Starting phenix.real_space_refine on Sat Apr 13 09:22:18 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ovw_17224/04_2024/8ovw_17224.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ovw_17224/04_2024/8ovw_17224.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ovw_17224/04_2024/8ovw_17224.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ovw_17224/04_2024/8ovw_17224.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ovw_17224/04_2024/8ovw_17224.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ovw_17224/04_2024/8ovw_17224.pdb" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.005 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 54 5.49 5 S 109 5.16 5 C 17953 2.51 5 N 4873 2.21 5 O 5472 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 236": "OE1" <-> "OE2" Residue "A ARG 252": "NH1" <-> "NH2" Residue "A GLU 275": "OE1" <-> "OE2" Residue "A GLU 289": "OE1" <-> "OE2" Residue "A GLU 305": "OE1" <-> "OE2" Residue "A GLU 314": "OE1" <-> "OE2" Residue "B GLU 229": "OE1" <-> "OE2" Residue "B ARG 234": "NH1" <-> "NH2" Residue "B GLU 253": "OE1" <-> "OE2" Residue "B GLU 272": "OE1" <-> "OE2" Residue "B GLU 279": "OE1" <-> "OE2" Residue "B TYR 310": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 312": "OE1" <-> "OE2" Residue "H GLU 10": "OE1" <-> "OE2" Residue "H ARG 32": "NH1" <-> "NH2" Residue "H ARG 51": "NH1" <-> "NH2" Residue "H PHE 83": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 92": "OE1" <-> "OE2" Residue "H TYR 98": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ASP 122": "OD1" <-> "OD2" Residue "H GLU 155": "OE1" <-> "OE2" Residue "H GLU 159": "OE1" <-> "OE2" Residue "H GLU 163": "OE1" <-> "OE2" Residue "I ARG 99": "NH1" <-> "NH2" Residue "I ARG 193": "NH1" <-> "NH2" Residue "I PHE 230": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 246": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ARG 328": "NH1" <-> "NH2" Residue "I GLU 358": "OE1" <-> "OE2" Residue "I GLU 377": "OE1" <-> "OE2" Residue "I ASP 389": "OD1" <-> "OD2" Residue "I PHE 458": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 507": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 512": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 530": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ARG 579": "NH1" <-> "NH2" Residue "I ASP 587": "OD1" <-> "OD2" Residue "I PHE 630": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I GLU 651": "OE1" <-> "OE2" Residue "I GLU 654": "OE1" <-> "OE2" Residue "I PHE 660": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I GLU 668": "OE1" <-> "OE2" Residue "I PHE 670": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K GLU 44": "OE1" <-> "OE2" Residue "K GLU 51": "OE1" <-> "OE2" Residue "K GLU 55": "OE1" <-> "OE2" Residue "K ARG 119": "NH1" <-> "NH2" Residue "K PHE 155": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K TYR 159": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ASP 168": "OD1" <-> "OD2" Residue "K GLU 169": "OE1" <-> "OE2" Residue "K GLU 187": "OE1" <-> "OE2" Residue "K GLU 218": "OE1" <-> "OE2" Residue "K PHE 233": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L GLU 30": "OE1" <-> "OE2" Residue "L TYR 56": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 86": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ASP 93": "OD1" <-> "OD2" Residue "L GLU 97": "OE1" <-> "OE2" Residue "L GLU 106": "OE1" <-> "OE2" Residue "L TYR 107": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L GLU 117": "OE1" <-> "OE2" Residue "L GLU 135": "OE1" <-> "OE2" Residue "L GLU 164": "OE1" <-> "OE2" Residue "L GLU 168": "OE1" <-> "OE2" Residue "L TYR 184": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N ARG 67": "NH1" <-> "NH2" Residue "N ARG 68": "NH1" <-> "NH2" Residue "N GLU 102": "OE1" <-> "OE2" Residue "N ARG 158": "NH1" <-> "NH2" Residue "N PHE 204": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N TYR 220": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N GLU 265": "OE1" <-> "OE2" Residue "N GLU 301": "OE1" <-> "OE2" Residue "N ASP 304": "OD1" <-> "OD2" Residue "N GLU 320": "OE1" <-> "OE2" Residue "N PHE 333": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N GLU 392": "OE1" <-> "OE2" Residue "N PHE 447": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O GLU 161": "OE1" <-> "OE2" Residue "O TYR 163": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O PHE 178": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O GLU 200": "OE1" <-> "OE2" Residue "O ARG 212": "NH1" <-> "NH2" Residue "O TYR 221": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O ARG 227": "NH1" <-> "NH2" Residue "O ASP 245": "OD1" <-> "OD2" Residue "O PHE 309": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O PHE 318": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O GLU 356": "OE1" <-> "OE2" Residue "P PHE 104": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P ARG 124": "NH1" <-> "NH2" Residue "P GLU 126": "OE1" <-> "OE2" Residue "P PHE 189": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P ARG 267": "NH1" <-> "NH2" Residue "P ARG 284": "NH1" <-> "NH2" Residue "P ARG 287": "NH1" <-> "NH2" Residue "P PHE 300": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P GLU 339": "OE1" <-> "OE2" Residue "P TYR 342": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P TYR 348": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P GLU 356": "OE1" <-> "OE2" Residue "P TYR 367": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q GLU 129": "OE1" <-> "OE2" Residue "Q GLU 137": "OE1" <-> "OE2" Residue "Q GLU 140": "OE1" <-> "OE2" Residue "Q GLU 147": "OE1" <-> "OE2" Residue "Q GLU 167": "OE1" <-> "OE2" Residue "Q GLU 182": "OE1" <-> "OE2" Residue "Q GLU 184": "OE1" <-> "OE2" Residue "Q GLU 195": "OE1" <-> "OE2" Residue "Q GLU 204": "OE1" <-> "OE2" Residue "Q GLU 208": "OE1" <-> "OE2" Residue "Q PHE 223": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q ARG 264": "NH1" <-> "NH2" Residue "Q GLU 271": "OE1" <-> "OE2" Residue "Q ARG 286": "NH1" <-> "NH2" Residue "Q GLU 289": "OE1" <-> "OE2" Residue "Q TYR 306": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q TYR 363": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q GLU 372": "OE1" <-> "OE2" Residue "Q GLU 388": "OE1" <-> "OE2" Residue "T GLU 323": "OE1" <-> "OE2" Residue "T GLU 351": "OE1" <-> "OE2" Residue "T TYR 359": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U GLU 147": "OE1" <-> "OE2" Residue "U ASP 163": "OD1" <-> "OD2" Residue "U TYR 204": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U ARG 212": "NH1" <-> "NH2" Residue "U GLU 214": "OE1" <-> "OE2" Residue "U GLU 226": "OE1" <-> "OE2" Residue "U GLU 229": "OE1" <-> "OE2" Residue "W GLU 68": "OE1" <-> "OE2" Residue "W GLU 79": "OE1" <-> "OE2" Residue "W ASP 87": "OD1" <-> "OD2" Residue "Y TYR 67": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y GLU 96": "OE1" <-> "OE2" Residue "Y GLU 115": "OE1" <-> "OE2" Residue "Y ASP 149": "OD1" <-> "OD2" Residue "Z TYR 10": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z ASP 13": "OD1" <-> "OD2" Residue "Z GLU 24": "OE1" <-> "OE2" Residue "Z TYR 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z GLU 36": "OE1" <-> "OE2" Residue "Z TYR 43": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z GLU 44": "OE1" <-> "OE2" Residue "Z ARG 49": "NH1" <-> "NH2" Residue "Z ARG 52": "NH1" <-> "NH2" Residue "Z GLU 79": "OE1" <-> "OE2" Time to flip residues: 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 28461 Number of models: 1 Model: "" Number of chains: 17 Chain: "A" Number of atoms: 822 Number of conformers: 1 Conformer: "" Number of residues, atoms: 101, 822 Classifications: {'peptide': 101} Link IDs: {'PTRANS': 1, 'TRANS': 99} Chain: "B" Number of atoms: 876 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 876 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 1, 'TRANS': 105} Chain: "D" Number of atoms: 553 Number of conformers: 1 Conformer: "" Number of residues, atoms: 27, 553 Classifications: {'DNA': 27} Link IDs: {'rna3p': 26} Chain: "H" Number of atoms: 1412 Number of conformers: 1 Conformer: "" Number of residues, atoms: 171, 1412 Classifications: {'peptide': 171} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 167} Chain breaks: 1 Chain: "I" Number of atoms: 5496 Number of conformers: 1 Conformer: "" Number of residues, atoms: 679, 5496 Classifications: {'peptide': 679} Link IDs: {'PTRANS': 27, 'TRANS': 651} Chain breaks: 4 Chain: "K" Number of atoms: 1762 Number of conformers: 1 Conformer: "" Number of residues, atoms: 219, 1762 Classifications: {'peptide': 219} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 6, 'TRANS': 212} Chain breaks: 2 Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "L" Number of atoms: 1941 Number of conformers: 1 Conformer: "" Number of residues, atoms: 241, 1941 Classifications: {'peptide': 241} Link IDs: {'PTRANS': 9, 'TRANS': 231} Chain: "N" Number of atoms: 3166 Number of conformers: 1 Conformer: "" Number of residues, atoms: 391, 3166 Classifications: {'peptide': 391} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 21, 'TRANS': 369} Chain breaks: 3 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "O" Number of atoms: 1979 Number of conformers: 1 Conformer: "" Number of residues, atoms: 241, 1979 Classifications: {'peptide': 241} Link IDs: {'PTRANS': 6, 'TRANS': 234} Chain breaks: 1 Chain: "P" Number of atoms: 2116 Number of conformers: 1 Conformer: "" Number of residues, atoms: 257, 2116 Classifications: {'peptide': 257} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 6, 'TRANS': 250} Chain breaks: 2 Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'ARG:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 8 Chain: "Q" Number of atoms: 2144 Number of conformers: 1 Conformer: "" Number of residues, atoms: 258, 2144 Classifications: {'peptide': 258} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 8, 'TRANS': 249} Chain breaks: 1 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 23 Unresolved non-hydrogen angles: 28 Unresolved non-hydrogen dihedrals: 19 Planarities with less than four sites: {'GLU:plan': 2, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 18 Chain: "T" Number of atoms: 761 Number of conformers: 1 Conformer: "" Number of residues, atoms: 92, 761 Classifications: {'peptide': 92} Link IDs: {'PTRANS': 3, 'TRANS': 88} Chain: "U" Number of atoms: 1485 Number of conformers: 1 Conformer: "" Number of residues, atoms: 184, 1485 Classifications: {'peptide': 184} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 2, 'TRANS': 181} Chain breaks: 1 Unresolved non-hydrogen bonds: 21 Unresolved non-hydrogen angles: 27 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1, 'ASN:plan1': 2} Unresolved non-hydrogen planarities: 14 Chain: "W" Number of atoms: 551 Number of conformers: 1 Conformer: "" Number of residues, atoms: 69, 551 Classifications: {'peptide': 69} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 67} Chain breaks: 1 Chain: "Y" Number of atoms: 1663 Number of conformers: 1 Conformer: "" Number of residues, atoms: 223, 1663 Classifications: {'peptide': 223} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 29} Link IDs: {'PTRANS': 5, 'TRANS': 217} Chain breaks: 2 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 106 Unresolved non-hydrogen angles: 129 Unresolved non-hydrogen dihedrals: 89 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'TYR:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 4, 'PHE:plan': 1, 'GLU:plan': 3, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 45 Chain: "Z" Number of atoms: 1180 Number of conformers: 1 Conformer: "" Number of residues, atoms: 151, 1180 Classifications: {'peptide': 151} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 19} Link IDs: {'PTRANS': 2, 'TRANS': 148} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 65 Unresolved non-hydrogen angles: 85 Unresolved non-hydrogen dihedrals: 49 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'GLN:plan1': 2, 'TYR:plan': 1, 'ASN:plan1': 2, 'ASP:plan': 1, 'GLU:plan': 2, 'ASN%COO:plan1': 1} Unresolved non-hydrogen planarities: 35 Chain: "E" Number of atoms: 554 Number of conformers: 1 Conformer: "" Number of residues, atoms: 27, 554 Classifications: {'DNA': 27} Link IDs: {'rna3p': 26} Time building chain proxies: 14.65, per 1000 atoms: 0.51 Number of scatterers: 28461 At special positions: 0 Unit cell: (131.152, 187.36, 176.821, 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) S 109 16.00 P 54 15.00 O 5472 8.00 N 4873 7.00 C 17953 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: 11.39 Conformation dependent library (CDL) restraints added in 4.8 seconds 6636 Ramachandran restraints generated. 