Starting phenix.real_space_refine on Sat Mar 16 22:03:00 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sik_40508/03_2024/8sik_40508.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sik_40508/03_2024/8sik_40508.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sik_40508/03_2024/8sik_40508.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sik_40508/03_2024/8sik_40508.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sik_40508/03_2024/8sik_40508.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sik_40508/03_2024/8sik_40508.pdb" } resolution = 2.9 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= 0.002 sd= 0.043 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: 5 Type Number sf(0) Gaussians Ca 8 9.91 5 S 80 5.16 5 C 10196 2.51 5 N 2708 2.21 5 O 2840 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B GLU 12": "OE1" <-> "OE2" Residue "B GLU 15": "OE1" <-> "OE2" Residue "B PHE 20": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 46": "OE1" <-> "OE2" Residue "B ASP 51": "OD1" <-> "OD2" Residue "B PHE 69": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 85": "OE1" <-> "OE2" Residue "B ASP 96": "OD1" <-> "OD2" Residue "A GLU 170": "OE1" <-> "OE2" Residue "A ASP 202": "OD1" <-> "OD2" Residue "A TYR 395": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 15": "OE1" <-> "OE2" Residue "D GLU 68": "OE1" <-> "OE2" Residue "D PHE 69": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 84": "OE1" <-> "OE2" Residue "D GLU 85": "OE1" <-> "OE2" Residue "D GLU 88": "OE1" <-> "OE2" Residue "D TYR 139": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 141": "OE1" <-> "OE2" Residue "F GLU 15": "OE1" <-> "OE2" Residue "F ASP 51": "OD1" <-> "OD2" Residue "F GLU 68": "OE1" <-> "OE2" Residue "F PHE 69": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 84": "OE1" <-> "OE2" Residue "F GLU 85": "OE1" <-> "OE2" Residue "F GLU 88": "OE1" <-> "OE2" Residue "F ASP 96": "OD1" <-> "OD2" Residue "F TYR 139": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 140": "OE1" <-> "OE2" Residue "F GLU 141": "OE1" <-> "OE2" Residue "H GLU 15": "OE1" <-> "OE2" Residue "H ASP 23": "OD1" <-> "OD2" Residue "H GLU 32": "OE1" <-> "OE2" Residue "H GLU 68": "OE1" <-> "OE2" Residue "H PHE 69": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 85": "OE1" <-> "OE2" Residue "H ASP 96": "OD1" <-> "OD2" Residue "H TYR 139": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 115": "OE1" <-> "OE2" Residue "G GLU 170": "OE1" <-> "OE2" Residue "G ASP 202": "OD1" <-> "OD2" Residue "C PHE 113": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 115": "OE1" <-> "OE2" Residue "E PHE 113": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 115": "OE1" <-> "OE2" Residue "E ASP 202": "OD1" <-> "OD2" Residue "E GLU 508": "OE1" <-> "OE2" Residue "E ASP 537": "OD1" <-> "OD2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 15832 Number of models: 1 Model: "" Number of chains: 12 Chain: "B" Number of atoms: 1108 Number of conformers: 1 Conformer: "" Number of residues, atoms: 144, 1108 Classifications: {'peptide': 144} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 2, 'TRANS': 141} Unresolved non-hydrogen bonds: 27 Unresolved non-hydrogen angles: 32 Unresolved non-hydrogen dihedrals: 22 Planarities with less than four sites: {'ASP:plan': 5} Unresolved non-hydrogen planarities: 15 Chain: "A" Number of atoms: 2848 Number of conformers: 1 Conformer: "" Number of residues, atoms: 352, 2848 Classifications: {'peptide': 352} Link IDs: {'PTRANS': 7, 'TRANS': 344} Chain breaks: 2 Chain: "D" Number of atoms: 1108 Number of conformers: 1 Conformer: "" Number of residues, atoms: 144, 1108 Classifications: {'peptide': 144} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 2, 'TRANS': 141} Unresolved non-hydrogen bonds: 27 Unresolved non-hydrogen angles: 32 Unresolved non-hydrogen dihedrals: 22 Planarities with less than four sites: {'ASP:plan': 5} Unresolved non-hydrogen planarities: 15 Chain: "F" Number of atoms: 1108 Number of conformers: 1 Conformer: "" Number of residues, atoms: 144, 1108 Classifications: {'peptide': 144} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 2, 'TRANS': 141} Unresolved non-hydrogen bonds: 27 Unresolved non-hydrogen angles: 32 Unresolved non-hydrogen dihedrals: 22 Planarities with less than four sites: {'ASP:plan': 5} Unresolved non-hydrogen planarities: 15 Chain: "H" Number of atoms: 1108 Number of conformers: 1 Conformer: "" Number of residues, atoms: 144, 1108 Classifications: {'peptide': 144} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 2, 'TRANS': 141} Unresolved non-hydrogen bonds: 27 Unresolved non-hydrogen angles: 32 Unresolved non-hydrogen dihedrals: 22 Planarities with less than four sites: {'ASP:plan': 5} Unresolved non-hydrogen planarities: 15 Chain: "G" Number of atoms: 2848 Number of conformers: 1 Conformer: "" Number of residues, atoms: 352, 2848 Classifications: {'peptide': 352} Link IDs: {'PTRANS': 7, 'TRANS': 344} Chain breaks: 2 Chain: "C" Number of atoms: 2848 Number of conformers: 1 Conformer: "" Number of residues, atoms: 352, 2848 Classifications: {'peptide': 352} Link IDs: {'PTRANS': 7, 'TRANS': 344} Chain breaks: 2 Chain: "E" Number of atoms: 2848 Number of conformers: 1 Conformer: "" Number of residues, atoms: 352, 2848 Classifications: {'peptide': 352} Link IDs: {'PTRANS': 7, 'TRANS': 344} Chain breaks: 2 Chain: "B" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' CA': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' CA': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' CA': 1} Classifications: {'undetermined': 1} Chain: "H" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' CA': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Residues with excluded nonbonded symmetry interactions: 4 residue: pdb="CA CA B 202 " occ=0.46 residue: pdb="CA CA F 201 " occ=0.45 residue: pdb="CA CA H 201 " occ=0.51 residue: pdb="CA CA H 203 " occ=0.49 Time building chain proxies: 8.23, per 1000 atoms: 0.52 Number of scatterers: 15832 At special positions: 0 Unit cell: (113.265, 113.265, 124.172, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Ca 8 19.99 S 80 16.00 O 2840 8.00 N 2708 7.00 C 10196 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=0, symmetry=0 Time building additional restraints: 6.65 Conformation dependent library (CDL) restraints added in 2.7 seconds 3904 Ramachandran restraints generated. 1952 Oldfield, 0 Emsley, 1952 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3680 Finding SS restraints... Secondary structure from input PDB file: 104 helices and 4 sheets defined 81.3% alpha, 0.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.68 Creating SS restraints... Processing helix chain 'B' and resid 6 through 22 Processing helix chain 'B' and resid 29 through 41 Processing helix chain 'B' and resid 45 through 57 removed outlier: 3.604A pdb=" N GLU B 55 " --> pdb=" O ASP B 51 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N VAL B 56 " --> pdb=" O MET B 52 " (cutoff:3.500A) Processing helix chain 'B' and resid 65 through 74 Processing helix chain 'B' and resid 79 through 92 removed outlier: 3.593A pdb=" N VAL B 92 " --> pdb=" O GLU B 88 " (cutoff:3.500A) Processing helix chain 'B' and resid 103 through 113 Processing helix chain 'B' and resid 118 through 129 Processing helix chain 'B' and resid 139 through 149 removed outlier: 3.745A pdb=" N LYS B 149 " --> pdb=" O MET B 145 " (cutoff:3.500A) Processing helix chain 'A' and resid 105 through 115 Processing helix chain 'A' and resid 120 through 144 removed outlier: 3.783A pdb=" N THR A 144 " --> pdb=" O SER A 140 " (cutoff:3.500A) Processing helix chain 'A' and resid 148 through 178 removed outlier: 3.539A pdb=" N PHE A 157 " --> pdb=" O THR A 153 " (cutoff:3.500A) removed outlier: 4.676A pdb=" N TRP A 158 " --> pdb=" O GLY A 154 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N MET A 159 " --> pdb=" O THR A 155 " (cutoff:3.500A) Processing helix chain 'A' and resid 179 through 181 No H-bonds generated for 'chain 'A' and resid 179 through 181' Processing helix chain 'A' and resid 185 through 196 removed outlier: 3.720A pdb=" N GLY A 189 " --> pdb=" O VAL A 185 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N LYS A 196 " --> pdb=" O ARG A 192 " (cutoff:3.500A) Processing helix chain 'A' and resid 196 through 216 Processing helix chain 'A' and resid 224 through 237 removed outlier: 4.179A pdb=" N ILE A 230 " --> pdb=" O ALA A 226 " (cutoff:3.500A) Processing helix chain 'A' and resid 238 through 242 removed outlier: 3.527A pdb=" N VAL A 241 " --> pdb=" O MET A 238 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N ASP A 242 " --> pdb=" O LEU A 239 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 238 through 242' Processing helix chain 'A' and resid 245 through 258 removed outlier: 3.607A pdb=" N VAL A 254 " --> pdb=" O LEU A 250 " (cutoff:3.500A) Processing helix chain 'A' and resid 258 through 284 Processing helix chain 'A' and resid 298 through 311 Processing helix chain 'A' and resid 322 through 358 removed