Starting phenix.real_space_refine on Mon Jul 22 16:56:44 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8qyj_18755/07_2024/8qyj_18755.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8qyj_18755/07_2024/8qyj_18755.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.73 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8qyj_18755/07_2024/8qyj_18755.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8qyj_18755/07_2024/8qyj_18755.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8qyj_18755/07_2024/8qyj_18755.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8qyj_18755/07_2024/8qyj_18755.cif" } resolution = 2.73 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.008 sd= 0.129 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 114 5.16 5 C 12336 2.51 5 N 3306 2.21 5 O 3646 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 120": "OE1" <-> "OE2" Residue "A PHE 173": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 130": "OE1" <-> "OE2" Residue "G GLU 174": "OE1" <-> "OE2" Residue "G GLU 180": "OE1" <-> "OE2" Residue "H GLU 82": "OE1" <-> "OE2" Residue "J GLU 65": "OE1" <-> "OE2" Residue "J GLU 76": "OE1" <-> "OE2" Residue "L GLU 107": "OE1" <-> "OE2" Residue "M GLU 114": "OE1" <-> "OE2" Residue "M GLU 121": "OE1" <-> "OE2" Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/chem_data/mon_lib" Total number of atoms: 19402 Number of models: 1 Model: "" Number of chains: 13 Chain: "A" Number of atoms: 1766 Number of conformers: 1 Conformer: "" Number of residues, atoms: 228, 1766 Classifications: {'peptide': 228} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 10, 'TRANS': 217} Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 23 Unresolved non-hydrogen dihedrals: 16 Planarities with less than four sites: {'TYR:plan': 1, 'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 16 Chain: "B" Number of atoms: 1841 Number of conformers: 1 Conformer: "" Number of residues, atoms: 236, 1841 Classifications: {'peptide': 236} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 5, 'TRANS': 230} Chain breaks: 1 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'GLN:plan1': 2} Unresolved non-hydrogen planarities: 8 Chain: "C" Number of atoms: 1847 Number of conformers: 1 Conformer: "" Number of residues, atoms: 236, 1847 Classifications: {'peptide': 236} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 6, 'TRANS': 229} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 13 Unresolved non-hydrogen dihedrals: 11 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "D" Number of atoms: 1848 Number of conformers: 1 Conformer: "" Number of residues, atoms: 242, 1848 Unusual residues: {'ACE': 1} Classifications: {'peptide': 241, 'undetermined': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'ACE_C-N': 1, 'PTRANS': 8, 'TRANS': 232} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "E" Number of atoms: 1886 Number of conformers: 1 Conformer: "" Number of residues, atoms: 240, 1886 Unusual residues: {'ACE': 1} Classifications: {'peptide': 239, 'undetermined': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'ACE_C-N': 1, 'PTRANS': 9, 'TRANS': 229} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "F" Number of atoms: 1872 Number of conformers: 1 Conformer: "" Number of residues, atoms: 240, 1872 Classifications: {'peptide': 240} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 5, 'TRANS': 234} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "G" Number of atoms: 1787 Number of conformers: 1 Conformer: "" Number of residues, atoms: 235, 1787 Classifications: {'peptide': 235} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PTRANS': 8, 'TRANS': 226} Chain breaks: 1 Unresolved non-hydrogen bonds: 44 Unresolved non-hydrogen angles: 51 Unresolved non-hydrogen dihedrals: 37 Planarities with less than four sites: {'GLU:plan': 6, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 27 Chain: "H" Number of atoms: 408 Number of conformers: 1 Conformer: "" Number of residues, atoms: 52, 408 Classifications: {'peptide': 52} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 49} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Chain: "I" Number of atoms: 1933 Number of conformers: 1 Conformer: "" Number of residues, atoms: 243, 1933 Classifications: {'peptide': 243} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 231} Chain breaks: 1 Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 19 Unresolved non-hydrogen dihedrals: 15 Planarities with less than four sites: {'GLU:plan': 2} Unresolved non-hydrogen planarities: 8 Chain: "J" Number of atoms: 1909 Number of conformers: 1 Conformer: "" Number of residues, atoms: 248, 1909 Unusual residues: {'ACE': 1} Classifications: {'peptide': 247, 'undetermined': 1} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'ACE_C-N': 1, 'PTRANS': 15, 'TRANS': 231} Chain breaks: 2 Unresolved non-hydrogen bonds: 32 Unresolved non-hydrogen angles: 36 Unresolved non-hydrogen dihedrals: 28 Planarities with less than four sites: {'GLU:plan': 2, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 18 Chain: "K" Number of atoms: 512 Number of conformers: 1 Conformer: "" Number of residues, atoms: 70, 512 Classifications: {'peptide': 70} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 3, 'TRANS': 66} Chain breaks: 3 Unresolved non-hydrogen bonds: 25 Unresolved non-hydrogen angles: 32 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'TYR:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 10 Chain: "L" Number of atoms: 885 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 885 Classifications: {'peptide': 118} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 113} Chain: "M" Number of atoms: 908 Number of conformers: 1 Conformer: "" Number of residues, atoms: 113, 908 Classifications: {'peptide': 113} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 109} Time building chain proxies: 10.70, per 1000 atoms: 0.55 Number of scatterers: 19402 At special positions: 0 Unit cell: (123.424, 141.299, 133.638, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 114 16.00 O 3646 8.00 N 3306 7.00 C 12336 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 6.93 Conformation dependent library (CDL) restraints added in 3.5 seconds 4912 Ramachandran restraints generated. 2456 Oldfield, 0 Emsley, 2456 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4682 Finding SS restraints... Secondary structure from input PDB file: 84 helices and 22 sheets defined 40.3% alpha, 21.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.59 Creating SS restraints... Processing helix chain 'A' and resid 19 through 31 removed outlier: 3.644A pdb=" N GLY A 31 " --> pdb=" O ALA A 27 " (cutoff:3.500A) Processing helix chain 'A' and resid 79 through 102 removed outlier: 3.681A pdb=" N HIS A 88 " --> pdb=" O ARG A 84 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N ARG A 89 " --> pdb=" O VAL A 85 " (cutoff:3.500A) Processing helix chain 'A' and resid 106 through 121 removed outlier: 3.930A pdb=" N TYR A 121 " --> pdb=" O VAL A 117 " (cutoff:3.500A) Processing helix chain 'A' and resid 166 through 177 Processing helix chain 'A' and resid 183 through 197 Processing helix chain 'A' and resid 222 through 233 removed outlier: 3.536A pdb=" N ALA A 232 " --> pdb=" O ASP A 228 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N ILE A 233 " --> pdb=" O TYR A 229 " (cutoff:3.500A) Processing helix chain 'B' and resid 18 through 29 Processing helix chain 'B' and resid 79 through 102 Processing helix chain 'B' and resid 106 through 121 removed outlier: 3.601A pdb=" N ILE B 117 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N TYR B 121 " --> pdb=" O ILE B 117 " (cutoff:3.500A) Processing helix chain 'B' and resid 167 through 179 removed outlier: 3.610A pdb=" N ALA B 171 " --> pdb=" O ASN B 167 " (cutoff:3.500A) Processing helix chain 'B' and resid 185 through 201 Processing helix chain 'B' and resid 229 through 248 Processing helix chain 'C' and resid 16 through 27 Processing helix chain 'C' and resid 55 through 60 removed outlier: 3.599A pdb=" N THR C 58 " --> pdb=" O ASP C 55 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N VAL C 59 " --> pdb=" O GLU C 56 " (cutoff:3.500A) removed outlier: 4.094A pdb=" N ARG C 60 " --> pdb=" O ARG C 57 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 55 through 