3318 Oldfield, 0 Emsley, 3318 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6548 Finding SS restraints... Secondary structure from input PDB file: 139 helices and 16 sheets defined 67.1% alpha, 9.5% beta 25 base pairs and 44 stacking pairs defined. Time for finding SS restraints: 9.18 Creating SS restraints... Processing helix chain 'A' and resid 229 through 249 removed outlier: 3.619A pdb=" N ARG A 233 " --> pdb=" O GLU A 229 " (cutoff:3.500A) Processing helix chain 'A' and resid 255 through 320 Processing helix chain 'B' and resid 219 through 248 Processing helix chain 'B' and resid 255 through 324 Processing helix chain 'H' and resid 5 through 39 Processing helix chain 'H' and resid 46 through 74 removed outlier: 3.846A pdb=" N LEU H 52 " --> pdb=" O THR H 48 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N LEU H 72 " --> pdb=" O LEU H 68 " (cutoff:3.500A) Processing helix chain 'H' and resid 80 through 94 removed outlier: 3.648A pdb=" N THR H 84 " --> pdb=" O ASN H 80 " (cutoff:3.500A) Processing helix chain 'H' and resid 96 through 133 removed outlier: 3.543A pdb=" N LEU H 100 " --> pdb=" O LEU H 96 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N LEU H 101 " --> pdb=" O ASP H 97 " (cutoff:3.500A) Processing helix chain 'H' and resid 148 through 172 removed outlier: 3.806A pdb=" N GLU H 153 " --> pdb=" O GLY H 149 " (cutoff:3.500A) Processing helix chain 'I' and resid 3 through 13 Processing helix chain 'I' and resid 26 through 38 Processing helix chain 'I' and resid 41 through 55 removed outlier: 3.570A pdb=" N THR I 55 " --> pdb=" O LEU I 51 " (cutoff:3.500A) Processing helix chain 'I' and resid 59 through 70 Processing helix chain 'I' and resid 78 through 89 removed outlier: 3.615A pdb=" N LEU I 82 " --> pdb=" O THR I 78 " (cutoff:3.500A) Processing helix chain 'I' and resid 103 through 117 Processing helix chain 'I' and resid 131 through 139 Processing helix chain 'I' and resid 145 through 157 removed outlier: 4.005A pdb=" N THR I 150 " --> pdb=" O GLN I 146 " (cutoff:3.500A) Proline residue: I 151 - end of helix Processing helix chain 'I' and resid 164 through 176 Processing helix chain 'I' and resid 182 through 199 removed outlier: 3.857A pdb=" N GLY I 199 " --> pdb=" O GLN I 195 " (cutoff:3.500A) Processing helix chain 'I' and resid 204 through 211 Processing helix chain 'I' and resid 216 through 222 Processing helix chain 'I' and resid 227 through 241 Processing helix chain 'I' and resid 247 through 264 removed outlier: 3.655A pdb=" N ILE I 262 " --> pdb=" O TYR I 258 " (cutoff:3.500A) Processing helix chain 'I' and resid 265 through 267 No H-bonds generated for 'chain 'I' and resid 265 through 267' Processing helix chain 'I' and resid 295 through 302 removed outlier: 3.819A pdb=" N LEU I 299 " --> pdb=" O SER I 295 " (cutoff:3.500A) removed outlier: 4.086A pdb=" N ALA I 300 " --> pdb=" O LEU I 296 " (cutoff:3.500A) removed outlier: 4.253A pdb=" N GLN I 301 " --> pdb=" O GLU I 297 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N ASN I 302 " --> pdb=" O GLN I 298 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 295 through 302' Processing helix chain 'I' and resid 311 through 317 Processing helix chain 'I' and resid 332 through 337 removed outlier: 3.800A pdb=" N LEU I 336 " --> pdb=" O ARG I 333 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N LYS I 337 " --> pdb=" O ASP I 334 " (cutoff:3.500A) Processing helix chain 'I' and resid 339 through 348 Processing helix chain 'I' and resid 354 through 369 Processing helix chain 'I' and resid 378 through 387 Processing helix chain 'I' and resid 389 through 401 removed outlier: 3.527A pdb=" N SER I 393 " --> pdb=" O ASP I 389 " (cutoff:3.500A) Processing helix chain 'I' and resid 402 through 409 Processing helix chain 'I' and resid 409 through 421 removed outlier: 3.534A pdb=" N LEU I 413 " --> pdb=" O ASP I 409 " (cutoff:3.500A) Processing helix chain 'I' and resid 422 through 424 No H-bonds generated for 'chain 'I' and resid 422 through 424' Processing helix chain 'I' and resid 431 through 450 removed outlier: 4.200A pdb=" N ASP I 450 " --> pdb=" O TRP I 446 " (cutoff:3.500A) Processing helix chain 'I' and resid 456 through 475 removed outlier: 3.896A pdb=" N ASP I 475 " --> pdb=" O ASN I 471 " (cutoff:3.500A) Processing helix chain 'I' and resid 478 through 494 Processing helix chain 'I' and resid 505 through 524 removed outlier: 3.532A pdb=" N LYS I 524 " --> pdb=" O THR I 520 " (cutoff:3.500A) Processing helix chain 'I' and resid 531 through 535 removed outlier: 3.623A pdb=" N TYR I 534 " --> pdb=" O ALA I 531 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N LEU I 535 " --> pdb=" O ILE I 532 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 531 through 535' Processing helix chain 'I' and resid 538 through 548 removed outlier: 3.798A pdb=" N MET I 542 " --> pdb=" O GLY I 538 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N LYS I 544 " --> pdb=" O ASP I 540 " (cutoff:3.500A) Processing helix chain 'I' and resid 550 through 569 Processing helix chain 'I' and resid 577 through 593 Processing helix chain 'I' and resid 607 through 616 removed outlier: 3.763A pdb=" N PHE I 611 " --> pdb=" O SER I 607 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N LEU I 615 " --> pdb=" O PHE I 611 " (cutoff:3.500A) Processing helix chain 'I' and resid 639 through 654 removed outlier: 3.526A pdb=" N CYS I 643 " --> pdb=" O LEU I 639 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N ILE I 644 " --> pdb=" O SER I 640 " (cutoff:3.500A) Processing helix chain 'I' and resid 666 through 677 removed outlier: 3.586A pdb=" N HIS I 677 " --> pdb=" O PHE I 673 " (cutoff:3.500A) Processing helix chain 'I' and resid 677 through 684 removed outlier: 3.667A pdb=" N GLN I 683 " --> pdb=" O ASP I 679 " (cutoff:3.500A) Processing helix chain 'I' and resid 692 through 705 Processing helix chain 'I' and resid 711 through 721 removed outlier: 4.120A pdb=" N ALA I 715 " --> pdb=" O TYR I 711 " (cutoff:3.500A) Processing helix chain 'I' and resid 725 through 729 removed outlier: 3.767A pdb=" N SER I 729 " --> pdb=" O SER I 726 " (cutoff:3.500A) Processing helix chain 'K' and resid 6 through 40 Processing helix chain 'K' and resid 49 through 58 Processing helix chain 'K' and resid 70 through 130 removed outlier: 3.875A pdb=" N SER K 130 " --> pdb=" O THR K 126 " (cutoff:3.500A) Processing helix chain 'K' and resid 138 through 159 Processing helix chain 'K' and resid 159 through 165 Processing helix chain 'K' and resid 166 through 169 Processing helix chain 'K' and resid 170 through 187 removed outlier: 3.840A pdb=" N LEU K 174 " --> pdb=" O SER K 170 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N GLU K 177 " --> pdb=" O SER K 173 " (cutoff:3.500A) Processing helix chain 'K' and resid 201 through 211 Processing helix chain 'L' and resid 19 through 28 removed outlier: 3.738A pdb=" N LEU L 23 " --> pdb=" O GLY L 19 " (cutoff:3.500A) Processing helix chain 'L' and resid 43 through 47 removed outlier: 3.526A pdb=" N GLY L 47 " --> pdb=" O PRO L 44 " (cutoff:3.500A) Processing helix chain 'L' and resid 94 through 108 removed outlier: 3.922A pdb=" N VAL L 98 " --> pdb=" O ASN L 94 " (cutoff:3.500A) Processing helix chain 'L' and resid 117 through 128 Processing helix chain 'L' and resid 153 through 157 Processing helix chain 'L' and resid 166 through 178 Processing helix chain 'L' and resid 182 through 187 Processing helix chain 'L' and resid 187 through 197 Processing helix chain 'L' and resid 229 through 240 Processing helix chain 'N' and resid 16 through 25 Processing helix chain 'N' and resid 28 through 43 Processing helix chain 'N' and resid 50 through 64 Processing helix chain 'N' and resid 67 through 78 removed outlier: 3.892A pdb=" N ILE N 71 " --> pdb=" O ARG N 67 " (cutoff:3.500A) Processing helix chain 'N' and resid 85 through 100 removed outlier: 3.713A pdb=" N ASP N 93 " --> pdb=" O LEU N 89 " (cutoff:3.500A) Processing helix chain 'N' and resid 101 through 103 No H-bonds generated for 'chain 'N' and resid 101 through 103' Processing helix chain 'N' and resid 124 through 137 Processing helix chain 'N' and resid 218 through 234 removed outlier: 3.777A pdb=" N SER N 233 " --> pdb=" O SER N 229 " (cutoff:3.500A) removed outlier: 4.530A pdb=" N GLU N 234 " --> pdb=" O ARG N 230 " (cutoff:3.500A) Processing helix chain 'N' and resid 250 through 258 removed outlier: 3.565A pdb=" N ILE N 254 " --> pdb=" O SER N 250 " (cutoff:3.500A) Processing helix chain 'N' and resid 267 through 269 No H-bonds generated for 'chain 'N' and resid 267 through 269' Processing helix chain 'N' and resid 270 through 276 removed outlier: 3.587A pdb=" N ALA N 274 " --> pdb=" O TRP N 270 " (cutoff:3.500A) Processing helix chain 'N' and resid 289 through 294 Processing helix chain 'N' and resid 318 through 335 Processing helix chain 'N' and resid 408 through 419 Processing helix chain 'N' and resid 428 through 433 Processing helix chain 'O' and resid 134 through 139 removed outlier: 4.142A pdb=" N THR O 138 " --> pdb=" O THR O 134 " (cutoff:3.500A) Processing helix chain 'O' and resid 139 through 148 removed outlier: 3.709A pdb=" N ARG O 143 " --> pdb=" O SER O 139 " (cutoff:3.500A) Processing helix chain 'O' and resid 154 through 172 Processing helix chain 'O' and resid 182 through 184 No H-bonds generated for 'chain 'O' and resid 182 through 184' Processing helix chain 'O' and resid 245 through 253 Processing helix chain 'O' and resid 254 through 256 No H-bonds generated for 'chain 'O' and resid 254 through 256' Processing helix chain 'O' and resid 260 through 291 removed outlier: 3.754A pdb=" N GLN O 274 " --> pdb=" O ARG O 270 " (cutoff:3.500A) Processing helix chain 'O' and resid 338 through 348 Processing helix chain 'O' and resid 352 through 364 removed outlier: 3.764A pdb=" N ALA O 364 " --> pdb=" O ASN O 360 " (cutoff:3.500A) Processing helix chain 'P' and resid 99 through 112 Processing helix chain 'P' and resid 133 through 140 Processing helix chain 'P' and resid 149 through 160 Processing helix chain 'P' and resid 224 through 232 Processing helix chain 'P' and resid 236 through 266 removed outlier: 3.618A pdb=" N CYS P 240 " --> pdb=" O ASN P 236 " (cutoff:3.500A) Processing helix chain 'P' and resid 333 through 349 Processing helix chain 'P' and resid 350 through 363 Processing helix chain 'P' and resid 364 through 368 removed outlier: 3.838A pdb=" N ALA P 368 " --> pdb=" O ASP P 365 " (cutoff:3.500A) Processing helix chain 'Q' and resid 129 through 141 removed outlier: 3.728A pdb=" N VAL Q 133 " --> pdb=" O GLU Q 129 " (cutoff:3.500A) Processing helix chain 'Q' and resid 155 through 181 Processing helix chain 'Q' and resid 181 through 190 removed outlier: 3.549A pdb=" N MET Q 185 " --> pdb=" O TYR Q 181 " (cutoff:3.500A) Processing helix chain 'Q' and resid 192 through 220 removed outlier: 3.551A pdb=" N VAL Q 196 " --> pdb=" O ASP Q 192 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N GLN Q 220 " --> pdb=" O LYS Q 216 " (cutoff:3.500A) Processing helix chain 'Q' and resid 233 through 290 removed outlier: 3.576A pdb=" N ILE Q 237 " --> pdb=" O ASP Q 233 " (cutoff:3.500A) Processing helix chain 'Q' and resid 297 through 299 No H-bonds generated for 'chain 'Q' and resid 297 through 299' Processing helix chain 'Q' and resid 300 through 308 Processing helix chain 'Q' and resid 321 through 332 removed outlier: 4.045A pdb=" N HIS Q 330 " --> pdb=" O ARG Q 326 " (cutoff:3.500A) Processing helix chain 'Q' and resid 349 through 357 Processing helix chain 'Q' and resid 358 through 382 removed outlier: 4.019A pdb=" N GLU Q 362 " --> pdb=" O PRO Q 358 " (cutoff:3.500A) Processing helix chain 'Q' and resid 382 through 389 removed outlier: 3.642A pdb=" N VAL Q 389 " --> pdb=" O GLU Q 385 " (cutoff:3.500A) Processing helix chain 'T' and resid 274 through 283 Processing helix chain 'T' and resid 284 through 289 Processing helix chain 'T' and resid 294 through 316 removed outlier: 4.112A pdb=" N LEU T 306 " --> pdb=" O GLN T 302 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N ASN T 307 " --> pdb=" O GLU T 303 " (cutoff:3.500A) Processing helix chain 'T' and resid 320 through 331 removed outlier: 3.863A pdb=" N LEU T 324 " --> pdb=" O GLN T 320 " (cutoff:3.500A) removed outlier: 4.085A pdb=" N VAL T 325 " --> pdb=" O LYS T 321 " (cutoff:3.500A) Processing helix chain 'T' and resid 336 through 344 Processing helix chain 'T' and resid 349 through 360 Processing helix chain 'U' and resid 134 through 149 Processing helix chain 'U' and resid 150 through 161 Processing helix chain 'U' and resid 164 through 232 removed outlier: 3.995A pdb=" N ASN U 200 " --> pdb=" O ASN U 196 " (cutoff:3.500A) Processing helix chain 'U' and resid 233 through 265 removed outlier: 3.599A pdb=" N HIS U 237 " --> pdb=" O GLY U 233 " (cutoff:3.500A) Processing helix chain 'U' and resid 286 through 299 removed outlier: 3.506A pdb=" N LEU U 290 " --> pdb=" O ASP U 286 " (cutoff:3.500A) Processing helix chain 'U' and resid 305 through 321 Processing helix chain 'W' and resid 2 through 15 Processing helix chain 'W' and resid 37 through 69 Processing helix chain 'W' and resid 74 through 88 Processing helix chain 'Y' and resid 3 through 16 removed outlier: 3.673A pdb=" N SER Y 7 " --> pdb=" O ASP Y 3 " (cutoff:3.500A) Processing helix chain 'Y' and resid 17 through 30 Processing helix chain 'Y' and resid 36 through 50 Processing helix chain 'Y' and resid 55 through 84 Processing helix chain 'Y' and resid 94 through 102 Processing helix chain 'Y' and resid 109 through 119 removed outlier: 3.623A pdb=" N LYS Y 119 " --> pdb=" O GLU Y 115 " (cutoff:3.500A) Processing helix chain 'Y' and resid 137 through 186 removed outlier: 3.595A pdb=" N GLU Y 186 " --> pdb=" O LYS Y 182 " (cutoff:3.500A) Processing helix chain 'Y' and resid 191 through 219 removed outlier: 4.528A pdb=" N ALA Y 195 " --> pdb=" O SER Y 191 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N PHE Y 219 " --> pdb=" O ALA Y 215 " (cutoff:3.500A) Processing helix chain 'Y' and resid 222 through 238 Processing helix chain 'Z' and resid 4 through 13 Processing helix chain 'Z' and resid 15 through 20 Processing helix chain 'Z' and resid 21 through 29 Processing helix chain 'Z' and resid 35 through 84 Processing helix chain 'Z' and resid 86 through 127 removed outlier: 3.540A pdb=" N LEU Z 90 " --> pdb=" O SER Z 86 " (cutoff:3.500A) Processing helix chain 'Z' and resid 134 through 153 removed outlier: 3.547A pdb=" N ASN Z 153 " --> pdb=" O LEU Z 149 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'I' and resid 288 through 289 removed outlier: 6.510A pdb=" N VAL I 288 " --> pdb=" O HIS I 307 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'K' and resid 214 through 218 removed outlier: 3.699A pdb=" N LYS K 229 " --> pdb=" O THR K 215 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'L' and resid 35 through 36 removed outlier: 3.798A pdb=" N MET L 85 " --> pdb=" O ILE L 10 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N TRP L 112 " --> pdb=" O GLY L 9 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'L' and resid 35 through 36 removed outlier: 3.798A pdb=" N MET L 85 " --> pdb=" O ILE L 10 