Starting phenix.real_space_refine on Sat Feb 7 03:24:12 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9o04_49966/02_2026/9o04_49966.cif Found real_map, /net/cci-nas-00/data/ceres_data/9o04_49966/02_2026/9o04_49966.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9o04_49966/02_2026/9o04_49966.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9o04_49966/02_2026/9o04_49966.map" model { file = "/net/cci-nas-00/data/ceres_data/9o04_49966/02_2026/9o04_49966.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9o04_49966/02_2026/9o04_49966.cif" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } 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= 0.005 sd= 1.067 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians Mn 16 7.51 5 S 180 5.16 5 C 18628 2.51 5 N 5023 2.21 5 O 5506 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 61 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 29353 Number of models: 1 Model: "" Number of chains: 23 Chain: "A" Number of atoms: 1136 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 133, 1126 Classifications: {'peptide': 133} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'TRANS': 132} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASN:plan1': 1} Unresolved non-hydrogen planarities: 3 Conformer: "B" Number of residues, atoms: 133, 1126 Classifications: {'peptide': 133} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'TRANS': 132} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASN:plan1': 1} Unresolved non-hydrogen planarities: 3 bond proxies already assigned to first conformer: 1122 Chain: "B" Number of atoms: 1110 Number of conformers: 1 Conformer: "" Number of residues, atoms: 131, 1110 Classifications: {'peptide': 131} Link IDs: {'TRANS': 130} Chain: "C" Number of atoms: 3029 Number of conformers: 1 Conformer: "" Number of residues, atoms: 382, 3029 Classifications: {'peptide': 382} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 28, 'TRANS': 352} Chain breaks: 2 Chain: "D" Number of atoms: 2401 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 295, 2392 Classifications: {'peptide': 295} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 11, 'TRANS': 283} Chain breaks: 1 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 1 Planarities with less than four sites: {'MLL%COO:plan-1': 1} Unresolved non-hydrogen planarities: 1 Conformer: "B" Number of residues, atoms: 295, 2392 Classifications: {'peptide': 295} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 11, 'TRANS': 283} Chain breaks: 1 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 1 Planarities with less than four sites: {'MLL%COO:plan-1': 1} Unresolved non-hydrogen planarities: 1 bond proxies already assigned to first conformer: 2439 Chain: "E" Number of atoms: 2344 Number of conformers: 1 Conformer: "" Number of residues, atoms: 291, 2344 Classifications: {'peptide': 291} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 11, 'TRANS': 279} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 5 Chain: "F" Number of atoms: 1092 Number of conformers: 1 Conformer: "" Number of residues, atoms: 136, 1092 Classifications: {'peptide': 136} Link IDs: {'PTRANS': 5, 'TRANS': 130} Chain breaks: 2 Chain: "G" Number of atoms: 3036 Number of conformers: 1 Conformer: "" Number of residues, atoms: 383, 3036 Classifications: {'peptide': 383} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 30, 'TRANS': 352} Chain breaks: 2 Chain: "H" Number of atoms: 1092 Number of conformers: 1 Conformer: "" Number of residues, atoms: 136, 1092 Classifications: {'peptide': 136} Link IDs: {'PTRANS': 5, 'TRANS': 130} Chain breaks: 2 Chain: "I" Number of atoms: 2344 Number of conformers: 1 Conformer: "" Number of residues, atoms: 291, 2344 Classifications: {'peptide': 291} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 11, 'TRANS': 279} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 5 Chain: "J" Number of atoms: 2377 Number of conformers: 1 Conformer: "" Number of residues, atoms: 294, 2377 Classifications: {'peptide': 294} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 11, 'TRANS': 282} Chain breaks: 1 Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'MLL%COO:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "K" Number of atoms: 2344 Number of conformers: 1 Conformer: "" Number of residues, atoms: 291, 2344 Classifications: {'peptide': 291} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 11, 'TRANS': 279} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 5 Chain: "L" Number of atoms: 2344 Number of conformers: 1 Conformer: "" Number of residues, atoms: 291, 2344 Classifications: {'peptide': 291} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 11, 'TRANS': 279} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 5 Chain: "M" Number of atoms: 2344 Number of conformers: 1 Conformer: "" Number of residues, atoms: 291, 2344 Classifications: {'peptide': 291} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 11, 'TRANS': 279} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 5 Chain: "N" Number of atoms: 2344 Number of conformers: 1 Conformer: "" Number of residues, atoms: 291, 2344 Classifications: {'peptide': 291} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 11, 'TRANS': 279} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 5 Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MN': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "I" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "J" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "K" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "L" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "M" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MN': 1} Classifications: {'undetermined': 1} Chain: "N" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Residues with excluded nonbonded symmetry interactions: 2 residue: pdb=" N AHIS A 154 " occ=0.47 ... (18 atoms not shown) pdb=" NE2BHIS A 154 " occ=0.53 residue: pdb=" N AGLU D 9 " occ=0.50 ... (16 atoms not shown) pdb=" OE2BGLU D 9 " occ=0.50 Time building chain proxies: 7.27, per 1000 atoms: 0.25 Number of scatterers: 29353 At special positions: 0 Unit cell: (111.454, 217.042, 213.69, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Mn 16 24.99 S 180 16.00 O 5506 8.00 N 5023 7.00 C 18628 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 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: 2.45 Conformation dependent library (CDL) restraints added in 1.2 seconds 7184 Ramachandran restraints generated. 3592 Oldfield, 0 Emsley, 3592 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6784 Finding SS restraints... Secondary structure from input PDB file: 117 helices and 44 sheets defined 42.2% alpha, 11.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.99 Creating SS restraints... Processing helix chain 'A' and resid 91 through 223 removed outlier: 3.829A pdb=" N ARG A 95 " --> pdb=" O ASN A 91 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N ALA A 97 " --> pdb=" O ASP A 93 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N SER A 187 " --> pdb=" O ASN A 183 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N LYS A 188 " --> pdb=" O ASP A 184 " (cutoff:3.500A) removed outlier: 4.535A pdb=" N ILE A 200 " --> pdb=" O ARG A 196 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N ASP A 201 " --> pdb=" O ARG A 197 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N LYS A 223 " --> pdb=" O LYS A 219 " (cutoff:3.500A) Processing helix chain 'B' and resid 94 through 223 removed outlier: 4.003A pdb=" N VAL B 99 " --> pdb=" O ARG B 95 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N GLN B 161 " --> pdb=" O ALA B 157 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N GLU B 182 " --> pdb=" O ILE B 178 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N GLN B 208 " --> pdb=" O ASN B 204 " (cutoff:3.500A) removed outlier: 4.176A pdb=" N LYS B 219 " --> pdb=" O ASN B 215 " (cutoff:3.500A) Processing helix chain 'C' and resid 46 through 50 Processing helix chain 'C' and resid 51 through 60 removed outlier: 3.756A pdb=" N TYR C 57 " --> pdb=" O GLU C 53 " (cutoff:3.500A) Processing helix chain 'C' and resid 66 through 72 removed outlier: 3.667A pdb=" N ALA C 72 " --> pdb=" O HIS C 68 " (cutoff:3.500A) Processing helix chain 'C' and resid 75 through 100 Processing helix chain 'C' and resid 331 through 335 Processing helix chain 'C' and resid 338 through 342 removed outlier: 3.546A pdb=" N HIS C 342 " --> pdb=" O LEU C 339 " (cutoff:3.500A) Processing helix chain 'D' and resid 5 through 18 Processing helix chain 'D' and resid 24 through 39 removed outlier: 3.540A pdb=" N GLU D 37 " --> pdb=" O GLU D 33 " (cutoff:3.500A) Processing helix chain 'D' and resid 61 through 73 Processing helix chain 'D' and resid 92 through 107 Processing helix chain 'D' and resid 120 through 125 Processing helix chain 'D' and resid 129 through 138 Processing helix chain 'D' and resid 140 through 151 removed outlier: 3.539A pdb=" N LYS D 144 " --> pdb=" O ALA D 140 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N ASP D 151 " --> pdb=" O THR D 147 " (cutoff:3.500A) Processing helix chain 'D' and resid 176 through 180 Processing helix chain 'D' and resid 193 through 201 Processing helix chain 'D' and resid 221 through 233 removed outlier: 3.532A pdb=" N SER D 225 " --> pdb=" O GLY D 221 " (cutoff:3.500A) Processing helix chain 'D' and resid 264 through 268 Processing helix chain 'E' and resid 5 through 19 removed outlier: 3.974A pdb=" N GLU E 19 " --> pdb=" O GLU E 15 " (cutoff:3.500A) Processing helix chain 'E' and resid 24 through 42 removed outlier: 4.205A pdb=" N GLU E 37 " --> pdb=" O GLU E 33 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N ILE E 38 " --> pdb=" O LYS E 34 " (cutoff:3.500A) Processing helix chain 'E' and resid 61 through 73 Processing helix chain 'E' and resid 92 through 107 removed outlier: 4.066A pdb=" N THR E 96 " --> pdb=" O TYR E 92 " (cutoff:3.500A) Processing helix chain 'E' and resid 122 through 128 removed outlier: 3.541A pdb=" N VAL E 126 " --> pdb=" O GLN E 122 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N GLY E 128 " --> pdb=" O THR E 124 " (cutoff:3.500A) Processing helix chain 'E' and resid 128 through 138 Processing helix chain 'E' and resid 140 through 153 removed outlier: 3.602A pdb=" N TYR E 152 " --> pdb=" O ASP E 148 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N LEU E 153 " --> pdb=" O LEU E 149 " (cutoff:3.500A) Processing helix chain 'E' and resid 176 through 183 removed outlier: 3.969A pdb=" N ILE E 180 " --> pdb=" O THR E 176 " (cutoff:3.500A) Processing helix chain 'E' and resid 193 through 201 removed outlier: 3.564A pdb=" N LEU E 199 " --> pdb=" O MET E 195 " (cutoff:3.500A) Processing helix chain 'E' and resid 221 through 232 removed outlier: 3.539A pdb=" N SER E 225 " --> pdb=" O GLY E 221 " (cutoff:3.500A) Processing helix chain 'E' and resid 264 through 268 Processing helix chain 'F' and resid 17 through 21 Processing helix chain 'F' and resid 24 through 32 removed outlier: 4.162A pdb=" N MET F 30 " --> pdb=" O THR F 26 " (cutoff:3.500A) removed outlier: 4.525A pdb=" N GLU F 32 " --> pdb=" O LYS F 28 " (cutoff:3.500A) Processing helix chain 'F' and resid 51 through 65 removed outlier: 3.604A pdb=" N LEU F 55 " --> pdb=" O ASN F 51 " (cutoff:3.500A) removed outlier: 4.241A pdb=" N LYS F 57 " --> pdb=" O ALA F 53 " (cutoff:3.500A) Processing helix chain 'F' and resid 87 through 93 removed outlier: 4.184A pdb=" N GLU F 91 " --> pdb=" O VAL F 87 " (cutoff:3.500A) Processing helix chain 'F' and resid 98 through 110 removed outlier: 3.698A pdb=" N GLU F 102 " --> pdb=" O GLY F 98 " (cutoff:3.500A) Processing helix chain 'F' and resid 113 through 128 removed outlier: 4.275A pdb=" N MET F 126 " --> pdb=" O THR F 122 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N ILE F 127 " --> pdb=" O VAL F 123 " (cutoff:3.500A) Processing helix chain 'F' and resid 131 through 139 removed outlier: 3.710A pdb=" N ILE F 135 " --> pdb=" O THR F 131 " (cutoff:3.500A) Processing helix chain 'F' and resid 150 through 155 removed outlier: 4.092A pdb=" N ARG F 154 " --> pdb=" O GLU F 150 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N LYS F 155 " --> pdb=" O ALA F 151 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 150 through 155' Processing helix chain 'G' and resid 51 through 60 Processing helix chain 'G' and resid 67 through 73 Processing helix chain 'G' and resid 76 through 100 removed outlier: 3.965A pdb=" N ARG G 80 " --> pdb=" O LYS G 76 " (cutoff:3.500A) Processing helix chain 'G' and resid 331 through 335 removed outlier: 3.580A pdb=" N HIS G 334 " --> pdb=" O ASN G 331 " (cutoff:3.500A) Processing helix chain 'G' and resid 667 through 671 removed outlier: 4.069A pdb=" N VAL G 670 " --> pdb=" O SER G 667 " (cutoff:3.500A) Processing helix chain 'H' and resid 17 through 23 removed outlier: 4.013A pdb=" N GLN H 23 " --> pdb=" O GLU H 19 " (cutoff:3.500A) Processing helix chain 'H' and resid 24 through 34 removed outlier: 3.575A pdb=" N LYS H 28 " --> pdb=" O SER H 24 " (cutoff:3.500A) Processing helix chain 'H' and resid 51 through 65 Processing helix chain 'H' and resid 88 through 92 removed outlier: 3.864A pdb=" N GLU H 91 " --> pdb=" O TRP H 88 " (cutoff:3.500A) Processing helix chain 'H' and resid 96 through 111 removed outlier: 3.977A pdb=" N LEU H 100 " --> pdb=" O ASP H 96 " (cutoff:3.500A) Processing helix chain 'H' and resid 112 through 128 removed outlier: 3.884A pdb=" N MET H 126 " --> pdb=" O THR H 122 " (cutoff:3.500A) Processing helix chain 'H' and resid 131 through 140 Processing helix chain 'H' and resid 149 through 155 Processing helix chain 'I' and resid 5 through 19 Processing helix chain 'I' and resid 24 through 41 removed outlier: 4.422A pdb=" N GLU I 37 " --> pdb=" O GLU I 33 " (cutoff:3.500A) removed outlier: 4.170A pdb=" N ILE I 38 " --> pdb=" O LYS I 34 " (cutoff:3.500A) Processing helix chain 'I' and resid 61 through 73 Processing helix chain 'I' and resid 92 through 107 removed outlier: 3.720A pdb=" N THR I 96 " --> pdb=" O TYR I 92 " (cutoff:3.500A) Processing helix chain 'I' and resid 120 through 128 removed outlier: 3.828A pdb=" N GLY I 128 " --> pdb=" O THR I 124 " (cutoff:3.500A) Processing helix chain 'I' and resid 128 through 138 Processing helix chain 'I' and resid 140 through 152 removed outlier: 3.870A pdb=" N TYR I 152 " --> pdb=" O ASP I 148 " (cutoff:3.500A) Processing helix chain 'I' and resid 176 through 181 removed outlier: 3.895A pdb=" N ILE I 180 " --> pdb=" O THR I 176 " (cutoff:3.500A) Processing helix chain 'I' and resid 193 through 198 Processing helix chain 'I' and resid 221 through 233 removed outlier: 3.641A pdb=" N SER I 225 " --> pdb=" O GLY I 221 " (cutoff:3.500A) Processing helix chain 'I' and resid 264 through 268 Processing helix chain 'J' and resid 5 through 19 Processing helix chain 'J' and resid 24 through 41 removed outlier: 4.025A pdb=" N GLU J 37 " --> pdb=" O GLU J 33 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N ILE J 38 " --> pdb=" O LYS J 34 " (cutoff:3.500A) Processing helix chain 'J' and resid 61 through 73 Processing helix chain 'J' and resid 92 through 107 removed outlier: 3.685A pdb=" N THR J 96 " --> pdb=" O TYR J 92 " (cutoff:3.500A) Processing helix chain 'J' and resid 120 through 128 Processing helix chain 'J' and resid 128 through 138 Processing helix chain 'J' and resid 141 through 151 Processing helix chain 'J' and resid 176 through 182 removed outlier: 3.598A pdb=" N ILE J 180 " --> pdb=" O THR J 176 " (cutoff:3.500A) Processing helix chain 'J' and resid 193 through 201 removed outlier: 3.592A pdb=" N ASP J 197 " --> pdb=" O GLY J 193 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N LEU J 198 " --> pdb=" O PRO J 194 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N LEU J 199 " --> pdb=" O MET J 195 " (cutoff:3.500A) Processing helix chain 'J' and resid 221 through 233 removed outlier: 3.508A pdb=" N SER J 225 " --> pdb=" O GLY J 221 " (cutoff:3.500A) Processing helix chain 'J' and resid 264 through 268 Processing helix chain 'K' and resid 5 through 19 removed outlier: 3.642A pdb=" N GLU K 19 " --> pdb=" O GLU K 15 " (cutoff:3.500A) Processing helix chain 'K' and resid 24 through 42 removed outlier: 4.508A pdb=" N GLU K 37 " --> pdb=" O GLU K 33 " (cutoff:3.500A) removed outlier: 4.450A pdb=" N ILE K 38 " --> pdb=" O LYS K 34 " (cutoff:3.500A) Processing helix chain 'K' and resid 61 through 73 Processing helix chain 'K' and resid 92 through 107 Processing helix chain 'K' and resid 122 through 128 removed outlier: 3.727A pdb=" N VAL K 126 " --> pdb=" O GLN K 122 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N GLY K 128 " --> pdb=" O THR K 124 " (cutoff:3.500A) Processing helix chain 'K' and resid 128 through 138 Processing helix chain 'K' and resid 141 through 151 removed outlier: 3.763A pdb=" N TYR K 145 " --> pdb=" O ASN K 141 " (cutoff:3.500A) Processing helix chain 'K' and resid 176 through 181 removed outlier: 3.787A pdb=" N ILE K 180 " --> pdb=" O THR K 176 " (cutoff:3.500A) Processing helix chain 'K' and resid 193 through 201 Processing helix chain 'K' and resid 221 through 231 removed outlier: 4.230A pdb=" N ALA K 231 " --> pdb=" O THR K 227 " (cutoff:3.500A) Processing helix chain 'K' and resid 264 through 268 Processing helix chain 'L' and resid 5 through 19 Processing helix chain 'L' and resid 24 through 42 removed outlier: 4.262A pdb=" N GLU L 37 " --> pdb=" O GLU L 33 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N ILE L 38 " --> pdb=" O LYS L 34 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N GLU L 42 " --> pdb=" O ILE L 38 " (cutoff:3.500A) Processing helix chain 'L' and resid 61 through 73 Processing helix chain 'L' and resid 92 through 107 Processing helix chain 'L' and resid 120 through 128 removed outlier: 4.130A pdb=" N THR L 124 " --> pdb=" O SER L 120 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N GLN L 125 " --> pdb=" O ARG L 121 " (cutoff:3.500A) removed outlier: 