Starting phenix.real_space_refine on Thu Feb 22 15:55:21 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lex_23293/02_2024/7lex_23293.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lex_23293/02_2024/7lex_23293.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lex_23293/02_2024/7lex_23293.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lex_23293/02_2024/7lex_23293.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lex_23293/02_2024/7lex_23293.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lex_23293/02_2024/7lex_23293.pdb" } resolution = 3.6 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= 0.053 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 126 5.16 5 C 21822 2.51 5 N 5856 2.21 5 O 6792 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 180": "NH1" <-> "NH2" Residue "E PHE 139": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 180": "NH1" <-> "NH2" Residue "C ARG 180": "NH1" <-> "NH2" Residue "H PHE 139": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 139": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ARG 180": "NH1" <-> "NH2" Residue "L PHE 139": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M ARG 180": "NH1" <-> "NH2" Residue "N ARG 180": "NH1" <-> "NH2" Residue "O PHE 139": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P PHE 139": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.12s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 34596 Number of models: 1 Model: "" Number of chains: 18 Chain: "A" Number of atoms: 2409 Number of conformers: 1 Conformer: "" Number of residues, atoms: 317, 2409 Classifications: {'peptide': 317} Link IDs: {'CIS': 1, 'PTRANS': 21, 'TRANS': 294} Chain: "D" Number of atoms: 1717 Number of conformers: 1 Conformer: "" Number of residues, atoms: 228, 1717 Classifications: {'peptide': 228} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'CIS': 2, 'PCIS': 2, 'PTRANS': 12, 'TRANS': 211} Chain breaks: 3 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "E" Number of atoms: 1640 Number of conformers: 1 Conformer: "" Number of residues, atoms: 214, 1640 Classifications: {'peptide': 214} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'CIS': 1, 'PCIS': 2, 'PTRANS': 10, 'TRANS': 200} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "B" Number of atoms: 2409 Number of conformers: 1 Conformer: "" Number of residues, atoms: 317, 2409 Classifications: {'peptide': 317} Link IDs: {'CIS': 1, 'PTRANS': 21, 'TRANS': 294} Chain: "C" Number of atoms: 2409 Number of conformers: 1 Conformer: "" Number of residues, atoms: 317, 2409 Classifications: {'peptide': 317} Link IDs: {'CIS': 1, 'PTRANS': 21, 'TRANS': 294} Chain: "H" Number of atoms: 1640 Number of conformers: 1 Conformer: "" Number of residues, atoms: 214, 1640 Classifications: {'peptide': 214} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'CIS': 1, 'PCIS': 2, 'PTRANS': 10, 'TRANS': 200} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "I" Number of atoms: 1640 Number of conformers: 1 Conformer: "" Number of residues, atoms: 214, 1640 Classifications: {'peptide': 214} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'CIS': 1, 'PCIS': 2, 'PTRANS': 10, 'TRANS': 200} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "J" Number of atoms: 2409 Number of conformers: 1 Conformer: "" Number of residues, atoms: 317, 2409 Classifications: {'peptide': 317} Link IDs: {'CIS': 1, 'PTRANS': 21, 'TRANS': 294} Chain: "L" Number of atoms: 1640 Number of conformers: 1 Conformer: "" Number of residues, atoms: 214, 1640 Classifications: {'peptide': 214} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'CIS': 1, 'PCIS': 2, 'PTRANS': 10, 'TRANS': 200} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "M" Number of atoms: 2409 Number of conformers: 1 Conformer: "" Number of residues, atoms: 317, 2409 Classifications: {'peptide': 317} Link IDs: {'CIS': 1, 'PTRANS': 21, 'TRANS': 294} Chain: "N" Number of atoms: 2409 Number of conformers: 1 Conformer: "" Number of residues, atoms: 317, 2409 Classifications: {'peptide': 317} Link IDs: {'CIS': 1, 'PTRANS': 21, 'TRANS': 294} Chain: "O" Number of atoms: 1640 Number of conformers: 1 Conformer: "" Number of residues, atoms: 214, 1640 Classifications: {'peptide': 214} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'CIS': 1, 'PCIS': 2, 'PTRANS': 10, 'TRANS': 200} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "P" Number of atoms: 1640 Number of conformers: 1 Conformer: "" Number of residues, atoms: 214, 1640 Classifications: {'peptide': 214} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'CIS': 1, 'PCIS': 2, 'PTRANS': 10, 'TRANS': 200} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "F" Number of atoms: 1717 Number of conformers: 1 Conformer: "" Number of residues, atoms: 228, 1717 Classifications: {'peptide': 228} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'CIS': 2, 'PCIS': 2, 'PTRANS': 12, 'TRANS': 211} Chain breaks: 3 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "G" Number of atoms: 1717 Number of conformers: 1 Conformer: "" Number of residues, atoms: 228, 1717 Classifications: {'peptide': 228} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'CIS': 2, 'PCIS': 2, 'PTRANS': 12, 'TRANS': 211} Chain breaks: 3 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "K" Number of atoms: 1717 Number of conformers: 1 Conformer: "" Number of residues, atoms: 228, 1717 Classifications: {'peptide': 228} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'CIS': 2, 'PCIS': 2, 'PTRANS': 12, 'TRANS': 211} Chain breaks: 3 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "Q" Number of atoms: 1717 Number of conformers: 1 Conformer: "" Number of residues, atoms: 228, 1717 Classifications: {'peptide': 228} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'CIS': 2, 'PCIS': 2, 'PTRANS': 12, 'TRANS': 211} Chain breaks: 3 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "R" Number of atoms: 1717 Number of conformers: 1 Conformer: "" Number of residues, atoms: 228, 1717 Classifications: {'peptide': 228} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'CIS': 2, 'PCIS': 2, 'PTRANS': 12, 'TRANS': 211} Chain breaks: 3 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Time building chain proxies: 18.49, per 1000 atoms: 0.53 Number of scatterers: 34596 At special positions: 0 Unit cell: (121.68, 115.44, 246.48, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 126 16.00 O 6792 8.00 N 5856 7.00 C 21822 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=24, symmetry=0 Simple disulfide: pdb=" SG CYS D 22 " - pdb=" SG CYS D 96 " distance=2.03 Simple disulfide: pdb=" SG CYS D 152 " - pdb=" SG CYS D 207 " distance=2.03 Simple disulfide: pdb=" SG CYS E 23 " - pdb=" SG CYS E 88 " distance=2.03 Simple disulfide: pdb=" SG CYS E 134 " - pdb=" SG CYS E 194 " distance=2.03 Simple disulfide: pdb=" SG CYS H 23 " - pdb=" SG CYS H 88 " distance=2.03 Simple disulfide: pdb=" SG CYS H 134 " - pdb=" SG CYS H 194 " distance=2.03 Simple disulfide: pdb=" SG CYS I 23 " - pdb=" SG CYS I 88 " distance=2.03 Simple disulfide: pdb=" SG CYS I 134 " - pdb=" SG CYS I 194 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.03 Simple disulfide: pdb=" SG CYS L 134 " - pdb=" SG CYS L 194 " distance=2.03 Simple disulfide: pdb=" SG CYS O 23 " - pdb=" SG CYS O 88 " distance=2.03 Simple disulfide: pdb=" SG CYS O 134 " - pdb=" SG CYS O 194 " distance=2.03 Simple disulfide: pdb=" SG CYS P 23 " - pdb=" SG CYS P 88 " distance=2.03 Simple disulfide: pdb=" SG CYS P 134 " - pdb=" SG CYS P 194 " distance=2.03 Simple disulfide: pdb=" SG CYS F 22 " - pdb=" SG CYS F 96 " distance=2.03 Simple disulfide: pdb=" SG CYS F 152 " - pdb=" SG CYS F 207 " distance=2.03 Simple disulfide: pdb=" SG CYS G 22 " - pdb=" SG CYS G 96 " distance=2.04 Simple disulfide: pdb=" SG CYS G 152 " - pdb=" SG CYS G 207 " distance=2.03 Simple disulfide: pdb=" SG CYS K 22 " - pdb=" SG CYS K 96 " distance=2.03 Simple disulfide: pdb=" SG CYS K 152 " - pdb=" SG CYS K 207 " distance=2.03 Simple disulfide: pdb=" SG CYS Q 22 " - pdb=" SG CYS Q 96 " distance=2.03 Simple disulfide: pdb=" SG CYS Q 152 " - pdb=" SG CYS Q 207 " distance=2.03 Simple disulfide: pdb=" SG CYS R 22 " - pdb=" SG CYS R 96 " distance=2.03 Simple disulfide: pdb=" SG CYS R 152 " - pdb=" SG CYS R 207 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 13.29 Conformation dependent library (CDL) restraints added in 6.7 seconds 8940 Ramachandran restraints generated. 4470 Oldfield, 0 Emsley, 4470 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8280 Finding SS restraints... Secondary structure from input PDB file: 96 helices and 72 sheets defined 20.2% alpha, 23.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.13 Creating SS restraints... Processing helix chain 'A' and resid 23 through 25 No H-bonds generated for 'chain 'A' and resid 23 through 25' Processing helix chain 'A' and resid 26 through 34 removed outlier: 3.737A pdb=" N VAL A 30 " --> pdb=" O GLU A 26 " (cutoff:3.500A) Processing helix chain 'A' and resid 35 through 41 Processing helix chain 'A' and resid 69 through 90 removed outlier: 3.811A pdb=" N VAL A 73 " --> pdb=" O ASN A 69 " (cutoff:3.500A) Processing helix chain 'A' and resid 100 through 102 No H-bonds generated for 'chain 'A' and resid 100 through 102' Processing helix chain 'A' and resid 103 through 113 removed outlier: 4.059A pdb=" N HIS A 111 " --> pdb=" O SER A 107 " (cutoff:3.500A) Processing helix chain 'A' and resid 144 through 148 removed outlier: 3.610A pdb=" N PHE A 147 " --> pdb=" O PRO A 144 " (cutoff:3.500A) Processing helix chain 'A' and resid 149 through 153 Processing helix chain 'A' and resid 170 through 172 No H-bonds generated for 'chain 'A' and resid 170 through 172' Processing helix chain 'A' and resid 183 through 193 Processing helix chain 'A' and resid 200 through 221 removed outlier: 7.068A pdb=" N ILE A 208 " --> pdb=" O ASP A 204 " (cutoff:3.500A) removed outlier: 8.664A pdb=" N GLY A 209 " --> pdb=" O ARG A 205 " (cutoff:3.500A) removed outlier: 4.257A pdb=" N LYS A 210 " --> pdb=" O LEU A 206 " (cutoff:3.500A) Processing helix chain 'A' and resid 253 through 266 Processing helix chain 'A' and resid 285 through 304 removed outlier: 3.554A pdb=" N VAL A 289 " --> pdb=" O THR A 285 " (cutoff:3.500A) Processing helix chain 'E' and resid 79 through 83 removed outlier: 4.057A pdb=" N PHE E 83 " --> pdb=" O PRO E 80 " (cutoff:3.500A) Processing helix chain 'E' and resid 121 through 126 Processing helix chain 'E' and resid 183 through 189 removed outlier: 4.177A pdb=" N HIS E 189 " --> pdb=" O GLU E 185 " (cutoff:3.500A) Processing helix chain 'B' and resid 23 through 25 No H-bonds generated for 'chain 'B' and resid 23 through 25' Processing helix chain 'B' and resid 26 through 34 removed outlier: 3.737A pdb=" N VAL B 30 " --> pdb=" O GLU B 26 " (cutoff:3.500A) Processing helix chain 'B' and resid 35 through 41 Processing helix chain 'B' and resid 69 through 90 removed outlier: 3.809A pdb=" N VAL B 73 " --> pdb=" O ASN B 69 " (cutoff:3.500A) Processing helix chain 'B' and resid 100 through 102 No H-bonds generated for 'chain 'B' and resid 100 through 102' Processing helix chain 'B' and resid 103 through 113 removed outlier: 4.060A pdb=" N HIS B 111 " --> pdb=" O SER B 107 " (cutoff:3.500A) Processing helix chain 'B' and resid 144 through 148 removed outlier: 3.611A pdb=" N PHE B 147 " --> pdb=" O PRO B 144 " (cutoff:3.500A) Processing helix chain 'B' and resid 149 through 153 Processing helix chain 'B' and resid 170 through 172 No H-bonds generated for 'chain 'B' and resid 170 through 172' Processing helix chain 'B' and resid 183 through 193 Processing helix chain 'B' and resid 200 through 221 removed outlier: 7.068A pdb=" N ILE B 208 " --> pdb=" O ASP B 204 " (cutoff:3.500A) removed outlier: 8.665A pdb=" N GLY B 209 " --> pdb=" O ARG B 205 " (cutoff:3.500A) removed outlier: 4.257A pdb=" N LYS B 210 " --> pdb=" O LEU B 206 " (cutoff:3.500A) Processing helix chain 'B' and resid 253 through 266 Processing helix chain 'B' and resid 285 through 304 removed outlier: 3.553A pdb=" N VAL B 289 " --> pdb=" O THR B 285 " (cutoff:3.500A) Processing helix chain 'C' and resid 