outlier: 3.863A pdb=" N ILE A 337 " --> pdb=" O SER A 333 " (cutoff:3.500A) removed outlier: 4.822A pdb=" N SER A 338 " --> pdb=" O VAL A 334 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N PHE A 339 " --> pdb=" O PHE A 335 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N PHE A 340 " --> pdb=" O ALA A 336 " (cutoff:3.500A) Proline residue: A 343 - end of helix Processing helix chain 'A' and resid 359 through 361 No H-bonds generated for 'chain 'A' and resid 359 through 361' Processing helix chain 'A' and resid 363 through 366 Processing helix chain 'A' and resid 367 through 384 Processing helix chain 'A' and resid 389 through 396 removed outlier: 3.862A pdb=" N TRP A 392 " --> pdb=" O SER A 389 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N LYS A 393 " --> pdb=" O SER A 390 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N ILE A 394 " --> pdb=" O THR A 391 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N TYR A 395 " --> pdb=" O TRP A 392 " (cutoff:3.500A) Processing helix chain 'A' and resid 509 through 533 removed outlier: 4.024A pdb=" N THR A 513 " --> pdb=" O HIS A 509 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N VAL A 516 " --> pdb=" O ALA A 512 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N ARG A 519 " --> pdb=" O LYS A 515 " (cutoff:3.500A) Processing helix chain 'A' and resid 537 through 568 removed outlier: 3.585A pdb=" N VAL A 541 " --> pdb=" O ASP A 537 " (cutoff:3.500A) Processing helix chain 'D' and resid 7 through 22 Processing helix chain 'D' and resid 29 through 41 Processing helix chain 'D' and resid 45 through 57 removed outlier: 3.560A pdb=" N GLU D 55 " --> pdb=" O ASP D 51 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N VAL D 56 " --> pdb=" O MET D 52 " (cutoff:3.500A) Processing helix chain 'D' and resid 65 through 74 Processing helix chain 'D' and resid 79 through 92 removed outlier: 3.593A pdb=" N VAL D 92 " --> pdb=" O GLU D 88 " (cutoff:3.500A) Processing helix chain 'D' and resid 103 through 113 Processing helix chain 'D' and resid 118 through 129 Processing helix chain 'D' and resid 139 through 149 removed outlier: 3.525A pdb=" N VAL D 143 " --> pdb=" O TYR D 139 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N LYS D 149 " --> pdb=" O MET D 145 " (cutoff:3.500A) Processing helix chain 'F' and resid 7 through 22 Processing helix chain 'F' and resid 29 through 41 Processing helix chain 'F' and resid 45 through 57 removed outlier: 3.571A pdb=" N GLU F 55 " --> pdb=" O ASP F 51 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N VAL F 56 " --> pdb=" O MET F 52 " (cutoff:3.500A) Processing helix chain 'F' and resid 65 through 74 Processing helix chain 'F' and resid 79 through 92 removed outlier: 3.589A pdb=" N VAL F 92 " --> pdb=" O GLU F 88 " (cutoff:3.500A) Processing helix chain 'F' and resid 103 through 113 Processing helix chain 'F' and resid 118 through 129 Processing helix chain 'F' and resid 139 through 147 Processing helix chain 'H' and resid 7 through 22 Processing helix chain 'H' and resid 29 through 41 Processing helix chain 'H' and resid 45 through 57 removed outlier: 3.564A pdb=" N GLU H 55 " --> pdb=" O ASP H 51 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N VAL H 56 " --> pdb=" O MET H 52 " (cutoff:3.500A) Processing helix chain 'H' and resid 65 through 74 Processing helix chain 'H' and resid 79 through 92 removed outlier: 3.616A pdb=" N VAL H 92 " --> pdb=" O GLU H 88 " (cutoff:3.500A) Processing helix chain 'H' and resid 103 through 113 Processing helix chain 'H' and resid 118 through 129 Processing helix chain 'H' and resid 139 through 149 removed outlier: 3.839A pdb=" N LYS H 149 " --> pdb=" O MET H 145 " (cutoff:3.500A) Processing helix chain 'G' and resid 105 through 115 Processing helix chain 'G' and resid 120 through 145 removed outlier: 3.830A pdb=" N THR G 144 " --> pdb=" O SER G 140 " (cutoff:3.500A) removed outlier: 4.098A pdb=" N ILE G 145 " --> pdb=" O VAL G 141 " (cutoff:3.500A) Processing helix chain 'G' and resid 148 through 178 removed outlier: 3.541A pdb=" N PHE G 157 " --> pdb=" O THR G 153 " (cutoff:3.500A) removed outlier: 4.539A pdb=" N TRP G 158 " --> pdb=" O GLY G 154 " (cutoff:3.500A) Processing helix chain 'G' and resid 179 through 181 No H-bonds generated for 'chain 'G' and resid 179 through 181' Processing helix chain 'G' and resid 185 through 194 removed outlier: 3.646A pdb=" N GLY G 189 " --> pdb=" O VAL G 185 " (cutoff:3.500A) Processing helix chain 'G' and resid 196 through 216 Processing helix chain 'G' and resid 224 through 237 removed outlier: 4.338A pdb=" N ILE G 230 " --> pdb=" O ALA G 226 " (cutoff:3.500A) Processing helix chain 'G' and resid 238 through 242 removed outlier: 3.562A pdb=" N VAL G 241 " --> pdb=" O MET G 238 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N ASP G 242 " --> pdb=" O LEU G 239 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 238 through 242' Processing helix chain 'G' and resid 245 through 258 removed outlier: 3.609A pdb=" N VAL G 254 " --> pdb=" O LEU G 250 " (cutoff:3.500A) Processing helix chain 'G' and resid 258 through 284 Processing helix chain 'G' and resid 298 through 311 Processing helix chain 'G' and resid 322 through 358 removed outlier: 3.838A pdb=" N ILE G 337 " --> pdb=" O SER G 333 " (cutoff:3.500A) removed outlier: 4.840A pdb=" N SER G 338 " --> pdb=" O VAL G 334 " (cutoff:3.500A) removed outlier: 4.051A pdb=" N PHE G 339 " --> pdb=" O PHE G 335 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N PHE G 340 " --> pdb=" O ALA G 336 " (cutoff:3.500A) Proline residue: G 343 - end of helix Processing helix chain 'G' and resid 359 through 361 No H-bonds generated for 'chain 'G' and resid 359 through 361' Processing helix chain 'G' and resid 363 through 366 Processing helix chain 'G' and resid 367 through 384 Processing helix chain 'G' and resid 389 through 396 removed outlier: 3.911A pdb=" N TRP G 392 " --> pdb=" O SER G 389 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N LYS G 393 " --> pdb=" O SER G 390 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N ILE G 394 " --> pdb=" O THR G 391 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N TYR G 395 " --> pdb=" O TRP G 392 " (cutoff:3.500A) Processing helix chain 'G' and resid 509 through 533 removed outlier: 4.185A pdb=" N THR G 513 " --> pdb=" O HIS G 509 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N VAL G 516 " --> pdb=" O ALA G 512 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ARG G 519 " --> pdb=" O LYS G 515 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ARG G 533 " --> pdb=" O PHE G 529 " (cutoff:3.500A) Processing helix chain 'G' and resid 537 through 568 removed outlier: 3.572A pdb=" N VAL G 541 " --> pdb=" O ASP G 537 " (cutoff:3.500A) Processing helix chain 'C' and resid 105 through 115 Processing helix chain 'C' and resid 120 through 145 removed outlier: 3.702A pdb=" N THR C 144 " --> pdb=" O SER C 140 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N ILE C 145 " --> pdb=" O VAL C 141 " (cutoff:3.500A) Processing helix chain 'C' and resid 148 through 178 removed outlier: 3.593A pdb=" N PHE C 157 " --> pdb=" O THR C 153 " (cutoff:3.500A) removed outlier: 4.515A pdb=" N TRP C 158 " --> pdb=" O GLY C 154 " (cutoff:3.500A) Processing helix chain 'C' and resid 179 through 181 No H-bonds generated for 'chain 'C' and resid 179 through 181' Processing helix chain 'C' and resid 185 through 195 removed outlier: 3.654A pdb=" N GLY C 189 " --> pdb=" O VAL C 185 " (cutoff:3.500A) Processing helix chain 'C' and resid 196 through 216 Processing helix chain 'C' and resid 224 through 237 removed outlier: 4.236A pdb=" N ILE C 230 " --> pdb=" O ALA C 226 " (cutoff:3.500A) Processing helix chain 'C' and resid 238 through 242 removed outlier: 3.593A pdb=" N ASP C 242 " --> pdb=" O LEU C 239 " (cutoff:3.500A) Processing helix chain 'C' and resid 245 through 258 removed outlier: 3.604A pdb=" N VAL C 254 " --> pdb=" O LEU C 250 " (cutoff:3.500A) Processing helix chain 'C' and resid 258 through 284 Processing helix chain 'C' and resid 298 through 311 Processing helix chain 'C' and resid 322 through 358 removed outlier: 3.891A pdb=" N ILE C 337 " --> pdb=" O SER C 333 " (cutoff:3.500A) removed outlier: 4.857A pdb=" N SER C 338 " --> pdb=" O VAL C 334 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N PHE C 339 " --> pdb=" O PHE C 335 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N PHE C 340 " --> pdb=" O ALA C 336 " (cutoff:3.500A) Proline residue: C 343 - end of helix Processing helix chain 'C' and resid 359 through 361 No H-bonds generated for 'chain 'C' and resid 359 through 361' Processing helix chain 'C' and resid 363 through 366 Processing helix chain 'C' and resid 367 through 384 Processing helix chain 'C' and resid 389 through 396 removed outlier: 3.876A pdb=" N TRP C 392 " --> pdb=" O SER C 389 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N LYS C 393 " --> pdb=" O SER C 390 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N ILE C 394 " --> pdb=" O THR C 391 