb=" N ILE A 415 " --> pdb=" O VAL A 233 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'D' and resid 114 through 116 Processing sheet with id= D, first strand: chain 'B' and resid 18 through 22 removed outlier: 3.735A pdb=" N LYS B 18 " --> pdb=" O ILE B 185 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 229 through 233 removed outlier: 6.411A pdb=" N TYR B 359 " --> pdb=" O ALA B 230 " (cutoff:3.500A) removed outlier: 8.097A pdb=" N VAL B 232 " --> pdb=" O TYR B 359 " (cutoff:3.500A) removed outlier: 6.564A pdb=" N ALA B 361 " --> pdb=" O VAL B 232 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'E' and resid 106 through 108 removed outlier: 3.630A pdb=" N ILE E 106 " --> pdb=" O VAL E 113 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N ARG E 116 " --> pdb=" O LEU E 150 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N LEU E 150 " --> pdb=" O ARG E 116 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'E' and resid 173 through 175 Processing sheet with id= H, first strand: chain 'E' and resid 203 through 205 696 hydrogen bonds defined for protein. 1806 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: 10.49 Time building geometry restraints manager: 23.98 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.12: 13655 1.12 - 1.41: 6289 1.41 - 1.70: 8708 1.70 - 1.98: 72 1.98 - 2.27: 15 Bond restraints: 28739 Sorted by residual: bond pdb=" C CYS D 82 " pdb=" O CYS D 82 " ideal model delta sigma weight residual 1.237 1.076 0.161 1.17e-02 7.31e+03 1.89e+02 bond pdb=" C2D HEC D 301 " pdb=" C3D HEC D 301 " ideal model delta sigma weight residual 1.544 1.332 0.212 2.00e-02 2.50e+03 1.13e+02 bond pdb=" CAB HEC D 301 " pdb=" CBB HEC D 301 " ideal model delta sigma weight residual 1.544 1.332 0.212 2.00e-02 2.50e+03 1.12e+02 bond pdb=" CAC HEC D 301 " pdb=" CBC HEC D 301 " ideal model delta sigma weight residual 1.544 1.336 0.208 2.00e-02 2.50e+03 1.08e+02 bond pdb=" C ILE F 30 " pdb=" N SER F 31 " ideal model delta sigma weight residual 1.331 1.234 0.097 1.48e-02 4.57e+03 4.26e+01 ... (remaining 28734 not shown) Histogram of bond angle deviations from ideal: 86.63 - 104.92: 310 104.92 - 123.20: 48509 123.20 - 141.49: 2760 141.49 - 159.77: 0 159.77 - 178.05: 6 Bond angle restraints: 51585 Sorted by residual: angle pdb=" S1 FES E 301 " pdb="FE1 FES E 301 " pdb=" S2 FES E 301 " ideal model delta sigma weight residual 104.33 86.63 17.70 1.20e+00 6.94e-01 2.17e+02 angle pdb=" S1 FES E 301 " pdb="FE2 FES E 301 " pdb=" S2 FES E 301 " ideal model delta sigma weight residual 104.33 88.19 16.14 1.14e+00 7.69e-01 2.01e+02 angle pdb="FE1 FES E 301 " pdb=" S2 FES E 301 " pdb="FE2 FES E 301 " ideal model delta sigma weight residual 75.66 89.74 -14.08 1.14e+00 7.69e-01 1.53e+02 angle pdb="FE1 FES E 301 " pdb=" S1 FES E 301 " pdb="FE2 FES E 301 " ideal model delta sigma weight residual 75.66 90.33 -14.67 1.20e+00 6.94e-01 1.50e+02 angle pdb=" CA CYS D 82 " pdb=" C CYS D 82 " pdb=" O CYS D 82 " ideal model delta sigma weight residual 120.55 109.72 10.83 1.06e+00 8.90e-01 1.04e+02 ... (remaining 51580 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.28: 13327 35.28 - 70.56: 315 70.56 - 105.84: 35 105.84 - 141.12: 1 141.12 - 176.40: 1 Dihedral angle restraints: 13679 sinusoidal: 7049 harmonic: 6630 Sorted by residual: dihedral pdb=" CD ARG D 282 " pdb=" NE ARG D 282 " pdb=" CZ ARG D 282 " pdb=" NH1 ARG D 282 " ideal model delta sinusoidal sigma weight residual 0.00 176.40 -176.40 1 1.00e+01 1.00e-02 1.92e+02 dihedral pdb=" C PRO E 192 " pdb=" N PRO E 192 " pdb=" CA PRO E 192 " pdb=" CB PRO E 192 " ideal model delta harmonic sigma weight residual -120.70 -103.51 -17.19 0 2.50e+00 1.60e-01 4.73e+01 dihedral pdb=" C HIS E 117 " pdb=" N HIS E 117 " pdb=" CA HIS E 117 " pdb=" CB HIS E 117 " ideal model delta harmonic sigma weight residual -122.60 -139.00 16.40 0 2.50e+00 1.60e-01 4.30e+01 ... (remaining 13676 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.102: 2148 0.102 - 0.204: 116 0.204 - 0.306: 15 0.306 - 0.408: 4 0.408 - 0.510: 1 Chirality restraints: 2284 Sorted by residual: chirality pdb=" CA HIS E 117 " pdb=" N HIS E 117 " pdb=" C HIS E 117 " pdb=" CB HIS E 117 " both_signs ideal model delta sigma weight residual False 2.51 2.00 0.51 2.00e-01 2.50e+01 6.50e+00 chirality pdb=" CA ILE E 188 " pdb=" N ILE E 188 " pdb=" C ILE E 188 " pdb=" CB ILE E 188 " both_signs ideal model delta sigma weight residual False 2.43 2.83 -0.39 2.00e-01 2.50e+01 3.90e+00 chirality pdb=" CA PRO E 192 " pdb=" N PRO E 192 " pdb=" C PRO E 192 " pdb=" CB PRO E 192 " both_signs ideal model delta sigma weight residual False 2.72 3.08 -0.36 2.00e-01 2.50e+01 3.29e+00 ... (remaining 2281 not shown) Planarity restraints: 4301 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ARG E 189 " -0.041 2.00e-02 2.50e+03 8.10e-02 6.55e+01 pdb=" C ARG E 189 " 0.140 2.00e-02 2.50e+03 pdb=" O ARG E 189 " -0.052 2.00e-02 2.50e+03 pdb=" N LYS E 190 " -0.048 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB HIS K 96 " 0.056 2.00e-02 2.50e+03 4.00e-02 3.60e+01 pdb=" CG HIS K 96 " -0.069 2.00e-02 2.50e+03 pdb=" ND1 HIS K 96 " 0.001 2.00e-02 2.50e+03 pdb=" CD2 HIS K 96 " -0.053 2.00e-02 2.50e+03 pdb=" CE1 HIS K 96 " -0.006 2.00e-02 2.50e+03 pdb=" NE2 HIS K 96 " 0.060 2.00e-02 2.50e+03 pdb=" HD1 HIS K 96 " -0.001 2.00e-02 2.50e+03 pdb=" HD2 HIS K 96 " 0.009 2.00e-02 2.50e+03 pdb=" HE1 HIS K 96 " 0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE K 184 " -0.014 2.00e-02 2.50e+03 2.57e-02 1.98e+01 pdb=" CG PHE K 184 " 0.067 2.00e-02 2.50e+03 pdb=" CD1 PHE K 184 " -0.021 2.00e-02 2.50e+03 pdb=" CD2 PHE K 184 " -0.049 2.00e-02 2.50e+03 pdb=" CE1 PHE K 184 " -0.002 2.00e-02 2.50e+03 pdb=" CE2 PHE K 184 " 0.018 2.00e-02 2.50e+03 pdb=" CZ PHE K 184 " -0.001 2.00e-02 2.50e+03 pdb=" HD1 PHE K 184 " -0.000 2.00e-02 2.50e+03 pdb=" HD2 PHE K 184 " 0.005 2.00e-02 2.50e+03 pdb=" HE1 PHE K 184 " -0.003 2.00e-02 2.50e+03 pdb=" HE2 PHE K 184 " -0.004 2.00e-02 2.50e+03 pdb=" HZ PHE K 184 " 0.004 2.00e-02 2.50e+03 ... (remaining 4298 not shown) Histogram of nonbonded interaction distances: 1.10 - 1.80: 113 1.80 - 2.50: 21269 2.50 - 3.20: 89476 3.20 - 3.90: 117062 3.90 - 4.60: 185073 Nonbonded interactions: 412993 Sorted by model distance: nonbonded pdb=" H LYS F 36 " pdb=" O TYR M 40 " model vdw 1.103 1.850 nonbonded pdb="HD21 ASN K 149 " pdb=" N GLY E 160 " model vdw 1.199 2.600 nonbonded pdb=" HB2 GLN A 156 " pdb=" HG3 GLN M 34 " model vdw 1.227 2.440 nonbonded pdb=" HB THR K 265 " pdb=" CB VAL E 162 " model vdw 1.285 2.920 nonbonded pdb=" HE2 PHE I 30 " pdb="HD12 LEU M 63 " model vdw 1.335 2.270 ... (remaining 412988 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: 1.210 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: 0.440 Extract box with map and model: 6.420 Check model and map are aligned: 0.450 Set scattering table: 0.280 Process input model: 91.990 Find NCS groups from input model: 0.600 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.840 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 104.310 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6543 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 : 0.007 0.212 15075 Z= 0.464 Angle : 0.824 17.696 20544 Z= 0.536 Chirality : 0.053 0.510 2284 Planarity : 0.005 0.081 2625 Dihedral : 13.600 176.404 5270 Min Nonbonded Distance : 1.840 Molprobity Statistics. All-atom Clashscore : 11.85 Ramachandran Plot: Outliers : 0.32 % Allowed : 4.35 % Favored : 95.34 % Rotamer: Outliers : 0.27 % Allowed : 0.20 % Favored : 99.53 % Cbeta Deviations : 0.22 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.14 (0.20), residues: 1887 helix: 0.55 (0.17), residues: 970 sheet: -0.60 (0.38), residues: 174 loop : -0.15 (0.24), residues: 743 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP K 142 HIS 0.037 0.001 HIS K 96 PHE 0.068 0.002 PHE K 184 TYR 0.023 0.002 TYR K 132 ARG 0.008 0.001 ARG D 282 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3774 Ramachandran restraints generated. 