23 through 25 No H-bonds generated for 'chain 'C' and resid 23 through 25' Processing helix chain 'C' and resid 26 through 34 removed outlier: 3.735A pdb=" N VAL C 30 " --> pdb=" O GLU C 26 " (cutoff:3.500A) Processing helix chain 'C' and resid 35 through 41 Processing helix chain 'C' and resid 69 through 90 removed outlier: 3.810A pdb=" N VAL C 73 " --> pdb=" O ASN C 69 " (cutoff:3.500A) Processing helix chain 'C' and resid 100 through 102 No H-bonds generated for 'chain 'C' and resid 100 through 102' Processing helix chain 'C' and resid 103 through 113 removed outlier: 4.060A pdb=" N HIS C 111 " --> pdb=" O SER C 107 " (cutoff:3.500A) Processing helix chain 'C' and resid 144 through 148 removed outlier: 3.610A pdb=" N PHE C 147 " --> pdb=" O PRO C 144 " (cutoff:3.500A) Processing helix chain 'C' and resid 149 through 153 Processing helix chain 'C' and resid 170 through 172 No H-bonds generated for 'chain 'C' and resid 170 through 172' Processing helix chain 'C' and resid 183 through 193 Processing helix chain 'C' and resid 200 through 221 removed outlier: 7.068A pdb=" N ILE C 208 " --> pdb=" O ASP C 204 " (cutoff:3.500A) removed outlier: 8.665A pdb=" N GLY C 209 " --> pdb=" O ARG C 205 " (cutoff:3.500A) removed outlier: 4.258A pdb=" N LYS C 210 " --> pdb=" O LEU C 206 " (cutoff:3.500A) Processing helix chain 'C' and resid 253 through 266 Processing helix chain 'C' and resid 285 through 304 removed outlier: 3.554A pdb=" N VAL C 289 " --> pdb=" O THR C 285 " (cutoff:3.500A) Processing helix chain 'H' and resid 79 through 83 removed outlier: 4.057A pdb=" N PHE H 83 " --> pdb=" O PRO H 80 " (cutoff:3.500A) Processing helix chain 'H' and resid 121 through 126 Processing helix chain 'H' and resid 183 through 189 removed outlier: 4.177A pdb=" N HIS H 189 " --> pdb=" O GLU H 185 " (cutoff:3.500A) Processing helix chain 'I' and resid 79 through 83 removed outlier: 4.058A pdb=" N PHE I 83 " --> pdb=" O PRO I 80 " (cutoff:3.500A) Processing helix chain 'I' and resid 121 through 126 Processing helix chain 'I' and resid 183 through 189 removed outlier: 4.176A pdb=" N HIS I 189 " --> pdb=" O GLU I 185 " (cutoff:3.500A) Processing helix chain 'J' and resid 23 through 25 No H-bonds generated for 'chain 'J' and resid 23 through 25' Processing helix chain 'J' and resid 26 through 34 removed outlier: 3.736A pdb=" N VAL J 30 " --> pdb=" O GLU J 26 " (cutoff:3.500A) Processing helix chain 'J' and resid 35 through 41 Processing helix chain 'J' and resid 69 through 90 removed outlier: 3.810A pdb=" N VAL J 73 " --> pdb=" O ASN J 69 " (cutoff:3.500A) Processing helix chain 'J' and resid 100 through 102 No H-bonds generated for 'chain 'J' and resid 100 through 102' Processing helix chain 'J' and resid 103 through 113 removed outlier: 4.060A pdb=" N HIS J 111 " --> pdb=" O SER J 107 " (cutoff:3.500A) Processing helix chain 'J' and resid 144 through 148 removed outlier: 3.611A pdb=" N PHE J 147 " --> pdb=" O PRO J 144 " (cutoff:3.500A) Processing helix chain 'J' and resid 149 through 153 Processing helix chain 'J' and resid 170 through 172 No H-bonds generated for 'chain 'J' and resid 170 through 172' Processing helix chain 'J' and resid 183 through 193 Processing helix chain 'J' and resid 200 through 221 removed outlier: 7.068A pdb=" N ILE J 208 " --> pdb=" O ASP J 204 " (cutoff:3.500A) removed outlier: 8.665A pdb=" N GLY J 209 " --> pdb=" O ARG J 205 " (cutoff:3.500A) removed outlier: 4.256A pdb=" N LYS J 210 " --> pdb=" O LEU J 206 " (cutoff:3.500A) Processing helix chain 'J' and resid 253 through 266 Processing helix chain 'J' and resid 285 through 304 removed outlier: 3.554A pdb=" N VAL J 289 " --> pdb=" O THR J 285 " (cutoff:3.500A) Processing helix chain 'L' and resid 79 through 83 removed outlier: 4.057A pdb=" N PHE L 83 " --> pdb=" O PRO L 80 " (cutoff:3.500A) Processing helix chain 'L' and resid 121 through 126 Processing helix chain 'L' and resid 183 through 189 removed outlier: 4.177A pdb=" N HIS L 189 " --> pdb=" O GLU L 185 " (cutoff:3.500A) Processing helix chain 'M' and resid 23 through 25 No H-bonds generated for 'chain 'M' and resid 23 through 25' Processing helix chain 'M' and resid 26 through 34 removed outlier: 3.737A pdb=" N VAL M 30 " --> pdb=" O GLU M 26 " (cutoff:3.500A) Processing helix chain 'M' and resid 35 through 41 Processing helix chain 'M' and resid 69 through 90 removed outlier: 3.810A pdb=" N VAL M 73 " --> pdb=" O ASN M 69 " (cutoff:3.500A) Processing helix chain 'M' and resid 100 through 102 No H-bonds generated for 'chain 'M' and resid 100 through 102' Processing helix chain 'M' and resid 103 through 113 removed outlier: 4.060A pdb=" N HIS M 111 " --> pdb=" O SER M 107 " (cutoff:3.500A) Processing helix chain 'M' and resid 144 through 148 removed outlier: 3.610A pdb=" N PHE M 147 " --> pdb=" O PRO M 144 " (cutoff:3.500A) Processing helix chain 'M' and resid 149 through 153 Processing helix chain 'M' and resid 170 through 172 No H-bonds generated for 'chain 'M' and resid 170 through 172' Processing helix chain 'M' and resid 183 through 193 Processing helix chain 'M' and resid 200 through 221 removed outlier: 7.068A pdb=" N ILE M 208 " --> pdb=" O ASP M 204 " (cutoff:3.500A) removed outlier: 8.664A pdb=" N GLY M 209 " --> pdb=" O ARG M 205 " (cutoff:3.500A) removed outlier: 4.258A pdb=" N LYS M 210 " --> pdb=" O LEU M 206 " (cutoff:3.500A) Processing helix chain 'M' and resid 253 through 266 Processing helix chain 'M' and resid 285 through 304 removed outlier: 3.556A pdb=" N VAL M 289 " --> pdb=" O THR M 285 " (cutoff:3.500A) Processing helix chain 'N' and resid 23 through 25 No H-bonds generated for 'chain 'N' and resid 23 through 25' Processing helix chain 'N' and resid 26 through 34 removed outlier: 3.737A pdb=" N VAL N 30 " --> pdb=" O GLU N 26 " (cutoff:3.500A) Processing helix chain 'N' and resid 35 through 41 Processing helix chain 'N' and resid 69 through 90 removed outlier: 3.809A pdb=" N VAL N 73 " --> pdb=" O ASN N 69 " (cutoff:3.500A) Processing helix chain 'N' and resid 100 through 102 No H-bonds generated for 'chain 'N' and resid 100 through 102' Processing helix chain 'N' and resid 103 through 113 removed outlier: 4.059A pdb=" N HIS N 111 " --> pdb=" O SER N 107 " (cutoff:3.500A) Processing helix chain 'N' and resid 144 through 148 removed outlier: 3.611A pdb=" N PHE N 147 " --> pdb=" O PRO N 144 " (cutoff:3.500A) Processing helix chain 'N' and resid 149 through 153 Processing helix chain 'N' and resid 170 through 172 No H-bonds generated for 'chain 'N' and resid 170 through 172' Processing helix chain 'N' and resid 183 through 193 Processing helix chain 'N' and resid 200 through 221 removed outlier: 7.069A pdb=" N ILE N 208 " --> pdb=" O ASP N 204 " (cutoff:3.500A) removed outlier: 8.665A pdb=" N GLY N 209 " --> pdb=" O ARG N 205 " (cutoff:3.500A) removed outlier: 4.257A pdb=" N LYS N 210 " --> pdb=" O LEU N 206 " (cutoff:3.500A) Processing helix chain 'N' and resid 253 through 266 Processing helix chain 'N' and resid 285 through 304 removed outlier: 3.553A pdb=" N VAL N 289 " --> pdb=" O THR N 285 " (cutoff:3.500A) Processing helix chain 'O' and resid 79 through 83 removed outlier: 4.056A pdb=" N PHE O 83 " --> pdb=" O PRO O 80 " (cutoff:3.500A) Processing helix chain 'O' and resid 121 through 126 Processing helix chain 'O' and resid 183 through 189 removed outlier: 4.177A pdb=" N HIS O 189 " --> pdb=" O GLU O 185 " (cutoff:3.500A) Processing helix chain 'P' and resid 79 through 83 removed outlier: 4.057A pdb=" N PHE P 83 " --> pdb=" O PRO P 80 " (cutoff:3.500A) Processing helix chain 'P' and resid 121 through 126 Processing helix chain 'P' and resid 183 through 189 removed outlier: 4.177A pdb=" N HIS P 189 " --> pdb=" O GLU P 185 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 48 through 49 removed outlier: 6.891A pdb=" N ILE A 8 " --> pdb=" O LYS A 48 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N SER A 94 " --> pdb=" O SER A 271 " (cutoff:3.500A) removed outlier: 6.390A pdb=" N ILE A 227 " --> pdb=" O SER A 271 " (cutoff:3.500A) removed outlier: 6.018A pdb=" N LEU A 273 " --> pdb=" O ILE A 227 " (cutoff:3.500A) removed outlier: 6.867A pdb=" N LEU A 229 " --> pdb=" O LEU A 273 " (cutoff:3.500A) removed outlier: 5.850A pdb=" N ILE A 275 " --> pdb=" O LEU A 229 " (cutoff:3.500A) removed outlier: 7.149A pdb=" N PHE A 231 " --> pdb=" O ILE A 275 " (cutoff:3.500A) removed outlier: 6.451A pdb=" N GLY A 119 " --> pdb=" O HIS A 228 " (cutoff:3.500A) removed outlier: 7.000A pdb=" N SER A 230 " --> pdb=" O GLY A 119 " (cutoff:3.500A) removed outlier: 6.345A pdb=" N ILE A 121 " --> pdb=" O SER A 230 " (cutoff:3.500A) removed outlier: 7.028A pdb=" N ASP A 232 " --> pdb=" O ILE A 121 " (cutoff:3.500A) removed outlier: 6.627A pdb=" N VAL A 123 " --> pdb=" O ASP A 232 " (cutoff:3.500A) removed outlier: 7.759A pdb=" N PHE A 198 " --> pdb=" O ILE A 174 " (cutoff:3.500A) removed outlier: 6.343A pdb=" N TYR A 176 " --> pdb=" O PHE A 198 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'D' and resid 3 through 7 removed outlier: 3.688A pdb=" N SER D 25 " --> pdb=" O GLN D 3 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N MET D 81 " --> pdb=" O VAL D 20 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'D' and resid 46 through 50 removed outlier: 5.959A pdb=" N TRP D 36 " --> pdb=" O MET D 48 " (cutoff:3.500A) removed outlier: 4.851A pdb=" N TRP D 50 " --> pdb=" O ILE D 34 " (cutoff:3.500A) removed outlier: 6.758A pdb=" N ILE D 34 " --> pdb=" O TRP D 50 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 92 through 93 Processing sheet with id=AA5, first strand: chain 'D' and resid 132 through 133 removed outlier: 3.682A pdb=" N SER D 192 " --> pdb=" O CYS D 152 " (cutoff:3.500A) removed outlier: 5.951A pdb=" N THR D 188 " --> pdb=" O GLY D 156 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'D' and resid 132 through 133 removed outlier: 3.682A pdb=" N SER D 192 " --> pdb=" O CYS D 152 " (cutoff:3.500A) removed outlier: 5.951A pdb=" N THR D 188 " --> pdb=" O GLY D 156 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 163 through 166 removed outlier: 3.587A pdb=" N THR D 165 " --> pdb=" O ASN D 208 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N CYS D 207 " --> pdb=" O LYS D 220 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'E' and resid 10 through 12 removed outlier: 6.919A pdb=" N LEU E 11 " --> pdb=" O GLU E 105 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'E' and resid 21 through 24 removed outlier: 3.682A pdb=" N LEU E 73 " --> pdb=" O LEU E 21 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'E' and resid 45 through 48 removed outlier: 3.728A pdb=" N ARG E 45 " --> pdb=" O GLN E 37 " (cutoff:3.500A) removed outlier: 6.453A pdb=" N TRP E 35 " --> pdb=" O LEU E 47 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'E' and resid 114 through 118 removed outlier: 3.594A pdb=" N ASN E 137 " --> pdb=" O THR E 114 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N VAL E 133 " --> pdb=" O PHE E 118 " (cutoff:3.500A) removed outlier: 5.597A pdb=" N TYR E 173 " --> pdb=" O ASN E 138 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'E' and resid 153 through 154 removed outlier: 3.601A pdb=" N ASN E 145 " --> pdb=" O THR E 197 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N LYS E 149 " --> pdb=" O THR E 193 " (cutoff:3.500A) removed outlier: 4.247A pdb=" N THR E 193 " --> pdb=" O LYS E 149 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 48 through 49 removed outlier: 6.891A pdb=" N ILE B 8 " --> pdb=" O LYS B 48 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N SER B 94 " --> pdb=" O SER B 271 " (cutoff:3.500A) removed outlier: 6.390A pdb=" N ILE B 227 " --> pdb=" O SER B 271 " (cutoff:3.500A) removed outlier: 6.018A pdb=" N LEU B 273 " --> pdb=" O ILE B 227 " (cutoff:3.500A) removed outlier: 6.866A pdb=" N LEU B 229 " --> pdb=" O LEU B 273 " (cutoff:3.500A) removed outlier: 5.851A pdb=" N ILE B 275 " --> pdb=" O LEU B 229 " (cutoff:3.500A) removed outlier: 7.149A pdb=" N PHE B 231 " --> pdb=" O ILE B 275 " (cutoff:3.500A) removed outlier: 6.452A pdb=" N GLY B 119 " --> pdb=" O HIS B 228 " (cutoff:3.500A) removed outlier: 