Starting phenix.real_space_refine on Thu Feb 15 08:12:03 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dg8_27418/02_2024/8dg8_27418.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dg8_27418/02_2024/8dg8_27418.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.62 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dg8_27418/02_2024/8dg8_27418.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dg8_27418/02_2024/8dg8_27418.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dg8_27418/02_2024/8dg8_27418.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dg8_27418/02_2024/8dg8_27418.pdb" } resolution = 3.62 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.167 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: 4 Type Number sf(0) Gaussians S 60 5.16 5 C 7323 2.51 5 N 1943 2.21 5 O 2291 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B TYR 376": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 437": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ASP 26": "OD1" <-> "OD2" Residue "L TYR 49": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L GLU 81": "OE1" <-> "OE2" Residue "A TYR 83": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 371": "OD1" <-> "OD2" Residue "C GLU 145": "OE1" <-> "OE2" Residue "C ASP 441": "OD1" <-> "OD2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 11617 Number of models: 1 Model: "" Number of chains: 8 Chain: "B" Number of atoms: 3251 Number of conformers: 1 Conformer: "" Number of residues, atoms: 422, 3251 Classifications: {'peptide': 422} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 15, 'TRANS': 406} Chain breaks: 2 Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASN:plan1': 1} Unresolved non-hydrogen planarities: 3 Chain: "H" Number of atoms: 955 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 955 Classifications: {'peptide': 125} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 4, 'TRANS': 120} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "L" Number of atoms: 783 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 783 Classifications: {'peptide': 103} Link IDs: {'PTRANS': 4, 'TRANS': 98} Chain breaks: 1 Chain: "A" Number of atoms: 3251 Number of conformers: 1 Conformer: "" Number of residues, atoms: 422, 3251 Classifications: {'peptide': 422} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 15, 'TRANS': 406} Chain breaks: 2 Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASN:plan1': 1} Unresolved non-hydrogen planarities: 3 Chain: "C" Number of atoms: 3251 Number of conformers: 1 Conformer: "" Number of residues, atoms: 422, 3251 Classifications: {'peptide': 422} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 15, 'TRANS': 406} Chain breaks: 2 Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASN:plan1': 1} Unresolved non-hydrogen planarities: 3 Chain: "B" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "A" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "C" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Time building chain proxies: 6.67, per 1000 atoms: 0.57 Number of scatterers: 11617 At special positions: 0 Unit cell: (124.491, 104.943, 117.289, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 60 16.00 O 2291 8.00 N 1943 7.00 C 7323 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=23, symmetry=0 Simple disulfide: pdb=" SG CYS B 63 " - pdb=" SG CYS B 192 " distance=2.03 Simple disulfide: pdb=" SG CYS B 162 " - pdb=" SG CYS B 168 " distance=2.04 Simple disulfide: pdb=" SG CYS B 213 " - pdb=" SG CYS B 230 " distance=2.03 Simple disulfide: pdb=" SG CYS B 331 " - pdb=" SG CYS B 340 " distance=2.03 Simple disulfide: pdb=" SG CYS B 355 " - pdb=" SG CYS B 363 " distance=2.03 Simple disulfide: pdb=" SG CYS B 387 " - pdb=" SG CYS B 392 " distance=2.03 Simple disulfide: pdb=" SG CYS B 394 " - pdb=" SG CYS B 417 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 92 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.03 Simple disulfide: pdb=" SG CYS A 63 " - pdb=" SG CYS A 192 " distance=2.03 Simple disulfide: pdb=" SG CYS A 162 " - pdb=" SG CYS A 168 " distance=2.03 Simple disulfide: pdb=" SG CYS A 213 " - pdb=" SG CYS A 230 " distance=2.04 Simple disulfide: pdb=" SG CYS A 331 " - pdb=" SG CYS A 340 " distance=2.03 Simple disulfide: pdb=" SG CYS A 355 " - pdb=" SG CYS A 363 " distance=2.03 Simple disulfide: pdb=" SG CYS A 387 " - pdb=" SG CYS A 392 " distance=2.03 Simple disulfide: pdb=" SG CYS A 394 " - pdb=" SG CYS A 417 " distance=2.04 Simple disulfide: pdb=" SG CYS C 63 " - pdb=" SG CYS C 192 " distance=2.03 Simple disulfide: pdb=" SG CYS C 162 " - pdb=" SG CYS C 168 " distance=2.03 Simple disulfide: pdb=" SG CYS C 213 " - pdb=" SG CYS C 230 " distance=2.03 Simple disulfide: pdb=" SG CYS C 331 " - pdb=" SG CYS C 340 " distance=2.03 Simple disulfide: pdb=" SG CYS C 355 " - pdb=" SG CYS C 363 " distance=2.03 Simple disulfide: pdb=" SG CYS C 387 " - pdb=" SG CYS C 392 " distance=2.03 Simple disulfide: pdb=" SG CYS C 394 " - pdb=" SG CYS C 417 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied NAG-ASN " NAG A 601 " - " ASN A 238 " " NAG A 602 " - " ASN A 359 " " NAG A 603 " - " ASN A 446 " " NAG B 601 " - " ASN B 238 " " NAG B 602 " - " ASN B 359 " " NAG B 603 " - " ASN B 446 " " NAG C 601 " - " ASN C 238 " " NAG C 602 " - " ASN C 359 " " NAG C 603 " - " ASN C 446 " Time building additional restraints: 5.03 Conformation dependent library (CDL) restraints added in 2.4 seconds 2940 Ramachandran restraints generated. 1470 Oldfield, 0 Emsley, 1470 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2794 Finding SS restraints... Secondary structure from input PDB file: 40 helices and 24 sheets defined 29.3% alpha, 21.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.41 Creating SS restraints... Processing helix chain 'B' and resid 25 through 28 Processing helix chain 'B' and resid 64 through 84 removed outlier: 3.500A pdb=" N LYS B 72 " --> pdb=" O ILE B 68 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N LEU B 74 " --> pdb=" O GLN B 70 " (cutoff:3.500A) removed outlier: 4.303A pdb=" N LEU B 75 " --> pdb=" O TYR B 71 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N ASP B 76 " --> pdb=" O LYS B 72 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N ARG B 77 " --> pdb=" O ARG B 73 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N LEU B 78 " --> pdb=" O LEU B 74 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N ILE B 79 " --> pdb=" O LEU B 75 " (cutoff:3.500A) Proline residue: B 81 - end of helix Processing helix chain 'B' and resid 124 through 152 removed outlier: 4.090A pdb=" N ALA B 130 " --> pdb=" O ALA B 126 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N LEU B 134 " --> pdb=" O ALA B 130 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N ALA B 137 " --> pdb=" O ALA B 133 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N LYS B 138 " --> pdb=" O LEU B 134 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N GLN B 139 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N SER B 142 " --> pdb=" O LYS B 138 " (cutoff:3.500A) removed outlier: 4.697A pdb=" N ASP B 143 " --> pdb=" O GLN B 139 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N LYS B 146 " --> pdb=" O SER B 142 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N ALA B 150 " --> pdb=" O LYS B 146 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N ARG B 152 " --> pdb=" O LYS B 148 " (cutoff:3.500A) Processing helix chain 'B' and resid 175 through 190 removed outlier: 3.699A pdb=" N LYS B 181 " --> pdb=" O ASP B 177 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N VAL B 184 " --> pdb=" O ASN B 180 " (cutoff:3.500A) Proline residue: B 185 - end of helix removed outlier: 4.559A pdb=" N ALA B 188 " --> pdb=" O VAL B 184 " (cutoff:3.500A) Processing helix chain 'B' and resid 195 through 210 removed outlier: 3.594A pdb=" N LEU B 199 " --> pdb=" O ALA B 195 " (cutoff:3.500A) Processing helix chain 'B' and resid 228 through 236 removed outlier: 3.927A pdb=" N TYR B 235 " --> pdb=" O ILE B 231 " (cutoff:3.500A) Processing helix chain 'B' and resid 238 through 243 removed outlier: 3.866A pdb=" N ILE B 242 " --> pdb=" O ASN B 238 " (cutoff:3.500A) Processing helix chain 'B' and resid 245 through 249 Processing helix chain 'B' and resid 252 through 261 removed outlier: 3.637A pdb=" N LEU B 256 " --> pdb=" O ASP B 252 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N LEU B 257 " --> pdb=" O ILE B 253 " (cutoff:3.500A) Processing helix chain 'B' and resid 349 through 355 Processing helix chain 'B' and resid 356 through 358 No H-bonds generated for 'chain 'B' and resid 356 through 358' Processing helix chain 'B' and resid 452 through 471 Processing helix chain 'H' and resid 61 through 64 Processing helix chain 'H' and resid 100A through 100E removed outlier: 4.376A pdb=" N TRP H 100D" --> pdb=" O ASP H 100A" (cutoff:3.500A) Processing helix chain 'A' and resid 25 through 28 Processing helix chain 'A' and resid 60 through 65 Processing helix chain 'A' and resid 66 through 74 removed outlier: 3.760A pdb=" N GLN A 70 " --> pdb=" O GLN A 66 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N TYR A 71 " --> pdb=" O GLN A 67 " (cutoff:3.500A) removed outlier: 4.136A pdb=" N LYS A 72 " --> pdb=" O ILE A 68 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N ARG A 73 " --> pdb=" O