4.350A pdb=" N VAL L 126 " --> pdb=" O GLN L 122 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N GLY L 128 " --> pdb=" O THR L 124 " (cutoff:3.500A) Processing helix chain 'L' and resid 128 through 138 Processing helix chain 'L' and resid 140 through 151 removed outlier: 3.956A pdb=" N LYS L 144 " --> pdb=" O ALA L 140 " (cutoff:3.500A) Processing helix chain 'L' and resid 176 through 182 Processing helix chain 'L' and resid 193 through 201 removed outlier: 3.865A pdb=" N LEU L 199 " --> pdb=" O MET L 195 " (cutoff:3.500A) Processing helix chain 'L' and resid 221 through 233 removed outlier: 3.562A pdb=" N SER L 225 " --> pdb=" O GLY L 221 " (cutoff:3.500A) Processing helix chain 'L' and resid 264 through 268 removed outlier: 3.523A pdb=" N ARG L 268 " --> pdb=" O TYR L 265 " (cutoff:3.500A) Processing helix chain 'M' and resid 5 through 19 Processing helix chain 'M' and resid 24 through 41 removed outlier: 4.210A pdb=" N GLU M 37 " --> pdb=" O GLU M 33 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N ILE M 38 " --> pdb=" O LYS M 34 " (cutoff:3.500A) Processing helix chain 'M' and resid 61 through 73 Processing helix chain 'M' and resid 92 through 107 removed outlier: 3.730A pdb=" N THR M 96 " --> pdb=" O TYR M 92 " (cutoff:3.500A) Processing helix chain 'M' and resid 122 through 126 Processing helix chain 'M' and resid 128 through 138 Processing helix chain 'M' and resid 140 through 151 Processing helix chain 'M' and resid 179 through 183 removed outlier: 3.551A pdb=" N LEU M 183 " --> pdb=" O ILE M 180 " (cutoff:3.500A) Processing helix chain 'M' and resid 195 through 200 removed outlier: 3.656A pdb=" N TRP M 200 " --> pdb=" O CYS M 196 " (cutoff:3.500A) Processing helix chain 'M' and resid 221 through 233 removed outlier: 3.547A pdb=" N SER M 225 " --> pdb=" O GLY M 221 " (cutoff:3.500A) Processing helix chain 'M' and resid 264 through 268 Processing helix chain 'N' and resid 5 through 19 Processing helix chain 'N' and resid 24 through 41 removed outlier: 4.053A pdb=" N GLU N 37 " --> pdb=" O GLU N 33 " (cutoff:3.500A) removed outlier: 4.171A pdb=" N ILE N 38 " --> pdb=" O LYS N 34 " (cutoff:3.500A) Processing helix chain 'N' and resid 61 through 73 Processing helix chain 'N' and resid 93 through 107 removed outlier: 3.613A pdb=" N VAL N 97 " --> pdb=" O SER N 93 " (cutoff:3.500A) Processing helix chain 'N' and resid 122 through 127 removed outlier: 3.743A pdb=" N VAL N 126 " --> pdb=" O GLN N 122 " (cutoff:3.500A) Processing helix chain 'N' and resid 128 through 138 Processing helix chain 'N' and resid 140 through 151 Processing helix chain 'N' and resid 176 through 182 removed outlier: 3.770A pdb=" N ILE N 180 " --> pdb=" O THR N 176 " (cutoff:3.500A) Processing helix chain 'N' and resid 195 through 200 removed outlier: 3.964A pdb=" N LEU N 199 " --> pdb=" O MET N 195 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N TRP N 200 " --> pdb=" O CYS N 196 " (cutoff:3.500A) No H-bonds generated for 'chain 'N' and resid 195 through 200' Processing helix chain 'N' and resid 221 through 233 removed outlier: 3.654A pdb=" N SER N 225 " --> pdb=" O GLY N 221 " (cutoff:3.500A) Processing helix chain 'N' and resid 264 through 268 Processing sheet with id=AA1, first strand: chain 'C' and resid 102 through 103 Processing sheet with id=AA2, first strand: chain 'C' and resid 123 through 127 removed outlier: 6.456A pdb=" N ASP C 150 " --> pdb=" O GLY C 137 " (cutoff:3.500A) removed outlier: 6.211A pdb=" N CYS C 139 " --> pdb=" O PHE C 148 " (cutoff:3.500A) removed outlier: 6.120A pdb=" N PHE C 148 " --> pdb=" O CYS C 139 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 178 through 181 removed outlier: 4.184A pdb=" N ILE C 210 " --> pdb=" O ILE C 223 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N SER C 214 " --> pdb=" O TRP C 219 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N TRP C 219 " --> pdb=" O SER C 214 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 192 through 193 Processing sheet with id=AA5, first strand: chain 'C' and resid 244 through 245 removed outlier: 3.530A pdb=" N LEU C 263 " --> pdb=" O MET C 244 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 275 through 276 removed outlier: 4.458A pdb=" N TRP C 324 " --> pdb=" O SER C 276 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N ILE C 298 " --> pdb=" O TRP C 313 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 328 through 330 removed outlier: 6.065A pdb=" N LYS C 328 " --> pdb=" O VAL C 660 " (cutoff:3.500A) removed outlier: 7.586A pdb=" N TRP C 662 " --> pdb=" O LYS C 328 " (cutoff:3.500A) removed outlier: 7.335A pdb=" N GLU C 330 " --> pdb=" O TRP C 662 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N LYS C 661 " --> pdb=" O ASP C 650 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 45 through 48 removed outlier: 6.494A pdb=" N GLN D 46 " --> pdb=" O LEU D 158 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'D' and resid 111 through 113 Processing sheet with id=AB1, first strand: chain 'D' and resid 210 through 211 Processing sheet with id=AB2, first strand: chain 'E' and resid 45 through 48 removed outlier: 4.271A pdb=" N GLN E 46 " --> pdb=" O THR E 156 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'E' and resid 80 through 81 removed outlier: 6.957A pdb=" N THR E 53 " --> pdb=" O LEU E 81 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'E' and resid 202 through 203 removed outlier: 6.450A pdb=" N ASP E 202 " --> pdb=" O PHE E 220 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'E' and resid 237 through 239 removed outlier: 6.384A pdb=" N VAL E 237 " --> pdb=" O VAL E 257 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'E' and resid 273 through 275 Processing sheet with id=AB7, first strand: chain 'G' and resid 102 through 104 Processing sheet with id=AB8, first strand: chain 'G' and resid 123 through 127 Processing sheet with id=AB9, first strand: chain 'G' and resid 167 through 168 removed outlier: 6.888A pdb=" N SER G 167 " --> pdb=" O TRP G 220 " (cutoff:3.500A) removed outlier: 8.546A pdb=" N CYS G 222 " --> pdb=" O SER G 167 " (cutoff:3.500A) removed outlier: 4.341A pdb=" N ILE G 210 " --> pdb=" O ILE G 223 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'G' and resid 192 through 193 Processing sheet with id=AC2, first strand: chain 'G' and resid 236 through 240 removed outlier: 3.684A pdb=" N ALA G 269 " --> pdb=" O ASP G 264 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'G' and resid 287 through 292 removed outlier: 5.358A pdb=" N GLN G 288 " --> pdb=" O LEU G 299 " (cutoff:3.500A) removed outlier: 7.749A pdb=" N LEU G 299 " --> pdb=" O GLN G 288 " (cutoff:3.500A) removed outlier: 6.113A pdb=" N VAL G 290 " --> pdb=" O LEU G 297 " (cutoff:3.500A) removed outlier: 6.299A pdb=" N LEU G 297 " --> pdb=" O VAL G 290 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ALA G 323 " --> pdb=" O HIS G 316 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'G' and resid 328 through 330 Processing sheet with id=AC5, first strand: chain 'G' and resid 344 through 347 removed outlier: 3.607A pdb=" N VAL G 351 " --> pdb=" O LEU G 649 " (cutoff:3.500A) removed outlier: 4.269A pdb=" N SER G 355 " --> pdb=" O GLN G 645 " (cutoff:3.500A) removed outlier: 4.222A pdb=" N GLN G 645 " --> pdb=" O SER G 355 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'H' and resid 14 through 16 removed outlier: 7.393A pdb=" N LYS H 5 " --> pdb=" O VAL H 45 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'I' and resid 45 through 48 removed outlier: 6.115A pdb=" N GLN I 46 " --> pdb=" O LEU I 158 " (cutoff:3.500A) removed outlier: 6.200A pdb=" N VAL I 237 " --> pdb=" O VAL I 257 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'I' and resid 111 through 113 removed outlier: 3.712A pdb=" N THR I 112 " --> pdb=" O TYR I 80 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N ILE I 275 " --> pdb=" O LEU I 287 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'I' and resid 202 through 203 removed outlier: 3.660A pdb=" N ASP I 202 " --> pdb=" O TYR I 218 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N PHE I 220 " --> pdb=" O ASP I 202 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'J' and resid 45 through 48 removed outlier: 6.293A pdb=" N GLN J 46 " --> pdb=" O LEU J 158 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'J' and resid 111 through 113 Processing sheet with id=AD3, first strand: chain 'J' and resid 202 through 203 Processing sheet with id=AD4, first strand: chain 'K' and resid 46 through 48 removed outlier: 6.112A pdb=" N GLN K 46 " --> pdb=" O LEU K 158 " (cutoff:3.500A) removed outlier: 6.215A pdb=" N PHE K 164 " --> pdb=" O SER K 238 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N VAL K 257 " --> pdb=" O VAL K 237 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'K' and resid 202 through 203 removed outlier: 3.644A pdb=" N PHE K 220 " --> pdb=" O ASP K 202 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'K' and resid 273 through 275 Processing sheet with id=AD7, first strand: chain 'L' and resid 45 through 48 removed outlier: 6.742A pdb=" N GLN L 46 " --> pdb=" O LEU L 158 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'L' and resid 53 through 55 Processing sheet with id=AD9, first strand: chain 'L' and resid 202 through 203 removed outlier: 3.628A pdb=" N ASP L 202 " --> pdb=" O TYR L 218 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N PHE L 220 " --> pdb=" O ASP L 202 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'L' and resid 273 through 277 Processing sheet with id=AE2, first strand: chain 'M' and resid 45 through 48 removed outlier: 6.009A pdb=" N GLN M 46 " --> pdb=" O LEU M 158 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N PHE M 164 " --> pdb=" O LEU M 236 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N SER M 238 " --> pdb=" O PHE M 164 " (cutoff:3.500A) removed outlier: 4.179A pdb=" N LEU M 166 " --> pdb=" O SER M 238 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N VAL M 257 " --> pdb=" O VAL M 237 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'M' and resid 111 through 113 removed outlier: 7.041A pdb=" N TYR M 80 " --> pdb=" O THR M 112 " (cutoff:3.500A) removed outlier: 6.524A pdb=" N THR M 53 " --> pdb=" O LEU M 81 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'M' and resid 202 through 203 removed outlier: 7.286A pdb=" N ASP M 202 " --> pdb=" O PHE M 220 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'N' and resid 45 through 48 removed outlier: 6.237A pdb=" N GLN N 46 " --> pdb=" O LEU N 158 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'N' and resid 81 through 82 Processing sheet with id=AE7, first strand: chain 'N' and resid 202 through 203 removed outlier: 3.599A pdb=" N ASP N 202 " --> pdb=" O TYR N 218 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N PHE N 220 " --> pdb=" O ASP N 202 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'N' and resid 237 through 239 removed outlier: 3.508A pdb=" N VAL N 257 " --> pdb=" O VAL N 237 " (cutoff:3.500A) 1294 hydrogen bonds defined for protein. 3566 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: 5.69 Time building geometry restraints manager: 3.22 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 6258 1.33 - 1.46: 8185 1.46 - 1.59: 15351 1.59 - 1.71: 1 1.71 - 1.84: 250 Bond restraints: 30045 Sorted by residual: bond pdb=" N PRO F 44 " pdb=" CD PRO F 44 " ideal model delta sigma weight residual 1.473 1.561 -0.088 1.40e-02 5.10e+03 3.91e+01 bond pdb=" C MLL D 309 " pdb=" OXT MLL D 309 " ideal model delta sigma weight residual 1.231 1.326 -0.095 2.00e-02 2.50e+03 2.27e+01 bond pdb=" C MLL J 309 " pdb=" OXT MLL J 309 " ideal model delta sigma weight residual 1.231 1.326 -0.095 2.00e-02 2.50e+03 2.23e+01 bond pdb=" N ASP H 96 " pdb=" CA ASP H 96 " ideal model delta sigma weight residual 1.454 1.509 -0.055 1.32e-02 5.74e+03 1.73e+01 bond pdb=" N VAL N 87 " pdb=" CA VAL N 87 " ideal model delta sigma weight residual 1.459 1.510 -0.051 1.25e-02 6.40e+03 1.68e+01 ... (remaining 30040 not shown) Histogram of bond angle deviations from ideal: 0.00 - 7.17: 40522 7.17 - 14.35: 174 14.35 - 21.52: 15 21.52 - 28.70: 7 28.70 - 35.87: 3 Bond angle restraints: 40721 Sorted by residual: angle pdb=" N TYR N 86 " pdb=" CA TYR N 86 " pdb=" C TYR N 86 " ideal model delta sigma weight residual 112.90 141.69 -28.79 1.31e+00 5.83e-01 4.83e+02 angle pdb=" N GLN F 97 " pdb=" CA GLN F 97 " pdb=" C GLN F 97 " ideal model delta sigma weight residual 112.72 140.06 -27.34 1.28e+00 6.10e-01 4.56e+02 angle pdb=" N GLN H 97 " pdb=" CA GLN H 97 " pdb=" C GLN H 97 " ideal model delta sigma weight residual 112.54 136.79 -24.25 1.22e+00 6.72e-01 3.95e+02 angle pdb=" N GLN F 23 " pdb=" CA GLN F 23 " pdb=" C GLN F 23 " ideal model delta sigma weight residual 111.33 133.02 -21.69 1.21e+00 6.83e-01 3.21e+02 angle pdb=" C GLN H 97 " pdb=" CA GLN H 97 " pdb=" CB GLN H 97 " ideal model delta sigma weight residual 110.31 74.44 35.87 2.09e+00 2.29e-01 2.95e+02 ... (remaining 40716 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.92: 15292 17.92 - 35.84: 1965 35.84 - 53.76: 458 53.76 - 71.68: 102 71.68 - 89.60: 35 Dihedral angle restraints: 17852 sinusoidal: 7296 harmonic: 10556 Sorted by residual: dihedral pdb=" C GLN H 97 " pdb=" N GLN H 97 " pdb=" CA GLN H 97 " pdb=" CB GLN H 97 " ideal model delta harmonic sigma weight residual -122.60 -71.02 -51.58 0 2.50e+00 1.60e-01 4.26e+02 dihedral pdb=" N GLN H 97 " pdb=" C GLN H 97 " pdb=" CA GLN H 97 " pdb=" CB GLN H 97 " ideal model delta harmonic sigma weight residual 122.80 78.43 44.37 0 2.50e+00 1.60e-01 3.15e+02 dihedral pdb=" C ASP H 96 " pdb=" N ASP H 96 " pdb=" CA ASP H 96 " pdb=" CB ASP H 96 " ideal model delta harmonic sigma weight residual -122.60 -81.31 -41.29 0 2.50e+00 1.60e-01 2.73e+02 ... (remaining 17849 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.230: 4309 0.230 - 0.459: 44 0.459 - 0.689: 6 0.689 - 0.919: 2 0.919 - 1.149: 1 Chirality restraints: 4362 Sorted by residual: chirality pdb=" CA GLN H 158 " pdb=" N GLN H 158 " pdb=" C GLN H 158 " pdb=" CB GLN H 158 " both_signs ideal model delta sigma weight residual False 2.51 1.36 1.15 2.00e-01 2.50e+01 3.30e+01 chirality pdb=" CA GLN F 97 " pdb=" N GLN F 97 " pdb=" C GLN F 97 " pdb=" CB GLN F 97 " both_signs ideal model delta sigma weight residual False 2.51 1.71 0.80 2.00e-01 2.50e+01 1.60e+01 chirality pdb=" CA LYS F 128 " pdb=" N LYS F 128 " pdb=" C LYS F 128 " pdb=" CB LYS F 128 " both_signs ideal model delta sigma weight residual False 2.51 1.81 0.70 2.00e-01 2.50e+01 1.24e+01 ... (remaining 4359 not shown) Planarity restraints: 5290 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA TYR N 86 " -0.042 2.00e-02 2.50e+03 8.40e-02 7.06e+01 pdb=" C TYR N 86 " 0.145 2.00e-02 2.50e+03 pdb=" O TYR N 86 " -0.055 2.00e-02 2.50e+03 pdb=" N VAL N 87 " -0.049 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG H 154 " -0.595 9.50e-02 1.11e+02 2.67e-01 4.36e+01 pdb=" NE ARG H 154 " 0.036 2.00e-02 2.50e+03 pdb=" CZ ARG H 154 " 0.004 2.00e-02 2.50e+03 pdb=" NH1 ARG H 154 " 0.005 2.00e-02 2.50e+03 pdb=" NH2 ARG H 154 " -0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE N 150 " 0.027 2.00e-02 2.50e+03 3.99e-02 2.79e+01 pdb=" CG PHE N 150 " -0.091 2.00e-02 2.50e+03 pdb=" CD1 PHE N 150 " 0.032 2.00e-02 2.50e+03 pdb=" CD2 PHE N 150 " 0.034 2.00e-02 2.50e+03 pdb=" CE1 PHE N 150 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 PHE N 150 " -0.002 2.00e-02 2.50e+03 pdb=" CZ PHE N 150 " -0.001 2.00e-02 2.50e+03 ... (remaining 5287 not shown) Histogram of nonbonded interaction distances: 1.42 - 2.12: 7 2.12 - 2.81: 7903 2.81 - 3.51: 40655 3.51 - 4.20: 67993 4.20 - 4.90: 122288 Nonbonded interactions: 238846 Sorted by model distance: nonbonded pdb=" OXT MLL D 309 " pdb=" C10 MLL D 309 " model vdw 1.425 3.460 nonbonded pdb=" OXT MLL J 309 " pdb=" C10 MLL J 309 " model vdw 1.426 3.460 nonbonded pdb="MN MN K 401 " pdb="MN MN K 402 " model vdw 1.878 1.600 nonbonded pdb=" O GLN F 97 " pdb=" CE2 PHE F 101 " model vdw 1.989 3.340 nonbonded pdb=" O LYS F 113 " pdb=" OD1 ASP F 117 " model vdw 2.026 3.040 ... (remaining 238841 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 93 through 153 or resid 155 through 223)) selection = (chain 'B' and (resid 93 through 153 or resid 155 through 223)) } ncs_group { reference = chain 'C' selection = (chain 'G' and (resid 45 through 696 or resid 706 through 717)) } ncs_group { reference = (chain 'D' and (resid 4 through 7 or (resid 8 and (name N or name CA or name C o \ r name O or name CB )) or resid 10 through 294 or resid 402)) selection = (chain 'E' and (resid 4 through 8 or resid 10 through 294 or resid 402)) selection = (chain 'I' and (resid 4 through 8 or resid 10 through 294 or resid 402)) selection = (chain 'J' and (resid 4 through 8 or resid 10 through 294 or resid 402)) selection = (chain 'K' and (resid 4 through 8 or resid 10 through 294 or resid 402)) selection = (chain 'L' and (resid 4 through 8 or resid 10 through 294 or resid 402)) selection = (chain 'M' and (resid 4 through 8 or resid 10 through 401)) selection = (chain 'N' and (resid 4 through 8 or resid 10 through 294 or resid 402)) } ncs_group { reference = chain 'F' selection = chain 'H' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.47 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 7.010 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.500 Check model and map are aligned: 0.070 Set scattering table: 0.080 Process input model: 26.100 Find NCS groups from input model: 0.660 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.270 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.790 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6980 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 : 0.007 0.095 30045 Z= 0.333 Angle : 1.416 35.874 40721 Z= 0.796 Chirality : 0.078 1.149 4362 Planarity : 0.010 0.267 5290 Dihedral : 16.930 89.597 11068 Min Nonbonded Distance : 1.425 Molprobity Statistics. All-atom Clashscore : 9.56 Ramachandran Plot: Outliers : 0.03 % Allowed : 7.50 % Favored : 92.47 % Rotamer: Outliers : 1.40 % Allowed : 28.45 % Favored : 70.15 % Cbeta Deviations : 0.38 % Peptide Plane: Cis-proline : 0.64 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.81 (0.14), residues: 3592 helix: 0.38 (0.14), residues: 1347 sheet: -2.03 (0.22), residues: 566 loop : -2.26 (0.14), residues: 1679 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG E 115 TYR 0.070 0.002 TYR M 145 PHE 0.091 0.003 PHE N 150 TRP 0.068 0.003 TRP A 218 HIS 0.026 0.002 HIS E 230 Details of bonding type rmsd covalent geometry : bond 0.00651 (30045) covalent geometry : angle 1.41567 (40721) hydrogen bonds : bond 0.13932 ( 1294) hydrogen bonds : angle 6.71522 ( 3566) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7184 Ramachandran restraints generated. 