60' Processing helix chain 'C' and resid 76 through 99 removed outlier: 3.624A pdb=" N ALA C 80 " --> pdb=" O LEU C 76 " (cutoff:3.500A) Processing helix chain 'C' and resid 103 through 117 Processing helix chain 'C' and resid 118 through 120 No H-bonds generated for 'chain 'C' and resid 118 through 120' Processing helix chain 'C' and resid 164 through 176 Processing helix chain 'C' and resid 183 through 196 Processing helix chain 'C' and resid 201 through 204 removed outlier: 4.391A pdb=" N LYS C 204 " --> pdb=" O SER C 201 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 201 through 204' Processing helix chain 'C' and resid 221 through 241 Processing helix chain 'D' and resid 21 through 30 Processing helix chain 'D' and resid 31 through 34 Processing helix chain 'D' and resid 60 through 64 Processing helix chain 'D' and resid 84 through 104 removed outlier: 4.497A pdb=" N LEU D 88 " --> pdb=" O ASP D 84 " (cutoff:3.500A) Processing helix chain 'D' and resid 108 through 121 removed outlier: 3.836A pdb=" N LEU D 119 " --> pdb=" O ALA D 115 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N LEU D 121 " --> pdb=" O SER D 117 " (cutoff:3.500A) Processing helix chain 'D' and resid 173 through 183 removed outlier: 3.934A pdb=" N GLU D 183 " --> pdb=" O SER D 179 " (cutoff:3.500A) Processing helix chain 'D' and resid 190 through 206 Processing helix chain 'D' and resid 230 through 239 Processing helix chain 'E' and resid 3 through 7 removed outlier: 4.074A pdb=" N ASP E 7 " --> pdb=" O ASN E 4 " (cutoff:3.500A) Processing helix chain 'E' and resid 19 through 27 removed outlier: 3.907A pdb=" N GLU E 23 " --> pdb=" O ILE E 19 " (cutoff:3.500A) Processing helix chain 'E' and resid 28 through 32 Processing helix chain 'E' and resid 78 through 100 Processing helix chain 'E' and resid 104 through 118 removed outlier: 4.008A pdb=" N ILE E 118 " --> pdb=" O SER E 114 " (cutoff:3.500A) Processing helix chain 'E' and resid 119 through 121 No H-bonds generated for 'chain 'E' and resid 119 through 121' Processing helix chain 'E' and resid 165 through 175 Processing helix chain 'E' and resid 176 through 179 removed outlier: 3.822A pdb=" N PHE E 179 " --> pdb=" O MET E 176 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 176 through 179' Processing helix chain 'E' and resid 183 through 197 removed outlier: 3.661A pdb=" N GLU E 197 " --> pdb=" O ARG E 193 " (cutoff:3.500A) Processing helix chain 'E' and resid 225 through 228 Processing helix chain 'E' and resid 229 through 234 Processing helix chain 'F' and resid 21 through 30 removed outlier: 3.602A pdb=" N GLU F 25 " --> pdb=" O VAL F 21 " (cutoff:3.500A) Processing helix chain 'F' and resid 81 through 104 Processing helix chain 'F' and resid 108 through 122 Processing helix chain 'F' and resid 169 through 178 Processing helix chain 'F' and resid 179 through 180 No H-bonds generated for 'chain 'F' and resid 179 through 180' Processing helix chain 'F' and resid 181 through 185 removed outlier: 3.530A pdb=" N MET F 185 " --> pdb=" O MET F 182 " (cutoff:3.500A) Processing helix chain 'F' and resid 186 through 201 removed outlier: 4.358A pdb=" N LYS F 192 " --> pdb=" O ARG F 188 " (cutoff:3.500A) Processing helix chain 'F' and resid 220 through 222 No H-bonds generated for 'chain 'F' and resid 220 through 222' Processing helix chain 'F' and resid 229 through 244 Processing helix chain 'G' and resid 22 through 31 removed outlier: 3.553A pdb=" N GLU G 26 " --> pdb=" O LEU G 22 " (cutoff:3.500A) Processing helix chain 'G' and resid 32 through 35 removed outlier: 3.558A pdb=" N GLY G 35 " --> pdb=" O ILE G 32 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 32 through 35' Processing helix chain 'G' and resid 62 through 66 Processing helix chain 'G' and resid 83 through 106 Processing helix chain 'G' and resid 110 through 125 removed outlier: 3.720A pdb=" N VAL G 124 " --> pdb=" O ASP G 120 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N TYR G 125 " --> pdb=" O ILE G 121 " (cutoff:3.500A) Processing helix chain 'G' and resid 171 through 186 removed outlier: 3.794A pdb=" N LYS G 181 " --> pdb=" O SER G 177 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N LYS G 182 " --> pdb=" O PHE G 178 " (cutoff:3.500A) Processing helix chain 'G' and resid 190 through 207 Processing helix chain 'G' and resid 231 through 243 Processing helix chain 'H' and resid 63 through 71 Processing helix chain 'H' and resid 73 through 87 removed outlier: 3.726A pdb=" N LEU H 77 " --> pdb=" O LEU H 73 " (cutoff:3.500A) Processing helix chain 'H' and resid 99 through 107 Processing helix chain 'I' and resid 35 through 45 Processing helix chain 'I' and resid 61 through 66 removed outlier: 3.715A pdb=" N TYR I 66 " --> pdb=" O LEU I 62 " (cutoff:3.500A) Processing helix chain 'I' and resid 76 through 87 Processing helix chain 'I' and resid 145 through 154 Processing helix chain 'I' and resid 173 through 175 No H-bonds generated for 'chain 'I' and resid 173 through 175' Processing helix chain 'I' and resid 180 through 184 removed outlier: 3.580A pdb=" N SER I 183 " --> pdb=" O SER I 180 " (cutoff:3.500A) Processing helix chain 'I' and resid 214 through 226 Processing helix chain 'I' and resid 243 through 249 Processing helix chain 'I' and resid 250 through 256 Processing helix chain 'I' and resid 265 through 277 removed outlier: 4.066A pdb=" N SER I 269 " --> pdb=" O ASN I 265 " (cutoff:3.500A) Processing helix chain 'J' and resid 23 through 25 No H-bonds generated for 'chain 'J' and resid 23 through 25' Processing helix chain 'J' and resid 26 through 40 Processing helix chain 'J' and resid 99 through 114 removed outlier: 3.575A pdb=" N GLY J 114 " --> pdb=" O VAL J 110 " (cutoff:3.500A) Processing helix chain 'J' and resid 132 through 136 removed outlier: 3.554A pdb=" N SER J 136 " --> pdb=" O GLN J 133 " (cutoff:3.500A) Processing helix chain 'J' and resid 148 through 159 Processing helix chain 'J' and resid 186 through 198 Processing helix chain 'J' and resid 213 through 229 removed outlier: 3.964A pdb=" N TRP J 227 " --> pdb=" O TYR J 223 " (cutoff:3.500A) Processing helix chain 'K' and resid 98 through 114 Processing helix chain 'K' and resid 118 through 130 removed outlier: 3.533A pdb=" N ALA K 122 " --> pdb=" O ARG K 118 " (cutoff:3.500A) Processing helix chain 'L' and resid 72 through 90 removed outlier: 5.950A pdb=" N PHE L 85 " --> pdb=" O ASN L 81 " (cutoff:3.500A) removed outlier: 5.267A pdb=" N VAL L 86 " --> pdb=" O LEU L 82 " (cutoff:3.500A) Processing helix chain 'L' and resid 105 through 119 removed outlier: 3.703A pdb=" N GLU L 114 " --> pdb=" O LYS L 110 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N VAL L 115 " --> pdb=" O ALA L 111 " (cutoff:3.500A) Processing helix chain 'M' and resid 74 through 88 Processing helix chain 'M' and resid 103 through 119 Processing helix chain 'M' and resid 120 through 123 removed outlier: 3.613A pdb=" N PHE M 123 " --> pdb=" O PRO M 120 " (cutoff:3.500A) No H-bonds generated for 'chain 'M' and resid 120 through 123' Processing sheet with id=AA1, first strand: chain 'A' and resid 160 through 163 Processing sheet with id=AA2, first strand: chain 'A' and resid 66 through 67 Processing sheet with id=AA3, first strand: chain 'B' and resid 161 through 164 Processing sheet with id=AA4, first strand: chain 'B' and resid 65 through 67 removed outlier: 3.558A pdb=" N LEU B 134 " --> pdb=" O SER B 150 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N GLY B 138 " --> pdb=" O GLN B 146 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N GLY B 157 " --> pdb=" O GLN B 149 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 158 through 161 Processing sheet with id=AA6, first strand: chain 'C' and resid 62 through 64 removed outlier: 3.513A pdb=" N GLY C 135 " --> pdb=" O ARG C 143 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 167 through 170 Processing sheet with id=AA8, first strand: chain 'D' and resid 67 through 71 removed outlier: 6.526A pdb=" N ILE D 74 " --> pdb=" O ILE D 70 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'E' and resid 158 through 161 removed outlier: 5.354A pdb=" N GLY E 216 " --> pdb=" O GLU E 220 " (cutoff:3.500A) removed outlier: 4.959A pdb=" N GLU E 220 " --> pdb=" O GLY E 216 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'E' and resid 63 