LYS A 69 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N LEU A 74 " --> pdb=" O GLN A 70 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 66 through 74' Processing helix chain 'A' and resid 75 through 83 removed outlier: 3.590A pdb=" N ILE A 79 " --> pdb=" O LEU A 75 " (cutoff:3.500A) Proline residue: A 81 - end of helix Processing helix chain 'A' and resid 124 through 152 removed outlier: 3.542A pdb=" N LYS A 138 " --> pdb=" O LEU A 134 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N GLN A 139 " --> pdb=" O VAL A 135 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N ALA A 140 " --> pdb=" O GLU A 136 " (cutoff:3.500A) removed outlier: 4.492A pdb=" N SER A 142 " --> pdb=" O LYS A 138 " (cutoff:3.500A) removed outlier: 5.484A pdb=" N ASP A 143 " --> pdb=" O GLN A 139 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N ALA A 150 " --> pdb=" O LYS A 146 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N ARG A 152 " --> pdb=" O LYS A 148 " (cutoff:3.500A) Processing helix chain 'A' and resid 175 through 183 Processing helix chain 'A' and resid 184 through 189 Processing helix chain 'A' and resid 195 through 215 removed outlier: 4.613A pdb=" N CYS A 213 " --> pdb=" O GLU A 209 " (cutoff:3.500A) Processing helix chain 'A' and resid 228 through 234 Processing helix chain 'A' and resid 245 through 250 removed outlier: 4.450A pdb=" N LYS A 250 " --> pdb=" O SER A 246 " (cutoff:3.500A) Processing helix chain 'A' and resid 252 through 259 Processing helix chain 'A' and resid 349 through 356 removed outlier: 4.034A pdb=" N LEU A 356 " --> pdb=" O MET A 352 " (cutoff:3.500A) Processing helix chain 'A' and resid 452 through 469 removed outlier: 3.612A pdb=" N LYS A 462 " --> pdb=" O ILE A 458 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N GLU A 469 " --> pdb=" O SER A 465 " (cutoff:3.500A) Processing helix chain 'C' and resid 64 through 71 removed outlier: 4.267A pdb=" N LYS C 69 " --> pdb=" O ASP C 65 " (cutoff:3.500A) removed outlier: 4.391A pdb=" N GLN C 70 " --> pdb=" O GLN C 66 " (cutoff:3.500A) Processing helix chain 'C' and resid 72 through 78 removed outlier: 3.521A pdb=" N ASP C 76 " --> pdb=" O LYS C 72 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ARG C 77 " --> pdb=" O ARG C 73 " (cutoff:3.500A) Processing helix chain 'C' and resid 79 through 87 Processing helix chain 'C' and resid 124 through 136 removed outlier: 3.978A pdb=" N ALA C 133 " --> pdb=" O THR C 129 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N LEU C 134 " --> pdb=" O ALA C 130 " (cutoff:3.500A) Processing helix chain 'C' and resid 136 through 151 removed outlier: 3.595A pdb=" N ALA C 140 " --> pdb=" O GLU C 136 " (cutoff:3.500A) removed outlier: 5.146A pdb=" N SER C 142 " --> pdb=" O LYS C 138 " (cutoff:3.500A) removed outlier: 5.570A pdb=" N ASP C 143 " --> pdb=" O GLN C 139 " (cutoff:3.500A) Processing helix chain 'C' and resid 175 through 190 removed outlier: 4.134A pdb=" N VAL C 184 " --> pdb=" O ASN C 180 " (cutoff:3.500A) Proline residue: C 185 - end of helix removed outlier: 4.993A pdb=" N ALA C 188 " --> pdb=" O VAL C 184 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ARG C 189 " --> pdb=" O PRO C 185 " (cutoff:3.500A) Processing helix chain 'C' and resid 195 through 214 removed outlier: 3.517A pdb=" N ASN C 212 " --> pdb=" O SER C 208 " (cutoff:3.500A) Processing helix chain 'C' and resid 228 through 234 Processing helix chain 'C' and resid 238 through 243 removed outlier: 3.625A pdb=" N ILE C 242 " --> pdb=" O ASN C 238 " (cutoff:3.500A) Processing helix chain 'C' and resid 252 through 260 removed outlier: 4.213A pdb=" N LEU C 257 " --> pdb=" O ILE C 253 " (cutoff:3.500A) removed outlier: 4.841A pdb=" N PHE C 258 " --> pdb=" O TYR C 254 " (cutoff:3.500A) Processing helix chain 'C' and resid 349 through 358 removed outlier: 4.011A pdb=" N LEU C 356 " --> pdb=" O MET C 352 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N GLY C 358 " --> pdb=" O SER C 354 " (cutoff:3.500A) Processing helix chain 'C' and resid 452 through 469 removed outlier: 3.869A pdb=" N LEU C 467 " --> pdb=" O VAL C 463 " (cutoff:3.500A) removed outlier: 4.469A pdb=" N GLU C 469 " --> pdb=" O SER C 465 " (cutoff:3.500A) Processing helix chain 'C' and resid 470 through 472 No H-bonds generated for 'chain 'C' and resid 470 through 472' Processing sheet with id=AA1, first strand: chain 'B' and resid 30 through 33 removed outlier: 4.080A pdb=" N HIS B 315 " --> pdb=" O ALA B 326 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 281 through 286 removed outlier: 4.528A pdb=" N ASN B 43 " --> pdb=" O LEU B 284 " (cutoff:3.500A) removed outlier: 7.695A pdb=" N THR B 286 " --> pdb=" O SER B 41 " (cutoff:3.500A) removed outlier: 6.185A pdb=" N SER B 41 " --> pdb=" O THR B 286 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 158 through 159 removed outlier: 3.721A pdb=" N ASP B 268 " --> pdb=" O THR B 277 " (cutoff:3.500A) removed outlier: 6.555A pdb=" N GLN B 279 " --> pdb=" O VAL B 266 " (cutoff:3.500A) removed outlier: 5.943A pdb=" N VAL B 266 " --> pdb=" O GLN B 279 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N ILE B 226 " --> pdb=" O VAL B 264 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 301 through 303 Processing sheet with id=AA5, first strand: chain 'B' and resid 376 through 377 removed outlier: 3.534A pdb=" N ALA B 385 " --> pdb=" O LYS B 410 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'H' and resid 4 through 5 Processing sheet with id=AA7, first strand: chain 'H' and resid 57 through 59 removed outlier: 5.146A pdb=" N TRP H 47 " --> pdb=" O ARG H 38 " (cutoff:3.500A) removed outlier: 5.966A pdb=" N ARG H 38 " --> pdb=" O TRP H 47 " (cutoff:3.500A) removed outlier: 4.134A pdb=" N ALA H 49 " --> pdb=" O TRP H 36 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N HIS H 102 " --> pdb=" O LYS H 94 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'H' and resid 57 through 59 removed outlier: 5.146A pdb=" N TRP H 47 " --> pdb=" O ARG H 38 " (cutoff:3.500A) removed outlier: 5.966A pdb=" N ARG H 38 " --> pdb=" O TRP H 47 " (cutoff:3.500A) removed outlier: 4.134A pdb=" N ALA H 49 " --> pdb=" O TRP H 36 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'L' and resid 9 through 12 removed outlier: 3.723A pdb=" N THR L 105 " --> pdb=" O VAL L 11 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'L' and resid 18 through 24 Processing sheet with id=AB2, first strand: chain 'L' and resid 45 through 50 removed outlier: 6.899A pdb=" N TRP L 35 " --> pdb=" O VAL L 47 " (cutoff:3.500A) removed outlier: 4.385A pdb=" N TYR L 49 " --> pdb=" O VAL L 33 " (cutoff:3.500A) removed outlier: 6.764A pdb=" N VAL L 33 " --> pdb=" O TYR L 49 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 30 through 32 removed outlier: 3.501A pdb=" N ASP A 297 " --> pdb=" O LEU A 31 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 30 through 32 removed outlier: 3.501A pdb=" N ASP A 297 " --> pdb=" O LEU A 31 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N ASN A 43 " --> pdb=" O LEU A 284 " (cutoff:3.500A) removed outlier: 6.966A pdb=" N THR A 286 " --> pdb=" O SER A 41 " (cutoff:3.500A) removed outlier: 5.364A pdb=" N SER A 41 " --> pdb=" O THR A 286 " (cutoff:3.500A) removed outlier: 6.234A pdb=" N LEU A 288 " --> pdb=" O LYS A 39 " (cutoff:3.500A) removed outlier: 5.306A pdb=" N LYS A 39 " --> pdb=" O LEU A 288 " (cutoff:3.500A) removed outlier: 9.446A pdb=" N ASN A 290 " --> pdb=" O GLY A 37 " (cutoff:3.500A) removed outlier: 9.668A pdb=" N GLY A 37 " --> pdb=" O ASN A 290 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 158 through 164 removed outlier: 3.621A pdb=" N SER A 163 " --> pdb=" O ASN A 167 " (cutoff:3.500A) removed outlier: 6.995A pdb=" N ASN A 167 " --> pdb=" O SER A 163 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N TYR A 48 " --> pdb=" O CYS A 168 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N VAL A 170 " --> pdb=" O TYR A 48 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N ILE A 172 " --> pdb=" O ILE A 50 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N ASP A 268 " --> pdb=" O THR A 277 " (cutoff:3.500A) removed outlier: 6.354A pdb=" N GLN A 279 " --> pdb=" O VAL A 266 " (cutoff:3.500A) removed outlier: 5.954A pdb=" N VAL A 266 " --> pdb=" O GLN A 279 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N ILE A 226 " --> pdb=" O VAL A 264 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 308 through 309 Processing sheet with id=AB7, first strand: chain 'A' and resid 376 through 377 removed outlier: 3.695A pdb=" N ALA A 385 " --> pdb=" O LYS A 410 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 419 through 420 Processing sheet with id=AB9, first strand: chain 'C' and resid 285 through 286 removed outlier: 4.973A pdb=" N LYS C 295 " --> pdb=" O ASN C 33 " (cutoff:3.500A) removed outlier: 6.250A pdb=" N ILE C 293 " --> pdb=" O PRO C 35 " (cutoff:3.500A) removed outlier: 5.387A pdb=" N GLY C 37 " --> pdb=" O THR C 291 " (cutoff:3.500A) removed outlier: 8.042A pdb=" N THR C 291 " --> pdb=" O GLY C 37 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 285 through 286 removed outlier: 8.047A pdb=" N TYR C 338 " --> pdb=" O PRO C 35 " (cutoff:3.500A) removed outlier: 6.046A pdb=" N GLY C 37 " --> pdb=" O TYR C 338 " (cutoff:3.500A) removed outlier: 7.472A pdb=" N CYS C 340 " --> pdb=" O GLY C 37 " (cutoff:3.500A) removed outlier: 6.061A pdb=" N LYS C 39 " --> pdb=" O CYS C 340 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 158 through 161 removed outlier: 3.629A pdb=" N VAL C 161 " --> pdb=" O ILE C 169 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N ILE C 169 " --> pdb=" O VAL C 161 " (cutoff:3.500A) removed outlier: 9.427A pdb=" N VAL C 170 " --> pdb=" O THR C 46 " (cutoff:3.500A) removed outlier: 6.551A pdb=" N TYR C 48 " --> pdb=" O VAL C 170 " (cutoff:3.500A) removed outlier: 8.038A pdb=" N ILE C 172 " --> pdb=" O TYR C 48 " (cutoff:3.500A) removed outlier: 6.561A pdb=" N ILE C 50 " --> pdb=" O ILE C 172 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N ASP C 268 " --> pdb=" O THR C 277 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 226 through 227 Processing sheet with id=AC4, first strand: chain 'C' and resid 301 through 303 removed outlier: 4.350A pdb=" N THR C 367 " --> pdb=" O VAL C 449 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'C' and resid 376 through 377 Processing sheet with id=AC6, first strand: chain 'C' and resid 392 through 394 387 hydrogen bonds defined for protein. 