1887 Oldfield, 0 Emsley, 1887 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3774 Ramachandran restraints generated. 1887 Oldfield, 0 Emsley, 1887 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ALA 112 is missing expected H atoms. Skipping. Residue LYS 124 is missing expected H atoms. Skipping. Residue LYS 36 is missing expected H atoms. Skipping. Residue TYR 43 is missing expected H atoms. Skipping. Residue LYS 80 is missing expected H atoms. Skipping. Residue SER 214 is missing expected H atoms. Skipping. Residue LYS 218 is missing expected H atoms. Skipping. Residue LEU 220 is missing expected H atoms. Skipping. Residue TYR 32 is missing expected H atoms. Skipping. Evaluate side-chains 372 residues out of total 1606 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 368 time to evaluate : 2.164 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: A 35 GLU cc_start: 0.7064 (tm-30) cc_final: 0.6626 (tt0) REVERT: A 126 LYS cc_start: 0.7446 (ttpp) cc_final: 0.7190 (tppt) REVERT: A 174 LEU cc_start: 0.8971 (mt) cc_final: 0.8754 (mt) REVERT: A 252 GLU cc_start: 0.8145 (mm-30) cc_final: 0.7847 (mm-30) REVERT: A 256 SER cc_start: 0.8715 (m) cc_final: 0.8319 (p) REVERT: A 276 SER cc_start: 0.8410 (t) cc_final: 0.8197 (p) REVERT: A 391 LYS cc_start: 0.8051 (ttmm) cc_final: 0.7849 (mtpt) REVERT: A 396 LYS cc_start: 0.7654 (mmtt) cc_final: 0.7351 (mppt) REVERT: K 52 MET cc_start: 0.8702 (mtt) cc_final: 0.8445 (mtm) REVERT: K 60 LEU cc_start: 0.7876 (mt) cc_final: 0.7553 (mt) REVERT: K 261 ASN cc_start: 0.7427 (t0) cc_final: 0.7206 (t0) REVERT: D 79 ARG cc_start: 0.7561 (mtp-110) cc_final: 0.6873 (mtp85) REVERT: D 193 SER cc_start: 0.8023 (m) cc_final: 0.7804 (p) REVERT: D 231 ASP cc_start: 0.8256 (m-30) cc_final: 0.8035 (m-30) REVERT: D 241 GLU cc_start: 0.8412 (mt-10) cc_final: 0.8177 (mt-10) REVERT: D 246 ASP cc_start: 0.7957 (m-30) cc_final: 0.7657 (m-30) REVERT: G 31 LYS cc_start: 0.8125 (ttmm) cc_final: 0.6565 (tmtt) REVERT: G 61 LYS cc_start: 0.7570 (tmmt) cc_final: 0.6931 (ttmt) REVERT: G 92 LYS cc_start: 0.8068 (mtpt) cc_final: 0.7765 (mtmm) REVERT: F 27 GLN cc_start: 0.7690 (mt0) cc_final: 0.7473 (tt0) REVERT: H 91 GLU cc_start: 0.7891 (mm-30) cc_final: 0.7594 (mm-30) REVERT: I 36 LYS cc_start: 0.8176 (ttpp) cc_final: 0.7703 (ttmm) REVERT: I 53 LYS cc_start: 0.8507 (mtpp) cc_final: 0.8208 (mtpt) REVERT: B 113 GLN cc_start: 0.8169 (tt0) cc_final: 0.7904 (tp40) REVERT: B 132 LYS cc_start: 0.7791 (ttpp) cc_final: 0.7590 (ttmt) REVERT: B 152 ARG cc_start: 0.7169 (mtt180) cc_final: 0.6413 (mmm160) REVERT: B 190 GLU cc_start: 0.7230 (mt-10) cc_final: 0.6858 (mt-10) REVERT: B 208 TYR cc_start: 0.5797 (m-80) cc_final: 0.5421 (m-80) REVERT: B 238 SER cc_start: 0.8418 (m) cc_final: 0.8059 (t) REVERT: B 370 TYR cc_start: 0.7765 (m-80) cc_final: 0.7418 (m-80) REVERT: E 86 LEU cc_start: 0.7858 (OUTLIER) cc_final: 0.7594 (mt) outliers start: 4 outliers final: 0 residues processed: 370 average time/residue: 0.6692 time to fit residues: 356.2949 Evaluate side-chains 264 residues out of total 1606 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 263 time to evaluate : 2.072 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 86 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 187 random chunks: chunk 157 optimal weight: 1.9990 chunk 141 optimal weight: 0.7980 chunk 78 optimal weight: 1.9990 chunk 48 optimal weight: 1.9990 chunk 95 optimal weight: 0.9980 chunk 75 optimal weight: 1.9990 chunk 146 optimal weight: 0.5980 chunk 56 optimal weight: 2.9990 chunk 89 optimal weight: 0.9990 chunk 109 optimal weight: 0.7980 chunk 169 optimal weight: 0.0050 overall best weight: 0.6394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 57 HIS K 14 ASN ** K 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 177 GLN ** D 150 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 223 ASN B 287 GLN ** M 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6601 moved from start: 0.1895 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 15075 Z= 0.210 Angle : 0.560 12.011 20544 Z= 0.281 Chirality : 0.039 0.166 2284 Planarity : 0.004 0.050 2625 Dihedral : 8.143 176.935 2086 Min Nonbonded Distance : 1.922 Molprobity Statistics. All-atom Clashscore : 9.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.76 % Favored : 96.24 % Rotamer: Outliers : 0.67 % Allowed : 5.78 % Favored : 93.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.40 (0.20), residues: 1887 helix: 0.77 (0.17), residues: 969 sheet: -0.46 (0.39), residues: 171 loop : -0.06 (0.25), residues: 747 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP K 142 HIS 0.007 0.001 HIS K 96 PHE 0.013 0.001 PHE I 30 TYR 0.015 0.001 TYR K 132 ARG 0.004 0.000 ARG D 282 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3774 Ramachandran restraints generated. 1887 Oldfield, 0 Emsley, 1887 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3774 Ramachandran restraints generated. 1887 Oldfield, 0 Emsley, 1887 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ALA 112 is missing expected H atoms. Skipping. Residue LYS 124 is missing expected H atoms. Skipping. Residue LYS 36 is missing expected H atoms. Skipping. Residue TYR 43 is missing expected H atoms. Skipping. Residue LYS 80 is missing expected H atoms. Skipping. Residue SER 214 is missing expected H atoms. Skipping. Residue LYS 218 is missing expected H atoms. Skipping. Residue LEU 220 is missing expected H atoms. Skipping. Residue TYR 32 is missing expected H atoms. Skipping. Evaluate side-chains 280 residues out of total 1606 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 270 time to evaluate : 2.126 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: A 35 GLU cc_start: 0.7158 (tm-30) cc_final: 0.6698 (tt0) REVERT: A 126 LYS cc_start: 0.7420 (ttpp) cc_final: 0.7131 (tppt) REVERT: A 252 GLU cc_start: 0.8140 (mm-30) cc_final: 0.7842 (mm-30) REVERT: A 256 SER cc_start: 0.8741 (m) cc_final: 0.8365 (p) REVERT: A 276 SER cc_start: 0.8512 (t) cc_final: 0.8245 (p) REVERT: A 396 LYS cc_start: 0.7686 (mmtt) cc_final: 0.7230 (mppt) REVERT: K 52 MET cc_start: 0.8769 (mtt) cc_final: 0.8550 (mtm) REVERT: K 77 LEU cc_start: 0.8276 (tp) cc_final: 0.8068 (tp) REVERT: K 261 ASN cc_start: 0.7547 (t0) cc_final: 0.7295 (t0) REVERT: D 48 HIS cc_start: 0.8346 (t70) cc_final: 0.8116 (t70) REVERT: D 79 ARG cc_start: 0.7557 (mtp-110) cc_final: 0.6875 (mtp85) REVERT: D 241 GLU cc_start: 0.8343 (mt-10) cc_final: 0.8108 (mt-10) REVERT: D 243 GLU cc_start: 0.7772 (pm20) cc_final: 0.7476 (pm20) REVERT: D 246 ASP cc_start: 0.8010 (m-30) cc_final: 0.7689 (m-30) REVERT: G 61 LYS cc_start: 0.7662 (tmmt) cc_final: 0.6991 (ttmt) REVERT: G 92 LYS cc_start: 0.8190 (mtpt) cc_final: 0.7987 (mtmm) REVERT: F 27 GLN cc_start: 0.7743 (mt0) cc_final: 0.7452 (tt0) REVERT: I 36 LYS cc_start: 0.8231 (ttpp) cc_final: 0.7685 (ttmm) REVERT: I 53 LYS cc_start: 0.8556 (mtpp) cc_final: 0.8343 (mtpt) REVERT: B 113 GLN cc_start: 0.8150 (tt0) cc_final: 0.7907 (tp40) REVERT: B 