3592 Oldfield, 0 Emsley, 3592 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7184 Ramachandran restraints generated. 3592 Oldfield, 0 Emsley, 3592 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 489 residues out of total 3218 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 444 time to evaluate : 0.982 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: B 121 GLN cc_start: 0.7327 (mm-40) cc_final: 0.7122 (mm-40) REVERT: B 137 GLU cc_start: 0.8029 (tt0) cc_final: 0.7703 (tt0) REVERT: C 95 LYS cc_start: 0.8631 (pttt) cc_final: 0.8357 (pttm) REVERT: C 202 GLN cc_start: 0.8872 (OUTLIER) cc_final: 0.8558 (tt0) REVERT: C 356 GLN cc_start: 0.7545 (tt0) cc_final: 0.7260 (tt0) REVERT: D 135 ARG cc_start: 0.8276 (ptt180) cc_final: 0.7851 (ptm160) REVERT: D 277 GLU cc_start: 0.8357 (tt0) cc_final: 0.7869 (mt-10) REVERT: E 36 LYS cc_start: 0.8568 (mmmm) cc_final: 0.8050 (pttm) REVERT: E 83 MET cc_start: 0.5669 (mmt) cc_final: 0.4423 (mtt) REVERT: E 143 TRP cc_start: 0.7031 (t60) cc_final: 0.6707 (t60) REVERT: F 30 MET cc_start: 0.6931 (OUTLIER) cc_final: 0.6624 (pp-130) REVERT: G 133 MET cc_start: 0.8203 (ttp) cc_final: 0.7898 (ttp) REVERT: H 57 LYS cc_start: 0.3855 (mtpt) cc_final: 0.3567 (tttp) REVERT: H 62 CYS cc_start: 0.3404 (OUTLIER) cc_final: 0.2729 (t) REVERT: H 112 ILE cc_start: 0.1093 (OUTLIER) cc_final: 0.0727 (mm) REVERT: I 145 TYR cc_start: 0.7199 (m-10) cc_final: 0.6999 (m-10) REVERT: I 205 ASP cc_start: 0.7943 (p0) cc_final: 0.7669 (p0) REVERT: I 248 TYR cc_start: 0.8414 (p90) cc_final: 0.7652 (p90) REVERT: J 135 ARG cc_start: 0.7459 (ttp80) cc_final: 0.7142 (ttp80) REVERT: K 34 LYS cc_start: 0.8457 (mtmm) cc_final: 0.8244 (mtmm) REVERT: K 132 GLU cc_start: 0.7992 (tt0) cc_final: 0.7782 (tt0) REVERT: L 21 LYS cc_start: 0.8472 (tttp) cc_final: 0.7853 (ttpp) REVERT: L 91 TYR cc_start: 0.7612 (t80) cc_final: 0.6942 (t80) REVERT: L 283 LYS cc_start: 0.7762 (tppt) cc_final: 0.7279 (mmmt) REVERT: M 83 MET cc_start: 0.1919 (OUTLIER) cc_final: 0.1165 (ttt) REVERT: M 134 LEU cc_start: 0.7533 (mt) cc_final: 0.7122 (tt) REVERT: M 242 GLN cc_start: 0.7917 (mm110) cc_final: 0.7644 (mm-40) REVERT: M 246 GLU cc_start: 0.7495 (mm-30) cc_final: 0.7109 (tp30) REVERT: N 230 HIS cc_start: 0.6935 (m-70) cc_final: 0.6639 (m-70) REVERT: N 276 MET cc_start: 0.4998 (ttt) cc_final: 0.4129 (tmm) outliers start: 45 outliers final: 26 residues processed: 474 average time/residue: 0.1866 time to fit residues: 140.4625 Evaluate side-chains 437 residues out of total 3218 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 406 time to evaluate : 1.002 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 188 LYS Chi-restraints excluded: chain C residue 74 VAL Chi-restraints excluded: chain C residue 111 TYR Chi-restraints excluded: chain C residue 202 GLN Chi-restraints excluded: chain C residue 263 LEU Chi-restraints excluded: chain D residue 85 ASP Chi-restraints excluded: chain D residue 86 TYR Chi-restraints excluded: chain E residue 21 LYS Chi-restraints excluded: chain E residue 97 VAL Chi-restraints excluded: chain F residue 16 VAL Chi-restraints excluded: chain F residue 30 MET Chi-restraints excluded: chain F residue 44 PRO Chi-restraints excluded: chain F residue 85 ILE Chi-restraints excluded: chain F residue 93 LEU Chi-restraints excluded: chain F residue 104 ILE Chi-restraints excluded: chain F residue 117 ASP Chi-restraints excluded: chain F residue 144 ASP Chi-restraints excluded: chain G residue 288 GLN Chi-restraints excluded: chain H residue 62 CYS Chi-restraints excluded: chain H residue 112 ILE Chi-restraints excluded: chain H residue 113 LYS Chi-restraints excluded: chain H residue 145 PHE Chi-restraints excluded: chain I residue 280 ASP Chi-restraints excluded: chain J residue 12 GLN Chi-restraints excluded: chain K residue 33 GLU Chi-restraints excluded: chain L residue 253 ASP Chi-restraints excluded: chain M residue 83 MET Chi-restraints excluded: chain M residue 87 VAL Chi-restraints excluded: chain M residue 88 ASP Chi-restraints excluded: chain N residue 224 ILE Chi-restraints excluded: chain N residue 245 MET Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 197 optimal weight: 2.9990 chunk 215 optimal weight: 0.8980 chunk 20 optimal weight: 0.9980 chunk 132 optimal weight: 1.9990 chunk 261 optimal weight: 0.3980 chunk 248 optimal weight: 3.9990 chunk 207 optimal weight: 3.9990 chunk 155 optimal weight: 2.9990 chunk 244 optimal weight: 1.9990 chunk 183 optimal weight: 9.9990 chunk 298 optimal weight: 0.9990 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 215 ASN B 102 GLN C 288 GLN E 118 HIS ** F 65 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 288 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 334 HIS H 97 GLN ** H 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 125 ASN K 79 ASN ** K 118 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 230 HIS K 249 ASN L 61 GLN N 63 HIS N 122 GLN ** N 229 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4522 r_free = 0.4522 target = 0.205082 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3898 r_free = 0.3898 target = 0.152897 restraints weight = 76100.175| |-----------------------------------------------------------------------------| r_work (start): 0.3912 rms_B_bonded: 4.19 r_work: 0.3704 rms_B_bonded: 3.85 restraints_weight: 0.5000 r_work (final): 0.3704 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3712 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3712 r_free = 0.3712 target_work(ls_wunit_k1) = 0.137 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3712 r_free = 0.3712 target_work(ls_wunit_k1) = 0.137 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3712 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7493 moved from start: 0.1396 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 30045 Z= 0.162 Angle : 0.679 12.644 40721 Z= 0.356 Chirality : 0.045 0.245 4362 Planarity : 0.005 0.067 5290 Dihedral : 6.079 78.473 4035 Min Nonbonded Distance : 1.908 Molprobity Statistics. All-atom Clashscore : 10.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.35 % Favored : 94.65 % Rotamer: Outliers : 3.84 % Allowed : 22.36 % Favored : 73.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.64 % Cis-general : 0.00 % Twisted Proline : 0.64 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.20 (0.14), residues: 3592 helix: 1.07 (0.14), residues: 1372 sheet: -2.05 (0.21), residues: 645 loop : -1.94 (0.15), residues: 1575 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG E 268 TYR 0.044 0.001 TYR E 145 PHE 0.020 0.002 PHE L 164 TRP 0.026 0.001 TRP A 218 HIS 0.013 0.001 HIS E 230 Details of bonding type rmsd covalent geometry : bond 0.00369 (30045) covalent geometry : angle 0.67935 (40721) hydrogen bonds : bond 0.05095 ( 1294) hydrogen bonds : angle 5.17752 ( 3566) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7184 Ramachandran restraints generated. 3592 Oldfield, 0 Emsley, 3592 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7184 Ramachandran restraints generated. 3592 Oldfield, 0 Emsley, 3592 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 556 residues out of total 3218 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 123 poor density : 433 time to evaluate : 0.865 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 137 GLU cc_start: 0.8385 (tt0) cc_final: 0.8145 (tt0) REVERT: C 88 GLN cc_start: 0.8151 (OUTLIER) cc_final: 0.7200 (mp10) REVERT: C 256 MET cc_start: 0.8671 (mmm) cc_final: 0.8455 (mmm) REVERT: C 266 GLU cc_start: 0.8131 (mm-30) cc_final: 0.7724 (mm-30) REVERT: C 356 GLN cc_start: 0.8221 (tt0) cc_final: 0.7265 (tt0) REVERT: C 647 TYR cc_start: 0.8669 (m-80) cc_final: 0.8216 (m-80) REVERT: D 86 TYR cc_start: 0.8476 (OUTLIER) cc_final: 0.7633 (p90) REVERT: D 110 ARG cc_start: 0.8751 (mmm160) cc_final: 0.8320 (mmt180) REVERT: E 24 SER cc_start: 0.5396 (OUTLIER) cc_final: 0.5142 (p) REVERT: E 70 ARG cc_start: 0.5417 (OUTLIER) cc_final: 0.4843 (ptt180) REVERT: E 83 MET cc_start: 0.5500 (mmt) cc_final: 0.4230 (mtt) REVERT: E 95 GLU cc_start: 0.8443 (mp0) cc_final: 0.7882 (mp0) REVERT: E 209 TRP cc_start: 0.6224 (m100) cc_final: 0.5898 (m100) REVERT: E 244 VAL cc_start: 0.6313 (OUTLIER) cc_final: 0.6104 (m) REVERT: G 158 SER cc_start: 0.7700 (OUTLIER) cc_final: 0.7483 (p) REVERT: G 264 ASP cc_start: 0.7077 (t0) cc_final: 0.6686 (t0) REVERT: G 695 MET cc_start: 0.6401 (OUTLIER) cc_final: 0.5993 (mmm) REVERT: H 145 PHE cc_start: 0.2072 (OUTLIER) cc_final: 0.0576 (p90) REVERT: I 19 GLU cc_start: 0.7969 (tm-30) cc_final: 0.7648 (tm-30) REVERT: I 21 LYS cc_start: 0.7770 (mmmt) cc_final: 0.7424 (mmmt) REVERT: I 77 ASP cc_start: 0.7533 (p0) cc_final: 0.7331 (p0) REVERT: I 145 TYR cc_start: 0.7298 (m-10) cc_final: 0.6940 (m-10) REVERT: I 214 ARG cc_start: 0.8695 (OUTLIER) cc_final: 0.8457 (mtp180) REVERT: I 248 TYR cc_start: 0.8279 (p90) cc_final: 0.7501 (p90) REVERT: J 19 GLU cc_start: 0.7281 (mm-30) cc_final: 0.7065 (mm-30) REVERT: J 115 ARG cc_start: 0.8578 (OUTLIER) cc_final: 0.8209 (ttt180) REVERT: K 34 LYS cc_start: 0.8633 (mtmm) cc_final: 0.8362 (mttm) REVERT: K 145 TYR cc_start: 0.7625 (m-80) cc_final: 0.7411 (m-80) REVERT: K 201 SER cc_start: 0.7703 (m) cc_final: 0.7083 (p) REVERT: L 21 LYS cc_start: 0.8499 (tttp) cc_final: 0.7980 (ttpp) REVERT: M 145 TYR cc_start: 0.7008 (m-80) cc_final: 0.6713 (m-10) REVERT: M 224 ILE cc_start: 0.7482 (OUTLIER) cc_final: 0.7209 (pt) REVERT: M 246 GLU cc_start: 0.7335 (mm-30) cc_final: 0.6931 (tp30) REVERT: N 83 MET cc_start: 0.5073 (tpt) cc_final: 0.4320 (mmm) REVERT: N 244 VAL cc_start: 0.2462 (OUTLIER) cc_final: 0.2064 (t) outliers start: 123 outliers final: 65 residues processed: 527 average time/residue: 0.1917 time to fit residues: 160.2671 Evaluate side-chains 452 residues out of total 3218 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 375 time to evaluate : 1.189 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 124 GLN Chi-restraints excluded: chain A residue 188 LYS Chi-restraints excluded: chain B residue 130 LEU Chi-restraints excluded: chain B residue 198 GLU Chi-restraints excluded: chain C residue 68 HIS Chi-restraints excluded: chain C residue 74 VAL Chi-restraints excluded: chain C residue 82 ILE Chi-restraints excluded: chain C residue 88 GLN Chi-restraints excluded: chain C residue 89 CYS Chi-restraints excluded: chain C residue 181 VAL Chi-restraints excluded: chain C residue 224 VAL Chi-restraints excluded: chain C residue 263 LEU Chi-restraints excluded: chain C residue 274 ASN Chi-restraints excluded: chain C residue 290 VAL Chi-restraints excluded: chain C residue 329 VAL Chi-restraints excluded: chain C residue 350 CYS Chi-restraints excluded: chain C residue 664 VAL Chi-restraints excluded: chain C residue 671 VAL Chi-restraints excluded: chain D residue 86 TYR Chi-restraints excluded: chain D residue 202 ASP Chi-restraints excluded: chain E residue 5 VAL Chi-restraints excluded: chain E residue 24 SER Chi-restraints excluded: chain E residue 52 VAL Chi-restraints excluded: chain E residue 65 LEU Chi-restraints excluded: chain E residue 66 MET Chi-restraints excluded: chain E residue 70 ARG Chi-restraints excluded: chain E residue 78 THR Chi-restraints excluded: chain E residue 97 VAL Chi-restraints excluded: chain E residue 126 VAL Chi-restraints excluded: chain E residue 244 VAL Chi-restraints excluded: chain F residue 16 VAL Chi-restraints excluded: chain F residue 85 ILE Chi-restraints excluded: chain F residue 93 LEU Chi-restraints excluded: chain F residue 141 ILE Chi-restraints excluded: chain G residue 117 THR Chi-restraints excluded: chain G residue 158 SER Chi-restraints excluded: chain G residue 196 SER Chi-restraints excluded: chain G residue 210 ILE Chi-restraints excluded: chain G residue 257 SER Chi-restraints excluded: chain G residue 288 GLN Chi-restraints excluded: chain G residue 302 CYS Chi-restraints excluded: chain G residue 334 HIS Chi-restraints excluded: chain G residue 339 LEU Chi-restraints excluded: chain G residue 664 VAL Chi-restraints excluded: chain G residue 695 MET Chi-restraints excluded: chain H residue 145 PHE Chi-restraints excluded: chain I residue 111 ILE Chi-restraints excluded: chain I residue 196 CYS Chi-restraints excluded: chain I residue 214 ARG Chi-restraints excluded: chain I residue 258 THR Chi-restraints excluded: chain J residue 40 THR Chi-restraints excluded: chain J residue 115 ARG Chi-restraints excluded: chain J residue 246 GLU Chi-restraints excluded: chain J residue 258 THR Chi-restraints excluded: chain K residue 33 GLU Chi-restraints excluded: chain K residue 134 LEU Chi-restraints excluded: chain K residue 156 THR Chi-restraints excluded: chain K residue 257 VAL Chi-restraints excluded: chain L residue 17 LEU Chi-restraints excluded: chain L residue 134 LEU Chi-restraints excluded: chain L residue 158 LEU Chi-restraints excluded: chain L residue 230 HIS Chi-restraints excluded: chain M residue 17 LEU Chi-restraints excluded: chain M residue 87 VAL Chi-restraints excluded: chain M residue 88 ASP Chi-restraints excluded: chain M residue 94 VAL Chi-restraints excluded: chain M residue 126 VAL Chi-restraints excluded: chain M residue 189 VAL Chi-restraints excluded: chain M residue 224 ILE Chi-restraints excluded: chain N residue 28 VAL Chi-restraints excluded: chain N residue 54 VAL Chi-restraints excluded: chain N residue 97 VAL Chi-restraints excluded: chain N residue 152 TYR Chi-restraints excluded: chain N residue 184 ASP Chi-restraints excluded: chain N residue 224 ILE Chi-restraints excluded: chain N residue 244 VAL Chi-restraints excluded: chain N residue 266 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 31 optimal weight: 0.8980 chunk 219 optimal weight: 0.7980 chunk 115 optimal weight: 5.9990 chunk 243 optimal weight: 1.9990 chunk 44 optimal weight: 1.9990 chunk 139 optimal weight: 7.9990 chunk 187 optimal weight: 1.9990 chunk 23 optimal weight: 8.9990 chunk 320 optimal weight: 6.9990 chunk 54 optimal weight: 0.7980 chunk 118 optimal weight: 0.8980 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 288 GLN E 272 GLN ** F 64 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 65 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 286 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 288 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 118 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 179 HIS ** N 229 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4507 r_free = 0.4507 target = 0.203631 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3857 r_free = 0.3857 target = 0.149846 restraints weight = 61377.832| |-----------------------------------------------------------------------------| r_work (start): 0.3876 rms_B_bonded: 3.88 r_work: 0.3688 rms_B_bonded: 3.80 restraints_weight: 0.5000 r_work (final): 0.3688 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3659 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3659 r_free = 0.3659 target_work(ls_wunit_k1) = 0.133 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3659 r_free = 0.3659 target_work(ls_wunit_k1) = 0.133 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3659 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7521 moved from start: 0.1882 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 30045 Z= 0.153 Angle : 0.634 10.091 40721 Z= 0.329 Chirality : 0.044 0.246 4362 Planarity : 0.004 0.067 5290 Dihedral : 5.300 72.586 3992 Min Nonbonded Distance : 1.646 Molprobity Statistics. All-atom Clashscore : 10.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.41 % Favored : 94.59 % Rotamer: Outliers : 3.96 % Allowed : 22.49 % Favored : 73.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.64 % Cis-general : 0.00 % Twisted Proline : 0.64 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.03 (0.14), residues: 3592 helix: 1.22 (0.14), residues: 1375 sheet: -1.91 (0.21), residues: 637 loop : -1.88 (0.15), residues: 1580 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG B 197 TYR 0.032 0.001 TYR N 145 PHE 0.020 0.001 PHE L 164 TRP 0.022 0.001 TRP A 218 HIS 0.020 0.001 HIS G 334 Details of bonding type rmsd covalent geometry : bond 0.00353 (30045) covalent geometry : angle 0.63396 (40721) hydrogen bonds : bond 0.04793 ( 1294) hydrogen bonds : angle 4.85360 ( 3566) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7184 Ramachandran restraints generated. 3592 Oldfield, 0 Emsley, 3592 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7184 Ramachandran restraints generated. 