1038 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: 3.75 Time building geometry restraints manager: 5.43 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 3800 1.34 - 1.46: 2514 1.46 - 1.59: 5398 1.59 - 1.71: 0 1.71 - 1.84: 74 Bond restraints: 11786 Sorted by residual: bond pdb=" CA SER B 357 " pdb=" CB SER B 357 " ideal model delta sigma weight residual 1.528 1.469 0.059 1.34e-02 5.57e+03 1.96e+01 bond pdb=" C1 NAG A 601 " pdb=" O5 NAG A 601 " ideal model delta sigma weight residual 1.406 1.493 -0.087 2.00e-02 2.50e+03 1.88e+01 bond pdb=" CA SER B 361 " pdb=" CB SER B 361 " ideal model delta sigma weight residual 1.530 1.476 0.055 1.69e-02 3.50e+03 1.05e+01 bond pdb=" C1 NAG C 602 " pdb=" O5 NAG C 602 " ideal model delta sigma weight residual 1.406 1.455 -0.049 2.00e-02 2.50e+03 6.10e+00 bond pdb=" N SER B 361 " pdb=" CA SER B 361 " ideal model delta sigma weight residual 1.457 1.486 -0.028 1.29e-02 6.01e+03 4.82e+00 ... (remaining 11781 not shown) Histogram of bond angle deviations from ideal: 99.14 - 106.12: 219 106.12 - 113.11: 6704 113.11 - 120.09: 3884 120.09 - 127.08: 5096 127.08 - 134.06: 85 Bond angle restraints: 15988 Sorted by residual: angle pdb=" CA ASN B 359 " pdb=" CB ASN B 359 " pdb=" CG ASN B 359 " ideal model delta sigma weight residual 112.60 105.66 6.94 1.00e+00 1.00e+00 4.82e+01 angle pdb=" N SER B 357 " pdb=" CA SER B 357 " pdb=" C SER B 357 " ideal model delta sigma weight residual 111.87 103.19 8.68 1.41e+00 5.03e-01 3.79e+01 angle pdb=" N VAL B 328 " pdb=" CA VAL B 328 " pdb=" C VAL B 328 " ideal model delta sigma weight residual 111.91 107.52 4.39 8.90e-01 1.26e+00 2.44e+01 angle pdb=" C ASN A 380 " pdb=" CA ASN A 380 " pdb=" CB ASN A 380 " ideal model delta sigma weight residual 116.63 110.91 5.72 1.16e+00 7.43e-01 2.44e+01 angle pdb=" C LEU B 356 " pdb=" N SER B 357 " pdb=" CA SER B 357 " ideal model delta sigma weight residual 122.79 116.34 6.45 1.63e+00 3.76e-01 1.57e+01 ... (remaining 15983 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 25.02: 6994 25.02 - 50.04: 312 50.04 - 75.06: 34 75.06 - 100.08: 14 100.08 - 125.10: 1 Dihedral angle restraints: 7355 sinusoidal: 3024 harmonic: 4331 Sorted by residual: dihedral pdb=" CB CYS A 63 " pdb=" SG CYS A 63 " pdb=" SG CYS A 192 " pdb=" CB CYS A 192 " ideal model delta sinusoidal sigma weight residual -86.00 -9.36 -76.64 1 1.00e+01 1.00e-02 7.38e+01 dihedral pdb=" CB CYS A 213 " pdb=" SG CYS A 213 " pdb=" SG CYS A 230 " pdb=" CB CYS A 230 " ideal model delta sinusoidal sigma weight residual -86.00 -162.25 76.25 1 1.00e+01 1.00e-02 7.32e+01 dihedral pdb=" CB CYS B 162 " pdb=" SG CYS B 162 " pdb=" SG CYS B 168 " pdb=" CB CYS B 168 " ideal model delta sinusoidal sigma weight residual 93.00 38.72 54.28 1 1.00e+01 1.00e-02 4.00e+01 ... (remaining 7352 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.077: 1733 0.077 - 0.153: 201 0.153 - 0.230: 6 0.230 - 0.306: 2 0.306 - 0.383: 3 Chirality restraints: 1945 Sorted by residual: chirality pdb=" C1 NAG C 602 " pdb=" ND2 ASN C 359 " pdb=" C2 NAG C 602 " pdb=" O5 NAG C 602 " both_signs ideal model delta sigma weight residual False -2.40 -2.78 0.38 2.00e-01 2.50e+01 3.66e+00 chirality pdb=" CB ILE A 50 " pdb=" CA ILE A 50 " pdb=" CG1 ILE A 50 " pdb=" CG2 ILE A 50 " both_signs ideal model delta sigma weight residual False 2.64 2.29 0.36 2.00e-01 2.50e+01 3.21e+00 chirality pdb=" CB ILE B 50 " pdb=" CA ILE B 50 " pdb=" CG1 ILE B 50 " pdb=" CG2 ILE B 50 " both_signs ideal model delta sigma weight residual False 2.64 2.30 0.34 2.00e-01 2.50e+01 2.96e+00 ... (remaining 1942 not shown) Planarity restraints: 2035 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG B 602 " 0.279 2.00e-02 2.50e+03 2.37e-01 7.03e+02 pdb=" C7 NAG B 602 " -0.071 2.00e-02 2.50e+03 pdb=" C8 NAG B 602 " 0.175 2.00e-02 2.50e+03 pdb=" N2 NAG B 602 " -0.409 2.00e-02 2.50e+03 pdb=" O7 NAG B 602 " 0.027 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU B 356 " -0.022 2.00e-02 2.50e+03 4.47e-02 2.00e+01 pdb=" C LEU B 356 " 0.077 2.00e-02 2.50e+03 pdb=" O LEU B 356 " -0.029 2.00e-02 2.50e+03 pdb=" N SER B 357 " -0.027 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 238 " -0.001 2.00e-02 2.50e+03 3.62e-02 1.64e+01 pdb=" CG ASN A 238 " 0.046 2.00e-02 2.50e+03 pdb=" OD1 ASN A 238 " -0.044 2.00e-02 2.50e+03 pdb=" ND2 ASN A 238 " 0.035 2.00e-02 2.50e+03 pdb=" C1 NAG A 601 " -0.036 2.00e-02 2.50e+03 ... (remaining 2032 not shown) Histogram of nonbonded interaction distances: 2.13 - 2.68: 358 2.68 - 3.24: 12316 3.24 - 3.79: 17549 3.79 - 4.35: 23828 4.35 - 4.90: 37648 Nonbonded interactions: 91699 Sorted by model distance: nonbonded pdb=" OH TYR C 251 " pdb=" O PRO C 283 " model vdw 2.129 2.440 nonbonded pdb=" OG1 THR C 393 " pdb=" O GLY C 396 " model vdw 2.145 2.440 nonbonded pdb=" ND2 ASN A 349 " pdb=" OD1 ASP C 455 " model vdw 2.154 2.520 nonbonded pdb=" NE2 GLN C 403 " pdb=" O GLY C 408 " model vdw 2.195 2.520 nonbonded pdb=" O ILE C 151 " pdb=" NZ LYS C 173 " model vdw 2.198 2.520 ... (remaining 91694 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.370 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: 0.010 Extract box with map and model: 7.290 Check model and map are aligned: 0.190 Set scattering table: 0.120 Process input model: 35.690 Find NCS groups from input model: 0.650 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.690 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 48.080 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5442 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 : 0.004 0.087 11786 Z= 0.236 Angle : 0.717 10.362 15988 Z= 0.391 Chirality : 0.049 0.383 1945 Planarity : 0.007 0.237 2026 Dihedral : 14.018 125.103 4492 Min Nonbonded Distance : 2.129 Molprobity Statistics. All-atom Clashscore : 16.01 Ramachandran Plot: Outliers : 0.07 % Allowed : 8.37 % Favored : 91.56 % Rotamer: Outliers : 0.15 % Allowed : 0.31 % Favored : 99.54 % 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: -2.83 (0.20), residues: 1470 helix: -1.54 (0.26), residues: 379 sheet: -1.41 (0.31), residues: 273 loop : -2.25 (0.20), residues: 818 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP H 47 HIS 0.005 0.001 HIS C 414 PHE 0.009 0.001 PHE L 62 TYR 0.014 0.001 TYR A 83 ARG 0.004 0.000 ARG H 71 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2940 Ramachandran restraints generated. 1470 Oldfield, 0 Emsley, 1470 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2940 Ramachandran restraints generated. 1470 Oldfield, 0 Emsley, 1470 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 211 residues out of total 1312 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 209 time to evaluate : 1.303 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 208 SER cc_start: 0.6852 (m) cc_final: 0.6531 (p) REVERT: B 281 ARG cc_start: 0.7336 (mtm-85) cc_final: 0.6930 (ptt180) REVERT: B 284 LEU cc_start: 0.6724 (tp) cc_final: 0.6132 (mt) REVERT: B 289 LEU cc_start: 0.7135 (mt) cc_final: 0.6892 (mp) REVERT: B 425 MET cc_start: 0.4509 (mtp) cc_final: 0.4245 (mtm) REVERT: H 3 GLN cc_start: 0.6844 (OUTLIER) cc_final: 0.6608 (pm20) REVERT: H 89 VAL cc_start: 0.8152 (m) cc_final: 0.7674 (p) REVERT: H 100 GLU cc_start: 0.6064 (tp30) cc_final: 0.5388 (tt0) REVERT: L 31 TYR cc_start: 0.6902 (m-80) cc_final: 0.6577 (m-80) REVERT: L 32 TYR cc_start: 0.6470 (m-10) cc_final: 0.5910 (m-10) REVERT: A 70 GLN cc_start: 0.8674 (tm-30) cc_final: 0.8214 (mm-40) REVERT: A 78 LEU cc_start: 0.6034 (pp) cc_final: 0.5593 (tt) REVERT: A 270 ASP cc_start: 0.5827 (t0) cc_final: 0.5350 (t0) REVERT: A 414 HIS cc_start: 0.4695 (p-80) cc_final: 0.4436 (p-80) REVERT: A 462 LYS cc_start: 0.7438 (ttpp) cc_final: 0.7016 (tmmt) REVERT: C 48 TYR cc_start: 0.7629 (m-80) cc_final: 0.6894 (m-80) REVERT: C 49 LEU cc_start: 0.5722 (mt) cc_final: 0.5363 (mp) REVERT: C 56 LYS cc_start: 0.7100 (tmtt) cc_final: 0.6883 (tppp) REVERT: C 236 ARG cc_start: 0.7090 (mtt90) cc_final: 0.5386 (mmt180) REVERT: C 278 LEU cc_start: 0.7413 (mp) cc_final: 0.7103 (mt) outliers start: 2 outliers final: 0 residues processed: 210 average time/residue: 0.2300 time to fit residues: 69.8197 Evaluate side-chains 152 residues out of total 1312 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 151 time to evaluate : 1.333 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 3 GLN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 124 optimal weight: 3.9990 chunk 112 optimal weight: 2.9990 chunk 62 optimal weight: 5.9990 chunk 38 optimal weight: 0.0970 chunk 75 optimal weight: 4.9990 chunk 59 optimal weight: 3.9990 chunk 116 optimal weight: 0.7980 chunk 44 optimal weight: 3.9990 chunk 70 optimal weight: 1.9990 chunk 86 optimal weight: 0.1980 chunk 134 optimal weight: 0.