148 GLU cc_start: 0.8226 (tt0) cc_final: 0.7985 (tt0) REVERT: B 152 ARG cc_start: 0.7686 (mtt180) cc_final: 0.6283 (mmm160) REVERT: B 208 TYR cc_start: 0.5740 (m-80) cc_final: 0.5371 (m-80) REVERT: B 225 PHE cc_start: 0.6745 (m-80) cc_final: 0.6349 (m-10) REVERT: B 238 SER cc_start: 0.8451 (m) cc_final: 0.8103 (t) REVERT: B 330 GLU cc_start: 0.7841 (mm-30) cc_final: 0.7620 (mm-30) REVERT: B 356 LYS cc_start: 0.8721 (mmmt) cc_final: 0.8293 (mmmm) REVERT: B 370 TYR cc_start: 0.8028 (m-80) cc_final: 0.7577 (m-80) REVERT: E 86 LEU cc_start: 0.7907 (OUTLIER) cc_final: 0.7455 (mt) outliers start: 10 outliers final: 9 residues processed: 276 average time/residue: 0.6368 time to fit residues: 255.9544 Evaluate side-chains 261 residues out of total 1606 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 251 time to evaluate : 2.200 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 SER Chi-restraints excluded: chain A residue 132 SER Chi-restraints excluded: chain G residue 122 ASN Chi-restraints excluded: chain B residue 77 THR Chi-restraints excluded: chain B residue 87 LEU Chi-restraints excluded: chain B residue 226 THR Chi-restraints excluded: chain B residue 235 SER Chi-restraints excluded: chain B residue 265 THR Chi-restraints excluded: chain E residue 82 SER Chi-restraints excluded: chain E residue 86 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 187 random chunks: chunk 94 optimal weight: 0.4980 chunk 52 optimal weight: 0.9980 chunk 141 optimal weight: 2.9990 chunk 115 optimal weight: 2.9990 chunk 46 optimal weight: 2.9990 chunk 170 optimal weight: 4.9990 chunk 183 optimal weight: 20.0000 chunk 151 optimal weight: 1.9990 chunk 168 optimal weight: 0.6980 chunk 57 optimal weight: 0.1980 chunk 136 optimal weight: 3.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 57 HIS ** K 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 150 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 41 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 287 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6664 moved from start: 0.2450 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.069 15075 Z= 0.250 Angle : 0.538 9.979 20544 Z= 0.272 Chirality : 0.039 0.155 2284 Planarity : 0.004 0.051 2625 Dihedral : 7.616 179.676 2086 Min Nonbonded Distance : 1.937 Molprobity Statistics. All-atom Clashscore : 9.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.03 % Favored : 95.97 % Rotamer: Outliers : 1.14 % Allowed : 6.78 % Favored : 92.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.57 (0.20), residues: 1887 helix: 0.98 (0.17), residues: 972 sheet: -0.56 (0.39), residues: 169 loop : -0.03 (0.25), residues: 746 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP K 142 HIS 0.006 0.001 HIS D 48 PHE 0.012 0.001 PHE K 90 TYR 0.015 0.001 TYR K 358 ARG 0.003 0.000 ARG H 92 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3774 Ramachandran restraints generated. 1887 Oldfield, 0 Emsley, 1887 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3774 Ramachandran restraints generated. 1887 Oldfield, 0 Emsley, 1887 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ALA 112 is missing expected H atoms. Skipping. Residue LYS 124 is missing expected H atoms. Skipping. Residue LYS 36 is missing expected H atoms. Skipping. Residue TYR 43 is missing expected H atoms. Skipping. Residue LYS 80 is missing expected H atoms. Skipping. Residue SER 214 is missing expected H atoms. Skipping. Residue LYS 218 is missing expected H atoms. Skipping. Residue LEU 220 is missing expected H atoms. Skipping. Residue TYR 32 is missing expected H atoms. Skipping. Evaluate side-chains 281 residues out of total 1606 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 264 time to evaluate : 2.230 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: A 35 GLU cc_start: 0.7262 (tm-30) cc_final: 0.6778 (tt0) REVERT: A 126 LYS cc_start: 0.7488 (ttpp) cc_final: 0.7237 (tppt) REVERT: A 252 GLU cc_start: 0.8156 (mm-30) cc_final: 0.7825 (mm-30) REVERT: A 256 SER cc_start: 0.8751 (m) cc_final: 0.8366 (p) REVERT: A 276 SER cc_start: 0.8500 (t) cc_final: 0.8222 (p) REVERT: A 396 LYS cc_start: 0.7754 (mmtt) cc_final: 0.7267 (mppt) REVERT: K 52 MET cc_start: 0.8764 (mtt) cc_final: 0.8563 (mtm) REVERT: K 59 GLU cc_start: 0.8189 (pt0) cc_final: 0.7921 (pt0) REVERT: K 261 ASN cc_start: 0.7858 (t0) cc_final: 0.7471 (t0) REVERT: D 79 ARG cc_start: 0.7545 (mtp-110) cc_final: 0.6956 (mtp85) REVERT: D 241 GLU cc_start: 0.8232 (mt-10) cc_final: 0.8005 (mt-10) REVERT: D 243 GLU cc_start: 0.7782 (pm20) cc_final: 0.7418 (pm20) REVERT: D 246 ASP cc_start: 0.8041 (m-30) cc_final: 0.7763 (m-30) REVERT: F 27 GLN cc_start: 0.7673 (mt0) cc_final: 0.7305 (tt0) REVERT: I 36 LYS cc_start: 0.8317 (ttpp) cc_final: 0.7780 (ttmm) REVERT: I 53 LYS cc_start: 0.8512 (mtpp) cc_final: 0.8299 (mtpt) REVERT: B 113 GLN cc_start: 0.8172 (tt0) cc_final: 0.7875 (tp40) REVERT: B 148 GLU cc_start: 0.8352 (tt0) cc_final: 0.8151 (tt0) REVERT: B 152 ARG cc_start: 0.7988 (mtt180) cc_final: 0.6346 (mmm160) REVERT: B 208 TYR cc_start: 0.5911 (m-80) cc_final: 0.5415 (m-80) REVERT: B 225 PHE cc_start: 0.6818 (m-80) cc_final: 0.6409 (m-10) REVERT: B 238 SER cc_start: 0.8579 (m) cc_final: 0.8219 (t) REVERT: B 356 LYS cc_start: 0.8754 (mmmt) cc_final: 0.8354 (mmmm) REVERT: E 86 LEU cc_start: 0.7890 (OUTLIER) cc_final: 0.7380 (mt) outliers start: 17 outliers final: 15 residues processed: 275 average time/residue: 0.6100 time to fit residues: 245.0944 Evaluate side-chains 261 residues out of total 1606 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 245 time to evaluate : 2.332 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 SER Chi-restraints excluded: chain A residue 132 SER Chi-restraints excluded: chain A residue 288 SER Chi-restraints excluded: chain K residue 10 LEU Chi-restraints excluded: chain K residue 64 SER Chi-restraints excluded: chain G residue 58 THR Chi-restraints excluded: chain G residue 60 ILE Chi-restraints excluded: chain I residue 40 GLU Chi-restraints excluded: chain B residue 87 LEU Chi-restraints excluded: chain B residue 164 SER Chi-restraints excluded: chain B residue 199 LYS Chi-restraints excluded: chain B residue 226 THR Chi-restraints excluded: chain B residue 235 SER Chi-restraints excluded: chain B residue 265 THR Chi-restraints excluded: chain E residue 82 SER Chi-restraints excluded: chain E residue 86 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 187 random chunks: chunk 168 optimal weight: 0.9990 chunk 127 optimal weight: 7.9990 chunk 88 optimal weight: 2.9990 chunk 18 optimal weight: 2.9990 chunk 81 optimal weight: 1.9990 chunk 114 optimal weight: 1.9990 chunk 170 optimal weight: 4.9990 chunk 180 optimal weight: 30.0000 chunk 89 optimal weight: 0.6980 chunk 161 optimal weight: 2.9990 chunk 48 optimal weight: 1.9990 overall best weight: 1.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 57 HIS ** A 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 57 ASN ** K 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 150 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 41 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6764 moved from start: 0.3335 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.065 15075 Z= 0.351 Angle : 0.591 9.841 20544 Z= 0.306 Chirality : 0.041 0.155 2284 Planarity : 0.004 0.055 2625 Dihedral : 7.777 179.778 2086 Min Nonbonded Distance : 1.971 Molprobity Statistics. All-atom Clashscore : 10.