3592 Oldfield, 0 Emsley, 3592 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 541 residues out of total 3218 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 127 poor density : 414 time to evaluate : 1.240 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: B 137 GLU cc_start: 0.8375 (tt0) cc_final: 0.8085 (tt0) REVERT: C 88 GLN cc_start: 0.8091 (OUTLIER) cc_final: 0.7208 (mp10) REVERT: C 133 MET cc_start: 0.8909 (ttp) cc_final: 0.8602 (ttt) REVERT: C 256 MET cc_start: 0.8662 (mmm) cc_final: 0.8456 (mmm) REVERT: C 266 GLU cc_start: 0.8134 (mm-30) cc_final: 0.7725 (mm-30) REVERT: C 356 GLN cc_start: 0.8267 (tt0) cc_final: 0.7849 (tt0) REVERT: C 675 GLU cc_start: 0.8676 (OUTLIER) cc_final: 0.8107 (tt0) REVERT: D 17 LEU cc_start: 0.8673 (OUTLIER) cc_final: 0.8255 (mm) REVERT: D 86 TYR cc_start: 0.8761 (OUTLIER) cc_final: 0.7624 (p90) REVERT: D 115 ARG cc_start: 0.8542 (OUTLIER) cc_final: 0.7721 (ttm170) REVERT: E 24 SER cc_start: 0.5251 (OUTLIER) cc_final: 0.5013 (p) REVERT: E 83 MET cc_start: 0.5658 (mmt) cc_final: 0.4580 (mtt) REVERT: E 86 TYR cc_start: 0.7440 (m-10) cc_final: 0.7138 (m-10) REVERT: E 95 GLU cc_start: 0.8434 (mp0) cc_final: 0.8165 (mp0) REVERT: G 158 SER cc_start: 0.7681 (OUTLIER) cc_final: 0.7460 (p) REVERT: G 264 ASP cc_start: 0.7045 (t0) cc_final: 0.6616 (t0) REVERT: H 145 PHE cc_start: 0.2341 (OUTLIER) cc_final: 0.0878 (p90) REVERT: I 19 GLU cc_start: 0.8101 (tm-30) cc_final: 0.7787 (tm-30) REVERT: I 21 LYS cc_start: 0.7848 (mmmt) cc_final: 0.7610 (mmmt) REVERT: I 214 ARG cc_start: 0.8727 (OUTLIER) cc_final: 0.8457 (mtp180) REVERT: I 248 TYR cc_start: 0.8277 (p90) cc_final: 0.7569 (p90) REVERT: I 268 ARG cc_start: 0.8371 (ptp90) cc_final: 0.8127 (ptp90) REVERT: J 19 GLU cc_start: 0.7288 (mm-30) cc_final: 0.6802 (mt-10) REVERT: J 115 ARG cc_start: 0.8571 (OUTLIER) cc_final: 0.8153 (ttt180) REVERT: K 201 SER cc_start: 0.7709 (m) cc_final: 0.7158 (p) REVERT: M 134 LEU cc_start: 0.7283 (mt) cc_final: 0.6867 (pp) REVERT: M 145 TYR cc_start: 0.6955 (m-80) cc_final: 0.6542 (m-80) REVERT: M 212 SER cc_start: 0.6477 (OUTLIER) cc_final: 0.6254 (p) REVERT: M 224 ILE cc_start: 0.7750 (OUTLIER) cc_final: 0.7303 (mp) REVERT: N 83 MET cc_start: 0.5118 (tpt) cc_final: 0.4405 (mmm) REVERT: N 89 ARG cc_start: 0.6088 (ptp-110) cc_final: 0.5828 (ptp90) REVERT: N 244 VAL cc_start: 0.2061 (OUTLIER) cc_final: 0.1423 (t) REVERT: N 245 MET cc_start: 0.6113 (tmm) cc_final: 0.5864 (tmm) REVERT: N 256 VAL cc_start: 0.1994 (OUTLIER) cc_final: 0.1636 (p) REVERT: N 264 ASN cc_start: 0.8495 (t0) cc_final: 0.8286 (t0) REVERT: N 276 MET cc_start: 0.3951 (ttm) cc_final: 0.3387 (tmm) outliers start: 127 outliers final: 79 residues processed: 513 average time/residue: 0.1833 time to fit residues: 151.5158 Evaluate side-chains 471 residues out of total 3218 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 378 time to evaluate : 1.218 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 124 GLN Chi-restraints excluded: chain A residue 188 LYS Chi-restraints excluded: chain B residue 99 VAL Chi-restraints excluded: chain B residue 106 GLU Chi-restraints excluded: chain B residue 198 GLU Chi-restraints excluded: chain C residue 68 HIS Chi-restraints excluded: chain C residue 74 VAL Chi-restraints excluded: chain C residue 82 ILE Chi-restraints excluded: chain C residue 88 GLN Chi-restraints excluded: chain C residue 89 CYS Chi-restraints excluded: chain C residue 97 VAL Chi-restraints excluded: chain C residue 181 VAL Chi-restraints excluded: chain C residue 200 LEU Chi-restraints excluded: chain C residue 224 VAL Chi-restraints excluded: chain C residue 271 SER Chi-restraints excluded: chain C residue 274 ASN Chi-restraints excluded: chain C residue 290 VAL Chi-restraints excluded: chain C residue 350 CYS Chi-restraints excluded: chain C residue 664 VAL Chi-restraints excluded: chain C residue 671 VAL Chi-restraints excluded: chain C residue 675 GLU Chi-restraints excluded: chain D residue 17 LEU Chi-restraints excluded: chain D residue 86 TYR Chi-restraints excluded: chain D residue 115 ARG Chi-restraints excluded: chain D residue 135 ARG Chi-restraints excluded: chain D residue 202 ASP Chi-restraints excluded: chain E residue 5 VAL Chi-restraints excluded: chain E residue 24 SER Chi-restraints excluded: chain E residue 27 GLN Chi-restraints excluded: chain E residue 52 VAL Chi-restraints excluded: chain E residue 65 LEU Chi-restraints excluded: chain E residue 66 MET Chi-restraints excluded: chain E residue 78 THR Chi-restraints excluded: chain E residue 97 VAL Chi-restraints excluded: chain E residue 113 ILE Chi-restraints excluded: chain E residue 126 VAL Chi-restraints excluded: chain E residue 142 VAL Chi-restraints excluded: chain E residue 256 VAL Chi-restraints excluded: chain F residue 85 ILE Chi-restraints excluded: chain F residue 87 VAL Chi-restraints excluded: chain F residue 93 LEU Chi-restraints excluded: chain F residue 125 ASN Chi-restraints excluded: chain F residue 141 ILE Chi-restraints excluded: chain G residue 117 THR Chi-restraints excluded: chain G residue 158 SER Chi-restraints excluded: chain G residue 196 SER Chi-restraints excluded: chain G residue 210 ILE Chi-restraints excluded: chain G residue 302 CYS Chi-restraints excluded: chain G residue 339 LEU Chi-restraints excluded: chain G residue 682 VAL Chi-restraints excluded: chain H residue 145 PHE Chi-restraints excluded: chain I residue 111 ILE Chi-restraints excluded: chain I residue 196 CYS Chi-restraints excluded: chain I residue 214 ARG Chi-restraints excluded: chain I residue 235 THR Chi-restraints excluded: chain I residue 258 THR Chi-restraints excluded: chain I residue 280 ASP Chi-restraints excluded: chain J residue 115 ARG Chi-restraints excluded: chain J residue 246 GLU Chi-restraints excluded: chain J residue 258 THR Chi-restraints excluded: chain K residue 25 GLU Chi-restraints excluded: chain K residue 27 GLN Chi-restraints excluded: chain K residue 87 VAL Chi-restraints excluded: chain K residue 113 ILE Chi-restraints excluded: chain K residue 134 LEU Chi-restraints excluded: chain K residue 156 THR Chi-restraints excluded: chain K residue 170 LEU Chi-restraints excluded: chain K residue 244 VAL Chi-restraints excluded: chain K residue 257 VAL Chi-restraints excluded: chain L residue 17 LEU Chi-restraints excluded: chain L residue 46 GLN Chi-restraints excluded: chain L residue 120 SER Chi-restraints excluded: chain L residue 134 LEU Chi-restraints excluded: chain L residue 158 LEU Chi-restraints excluded: chain L residue 170 LEU Chi-restraints excluded: chain L residue 230 HIS Chi-restraints excluded: chain L residue 277 GLU Chi-restraints excluded: chain M residue 4 LYS Chi-restraints excluded: chain M residue 17 LEU Chi-restraints excluded: chain M residue 88 ASP Chi-restraints excluded: chain M residue 126 VAL Chi-restraints excluded: chain M residue 189 VAL Chi-restraints excluded: chain M residue 212 SER Chi-restraints excluded: chain M residue 224 ILE Chi-restraints excluded: chain M residue 244 VAL Chi-restraints excluded: chain N residue 28 VAL Chi-restraints excluded: chain N residue 54 VAL Chi-restraints excluded: chain N residue 97 VAL Chi-restraints excluded: chain N residue 152 TYR Chi-restraints excluded: chain N residue 184 ASP Chi-restraints excluded: chain N residue 224 ILE Chi-restraints excluded: chain N residue 244 VAL Chi-restraints excluded: chain N residue 256 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 111 optimal weight: 0.2980 chunk 149 optimal weight: 0.9980 chunk 276 optimal weight: 0.8980 chunk 221 optimal weight: 2.9990 chunk 6 optimal weight: 0.5980 chunk 96 optimal weight: 0.7980 chunk 184 optimal weight: 7.9990 chunk 9 optimal weight: 0.6980 chunk 232 optimal weight: 0.0050 chunk 197 optimal weight: 3.9990 chunk 336 optimal weight: 7.9990 overall best weight: 0.4794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 271 ASN ** E 230 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 64 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 65 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 286 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 288 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 331 ASN ** H 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 117 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 118 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 229 ASN ** 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 = 0.4531 r_free = 0.4531 target = 0.205928 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3935 r_free = 0.3935 target = 0.154736 restraints weight = 69938.654| |-----------------------------------------------------------------------------| r_work (start): 0.3952 rms_B_bonded: 3.73 r_work: 0.3726 rms_B_bonded: 3.80 restraints_weight: 0.5000 r_work (final): 0.3726 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3703 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3703 r_free = 0.3703 target_work(ls_wunit_k1) = 0.136 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3703 r_free = 0.3703 target_work(ls_wunit_k1) = 0.136 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3703 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7476 moved from start: 0.2136 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 30045 Z= 0.117 Angle : 0.588 11.560 40721 Z= 0.303 Chirality : 0.042 0.186 4362 Planarity : 0.004 0.068 5290 Dihedral : 4.922 74.282 3982 Min Nonbonded Distance : 1.474 Molprobity Statistics. All-atom Clashscore : 9.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.94 % Favored : 95.06 % Rotamer: Outliers : 3.65 % Allowed : 23.08 % Favored : 73.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.64 % Cis-general : 0.00 % Twisted Proline : 0.64 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.87 (0.14), residues: 3592 helix: 1.28 (0.14), residues: 1413 sheet: -1.71 (0.21), residues: 619 loop : -1.85 (0.15), residues: 1560 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG E 70 TYR 0.027 0.001 TYR N 145 PHE 0.014 0.001 PHE L 164 TRP 0.016 0.001 TRP A 218 HIS 0.009 0.001 HIS E 230 Details of bonding type rmsd covalent geometry : bond 0.00256 (30045) covalent geometry : angle 0.58795 (40721) hydrogen bonds : bond 0.04295 ( 1294) hydrogen bonds : angle 4.65873 ( 3566) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7184 Ramachandran restraints generated. 3592 Oldfield, 0 Emsley, 3592 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7184 Ramachandran restraints generated. 3592 Oldfield, 0 Emsley, 3592 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 547 residues out of total 3218 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 117 poor density : 430 time to evaluate : 0.812 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: B 137 GLU cc_start: 0.8376 (tt0) cc_final: 0.8171 (tt0) REVERT: C 88 GLN cc_start: 0.8070 (OUTLIER) cc_final: 0.7180 (mp10) REVERT: C 133 MET cc_start: 0.8903 (ttp) cc_final: 0.8684 (ttt) REVERT: C 163 ARG cc_start: 0.8920 (ttt-90) cc_final: 0.8643 (tpt-90) REVERT: C 266 GLU cc_start: 0.8133 (mm-30) cc_final: 0.7796 (mm-30) REVERT: C 356 GLN cc_start: 0.8250 (tt0) cc_final: 0.7825 (tt0) REVERT: C 675 GLU cc_start: 0.8647 (OUTLIER) cc_final: 0.8083 (tt0) REVERT: D 33 GLU cc_start: 0.8157 (mm-30) cc_final: 0.7831 (mm-30) REVERT: D 86 TYR cc_start: 0.8656 (OUTLIER) cc_final: 0.7924 (p90) REVERT: E 29 LYS cc_start: 0.9193 (tppt) cc_final: 0.8992 (tppt) REVERT: E 41 LYS cc_start: 0.8871 (mmtm) cc_final: 0.8611 (mmtm) REVERT: E 83 MET cc_start: 0.5441 (mmt) cc_final: 0.4408 (mtt) REVERT: G 158 SER cc_start: 0.7884 (OUTLIER) cc_final: 0.7633 (p) REVERT: G 264 ASP cc_start: 0.7055 (t0) cc_final: 0.6578 (t0) REVERT: H 145 PHE cc_start: 0.2382 (OUTLIER) cc_final: 0.0960 (p90) REVERT: I 19 GLU cc_start: 0.8104 (OUTLIER) cc_final: 0.7745 (tm-30) REVERT: I 77 ASP cc_start: 0.7609 (p0) cc_final: 0.7408 (p0) REVERT: I 111 ILE cc_start: 0.8623 (OUTLIER) cc_final: 0.8285 (pt) REVERT: I 137 TYR cc_start: 0.6924 (m-10) cc_final: 0.6664 (m-10) REVERT: I 149 LEU cc_start: 0.8872 (OUTLIER) cc_final: 0.8662 (tt) REVERT: I 248 TYR cc_start: 0.8300 (p90) cc_final: 0.7649 (p90) REVERT: I 287 LEU cc_start: 0.8400 (mm) cc_final: 0.8036 (mt) REVERT: J 19 GLU cc_start: 0.7097 (mm-30) cc_final: 0.6695 (mt-10) REVERT: K 33 GLU cc_start: 0.8734 (pt0) cc_final: 0.8240 (pp20) REVERT: K 34 LYS cc_start: 0.8464 (mtmm) cc_final: 0.8026 (mttm) REVERT: K 243 LEU cc_start: 0.7275 (tp) cc_final: 0.7039 (tp) REVERT: K 290 ASP cc_start: 0.5993 (OUTLIER) cc_final: 0.5762 (m-30) REVERT: L 12 GLN cc_start: 0.8908 (tp-100) cc_final: 0.8647 (tp40) REVERT: L 16 GLN cc_start: 0.8349 (mt0) cc_final: 0.7641 (mt0) REVERT: M 100 LEU cc_start: 0.8053 (mt) cc_final: 0.7776 (mt) REVERT: M 134 LEU cc_start: 0.7268 (mt) cc_final: 0.6896 (pp) REVERT: M 212 SER cc_start: 0.6516 (OUTLIER) cc_final: 0.6305 (p) REVERT: M 224 ILE cc_start: 0.7745 (OUTLIER) cc_final: 0.7319 (mp) REVERT: M 246 GLU cc_start: 0.7335 (mm-30) cc_final: 0.6777 (tp30) REVERT: N 83 MET cc_start: 0.4913 (tpt) cc_final: 0.3872 (mmm) REVERT: N 256 VAL cc_start: 0.1758 (OUTLIER) cc_final: 0.1376 (p) REVERT: N 264 ASN cc_start: 0.8474 (t0) cc_final: 0.8248 (t0) outliers start: 117 outliers final: 71 residues processed: 514 average time/residue: 0.1801 time to fit residues: 148.4040 Evaluate side-chains 479 residues out of total 3218 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 396 time to evaluate : 1.120 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 106 GLU Chi-restraints excluded: chain B residue 130 LEU Chi-restraints excluded: chain C residue 74 VAL Chi-restraints excluded: chain C residue 82 ILE Chi-restraints excluded: chain C residue 88 GLN Chi-restraints excluded: chain C residue 89 CYS Chi-restraints excluded: chain C residue 97 VAL Chi-restraints excluded: chain C residue 200 LEU Chi-restraints excluded: chain C residue 224 VAL Chi-restraints excluded: chain C residue 263 LEU Chi-restraints excluded: chain C residue 274 ASN Chi-restraints excluded: chain C residue 350 CYS Chi-restraints excluded: chain C residue 664 VAL Chi-restraints excluded: chain C residue 671 VAL Chi-restraints excluded: chain C residue 675 GLU Chi-restraints excluded: chain D residue 10 LEU Chi-restraints excluded: chain D residue 78 THR Chi-restraints excluded: chain D residue 86 TYR Chi-restraints excluded: chain D residue 135 ARG Chi-restraints excluded: chain D residue 202 ASP Chi-restraints excluded: chain E residue 5 VAL Chi-restraints excluded: chain E residue 52 VAL Chi-restraints excluded: chain E residue 65 LEU Chi-restraints excluded: chain E residue 66 MET Chi-restraints excluded: chain E residue 78 THR Chi-restraints excluded: chain E residue 97 VAL Chi-restraints excluded: chain E residue 111 ILE Chi-restraints excluded: chain E residue 126 VAL Chi-restraints excluded: chain E residue 142 VAL Chi-restraints excluded: chain E residue 256 VAL Chi-restraints excluded: chain F residue 5 LYS Chi-restraints excluded: chain F residue 85 ILE Chi-restraints excluded: chain F residue 141 ILE Chi-restraints excluded: chain F residue 146 THR Chi-restraints excluded: chain G residue 117 THR Chi-restraints excluded: chain G residue 158 SER Chi-restraints excluded: chain G residue 210 ILE Chi-restraints excluded: chain G residue 257 SER Chi-restraints excluded: chain G residue 302 CYS Chi-restraints excluded: chain G residue 664 VAL Chi-restraints excluded: chain H residue 145 PHE Chi-restraints excluded: chain I residue 19 GLU Chi-restraints excluded: chain I residue 111 ILE Chi-restraints excluded: chain I residue 149 LEU Chi-restraints excluded: chain I residue 211 ILE Chi-restraints excluded: chain I residue 258 THR Chi-restraints excluded: chain J residue 40 THR Chi-restraints excluded: chain J residue 246 GLU Chi-restraints excluded: chain J residue 258 THR Chi-restraints excluded: chain K residue 25 GLU Chi-restraints excluded: chain K residue 27 GLN Chi-restraints excluded: chain K residue 87 VAL Chi-restraints excluded: chain K residue 134 LEU Chi-restraints excluded: chain K residue 156 THR Chi-restraints excluded: chain K residue 244 VAL Chi-restraints excluded: chain K residue 257 VAL Chi-restraints excluded: chain K residue 284 TYR Chi-restraints excluded: chain K residue 290 ASP Chi-restraints excluded: chain L residue 17 LEU Chi-restraints excluded: chain L residue 46 GLN Chi-restraints excluded: chain L residue 86 TYR Chi-restraints excluded: chain L residue 120 SER Chi-restraints excluded: chain L residue 134 LEU Chi-restraints excluded: chain L residue 158 LEU Chi-restraints excluded: chain L residue 170 LEU Chi-restraints excluded: chain L residue 230 HIS Chi-restraints excluded: chain L residue 257 VAL Chi-restraints excluded: chain M residue 4 LYS Chi-restraints excluded: chain M residue 17 LEU Chi-restraints excluded: chain M residue 48 VAL Chi-restraints excluded: chain M residue 88 ASP Chi-restraints excluded: chain M residue 126 VAL Chi-restraints excluded: chain M residue 189 VAL Chi-restraints excluded: chain M residue 212 SER Chi-restraints excluded: chain M residue 224 ILE Chi-restraints excluded: chain M residue 244 VAL Chi-restraints excluded: chain N residue 65 LEU Chi-restraints excluded: chain N residue 97 VAL Chi-restraints excluded: chain N residue 152 TYR Chi-restraints excluded: chain N residue 184 ASP Chi-restraints excluded: chain N residue 224 ILE Chi-restraints excluded: chain N residue 234 LEU Chi-restraints excluded: chain N residue 256 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 256 optimal weight: 2.9990 chunk 314 optimal weight: 3.9990 chunk 302 optimal weight: 0.9980 chunk 211 optimal weight: 3.9990 chunk 151 optimal weight: 0.7980 chunk 287 optimal weight: 0.6980 chunk 24 optimal weight: 0.7980 chunk 88 optimal weight: 4.9990 chunk 178 optimal weight: 8.9990 chunk 107 optimal weight: 0.8980 chunk 312 optimal weight: 10.0000 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 121 GLN ** F 64 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 65 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 145 ASN ** G 286 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 288 GLN ** H 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 79 ASN ** K 118 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 122 GLN K 232 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4511 r_free = 0.4511 target = 0.203828 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3905 r_free = 0.3905 target = 0.151865 restraints weight = 75708.190| |-----------------------------------------------------------------------------| r_work (start): 0.3887 rms_B_bonded: 3.94 r_work: 0.3652 rms_B_bonded: 3.93 restraints_weight: 0.5000 r_work (final): 0.3652 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3664 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3664 r_free = 0.3664 target_work(ls_wunit_k1) = 0.134 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3664 r_free = 0.3664 target_work(ls_wunit_k1) = 0.134 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3664 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7482 moved from start: 0.2399 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 30045 Z= 0.132 Angle : 0.600 13.759 40721 Z= 0.308 Chirality : 0.042 0.192 4362 Planarity : 0.004 0.068 5290 Dihedral : 4.856 74.894 3976 Min Nonbonded Distance : 1.484 Molprobity Statistics. All-atom Clashscore : 9.