Starting phenix.real_space_refine on Sun Feb 18 14:56:46 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pdz_13343/02_2024/7pdz_13343_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pdz_13343/02_2024/7pdz_13343.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pdz_13343/02_2024/7pdz_13343.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pdz_13343/02_2024/7pdz_13343.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pdz_13343/02_2024/7pdz_13343_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pdz_13343/02_2024/7pdz_13343_updated.pdb" } resolution = 3.8 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.004 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 16 5.49 5 Mg 6 5.21 5 S 155 5.16 5 C 13971 2.51 5 N 3750 2.21 5 O 4287 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "E GLU 22": "OE1" <-> "OE2" Residue "E GLU 99": "OE1" <-> "OE2" Residue "E PHE 249": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 28": "OE1" <-> "OE2" Residue "F GLU 31": "OE1" <-> "OE2" Residue "F GLU 78": "OE1" <-> "OE2" Residue "F GLU 104": "OE1" <-> "OE2" Residue "F ARG 172": "NH1" <-> "NH2" Residue "F ARG 260": "NH1" <-> "NH2" Residue "I ARG 39": "NH1" <-> "NH2" Residue "I TYR 240": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I GLU 270": "OE1" <-> "OE2" Residue "J ARG 39": "NH1" <-> "NH2" Residue "J GLU 83": "OE1" <-> "OE2" Residue "J GLU 270": "OE1" <-> "OE2" Residue "K GLU 167": "OE1" <-> "OE2" Residue "K GLU 226": "OE1" <-> "OE2" Residue "K GLU 237": "OE1" <-> "OE2" Residue "K GLU 253": "OE1" <-> "OE2" Residue "K PHE 255": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K GLU 334": "OE1" <-> "OE2" Residue "L PHE 31": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 200": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 218": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N TYR 166": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N TYR 240": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N GLU 270": "OE1" <-> "OE2" Residue "N GLU 334": "OE1" <-> "OE2" Residue "O PHE 255": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O GLU 270": "OE1" <-> "OE2" Residue "O GLU 334": "OE1" <-> "OE2" Time to flip residues: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 22185 Number of models: 1 Model: "" Number of chains: 19 Chain: "E" Number of atoms: 2146 Number of conformers: 1 Conformer: "" Number of residues, atoms: 272, 2146 Classifications: {'peptide': 272} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 262} Chain: "F" Number of atoms: 2212 Number of conformers: 1 Conformer: "" Number of residues, atoms: 272, 2212 Classifications: {'peptide': 272} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 261} Chain: "I" Number of atoms: 2894 Number of conformers: 1 Conformer: "" Number of residues, atoms: 371, 2894 Classifications: {'peptide': 371} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 351} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'HIC:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "J" Number of atoms: 2894 Number of conformers: 1 Conformer: "" Number of residues, atoms: 371, 2894 Classifications: {'peptide': 371} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 351} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'HIC:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "K" Number of atoms: 2894 Number of conformers: 1 Conformer: "" Number of residues, atoms: 371, 2894 Classifications: {'peptide': 371} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 351} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'HIC:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "L" Number of atoms: 2894 Number of conformers: 1 Conformer: "" Number of residues, atoms: 371, 2894 Classifications: {'peptide': 371} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 351} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'HIC:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "N" Number of atoms: 2894 Number of conformers: 1 Conformer: "" Number of residues, atoms: 371, 2894 Classifications: {'peptide': 371} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 351} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'HIC:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "O" Number of atoms: 2894 Number of conformers: 1 Conformer: "" Number of residues, atoms: 371, 2894 Classifications: {'peptide': 371} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 351} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'HIC:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "Q" Number of atoms: 55 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 55 Classifications: {'peptide': 7} Modifications used: {'DTH_chir_02_both': 1, 'PEPT-D': 1} Link IDs: {'TRANS': 6} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'EEP:plan-1': 1, 'HYP:plan-1': 1} Unresolved non-hydrogen planarities: 2 Chain: "R" Number of atoms: 55 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 55 Classifications: {'peptide': 7} Modifications used: {'DTH_chir_02_both': 1, 'PEPT-D': 1} Link IDs: {'TRANS': 6} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'EEP:plan-1': 1, 'HYP:plan-1': 1} Unresolved non-hydrogen planarities: 2 Chain: "S" Number of atoms: 55 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 55 Classifications: {'peptide': 7} Modifications used: {'DTH_chir_02_both': 1, 'PEPT-D': 1} Link IDs: {'TRANS': 6} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'EEP:plan-1': 1, 'HYP:plan-1': 1} Unresolved non-hydrogen planarities: 2 Chain: "T" Number of atoms: 55 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 55 Classifications: {'peptide': 7} Modifications used: {'DTH_chir_02_both': 1, 'PEPT-D': 1} Link IDs: {'TRANS': 6} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'EEP:plan-1': 1, 'HYP:plan-1': 1} Unresolved non-hydrogen planarities: 2 Chain: "P" Number of atoms: 55 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 55 Classifications: {'peptide': 7} Modifications used: {'DTH_chir_02_both': 1, 'PEPT-D': 1} Link IDs: {'TRANS': 6} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'EEP:plan-1': 1, 'HYP:plan-1': 1} Unresolved non-hydrogen planarities: 2 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "K" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {' MG': 1, 'ADP': 1, 'PO4': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "L" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {' MG': 1, 'ADP': 1, 'PO4': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "N" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {' MG': 1, 'ADP': 1, 'PO4': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "O" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {' MG': 1, 'ADP': 1, 'PO4': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Time building chain proxies: 12.81, per 1000 atoms: 0.58 Number of scatterers: 22185 At special positions: 0 Unit cell: (108.9, 94.38, 254.1, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 155 16.00 P 16 15.00 Mg 6 11.99 O 4287 8.00 N 3750 7.00 C 13971 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=7, symmetry=0 Number of additional bonds: simple=7, symmetry=0 Coordination: Other bonds: Time building additional restraints: 10.01 Conformation dependent library (CDL) restraints added in 4.6 seconds 5472 Ramachandran restraints generated. 2736 Oldfield, 0 Emsley, 2736 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Skipped Input residue name is d-peptide pdb=" CB DTH Q 6 " pdb=" CB DTH R 6 " pdb=" CB DTH S 6 " pdb=" CB DTH T 6 " pdb=" CB DTH P 6 " Number of C-beta restraints generated: 5202 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 137 helices and 27 sheets defined 44.0% alpha, 14.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.34 Creating SS restraints... Processing helix chain 'E' and resid 2 through 15 Processing helix chain 'E' and resid 18 through 31 removed outlier: 3.508A pdb=" N ILE E 21 " --> pdb=" O PRO E 18 " (cutoff:3.500A) removed outlier: 5.212A pdb=" N GLU E 22 " --> pdb=" O GLN E 19 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N ASP E 27 " --> pdb=" O ASN E 24 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N ILE E 29 " --> pdb=" O SER E 26 " (cutoff:3.500A) Processing helix chain 'E' and resid 36 through 42 Processing helix chain 'E' and resid 91 through 112 Processing helix chain 'E' and resid 209 through 244 removed outlier: 4.101A pdb=" N VAL E 240 " --> pdb=" O THR E 236 " (cutoff:3.500A) Processing helix chain 'E' and resid 247 through 271 removed outlier: 3.718A pdb=" N ARG E 268 " --> pdb=" O GLU E 264 " (cutoff:3.500A) Processing helix chain 'F' and resid 11 through 23 Processing helix chain 'F' and resid 29 through 39 Processing helix chain 'F' and resid 44 through 61 removed outlier: 3.850A pdb=" N GLY F 49 " --> pdb=" O LEU F 45 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N HIS F 52 " --> pdb=" O GLU F 48 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N GLN F 56 " --> pdb=" O HIS F 52 " (cutoff:3.500A) Processing helix chain 'F' and resid 116 through 133 removed outlier: 3.657A pdb=" N TRP F 120 " --> pdb=" O GLY F 116 " (cutoff:3.500A) removed outlier: 4.286A pdb=" N ARG F 121 " --> pdb=" O LEU F 117 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N SER F 123 " --> pdb=" O SER F 119 " (cutoff:3.500A) removed outlier: 4.399A pdb=" N CYS F 124 " --> pdb=" O TRP F 120 " (cutoff:3.500A) removed outlier: 4.114A pdb=" N ALA F 130 " --> pdb=" O SER F 126 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N TYR F 131 " --> pdb=" O ALA F 127 " (cutoff:3.500A) Processing helix chain 'F' and resid 165 through 167 No H-bonds generated for 'chain 'F' and resid 165 through 167' Processing helix chain 'F' and resid 221 through 245 Processing helix chain 'F' and resid 250 through 258 Processing helix chain 'F' and resid 271 through 276 Processing helix chain 'I' and resid 45 through 47 No H-bonds generated for 'chain 'I' and resid 45 through 47' Processing helix chain 'I' and resid 55 through 60 Processing helix chain 'I' and resid 62 through 64 No H-bonds generated for 'chain 'I' and resid 62 through 64' Processing helix chain 'I' and resid 79 through 91 Processing helix chain 'I' and resid 98 through 100 No H-bonds generated for 'chain 'I' and resid 98 through 100' Processing helix chain 'I' and resid 113 through 125 removed outlier: 3.735A pdb=" N GLU I 117 " --> pdb=" O LYS I 113 " (cutoff:3.500A) Processing helix chain 'I' and resid 137 through 144 removed outlier: 3.520A pdb=" N SER I 141 " --> pdb=" O GLN I 137 " (cutoff:3.500A) Processing helix chain 'I' and resid 172 through 174 No H-bonds generated for 'chain 'I' and resid 172 through 174' Processing helix chain 'I' and resid 182 through 196 removed outlier: 4.096A pdb=" N ARG I 196 " --> pdb=" O ILE I 192 " (cutoff:3.500A) Processing helix chain 'I' and resid 203 through 213 removed outlier: 3.530A pdb=" N GLU I 207 " --> pdb=" O THR I 203 " (cutoff:3.500A) Processing helix chain 'I' and resid 223 