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.40 % Favored : 95.60 % Rotamer: Outliers : 1.54 % Allowed : 7.92 % Favored : 90.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.24 (0.20), residues: 1887 helix: 0.74 (0.17), residues: 975 sheet: -0.77 (0.38), residues: 181 loop : -0.22 (0.24), residues: 731 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP K 142 HIS 0.010 0.002 HIS K 197 PHE 0.021 0.002 PHE G 14 TYR 0.018 0.002 TYR K 358 ARG 0.004 0.001 ARG G 18 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3774 Ramachandran restraints generated. 1887 Oldfield, 0 Emsley, 1887 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3774 Ramachandran restraints generated. 1887 Oldfield, 0 Emsley, 1887 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ALA 112 is missing expected H atoms. Skipping. Residue LYS 124 is missing expected H atoms. Skipping. Residue LYS 36 is missing expected H atoms. Skipping. Residue TYR 43 is missing expected H atoms. Skipping. Residue LYS 80 is missing expected H atoms. Skipping. Residue SER 214 is missing expected H atoms. Skipping. Residue LYS 218 is missing expected H atoms. Skipping. Residue LEU 220 is missing expected H atoms. Skipping. Residue TYR 32 is missing expected H atoms. Skipping. Evaluate side-chains 283 residues out of total 1606 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 260 time to evaluate : 2.386 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 35 GLU cc_start: 0.7238 (tm-30) cc_final: 0.6808 (tt0) REVERT: A 252 GLU cc_start: 0.8203 (mm-30) cc_final: 0.7817 (mm-30) REVERT: A 256 SER cc_start: 0.8803 (m) cc_final: 0.8314 (p) REVERT: A 276 SER cc_start: 0.8531 (t) cc_final: 0.8080 (p) REVERT: A 396 LYS cc_start: 0.7861 (mmtt) cc_final: 0.7415 (mppt) REVERT: K 52 MET cc_start: 0.8832 (mtt) cc_final: 0.8602 (mtm) REVERT: K 261 ASN cc_start: 0.8357 (t0) cc_final: 0.7897 (t0) REVERT: D 79 ARG cc_start: 0.7483 (mtp-110) cc_final: 0.6896 (mtp85) REVERT: D 143 GLU cc_start: 0.8399 (tt0) cc_final: 0.8192 (tt0) REVERT: D 170 ASP cc_start: 0.7994 (m-30) cc_final: 0.7783 (m-30) REVERT: D 206 MET cc_start: 0.8915 (ttp) cc_final: 0.8602 (ttp) REVERT: D 246 ASP cc_start: 0.8038 (m-30) cc_final: 0.7780 (m-30) REVERT: G 99 ASP cc_start: 0.7137 (t0) cc_final: 0.6916 (t70) REVERT: G 109 GLU cc_start: 0.7122 (tp30) cc_final: 0.6613 (mt-10) REVERT: F 54 LYS cc_start: 0.8121 (tttp) cc_final: 0.7628 (tppt) REVERT: H 67 ASP cc_start: 0.7118 (m-30) cc_final: 0.6734 (m-30) REVERT: I 36 LYS cc_start: 0.8435 (ttpp) cc_final: 0.7912 (ttmm) REVERT: I 53 LYS cc_start: 0.8484 (mtpp) cc_final: 0.8258 (mtpt) REVERT: B 113 GLN cc_start: 0.8020 (tt0) cc_final: 0.7784 (tp40) REVERT: B 152 ARG cc_start: 0.8348 (mtt180) cc_final: 0.6382 (mmm160) REVERT: B 190 GLU cc_start: 0.7307 (mt-10) cc_final: 0.6995 (mt-10) REVERT: B 204 SER cc_start: 0.8223 (p) cc_final: 0.7982 (p) REVERT: B 238 SER cc_start: 0.8720 (m) cc_final: 0.8306 (t) REVERT: B 356 LYS cc_start: 0.8693 (mmmt) cc_final: 0.8313 (mmmm) REVERT: M 60 MET cc_start: 0.8596 (ttm) cc_final: 0.8371 (ttm) outliers start: 23 outliers final: 20 residues processed: 278 average time/residue: 0.6200 time to fit residues: 248.4018 Evaluate side-chains 264 residues out of total 1606 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 244 time to evaluate : 2.040 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 SER Chi-restraints excluded: chain A residue 132 SER Chi-restraints excluded: chain A residue 288 SER Chi-restraints excluded: chain K residue 64 SER Chi-restraints excluded: chain D residue 65 THR Chi-restraints excluded: chain D residue 105 GLU Chi-restraints excluded: chain D residue 174 SER Chi-restraints excluded: chain G residue 58 THR Chi-restraints excluded: chain G residue 60 ILE Chi-restraints excluded: chain F residue 9 THR Chi-restraints excluded: chain I residue 32 VAL Chi-restraints excluded: chain B residue 40 SER Chi-restraints excluded: chain B residue 87 LEU Chi-restraints excluded: chain B residue 164 SER Chi-restraints excluded: chain B residue 226 THR Chi-restraints excluded: chain B residue 229 GLU Chi-restraints excluded: chain B residue 235 SER Chi-restraints excluded: chain B residue 265 THR Chi-restraints excluded: chain E residue 82 SER Chi-restraints excluded: chain E residue 86 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 187 random chunks: chunk 150 optimal weight: 1.9990 chunk 102 optimal weight: 1.9990 chunk 2 optimal weight: 2.9990 chunk 134 optimal weight: 2.9990 chunk 74 optimal weight: 1.9990 chunk 154 optimal weight: 1.9990 chunk 124 optimal weight: 0.9990 chunk 0 optimal weight: 2.9990 chunk 92 optimal weight: 1.9990 chunk 162 optimal weight: 1.9990 chunk 45 optimal weight: 1.9990 overall best weight: 1.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 57 HIS ** K 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 150 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 86 GLN ** I 41 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 179 GLN B 287 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6797 moved from start: 0.3861 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.070 15075 Z= 0.390 Angle : 0.582 9.663 20544 Z= 0.302 Chirality : 0.041 0.159 2284 Planarity : 0.004 0.043 2625 Dihedral : 7.772 178.288 2086 Min Nonbonded Distance : 1.987 Molprobity Statistics. All-atom Clashscore : 10.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.40 % Favored : 95.60 % Rotamer: Outliers : 1.68 % Allowed : 9.34 % Favored : 88.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.11 (0.20), residues: 1887 helix: 0.67 (0.17), residues: 968 sheet: -0.87 (0.38), residues: 176 loop : -0.33 (0.24), residues: 743 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP K 142 HIS 0.009 0.001 HIS K 197 PHE 0.019 0.001 PHE K 89 TYR 0.026 0.002 TYR H 107 ARG 0.003 0.001 ARG F 87 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3774 Ramachandran restraints generated. 1887 Oldfield, 0 Emsley, 1887 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3774 Ramachandran restraints generated. 1887 Oldfield, 0 Emsley, 1887 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ALA 112 is missing expected H atoms. Skipping. Residue LYS 124 is missing expected H atoms. Skipping. Residue LYS 36 is missing expected H atoms. Skipping. Residue TYR 43 is missing expected H atoms. Skipping. Residue LYS 80 is missing expected H atoms. Skipping. Residue SER 214 is missing expected H atoms. Skipping. Residue LYS 218 is missing expected H atoms. Skipping. Residue LEU 220 is missing expected H atoms. Skipping. Residue TYR 32 is missing expected H atoms. Skipping. Evaluate side-chains 290 residues out of total 1606 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 265 time to evaluate : 2.562 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: A 35 GLU cc_start: 0.7265 (tm-30) cc_final: 0.6792 (tt0) REVERT: A 252 GLU cc_start: 0.8190 (mm-30) cc_final: 0.7834 (mm-30) REVERT: A 256 SER cc_start: 0.8707 (m) cc_final: 0.8388 (p) REVERT: A 276 SER cc_start: 0.8572 (t) cc_final: 0.8079 (p) REVERT: A 396 LYS cc_start: 0.7795 (mmtt) cc_final: 0.7312 (mppt) REVERT: K 52 MET cc_start: 0.8909 (mtt) cc_final: 0.8632 (mtm) REVERT: K 112 MET cc_start: 0.7741 (ttp) cc_final: 0.7506 (ttp) REVERT: K 261 ASN cc_start: 0.8529 (t0) cc_final: 0.8121 (t0) REVERT: D 79 ARG cc_start: 0.7605 (mtp-110) cc_final: 0.7029 (mtp85) REVERT: D 142 ASN cc_start: 0.8167 (p0) cc_final: 0.7966 (p0) REVERT: D 143 GLU cc_start: 0.8454 (tt0) cc_final: 