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N TYR C 395 " --> pdb=" O TRP C 392 " (cutoff:3.500A) Processing helix chain 'C' and resid 509 through 533 removed outlier: 4.337A pdb=" N THR C 513 " --> pdb=" O HIS C 509 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N VAL C 516 " --> pdb=" O ALA C 512 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ARG C 519 " --> pdb=" O LYS C 515 " (cutoff:3.500A) Processing helix chain 'C' and resid 537 through 568 removed outlier: 3.587A pdb=" N VAL C 541 " --> pdb=" O ASP C 537 " (cutoff:3.500A) Processing helix chain 'E' and resid 105 through 115 Processing helix chain 'E' and resid 120 through 145 removed outlier: 3.804A pdb=" N THR E 144 " --> pdb=" O SER E 140 " (cutoff:3.500A) removed outlier: 4.074A pdb=" N ILE E 145 " --> pdb=" O VAL E 141 " (cutoff:3.500A) Processing helix chain 'E' and resid 148 through 178 removed outlier: 3.708A pdb=" N PHE E 157 " --> pdb=" O THR E 153 " (cutoff:3.500A) removed outlier: 4.648A pdb=" N TRP E 158 " --> pdb=" O GLY E 154 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N MET E 159 " --> pdb=" O THR E 155 " (cutoff:3.500A) Processing helix chain 'E' and resid 179 through 181 No H-bonds generated for 'chain 'E' and resid 179 through 181' Processing helix chain 'E' and resid 185 through 194 removed outlier: 3.626A pdb=" N GLY E 189 " --> pdb=" O VAL E 185 " (cutoff:3.500A) Processing helix chain 'E' and resid 196 through 216 Processing helix chain 'E' and resid 224 through 237 removed outlier: 4.242A pdb=" N ILE E 230 " --> pdb=" O ALA E 226 " (cutoff:3.500A) Processing helix chain 'E' and resid 238 through 242 removed outlier: 3.571A pdb=" N ASP E 242 " --> pdb=" O LEU E 239 " (cutoff:3.500A) Processing helix chain 'E' and resid 245 through 258 removed outlier: 3.630A pdb=" N VAL E 254 " --> pdb=" O LEU E 250 " (cutoff:3.500A) Processing helix chain 'E' and resid 258 through 285 Processing helix chain 'E' and resid 298 through 311 Processing helix chain 'E' and resid 322 through 358 removed outlier: 3.877A pdb=" N ILE E 337 " --> pdb=" O SER E 333 " (cutoff:3.500A) removed outlier: 4.858A pdb=" N SER E 338 " --> pdb=" O VAL E 334 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N PHE E 339 " --> pdb=" O PHE E 335 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N PHE E 340 " --> pdb=" O ALA E 336 " (cutoff:3.500A) Proline residue: E 343 - end of helix Processing helix chain 'E' and resid 359 through 361 No H-bonds generated for 'chain 'E' and resid 359 through 361' Processing helix chain 'E' and resid 363 through 366 Processing helix chain 'E' and resid 367 through 384 Processing helix chain 'E' and resid 389 through 396 removed outlier: 3.856A pdb=" N TRP E 392 " --> pdb=" O SER E 389 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N LYS E 393 " --> pdb=" O SER E 390 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N ILE E 394 " --> pdb=" O THR E 391 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N TYR E 395 " --> pdb=" O TRP E 392 " (cutoff:3.500A) Processing helix chain 'E' and resid 509 through 533 removed outlier: 4.267A pdb=" N THR E 513 " --> pdb=" O HIS E 509 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N VAL E 516 " --> pdb=" O ALA E 512 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N ARG E 519 " --> pdb=" O LYS E 515 " (cutoff:3.500A) Processing helix chain 'E' and resid 537 through 567 removed outlier: 3.581A pdb=" N VAL E 541 " --> pdb=" O ASP E 537 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 100 through 102 Processing sheet with id=AA2, first strand: chain 'D' and resid 100 through 102 Processing sheet with id=AA3, first strand: chain 'F' and resid 100 through 102 Processing sheet with id=AA4, first strand: chain 'H' and resid 100 through 102 1112 hydrogen bonds defined for protein. 3306 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: 4.85 Time building geometry restraints manager: 7.15 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 5098 1.34 - 1.46: 2385 1.46 - 1.57: 8533 1.57 - 1.69: 0 1.69 - 1.81: 136 Bond restraints: 16152 Sorted by residual: bond pdb=" C ILE A 368 " pdb=" N PRO A 369 " ideal model delta sigma weight residual 1.335 1.359 -0.024 1.36e-02 5.41e+03 3.13e+00 bond pdb=" C ILE C 368 " pdb=" N PRO C 369 " ideal model delta sigma weight residual 1.335 1.359 -0.024 1.36e-02 5.41e+03 3.05e+00 bond pdb=" C GLY D 26 " pdb=" O GLY D 26 " ideal model delta sigma weight residual 1.239 1.222 0.017 1.09e-02 8.42e+03 2.44e+00 bond pdb=" CA LYS D 22 " pdb=" C LYS D 22 " ideal model delta sigma weight residual 1.523 1.541 -0.018 1.34e-02 5.57e+03 1.85e+00 bond pdb=" CB ILE B 131 " pdb=" CG1 ILE B 131 " ideal model delta sigma weight residual 1.530 1.550 -0.020 2.00e-02 2.50e+03 1.00e+00 ... (remaining 16147 not shown) Histogram of bond angle deviations from ideal: 100.20 - 106.97: 280 106.97 - 113.74: 8908 113.74 - 120.51: 6659 120.51 - 127.27: 5829 127.27 - 134.04: 148 Bond angle restraints: 21824 Sorted by residual: angle pdb=" N ILE A 227 " pdb=" CA ILE A 227 " pdb=" C ILE A 227 " ideal model delta sigma weight residual 112.96 109.20 3.76 1.00e+00 1.00e+00 1.41e+01 angle pdb=" CB ILE B 131 " pdb=" CG1 ILE B 131 " pdb=" CD1 ILE B 131 " ideal model delta sigma weight residual 113.80 120.89 -7.09 2.10e+00 2.27e-01 1.14e+01 angle pdb=" N GLY D 26 " pdb=" CA GLY D 26 " pdb=" C GLY D 26 " ideal model delta sigma weight residual 114.95 110.49 4.46 1.41e+00 5.03e-01 1.00e+01 angle pdb=" CG ARG E 507 " pdb=" CD ARG E 507 " pdb=" NE ARG E 507 " ideal model delta sigma weight residual 112.00 118.29 -6.29 2.20e+00 2.07e-01 8.17e+00 angle pdb=" CA GLU D 12 " pdb=" CB GLU D 12 " pdb=" CG GLU D 12 " ideal model delta sigma weight residual 114.10 119.41 -5.31 2.00e+00 2.50e-01 7.04e+00 ... (remaining 21819 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.48: 8299 17.48 - 34.96: 897 34.96 - 52.44: 251 52.44 - 69.93: 20 69.93 - 87.41: 25 Dihedral angle restraints: 9492 sinusoidal: 3776 harmonic: 5716 Sorted by residual: dihedral pdb=" CA GLN E 234 " pdb=" C GLN E 234 " pdb=" N ILE E 235 " pdb=" CA ILE E 235 " ideal model delta harmonic sigma weight residual 180.00 158.37 21.63 0 5.00e+00 4.00e-02 1.87e+01 dihedral pdb=" CG ARG G 109 " pdb=" CD ARG G 109 " pdb=" NE ARG G 109 " pdb=" CZ ARG G 109 " ideal model delta sinusoidal sigma weight residual 90.00 134.49 -44.49 2 1.50e+01 4.44e-03 1.05e+01 dihedral pdb=" CB GLU A 170 " pdb=" CG GLU A 170 " pdb=" CD GLU A 170 " pdb=" OE1 GLU A 170 " ideal model delta sinusoidal sigma weight residual 0.00 -86.93 86.93 1 3.00e+01 1.11e-03 1.01e+01 ... (remaining 9489 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.049: 1972 0.049 - 0.097: 406 0.097 - 0.146: 60 0.146 - 0.194: 1 0.194 - 0.243: 5 Chirality restraints: 2444 Sorted by residual: chirality pdb=" CG LEU G 191 " pdb=" CB LEU G 191 " pdb=" CD1 LEU G 191 " pdb=" CD2 LEU G 191 " both_signs ideal model delta sigma weight residual False -2.59 -2.35 -0.24 2.00e-01 2.50e+01 1.48e+00 chirality pdb=" CA ASN F 43 " pdb=" N ASN F 43 " pdb=" C ASN F 43 " pdb=" CB ASN F 43 " both_signs ideal model delta sigma weight residual False 2.51 2.29 0.22 2.00e-01 2.50e+01 1.24e+00 chirality pdb=" CG LEU E 191 " pdb=" CB LEU E 191 " pdb=" CD1 LEU E 191 " pdb=" CD2 LEU E 191 " both_signs ideal model delta sigma weight residual False -2.59 -2.38 -0.21 2.00e-01 2.50e+01 1.09e+00 ... (remaining 2441 not shown) Planarity restraints: 2752 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASP D 21 " -0.012 2.00e-02 2.50e+03 2.35e-02 5.54e+00 pdb=" C ASP D 21 " 0.041 2.00e-02 2.50e+03 pdb=" O ASP D 21 " -0.015 2.00e-02 2.50e+03 pdb=" N LYS D 22 " -0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG G 507 " 0.196 9.50e-02 1.11e+02 8.81e-02 5.33e+00 pdb=" NE ARG G 507 " -0.016 2.00e-02 2.50e+03 pdb=" CZ ARG G 507 " 0.011 2.00e-02 2.50e+03 pdb=" NH1 ARG G 507 " -0.006 2.00e-02 2.50e+03 pdb=" NH2 ARG G 507 " 0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE B 131 " 0.007 2.00e-02 2.50e+03 1.46e-02 2.15e+00 pdb=" C ILE B 131 " -0.025 2.00e-02 2.50e+03 pdb=" O ILE B 131 " 0.010 2.00e-02 2.50e+03 pdb=" N ASP B 132 " 0.008 2.00e-02 2.50e+03 ... (remaining 2749 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.74: 1625 2.74 - 3.28: 16120 3.28 - 3.82: 26892 3.82 - 4.36: 31323 4.36 - 4.90: 55056 Nonbonded interactions: 131016 Sorted by model distance: nonbonded pdb=" OE2 GLU H 68 " pdb="CA CA H 203 " model vdw 2.206 2.510 nonbonded pdb=" OE1 GLU H 55 " pdb=" NZ LYS G 527 " model vdw 2.209 2.520 nonbonded pdb=" OD1 ASN H 61 " pdb="CA CA H 203 " model vdw 2.211 2.510 nonbonded pdb=" OE1 GLU H 124 " pdb=" OG SER G 390 " model vdw 2.255 2.440 nonbonded pdb=" OE1 GLU B 124 " pdb=" OG SER A 390 " model vdw 2.268 2.440 ... (remaining 131011 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'E' selection = chain 'G' } ncs_group { reference = (chain 'B' and (resid 6 through 149 or resid 201)) selection = (chain 'D' and (resid 6 through 149 or resid 201)) selection = chain 'F' selection = (chain 'H' and (resid 6 through 149 or resid 201)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.45 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.660 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 9.910 Check model and map are aligned: 0.250 Set scattering table: 0.120 Process input model: 42.900 Find NCS groups from input model: 1.090 Set up NCS constraints: 0.100 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:18.450 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 76.490 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7502 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 : 0.003 0.026 16152 Z= 0.181 Angle : 0.506 8.678 21824 Z= 0.296 Chirality : 0.039 0.243 2444 Planarity : 0.004 0.088 2752 Dihedral : 15.666 87.408 5812 Min Nonbonded Distance : 2.206 Molprobity Statistics. All-atom Clashscore : 6.