through 232 Processing helix chain 'I' and resid 234 through 236 No H-bonds generated for 'chain 'I' and resid 234 through 236' Processing helix chain 'I' and resid 253 through 262 Proline residue: I 258 - end of helix removed outlier: 4.683A pdb=" N LEU I 261 " --> pdb=" O CYS I 257 " (cutoff:3.500A) removed outlier: 4.247A pdb=" N PHE I 262 " --> pdb=" O PRO I 258 " (cutoff:3.500A) Processing helix chain 'I' and resid 264 through 267 Processing helix chain 'I' and resid 274 through 284 removed outlier: 4.194A pdb=" N LYS I 284 " --> pdb=" O ASN I 280 " (cutoff:3.500A) Processing helix chain 'I' and resid 287 through 296 removed outlier: 4.537A pdb=" N LYS I 291 " --> pdb=" O ASP I 288 " (cutoff:3.500A) removed outlier: 4.382A pdb=" N ALA I 295 " --> pdb=" O ASP I 292 " (cutoff:3.500A) Processing helix chain 'I' and resid 302 through 305 Processing helix chain 'I' and resid 309 through 320 removed outlier: 3.707A pdb=" N ALA I 319 " --> pdb=" O LYS I 315 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N LEU I 320 " --> pdb=" O GLU I 316 " (cutoff:3.500A) Processing helix chain 'I' and resid 338 through 348 Processing helix chain 'I' and resid 350 through 355 Processing helix chain 'I' and resid 359 through 374 Proline residue: I 367 - end of helix removed outlier: 5.401A pdb=" N VAL I 370 " --> pdb=" O GLY I 366 " (cutoff:3.500A) removed outlier: 4.473A pdb=" N HIS I 371 " --> pdb=" O PRO I 367 " (cutoff:3.500A) removed outlier: 4.205A pdb=" N ARG I 372 " --> pdb=" O SER I 368 " (cutoff:3.500A) removed outlier: 4.840A pdb=" N LYS I 373 " --> pdb=" O ILE I 369 " (cutoff:3.500A) Processing helix chain 'J' and resid 45 through 47 No H-bonds generated for 'chain 'J' and resid 45 through 47' Processing helix chain 'J' and resid 56 through 60 Processing helix chain 'J' and resid 62 through 64 No H-bonds generated for 'chain 'J' and resid 62 through 64' Processing helix chain 'J' and resid 79 through 91 Processing helix chain 'J' and resid 98 through 100 No H-bonds generated for 'chain 'J' and resid 98 through 100' Processing helix chain 'J' and resid 113 through 125 Processing helix chain 'J' and resid 137 through 145 removed outlier: 3.827A pdb=" N SER J 145 " --> pdb=" O SER J 141 " (cutoff:3.500A) Processing helix chain 'J' and resid 172 through 174 No H-bonds generated for 'chain 'J' and resid 172 through 174' Processing helix chain 'J' and resid 182 through 196 removed outlier: 3.670A pdb=" N GLU J 195 " --> pdb=" O LYS J 191 " (cutoff:3.500A) removed outlier: 4.099A pdb=" N ARG J 196 " --> pdb=" O ILE J 192 " (cutoff:3.500A) Processing helix chain 'J' and resid 203 through 216 Processing helix chain 'J' and resid 223 through 230 Processing helix chain 'J' and resid 234 through 236 No H-bonds generated for 'chain 'J' and resid 234 through 236' Processing helix chain 'J' and resid 252 through 261 Proline residue: J 258 - end of helix removed outlier: 4.745A pdb=" N LEU J 261 " --> pdb=" O CYS J 257 " (cutoff:3.500A) Processing helix chain 'J' and resid 264 through 267 Processing helix chain 'J' and resid 274 through 282 Processing helix chain 'J' and resid 287 through 296 removed outlier: 3.918A pdb=" N ARG J 290 " --> pdb=" O VAL J 287 " (cutoff:3.500A) removed outlier: 4.329A pdb=" N LYS J 291 " --> pdb=" O ASP J 288 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N ALA J 295 " --> pdb=" O ASP J 292 " (cutoff:3.500A) Processing helix chain 'J' and resid 302 through 305 Processing helix chain 'J' and resid 309 through 320 removed outlier: 3.927A pdb=" N ALA J 319 " --> pdb=" O LYS J 315 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N LEU J 320 " --> pdb=" O GLU J 316 " (cutoff:3.500A) Processing helix chain 'J' and resid 338 through 348 Processing helix chain 'J' and resid 352 through 354 No H-bonds generated for 'chain 'J' and resid 352 through 354' Processing helix chain 'J' and resid 359 through 373 Proline residue: J 367 - end of helix removed outlier: 5.143A pdb=" N VAL J 370 " --> pdb=" O GLY J 366 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N ARG J 372 " --> pdb=" O SER J 368 " (cutoff:3.500A) Processing helix chain 'K' and resid 45 through 47 No H-bonds generated for 'chain 'K' and resid 45 through 47' Processing helix chain 'K' and resid 55 through 60 Processing helix chain 'K' and resid 62 through 64 No H-bonds generated for 'chain 'K' and resid 62 through 64' Processing helix chain 'K' and resid 79 through 91 Processing helix chain 'K' and resid 98 through 100 No H-bonds generated for 'chain 'K' and resid 98 through 100' Processing helix chain 'K' and resid 113 through 125 removed outlier: 3.521A pdb=" N GLU K 117 " --> pdb=" O LYS K 113 " (cutoff:3.500A) Processing helix chain 'K' and resid 137 through 145 Processing helix chain 'K' and resid 172 through 174 No H-bonds generated for 'chain 'K' and resid 172 through 174' Processing helix chain 'K' and resid 182 through 196 removed outlier: 3.535A pdb=" N LYS K 191 " --> pdb=" O ASP K 187 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N GLU K 195 " --> pdb=" O LYS K 191 " (cutoff:3.500A) removed outlier: 4.379A pdb=" N ARG K 196 " --> pdb=" O ILE K 192 " (cutoff:3.500A) Processing helix chain 'K' and resid 203 through 215 removed outlier: 3.501A pdb=" N GLU K 207 " --> pdb=" O THR K 203 " (cutoff:3.500A) Processing helix chain 'K' and resid 223 through 232 Processing helix chain 'K' and resid 254 through 262 Proline residue: K 258 - end of helix removed outlier: 5.234A pdb=" N LEU K 261 " --> pdb=" O CYS K 257 " (cutoff:3.500A) removed outlier: 4.133A pdb=" N PHE K 262 " --> pdb=" O PRO K 258 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 254 through 262' Processing helix chain 'K' and resid 264 through 267 Processing helix chain 'K' and resid 274 through 284 Processing helix chain 'K' and resid 290 through 296 Processing helix chain 'K' and resid 302 through 305 Processing helix chain 'K' and resid 309 through 320 Processing helix chain 'K' and resid 335 through 337 No H-bonds generated for 'chain 'K' and resid 335 through 337' Processing helix chain 'K' and resid 342 through 348 Processing helix chain 'K' and resid 350 through 354 removed outlier: 4.109A pdb=" N GLN K 354 " --> pdb=" O THR K 351 " (cutoff:3.500A) Processing helix chain 'K' and resid 359 through 370 Proline residue: K 367 - end of helix removed outlier: 4.906A pdb=" N VAL K 370 " --> pdb=" O GLY K 366 " (cutoff:3.500A) Processing helix chain 'L' and resid 45 through 47 No H-bonds generated for 'chain 'L' and resid 45 through 47' Processing helix chain 'L' and resid 55 through 60 Processing helix chain 'L' and resid 62 through 64 No H-bonds generated for 'chain 'L' and resid 62 through 64' Processing helix chain 'L' and resid 79 through 91 Processing helix chain 'L' and resid 98 through 100 No H-bonds generated for 'chain 'L' and resid 98 through 100' Processing helix chain 'L' and resid 113 through 125 Processing helix chain 'L' and resid 137 through 145 Processing helix chain 'L' and resid 172 through 174 No H-bonds generated for 'chain 'L' and resid 172 through 174' Processing helix chain 'L' and resid 182 through 196 removed outlier: 3.710A pdb=" N GLU L 195 " --> pdb=" O LYS L 191 " (cutoff:3.500A) removed outlier: 4.126A pdb=" N ARG L 196 " --> pdb=" O ILE L 192 " (cutoff:3.500A) Processing helix chain 'L' and resid 203 through 214 Processing helix chain 'L' and resid 223 through 232 Processing helix chain 'L' and resid 252 through 261 Proline residue: L 258 - end of helix removed outlier: 4.982A pdb=" N LEU L 261 " --> pdb=" O CYS L 257 " (cutoff:3.500A) Processing helix chain 'L' and resid 264 through 267 Processing helix chain 'L' and resid 274 through 284 Processing helix chain 'L' and resid 288 through 294 removed outlier: 4.830A pdb=" N ASP L 292 " --> pdb=" O ASP L 288 " (cutoff:3.500A) removed outlier: 4.896A pdb=" N LEU L 293 " --> pdb=" O ILE L 289 " (cutoff:3.500A) Processing helix chain 'L' and resid 302 through 305 Processing helix chain 'L' and resid 309 through 320 removed outlier: 4.027A pdb=" N ALA L 319 " --> pdb=" O LYS L 315 " (cutoff:3.500A) Processing helix chain 'L' and resid 335 through 348 removed outlier: 3.583A pdb=" N SER L 338 " --> pdb=" O ARG L 335 " (cutoff:3.500A) removed outlier: 5.917A pdb=" N VAL L 339 " --> pdb=" O LYS L 336 " (cutoff:3.500A) Processing helix chain 'L' and resid 351 through 354 Processing helix chain 'L' and resid 359 through 365 removed outlier: 3.648A pdb=" N GLU L 364 " --> pdb=" O GLN L 360 " (cutoff:3.500A) Processing helix chain 'L' and resid 367 through 371 removed outlier: 3.578A pdb=" N HIS L 371 " --> pdb=" O SER L 368 " (cutoff:3.500A) Processing helix chain 'N' and resid 45 through 47 No H-bonds generated for 'chain 'N' and resid 45 through 47' Processing helix chain 'N' and resid 55 through 60 Processing helix chain 'N' and resid 62 through 64 No H-bonds generated for 'chain 'N' and resid 62 through 64' Processing helix chain 'N' and resid 79 through 91 Processing helix chain 'N' and resid 98 through 100 No H-bonds generated for 'chain 'N' and resid 98 through 100' Processing helix chain 'N' and resid 113 through 125 Processing helix chain 'N' and resid 137 through 145 Processing helix chain 'N' and resid 172 through 174 No H-bonds generated for 'chain 'N' and resid 172 through 174' Processing helix chain 'N' and resid 182 through 196 removed outlier: 3.561A pdb=" N LYS N 191 " --> pdb=" O ASP N 187 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N THR N 194 " --> pdb=" O MET N 190 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N GLU N 195 " --> pdb=" O LYS N 191 " (cutoff:3.500A) removed outlier: 4.217A pdb=" N ARG N 196 " --> pdb=" O ILE N 192 " (cutoff:3.500A) Processing helix chain 'N' and resid 203 through 216 Processing helix chain 'N' and resid 223 through 233 removed outlier: 3.679A pdb=" N SER N 232 " --> pdb=" O ALA N 228 " (cutoff:3.500A) Processing helix chain 'N' and resid 252 through 261 removed outlier: 4.715A pdb=" N CYS N 257 " --> pdb=" O ARG N 254 " (cutoff:3.500A) Proline residue: N 258 - end of helix Processing helix chain 'N' and resid 264 through 267 Processing helix chain 'N' and resid 274 through 283 Processing helix chain 'N' and resid 290 through 295 Processing helix chain 'N' and resid 302 through 305 Processing helix chain 'N' and resid 309 through 320 removed outlier: 3.534A pdb=" N ALA N 319 " --> pdb=" O LYS N 315 " (cutoff:3.500A) Processing helix chain 'N' and resid 335 through 348 removed outlier: 5.162A pdb=" N VAL N 339 " --> pdb=" O LYS N 336 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N GLY N 342 " --> pdb=" O VAL N 339 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N GLY N 343 " --> pdb=" O TRP N 340 " (cutoff:3.500A) Processing helix chain 'N' and resid 351 through 354 Processing helix chain 'N' and resid 359 through 371 Proline residue: N 367 - end of helix removed outlier: 5.034A pdb=" N VAL N 370 " --> pdb=" O GLY N 366 " (cutoff:3.500A) removed outlier: 