0.8041 (tt0) REVERT: D 151 GLN cc_start: 0.8589 (mp10) cc_final: 0.8202 (mp10) REVERT: D 170 ASP cc_start: 0.8050 (m-30) cc_final: 0.7839 (m-30) REVERT: D 206 MET cc_start: 0.8955 (ttp) cc_final: 0.8682 (ttp) REVERT: G 98 GLU cc_start: 0.7392 (mt-10) cc_final: 0.6961 (mt-10) REVERT: G 109 GLU cc_start: 0.7142 (tp30) cc_final: 0.6580 (mt-10) REVERT: G 117 LYS cc_start: 0.7753 (ttmt) cc_final: 0.6974 (tptt) REVERT: G 119 GLU cc_start: 0.8113 (tp30) cc_final: 0.7865 (tp30) REVERT: F 54 LYS cc_start: 0.8078 (tttp) cc_final: 0.7607 (tppt) REVERT: H 67 ASP cc_start: 0.7172 (m-30) cc_final: 0.6755 (m-30) REVERT: I 36 LYS cc_start: 0.8451 (ttpp) cc_final: 0.7951 (ttmm) REVERT: I 53 LYS cc_start: 0.8462 (mtpp) cc_final: 0.8235 (mtpt) REVERT: B 59 ASN cc_start: 0.7664 (OUTLIER) cc_final: 0.7321 (m-40) REVERT: B 152 ARG cc_start: 0.8468 (mtt180) cc_final: 0.6484 (mmm160) REVERT: B 183 GLU cc_start: 0.7186 (pt0) cc_final: 0.6881 (pt0) REVERT: B 186 SER cc_start: 0.7836 (t) cc_final: 0.7430 (p) REVERT: B 190 GLU cc_start: 0.7625 (mt-10) cc_final: 0.7310 (mt-10) REVERT: B 238 SER cc_start: 0.8738 (m) cc_final: 0.8305 (t) REVERT: B 356 LYS cc_start: 0.8622 (mmmt) cc_final: 0.8249 (mmmm) REVERT: M 50 ARG cc_start: 0.6721 (tmt-80) cc_final: 0.5436 (ptp90) REVERT: M 60 MET cc_start: 0.8709 (ttm) cc_final: 0.8294 (ttm) outliers start: 25 outliers final: 19 residues processed: 284 average time/residue: 0.6878 time to fit residues: 284.7066 Evaluate side-chains 270 residues out of total 1606 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 250 time to evaluate : 2.416 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 SER Chi-restraints excluded: chain A residue 132 SER Chi-restraints excluded: chain A residue 288 SER Chi-restraints excluded: chain K residue 14 ASN Chi-restraints excluded: chain K residue 64 SER Chi-restraints excluded: chain D residue 65 THR Chi-restraints excluded: chain D residue 105 GLU Chi-restraints excluded: chain D residue 174 SER Chi-restraints excluded: chain G residue 18 ARG Chi-restraints excluded: chain G residue 60 ILE Chi-restraints excluded: chain G residue 66 GLU Chi-restraints excluded: chain F residue 9 THR Chi-restraints excluded: chain B residue 40 SER Chi-restraints excluded: chain B residue 59 ASN Chi-restraints excluded: chain B residue 87 LEU Chi-restraints excluded: chain B residue 226 THR Chi-restraints excluded: chain B residue 232 VAL Chi-restraints excluded: chain B residue 235 SER Chi-restraints excluded: chain B residue 265 THR Chi-restraints excluded: chain E residue 82 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 187 random chunks: chunk 60 optimal weight: 0.5980 chunk 162 optimal weight: 1.9990 chunk 35 optimal weight: 1.9990 chunk 106 optimal weight: 2.9990 chunk 44 optimal weight: 0.6980 chunk 180 optimal weight: 0.0470 chunk 150 optimal weight: 2.9990 chunk 83 optimal weight: 1.9990 chunk 15 optimal weight: 2.9990 chunk 59 optimal weight: 0.6980 chunk 94 optimal weight: 1.9990 overall best weight: 0.8080 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 57 HIS A 398 ASN ** K 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 41 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6767 moved from start: 0.4002 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 15075 Z= 0.222 Angle : 0.516 8.677 20544 Z= 0.265 Chirality : 0.038 0.154 2284 Planarity : 0.004 0.039 2625 Dihedral : 7.451 178.892 2084 Min Nonbonded Distance : 1.983 Molprobity Statistics. All-atom Clashscore : 10.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.76 % Favored : 96.24 % Rotamer: Outliers : 1.21 % Allowed : 10.34 % Favored : 88.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.41 (0.20), residues: 1887 helix: 0.94 (0.17), residues: 967 sheet: -0.82 (0.38), residues: 175 loop : -0.19 (0.24), residues: 745 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP K 142 HIS 0.005 0.001 HIS K 343 PHE 0.015 0.001 PHE A 327 TYR 0.012 0.001 TYR H 107 ARG 0.003 0.000 ARG A 429 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3774 Ramachandran restraints generated. 1887 Oldfield, 0 Emsley, 1887 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3774 Ramachandran restraints generated. 1887 Oldfield, 0 Emsley, 1887 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ALA 112 is missing expected H atoms. Skipping. Residue LYS 124 is missing expected H atoms. Skipping. Residue LYS 36 is missing expected H atoms. Skipping. Residue TYR 43 is missing expected H atoms. Skipping. Residue LYS 80 is missing expected H atoms. Skipping. Residue SER 214 is missing expected H atoms. Skipping. Residue LYS 218 is missing expected H atoms. Skipping. Residue LEU 220 is missing expected H atoms. Skipping. Residue TYR 32 is missing expected H atoms. Skipping. Evaluate side-chains 270 residues out of total 1606 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 252 time to evaluate : 2.234 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 35 GLU cc_start: 0.7273 (tm-30) cc_final: 0.6814 (tt0) REVERT: A 210 GLU cc_start: 0.7871 (tm-30) cc_final: 0.7380 (tp30) REVERT: A 252 GLU cc_start: 0.8170 (mm-30) cc_final: 0.7795 (mm-30) REVERT: A 256 SER cc_start: 0.8714 (m) cc_final: 0.8386 (p) REVERT: A 276 SER cc_start: 0.8525 (t) cc_final: 0.8017 (p) REVERT: A 396 LYS cc_start: 0.7801 (mmtt) cc_final: 0.7317 (mppt) REVERT: K 52 MET cc_start: 0.8897 (mtt) cc_final: 0.8619 (mtm) REVERT: K 112 MET cc_start: 0.7825 (ttp) cc_final: 0.7615 (ttp) REVERT: K 261 ASN cc_start: 0.8453 (t0) cc_final: 0.8047 (t0) REVERT: D 79 ARG cc_start: 0.7666 (mtp-110) cc_final: 0.7039 (mtp85) REVERT: D 151 GLN cc_start: 0.8592 (mp10) cc_final: 0.8115 (mp10) REVERT: G 98 GLU cc_start: 0.7420 (mt-10) cc_final: 0.7092 (mt-10) REVERT: G 109 GLU cc_start: 0.7135 (tp30) cc_final: 0.6814 (tp30) REVERT: G 117 LYS cc_start: 0.7670 (ttmt) cc_final: 0.6867 (tptt) REVERT: G 119 GLU cc_start: 0.8090 (tp30) cc_final: 0.7837 (tp30) REVERT: F 54 LYS cc_start: 0.8054 (tttp) cc_final: 0.7594 (tppt) REVERT: H 67 ASP cc_start: 0.7155 (m-30) cc_final: 0.6773 (m-30) REVERT: I 36 LYS cc_start: 0.8457 (ttpp) cc_final: 0.7963 (ttmm) REVERT: I 53 LYS cc_start: 0.8426 (mtpp) cc_final: 0.8205 (mtpt) REVERT: B 59 ASN cc_start: 0.7613 (OUTLIER) cc_final: 0.7293 (m-40) REVERT: B 152 ARG cc_start: 0.8407 (mtt180) cc_final: 0.6548 (mmm160) REVERT: B 183 GLU cc_start: 0.7104 (pt0) cc_final: 0.6814 (pt0) REVERT: B 190 GLU cc_start: 0.7443 (mt-10) cc_final: 0.7139 (mt-10) REVERT: B 225 PHE cc_start: 0.7272 (m-80) cc_final: 0.6905 (m-10) REVERT: B 238 SER cc_start: 0.8694 (m) cc_final: 0.8314 (t) REVERT: B 356 LYS cc_start: 0.8664 (mmmt) cc_final: 0.8275 (mmmm) REVERT: M 50 ARG cc_start: 0.6604 (tmt-80) cc_final: 0.5331 (ptp90) REVERT: M 60 MET cc_start: 0.8695 (ttm) cc_final: 0.8391 (ttp) outliers start: 18 outliers final: 16 residues processed: 267 average time/residue: 0.6312 time to fit residues: 241.7893 Evaluate side-chains 258 residues out of total 1606 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 241 time to evaluate : 2.152 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 SER Chi-restraints excluded: chain A residue 132 SER Chi-restraints excluded: chain A residue 288 SER Chi-restraints excluded: chain K residue 64 SER Chi-restraints excluded: chain D residue 65 THR Chi-restraints excluded: chain D residue 105 GLU Chi-restraints excluded: chain D residue 174 SER Chi-restraints excluded: chain G residue 18 ARG Chi-restraints excluded: chain G residue 60 ILE