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.69 % Favored : 98.31 % Rotamer: Outliers : 0.96 % Allowed : 19.64 % Favored : 79.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.43 (0.19), residues: 1952 helix: 2.13 (0.13), residues: 1504 sheet: None (None), residues: 0 loop : -0.12 (0.28), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP G 323 HIS 0.005 0.001 HIS E 363 PHE 0.013 0.001 PHE E 332 TYR 0.017 0.001 TYR D 139 ARG 0.013 0.001 ARG G 507 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3904 Ramachandran restraints generated. 1952 Oldfield, 0 Emsley, 1952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3904 Ramachandran restraints generated. 1952 Oldfield, 0 Emsley, 1952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 218 residues out of total 1692 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 202 time to evaluate : 1.808 Fit side-chains REVERT: G 195 ARG cc_start: 0.6353 (mtp180) cc_final: 0.5956 (mtm110) REVERT: C 191 LEU cc_start: 0.6722 (mp) cc_final: 0.6407 (mm) outliers start: 16 outliers final: 12 residues processed: 216 average time/residue: 1.4274 time to fit residues: 336.6977 Evaluate side-chains 207 residues out of total 1692 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 195 time to evaluate : 1.683 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 39 SER Chi-restraints excluded: chain A residue 310 VAL Chi-restraints excluded: chain D residue 39 SER Chi-restraints excluded: chain F residue 39 SER Chi-restraints excluded: chain H residue 39 SER Chi-restraints excluded: chain G residue 230 ILE Chi-restraints excluded: chain G residue 310 VAL Chi-restraints excluded: chain G residue 567 ILE Chi-restraints excluded: chain C residue 310 VAL Chi-restraints excluded: chain C residue 366 ARG Chi-restraints excluded: chain E residue 230 ILE Chi-restraints excluded: chain E residue 310 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 165 optimal weight: 5.9990 chunk 148 optimal weight: 0.9980 chunk 82 optimal weight: 7.9990 chunk 50 optimal weight: 3.9990 chunk 100 optimal weight: 8.9990 chunk 79 optimal weight: 2.9990 chunk 153 optimal weight: 0.0000 chunk 59 optimal weight: 2.9990 chunk 93 optimal weight: 4.9990 chunk 114 optimal weight: 0.9980 chunk 177 optimal weight: 2.9990 overall best weight: 1.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 357 GLN G 234 GLN G 359 GLN ** E 234 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7542 moved from start: 0.0568 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 16152 Z= 0.276 Angle : 0.486 7.751 21824 Z= 0.268 Chirality : 0.040 0.214 2444 Planarity : 0.004 0.045 2752 Dihedral : 4.083 38.488 2182 Min Nonbonded Distance : 2.133 Molprobity Statistics. All-atom Clashscore : 6.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % Rotamer: Outliers : 3.73 % Allowed : 17.05 % Favored : 79.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.29 (0.19), residues: 1952 helix: 2.01 (0.13), residues: 1516 sheet: None (None), residues: 0 loop : -0.15 (0.29), residues: 436 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP G 323 HIS 0.003 0.001 HIS C 240 PHE 0.015 0.002 PHE C 332 TYR 0.015 0.002 TYR C 545 ARG 0.006 0.000 ARG G 507 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3904 Ramachandran restraints generated. 1952 Oldfield, 0 Emsley, 1952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3904 Ramachandran restraints generated. 1952 Oldfield, 0 Emsley, 1952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 263 residues out of total 1692 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 201 time to evaluate : 2.063 Fit side-chains REVERT: B 131 ILE cc_start: 0.4351 (OUTLIER) cc_final: 0.4089 (pp) REVERT: D 12 GLU cc_start: 0.7243 (OUTLIER) cc_final: 0.6834 (pm20) REVERT: D 68 GLU cc_start: 0.7178 (OUTLIER) cc_final: 0.6836 (mt-10) REVERT: F 42 GLN cc_start: 0.8109 (OUTLIER) cc_final: 0.6650 (mp10) REVERT: F 68 GLU cc_start: 0.7418 (OUTLIER) cc_final: 0.7087 (mt-10) REVERT: F 140 GLU cc_start: 0.6972 (OUTLIER) cc_final: 0.6271 (mp0) REVERT: H 141 GLU cc_start: 0.7180 (OUTLIER) cc_final: 0.6643 (pp20) REVERT: G 195 ARG cc_start: 0.6399 (mtp180) cc_final: 0.5922 (mtm110) outliers start: 62 outliers final: 22 residues processed: 239 average time/residue: 1.5089 time to fit residues: 392.1559 Evaluate side-chains 227 residues out of total 1692 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 198 time to evaluate : 1.455 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 131 ILE Chi-restraints excluded: chain B residue 137 VAL Chi-restraints excluded: chain A residue 172 VAL Chi-restraints excluded: chain A residue 310 VAL Chi-restraints excluded: chain A residue 366 ARG Chi-restraints excluded: chain A residue 567 ILE Chi-restraints excluded: chain D residue 12 GLU Chi-restraints excluded: chain D residue 29 THR Chi-restraints excluded: chain D residue 68 GLU Chi-restraints excluded: chain D residue 131 ILE Chi-restraints excluded: chain D residue 137 VAL Chi-restraints excluded: chain F residue 29 THR Chi-restraints excluded: chain F residue 42 GLN Chi-restraints excluded: chain F residue 68 GLU Chi-restraints excluded: chain F residue 125 MET Chi-restraints excluded: chain F residue 137 VAL Chi-restraints excluded: chain F residue 140 GLU Chi-restraints excluded: chain H residue 29 THR Chi-restraints excluded: chain H residue 141 GLU Chi-restraints excluded: chain G residue 172 VAL Chi-restraints excluded: chain G residue 230 ILE Chi-restraints excluded: chain G residue 310 VAL Chi-restraints excluded: chain G residue 366 ARG Chi-restraints excluded: chain C residue 172 VAL Chi-restraints excluded: chain C residue 285 LYS Chi-restraints excluded: chain C residue 567 ILE Chi-restraints excluded: chain E residue 172 VAL Chi-restraints excluded: chain E residue 230 ILE Chi-restraints excluded: chain E residue 567 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 98 optimal weight: 4.9990 chunk 55 optimal weight: 2.9990 chunk 148 optimal weight: 1.9990 chunk 121 optimal weight: 1.9990 chunk 49 optimal weight: 10.0000 chunk 178 optimal weight: 0.7980 chunk 192 optimal weight: 0.4980 chunk 158 optimal weight: 0.9990 chunk 176 optimal weight: 1.9990 chunk 60 optimal weight: 0.6980 chunk 143 optimal weight: 0.6980 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 359 GLN ** D 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 234 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 359 GLN C 357 GLN ** C 359 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 234 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 357 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7502 moved from start: 0.0616 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 16152 Z= 0.158 Angle : 0.422 7.224 21824 Z= 0.232 Chirality : 0.037 0.238 2444 Planarity : 0.003 0.030 2752 Dihedral : 3.442 25.717 2170 Min Nonbonded Distance : 2.262 Molprobity Statistics. All-atom Clashscore : 5.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % Rotamer: Outliers : 2.95 % Allowed : 18.31 % Favored : 78.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.64 (0.19), residues: 1952 helix: 2.29 (0.13), residues: 1516 sheet: None (None), residues: 0 loop : -0.18 (0.29), residues: 436 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 379 HIS 0.003 0.001 HIS E 240 PHE 0.012 0.001 PHE C 332 TYR 0.011 0.001 TYR C 545 ARG 0.006 0.000 ARG E 109 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3904 Ramachandran restraints generated. 1952 Oldfield, 0 Emsley, 1952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3904 Ramachandran restraints generated. 