4.924A pdb=" N HIS N 371 " --> pdb=" O PRO N 367 " (cutoff:3.500A) Processing helix chain 'O' and resid 55 through 60 Processing helix chain 'O' and resid 79 through 91 Processing helix chain 'O' and resid 98 through 100 No H-bonds generated for 'chain 'O' and resid 98 through 100' Processing helix chain 'O' and resid 113 through 125 Processing helix chain 'O' and resid 137 through 145 removed outlier: 3.615A pdb=" N SER O 145 " --> pdb=" O SER O 141 " (cutoff:3.500A) Processing helix chain 'O' and resid 172 through 174 No H-bonds generated for 'chain 'O' and resid 172 through 174' Processing helix chain 'O' and resid 182 through 196 removed outlier: 3.772A pdb=" N THR O 194 " --> pdb=" O MET O 190 " (cutoff:3.500A) removed outlier: 4.161A pdb=" N GLU O 195 " --> pdb=" O LYS O 191 " (cutoff:3.500A) removed outlier: 4.585A pdb=" N ARG O 196 " --> pdb=" O ILE O 192 " (cutoff:3.500A) Processing helix chain 'O' and resid 203 through 214 Processing helix chain 'O' and resid 223 through 232 Processing helix chain 'O' and resid 234 through 236 No H-bonds generated for 'chain 'O' and resid 234 through 236' Processing helix chain 'O' and resid 252 through 262 Proline residue: O 258 - end of helix removed outlier: 4.791A pdb=" N LEU O 261 " --> pdb=" O CYS O 257 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N PHE O 262 " --> pdb=" O PRO O 258 " (cutoff:3.500A) Processing helix chain 'O' and resid 264 through 267 Processing helix chain 'O' and resid 274 through 284 Processing helix chain 'O' and resid 289 through 294 removed outlier: 3.817A pdb=" N TYR O 294 " --> pdb=" O LYS O 291 " (cutoff:3.500A) Processing helix chain 'O' and resid 302 through 305 Processing helix chain 'O' and resid 309 through 320 removed outlier: 3.646A pdb=" N ALA O 319 " --> pdb=" O LYS O 315 " (cutoff:3.500A) Processing helix chain 'O' and resid 338 through 348 Processing helix chain 'O' and resid 350 through 354 Processing helix chain 'O' and resid 359 through 371 removed outlier: 3.671A pdb=" N GLU O 364 " --> pdb=" O GLN O 360 " (cutoff:3.500A) Proline residue: O 367 - end of helix removed outlier: 5.558A pdb=" N VAL O 370 " --> pdb=" O GLY O 366 " (cutoff:3.500A) removed outlier: 5.023A pdb=" N HIS O 371 " --> pdb=" O PRO O 367 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'E' and resid 48 through 52 removed outlier: 4.155A pdb=" N LYS E 48 " --> pdb=" O LEU E 61 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N LYS E 57 " --> pdb=" O ASP E 52 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'E' and resid 116 through 124 removed outlier: 3.505A pdb=" N PHE E 128 " --> pdb=" O VAL E 156 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'F' and resid 64 through 66 Processing sheet with id= D, first strand: chain 'F' and resid 140 through 148 removed outlier: 3.611A pdb=" N PHE F 140 " --> pdb=" O GLU F 159 " (cutoff:3.500A) removed outlier: 4.173A pdb=" N LYS F 146 " --> pdb=" O THR F 153 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N THR F 153 " --> pdb=" O LYS F 146 " (cutoff:3.500A) removed outlier: 4.791A pdb=" N GLN F 152 " --> pdb=" O ILE F 181 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N ILE F 158 " --> pdb=" O SER F 175 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N GLN F 164 " --> pdb=" O TRP F 169 " (cutoff:3.500A) removed outlier: 4.179A pdb=" N TRP F 169 " --> pdb=" O GLN F 164 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'I' and resid 132 through 136 removed outlier: 6.793A pdb=" N VAL I 103 " --> pdb=" O TYR I 133 " (cutoff:3.500A) removed outlier: 8.174A pdb=" N ALA I 135 " --> pdb=" O VAL I 103 " (cutoff:3.500A) removed outlier: 6.874A pdb=" N LEU I 105 " --> pdb=" O ALA I 135 " (cutoff:3.500A) removed outlier: 6.819A pdb=" N LEU I 8 " --> pdb=" O LEU I 104 " (cutoff:3.500A) removed outlier: 8.044A pdb=" N THR I 106 " --> pdb=" O LEU I 8 " (cutoff:3.500A) removed outlier: 7.763A pdb=" N VAL I 10 " --> pdb=" O THR I 106 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'I' and resid 34 through 38 Processing sheet with id= G, first strand: chain 'I' and resid 297 through 300 removed outlier: 6.309A pdb=" N ILE I 151 " --> pdb=" O VAL I 298 " (cutoff:3.500A) removed outlier: 7.736A pdb=" N SER I 300 " --> pdb=" O ILE I 151 " (cutoff:3.500A) removed outlier: 6.250A pdb=" N MET I 153 " --> pdb=" O SER I 300 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'I' and resid 238 through 241 removed outlier: 3.580A pdb=" N TYR I 240 " --> pdb=" O ILE I 248 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'J' and resid 132 through 136 removed outlier: 6.676A pdb=" N VAL J 103 " --> pdb=" O TYR J 133 " (cutoff:3.500A) removed outlier: 7.892A pdb=" N ALA J 135 " --> pdb=" O VAL J 103 " (cutoff:3.500A) removed outlier: 6.808A pdb=" N LEU J 105 " --> pdb=" O ALA J 135 " (cutoff:3.500A) removed outlier: 6.723A pdb=" N LEU J 8 " --> pdb=" O LEU J 104 " (cutoff:3.500A) removed outlier: 8.020A pdb=" N THR J 106 " --> pdb=" O LEU J 8 " (cutoff:3.500A) removed outlier: 7.640A pdb=" N VAL J 10 " --> pdb=" O THR J 106 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'J' and resid 34 through 38 Processing sheet with id= K, first strand: chain 'J' and resid 297 through 300 removed outlier: 6.480A pdb=" N ILE J 151 " --> pdb=" O VAL J 298 " (cutoff:3.500A) removed outlier: 7.797A pdb=" N SER J 300 " --> pdb=" O ILE J 151 " (cutoff:3.500A) removed outlier: 6.507A pdb=" N MET J 153 " --> pdb=" O SER J 300 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'J' and resid 238 through 241 Processing sheet with id= M, first strand: chain 'K' and resid 132 through 136 removed outlier: 6.733A pdb=" N VAL K 103 " --> pdb=" O TYR K 133 " (cutoff:3.500A) removed outlier: 7.853A pdb=" N ALA K 135 " --> pdb=" O VAL K 103 " (cutoff:3.500A) removed outlier: 6.713A pdb=" N LEU K 105 " --> pdb=" O ALA K 135 " (cutoff:3.500A) removed outlier: 6.490A pdb=" N LEU K 8 " --> pdb=" O LEU K 104 " (cutoff:3.500A) removed outlier: 8.100A pdb=" N THR K 106 " --> pdb=" O LEU K 8 " (cutoff:3.500A) removed outlier: 7.910A pdb=" N VAL K 10 " --> pdb=" O THR K 106 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'K' and resid 52 through 54 Processing sheet with id= O, first strand: chain 'K' and resid 160 through 165 Processing sheet with id= P, first strand: chain 'K' and resid 238 through 241 Processing sheet with id= Q, first strand: chain 'L' and resid 132 through 136 removed outlier: 6.647A pdb=" N VAL L 103 " --> pdb=" O TYR L 133 " (cutoff:3.500A) removed outlier: 7.559A pdb=" N ALA L 135 " --> pdb=" O VAL L 103 " (cutoff:3.500A) removed outlier: 6.715A pdb=" N LEU L 105 " --> pdb=" O ALA L 135 " (cutoff:3.500A) removed outlier: 6.509A pdb=" N LEU L 8 " --> pdb=" O LEU L 104 " (cutoff:3.500A) removed outlier: 7.822A pdb=" N THR L 106 " --> pdb=" O LEU L 8 " (cutoff:3.500A) removed outlier: 7.780A pdb=" N VAL L 10 " --> pdb=" O THR L 106 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N PHE L 31 " --> pdb=" O CYS L 17 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'L' and resid 35 through 38 Processing sheet with id= S, first strand: chain 'L' and resid 297 through 300 removed outlier: 6.153A pdb=" N ILE L 151 " --> pdb=" O VAL L 298 " (cutoff:3.500A) removed outlier: 7.480A pdb=" N SER L 300 " --> pdb=" O ILE L 151 " (cutoff:3.500A) removed outlier: 6.275A pdb=" N MET L 153 " --> pdb=" O SER L 300 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'L' and resid 238 through 241 Processing sheet with id= U, first strand: chain 'N' and resid 18 through 21 removed outlier: 3.531A pdb=" N THR N 106 " --> pdb=" O VAL N 10 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'N' and resid 35 through 38 Processing sheet with id= W, first strand: chain 'N' and resid 297 through 300 removed outlier: 6.255A pdb=" N ILE N 151 " --> pdb=" O VAL N 298 " (cutoff:3.500A) removed outlier: 7.492A pdb=" N SER N 300 " --> pdb=" O ILE N 151 " (cutoff:3.500A) removed outlier: 6.057A pdb=" N MET N 153 " --> pdb=" O SER N 300 " (cutoff:3.500A) Processing sheet with id= X, first strand: chain 'N' and resid 239 through 241 Processing sheet with id= Y, first strand: chain 'O' and resid 132 through 136 removed outlier: 6.780A pdb=" N VAL O 103 " --> pdb=" O TYR O 133 " (cutoff:3.500A) removed outlier: 7.700A pdb=" N ALA O 135 " --> pdb=" O VAL O 103 " (cutoff:3.500A) removed outlier: 6.850A pdb=" N LEU O 105 " --> pdb=" O ALA O 135 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N LEU O 8 " --> pdb=" O LEU O 104 " (cutoff:3.500A) removed outlier: 7.739A pdb=" N THR O 106 " --> pdb=" O LEU O 8 " (cutoff:3.500A) removed outlier: 7.378A pdb=" N VAL O 10 " --> pdb=" O THR O 106 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N PHE O 31 " --> pdb=" O CYS O 17 " (cutoff:3.500A) Processing sheet with id= Z, first strand: chain 'O' and resid 297 through 300 removed outlier: 6.108A pdb=" N ILE O 151 " --> pdb=" O VAL O 298 " (cutoff:3.500A) removed outlier: 7.484A pdb=" N SER O 300 " --> pdb=" O ILE O 151 " (cutoff:3.500A) removed outlier: 6.330A pdb=" N MET O 153 " --> pdb=" O SER O 300 " (cutoff:3.500A) Processing sheet with id= AA, first strand: chain 'O' and resid 238 through 241 870 hydrogen bonds defined for protein. 2334 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: 6.80 Time building geometry restraints manager: 10.85 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.34: 6831 1.34 - 1.49: 6868 1.49 - 1.63: 8701 1.63 - 1.78: 54 1.78 - 1.93: 206 Bond restraints: 22660 Sorted by residual: bond pdb=" N HYP P 1 " pdb=" CA HYP P 1 " ideal model delta sigma weight residual 1.466 1.313 0.153 1.50e-02 4.44e+03 1.04e+02 bond pdb=" N HYP S 1 " pdb=" CA HYP S 1 " ideal model delta sigma weight residual 1.466 1.314 0.152 1.50e-02 4.44e+03 1.02e+02 bond pdb=" CA HYP P 1 " pdb=" C HYP P 1 " ideal model delta sigma weight residual 1.525 1.313 0.212 2.10e-02 2.27e+03 1.02e+02 bond pdb=" CA HYP Q 1 " pdb=" C HYP Q 1 " ideal model delta sigma weight residual 1.525 1.315 0.210 2.10e-02 2.27e+03 9.98e+01 bond pdb=" N HYP Q 1 " pdb=" CA HYP Q 1 " ideal model delta sigma weight residual 1.466 1.317 0.149 1.50e-02 4.44e+03 9.92e+01 ... (remaining 22655 not shown) Histogram of bond angle deviations from ideal: 96.28 - 104.35: 493 104.35 - 112.42: 9292 112.42 - 120.49: 12022 120.49 - 128.56: 8689 128.56 - 136.63: 238 Bond angle restraints: 30734 Sorted by residual: angle pdb=" N PRO K 32 " pdb=" CA PRO K 32 " pdb=" C PRO K 32 " ideal model delta sigma weight residual 111.03 98.97 12.06 1.54e+00 4.22e-01 6.14e+01 angle pdb=" CA TYR I 143 " pdb=" CB TYR I 143 " pdb=" CG TYR I 143 " ideal model delta sigma weight residual 113.90 127.03 -13.13 1.80e+00 3.09e-01 5.32e+01 angle pdb=" CA PHE F 54 " pdb=" CB PHE F 54 " pdb=" CG PHE F 54 " ideal model delta sigma weight residual 113.80 121.07 -7.27 1.00e+00 1.00e+00 5.29e+01 angle pdb=" N TRP L 340 " pdb=" CA TRP L 340 " pdb=" C TRP L 340 " ideal model delta sigma weight residual 111.28 103.57 7.71 1.09e+00 8.42e-01 5.00e+01 