Chi-restraints excluded: chain F residue 9 THR Chi-restraints excluded: chain B residue 40 SER Chi-restraints excluded: chain B residue 59 ASN Chi-restraints excluded: chain B residue 87 LEU Chi-restraints excluded: chain B residue 232 VAL Chi-restraints excluded: chain B residue 235 SER Chi-restraints excluded: chain B residue 265 THR Chi-restraints excluded: chain E residue 82 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 187 random chunks: chunk 174 optimal weight: 0.0980 chunk 20 optimal weight: 2.9990 chunk 103 optimal weight: 1.9990 chunk 132 optimal weight: 2.9990 chunk 102 optimal weight: 1.9990 chunk 152 optimal weight: 1.9990 chunk 101 optimal weight: 0.9990 chunk 180 optimal weight: 0.9990 chunk 112 optimal weight: 0.3980 chunk 109 optimal weight: 0.0170 chunk 83 optimal weight: 2.9990 overall best weight: 0.5022 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 57 HIS A 329 HIS ** K 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 177 GLN ** I 41 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6752 moved from start: 0.4060 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 15075 Z= 0.187 Angle : 0.498 7.802 20544 Z= 0.252 Chirality : 0.038 0.151 2284 Planarity : 0.003 0.036 2625 Dihedral : 7.252 179.070 2084 Min Nonbonded Distance : 1.986 Molprobity Statistics. All-atom Clashscore : 10.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.08 % Favored : 95.92 % Rotamer: Outliers : 1.21 % Allowed : 10.61 % Favored : 88.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.67 (0.20), residues: 1887 helix: 1.15 (0.17), residues: 972 sheet: -0.75 (0.39), residues: 175 loop : -0.06 (0.24), residues: 740 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP K 142 HIS 0.003 0.001 HIS K 197 PHE 0.019 0.001 PHE G 14 TYR 0.009 0.001 TYR K 358 ARG 0.002 0.000 ARG A 429 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3774 Ramachandran restraints generated. 1887 Oldfield, 0 Emsley, 1887 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3774 Ramachandran restraints generated. 1887 Oldfield, 0 Emsley, 1887 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ALA 112 is missing expected H atoms. Skipping. Residue LYS 124 is missing expected H atoms. Skipping. Residue LYS 36 is missing expected H atoms. Skipping. Residue TYR 43 is missing expected H atoms. Skipping. Residue LYS 80 is missing expected H atoms. Skipping. Residue SER 214 is missing expected H atoms. Skipping. Residue LYS 218 is missing expected H atoms. Skipping. Residue LEU 220 is missing expected H atoms. Skipping. Residue TYR 32 is missing expected H atoms. Skipping. Evaluate side-chains 264 residues out of total 1606 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 246 time to evaluate : 2.018 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: A 35 GLU cc_start: 0.7271 (tm-30) cc_final: 0.6848 (tt0) REVERT: A 252 GLU cc_start: 0.8138 (mm-30) cc_final: 0.7789 (mm-30) REVERT: A 256 SER cc_start: 0.8704 (m) cc_final: 0.8357 (p) REVERT: A 396 LYS cc_start: 0.7806 (mmtt) cc_final: 0.7307 (mppt) REVERT: K 112 MET cc_start: 0.7928 (ttp) cc_final: 0.7703 (ttp) REVERT: K 261 ASN cc_start: 0.8376 (t0) cc_final: 0.7949 (t0) REVERT: D 79 ARG cc_start: 0.7660 (mtp-110) cc_final: 0.7047 (mtp85) REVERT: D 151 GLN cc_start: 0.8528 (mp10) cc_final: 0.8148 (mp10) REVERT: D 206 MET cc_start: 0.8908 (ttp) cc_final: 0.8649 (ttp) REVERT: G 98 GLU cc_start: 0.7402 (mt-10) cc_final: 0.7090 (mt-10) REVERT: G 109 GLU cc_start: 0.7133 (tp30) cc_final: 0.6824 (tp30) REVERT: G 119 GLU cc_start: 0.8101 (tp30) cc_final: 0.7841 (tp30) REVERT: F 54 LYS cc_start: 0.8057 (tttp) cc_final: 0.7561 (tppt) REVERT: H 67 ASP cc_start: 0.7163 (m-30) cc_final: 0.6765 (m-30) REVERT: I 36 LYS cc_start: 0.8461 (ttpp) cc_final: 0.7971 (ttmm) REVERT: B 59 ASN cc_start: 0.7561 (OUTLIER) cc_final: 0.7262 (m-40) REVERT: B 152 ARG cc_start: 0.8354 (mtt180) cc_final: 0.6495 (mmm160) REVERT: B 183 GLU cc_start: 0.7051 (pt0) cc_final: 0.6597 (pt0) REVERT: B 186 SER cc_start: 0.7836 (t) cc_final: 0.7453 (p) REVERT: B 190 GLU cc_start: 0.7398 (mt-10) cc_final: 0.7099 (mt-10) REVERT: B 238 SER cc_start: 0.8648 (m) cc_final: 0.8281 (t) REVERT: B 356 LYS cc_start: 0.8612 (mmmt) cc_final: 0.8235 (mmmm) REVERT: M 50 ARG cc_start: 0.6675 (tmt-80) cc_final: 0.5403 (ptp90) REVERT: M 60 MET cc_start: 0.8658 (ttm) cc_final: 0.8388 (ttp) outliers start: 18 outliers final: 15 residues processed: 262 average time/residue: 0.6369 time to fit residues: 239.6096 Evaluate side-chains 248 residues out of total 1606 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 232 time to evaluate : 2.123 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 SER Chi-restraints excluded: chain A residue 132 SER Chi-restraints excluded: chain A residue 288 SER Chi-restraints excluded: chain K residue 10 LEU Chi-restraints excluded: chain K residue 64 SER Chi-restraints excluded: chain D residue 65 THR Chi-restraints excluded: chain D residue 174 SER Chi-restraints excluded: chain G residue 18 ARG Chi-restraints excluded: chain G residue 60 ILE Chi-restraints excluded: chain F residue 9 THR Chi-restraints excluded: chain I residue 32 VAL Chi-restraints excluded: chain B residue 59 ASN Chi-restraints excluded: chain B residue 87 LEU Chi-restraints excluded: chain B residue 164 SER Chi-restraints excluded: chain B residue 235 SER Chi-restraints excluded: chain E residue 82 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 187 random chunks: chunk 111 optimal weight: 1.9990 chunk 71 optimal weight: 0.9980 chunk 107 optimal weight: 1.9990 chunk 54 optimal weight: 1.9990 chunk 35 optimal weight: 1.9990 chunk 34 optimal weight: 0.8980 chunk 114 optimal weight: 1.9990 chunk 122 optimal weight: 3.9990 chunk 89 optimal weight: 3.9990 chunk 16 optimal weight: 3.9990 chunk 141 optimal weight: 1.9990 overall best weight: 1.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 57 HIS A 129 GLN ** K 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 150 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 41 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6801 moved from start: 0.4230 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.068 15075 Z= 0.367 Angle : 0.564 8.931 20544 Z= 0.290 Chirality : 0.040 0.155 2284 Planarity : 0.004 0.035 2625 Dihedral : 7.452 179.271 2084 Min Nonbonded Distance : 1.996 Molprobity Statistics. All-atom Clashscore : 10.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.50 % Favored : 95.50 % Rotamer: Outliers : 1.28 % Allowed : 10.95 % Favored : 87.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.43 (0.20), residues: 1887 helix: 1.02 (0.17), residues: 963 sheet: -0.81 (0.39), residues: 175 loop : -0.27 (0.24), residues: 749 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP K 142 HIS 0.008 0.001 HIS I 41 PHE 0.022 0.001 PHE K 89 TYR 0.012 0.001 TYR K 358 ARG 0.002 0.000 ARG A 429 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3774 Ramachandran restraints generated. 1887 Oldfield, 0 Emsley, 1887 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3774 Ramachandran restraints generated. 