6.999A pdb=" N SER B 230 " --> pdb=" O GLY B 119 " (cutoff:3.500A) removed outlier: 6.345A pdb=" N ILE B 121 " --> pdb=" O SER B 230 " (cutoff:3.500A) removed outlier: 7.026A pdb=" N ASP B 232 " --> pdb=" O ILE B 121 " (cutoff:3.500A) removed outlier: 6.627A pdb=" N VAL B 123 " --> pdb=" O ASP B 232 " (cutoff:3.500A) removed outlier: 7.759A pdb=" N PHE B 198 " --> pdb=" O ILE B 174 " (cutoff:3.500A) removed outlier: 6.343A pdb=" N TYR B 176 " --> pdb=" O PHE B 198 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 48 through 49 removed outlier: 6.891A pdb=" N ILE C 8 " --> pdb=" O LYS C 48 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N SER C 94 " --> pdb=" O SER C 271 " (cutoff:3.500A) removed outlier: 6.391A pdb=" N ILE C 227 " --> pdb=" O SER C 271 " (cutoff:3.500A) removed outlier: 6.018A pdb=" N LEU C 273 " --> pdb=" O ILE C 227 " (cutoff:3.500A) removed outlier: 6.867A pdb=" N LEU C 229 " --> pdb=" O LEU C 273 " (cutoff:3.500A) removed outlier: 5.851A pdb=" N ILE C 275 " --> pdb=" O LEU C 229 " (cutoff:3.500A) removed outlier: 7.149A pdb=" N PHE C 231 " --> pdb=" O ILE C 275 " (cutoff:3.500A) removed outlier: 6.452A pdb=" N GLY C 119 " --> pdb=" O HIS C 228 " (cutoff:3.500A) removed outlier: 6.998A pdb=" N SER C 230 " --> pdb=" O GLY C 119 " (cutoff:3.500A) removed outlier: 6.346A pdb=" N ILE C 121 " --> pdb=" O SER C 230 " (cutoff:3.500A) removed outlier: 7.025A pdb=" N ASP C 232 " --> pdb=" O ILE C 121 " (cutoff:3.500A) removed outlier: 6.628A pdb=" N VAL C 123 " --> pdb=" O ASP C 232 " (cutoff:3.500A) removed outlier: 7.758A pdb=" N PHE C 198 " --> pdb=" O ILE C 174 " (cutoff:3.500A) removed outlier: 6.343A pdb=" N TYR C 176 " --> pdb=" O PHE C 198 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'H' and resid 10 through 12 removed outlier: 6.919A pdb=" N LEU H 11 " --> pdb=" O GLU H 105 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB6 Processing sheet with id=AB7, first strand: chain 'H' and resid 21 through 24 removed outlier: 3.682A pdb=" N LEU H 73 " --> pdb=" O LEU H 21 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'H' and resid 45 through 48 removed outlier: 3.729A pdb=" N ARG H 45 " --> pdb=" O GLN H 37 " (cutoff:3.500A) removed outlier: 6.453A pdb=" N TRP H 35 " --> pdb=" O LEU H 47 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'H' and resid 114 through 118 removed outlier: 3.594A pdb=" N ASN H 137 " --> pdb=" O THR H 114 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N VAL H 133 " --> pdb=" O PHE H 118 " (cutoff:3.500A) removed outlier: 5.595A pdb=" N TYR H 173 " --> pdb=" O ASN H 138 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'H' and resid 153 through 154 removed outlier: 3.603A pdb=" N ASN H 145 " --> pdb=" O THR H 197 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N LYS H 149 " --> pdb=" O THR H 193 " (cutoff:3.500A) removed outlier: 4.246A pdb=" N THR H 193 " --> pdb=" O LYS H 149 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'I' and resid 10 through 12 removed outlier: 6.919A pdb=" N LEU I 11 " --> pdb=" O GLU I 105 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC2 Processing sheet with id=AC3, first strand: chain 'I' and resid 21 through 24 removed outlier: 3.682A pdb=" N LEU I 73 " --> pdb=" O LEU I 21 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'I' and resid 45 through 48 removed outlier: 3.728A pdb=" N ARG I 45 " --> pdb=" O GLN I 37 " (cutoff:3.500A) removed outlier: 6.453A pdb=" N TRP I 35 " --> pdb=" O LEU I 47 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'I' and resid 114 through 118 removed outlier: 3.594A pdb=" N ASN I 137 " --> pdb=" O THR I 114 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N VAL I 133 " --> pdb=" O PHE I 118 " (cutoff:3.500A) removed outlier: 5.595A pdb=" N TYR I 173 " --> pdb=" O ASN I 138 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'I' and resid 153 through 154 removed outlier: 3.602A pdb=" N ASN I 145 " --> pdb=" O THR I 197 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N LYS I 149 " --> pdb=" O THR I 193 " (cutoff:3.500A) removed outlier: 4.246A pdb=" N THR I 193 " --> pdb=" O LYS I 149 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'J' and resid 48 through 49 removed outlier: 6.891A pdb=" N ILE J 8 " --> pdb=" O LYS J 48 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N SER J 94 " --> pdb=" O SER J 271 " (cutoff:3.500A) removed outlier: 6.390A pdb=" N ILE J 227 " --> pdb=" O SER J 271 " (cutoff:3.500A) removed outlier: 6.019A pdb=" N LEU J 273 " --> pdb=" O ILE J 227 " (cutoff:3.500A) removed outlier: 6.868A pdb=" N LEU J 229 " --> pdb=" O LEU J 273 " (cutoff:3.500A) removed outlier: 5.851A pdb=" N ILE J 275 " --> pdb=" O LEU J 229 " (cutoff:3.500A) removed outlier: 7.148A pdb=" N PHE J 231 " --> pdb=" O ILE J 275 " (cutoff:3.500A) removed outlier: 6.453A pdb=" N GLY J 119 " --> pdb=" O HIS J 228 " (cutoff:3.500A) removed outlier: 6.999A pdb=" N SER J 230 " --> pdb=" O GLY J 119 " (cutoff:3.500A) removed outlier: 6.347A pdb=" N ILE J 121 " --> pdb=" O SER J 230 " (cutoff:3.500A) removed outlier: 7.027A pdb=" N ASP J 232 " --> pdb=" O ILE J 121 " (cutoff:3.500A) removed outlier: 6.627A pdb=" N VAL J 123 " --> pdb=" O ASP J 232 " (cutoff:3.500A) removed outlier: 7.759A pdb=" N PHE J 198 " --> pdb=" O ILE J 174 " (cutoff:3.500A) removed outlier: 6.341A pdb=" N TYR J 176 " --> pdb=" O PHE J 198 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'L' and resid 10 through 12 removed outlier: 6.919A pdb=" N LEU L 11 " --> pdb=" O GLU L 105 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC8 Processing sheet with id=AC9, first strand: chain 'L' and resid 21 through 24 removed outlier: 3.683A pdb=" N LEU L 73 " --> pdb=" O LEU L 21 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'L' and resid 45 through 48 removed outlier: 3.730A pdb=" N ARG L 45 " --> pdb=" O GLN L 37 " (cutoff:3.500A) removed outlier: 6.454A pdb=" N TRP L 35 " --> pdb=" O LEU L 47 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'L' and resid 114 through 118 removed outlier: 3.594A pdb=" N ASN L 137 " --> pdb=" O THR L 114 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N VAL L 133 " --> pdb=" O PHE L 118 " (cutoff:3.500A) removed outlier: 5.596A pdb=" N TYR L 173 " --> pdb=" O ASN L 138 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'L' and resid 153 through 154 removed outlier: 3.602A pdb=" N ASN L 145 " --> pdb=" O THR L 197 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N LYS L 149 " --> pdb=" O THR L 193 " (cutoff:3.500A) removed outlier: 4.245A pdb=" N THR L 193 " --> pdb=" O LYS L 149 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'M' and resid 48 through 49 removed outlier: 6.892A pdb=" N ILE M 8 " --> pdb=" O LYS M 48 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N SER M 94 " --> pdb=" O SER M 271 " (cutoff:3.500A) removed outlier: 6.391A pdb=" N ILE M 227 " --> pdb=" O SER M 271 " (cutoff:3.500A) removed outlier: 6.019A pdb=" N LEU M 273 " --> pdb=" O ILE M 227 " (cutoff:3.500A) removed outlier: 6.868A pdb=" N LEU M 229 " --> pdb=" O LEU M 273 " (cutoff:3.500A) removed outlier: 5.851A pdb=" N ILE M 275 " --> pdb=" O LEU M 229 " (cutoff:3.500A) removed outlier: 7.149A pdb=" N PHE M 231 " --> pdb=" O ILE M 275 " (cutoff:3.500A) removed outlier: 6.451A pdb=" N GLY M 119 " --> pdb=" O HIS M 228 " (cutoff:3.500A) removed outlier: 6.999A pdb=" N SER M 230 " --> pdb=" O GLY M 119 " (cutoff:3.500A) removed outlier: 6.346A pdb=" N ILE M 121 " --> pdb=" O SER M 230 " (cutoff:3.500A) removed outlier: 7.027A pdb=" N ASP M 232 " --> pdb=" O ILE M 121 " (cutoff:3.500A) removed outlier: 6.628A pdb=" N VAL M 123 " --> pdb=" O ASP M 232 " (cutoff:3.500A) removed outlier: 7.759A pdb=" N PHE M 198 " --> pdb=" O ILE M 174 " (cutoff:3.500A) removed outlier: 6.341A pdb=" N TYR M 176 " --> pdb=" O PHE M 198 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'N' and resid 48 through 49 removed outlier: 6.891A pdb=" N ILE N 8 " --> pdb=" O LYS N 48 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N SER N 94 " --> pdb=" O SER N 271 " (cutoff:3.500A) removed outlier: 6.391A pdb=" N ILE N 227 " --> pdb=" O SER N 271 " (cutoff:3.500A) removed outlier: 6.019A pdb=" N LEU N 273 " --> pdb=" O ILE N 227 " (cutoff:3.500A) removed outlier: 6.867A pdb=" N LEU N 229 " --> pdb=" O LEU N 273 " (cutoff:3.500A) removed outlier: 5.851A pdb=" N ILE N 275 " --> pdb=" O LEU N 229 " (cutoff:3.500A) removed outlier: 7.148A pdb=" N PHE N 231 " --> pdb=" O ILE N 275 " (cutoff:3.500A) removed outlier: 6.453A pdb=" N GLY N 119 " --> pdb=" O HIS N 228 " (cutoff:3.500A) removed outlier: 6.999A pdb=" N SER N 230 " --> pdb=" O GLY N 119 " (cutoff:3.500A) removed outlier: 6.345A pdb=" N ILE N 121 " --> pdb=" O SER N 230 " (cutoff:3.500A) removed outlier: 7.027A pdb=" N ASP N 232 " --> pdb=" O ILE N 121 " (cutoff:3.500A) removed outlier: 6.628A pdb=" N VAL N 123 " --> pdb=" O ASP N 232 " (cutoff:3.500A) removed outlier: 7.760A pdb=" N PHE N 198 " --> pdb=" O ILE N 174 " (cutoff:3.500A) removed outlier: 6.343A pdb=" N TYR N 176 " --> pdb=" O PHE N 198 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'O' and resid 10 through 12 removed outlier: 6.919A pdb=" N LEU O 11 " --> pdb=" O GLU O 105 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD6 Processing sheet with id=AD7, first strand: chain 'O' and resid 21 through 24 removed outlier: 3.682A pdb=" N LEU O 73 " --> pdb=" O LEU O 21 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'O' and resid 45 through 48 removed outlier: 3.729A pdb=" N ARG O 45 " --> pdb=" O GLN O 37 " (cutoff:3.500A) removed outlier: 6.453A pdb=" N TRP O 35 " --> pdb=" O LEU O 47 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'O' and resid 114 through 118 removed outlier: 3.594A pdb=" N ASN O 137 " --> pdb=" O THR O 114 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N VAL O 133 " --> pdb=" O PHE O 118 " (cutoff:3.500A) removed outlier: 5.594A pdb=" N TYR O 173 " --> pdb=" O ASN O 138 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'O' and resid 153 through 154 removed outlier: 3.603A pdb=" N ASN O 145 " --> pdb=" O THR O 197 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N LYS O 149 " --> pdb=" O THR O 193 " (cutoff:3.500A) removed outlier: 4.246A pdb=" N THR O 193 " --> pdb=" O LYS O 149 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'P' and resid 10 through 12 removed outlier: 6.919A pdb=" N LEU P 11 " --> pdb=" O GLU P 105 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE2 Processing sheet with id=AE3, first strand: chain 'P' and resid 21 through 24 removed outlier: 3.682A pdb=" N LEU P 73 " --> pdb=" O LEU P 21 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'P' and resid 45 through 48 removed outlier: 3.727A pdb=" N ARG P 45 " --> pdb=" O GLN P 37 " (cutoff:3.500A) removed outlier: 6.452A pdb=" N TRP P 35 " --> pdb=" O LEU P 47 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'P' and resid 114 through 118 removed outlier: 3.595A pdb=" N ASN P 137 " --> pdb=" O THR P 114 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N VAL P 133 " --> pdb=" O PHE P 118 " (cutoff:3.500A) removed outlier: 5.595A pdb=" N TYR P 173 " --> pdb=" O ASN P 138 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'P' and resid 153 through 154 removed outlier: 3.601A pdb=" N ASN P 145 " --> pdb=" O THR P 197 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N LYS P 149 " --> pdb=" O THR P 193 " (cutoff:3.500A) removed outlier: 4.247A pdb=" N THR P 193 " --> pdb=" O LYS P 149 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'F' and resid 3 through 7 removed outlier: 3.689A pdb=" N SER F 25 " --> pdb=" O GLN F 3 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N MET F 81 " --> pdb=" O VAL F 20 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'F' and resid 46 through 50 removed outlier: 5.959A pdb=" N TRP F 36 " --> pdb=" O MET F 48 " (cutoff:3.500A) removed outlier: 4.851A pdb=" N TRP F 50 " --> pdb=" O ILE F 34 " (cutoff:3.500A) removed outlier: 6.759A pdb=" N ILE F 34 " --> pdb=" O TRP F 50 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'F' and resid 92 through 93 Processing sheet with id=AF1, first