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N SER L 220 " --> pdb=" O MET L 217 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N VAL L 222 " --> pdb=" O LYS L 215 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'L' and resid 130 through 132 Processing sheet with id=AA6, first strand: chain 'N' and resid 141 through 148 removed outlier: 3.943A pdb=" N HIS N 141 " --> pdb=" O PHE N 162 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N VAL N 202 " --> pdb=" O THR N 157 " (cutoff:3.500A) removed outlier: 6.209A pdb=" N TYR N 201 " --> pdb=" O SER N 214 " (cutoff:3.500A) removed outlier: 7.516A pdb=" N ILE N 210 " --> pdb=" O PRO N 205 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'N' and resid 141 through 148 removed outlier: 3.943A pdb=" N HIS N 141 " --> pdb=" O PHE N 162 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N VAL N 202 " --> pdb=" O THR N 157 " (cutoff:3.500A) removed outlier: 6.209A pdb=" N TYR N 201 " --> pdb=" O SER N 214 " (cutoff:3.500A) removed outlier: 7.516A pdb=" N ILE N 210 " --> pdb=" O PRO N 205 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'N' and resid 295 through 298 Processing sheet with id=AA9, first strand: chain 'O' and resid 175 through 180 removed outlier: 4.360A pdb=" N LEU O 180 " --> pdb=" O MET O 201 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N MET O 201 " --> pdb=" O LEU O 180 " (cutoff:3.500A) removed outlier: 6.625A pdb=" N LYS O 225 " --> pdb=" O LEU O 235 " (cutoff:3.500A) removed outlier: 5.612A pdb=" N LEU O 235 " --> pdb=" O LYS O 225 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'O' and resid 186 through 188 Processing sheet with id=AB2, first strand: chain 'O' and resid 209 through 210 Processing sheet with id=AB3, first strand: chain 'O' and resid 305 through 309 removed outlier: 6.212A pdb=" N LYS O 320 " --> pdb=" O ILE O 324 " (cutoff:3.500A) removed outlier: 5.254A pdb=" N ILE O 324 " --> pdb=" O LYS O 320 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'P' and resid 165 through 171 removed outlier: 3.518A pdb=" N GLN P 170 " --> pdb=" O VAL P 184 " (cutoff:3.500A) removed outlier: 7.202A pdb=" N VAL P 184 " --> pdb=" O GLN P 170 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'P' and resid 165 through 171 removed outlier: 3.518A pdb=" N GLN P 170 " --> pdb=" O VAL P 184 " (cutoff:3.500A) removed outlier: 7.202A pdb=" N VAL P 184 " --> pdb=" O GLN P 170 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N PHE P 197 " --> pdb=" O PHE P 189 " (cutoff:3.500A) removed outlier: 6.990A pdb=" N GLU P 198 " --> pdb=" O ILE P 220 " (cutoff:3.500A) removed outlier: 4.867A pdb=" N ILE P 220 " --> pdb=" O GLU P 198 " (cutoff:3.500A) removed outlier: 6.729A pdb=" N GLN P 200 " --> pdb=" O LEU P 218 " (cutoff:3.500A) removed outlier: 4.276A pdb=" N LYS P 214 " --> pdb=" O PHE P 204 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'P' and resid 270 through 274 removed outlier: 3.550A pdb=" N SER P 322 " --> pdb=" O ASN P 299 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'P' and resid 270 through 274 removed outlier: 3.550A pdb=" N SER P 322 " --> pdb=" O ASN P 299 " (cutoff:3.500A) removed outlier: 6.619A pdb=" N SER P 319 " --> pdb=" O MET Q 335 " (cutoff:3.500A) 1869 hydrogen bonds defined for protein. 5517 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 62 hydrogen bonds 124 hydrogen bond angles 0 basepair planarities 25 basepair parallelities 44 stacking parallelities Total time for adding SS restraints: 10.08 Time building geometry restraints manager: 12.35 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 4921 1.32 - 1.45: 7342 1.45 - 1.57: 16490 1.57 - 1.70: 106 1.70 - 1.82: 182 Bond restraints: 29041 Sorted by residual: bond pdb=" N ARG P 308 " pdb=" CA ARG P 308 " ideal model delta sigma weight residual 1.458 1.531 -0.073 1.90e-02 2.77e+03 1.47e+01 bond pdb=" C ALA I 241 " pdb=" N HIS I 242 " ideal model delta sigma weight residual 1.328 1.377 -0.049 1.44e-02 4.82e+03 1.15e+01 bond pdb=" N LYS Q 222 " pdb=" CA LYS Q 222 " ideal model delta sigma weight residual 1.456 1.497 -0.040 1.21e-02 6.83e+03 1.10e+01 bond pdb=" N ALA Q 221 " pdb=" CA ALA Q 221 " ideal model delta sigma weight residual 1.455 1.495 -0.040 1.29e-02 6.01e+03 9.61e+00 bond pdb=" N HIS I 242 " pdb=" CA HIS I 242 " ideal model delta sigma weight residual 1.454 1.492 -0.038 1.29e-02 6.01e+03 8.68e+00 ... (remaining 29036 not shown) Histogram of bond angle deviations from ideal: 97.68 - 105.02: 553 105.02 - 112.36: 14935 112.36 - 119.69: 9967 119.69 - 127.03: 13588 127.03 - 134.37: 360 Bond angle restraints: 39403 Sorted by residual: angle pdb=" N PRO Y 223 " pdb=" CA PRO Y 223 " pdb=" CB PRO Y 223 " ideal model delta sigma weight residual 103.44 110.05 -6.61 1.12e+00 7.97e-01 3.48e+01 angle pdb=" N PRO Z 137 " pdb=" CA PRO Z 137 " pdb=" CB PRO Z 137 " ideal model delta sigma weight residual 103.44 110.02 -6.58 1.12e+00 7.97e-01 3.45e+01 angle pdb=" N GLN Y 45 " pdb=" CA GLN Y 45 " pdb=" CB GLN Y 45 " ideal model delta sigma weight residual 110.30 118.32 -8.02 1.54e+00 4.22e-01 2.71e+01 angle pdb=" N GLN H 14 " pdb=" CA GLN H 14 " pdb=" CB GLN H 14 " ideal model delta sigma weight residual 110.28 118.15 -7.87 1.55e+00 4.16e-01 2.58e+01 angle pdb=" CA ILE Z 136 " pdb=" C ILE Z 136 " pdb=" N PRO Z 137 " ideal model delta sigma weight residual 121.00 117.30 3.70 8.30e-01 1.45e+00 1.98e+01 ... (remaining 39398 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.95: 15566 17.95 - 35.90: 1595 35.90 - 53.85: 406 53.85 - 71.79: 90 71.79 - 89.74: 53 Dihedral angle restraints: 17710 sinusoidal: 7703 harmonic: 10007 Sorted by residual: dihedral pdb=" CA ASP Y 187 " pdb=" C ASP Y 187 " pdb=" N ASP Y 188 " pdb=" CA ASP Y 188 " ideal model delta harmonic sigma weight residual -180.00 -134.75 -45.25 0 5.00e+00 4.00e-02 8.19e+01 dihedral pdb=" CD ARG U 167 " pdb=" NE ARG U 167 " pdb=" CZ ARG U 167 " pdb=" NH1 ARG U 167 " ideal model delta sinusoidal sigma weight residual 0.00 79.94 -79.94 1 1.00e+01 1.00e-02 7.92e+01 dihedral pdb=" CA SER I 202 " pdb=" C SER I 202 " pdb=" N GLN I 203 " pdb=" CA GLN I 203 " ideal model delta harmonic sigma weight residual -180.00 -142.38 -37.62 0 5.00e+00 4.00e-02 5.66e+01 ... (remaining 17707 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.073: 4078 0.073 - 0.146: 410 0.146 - 0.219: 31 0.219 - 0.292: 9 0.292 - 0.365: 2 Chirality restraints: 4530 Sorted by residual: chirality pdb=" CG LEU H 114 " pdb=" CB LEU H 114 " pdb=" CD1 LEU H 114 " pdb=" CD2 LEU H 114 " both_signs ideal model delta sigma weight residual False -2.59 -2.22 -0.37 2.00e-01 2.50e+01 3.33e+00 chirality pdb=" CB VAL H 43 " pdb=" CA VAL H 43 " pdb=" CG1 VAL H 43 " pdb=" CG2 VAL H 43 " both_signs ideal model delta sigma weight residual False -2.63 -2.33 -0.30 2.00e-01 2.50e+01 2.27e+00 chirality pdb=" CB THR K 140 " pdb=" CA THR K 140 " pdb=" OG1 THR K 140 " pdb=" CG2 THR K 140 " both_signs ideal model delta sigma weight residual False 2.55 2.28 0.28 2.00e-01 2.50e+01 1.89e+00 ... (remaining 4527 not shown) Planarity restraints: 4802 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG U 167 " -1.083 9.50e-02 1.11e+02 4.86e-01 1.42e+02 pdb=" NE ARG U 167 " 0.065 2.00e-02 2.50e+03 pdb=" CZ ARG U 167 " 0.012 2.00e-02 2.50e+03 pdb=" NH1 ARG U 167 " -0.010 2.00e-02 2.50e+03 pdb=" NH2 ARG U 167 " -0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ARG Q 219 " -0.035 2.00e-02 2.50e+03 6.86e-02 4.70e+01 pdb=" C ARG Q 219 " 0.119 2.00e-02 2.50e+03 pdb=" O ARG Q 219 " -0.045 2.00e-02 2.50e+03 pdb=" N GLN Q 220 " -0.039 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA I 241 " 0.029 2.00e-02 2.50e+03 5.67e-02 3.21e+01 pdb=" C ALA I 241 " -0.098 2.00e-02 2.50e+03 pdb=" O ALA I 241 " 0.037 2.00e-02 2.50e+03 pdb=" N HIS I 242 " 0.032 2.00e-02 2.50e+03 ... (remaining 4799 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 2684 2.75 - 3.29: 28468 3.29 - 3.82: 49026 3.82 - 4.36: 55544 4.36 - 4.90: 95211 Nonbonded interactions: 230933 Sorted by model distance: nonbonded pdb=" OG SER N 233 " pdb=" O GLU N 236 " model vdw 2.212 2.440 nonbonded pdb=" O ILE K 171 " pdb=" OG1 THR K 175 " model vdw 2.232 2.440 nonbonded pdb=" OG SER Q 249 " pdb=" OD1 ASN Y 6 " model vdw 2.264 2.440 nonbonded pdb=" O ILE I 204 " pdb=" OG SER I 207 " model vdw 2.272 2.440 nonbonded pdb=" OH TYR L 148 " pdb=" OE1 GLN L 160 " model vdw 2.277 2.440 ... (remaining 230928 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = (chain 'B' and resid 221 through 321) } 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=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.940 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 6.540 Check model and map are aligned: 0.400 Set scattering table: 0.280 Process input model: 78.450 Find NCS groups from input model: 0.970 Set up NCS constraints: 0.100 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.780 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 91.490 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7630 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.073 29041 Z= 0.239 Angle : 0.784 12.777 39403 Z= 0.432 Chirality : 0.046 0.365 4530 Planarity : 0.009 0.486 4802 Dihedral : 16.453 89.742 11162 Min Nonbonded Distance : 2.212 Molprobity Statistics. All-atom Clashscore : 5.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.13 % Favored : 96.87 % Rotamer: Outliers : 0.13 % Allowed : 0.52 % Favored : 99.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.15 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.07 (0.14), residues: 3318 helix: 0.74 (0.11), residues: 2094 sheet: -0.72 (0.33), residues: 246 loop : -1.45 (0.19), residues: 978 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP I 136 HIS 0.007 0.001 HIS L 131 PHE 0.054 0.002 PHE H 83 TYR 0.052 0.001 TYR Q 363 ARG 0.026 0.001 ARG K 139 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6636 Ramachandran restraints generated. 3318 Oldfield, 0 Emsley, 3318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6636 Ramachandran restraints generated. 3318 Oldfield, 0 Emsley, 3318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 643 residues out of total 3136 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 639 time to evaluate : 3.397 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 225 ASP cc_start: 0.6166 (m-30) cc_final: 0.5694 (t70) REVERT: B 219 TRP cc_start: 0.6206 (t-100) cc_final: 0.5852 (t60) REVERT: B 222 GLN cc_start: 0.7065 (tp40) cc_final: 0.6751 (tp40) REVERT: B 223 ARG cc_start: 0.7279 (mtt180) cc_final: 0.6953 (mtt-85) REVERT: B 315 TYR cc_start: 0.6057 (t80) cc_final: 0.5396 (t80) REVERT: B 316 MET cc_start: 0.7176 (mmm) cc_final: 0.6904 (mmm) REVERT: B 322 LYS cc_start: 0.6868 (mttm) cc_final: 0.6503 (tmmt) REVERT: H 7 LYS cc_start: 0.7832 (mttt) cc_final: 0.7552 (mptt) REVERT: H 14 GLN cc_start: 0.6559 (pm20) cc_final: 0.5898 (tt0) REVERT: H 31 ASP cc_start: 0.8071 (m-30) cc_final: 0.7829 (m-30) REVERT: H 51 ARG cc_start: 0.7721 (tpp80) cc_final: 0.7330 (tpp80) REVERT: H 60 GLN cc_start: 0.8071 (tt0) cc_final: 0.7751 (tt0) REVERT: H 71 ARG cc_start: 0.5774 (ttm-80) cc_final: 0.4947 (mtt180) REVERT: H 74 GLU cc_start: 0.5251 (tt0) cc_final: 0.4724 (tp30) REVERT: H 75 LYS cc_start: 0.5610 (mtpp) cc_final: 0.5041 (pttm) REVERT: H 125 MET cc_start: 0.7738 (tpp) cc_final: 0.7435 (tpp) REVERT: H 127 LYS cc_start: 0.7646 (mmtp) cc_final: 0.7250 (mmmt) REVERT: H 154 VAL cc_start: 0.7556 (p) cc_final: 0.7115 (p) REVERT: H 166 ILE cc_start: 0.6657 (mm) cc_final: 0.6403 (mt) REVERT: I 148 TRP cc_start: 0.7275 (m100) cc_final: 0.6195 (m100) REVERT: I 264 GLN cc_start: 0.7613 (pt0) cc_final: 0.6961 (tt0) REVERT: I 311 ASP cc_start: 0.6961 (t0) cc_final: 0.6563 (t0) REVERT: I 331 MET cc_start: 0.4962 (mmp) cc_final: 0.4165 (mtm) REVERT: I 438 LYS cc_start: 0.8093 (tttm) cc_final: 0.7871 (mmtm) REVERT: I 533 GLN cc_start: 0.8034 (pt0) cc_final: 0.7432 (tt0) REVERT: I 582 ASN cc_start: 0.6435 (m-40) cc_final: 0.5829 (m-40) REVERT: I 677 HIS cc_start: 0.5532 (m90) cc_final: 0.5014 (m170) REVERT: K 13 LYS cc_start: 0.8061 (mttt) cc_final: 0.7769 (tptp) REVERT: K 54 THR cc_start: 0.8246 (m) cc_final: 0.7968 (m) REVERT: K 56 LEU cc_start: 0.8490 (tp) cc_final: 0.8195 (tt) REVERT: K 94 ASN cc_start: 0.7341 (m-40) cc_final: 0.6938 (t0) REVERT: K 149 TRP cc_start: 0.5691 (m100) cc_final: 0.5423 (m100) REVERT: K 179 MET cc_start: 0.7303 (mmm) cc_final: 0.6850 (mmp) REVERT: K 183 LYS cc_start: 0.5806 (mptt) cc_final: 0.5118 (tppt) REVERT: L 215 LYS cc_start: 0.7877 (ptmm) cc_final: 0.7652 (ptpt) REVERT: N 25 MET cc_start: 0.7741 (mmm) cc_final: 0.7445 (mmm) REVERT: O 123 MET cc_start: 0.1781 (tpt) cc_final: 0.0536 (ptp) REVERT: O 124 PHE cc_start: 0.6335 (m-80) cc_final: 0.5886 (m-10) REVERT: O 360 ASN cc_start: 0.7756 (t0) cc_final: 0.6386 (p0) REVERT: O 361 HIS cc_start: 0.7432 (t70) cc_final: 0.7130 (t70) REVERT: P 136 LYS cc_start: 0.8636 (tttp) cc_final: 0.8414 (tttm) REVERT: Q 153 LYS cc_start: 0.6675 (mttt) cc_final: 0.6331 (pttp) REVERT: Q 200 TYR cc_start: 0.6478 (t80) cc_final: 0.6107 (t80) REVERT: Q 222 LYS cc_start: 0.4327 (OUTLIER) cc_final: 0.3958 (mtmm) REVERT: Q 380 ASP cc_start: 0.8649 (m-30) cc_final: 0.8295 (m-30) REVERT: T 288 GLU cc_start: 0.6931 (tt0) cc_final: 0.6521 (tt0) REVERT: T 291 ILE cc_start: 0.4658 (mm) cc_final: 0.4447 (mm) REVERT: T 316 ILE cc_start: 0.5882 (mp) cc_final: 0.5634 (pt) REVERT: T 338 ASP cc_start: 0.5412 (t0) cc_final: 0.4837 (m-30) REVERT: T 340 MET cc_start: 0.6350 (mmm) cc_final: 0.5626 (mmm) REVERT: U 176 ARG cc_start: 0.5424 (mmp80) cc_final: 0.5076 (mmp-170) REVERT: W 8 ASN cc_start: 0.6095 (m-40) cc_final: 0.5875 (m-40) REVERT: W 41 ASN cc_start: 0.6916 (m-40) cc_final: 0.6666 (m-40) REVERT: W 64 ARG cc_start: 0.6703 (mtt-85) cc_final: 0.6374 (mtt-85) REVERT: Y 60 ASP cc_start: 0.7278 (t70) cc_final: 0.6790 (t70) REVERT: Z 30 GLN cc_start: 0.4786 (mt0) cc_final: 0.4213 (mm-40) REVERT: Z 36 GLU cc_start: 0.6485 (tt0) cc_final: 0.5818 (mm-30) REVERT: Z 50 ASP cc_start: 0.4097 (p0) cc_final: 0.3665 (p0) REVERT: Z 77 GLU cc_start: 0.7557 (mt-10) cc_final: 0.7247 (mt-10) REVERT: Z 81 LEU cc_start: 0.8214 (tt) cc_final: 0.7977 (pp) outliers start: 4 outliers final: 0 residues processed: 643 average time/residue: 0.4620 time to fit residues: 450.5978 Evaluate side-chains 381 residues out of total 3136 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 380 time to evaluate : 3.886 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Q residue 222 LYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 283 optimal weight: 0.9980 chunk 254 optimal weight: 2.9990 chunk 141 optimal weight: 0.9990 chunk 86 optimal weight: 7.9990 chunk 171 optimal weight: 2.9990 chunk 136 optimal weight: 0.9980 chunk 263 optimal weight: 4.9990 chunk 101 optimal weight: 10.0000 chunk 160 optimal weight: 0.0370 chunk 196 optimal weight: 5.9990 chunk 305 optimal weight: 0.5980 overall best weight: 0.7260 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 222 GLN ** H 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 40 ASN ** H 50 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 62 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 107 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 171 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 107 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 212 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 467 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 123 HIS N 73 ASN N 435 ASN ** P 166 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 135 GLN U 165 GLN Y 59 GLN Y 79 GLN ** Y 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7672 moved from start: 0.1770 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 29041 Z= 0.162 Angle : 0.554 10.580 39403 Z= 0.295 Chirality : 0.039 0.245 4530 Planarity : 0.004 0.050 4802 Dihedral : 13.232 77.859 4214 Min Nonbonded Distance : 2.150 Molprobity Statistics. All-atom Clashscore : 9.