through 65 removed outlier: 3.622A pdb=" N LEU E 132 " --> pdb=" O THR E 147 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'E' and resid 63 through 65 removed outlier: 3.507A pdb=" N GLY E 76 " --> pdb=" O THR I 288 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'F' and resid 163 through 166 removed outlier: 4.042A pdb=" N GLY F 45 " --> pdb=" O CYS F 42 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N TRP F 216 " --> pdb=" O GLU F 226 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'F' and resid 67 through 69 Processing sheet with id=AB5, first strand: chain 'G' and resid 165 through 169 removed outlier: 5.642A pdb=" N THR G 38 " --> pdb=" O GLN G 53 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N GLN G 53 " --> pdb=" O THR G 38 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'G' and resid 69 through 73 removed outlier: 6.575A pdb=" N ILE G 76 " --> pdb=" O ILE G 72 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N GLY G 148 " --> pdb=" O ASP G 144 " (cutoff:3.500A) removed outlier: 4.317A pdb=" N VAL G 151 " --> pdb=" O PHE G 163 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N CYS G 161 " --> pdb=" O LYS G 153 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'I' and resid 48 through 50 removed outlier: 6.964A pdb=" N PHE I 123 " --> pdb=" O VAL I 96 " (cutoff:3.500A) removed outlier: 4.435A pdb=" N CYS I 98 " --> pdb=" O CYS I 121 " (cutoff:3.500A) removed outlier: 7.230A pdb=" N CYS I 121 " --> pdb=" O CYS I 98 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N VAL I 122 " --> pdb=" O GLN I 136 " (cutoff:3.500A) removed outlier: 5.657A pdb=" N VAL I 132 " --> pdb=" O LEU I 126 " (cutoff:3.500A) removed outlier: 6.426A pdb=" N LYS I 70 " --> pdb=" O PHE I 133 " (cutoff:3.500A) removed outlier: 8.066A pdb=" N CYS I 135 " --> pdb=" O LYS I 70 " (cutoff:3.500A) removed outlier: 6.463A pdb=" N ILE I 72 " --> pdb=" O CYS I 135 " (cutoff:3.500A) removed outlier: 7.608A pdb=" N CYS I 137 " --> pdb=" O ILE I 72 " (cutoff:3.500A) removed outlier: 6.191A pdb=" N ALA I 74 " --> pdb=" O CYS I 137 " (cutoff:3.500A) removed outlier: 4.437A pdb=" N CYS I 169 " --> pdb=" O ILE I 75 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'I' and resid 212 through 213 Processing sheet with id=AB9, first strand: chain 'J' and resid 2 through 4 removed outlier: 3.534A pdb=" N SER J 42 " --> pdb=" O SER J 79 " (cutoff:3.500A) removed outlier: 7.020A pdb=" N VAL J 77 " --> pdb=" O ILE J 44 " (cutoff:3.500A) removed outlier: 5.144A pdb=" N TYR J 46 " --> pdb=" O ALA J 75 " (cutoff:3.500A) removed outlier: 8.191A pdb=" N ALA J 75 " --> pdb=" O TYR J 46 " (cutoff:3.500A) removed outlier: 6.970A pdb=" N LEU J 90 " --> pdb=" O PRO J 20 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'J' and resid 2 through 4 removed outlier: 3.534A pdb=" N SER J 42 " --> pdb=" O SER J 79 " (cutoff:3.500A) removed outlier: 7.020A pdb=" N VAL J 77 " --> pdb=" O ILE J 44 " (cutoff:3.500A) removed outlier: 5.144A pdb=" N TYR J 46 " --> pdb=" O ALA J 75 " (cutoff:3.500A) removed outlier: 8.191A pdb=" N ALA J 75 " --> pdb=" O TYR J 46 " (cutoff:3.500A) removed outlier: 6.970A pdb=" N LEU J 90 " --> pdb=" O PRO J 20 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'K' and resid 78 through 81 removed outlier: 5.032A pdb=" N PHE K 79 " --> pdb=" O CYS K 86 " (cutoff:3.500A) removed outlier: 6.862A pdb=" N CYS K 86 " --> pdb=" O PHE K 79 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N GLY K 145 " --> pdb=" O HIS K 152 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'L' and resid 8 through 16 removed outlier: 4.224A pdb=" N ILE L 8 " --> pdb=" O ALA L 27 " (cutoff:3.500A) removed outlier: 6.021A pdb=" N ILE L 32 " --> pdb=" O LEU L 96 " (cutoff:3.500A) removed outlier: 7.461A pdb=" N ALA L 98 " --> pdb=" O ILE L 32 " (cutoff:3.500A) removed outlier: 6.606A pdb=" N VAL L 34 " --> pdb=" O ALA L 98 " (cutoff:3.500A) removed outlier: 8.067A pdb=" N ALA L 100 " --> pdb=" O VAL L 34 " (cutoff:3.500A) removed outlier: 6.910A pdb=" N VAL L 36 " --> pdb=" O ALA L 100 " (cutoff:3.500A) removed outlier: 6.538A pdb=" N LEU L 45 " --> pdb=" O LEU L 67 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'M' and resid 13 through 21 removed outlier: 3.626A pdb=" N SER M 36 " --> pdb=" O LEU M 33 " (cutoff:3.500A) removed outlier: 6.309A pdb=" N LEU M 37 " --> pdb=" O PHE M 92 " (cutoff:3.500A) removed outlier: 7.985A pdb=" N SER M 94 " --> pdb=" O LEU M 37 " (cutoff:3.500A) removed outlier: 6.701A pdb=" N LEU M 39 " --> pdb=" O SER M 94 " (cutoff:3.500A) removed outlier: 6.539A pdb=" N LEU M 50 " --> pdb=" O LEU M 67 " (cutoff:3.500A) 1026 hydrogen bonds defined for protein. 2925 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: 5.93 Time building geometry restraints manager: 7.62 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 6323 1.34 - 1.46: 2532 1.46 - 1.57: 10719 1.57 - 1.69: 0 1.69 - 1.81: 174 Bond restraints: 19748 Sorted by residual: bond pdb=" C ACE D 0 " pdb=" O ACE D 0 " ideal model delta sigma weight residual 1.199 1.230 -0.031 2.00e-02 2.50e+03 2.35e+00 bond pdb=" C ACE J 0 " pdb=" O ACE J 0 " ideal model delta sigma weight residual 1.199 1.229 -0.030 2.00e-02 2.50e+03 2.32e+00 bond pdb=" C ACE E 0 " pdb=" O ACE E 0 " ideal model delta sigma weight residual 1.199 1.229 -0.030 2.00e-02 2.50e+03 2.18e+00 bond pdb=" CD GLU M 117 " pdb=" OE1 GLU M 117 " ideal model delta sigma weight residual 1.249 1.230 0.019 1.90e-02 2.77e+03 1.02e+00 bond pdb=" CA ASN K 83 " pdb=" CB ASN K 83 " ideal model delta sigma weight residual 1.530 1.547 -0.017 1.69e-02 3.50e+03 1.01e+00 ... (remaining 19743 not shown) Histogram of bond angle deviations from ideal: 100.11 - 106.88: 488 106.88 - 113.66: 10983 113.66 - 120.44: 7239 120.44 - 127.21: 7832 127.21 - 133.99: 172 Bond angle restraints: 26714 Sorted by residual: angle pdb=" N GLU M 117 " pdb=" CA GLU M 117 " pdb=" CB GLU M 117 " ideal model delta sigma weight residual 110.40 116.35 -5.95 1.63e+00 3.76e-01 1.33e+01 angle pdb=" N THR D 213 " pdb=" CA THR D 213 " pdb=" C THR D 213 " ideal model delta sigma weight residual 114.56 109.94 4.62 1.27e+00 6.20e-01 1.32e+01 angle pdb=" C MET M 116 " pdb=" N GLU M 117 " pdb=" CA GLU M 117 " ideal model delta sigma weight residual 121.14 115.02 6.12 1.75e+00 3.27e-01 1.22e+01 angle pdb=" C PRO K 82 " pdb=" N ASN K 83 " pdb=" CA ASN K 83 " ideal model delta sigma weight residual 121.54 128.10 -6.56 1.91e+00 2.74e-01 1.18e+01 angle pdb=" N GLU C 237 " pdb=" CA GLU C 237 " pdb=" CB GLU C 237 " ideal model delta sigma weight residual 110.28 115.10 -4.82 1.55e+00 4.16e-01 9.68e+00 ... (remaining 26709 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.57: 10885 17.57 - 35.14: 884 35.14 - 52.71: 129 52.71 - 70.28: 36 70.28 - 87.86: 24 Dihedral angle restraints: 11958 sinusoidal: 4710 harmonic: 7248 Sorted by residual: dihedral pdb=" CA TRP F 216 " pdb=" C TRP F 216 " pdb=" N VAL F 217 " pdb=" CA VAL F 217 " ideal model delta harmonic sigma weight residual 180.00 161.07 18.93 0 5.00e+00 4.00e-02 1.43e+01 dihedral pdb=" CA ASN D 104 " pdb=" C ASN D 104 " pdb=" N GLU D 105 " pdb=" CA GLU D 105 " ideal model delta harmonic sigma weight residual 180.00 161.83 18.17 0 5.00e+00 4.00e-02 1.32e+01 dihedral pdb=" CA ASP E 94 " pdb=" CB ASP E 94 " pdb=" CG ASP E 94 " pdb=" OD1 ASP E 94 " ideal model delta sinusoidal sigma weight residual -30.00 -87.99 57.99 1 2.00e+01 2.50e-03 1.13e+01 ... (remaining 11955 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.029: 1941 0.029 - 0.058: 710 0.058 - 0.088: 211 0.088 - 0.117: 191 0.117 - 0.146: 26 Chirality restraints: 3079 Sorted by residual: chirality pdb=" CA GLU C 237 " pdb=" N GLU C 237 " pdb=" C GLU C 237 " pdb=" CB GLU C 237 " both_signs ideal model delta sigma weight residual False 2.51 2.36 0.15 2.00e-01 2.50e+01 5.34e-01 chirality pdb=" CA ILE K 84 " pdb=" N ILE K 84 " pdb=" C ILE K 84 " pdb=" CB ILE K 84 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.81e-01 chirality pdb=" CB THR D 113 " pdb=" CA THR D 113 " pdb=" OG1 THR D 113 " pdb=" CG2 THR D 113 " both_signs ideal model delta sigma weight residual False 2.55 2.41 0.14 2.00e-01 2.50e+01 4.71e-01 ... (remaining 3076 not shown) Planarity restraints: 3404 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP F 216 " -0.017 2.00e-02 2.50e+03 1.71e-02 7.28e+00 