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 380 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 461 ASN ** L 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 89 GLN A 155 ASN A 349 ASN C 127 GLN ** C 155 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 206 HIS C 290 ASN ** C 447 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5520 moved from start: 0.1644 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 11786 Z= 0.274 Angle : 0.748 9.209 15988 Z= 0.383 Chirality : 0.051 0.314 1945 Planarity : 0.005 0.054 2026 Dihedral : 8.685 114.429 1780 Min Nonbonded Distance : 2.054 Molprobity Statistics. All-atom Clashscore : 15.24 Ramachandran Plot: Outliers : 0.07 % Allowed : 8.71 % Favored : 91.22 % Rotamer: Outliers : 1.38 % Allowed : 9.04 % Favored : 89.58 % 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: -2.87 (0.20), residues: 1470 helix: -1.53 (0.24), residues: 389 sheet: -1.27 (0.31), residues: 281 loop : -2.38 (0.20), residues: 800 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP C 308 HIS 0.006 0.001 HIS C 414 PHE 0.019 0.002 PHE A 437 TYR 0.024 0.002 TYR C 71 ARG 0.007 0.001 ARG L 61 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2940 Ramachandran restraints generated. 1470 Oldfield, 0 Emsley, 1470 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2940 Ramachandran restraints generated. 1470 Oldfield, 0 Emsley, 1470 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 1312 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 161 time to evaluate : 1.382 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 42 GLN cc_start: 0.5981 (pt0) cc_final: 0.5772 (pt0) REVERT: B 281 ARG cc_start: 0.7200 (mtm-85) cc_final: 0.6884 (ptt90) REVERT: B 284 LEU cc_start: 0.6807 (tp) cc_final: 0.6184 (mt) REVERT: B 289 LEU cc_start: 0.7281 (mt) cc_final: 0.7061 (mp) REVERT: B 354 SER cc_start: 0.6616 (t) cc_final: 0.6364 (p) REVERT: H 100 GLU cc_start: 0.6281 (tp30) cc_final: 0.5560 (tt0) REVERT: L 32 TYR cc_start: 0.6595 (m-10) cc_final: 0.6086 (m-10) REVERT: A 56 LYS cc_start: 0.6909 (tptm) cc_final: 0.6294 (mmtt) REVERT: A 70 GLN cc_start: 0.8686 (tm-30) cc_final: 0.8142 (mp10) REVERT: A 78 LEU cc_start: 0.6278 (pp) cc_final: 0.5834 (tt) REVERT: A 136 GLU cc_start: 0.6285 (mt-10) cc_final: 0.6079 (tm-30) REVERT: A 270 ASP cc_start: 0.5450 (t0) cc_final: 0.5123 (t0) REVERT: A 333 GLU cc_start: 0.8088 (tp30) cc_final: 0.7819 (mm-30) REVERT: A 414 HIS cc_start: 0.4773 (p-80) cc_final: 0.4541 (p-80) REVERT: C 38 MET cc_start: 0.6588 (tpt) cc_final: 0.6058 (tpt) REVERT: C 48 TYR cc_start: 0.7582 (m-80) cc_final: 0.6889 (m-80) REVERT: C 49 LEU cc_start: 0.5634 (mt) cc_final: 0.5348 (mt) REVERT: C 56 LYS cc_start: 0.7451 (tmtt) cc_final: 0.6913 (tppp) REVERT: C 158 VAL cc_start: 0.6471 (t) cc_final: 0.6199 (p) REVERT: C 236 ARG cc_start: 0.6901 (mtt90) cc_final: 0.5252 (mmt180) outliers start: 18 outliers final: 11 residues processed: 172 average time/residue: 0.2468 time to fit residues: 61.2426 Evaluate side-chains 149 residues out of total 1312 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 138 time to evaluate : 1.347 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 422 ILE Chi-restraints excluded: chain H residue 48 VAL Chi-restraints excluded: chain H residue 110 THR Chi-restraints excluded: chain L residue 19 VAL Chi-restraints excluded: chain L residue 45 LEU Chi-restraints excluded: chain A residue 24 LYS Chi-restraints excluded: chain A residue 134 LEU Chi-restraints excluded: chain A residue 397 ILE Chi-restraints excluded: chain A residue 419 THR Chi-restraints excluded: chain C residue 388 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 74 optimal weight: 2.9990 chunk 41 optimal weight: 0.6980 chunk 111 optimal weight: 6.9990 chunk 91 optimal weight: 1.9990 chunk 37 optimal weight: 0.7980 chunk 134 optimal weight: 0.5980 chunk 145 optimal weight: 1.9990 chunk 119 optimal weight: 2.9990 chunk 133 optimal weight: 1.9990 chunk 45 optimal weight: 1.9990 chunk 108 optimal weight: 1.9990 overall best weight: 1.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 3 GLN ** L 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 37 GLN A 155 ASN ** A 362 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 407 GLN ** C 447 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5582 moved from start: 0.2222 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.071 11786 Z= 0.341 Angle : 0.749 10.710 15988 Z= 0.386 Chirality : 0.051 0.392 1945 Planarity : 0.005 0.049 2026 Dihedral : 8.248 107.881 1777 Min Nonbonded Distance : 2.053 Molprobity Statistics. All-atom Clashscore : 16.57 Ramachandran Plot: Outliers : 0.07 % Allowed : 9.86 % Favored : 90.07 % Rotamer: Outliers : 3.37 % Allowed : 12.64 % Favored : 83.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.87 (0.20), residues: 1470 helix: -1.38 (0.25), residues: 383 sheet: -1.22 (0.31), residues: 278 loop : -2.48 (0.20), residues: 809 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP C 308 HIS 0.006 0.002 HIS C 414 PHE 0.022 0.003 PHE A 378 TYR 0.023 0.002 TYR L 49 ARG 0.005 0.001 ARG A 281 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2940 Ramachandran restraints generated. 1470 Oldfield, 0 Emsley, 1470 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2940 Ramachandran restraints generated. 1470 Oldfield, 0 Emsley, 1470 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 1312 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 142 time to evaluate : 1.356 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 281 ARG cc_start: 0.7231 (mtm-85) cc_final: 0.6845 (ptt90) REVERT: B 284 LEU cc_start: 0.6869 (tp) cc_final: 0.6276 (mt) REVERT: B 289 LEU cc_start: 0.7368 (mt) cc_final: 0.7152 (mp) REVERT: B 354 SER cc_start: 0.7161 (t) cc_final: 0.6801 (p) REVERT: B 460 LEU cc_start: 0.4377 (OUTLIER) cc_final: 0.4150 (pp) REVERT: H 3 GLN cc_start: 0.6608 (OUTLIER) cc_final: 0.6301 (pm20) REVERT: H 100 GLU cc_start: 0.6355 (tp30) cc_final: 0.5538 (tt0) REVERT: L 32 TYR cc_start: 0.6891 (m-10) cc_final: 0.6201 (m-10) REVERT: A 24 LYS cc_start: 0.8661 (OUTLIER) cc_final: 0.8461 (ptmt) REVERT: A 67 GLN cc_start: 0.8119 (tm-30) cc_final: 0.7903 (tm-30) REVERT: A 70 GLN cc_start: 0.8654 (tm-30) cc_final: 0.8001 (mp10) REVERT: A 136 GLU cc_start: 0.6450 (mt-10) cc_final: 0.6117 (tm-30) REVERT: A 327 ASP cc_start: 0.6444 (m-30) cc_final: 0.6202 (m-30) REVERT: A 366 THR cc_start: 0.6898 (OUTLIER) cc_final: 0.5769 (m) REVERT: A 378 PHE cc_start: 0.7830 (m-10) cc_final: 0.7563 (m-10) REVERT: A 411 ILE cc_start: 0.5998 (mm) cc_final: 0.5793 (mm) REVERT: A 417 CYS cc_start: 0.6442 (t) cc_final: 0.5914 (t) REVERT: A 437 PHE cc_start: 0.6855 (t80) cc_final: 0.6515 (t80) REVERT: A 465 SER cc_start: 0.9017 (t) cc_final: 0.8674 (m) REVERT: C 38 MET cc_start: 0.6681 (tpt) cc_final: 0.6087 (tpt) REVERT: C 56 LYS cc_start: 0.7500 (tmtt) cc_final: 0.7008 (tmtt) REVERT: C 231 ILE cc_start: 0.5694 (mm) cc_final: 0.5481 (mt) REVERT: C 236 ARG cc_start: 0.6887 (mtt90) cc_final: 0.5194 (mmt180) outliers start: 44 outliers final: 25 residues processed: 172 average time/residue: 0.2414 time to fit residues: 60.4086 Evaluate side-chains 159 residues out of total 1312 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 130 time to evaluate : 1.305 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 162 CYS Chi-restraints excluded: chain B residue 170 VAL Chi-restraints excluded: chain B residue 210 LEU Chi-restraints excluded: chain B residue 211 THR Chi-restraints excluded: chain B residue 288 LEU Chi-restraints excluded: chain B residue 388 ILE Chi-restraints excluded: chain B residue 419 THR Chi-restraints excluded: chain B residue 422 ILE Chi-restraints excluded: chain B residue 449 VAL Chi-restraints excluded: chain B residue 460 LEU Chi-restraints excluded: chain H residue 3 GLN Chi-restraints excluded: chain H residue 46 GLU Chi-restraints excluded: chain H residue 48 VAL Chi-restraints excluded: chain H residue 110 THR Chi-restraints excluded: chain L residue 19 VAL Chi-restraints excluded: chain A residue 24 LYS Chi-restraints excluded: chain A residue 124 THR Chi-restraints excluded: chain A residue 134 LEU Chi-restraints excluded: chain A residue 347 VAL Chi-restraints excluded: chain A residue 366 THR Chi-restraints excluded: chain A residue 379 VAL Chi-restraints excluded: chain A residue 397 ILE Chi-restraints excluded: chain A residue 413 THR Chi-restraints excluded: chain A residue 419 THR Chi-restraints excluded: chain C residue 169 ILE Chi-restraints excluded: chain C residue 170 VAL Chi-restraints excluded: chain C residue 317 MET Chi-restraints excluded: chain C residue 388 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 133 optimal weight: 2.9990 chunk 101 optimal weight: 3.9990 chunk 69 optimal weight: 4.9990 chunk 14 optimal weight: 0.0370 chunk 64 optimal weight: 0.9990 chunk 90 optimal weight: 0.5980 chunk 135 optimal weight: 0.5980 chunk 143 optimal weight: 0.9980 chunk 70 optimal weight: 1.9990 chunk 128 optimal weight: 0.7980 chunk 38 optimal weight: 0.0570 overall best weight: 0.4176 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 380 ASN H 3 GLN ** L 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 155 ASN A 362 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5510 moved from start: 0.2391 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 11786 Z= 0.193 Angle : 0.664 10.964 15988 Z= 0.338 Chirality : 0.048 0.340 1945 Planarity : 0.004 0.049 2026 Dihedral : 7.709 101.988 1777 Min Nonbonded Distance : 2.100 Molprobity Statistics. All-atom Clashscore : 14.47 Ramachandran Plot: Outliers : 0.07 % Allowed : 8.16 % Favored : 91.77 % Rotamer: Outliers : 2.91 % Allowed : 14.71 % Favored : 82.