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 1.34 % Allowed : 7.83 % Favored : 90.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.00 (0.15), residues: 3318 helix: 1.66 (0.11), residues: 2119 sheet: -0.59 (0.33), residues: 242 loop : -1.25 (0.20), residues: 957 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP T 298 HIS 0.009 0.001 HIS K 123 PHE 0.024 0.002 PHE T 341 TYR 0.026 0.001 TYR Q 306 ARG 0.007 0.000 ARG K 39 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6636 Ramachandran restraints generated. 3318 Oldfield, 0 Emsley, 3318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6636 Ramachandran restraints generated. 3318 Oldfield, 0 Emsley, 3318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 447 residues out of total 3136 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 406 time to evaluate : 3.407 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 225 ASP cc_start: 0.6174 (m-30) cc_final: 0.5685 (t70) REVERT: B 222 GLN cc_start: 0.6886 (tp-100) cc_final: 0.6625 (tp40) REVERT: B 223 ARG cc_start: 0.7341 (mtt180) cc_final: 0.6947 (mtt-85) REVERT: B 315 TYR cc_start: 0.5804 (t80) cc_final: 0.5602 (t80) REVERT: B 322 LYS cc_start: 0.6843 (mttm) cc_final: 0.6482 (tmmt) REVERT: H 7 LYS cc_start: 0.7805 (mttt) cc_final: 0.7496 (mptt) REVERT: H 14 GLN cc_start: 0.6844 (pm20) cc_final: 0.6552 (tm-30) REVERT: H 51 ARG cc_start: 0.7712 (tpp80) cc_final: 0.7114 (tpp80) REVERT: H 71 ARG cc_start: 0.5729 (ttm-80) cc_final: 0.5349 (ttm-80) REVERT: H 74 GLU cc_start: 0.5315 (tt0) cc_final: 0.4879 (tp30) REVERT: H 75 LYS cc_start: 0.5583 (mtpp) cc_final: 0.5224 (pttm) REVERT: H 97 ASP cc_start: 0.7161 (OUTLIER) cc_final: 0.6793 (p0) REVERT: H 127 LYS cc_start: 0.7327 (mmtp) cc_final: 0.7093 (mmmt) REVERT: I 65 TYR cc_start: 0.6772 (OUTLIER) cc_final: 0.6546 (m-80) REVERT: I 148 TRP cc_start: 0.7321 (m100) cc_final: 0.6314 (m100) REVERT: I 264 GLN cc_start: 0.7691 (pt0) cc_final: 0.7151 (tt0) REVERT: I 489 MET cc_start: 0.8303 (mmp) cc_final: 0.8008 (mmp) REVERT: I 533 GLN cc_start: 0.8015 (pt0) cc_final: 0.7476 (tt0) REVERT: I 578 VAL cc_start: 0.7359 (t) cc_final: 0.7078 (p) REVERT: I 582 ASN cc_start: 0.5804 (m-40) cc_final: 0.5428 (m-40) REVERT: I 596 LYS cc_start: 0.7080 (ptpt) cc_final: 0.6761 (mmtm) REVERT: K 94 ASN cc_start: 0.7271 (m-40) cc_final: 0.6909 (t0) REVERT: K 183 LYS cc_start: 0.6001 (mptt) cc_final: 0.5577 (pptt) REVERT: L 215 LYS cc_start: 0.7753 (ptmm) cc_final: 0.7494 (ptpt) REVERT: N 25 MET cc_start: 0.8127 (mmm) cc_final: 0.7769 (mmm) REVERT: N 317 GLU cc_start: 0.7400 (tp30) cc_final: 0.6960 (mp0) REVERT: O 123 MET cc_start: 0.1937 (tpt) cc_final: 0.0633 (ptp) REVERT: O 124 PHE cc_start: 0.6306 (m-80) cc_final: 0.5879 (m-10) REVERT: Q 153 LYS cc_start: 0.6768 (mttt) cc_final: 0.6363 (pttp) REVERT: Q 188 MET cc_start: 0.6025 (OUTLIER) cc_final: 0.5472 (ptp) REVERT: Q 222 LYS cc_start: 0.3815 (OUTLIER) cc_final: 0.3114 (mtmm) REVERT: Q 271 GLU cc_start: 0.7446 (tm-30) cc_final: 0.7172 (tm-30) REVERT: Q 383 GLU cc_start: 0.7812 (tm-30) cc_final: 0.7453 (tm-30) REVERT: T 290 ARG cc_start: 0.7289 (mtm180) cc_final: 0.7074 (mtp85) REVERT: T 309 MET cc_start: 0.6897 (ppp) cc_final: 0.6557 (ppp) REVERT: T 338 ASP cc_start: 0.5506 (t0) cc_final: 0.4941 (m-30) REVERT: T 340 MET cc_start: 0.6440 (mmm) cc_final: 0.5709 (mmm) REVERT: W 8 ASN cc_start: 0.6123 (m-40) cc_final: 0.5890 (m-40) REVERT: W 41 ASN cc_start: 0.6791 (m-40) cc_final: 0.6472 (m-40) REVERT: Z 30 GLN cc_start: 0.4620 (mt0) cc_final: 0.4136 (mm-40) REVERT: Z 50 ASP cc_start: 0.3313 (p0) cc_final: 0.3075 (p0) REVERT: Z 77 GLU cc_start: 0.7568 (mt-10) cc_final: 0.7267 (mt-10) REVERT: Z 81 LEU cc_start: 0.8345 (tt) cc_final: 0.8054 (pp) outliers start: 41 outliers final: 25 residues processed: 432 average time/residue: 0.4433 time to fit residues: 296.8890 Evaluate side-chains 355 residues out of total 3136 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 326 time to evaluate : 3.583 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 313 ILE Chi-restraints excluded: chain H residue 62 ASN Chi-restraints excluded: chain H residue 97 ASP Chi-restraints excluded: chain I residue 65 TYR Chi-restraints excluded: chain I residue 242 HIS Chi-restraints excluded: chain I residue 466 LEU Chi-restraints excluded: chain I residue 526 THR Chi-restraints excluded: chain I residue 579 ARG Chi-restraints excluded: chain I residue 610 PHE Chi-restraints excluded: chain K residue 92 LEU Chi-restraints excluded: chain L residue 35 ILE Chi-restraints excluded: chain L residue 208 VAL Chi-restraints excluded: chain N residue 237 THR Chi-restraints excluded: chain N residue 248 VAL Chi-restraints excluded: chain O residue 353 ASP Chi-restraints excluded: chain P residue 154 LEU Chi-restraints excluded: chain P residue 198 GLU Chi-restraints excluded: chain P residue 213 LEU Chi-restraints excluded: chain Q residue 188 MET Chi-restraints excluded: chain Q residue 222 LYS Chi-restraints excluded: chain Q residue 277 MET Chi-restraints excluded: chain Q residue 288 THR Chi-restraints excluded: chain T residue 276 MET Chi-restraints excluded: chain T residue 305 SER Chi-restraints excluded: chain T residue 342 GLU Chi-restraints excluded: chain W residue 73 VAL Chi-restraints excluded: chain Y residue 16 LEU Chi-restraints excluded: chain Y residue 36 ASN Chi-restraints excluded: chain Y residue 205 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 169 optimal weight: 0.8980 chunk 94 optimal weight: 0.0570 chunk 253 optimal weight: 6.9990 chunk 207 optimal weight: 8.9990 chunk 84 optimal weight: 6.9990 chunk 305 optimal weight: 0.1980 chunk 330 optimal weight: 2.9990 chunk 272 optimal weight: 0.0770 chunk 303 optimal weight: 6.9990 chunk 104 optimal weight: 9.9990 chunk 245 optimal weight: 9.9990 overall best weight: 0.8458 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 50 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 60 GLN ** H 62 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 171 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 88 HIS ** I 467 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 677 HIS ** K 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 123 HIS L 238 GLN ** N 165 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 166 GLN U 196 ASN Y 79 GLN ** Y 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7685 moved from start: 0.2182 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.047 29041 Z= 0.155 Angle : 0.515 9.431 39403 Z= 0.273 Chirality : 0.038 0.235 4530 Planarity : 0.003 0.047 4802 Dihedral : 13.140 73.340 4214 Min Nonbonded Distance : 2.201 Molprobity Statistics. All-atom Clashscore : 9.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer: Outliers : 1.60 % Allowed : 10.17 % Favored : 88.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.47 (0.15), residues: 3318 helix: 2.05 (0.11), residues: 2121 sheet: -0.63 (0.32), residues: 248 loop : -1.09 (0.20), residues: 949 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP T 298 HIS 0.009 0.001 HIS K 123 PHE 0.022 0.001 PHE T 341 TYR 0.027 0.001 TYR I 641 ARG 0.003 0.000 ARG Q 198 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6636 Ramachandran restraints generated. 3318 Oldfield, 0 Emsley, 3318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6636 Ramachandran restraints generated. 3318 Oldfield, 0 Emsley, 3318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 408 residues out of total 3136 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 359 time to evaluate : 3.643 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 225 ASP cc_start: 0.6111 (m-30) cc_final: 0.5619 (t70) REVERT: B 222 GLN cc_start: 0.6973 (tp-100) cc_final: 0.6669 (tp40) REVERT: B 223 ARG cc_start: 0.7336 (mtt180) cc_final: 0.6936 (mtt-85) REVERT: B 322 LYS cc_start: 0.6861 (mttm) cc_final: 0.6499 (tmmt) REVERT: H 7 LYS cc_start: 0.7735 (mttt) cc_final: 0.7463 (mptt) REVERT: H 14 GLN cc_start: 0.6995 (OUTLIER) cc_final: 0.6505 (tm-30) REVERT: H 51 ARG cc_start: 0.7749 (tpp80) cc_final: 0.7114 (tpp80) REVERT: H 75 LYS cc_start: 0.5662 (mtpp) cc_final: 0.5093 (pttm) REVERT: H 97 ASP cc_start: 0.7138 (OUTLIER) cc_final: 0.6623 (p0) REVERT: H 98 TYR cc_start: 0.7225 (t80) cc_final: 0.6932 (t80) REVERT: I 65 TYR cc_start: 0.6749 (OUTLIER) cc_final: 0.6531 (m-80) REVERT: I 148 TRP cc_start: 0.7364 (m100) cc_final: 0.6358 (m100) REVERT: I 264 GLN cc_start: 0.7650 (pt0) cc_final: 0.7147 (tt0) REVERT: I 311 ASP cc_start: 0.6420 (t0) cc_final: 0.5956 (t0) REVERT: I 533 GLN cc_start: 0.8100 (pt0) cc_final: 0.7781 (mt0) REVERT: I 578 VAL cc_start: 0.7301 (t) cc_final: 0.7013 (p) REVERT: I 580 MET cc_start: 0.8078 (mtp) cc_final: 0.7689 (ttt) REVERT: I 582 ASN cc_start: 0.6204 (m-40) cc_final: 0.5764 (m-40) REVERT: I 596 LYS cc_start: 0.7005 (ptpt) cc_final: 0.6755 (mmtm) REVERT: K 15 LEU cc_start: 0.7710 (mt) cc_final: 0.7492 (mm) REVERT: K 53 PHE cc_start: 0.7450 (t80) cc_final: 0.7065 (t80) REVERT: K 94 ASN cc_start: 0.7158 (m-40) cc_final: 0.6838 (t0) REVERT: K 183 LYS cc_start: 0.6020 (mptt) cc_final: 0.5571 (pptt) REVERT: L 215 LYS cc_start: 0.7790 (ptmm) cc_final: 0.7576 (ptpt) REVERT: N 5 LEU cc_start: 0.7452 (OUTLIER) cc_final: 0.7066 (tt) REVERT: N 21 PHE cc_start: 0.7838 (t80) cc_final: 0.7558 (t80) REVERT: N 102 GLU cc_start: 0.7695 (pm20) cc_final: 0.7492 (pm20) REVERT: N 317 GLU cc_start: 0.7364 (tp30) cc_final: 0.6951 (mp0) REVERT: O 123 MET cc_start: 0.1973 (tpt) cc_final: 0.0595 (ptp) REVERT: O 124 PHE cc_start: 0.6304 (m-80) cc_final: 0.5935 (m-10) REVERT: Q 153 LYS cc_start: 0.6754 (mttt) cc_final: 0.6289 (pttp) REVERT: Q 158 MET cc_start: 0.8047 (OUTLIER) cc_final: 0.7698 (ttm) REVERT: Q 222 LYS cc_start: 0.3762 (OUTLIER) cc_final: 0.3095 (mtmm) REVERT: Q 259 GLU cc_start: 0.7729 (mm-30) cc_final: 0.7370 (tp30) REVERT: Q 271 GLU cc_start: 0.7528 (tm-30) cc_final: 0.7255 (tm-30) REVERT: Q 383 GLU cc_start: 0.7818 (tm-30) cc_final: 0.7509 (tm-30) REVERT: T 290 ARG cc_start: 0.7285 (mtm180) cc_final: 0.6975 (mtp85) REVERT: T 309 MET cc_start: 0.7005 (ppp) cc_final: 0.6682 (ppp) REVERT: T 338 ASP cc_start: 0.5590 (t0) cc_final: 0.4949 (m-30) REVERT: T 340 MET cc_start: 0.6549 (mmm) cc_final: 0.5762 (mmm) REVERT: U 167 ARG cc_start: 0.2609 (tpt170) cc_final: 0.2069 (mmt180) REVERT: U 170 LEU cc_start: 0.5901 (OUTLIER) cc_final: 0.5618 (tt) REVERT: U 178 PHE cc_start: 0.8050 (m-80) cc_final: 0.7775 (m-80) REVERT: U 228 GLN cc_start: 0.7827 (mm110) cc_final: 0.7594 (mt0) REVERT: W 42 LYS cc_start: 0.5835 (tptt) cc_final: 0.5038 (mmtm) REVERT: Z 30 GLN cc_start: 0.4777 (mt0) cc_final: 0.4254 (mm-40) REVERT: Z 77 GLU cc_start: 0.7575 (mt-10) cc_final: 0.7285 (mt-10) REVERT: Z 81 LEU cc_start: 0.8344 (tt) cc_final: 0.8057 (pp) outliers start: 49 outliers final: 26 residues processed: 387 average time/residue: 0.4291 time to fit residues: 260.5483 Evaluate side-chains 362 residues out of total 3136 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 329 time to evaluate : 3.609 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 14 GLN Chi-restraints excluded: chain H residue 62 ASN Chi-restraints excluded: chain H residue 97 ASP Chi-restraints excluded: chain H residue 122 ASP Chi-restraints excluded: chain I residue 65 TYR Chi-restraints excluded: chain I residue 242 HIS Chi-restraints excluded: chain I residue 257 MET Chi-restraints excluded: chain I residue 466 LEU Chi-restraints excluded: chain I residue 610 PHE Chi-restraints excluded: chain I residue 633 ILE Chi-restraints excluded: chain I residue 665 ILE Chi-restraints excluded: chain K residue 92 LEU Chi-restraints excluded: chain L residue 35 ILE Chi-restraints excluded: chain L residue 208 VAL Chi-restraints excluded: chain L residue 222 VAL Chi-restraints excluded: chain N residue 5 LEU Chi-restraints excluded: chain N residue 248 VAL Chi-restraints excluded: chain O residue 188 ILE Chi-restraints excluded: chain O residue 353 ASP Chi-restraints excluded: chain O residue 361 HIS Chi-restraints excluded: chain P residue 154 LEU Chi-restraints excluded: chain P residue 198 GLU Chi-restraints excluded: chain Q residue 158 MET Chi-restraints excluded: chain Q residue 222 LYS Chi-restraints excluded: chain Q residue 277 MET Chi-restraints excluded: chain Q residue 288 THR Chi-restraints excluded: chain T residue 305 SER Chi-restraints excluded: chain U residue 166 PHE Chi-restraints excluded: chain U residue 170 LEU Chi-restraints excluded: chain W residue 73 VAL Chi-restraints excluded: chain Y residue 16 LEU Chi-restraints excluded: chain Y residue 203 VAL Chi-restraints excluded: chain Y residue 205 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 302 optimal weight: 6.9990 chunk 229 optimal weight: 5.9990 chunk 158 optimal weight: 0.7980 chunk 33 optimal weight: 0.9990 chunk 145 optimal weight: 2.9990 chunk 205 optimal weight: 0.4980 chunk 306 optimal weight: 1.9990 chunk 324 optimal weight: 7.9990 chunk 160 optimal weight: 4.9990 chunk 290 optimal weight: 3.9990 chunk 87 optimal weight: 0.8980 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 50 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 62 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 171 HIS ** I 467 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 123 HIS P 166 GLN P 200 GLN Y 79 GLN Y 170 GLN ** Y 172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7700 moved from start: 0.2441 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 29041 Z= 0.159 Angle : 0.509 12.933 39403 Z= 0.267 Chirality : 0.038 0.287 4530 Planarity : 0.003 0.045 4802 Dihedral : 13.070 72.000 4214 Min Nonbonded Distance : 2.216 Molprobity Statistics. All-atom Clashscore : 9.