pdb=" CG TRP F 216 " 0.045 2.00e-02 2.50e+03 pdb=" CD1 TRP F 216 " -0.024 2.00e-02 2.50e+03 pdb=" CD2 TRP F 216 " -0.000 2.00e-02 2.50e+03 pdb=" NE1 TRP F 216 " 0.003 2.00e-02 2.50e+03 pdb=" CE2 TRP F 216 " 0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP F 216 " -0.001 2.00e-02 2.50e+03 pdb=" CZ2 TRP F 216 " 0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP F 216 " -0.006 2.00e-02 2.50e+03 pdb=" CH2 TRP F 216 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C SER F 16 " 0.029 5.00e-02 4.00e+02 4.38e-02 3.06e+00 pdb=" N PRO F 17 " -0.076 5.00e-02 4.00e+02 pdb=" CA PRO F 17 " 0.022 5.00e-02 4.00e+02 pdb=" CD PRO F 17 " 0.024 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA PRO K 82 " 0.008 2.00e-02 2.50e+03 1.65e-02 2.71e+00 pdb=" C PRO K 82 " -0.028 2.00e-02 2.50e+03 pdb=" O PRO K 82 " 0.011 2.00e-02 2.50e+03 pdb=" N ASN K 83 " 0.010 2.00e-02 2.50e+03 ... (remaining 3401 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.77: 3135 2.77 - 3.30: 16805 3.30 - 3.83: 29800 3.83 - 4.37: 34705 4.37 - 4.90: 64645 Nonbonded interactions: 149090 Sorted by model distance: nonbonded pdb=" O ARG K 124 " pdb=" NE2 GLN K 128 " model vdw 2.235 2.520 nonbonded pdb=" OG SER E 33 " pdb=" NZ LYS E 62 " model vdw 2.235 2.520 nonbonded pdb=" OD2 ASP B 151 " pdb=" OG SER B 153 " model vdw 2.239 2.440 nonbonded pdb=" OH TYR I 175 " pdb=" OE1 GLU I 207 " model vdw 2.248 2.440 nonbonded pdb=" OG SER L 29 " pdb=" O PRO M 45 " model vdw 2.259 2.440 ... (remaining 149085 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.490 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.780 Check model and map are aligned: 0.130 Set scattering table: 0.170 Process input model: 50.920 Find NCS groups from input model: 0.610 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: 0.000 Load rotamer database and sin/cos tables:11.950 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 66.130 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8521 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 : 0.002 0.048 19748 Z= 0.136 Angle : 0.442 10.682 26714 Z= 0.238 Chirality : 0.041 0.146 3079 Planarity : 0.004 0.044 3404 Dihedral : 13.648 87.855 7276 Min Nonbonded Distance : 2.235 Molprobity Statistics. All-atom Clashscore : 2.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer: Outliers : 0.00 % Allowed : 0.14 % Favored : 99.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.76 (0.17), residues: 2456 helix: 2.87 (0.18), residues: 889 sheet: 0.99 (0.23), residues: 550 loop : -0.29 (0.19), residues: 1017 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.045 0.001 TRP F 216 HIS 0.003 0.000 HIS D 186 PHE 0.013 0.001 PHE G 9 TYR 0.007 0.001 TYR B 156 ARG 0.002 0.000 ARG H 106 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4912 Ramachandran restraints generated. 2456 Oldfield, 0 Emsley, 2456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4912 Ramachandran restraints generated. 2456 Oldfield, 0 Emsley, 2456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 285 residues out of total 2149 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 285 time to evaluate : 2.184 Fit side-chains REVERT: F 171 GLN cc_start: 0.7521 (tp-100) cc_final: 0.7028 (tp-100) REVERT: M 121 GLU cc_start: 0.7673 (pm20) cc_final: 0.7403 (pm20) outliers start: 0 outliers final: 0 residues processed: 285 average time/residue: 1.4419 time to fit residues: 456.8004 Evaluate side-chains 224 residues out of total 2149 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 224 time to evaluate : 2.369 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 245 random chunks: chunk 206 optimal weight: 2.9990 chunk 185 optimal weight: 0.5980 chunk 103 optimal weight: 3.9990 chunk 63 optimal weight: 3.9990 chunk 125 optimal weight: 4.9990 chunk 99 optimal weight: 2.9990 chunk 192 optimal weight: 5.9990 chunk 74 optimal weight: 2.9990 chunk 116 optimal weight: 6.9990 chunk 142 optimal weight: 4.9990 chunk 222 optimal weight: 10.0000 overall best weight: 2.7188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 214 ASN B 69 ASN B 84 ASN B 155 ASN ** B 230 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 205 ASN G 224 ASN I 280 ASN J 152 GLN J 159 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8597 moved from start: 0.1049 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 19748 Z= 0.284 Angle : 0.546 9.923 26714 Z= 0.291 Chirality : 0.044 0.172 3079 Planarity : 0.005 0.048 3404 Dihedral : 4.071 20.876 2690 Min Nonbonded Distance : 2.274 Molprobity Statistics. All-atom Clashscore : 2.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.69 % Favored : 97.31 % Rotamer: Outliers : 1.71 % Allowed : 7.93 % Favored : 90.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.56 (0.17), residues: 2456 helix: 2.78 (0.18), residues: 897 sheet: 1.04 (0.22), residues: 549 loop : -0.62 (0.18), residues: 1010 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP F 216 HIS 0.005 0.001 HIS E 65 PHE 0.014 0.001 PHE A 173 TYR 0.013 0.001 TYR B 136 ARG 0.002 0.000 ARG L 93 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4912 Ramachandran restraints generated. 2456 Oldfield, 0 Emsley, 2456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4912 Ramachandran restraints generated. 2456 Oldfield, 0 Emsley, 2456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 250 residues out of total 2149 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 214 time to evaluate : 2.260 Fit side-chains REVERT: D 207 GLU cc_start: 0.7451 (OUTLIER) cc_final: 0.6532 (mp0) REVERT: E 60 GLN cc_start: 0.8273 (OUTLIER) cc_final: 0.8003 (mt0) REVERT: E 203 GLN cc_start: 0.7893 (OUTLIER) cc_final: 0.7561 (mt0) REVERT: F 171 GLN cc_start: 0.7612 (tp-100) cc_final: 0.7142 (tp-100) REVERT: G 112 ASP cc_start: 0.8637 (OUTLIER) cc_final: 0.8254 (p0) REVERT: G 130 GLU cc_start: 0.7692 (OUTLIER) cc_final: 0.7155 (mp0) REVERT: K 128 GLN cc_start: 0.6682 (OUTLIER) cc_final: 0.5809 (mp10) REVERT: M 121 GLU cc_start: 0.7746 (pm20) cc_final: 0.7463 (pm20) outliers start: 36 outliers final: 13 residues processed: 229 average time/residue: 1.4566 time to fit residues: 372.1504 Evaluate side-chains 225 residues out of total 2149 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 206 time to evaluate : 2.182 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 228 ASP Chi-restraints excluded: chain B residue 87 THR Chi-restraints excluded: chain C residue 216 SER Chi-restraints excluded: chain D residue 205 VAL Chi-restraints excluded: chain D residue 207 GLU Chi-restraints excluded: chain D residue 228 MET Chi-restraints excluded: chain E residue 60 GLN Chi-restraints excluded: chain E residue 203 GLN Chi-restraints excluded: chain G residue 112 ASP Chi-restraints excluded: chain G residue 130 GLU Chi-restraints excluded: chain I residue 60 VAL Chi-restraints excluded: chain K residue 80 ILE Chi-restraints excluded: chain K residue 97 MET Chi-restraints excluded: chain K residue 119 VAL Chi-restraints excluded: chain K residue 128 GLN Chi-restraints excluded: chain L residue 9 SER Chi-restraints excluded: chain L residue 29 SER Chi-restraints excluded: chain L residue 63 THR Chi-restraints excluded: chain M residue 54 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 245 random chunks: chunk 123 optimal weight: 0.9980 chunk 69 optimal weight: 1.9990 chunk 185 optimal weight: 0.9980 chunk 151 optimal weight: 0.6980 chunk 61 optimal weight: 3.9990 chunk 222 optimal weight: 9.9990 chunk 240 optimal weight: 8.9990 chunk 198 optimal weight: 3.9990 chunk 221 optimal weight: 10.0000 chunk 75 optimal weight: 0.9990 chunk 178 optimal weight: 4.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 69 ASN ** B 230 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 224 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8554 moved from start: 0.1069 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 19748 Z= 0.148 Angle : 0.455 10.369 26714 Z= 0.245 Chirality : 0.041 0.145 3079 Planarity : 0.004 0.048 3404 Dihedral : 3.849 18.639 2690 Min Nonbonded Distance : 2.256 Molprobity Statistics. All-atom Clashscore : 2.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.83 % Favored : 98.17 % Rotamer: Outliers : 1.61 % Allowed : 9.97 % Favored : 88.