strand: chain 'F' and resid 132 through 133 removed outlier: 3.684A pdb=" N SER F 192 " --> pdb=" O CYS F 152 " (cutoff:3.500A) removed outlier: 5.951A pdb=" N THR F 188 " --> pdb=" O GLY F 156 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'F' and resid 132 through 133 removed outlier: 3.684A pdb=" N SER F 192 " --> pdb=" O CYS F 152 " (cutoff:3.500A) removed outlier: 5.951A pdb=" N THR F 188 " --> pdb=" O GLY F 156 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'F' and resid 163 through 166 removed outlier: 3.587A pdb=" N THR F 165 " --> pdb=" O ASN F 208 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N CYS F 207 " --> pdb=" O LYS F 220 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'G' and resid 3 through 7 removed outlier: 3.689A pdb=" N SER G 25 " --> pdb=" O GLN G 3 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N MET G 81 " --> pdb=" O VAL G 20 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'G' and resid 46 through 50 removed outlier: 5.958A pdb=" N TRP G 36 " --> pdb=" O MET G 48 " (cutoff:3.500A) removed outlier: 4.849A pdb=" N TRP G 50 " --> pdb=" O ILE G 34 " (cutoff:3.500A) removed outlier: 6.758A pdb=" N ILE G 34 " --> pdb=" O TRP G 50 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'G' and resid 92 through 93 Processing sheet with id=AF7, first strand: chain 'G' and resid 132 through 133 removed outlier: 3.684A pdb=" N SER G 192 " --> pdb=" O CYS G 152 " (cutoff:3.500A) removed outlier: 5.950A pdb=" N THR G 188 " --> pdb=" O GLY G 156 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'G' and resid 132 through 133 removed outlier: 3.684A pdb=" N SER G 192 " --> pdb=" O CYS G 152 " (cutoff:3.500A) removed outlier: 5.950A pdb=" N THR G 188 " --> pdb=" O GLY G 156 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'G' and resid 163 through 166 removed outlier: 3.587A pdb=" N THR G 165 " --> pdb=" O ASN G 208 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N CYS G 207 " --> pdb=" O LYS G 220 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'K' and resid 3 through 7 removed outlier: 3.689A pdb=" N SER K 25 " --> pdb=" O GLN K 3 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N MET K 81 " --> pdb=" O VAL K 20 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'K' and resid 46 through 50 removed outlier: 5.957A pdb=" N TRP K 36 " --> pdb=" O MET K 48 " (cutoff:3.500A) removed outlier: 4.852A pdb=" N TRP K 50 " --> pdb=" O ILE K 34 " (cutoff:3.500A) removed outlier: 6.758A pdb=" N ILE K 34 " --> pdb=" O TRP K 50 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'K' and resid 92 through 93 Processing sheet with id=AG4, first strand: chain 'K' and resid 132 through 133 removed outlier: 3.683A pdb=" N SER K 192 " --> pdb=" O CYS K 152 " (cutoff:3.500A) removed outlier: 5.951A pdb=" N THR K 188 " --> pdb=" O GLY K 156 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'K' and resid 132 through 133 removed outlier: 3.683A pdb=" N SER K 192 " --> pdb=" O CYS K 152 " (cutoff:3.500A) removed outlier: 5.951A pdb=" N THR K 188 " --> pdb=" O GLY K 156 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'K' and resid 163 through 166 removed outlier: 3.586A pdb=" N THR K 165 " --> pdb=" O ASN K 208 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N CYS K 207 " --> pdb=" O LYS K 220 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'Q' and resid 3 through 7 removed outlier: 3.689A pdb=" N SER Q 25 " --> pdb=" O GLN Q 3 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N MET Q 81 " --> pdb=" O VAL Q 20 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'Q' and resid 46 through 50 removed outlier: 5.959A pdb=" N TRP Q 36 " --> pdb=" O MET Q 48 " (cutoff:3.500A) removed outlier: 4.850A pdb=" N TRP Q 50 " --> pdb=" O ILE Q 34 " (cutoff:3.500A) removed outlier: 6.758A pdb=" N ILE Q 34 " --> pdb=" O TRP Q 50 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'Q' and resid 92 through 93 Processing sheet with id=AH1, first strand: chain 'Q' and resid 132 through 133 removed outlier: 3.681A pdb=" N SER Q 192 " --> pdb=" O CYS Q 152 " (cutoff:3.500A) removed outlier: 5.952A pdb=" N THR Q 188 " --> pdb=" O GLY Q 156 " (cutoff:3.500A) Processing sheet with id=AH2, first strand: chain 'Q' and resid 132 through 133 removed outlier: 3.681A pdb=" N SER Q 192 " --> pdb=" O CYS Q 152 " (cutoff:3.500A) removed outlier: 5.952A pdb=" N THR Q 188 " --> pdb=" O GLY Q 156 " (cutoff:3.500A) Processing sheet with id=AH3, first strand: chain 'Q' and resid 163 through 166 removed outlier: 3.587A pdb=" N THR Q 165 " --> pdb=" O ASN Q 208 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N CYS Q 207 " --> pdb=" O LYS Q 220 " (cutoff:3.500A) Processing sheet with id=AH4, first strand: chain 'R' and resid 3 through 7 removed outlier: 3.688A pdb=" N SER R 25 " --> pdb=" O GLN R 3 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N MET R 81 " --> pdb=" O VAL R 20 " (cutoff:3.500A) Processing sheet with id=AH5, first strand: chain 'R' and resid 46 through 50 removed outlier: 5.958A pdb=" N TRP R 36 " --> pdb=" O MET R 48 " (cutoff:3.500A) removed outlier: 4.851A pdb=" N TRP R 50 " --> pdb=" O ILE R 34 " (cutoff:3.500A) removed outlier: 6.758A pdb=" N ILE R 34 " --> pdb=" O TRP R 50 " (cutoff:3.500A) Processing sheet with id=AH6, first strand: chain 'R' and resid 92 through 93 Processing sheet with id=AH7, first strand: chain 'R' and resid 132 through 133 removed outlier: 3.682A pdb=" N SER R 192 " --> pdb=" O CYS R 152 " (cutoff:3.500A) removed outlier: 5.951A pdb=" N THR R 188 " --> pdb=" O GLY R 156 " (cutoff:3.500A) Processing sheet with id=AH8, first strand: chain 'R' and resid 132 through 133 removed outlier: 3.682A pdb=" N SER R 192 " --> pdb=" O CYS R 152 " (cutoff:3.500A) removed outlier: 5.951A pdb=" N THR R 188 " --> pdb=" O GLY R 156 " (cutoff:3.500A) Processing sheet with id=AH9, first strand: chain 'R' and resid 163 through 166 removed outlier: 3.587A pdb=" N THR R 165 " --> pdb=" O ASN R 208 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N CYS R 207 " --> pdb=" O LYS R 220 " (cutoff:3.500A) 1110 hydrogen bonds defined for protein. 2952 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 13.90 Time building geometry restraints manager: 14.41 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.43: 14694 1.43 - 1.63: 20508 1.63 - 1.84: 174 1.84 - 2.04: 0 2.04 - 2.25: 6 Bond restraints: 35382 Sorted by residual: bond pdb=" C LYS P 107 " pdb=" N ARG P 108 " ideal model delta sigma weight residual 1.331 2.246 -0.916 1.39e-02 5.18e+03 4.34e+03 bond pdb=" C LYS I 107 " pdb=" N ARG I 108 " ideal model delta sigma weight residual 1.331 2.246 -0.916 1.39e-02 5.18e+03 4.34e+03 bond pdb=" C LYS O 107 " pdb=" N ARG O 108 " ideal model delta sigma weight residual 1.331 2.246 -0.915 1.39e-02 5.18e+03 4.34e+03 bond pdb=" C LYS L 107 " pdb=" N ARG L 108 " ideal model delta sigma weight residual 1.331 2.245 -0.915 1.39e-02 5.18e+03 4.33e+03 bond pdb=" C LYS H 107 " pdb=" N ARG H 108 " ideal model delta sigma weight residual 1.331 2.245 -0.915 1.39e-02 5.18e+03 4.33e+03 ... (remaining 35377 not shown) Histogram of bond angle deviations from ideal: 99.45 - 106.38: 1340 106.38 - 113.32: 19457 113.32 - 120.25: 12467 120.25 - 127.19: 14394 127.19 - 134.12: 486 Bond angle restraints: 48144 Sorted by residual: angle pdb=" C GLN R 65 " pdb=" N GLY R 66 " pdb=" CA GLY R 66 " ideal model delta sigma weight residual 121.70 130.27 -8.57 1.80e+00 3.09e-01 2.27e+01 angle pdb=" C GLN Q 65 " pdb=" N GLY Q 66 " pdb=" CA GLY Q 66 " ideal model delta sigma weight residual 121.70 130.24 -8.54 1.80e+00 3.09e-01 2.25e+01 angle pdb=" C GLN G 65 " pdb=" N GLY G 66 " pdb=" CA GLY G 66 " ideal model delta sigma weight residual 121.70 130.22 -8.52 1.80e+00 3.09e-01 2.24e+01 angle pdb=" C GLN K 65 " pdb=" N GLY K 66 " pdb=" CA GLY K 66 " ideal model delta sigma weight residual 121.70 130.15 -8.45 1.80e+00 3.09e-01 2.20e+01 angle pdb=" C GLN F 65 " pdb=" N GLY F 66 " pdb=" CA GLY F 66 " ideal model delta sigma weight residual 121.70 130.14 -8.44 1.80e+00 3.09e-01 2.20e+01 ... (remaining 48139 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 12.01: 19314 12.01 - 24.02: 1387 24.02 - 36.03: 347 36.03 - 48.05: 96 48.05 - 60.06: 12 Dihedral angle restraints: 21156 sinusoidal: 8172 harmonic: 12984 Sorted by residual: dihedral pdb=" CA LYS G 13 " pdb=" C LYS G 13 " pdb=" N PRO G 14 " pdb=" CA PRO G 14 " ideal model delta harmonic sigma weight residual 180.00 134.49 45.51 0 5.00e+00 4.00e-02 8.28e+01 dihedral pdb=" CA LYS K 13 " pdb=" C LYS K 13 " pdb=" N PRO K 14 " pdb=" CA PRO K 14 " ideal model delta harmonic sigma weight residual 180.00 134.50 45.50 0 5.00e+00 4.00e-02 8.28e+01 dihedral pdb=" CA LYS D 13 " pdb=" C LYS D 13 " pdb=" N PRO D 14 " pdb=" CA PRO D 14 " ideal model delta harmonic sigma weight residual 180.00 134.53 45.47 0 5.00e+00 4.00e-02 8.27e+01 ... (remaining 21153 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.043: 3382 0.043 - 0.086: 1317 0.086 - 0.129: 595 0.129 - 0.171: 141 0.171 - 0.214: 43 Chirality restraints: 5478 Sorted by residual: chirality pdb=" CA TYR P 49 " pdb=" N TYR P 49 " pdb=" C TYR P 49 " pdb=" CB TYR P 49 " both_signs ideal model delta sigma weight residual False 2.51 2.30 0.21 2.00e-01 2.50e+01 1.15e+00 chirality pdb=" CA TYR E 49 " pdb=" N TYR E 49 " pdb=" C TYR E 49 " pdb=" CB TYR E 49 " both_signs ideal model delta sigma weight residual False 2.51 2.30 0.21 2.00e-01 2.50e+01 1.15e+00 chirality pdb=" CA TYR O 49 " pdb=" N TYR O 49 " pdb=" C TYR O 49 " pdb=" CB TYR O 49 " both_signs ideal model delta sigma weight residual False 2.51 2.30 0.21 2.00e-01 2.50e+01 1.15e+00 ... (remaining 5475 not shown) Planarity restraints: 6168 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LYS Q 13 " -0.078 5.00e-02 4.00e+02 1.20e-01 2.29e+01 pdb=" N PRO Q 14 " 0.207 5.00e-02 4.00e+02 pdb=" CA PRO Q 14 " -0.063 5.00e-02 4.00e+02 pdb=" CD PRO Q 14 " -0.065 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS R 13 " 0.078 5.00e-02 4.00e+02 1.19e-01 2.28e+01 pdb=" N PRO R 14 " -0.207 5.00e-02 4.00e+02 pdb=" CA PRO R 14 " 0.063 5.00e-02 4.00e+02 pdb=" CD PRO R 14 " 0.065 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS G 13 " -0.078 5.00e-02 4.00e+02 1.19e-01 2.27e+01 pdb=" N PRO G 14 " 0.206 5.00e-02 4.00e+02 pdb=" CA PRO G 14 " -0.063 5.00e-02 4.00e+02 pdb=" CD PRO G 14 " -0.065 5.00e-02 4.00e+02 ... (remaining 6165 not shown) Histogram of nonbonded interaction distances: 2.27 - 2.80: 8773 2.80 - 3.32: 31061 3.32 - 3.85: 61102 3.85 - 4.37: 70092 4.37 - 4.90: 117972 Nonbonded interactions: 289000 Sorted by model distance: nonbonded pdb=" O ARG M 32 " pdb=" OG SER Q 75 " model vdw 2.269 2.440 nonbonded pdb=" O ARG B 32 " pdb=" OG SER F 75 " model vdw 2.269 2.440 nonbonded pdb=" O ALA Q 101 " pdb=" OG SER Q 106 " model vdw 2.276 2.440 nonbonded pdb=" O ALA R 101 " pdb=" OG SER R 106 " model vdw 2.276 2.440 nonbonded pdb=" O ALA F 101 " pdb=" OG SER F 106 " model vdw 2.276 2.440 ... (remaining 288995 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'J' selection = chain 'M' selection = chain 'N' } ncs_group { reference = chain 'D' selection = chain 'F' selection = chain 'G' selection = chain 'K' selection = chain 'Q' selection = chain 'R' } ncs_group { reference = chain 'E' selection = chain 'H' selection = chain 'I' selection = chain 'L' selection = chain 'O' selection = chain 'P' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.810 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: 0.030 Extract box with map and model: 10.220 Check model and map are aligned: 0.570 Set scattering table: 0.310 Process input model: 91.170 Find NCS groups from input model: 2.490 Set up NCS constraints: 0.280 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:2.980 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 109.870 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5446 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 : 0.013 0.916 35382 Z= 0.886 Angle : 1.032 15.244 48144 Z= 0.553 Chirality : 0.057 0.214 5478 Planarity : 0.009 0.120 6168 Dihedral : 9.442 60.058 12804 Min Nonbonded Distance : 2.269 Molprobity Statistics. All-atom Clashscore : 6.70 Ramachandran Plot: Outliers : 0.89 % Allowed : 8.70 % Favored : 90.40 % Rotamer: Outliers : 0.31 % Allowed : 3.12 % Favored : 96.