1952 Oldfield, 0 Emsley, 1952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 248 residues out of total 1692 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 199 time to evaluate : 1.883 Fit side-chains REVERT: A 557 LYS cc_start: 0.6833 (OUTLIER) cc_final: 0.6473 (mtpt) REVERT: D 12 GLU cc_start: 0.7295 (OUTLIER) cc_final: 0.6815 (pm20) REVERT: D 68 GLU cc_start: 0.7177 (OUTLIER) cc_final: 0.6787 (mt-10) REVERT: F 68 GLU cc_start: 0.7393 (OUTLIER) cc_final: 0.7048 (mt-10) REVERT: F 140 GLU cc_start: 0.6889 (OUTLIER) cc_final: 0.6146 (mp0) REVERT: H 141 GLU cc_start: 0.7122 (OUTLIER) cc_final: 0.6621 (pp20) REVERT: G 195 ARG cc_start: 0.6348 (mtp180) cc_final: 0.5848 (mtm110) REVERT: G 508 GLU cc_start: 0.6267 (OUTLIER) cc_final: 0.5830 (mp0) REVERT: C 533 ARG cc_start: 0.7549 (mtp85) cc_final: 0.7043 (mtm180) outliers start: 49 outliers final: 19 residues processed: 232 average time/residue: 1.5276 time to fit residues: 385.1708 Evaluate side-chains 221 residues out of total 1692 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 195 time to evaluate : 1.678 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 125 MET Chi-restraints excluded: chain A residue 366 ARG Chi-restraints excluded: chain A residue 557 LYS Chi-restraints excluded: chain D residue 12 GLU Chi-restraints excluded: chain D residue 29 THR Chi-restraints excluded: chain D residue 68 GLU Chi-restraints excluded: chain D residue 131 ILE Chi-restraints excluded: chain F residue 29 THR Chi-restraints excluded: chain F residue 39 SER Chi-restraints excluded: chain F residue 68 GLU Chi-restraints excluded: chain F residue 140 GLU Chi-restraints excluded: chain H residue 29 THR Chi-restraints excluded: chain H residue 39 SER Chi-restraints excluded: chain H residue 141 GLU Chi-restraints excluded: chain G residue 163 LEU Chi-restraints excluded: chain G residue 230 ILE Chi-restraints excluded: chain G residue 366 ARG Chi-restraints excluded: chain G residue 508 GLU Chi-restraints excluded: chain G residue 567 ILE Chi-restraints excluded: chain C residue 163 LEU Chi-restraints excluded: chain C residue 310 VAL Chi-restraints excluded: chain C residue 366 ARG Chi-restraints excluded: chain C residue 567 ILE Chi-restraints excluded: chain E residue 163 LEU Chi-restraints excluded: chain E residue 230 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 176 optimal weight: 0.9980 chunk 134 optimal weight: 0.7980 chunk 92 optimal weight: 0.8980 chunk 19 optimal weight: 10.0000 chunk 85 optimal weight: 0.2980 chunk 119 optimal weight: 0.0980 chunk 178 optimal weight: 0.8980 chunk 189 optimal weight: 4.9990 chunk 93 optimal weight: 0.9990 chunk 169 optimal weight: 2.9990 chunk 51 optimal weight: 4.9990 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 357 GLN A 359 GLN ** D 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 234 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 357 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 359 GLN ** C 359 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 234 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 357 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 359 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7488 moved from start: 0.0720 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 16152 Z= 0.142 Angle : 0.416 7.606 21824 Z= 0.227 Chirality : 0.037 0.241 2444 Planarity : 0.003 0.031 2752 Dihedral : 3.273 16.596 2168 Min Nonbonded Distance : 2.281 Molprobity Statistics. All-atom Clashscore : 5.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % Rotamer: Outliers : 2.95 % Allowed : 18.19 % Favored : 78.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.62 (0.19), residues: 1952 helix: 2.27 (0.13), residues: 1544 sheet: None (None), residues: 0 loop : -0.38 (0.29), residues: 408 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 379 HIS 0.003 0.001 HIS E 363 PHE 0.011 0.001 PHE E 332 TYR 0.011 0.001 TYR C 545 ARG 0.007 0.000 ARG E 507 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3904 Ramachandran restraints generated. 1952 Oldfield, 0 Emsley, 1952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3904 Ramachandran restraints generated. 1952 Oldfield, 0 Emsley, 1952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 253 residues out of total 1692 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 204 time to evaluate : 1.720 Fit side-chains REVERT: B 141 GLU cc_start: 0.7137 (pt0) cc_final: 0.6779 (pp20) REVERT: A 557 LYS cc_start: 0.6814 (OUTLIER) cc_final: 0.6448 (mtpt) REVERT: D 12 GLU cc_start: 0.7294 (OUTLIER) cc_final: 0.6815 (pm20) REVERT: D 68 GLU cc_start: 0.7151 (OUTLIER) cc_final: 0.6763 (mt-10) REVERT: F 39 SER cc_start: 0.8516 (OUTLIER) cc_final: 0.8252 (p) REVERT: F 42 GLN cc_start: 0.8123 (OUTLIER) cc_final: 0.6644 (mp10) REVERT: F 68 GLU cc_start: 0.7341 (OUTLIER) cc_final: 0.6997 (mt-10) REVERT: F 112 ASN cc_start: 0.8475 (m110) cc_final: 0.8060 (m-40) REVERT: F 140 GLU cc_start: 0.6879 (OUTLIER) cc_final: 0.6100 (mp0) REVERT: H 141 GLU cc_start: 0.7083 (OUTLIER) cc_final: 0.6605 (pp20) REVERT: G 195 ARG cc_start: 0.6288 (mtp180) cc_final: 0.5800 (mtm110) REVERT: C 533 ARG cc_start: 0.7477 (mtp85) cc_final: 0.6742 (mtm110) REVERT: E 560 GLN cc_start: 0.6525 (tp-100) cc_final: 0.6029 (mt0) outliers start: 49 outliers final: 19 residues processed: 240 average time/residue: 1.5124 time to fit residues: 394.5184 Evaluate side-chains 227 residues out of total 1692 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 200 time to evaluate : 1.813 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain A residue 163 LEU Chi-restraints excluded: chain A residue 366 ARG Chi-restraints excluded: chain A residue 557 LYS Chi-restraints excluded: chain D residue 12 GLU Chi-restraints excluded: chain D residue 29 THR Chi-restraints excluded: chain D residue 68 GLU Chi-restraints excluded: chain D residue 131 ILE Chi-restraints excluded: chain F residue 29 THR Chi-restraints excluded: chain F residue 39 SER Chi-restraints excluded: chain F residue 42 GLN Chi-restraints excluded: chain F residue 68 GLU Chi-restraints excluded: chain F residue 131 ILE Chi-restraints excluded: chain F residue 140 GLU Chi-restraints excluded: chain H residue 29 THR Chi-restraints excluded: chain H residue 39 SER Chi-restraints excluded: chain H residue 141 GLU Chi-restraints excluded: chain G residue 163 LEU Chi-restraints excluded: chain G residue 310 VAL Chi-restraints excluded: chain G residue 567 ILE Chi-restraints excluded: chain C residue 163 LEU Chi-restraints excluded: chain C residue 366 ARG Chi-restraints excluded: chain C residue 513 THR Chi-restraints excluded: chain C residue 567 ILE Chi-restraints excluded: chain E residue 163 LEU Chi-restraints excluded: chain E residue 230 ILE Chi-restraints excluded: chain E residue 310 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 157 optimal weight: 1.9990 chunk 107 optimal weight: 0.6980 chunk 2 optimal weight: 5.9990 chunk 141 optimal weight: 2.9990 chunk 78 optimal weight: 2.9990 chunk 161 optimal weight: 0.9980 chunk 130 optimal weight: 4.9990 chunk 0 optimal weight: 10.0000 chunk 96 optimal weight: 5.9990 chunk 170 optimal weight: 4.9990 chunk 47 optimal weight: 3.9990 overall best weight: 1.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 108 HIS F 112 ASN G 234 GLN G 359 GLN ** E 234 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7560 moved from start: 0.0964 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 16152 Z= 0.328 Angle : 0.510 7.114 21824 Z= 0.280 Chirality : 0.041 0.269 2444 Planarity : 0.004 0.035 2752 Dihedral : 3.591 17.575 2166 Min Nonbonded Distance : 2.209 Molprobity Statistics. All-atom Clashscore : 6.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.74 % Favored : 98.26 % Rotamer: Outliers : 4.46 % Allowed : 16.81 % Favored : 78.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.08 (0.18), residues: 1952 helix: 1.86 (0.13), residues: 1548 sheet: None (None), residues: 0 loop : -0.45 (0.28), residues: 404 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP E 323 HIS 0.004 0.001 HIS E 510 PHE 0.016 0.002 PHE C 332 TYR 0.018 0.002 TYR H 139 ARG 0.006 0.000 ARG E 507 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3904 Ramachandran restraints generated. 1952 Oldfield, 0 Emsley, 1952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3904 Ramachandran restraints generated. 