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.79 (0.17), residues: 2456 helix: 2.98 (0.18), residues: 897 sheet: 1.26 (0.22), residues: 536 loop : -0.53 (0.18), residues: 1023 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP F 216 HIS 0.004 0.001 HIS E 65 PHE 0.015 0.001 PHE A 173 TYR 0.008 0.001 TYR B 156 ARG 0.002 0.000 ARG H 106 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4912 Ramachandran restraints generated. 2456 Oldfield, 0 Emsley, 2456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4912 Ramachandran restraints generated. 2456 Oldfield, 0 Emsley, 2456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 249 residues out of total 2149 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 215 time to evaluate : 2.457 Fit side-chains REVERT: D 207 GLU cc_start: 0.7377 (OUTLIER) cc_final: 0.6528 (mp0) REVERT: F 171 GLN cc_start: 0.7537 (tp-100) cc_final: 0.7080 (tp-100) REVERT: G 112 ASP cc_start: 0.8524 (OUTLIER) cc_final: 0.8113 (p0) REVERT: K 97 MET cc_start: 0.6817 (OUTLIER) cc_final: 0.6422 (ttm) REVERT: K 128 GLN cc_start: 0.6684 (OUTLIER) cc_final: 0.5810 (mp10) REVERT: M 121 GLU cc_start: 0.7727 (pm20) cc_final: 0.7458 (pm20) outliers start: 34 outliers final: 16 residues processed: 228 average time/residue: 1.5255 time to fit residues: 386.8883 Evaluate side-chains 226 residues out of total 2149 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 206 time to evaluate : 2.541 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 228 ASP Chi-restraints excluded: chain C residue 216 SER Chi-restraints excluded: chain C residue 237 GLU Chi-restraints excluded: chain D residue 104 ASN Chi-restraints excluded: chain D residue 133 MET Chi-restraints excluded: chain D residue 148 GLU Chi-restraints excluded: chain D residue 205 VAL Chi-restraints excluded: chain D residue 207 GLU Chi-restraints excluded: chain D residue 228 MET Chi-restraints excluded: chain E residue 227 ASP Chi-restraints excluded: chain G residue 90 GLN Chi-restraints excluded: chain G residue 112 ASP Chi-restraints excluded: chain I residue 60 VAL Chi-restraints excluded: chain J residue 55 MET Chi-restraints excluded: chain K residue 80 ILE Chi-restraints excluded: chain K residue 97 MET Chi-restraints excluded: chain K residue 119 VAL Chi-restraints excluded: chain K residue 128 GLN Chi-restraints excluded: chain M residue 54 MET Chi-restraints excluded: chain M residue 65 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 245 random chunks: chunk 220 optimal weight: 6.9990 chunk 167 optimal weight: 7.9990 chunk 115 optimal weight: 2.9990 chunk 24 optimal weight: 10.0000 chunk 106 optimal weight: 0.6980 chunk 149 optimal weight: 0.9980 chunk 223 optimal weight: 1.9990 chunk 236 optimal weight: 6.9990 chunk 116 optimal weight: 9.9990 chunk 212 optimal weight: 4.9990 chunk 63 optimal weight: 0.7980 overall best weight: 1.4984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 214 ASN B 88 ASN B 146 GLN ** B 230 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 224 ASN ** K 83 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8567 moved from start: 0.1171 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 19748 Z= 0.178 Angle : 0.470 10.500 26714 Z= 0.252 Chirality : 0.042 0.164 3079 Planarity : 0.004 0.049 3404 Dihedral : 3.868 18.454 2690 Min Nonbonded Distance : 2.263 Molprobity Statistics. All-atom Clashscore : 2.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 1.71 % Allowed : 11.21 % Favored : 87.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.79 (0.17), residues: 2456 helix: 2.98 (0.18), residues: 896 sheet: 1.22 (0.22), residues: 538 loop : -0.51 (0.18), residues: 1022 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP F 216 HIS 0.004 0.001 HIS E 65 PHE 0.013 0.001 PHE A 173 TYR 0.010 0.001 TYR B 136 ARG 0.002 0.000 ARG D 10 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4912 Ramachandran restraints generated. 2456 Oldfield, 0 Emsley, 2456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4912 Ramachandran restraints generated. 2456 Oldfield, 0 Emsley, 2456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 249 residues out of total 2149 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 213 time to evaluate : 2.180 Fit side-chains REVERT: D 148 GLU cc_start: 0.7611 (OUTLIER) cc_final: 0.7390 (pm20) REVERT: D 207 GLU cc_start: 0.7361 (OUTLIER) cc_final: 0.6459 (mp0) REVERT: E 203 GLN cc_start: 0.7862 (OUTLIER) cc_final: 0.7512 (mt0) REVERT: F 171 GLN cc_start: 0.7577 (tp-100) cc_final: 0.7116 (tp-100) REVERT: G 112 ASP cc_start: 0.8558 (OUTLIER) cc_final: 0.8170 (p0) REVERT: G 130 GLU cc_start: 0.7702 (OUTLIER) cc_final: 0.7245 (mp0) REVERT: H 80 GLN cc_start: 0.8276 (OUTLIER) cc_final: 0.8003 (tt0) REVERT: K 97 MET cc_start: 0.6784 (OUTLIER) cc_final: 0.6418 (ttm) REVERT: K 128 GLN cc_start: 0.6611 (OUTLIER) cc_final: 0.5714 (mp10) REVERT: M 117 GLU cc_start: 0.6861 (tp30) cc_final: 0.6610 (mp0) REVERT: M 121 GLU cc_start: 0.7724 (pm20) cc_final: 0.7449 (pm20) outliers start: 36 outliers final: 18 residues processed: 228 average time/residue: 1.4079 time to fit residues: 357.4075 Evaluate side-chains 231 residues out of total 2149 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 205 time to evaluate : 2.533 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 228 ASP Chi-restraints excluded: chain B residue 87 THR Chi-restraints excluded: chain C residue 216 SER Chi-restraints excluded: chain C residue 237 GLU Chi-restraints excluded: chain D residue 104 ASN Chi-restraints excluded: chain D residue 148 GLU Chi-restraints excluded: chain D residue 205 VAL Chi-restraints excluded: chain D residue 207 GLU Chi-restraints excluded: chain D residue 228 MET Chi-restraints excluded: chain E residue 203 GLN Chi-restraints excluded: chain E residue 227 ASP Chi-restraints excluded: chain G residue 90 GLN Chi-restraints excluded: chain G residue 112 ASP Chi-restraints excluded: chain G residue 130 GLU Chi-restraints excluded: chain G residue 146 GLU Chi-restraints excluded: chain H residue 80 GLN Chi-restraints excluded: chain H residue 86 VAL Chi-restraints excluded: chain I residue 60 VAL Chi-restraints excluded: chain J residue 55 MET Chi-restraints excluded: chain K residue 80 ILE Chi-restraints excluded: chain K residue 97 MET Chi-restraints excluded: chain K residue 119 VAL Chi-restraints excluded: chain K residue 128 GLN Chi-restraints excluded: chain L residue 63 THR Chi-restraints excluded: chain M residue 54 MET Chi-restraints excluded: chain M residue 65 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 245 random chunks: chunk 197 optimal weight: 2.9990 chunk 134 optimal weight: 6.9990 chunk 3 optimal weight: 0.5980 chunk 176 optimal weight: 0.6980 chunk 97 optimal weight: 8.9990 chunk 202 optimal weight: 0.8980 chunk 163 optimal weight: 6.9990 chunk 0 optimal weight: 10.0000 chunk 120 optimal weight: 6.9990 chunk 212 optimal weight: 6.9990 chunk 59 optimal weight: 5.9990 overall best weight: 2.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 214 ASN B 146 GLN ** B 230 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 224 ASN ** K 83 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8597 moved from start: 0.1297 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 19748 Z= 0.236 Angle : 0.507 10.092 26714 Z= 0.273 Chirality : 0.043 0.167 3079 Planarity : 0.004 0.051 3404 Dihedral : 4.051 20.699 2690 Min Nonbonded Distance : 2.241 Molprobity Statistics. All-atom Clashscore : 2.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 2.14 % Allowed : 11.92 % Favored : 85.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.66 (0.17), residues: 2456 helix: 2.88 (0.17), residues: 896 sheet: 1.21 (0.22), residues: 535 loop : -0.62 (0.18), residues: 1025 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP F 216 HIS 0.005 0.001 HIS E 65 PHE 0.013 0.001 PHE A 173 TYR 0.013 0.001 TYR B 136 ARG 0.002 0.000 ARG F 233 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4912 Ramachandran restraints generated. 2456 Oldfield, 0 Emsley, 2456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4912 Ramachandran restraints generated. 