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.51 % Cis-general : 0.57 % Twisted Proline : 2.13 % Twisted General : 0.57 % 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: -4.14 (0.11), residues: 4470 helix: -2.46 (0.13), residues: 786 sheet: -2.91 (0.13), residues: 1350 loop : -2.72 (0.11), residues: 2334 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.004 TRP Q 115 HIS 0.013 0.003 HIS R 109 PHE 0.051 0.004 PHE E 71 TYR 0.044 0.003 TYR L 49 ARG 0.008 0.001 ARG C 180 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8940 Ramachandran restraints generated. 4470 Oldfield, 0 Emsley, 4470 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8940 Ramachandran restraints generated. 4470 Oldfield, 0 Emsley, 4470 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 379 residues out of total 3864 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 367 time to evaluate : 4.226 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: N 52 ASP cc_start: 0.5829 (m-30) cc_final: 0.4927 (p0) REVERT: P 187 GLU cc_start: 0.0354 (mm-30) cc_final: -0.0350 (mm-30) REVERT: G 168 SER cc_start: 0.6787 (m) cc_final: 0.6584 (p) REVERT: R 73 ASP cc_start: 0.7681 (t70) cc_final: 0.6919 (t70) outliers start: 12 outliers final: 3 residues processed: 375 average time/residue: 0.6369 time to fit residues: 353.7156 Evaluate side-chains 148 residues out of total 3864 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 145 time to evaluate : 4.424 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 83 LEU Chi-restraints excluded: chain F residue 83 LEU Chi-restraints excluded: chain G residue 83 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 444 random chunks: chunk 374 optimal weight: 9.9990 chunk 336 optimal weight: 3.9990 chunk 186 optimal weight: 5.9990 chunk 114 optimal weight: 6.9990 chunk 227 optimal weight: 20.0000 chunk 179 optimal weight: 7.9990 chunk 348 optimal weight: 30.0000 chunk 134 optimal weight: 0.9980 chunk 211 optimal weight: 8.9990 chunk 259 optimal weight: 6.9990 chunk 403 optimal weight: 30.0000 overall best weight: 4.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 90 ASN A 141 HIS A 294 ASN A 319 ASN D 6 GLN D 31 ASN D 39 GLN D 59 ASN D 183 GLN E 38 GLN E 137 ASN ** E 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 141 HIS B 319 ASN C 141 HIS C 319 ASN ** H 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 137 ASN ** H 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 38 GLN I 137 ASN J 126 HIS J 141 HIS J 319 ASN ** L 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 137 ASN M 60 ASN M 126 HIS M 141 HIS ** N 115 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 126 HIS N 141 HIS N 319 ASN O 90 GLN O 137 ASN ** P 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 137 ASN F 6 GLN F 31 ASN ** F 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 59 ASN G 31 ASN G 39 GLN G 59 ASN K 3 GLN ** K 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 31 ASN ** K 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 59 ASN ** K 109 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 183 GLN Q 6 GLN Q 31 ASN Q 109 HIS R 6 GLN R 31 ASN R 59 ASN Total number of N/Q/H flips: 47 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5809 moved from start: 0.3194 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.110 35382 Z= 0.369 Angle : 0.812 13.509 48144 Z= 0.407 Chirality : 0.047 0.207 5478 Planarity : 0.007 0.121 6168 Dihedral : 7.055 42.145 4884 Min Nonbonded Distance : 2.021 Molprobity Statistics. All-atom Clashscore : 22.13 Ramachandran Plot: Outliers : 0.31 % Allowed : 9.97 % Favored : 89.71 % Rotamer: Outliers : 1.85 % Allowed : 6.32 % Favored : 91.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.51 % Cis-general : 0.57 % Twisted Proline : 2.13 % Twisted General : 0.40 % 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: -2.90 (0.12), residues: 4482 helix: -0.28 (0.17), residues: 810 sheet: -2.40 (0.13), residues: 1350 loop : -2.21 (0.13), residues: 2322 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.003 TRP P 35 HIS 0.013 0.002 HIS O 91 PHE 0.022 0.002 PHE N 64 TYR 0.035 0.002 TYR H 49 ARG 0.014 0.001 ARG P 54 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8964 Ramachandran restraints generated. 4482 Oldfield, 0 Emsley, 4482 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8964 Ramachandran restraints generated. 4482 Oldfield, 0 Emsley, 4482 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 225 residues out of total 3864 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 154 time to evaluate : 4.248 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 183 LYS cc_start: 0.5683 (OUTLIER) cc_final: 0.4881 (tppt) REVERT: C 212 MET cc_start: 0.6226 (mmm) cc_final: 0.5928 (mmm) REVERT: P 54 ARG cc_start: 0.3360 (mmp80) cc_final: 0.2721 (mmp80) REVERT: K 48 MET cc_start: 0.4110 (ptt) cc_final: 0.3905 (mtm) outliers start: 71 outliers final: 25 residues processed: 221 average time/residue: 0.5154 time to fit residues: 182.6786 Evaluate side-chains 147 residues out of total 3864 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 121 time to evaluate : 4.251 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 101 HIS Chi-restraints excluded: chain A residue 264 ILE Chi-restraints excluded: chain D residue 74 THR Chi-restraints excluded: chain D residue 83 LEU Chi-restraints excluded: chain E residue 3 VAL Chi-restraints excluded: chain E residue 156 GLN Chi-restraints excluded: chain E residue 165 ASP Chi-restraints excluded: chain E residue 183 LYS Chi-restraints excluded: chain B residue 101 HIS Chi-restraints excluded: chain B residue 264 ILE Chi-restraints excluded: chain C residue 96 VAL Chi-restraints excluded: chain C residue 101 HIS Chi-restraints excluded: chain H residue 93 LEU Chi-restraints excluded: chain H residue 169 LYS Chi-restraints excluded: chain H residue 183 LYS Chi-restraints excluded: chain L residue 122 SER Chi-restraints excluded: chain M residue 101 HIS Chi-restraints excluded: chain O residue 75 ILE Chi-restraints excluded: chain P residue 3 VAL Chi-restraints excluded: chain F residue 58 THR Chi-restraints excluded: chain F residue 74 THR Chi-restraints excluded: chain F residue 83 LEU Chi-restraints excluded: chain G residue 83 LEU Chi-restraints excluded: chain Q residue 18 VAL Chi-restraints excluded: chain R residue 18 VAL Chi-restraints excluded: chain R residue 37 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 444 random chunks: chunk 224 optimal weight: 8.9990 chunk 125 optimal weight: 6.9990 chunk 335 optimal weight: 6.9990 chunk 274 optimal weight: 10.0000 chunk 111 optimal weight: 4.9990 chunk 403 optimal weight: 7.9990 chunk 436 optimal weight: 30.0000 chunk 359 optimal weight: 1.9990 chunk 400 optimal weight: 7.9990 chunk 137 optimal weight: 20.0000 chunk 324 optimal weight: 0.4980 overall best weight: 4.2988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 39 GLN E 156 GLN ** B 319 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 90 ASN ** H 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 90 ASN M 90 ASN ** O 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 109 HIS ** K 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 109 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 59 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5859 moved from start: 0.4084 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.071 35382 Z= 0.319 Angle : 0.750 14.531 48144 Z= 0.372 Chirality : 0.046 0.201 5478 Planarity : 0.006 0.130 6168 Dihedral : 6.658 43.256 4884 Min Nonbonded Distance : 2.073 Molprobity Statistics. All-atom Clashscore : 20.26 Ramachandran Plot: Outliers : 0.20 % Allowed : 10.62 % Favored : 89.18 % Rotamer: Outliers : 1.87 % Allowed : 7.38 % Favored : 90.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.51 % Cis-general : 0.57 % Twisted Proline : 2.13 % Twisted General : 0.31 % 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: -2.30 (0.12), residues: 4482 helix: 0.51 (0.18), residues: 804 sheet: -1.95 (0.14), residues: 1242 loop : -2.02 (0.13), residues: 2436 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP F 50 HIS 0.009 0.002 HIS O 91 PHE 0.035 0.002 PHE C 64 TYR 0.032 0.002 TYR H 49 ARG 0.010 0.001 ARG H 24 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8964 Ramachandran restraints generated. 4482 Oldfield, 0 Emsley, 4482 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8964 Ramachandran restraints generated. 4482 Oldfield, 0 Emsley, 4482 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 202 residues out of total 3864 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 130 time to evaluate : 4.544 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 110 ASP cc_start: 0.3991 (m-30) cc_final: 0.3257 (m-30) REVERT: P 54 ARG cc_start: 0.2537 (mmp80) cc_final: 0.2299 (mmp80) REVERT: Q 82 GLU cc_start: 0.4709 (mp0) cc_final: 0.4500 (mp0) outliers start: 72 outliers final: 40 residues processed: 197 average time/residue: 0.5074 time to fit residues: 161.5519 Evaluate side-chains 148 residues out of total 3864 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 108 time to evaluate : 4.140 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 ASP Chi-restraints excluded: chain A residue 97 LEU Chi-restraints excluded: chain A residue 101 HIS Chi-restraints excluded: chain A residue 264 ILE Chi-restraints excluded: chain D residue 28 THR Chi-restraints excluded: chain D residue 48 MET Chi-restraints excluded: chain D residue 74 THR Chi-restraints excluded: chain D residue 83 LEU Chi-restraints excluded: chain E residue 3 VAL Chi-restraints excluded: chain E residue 11 LEU Chi-restraints excluded: chain E residue 48 ILE Chi-restraints excluded: chain E residue 82 ASP Chi-restraints excluded: chain E residue 93 LEU Chi-restraints excluded: chain E residue 102 THR Chi-restraints excluded: chain E residue 165 ASP Chi-restraints excluded: chain E residue 183 LYS Chi-restraints excluded: chain B residue 97 LEU Chi-restraints excluded: chain B residue 101 HIS Chi-restraints excluded: chain B residue 264 ILE Chi-restraints excluded: chain C residue 96 VAL Chi-restraints excluded: chain C residue 97 LEU Chi-restraints excluded: chain C residue 101 HIS Chi-restraints excluded: chain H residue 93 LEU Chi-restraints excluded: chain H residue 102 THR Chi-restraints excluded: chain H residue 169 LYS Chi-restraints excluded: chain I residue 93 LEU Chi-restraints excluded: chain L residue 122 SER Chi-restraints excluded: chain M residue 97 LEU Chi-restraints excluded: chain M residue 101 HIS Chi-restraints excluded: chain O residue 14 SER Chi-restraints excluded: chain O residue 48 ILE Chi-restraints excluded: chain P residue 3 VAL Chi-restraints excluded: chain P residue 102 THR Chi-restraints excluded: chain P residue 108 ARG Chi-restraints excluded: chain F residue 83 LEU Chi-restraints excluded: chain G residue 68 VAL Chi-restraints excluded: chain G residue 74 THR Chi-restraints excluded: chain G residue 83 LEU Chi-restraints excluded: chain K residue 89 ASP Chi-restraints excluded: chain R residue 89 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 444 random chunks: chunk 399 optimal weight: 7.9990 chunk 303 optimal weight: 0.0060 chunk 209 optimal weight: 4.9990 chunk 44 optimal weight: 8.9990 chunk 192 optimal weight: 0.0060 chunk 271 optimal weight: 50.0000 chunk 405 optimal weight: 9.9990 chunk 429 optimal weight: 10.0000 chunk 211 optimal weight: 5.9990 chunk 384 optimal weight: 6.9990 chunk 115 optimal weight: 5.9990 overall best weight: 3.4018 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 90 ASN B 130 ASN ** B 319 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 212 ASN ** N 115 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 38 GLN F 183 GLN G 6 GLN ** G 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 109 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5866 moved from start: 0.4559 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 35382 Z= 0.271 Angle : 0.711 13.450 48144 Z= 0.351 Chirality : 0.045 0.174 5478 Planarity : 0.005 0.119 6168 Dihedral : 6.410 49.112 4884 Min Nonbonded Distance : 2.066 Molprobity Statistics. All-atom Clashscore : 20.21 Ramachandran Plot: Outliers : 0.13 % Allowed : 10.82 % Favored : 89.05 % Rotamer: Outliers : 1.74 % Allowed : 8.22 % Favored : 90.