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -2.67 (0.21), residues: 1470 helix: -1.22 (0.26), residues: 386 sheet: -1.27 (0.31), residues: 276 loop : -2.28 (0.20), residues: 808 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP C 308 HIS 0.007 0.001 HIS A 414 PHE 0.017 0.002 PHE A 437 TYR 0.018 0.001 TYR L 49 ARG 0.003 0.000 ARG L 61 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2940 Ramachandran restraints generated. 1470 Oldfield, 0 Emsley, 1470 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2940 Ramachandran restraints generated. 1470 Oldfield, 0 Emsley, 1470 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 1312 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 149 time to evaluate : 1.316 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 281 ARG cc_start: 0.7130 (mtm-85) cc_final: 0.6813 (ptt90) REVERT: B 284 LEU cc_start: 0.6854 (tp) cc_final: 0.6292 (mt) REVERT: B 289 LEU cc_start: 0.7497 (mt) cc_final: 0.7261 (mp) REVERT: B 354 SER cc_start: 0.6902 (t) cc_final: 0.6612 (p) REVERT: H 100 GLU cc_start: 0.6160 (tp30) cc_final: 0.5471 (tt0) REVERT: L 31 TYR cc_start: 0.7253 (m-80) cc_final: 0.6698 (m-80) REVERT: L 32 TYR cc_start: 0.6709 (m-10) cc_final: 0.6153 (m-10) REVERT: A 67 GLN cc_start: 0.8104 (tm-30) cc_final: 0.7841 (tm-30) REVERT: A 70 GLN cc_start: 0.8619 (tm-30) cc_final: 0.8002 (mp10) REVERT: A 73 ARG cc_start: 0.7333 (mmm160) cc_final: 0.7075 (mmm160) REVERT: A 378 PHE cc_start: 0.7531 (m-10) cc_final: 0.7325 (m-10) REVERT: A 411 ILE cc_start: 0.6069 (mm) cc_final: 0.5838 (mm) REVERT: A 417 CYS cc_start: 0.6509 (t) cc_final: 0.6031 (t) REVERT: A 437 PHE cc_start: 0.6761 (t80) cc_final: 0.6511 (t80) REVERT: A 460 LEU cc_start: 0.4735 (OUTLIER) cc_final: 0.4498 (pp) REVERT: A 465 SER cc_start: 0.8977 (t) cc_final: 0.8633 (m) REVERT: C 38 MET cc_start: 0.6656 (tpt) cc_final: 0.6150 (tpt) REVERT: C 56 LYS cc_start: 0.7487 (tmtt) cc_final: 0.6984 (tmtt) REVERT: C 158 VAL cc_start: 0.6512 (t) cc_final: 0.6256 (p) REVERT: C 231 ILE cc_start: 0.5682 (mm) cc_final: 0.5481 (mt) REVERT: C 236 ARG cc_start: 0.6850 (mtt90) cc_final: 0.5211 (mmt180) outliers start: 38 outliers final: 14 residues processed: 180 average time/residue: 0.2548 time to fit residues: 65.8925 Evaluate side-chains 146 residues out of total 1312 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 131 time to evaluate : 1.281 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 162 CYS Chi-restraints excluded: chain B residue 211 THR Chi-restraints excluded: chain B residue 426 LEU Chi-restraints excluded: chain H residue 46 GLU Chi-restraints excluded: chain H residue 48 VAL Chi-restraints excluded: chain H residue 82 MET Chi-restraints excluded: chain H residue 82 LEU Chi-restraints excluded: chain L residue 19 VAL Chi-restraints excluded: chain L residue 52 ASN Chi-restraints excluded: chain A residue 134 LEU Chi-restraints excluded: chain A residue 379 VAL Chi-restraints excluded: chain A residue 422 ILE Chi-restraints excluded: chain A residue 460 LEU Chi-restraints excluded: chain C residue 449 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 119 optimal weight: 3.9990 chunk 81 optimal weight: 0.6980 chunk 2 optimal weight: 1.9990 chunk 106 optimal weight: 1.9990 chunk 59 optimal weight: 3.9990 chunk 122 optimal weight: 5.9990 chunk 98 optimal weight: 0.8980 chunk 0 optimal weight: 1.9990 chunk 73 optimal weight: 4.9990 chunk 128 optimal weight: 5.9990 chunk 36 optimal weight: 0.5980 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 42 GLN B 380 ASN H 3 GLN ** L 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 95BHIS A 155 ASN C 461 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5594 moved from start: 0.2710 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.067 11786 Z= 0.341 Angle : 0.738 12.350 15988 Z= 0.375 Chirality : 0.051 0.363 1945 Planarity : 0.005 0.050 2026 Dihedral : 7.733 98.541 1777 Min Nonbonded Distance : 2.050 Molprobity Statistics. All-atom Clashscore : 16.53 Ramachandran Plot: Outliers : 0.07 % Allowed : 10.14 % Favored : 89.80 % Rotamer: Outliers : 4.44 % Allowed : 15.71 % Favored : 79.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.70 (0.21), residues: 1470 helix: -1.22 (0.26), residues: 376 sheet: -1.22 (0.31), residues: 279 loop : -2.33 (0.20), residues: 815 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP C 308 HIS 0.009 0.002 HIS A 414 PHE 0.018 0.002 PHE A 437 TYR 0.020 0.002 TYR C 309 ARG 0.005 0.001 ARG B 306 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2940 Ramachandran restraints generated. 1470 Oldfield, 0 Emsley, 1470 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2940 Ramachandran restraints generated. 1470 Oldfield, 0 Emsley, 1470 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 196 residues out of total 1312 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 138 time to evaluate : 1.330 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 281 ARG cc_start: 0.7123 (mtm-85) cc_final: 0.6772 (ptt90) REVERT: B 284 LEU cc_start: 0.6810 (tp) cc_final: 0.6214 (mt) REVERT: B 289 LEU cc_start: 0.7507 (mt) cc_final: 0.7280 (mp) REVERT: B 354 SER cc_start: 0.7387 (t) cc_final: 0.6989 (p) REVERT: H 100 GLU cc_start: 0.6274 (tp30) cc_final: 0.5539 (tt0) REVERT: L 32 TYR cc_start: 0.7057 (m-10) cc_final: 0.6366 (m-10) REVERT: L 60 ASP cc_start: 0.5163 (OUTLIER) cc_final: 0.3796 (t70) REVERT: A 67 GLN cc_start: 0.8141 (tm-30) cc_final: 0.7848 (tm-30) REVERT: A 70 GLN cc_start: 0.8618 (tm-30) cc_final: 0.7871 (mp10) REVERT: A 136 GLU cc_start: 0.6501 (mt-10) cc_final: 0.6181 (tm-30) REVERT: A 349 ASN cc_start: 0.6788 (OUTLIER) cc_final: 0.6530 (m-40) REVERT: A 411 ILE cc_start: 0.6417 (mm) cc_final: 0.6166 (mm) REVERT: A 417 CYS cc_start: 0.6644 (t) cc_final: 0.6268 (t) REVERT: A 460 LEU cc_start: 0.4758 (OUTLIER) cc_final: 0.4553 (pp) REVERT: A 465 SER cc_start: 0.9074 (t) cc_final: 0.8668 (m) REVERT: C 38 MET cc_start: 0.6740 (tpt) cc_final: 0.6116 (tpt) REVERT: C 56 LYS cc_start: 0.7492 (tmtt) cc_final: 0.7066 (tmtt) REVERT: C 88 LEU cc_start: 0.6353 (OUTLIER) cc_final: 0.6102 (pp) REVERT: C 236 ARG cc_start: 0.6850 (mtt90) cc_final: 0.5248 (mmt180) outliers start: 58 outliers final: 34 residues processed: 181 average time/residue: 0.2357 time to fit residues: 61.3093 Evaluate side-chains 172 residues out of total 1312 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 134 time to evaluate : 1.248 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 46 THR Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 162 CYS Chi-restraints excluded: chain B residue 210 LEU Chi-restraints excluded: chain B residue 211 THR Chi-restraints excluded: chain B residue 234 LEU Chi-restraints excluded: chain B residue 288 LEU Chi-restraints excluded: chain B residue 388 ILE Chi-restraints excluded: chain B residue 394 CYS Chi-restraints excluded: chain B residue 419 THR Chi-restraints excluded: chain B residue 422 ILE Chi-restraints excluded: chain B residue 426 LEU Chi-restraints excluded: chain B residue 449 VAL Chi-restraints excluded: chain H residue 46 GLU Chi-restraints excluded: chain H residue 48 VAL Chi-restraints excluded: chain H residue 82 LEU Chi-restraints excluded: chain H residue 110 THR Chi-restraints excluded: chain L residue 19 VAL Chi-restraints excluded: chain L residue 45 LEU Chi-restraints excluded: chain L residue 51 LYS Chi-restraints excluded: chain L residue 52 ASN Chi-restraints excluded: chain L residue 60 ASP Chi-restraints excluded: chain A residue 124 THR Chi-restraints excluded: chain A residue 134 LEU Chi-restraints excluded: chain A residue 333 GLU Chi-restraints excluded: chain A residue 347 VAL Chi-restraints excluded: chain A residue 349 ASN Chi-restraints excluded: chain A residue 379 VAL Chi-restraints excluded: chain A residue 397 ILE Chi-restraints excluded: chain A residue 413 THR Chi-restraints excluded: chain A residue 460 LEU Chi-restraints excluded: chain C residue 88 LEU Chi-restraints excluded: chain C residue 169 ILE Chi-restraints excluded: chain C residue 170 VAL Chi-restraints excluded: chain C residue 172 ILE Chi-restraints excluded: chain C residue 210 LEU Chi-restraints excluded: chain C residue 317 MET Chi-restraints excluded: chain C residue 449 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 48 optimal weight: 0.0870 chunk 128 optimal weight: 0.8980 chunk 28 optimal weight: 2.9990 chunk 83 optimal weight: 2.9990 chunk 35 optimal weight: 1.9990 chunk 143 optimal weight: 0.6980 chunk 118 optimal weight: 0.9980 chunk 66 optimal weight: 1.9990 chunk 11 optimal weight: 0.6980 chunk 47 optimal weight: 0.8980 chunk 75 optimal weight: 3.9990 overall best weight: 0.6558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 3 GLN ** L 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 155 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5548 moved from start: 0.2845 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 11786 Z= 0.231 Angle : 0.686 11.498 15988 Z= 0.346 Chirality : 0.049 0.332 1945 Planarity : 0.004 0.051 2026 Dihedral : 7.441 94.873 1777 Min Nonbonded Distance : 2.089 Molprobity Statistics. All-atom Clashscore : 15.28 Ramachandran Plot: Outliers : 0.07 % Allowed : 9.05 % Favored : 90.88 % Rotamer: Outliers : 3.83 % Allowed : 17.55 % Favored : 78.62 % 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: -2.58 (0.21), residues: 1470 helix: -0.98 (0.27), residues: 374 sheet: -1.25 (0.31), residues: 287 loop : -2.29 (0.20), residues: 809 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP C 308 HIS 0.009 0.001 HIS A 414 PHE 0.026 0.002 PHE A 378 TYR 0.018 0.002 TYR L 49 ARG 0.009 0.000 ARG A 73 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2940 Ramachandran restraints generated. 