2456 Oldfield, 0 Emsley, 2456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 249 residues out of total 2149 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 204 time to evaluate : 2.179 Fit side-chains REVERT: D 207 GLU cc_start: 0.7399 (OUTLIER) cc_final: 0.6471 (mp0) REVERT: E 203 GLN cc_start: 0.7861 (OUTLIER) cc_final: 0.7505 (mt0) REVERT: F 171 GLN cc_start: 0.7654 (tp-100) cc_final: 0.7161 (tp-100) REVERT: G 112 ASP cc_start: 0.8610 (OUTLIER) cc_final: 0.8236 (p0) REVERT: G 130 GLU cc_start: 0.7732 (OUTLIER) cc_final: 0.7208 (mp0) REVERT: H 80 GLN cc_start: 0.8285 (OUTLIER) cc_final: 0.7999 (tt0) REVERT: H 110 GLU cc_start: 0.8282 (OUTLIER) cc_final: 0.7860 (mt-10) REVERT: I 283 GLN cc_start: 0.8787 (OUTLIER) cc_final: 0.8516 (mt0) REVERT: K 128 GLN cc_start: 0.6648 (OUTLIER) cc_final: 0.5726 (mp10) REVERT: M 117 GLU cc_start: 0.6995 (tp30) cc_final: 0.6685 (mp0) REVERT: M 121 GLU cc_start: 0.7756 (pm20) cc_final: 0.7461 (pm20) outliers start: 45 outliers final: 23 residues processed: 226 average time/residue: 1.5466 time to fit residues: 387.8367 Evaluate side-chains 233 residues out of total 2149 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 202 time to evaluate : 2.320 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 LEU Chi-restraints excluded: chain A residue 150 ASP Chi-restraints excluded: chain A residue 228 ASP Chi-restraints excluded: chain B residue 87 THR Chi-restraints excluded: chain C residue 216 SER Chi-restraints excluded: chain C residue 237 GLU Chi-restraints excluded: chain D residue 104 ASN Chi-restraints excluded: chain D residue 148 GLU Chi-restraints excluded: chain D residue 205 VAL Chi-restraints excluded: chain D residue 207 GLU Chi-restraints excluded: chain D residue 228 MET Chi-restraints excluded: chain E residue 203 GLN Chi-restraints excluded: chain G residue 90 GLN Chi-restraints excluded: chain G residue 112 ASP Chi-restraints excluded: chain G residue 130 GLU Chi-restraints excluded: chain G residue 146 GLU Chi-restraints excluded: chain H residue 80 GLN Chi-restraints excluded: chain H residue 86 VAL Chi-restraints excluded: chain H residue 110 GLU Chi-restraints excluded: chain I residue 60 VAL Chi-restraints excluded: chain I residue 283 GLN Chi-restraints excluded: chain J residue 55 MET Chi-restraints excluded: chain J residue 144 THR Chi-restraints excluded: chain K residue 80 ILE Chi-restraints excluded: chain K residue 97 MET Chi-restraints excluded: chain K residue 119 VAL Chi-restraints excluded: chain K residue 128 GLN Chi-restraints excluded: chain L residue 29 SER Chi-restraints excluded: chain L residue 63 THR Chi-restraints excluded: chain M residue 54 MET Chi-restraints excluded: chain M residue 65 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 245 random chunks: chunk 79 optimal weight: 3.9990 chunk 213 optimal weight: 2.9990 chunk 46 optimal weight: 2.9990 chunk 139 optimal weight: 5.9990 chunk 58 optimal weight: 0.4980 chunk 237 optimal weight: 6.9990 chunk 196 optimal weight: 3.9990 chunk 109 optimal weight: 4.9990 chunk 19 optimal weight: 0.8980 chunk 78 optimal weight: 4.9990 chunk 124 optimal weight: 5.9990 overall best weight: 2.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 214 ASN ** B 230 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 224 ASN ** K 83 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8599 moved from start: 0.1351 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 19748 Z= 0.243 Angle : 0.514 9.918 26714 Z= 0.276 Chirality : 0.043 0.171 3079 Planarity : 0.004 0.053 3404 Dihedral : 4.084 21.561 2690 Min Nonbonded Distance : 2.221 Molprobity Statistics. All-atom Clashscore : 2.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer: Outliers : 2.28 % Allowed : 12.39 % Favored : 85.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.60 (0.17), residues: 2456 helix: 2.85 (0.17), residues: 896 sheet: 1.17 (0.22), residues: 537 loop : -0.67 (0.18), residues: 1023 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP I 149 HIS 0.005 0.001 HIS E 65 PHE 0.013 0.001 PHE A 173 TYR 0.012 0.001 TYR B 136 ARG 0.002 0.000 ARG F 233 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4912 Ramachandran restraints generated. 2456 Oldfield, 0 Emsley, 2456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4912 Ramachandran restraints generated. 2456 Oldfield, 0 Emsley, 2456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 252 residues out of total 2149 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 204 time to evaluate : 2.473 Fit side-chains REVERT: C 23 GLN cc_start: 0.8684 (OUTLIER) cc_final: 0.8137 (mt0) REVERT: D 207 GLU cc_start: 0.7383 (OUTLIER) cc_final: 0.6446 (mp0) REVERT: F 28 MET cc_start: 0.8788 (mtp) cc_final: 0.8560 (mtm) REVERT: F 100 ARG cc_start: 0.8029 (OUTLIER) cc_final: 0.7726 (tpt90) REVERT: F 171 GLN cc_start: 0.7671 (tp-100) cc_final: 0.7131 (tp-100) REVERT: G 112 ASP cc_start: 0.8608 (OUTLIER) cc_final: 0.8225 (p0) REVERT: G 130 GLU cc_start: 0.7765 (OUTLIER) cc_final: 0.7223 (mp0) REVERT: H 80 GLN cc_start: 0.8281 (OUTLIER) cc_final: 0.7995 (tt0) REVERT: H 110 GLU cc_start: 0.8322 (OUTLIER) cc_final: 0.7828 (mt-10) REVERT: I 283 GLN cc_start: 0.8795 (OUTLIER) cc_final: 0.8529 (mt0) REVERT: M 117 GLU cc_start: 0.7032 (OUTLIER) cc_final: 0.6720 (mp0) REVERT: M 121 GLU cc_start: 0.7776 (pm20) cc_final: 0.7484 (pm20) outliers start: 48 outliers final: 27 residues processed: 230 average time/residue: 1.5047 time to fit residues: 383.3146 Evaluate side-chains 238 residues out of total 2149 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 202 time to evaluate : 2.284 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 LEU Chi-restraints excluded: chain A residue 150 ASP Chi-restraints excluded: chain A residue 228 ASP Chi-restraints excluded: chain B residue 87 THR Chi-restraints excluded: chain C residue 23 GLN Chi-restraints excluded: chain C residue 216 SER Chi-restraints excluded: chain D residue 104 ASN Chi-restraints excluded: chain D residue 148 GLU Chi-restraints excluded: chain D residue 205 VAL Chi-restraints excluded: chain D residue 207 GLU Chi-restraints excluded: chain D residue 228 MET Chi-restraints excluded: chain E residue 227 ASP Chi-restraints excluded: chain F residue 100 ARG Chi-restraints excluded: chain F residue 170 ARG Chi-restraints excluded: chain G residue 90 GLN Chi-restraints excluded: chain G residue 112 ASP Chi-restraints excluded: chain G residue 130 GLU Chi-restraints excluded: chain G residue 146 GLU Chi-restraints excluded: chain G residue 170 VAL Chi-restraints excluded: chain H residue 80 GLN Chi-restraints excluded: chain H residue 86 VAL Chi-restraints excluded: chain H residue 110 GLU Chi-restraints excluded: chain I residue 60 VAL Chi-restraints excluded: chain I residue 283 GLN Chi-restraints excluded: chain J residue 16 THR Chi-restraints excluded: chain J residue 55 MET Chi-restraints excluded: chain J residue 93 ILE Chi-restraints excluded: chain J residue 144 THR Chi-restraints excluded: chain K residue 80 ILE Chi-restraints excluded: chain K residue 97 MET Chi-restraints excluded: chain K residue 119 VAL Chi-restraints excluded: chain L residue 29 SER Chi-restraints excluded: chain L residue 63 THR Chi-restraints excluded: chain M residue 54 MET Chi-restraints excluded: chain M residue 65 THR Chi-restraints excluded: chain M residue 117 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 245 random chunks: chunk 228 optimal weight: 1.9990 chunk 26 optimal weight: 10.0000 chunk 135 optimal weight: 1.9990 chunk 173 optimal weight: 5.9990 chunk 134 optimal weight: 6.9990 chunk 199 optimal weight: 10.0000 chunk 132 optimal weight: 5.9990 chunk 236 optimal weight: 5.9990 chunk 147 optimal weight: 9.9990 chunk 143 optimal weight: 1.9990 chunk 109 optimal weight: 8.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 214 ASN F 181 GLN G 224 ASN ** K 83 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8632 moved from start: 0.1497 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 19748 Z= 0.358 Angle : 0.583 9.502 26714 Z= 0.311 Chirality : 0.045 0.182 3079 Planarity : 0.005 0.054 3404 Dihedral : 4.341 24.862 2690 Min Nonbonded Distance : 2.235 Molprobity Statistics. All-atom Clashscore : 2.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Rotamer: Outliers : 2.33 % Allowed : 13.01 % Favored : 84.