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.51 % Cis-general : 0.57 % Twisted Proline : 2.13 % Twisted General : 0.26 % 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: -2.10 (0.13), residues: 4482 helix: 0.82 (0.19), residues: 804 sheet: -1.82 (0.13), residues: 1374 loop : -1.91 (0.13), residues: 2304 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP F 50 HIS 0.008 0.001 HIS O 91 PHE 0.012 0.002 PHE G 29 TYR 0.029 0.002 TYR H 49 ARG 0.008 0.001 ARG L 54 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8964 Ramachandran restraints generated. 4482 Oldfield, 0 Emsley, 4482 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8964 Ramachandran restraints generated. 4482 Oldfield, 0 Emsley, 4482 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 3864 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 121 time to evaluate : 4.153 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 81 MET cc_start: 0.6721 (tmm) cc_final: 0.6472 (tmm) REVERT: E 183 LYS cc_start: 0.5359 (OUTLIER) cc_final: 0.4431 (tppt) REVERT: C 118 LEU cc_start: 0.7117 (OUTLIER) cc_final: 0.6896 (pp) REVERT: L 110 ASP cc_start: 0.4158 (m-30) cc_final: 0.3515 (m-30) outliers start: 67 outliers final: 39 residues processed: 183 average time/residue: 0.5356 time to fit residues: 157.9939 Evaluate side-chains 149 residues out of total 3864 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 108 time to evaluate : 4.357 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 97 LEU Chi-restraints excluded: chain A residue 101 HIS Chi-restraints excluded: chain A residue 264 ILE Chi-restraints excluded: chain D residue 28 THR Chi-restraints excluded: chain D residue 74 THR Chi-restraints excluded: chain E residue 3 VAL Chi-restraints excluded: chain E residue 48 ILE Chi-restraints excluded: chain E residue 70 ASP Chi-restraints excluded: chain E residue 93 LEU Chi-restraints excluded: chain E residue 102 THR Chi-restraints excluded: chain E residue 183 LYS Chi-restraints excluded: chain B residue 97 LEU Chi-restraints excluded: chain B residue 101 HIS Chi-restraints excluded: chain B residue 126 HIS Chi-restraints excluded: chain B residue 264 ILE Chi-restraints excluded: chain C residue 96 VAL Chi-restraints excluded: chain C residue 97 LEU Chi-restraints excluded: chain C residue 101 HIS Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain H residue 93 LEU Chi-restraints excluded: chain H residue 102 THR Chi-restraints excluded: chain H residue 143 ASP Chi-restraints excluded: chain H residue 169 LYS Chi-restraints excluded: chain I residue 93 LEU Chi-restraints excluded: chain L residue 29 VAL Chi-restraints excluded: chain L residue 102 THR Chi-restraints excluded: chain M residue 97 LEU Chi-restraints excluded: chain M residue 101 HIS Chi-restraints excluded: chain P residue 3 VAL Chi-restraints excluded: chain P residue 102 THR Chi-restraints excluded: chain P residue 108 ARG Chi-restraints excluded: chain F residue 64 LEU Chi-restraints excluded: chain F residue 74 THR Chi-restraints excluded: chain G residue 68 VAL Chi-restraints excluded: chain G residue 74 THR Chi-restraints excluded: chain G residue 83 LEU Chi-restraints excluded: chain G residue 222 ILE Chi-restraints excluded: chain K residue 89 ASP Chi-restraints excluded: chain K residue 182 LEU Chi-restraints excluded: chain Q residue 18 VAL Chi-restraints excluded: chain R residue 28 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 444 random chunks: chunk 357 optimal weight: 10.0000 chunk 243 optimal weight: 0.4980 chunk 6 optimal weight: 2.9990 chunk 319 optimal weight: 30.0000 chunk 177 optimal weight: 30.0000 chunk 366 optimal weight: 0.6980 chunk 296 optimal weight: 6.9990 chunk 0 optimal weight: 10.0000 chunk 219 optimal weight: 0.0030 chunk 385 optimal weight: 0.0770 chunk 108 optimal weight: 4.9990 overall best weight: 0.8550 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 319 ASN ** C 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 143 GLN O 53 ASN ** G 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 109 HIS ** Q 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5752 moved from start: 0.4622 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 35382 Z= 0.163 Angle : 0.663 10.746 48144 Z= 0.325 Chirality : 0.044 0.164 5478 Planarity : 0.005 0.107 6168 Dihedral : 5.934 38.816 4880 Min Nonbonded Distance : 2.106 Molprobity Statistics. All-atom Clashscore : 15.79 Ramachandran Plot: Outliers : 0.11 % Allowed : 9.37 % Favored : 90.52 % Rotamer: Outliers : 1.72 % Allowed : 8.42 % Favored : 89.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.51 % Cis-general : 0.57 % Twisted Proline : 1.77 % Twisted General : 0.12 % 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: -1.83 (0.13), residues: 4482 helix: 1.11 (0.19), residues: 798 sheet: -1.80 (0.13), residues: 1422 loop : -1.63 (0.14), residues: 2262 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP O 163 HIS 0.006 0.001 HIS E 91 PHE 0.011 0.001 PHE O 98 TYR 0.027 0.001 TYR H 49 ARG 0.007 0.000 ARG O 108 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8964 Ramachandran restraints generated. 4482 Oldfield, 0 Emsley, 4482 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8964 Ramachandran restraints generated. 4482 Oldfield, 0 Emsley, 4482 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 3864 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 129 time to evaluate : 4.687 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 81 MET cc_start: 0.6758 (tmm) cc_final: 0.6383 (tmm) REVERT: D 83 LEU cc_start: 0.6645 (OUTLIER) cc_final: 0.6316 (mm) REVERT: E 175 MET cc_start: 0.5841 (mmm) cc_final: 0.4892 (mmm) REVERT: E 183 LYS cc_start: 0.4968 (OUTLIER) cc_final: 0.4308 (tppt) REVERT: J 183 ASP cc_start: 0.4507 (OUTLIER) cc_final: 0.4051 (t70) REVERT: N 52 ASP cc_start: 0.5804 (m-30) cc_final: 0.5198 (p0) outliers start: 66 outliers final: 37 residues processed: 189 average time/residue: 0.5002 time to fit residues: 153.7181 Evaluate side-chains 140 residues out of total 3864 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 100 time to evaluate : 3.975 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 97 LEU Chi-restraints excluded: chain A residue 126 HIS Chi-restraints excluded: chain D residue 28 THR Chi-restraints excluded: chain D residue 64 LEU Chi-restraints excluded: chain D residue 78 THR Chi-restraints excluded: chain D residue 83 LEU Chi-restraints excluded: chain D residue 222 ILE Chi-restraints excluded: chain E residue 3 VAL Chi-restraints excluded: chain E residue 11 LEU Chi-restraints excluded: chain E residue 70 ASP Chi-restraints excluded: chain E residue 93 LEU Chi-restraints excluded: chain E residue 102 THR Chi-restraints excluded: chain E residue 183 LYS Chi-restraints excluded: chain B residue 97 LEU Chi-restraints excluded: chain B residue 101 HIS Chi-restraints excluded: chain C residue 97 LEU Chi-restraints excluded: chain C residue 101 HIS Chi-restraints excluded: chain C residue 126 HIS Chi-restraints excluded: chain H residue 102 THR Chi-restraints excluded: chain I residue 93 LEU Chi-restraints excluded: chain I residue 150 ILE Chi-restraints excluded: chain J residue 183 ASP Chi-restraints excluded: chain L residue 102 THR Chi-restraints excluded: chain L residue 122 SER Chi-restraints excluded: chain M residue 97 LEU Chi-restraints excluded: chain O residue 48 ILE Chi-restraints excluded: chain O residue 150 ILE Chi-restraints excluded: chain P residue 3 VAL Chi-restraints excluded: chain P residue 108 ARG Chi-restraints excluded: chain F residue 74 THR Chi-restraints excluded: chain F residue 78 THR Chi-restraints excluded: chain G residue 18 VAL Chi-restraints excluded: chain G residue 64 LEU Chi-restraints excluded: chain G residue 74 THR Chi-restraints excluded: chain G residue 83 LEU Chi-restraints excluded: chain G residue 222 ILE Chi-restraints excluded: chain Q residue 18 VAL Chi-restraints excluded: chain Q residue 83 LEU Chi-restraints excluded: chain R residue 18 VAL Chi-restraints excluded: chain R residue 120 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 444 random chunks: chunk 144 optimal weight: 5.9990 chunk 386 optimal weight: 6.9990 chunk 84 optimal weight: 8.9990 chunk 251 optimal weight: 7.9990 chunk 105 optimal weight: 10.0000 chunk 429 optimal weight: 30.0000 chunk 356 optimal weight: 8.9990 chunk 198 optimal weight: 30.0000 chunk 35 optimal weight: 10.0000 chunk 142 optimal weight: 7.9990 chunk 225 optimal weight: 30.0000 overall best weight: 7.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 139 ASN B 90 ASN B 139 ASN C 90 ASN H 38 GLN H 212 ASN M 101 HIS ** N 115 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 143 GLN ** P 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 39 GLN G 39 GLN ** G 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 59 ASN Q 59 ASN ** Q 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6037 moved from start: 0.5699 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.122 35382 Z= 0.506 Angle : 0.854 15.889 48144 Z= 0.424 Chirality : 0.048 0.230 5478 Planarity : 0.006 0.125 6168 Dihedral : 6.518 41.638 4880 Min Nonbonded Distance : 1.988 Molprobity Statistics. All-atom Clashscore : 28.72 Ramachandran Plot: Outliers : 0.18 % Allowed : 11.62 % Favored : 88.20 % Rotamer: Outliers : 2.24 % Allowed : 9.10 % Favored : 88.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.51 % Cis-general : 0.57 % Twisted Proline : 1.77 % Twisted General : 0.21 % 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 (0.13), residues: 4482 helix: 0.55 (0.18), residues: 840 sheet: -1.66 (0.14), residues: 1386 loop : -1.90 (0.13), residues: 2256 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP E 163 HIS 0.014 0.002 HIS A 101 PHE 0.025 0.002 PHE I 71 TYR 0.034 0.002 TYR E 49 ARG 0.008 0.001 ARG H 24 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8964 Ramachandran restraints generated. 4482 Oldfield, 0 Emsley, 4482 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8964 Ramachandran restraints generated. 