angle pdb=" CA PHE F 228 " pdb=" CB PHE F 228 " pdb=" CG PHE F 228 " ideal model delta sigma weight residual 113.80 120.74 -6.94 1.00e+00 1.00e+00 4.82e+01 ... (remaining 30729 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.78: 13363 34.78 - 69.57: 238 69.57 - 104.35: 31 104.35 - 139.13: 5 139.13 - 173.92: 4 Dihedral angle restraints: 13641 sinusoidal: 5538 harmonic: 8103 Sorted by residual: dihedral pdb=" C5' ADP N 401 " pdb=" O5' ADP N 401 " pdb=" PA ADP N 401 " pdb=" O2A ADP N 401 " ideal model delta sinusoidal sigma weight residual 300.00 126.09 173.92 1 2.00e+01 2.50e-03 4.79e+01 dihedral pdb=" C5' ADP J 401 " pdb=" O5' ADP J 401 " pdb=" PA ADP J 401 " pdb=" O2A ADP J 401 " ideal model delta sinusoidal sigma weight residual -60.00 113.39 -173.39 1 2.00e+01 2.50e-03 4.78e+01 dihedral pdb=" C5' ADP L 401 " pdb=" O5' ADP L 401 " pdb=" PA ADP L 401 " pdb=" O2A ADP L 401 " ideal model delta sinusoidal sigma weight residual -60.00 99.03 -159.02 1 2.00e+01 2.50e-03 4.64e+01 ... (remaining 13638 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.159: 2582 0.159 - 0.319: 535 0.319 - 0.478: 184 0.478 - 0.638: 91 0.638 - 0.797: 11 Chirality restraints: 3403 Sorted by residual: chirality pdb=" CA HYP T 1 " pdb=" N HYP T 1 " pdb=" C HYP T 1 " pdb=" CB HYP T 1 " both_signs ideal model delta sigma weight residual False 2.72 1.92 0.80 2.00e-01 2.50e+01 1.59e+01 chirality pdb=" CG LEU F 117 " pdb=" CB LEU F 117 " pdb=" CD1 LEU F 117 " pdb=" CD2 LEU F 117 " both_signs ideal model delta sigma weight residual False -2.59 -1.83 -0.76 2.00e-01 2.50e+01 1.43e+01 chirality pdb=" CA HYP R 1 " pdb=" N HYP R 1 " pdb=" C HYP R 1 " pdb=" CB HYP R 1 " both_signs ideal model delta sigma weight residual False 2.72 1.97 0.75 2.00e-01 2.50e+01 1.41e+01 ... (remaining 3400 not shown) Planarity restraints: 3923 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP F 271 " 0.152 2.00e-02 2.50e+03 7.47e-02 1.39e+02 pdb=" CG TRP F 271 " -0.039 2.00e-02 2.50e+03 pdb=" CD1 TRP F 271 " -0.061 2.00e-02 2.50e+03 pdb=" CD2 TRP F 271 " -0.058 2.00e-02 2.50e+03 pdb=" NE1 TRP F 271 " -0.033 2.00e-02 2.50e+03 pdb=" CE2 TRP F 271 " 0.003 2.00e-02 2.50e+03 pdb=" CE3 TRP F 271 " -0.084 2.00e-02 2.50e+03 pdb=" CZ2 TRP F 271 " 0.102 2.00e-02 2.50e+03 pdb=" CZ3 TRP F 271 " -0.041 2.00e-02 2.50e+03 pdb=" CH2 TRP F 271 " 0.060 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP J 340 " -0.125 2.00e-02 2.50e+03 6.06e-02 9.20e+01 pdb=" CG TRP J 340 " 0.048 2.00e-02 2.50e+03 pdb=" CD1 TRP J 340 " 0.025 2.00e-02 2.50e+03 pdb=" CD2 TRP J 340 " 0.055 2.00e-02 2.50e+03 pdb=" NE1 TRP J 340 " 0.027 2.00e-02 2.50e+03 pdb=" CE2 TRP J 340 " 0.002 2.00e-02 2.50e+03 pdb=" CE3 TRP J 340 " 0.077 2.00e-02 2.50e+03 pdb=" CZ2 TRP J 340 " -0.064 2.00e-02 2.50e+03 pdb=" CZ3 TRP J 340 " 0.019 2.00e-02 2.50e+03 pdb=" CH2 TRP J 340 " -0.064 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR O 240 " 0.111 2.00e-02 2.50e+03 5.62e-02 6.33e+01 pdb=" CG TYR O 240 " -0.071 2.00e-02 2.50e+03 pdb=" CD1 TYR O 240 " -0.037 2.00e-02 2.50e+03 pdb=" CD2 TYR O 240 " -0.048 2.00e-02 2.50e+03 pdb=" CE1 TYR O 240 " -0.017 2.00e-02 2.50e+03 pdb=" CE2 TYR O 240 " -0.007 2.00e-02 2.50e+03 pdb=" CZ TYR O 240 " 0.007 2.00e-02 2.50e+03 pdb=" OH TYR O 240 " 0.062 2.00e-02 2.50e+03 ... (remaining 3920 not shown) Histogram of nonbonded interaction distances: 1.82 - 2.44: 67 2.44 - 3.05: 13981 3.05 - 3.67: 33987 3.67 - 4.28: 51482 4.28 - 4.90: 83792 Nonbonded interactions: 183309 Sorted by model distance: nonbonded pdb=" CD1 TRP R 3 " pdb=" SG CYS R 7 " model vdw 1.820 3.620 nonbonded pdb=" CD1 TRP P 3 " pdb=" SG CYS P 7 " model vdw 1.820 3.620 nonbonded pdb=" CD1 TRP Q 3 " pdb=" SG CYS Q 7 " model vdw 1.824 3.620 nonbonded pdb=" CD1 TRP S 3 " pdb=" SG CYS S 7 " model vdw 1.825 3.620 nonbonded pdb=" CD1 TRP T 3 " pdb=" SG CYS T 7 " model vdw 1.826 3.620 ... (remaining 183304 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 'I' and resid 5 through 375) selection = (chain 'J' and resid 5 through 375) selection = (chain 'K' and resid 5 through 375) selection = (chain 'L' and resid 5 through 375) selection = (chain 'N' and resid 5 through 375) selection = (chain 'O' and resid 5 through 375) } ncs_group { reference = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'T' } 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: 4.700 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 12.830 Check model and map are aligned: 0.360 Set scattering table: 0.210 Process input model: 62.430 Find NCS groups from input model: 1.630 Set up NCS constraints: 0.170 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:2.680 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 85.030 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7575 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 : 0.023 0.212 22660 Z= 1.473 Angle : 1.958 13.131 30734 Z= 1.187 Chirality : 0.173 0.797 3403 Planarity : 0.013 0.127 3923 Dihedral : 15.056 173.918 8439 Min Nonbonded Distance : 1.820 Molprobity Statistics. All-atom Clashscore : 4.89 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.77 % Favored : 94.19 % Rotamer: Outliers : 0.21 % Allowed : 6.28 % Favored : 93.51 % Cbeta Deviations : 0.88 % Peptide Plane: Cis-proline : 1.50 % 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: -2.08 (0.14), residues: 2736 helix: -2.05 (0.12), residues: 1150 sheet: 0.08 (0.24), residues: 422 loop : -1.01 (0.18), residues: 1164 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.152 0.016 TRP F 271 HIS 0.027 0.004 HIS F 135 PHE 0.084 0.010 PHE L 31 TYR 0.111 0.016 TYR O 240 ARG 0.044 0.003 ARG J 196 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5472 Ramachandran restraints generated. 2736 Oldfield, 0 Emsley, 2736 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5472 Ramachandran restraints generated. 2736 Oldfield, 0 Emsley, 2736 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 618 residues out of total 2372 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 613 time to evaluate : 2.526 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 88 MET cc_start: 0.7817 (mmm) cc_final: 0.7412 (tpp) REVERT: E 94 ARG cc_start: 0.8090 (tpt170) cc_final: 0.7822 (tpt170) REVERT: E 110 LEU cc_start: 0.8124 (mt) cc_final: 0.7916 (mt) REVERT: E 187 MET cc_start: 0.8252 (mtp) cc_final: 0.7646 (mpp) REVERT: E 227 THR cc_start: 0.8242 (m) cc_final: 0.7408 (p) REVERT: F 197 HIS cc_start: 0.7446 (t-170) cc_final: 0.6293 (t70) REVERT: F 266 ARG cc_start: 0.7972 (mmt90) cc_final: 0.7438 (mtp180) REVERT: I 86 TRP cc_start: 0.8451 (m-10) cc_final: 0.8108 (m-10) REVERT: I 92 ASN cc_start: 0.8926 (m-40) cc_final: 0.8688 (m-40) REVERT: I 263 GLN cc_start: 0.8540 (mt0) cc_final: 0.7938 (mp10) REVERT: J 16 MET cc_start: 0.7460 (mtp) cc_final: 0.7233 (mtm) REVERT: J 292 ASP cc_start: 0.8309 (m-30) cc_final: 0.7683 (t0) REVERT: J 356 TRP cc_start: 0.6575 (m100) cc_final: 0.5997 (m-10) REVERT: K 203 THR cc_start: 0.8500 (p) cc_final: 0.8233 (t) REVERT: L 134 VAL cc_start: 0.9114 (t) cc_final: 0.8168 (t) REVERT: L 242 LEU cc_start: 0.8791 (mt) cc_final: 0.8241 (mt) REVERT: L 280 ASN cc_start: 0.8487 (m-40) cc_final: 0.8285 (m-40) REVERT: L 371 HIS cc_start: 0.6291 (m-70) cc_final: 0.5970 (m90) REVERT: N 65 LEU cc_start: 0.8238 (mt) cc_final: 0.8000 (mt) REVERT: N 141 SER cc_start: 0.8292 (m) cc_final: 0.8008 (t) REVERT: N 171 LEU cc_start: 0.8966 (mp) cc_final: 0.8650 (mm) REVERT: N 305 MET cc_start: 0.8636 (mmm) cc_final: 0.8350 (mmm) REVERT: O 119 MET cc_start: 0.9034 (mtm) cc_final: 0.8571 (mtp) outliers start: 5 outliers final: 4 residues processed: 618 average time/residue: 0.3750 time to fit residues: 341.7617 Evaluate side-chains 303 residues out of total 2372 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 299 time to evaluate : 2.483 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Q residue 7 CYS Chi-restraints excluded: chain S residue 7 CYS Chi-restraints excluded: chain T residue 7 CYS Chi-restraints excluded: chain P residue 7 CYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 276 random chunks: chunk 233 optimal weight: 0.9980 chunk 209 optimal weight: 0.8980 chunk 116 optimal weight: 0.9990 chunk 71 optimal weight: 1.9990 chunk 141 optimal weight: 0.9990 chunk 111 optimal weight: 0.8980 chunk 216 optimal weight: 0.9980 chunk 83 optimal weight: 7.9990 chunk 131 optimal weight: 6.9990 chunk 161 optimal weight: 0.5980 chunk 250 optimal weight: 0.7980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 20 GLN E 196 GLN E 209 HIS E 212 ASN E 270 GLN F 79 HIS ** F 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 203 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 41 GLN I 88 HIS ** I 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 87 HIS L 246 GLN ** L 360 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7669 moved from start: 0.3369 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 22660 Z= 0.243 Angle : 0.754 8.992 30734 Z= 0.385 Chirality : 0.048 0.231 3403 Planarity : 0.005 0.061 3923 Dihedral : 10.533 171.342 3179 Min Nonbonded Distance : 2.010 Molprobity Statistics. All-atom Clashscore : 10.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % Rotamer: Outliers : 2.49 % Allowed : 12.77 % Favored : 84.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.71 (0.15), residues: 2736 helix: -0.55 (0.14), residues: 1193 sheet: -0.07 (0.22), residues: 534 loop : -0.31 (0.19), residues: 1009 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.051 0.003 TRP F 271 HIS 0.008 0.001 HIS I 40 PHE 0.023 0.002 PHE N 31 TYR 0.023 0.002 TYR K 294 ARG 0.006 0.001 ARG E 225 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5472 Ramachandran restraints generated. 2736 Oldfield, 0 Emsley, 2736 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5472 Ramachandran restraints generated. 