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.35 (0.17), residues: 2456 helix: 2.66 (0.17), residues: 895 sheet: 1.07 (0.22), residues: 532 loop : -0.84 (0.18), residues: 1029 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP I 149 HIS 0.006 0.001 HIS E 65 PHE 0.015 0.002 PHE E 97 TYR 0.014 0.002 TYR B 136 ARG 0.003 0.000 ARG F 233 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4912 Ramachandran restraints generated. 2456 Oldfield, 0 Emsley, 2456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4912 Ramachandran restraints generated. 2456 Oldfield, 0 Emsley, 2456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 253 residues out of total 2149 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 204 time to evaluate : 2.321 Fit side-chains REVERT: A 18 LYS cc_start: 0.7925 (mmpt) cc_final: 0.7699 (mmpt) REVERT: C 23 GLN cc_start: 0.8683 (OUTLIER) cc_final: 0.8139 (mt0) REVERT: D 207 GLU cc_start: 0.7408 (OUTLIER) cc_final: 0.6446 (mp0) REVERT: F 28 MET cc_start: 0.8810 (mtp) cc_final: 0.8579 (mtm) REVERT: F 100 ARG cc_start: 0.8079 (OUTLIER) cc_final: 0.7863 (tpt90) REVERT: F 171 GLN cc_start: 0.7761 (tp-100) cc_final: 0.7208 (tp-100) REVERT: G 112 ASP cc_start: 0.8700 (OUTLIER) cc_final: 0.8342 (p0) REVERT: G 130 GLU cc_start: 0.7785 (OUTLIER) cc_final: 0.7194 (mp0) REVERT: H 80 GLN cc_start: 0.8299 (OUTLIER) cc_final: 0.8006 (tt0) REVERT: H 81 MET cc_start: 0.8284 (OUTLIER) cc_final: 0.7947 (mtp) REVERT: H 110 GLU cc_start: 0.8343 (OUTLIER) cc_final: 0.7807 (mt-10) REVERT: I 283 GLN cc_start: 0.8794 (OUTLIER) cc_final: 0.8536 (mt0) REVERT: K 128 GLN cc_start: 0.6683 (OUTLIER) cc_final: 0.5704 (mp10) REVERT: M 117 GLU cc_start: 0.7017 (OUTLIER) cc_final: 0.6633 (mp0) REVERT: M 121 GLU cc_start: 0.7779 (pm20) cc_final: 0.7472 (pm20) outliers start: 49 outliers final: 29 residues processed: 233 average time/residue: 1.5511 time to fit residues: 400.4941 Evaluate side-chains 241 residues out of total 2149 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 201 time to evaluate : 2.361 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 LEU Chi-restraints excluded: chain A residue 150 ASP Chi-restraints excluded: chain A residue 228 ASP Chi-restraints excluded: chain B residue 87 THR Chi-restraints excluded: chain C residue 23 GLN Chi-restraints excluded: chain C residue 216 SER Chi-restraints excluded: chain D residue 104 ASN Chi-restraints excluded: chain D residue 113 THR Chi-restraints excluded: chain D residue 148 GLU Chi-restraints excluded: chain D residue 205 VAL Chi-restraints excluded: chain D residue 207 GLU Chi-restraints excluded: chain D residue 228 MET Chi-restraints excluded: chain E residue 10 VAL Chi-restraints excluded: chain F residue 100 ARG Chi-restraints excluded: chain F residue 170 ARG Chi-restraints excluded: chain G residue 90 GLN Chi-restraints excluded: chain G residue 112 ASP Chi-restraints excluded: chain G residue 130 GLU Chi-restraints excluded: chain G residue 146 GLU Chi-restraints excluded: chain G residue 170 VAL Chi-restraints excluded: chain G residue 234 GLU Chi-restraints excluded: chain H residue 80 GLN Chi-restraints excluded: chain H residue 81 MET Chi-restraints excluded: chain H residue 86 VAL Chi-restraints excluded: chain H residue 110 GLU Chi-restraints excluded: chain I residue 195 GLN Chi-restraints excluded: chain I residue 283 GLN Chi-restraints excluded: chain J residue 16 THR Chi-restraints excluded: chain J residue 55 MET Chi-restraints excluded: chain J residue 93 ILE Chi-restraints excluded: chain J residue 144 THR Chi-restraints excluded: chain K residue 80 ILE Chi-restraints excluded: chain K residue 97 MET Chi-restraints excluded: chain K residue 119 VAL Chi-restraints excluded: chain K residue 128 GLN Chi-restraints excluded: chain L residue 29 SER Chi-restraints excluded: chain L residue 63 THR Chi-restraints excluded: chain M residue 54 MET Chi-restraints excluded: chain M residue 65 THR Chi-restraints excluded: chain M residue 117 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 245 random chunks: chunk 146 optimal weight: 0.9990 chunk 94 optimal weight: 2.9990 chunk 141 optimal weight: 0.8980 chunk 71 optimal weight: 0.1980 chunk 46 optimal weight: 0.8980 chunk 45 optimal weight: 0.3980 chunk 150 optimal weight: 2.9990 chunk 160 optimal weight: 6.9990 chunk 116 optimal weight: 4.9990 chunk 22 optimal weight: 2.9990 chunk 185 optimal weight: 0.8980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 214 ASN F 64 ASN G 224 ASN ** K 83 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8542 moved from start: 0.1345 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 19748 Z= 0.136 Angle : 0.456 10.383 26714 Z= 0.246 Chirality : 0.041 0.164 3079 Planarity : 0.004 0.053 3404 Dihedral : 3.885 20.055 2690 Min Nonbonded Distance : 2.193 Molprobity Statistics. All-atom Clashscore : 2.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.91 % Favored : 98.09 % Rotamer: Outliers : 1.38 % Allowed : 14.29 % Favored : 84.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.74 (0.17), residues: 2456 helix: 2.95 (0.18), residues: 898 sheet: 1.19 (0.22), residues: 538 loop : -0.56 (0.18), residues: 1020 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP I 149 HIS 0.003 0.001 HIS E 65 PHE 0.012 0.001 PHE A 173 TYR 0.010 0.001 TYR B 156 ARG 0.002 0.000 ARG H 106 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4912 Ramachandran restraints generated. 2456 Oldfield, 0 Emsley, 2456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4912 Ramachandran restraints generated. 2456 Oldfield, 0 Emsley, 2456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 237 residues out of total 2149 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 208 time to evaluate : 2.347 Fit side-chains REVERT: D 148 GLU cc_start: 0.7597 (OUTLIER) cc_final: 0.7359 (pm20) REVERT: D 207 GLU cc_start: 0.7360 (OUTLIER) cc_final: 0.6574 (mp0) REVERT: F 28 MET cc_start: 0.8735 (mtp) cc_final: 0.8456 (mtm) REVERT: F 171 GLN cc_start: 0.7614 (tp-100) cc_final: 0.7075 (tp-100) REVERT: G 112 ASP cc_start: 0.8492 (OUTLIER) cc_final: 0.8096 (p0) REVERT: H 80 GLN cc_start: 0.8255 (OUTLIER) cc_final: 0.8012 (tt0) REVERT: H 110 GLU cc_start: 0.8287 (OUTLIER) cc_final: 0.7727 (mt-10) REVERT: K 128 GLN cc_start: 0.6542 (OUTLIER) cc_final: 0.5578 (mp10) REVERT: M 117 GLU cc_start: 0.7047 (tp30) cc_final: 0.6642 (mp0) REVERT: M 121 GLU cc_start: 0.7793 (pm20) cc_final: 0.7506 (pm20) outliers start: 29 outliers final: 14 residues processed: 223 average time/residue: 1.5382 time to fit residues: 380.3044 Evaluate side-chains 221 residues out of total 2149 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 201 time to evaluate : 2.270 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 150 ASP Chi-restraints excluded: chain A residue 228 ASP Chi-restraints excluded: chain C residue 216 SER Chi-restraints excluded: chain D residue 104 ASN Chi-restraints excluded: chain D residue 148 GLU Chi-restraints excluded: chain D residue 205 VAL Chi-restraints excluded: chain D residue 207 GLU Chi-restraints excluded: chain F residue 170 ARG Chi-restraints excluded: chain G residue 90 GLN Chi-restraints excluded: chain G residue 112 ASP Chi-restraints excluded: chain G residue 170 VAL Chi-restraints excluded: chain H residue 80 GLN Chi-restraints excluded: chain H residue 86 VAL Chi-restraints excluded: chain H residue 110 GLU Chi-restraints excluded: chain I residue 195 GLN Chi-restraints excluded: chain J residue 16 THR Chi-restraints excluded: chain K residue 80 ILE Chi-restraints excluded: chain K residue 119 VAL Chi-restraints excluded: chain K residue 128 GLN Chi-restraints excluded: chain M residue 65 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 245 random chunks: chunk 214 optimal weight: 2.9990 chunk 226 optimal weight: 10.0000 chunk 206 optimal weight: 10.0000 chunk 220 optimal weight: 0.6980 chunk 132 optimal weight: 0.9980 chunk 95 optimal weight: 0.2980 chunk 172 optimal weight: 4.9990 chunk 67 optimal weight: 4.9990 chunk 198 optimal weight: 0.9980 chunk 208 optimal weight: 4.9990 chunk 219 optimal weight: 5.9990 overall best weight: 1.1982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 214 ASN B 146 GLN F 181 GLN G 224 ASN ** K 83 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8559 moved from start: 0.1341 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 19748 Z= 0.160 Angle : 0.470 10.009 26714 Z= 0.252 Chirality : 0.041 0.160 3079 Planarity : 0.004 0.052 3404 Dihedral : 3.839 18.900 2690 Min Nonbonded Distance : 2.193 Molprobity Statistics. All-atom Clashscore : 2.