4482 Oldfield, 0 Emsley, 4482 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 210 residues out of total 3864 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 86 poor density : 124 time to evaluate : 4.230 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 183 LYS cc_start: 0.5716 (OUTLIER) cc_final: 0.4571 (tppt) REVERT: C 118 LEU cc_start: 0.7360 (OUTLIER) cc_final: 0.7134 (pp) REVERT: M 101 HIS cc_start: -0.3896 (OUTLIER) cc_final: -0.4814 (m170) REVERT: O 138 ASN cc_start: 0.7828 (m-40) cc_final: 0.7578 (m-40) outliers start: 86 outliers final: 52 residues processed: 205 average time/residue: 0.4821 time to fit residues: 163.7136 Evaluate side-chains 162 residues out of total 3864 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 107 time to evaluate : 4.240 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 97 LEU Chi-restraints excluded: chain A residue 126 HIS Chi-restraints excluded: chain A residue 174 ILE Chi-restraints excluded: chain A residue 264 ILE Chi-restraints excluded: chain D residue 28 THR Chi-restraints excluded: chain D residue 64 LEU Chi-restraints excluded: chain D residue 74 THR Chi-restraints excluded: chain D residue 78 THR Chi-restraints excluded: chain E residue 48 ILE Chi-restraints excluded: chain E residue 70 ASP Chi-restraints excluded: chain E residue 82 ASP Chi-restraints excluded: chain E residue 93 LEU Chi-restraints excluded: chain E residue 183 LYS Chi-restraints excluded: chain B residue 97 LEU Chi-restraints excluded: chain B residue 101 HIS Chi-restraints excluded: chain B residue 126 HIS Chi-restraints excluded: chain C residue 97 LEU Chi-restraints excluded: chain C residue 101 HIS Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 126 HIS Chi-restraints excluded: chain H residue 93 LEU Chi-restraints excluded: chain H residue 102 THR Chi-restraints excluded: chain H residue 143 ASP Chi-restraints excluded: chain H residue 169 LYS Chi-restraints excluded: chain I residue 93 LEU Chi-restraints excluded: chain I residue 132 VAL Chi-restraints excluded: chain I residue 150 ILE Chi-restraints excluded: chain I residue 154 GLU Chi-restraints excluded: chain L residue 29 VAL Chi-restraints excluded: chain L residue 102 THR Chi-restraints excluded: chain L residue 122 SER Chi-restraints excluded: chain M residue 97 LEU Chi-restraints excluded: chain M residue 101 HIS Chi-restraints excluded: chain M residue 276 MET Chi-restraints excluded: chain O residue 14 SER Chi-restraints excluded: chain O residue 48 ILE Chi-restraints excluded: chain O residue 150 ILE Chi-restraints excluded: chain O residue 163 TRP Chi-restraints excluded: chain P residue 3 VAL Chi-restraints excluded: chain P residue 102 THR Chi-restraints excluded: chain F residue 58 THR Chi-restraints excluded: chain F residue 64 LEU Chi-restraints excluded: chain F residue 74 THR Chi-restraints excluded: chain F residue 78 THR Chi-restraints excluded: chain F residue 150 LEU Chi-restraints excluded: chain G residue 63 LYS Chi-restraints excluded: chain G residue 64 LEU Chi-restraints excluded: chain G residue 68 VAL Chi-restraints excluded: chain G residue 74 THR Chi-restraints excluded: chain G residue 83 LEU Chi-restraints excluded: chain G residue 222 ILE Chi-restraints excluded: chain K residue 74 THR Chi-restraints excluded: chain K residue 182 LEU Chi-restraints excluded: chain Q residue 83 LEU Chi-restraints excluded: chain R residue 18 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 444 random chunks: chunk 414 optimal weight: 40.0000 chunk 48 optimal weight: 0.0040 chunk 244 optimal weight: 20.0000 chunk 313 optimal weight: 7.9990 chunk 243 optimal weight: 6.9990 chunk 361 optimal weight: 4.9990 chunk 239 optimal weight: 8.9990 chunk 427 optimal weight: 30.0000 chunk 267 optimal weight: 9.9990 chunk 260 optimal weight: 0.6980 chunk 197 optimal weight: 30.0000 overall best weight: 4.1398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 3 GLN B 90 ASN C 90 ASN L 27 GLN ** L 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 115 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 115 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 143 GLN ** P 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5953 moved from start: 0.5865 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.073 35382 Z= 0.301 Angle : 0.739 13.401 48144 Z= 0.363 Chirality : 0.045 0.189 5478 Planarity : 0.005 0.117 6168 Dihedral : 6.258 43.115 4880 Min Nonbonded Distance : 2.046 Molprobity Statistics. All-atom Clashscore : 23.68 Ramachandran Plot: Outliers : 0.16 % Allowed : 10.75 % Favored : 89.09 % Rotamer: Outliers : 1.74 % Allowed : 10.06 % Favored : 88.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.51 % Cis-general : 0.57 % Twisted Proline : 1.06 % Twisted General : 0.19 % 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 (0.13), residues: 4482 helix: 0.83 (0.18), residues: 828 sheet: -1.70 (0.14), residues: 1356 loop : -1.76 (0.13), residues: 2298 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP O 163 HIS 0.024 0.002 HIS M 101 PHE 0.030 0.002 PHE C 64 TYR 0.031 0.002 TYR H 49 ARG 0.014 0.001 ARG C 222 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8964 Ramachandran restraints generated. 4482 Oldfield, 0 Emsley, 4482 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8964 Ramachandran restraints generated. 4482 Oldfield, 0 Emsley, 4482 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 3864 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 116 time to evaluate : 3.986 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 183 LYS cc_start: 0.5712 (OUTLIER) cc_final: 0.4587 (tppt) REVERT: C 118 LEU cc_start: 0.7181 (OUTLIER) cc_final: 0.6923 (pp) REVERT: M 42 GLU cc_start: -0.2538 (OUTLIER) cc_final: -0.3290 (mp0) REVERT: N 52 ASP cc_start: 0.5698 (m-30) cc_final: 0.5000 (p0) REVERT: O 138 ASN cc_start: 0.7883 (m-40) cc_final: 0.7609 (m-40) REVERT: Q 23 LYS cc_start: 0.7875 (OUTLIER) cc_final: 0.6092 (ptpp) outliers start: 67 outliers final: 46 residues processed: 179 average time/residue: 0.4807 time to fit residues: 141.9982 Evaluate side-chains 157 residues out of total 3864 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 107 time to evaluate : 4.096 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 97 LEU Chi-restraints excluded: chain A residue 126 HIS Chi-restraints excluded: chain A residue 139 ASN Chi-restraints excluded: chain A residue 264 ILE Chi-restraints excluded: chain D residue 28 THR Chi-restraints excluded: chain D residue 64 LEU Chi-restraints excluded: chain D residue 74 THR Chi-restraints excluded: chain D residue 78 THR Chi-restraints excluded: chain E residue 48 ILE Chi-restraints excluded: chain E residue 70 ASP Chi-restraints excluded: chain E residue 82 ASP Chi-restraints excluded: chain E residue 93 LEU Chi-restraints excluded: chain E residue 132 VAL Chi-restraints excluded: chain E residue 183 LYS Chi-restraints excluded: chain B residue 97 LEU Chi-restraints excluded: chain B residue 101 HIS Chi-restraints excluded: chain B residue 126 HIS Chi-restraints excluded: chain B residue 260 ILE Chi-restraints excluded: chain C residue 97 LEU Chi-restraints excluded: chain C residue 101 HIS Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 126 HIS Chi-restraints excluded: chain H residue 93 LEU Chi-restraints excluded: chain H residue 102 THR Chi-restraints excluded: chain H residue 143 ASP Chi-restraints excluded: chain I residue 93 LEU Chi-restraints excluded: chain I residue 132 VAL Chi-restraints excluded: chain I residue 150 ILE Chi-restraints excluded: chain I residue 154 GLU Chi-restraints excluded: chain L residue 102 THR Chi-restraints excluded: chain L residue 122 SER Chi-restraints excluded: chain L residue 213 GLU Chi-restraints excluded: chain M residue 42 GLU Chi-restraints excluded: chain M residue 97 LEU Chi-restraints excluded: chain O residue 48 ILE Chi-restraints excluded: chain O residue 150 ILE Chi-restraints excluded: chain O residue 163 TRP Chi-restraints excluded: chain P residue 3 VAL Chi-restraints excluded: chain P residue 102 THR Chi-restraints excluded: chain F residue 74 THR Chi-restraints excluded: chain F residue 78 THR Chi-restraints excluded: chain G residue 63 LYS Chi-restraints excluded: chain G residue 64 LEU Chi-restraints excluded: chain G residue 74 THR Chi-restraints excluded: chain G residue 222 ILE Chi-restraints excluded: chain K residue 74 THR Chi-restraints excluded: chain K residue 182 LEU Chi-restraints excluded: chain Q residue 23 LYS Chi-restraints excluded: chain Q residue 83 LEU Chi-restraints excluded: chain R residue 18 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 444 random chunks: chunk 264 optimal weight: 20.0000 chunk 170 optimal weight: 7.9990 chunk 255 optimal weight: 6.9990 chunk 128 optimal weight: 0.0470 chunk 84 optimal weight: 0.8980 chunk 82 optimal weight: 3.9990 chunk 272 optimal weight: 0.5980 chunk 291 optimal weight: 50.0000 chunk 211 optimal weight: 30.0000 chunk 39 optimal weight: 0.8980 chunk 336 optimal weight: 6.9990 overall best weight: 1.2880 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 90 GLN M 101 HIS M 115 HIS ** N 115 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 3 GLN ** G 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5838 moved from start: 0.5813 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 35382 Z= 0.180 Angle : 0.691 14.795 48144 Z= 0.337 Chirality : 0.044 0.193 5478 Planarity : 0.005 0.109 6168 Dihedral : 5.864 39.677 4878 Min Nonbonded Distance : 2.101 Molprobity Statistics. All-atom Clashscore : 18.68 Ramachandran Plot: Outliers : 0.11 % Allowed : 10.11 % Favored : 89.78 % Rotamer: Outliers : 1.51 % Allowed : 10.43 % Favored : 88.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.51 % Cis-general : 0.57 % Twisted Proline : 0.71 % Twisted General : 0.07 % 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: -1.57 (0.13), residues: 4482 helix: 1.13 (0.19), residues: 822 sheet: -1.46 (0.14), residues: 1326 loop : -1.58 (0.14), residues: 2334 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.002 TRP L 148 HIS 0.008 0.001 HIS A 101 PHE 0.018 0.001 PHE C 64 TYR 0.029 0.001 TYR H 49 ARG 0.011 0.000 ARG C 222 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8964 Ramachandran restraints generated. 4482 Oldfield, 0 Emsley, 4482 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8964 Ramachandran restraints generated. 4482 Oldfield, 0 Emsley, 4482 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 3864 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 120 time to evaluate : 4.805 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 175 MET cc_start: 0.5850 (mmm) cc_final: 0.5461 (mmm) REVERT: E 183 LYS cc_start: 0.5648 (OUTLIER) cc_final: 0.4618 (tppt) REVERT: L 213 GLU cc_start: -0.2323 (OUTLIER) cc_final: -0.2780 (pp20) REVERT: M 42 GLU cc_start: -0.2484 (OUTLIER) cc_final: -0.3245 (mp0) REVERT: N 52 ASP cc_start: 0.5603 (m-30) cc_final: 0.4898 (p0) REVERT: N 212 MET cc_start: 0.1493 (tmm) cc_final: 0.0235 (mmm) REVERT: P 54 ARG cc_start: 0.2812 (mmp80) cc_final: 0.0412 (mmm-85) REVERT: P 81 GLU cc_start: 0.6683 (tm-30) cc_final: 0.6345 (pt0) outliers start: 58 outliers final: 41 residues processed: 174 average time/residue: 0.5275 time to fit residues: 150.0573 Evaluate side-chains 150 residues out of total 3864 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 106 time to evaluate : 4.551 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 97 LEU Chi-restraints excluded: chain A residue 126 HIS Chi-restraints excluded: chain A residue 264 ILE Chi-restraints excluded: chain D residue 28 THR Chi-restraints excluded: chain D residue 64 LEU Chi-restraints excluded: chain D residue 74 THR Chi-restraints excluded: chain D residue 78 THR Chi-restraints excluded: chain E residue 11 LEU Chi-restraints excluded: chain E residue 49 TYR Chi-restraints excluded: chain E residue 70 ASP Chi-restraints excluded: chain E residue 93 LEU Chi-restraints excluded: chain E residue 132 VAL Chi-restraints excluded: chain E residue 183 LYS Chi-restraints excluded: chain B residue 97 LEU Chi-restraints excluded: chain B residue 126 HIS Chi-restraints excluded: chain C residue 97 LEU Chi-restraints excluded: chain C residue 101 HIS Chi-restraints excluded: chain C residue 126 HIS Chi-restraints excluded: chain H residue 93 LEU Chi-restraints excluded: chain H residue 102 THR Chi-restraints excluded: chain H residue 169 LYS Chi-restraints excluded: chain I residue 93 LEU Chi-restraints excluded: chain I residue 132 VAL Chi-restraints excluded: chain I residue 150 ILE Chi-restraints excluded: chain L residue 4 MET Chi-restraints excluded: chain L residue 102 THR Chi-restraints excluded: chain L residue 122 SER Chi-restraints excluded: chain L residue 213 GLU Chi-restraints excluded: chain M residue 42 GLU Chi-restraints excluded: chain M residue 97 LEU Chi-restraints excluded: chain O residue 48 ILE Chi-restraints excluded: chain O residue 150 ILE Chi-restraints excluded: chain P residue 3 VAL Chi-restraints excluded: chain P residue 102 THR Chi-restraints excluded: chain F residue 78 THR Chi-restraints excluded: chain F residue 150 LEU Chi-restraints excluded: chain G residue 64 LEU Chi-restraints excluded: chain G residue 74 THR Chi-restraints excluded: chain G residue 222 ILE Chi-restraints excluded: chain K residue 48 MET Chi-restraints excluded: chain K residue 74 THR Chi-restraints excluded: chain K residue 182 LEU Chi-restraints excluded: chain Q residue 83 LEU Chi-restraints excluded: chain R residue 18 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 444 random chunks: chunk 389 optimal weight: 3.9990 chunk 409 optimal weight: 30.0000 chunk 374 optimal weight: 0.6980 chunk 398 optimal weight: 10.0000 chunk 240 optimal weight: 50.0000 chunk 173 optimal weight: 20.0000 chunk 313 optimal weight: 0.0070 chunk 122 optimal weight: 2.9990 chunk 360 optimal weight: 6.9990 chunk 377 optimal weight: 6.9990 chunk 397 optimal weight: 50.0000 overall best weight: 2.9404 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 115 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 319 ASN ** O 91 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5900 moved from start: 0.6027 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 35382 Z= 0.244 Angle : 0.706 14.065 48144 Z= 0.345 Chirality : 0.044 0.196 5478 Planarity : 0.005 0.110 6168 Dihedral : 5.896 40.401 4878 Min Nonbonded Distance : 2.080 Molprobity Statistics. All-atom Clashscore : 21.19 Ramachandran Plot: Outliers : 0.16 % Allowed : 10.44 % Favored : 89.40 % Rotamer: Outliers : 1.51 % Allowed : 10.50 % Favored : 87.