2736 Oldfield, 0 Emsley, 2736 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 356 residues out of total 2372 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 297 time to evaluate : 2.782 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 13 MET cc_start: 0.6811 (ppp) cc_final: 0.6434 (ppp) REVERT: E 186 THR cc_start: 0.8495 (OUTLIER) cc_final: 0.8042 (m) REVERT: E 193 LEU cc_start: 0.9086 (mt) cc_final: 0.8830 (tp) REVERT: E 212 ASN cc_start: 0.7779 (OUTLIER) cc_final: 0.7538 (m110) REVERT: I 16 MET cc_start: 0.5448 (mmm) cc_final: 0.5210 (mmm) REVERT: I 269 MET cc_start: 0.7100 (mmt) cc_final: 0.6613 (mpp) REVERT: J 292 ASP cc_start: 0.8195 (m-30) cc_final: 0.7756 (t0) REVERT: L 153 MET cc_start: 0.8146 (ttp) cc_final: 0.7825 (tmm) REVERT: L 227 MET cc_start: 0.8331 (ttm) cc_final: 0.8129 (ttm) REVERT: L 371 HIS cc_start: 0.6778 (m-70) cc_final: 0.6566 (m90) REVERT: N 65 LEU cc_start: 0.8147 (mt) cc_final: 0.7782 (mt) REVERT: N 141 SER cc_start: 0.8349 (m) cc_final: 0.7701 (t) REVERT: N 338 SER cc_start: 0.8535 (OUTLIER) cc_final: 0.8195 (m) REVERT: O 16 MET cc_start: 0.6565 (mmm) cc_final: 0.6294 (mmm) REVERT: O 47 MET cc_start: -0.4051 (mmt) cc_final: -0.5537 (ttm) REVERT: O 153 MET cc_start: 0.8109 (tmm) cc_final: 0.7880 (tmm) REVERT: O 313 MET cc_start: 0.8966 (mmm) cc_final: 0.8695 (tpt) outliers start: 59 outliers final: 29 residues processed: 341 average time/residue: 0.3337 time to fit residues: 174.9477 Evaluate side-chains 260 residues out of total 2372 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 228 time to evaluate : 2.349 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 186 THR Chi-restraints excluded: chain E residue 212 ASN Chi-restraints excluded: chain F residue 71 ASP Chi-restraints excluded: chain F residue 121 ARG Chi-restraints excluded: chain F residue 136 TYR Chi-restraints excluded: chain F residue 173 TRP Chi-restraints excluded: chain F residue 265 THR Chi-restraints excluded: chain I residue 49 GLN Chi-restraints excluded: chain I residue 88 HIS Chi-restraints excluded: chain I residue 145 SER Chi-restraints excluded: chain I residue 149 THR Chi-restraints excluded: chain I residue 193 LEU Chi-restraints excluded: chain I residue 326 LYS Chi-restraints excluded: chain J residue 77 THR Chi-restraints excluded: chain J residue 89 THR Chi-restraints excluded: chain J residue 189 LEU Chi-restraints excluded: chain K residue 248 ILE Chi-restraints excluded: chain K residue 324 THR Chi-restraints excluded: chain K residue 334 GLU Chi-restraints excluded: chain K residue 337 TYR Chi-restraints excluded: chain L residue 82 MET Chi-restraints excluded: chain N residue 8 LEU Chi-restraints excluded: chain N residue 201 THR Chi-restraints excluded: chain N residue 278 THR Chi-restraints excluded: chain N residue 294 TYR Chi-restraints excluded: chain N residue 338 SER Chi-restraints excluded: chain N residue 355 MET Chi-restraints excluded: chain O residue 56 ASP Chi-restraints excluded: chain O residue 81 ASP Chi-restraints excluded: chain O residue 89 THR Chi-restraints excluded: chain O residue 171 LEU Chi-restraints excluded: chain O residue 257 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 276 random chunks: chunk 139 optimal weight: 2.9990 chunk 77 optimal weight: 5.9990 chunk 208 optimal weight: 1.9990 chunk 170 optimal weight: 2.9990 chunk 69 optimal weight: 9.9990 chunk 251 optimal weight: 0.0670 chunk 271 optimal weight: 2.9990 chunk 223 optimal weight: 3.9990 chunk 248 optimal weight: 0.7980 chunk 85 optimal weight: 10.0000 chunk 201 optimal weight: 8.9990 overall best weight: 1.7724 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 212 ASN F 92 ASN ** F 203 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 92 ASN K 353 GLN ** L 360 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 173 HIS O 87 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7778 moved from start: 0.4097 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.095 22660 Z= 0.309 Angle : 0.699 9.306 30734 Z= 0.350 Chirality : 0.047 0.251 3403 Planarity : 0.005 0.083 3923 Dihedral : 9.641 146.724 3175 Min Nonbonded Distance : 1.837 Molprobity Statistics. All-atom Clashscore : 12.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.95 % Favored : 96.05 % Rotamer: Outliers : 2.49 % Allowed : 14.04 % Favored : 83.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.43 (0.16), residues: 2736 helix: -0.21 (0.15), residues: 1182 sheet: 0.02 (0.23), residues: 490 loop : -0.28 (0.19), residues: 1064 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.058 0.003 TRP F 271 HIS 0.023 0.001 HIS I 88 PHE 0.020 0.002 PHE O 352 TYR 0.019 0.002 TYR F 198 ARG 0.008 0.001 ARG I 290 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5472 Ramachandran restraints generated. 2736 Oldfield, 0 Emsley, 2736 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5472 Ramachandran restraints generated. 2736 Oldfield, 0 Emsley, 2736 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 292 residues out of total 2372 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 233 time to evaluate : 2.742 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 13 MET cc_start: 0.6480 (ppp) cc_final: 0.6189 (ppp) REVERT: E 186 THR cc_start: 0.8327 (OUTLIER) cc_final: 0.7807 (m) REVERT: E 193 LEU cc_start: 0.9128 (mt) cc_final: 0.8892 (tp) REVERT: E 197 MET cc_start: 0.8264 (tmm) cc_final: 0.8062 (tmm) REVERT: F 197 HIS cc_start: 0.6069 (t70) cc_final: 0.3914 (t70) REVERT: F 199 TYR cc_start: 0.8470 (p90) cc_final: 0.7959 (p90) REVERT: I 16 MET cc_start: 0.5337 (mmm) cc_final: 0.5098 (mmm) REVERT: I 269 MET cc_start: 0.7394 (mmt) cc_final: 0.6844 (mpp) REVERT: J 173 HIS cc_start: 0.7103 (OUTLIER) cc_final: 0.6457 (p-80) REVERT: J 292 ASP cc_start: 0.8247 (m-30) cc_final: 0.7813 (t0) REVERT: J 326 LYS cc_start: 0.8167 (mmmt) cc_final: 0.7946 (mmmt) REVERT: K 325 MET cc_start: 0.8658 (tpt) cc_final: 0.8360 (tpt) REVERT: L 153 MET cc_start: 0.8193 (ttp) cc_final: 0.7602 (tmm) REVERT: L 313 MET cc_start: 0.8913 (mmm) cc_final: 0.8400 (ttm) REVERT: L 355 MET cc_start: 0.8118 (mmt) cc_final: 0.7882 (mmt) REVERT: L 371 HIS cc_start: 0.6990 (m-70) cc_final: 0.6626 (m90) REVERT: N 65 LEU cc_start: 0.8273 (mt) cc_final: 0.7910 (mt) REVERT: N 227 MET cc_start: 0.8688 (tpt) cc_final: 0.8417 (tpt) REVERT: O 16 MET cc_start: 0.6894 (mmm) cc_final: 0.6551 (mmm) REVERT: O 132 MET cc_start: 0.8020 (ttp) cc_final: 0.7776 (ttp) REVERT: O 153 MET cc_start: 0.8464 (tmm) cc_final: 0.8135 (tmm) REVERT: O 227 MET cc_start: 0.8723 (mmm) cc_final: 0.8299 (mmm) outliers start: 59 outliers final: 34 residues processed: 280 average time/residue: 0.3397 time to fit residues: 148.9454 Evaluate side-chains 240 residues out of total 2372 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 204 time to evaluate : 2.535 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 186 THR Chi-restraints excluded: chain F residue 136 TYR Chi-restraints excluded: chain F residue 173 TRP Chi-restraints excluded: chain F residue 265 THR Chi-restraints excluded: chain I residue 49 GLN Chi-restraints excluded: chain I residue 151 ILE Chi-restraints excluded: chain I residue 152 VAL Chi-restraints excluded: chain I residue 162 THR Chi-restraints excluded: chain I residue 193 LEU Chi-restraints excluded: chain I residue 326 LYS Chi-restraints excluded: chain J residue 77 THR Chi-restraints excluded: chain J residue 173 HIS Chi-restraints excluded: chain J residue 189 LEU Chi-restraints excluded: chain K residue 54 VAL Chi-restraints excluded: chain K residue 324 THR Chi-restraints excluded: chain K residue 334 GLU Chi-restraints excluded: chain K residue 337 TYR Chi-restraints excluded: chain L residue 60 SER Chi-restraints excluded: chain L residue 82 MET Chi-restraints excluded: chain L residue 134 VAL Chi-restraints excluded: chain L residue 201 THR Chi-restraints excluded: chain L residue 227 MET Chi-restraints excluded: chain L residue 361 GLU Chi-restraints excluded: chain N residue 8 LEU Chi-restraints excluded: chain N residue 201 THR Chi-restraints excluded: chain N residue 221 LEU Chi-restraints excluded: chain N residue 294 TYR Chi-restraints excluded: chain N residue 338 SER Chi-restraints excluded: chain O residue 56 ASP Chi-restraints excluded: chain O residue 81 ASP Chi-restraints excluded: chain O residue 85 ILE Chi-restraints excluded: chain O residue 89 THR Chi-restraints excluded: chain O residue 159 VAL Chi-restraints excluded: chain O residue 203 THR Chi-restraints excluded: chain O residue 257 CYS Chi-restraints excluded: chain T residue 7 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 276 random chunks: chunk 248 optimal weight: 5.9990 chunk 188 optimal weight: 3.9990 chunk 130 optimal weight: 0.0970 chunk 27 optimal weight: 5.9990 chunk 119 optimal weight: 0.7980 chunk 168 optimal weight: 0.5980 chunk 251 optimal weight: 0.7980 chunk 266 optimal weight: 0.5980 chunk 131 optimal weight: 3.9990 chunk 238 optimal weight: 0.0570 chunk 71 optimal weight: 6.9990 overall best weight: 0.4296 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 152 HIS ** E 212 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 203 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 223 GLN I 88 HIS K 137 GLN L 360 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7724 moved from start: 0.4463 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 22660 Z= 0.162 Angle : 0.618 8.100 30734 Z= 0.305 Chirality : 0.044 0.220 3403 Planarity : 0.004 0.063 3923 Dihedral : 8.770 133.474 3175 Min Nonbonded Distance : 1.980 Molprobity Statistics. All-atom Clashscore : 11.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 1.94 % Allowed : 14.76 % Favored : 83.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.08 (0.16), residues: 2736 helix: 0.03 (0.15), residues: 1171 sheet: 0.19 (0.22), residues: 540 loop : -0.02 (0.19), residues: 1025 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.045 0.002 TRP F 169 HIS 0.006 0.001 HIS O 161 PHE 0.019 0.001 PHE L 352 TYR 0.015 0.001 TYR F 198 ARG 0.005 0.000 ARG E 225 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5472 Ramachandran restraints generated. 2736 Oldfield, 0 Emsley, 2736 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5472 Ramachandran restraints generated. 2736 Oldfield, 0 Emsley, 2736 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 293 residues out of total 2372 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 247 time to evaluate : 2.580 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 13 MET cc_start: 0.6567 (ppp) cc_final: 0.6317 (ppp) REVERT: F 173 TRP cc_start: 0.7726 (OUTLIER) cc_final: 0.7520 (t60) REVERT: I 47 MET cc_start: 0.5628 (tmm) cc_final: 0.5185 (tmm) REVERT: I 92 ASN cc_start: 0.9015 (m110) cc_final: 0.8742 (m-40) REVERT: I 227 MET cc_start: 0.8131 (OUTLIER) cc_final: 0.7861 (tpt) REVERT: J 111 ASN cc_start: 0.7798 (m110) cc_final: 0.7586 (m-40) REVERT: J 292 ASP cc_start: 0.8222 (m-30) cc_final: 0.7752 (t0) REVERT: L 153 MET cc_start: 0.8245 (ttp) cc_final: 0.7707 (tmm) REVERT: L 313 MET cc_start: 0.8748 (mmm) cc_final: 0.8505 (ttm) REVERT: N 65 LEU cc_start: 0.8182 (mt) cc_final: 0.7903 (mt) REVERT: N 141 SER cc_start: 0.8371 (m) cc_final: 0.7992 (t) REVERT: N 227 MET cc_start: 0.8667 (tpt) cc_final: 0.8388 (tpt) REVERT: O 16 MET cc_start: 0.6813 (mmm) cc_final: 0.6498 (mmm) REVERT: O 44 MET cc_start: 0.2888 (ptt) cc_final: 0.2652 (ptt) REVERT: O 227 MET cc_start: 0.8719 (mmm) cc_final: 0.8332 (mmm) outliers start: 46 outliers final: 23 residues processed: 278 average time/residue: 0.3339 time to fit residues: 145.9992 Evaluate side-chains 236 residues out of total 2372 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 211 time to evaluate : 2.364 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 186 THR Chi-restraints excluded: chain F residue 136 TYR Chi-restraints excluded: chain F residue 173 TRP Chi-restraints excluded: chain F residue 265 THR Chi-restraints excluded: chain I residue 49 GLN Chi-restraints excluded: chain I residue 149 THR Chi-restraints excluded: chain I residue 151 ILE Chi-restraints excluded: chain I residue 