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Rotamer: Outliers : 1.70 % Allowed : 11.31 % Favored : 86.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.74 (0.15), residues: 3318 helix: 2.28 (0.11), residues: 2125 sheet: -0.58 (0.32), residues: 248 loop : -1.01 (0.20), residues: 945 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP T 298 HIS 0.010 0.001 HIS K 123 PHE 0.022 0.001 PHE T 341 TYR 0.025 0.001 TYR I 641 ARG 0.006 0.000 ARG U 187 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6636 Ramachandran restraints generated. 3318 Oldfield, 0 Emsley, 3318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6636 Ramachandran restraints generated. 3318 Oldfield, 0 Emsley, 3318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 403 residues out of total 3136 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 351 time to evaluate : 3.784 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 225 ASP cc_start: 0.6103 (m-30) cc_final: 0.5650 (t70) REVERT: B 222 GLN cc_start: 0.6988 (tp-100) cc_final: 0.6626 (tp40) REVERT: B 223 ARG cc_start: 0.7396 (mtt180) cc_final: 0.6951 (mtt-85) REVERT: B 322 LYS cc_start: 0.6885 (mttm) cc_final: 0.6506 (tmmt) REVERT: H 7 LYS cc_start: 0.7726 (mttt) cc_final: 0.7455 (mptt) REVERT: H 14 GLN cc_start: 0.7096 (OUTLIER) cc_final: 0.6373 (tm-30) REVERT: H 51 ARG cc_start: 0.7618 (tpp80) cc_final: 0.7187 (tpp80) REVERT: H 75 LYS cc_start: 0.5649 (mtpp) cc_final: 0.5050 (pttm) REVERT: H 97 ASP cc_start: 0.7093 (OUTLIER) cc_final: 0.6560 (p0) REVERT: H 98 TYR cc_start: 0.7149 (t80) cc_final: 0.6760 (t80) REVERT: H 166 ILE cc_start: 0.6806 (mm) cc_final: 0.6543 (mt) REVERT: I 65 TYR cc_start: 0.6703 (OUTLIER) cc_final: 0.6465 (m-80) REVERT: I 148 TRP cc_start: 0.7391 (m100) cc_final: 0.6391 (m100) REVERT: I 176 MET cc_start: 0.6785 (mtp) cc_final: 0.6291 (mmm) REVERT: I 264 GLN cc_start: 0.7568 (pt0) cc_final: 0.7111 (tt0) REVERT: I 311 ASP cc_start: 0.6548 (t0) cc_final: 0.6072 (t0) REVERT: I 533 GLN cc_start: 0.8161 (pt0) cc_final: 0.7791 (mt0) REVERT: I 578 VAL cc_start: 0.7299 (t) cc_final: 0.7020 (p) REVERT: I 582 ASN cc_start: 0.6052 (m-40) cc_final: 0.5605 (m-40) REVERT: I 596 LYS cc_start: 0.7099 (ptpt) cc_final: 0.6853 (mmtm) REVERT: K 53 PHE cc_start: 0.7405 (t80) cc_final: 0.7153 (t80) REVERT: K 90 LEU cc_start: 0.8023 (OUTLIER) cc_final: 0.7423 (mm) REVERT: K 94 ASN cc_start: 0.7163 (m-40) cc_final: 0.6857 (t0) REVERT: K 183 LYS cc_start: 0.6011 (mptt) cc_final: 0.5648 (pptt) REVERT: N 5 LEU cc_start: 0.7411 (OUTLIER) cc_final: 0.7033 (tt) REVERT: N 37 LEU cc_start: 0.8545 (mp) cc_final: 0.8327 (mp) REVERT: N 317 GLU cc_start: 0.7407 (tp30) cc_final: 0.6798 (mp0) REVERT: O 123 MET cc_start: 0.2051 (tpt) cc_final: 0.0576 (ptp) REVERT: O 124 PHE cc_start: 0.6299 (m-80) cc_final: 0.6009 (m-10) REVERT: P 104 PHE cc_start: 0.7936 (t80) cc_final: 0.7719 (t80) REVERT: Q 153 LYS cc_start: 0.6816 (mttt) cc_final: 0.6274 (pttp) REVERT: Q 222 LYS cc_start: 0.3828 (OUTLIER) cc_final: 0.3263 (mtmm) REVERT: Q 236 TYR cc_start: 0.8460 (t80) cc_final: 0.8231 (t80) REVERT: Q 259 GLU cc_start: 0.7761 (mm-30) cc_final: 0.7456 (tp30) REVERT: Q 271 GLU cc_start: 0.7441 (tm-30) cc_final: 0.7143 (tm-30) REVERT: T 290 ARG cc_start: 0.7268 (mtm180) cc_final: 0.7054 (mtp85) REVERT: T 309 MET cc_start: 0.7089 (ppp) cc_final: 0.6778 (ppp) REVERT: T 338 ASP cc_start: 0.5509 (t0) cc_final: 0.4957 (m-30) REVERT: T 340 MET cc_start: 0.6504 (mmm) cc_final: 0.5721 (mmm) REVERT: U 167 ARG cc_start: 0.2322 (tpt170) cc_final: 0.1849 (mmt180) REVERT: U 178 PHE cc_start: 0.8080 (m-80) cc_final: 0.7729 (m-80) REVERT: U 228 GLN cc_start: 0.7840 (mm110) cc_final: 0.7627 (mt0) REVERT: Z 15 LEU cc_start: 0.5910 (mt) cc_final: 0.5516 (tp) REVERT: Z 30 GLN cc_start: 0.4913 (mt0) cc_final: 0.4425 (mm-40) REVERT: Z 46 LEU cc_start: 0.7171 (mt) cc_final: 0.6859 (mm) REVERT: Z 49 ARG cc_start: 0.5778 (ppt170) cc_final: 0.5558 (ppt170) REVERT: Z 77 GLU cc_start: 0.7580 (mt-10) cc_final: 0.7352 (mt-10) outliers start: 52 outliers final: 34 residues processed: 382 average time/residue: 0.4360 time to fit residues: 261.4316 Evaluate side-chains 358 residues out of total 3136 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 318 time to evaluate : 5.022 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 313 ILE Chi-restraints excluded: chain H residue 14 GLN Chi-restraints excluded: chain H residue 62 ASN Chi-restraints excluded: chain H residue 97 ASP Chi-restraints excluded: chain H residue 122 ASP Chi-restraints excluded: chain I residue 65 TYR Chi-restraints excluded: chain I residue 204 ILE Chi-restraints excluded: chain I residue 242 HIS Chi-restraints excluded: chain I residue 257 MET Chi-restraints excluded: chain I residue 466 LEU Chi-restraints excluded: chain I residue 526 THR Chi-restraints excluded: chain I residue 579 ARG Chi-restraints excluded: chain I residue 633 ILE Chi-restraints excluded: chain K residue 90 LEU Chi-restraints excluded: chain K residue 92 LEU Chi-restraints excluded: chain K residue 104 LEU Chi-restraints excluded: chain K residue 208 LEU Chi-restraints excluded: chain L residue 35 ILE Chi-restraints excluded: chain L residue 83 VAL Chi-restraints excluded: chain L residue 208 VAL Chi-restraints excluded: chain L residue 222 VAL Chi-restraints excluded: chain N residue 5 LEU Chi-restraints excluded: chain N residue 10 ASN Chi-restraints excluded: chain N residue 248 VAL Chi-restraints excluded: chain O residue 310 VAL Chi-restraints excluded: chain O residue 353 ASP Chi-restraints excluded: chain O residue 361 HIS Chi-restraints excluded: chain P residue 154 LEU Chi-restraints excluded: chain P residue 198 GLU Chi-restraints excluded: chain Q residue 222 LYS Chi-restraints excluded: chain Q residue 277 MET Chi-restraints excluded: chain Q residue 288 THR Chi-restraints excluded: chain T residue 305 SER Chi-restraints excluded: chain U residue 133 THR Chi-restraints excluded: chain U residue 278 SER Chi-restraints excluded: chain W residue 73 VAL Chi-restraints excluded: chain Y residue 16 LEU Chi-restraints excluded: chain Y residue 36 ASN Chi-restraints excluded: chain Y residue 203 VAL Chi-restraints excluded: chain Y residue 205 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 270 optimal weight: 10.0000 chunk 184 optimal weight: 0.1980 chunk 4 optimal weight: 8.9990 chunk 241 optimal weight: 5.9990 chunk 134 optimal weight: 1.9990 chunk 277 optimal weight: 1.9990 chunk 224 optimal weight: 4.9990 chunk 0 optimal weight: 10.0000 chunk 165 optimal weight: 3.9990 chunk 291 optimal weight: 2.9990 chunk 81 optimal weight: 0.0570 overall best weight: 1.4504 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 62 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 171 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 467 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 123 HIS T 314 GLN Y 79 GLN Y 170 GLN ** Y 172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7729 moved from start: 0.2700 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 29041 Z= 0.188 Angle : 0.516 10.017 39403 Z= 0.271 Chirality : 0.038 0.264 4530 Planarity : 0.003 0.046 4802 Dihedral : 13.064 71.235 4214 Min Nonbonded Distance : 2.187 Molprobity Statistics. All-atom Clashscore : 9.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 1.96 % Allowed : 12.78 % Favored : 85.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.90 (0.15), residues: 3318 helix: 2.41 (0.11), residues: 2123 sheet: -0.55 (0.32), residues: 249 loop : -0.94 (0.21), residues: 946 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP T 298 HIS 0.010 0.001 HIS K 123 PHE 0.029 0.001 PHE Q 130 TYR 0.021 0.001 TYR Y 91 ARG 0.007 0.000 ARG H 71 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6636 Ramachandran restraints generated. 3318 Oldfield, 0 Emsley, 3318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6636 Ramachandran restraints generated. 3318 Oldfield, 0 Emsley, 3318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 403 residues out of total 3136 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 343 time to evaluate : 3.384 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 225 ASP cc_start: 0.6095 (m-30) cc_final: 0.5609 (t70) REVERT: B 222 GLN cc_start: 0.7036 (tp-100) cc_final: 0.6606 (tp40) REVERT: B 223 ARG cc_start: 0.7385 (mtt180) cc_final: 0.7118 (mtt-85) REVERT: B 322 LYS cc_start: 0.6827 (mttm) cc_final: 0.6501 (tmmt) REVERT: H 7 LYS cc_start: 0.7725 (mttt) cc_final: 0.7447 (mptt) REVERT: H 14 GLN cc_start: 0.7002 (OUTLIER) cc_final: 0.6347 (tm-30) REVERT: H 51 ARG cc_start: 0.7665 (tpp80) cc_final: 0.7241 (tpp80) REVERT: H 71 ARG cc_start: 0.5829 (ttm110) cc_final: 0.4821 (ttp-170) REVERT: H 75 LYS cc_start: 0.5512 (mtpp) cc_final: 0.4930 (pttm) REVERT: H 97 ASP cc_start: 0.7009 (OUTLIER) cc_final: 0.6482 (p0) REVERT: H 98 TYR cc_start: 0.7222 (t80) cc_final: 0.6838 (t80) REVERT: H 166 ILE cc_start: 0.6764 (mm) cc_final: 0.6521 (mt) REVERT: I 148 TRP cc_start: 0.7450 (m100) cc_final: 0.6531 (m100) REVERT: I 173 ARG cc_start: 0.8192 (ttm170) cc_final: 0.7712 (mtp180) REVERT: I 176 MET cc_start: 0.6834 (mtp) cc_final: 0.6317 (mmm) REVERT: I 264 GLN cc_start: 0.7537 (pt0) cc_final: 0.7115 (tt0) REVERT: I 311 ASP cc_start: 0.6745 (t0) cc_final: 0.6240 (t0) REVERT: I 331 MET cc_start: 0.4867 (mmp) cc_final: 0.3787 (mtm) REVERT: I 533 GLN cc_start: 0.8206 (pt0) cc_final: 0.7856 (mt0) REVERT: I 578 VAL cc_start: 0.7387 (t) cc_final: 0.7057 (p) REVERT: I 580 MET cc_start: 0.8002 (mtp) cc_final: 0.7729 (ttt) REVERT: I 582 ASN cc_start: 0.6213 (m-40) cc_final: 0.5747 (m-40) REVERT: I 596 LYS cc_start: 0.7130 (ptpt) cc_final: 0.6910 (mptt) REVERT: I 622 THR cc_start: 0.5271 (m) cc_final: 0.4996 (p) REVERT: K 53 PHE cc_start: 0.7519 (t80) cc_final: 0.7019 (t80) REVERT: K 90 LEU cc_start: 0.8152 (OUTLIER) cc_final: 0.7631 (mm) REVERT: K 94 ASN cc_start: 0.7104 (m-40) cc_final: 0.6869 (t0) REVERT: K 183 LYS cc_start: 0.6095 (mptt) cc_final: 0.5519 (tppt) REVERT: K 231 ILE cc_start: 0.7875 (OUTLIER) cc_final: 0.7463 (mt) REVERT: N 5 LEU cc_start: 0.7183 (OUTLIER) cc_final: 0.6823 (tt) REVERT: N 317 GLU cc_start: 0.7384 (tp30) cc_final: 0.6792 (mp0) REVERT: O 123 MET cc_start: 0.2310 (tpt) cc_final: 0.0866 (ptp) REVERT: Q 153 LYS cc_start: 0.6902 (mttt) cc_final: 0.6280 (pttp) REVERT: Q 178 PHE cc_start: 0.5401 (m-10) cc_final: 0.4781 (m-10) REVERT: Q 222 LYS cc_start: 0.3909 (OUTLIER) cc_final: 0.3673 (mtmm) REVERT: Q 259 GLU cc_start: 0.7786 (mm-30) cc_final: 0.7475 (tp30) REVERT: Q 271 GLU cc_start: 0.7472 (tm-30) cc_final: 0.7155 (tm-30) REVERT: Q 387 LYS cc_start: 0.7732 (ttmt) cc_final: 0.7067 (tptt) REVERT: T 309 MET cc_start: 0.7196 (ppp) cc_final: 0.6784 (ppp) REVERT: T 324 LEU cc_start: 0.6624 (OUTLIER) cc_final: 0.6026 (tp) REVERT: T 338 ASP cc_start: 0.5162 (t0) cc_final: 0.4830 (m-30) REVERT: T 340 MET cc_start: 0.6526 (mmm) cc_final: 0.5698 (mmm) REVERT: U 167 ARG cc_start: 0.2904 (tpt170) cc_final: 0.2604 (mmt180) REVERT: U 171 TYR cc_start: 0.5816 (m-10) cc_final: 0.5522 (m-10) REVERT: U 178 PHE cc_start: 0.8085 (m-80) cc_final: 0.7761 (m-80) REVERT: U 228 GLN cc_start: 0.7869 (mm110) cc_final: 0.7659 (mt0) REVERT: W 64 ARG cc_start: 0.6578 (mtt-85) cc_final: 0.6271 (mtt180) REVERT: Z 30 GLN cc_start: 0.5009 (mt0) cc_final: 0.4588 (mm110) REVERT: Z 46 LEU cc_start: 0.7305 (mt) cc_final: 0.6960 (mm) REVERT: Z 49 ARG cc_start: 0.5684 (ppt170) cc_final: 0.5432 (ppt170) REVERT: Z 77 GLU cc_start: 0.7584 (mt-10) cc_final: 0.7306 (mt-10) outliers start: 60 outliers final: 40 residues processed: 380 average time/residue: 0.4336 time to fit residues: 257.7412 Evaluate side-chains 369 residues out of total 3136 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 322 time to evaluate : 3.394 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 313 ILE Chi-restraints excluded: chain H residue 14 GLN Chi-restraints excluded: chain H residue 62 ASN Chi-restraints excluded: chain H residue 81 VAL Chi-restraints excluded: chain H residue 97 ASP Chi-restraints excluded: chain H residue 122 ASP Chi-restraints excluded: chain I residue 84 GLU Chi-restraints excluded: chain I residue 204 ILE Chi-restraints excluded: chain I residue 