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.99 % Favored : 95.01 % Rotamer: Outliers : 4.21 % Allowed : 22.52 % Favored : 73.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.64 % Cis-general : 0.00 % Twisted Proline : 0.64 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.88 (0.14), residues: 3592 helix: 1.25 (0.14), residues: 1421 sheet: -1.84 (0.20), residues: 683 loop : -1.77 (0.15), residues: 1488 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG K 268 TYR 0.048 0.001 TYR E 145 PHE 0.025 0.001 PHE N 150 TRP 0.017 0.001 TRP A 218 HIS 0.007 0.001 HIS D 241 Details of bonding type rmsd covalent geometry : bond 0.00303 (30045) covalent geometry : angle 0.59955 (40721) hydrogen bonds : bond 0.04307 ( 1294) hydrogen bonds : angle 4.60232 ( 3566) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7184 Ramachandran restraints generated. 3592 Oldfield, 0 Emsley, 3592 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7184 Ramachandran restraints generated. 3592 Oldfield, 0 Emsley, 3592 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 548 residues out of total 3218 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 135 poor density : 413 time to evaluate : 1.031 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: B 137 GLU cc_start: 0.8393 (tt0) cc_final: 0.7964 (tt0) REVERT: B 168 GLU cc_start: 0.8589 (OUTLIER) cc_final: 0.8287 (mt-10) REVERT: B 198 GLU cc_start: 0.8565 (OUTLIER) cc_final: 0.8355 (tm-30) REVERT: C 88 GLN cc_start: 0.8037 (OUTLIER) cc_final: 0.7158 (mp10) REVERT: C 133 MET cc_start: 0.8906 (ttp) cc_final: 0.8594 (ttt) REVERT: C 163 ARG cc_start: 0.8991 (ttt-90) cc_final: 0.8697 (tpt-90) REVERT: C 266 GLU cc_start: 0.8174 (mm-30) cc_final: 0.7781 (mm-30) REVERT: C 356 GLN cc_start: 0.8282 (tt0) cc_final: 0.7845 (tt0) REVERT: C 675 GLU cc_start: 0.8638 (OUTLIER) cc_final: 0.8075 (tt0) REVERT: D 17 LEU cc_start: 0.8588 (OUTLIER) cc_final: 0.8149 (mm) REVERT: D 33 GLU cc_start: 0.8152 (mm-30) cc_final: 0.7759 (mm-30) REVERT: D 86 TYR cc_start: 0.8778 (OUTLIER) cc_final: 0.7916 (p90) REVERT: E 24 SER cc_start: 0.5101 (OUTLIER) cc_final: 0.4815 (p) REVERT: E 41 LYS cc_start: 0.9005 (mmtm) cc_final: 0.8766 (mmtm) REVERT: E 83 MET cc_start: 0.5526 (mmt) cc_final: 0.4698 (mtt) REVERT: E 95 GLU cc_start: 0.8351 (mp0) cc_final: 0.7744 (mp0) REVERT: G 158 SER cc_start: 0.7779 (OUTLIER) cc_final: 0.7527 (p) REVERT: G 264 ASP cc_start: 0.6971 (t0) cc_final: 0.6520 (t0) REVERT: G 710 LEU cc_start: 0.6311 (OUTLIER) cc_final: 0.5896 (tp) REVERT: H 145 PHE cc_start: 0.2343 (OUTLIER) cc_final: 0.0930 (p90) REVERT: I 19 GLU cc_start: 0.8214 (OUTLIER) cc_final: 0.7867 (tm-30) REVERT: I 145 TYR cc_start: 0.7285 (m-10) cc_final: 0.6981 (m-10) REVERT: I 214 ARG cc_start: 0.8731 (OUTLIER) cc_final: 0.8503 (mtp180) REVERT: I 248 TYR cc_start: 0.8357 (p90) cc_final: 0.7638 (p90) REVERT: J 19 GLU cc_start: 0.7192 (mm-30) cc_final: 0.6857 (mt-10) REVERT: J 115 ARG cc_start: 0.8575 (OUTLIER) cc_final: 0.8148 (ttt180) REVERT: J 160 ASP cc_start: 0.8387 (m-30) cc_final: 0.8173 (m-30) REVERT: K 33 GLU cc_start: 0.8786 (pt0) cc_final: 0.8323 (pp20) REVERT: K 34 LYS cc_start: 0.8485 (mtmm) cc_final: 0.8123 (mtmt) REVERT: K 141 ASN cc_start: 0.7943 (p0) cc_final: 0.7470 (t0) REVERT: K 183 LEU cc_start: 0.7595 (OUTLIER) cc_final: 0.7331 (tt) REVERT: K 290 ASP cc_start: 0.6011 (OUTLIER) cc_final: 0.5786 (m-30) REVERT: L 12 GLN cc_start: 0.8947 (tp-100) cc_final: 0.8482 (tp-100) REVERT: L 16 GLN cc_start: 0.8426 (mt0) cc_final: 0.7729 (mt0) REVERT: M 134 LEU cc_start: 0.7309 (mt) cc_final: 0.6970 (pp) REVERT: M 145 TYR cc_start: 0.7169 (m-10) cc_final: 0.6698 (m-80) REVERT: M 212 SER cc_start: 0.6372 (OUTLIER) cc_final: 0.6118 (p) REVERT: M 224 ILE cc_start: 0.7638 (OUTLIER) cc_final: 0.7206 (mp) REVERT: N 83 MET cc_start: 0.5192 (tpt) cc_final: 0.4849 (mmm) REVERT: N 89 ARG cc_start: 0.5958 (ptp-110) cc_final: 0.5710 (ptp-170) REVERT: N 256 VAL cc_start: 0.1719 (OUTLIER) cc_final: 0.1350 (p) REVERT: N 264 ASN cc_start: 0.8527 (t0) cc_final: 0.8326 (t0) outliers start: 135 outliers final: 96 residues processed: 513 average time/residue: 0.1761 time to fit residues: 145.7285 Evaluate side-chains 495 residues out of total 3218 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 114 poor density : 381 time to evaluate : 0.807 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 124 GLN Chi-restraints excluded: chain B residue 99 VAL Chi-restraints excluded: chain B residue 106 GLU Chi-restraints excluded: chain B residue 130 LEU Chi-restraints excluded: chain B residue 168 GLU Chi-restraints excluded: chain B residue 198 GLU Chi-restraints excluded: chain C residue 68 HIS Chi-restraints excluded: chain C residue 74 VAL Chi-restraints excluded: chain C residue 82 ILE Chi-restraints excluded: chain C residue 88 GLN Chi-restraints excluded: chain C residue 89 CYS Chi-restraints excluded: chain C residue 97 VAL Chi-restraints excluded: chain C residue 181 VAL Chi-restraints excluded: chain C residue 200 LEU Chi-restraints excluded: chain C residue 224 VAL Chi-restraints excluded: chain C residue 263 LEU Chi-restraints excluded: chain C residue 271 SER Chi-restraints excluded: chain C residue 274 ASN Chi-restraints excluded: chain C residue 290 VAL Chi-restraints excluded: chain C residue 350 CYS Chi-restraints excluded: chain C residue 664 VAL Chi-restraints excluded: chain C residue 671 VAL Chi-restraints excluded: chain C residue 675 GLU Chi-restraints excluded: chain D residue 10 LEU Chi-restraints excluded: chain D residue 17 LEU Chi-restraints excluded: chain D residue 55 CYS Chi-restraints excluded: chain D residue 78 THR Chi-restraints excluded: chain D residue 86 TYR Chi-restraints excluded: chain D residue 135 ARG Chi-restraints excluded: chain D residue 202 ASP Chi-restraints excluded: chain E residue 5 VAL Chi-restraints excluded: chain E residue 24 SER Chi-restraints excluded: chain E residue 27 GLN Chi-restraints excluded: chain E residue 52 VAL Chi-restraints excluded: chain E residue 65 LEU Chi-restraints excluded: chain E residue 66 MET Chi-restraints excluded: chain E residue 78 THR Chi-restraints excluded: chain E residue 97 VAL Chi-restraints excluded: chain E residue 111 ILE Chi-restraints excluded: chain E residue 126 VAL Chi-restraints excluded: chain E residue 142 VAL Chi-restraints excluded: chain E residue 165 CYS Chi-restraints excluded: chain E residue 256 VAL Chi-restraints excluded: chain F residue 85 ILE Chi-restraints excluded: chain F residue 87 VAL Chi-restraints excluded: chain F residue 141 ILE Chi-restraints excluded: chain F residue 146 THR Chi-restraints excluded: chain G residue 117 THR Chi-restraints excluded: chain G residue 158 SER Chi-restraints excluded: chain G residue 196 SER Chi-restraints excluded: chain G residue 210 ILE Chi-restraints excluded: chain G residue 257 SER Chi-restraints excluded: chain G residue 302 CYS Chi-restraints excluded: chain G residue 317 MET Chi-restraints excluded: chain G residue 332 GLU Chi-restraints excluded: chain G residue 664 VAL Chi-restraints excluded: chain G residue 710 LEU Chi-restraints excluded: chain H residue 145 PHE Chi-restraints excluded: chain I residue 19 GLU Chi-restraints excluded: chain I residue 111 ILE Chi-restraints excluded: chain I residue 149 LEU Chi-restraints excluded: chain I residue 196 CYS Chi-restraints excluded: chain I residue 214 ARG Chi-restraints excluded: chain I residue 235 THR Chi-restraints excluded: chain I residue 258 THR Chi-restraints excluded: chain J residue 40 THR Chi-restraints excluded: chain J residue 115 ARG Chi-restraints excluded: chain J residue 245 MET Chi-restraints excluded: chain J residue 246 GLU Chi-restraints excluded: chain J residue 258 THR Chi-restraints excluded: chain K residue 25 GLU Chi-restraints excluded: chain K residue 27 GLN Chi-restraints excluded: chain K residue 48 VAL Chi-restraints excluded: chain K residue 79 ASN Chi-restraints excluded: chain K residue 87 VAL Chi-restraints excluded: chain K residue 113 ILE Chi-restraints excluded: chain K residue 134 LEU Chi-restraints excluded: chain K residue 156 THR Chi-restraints excluded: chain K residue 170 LEU Chi-restraints excluded: chain K residue 183 LEU Chi-restraints excluded: chain K residue 234 LEU Chi-restraints excluded: chain K residue 257 VAL Chi-restraints excluded: chain K residue 284 TYR Chi-restraints excluded: chain K residue 290 ASP Chi-restraints excluded: chain L residue 17 LEU Chi-restraints excluded: chain L residue 46 GLN Chi-restraints excluded: chain L residue 86 TYR Chi-restraints excluded: chain L residue 120 SER Chi-restraints excluded: chain L residue 126 VAL Chi-restraints excluded: chain L residue 134 LEU Chi-restraints excluded: chain L residue 170 LEU Chi-restraints excluded: chain L residue 230 HIS Chi-restraints excluded: chain L residue 257 VAL Chi-restraints excluded: chain L residue 277 GLU Chi-restraints excluded: chain M residue 4 LYS Chi-restraints excluded: chain M residue 17 LEU Chi-restraints excluded: chain M residue 48 VAL Chi-restraints excluded: chain M residue 88 ASP Chi-restraints excluded: chain M residue 126 VAL Chi-restraints excluded: chain M residue 189 VAL Chi-restraints excluded: chain M residue 212 SER Chi-restraints excluded: chain M residue 224 ILE Chi-restraints excluded: chain M residue 244 VAL Chi-restraints excluded: chain N residue 33 GLU Chi-restraints excluded: chain N residue 54 VAL Chi-restraints excluded: chain N residue 65 LEU Chi-restraints excluded: chain N residue 97 VAL Chi-restraints excluded: chain N residue 152 TYR Chi-restraints excluded: chain N residue 184 ASP Chi-restraints excluded: chain N residue 224 ILE Chi-restraints excluded: chain N residue 234 LEU Chi-restraints excluded: chain N residue 256 VAL Chi-restraints excluded: chain N residue 257 VAL Chi-restraints excluded: chain N residue 287 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 226 optimal weight: 2.9990 chunk 60 optimal weight: 8.9990 chunk 220 optimal weight: 1.9990 chunk 304 optimal weight: 0.8980 chunk 171 optimal weight: 5.9990 chunk 200 optimal weight: 0.9990 chunk 262 optimal weight: 3.9990 chunk 187 optimal weight: 3.9990 chunk 25 optimal weight: 0.8980 chunk 302 optimal weight: 0.8980 chunk 292 optimal weight: 0.9980 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 102 GLN ** F 64 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 65 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 286 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 79 ASN ** K 118 HIS ** 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 = 0.4505 r_free = 0.4505 target = 0.202986 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3920 r_free = 0.3920 target = 0.152841 restraints weight = 69285.112| |-----------------------------------------------------------------------------| r_work (start): 0.3905 rms_B_bonded: 3.62 r_work: 0.3664 rms_B_bonded: 3.76 restraints_weight: 0.5000 r_work (final): 0.3664 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3690 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3690 r_free = 0.3690 target_work(ls_wunit_k1) = 0.135 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3690 r_free = 0.3690 target_work(ls_wunit_k1) = 0.135 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3690 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7569 moved from start: 0.2606 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 30045 Z= 0.139 Angle : 0.606 13.428 40721 Z= 0.311 Chirality : 0.042 0.201 4362 Planarity : 0.004 0.067 5290 Dihedral : 4.913 75.248 3976 Min Nonbonded Distance : 1.425 Molprobity Statistics. All-atom Clashscore : 9.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.13 % Favored : 94.87 % Rotamer: Outliers : 4.43 % Allowed : 22.93 % Favored : 72.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.64 % Cis-general : 0.00 % Twisted Proline : 0.64 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.90 (0.14), residues: 3592 helix: 1.25 (0.14), residues: 1421 sheet: -1.94 (0.20), residues: 690 loop : -1.73 (0.15), residues: 1481 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG B 197 TYR 0.045 0.001 TYR N 145 PHE 0.014 0.001 PHE L 164 TRP 0.017 0.001 TRP A 218 HIS 0.007 0.001 HIS E 230 Details of bonding type rmsd covalent geometry : bond 0.00322 (30045) covalent geometry : angle 0.60587 (40721) hydrogen bonds : bond 0.04294 ( 1294) hydrogen bonds : angle 4.59166 ( 3566) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7184 Ramachandran restraints generated. 3592 Oldfield, 0 Emsley, 3592 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7184 Ramachandran restraints generated. 3592 Oldfield, 0 Emsley, 3592 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 544 residues out of total 3218 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 142 poor density : 402 time to evaluate : 1.231 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: A 160 GLU cc_start: 0.8402 (tm-30) cc_final: 0.8186 (tm-30) REVERT: A 175 MET cc_start: 0.8284 (mmt) cc_final: 0.7759 (mmt) REVERT: B 137 GLU cc_start: 0.8368 (tt0) cc_final: 0.7977 (tt0) REVERT: B 159 LEU cc_start: 0.8569 (OUTLIER) cc_final: 0.8302 (tp) REVERT: B 198 GLU cc_start: 0.8520 (OUTLIER) cc_final: 0.8151 (tm-30) REVERT: C 88 GLN cc_start: 0.8114 (OUTLIER) cc_final: 0.7223 (mp10) REVERT: C 133 MET cc_start: 0.8914 (ttp) cc_final: 0.8626 (ttt) REVERT: C 163 ARG cc_start: 0.8954 (ttt-90) cc_final: 0.8674 (tpt-90) REVERT: C 266 GLU cc_start: 0.8223 (mm-30) cc_final: 0.7876 (mm-30) REVERT: C 356 GLN cc_start: 0.8292 (tt0) cc_final: 0.7856 (tt0) REVERT: C 675 GLU cc_start: 0.8698 (OUTLIER) cc_final: 0.8127 (tt0) REVERT: D 17 LEU cc_start: 0.8832 (OUTLIER) cc_final: 0.8420 (mm) REVERT: D 33 GLU cc_start: 0.8207 (mm-30) cc_final: 0.7839 (mm-30) REVERT: D 86 TYR cc_start: 0.8753 (OUTLIER) cc_final: 0.7700 (p90) REVERT: E 41 LYS cc_start: 0.9025 (mmtm) cc_final: 0.8780 (mmtm) REVERT: E 83 MET cc_start: 0.5628 (mmt) cc_final: 0.5384 (mtp) REVERT: G 158 SER cc_start: 0.7948 (OUTLIER) cc_final: 0.7678 (p) REVERT: G 264 ASP cc_start: 0.7057 (t0) cc_final: 0.6643 (t0) REVERT: G 710 LEU cc_start: 0.6487 (OUTLIER) cc_final: 0.6075 (tp) REVERT: H 145 PHE cc_start: 0.2387 (OUTLIER) cc_final: 0.1015 (p90) REVERT: I 19 GLU cc_start: 0.8185 (OUTLIER) cc_final: 0.7839 (tm-30) REVERT: I 214 ARG cc_start: 0.8722 (OUTLIER) cc_final: 0.8499 (mtp180) REVERT: I 248 TYR cc_start: 0.8296 (p90) cc_final: 0.7574 (p90) REVERT: I 288 GLN cc_start: 0.8041 (OUTLIER) cc_final: 0.7764 (mt0) REVERT: J 19 GLU cc_start: 0.7218 (mm-30) cc_final: 0.6959 (mt-10) REVERT: J 115 ARG cc_start: 0.8543 (OUTLIER) cc_final: 0.8139 (ttt180) REVERT: J 132 GLU cc_start: 0.7255 (OUTLIER) cc_final: 0.6171 (tp30) REVERT: J 160 ASP cc_start: 0.8354 (m-30) cc_final: 0.8147 (m-30) REVERT: K 27 GLN cc_start: 0.7413 (OUTLIER) cc_final: 0.7014 (mt0) REVERT: K 33 GLU cc_start: 0.8745 (pt0) cc_final: 0.8297 (pp20) REVERT: K 183 LEU cc_start: 0.7714 (OUTLIER) cc_final: 0.7468 (tt) REVERT: K 238 SER cc_start: 0.4653 (OUTLIER) cc_final: 0.4169 (t) REVERT: K 290 ASP cc_start: 0.5732 (OUTLIER) cc_final: 0.5521 (m-30) REVERT: M 134 LEU cc_start: 0.7198 (mt) cc_final: 0.6891 (pp) REVERT: M 212 SER cc_start: 0.6485 (OUTLIER) cc_final: 0.6224 (p) REVERT: M 224 ILE cc_start: 0.7733 (OUTLIER) cc_final: 0.7298 (mp) REVERT: N 83 MET cc_start: 0.5485 (tpt) cc_final: 0.4604 (mmm) REVERT: N 256 VAL cc_start: 0.1858 (OUTLIER) cc_final: 0.1514 (p) outliers start: 142 outliers final: 96 residues processed: 516 average time/residue: 0.1783 time to fit residues: 148.7158 Evaluate side-chains 495 residues out of total 3218 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 117 poor density : 378 time to evaluate : 1.046 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 124 GLN Chi-restraints excluded: chain B residue 99 VAL Chi-restraints excluded: chain B residue 102 GLN Chi-restraints excluded: chain B residue 106 GLU Chi-restraints excluded: chain B residue 130 LEU Chi-restraints excluded: chain B residue 159 LEU Chi-restraints excluded: chain B residue 187 SER Chi-restraints excluded: chain B residue 198 GLU Chi-restraints excluded: chain C residue 68 HIS Chi-restraints excluded: chain C residue 74 VAL Chi-restraints excluded: chain C residue 82 ILE Chi-restraints excluded: chain C residue 88 GLN Chi-restraints excluded: chain C residue 89 CYS Chi-restraints excluded: chain C residue 97 VAL Chi-restraints excluded: chain C residue 181 VAL Chi-restraints excluded: chain C residue 200 LEU Chi-restraints excluded: chain C residue 224 VAL Chi-restraints excluded: chain C residue 232 MET Chi-restraints excluded: chain C residue 263 LEU Chi-restraints excluded: chain C residue 271 SER Chi-restraints excluded: chain C residue 274 ASN Chi-restraints excluded: chain C residue 290 VAL Chi-restraints excluded: chain C residue 350 CYS Chi-restraints excluded: chain C residue 664 VAL Chi-restraints excluded: chain C residue 671 VAL Chi-restraints excluded: chain C residue 675 GLU Chi-restraints excluded: chain D residue 10 LEU Chi-restraints excluded: chain D residue 17 LEU Chi-restraints excluded: chain D residue 55 CYS Chi-restraints excluded: chain D residue 78 THR Chi-restraints excluded: chain D residue 86 TYR Chi-restraints excluded: chain D residue 135 ARG Chi-restraints excluded: chain D residue 202 ASP Chi-restraints excluded: chain E residue 5 VAL Chi-restraints