152 VAL Chi-restraints excluded: chain I residue 153 MET Chi-restraints excluded: chain I residue 162 THR Chi-restraints excluded: chain I residue 227 MET Chi-restraints excluded: chain J residue 77 THR Chi-restraints excluded: chain J residue 189 LEU Chi-restraints excluded: chain K residue 143 TYR Chi-restraints excluded: chain K residue 334 GLU Chi-restraints excluded: chain K residue 337 TYR Chi-restraints excluded: chain L residue 142 LEU Chi-restraints excluded: chain L residue 227 MET Chi-restraints excluded: chain L residue 361 GLU Chi-restraints excluded: chain N residue 201 THR Chi-restraints excluded: chain N residue 221 LEU Chi-restraints excluded: chain N residue 294 TYR Chi-restraints excluded: chain O residue 159 VAL Chi-restraints excluded: chain O residue 203 THR Chi-restraints excluded: chain T residue 7 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 276 random chunks: chunk 222 optimal weight: 0.8980 chunk 151 optimal weight: 0.7980 chunk 3 optimal weight: 7.9990 chunk 198 optimal weight: 0.9990 chunk 110 optimal weight: 5.9990 chunk 227 optimal weight: 3.9990 chunk 184 optimal weight: 3.9990 chunk 0 optimal weight: 50.0000 chunk 136 optimal weight: 3.9990 chunk 239 optimal weight: 0.0980 chunk 67 optimal weight: 7.9990 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 212 ASN F 223 GLN ** L 371 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7790 moved from start: 0.4799 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 22660 Z= 0.243 Angle : 0.653 8.016 30734 Z= 0.320 Chirality : 0.045 0.222 3403 Planarity : 0.004 0.047 3923 Dihedral : 8.126 129.792 3175 Min Nonbonded Distance : 1.876 Molprobity Statistics. All-atom Clashscore : 13.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.80 % Favored : 96.20 % Rotamer: Outliers : 2.23 % Allowed : 16.65 % Favored : 81.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.03 (0.16), residues: 2736 helix: 0.13 (0.15), residues: 1144 sheet: 0.11 (0.22), residues: 540 loop : -0.01 (0.19), residues: 1052 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.052 0.002 TRP I 356 HIS 0.006 0.001 HIS K 161 PHE 0.017 0.001 PHE J 223 TYR 0.020 0.002 TYR F 198 ARG 0.005 0.000 ARG E 225 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5472 Ramachandran restraints generated. 2736 Oldfield, 0 Emsley, 2736 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5472 Ramachandran restraints generated. 2736 Oldfield, 0 Emsley, 2736 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 268 residues out of total 2372 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 215 time to evaluate : 2.781 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 13 MET cc_start: 0.6705 (ppp) cc_final: 0.6494 (ppp) REVERT: E 122 TRP cc_start: 0.6963 (p90) cc_final: 0.6672 (p90) REVERT: F 199 TYR cc_start: 0.8479 (p90) cc_final: 0.7968 (p90) REVERT: I 16 MET cc_start: 0.4827 (mmm) cc_final: 0.4627 (mmm) REVERT: J 173 HIS cc_start: 0.7013 (OUTLIER) cc_final: 0.6168 (p-80) REVERT: J 292 ASP cc_start: 0.8183 (m-30) cc_final: 0.7804 (t0) REVERT: J 355 MET cc_start: 0.8089 (mmt) cc_final: 0.7782 (mmm) REVERT: K 184 ASP cc_start: 0.8308 (OUTLIER) cc_final: 0.8026 (t70) REVERT: K 221 LEU cc_start: 0.9065 (tt) cc_final: 0.8827 (tp) REVERT: K 325 MET cc_start: 0.8436 (tpt) cc_final: 0.8204 (tmm) REVERT: L 153 MET cc_start: 0.8352 (ttp) cc_final: 0.7821 (tmm) REVERT: L 313 MET cc_start: 0.8793 (mmm) cc_final: 0.8514 (ttm) REVERT: O 16 MET cc_start: 0.7151 (mmm) cc_final: 0.6824 (mmm) outliers start: 53 outliers final: 40 residues processed: 252 average time/residue: 0.3409 time to fit residues: 135.3116 Evaluate side-chains 246 residues out of total 2372 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 204 time to evaluate : 2.592 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 6 LEU Chi-restraints excluded: chain E residue 10 LEU Chi-restraints excluded: chain E residue 186 THR Chi-restraints excluded: chain E residue 228 LEU Chi-restraints excluded: chain F residue 121 ARG Chi-restraints excluded: chain F residue 136 TYR Chi-restraints excluded: chain F residue 173 TRP Chi-restraints excluded: chain F residue 220 ASN Chi-restraints excluded: chain F residue 265 THR Chi-restraints excluded: chain I residue 49 GLN Chi-restraints excluded: chain I residue 149 THR Chi-restraints excluded: chain I residue 151 ILE Chi-restraints excluded: chain I residue 152 VAL Chi-restraints excluded: chain I residue 153 MET Chi-restraints excluded: chain I residue 227 MET Chi-restraints excluded: chain J residue 77 THR Chi-restraints excluded: chain J residue 173 HIS Chi-restraints excluded: chain J residue 189 LEU Chi-restraints excluded: chain K residue 54 VAL Chi-restraints excluded: chain K residue 115 ASN Chi-restraints excluded: chain K residue 184 ASP Chi-restraints excluded: chain K residue 334 GLU Chi-restraints excluded: chain K residue 337 TYR Chi-restraints excluded: chain L residue 16 MET Chi-restraints excluded: chain L residue 60 SER Chi-restraints excluded: chain L residue 134 VAL Chi-restraints excluded: chain L residue 227 MET Chi-restraints excluded: chain L residue 371 HIS Chi-restraints excluded: chain N residue 8 LEU Chi-restraints excluded: chain N residue 201 THR Chi-restraints excluded: chain N residue 221 LEU Chi-restraints excluded: chain N residue 282 ILE Chi-restraints excluded: chain N residue 294 TYR Chi-restraints excluded: chain O residue 81 ASP Chi-restraints excluded: chain O residue 85 ILE Chi-restraints excluded: chain O residue 89 THR Chi-restraints excluded: chain O residue 132 MET Chi-restraints excluded: chain O residue 159 VAL Chi-restraints excluded: chain O residue 203 THR Chi-restraints excluded: chain O residue 257 CYS Chi-restraints excluded: chain O residue 293 LEU Chi-restraints excluded: chain T residue 7 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 276 random chunks: chunk 89 optimal weight: 0.0040 chunk 240 optimal weight: 4.9990 chunk 52 optimal weight: 0.9980 chunk 156 optimal weight: 0.9990 chunk 65 optimal weight: 0.7980 chunk 267 optimal weight: 2.9990 chunk 221 optimal weight: 0.6980 chunk 123 optimal weight: 0.9980 chunk 22 optimal weight: 2.9990 chunk 88 optimal weight: 0.9980 chunk 140 optimal weight: 3.9990 overall best weight: 0.6992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 223 GLN I 92 ASN J 41 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7763 moved from start: 0.5027 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 22660 Z= 0.172 Angle : 0.618 8.737 30734 Z= 0.300 Chirality : 0.044 0.184 3403 Planarity : 0.004 0.045 3923 Dihedral : 7.717 130.114 3175 Min Nonbonded Distance : 1.925 Molprobity Statistics. All-atom Clashscore : 12.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer: Outliers : 1.94 % Allowed : 16.95 % Favored : 81.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.25 (0.16), residues: 2736 helix: 0.45 (0.16), residues: 1104 sheet: 0.15 (0.22), residues: 540 loop : 0.10 (0.19), residues: 1092 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.071 0.002 TRP F 271 HIS 0.008 0.001 HIS I 275 PHE 0.013 0.001 PHE F 29 TYR 0.018 0.001 TYR F 198 ARG 0.006 0.000 ARG F 174 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5472 Ramachandran restraints generated. 2736 Oldfield, 0 Emsley, 2736 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5472 Ramachandran restraints generated. 2736 Oldfield, 0 Emsley, 2736 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 269 residues out of total 2372 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 223 time to evaluate : 2.785 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 199 TYR cc_start: 0.8441 (p90) cc_final: 0.7918 (p90) REVERT: J 72 GLU cc_start: 0.7901 (mm-30) cc_final: 0.7670 (mm-30) REVERT: J 227 MET cc_start: 0.9208 (tpp) cc_final: 0.8869 (mpp) REVERT: J 292 ASP cc_start: 0.8224 (m-30) cc_final: 0.7786 (t0) REVERT: J 355 MET cc_start: 0.8083 (mmt) cc_final: 0.7814 (mmm) REVERT: J 356 TRP cc_start: 0.7214 (m100) cc_final: 0.6315 (m-10) REVERT: K 16 MET cc_start: 0.7972 (mmt) cc_final: 0.7611 (mmm) REVERT: L 153 MET cc_start: 0.8334 (ttp) cc_final: 0.7766 (tmm) REVERT: L 294 TYR cc_start: 0.8464 (OUTLIER) cc_final: 0.7967 (m-10) REVERT: L 313 MET cc_start: 0.8728 (mmm) cc_final: 0.8432 (ttm) REVERT: N 141 SER cc_start: 0.8409 (m) cc_final: 0.8055 (t) REVERT: O 16 MET cc_start: 0.7098 (mmm) cc_final: 0.6764 (mmm) REVERT: O 227 MET cc_start: 0.8812 (mmm) cc_final: 0.8586 (mmm) outliers start: 46 outliers final: 37 residues processed: 253 average time/residue: 0.3507 time to fit residues: 141.6194 Evaluate side-chains 245 residues out of total 2372 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 207 time to evaluate : 2.738 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 6 LEU Chi-restraints excluded: chain E residue 186 THR Chi-restraints excluded: chain E residue 228 LEU Chi-restraints excluded: chain F residue 121 ARG Chi-restraints excluded: chain F residue 136 TYR Chi-restraints excluded: chain F residue 173 TRP Chi-restraints excluded: chain F residue 265 THR Chi-restraints excluded: chain I residue 49 GLN Chi-restraints excluded: chain I residue 145 SER Chi-restraints excluded: chain I residue 149 THR Chi-restraints excluded: chain I residue 151 ILE Chi-restraints excluded: chain I residue 152 VAL Chi-restraints excluded: chain I residue 153 MET Chi-restraints excluded: chain J residue 77 THR Chi-restraints excluded: chain J residue 153 MET Chi-restraints excluded: chain J residue 189 LEU Chi-restraints excluded: chain K residue 115 ASN Chi-restraints excluded: chain K residue 143 TYR Chi-restraints excluded: chain K residue 334 GLU Chi-restraints excluded: chain K residue 337 TYR Chi-restraints excluded: chain L residue 16 MET Chi-restraints excluded: chain L residue 60 SER Chi-restraints excluded: chain L residue 85 ILE Chi-restraints excluded: chain L residue 134 VAL Chi-restraints excluded: chain L residue 227 MET Chi-restraints excluded: chain L residue 294 TYR Chi-restraints excluded: chain L residue 371 HIS Chi-restraints excluded: chain N residue 106 THR Chi-restraints excluded: chain N residue 201 THR Chi-restraints excluded: chain N residue 221 LEU Chi-restraints excluded: chain N residue 294 TYR Chi-restraints excluded: chain O residue 81 ASP Chi-restraints excluded: chain O residue 129 THR Chi-restraints excluded: chain O residue 132 MET Chi-restraints excluded: chain O residue 159 VAL Chi-restraints excluded: chain O residue 203 THR Chi-restraints excluded: chain O residue 257 CYS Chi-restraints excluded: chain T residue 7 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 276 random chunks: chunk 257 optimal weight: 1.9990 chunk 30 optimal weight: 10.0000 chunk 152 optimal weight: 0.7980 chunk 195 optimal weight: 0.0470 chunk 151 optimal weight: 2.9990 chunk 224 optimal weight: 0.9990 chunk 149 optimal weight: 4.9990 chunk 266 optimal weight: 0.9990 chunk 166 optimal weight: 7.9990 chunk 162 optimal weight: 5.9990 chunk 122 optimal weight: 6.9990 overall best weight: 0.9684 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 109 GLN F 223 GLN I 92 ASN J 41 GLN N 280 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7784 moved from start: 0.5231 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 22660 Z= 0.202 Angle : 0.631 10.928 30734 Z= 0.305 Chirality : 0.044 0.180 3403 Planarity : 0.004 0.045 3923 Dihedral : 7.408 127.487 3175 Min Nonbonded Distance : 1.921 Molprobity Statistics. All-atom Clashscore : 12.