1887 Oldfield, 0 Emsley, 1887 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ALA 112 is missing expected H atoms. Skipping. Residue LYS 124 is missing expected H atoms. Skipping. Residue LYS 36 is missing expected H atoms. Skipping. Residue TYR 43 is missing expected H atoms. Skipping. Residue LYS 80 is missing expected H atoms. Skipping. Residue SER 214 is missing expected H atoms. Skipping. Residue LYS 218 is missing expected H atoms. Skipping. Residue LEU 220 is missing expected H atoms. Skipping. Residue TYR 32 is missing expected H atoms. Skipping. Evaluate side-chains 258 residues out of total 1606 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 239 time to evaluate : 2.294 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 35 GLU cc_start: 0.7259 (tm-30) cc_final: 0.6800 (tt0) REVERT: A 252 GLU cc_start: 0.8195 (mm-30) cc_final: 0.7844 (mm-30) REVERT: A 256 SER cc_start: 0.8716 (m) cc_final: 0.8378 (p) REVERT: A 276 SER cc_start: 0.8431 (t) cc_final: 0.7965 (p) REVERT: A 396 LYS cc_start: 0.7819 (mmtt) cc_final: 0.7500 (mppt) REVERT: A 411 ARG cc_start: 0.7776 (mmm-85) cc_final: 0.7415 (mpt180) REVERT: K 52 MET cc_start: 0.8861 (mtt) cc_final: 0.8546 (mtm) REVERT: K 112 MET cc_start: 0.7876 (ttp) cc_final: 0.7660 (ttp) REVERT: K 261 ASN cc_start: 0.8464 (t0) cc_final: 0.8098 (t0) REVERT: D 79 ARG cc_start: 0.7690 (mtp-110) cc_final: 0.7069 (mtp85) REVERT: D 142 ASN cc_start: 0.8167 (p0) cc_final: 0.7946 (p0) REVERT: D 151 GLN cc_start: 0.8553 (mp10) cc_final: 0.8211 (mp10) REVERT: G 98 GLU cc_start: 0.7406 (mt-10) cc_final: 0.7081 (mt-10) REVERT: G 109 GLU cc_start: 0.7195 (tp30) cc_final: 0.6813 (tp30) REVERT: G 117 LYS cc_start: 0.7717 (ttmt) cc_final: 0.6937 (tptt) REVERT: G 119 GLU cc_start: 0.8163 (tp30) cc_final: 0.7923 (tp30) REVERT: F 54 LYS cc_start: 0.8065 (tttp) cc_final: 0.7577 (tppt) REVERT: H 67 ASP cc_start: 0.7252 (m-30) cc_final: 0.6858 (m-30) REVERT: I 36 LYS cc_start: 0.8462 (ttpp) cc_final: 0.7984 (ttmm) REVERT: B 59 ASN cc_start: 0.7743 (OUTLIER) cc_final: 0.7436 (m-40) REVERT: B 152 ARG cc_start: 0.8433 (mtt180) cc_final: 0.6534 (mmm160) REVERT: B 190 GLU cc_start: 0.7813 (mt-10) cc_final: 0.7501 (mt-10) REVERT: B 238 SER cc_start: 0.8738 (m) cc_final: 0.8305 (t) REVERT: B 356 LYS cc_start: 0.8609 (mmmt) cc_final: 0.8240 (mmmm) REVERT: M 50 ARG cc_start: 0.6751 (tmt-80) cc_final: 0.5493 (ptp90) REVERT: M 60 MET cc_start: 0.8661 (ttm) cc_final: 0.8409 (ttp) outliers start: 19 outliers final: 17 residues processed: 254 average time/residue: 0.6931 time to fit residues: 250.2263 Evaluate side-chains 251 residues out of total 1606 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 233 time to evaluate : 2.151 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 SER Chi-restraints excluded: chain A residue 132 SER Chi-restraints excluded: chain A residue 288 SER Chi-restraints excluded: chain K residue 64 SER Chi-restraints excluded: chain D residue 65 THR Chi-restraints excluded: chain G residue 18 ARG Chi-restraints excluded: chain G residue 60 ILE Chi-restraints excluded: chain F residue 9 THR Chi-restraints excluded: chain I residue 24 PHE Chi-restraints excluded: chain I residue 32 VAL Chi-restraints excluded: chain B residue 40 SER Chi-restraints excluded: chain B residue 59 ASN Chi-restraints excluded: chain B residue 87 LEU Chi-restraints excluded: chain B residue 164 SER Chi-restraints excluded: chain B residue 226 THR Chi-restraints excluded: chain B residue 235 SER Chi-restraints excluded: chain B residue 265 THR Chi-restraints excluded: chain E residue 82 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 187 random chunks: chunk 163 optimal weight: 2.9990 chunk 172 optimal weight: 2.9990 chunk 157 optimal weight: 1.9990 chunk 167 optimal weight: 2.9990 chunk 101 optimal weight: 0.9980 chunk 73 optimal weight: 1.9990 chunk 131 optimal weight: 0.9990 chunk 51 optimal weight: 0.3980 chunk 151 optimal weight: 3.9990 chunk 158 optimal weight: 0.9980 chunk 110 optimal weight: 1.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 57 HIS ** K 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 41 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6785 moved from start: 0.4337 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 15075 Z= 0.273 Angle : 0.529 8.477 20544 Z= 0.270 Chirality : 0.039 0.164 2284 Planarity : 0.004 0.036 2625 Dihedral : 7.348 178.666 2084 Min Nonbonded Distance : 2.002 Molprobity Statistics. All-atom Clashscore : 10.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.45 % Favored : 95.55 % Rotamer: Outliers : 1.07 % Allowed : 11.35 % Favored : 87.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.55 (0.20), residues: 1887 helix: 1.11 (0.17), residues: 964 sheet: -0.75 (0.39), residues: 175 loop : -0.21 (0.24), residues: 748 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP K 142 HIS 0.008 0.001 HIS I 41 PHE 0.023 0.001 PHE K 89 TYR 0.010 0.001 TYR F 28 ARG 0.003 0.000 ARG B 153 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3774 Ramachandran restraints generated. 1887 Oldfield, 0 Emsley, 1887 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3774 Ramachandran restraints generated. 1887 Oldfield, 0 Emsley, 1887 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ALA 112 is missing expected H atoms. Skipping. Residue LYS 124 is missing expected H atoms. Skipping. Residue LYS 36 is missing expected H atoms. Skipping. Residue TYR 43 is missing expected H atoms. Skipping. Residue LYS 80 is missing expected H atoms. Skipping. Residue SER 214 is missing expected H atoms. Skipping. Residue LYS 218 is missing expected H atoms. Skipping. Residue LEU 220 is missing expected H atoms. Skipping. Residue TYR 32 is missing expected H atoms. Skipping. Evaluate side-chains 257 residues out of total 1606 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 241 time to evaluate : 2.191 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 35 GLU cc_start: 0.7269 (tm-30) cc_final: 0.6833 (tt0) REVERT: A 252 GLU cc_start: 0.8178 (mm-30) cc_final: 0.7685 (mm-30) REVERT: A 256 SER cc_start: 0.8712 (m) cc_final: 0.8299 (p) REVERT: A 276 SER cc_start: 0.8464 (t) cc_final: 0.7948 (p) REVERT: A 396 LYS cc_start: 0.7790 (mmtt) cc_final: 0.7300 (mtmt) REVERT: K 112 MET cc_start: 0.7908 (ttp) cc_final: 0.7701 (ttp) REVERT: K 261 ASN cc_start: 0.8401 (t0) cc_final: 0.8072 (t0) REVERT: D 79 ARG cc_start: 0.7655 (mtp-110) cc_final: 0.7077 (mtp85) REVERT: D 206 MET cc_start: 0.8914 (ttp) cc_final: 0.8648 (ttp) REVERT: G 98 GLU cc_start: 0.7387 (mt-10) cc_final: 0.7029 (mt-10) REVERT: G 109 GLU cc_start: 0.7170 (tp30) cc_final: 0.6821 (tp30) REVERT: G 117 LYS cc_start: 0.7679 (ttmt) cc_final: 0.6939 (tptt) REVERT: G 119 GLU cc_start: 0.8175 (tp30) cc_final: 0.7964 (tp30) REVERT: F 54 LYS cc_start: 0.8063 (tttp) cc_final: 0.7576 (tppt) REVERT: H 67 ASP cc_start: 0.7236 (m-30) cc_final: 0.6839 (m-30) REVERT: I 36 LYS cc_start: 0.8440 (ttpp) cc_final: 0.7975 (ttmm) REVERT: I 43 LYS cc_start: 0.7890 (ptpp) cc_final: 0.7596 (ptpp) REVERT: B 59 ASN cc_start: 0.7678 (OUTLIER) cc_final: 0.7364 (m-40) REVERT: B 152 ARG cc_start: 0.8401 (mtt180) cc_final: 0.6477 (mmm160) REVERT: B 190 GLU cc_start: 0.7607 (mt-10) cc_final: 0.7299 (mt-10) REVERT: B 238 SER cc_start: 0.8695 (m) cc_final: 0.8296 (t) REVERT: M 54 TYR cc_start: 0.6350 (t80) cc_final: 0.6142 (t80) REVERT: M 60 MET cc_start: 0.8653 (ttm) cc_final: 0.8398 (ttp) outliers start: 16 outliers final: 15 residues processed: 256 average time/residue: 0.6671 time to fit residues: 243.9253 Evaluate side-chains 251 residues out of total 1606 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 235 time to evaluate : 2.319 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 SER Chi-restraints excluded: chain A residue 132 SER Chi-restraints excluded: chain A residue 288 SER Chi-restraints excluded: chain