1952 Oldfield, 0 Emsley, 1952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 276 residues out of total 1692 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 74 poor density : 202 time to evaluate : 1.883 Fit side-chains REVERT: B 141 GLU cc_start: 0.7250 (pt0) cc_final: 0.6905 (pp20) REVERT: A 557 LYS cc_start: 0.6735 (OUTLIER) cc_final: 0.5930 (ttpt) REVERT: D 12 GLU cc_start: 0.7291 (OUTLIER) cc_final: 0.6999 (pm20) REVERT: D 68 GLU cc_start: 0.7184 (OUTLIER) cc_final: 0.6854 (mt-10) REVERT: F 31 LYS cc_start: 0.7465 (mppt) cc_final: 0.6987 (mtpm) REVERT: F 42 GLN cc_start: 0.8202 (OUTLIER) cc_final: 0.6701 (mp10) REVERT: F 68 GLU cc_start: 0.7470 (OUTLIER) cc_final: 0.7156 (mt-10) REVERT: F 146 MET cc_start: 0.7770 (mtp) cc_final: 0.7359 (ttp) REVERT: H 141 GLU cc_start: 0.7125 (OUTLIER) cc_final: 0.6634 (pp20) REVERT: G 195 ARG cc_start: 0.6422 (mtp180) cc_final: 0.5995 (mtm110) REVERT: G 508 GLU cc_start: 0.6262 (OUTLIER) cc_final: 0.5873 (mp0) outliers start: 74 outliers final: 35 residues processed: 253 average time/residue: 1.4757 time to fit residues: 406.8256 Evaluate side-chains 246 residues out of total 1692 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 204 time to evaluate : 1.717 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain A residue 163 LEU Chi-restraints excluded: chain A residue 172 VAL Chi-restraints excluded: chain A residue 312 THR Chi-restraints excluded: chain A residue 366 ARG Chi-restraints excluded: chain A residue 506 LEU Chi-restraints excluded: chain A residue 557 LYS Chi-restraints excluded: chain A residue 567 ILE Chi-restraints excluded: chain D residue 12 GLU Chi-restraints excluded: chain D residue 29 THR Chi-restraints excluded: chain D residue 68 GLU Chi-restraints excluded: chain D residue 131 ILE Chi-restraints excluded: chain F residue 29 THR Chi-restraints excluded: chain F residue 39 SER Chi-restraints excluded: chain F residue 42 GLN Chi-restraints excluded: chain F residue 68 GLU Chi-restraints excluded: chain F residue 131 ILE Chi-restraints excluded: chain H residue 29 THR Chi-restraints excluded: chain H residue 39 SER Chi-restraints excluded: chain H residue 131 ILE Chi-restraints excluded: chain H residue 141 GLU Chi-restraints excluded: chain G residue 163 LEU Chi-restraints excluded: chain G residue 172 VAL Chi-restraints excluded: chain G residue 210 MET Chi-restraints excluded: chain G residue 310 VAL Chi-restraints excluded: chain G residue 366 ARG Chi-restraints excluded: chain G residue 508 GLU Chi-restraints excluded: chain G residue 567 ILE Chi-restraints excluded: chain C residue 163 LEU Chi-restraints excluded: chain C residue 172 VAL Chi-restraints excluded: chain C residue 285 LYS Chi-restraints excluded: chain C residue 310 VAL Chi-restraints excluded: chain C residue 342 LEU Chi-restraints excluded: chain C residue 366 ARG Chi-restraints excluded: chain C residue 567 ILE Chi-restraints excluded: chain E residue 163 LEU Chi-restraints excluded: chain E residue 172 VAL Chi-restraints excluded: chain E residue 230 ILE Chi-restraints excluded: chain E residue 285 LYS Chi-restraints excluded: chain E residue 310 VAL Chi-restraints excluded: chain E residue 312 THR Chi-restraints excluded: chain E residue 567 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 63 optimal weight: 10.0000 chunk 170 optimal weight: 5.9990 chunk 37 optimal weight: 0.7980 chunk 111 optimal weight: 0.9980 chunk 46 optimal weight: 2.9990 chunk 189 optimal weight: 3.9990 chunk 157 optimal weight: 0.9980 chunk 87 optimal weight: 0.5980 chunk 15 optimal weight: 0.7980 chunk 62 optimal weight: 0.9990 chunk 99 optimal weight: 0.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 357 GLN A 359 GLN ** D 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 144 GLN H 42 GLN ** G 234 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 357 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 359 GLN C 357 GLN C 359 GLN ** E 234 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 357 GLN ** E 359 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7513 moved from start: 0.0916 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 16152 Z= 0.173 Angle : 0.441 6.849 21824 Z= 0.240 Chirality : 0.037 0.255 2444 Planarity : 0.003 0.036 2752 Dihedral : 3.387 18.638 2166 Min Nonbonded Distance : 2.252 Molprobity Statistics. All-atom Clashscore : 6.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.69 % Favored : 98.31 % Rotamer: Outliers : 2.77 % Allowed : 18.37 % Favored : 78.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.42 (0.19), residues: 1952 helix: 2.13 (0.13), residues: 1544 sheet: None (None), residues: 0 loop : -0.45 (0.29), residues: 408 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP G 323 HIS 0.002 0.001 HIS E 240 PHE 0.012 0.001 PHE G 332 TYR 0.011 0.001 TYR C 545 ARG 0.008 0.000 ARG E 507 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3904 Ramachandran restraints generated. 1952 Oldfield, 0 Emsley, 1952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3904 Ramachandran restraints generated. 1952 Oldfield, 0 Emsley, 1952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 247 residues out of total 1692 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 201 time to evaluate : 1.907 Fit side-chains REVERT: B 141 GLU cc_start: 0.7203 (OUTLIER) cc_final: 0.6881 (pp20) REVERT: A 557 LYS cc_start: 0.6764 (OUTLIER) cc_final: 0.5942 (ttpt) REVERT: D 12 GLU cc_start: 0.7260 (OUTLIER) cc_final: 0.6969 (pm20) REVERT: D 68 GLU cc_start: 0.7173 (OUTLIER) cc_final: 0.6781 (mt-10) REVERT: F 31 LYS cc_start: 0.7461 (mppt) cc_final: 0.7005 (mtpm) REVERT: F 39 SER cc_start: 0.8514 (OUTLIER) cc_final: 0.8260 (p) REVERT: F 42 GLN cc_start: 0.8184 (OUTLIER) cc_final: 0.6698 (mp10) REVERT: F 68 GLU cc_start: 0.7388 (OUTLIER) cc_final: 0.7072 (mt-10) REVERT: H 141 GLU cc_start: 0.7107 (OUTLIER) cc_final: 0.6635 (pp20) REVERT: G 195 ARG cc_start: 0.6366 (mtp180) cc_final: 0.5955 (mtm110) REVERT: C 533 ARG cc_start: 0.7506 (mtp85) cc_final: 0.6795 (mtm110) outliers start: 46 outliers final: 23 residues processed: 233 average time/residue: 1.5326 time to fit residues: 388.1084 Evaluate side-chains 229 residues out of total 1692 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 198 time to evaluate : 1.809 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 141 GLU Chi-restraints excluded: chain A residue 163 LEU Chi-restraints excluded: chain A residue 172 VAL Chi-restraints excluded: chain A residue 366 ARG Chi-restraints excluded: chain A residue 557 LYS Chi-restraints excluded: chain A residue 567 ILE Chi-restraints excluded: chain D residue 12 GLU Chi-restraints excluded: chain D residue 29 THR Chi-restraints excluded: chain D residue 68 GLU Chi-restraints excluded: chain D residue 131 ILE Chi-restraints excluded: chain F residue 29 THR Chi-restraints excluded: chain F residue 39 SER Chi-restraints excluded: chain F residue 42 GLN Chi-restraints excluded: chain F residue 68 GLU Chi-restraints excluded: chain F residue 131 ILE Chi-restraints excluded: chain H residue 39 SER Chi-restraints excluded: chain H residue 131 ILE Chi-restraints excluded: chain H residue 141 GLU Chi-restraints excluded: chain G residue 163 LEU Chi-restraints excluded: chain G residue 230 ILE Chi-restraints excluded: chain G residue 310 VAL Chi-restraints excluded: chain G residue 366 ARG Chi-restraints excluded: chain C residue 163 LEU Chi-restraints excluded: chain C residue 310 VAL Chi-restraints excluded: chain C residue 366 ARG Chi-restraints excluded: chain C residue 567 ILE Chi-restraints excluded: chain E residue 163 LEU Chi-restraints excluded: chain E residue 230 ILE Chi-restraints excluded: chain E residue 310 VAL Chi-restraints excluded: chain E residue 312 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 182 optimal weight: 0.6980 chunk 21 optimal weight: 5.9990 chunk 108 optimal weight: 2.9990 chunk 138 optimal weight: 0.9990 chunk 107 optimal weight: 0.9990 chunk 159 optimal weight: 6.9990 chunk 105 optimal weight: 0.9980 chunk 188 optimal weight: 2.9990 chunk 118 optimal weight: 3.9990 chunk 115 optimal weight: 1.9990 chunk 87 optimal weight: 0.3980 overall best weight: 0.8184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 359 GLN F 144 GLN ** G 234 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 357 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 359 GLN C 359 GLN ** E 234 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 359 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7509 moved from start: 0.0938 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 16152 Z= 0.171 Angle : 0.442 7.524 21824 Z= 0.240 Chirality : 0.037 0.253 2444 Planarity : 0.003 0.043 2752 Dihedral : 3.342 18.208 2166 Min Nonbonded Distance : 2.255 Molprobity Statistics. All-atom Clashscore : 6.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.74 % Favored : 98.26 % Rotamer: Outliers : 2.89 % Allowed : 18.67 % Favored : 78.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.53 (0.19), residues: 1952 helix: 2.20 (0.13), residues: 1544 sheet: None (None), residues: 0 loop : -0.36 (0.29), residues: 408 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP E 323 HIS 0.003 0.001 HIS E 363 PHE 0.013 0.001 PHE E 332 TYR 0.012 0.001 TYR C 545 ARG 0.009 0.000 ARG E 507 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3904 Ramachandran restraints generated. 1952 Oldfield, 0 Emsley, 1952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3904 Ramachandran restraints generated. 