1470 Oldfield, 0 Emsley, 1470 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2940 Ramachandran restraints generated. 1470 Oldfield, 0 Emsley, 1470 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 1312 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 139 time to evaluate : 1.403 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 78 LEU cc_start: 0.7212 (tp) cc_final: 0.6526 (mt) REVERT: B 270 ASP cc_start: 0.6429 (m-30) cc_final: 0.6212 (m-30) REVERT: B 281 ARG cc_start: 0.7085 (mtm-85) cc_final: 0.6767 (ptt90) REVERT: B 284 LEU cc_start: 0.6766 (tp) cc_final: 0.6171 (mt) REVERT: B 289 LEU cc_start: 0.7429 (mt) cc_final: 0.7211 (mp) REVERT: B 354 SER cc_start: 0.7352 (t) cc_final: 0.7014 (p) REVERT: H 100 GLU cc_start: 0.6225 (tp30) cc_final: 0.5552 (tt0) REVERT: L 32 TYR cc_start: 0.6903 (m-10) cc_final: 0.6298 (m-10) REVERT: L 60 ASP cc_start: 0.5461 (OUTLIER) cc_final: 0.4084 (t70) REVERT: A 24 LYS cc_start: 0.8737 (OUTLIER) cc_final: 0.8498 (ptmm) REVERT: A 67 GLN cc_start: 0.8097 (tm-30) cc_final: 0.7825 (tm-30) REVERT: A 70 GLN cc_start: 0.8397 (tm-30) cc_final: 0.7815 (mp10) REVERT: A 73 ARG cc_start: 0.8024 (mmm160) cc_final: 0.7751 (mmm160) REVERT: A 290 ASN cc_start: 0.6449 (t0) cc_final: 0.5659 (p0) REVERT: A 317 MET cc_start: 0.7719 (ttp) cc_final: 0.7431 (ttm) REVERT: A 349 ASN cc_start: 0.6699 (OUTLIER) cc_final: 0.6465 (m-40) REVERT: A 378 PHE cc_start: 0.7604 (m-10) cc_final: 0.7329 (m-10) REVERT: A 417 CYS cc_start: 0.6626 (t) cc_final: 0.6279 (t) REVERT: A 460 LEU cc_start: 0.4921 (OUTLIER) cc_final: 0.4681 (pp) REVERT: A 465 SER cc_start: 0.9093 (t) cc_final: 0.8714 (m) REVERT: C 38 MET cc_start: 0.6784 (tpt) cc_final: 0.6208 (tpt) REVERT: C 56 LYS cc_start: 0.7476 (tmtt) cc_final: 0.7041 (tmtt) REVERT: C 88 LEU cc_start: 0.6130 (OUTLIER) cc_final: 0.5891 (pp) REVERT: C 236 ARG cc_start: 0.6723 (mtt90) cc_final: 0.5117 (mmt180) outliers start: 50 outliers final: 32 residues processed: 178 average time/residue: 0.2400 time to fit residues: 61.3367 Evaluate side-chains 169 residues out of total 1312 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 132 time to evaluate : 1.414 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 46 THR Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 162 CYS Chi-restraints excluded: chain B residue 210 LEU Chi-restraints excluded: chain B residue 211 THR Chi-restraints excluded: chain B residue 288 LEU Chi-restraints excluded: chain B residue 349 ASN Chi-restraints excluded: chain B residue 388 ILE Chi-restraints excluded: chain B residue 422 ILE Chi-restraints excluded: chain B residue 426 LEU Chi-restraints excluded: chain B residue 449 VAL Chi-restraints excluded: chain H residue 46 GLU Chi-restraints excluded: chain H residue 48 VAL Chi-restraints excluded: chain H residue 82 MET Chi-restraints excluded: chain H residue 82 LEU Chi-restraints excluded: chain H residue 110 THR Chi-restraints excluded: chain L residue 19 VAL Chi-restraints excluded: chain L residue 51 LYS Chi-restraints excluded: chain L residue 52 ASN Chi-restraints excluded: chain L residue 60 ASP Chi-restraints excluded: chain A residue 24 LYS Chi-restraints excluded: chain A residue 134 LEU Chi-restraints excluded: chain A residue 230 CYS Chi-restraints excluded: chain A residue 333 GLU Chi-restraints excluded: chain A residue 349 ASN Chi-restraints excluded: chain A residue 360 ILE Chi-restraints excluded: chain A residue 365 ARG Chi-restraints excluded: chain A residue 379 VAL Chi-restraints excluded: chain A residue 413 THR Chi-restraints excluded: chain A residue 422 ILE Chi-restraints excluded: chain A residue 460 LEU Chi-restraints excluded: chain C residue 88 LEU Chi-restraints excluded: chain C residue 169 ILE Chi-restraints excluded: chain C residue 210 LEU Chi-restraints excluded: chain C residue 317 MET Chi-restraints excluded: chain C residue 413 THR Chi-restraints excluded: chain C residue 449 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 138 optimal weight: 0.8980 chunk 16 optimal weight: 5.9990 chunk 81 optimal weight: 0.5980 chunk 104 optimal weight: 0.9980 chunk 120 optimal weight: 0.0570 chunk 79 optimal weight: 8.9990 chunk 142 optimal weight: 5.9990 chunk 89 optimal weight: 0.3980 chunk 86 optimal weight: 1.9990 chunk 65 optimal weight: 0.8980 chunk 88 optimal weight: 0.5980 overall best weight: 0.5098 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 42 GLN B 395 ASN H 3 GLN ** L 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 155 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5523 moved from start: 0.2995 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 11786 Z= 0.208 Angle : 0.667 11.706 15988 Z= 0.338 Chirality : 0.048 0.373 1945 Planarity : 0.004 0.068 2026 Dihedral : 7.132 90.430 1777 Min Nonbonded Distance : 2.100 Molprobity Statistics. All-atom Clashscore : 14.77 Ramachandran Plot: Outliers : 0.07 % Allowed : 9.05 % Favored : 90.88 % Rotamer: Outliers : 4.14 % Allowed : 18.31 % Favored : 77.55 % 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: -2.43 (0.21), residues: 1470 helix: -0.86 (0.27), residues: 371 sheet: -1.21 (0.31), residues: 288 loop : -2.18 (0.20), residues: 811 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP C 308 HIS 0.008 0.001 HIS A 414 PHE 0.021 0.001 PHE A 378 TYR 0.017 0.001 TYR L 49 ARG 0.011 0.000 ARG A 73 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2940 Ramachandran restraints generated. 1470 Oldfield, 0 Emsley, 1470 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2940 Ramachandran restraints generated. 1470 Oldfield, 0 Emsley, 1470 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 1312 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 131 time to evaluate : 1.323 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 270 ASP cc_start: 0.6566 (m-30) cc_final: 0.6298 (m-30) REVERT: B 281 ARG cc_start: 0.7054 (mtm-85) cc_final: 0.6770 (ptt90) REVERT: B 284 LEU cc_start: 0.6766 (tp) cc_final: 0.6233 (mt) REVERT: B 289 LEU cc_start: 0.7450 (mt) cc_final: 0.7230 (mp) REVERT: B 354 SER cc_start: 0.7247 (t) cc_final: 0.6930 (p) REVERT: B 360 ILE cc_start: 0.5309 (pt) cc_final: 0.5080 (pt) REVERT: H 100 GLU cc_start: 0.6188 (tp30) cc_final: 0.5561 (tt0) REVERT: L 32 TYR cc_start: 0.6836 (m-10) cc_final: 0.6268 (m-10) REVERT: L 60 ASP cc_start: 0.5501 (OUTLIER) cc_final: 0.3996 (t70) REVERT: A 24 LYS cc_start: 0.8702 (OUTLIER) cc_final: 0.8465 (ptmm) REVERT: A 67 GLN cc_start: 0.8164 (tm-30) cc_final: 0.7864 (tm-30) REVERT: A 70 GLN cc_start: 0.8434 (tm-30) cc_final: 0.7838 (mp10) REVERT: A 73 ARG cc_start: 0.7987 (mmm160) cc_final: 0.7751 (mmm160) REVERT: A 274 TYR cc_start: 0.6665 (m-80) cc_final: 0.6298 (m-80) REVERT: A 290 ASN cc_start: 0.6419 (t0) cc_final: 0.5656 (p0) REVERT: A 317 MET cc_start: 0.7849 (ttp) cc_final: 0.7589 (ttm) REVERT: A 460 LEU cc_start: 0.4781 (OUTLIER) cc_final: 0.4517 (pp) REVERT: A 465 SER cc_start: 0.9089 (t) cc_final: 0.8706 (m) REVERT: C 31 LEU cc_start: 0.5653 (OUTLIER) cc_final: 0.5452 (tp) REVERT: C 38 MET cc_start: 0.6541 (tpt) cc_final: 0.5928 (tpt) REVERT: C 56 LYS cc_start: 0.7454 (tmtt) cc_final: 0.6953 (tppp) REVERT: C 236 ARG cc_start: 0.6694 (mtt90) cc_final: 0.5003 (mmt180) outliers start: 54 outliers final: 35 residues processed: 173 average time/residue: 0.2390 time to fit residues: 59.6831 Evaluate side-chains 164 residues out of total 1312 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 125 time to evaluate : 1.193 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 46 THR Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 162 CYS Chi-restraints excluded: chain B residue 172 ILE Chi-restraints excluded: chain B residue 210 LEU Chi-restraints excluded: chain B residue 211 THR Chi-restraints excluded: chain B residue 288 LEU Chi-restraints excluded: chain B residue 349 ASN Chi-restraints excluded: chain B residue 395 ASN Chi-restraints excluded: chain B residue 419 THR