K residue 10 LEU Chi-restraints excluded: chain K residue 64 SER Chi-restraints excluded: chain K residue 226 ILE Chi-restraints excluded: chain G residue 18 ARG Chi-restraints excluded: chain G residue 60 ILE Chi-restraints excluded: chain F residue 9 THR Chi-restraints excluded: chain I residue 32 VAL Chi-restraints excluded: chain B residue 40 SER Chi-restraints excluded: chain B residue 59 ASN Chi-restraints excluded: chain B residue 87 LEU Chi-restraints excluded: chain B residue 164 SER Chi-restraints excluded: chain B residue 235 SER Chi-restraints excluded: chain E residue 82 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 187 random chunks: chunk 177 optimal weight: 10.0000 chunk 108 optimal weight: 1.9990 chunk 84 optimal weight: 1.9990 chunk 123 optimal weight: 0.6980 chunk 186 optimal weight: 0.0270 chunk 171 optimal weight: 3.9990 chunk 148 optimal weight: 0.5980 chunk 15 optimal weight: 2.9990 chunk 114 optimal weight: 0.8980 chunk 90 optimal weight: 0.5980 chunk 117 optimal weight: 1.9990 overall best weight: 0.5638 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 57 HIS ** I 41 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6760 moved from start: 0.4383 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 15075 Z= 0.190 Angle : 0.498 7.531 20544 Z= 0.252 Chirality : 0.038 0.148 2284 Planarity : 0.003 0.036 2625 Dihedral : 7.154 179.015 2084 Min Nonbonded Distance : 1.996 Molprobity Statistics. All-atom Clashscore : 10.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.03 % Favored : 95.97 % Rotamer: Outliers : 1.14 % Allowed : 11.62 % Favored : 87.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.80 (0.20), residues: 1887 helix: 1.30 (0.17), residues: 969 sheet: -0.64 (0.40), residues: 175 loop : -0.06 (0.24), residues: 743 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP K 142 HIS 0.007 0.001 HIS I 41 PHE 0.020 0.001 PHE K 89 TYR 0.009 0.001 TYR K 358 ARG 0.003 0.000 ARG B 153 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3774 Ramachandran restraints generated. 1887 Oldfield, 0 Emsley, 1887 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3774 Ramachandran restraints generated. 1887 Oldfield, 0 Emsley, 1887 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ALA 112 is missing expected H atoms. Skipping. Residue LYS 124 is missing expected H atoms. Skipping. Residue LYS 36 is missing expected H atoms. Skipping. Residue TYR 43 is missing expected H atoms. Skipping. Residue LYS 80 is missing expected H atoms. Skipping. Residue SER 214 is missing expected H atoms. Skipping. Residue LYS 218 is missing expected H atoms. Skipping. Residue LEU 220 is missing expected H atoms. Skipping. Residue TYR 32 is missing expected H atoms. Skipping. Evaluate side-chains 259 residues out of total 1606 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 242 time to evaluate : 2.898 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: A 252 GLU cc_start: 0.8162 (mm-30) cc_final: 0.7668 (mm-30) REVERT: A 256 SER cc_start: 0.8711 (m) cc_final: 0.8279 (p) REVERT: A 396 LYS cc_start: 0.7780 (mmtt) cc_final: 0.7313 (mtmt) REVERT: A 411 ARG cc_start: 0.7724 (mmm-85) cc_final: 0.7327 (mpt180) REVERT: K 112 MET cc_start: 0.7920 (ttp) cc_final: 0.7702 (ttp) REVERT: K 261 ASN cc_start: 0.8366 (t0) cc_final: 0.8020 (t0) REVERT: D 79 ARG cc_start: 0.7601 (mtp-110) cc_final: 0.7057 (mtp85) REVERT: D 206 MET cc_start: 0.8881 (ttp) cc_final: 0.8640 (ttp) REVERT: G 86 GLN cc_start: 0.7954 (pt0) cc_final: 0.7676 (pt0) REVERT: G 109 GLU cc_start: 0.7151 (tp30) cc_final: 0.6544 (mt-10) REVERT: G 119 GLU cc_start: 0.8132 (tp30) cc_final: 0.7921 (tp30) REVERT: F 54 LYS cc_start: 0.8039 (tttp) cc_final: 0.7567 (tppt) REVERT: H 67 ASP cc_start: 0.7199 (m-30) cc_final: 0.6788 (m-30) REVERT: H 133 ARG cc_start: 0.8120 (mmm-85) cc_final: 0.7602 (mmt-90) REVERT: I 36 LYS cc_start: 0.8446 (ttpp) cc_final: 0.7981 (ttmm) REVERT: I 43 LYS cc_start: 0.7871 (ptpp) cc_final: 0.7546 (ptpp) REVERT: B 59 ASN cc_start: 0.7620 (OUTLIER) cc_final: 0.7326 (m-40) REVERT: B 152 ARG cc_start: 0.8327 (mtt180) cc_final: 0.6429 (mmm160) REVERT: B 183 GLU cc_start: 0.6982 (pt0) cc_final: 0.6553 (pt0) REVERT: B 190 GLU cc_start: 0.7418 (mt-10) cc_final: 0.7106 (mt-10) REVERT: B 238 SER cc_start: 0.8654 (m) cc_final: 0.8283 (t) REVERT: M 50 ARG cc_start: 0.6951 (tmt-80) cc_final: 0.5723 (ptp90) REVERT: M 54 TYR cc_start: 0.6364 (t80) cc_final: 0.6111 (t80) REVERT: M 60 MET cc_start: 0.8621 (ttm) cc_final: 0.8370 (ttp) outliers start: 17 outliers final: 15 residues processed: 255 average time/residue: 0.6811 time to fit residues: 248.3805 Evaluate side-chains 248 residues out of total 1606 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 232 time to evaluate : 2.168 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 SER Chi-restraints excluded: chain A residue 132 SER Chi-restraints excluded: chain A residue 288 SER Chi-restraints excluded: chain K residue 64 SER Chi-restraints excluded: chain K residue 226 ILE Chi-restraints excluded: chain D residue 105 GLU Chi-restraints excluded: chain G residue 18 ARG Chi-restraints excluded: chain G residue 60 ILE Chi-restraints excluded: chain F residue 9 THR Chi-restraints excluded: chain I residue 32 VAL Chi-restraints excluded: chain B residue 59 ASN Chi-restraints excluded: chain B residue 87 LEU Chi-restraints excluded: chain B residue 164 SER Chi-restraints excluded: chain B residue 226 THR Chi-restraints excluded: chain B residue 235 SER Chi-restraints excluded: chain E residue 82 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 187 random chunks: chunk 158 optimal weight: 1.9990 chunk 45 optimal weight: 1.9990 chunk 136 optimal weight: 1.9990 chunk 21 optimal weight: 2.9990 chunk 41 optimal weight: 2.9990 chunk 148 optimal weight: 0.5980 chunk 62 optimal weight: 0.0000 chunk 152 optimal weight: 1.9990 chunk 18 optimal weight: 1.9990 chunk 27 optimal weight: 0.2980 chunk 130 optimal weight: 5.9990 overall best weight: 0.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 57 HIS ** I 41 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.125316 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3101 r_free = 0.3101 target = 0.105683 restraints weight = 54480.024| |-----------------------------------------------------------------------------| r_work (start): 0.3270 rms_B_bonded: 2.15 r_work: 0.3149 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.3030 rms_B_bonded: 4.02 restraints_weight: 0.2500 r_work (final): 0.3030 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7827 moved from start: 0.4488 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 15075 Z= 0.259 Angle : 0.524 8.432 20544 Z= 0.265 Chirality : 0.038 0.151 2284 Planarity : 0.004 0.035 2625 Dihedral : 7.192 179.507 2084 Min Nonbonded Distance : 2.003 Molprobity Statistics. All-atom Clashscore : 10.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.29 % Favored : 95.71 % Rotamer: Outliers : 1.01 % Allowed : 11.89 % Favored : 87.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.74 (0.20), residues: 1887 helix: 1.27 (0.17), residues: 971 sheet: -0.69 (0.39), residues: 175 loop : -0.13 (0.24), residues: 741 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP K 142 HIS 0.007 0.001 HIS I 41 PHE 0.024 0.001 PHE K 89 TYR 0.011 0.001 TYR K 358 ARG 0.002 0.000 ARG B 153 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6707.95 seconds wall clock time: 119 minutes 57.97 seconds (7197.97 seconds total)