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.51 % Cis-general : 0.57 % Twisted Proline : 0.71 % 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: -1.51 (0.13), residues: 4482 helix: 1.39 (0.19), residues: 792 sheet: -1.43 (0.14), residues: 1338 loop : -1.58 (0.14), residues: 2352 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP F 36 HIS 0.013 0.001 HIS A 101 PHE 0.019 0.001 PHE C 64 TYR 0.029 0.001 TYR H 49 ARG 0.010 0.000 ARG C 222 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8964 Ramachandran restraints generated. 4482 Oldfield, 0 Emsley, 4482 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8964 Ramachandran restraints generated. 4482 Oldfield, 0 Emsley, 4482 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 3864 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 114 time to evaluate : 4.392 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 183 LYS cc_start: 0.5744 (OUTLIER) cc_final: 0.4651 (tppt) REVERT: C 118 LEU cc_start: 0.6968 (OUTLIER) cc_final: 0.6702 (pp) REVERT: L 213 GLU cc_start: -0.2464 (OUTLIER) cc_final: -0.2934 (pp20) REVERT: M 42 GLU cc_start: -0.2449 (OUTLIER) cc_final: -0.3196 (mp0) REVERT: N 52 ASP cc_start: 0.5587 (m-30) cc_final: 0.4824 (p0) REVERT: N 212 MET cc_start: 0.1524 (tmm) cc_final: 0.0273 (mmm) REVERT: O 143 ASP cc_start: 0.6264 (m-30) cc_final: 0.5060 (p0) outliers start: 58 outliers final: 44 residues processed: 168 average time/residue: 0.5021 time to fit residues: 139.4824 Evaluate side-chains 153 residues out of total 3864 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 105 time to evaluate : 4.267 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 97 LEU Chi-restraints excluded: chain A residue 126 HIS Chi-restraints excluded: chain A residue 139 ASN Chi-restraints excluded: chain A residue 264 ILE Chi-restraints excluded: chain D residue 28 THR Chi-restraints excluded: chain D residue 78 THR Chi-restraints excluded: chain E residue 11 LEU Chi-restraints excluded: chain E residue 49 TYR Chi-restraints excluded: chain E residue 70 ASP Chi-restraints excluded: chain E residue 82 ASP Chi-restraints excluded: chain E residue 93 LEU Chi-restraints excluded: chain E residue 102 THR Chi-restraints excluded: chain E residue 183 LYS Chi-restraints excluded: chain B residue 97 LEU Chi-restraints excluded: chain B residue 126 HIS Chi-restraints excluded: chain C residue 97 LEU Chi-restraints excluded: chain C residue 101 HIS Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 126 HIS Chi-restraints excluded: chain H residue 93 LEU Chi-restraints excluded: chain H residue 102 THR Chi-restraints excluded: chain H residue 143 ASP Chi-restraints excluded: chain H residue 169 LYS Chi-restraints excluded: chain I residue 93 LEU Chi-restraints excluded: chain I residue 132 VAL Chi-restraints excluded: chain I residue 150 ILE Chi-restraints excluded: chain L residue 4 MET Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 102 THR Chi-restraints excluded: chain L residue 122 SER Chi-restraints excluded: chain L residue 213 GLU Chi-restraints excluded: chain M residue 42 GLU Chi-restraints excluded: chain M residue 97 LEU Chi-restraints excluded: chain O residue 14 SER Chi-restraints excluded: chain O residue 48 ILE Chi-restraints excluded: chain O residue 150 ILE Chi-restraints excluded: chain O residue 163 TRP Chi-restraints excluded: chain P residue 3 VAL Chi-restraints excluded: chain F residue 78 THR Chi-restraints excluded: chain F residue 150 LEU Chi-restraints excluded: chain G residue 64 LEU Chi-restraints excluded: chain G residue 74 THR Chi-restraints excluded: chain G residue 222 ILE Chi-restraints excluded: chain K residue 48 MET Chi-restraints excluded: chain K residue 74 THR Chi-restraints excluded: chain K residue 182 LEU Chi-restraints excluded: chain Q residue 83 LEU Chi-restraints excluded: chain R residue 18 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 444 random chunks: chunk 261 optimal weight: 50.0000 chunk 421 optimal weight: 30.0000 chunk 257 optimal weight: 9.9990 chunk 200 optimal weight: 6.9990 chunk 293 optimal weight: 8.9990 chunk 442 optimal weight: 20.0000 chunk 407 optimal weight: 50.0000 chunk 352 optimal weight: 10.0000 chunk 36 optimal weight: 1.9990 chunk 272 optimal weight: 5.9990 chunk 215 optimal weight: 0.9990 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 115 HIS N 143 GLN ** O 91 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6005 moved from start: 0.6540 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.082 35382 Z= 0.358 Angle : 0.790 15.678 48144 Z= 0.387 Chirality : 0.046 0.209 5478 Planarity : 0.006 0.116 6168 Dihedral : 6.231 39.719 4878 Min Nonbonded Distance : 2.020 Molprobity Statistics. All-atom Clashscore : 27.16 Ramachandran Plot: Outliers : 0.22 % Allowed : 11.65 % Favored : 88.13 % Rotamer: Outliers : 1.53 % Allowed : 10.48 % Favored : 87.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.51 % Cis-general : 0.57 % Twisted Proline : 1.06 % Twisted General : 0.21 % 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: -1.68 (0.13), residues: 4482 helix: 1.15 (0.19), residues: 804 sheet: -1.58 (0.13), residues: 1470 loop : -1.59 (0.14), residues: 2208 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP K 115 HIS 0.017 0.002 HIS A 101 PHE 0.022 0.002 PHE C 64 TYR 0.036 0.002 TYR E 49 ARG 0.010 0.001 ARG C 222 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8964 Ramachandran restraints generated. 4482 Oldfield, 0 Emsley, 4482 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8964 Ramachandran restraints generated. 4482 Oldfield, 0 Emsley, 4482 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 3864 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 110 time to evaluate : 4.302 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 49 TYR cc_start: 0.5799 (OUTLIER) cc_final: 0.5541 (p90) REVERT: E 183 LYS cc_start: 0.5909 (OUTLIER) cc_final: 0.4899 (tppt) REVERT: C 118 LEU cc_start: 0.7223 (OUTLIER) cc_final: 0.6959 (pp) REVERT: L 213 GLU cc_start: -0.1932 (OUTLIER) cc_final: -0.2374 (pp20) REVERT: M 42 GLU cc_start: -0.2502 (OUTLIER) cc_final: -0.3246 (mp0) REVERT: N 212 MET cc_start: 0.1665 (tmm) cc_final: 0.0511 (mmm) REVERT: O 138 ASN cc_start: 0.7976 (m-40) cc_final: 0.7466 (m-40) REVERT: P 54 ARG cc_start: 0.2564 (mmp80) cc_final: 0.1062 (mmp80) REVERT: Q 23 LYS cc_start: 0.7778 (OUTLIER) cc_final: 0.6477 (ptpp) outliers start: 59 outliers final: 46 residues processed: 164 average time/residue: 0.4838 time to fit residues: 131.8393 Evaluate side-chains 156 residues out of total 3864 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 104 time to evaluate : 4.182 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 97 LEU Chi-restraints excluded: chain A residue 126 HIS Chi-restraints excluded: chain A residue 139 ASN Chi-restraints excluded: chain A residue 264 ILE Chi-restraints excluded: chain D residue 74 THR Chi-restraints excluded: chain D residue 78 THR Chi-restraints excluded: chain D residue 222 ILE Chi-restraints excluded: chain E residue 48 ILE Chi-restraints excluded: chain E residue 49 TYR Chi-restraints excluded: chain E residue 70 ASP Chi-restraints excluded: chain E residue 82 ASP Chi-restraints excluded: chain E residue 93 LEU Chi-restraints excluded: chain E residue 102 THR Chi-restraints excluded: chain E residue 132 VAL Chi-restraints excluded: chain E residue 183 LYS Chi-restraints excluded: chain B residue 97 LEU Chi-restraints excluded: chain B residue 126 HIS Chi-restraints excluded: chain C residue 97 LEU Chi-restraints excluded: chain C residue 101 HIS Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain H residue 93 LEU Chi-restraints excluded: chain H residue 102 THR Chi-restraints excluded: chain H residue 143 ASP Chi-restraints excluded: chain H residue 169 LYS Chi-restraints excluded: chain I residue 93 LEU Chi-restraints excluded: chain I residue 132 VAL Chi-restraints excluded: chain I residue 150 ILE Chi-restraints excluded: chain I residue 154 GLU Chi-restraints excluded: chain L residue 4 MET Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 102 THR Chi-restraints excluded: chain L residue 122 SER Chi-restraints excluded: chain L residue 213 GLU Chi-restraints excluded: chain M residue 42 GLU Chi-restraints excluded: chain M residue 97 LEU Chi-restraints excluded: chain O residue 14 SER Chi-restraints excluded: chain O residue 48 ILE Chi-restraints excluded: chain O residue 150 ILE Chi-restraints excluded: chain O residue 163 TRP Chi-restraints excluded: chain P residue 3 VAL Chi-restraints excluded: chain F residue 64 LEU Chi-restraints excluded: chain F residue 78 THR Chi-restraints excluded: chain F residue 150 LEU Chi-restraints excluded: chain G residue 64 LEU Chi-restraints excluded: chain G residue 74 THR Chi-restraints excluded: chain G residue 222 ILE Chi-restraints excluded: chain K residue 74 THR Chi-restraints excluded: chain K residue 182 LEU Chi-restraints excluded: chain Q residue 23 LYS Chi-restraints excluded: chain Q residue 83 LEU Chi-restraints excluded: chain R residue 18 VAL Chi-restraints excluded: chain R residue 81 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 444 random chunks: chunk 279 optimal weight: 5.9990 chunk 375 optimal weight: 20.0000 chunk 107 optimal weight: 1.9990 chunk 324 optimal weight: 5.9990 chunk 52 optimal weight: 6.9990 chunk 97 optimal weight: 0.8980 chunk 352 optimal weight: 7.9990 chunk 147 optimal weight: 30.0000 chunk 362 optimal weight: 0.1980 chunk 44 optimal weight: 5.9990 chunk 64 optimal weight: 7.9990 overall best weight: 3.0186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 124 GLN ** O 91 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 6 GLN ** Q 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4191 r_free = 0.4191 target = 0.082307 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.058178 restraints weight = 293156.725| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 50)----------------| | r_work = 0.3513 r_free = 0.3513 target = 0.059579 restraints weight = 113763.207| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3542 r_free = 0.3542 target = 0.060371 restraints weight = 58192.838| |-----------------------------------------------------------------------------| r_work (final): 0.3261 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7636 moved from start: 0.6560 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 35382 Z= 0.252 Angle : 0.733 13.621 48144 Z= 0.357 Chirality : 0.045 0.221 5478 Planarity : 0.005 0.112 6168 Dihedral : 6.032 41.054 4878 Min Nonbonded Distance : 2.058 Molprobity Statistics. All-atom Clashscore : 22.85 Ramachandran Plot: Outliers : 0.16 % Allowed : 10.58 % Favored : 89.27 % Rotamer: Outliers : 1.35 % Allowed : 10.79 % Favored : 87.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.51 % Cis-general : 0.57 % Twisted Proline : 0.71 % Twisted General : 0.12 % 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: -1.52 (0.13), residues: 4482 helix: 1.08 (0.19), residues: 828 sheet: -1.51 (0.14), residues: 1374 loop : -1.44 (0.14), residues: 2280 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP K 115 HIS 0.012 0.001 HIS A 101 PHE 0.018 0.002 PHE C 64 TYR 0.028 0.002 TYR H 49 ARG 0.009 0.001 ARG C 222 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5924.12 seconds wall clock time: 112 minutes 24.09 seconds (6744.09 seconds total)