242 HIS Chi-restraints excluded: chain I residue 257 MET Chi-restraints excluded: chain I residue 466 LEU Chi-restraints excluded: chain I residue 526 THR Chi-restraints excluded: chain I residue 579 ARG Chi-restraints excluded: chain I residue 633 ILE Chi-restraints excluded: chain I residue 665 ILE Chi-restraints excluded: chain K residue 90 LEU Chi-restraints excluded: chain K residue 92 LEU Chi-restraints excluded: chain K residue 123 HIS Chi-restraints excluded: chain K residue 208 LEU Chi-restraints excluded: chain K residue 231 ILE Chi-restraints excluded: chain L residue 83 VAL Chi-restraints excluded: chain L residue 208 VAL Chi-restraints excluded: chain L residue 222 VAL Chi-restraints excluded: chain N residue 5 LEU Chi-restraints excluded: chain N residue 10 ASN Chi-restraints excluded: chain N residue 237 THR Chi-restraints excluded: chain N residue 248 VAL Chi-restraints excluded: chain N residue 385 VAL Chi-restraints excluded: chain O residue 165 VAL Chi-restraints excluded: chain O residue 197 VAL Chi-restraints excluded: chain O residue 310 VAL Chi-restraints excluded: chain O residue 319 VAL Chi-restraints excluded: chain O residue 353 ASP Chi-restraints excluded: chain O residue 361 HIS Chi-restraints excluded: chain P residue 154 LEU Chi-restraints excluded: chain Q residue 222 LYS Chi-restraints excluded: chain Q residue 277 MET Chi-restraints excluded: chain Q residue 288 THR Chi-restraints excluded: chain T residue 305 SER Chi-restraints excluded: chain T residue 324 LEU Chi-restraints excluded: chain U residue 133 THR Chi-restraints excluded: chain U residue 166 PHE Chi-restraints excluded: chain U residue 278 SER Chi-restraints excluded: chain W residue 73 VAL Chi-restraints excluded: chain Y residue 16 LEU Chi-restraints excluded: chain Y residue 36 ASN Chi-restraints excluded: chain Y residue 205 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 109 optimal weight: 0.8980 chunk 292 optimal weight: 3.9990 chunk 64 optimal weight: 9.9990 chunk 190 optimal weight: 7.9990 chunk 80 optimal weight: 0.8980 chunk 325 optimal weight: 7.9990 chunk 269 optimal weight: 3.9990 chunk 150 optimal weight: 1.9990 chunk 27 optimal weight: 10.0000 chunk 107 optimal weight: 9.9990 chunk 170 optimal weight: 5.9990 overall best weight: 2.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 62 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 467 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 683 GLN ** K 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 231 ASN ** T 289 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 79 GLN Y 170 GLN ** Y 172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 106 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7769 moved from start: 0.2969 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 29041 Z= 0.252 Angle : 0.547 9.887 39403 Z= 0.286 Chirality : 0.040 0.213 4530 Planarity : 0.003 0.048 4802 Dihedral : 13.147 71.530 4214 Min Nonbonded Distance : 2.152 Molprobity Statistics. All-atom Clashscore : 10.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.13 % Favored : 96.87 % Rotamer: Outliers : 1.99 % Allowed : 13.60 % Favored : 84.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.85 (0.15), residues: 3318 helix: 2.36 (0.11), residues: 2125 sheet: -0.58 (0.32), residues: 244 loop : -0.96 (0.20), residues: 949 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP T 298 HIS 0.016 0.001 HIS K 123 PHE 0.022 0.002 PHE T 341 TYR 0.023 0.002 TYR Q 363 ARG 0.004 0.000 ARG H 71 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6636 Ramachandran restraints generated. 3318 Oldfield, 0 Emsley, 3318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6636 Ramachandran restraints generated. 3318 Oldfield, 0 Emsley, 3318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 386 residues out of total 3136 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 325 time to evaluate : 3.241 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 295 LEU cc_start: 0.8575 (OUTLIER) cc_final: 0.8313 (tt) REVERT: B 222 GLN cc_start: 0.7032 (tp-100) cc_final: 0.6577 (tp40) REVERT: B 322 LYS cc_start: 0.6853 (mttm) cc_final: 0.6519 (tmmt) REVERT: H 7 LYS cc_start: 0.7798 (mttt) cc_final: 0.7499 (mptt) REVERT: H 14 GLN cc_start: 0.7234 (OUTLIER) cc_final: 0.6462 (tm-30) REVERT: H 24 ARG cc_start: 0.8166 (ttp80) cc_final: 0.7913 (ttm170) REVERT: H 51 ARG cc_start: 0.7728 (tpp80) cc_final: 0.7306 (tpp80) REVERT: H 75 LYS cc_start: 0.5449 (mtpp) cc_final: 0.4853 (pttm) REVERT: H 166 ILE cc_start: 0.6801 (mm) cc_final: 0.6559 (mt) REVERT: I 148 TRP cc_start: 0.7509 (m100) cc_final: 0.6624 (m100) REVERT: I 173 ARG cc_start: 0.8216 (ttm170) cc_final: 0.7871 (mtp180) REVERT: I 264 GLN cc_start: 0.7559 (pt0) cc_final: 0.7165 (tt0) REVERT: I 311 ASP cc_start: 0.6870 (t0) cc_final: 0.6307 (t0) REVERT: I 331 MET cc_start: 0.4956 (mmp) cc_final: 0.3818 (mtm) REVERT: I 533 GLN cc_start: 0.8175 (pt0) cc_final: 0.7787 (mt0) REVERT: I 578 VAL cc_start: 0.7283 (t) cc_final: 0.6976 (p) REVERT: I 580 MET cc_start: 0.7983 (mtp) cc_final: 0.7635 (ttt) REVERT: I 582 ASN cc_start: 0.6100 (m-40) cc_final: 0.5644 (m-40) REVERT: I 622 THR cc_start: 0.5244 (m) cc_final: 0.4984 (p) REVERT: K 90 LEU cc_start: 0.8267 (OUTLIER) cc_final: 0.7898 (mm) REVERT: K 183 LYS cc_start: 0.6153 (mptt) cc_final: 0.5553 (tppt) REVERT: K 231 ILE cc_start: 0.7794 (OUTLIER) cc_final: 0.7311 (mt) REVERT: N 5 LEU cc_start: 0.7303 (OUTLIER) cc_final: 0.6948 (tt) REVERT: N 102 GLU cc_start: 0.7729 (pm20) cc_final: 0.7408 (pm20) REVERT: O 123 MET cc_start: 0.2016 (tpt) cc_final: 0.0788 (ptm) REVERT: Q 200 TYR cc_start: 0.6702 (t80) cc_final: 0.6494 (t80) REVERT: Q 222 LYS cc_start: 0.3730 (OUTLIER) cc_final: 0.3119 (mtmm) REVERT: Q 259 GLU cc_start: 0.7797 (mm-30) cc_final: 0.7573 (tp30) REVERT: Q 271 GLU cc_start: 0.7473 (tm-30) cc_final: 0.7154 (tm-30) REVERT: Q 387 LYS cc_start: 0.7518 (ttmt) cc_final: 0.7048 (tptt) REVERT: T 309 MET cc_start: 0.7226 (ppp) cc_final: 0.6865 (ppp) REVERT: T 324 LEU cc_start: 0.6255 (OUTLIER) cc_final: 0.6003 (tp) REVERT: T 340 MET cc_start: 0.6600 (mmm) cc_final: 0.5777 (mmm) REVERT: U 171 TYR cc_start: 0.5809 (m-10) cc_final: 0.5501 (m-10) REVERT: U 178 PHE cc_start: 0.8096 (m-80) cc_final: 0.7793 (m-80) REVERT: U 228 GLN cc_start: 0.7900 (mm110) cc_final: 0.7680 (mt0) REVERT: Y 3 ASP cc_start: 0.7333 (OUTLIER) cc_final: 0.7071 (m-30) REVERT: Y 158 GLN cc_start: 0.8221 (mt0) cc_final: 0.7799 (mt0) REVERT: Z 30 GLN cc_start: 0.5094 (mt0) cc_final: 0.4572 (mm-40) REVERT: Z 46 LEU cc_start: 0.7014 (mt) cc_final: 0.6677 (mm) REVERT: Z 49 ARG cc_start: 0.5584 (ppt170) cc_final: 0.5376 (ppt170) REVERT: Z 77 GLU cc_start: 0.7520 (mt-10) cc_final: 0.7257 (mt-10) outliers start: 61 outliers final: 41 residues processed: 366 average time/residue: 0.4844 time to fit residues: 285.4381 Evaluate side-chains 348 residues out of total 3136 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 299 time to evaluate : 3.470 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 295 LEU Chi-restraints excluded: chain B residue 313 ILE Chi-restraints excluded: chain H residue 14 GLN Chi-restraints excluded: chain H residue 62 ASN Chi-restraints excluded: chain H residue 81 VAL Chi-restraints excluded: chain H residue 97 ASP Chi-restraints excluded: chain H residue 122 ASP Chi-restraints excluded: chain I residue 84 GLU Chi-restraints excluded: chain I residue 204 ILE Chi-restraints excluded: chain I residue 242 HIS Chi-restraints excluded: chain I residue 255 ILE Chi-restraints excluded: chain I residue 257 MET Chi-restraints excluded: chain I residue 466 LEU Chi-restraints excluded: chain I residue 526 THR Chi-restraints excluded: chain I residue 579 ARG Chi-restraints excluded: chain I residue 633 ILE Chi-restraints excluded: chain I residue 665 ILE Chi-restraints excluded: chain K residue 90 LEU Chi-restraints excluded: chain K residue 92 LEU Chi-restraints excluded: chain K residue 104 LEU Chi-restraints excluded: chain K residue 126 THR Chi-restraints excluded: chain K residue 204 ILE Chi-restraints excluded: chain K residue 208 LEU Chi-restraints excluded: chain K residue 231 ILE Chi-restraints excluded: chain L residue 14 LEU Chi-restraints excluded: chain L residue 83 VAL Chi-restraints excluded: chain L residue 208 VAL Chi-restraints excluded: chain L residue 222 VAL Chi-restraints excluded: chain N residue 5 LEU Chi-restraints excluded: chain N residue 10 ASN Chi-restraints excluded: chain N residue 237 THR Chi-restraints excluded: chain N residue 248 VAL Chi-restraints excluded: chain O residue 197 VAL Chi-restraints excluded: chain O residue 262 ASP Chi-restraints excluded: chain O residue 305 MET Chi-restraints excluded: chain O residue 310 VAL Chi-restraints excluded: chain O residue 319 VAL Chi-restraints excluded: chain O residue 361 HIS Chi-restraints excluded: chain P residue 154 LEU Chi-restraints excluded: chain Q residue 222 LYS Chi-restraints excluded: chain Q residue 277 MET Chi-restraints excluded: chain Q residue 288 THR Chi-restraints excluded: chain T residue 305 SER Chi-restraints excluded: chain T residue 324 LEU Chi-restraints excluded: chain U residue 133 THR Chi-restraints excluded: chain U residue 278 SER Chi-restraints excluded: chain Y residue 3 ASP Chi-restraints excluded: chain Y residue 16 LEU Chi-restraints excluded: chain Y residue 205 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 313 optimal weight: 3.9990 chunk 36 optimal weight: 0.7980 chunk 185 optimal weight: 0.7980 chunk 237 optimal weight: 3.9990 chunk 183 optimal weight: 1.9990 chunk 273 optimal weight: 10.0000 chunk 181 optimal weight: 2.9990 chunk 323 optimal weight: 2.9990 chunk 202 optimal weight: 0.9990 chunk 197 optimal weight: 0.7980 chunk 149 optimal weight: 2.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 62 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 467 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 500 ASN ** I 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 683 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 123 HIS Y 79 GLN Y 170 GLN ** Y 172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7735 moved from start: 0.3044 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 29041 Z= 0.162 Angle : 0.515 9.401 39403 Z= 0.269 Chirality : 0.038 0.215 4530 Planarity : 0.003 0.050 4802 Dihedral : 13.051 70.394 4214 Min Nonbonded Distance : 2.161 Molprobity Statistics. All-atom Clashscore : 10.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 2.25 % Allowed : 13.86 % Favored : 83.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.99 (0.15), residues: 3318 helix: 2.47 (0.11), residues: 2128 sheet: -0.46 (0.33), residues: 244 loop : -0.92 (0.21), residues: 946 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP T 298 HIS 0.009 0.001 HIS K 123 PHE 0.021 0.001 PHE T 341 TYR 0.022 0.001 TYR Q 363 ARG 0.008 0.000 ARG H 71 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6636 Ramachandran restraints generated. 3318 Oldfield, 0 Emsley, 3318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6636 Ramachandran restraints generated. 3318 Oldfield, 0 Emsley, 3318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 388 residues out of total 3136 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 319 time to evaluate : 3.466 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 295 LEU cc_start: 0.8657 (OUTLIER) cc_final: 0.8402 (tt) REVERT: B 222 GLN cc_start: 0.7079 (tp-100) cc_final: 0.6616 (tp40) REVERT: B 315 TYR cc_start: 0.5366 (t80) cc_final: 0.4959 (t80) REVERT: B 322 LYS cc_start: 0.6833 (mttm) cc_final: 0.6484 (tmmt) REVERT: H 7 LYS cc_start: 0.7760 (mttt) cc_final: 0.7463 (mptt) REVERT: H 14 GLN cc_start: 0.7168 (OUTLIER) cc_final: 0.6391 (tm-30) REVERT: H 23 TYR cc_start: 0.8069 (t80) cc_final: 0.7706 (t80) REVERT: H 24 ARG cc_start: 0.8139 (ttp80) cc_final: 0.7903 (ttm170) REVERT: H 51 ARG cc_start: 0.7743 (tpp80) cc_final: 0.7327 (tpp80) REVERT: H 75 LYS cc_start: 0.5468 (mtpp) cc_final: 0.4837 (pttm) REVERT: H 166 ILE cc_start: 0.6944 (mm) cc_final: 0.6644 (mt) REVERT: H 175 THR cc_start: 0.7185 (p) cc_final: 0.6903 (p) REVERT: I 173 ARG cc_start: 0.8178 (ttm170) cc_final: 0.7846 (mtp180) REVERT: I 264 GLN cc_start: 0.7527 (pt0) cc_final: 0.7117 (tt0) REVERT: I 311 ASP cc_start: 0.6796 (t0) cc_final: 0.6220 (t0) REVERT: I 331 MET cc_start: 0.4984 (mmp) cc_final: 0.4272 (mtm) REVERT: I 533 GLN cc_start: 0.8102 (pt0) cc_final: 0.7706 (mt0) REVERT: I 578 VAL cc_start: 0.7295 (t) cc_final: 0.6997 (p) REVERT: I 580 MET cc_start: 0.7941 (mtp) cc_final: 0.7526 (ttt) REVERT: I 582 ASN cc_start: 0.6083 (m-40) cc_final: 0.5605 (m-40) REVERT: I 622 THR cc_start: 0.5182 (m) cc_final: 0.4919 (p) REVERT: K 79 LEU cc_start: 0.7595 (OUTLIER) cc_final: 0.7267 (mp) REVERT: K 90 LEU cc_start: 0.8225 (OUTLIER) cc_final: 0.7717 (mm) REVERT: K 183 LYS cc_start: 0.6203 (mptt) cc_final: 0.5562 (tppt) REVERT: K 231 ILE cc_start: 0.7655 (OUTLIER) cc_final: 0.7265 (mt) REVERT: N 5 LEU cc_start: 0.7215 (OUTLIER) cc_final: 0.6864 (tt) REVERT: O 123 MET cc_start: 0.2128 (tpt) cc_final: 0.0824 (ptm) REVERT: Q 222 LYS cc_start: 0.4158 (OUTLIER) cc_final: 0.3703 (mtmm) REVERT: Q 271 GLU cc_start: 0.7429 (tm-30) cc_final: 0.7090 (tm-30) REVERT: Q 387 LYS cc_start: 0.7462 (ttmt) cc_final: 0.6994 (tptt) REVERT: T 309 MET cc_start: 0.7241 (ppp) cc_final: 0.6809 (ppp) REVERT: T 324 LEU cc_start: 0.6327 (OUTLIER) cc_final: 0.6077 (tp) REVERT: T 340 MET cc_start: 0.6587 (mmm) cc_final: 0.5764 (mmm) REVERT: U 228 GLN cc_start: 0.7876 (mm110) cc_final: 0.7656 (mt0) REVERT: W 1 MET cc_start: 0.4353 (tmm) cc_final: 0.2996 (ttm) REVERT: Y 3 ASP cc_start: 0.7357 (OUTLIER) cc_final: 0.7130 (m-30) REVERT: Y 158 GLN cc_start: 0.8156 (mt0) cc_final: 0.7824 (mt0) REVERT: Z 30 GLN cc_start: 0.5087 (mt0) cc_final: 0.4578 (mm-40) REVERT: Z 46 LEU cc_start: 0.7277 (mt) cc_final: 0.6956 (mm) REVERT: Z 77 GLU cc_start: 0.7662 (mt-10) cc_final: 0.7356 (mt-10) outliers start: 69 outliers final: 44 residues processed: 367 average time/residue: 0.4437 time to fit residues: 256.9053 Evaluate side-chains 360 residues out of total 3136 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 307 time to evaluate : 3.777 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 295 LEU Chi-restraints excluded: chain B residue 313 ILE Chi-restraints excluded: chain H residue 14 GLN Chi-restraints excluded: chain H residue 62 ASN Chi-restraints excluded: chain H residue 97 ASP Chi-restraints excluded: chain H residue 122 ASP Chi-restraints excluded: chain I residue 84 GLU Chi-restraints excluded: chain I residue 163 VAL Chi-restraints excluded: chain I residue 204 ILE Chi-restraints excluded: chain I residue 242 HIS Chi-restraints excluded: chain I residue 257 MET Chi-restraints excluded: chain I residue 312 VAL Chi-restraints excluded: chain I residue 466 LEU Chi-restraints excluded: chain I residue 526 THR Chi-restraints excluded: chain I residue 579 ARG Chi-restraints excluded: chain I residue 633 ILE Chi-restraints excluded: chain I residue 665 ILE Chi-restraints excluded: chain K residue 79 LEU Chi-restraints excluded: chain K residue 81 LEU Chi-restraints excluded: chain K residue 90 LEU Chi-restraints excluded: chain K residue 92 LEU Chi-restraints excluded: chain K residue 104 LEU Chi-restraints excluded: chain K residue 123 HIS Chi-restraints excluded: chain K residue 126 THR Chi-restraints excluded: chain K residue 204 ILE Chi-restraints excluded: chain K residue 208 LEU Chi-restraints excluded: chain K residue 231 ILE Chi-restraints excluded: chain L residue 14 LEU Chi-restraints excluded: chain L residue 35 ILE Chi-restraints excluded: chain L residue 83 VAL Chi-restraints excluded: chain L residue 208 VAL Chi-restraints excluded: chain L residue 222 VAL Chi-restraints excluded: chain N residue 5 LEU Chi-restraints excluded: chain N residue 10 ASN Chi-restraints excluded: chain N residue 195 ILE Chi-restraints excluded: chain N residue 237 THR Chi-restraints excluded: chain N residue 248 VAL Chi-restraints excluded: chain N residue 385 VAL Chi-restraints excluded: chain N residue 399 THR Chi-restraints excluded: chain O residue 197 VAL Chi-restraints excluded: chain O residue 262 ASP Chi-restraints excluded: chain O residue 319 VAL Chi-restraints excluded: chain O residue 353 ASP Chi-restraints excluded: chain O residue 361 HIS Chi-restraints excluded: chain Q residue 222 LYS Chi-restraints excluded: chain Q residue 288 THR Chi-restraints excluded: chain Q residue 335 MET Chi-restraints excluded: chain T residue 324 LEU Chi-restraints excluded: chain U residue 133 THR Chi-restraints excluded: chain W residue 78 ILE Chi-restraints excluded: chain Y residue 3 ASP Chi-restraints excluded: chain Y residue 16 LEU Chi-restraints excluded: chain Y residue 205 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 200 optimal weight: 3.9990 chunk 129 optimal weight: 8.9990 chunk 193 optimal weight: 0.8980 chunk 97 optimal weight: 0.1980 chunk 63 optimal weight: 0.6980 chunk 62 optimal weight: 3.9990 chunk 205 optimal weight: 4.9990 chunk 220 optimal weight: 4.9990 chunk 160 optimal weight: 5.9990 chunk 30 optimal weight: 8.9990 chunk 254 optimal weight: 0.7980 overall best weight: 1.3182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 62 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 467 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 683 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 123 HIS ** K 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 289 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 79 GLN Y 170 GLN ** Y 172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7742 moved from start: 0.3136 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 29041 Z= 0.180 Angle : 0.524 9.016 39403 Z= 0.273 Chirality : 0.038 0.214 4530 Planarity : 0.003 0.043 4802 Dihedral : 13.036 69.981 4214 Min Nonbonded Distance : 2.150 Molprobity Statistics. All-atom Clashscore : 10.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.13 % Favored : 96.87 % Rotamer: Outliers : 2.05 % Allowed : 14.70 % Favored : 83.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: 2.04 (0.15), residues: 3318 helix: 2.50 (0.11), residues: 2128 sheet: -0.42 (0.33), residues: 244 loop : -0.89 (0.21), residues: 946 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP T 298 HIS 0.017 0.001 HIS K 123 PHE 0.021 0.001 PHE T 341 TYR 0.058 0.002 TYR U 171 ARG 0.009 0.000 ARG H 71 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6636 Ramachandran restraints generated. 3318 Oldfield, 0 Emsley, 3318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6636 Ramachandran restraints generated. 3318 Oldfield, 0 Emsley, 3318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 375 residues out of total 3136 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 312 time to evaluate : 3.162 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 295 LEU cc_start: 0.8662 (OUTLIER) cc_final: 0.8414 (tt) REVERT: B 222 GLN cc_start: 0.7080 (tp-100) cc_final: 0.6609 (tp40) REVERT: B 223 ARG cc_start: 0.7142 (mtt180) cc_final: 0.6719 (mtt-85) REVERT: B 315 TYR cc_start: 0.5468 (t80) cc_final: 0.5025 (t80) REVERT: B 322 LYS cc_start: 0.6821 (mttm) cc_final: 0.6484 (tmmt) REVERT: H 7 LYS cc_start: 0.7724 (mttt) cc_final: 0.7428 (mptt) REVERT: H 14 GLN cc_start: 0.7169 (OUTLIER) cc_final: 0.6400 (tm-30) REVERT: H 23 TYR cc_start: 0.8071 (t80) cc_final: 0.7750 (t80) REVERT: H 24 ARG cc_start: 0.8150 (ttp80) cc_final: 0.7910 (ttm170) REVERT: H 75 LYS cc_start: 0.5435 (mtpp) cc_final: 0.4800 (pttm) REVERT: H 166 ILE cc_start: 0.6893 (mm) cc_final: 0.6631 (mt) REVERT: H 175 THR cc_start: 0.7141 (p) cc_final: 0.6869 (p) REVERT: I 173 ARG cc_start: 0.8173 (ttm170) cc_final: 0.7843 (mtp180) REVERT: I 264 GLN cc_start: 0.7527 (pt0) cc_final: 0.7115 (tt0) REVERT: I 311 ASP cc_start: 0.6979 (t0) cc_final: 0.6359 (t0) REVERT: I 331 MET cc_start: 0.5149 (mmp) cc_final: 0.4417 (mtm) REVERT: I 533 GLN cc_start: 0.8088 (pt0) cc_final: 0.7703 (mt0) REVERT: I 578 VAL cc_start: 0.7357 (t) cc_final: 0.7075 (p) REVERT: I 580 MET cc_start: 0.7937 (mtp) cc_final: 0.7556 (ttt) REVERT: I 582 ASN cc_start: 0.6040 (m-40) cc_final: 0.5552 (m-40) REVERT: I 622 THR cc_start: 0.5145 (m) cc_final: 0.4883 (p) REVERT: K 79 LEU cc_start: 0.7542 (OUTLIER) cc_final: 0.7219 (mp) REVERT: K 90 LEU cc_start: 0.8126 (OUTLIER) cc_final: 0.7707 (mm) REVERT: K 231 ILE cc_start: 0.7655 (OUTLIER) cc_final: 0.7249 (mt) REVERT: N 5 LEU cc_start: 0.7231 (OUTLIER) cc_final: 0.6876 (tt) REVERT: O 123 MET cc_start: 0.1878 (tpt) cc_final: 0.0649 (ptm) REVERT: Q 222 LYS cc_start: 0.3724 (OUTLIER) cc_final: 0.3179 (mtmm) REVERT: Q 271 GLU cc_start: 0.7422 (tm-30) cc_final: 0.7107 (tm-30) REVERT: Q 387 LYS cc_start: 0.7622 (ttmt) cc_final: 0.7180 (tptt) REVERT: T 309 MET cc_start: 0.7242 (ppp) cc_final: 0.6786 (ppp) REVERT: T 316 ILE cc_start: 0.5565 (mp) cc_final: 0.5153 (pt) REVERT: T 324 LEU cc_start: 0.6445 (OUTLIER) cc_final: 0.6197 (tp) REVERT: T 340 MET cc_start: 0.6592 (mmm) cc_final: 0.5765 (mmm) REVERT: U 171 TYR cc_start: 0.5462 (m-10) cc_final: 0.5019 (m-80) REVERT: U 228 GLN cc_start: 0.7885 (mm110) cc_final: 0.7662 (mt0) REVERT: W 1 MET cc_start: 0.4129 (tmm) cc_final: 0.2663 (ttm) REVERT: Y 3 ASP cc_start: 0.7407 (OUTLIER) cc_final: 0.7178 (m-30) REVERT: Y 158 GLN cc_start: 0.8141 (mt0) cc_final: 0.7805 (mt0) REVERT: Z 30 GLN cc_start: 0.5066 (mt0) cc_final: 0.4639 (mm110) REVERT: Z 77 GLU cc_start: 0.7492 (mt-10) cc_final: 0.7225 (mt-10) outliers start: 63 outliers final: 46 residues processed: 355 average time/residue: 0.4172 time to fit residues: 234.8070 Evaluate side-chains 352 residues out of total 3136 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 297 time to evaluate : 3.772 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 295 LEU Chi-restraints excluded: chain B residue 313 ILE Chi-restraints excluded: chain H residue 14 GLN Chi-restraints excluded: chain H residue 62 ASN Chi-restraints excluded: chain H residue 97 ASP Chi-restraints excluded: chain H residue 122 ASP Chi-restraints excluded: chain I residue 84 GLU Chi-restraints excluded: chain I residue 163 VAL Chi-restraints excluded: chain I residue 204 ILE Chi-restraints excluded: chain I residue 242 HIS Chi-restraints excluded: chain I residue 257 MET Chi-restraints excluded: chain I residue 466 LEU Chi-restraints excluded: chain I residue 526 THR Chi-restraints excluded: chain I residue 579 ARG Chi-restraints excluded: chain I residue 633 ILE Chi-restraints excluded: chain I residue 665 ILE Chi-restraints excluded: chain K residue 41 LEU Chi-restraints excluded: chain K residue 79 LEU Chi-restraints excluded: chain K residue 90 LEU Chi-restraints excluded: chain K residue 92 LEU Chi-restraints excluded: chain K residue 104 LEU Chi-restraints excluded: chain K residue 123 HIS Chi-restraints excluded: chain K residue 126 THR Chi-restraints excluded: chain K residue 204 ILE Chi-restraints excluded: chain K residue 208 LEU Chi-restraints excluded: chain K residue 231 ILE Chi-restraints excluded: chain L residue 14 LEU Chi-restraints excluded: chain L residue 35 ILE Chi-restraints excluded: chain L residue 83 VAL Chi-restraints excluded: chain L residue 208 VAL Chi-restraints excluded: chain L residue 222 VAL Chi-restraints excluded: chain N residue 5 LEU Chi-restraints excluded: chain N residue 10 ASN Chi-restraints excluded: chain N residue 82 ASP Chi-restraints excluded: chain N residue 195 ILE Chi-restraints excluded: chain N residue 237 THR Chi-restraints excluded: chain N residue 248 VAL Chi-restraints excluded: chain N residue 385 VAL Chi-restraints excluded: chain N residue 399 THR Chi-restraints excluded: chain O residue 197 VAL Chi-restraints excluded: chain O residue 262 ASP Chi-restraints excluded: chain O residue 301 LEU Chi-restraints excluded: chain O residue 319 VAL Chi-restraints excluded: chain O residue 353 ASP Chi-restraints excluded: chain O residue 361 HIS Chi-restraints excluded: chain P residue 154 LEU Chi-restraints excluded: chain Q residue 222 LYS Chi-restraints excluded: chain Q residue 288 THR Chi-restraints excluded: chain Q residue 335 MET Chi-restraints excluded: chain T residue 324 LEU Chi-restraints excluded: chain U residue 133 THR Chi-restraints excluded: chain W residue 78 ILE Chi-restraints excluded: chain Y residue 3 ASP Chi-restraints excluded: chain Y residue 16 LEU Chi-restraints excluded: chain Y residue 205 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 294 optimal weight: 5.9990 chunk 310 optimal weight: 6.9990 chunk 283 optimal weight: 8.9990 chunk 301 optimal weight: 9.9990 chunk 181 optimal weight: 0.9980 chunk 131 optimal weight: 8.9990 chunk 236 optimal weight: 1.9990 chunk 92 optimal weight: 1.9990 chunk 272 optimal weight: 2.9990 chunk 285 optimal weight: 0.9990 chunk 300 optimal weight: 5.9990 overall best weight: 1.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 62 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 467 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 613 GLN ** I 683 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 123 HIS K 124 GLN O 295 HIS P 200 GLN Y 79 GLN Y 170 GLN ** Y 172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7758 moved from start: 0.3241 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 29041 Z= 0.213 Angle : 0.542 11.360 39403 Z= 0.281 Chirality : 0.039 0.219 4530 Planarity : 0.003 0.042 4802 Dihedral : 13.065 70.162 4214 Min Nonbonded Distance : 2.151 Molprobity Statistics. All-atom Clashscore : 10.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer: Outliers : 2.15 % Allowed : 14.77 % Favored : 83.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.99 (0.15), residues: 3318 helix: 2.46 (0.11), residues: 2131 sheet: -0.42 (0.33), residues: 244 loop : -0.92 (0.21), residues: 943 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP T 298 HIS 0.030 0.001 HIS K 123 PHE 0.023 0.001 PHE K 53 TYR 0.040 0.002 TYR U 171 ARG 0.011 0.000 ARG H 71 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6636 Ramachandran restraints generated. 3318 Oldfield, 0 Emsley, 3318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6636 Ramachandran restraints generated. 