1952 Oldfield, 0 Emsley, 1952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 248 residues out of total 1692 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 200 time to evaluate : 1.809 Fit side-chains REVERT: B 141 GLU cc_start: 0.7212 (pt0) cc_final: 0.6889 (pp20) REVERT: A 557 LYS cc_start: 0.6752 (OUTLIER) cc_final: 0.6480 (mtpt) REVERT: D 12 GLU cc_start: 0.7262 (OUTLIER) cc_final: 0.6998 (pm20) REVERT: F 39 SER cc_start: 0.8515 (OUTLIER) cc_final: 0.8263 (p) REVERT: F 42 GLN cc_start: 0.8188 (OUTLIER) cc_final: 0.6685 (mp10) REVERT: F 68 GLU cc_start: 0.7399 (OUTLIER) cc_final: 0.7080 (mt-10) REVERT: H 141 GLU cc_start: 0.7079 (OUTLIER) cc_final: 0.6616 (pp20) REVERT: G 195 ARG cc_start: 0.6330 (mtp180) cc_final: 0.5913 (mtm110) REVERT: C 533 ARG cc_start: 0.7484 (mtp85) cc_final: 0.6764 (mtm110) outliers start: 48 outliers final: 26 residues processed: 234 average time/residue: 1.5742 time to fit residues: 399.1473 Evaluate side-chains 230 residues out of total 1692 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 198 time to evaluate : 1.882 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain A residue 163 LEU Chi-restraints excluded: chain A residue 172 VAL Chi-restraints excluded: chain A residue 310 VAL Chi-restraints excluded: chain A residue 312 THR Chi-restraints excluded: chain A residue 366 ARG Chi-restraints excluded: chain A residue 557 LYS Chi-restraints excluded: chain A residue 567 ILE Chi-restraints excluded: chain D residue 12 GLU Chi-restraints excluded: chain D residue 29 THR Chi-restraints excluded: chain D residue 131 ILE Chi-restraints excluded: chain F residue 29 THR Chi-restraints excluded: chain F residue 39 SER Chi-restraints excluded: chain F residue 42 GLN Chi-restraints excluded: chain F residue 68 GLU Chi-restraints excluded: chain F residue 131 ILE Chi-restraints excluded: chain H residue 39 SER Chi-restraints excluded: chain H residue 131 ILE Chi-restraints excluded: chain H residue 141 GLU Chi-restraints excluded: chain G residue 163 LEU Chi-restraints excluded: chain G residue 230 ILE Chi-restraints excluded: chain G residue 310 VAL Chi-restraints excluded: chain G residue 366 ARG Chi-restraints excluded: chain C residue 163 LEU Chi-restraints excluded: chain C residue 285 LYS Chi-restraints excluded: chain C residue 310 VAL Chi-restraints excluded: chain C residue 366 ARG Chi-restraints excluded: chain C residue 567 ILE Chi-restraints excluded: chain E residue 230 ILE Chi-restraints excluded: chain E residue 310 VAL Chi-restraints excluded: chain E residue 312 THR Chi-restraints excluded: chain E residue 567 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 116 optimal weight: 0.2980 chunk 75 optimal weight: 0.8980 chunk 112 optimal weight: 1.9990 chunk 56 optimal weight: 3.9990 chunk 37 optimal weight: 1.9990 chunk 36 optimal weight: 0.9980 chunk 120 optimal weight: 0.5980 chunk 128 optimal weight: 4.9990 chunk 93 optimal weight: 4.9990 chunk 17 optimal weight: 1.9990 chunk 148 optimal weight: 0.7980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 357 GLN A 359 GLN ** D 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 234 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 357 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 359 GLN C 359 GLN E 357 GLN ** E 359 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7499 moved from start: 0.0976 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 16152 Z= 0.158 Angle : 0.441 8.119 21824 Z= 0.238 Chirality : 0.037 0.248 2444 Planarity : 0.003 0.043 2752 Dihedral : 3.294 17.771 2166 Min Nonbonded Distance : 2.265 Molprobity Statistics. All-atom Clashscore : 6.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer: Outliers : 2.59 % Allowed : 19.22 % Favored : 78.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.61 (0.19), residues: 1952 helix: 2.26 (0.13), residues: 1544 sheet: None (None), residues: 0 loop : -0.34 (0.29), residues: 408 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP C 323 HIS 0.002 0.001 HIS E 240 PHE 0.012 0.001 PHE G 332 TYR 0.011 0.001 TYR C 545 ARG 0.009 0.000 ARG E 507 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3904 Ramachandran restraints generated. 1952 Oldfield, 0 Emsley, 1952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3904 Ramachandran restraints generated. 1952 Oldfield, 0 Emsley, 1952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 244 residues out of total 1692 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 201 time to evaluate : 1.808 Fit side-chains REVERT: B 141 GLU cc_start: 0.7192 (OUTLIER) cc_final: 0.6875 (pp20) REVERT: A 557 LYS cc_start: 0.6750 (OUTLIER) cc_final: 0.6478 (mtpt) REVERT: D 12 GLU cc_start: 0.7270 (OUTLIER) cc_final: 0.6917 (pm20) REVERT: D 145 MET cc_start: 0.7619 (pp-130) cc_final: 0.7351 (pp-130) REVERT: F 39 SER cc_start: 0.8505 (OUTLIER) cc_final: 0.8251 (p) REVERT: F 68 GLU cc_start: 0.7410 (OUTLIER) cc_final: 0.7085 (mt-10) REVERT: F 112 ASN cc_start: 0.8451 (m-40) cc_final: 0.7982 (m-40) REVERT: H 141 GLU cc_start: 0.7063 (OUTLIER) cc_final: 0.6644 (pp20) REVERT: G 195 ARG cc_start: 0.6288 (mtp180) cc_final: 0.5874 (mtm110) REVERT: C 293 ARG cc_start: 0.6602 (OUTLIER) cc_final: 0.5936 (mtp-110) REVERT: C 533 ARG cc_start: 0.7424 (mtp85) cc_final: 0.6818 (mtm110) outliers start: 43 outliers final: 28 residues processed: 227 average time/residue: 1.5605 time to fit residues: 384.4322 Evaluate side-chains 236 residues out of total 1692 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 201 time to evaluate : 1.795 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 141 GLU Chi-restraints excluded: chain B residue 145 MET Chi-restraints excluded: chain A residue 163 LEU Chi-restraints excluded: chain A residue 172 VAL Chi-restraints excluded: chain A residue 310 VAL Chi-restraints excluded: chain A residue 312 THR Chi-restraints excluded: chain A residue 366 ARG Chi-restraints excluded: chain A residue 557 LYS Chi-restraints excluded: chain A residue 567 ILE Chi-restraints excluded: chain D residue 12 GLU Chi-restraints excluded: chain D residue 29 THR Chi-restraints excluded: chain D residue 131 ILE Chi-restraints excluded: chain F residue 29 THR Chi-restraints excluded: chain F residue 39 SER Chi-restraints excluded: chain F residue 68 GLU Chi-restraints excluded: chain F residue 131 ILE Chi-restraints excluded: chain H residue 39 SER Chi-restraints excluded: chain H residue 131 ILE Chi-restraints excluded: chain H residue 141 GLU Chi-restraints excluded: chain G residue 163 LEU Chi-restraints excluded: chain G residue 230 ILE Chi-restraints excluded: chain G residue 310 VAL Chi-restraints excluded: chain G residue 366 ARG Chi-restraints excluded: chain G residue 567 ILE Chi-restraints excluded: chain C residue 163 LEU Chi-restraints excluded: chain C residue 172 VAL Chi-restraints excluded: chain C residue 293 ARG Chi-restraints excluded: chain C residue 310 VAL Chi-restraints excluded: chain C residue 366 ARG Chi-restraints excluded: chain C residue 567 ILE Chi-restraints excluded: chain E residue 230 ILE Chi-restraints excluded: chain E residue 310 VAL Chi-restraints excluded: chain E residue 312 THR Chi-restraints excluded: chain E residue 567 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 171 optimal weight: 0.9980 chunk 180 optimal weight: 1.9990 chunk 165 optimal weight: 7.9990 chunk 176 optimal weight: 1.9990 chunk 105 optimal weight: 0.9980 chunk 76 optimal weight: 0.8980 chunk 138 optimal weight: 1.9990 chunk 54 optimal weight: 0.0030 chunk 159 optimal weight: 6.9990 chunk 166 optimal weight: 4.9990 chunk 175 optimal weight: 0.8980 overall best weight: 0.7590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 359 GLN ** G 234 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 359 GLN C 357 GLN C 359 GLN ** E 234 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 359 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7497 moved from start: 0.1002 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 16152 Z= 0.166 Angle : 0.448 8.127 21824 Z= 0.242 Chirality : 0.037 0.253 2444 Planarity : 0.003 0.042 2752 Dihedral : 3.272 17.432 2166 Min Nonbonded Distance : 2.266 Molprobity Statistics. All-atom Clashscore : 6.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 2.59 % Allowed : 19.22 % Favored : 78.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.61 (0.19), residues: 1952 helix: 2.25 (0.13), residues: 1544 sheet: None (None), residues: 0 loop : -0.33 (0.29), residues: 408 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP C 323 HIS 0.005 0.001 HIS E 363 PHE 0.012 0.001 PHE G 332 TYR 0.012 0.001 TYR C 545 ARG 0.008 0.000 ARG E 507 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3904 Ramachandran restraints generated. 1952 Oldfield, 0 Emsley, 1952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3904 Ramachandran restraints generated. 