Chi-restraints excluded: chain B residue 422 ILE Chi-restraints excluded: chain B residue 426 LEU Chi-restraints excluded: chain B residue 449 VAL Chi-restraints excluded: chain H residue 46 GLU Chi-restraints excluded: chain H residue 48 VAL Chi-restraints excluded: chain H residue 82 MET Chi-restraints excluded: chain H residue 82 LEU Chi-restraints excluded: chain H residue 110 THR Chi-restraints excluded: chain L residue 19 VAL Chi-restraints excluded: chain L residue 51 LYS Chi-restraints excluded: chain L residue 52 ASN Chi-restraints excluded: chain L residue 60 ASP Chi-restraints excluded: chain A residue 24 LYS Chi-restraints excluded: chain A residue 134 LEU Chi-restraints excluded: chain A residue 230 CYS Chi-restraints excluded: chain A residue 333 GLU Chi-restraints excluded: chain A residue 347 VAL Chi-restraints excluded: chain A residue 360 ILE Chi-restraints excluded: chain A residue 365 ARG Chi-restraints excluded: chain A residue 413 THR Chi-restraints excluded: chain A residue 422 ILE Chi-restraints excluded: chain A residue 460 LEU Chi-restraints excluded: chain C residue 31 LEU Chi-restraints excluded: chain C residue 169 ILE Chi-restraints excluded: chain C residue 210 LEU Chi-restraints excluded: chain C residue 317 MET Chi-restraints excluded: chain C residue 413 THR Chi-restraints excluded: chain C residue 449 VAL Chi-restraints excluded: chain C residue 452 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 56 optimal weight: 1.9990 chunk 85 optimal weight: 1.9990 chunk 42 optimal weight: 3.9990 chunk 28 optimal weight: 3.9990 chunk 27 optimal weight: 0.7980 chunk 90 optimal weight: 0.6980 chunk 97 optimal weight: 1.9990 chunk 70 optimal weight: 2.9990 chunk 13 optimal weight: 0.9980 chunk 112 optimal weight: 0.4980 chunk 129 optimal weight: 1.9990 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 395 ASN H 3 GLN ** L 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 155 ASN C 67 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5568 moved from start: 0.3121 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 11786 Z= 0.291 Angle : 0.709 11.968 15988 Z= 0.360 Chirality : 0.049 0.378 1945 Planarity : 0.005 0.056 2026 Dihedral : 7.188 87.686 1777 Min Nonbonded Distance : 2.071 Molprobity Statistics. All-atom Clashscore : 15.76 Ramachandran Plot: Outliers : 0.07 % Allowed : 9.80 % Favored : 90.14 % Rotamer: Outliers : 4.06 % Allowed : 18.70 % Favored : 77.24 % 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: -2.55 (0.21), residues: 1470 helix: -0.96 (0.26), residues: 380 sheet: -1.18 (0.31), residues: 284 loop : -2.30 (0.20), residues: 806 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP C 308 HIS 0.009 0.001 HIS A 414 PHE 0.024 0.002 PHE A 378 TYR 0.019 0.002 TYR A 309 ARG 0.007 0.000 ARG A 73 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2940 Ramachandran restraints generated. 1470 Oldfield, 0 Emsley, 1470 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2940 Ramachandran restraints generated. 1470 Oldfield, 0 Emsley, 1470 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 1312 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 133 time to evaluate : 1.347 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 281 ARG cc_start: 0.7127 (mtm-85) cc_final: 0.6830 (ptt90) REVERT: B 284 LEU cc_start: 0.6770 (tp) cc_final: 0.6207 (mt) REVERT: B 289 LEU cc_start: 0.7557 (mt) cc_final: 0.7345 (mp) REVERT: B 360 ILE cc_start: 0.5393 (pt) cc_final: 0.5176 (pt) REVERT: H 100 GLU cc_start: 0.6113 (tp30) cc_final: 0.5436 (tt0) REVERT: L 32 TYR cc_start: 0.6978 (m-10) cc_final: 0.6328 (m-10) REVERT: L 60 ASP cc_start: 0.5492 (OUTLIER) cc_final: 0.3870 (t70) REVERT: A 24 LYS cc_start: 0.8714 (OUTLIER) cc_final: 0.8426 (ptmm) REVERT: A 67 GLN cc_start: 0.8141 (tm-30) cc_final: 0.7825 (tm-30) REVERT: A 70 GLN cc_start: 0.8367 (tm-30) cc_final: 0.7805 (mp10) REVERT: A 73 ARG cc_start: 0.7992 (mmm160) cc_final: 0.7714 (mmm160) REVERT: A 290 ASN cc_start: 0.6380 (t0) cc_final: 0.5570 (p0) REVERT: A 317 MET cc_start: 0.7713 (ttp) cc_final: 0.7472 (ttm) REVERT: A 417 CYS cc_start: 0.6678 (t) cc_final: 0.6348 (t) REVERT: A 460 LEU cc_start: 0.4968 (OUTLIER) cc_final: 0.4736 (pp) REVERT: A 465 SER cc_start: 0.9092 (t) cc_final: 0.8720 (m) REVERT: C 38 MET cc_start: 0.6616 (tpt) cc_final: 0.5946 (tpt) REVERT: C 56 LYS cc_start: 0.7453 (tmtt) cc_final: 0.6961 (tppp) REVERT: C 236 ARG cc_start: 0.6645 (mtt90) cc_final: 0.5087 (mmt180) outliers start: 53 outliers final: 40 residues processed: 172 average time/residue: 0.2376 time to fit residues: 58.8119 Evaluate side-chains 172 residues out of total 1312 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 129 time to evaluate : 1.380 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 46 THR Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 162 CYS Chi-restraints excluded: chain B residue 172 ILE Chi-restraints excluded: chain B residue 210 LEU Chi-restraints excluded: chain B residue 211 THR Chi-restraints excluded: chain B residue 288 LEU Chi-restraints excluded: chain B residue 317 MET Chi-restraints excluded: chain B residue 349 ASN Chi-restraints excluded: chain B residue 388 ILE Chi-restraints excluded: chain B residue 395 ASN Chi-restraints excluded: chain B residue 419 THR Chi-restraints excluded: chain B residue 422 ILE Chi-restraints excluded: chain B residue 426 LEU Chi-restraints excluded: chain B residue 449 VAL Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain H residue 46 GLU Chi-restraints excluded: chain H residue 48 VAL Chi-restraints excluded: chain H residue 57 LEU Chi-restraints excluded: chain H residue 82 MET Chi-restraints excluded: chain H residue 82 LEU Chi-restraints excluded: chain H residue 108 LEU Chi-restraints excluded: chain H residue 110 THR Chi-restraints excluded: chain L residue 19 VAL Chi-restraints excluded: chain L residue 51 LYS Chi-restraints excluded: chain L residue 52 ASN Chi-restraints excluded: chain L residue 60 ASP Chi-restraints excluded: chain A residue 24 LYS Chi-restraints excluded: chain A residue 134 LEU Chi-restraints excluded: chain A residue 230 CYS Chi-restraints excluded: chain A residue 333 GLU Chi-restraints excluded: chain A residue 347 VAL Chi-restraints excluded: chain A residue 360 ILE Chi-restraints excluded: chain A residue 365 ARG Chi-restraints excluded: chain A residue 413 THR Chi-restraints excluded: chain A residue 422 ILE Chi-restraints excluded: chain A residue 460 LEU Chi-restraints excluded: chain C residue 169 ILE Chi-restraints excluded: chain C residue 172 ILE Chi-restraints excluded: chain C residue 210 LEU Chi-restraints excluded: chain C residue 317 MET Chi-restraints excluded: chain C residue 413 THR Chi-restraints excluded: chain C residue 449 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 136 optimal weight: 0.0980 chunk 124 optimal weight: 0.9990 chunk 132 optimal weight: 0.7980 chunk 80 optimal weight: 0.8980 chunk 57 optimal weight: 3.9990 chunk 104 optimal weight: 0.5980 chunk 40 optimal weight: 0.6980 chunk 120 optimal weight: 6.9990 chunk 125 optimal weight: 0.0970 chunk 87 optimal weight: 0.9990 chunk 140 optimal weight: 1.9990 overall best weight: 0.4578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 3 GLN ** L 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 155 ASN C 67 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5518 moved from start: 0.3189 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 11786 Z= 0.198 Angle : 0.660 12.300 15988 Z= 0.336 Chirality : 0.048 0.351 1945 Planarity : 0.004 0.054 2026 Dihedral : 6.932 83.993 1777 Min Nonbonded Distance : 2.103 Molprobity Statistics. All-atom Clashscore : 14.38 Ramachandran Plot: Outliers : 0.14 % Allowed : 8.44 % Favored : 91.43 % Rotamer: Outliers : 3.22 % Allowed : 19.62 % Favored : 77.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.44 (0.21), residues: 1470 helix: -0.83 (0.27), residues: 384 sheet: -1.21 (0.31), residues: 290 loop : -2.22 (0.20), residues: 796 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP C 308 HIS 0.009 0.001 HIS A 414 PHE 0.029 0.001 PHE A 378 TYR 0.016 0.001 TYR L 49 ARG 0.006 0.000 ARG A 73 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2940 Ramachandran restraints generated. 1470 Oldfield, 0 Emsley, 1470 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2940 Ramachandran restraints generated. 