3318 Oldfield, 0 Emsley, 3318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 375 residues out of total 3136 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 309 time to evaluate : 3.747 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 295 LEU cc_start: 0.8674 (OUTLIER) cc_final: 0.8421 (tt) REVERT: B 315 TYR cc_start: 0.5453 (t80) cc_final: 0.5155 (t80) REVERT: B 322 LYS cc_start: 0.6823 (mttm) cc_final: 0.6474 (tmmt) REVERT: H 7 LYS cc_start: 0.7762 (mttt) cc_final: 0.7463 (mptt) REVERT: H 14 GLN cc_start: 0.7205 (OUTLIER) cc_final: 0.6458 (tm-30) REVERT: H 23 TYR cc_start: 0.8029 (t80) cc_final: 0.7720 (t80) REVERT: H 24 ARG cc_start: 0.8185 (ttp80) cc_final: 0.7940 (ttm170) REVERT: H 75 LYS cc_start: 0.5424 (mtpp) cc_final: 0.4794 (pttm) REVERT: H 166 ILE cc_start: 0.6980 (mm) cc_final: 0.6683 (mt) REVERT: H 175 THR cc_start: 0.7250 (p) cc_final: 0.6990 (p) REVERT: I 173 ARG cc_start: 0.8173 (ttm170) cc_final: 0.7845 (mtp180) REVERT: I 264 GLN cc_start: 0.7527 (pt0) cc_final: 0.7126 (tt0) REVERT: I 311 ASP cc_start: 0.7076 (t0) cc_final: 0.6538 (t0) REVERT: I 331 MET cc_start: 0.5305 (mmp) cc_final: 0.4501 (mtm) REVERT: I 533 GLN cc_start: 0.8104 (pt0) cc_final: 0.7788 (mt0) REVERT: I 578 VAL cc_start: 0.7450 (t) cc_final: 0.7065 (p) REVERT: I 580 MET cc_start: 0.7945 (mtp) cc_final: 0.7612 (ttt) REVERT: I 582 ASN cc_start: 0.6055 (m-40) cc_final: 0.5545 (m-40) REVERT: I 622 THR cc_start: 0.5121 (m) cc_final: 0.4856 (p) REVERT: K 79 LEU cc_start: 0.7535 (OUTLIER) cc_final: 0.7199 (mp) REVERT: K 90 LEU cc_start: 0.8155 (OUTLIER) cc_final: 0.7765 (mm) REVERT: K 183 LYS cc_start: 0.6246 (mptt) cc_final: 0.5677 (tptm) REVERT: N 5 LEU cc_start: 0.7256 (OUTLIER) cc_final: 0.6903 (tt) REVERT: O 123 MET cc_start: 0.1889 (tpt) cc_final: 0.0678 (ptm) REVERT: Q 222 LYS cc_start: 0.3828 (OUTLIER) cc_final: 0.3228 (mtmm) REVERT: Q 387 LYS cc_start: 0.7597 (ttmt) cc_final: 0.7133 (tptt) REVERT: T 309 MET cc_start: 0.7268 (ppp) cc_final: 0.6807 (ppp) REVERT: T 324 LEU cc_start: 0.6437 (OUTLIER) cc_final: 0.6174 (tp) REVERT: T 331 MET cc_start: 0.6523 (mmm) cc_final: 0.6041 (mtt) REVERT: T 340 MET cc_start: 0.6597 (mmm) cc_final: 0.5772 (mmm) REVERT: U 171 TYR cc_start: 0.5406 (m-10) cc_final: 0.5118 (m-80) REVERT: U 228 GLN cc_start: 0.7915 (mm110) cc_final: 0.7685 (mt0) REVERT: Y 3 ASP cc_start: 0.7451 (OUTLIER) cc_final: 0.7183 (m-30) REVERT: Y 158 GLN cc_start: 0.8137 (mt0) cc_final: 0.7793 (mt0) REVERT: Z 77 GLU cc_start: 0.7496 (mt-10) cc_final: 0.7227 (mt-10) outliers start: 66 outliers final: 49 residues processed: 354 average time/residue: 0.4378 time to fit residues: 246.0096 Evaluate side-chains 352 residues out of total 3136 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 295 time to evaluate : 3.510 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 295 LEU Chi-restraints excluded: chain B residue 313 ILE Chi-restraints excluded: chain H residue 14 GLN Chi-restraints excluded: chain H residue 62 ASN Chi-restraints excluded: chain H residue 81 VAL Chi-restraints excluded: chain H residue 122 ASP Chi-restraints excluded: chain I residue 84 GLU Chi-restraints excluded: chain I residue 163 VAL Chi-restraints excluded: chain I residue 204 ILE Chi-restraints excluded: chain I residue 242 HIS Chi-restraints excluded: chain I residue 257 MET Chi-restraints excluded: chain I residue 466 LEU Chi-restraints excluded: chain I residue 526 THR Chi-restraints excluded: chain I residue 579 ARG Chi-restraints excluded: chain I residue 633 ILE Chi-restraints excluded: chain I residue 665 ILE Chi-restraints excluded: chain K residue 41 LEU Chi-restraints excluded: chain K residue 79 LEU Chi-restraints excluded: chain K residue 81 LEU Chi-restraints excluded: chain K residue 90 LEU Chi-restraints excluded: chain K residue 92 LEU Chi-restraints excluded: chain K residue 104 LEU Chi-restraints excluded: chain K residue 123 HIS Chi-restraints excluded: chain K residue 126 THR Chi-restraints excluded: chain K residue 204 ILE Chi-restraints excluded: chain K residue 208 LEU Chi-restraints excluded: chain K residue 231 ILE Chi-restraints excluded: chain L residue 14 LEU Chi-restraints excluded: chain L residue 35 ILE Chi-restraints excluded: chain L residue 83 VAL Chi-restraints excluded: chain L residue 208 VAL Chi-restraints excluded: chain L residue 222 VAL Chi-restraints excluded: chain N residue 5 LEU Chi-restraints excluded: chain N residue 10 ASN Chi-restraints excluded: chain N residue 30 THR Chi-restraints excluded: chain N residue 82 ASP Chi-restraints excluded: chain N residue 195 ILE Chi-restraints excluded: chain N residue 237 THR Chi-restraints excluded: chain N residue 248 VAL Chi-restraints excluded: chain N residue 385 VAL Chi-restraints excluded: chain N residue 399 THR Chi-restraints excluded: chain O residue 197 VAL Chi-restraints excluded: chain O residue 262 ASP Chi-restraints excluded: chain O residue 301 LEU Chi-restraints excluded: chain O residue 319 VAL Chi-restraints excluded: chain O residue 361 HIS Chi-restraints excluded: chain P residue 154 LEU Chi-restraints excluded: chain Q residue 222 LYS Chi-restraints excluded: chain Q residue 288 THR Chi-restraints excluded: chain Q residue 335 MET Chi-restraints excluded: chain T residue 324 LEU Chi-restraints excluded: chain U residue 133 THR Chi-restraints excluded: chain U residue 278 SER Chi-restraints excluded: chain W residue 78 ILE Chi-restraints excluded: chain Y residue 3 ASP Chi-restraints excluded: chain Y residue 16 LEU Chi-restraints excluded: chain Y residue 205 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 198 optimal weight: 0.9980 chunk 319 optimal weight: 0.0980 chunk 194 optimal weight: 0.8980 chunk 151 optimal weight: 6.9990 chunk 221 optimal weight: 3.9990 chunk 334 optimal weight: 8.9990 chunk 308 optimal weight: 1.9990 chunk 266 optimal weight: 1.9990 chunk 27 optimal weight: 7.9990 chunk 205 optimal weight: 2.9990 chunk 163 optimal weight: 0.9990 overall best weight: 0.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 222 GLN ** H 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 62 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 467 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 683 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 123 HIS Y 79 GLN Y 170 GLN ** Y 172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7737 moved from start: 0.3279 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 29041 Z= 0.163 Angle : 0.531 11.446 39403 Z= 0.275 Chirality : 0.038 0.221 4530 Planarity : 0.003 0.041 4802 Dihedral : 13.006 69.882 4214 Min Nonbonded Distance : 2.137 Molprobity Statistics. All-atom Clashscore : 10.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % Rotamer: Outliers : 1.96 % Allowed : 15.36 % Favored : 82.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: 2.06 (0.15), residues: 3318 helix: 2.51 (0.11), residues: 2130 sheet: -0.36 (0.33), residues: 244 loop : -0.90 (0.21), residues: 944 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP T 298 HIS 0.034 0.001 HIS K 123 PHE 0.020 0.001 PHE T 341 TYR 0.031 0.001 TYR U 171 ARG 0.011 0.000 ARG H 71 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6636 Ramachandran restraints generated. 3318 Oldfield, 0 Emsley, 3318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6636 Ramachandran restraints generated. 3318 Oldfield, 0 Emsley, 3318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 375 residues out of total 3136 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 315 time to evaluate : 3.350 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 295 LEU cc_start: 0.8661 (OUTLIER) cc_final: 0.8414 (tt) REVERT: A 315 TYR cc_start: 0.6720 (t80) cc_final: 0.6176 (t80) REVERT: B 315 TYR cc_start: 0.5459 (t80) cc_final: 0.5190 (t80) REVERT: B 322 LYS cc_start: 0.6825 (mttm) cc_final: 0.6490 (tmmt) REVERT: H 14 GLN cc_start: 0.7141 (OUTLIER) cc_final: 0.6397 (tm-30) REVERT: H 23 TYR cc_start: 0.8081 (t80) cc_final: 0.7764 (t80) REVERT: H 24 ARG cc_start: 0.8141 (ttp80) cc_final: 0.7906 (ttm170) REVERT: H 75 LYS cc_start: 0.5402 (mtpp) cc_final: 0.4785 (pttm) REVERT: H 166 ILE cc_start: 0.7038 (mm) cc_final: 0.6693 (mt) REVERT: H 175 THR cc_start: 0.7390 (p) cc_final: 0.7144 (p) REVERT: I 173 ARG cc_start: 0.8169 (ttm170) cc_final: 0.7846 (mtp180) REVERT: I 181 ARG cc_start: 0.7167 (mtm110) cc_final: 0.6963 (ttp-110) REVERT: I 264 GLN cc_start: 0.7461 (pt0) cc_final: 0.7070 (tt0) REVERT: I 311 ASP cc_start: 0.7017 (t0) cc_final: 0.6442 (t0) REVERT: I 331 MET cc_start: 0.5303 (mmp) cc_final: 0.4666 (mtm) REVERT: I 533 GLN cc_start: 0.8107 (pt0) cc_final: 0.7808 (mt0) REVERT: I 578 VAL cc_start: 0.7389 (t) cc_final: 0.7026 (p) REVERT: I 580 MET cc_start: 0.7973 (mtp) cc_final: 0.7622 (ttt) REVERT: I 582 ASN cc_start: 0.6108 (m-40) cc_final: 0.5605 (m-40) REVERT: I 622 THR cc_start: 0.5078 (m) cc_final: 0.4814 (p) REVERT: K 79 LEU cc_start: 0.7532 (OUTLIER) cc_final: 0.7198 (mp) REVERT: K 90 LEU cc_start: 0.8120 (OUTLIER) cc_final: 0.7734 (mm) REVERT: K 179 MET cc_start: 0.7347 (mmm) cc_final: 0.7047 (mmm) REVERT: K 231 ILE cc_start: 0.7665 (OUTLIER) cc_final: 0.7237 (mt) REVERT: N 5 LEU cc_start: 0.7221 (OUTLIER) cc_final: 0.6871 (tt) REVERT: O 123 MET cc_start: 0.2026 (tpt) cc_final: 0.0773 (ptm) REVERT: Q 222 LYS cc_start: 0.3807 (OUTLIER) cc_final: 0.3220 (mtmm) REVERT: Q 271 GLU cc_start: 0.7286 (tm-30) cc_final: 0.7063 (tm-30) REVERT: Q 387 LYS cc_start: 0.7554 (ttmt) cc_final: 0.7094 (tptt) REVERT: T 309 MET cc_start: 0.7258 (ppp) cc_final: 0.6760 (ppp) REVERT: T 316 ILE cc_start: 0.5852 (mp) cc_final: 0.5539 (pt) REVERT: T 324 LEU cc_start: 0.6400 (OUTLIER) cc_final: 0.6140 (tp) REVERT: T 331 MET cc_start: 0.6624 (mmm) cc_final: 0.6181 (mtt) REVERT: T 340 MET cc_start: 0.6502 (mmm) cc_final: 0.5694 (mmm) REVERT: W 1 MET cc_start: 0.4152 (tmm) cc_final: 0.2757 (ttm) REVERT: Y 3 ASP cc_start: 0.7421 (OUTLIER) cc_final: 0.7186 (m-30) REVERT: Y 19 LEU cc_start: 0.6722 (tt) cc_final: 0.6487 (tp) REVERT: Y 158 GLN cc_start: 0.8173 (mt0) cc_final: 0.7885 (mt0) REVERT: Z 34 SER cc_start: 0.5892 (m) cc_final: 0.5524 (p) REVERT: Z 77 GLU cc_start: 0.7455 (mt-10) cc_final: 0.7218 (mt-10) outliers start: 60 outliers final: 49 residues processed: 356 average time/residue: 0.4192 time to fit residues: 239.3599 Evaluate side-chains 359 residues out of total 3136 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 301 time to evaluate : 3.807 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 227 HIS Chi-restraints excluded: chain A residue 295 LEU Chi-restraints excluded: chain B residue 313 ILE Chi-restraints excluded: chain H residue 14 GLN Chi-restraints excluded: chain H residue 62 ASN Chi-restraints excluded: chain H residue 81 VAL Chi-restraints excluded: chain H residue 122 ASP Chi-restraints excluded: chain I residue 84 GLU Chi-restraints excluded: chain I residue 163 VAL Chi-restraints excluded: chain I residue 204 ILE Chi-restraints excluded: chain I residue 242 HIS Chi-restraints excluded: chain I residue 257 MET Chi-restraints excluded: chain I residue 466 LEU Chi-restraints excluded: chain I residue 526 THR Chi-restraints excluded: chain I residue 579 ARG Chi-restraints excluded: chain I residue 633 ILE Chi-restraints excluded: chain I residue 665 ILE Chi-restraints excluded: chain K residue 41 LEU Chi-restraints excluded: chain K residue 79 LEU Chi-restraints excluded: chain K residue 81 LEU Chi-restraints excluded: chain K residue 90 LEU Chi-restraints excluded: chain K residue 92 LEU Chi-restraints excluded: chain K residue 104 LEU Chi-restraints excluded: chain K residue 123 HIS Chi-restraints excluded: chain K residue 126 THR Chi-restraints excluded: chain K residue 204 ILE Chi-restraints excluded: chain K residue 208 LEU Chi-restraints excluded: chain K residue 231 ILE Chi-restraints excluded: chain L residue 14 LEU Chi-restraints excluded: chain L residue 35 ILE Chi-restraints excluded: chain L residue 83 VAL Chi-restraints excluded: chain L residue 208 VAL Chi-restraints excluded: chain L residue 222 VAL Chi-restraints excluded: chain N residue 5 LEU Chi-restraints excluded: chain N residue 10 ASN Chi-restraints excluded: chain N residue 30 THR Chi-restraints excluded: chain N residue 82 ASP Chi-restraints excluded: chain N residue 195 ILE Chi-restraints excluded: chain N residue 237 THR Chi-restraints excluded: chain N residue 248 VAL Chi-restraints excluded: chain N residue 385 VAL Chi-restraints excluded: chain N residue 399 THR Chi-restraints excluded: chain O residue 197 VAL Chi-restraints excluded: chain O residue 262 ASP Chi-restraints excluded: chain O residue 319 VAL Chi-restraints excluded: chain O residue 353 ASP Chi-restraints excluded: chain O residue 361 HIS Chi-restraints excluded: chain P residue 154 LEU Chi-restraints excluded: chain Q residue 222 LYS Chi-restraints excluded: chain Q residue 288 THR Chi-restraints excluded: chain Q residue 335 MET Chi-restraints excluded: chain T residue 324 LEU Chi-restraints excluded: chain U residue 133 THR Chi-restraints excluded: chain U residue 278 SER Chi-restraints excluded: chain W residue 78 ILE Chi-restraints excluded: chain Y residue 3 ASP Chi-restraints excluded: chain Y residue 16 LEU Chi-restraints excluded: chain Y residue 205 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 211 optimal weight: 1.9990 chunk 283 optimal weight: 1.9990 chunk 81 optimal weight: 0.0370 chunk 245 optimal weight: 7.9990 chunk 39 optimal weight: 10.0000 chunk 74 optimal weight: 1.9990 chunk 266 optimal weight: 0.9980 chunk 111 optimal weight: 3.9990 chunk 274 optimal weight: 0.0000 chunk 33 optimal weight: 1.9990 chunk 49 optimal weight: 7.9990 overall best weight: 1.0066 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 8 GLN ** H 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 62 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 467 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 677 HIS ** I 683 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 123 HIS U 228 GLN Y 170 GLN ** Y 172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 28 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3987 r_free = 0.3987 target = 0.135729 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3450 r_free = 0.3450 target = 0.099680 restraints weight = 59567.342| |-----------------------------------------------------------------------------| r_work (start): 0.3424 rms_B_bonded: 2.22 r_work: 0.3289 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.3172 rms_B_bonded: 4.88 restraints_weight: 0.2500 r_work (final): 0.3172 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8051 moved from start: 0.3332 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.073 29041 Z= 0.166 Angle : 0.531 11.058 39403 Z= 0.276 Chirality : 0.038 0.220 4530 Planarity : 0.004 0.126 4802 Dihedral : 12.981 69.445 4214 Min Nonbonded Distance : 2.144 Molprobity Statistics. All-atom Clashscore : 10.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.07 % Favored : 96.93 % Rotamer: Outliers : 2.02 % Allowed : 15.78 % Favored : 82.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: 2.09 (0.15), residues: 3318 helix: 2.51 (0.11), residues: 2136 sheet: -0.30 (0.33), residues: 244 loop : -0.88 (0.21), residues: 938 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP T 298 HIS 0.028 0.001 HIS K 123 PHE 0.027 0.001 PHE K 53 TYR 0.028 0.002 TYR Q 363 ARG 0.020 0.000 ARG P 369 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6888.04 seconds wall clock time: 126 minutes 36.54 seconds (7596.54 seconds total)