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 1.09 % Allowed : 15.00 % Favored : 83.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.79 (0.17), residues: 2456 helix: 2.99 (0.18), residues: 898 sheet: 1.25 (0.22), residues: 538 loop : -0.55 (0.18), residues: 1020 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP I 149 HIS 0.004 0.001 HIS E 65 PHE 0.015 0.001 PHE A 173 TYR 0.009 0.001 TYR B 136 ARG 0.002 0.000 ARG F 233 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4912 Ramachandran restraints generated. 2456 Oldfield, 0 Emsley, 2456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4912 Ramachandran restraints generated. 2456 Oldfield, 0 Emsley, 2456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 227 residues out of total 2149 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 204 time to evaluate : 2.493 Fit side-chains REVERT: D 207 GLU cc_start: 0.7320 (OUTLIER) cc_final: 0.6431 (mp0) REVERT: F 28 MET cc_start: 0.8736 (mtp) cc_final: 0.8460 (mtm) REVERT: F 171 GLN cc_start: 0.7636 (tp-100) cc_final: 0.7081 (tp-100) REVERT: G 112 ASP cc_start: 0.8539 (OUTLIER) cc_final: 0.8124 (p0) REVERT: H 80 GLN cc_start: 0.8260 (OUTLIER) cc_final: 0.8015 (tt0) REVERT: H 110 GLU cc_start: 0.8264 (OUTLIER) cc_final: 0.7690 (mt-10) REVERT: K 128 GLN cc_start: 0.6569 (OUTLIER) cc_final: 0.5614 (mp10) REVERT: M 117 GLU cc_start: 0.7050 (tp30) cc_final: 0.6656 (mp0) REVERT: M 121 GLU cc_start: 0.7771 (pm20) cc_final: 0.7527 (pm20) outliers start: 23 outliers final: 13 residues processed: 218 average time/residue: 1.5104 time to fit residues: 365.2835 Evaluate side-chains 217 residues out of total 2149 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 199 time to evaluate : 2.445 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 150 ASP Chi-restraints excluded: chain C residue 216 SER Chi-restraints excluded: chain D residue 104 ASN Chi-restraints excluded: chain D residue 205 VAL Chi-restraints excluded: chain D residue 207 GLU Chi-restraints excluded: chain E residue 10 VAL Chi-restraints excluded: chain G residue 90 GLN Chi-restraints excluded: chain G residue 112 ASP Chi-restraints excluded: chain G residue 170 VAL Chi-restraints excluded: chain H residue 80 GLN Chi-restraints excluded: chain H residue 86 VAL Chi-restraints excluded: chain H residue 110 GLU Chi-restraints excluded: chain J residue 16 THR Chi-restraints excluded: chain J residue 93 ILE Chi-restraints excluded: chain K residue 80 ILE Chi-restraints excluded: chain K residue 119 VAL Chi-restraints excluded: chain K residue 128 GLN Chi-restraints excluded: chain M residue 65 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 245 random chunks: chunk 144 optimal weight: 1.9990 chunk 232 optimal weight: 1.9990 chunk 142 optimal weight: 5.9990 chunk 110 optimal weight: 7.9990 chunk 161 optimal weight: 0.5980 chunk 244 optimal weight: 8.9990 chunk 224 optimal weight: 0.7980 chunk 194 optimal weight: 0.7980 chunk 20 optimal weight: 4.9990 chunk 150 optimal weight: 0.7980 chunk 119 optimal weight: 10.0000 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 214 ASN B 146 GLN F 64 ASN G 224 ASN ** K 83 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8544 moved from start: 0.1335 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 19748 Z= 0.145 Angle : 0.457 10.186 26714 Z= 0.245 Chirality : 0.041 0.157 3079 Planarity : 0.004 0.052 3404 Dihedral : 3.754 17.947 2690 Min Nonbonded Distance : 2.192 Molprobity Statistics. All-atom Clashscore : 2.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer: Outliers : 1.09 % Allowed : 15.05 % Favored : 83.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.86 (0.17), residues: 2456 helix: 3.03 (0.17), residues: 898 sheet: 1.28 (0.22), residues: 538 loop : -0.48 (0.18), residues: 1020 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP I 149 HIS 0.003 0.001 HIS E 65 PHE 0.013 0.001 PHE A 173 TYR 0.008 0.001 TYR B 156 ARG 0.001 0.000 ARG H 106 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4912 Ramachandran restraints generated. 2456 Oldfield, 0 Emsley, 2456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4912 Ramachandran restraints generated. 2456 Oldfield, 0 Emsley, 2456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 227 residues out of total 2149 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 204 time to evaluate : 2.341 Fit side-chains REVERT: D 207 GLU cc_start: 0.7323 (OUTLIER) cc_final: 0.6479 (mp0) REVERT: F 28 MET cc_start: 0.8716 (mtp) cc_final: 0.8443 (mtm) REVERT: F 171 GLN cc_start: 0.7582 (tp-100) cc_final: 0.7038 (tp-100) REVERT: G 112 ASP cc_start: 0.8499 (OUTLIER) cc_final: 0.8081 (p0) REVERT: H 80 GLN cc_start: 0.8244 (OUTLIER) cc_final: 0.8006 (tt0) REVERT: H 110 GLU cc_start: 0.8226 (OUTLIER) cc_final: 0.7616 (mt-10) REVERT: K 128 GLN cc_start: 0.6635 (OUTLIER) cc_final: 0.5678 (mp10) REVERT: M 117 GLU cc_start: 0.7042 (tp30) cc_final: 0.6647 (mp0) REVERT: M 121 GLU cc_start: 0.7749 (pm20) cc_final: 0.7506 (pm20) outliers start: 23 outliers final: 16 residues processed: 220 average time/residue: 1.4667 time to fit residues: 362.1573 Evaluate side-chains 222 residues out of total 2149 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 201 time to evaluate : 2.390 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 150 ASP Chi-restraints excluded: chain B residue 87 THR Chi-restraints excluded: chain C residue 216 SER Chi-restraints excluded: chain D residue 104 ASN Chi-restraints excluded: chain D residue 133 MET Chi-restraints excluded: chain D residue 205 VAL Chi-restraints excluded: chain D residue 207 GLU Chi-restraints excluded: chain E residue 10 VAL Chi-restraints excluded: chain G residue 90 GLN Chi-restraints excluded: chain G residue 112 ASP Chi-restraints excluded: chain G residue 170 VAL Chi-restraints excluded: chain H residue 80 GLN Chi-restraints excluded: chain H residue 86 VAL Chi-restraints excluded: chain H residue 110 GLU Chi-restraints excluded: chain I residue 195 GLN Chi-restraints excluded: chain J residue 16 THR Chi-restraints excluded: chain J residue 93 ILE Chi-restraints excluded: chain K residue 80 ILE Chi-restraints excluded: chain K residue 119 VAL Chi-restraints excluded: chain K residue 128 GLN Chi-restraints excluded: chain M residue 65 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 245 random chunks: chunk 154 optimal weight: 0.8980 chunk 207 optimal weight: 6.9990 chunk 59 optimal weight: 4.9990 chunk 179 optimal weight: 5.9990 chunk 28 optimal weight: 6.9990 chunk 54 optimal weight: 7.9990 chunk 194 optimal weight: 0.4980 chunk 81 optimal weight: 3.9990 chunk 199 optimal weight: 10.0000 chunk 24 optimal weight: 10.0000 chunk 35 optimal weight: 0.2980 overall best weight: 2.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 214 ASN B 84 ASN G 224 ASN ** K 83 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 = 0.3373 r_free = 0.3373 target = 0.107655 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2934 r_free = 0.2934 target = 0.077461 restraints weight = 29400.754| |-----------------------------------------------------------------------------| r_work (start): 0.2878 rms_B_bonded: 2.48 r_work: 0.2759 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.2638 rms_B_bonded: 4.57 restraints_weight: 0.2500 r_work (final): 0.2638 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8400 moved from start: 0.1415 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 19748 Z= 0.231 Angle : 0.515 9.837 26714 Z= 0.276 Chirality : 0.043 0.161 3079 Planarity : 0.004 0.053 3404 Dihedral : 4.001 20.148 2690 Min Nonbonded Distance : 2.182 Molprobity Statistics. All-atom Clashscore : 3.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer: Outliers : 1.23 % Allowed : 15.05 % Favored : 83.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.71 (0.17), residues: 2456 helix: 2.94 (0.18), residues: 896 sheet: 1.23 (0.22), residues: 537 loop : -0.62 (0.18), residues: 1023 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP I 149 HIS 0.005 0.001 HIS E 65 PHE 0.014 0.001 PHE A 173 TYR 0.012 0.001 TYR B 136 ARG 0.002 0.000 ARG F 233 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6984.63 seconds wall clock time: 123 minutes 40.99 seconds (7420.99 seconds total)