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.58 % Favored : 96.42 % Rotamer: Outliers : 2.11 % Allowed : 17.50 % Favored : 80.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.25 (0.16), residues: 2736 helix: 0.43 (0.16), residues: 1134 sheet: 0.14 (0.22), residues: 539 loop : 0.12 (0.19), residues: 1063 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.070 0.002 TRP F 169 HIS 0.005 0.001 HIS K 161 PHE 0.014 0.001 PHE J 223 TYR 0.017 0.001 TYR F 198 ARG 0.005 0.000 ARG L 95 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5472 Ramachandran restraints generated. 2736 Oldfield, 0 Emsley, 2736 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5472 Ramachandran restraints generated. 2736 Oldfield, 0 Emsley, 2736 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 258 residues out of total 2372 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 208 time to evaluate : 2.582 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 199 TYR cc_start: 0.8487 (p90) cc_final: 0.7959 (p90) REVERT: J 292 ASP cc_start: 0.8219 (m-30) cc_final: 0.7745 (t0) REVERT: K 16 MET cc_start: 0.8126 (mmt) cc_final: 0.7808 (mmm) REVERT: L 44 MET cc_start: 0.7768 (mtp) cc_final: 0.7467 (mtp) REVERT: L 153 MET cc_start: 0.8371 (ttp) cc_final: 0.7972 (tmm) REVERT: L 205 GLU cc_start: 0.7231 (mt-10) cc_final: 0.6869 (mp0) REVERT: L 313 MET cc_start: 0.8680 (mmm) cc_final: 0.8289 (ttt) REVERT: O 16 MET cc_start: 0.7180 (mmm) cc_final: 0.6841 (mmm) REVERT: O 44 MET cc_start: 0.1588 (ptt) cc_final: 0.1298 (ptt) REVERT: O 227 MET cc_start: 0.8841 (mmm) cc_final: 0.8588 (mmm) outliers start: 50 outliers final: 41 residues processed: 242 average time/residue: 0.3301 time to fit residues: 126.7009 Evaluate side-chains 244 residues out of total 2372 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 203 time to evaluate : 2.657 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 6 LEU Chi-restraints excluded: chain E residue 10 LEU Chi-restraints excluded: chain E residue 88 MET Chi-restraints excluded: chain E residue 152 HIS Chi-restraints excluded: chain E residue 186 THR Chi-restraints excluded: chain E residue 228 LEU Chi-restraints excluded: chain F residue 121 ARG Chi-restraints excluded: chain F residue 136 TYR Chi-restraints excluded: chain F residue 173 TRP Chi-restraints excluded: chain F residue 265 THR Chi-restraints excluded: chain I residue 49 GLN Chi-restraints excluded: chain I residue 145 SER Chi-restraints excluded: chain I residue 149 THR Chi-restraints excluded: chain I residue 151 ILE Chi-restraints excluded: chain I residue 152 VAL Chi-restraints excluded: chain I residue 153 MET Chi-restraints excluded: chain J residue 77 THR Chi-restraints excluded: chain J residue 189 LEU Chi-restraints excluded: chain K residue 54 VAL Chi-restraints excluded: chain K residue 115 ASN Chi-restraints excluded: chain K residue 143 TYR Chi-restraints excluded: chain K residue 334 GLU Chi-restraints excluded: chain K residue 337 TYR Chi-restraints excluded: chain L residue 16 MET Chi-restraints excluded: chain L residue 60 SER Chi-restraints excluded: chain L residue 85 ILE Chi-restraints excluded: chain L residue 134 VAL Chi-restraints excluded: chain L residue 227 MET Chi-restraints excluded: chain L residue 371 HIS Chi-restraints excluded: chain N residue 106 THR Chi-restraints excluded: chain N residue 201 THR Chi-restraints excluded: chain N residue 221 LEU Chi-restraints excluded: chain N residue 294 TYR Chi-restraints excluded: chain O residue 81 ASP Chi-restraints excluded: chain O residue 85 ILE Chi-restraints excluded: chain O residue 129 THR Chi-restraints excluded: chain O residue 132 MET Chi-restraints excluded: chain O residue 159 VAL Chi-restraints excluded: chain O residue 203 THR Chi-restraints excluded: chain O residue 257 CYS Chi-restraints excluded: chain T residue 7 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 276 random chunks: chunk 164 optimal weight: 5.9990 chunk 106 optimal weight: 3.9990 chunk 158 optimal weight: 0.1980 chunk 80 optimal weight: 7.9990 chunk 52 optimal weight: 6.9990 chunk 51 optimal weight: 4.9990 chunk 169 optimal weight: 0.0170 chunk 181 optimal weight: 1.9990 chunk 131 optimal weight: 4.9990 chunk 24 optimal weight: 9.9990 chunk 209 optimal weight: 5.9990 overall best weight: 2.2424 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 157 GLN F 223 GLN K 137 GLN L 115 ASN L 360 GLN N 280 ASN O 128 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7867 moved from start: 0.5504 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 22660 Z= 0.353 Angle : 0.716 11.690 30734 Z= 0.347 Chirality : 0.047 0.195 3403 Planarity : 0.005 0.046 3923 Dihedral : 7.579 130.000 3175 Min Nonbonded Distance : 1.826 Molprobity Statistics. All-atom Clashscore : 15.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.35 % Favored : 95.65 % Rotamer: Outliers : 2.49 % Allowed : 17.58 % Favored : 79.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.08 (0.16), residues: 2736 helix: 0.27 (0.15), residues: 1134 sheet: -0.21 (0.21), residues: 596 loop : -0.07 (0.20), residues: 1006 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.046 0.002 TRP F 271 HIS 0.010 0.001 HIS K 161 PHE 0.015 0.002 PHE J 223 TYR 0.022 0.002 TYR O 294 ARG 0.004 0.001 ARG L 95 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5472 Ramachandran restraints generated. 2736 Oldfield, 0 Emsley, 2736 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5472 Ramachandran restraints generated. 2736 Oldfield, 0 Emsley, 2736 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 260 residues out of total 2372 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 201 time to evaluate : 2.629 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 199 TYR cc_start: 0.8421 (p90) cc_final: 0.7900 (p90) REVERT: I 283 MET cc_start: 0.9047 (mmp) cc_final: 0.8790 (mmp) REVERT: J 47 MET cc_start: 0.7321 (ptt) cc_final: 0.6317 (ptt) REVERT: J 173 HIS cc_start: 0.7021 (OUTLIER) cc_final: 0.6210 (p-80) REVERT: J 292 ASP cc_start: 0.8245 (m-30) cc_final: 0.7854 (t0) REVERT: J 355 MET cc_start: 0.8103 (mmm) cc_final: 0.7732 (mmt) REVERT: K 16 MET cc_start: 0.8385 (mmt) cc_final: 0.7958 (mmm) REVERT: K 56 ASP cc_start: 0.8587 (OUTLIER) cc_final: 0.8381 (t0) REVERT: L 44 MET cc_start: 0.7797 (mtp) cc_final: 0.7535 (mtp) REVERT: L 153 MET cc_start: 0.8488 (ttp) cc_final: 0.8197 (tmm) REVERT: L 205 GLU cc_start: 0.7374 (OUTLIER) cc_final: 0.7075 (mp0) REVERT: L 294 TYR cc_start: 0.8504 (OUTLIER) cc_final: 0.7998 (m-80) REVERT: L 313 MET cc_start: 0.8730 (mmm) cc_final: 0.8416 (ttm) REVERT: N 227 MET cc_start: 0.8772 (mmm) cc_final: 0.8479 (tpt) REVERT: O 227 MET cc_start: 0.9041 (mmm) cc_final: 0.8799 (mmm) outliers start: 59 outliers final: 42 residues processed: 243 average time/residue: 0.3297 time to fit residues: 127.3383 Evaluate side-chains 237 residues out of total 2372 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 191 time to evaluate : 2.621 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 6 LEU Chi-restraints excluded: chain E residue 10 LEU Chi-restraints excluded: chain E residue 88 MET Chi-restraints excluded: chain E residue 154 VAL Chi-restraints excluded: chain E residue 186 THR Chi-restraints excluded: chain F residue 121 ARG Chi-restraints excluded: chain F residue 173 TRP Chi-restraints excluded: chain F residue 265 THR Chi-restraints excluded: chain I residue 49 GLN Chi-restraints excluded: chain I residue 115 ASN Chi-restraints excluded: chain I residue 145 SER Chi-restraints excluded: chain I residue 149 THR Chi-restraints excluded: chain I residue 151 ILE Chi-restraints excluded: chain I residue 152 VAL Chi-restraints excluded: chain I residue 153 MET Chi-restraints excluded: chain I residue 227 MET Chi-restraints excluded: chain J residue 77 THR Chi-restraints excluded: chain J residue 173 HIS Chi-restraints excluded: chain J residue 189 LEU Chi-restraints excluded: chain K residue 54 VAL Chi-restraints excluded: chain K residue 56 ASP Chi-restraints excluded: chain K residue 115 ASN Chi-restraints excluded: chain K residue 334 GLU Chi-restraints excluded: chain L residue 16 MET Chi-restraints excluded: chain L residue 60 SER Chi-restraints excluded: chain L residue 85 ILE Chi-restraints excluded: chain L residue 134 VAL Chi-restraints excluded: chain L residue 205 GLU Chi-restraints excluded: chain L residue 227 MET Chi-restraints excluded: chain L residue 294 TYR Chi-restraints excluded: chain L residue 371 HIS Chi-restraints excluded: chain N residue 106 THR Chi-restraints excluded: chain N residue 201 THR Chi-restraints excluded: chain N residue 221 LEU Chi-restraints excluded: chain N residue 294 TYR Chi-restraints excluded: chain N residue 329 ILE Chi-restraints excluded: chain N residue 338 SER Chi-restraints excluded: chain O residue 81 ASP Chi-restraints excluded: chain O residue 85 ILE Chi-restraints excluded: chain O residue 129 THR Chi-restraints excluded: chain O residue 132 MET Chi-restraints excluded: chain O residue 159 VAL Chi-restraints excluded: chain O residue 203 THR Chi-restraints excluded: chain O residue 257 CYS Chi-restraints excluded: chain O residue 293 LEU Chi-restraints excluded: chain T residue 7 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 276 random chunks: chunk 241 optimal weight: 0.9990 chunk 254 optimal weight: 0.9990 chunk 232 optimal weight: 0.9980 chunk 247 optimal weight: 0.9990 chunk 149 optimal weight: 0.6980 chunk 107 optimal weight: 0.7980 chunk 194 optimal weight: 0.6980 chunk 76 optimal weight: 5.9990 chunk 224 optimal weight: 1.9990 chunk 234 optimal weight: 0.2980 chunk 162 optimal weight: 0.7980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 223 GLN K 137 GLN L 115 ASN ** L 354 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 360 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 280 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7798 moved from start: 0.5628 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 22660 Z= 0.181 Angle : 0.653 12.626 30734 Z= 0.313 Chirality : 0.044 0.175 3403 Planarity : 0.004 0.046 3923 Dihedral : 7.329 135.991 3175 Min Nonbonded Distance : 1.958 Molprobity Statistics. All-atom Clashscore : 13.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % Rotamer: Outliers : 1.81 % Allowed : 18.04 % Favored : 80.