1952 Oldfield, 0 Emsley, 1952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 247 residues out of total 1692 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 204 time to evaluate : 1.807 Fit side-chains REVERT: B 141 GLU cc_start: 0.7190 (OUTLIER) cc_final: 0.6881 (pp20) REVERT: A 557 LYS cc_start: 0.6742 (OUTLIER) cc_final: 0.6482 (mtpt) REVERT: D 12 GLU cc_start: 0.7268 (OUTLIER) cc_final: 0.6920 (pm20) REVERT: F 39 SER cc_start: 0.8502 (OUTLIER) cc_final: 0.8250 (p) REVERT: F 68 GLU cc_start: 0.7436 (OUTLIER) cc_final: 0.7113 (mt-10) REVERT: F 112 ASN cc_start: 0.8454 (m-40) cc_final: 0.7981 (m-40) REVERT: H 141 GLU cc_start: 0.7076 (OUTLIER) cc_final: 0.6648 (pp20) REVERT: G 191 LEU cc_start: 0.6642 (mm) cc_final: 0.6387 (mp) REVERT: G 195 ARG cc_start: 0.6277 (mtp180) cc_final: 0.5838 (mtm110) REVERT: C 293 ARG cc_start: 0.6582 (OUTLIER) cc_final: 0.5910 (mtp-110) REVERT: C 533 ARG cc_start: 0.7417 (mtp85) cc_final: 0.6809 (mtm110) REVERT: E 191 LEU cc_start: 0.6451 (mp) cc_final: 0.6131 (mm) outliers start: 43 outliers final: 28 residues processed: 232 average time/residue: 1.5872 time to fit residues: 399.9155 Evaluate side-chains 238 residues out of total 1692 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 203 time to evaluate : 1.807 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 141 GLU Chi-restraints excluded: chain B residue 145 MET Chi-restraints excluded: chain A residue 163 LEU Chi-restraints excluded: chain A residue 172 VAL Chi-restraints excluded: chain A residue 310 VAL Chi-restraints excluded: chain A residue 312 THR Chi-restraints excluded: chain A residue 366 ARG Chi-restraints excluded: chain A residue 557 LYS Chi-restraints excluded: chain A residue 567 ILE Chi-restraints excluded: chain D residue 12 GLU Chi-restraints excluded: chain D residue 29 THR Chi-restraints excluded: chain F residue 29 THR Chi-restraints excluded: chain F residue 39 SER Chi-restraints excluded: chain F residue 68 GLU Chi-restraints excluded: chain F residue 131 ILE Chi-restraints excluded: chain H residue 39 SER Chi-restraints excluded: chain H residue 131 ILE Chi-restraints excluded: chain H residue 141 GLU Chi-restraints excluded: chain G residue 163 LEU Chi-restraints excluded: chain G residue 230 ILE Chi-restraints excluded: chain G residue 310 VAL Chi-restraints excluded: chain G residue 366 ARG Chi-restraints excluded: chain G residue 567 ILE Chi-restraints excluded: chain C residue 163 LEU Chi-restraints excluded: chain C residue 172 VAL Chi-restraints excluded: chain C residue 293 ARG Chi-restraints excluded: chain C residue 310 VAL Chi-restraints excluded: chain C residue 366 ARG Chi-restraints excluded: chain C residue 567 ILE Chi-restraints excluded: chain E residue 163 LEU Chi-restraints excluded: chain E residue 230 ILE Chi-restraints excluded: chain E residue 310 VAL Chi-restraints excluded: chain E residue 312 THR Chi-restraints excluded: chain E residue 567 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 115 optimal weight: 2.9990 chunk 186 optimal weight: 2.9990 chunk 113 optimal weight: 2.9990 chunk 88 optimal weight: 0.8980 chunk 129 optimal weight: 2.9990 chunk 195 optimal weight: 0.9990 chunk 179 optimal weight: 0.1980 chunk 155 optimal weight: 0.0030 chunk 16 optimal weight: 3.9990 chunk 120 optimal weight: 3.9990 chunk 95 optimal weight: 7.9990 overall best weight: 1.0194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 357 GLN A 359 GLN ** D 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 234 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 357 GLN G 359 GLN C 359 GLN ** E 234 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 357 GLN E 359 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7513 moved from start: 0.1021 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 16152 Z= 0.199 Angle : 0.470 7.495 21824 Z= 0.254 Chirality : 0.038 0.246 2444 Planarity : 0.003 0.044 2752 Dihedral : 3.348 18.403 2166 Min Nonbonded Distance : 2.241 Molprobity Statistics. All-atom Clashscore : 6.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % Rotamer: Outliers : 2.23 % Allowed : 19.58 % Favored : 78.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.47 (0.19), residues: 1952 helix: 2.16 (0.13), residues: 1544 sheet: None (None), residues: 0 loop : -0.37 (0.28), residues: 408 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP E 323 HIS 0.005 0.001 HIS E 363 PHE 0.013 0.001 PHE G 332 TYR 0.013 0.001 TYR G 545 ARG 0.008 0.000 ARG E 507 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3904 Ramachandran restraints generated. 1952 Oldfield, 0 Emsley, 1952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3904 Ramachandran restraints generated. 1952 Oldfield, 0 Emsley, 1952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 235 residues out of total 1692 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 198 time to evaluate : 1.682 Fit side-chains REVERT: B 141 GLU cc_start: 0.7191 (OUTLIER) cc_final: 0.6883 (pp20) REVERT: A 557 LYS cc_start: 0.6748 (OUTLIER) cc_final: 0.5949 (ttpt) REVERT: D 12 GLU cc_start: 0.7269 (OUTLIER) cc_final: 0.6914 (pm20) REVERT: F 39 SER cc_start: 0.8508 (OUTLIER) cc_final: 0.8246 (p) REVERT: F 68 GLU cc_start: 0.7513 (OUTLIER) cc_final: 0.7198 (mt-10) REVERT: H 141 GLU cc_start: 0.7117 (OUTLIER) cc_final: 0.6671 (pp20) REVERT: G 191 LEU cc_start: 0.6607 (mm) cc_final: 0.6299 (mp) REVERT: G 195 ARG cc_start: 0.6298 (mtp180) cc_final: 0.5850 (mtm110) REVERT: C 293 ARG cc_start: 0.6477 (OUTLIER) cc_final: 0.5875 (mtp-110) REVERT: C 533 ARG cc_start: 0.7441 (mtp85) cc_final: 0.6696 (mtm110) REVERT: E 191 LEU cc_start: 0.6443 (mp) cc_final: 0.6122 (mm) outliers start: 37 outliers final: 26 residues processed: 220 average time/residue: 1.5764 time to fit residues: 376.1545 Evaluate side-chains 230 residues out of total 1692 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 197 time to evaluate : 1.857 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 141 GLU Chi-restraints excluded: chain B residue 145 MET Chi-restraints excluded: chain A residue 163 LEU Chi-restraints excluded: chain A residue 172 VAL Chi-restraints excluded: chain A residue 310 VAL Chi-restraints excluded: chain A residue 312 THR Chi-restraints excluded: chain A residue 366 ARG Chi-restraints excluded: chain A residue 557 LYS Chi-restraints excluded: chain A residue 567 ILE Chi-restraints excluded: chain D residue 12 GLU Chi-restraints excluded: chain D residue 29 THR Chi-restraints excluded: chain F residue 29 THR Chi-restraints excluded: chain F residue 39 SER Chi-restraints excluded: chain F residue 68 GLU Chi-restraints excluded: chain F residue 131 ILE Chi-restraints excluded: chain H residue 39 SER Chi-restraints excluded: chain H residue 131 ILE Chi-restraints excluded: chain H residue 141 GLU Chi-restraints excluded: chain G residue 163 LEU Chi-restraints excluded: chain G residue 230 ILE Chi-restraints excluded: chain G residue 310 VAL Chi-restraints excluded: chain G residue 366 ARG Chi-restraints excluded: chain C residue 163 LEU Chi-restraints excluded: chain C residue 293 ARG Chi-restraints excluded: chain C residue 310 VAL Chi-restraints excluded: chain C residue 366 ARG Chi-restraints excluded: chain C residue 567 ILE Chi-restraints excluded: chain E residue 163 LEU Chi-restraints excluded: chain E residue 230 ILE Chi-restraints excluded: chain E residue 310 VAL Chi-restraints excluded: chain E residue 312 THR Chi-restraints excluded: chain E residue 567 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 123 optimal weight: 1.9990 chunk 165 optimal weight: 6.9990 chunk 47 optimal weight: 3.9990 chunk 143 optimal weight: 0.6980 chunk 22 optimal weight: 0.8980 chunk 43 optimal weight: 0.7980 chunk 155 optimal weight: 0.0020 chunk 65 optimal weight: 4.9990 chunk 159 optimal weight: 3.9990 chunk 19 optimal weight: 9.9990 chunk 28 optimal weight: 2.9990 overall best weight: 0.8790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 359 GLN ** D 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 234 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 359 GLN C 357 GLN C 359 GLN ** E 234 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 359 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4053 r_free = 0.4053 target = 0.183686 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3708 r_free = 0.3708 target = 0.149390 restraints weight = 15654.481| |-----------------------------------------------------------------------------| r_work (start): 0.3686 rms_B_bonded: 1.86 r_work: 0.3478 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.3329 rms_B_bonded: 4.46 restraints_weight: 0.2500 r_work (final): 0.3329 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3317 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3317 r_free = 0.3317 target_work(ls_wunit_k1) = 0.116 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3317 r_free = 0.3317 target_work(ls_wunit_k1) = 0.116 | | occupancies: max = 1.00 min = 0.31 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3317 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8115 moved from start: 0.1031 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 16152 Z= 0.183 Angle : 0.461 7.407 21824 Z= 0.249 Chirality : 0.037 0.236 2444 Planarity : 0.003 0.045 2752 Dihedral : 3.312 17.423 2166 Min Nonbonded Distance : 2.246 Molprobity Statistics. All-atom Clashscore : 6.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.90 % Favored : 98.10 % Rotamer: Outliers : 2.35 % Allowed : 19.76 % Favored : 77.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.55 (0.19), residues: 1952 helix: 2.21 (0.13), residues: 1540 sheet: None (None), residues: 0 loop : -0.34 (0.28), residues: 412 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP C 323 HIS 0.002 0.001 HIS G 363 PHE 0.013 0.001 PHE E 332 TYR 0.012 0.001 TYR C 545 ARG 0.009 0.000 ARG E 507 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6198.28 seconds wall clock time: 109 minutes 42.07 seconds (6582.07 seconds total)