excluded: chain E residue 52 VAL Chi-restraints excluded: chain E residue 65 LEU Chi-restraints excluded: chain E residue 66 MET Chi-restraints excluded: chain E residue 78 THR Chi-restraints excluded: chain E residue 97 VAL Chi-restraints excluded: chain E residue 111 ILE Chi-restraints excluded: chain E residue 126 VAL Chi-restraints excluded: chain E residue 142 VAL Chi-restraints excluded: chain E residue 165 CYS Chi-restraints excluded: chain E residue 256 VAL Chi-restraints excluded: chain F residue 5 LYS Chi-restraints excluded: chain F residue 85 ILE Chi-restraints excluded: chain F residue 87 VAL Chi-restraints excluded: chain F residue 141 ILE Chi-restraints excluded: chain F residue 146 THR Chi-restraints excluded: chain G residue 117 THR Chi-restraints excluded: chain G residue 158 SER Chi-restraints excluded: chain G residue 196 SER Chi-restraints excluded: chain G residue 210 ILE Chi-restraints excluded: chain G residue 257 SER Chi-restraints excluded: chain G residue 302 CYS Chi-restraints excluded: chain G residue 317 MET Chi-restraints excluded: chain G residue 332 GLU Chi-restraints excluded: chain G residue 664 VAL Chi-restraints excluded: chain G residue 710 LEU Chi-restraints excluded: chain H residue 55 LEU Chi-restraints excluded: chain H residue 145 PHE Chi-restraints excluded: chain I residue 19 GLU Chi-restraints excluded: chain I residue 111 ILE Chi-restraints excluded: chain I residue 149 LEU Chi-restraints excluded: chain I residue 196 CYS Chi-restraints excluded: chain I residue 214 ARG Chi-restraints excluded: chain I residue 258 THR Chi-restraints excluded: chain I residue 288 GLN Chi-restraints excluded: chain J residue 40 THR Chi-restraints excluded: chain J residue 113 ILE Chi-restraints excluded: chain J residue 115 ARG Chi-restraints excluded: chain J residue 132 GLU Chi-restraints excluded: chain J residue 245 MET Chi-restraints excluded: chain J residue 246 GLU Chi-restraints excluded: chain J residue 258 THR Chi-restraints excluded: chain K residue 25 GLU Chi-restraints excluded: chain K residue 27 GLN Chi-restraints excluded: chain K residue 87 VAL Chi-restraints excluded: chain K residue 113 ILE Chi-restraints excluded: chain K residue 134 LEU Chi-restraints excluded: chain K residue 156 THR Chi-restraints excluded: chain K residue 170 LEU Chi-restraints excluded: chain K residue 183 LEU Chi-restraints excluded: chain K residue 238 SER Chi-restraints excluded: chain K residue 257 VAL Chi-restraints excluded: chain K residue 284 TYR Chi-restraints excluded: chain K residue 290 ASP Chi-restraints excluded: chain L residue 17 LEU Chi-restraints excluded: chain L residue 46 GLN Chi-restraints excluded: chain L residue 86 TYR Chi-restraints excluded: chain L residue 120 SER Chi-restraints excluded: chain L residue 134 LEU Chi-restraints excluded: chain L residue 170 LEU Chi-restraints excluded: chain L residue 230 HIS Chi-restraints excluded: chain L residue 257 VAL Chi-restraints excluded: chain L residue 277 GLU Chi-restraints excluded: chain M residue 4 LYS Chi-restraints excluded: chain M residue 17 LEU Chi-restraints excluded: chain M residue 48 VAL Chi-restraints excluded: chain M residue 58 VAL Chi-restraints excluded: chain M residue 88 ASP Chi-restraints excluded: chain M residue 94 VAL Chi-restraints excluded: chain M residue 126 VAL Chi-restraints excluded: chain M residue 189 VAL Chi-restraints excluded: chain M residue 212 SER Chi-restraints excluded: chain M residue 224 ILE Chi-restraints excluded: chain M residue 244 VAL Chi-restraints excluded: chain N residue 28 VAL Chi-restraints excluded: chain N residue 54 VAL Chi-restraints excluded: chain N residue 65 LEU Chi-restraints excluded: chain N residue 97 VAL Chi-restraints excluded: chain N residue 184 ASP Chi-restraints excluded: chain N residue 224 ILE Chi-restraints excluded: chain N residue 234 LEU Chi-restraints excluded: chain N residue 256 VAL Chi-restraints excluded: chain N residue 257 VAL Chi-restraints excluded: chain N residue 287 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 64 optimal weight: 0.9980 chunk 158 optimal weight: 0.7980 chunk 214 optimal weight: 0.5980 chunk 139 optimal weight: 1.9990 chunk 216 optimal weight: 0.8980 chunk 168 optimal weight: 7.9990 chunk 334 optimal weight: 2.9990 chunk 62 optimal weight: 1.9990 chunk 86 optimal weight: 0.6980 chunk 325 optimal weight: 1.9990 chunk 13 optimal weight: 9.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 288 GLN ** F 64 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 65 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 286 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 232 ASN M 167 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4508 r_free = 0.4508 target = 0.203216 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3940 r_free = 0.3940 target = 0.155274 restraints weight = 65726.319| |-----------------------------------------------------------------------------| r_work (start): 0.3922 rms_B_bonded: 3.86 r_work: 0.3682 rms_B_bonded: 3.67 restraints_weight: 0.5000 r_work (final): 0.3682 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3703 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3703 r_free = 0.3703 target_work(ls_wunit_k1) = 0.136 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3703 r_free = 0.3703 target_work(ls_wunit_k1) = 0.136 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3703 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7575 moved from start: 0.2764 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 30045 Z= 0.131 Angle : 0.611 13.793 40721 Z= 0.313 Chirality : 0.042 0.207 4362 Planarity : 0.004 0.069 5290 Dihedral : 4.895 75.647 3976 Min Nonbonded Distance : 1.412 Molprobity Statistics. All-atom Clashscore : 10.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.33 % Favored : 94.67 % Rotamer: Outliers : 4.18 % Allowed : 23.39 % Favored : 72.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.64 % Cis-general : 0.00 % Twisted Proline : 0.64 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.86 (0.14), residues: 3592 helix: 1.29 (0.14), residues: 1421 sheet: -1.89 (0.20), residues: 705 loop : -1.72 (0.15), residues: 1466 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG K 268 TYR 0.046 0.001 TYR N 145 PHE 0.014 0.001 PHE M 289 TRP 0.016 0.001 TRP A 218 HIS 0.007 0.001 HIS E 230 Details of bonding type rmsd covalent geometry : bond 0.00300 (30045) covalent geometry : angle 0.61075 (40721) hydrogen bonds : bond 0.04286 ( 1294) hydrogen bonds : angle 4.55804 ( 3566) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7184 Ramachandran restraints generated. 3592 Oldfield, 0 Emsley, 3592 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7184 Ramachandran restraints generated. 3592 Oldfield, 0 Emsley, 3592 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 540 residues out of total 3218 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 134 poor density : 406 time to evaluate : 1.115 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: A 160 GLU cc_start: 0.8408 (tm-30) cc_final: 0.8192 (tm-30) REVERT: B 137 GLU cc_start: 0.8343 (tt0) cc_final: 0.7978 (tt0) REVERT: B 159 LEU cc_start: 0.8625 (OUTLIER) cc_final: 0.8370 (tp) REVERT: B 168 GLU cc_start: 0.8635 (OUTLIER) cc_final: 0.8332 (mt-10) REVERT: B 198 GLU cc_start: 0.8491 (OUTLIER) cc_final: 0.8144 (tm-30) REVERT: C 85 VAL cc_start: 0.7073 (OUTLIER) cc_final: 0.6645 (p) REVERT: C 88 GLN cc_start: 0.8140 (OUTLIER) cc_final: 0.7263 (mp10) REVERT: C 101 ASN cc_start: 0.8114 (t0) cc_final: 0.7882 (t0) REVERT: C 133 MET cc_start: 0.8913 (ttp) cc_final: 0.8659 (ttt) REVERT: C 163 ARG cc_start: 0.8911 (ttt-90) cc_final: 0.8654 (tpt-90) REVERT: C 266 GLU cc_start: 0.8216 (mm-30) cc_final: 0.7933 (mm-30) REVERT: C 356 GLN cc_start: 0.8277 (tt0) cc_final: 0.7860 (tt0) REVERT: C 675 GLU cc_start: 0.8687 (OUTLIER) cc_final: 0.8134 (tt0) REVERT: D 17 LEU cc_start: 0.8881 (OUTLIER) cc_final: 0.8478 (mm) REVERT: D 33 GLU cc_start: 0.8215 (mm-30) cc_final: 0.7862 (mm-30) REVERT: D 86 TYR cc_start: 0.8712 (OUTLIER) cc_final: 0.7730 (p90) REVERT: E 36 LYS cc_start: 0.8149 (pttp) cc_final: 0.7723 (mmtm) REVERT: E 41 LYS cc_start: 0.9011 (mmtm) cc_final: 0.8782 (mmtm) REVERT: E 83 MET cc_start: 0.5515 (mmt) cc_final: 0.5042 (mtt) REVERT: G 158 SER cc_start: 0.8066 (OUTLIER) cc_final: 0.7790 (p) REVERT: G 264 ASP cc_start: 0.7038 (t0) cc_final: 0.6634 (t0) REVERT: G 710 LEU cc_start: 0.6550 (OUTLIER) cc_final: 0.6106 (tp) REVERT: H 112 ILE cc_start: 0.0766 (OUTLIER) cc_final: 0.0485 (mm) REVERT: H 145 PHE cc_start: 0.2484 (OUTLIER) cc_final: 0.1026 (p90) REVERT: I 19 GLU cc_start: 0.8169 (OUTLIER) cc_final: 0.7820 (tm-30) REVERT: I 130 TYR cc_start: 0.8762 (t80) cc_final: 0.8490 (t80) REVERT: I 149 LEU cc_start: 0.8804 (OUTLIER) cc_final: 0.8555 (tt) REVERT: I 205 ASP cc_start: 0.7765 (p0) cc_final: 0.7461 (p0) REVERT: I 248 TYR cc_start: 0.8233 (p90) cc_final: 0.7550 (p90) REVERT: I 288 GLN cc_start: 0.7991 (OUTLIER) cc_final: 0.7726 (mt0) REVERT: J 132 GLU cc_start: 0.7283 (OUTLIER) cc_final: 0.6410 (tp30) REVERT: J 135 ARG cc_start: 0.7353 (ttp80) cc_final: 0.6605 (ptt180) REVERT: J 160 ASP cc_start: 0.8286 (m-30) cc_final: 0.8080 (m-30) REVERT: K 27 GLN cc_start: 0.7409 (OUTLIER) cc_final: 0.7191 (mt0) REVERT: K 34 LYS cc_start: 0.8501 (mtmm) cc_final: 0.8159 (mtmm) REVERT: K 89 ARG cc_start: 0.7613 (mmm-85) cc_final: 0.7270 (mpt-90) REVERT: K 183 LEU cc_start: 0.7724 (OUTLIER) cc_final: 0.7480 (tt) REVERT: K 238 SER cc_start: 0.4762 (OUTLIER) cc_final: 0.4278 (t) REVERT: L 16 GLN cc_start: 0.8348 (mt0) cc_final: 0.8080 (mt0) REVERT: M 49 ARG cc_start: 0.6220 (mmt180) cc_final: 0.4995 (ptp-170) REVERT: M 134 LEU cc_start: 0.7137 (mt) cc_final: 0.6867 (pp) REVERT: M 212 SER cc_start: 0.6575 (OUTLIER) cc_final: 0.6312 (p) REVERT: M 224 ILE cc_start: 0.7747 (OUTLIER) cc_final: 0.7369 (mp) REVERT: M 290 ASP cc_start: 0.7886 (m-30) cc_final: 0.7664 (t0) REVERT: N 83 MET cc_start: 0.5537 (tpt) cc_final: 0.4736 (mmm) REVERT: N 256 VAL cc_start: 0.1931 (OUTLIER) cc_final: 0.1597 (p) outliers start: 134 outliers final: 98 residues processed: 509 average time/residue: 0.1781 time to fit residues: 145.9316 Evaluate side-chains 504 residues out of total 3218 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 120 poor density : 384 time to evaluate : 1.032 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 124 GLN Chi-restraints excluded: chain B residue 106 GLU Chi-restraints excluded: chain B residue 130 LEU Chi-restraints excluded: chain B residue 159 LEU Chi-restraints excluded: chain B residue 168 GLU Chi-restraints excluded: chain B residue 187 SER Chi-restraints excluded: chain B residue 198 GLU Chi-restraints excluded: chain C residue 68 HIS Chi-restraints excluded: chain C residue 74 VAL Chi-restraints excluded: chain C residue 82 ILE Chi-restraints excluded: chain C residue 85 VAL Chi-restraints excluded: chain C residue 88 GLN Chi-restraints excluded: chain C residue 89 CYS Chi-restraints excluded: chain C residue 97 VAL Chi-restraints excluded: chain C residue 181 VAL Chi-restraints excluded: chain C residue 200 LEU Chi-restraints excluded: chain C residue 214 SER Chi-restraints excluded: chain C residue 224 VAL Chi-restraints excluded: chain C residue 232 MET Chi-restraints excluded: chain C residue 263 LEU Chi-restraints excluded: chain C residue 271 SER Chi-restraints excluded: chain C residue 274 ASN Chi-restraints excluded: chain C residue 290 VAL Chi-restraints excluded: chain C residue 350 CYS Chi-restraints excluded: chain C residue 664 VAL Chi-restraints excluded: chain C residue 671 VAL Chi-restraints excluded: chain C residue 675 GLU Chi-restraints excluded: chain D residue 10 LEU Chi-restraints excluded: chain D residue 17 LEU Chi-restraints excluded: chain D residue 55 CYS Chi-restraints excluded: chain D residue 78 THR Chi-restraints excluded: chain D residue 86 TYR Chi-restraints excluded: chain D residue 135 ARG Chi-restraints excluded: chain D residue 202 ASP Chi-restraints excluded: chain E residue 5 VAL Chi-restraints excluded: chain E residue 52 VAL Chi-restraints excluded: chain E residue 65 LEU Chi-restraints excluded: chain E residue 66 MET Chi-restraints excluded: chain E residue 78 THR Chi-restraints excluded: chain E residue 97 VAL Chi-restraints excluded: chain E residue 111 ILE Chi-restraints excluded: chain E residue 113 ILE Chi-restraints excluded: chain E residue 126 VAL Chi-restraints excluded: chain E residue 142 VAL Chi-restraints excluded: chain E residue 256 VAL Chi-restraints excluded: chain E residue 279 ASP Chi-restraints excluded: chain F residue 5 LYS Chi-restraints excluded: chain F residue 85 ILE Chi-restraints excluded: chain F residue 87 VAL Chi-restraints excluded: chain F residue 141 ILE Chi-restraints excluded: chain F residue 146 THR Chi-restraints excluded: chain G residue 117 THR Chi-restraints excluded: chain G residue 158 SER Chi-restraints excluded: chain G residue 196 SER Chi-restraints excluded: chain G residue 210 ILE Chi-restraints excluded: chain G residue 257 SER Chi-restraints excluded: chain G residue 317 MET Chi-restraints excluded: chain G residue 332 GLU Chi-restraints excluded: chain G residue 664 VAL Chi-restraints excluded: chain G residue 710 LEU Chi-restraints excluded: chain H residue 55 LEU Chi-restraints excluded: chain H residue 112 ILE Chi-restraints excluded: chain H residue 145 PHE Chi-restraints excluded: chain I residue 19 GLU Chi-restraints excluded: chain I residue 111 ILE Chi-restraints excluded: chain I residue 149 LEU Chi-restraints excluded: chain I residue 196 CYS Chi-restraints excluded: chain I residue 258 THR Chi-restraints excluded: chain I residue 288 GLN Chi-restraints excluded: chain J residue 40 THR Chi-restraints excluded: chain J residue 113 ILE Chi-restraints excluded: chain J residue 132 GLU Chi-restraints excluded: chain J residue 245 MET Chi-restraints excluded: chain J residue 246 GLU Chi-restraints excluded: chain J residue 258 THR Chi-restraints excluded: chain K residue 25 GLU Chi-restraints excluded: chain K residue 27 GLN Chi-restraints excluded: chain K residue 48 VAL Chi-restraints excluded: chain K residue 87 VAL Chi-restraints excluded: chain K residue 113 ILE Chi-restraints excluded: chain K residue 134 LEU Chi-restraints excluded: chain K residue 156 THR Chi-restraints excluded: chain K residue 170 LEU Chi-restraints excluded: chain K residue 183 LEU Chi-restraints excluded: chain K residue 201 SER Chi-restraints excluded: chain K residue 219 THR Chi-restraints excluded: chain K residue 238 SER Chi-restraints excluded: chain K residue 257 VAL Chi-restraints excluded: chain K residue 284 TYR Chi-restraints excluded: chain L residue 17 LEU Chi-restraints excluded: chain L residue 86 TYR Chi-restraints excluded: chain L residue 120 SER Chi-restraints excluded: chain L residue 134 LEU Chi-restraints excluded: chain L residue 170 LEU Chi-restraints excluded: chain L residue 230 HIS Chi-restraints excluded: chain L residue 257 VAL Chi-restraints excluded: chain L residue 277 GLU Chi-restraints excluded: chain M residue 4 LYS Chi-restraints excluded: chain M residue 17 LEU Chi-restraints excluded: chain M residue 48 VAL Chi-restraints excluded: chain M residue 58 VAL Chi-restraints excluded: chain M residue 88 ASP Chi-restraints excluded: chain M residue 94 VAL Chi-restraints excluded: chain M residue 96 THR Chi-restraints excluded: chain M residue 126 VAL Chi-restraints excluded: chain M residue 189 VAL Chi-restraints excluded: chain M residue 212 SER Chi-restraints excluded: chain M residue 224 ILE Chi-restraints excluded: chain M residue 244 VAL Chi-restraints excluded: chain N residue 54 VAL Chi-restraints excluded: chain N residue 65 LEU Chi-restraints excluded: chain N residue 97 VAL Chi-restraints excluded: chain N residue 145 TYR Chi-restraints excluded: chain N residue 146 PHE Chi-restraints excluded: chain N residue 184 ASP Chi-restraints excluded: chain N residue 224 ILE Chi-restraints excluded: chain N residue 234 LEU Chi-restraints excluded: chain N residue 256 VAL Chi-restraints excluded: chain N residue 257 VAL Chi-restraints excluded: chain N residue 287 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 170 optimal weight: 4.9990 chunk 58 optimal weight: 3.9990 chunk 34 optimal weight: 2.9990 chunk 184 optimal weight: 1.9990 chunk 267 optimal weight: 4.9990 chunk 75 optimal weight: 2.9990 chunk 67 optimal weight: 0.0870 chunk 308 optimal weight: 1.9990 chunk 289 optimal weight: 0.0980 chunk 187 optimal weight: 2.9990 chunk 351 optimal weight: 0.8980 overall best weight: 1.0162 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 102 GLN C 342 HIS ** F 64 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 286 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 272 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4500 r_free = 0.4500 target = 0.202664 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3885 r_free = 0.3885 target = 0.150510 restraints weight = 67905.018| |-----------------------------------------------------------------------------| r_work (start): 0.3879 rms_B_bonded: 3.47 r_work: 0.3685 rms_B_bonded: 3.58 restraints_weight: 0.5000 r_work (final): 0.3685 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3697 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3697 r_free = 0.3697 target_work(ls_wunit_k1) = 0.136 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3697 r_free = 0.3697 target_work(ls_wunit_k1) = 0.136 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3697 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7573 moved from start: 0.2924 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 30045 Z= 0.145 Angle : 0.625 14.531 40721 Z= 0.321 Chirality : 0.043 0.216 4362 Planarity : 0.004 0.069 5290 Dihedral : 4.982 77.651 3976 Min Nonbonded Distance : 1.408 Molprobity Statistics. All-atom Clashscore : 10.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.69 % Favored : 94.31 % Rotamer: Outliers : 4.18 % Allowed : 23.71 % Favored : 72.