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.12 (0.16), residues: 2736 helix: 0.41 (0.16), residues: 1147 sheet: -0.04 (0.21), residues: 584 loop : 0.01 (0.20), residues: 1005 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.002 TRP F 271 HIS 0.004 0.001 HIS K 161 PHE 0.014 0.001 PHE J 223 TYR 0.017 0.001 TYR F 277 ARG 0.006 0.000 ARG L 95 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5472 Ramachandran restraints generated. 2736 Oldfield, 0 Emsley, 2736 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5472 Ramachandran restraints generated. 2736 Oldfield, 0 Emsley, 2736 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 249 residues out of total 2372 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 206 time to evaluate : 2.514 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 13 MET cc_start: 0.6634 (ppp) cc_final: 0.5683 (ppp) REVERT: F 199 TYR cc_start: 0.8424 (p90) cc_final: 0.8021 (p90) REVERT: I 283 MET cc_start: 0.8986 (mmp) cc_final: 0.8729 (mmp) REVERT: J 153 MET cc_start: 0.8196 (OUTLIER) cc_final: 0.7905 (tpp) REVERT: J 292 ASP cc_start: 0.8218 (m-30) cc_final: 0.7811 (t0) REVERT: J 355 MET cc_start: 0.7928 (mmm) cc_final: 0.7722 (mmm) REVERT: K 16 MET cc_start: 0.8166 (mmt) cc_final: 0.7715 (mmm) REVERT: L 44 MET cc_start: 0.7761 (mtp) cc_final: 0.7558 (mtp) REVERT: L 205 GLU cc_start: 0.7360 (OUTLIER) cc_final: 0.7007 (mp0) REVERT: L 313 MET cc_start: 0.8645 (mmm) cc_final: 0.8260 (ttt) REVERT: N 123 MET cc_start: 0.9021 (mmm) cc_final: 0.8481 (tpp) REVERT: N 141 SER cc_start: 0.8430 (m) cc_final: 0.8084 (t) REVERT: O 44 MET cc_start: 0.1511 (ptt) cc_final: 0.1196 (ptt) REVERT: O 227 MET cc_start: 0.8962 (mmm) cc_final: 0.8752 (mmm) outliers start: 43 outliers final: 36 residues processed: 234 average time/residue: 0.3159 time to fit residues: 118.3623 Evaluate side-chains 231 residues out of total 2372 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 193 time to evaluate : 2.520 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 6 LEU Chi-restraints excluded: chain E residue 10 LEU Chi-restraints excluded: chain E residue 88 MET Chi-restraints excluded: chain E residue 133 LEU Chi-restraints excluded: chain E residue 186 THR Chi-restraints excluded: chain F residue 121 ARG Chi-restraints excluded: chain F residue 173 TRP Chi-restraints excluded: chain F residue 265 THR Chi-restraints excluded: chain I residue 149 THR Chi-restraints excluded: chain I residue 151 ILE Chi-restraints excluded: chain I residue 152 VAL Chi-restraints excluded: chain I residue 153 MET Chi-restraints excluded: chain I residue 227 MET Chi-restraints excluded: chain J residue 77 THR Chi-restraints excluded: chain J residue 153 MET Chi-restraints excluded: chain J residue 189 LEU Chi-restraints excluded: chain K residue 54 VAL Chi-restraints excluded: chain K residue 115 ASN Chi-restraints excluded: chain K residue 334 GLU Chi-restraints excluded: chain L residue 60 SER Chi-restraints excluded: chain L residue 85 ILE Chi-restraints excluded: chain L residue 115 ASN Chi-restraints excluded: chain L residue 134 VAL Chi-restraints excluded: chain L residue 205 GLU Chi-restraints excluded: chain L residue 227 MET Chi-restraints excluded: chain L residue 371 HIS Chi-restraints excluded: chain N residue 106 THR Chi-restraints excluded: chain N residue 201 THR Chi-restraints excluded: chain N residue 221 LEU Chi-restraints excluded: chain N residue 294 TYR Chi-restraints excluded: chain O residue 81 ASP Chi-restraints excluded: chain O residue 85 ILE Chi-restraints excluded: chain O residue 129 THR Chi-restraints excluded: chain O residue 132 MET Chi-restraints excluded: chain O residue 159 VAL Chi-restraints excluded: chain O residue 203 THR Chi-restraints excluded: chain O residue 293 LEU Chi-restraints excluded: chain T residue 7 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 276 random chunks: chunk 262 optimal weight: 0.7980 chunk 159 optimal weight: 0.7980 chunk 124 optimal weight: 0.0980 chunk 182 optimal weight: 4.9990 chunk 274 optimal weight: 0.9990 chunk 253 optimal weight: 0.5980 chunk 218 optimal weight: 0.0000 chunk 22 optimal weight: 2.9990 chunk 169 optimal weight: 0.4980 chunk 134 optimal weight: 0.9990 chunk 173 optimal weight: 0.9980 overall best weight: 0.3984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 223 GLN K 353 GLN L 115 ASN ** L 354 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 360 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 280 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7778 moved from start: 0.5732 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 22660 Z= 0.163 Angle : 0.659 13.590 30734 Z= 0.313 Chirality : 0.044 0.275 3403 Planarity : 0.004 0.045 3923 Dihedral : 7.134 134.782 3175 Min Nonbonded Distance : 1.958 Molprobity Statistics. All-atom Clashscore : 13.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % Rotamer: Outliers : 1.77 % Allowed : 18.30 % Favored : 79.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.32 (0.16), residues: 2736 helix: 0.46 (0.16), residues: 1148 sheet: 0.21 (0.21), residues: 613 loop : 0.17 (0.20), residues: 975 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.002 TRP F 271 HIS 0.005 0.001 HIS O 161 PHE 0.038 0.001 PHE N 352 TYR 0.017 0.001 TYR F 277 ARG 0.018 0.000 ARG L 116 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5472 Ramachandran restraints generated. 2736 Oldfield, 0 Emsley, 2736 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5472 Ramachandran restraints generated. 2736 Oldfield, 0 Emsley, 2736 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 245 residues out of total 2372 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 203 time to evaluate : 2.478 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 169 LEU cc_start: 0.8867 (tp) cc_final: 0.7779 (pt) REVERT: F 199 TYR cc_start: 0.8335 (p90) cc_final: 0.8030 (p90) REVERT: I 283 MET cc_start: 0.8958 (mmp) cc_final: 0.8731 (mmp) REVERT: J 72 GLU cc_start: 0.7945 (tp30) cc_final: 0.7678 (mm-30) REVERT: J 173 HIS cc_start: 0.6900 (OUTLIER) cc_final: 0.6030 (p-80) REVERT: J 292 ASP cc_start: 0.8230 (m-30) cc_final: 0.7752 (t0) REVERT: J 355 MET cc_start: 0.7809 (mmm) cc_final: 0.7499 (mmm) REVERT: K 16 MET cc_start: 0.8149 (mmt) cc_final: 0.7780 (mmm) REVERT: L 44 MET cc_start: 0.7812 (mtp) cc_final: 0.7556 (mtp) REVERT: L 134 VAL cc_start: 0.9062 (OUTLIER) cc_final: 0.8855 (t) REVERT: L 205 GLU cc_start: 0.7379 (mt-10) cc_final: 0.7062 (mp0) REVERT: L 294 TYR cc_start: 0.8423 (OUTLIER) cc_final: 0.7884 (m-10) REVERT: L 313 MET cc_start: 0.8587 (mmm) cc_final: 0.8259 (ttt) REVERT: N 123 MET cc_start: 0.8940 (mmm) cc_final: 0.8409 (tpp) REVERT: N 141 SER cc_start: 0.8389 (m) cc_final: 0.8049 (t) REVERT: N 339 VAL cc_start: 0.9218 (t) cc_final: 0.8890 (t) REVERT: O 44 MET cc_start: 0.1461 (ptt) cc_final: 0.1148 (ptt) outliers start: 42 outliers final: 32 residues processed: 235 average time/residue: 0.3207 time to fit residues: 120.9626 Evaluate side-chains 233 residues out of total 2372 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 198 time to evaluate : 2.844 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 88 MET Chi-restraints excluded: chain E residue 133 LEU Chi-restraints excluded: chain E residue 186 THR Chi-restraints excluded: chain E residue 238 ASP Chi-restraints excluded: chain F residue 173 TRP Chi-restraints excluded: chain F residue 265 THR Chi-restraints excluded: chain I residue 149 THR Chi-restraints excluded: chain I residue 151 ILE Chi-restraints excluded: chain I residue 152 VAL Chi-restraints excluded: chain I residue 153 MET Chi-restraints excluded: chain I residue 227 MET Chi-restraints excluded: chain J residue 77 THR Chi-restraints excluded: chain J residue 173 HIS Chi-restraints excluded: chain J residue 189 LEU Chi-restraints excluded: chain K residue 54 VAL Chi-restraints excluded: chain K residue 115 ASN Chi-restraints excluded: chain K residue 142 LEU Chi-restraints excluded: chain K residue 334 GLU Chi-restraints excluded: chain L residue 60 SER Chi-restraints excluded: chain L residue 85 ILE Chi-restraints excluded: chain L residue 134 VAL Chi-restraints excluded: chain L residue 227 MET Chi-restraints excluded: chain L residue 294 TYR Chi-restraints excluded: chain L residue 371 HIS Chi-restraints excluded: chain N residue 106 THR Chi-restraints excluded: chain N residue 201 THR Chi-restraints excluded: chain N residue 221 LEU Chi-restraints excluded: chain N residue 294 TYR Chi-restraints excluded: chain O residue 81 ASP Chi-restraints excluded: chain O residue 129 THR Chi-restraints excluded: chain O residue 132 MET Chi-restraints excluded: chain O residue 159 VAL Chi-restraints excluded: chain O residue 203 THR Chi-restraints excluded: chain O residue 293 LEU Chi-restraints excluded: chain T residue 7 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 276 random chunks: chunk 233 optimal weight: 3.9990 chunk 67 optimal weight: 4.9990 chunk 201 optimal weight: 9.9990 chunk 32 optimal weight: 7.9990 chunk 60 optimal weight: 0.0170 chunk 219 optimal weight: 0.9990 chunk 91 optimal weight: 1.9990 chunk 225 optimal weight: 0.4980 chunk 27 optimal weight: 0.9990 chunk 40 optimal weight: 10.0000 chunk 192 optimal weight: 0.9980 overall best weight: 0.7022 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 209 HIS F 223 GLN J 354 GLN L 115 ASN ** L 354 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 360 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 280 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3889 r_free = 0.3889 target = 0.099632 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.3242 r_free = 0.3242 target = 0.069198 restraints weight = 71205.571| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3292 r_free = 0.3292 target = 0.071284 restraints weight = 38801.301| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 56)----------------| | r_work = 0.3325 r_free = 0.3325 target = 0.072691 restraints weight = 25728.112| |-----------------------------------------------------------------------------| r_work (final): 0.3303 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7939 moved from start: 0.5836 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 22660 Z= 0.182 Angle : 0.663 12.719 30734 Z= 0.315 Chirality : 0.044 0.203 3403 Planarity : 0.004 0.045 3923 Dihedral : 7.007 132.380 3175 Min Nonbonded Distance : 1.929 Molprobity Statistics. All-atom Clashscore : 13.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.22 % Favored : 96.78 % Rotamer: Outliers : 1.85 % Allowed : 18.38 % Favored : 79.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.40 (0.16), residues: 2736 helix: 0.60 (0.16), residues: 1118 sheet: 0.17 (0.21), residues: 620 loop : 0.17 (0.20), residues: 998 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP F 271 HIS 0.005 0.001 HIS I 275 PHE 0.031 0.001 PHE N 352 TYR 0.016 0.001 TYR F 277 ARG 0.006 0.000 ARG L 95 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4323.35 seconds wall clock time: 80 minutes 22.32 seconds (4822.32 seconds total)