1470 Oldfield, 0 Emsley, 1470 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 1312 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 131 time to evaluate : 1.424 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 78 LEU cc_start: 0.7258 (tp) cc_final: 0.6415 (mt) REVERT: B 281 ARG cc_start: 0.7029 (mtm-85) cc_final: 0.6758 (ptt90) REVERT: B 284 LEU cc_start: 0.6797 (tp) cc_final: 0.6233 (mt) REVERT: B 357 SER cc_start: 0.7518 (t) cc_final: 0.7274 (p) REVERT: B 360 ILE cc_start: 0.5431 (pt) cc_final: 0.5230 (pt) REVERT: H 100 GLU cc_start: 0.6198 (tp30) cc_final: 0.5578 (tt0) REVERT: L 32 TYR cc_start: 0.6823 (m-10) cc_final: 0.6291 (m-10) REVERT: L 60 ASP cc_start: 0.5664 (OUTLIER) cc_final: 0.4162 (t70) REVERT: A 24 LYS cc_start: 0.8736 (OUTLIER) cc_final: 0.8472 (ptmm) REVERT: A 67 GLN cc_start: 0.8129 (tm-30) cc_final: 0.7807 (tm-30) REVERT: A 70 GLN cc_start: 0.8369 (tm-30) cc_final: 0.7814 (mp10) REVERT: A 73 ARG cc_start: 0.8036 (mmm160) cc_final: 0.7807 (mmm160) REVERT: A 274 TYR cc_start: 0.6663 (m-80) cc_final: 0.6326 (m-80) REVERT: A 290 ASN cc_start: 0.6316 (t0) cc_final: 0.5571 (p0) REVERT: A 317 MET cc_start: 0.7603 (ttp) cc_final: 0.7385 (ttm) REVERT: A 417 CYS cc_start: 0.6599 (t) cc_final: 0.6222 (t) REVERT: A 465 SER cc_start: 0.9142 (t) cc_final: 0.8755 (m) REVERT: C 38 MET cc_start: 0.6569 (tpt) cc_final: 0.5925 (tpt) REVERT: C 56 LYS cc_start: 0.7490 (tmtt) cc_final: 0.7000 (tppp) REVERT: C 236 ARG cc_start: 0.6641 (mtt90) cc_final: 0.5008 (mmt180) outliers start: 42 outliers final: 34 residues processed: 162 average time/residue: 0.2404 time to fit residues: 55.8692 Evaluate side-chains 165 residues out of total 1312 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 129 time to evaluate : 1.324 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 46 THR Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 162 CYS Chi-restraints excluded: chain B residue 172 ILE Chi-restraints excluded: chain B residue 210 LEU Chi-restraints excluded: chain B residue 211 THR Chi-restraints excluded: chain B residue 288 LEU Chi-restraints excluded: chain B residue 349 ASN Chi-restraints excluded: chain B residue 422 ILE Chi-restraints excluded: chain B residue 426 LEU Chi-restraints excluded: chain B residue 449 VAL Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain H residue 46 GLU Chi-restraints excluded: chain H residue 48 VAL Chi-restraints excluded: chain H residue 82 MET Chi-restraints excluded: chain H residue 82 LEU Chi-restraints excluded: chain H residue 108 LEU Chi-restraints excluded: chain L residue 19 VAL Chi-restraints excluded: chain L residue 51 LYS Chi-restraints excluded: chain L residue 52 ASN Chi-restraints excluded: chain L residue 60 ASP Chi-restraints excluded: chain A residue 24 LYS Chi-restraints excluded: chain A residue 134 LEU Chi-restraints excluded: chain A residue 230 CYS Chi-restraints excluded: chain A residue 333 GLU Chi-restraints excluded: chain A residue 347 VAL Chi-restraints excluded: chain A residue 360 ILE Chi-restraints excluded: chain A residue 365 ARG Chi-restraints excluded: chain A residue 413 THR Chi-restraints excluded: chain A residue 422 ILE Chi-restraints excluded: chain C residue 169 ILE Chi-restraints excluded: chain C residue 210 LEU Chi-restraints excluded: chain C residue 317 MET Chi-restraints excluded: chain C residue 413 THR Chi-restraints excluded: chain C residue 449 VAL Chi-restraints excluded: chain C residue 452 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 85 optimal weight: 2.9990 chunk 66 optimal weight: 1.9990 chunk 97 optimal weight: 0.0980 chunk 147 optimal weight: 0.6980 chunk 135 optimal weight: 0.8980 chunk 117 optimal weight: 6.9990 chunk 12 optimal weight: 0.0470 chunk 90 optimal weight: 0.3980 chunk 71 optimal weight: 2.9990 chunk 93 optimal weight: 0.0060 chunk 125 optimal weight: 0.0050 overall best weight: 0.1108 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 395 ASN H 3 GLN A 155 ASN C 67 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5431 moved from start: 0.3405 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 11786 Z= 0.155 Angle : 0.635 11.741 15988 Z= 0.322 Chirality : 0.047 0.321 1945 Planarity : 0.004 0.058 2026 Dihedral : 6.442 76.410 1777 Min Nonbonded Distance : 2.151 Molprobity Statistics. All-atom Clashscore : 13.48 Ramachandran Plot: Outliers : 0.14 % Allowed : 7.69 % Favored : 92.18 % Rotamer: Outliers : 2.30 % Allowed : 20.77 % Favored : 76.93 % 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: -2.22 (0.21), residues: 1470 helix: -0.72 (0.27), residues: 385 sheet: -1.02 (0.30), residues: 292 loop : -2.07 (0.21), residues: 793 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A 308 HIS 0.008 0.001 HIS A 414 PHE 0.019 0.001 PHE A 378 TYR 0.022 0.001 TYR A 438 ARG 0.006 0.000 ARG A 73 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2940 Ramachandran restraints generated. 1470 Oldfield, 0 Emsley, 1470 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2940 Ramachandran restraints generated. 1470 Oldfield, 0 Emsley, 1470 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 1312 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 141 time to evaluate : 1.435 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 70 GLN cc_start: 0.8052 (tm-30) cc_final: 0.7431 (tp40) REVERT: B 78 LEU cc_start: 0.7299 (tp) cc_final: 0.6458 (mt) REVERT: B 87 LYS cc_start: 0.7418 (pttm) cc_final: 0.7025 (ptpt) REVERT: B 263 LYS cc_start: 0.3614 (tttt) cc_final: 0.3358 (tttt) REVERT: B 281 ARG cc_start: 0.6838 (mtm-85) cc_final: 0.6628 (ptt90) REVERT: B 284 LEU cc_start: 0.6674 (tp) cc_final: 0.6171 (mt) REVERT: B 357 SER cc_start: 0.7326 (t) cc_final: 0.7104 (p) REVERT: H 100 GLU cc_start: 0.5911 (tp30) cc_final: 0.5363 (tt0) REVERT: L 31 TYR cc_start: 0.7277 (m-80) cc_final: 0.6632 (m-80) REVERT: L 32 TYR cc_start: 0.6716 (m-10) cc_final: 0.6183 (m-10) REVERT: L 60 ASP cc_start: 0.5400 (OUTLIER) cc_final: 0.3995 (t70) REVERT: A 67 GLN cc_start: 0.8055 (tm-30) cc_final: 0.7728 (tm-30) REVERT: A 70 GLN cc_start: 0.8339 (tm-30) cc_final: 0.7701 (mp10) REVERT: A 73 ARG cc_start: 0.8008 (mmm160) cc_final: 0.7782 (mmm160) REVERT: A 174 SER cc_start: 0.6972 (t) cc_final: 0.6097 (p) REVERT: A 274 TYR cc_start: 0.6564 (m-80) cc_final: 0.6260 (m-80) REVERT: A 290 ASN cc_start: 0.6480 (t0) cc_final: 0.5786 (p0) REVERT: A 317 MET cc_start: 0.7715 (ttp) cc_final: 0.7504 (ttm) REVERT: A 371 ASP cc_start: 0.7152 (t70) cc_final: 0.6339 (m-30) REVERT: A 417 CYS cc_start: 0.6559 (t) cc_final: 0.6263 (t) REVERT: A 465 SER cc_start: 0.8897 (t) cc_final: 0.8624 (m) REVERT: C 38 MET cc_start: 0.6473 (tpt) cc_final: 0.5813 (tpt) REVERT: C 56 LYS cc_start: 0.7435 (tmtt) cc_final: 0.6930 (tppp) REVERT: C 87 LYS cc_start: 0.4481 (tptp) cc_final: 0.3734 (ptmt) REVERT: C 158 VAL cc_start: 0.6273 (t) cc_final: 0.6022 (p) REVERT: C 236 ARG cc_start: 0.6616 (mtt90) cc_final: 0.5035 (mmt180) outliers start: 30 outliers final: 21 residues processed: 161 average time/residue: 0.2401 time to fit residues: 55.8180 Evaluate side-chains 153 residues out of total 1312 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 131 time to evaluate : 1.393 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 162 CYS Chi-restraints excluded: chain B residue 211 THR Chi-restraints excluded: chain B residue 288 LEU Chi-restraints excluded: chain B residue 419 THR Chi-restraints excluded: chain B residue 422 ILE Chi-restraints excluded: chain H residue 5 LEU Chi-restraints excluded: chain H residue 82 MET Chi-restraints excluded: chain H residue 82 LEU Chi-restraints excluded: chain L residue 19 VAL Chi-restraints excluded: chain L residue 51 LYS Chi-restraints excluded: chain L residue 60 ASP Chi-restraints excluded: chain A residue 134 LEU Chi-restraints excluded: chain A residue 333 GLU Chi-restraints excluded: chain A residue 347 VAL Chi-restraints excluded: chain A residue 360 ILE Chi-restraints excluded: chain A residue 365 ARG Chi-restraints excluded: chain A residue 422 ILE Chi-restraints excluded: chain C residue 93 ILE Chi-restraints excluded: chain C residue 169 ILE Chi-restraints excluded: chain C residue 413 THR Chi-restraints excluded: chain C residue 452 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 35 optimal weight: 0.1980 chunk 108 optimal weight: 0.9990 chunk 17 optimal weight: 0.6980 chunk 32 optimal weight: 0.0060 chunk 117 optimal weight: 5.9990 chunk 49 optimal weight: 5.9990 chunk 120 optimal weight: 6.9990 chunk 14 optimal weight: 4.9990 chunk 21 optimal weight: 0.7980 chunk 103 optimal weight: 2.9990 chunk 6 optimal weight: 0.6980 overall best weight: 0.4796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 155 ASN C 67 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4707 r_free = 0.4707 target = 0.240597 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.4644 r_free = 0.4644 target = 0.233177 restraints weight = 11723.583| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.4637 r_free = 0.4637 target = 0.232401 restraints weight = 15324.432| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.4618 r_free = 0.4618 target = 0.230354 restraints weight = 16755.061| |-----------------------------------------------------------------------------| r_work (final): 0.4624 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6240 moved from start: 0.3477 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 11786 Z= 0.194 Angle : 0.651 11.583 15988 Z= 0.328 Chirality : 0.048 0.339 1945 Planarity : 0.004 0.057 2026 Dihedral : 6.412 72.950 1777 Min Nonbonded Distance : 2.103 Molprobity Statistics. All-atom Clashscore : 13.65 Ramachandran Plot: Outliers : 0.14 % Allowed : 7.89 % Favored : 91.97 % Rotamer: Outliers : 2.22 % Allowed : 21.46 % Favored : 76.32 % 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: -2.29 (0.21), residues: 1470 helix: -0.74 (0.27), residues: 393 sheet: -0.96 (0.31), residues: 285 loop : -2.19 (0.21), residues: 792 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP H 103 HIS 0.013 0.001 HIS A 414 PHE 0.027 0.001 PHE A 378 TYR 0.015 0.001 TYR L 49 ARG 0.005 0.000 ARG A 73 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2350.60 seconds wall clock time: 44 minutes 1.62 seconds (2641.62 seconds total)