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.64 % Cis-general : 0.00 % Twisted Proline : 0.64 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.90 (0.14), residues: 3592 helix: 1.25 (0.14), residues: 1414 sheet: -1.87 (0.20), residues: 712 loop : -1.74 (0.15), residues: 1466 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.001 ARG B 197 TYR 0.045 0.001 TYR N 145 PHE 0.021 0.001 PHE N 150 TRP 0.018 0.001 TRP A 218 HIS 0.013 0.001 HIS G 281 Details of bonding type rmsd covalent geometry : bond 0.00337 (30045) covalent geometry : angle 0.62524 (40721) hydrogen bonds : bond 0.04380 ( 1294) hydrogen bonds : angle 4.57004 ( 3566) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7184 Ramachandran restraints generated. 3592 Oldfield, 0 Emsley, 3592 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7184 Ramachandran restraints generated. 3592 Oldfield, 0 Emsley, 3592 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 536 residues out of total 3218 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 134 poor density : 402 time to evaluate : 0.935 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: A 160 GLU cc_start: 0.8418 (tm-30) cc_final: 0.8178 (tm-30) REVERT: B 137 GLU cc_start: 0.8337 (tt0) cc_final: 0.7979 (tt0) REVERT: B 159 LEU cc_start: 0.8577 (OUTLIER) cc_final: 0.8328 (tp) REVERT: B 168 GLU cc_start: 0.8636 (OUTLIER) cc_final: 0.8318 (mt-10) REVERT: C 101 ASN cc_start: 0.8097 (t0) cc_final: 0.7869 (t0) REVERT: C 133 MET cc_start: 0.8920 (ttp) cc_final: 0.8624 (ttt) REVERT: C 163 ARG cc_start: 0.8914 (ttt-90) cc_final: 0.8628 (tpt-90) REVERT: C 266 GLU cc_start: 0.8207 (mm-30) cc_final: 0.7912 (mm-30) REVERT: C 356 GLN cc_start: 0.8283 (tt0) cc_final: 0.7855 (tt0) REVERT: C 675 GLU cc_start: 0.8697 (OUTLIER) cc_final: 0.8143 (tt0) REVERT: D 17 LEU cc_start: 0.8836 (OUTLIER) cc_final: 0.8422 (mm) REVERT: D 33 GLU cc_start: 0.8211 (mm-30) cc_final: 0.7849 (mm-30) REVERT: D 86 TYR cc_start: 0.8771 (OUTLIER) cc_final: 0.7773 (p90) REVERT: E 36 LYS cc_start: 0.8177 (pttp) cc_final: 0.7804 (mmtm) REVERT: E 37 GLU cc_start: 0.7648 (tm-30) cc_final: 0.7185 (tm-30) REVERT: E 41 LYS cc_start: 0.9048 (mmtm) cc_final: 0.8669 (mmtm) REVERT: E 83 MET cc_start: 0.5828 (mmt) cc_final: 0.5550 (mtt) REVERT: E 95 GLU cc_start: 0.8127 (mp0) cc_final: 0.7924 (mp0) REVERT: G 158 SER cc_start: 0.8086 (OUTLIER) cc_final: 0.7812 (p) REVERT: G 264 ASP cc_start: 0.7037 (t0) cc_final: 0.6627 (t0) REVERT: G 710 LEU cc_start: 0.6507 (OUTLIER) cc_final: 0.6046 (tp) REVERT: H 112 ILE cc_start: 0.0790 (OUTLIER) cc_final: 0.0505 (mm) REVERT: H 145 PHE cc_start: 0.2527 (OUTLIER) cc_final: 0.1102 (p90) REVERT: I 19 GLU cc_start: 0.8225 (OUTLIER) cc_final: 0.7872 (tm-30) REVERT: I 130 TYR cc_start: 0.8790 (t80) cc_final: 0.8576 (t80) REVERT: I 149 LEU cc_start: 0.8797 (OUTLIER) cc_final: 0.8549 (tt) REVERT: I 248 TYR cc_start: 0.8224 (p90) cc_final: 0.7547 (p90) REVERT: I 288 GLN cc_start: 0.8018 (OUTLIER) cc_final: 0.7725 (mt0) REVERT: J 115 ARG cc_start: 0.8539 (OUTLIER) cc_final: 0.8123 (ttt180) REVERT: J 132 GLU cc_start: 0.7285 (OUTLIER) cc_final: 0.6272 (tp30) REVERT: J 160 ASP cc_start: 0.8312 (m-30) cc_final: 0.8102 (m-30) REVERT: K 27 GLN cc_start: 0.7423 (OUTLIER) cc_final: 0.7222 (mt0) REVERT: K 33 GLU cc_start: 0.8689 (pt0) cc_final: 0.8265 (pp20) REVERT: K 34 LYS cc_start: 0.8318 (mtmm) cc_final: 0.7859 (mtmm) REVERT: K 183 LEU cc_start: 0.7801 (OUTLIER) cc_final: 0.7536 (tt) REVERT: K 238 SER cc_start: 0.4694 (OUTLIER) cc_final: 0.4272 (t) REVERT: K 249 ASN cc_start: 0.7951 (m110) cc_final: 0.7657 (m-40) REVERT: L 12 GLN cc_start: 0.8864 (tp-100) cc_final: 0.8549 (tp40) REVERT: L 16 GLN cc_start: 0.8430 (mt0) cc_final: 0.7735 (mt0) REVERT: L 46 GLN cc_start: 0.7033 (OUTLIER) cc_final: 0.6793 (tt0) REVERT: M 48 VAL cc_start: 0.2278 (OUTLIER) cc_final: 0.1879 (t) REVERT: M 49 ARG cc_start: 0.6307 (mmt180) cc_final: 0.5008 (ptp-170) REVERT: M 224 ILE cc_start: 0.7709 (OUTLIER) cc_final: 0.7246 (mp) REVERT: N 83 MET cc_start: 0.5657 (tpt) cc_final: 0.4845 (mmm) REVERT: N 256 VAL cc_start: 0.1907 (OUTLIER) cc_final: 0.1575 (p) outliers start: 134 outliers final: 97 residues processed: 510 average time/residue: 0.1732 time to fit residues: 142.3356 Evaluate side-chains 504 residues out of total 3218 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 118 poor density : 386 time to evaluate : 1.155 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 124 GLN Chi-restraints excluded: chain B residue 99 VAL Chi-restraints excluded: chain B residue 102 GLN Chi-restraints excluded: chain B residue 106 GLU Chi-restraints excluded: chain B residue 130 LEU Chi-restraints excluded: chain B residue 159 LEU Chi-restraints excluded: chain B residue 168 GLU Chi-restraints excluded: chain B residue 187 SER Chi-restraints excluded: chain C residue 68 HIS Chi-restraints excluded: chain C residue 74 VAL Chi-restraints excluded: chain C residue 82 ILE Chi-restraints excluded: chain C residue 88 GLN Chi-restraints excluded: chain C residue 89 CYS Chi-restraints excluded: chain C residue 97 VAL Chi-restraints excluded: chain C residue 181 VAL Chi-restraints excluded: chain C residue 200 LEU Chi-restraints excluded: chain C residue 214 SER Chi-restraints excluded: chain C residue 224 VAL Chi-restraints excluded: chain C residue 232 MET Chi-restraints excluded: chain C residue 263 LEU Chi-restraints excluded: chain C residue 271 SER Chi-restraints excluded: chain C residue 274 ASN Chi-restraints excluded: chain C residue 290 VAL Chi-restraints excluded: chain C residue 350 CYS Chi-restraints excluded: chain C residue 664 VAL Chi-restraints excluded: chain C residue 671 VAL Chi-restraints excluded: chain C residue 675 GLU Chi-restraints excluded: chain D residue 10 LEU Chi-restraints excluded: chain D residue 17 LEU Chi-restraints excluded: chain D residue 55 CYS Chi-restraints excluded: chain D residue 78 THR Chi-restraints excluded: chain D residue 86 TYR Chi-restraints excluded: chain D residue 135 ARG Chi-restraints excluded: chain D residue 202 ASP Chi-restraints excluded: chain E residue 5 VAL Chi-restraints excluded: chain E residue 52 VAL Chi-restraints excluded: chain E residue 65 LEU Chi-restraints excluded: chain E residue 66 MET Chi-restraints excluded: chain E residue 78 THR Chi-restraints excluded: chain E residue 97 VAL Chi-restraints excluded: chain E residue 111 ILE Chi-restraints excluded: chain E residue 126 VAL Chi-restraints excluded: chain E residue 142 VAL Chi-restraints excluded: chain E residue 256 VAL Chi-restraints excluded: chain F residue 5 LYS Chi-restraints excluded: chain F residue 85 ILE Chi-restraints excluded: chain F residue 87 VAL Chi-restraints excluded: chain F residue 141 ILE Chi-restraints excluded: chain F residue 146 THR Chi-restraints excluded: chain G residue 117 THR Chi-restraints excluded: chain G residue 158 SER Chi-restraints excluded: chain G residue 196 SER Chi-restraints excluded: chain G residue 210 ILE Chi-restraints excluded: chain G residue 317 MET Chi-restraints excluded: chain G residue 332 GLU Chi-restraints excluded: chain G residue 710 LEU Chi-restraints excluded: chain H residue 55 LEU Chi-restraints excluded: chain H residue 112 ILE Chi-restraints excluded: chain H residue 145 PHE Chi-restraints excluded: chain I residue 19 GLU Chi-restraints excluded: chain I residue 111 ILE Chi-restraints excluded: chain I residue 149 LEU Chi-restraints excluded: chain I residue 196 CYS Chi-restraints excluded: chain I residue 258 THR Chi-restraints excluded: chain I residue 288 GLN Chi-restraints excluded: chain J residue 40 THR Chi-restraints excluded: chain J residue 113 ILE Chi-restraints excluded: chain J residue 115 ARG Chi-restraints excluded: chain J residue 132 GLU Chi-restraints excluded: chain J residue 245 MET Chi-restraints excluded: chain J residue 246 GLU Chi-restraints excluded: chain J residue 258 THR Chi-restraints excluded: chain K residue 25 GLU Chi-restraints excluded: chain K residue 27 GLN Chi-restraints excluded: chain K residue 48 VAL Chi-restraints excluded: chain K residue 87 VAL Chi-restraints excluded: chain K residue 113 ILE Chi-restraints excluded: chain K residue 134 LEU Chi-restraints excluded: chain K residue 156 THR Chi-restraints excluded: chain K residue 170 LEU Chi-restraints excluded: chain K residue 183 LEU Chi-restraints excluded: chain K residue 201 SER Chi-restraints excluded: chain K residue 219 THR Chi-restraints excluded: chain K residue 238 SER Chi-restraints excluded: chain K residue 257 VAL Chi-restraints excluded: chain K residue 284 TYR Chi-restraints excluded: chain L residue 17 LEU Chi-restraints excluded: chain L residue 46 GLN Chi-restraints excluded: chain L residue 86 TYR Chi-restraints excluded: chain L residue 120 SER Chi-restraints excluded: chain L residue 134 LEU Chi-restraints excluded: chain L residue 170 LEU Chi-restraints excluded: chain L residue 230 HIS Chi-restraints excluded: chain L residue 257 VAL Chi-restraints excluded: chain M residue 4 LYS Chi-restraints excluded: chain M residue 17 LEU Chi-restraints excluded: chain M residue 48 VAL Chi-restraints excluded: chain M residue 58 VAL Chi-restraints excluded: chain M residue 87 VAL Chi-restraints excluded: chain M residue 88 ASP Chi-restraints excluded: chain M residue 94 VAL Chi-restraints excluded: chain M residue 96 THR Chi-restraints excluded: chain M residue 126 VAL Chi-restraints excluded: chain M residue 189 VAL Chi-restraints excluded: chain M residue 224 ILE Chi-restraints excluded: chain M residue 244 VAL Chi-restraints excluded: chain N residue 28 VAL Chi-restraints excluded: chain N residue 54 VAL Chi-restraints excluded: chain N residue 65 LEU Chi-restraints excluded: chain N residue 97 VAL Chi-restraints excluded: chain N residue 145 TYR Chi-restraints excluded: chain N residue 146 PHE Chi-restraints excluded: chain N residue 184 ASP Chi-restraints excluded: chain N residue 224 ILE Chi-restraints excluded: chain N residue 234 LEU Chi-restraints excluded: chain N residue 256 VAL Chi-restraints excluded: chain N residue 257 VAL Chi-restraints excluded: chain N residue 287 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 278 optimal weight: 3.9990 chunk 137 optimal weight: 2.9990 chunk 84 optimal weight: 0.9980 chunk 301 optimal weight: 4.9990 chunk 106 optimal weight: 6.9990 chunk 87 optimal weight: 0.0010 chunk 10 optimal weight: 5.9990 chunk 180 optimal weight: 8.9990 chunk 124 optimal weight: 8.9990 chunk 189 optimal weight: 3.9990 chunk 345 optimal weight: 0.9990 overall best weight: 1.7992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 179 HIS D 252 HIS ** G 286 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 272 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 162 GLN ** M 167 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 44 ASN N 232 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4468 r_free = 0.4468 target = 0.198614 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3843 r_free = 0.3843 target = 0.147809 restraints weight = 66028.890| |-----------------------------------------------------------------------------| r_work (start): 0.3849 rms_B_bonded: 3.42 r_work: 0.3629 rms_B_bonded: 3.69 restraints_weight: 0.5000 r_work (final): 0.3629 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3634 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3634 r_free = 0.3634 target_work(ls_wunit_k1) = 0.131 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3634 r_free = 0.3634 target_work(ls_wunit_k1) = 0.131 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3634 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7693 moved from start: 0.3204 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.057 30045 Z= 0.211 Angle : 0.696 13.922 40721 Z= 0.360 Chirality : 0.046 0.197 4362 Planarity : 0.005 0.069 5290 Dihedral : 5.365 79.665 3976 Min Nonbonded Distance : 1.379 Molprobity Statistics. All-atom Clashscore : 12.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.30 % Favored : 93.70 % Rotamer: Outliers : 4.02 % Allowed : 23.89 % Favored : 72.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.64 % Cis-general : 0.00 % Twisted Proline : 0.64 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.15 (0.14), residues: 3592 helix: 0.95 (0.14), residues: 1420 sheet: -1.84 (0.20), residues: 621 loop : -1.92 (0.15), residues: 1551 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG K 268 TYR 0.052 0.002 TYR E 145 PHE 0.020 0.002 PHE L 164 TRP 0.023 0.002 TRP A 218 HIS 0.010 0.001 HIS I 241 Details of bonding type rmsd covalent geometry : bond 0.00502 (30045) covalent geometry : angle 0.69617 (40721) hydrogen bonds : bond 0.04907 ( 1294) hydrogen bonds : angle 4.80213 ( 3566) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7184 Ramachandran restraints generated. 3592 Oldfield, 0 Emsley, 3592 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7184 Ramachandran restraints generated. 3592 Oldfield, 0 Emsley, 3592 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 523 residues out of total 3218 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 129 poor density : 394 time to evaluate : 1.135 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: A 160 GLU cc_start: 0.8469 (tm-30) cc_final: 0.8219 (tm-30) REVERT: B 106 GLU cc_start: 0.6884 (OUTLIER) cc_final: 0.6552 (pt0) REVERT: B 137 GLU cc_start: 0.8347 (tt0) cc_final: 0.7973 (tt0) REVERT: B 159 LEU cc_start: 0.8695 (OUTLIER) cc_final: 0.8447 (tp) REVERT: B 168 GLU cc_start: 0.8671 (OUTLIER) cc_final: 0.8353 (mt-10) REVERT: C 266 GLU cc_start: 0.8204 (mm-30) cc_final: 0.7848 (mm-30) REVERT: C 356 GLN cc_start: 0.8336 (tt0) cc_final: 0.7902 (tt0) REVERT: D 17 LEU cc_start: 0.8951 (OUTLIER) cc_final: 0.8503 (mm) REVERT: D 33 GLU cc_start: 0.8349 (mm-30) cc_final: 0.8070 (mm-30) REVERT: D 86 TYR cc_start: 0.8878 (OUTLIER) cc_final: 0.7434 (p90) REVERT: E 36 LYS cc_start: 0.8152 (pttp) cc_final: 0.7836 (mmtm) REVERT: E 41 LYS cc_start: 0.9048 (mmtm) cc_final: 0.8782 (mmtm) REVERT: G 158 SER cc_start: 0.8193 (OUTLIER) cc_final: 0.7909 (p) REVERT: G 264 ASP cc_start: 0.7068 (t0) cc_final: 0.6674 (t0) REVERT: G 710 LEU cc_start: 0.6621 (OUTLIER) cc_final: 0.6146 (tp) REVERT: H 112 ILE cc_start: 0.0703 (OUTLIER) cc_final: 0.0414 (mm) REVERT: H 145 PHE cc_start: 0.2470 (OUTLIER) cc_final: 0.1035 (p90) REVERT: I 19 GLU cc_start: 0.8279 (OUTLIER) cc_final: 0.7891 (tm-30) REVERT: I 149 LEU cc_start: 0.8806 (OUTLIER) cc_final: 0.8583 (tt) REVERT: I 248 TYR cc_start: 0.8213 (p90) cc_final: 0.7556 (p90) REVERT: I 288 GLN cc_start: 0.8096 (OUTLIER) cc_final: 0.6921 (mp10) REVERT: J 115 ARG cc_start: 0.8553 (OUTLIER) cc_final: 0.8155 (ttt180) REVERT: J 132 GLU cc_start: 0.7322 (OUTLIER) cc_final: 0.6266 (tp30) REVERT: K 27 GLN cc_start: 0.7498 (OUTLIER) cc_final: 0.7071 (mp10) REVERT: K 183 LEU cc_start: 0.7875 (OUTLIER) cc_final: 0.7613 (tt) REVERT: K 238 SER cc_start: 0.4986 (OUTLIER) cc_final: 0.4505 (t) REVERT: L 12 GLN cc_start: 0.8829 (tp-100) cc_final: 0.8460 (tp40) REVERT: L 16 GLN cc_start: 0.8464 (mt0) cc_final: 0.7754 (mt0) REVERT: L 46 GLN cc_start: 0.7134 (OUTLIER) cc_final: 0.6865 (tt0) REVERT: M 48 VAL cc_start: 0.2687 (OUTLIER) cc_final: 0.2267 (t) REVERT: M 49 ARG cc_start: 0.6563 (mmt180) cc_final: 0.5069 (ptp-170) REVERT: M 134 LEU cc_start: 0.7063 (mt) cc_final: 0.6560 (pp) REVERT: M 224 ILE cc_start: 0.7645 (OUTLIER) cc_final: 0.7193 (pt) REVERT: N 83 MET cc_start: 0.5553 (tpt) cc_final: 0.5171 (mmm) REVERT: N 256 VAL cc_start: 0.1862 (OUTLIER) cc_final: 0.1576 (p) outliers start: 129 outliers final: 94 residues processed: 500 average time/residue: 0.1752 time to fit residues: 140.9723 Evaluate side-chains 481 residues out of total 3218 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 115 poor density : 366 time to evaluate : 1.320 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 99 VAL Chi-restraints excluded: chain B residue 106 GLU Chi-restraints excluded: chain B residue 130 LEU Chi-restraints excluded: chain B residue 159 LEU Chi-restraints excluded: chain B residue 168 GLU Chi-restraints excluded: chain B residue 187 SER Chi-restraints excluded: chain C residue 68 HIS Chi-restraints excluded: chain C residue 74 VAL Chi-restraints excluded: chain C residue 82 ILE Chi-restraints excluded: chain C residue 88 GLN Chi-restraints excluded: chain C residue 89 CYS Chi-restraints excluded: chain C residue 181 VAL Chi-restraints excluded: chain C residue 200 LEU Chi-restraints excluded: chain C residue 214 SER Chi-restraints excluded: chain C residue 232 MET Chi-restraints excluded: chain C residue 263 LEU Chi-restraints excluded: chain C residue 271 SER Chi-restraints excluded: chain C residue 274 ASN Chi-restraints excluded: chain C residue 290 VAL Chi-restraints excluded: chain C residue 350 CYS Chi-restraints excluded: chain C residue 649 LEU Chi-restraints excluded: chain C residue 664 VAL Chi-restraints excluded: chain C residue 671 VAL Chi-restraints excluded: chain D residue 10 LEU Chi-restraints excluded: chain D residue 17 LEU Chi-restraints excluded: chain D residue 55 CYS Chi-restraints excluded: chain D residue 78 THR Chi-restraints excluded: chain D residue 86 TYR Chi-restraints excluded: chain D residue 135 ARG Chi-restraints excluded: chain E residue 5 VAL Chi-restraints excluded: chain E residue 65 LEU Chi-restraints excluded: chain E residue 66 MET Chi-restraints excluded: chain E residue 78 THR Chi-restraints excluded: chain E residue 97 VAL Chi-restraints excluded: chain E residue 111 ILE Chi-restraints excluded: chain E residue 126 VAL Chi-restraints excluded: chain E residue 142 VAL Chi-restraints excluded: chain E residue 256 VAL Chi-restraints excluded: chain E residue 279 ASP Chi-restraints excluded: chain F residue 5 LYS Chi-restraints excluded: chain F residue 85 ILE Chi-restraints excluded: chain F residue 87 VAL Chi-restraints excluded: chain F residue 141 ILE Chi-restraints excluded: chain F residue 146 THR Chi-restraints excluded: chain G residue 117 THR Chi-restraints excluded: chain G residue 158 SER Chi-restraints excluded: chain G residue 196 SER Chi-restraints excluded: chain G residue 210 ILE Chi-restraints excluded: chain G residue 317 MET Chi-restraints excluded: chain G residue 332 GLU Chi-restraints excluded: chain G residue 664 VAL Chi-restraints excluded: chain G residue 710 LEU Chi-restraints excluded: chain H residue 55 LEU Chi-restraints excluded: chain H residue 112 ILE Chi-restraints excluded: chain H residue 145 PHE Chi-restraints excluded: chain I residue 19 GLU Chi-restraints excluded: chain I residue 111 ILE Chi-restraints excluded: chain I residue 149 LEU Chi-restraints excluded: chain I residue 159 VAL Chi-restraints excluded: chain I residue 196 CYS Chi-restraints excluded: chain I residue 235 THR Chi-restraints excluded: chain I residue 258 THR Chi-restraints excluded: chain I residue 288 GLN Chi-restraints excluded: chain J residue 40 THR Chi-restraints excluded: chain J residue 113 ILE Chi-restraints excluded: chain J residue 115 ARG Chi-restraints excluded: chain J residue 132 GLU Chi-restraints excluded: chain J residue 246 GLU Chi-restraints excluded: chain J residue 258 THR Chi-restraints excluded: chain K residue 25 GLU Chi-restraints excluded: chain K residue 27 GLN Chi-restraints excluded: chain K residue 33 GLU Chi-restraints excluded: chain K residue 48 VAL Chi-restraints excluded: chain K residue 87 VAL Chi-restraints excluded: chain K residue 113 ILE Chi-restraints excluded: chain K residue 117 ASN Chi-restraints excluded: chain K residue 134 LEU Chi-restraints excluded: chain K residue 156 THR Chi-restraints excluded: chain K residue 170 LEU Chi-restraints excluded: chain K residue 183 LEU Chi-restraints excluded: chain K residue 201 SER Chi-restraints excluded: chain K residue 219 THR Chi-restraints excluded: chain K residue 238 SER Chi-restraints excluded: chain K residue 257 VAL Chi-restraints excluded: chain L residue 17 LEU Chi-restraints excluded: chain L residue 46 GLN Chi-restraints excluded: chain L residue 120 SER Chi-restraints excluded: chain L residue 126 VAL Chi-restraints excluded: chain L residue 134 LEU Chi-restraints excluded: chain L residue 158 LEU Chi-restraints excluded: chain L residue 230 HIS Chi-restraints excluded: chain L residue 257 VAL Chi-restraints excluded: chain M residue 17 LEU Chi-restraints excluded: chain M residue 48 VAL Chi-restraints excluded: chain M residue 58 VAL Chi-restraints excluded: chain M residue 88 ASP Chi-restraints excluded: chain M residue 94 VAL Chi-restraints excluded: chain M residue 96 THR Chi-restraints excluded: chain M residue 126 VAL Chi-restraints excluded: chain M residue 189 VAL Chi-restraints excluded: chain M residue 224 ILE Chi-restraints excluded: chain M residue 244 VAL Chi-restraints excluded: chain M residue 271 ASN Chi-restraints excluded: chain N residue 28 VAL Chi-restraints excluded: chain N residue 44 ASN Chi-restraints excluded: chain N residue 54 VAL Chi-restraints excluded: chain N residue 65 LEU Chi-restraints excluded: chain N residue 97 VAL Chi-restraints excluded: chain N residue 111 ILE Chi-restraints excluded: chain N residue 145 TYR Chi-restraints excluded: chain N residue 184 ASP Chi-restraints excluded: chain N residue 224 ILE Chi-restraints excluded: chain N residue 256 VAL Chi-restraints excluded: chain N residue 257 VAL Chi-restraints excluded: chain N residue 287 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 84 optimal weight: 0.9990 chunk 129 optimal weight: 0.9980 chunk 134 optimal weight: 7.9990 chunk 292 optimal weight: 0.8980 chunk 73 optimal weight: 0.6980 chunk 222 optimal weight: 0.9990 chunk 21 optimal weight: 0.9980 chunk 331 optimal weight: 0.9980 chunk 302 optimal weight: 0.9990 chunk 329 optimal weight: 0.7980 chunk 216 optimal weight: 0.7980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 162 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 125 GLN ** F 64 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 286 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 122 GLN ** K 249 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 272 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 167 HIS ** 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 = 0.4468 r_free = 0.4468 target = 0.198476 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3885 r_free = 0.3885 target = 0.147489 restraints weight = 79533.899| |-----------------------------------------------------------------------------| r_work (start): 0.3850 rms_B_bonded: 4.00 r_work: 0.3655 rms_B_bonded: 3.45 restraints_weight: 0.5000 r_work (final): 0.3655 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3661 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3661 r_free = 0.3661 target_work(ls_wunit_k1) = 0.133 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3661 r_free = 0.3661 target_work(ls_wunit_k1) = 0.133 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3661 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7656 moved from start: 0.3242 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.385 30045 Z= 0.217 Angle : 0.803 59.197 40721 Z= 0.437 Chirality : 0.047 0.991 4362 Planarity : 0.005 0.069 5290 Dihedral : 5.359 79.565 3976 Min Nonbonded Distance : 1.378 Molprobity Statistics. All-atom Clashscore : 14.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.27 % Favored : 93.73 % Rotamer: Outliers : 3.81 % Allowed : 24.49 % Favored : 71.71 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 0.64 % Cis-general : 0.00 % Twisted Proline : 0.64 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.17 (0.14), residues: 3592 helix: 0.93 (0.14), residues: 1420 sheet: -1.86 (0.20), residues: 621 loop : -1.93 (0.15), residues: 1551 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.033 0.001 ARG E 115 TYR 0.053 0.002 TYR E 145 PHE 0.073 0.002 PHE M 6 TRP 0.022 0.001 TRP A 218 HIS 0.023 0.001 HIS E 167 Details of bonding type rmsd covalent geometry : bond 0.00544 (30045) covalent geometry : angle 0.80258 (40721) hydrogen bonds : bond 0.04837 ( 1294) hydrogen bonds : angle 4.80752 ( 3566) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7184 Ramachandran restraints generated. 3592 Oldfield, 0 Emsley, 3592 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7184 Ramachandran restraints generated. 3592 Oldfield, 0 Emsley, 3592 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 489 residues out of total 3218 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 122 poor density : 367 time to evaluate : 1.103 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: A 160 GLU cc_start: 0.8457 (tm-30) cc_final: 0.8195 (tm-30) REVERT: B 106 GLU cc_start: 0.6866 (OUTLIER) cc_final: 0.6514 (pt0) REVERT: B 137 GLU cc_start: 0.8297 (tt0) cc_final: 0.7914 (tt0) REVERT: B 159 LEU cc_start: 0.8647 (OUTLIER) cc_final: 0.8400 (tp) REVERT: B 168 GLU cc_start: 0.8646 (OUTLIER) cc_final: 0.8322 (mt-10) REVERT: C 266 GLU cc_start: 0.8177 (mm-30) cc_final: 0.7819 (mm-30) REVERT: C 356 GLN cc_start: 0.8330 (tt0) cc_final: 0.7885 (tt0) REVERT: C 675 GLU cc_start: 0.8716 (OUTLIER) cc_final: 0.7907 (tt0) REVERT: D 17 LEU cc_start: 0.8896 (OUTLIER) cc_final: 0.8445 (mm) REVERT: D 33 GLU cc_start: 0.8313 (mm-30) cc_final: 0.8038 (mm-30) REVERT: D 86 TYR cc_start: 0.8881 (OUTLIER) cc_final: 0.7428 (p90) REVERT: E 36 LYS cc_start: 0.8171 (pttp) cc_final: 0.7851 (mmtm) REVERT: E 41 LYS cc_start: 0.9073 (mmtm) cc_final: 0.8797 (mmtm) REVERT: G 158 SER cc_start: 0.8164 (OUTLIER) cc_final: 0.7881 (p) REVERT: G 264 ASP cc_start: 0.7037 (t0) cc_final: 0.6638 (t0) REVERT: G 710 LEU cc_start: 0.6597 (OUTLIER) cc_final: 0.6127 (tp) REVERT: H 112 ILE cc_start: 0.0700 (OUTLIER) cc_final: 0.0411 (mm) REVERT: H 145 PHE cc_start: 0.2450 (OUTLIER) cc_final: 0.1015 (p90) REVERT: I 19 GLU cc_start: 0.8265 (OUTLIER) cc_final: 0.7884 (tm-30) REVERT: I 149 LEU cc_start: 0.8812 (OUTLIER) cc_final: 0.8586 (tt) REVERT: I 248 TYR cc_start: 0.8208 (p90) cc_final: 0.7539 (p90) REVERT: I 288 GLN cc_start: 0.8099 (OUTLIER) cc_final: 0.6911 (mp10) REVERT: J 115 ARG cc_start: 0.8541 (OUTLIER) cc_final: 0.8146 (ttt180) REVERT: J 132 GLU cc_start: 0.7234 (OUTLIER) cc_final: 0.6163 (tp30) REVERT: K 6 PHE cc_start: 0.3328 (OUTLIER) cc_final: 0.2581 (p90) REVERT: K 27 GLN cc_start: 0.7477 (OUTLIER) cc_final: 0.7055 (mp10) REVERT: K 183 LEU cc_start: 0.7861 (OUTLIER) cc_final: 0.7604 (tt) REVERT: K 238 SER cc_start: 0.4936 (OUTLIER) cc_final: 0.4420 (t) REVERT: L 12 GLN cc_start: 0.8814 (tp-100) cc_final: 0.8351 (tp-100) REVERT: L 16 GLN cc_start: 0.8455 (mt0) cc_final: 0.7771 (mt0) REVERT: L 46 GLN cc_start: 0.7081 (OUTLIER) cc_final: 0.6823 (tt0) REVERT: M 48 VAL cc_start: 0.2675 (OUTLIER) cc_final: 0.2245 (t) REVERT: M 49 ARG cc_start: 0.6599 (mmt180) cc_final: 0.5099 (ptp-170) REVERT: M 134 LEU cc_start: 0.7066 (mt) cc_final: 0.6575 (pp) REVERT: M 224 ILE cc_start: 0.7638 (OUTLIER) cc_final: 0.7185 (pt) REVERT: N 83 MET cc_start: 0.5532 (tpt) cc_final: 0.5161 (mmm) REVERT: N 256 VAL cc_start: 0.1872 (OUTLIER) cc_final: 0.1579 (p) outliers start: 122 outliers final: 97 residues processed: 471 average time/residue: 0.1659 time to fit residues: 127.1189 Evaluate side-chains 484 residues out of total 3218 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 120 poor density : 364 time to evaluate : 1.137 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 106 GLU Chi-restraints excluded: chain B residue 130 LEU Chi-restraints excluded: chain B residue 159 LEU Chi-restraints excluded: chain B residue 168 GLU Chi-restraints excluded: chain B residue 187 SER Chi-restraints excluded: chain C residue 68 HIS Chi-restraints excluded: chain C residue 74 VAL Chi-restraints excluded: chain C residue 82 ILE Chi-restraints excluded: chain C residue 88 GLN Chi-restraints excluded: chain C residue 89 CYS Chi-restraints excluded: chain C residue 181 VAL Chi-restraints excluded: chain C residue 200 LEU Chi-restraints excluded: chain C residue 214 SER Chi-restraints excluded: chain C residue 232 MET Chi-restraints excluded: chain C residue 263 LEU Chi-restraints excluded: chain C residue 271 SER Chi-restraints excluded: chain C residue 274 ASN Chi-restraints excluded: chain C residue 290 VAL Chi-restraints excluded: chain C residue 350 CYS Chi-restraints excluded: chain C residue 649 LEU Chi-restraints excluded: chain C residue 664 VAL Chi-restraints excluded: chain C residue 671 VAL Chi-restraints excluded: chain C residue 675 GLU Chi-restraints excluded: chain D residue 10 LEU Chi-restraints excluded: chain D residue 17 LEU Chi-restraints excluded: chain D residue 55 CYS Chi-restraints excluded: chain D residue 78 THR Chi-restraints excluded: chain D residue 86 TYR Chi-restraints excluded: chain D residue 135 ARG Chi-restraints excluded: chain E residue 5 VAL Chi-restraints excluded: chain E residue 65 LEU Chi-restraints excluded: chain E residue 66 MET Chi-restraints excluded: chain E residue 78 THR Chi-restraints excluded: chain E residue 97 VAL Chi-restraints excluded: chain E residue 111 ILE Chi-restraints excluded: chain E residue 125 GLN Chi-restraints excluded: chain E residue 126 VAL Chi-restraints excluded: chain E residue 141 ASN Chi-restraints excluded: chain E residue 142 VAL Chi-restraints excluded: chain E residue 256 VAL Chi-restraints excluded: chain E residue 279 ASP Chi-restraints excluded: chain F residue 5 LYS Chi-restraints excluded: chain F residue 85 ILE Chi-restraints excluded: chain F residue 87 VAL Chi-restraints excluded: chain F residue 141 ILE Chi-restraints excluded: chain F residue 146 THR Chi-restraints excluded: chain G residue 117 THR Chi-restraints excluded: chain G residue 158 SER Chi-restraints excluded: chain G residue 196 SER Chi-restraints excluded: chain G residue 210 ILE Chi-restraints excluded: chain G residue 302 CYS Chi-restraints excluded: chain G residue 317 MET Chi-restraints excluded: chain G residue 332 GLU Chi-restraints excluded: chain G residue 664 VAL Chi-restraints excluded: chain G residue 710 LEU Chi-restraints excluded: chain H residue 55 LEU Chi-restraints excluded: chain H residue 112 ILE Chi-restraints excluded: chain H residue 145 PHE Chi-restraints excluded: chain I residue 19 GLU Chi-restraints excluded: chain I residue 111 ILE Chi-restraints excluded: chain I residue 149 LEU Chi-restraints excluded: chain I residue 159 VAL Chi-restraints excluded: chain I residue 196 CYS Chi-restraints excluded: chain I residue 235 THR Chi-restraints excluded: chain I residue 258 THR Chi-restraints excluded: chain I residue 288 GLN Chi-restraints excluded: chain J residue 10 LEU Chi-restraints excluded: chain J residue 40 THR Chi-restraints excluded: chain J residue 113 ILE Chi-restraints excluded: chain J residue 115 ARG Chi-restraints excluded: chain J residue 132 GLU Chi-restraints excluded: chain J residue 246 GLU Chi-restraints excluded: chain J residue 258 THR Chi-restraints excluded: chain K residue 6 PHE Chi-restraints excluded: chain K residue 25 GLU Chi-restraints excluded: chain K residue 27 GLN Chi-restraints excluded: chain K residue 33 GLU Chi-restraints excluded: chain K residue 48 VAL Chi-restraints excluded: chain K residue 87 VAL Chi-restraints excluded: chain K residue 113 ILE Chi-restraints excluded: chain K residue 117 ASN Chi-restraints excluded: chain K residue 134 LEU Chi-restraints excluded: chain K residue 156 THR Chi-restraints excluded: chain K residue 170 LEU Chi-restraints excluded: chain K residue 183 LEU Chi-restraints excluded: chain K residue 201 SER Chi-restraints excluded: chain K residue 219 THR Chi-restraints excluded: chain K residue 238 SER Chi-restraints excluded: chain K residue 257 VAL Chi-restraints excluded: chain L residue 17 LEU Chi-restraints excluded: chain L residue 46 GLN Chi-restraints excluded: chain L residue 120 SER Chi-restraints excluded: chain L residue 134 LEU Chi-restraints excluded: chain L residue 158 LEU Chi-restraints excluded: chain L residue 170 LEU Chi-restraints excluded: chain L residue 230 HIS Chi-restraints excluded: chain L residue 257 VAL Chi-restraints excluded: chain M residue 17 LEU Chi-restraints excluded: chain M residue 48 VAL Chi-restraints excluded: chain M residue 58 VAL Chi-restraints excluded: chain M residue 88 ASP Chi-restraints excluded: chain M residue 94 VAL Chi-restraints excluded: chain M residue 96 THR Chi-restraints excluded: chain M residue 126 VAL Chi-restraints excluded: chain M residue 189 VAL Chi-restraints excluded: chain M residue 224 ILE Chi-restraints excluded: chain M residue 244 VAL Chi-restraints excluded: chain M residue 271 ASN Chi-restraints excluded: chain N residue 28 VAL Chi-restraints excluded: chain N residue 54 VAL Chi-restraints excluded: chain N residue 65 LEU Chi-restraints excluded: chain N residue 97 VAL Chi-restraints excluded: chain N residue 111 ILE Chi-restraints excluded: chain N residue 145 TYR Chi-restraints excluded: chain N residue 184 ASP Chi-restraints excluded: chain N residue 224 ILE Chi-restraints excluded: chain N residue 234 LEU Chi-restraints excluded: chain N residue 256 VAL Chi-restraints excluded: chain N residue 257 VAL Chi-restraints excluded: chain N residue 287 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 57 optimal weight: 1.9990 chunk 87 optimal weight: 0.9990 chunk 127 optimal weight: 6.9990 chunk 49 optimal weight: 1.9990 chunk 161 optimal weight: 0.9980 chunk 2 optimal weight: 1.9990 chunk 241 optimal weight: 0.0670 chunk 80 optimal weight: 3.9990 chunk 215 optimal weight: 0.9980 chunk 336 optimal weight: 2.9990 chunk 167 optimal weight: 6.9990 overall best weight: 1.0122 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 162 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 125 GLN ** F 64 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 286 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 249 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 272 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 167 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4463 r_free = 0.4463 target = 0.197996 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3870 r_free = 0.3870 target = 0.149488 restraints weight = 68104.146| |-----------------------------------------------------------------------------| r_work (start): 0.3876 rms_B_bonded: 3.92 r_work: 0.3623 rms_B_bonded: 3.85 restraints_weight: 0.5000 r_work (final): 0.3623 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3633 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3633 r_free = 0.3633 target_work(ls_wunit_k1) = 0.131 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3633 r_free = 0.3633 target_work(ls_wunit_k1) = 0.131 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3633 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7691 moved from start: 0.3244 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.401 30045 Z= 0.238 Angle : 0.852 59.199 40721 Z= 0.481 Chirality : 0.048 0.832 4362 Planarity : 0.005 0.127 5290 Dihedral : 5.356 79.545 3976 Min Nonbonded Distance : 1.377 Molprobity Statistics. All-atom Clashscore : 14.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.25 % Favored : 93.75 % Rotamer: Outliers : 3.81 % Allowed : 24.30 % Favored : 71.90 % Cbeta Deviations : 0.06 % Peptide Plane: Cis-proline : 0.64 % Cis-general : 0.00 % Twisted Proline : 0.64 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.17 (0.14), residues: 3592 helix: 0.93 (0.14), residues: 1420 sheet: -1.86 (0.20), residues: 621 loop : -1.93 (0.15), residues: 1551 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.024 0.001 ARG E 115 TYR 0.050 0.002 TYR E 145 PHE 0.049 0.002 PHE M 6 TRP 0.045 0.001 TRP E 13 HIS 0.018 0.001 HIS E 167 Details of bonding type rmsd covalent geometry : bond 0.00581 (30045) covalent geometry : angle 0.85229 (40721) hydrogen bonds : bond 0.04845 ( 1294) hydrogen bonds : angle 4.80907 ( 3566) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9466.72 seconds wall clock time: 162 minutes 15.58 seconds (9735.58 seconds total)