Starting phenix.real_space_refine on Fri Dec 8 12:30:05 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dwg_27753/12_2023/8dwg_27753_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dwg_27753/12_2023/8dwg_27753.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dwg_27753/12_2023/8dwg_27753_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.71 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dwg_27753/12_2023/8dwg_27753_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dwg_27753/12_2023/8dwg_27753_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dwg_27753/12_2023/8dwg_27753.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dwg_27753/12_2023/8dwg_27753.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dwg_27753/12_2023/8dwg_27753_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dwg_27753/12_2023/8dwg_27753_updated.pdb" } resolution = 2.71 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= 0.001 sd= 0.024 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 57 5.16 5 C 5356 2.51 5 N 1421 2.21 5 O 1516 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 17": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 21": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 15": "NH1" <-> "NH2" Residue "B ARG 24": "NH1" <-> "NH2" Residue "B ARG 32": "NH1" <-> "NH2" Residue "B PHE 100": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 115": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 117": "NH1" <-> "NH2" Residue "B PHE 125": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 151": "OE1" <-> "OE2" Residue "B PHE 164": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 182": "OE1" <-> "OE2" Residue "B PHE 192": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 197": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 212": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 233": "OD1" <-> "OD2" Residue "B TYR 243": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 59": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 66": "OD1" <-> "OD2" Residue "C ARG 68": "NH1" <-> "NH2" Residue "C ASP 83": "OD1" <-> "OD2" Residue "C TYR 105": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 111": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 124": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 134": "NH1" <-> "NH2" Residue "C ARG 137": "NH1" <-> "NH2" Residue "C PHE 151": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 163": "OD1" <-> "OD2" Residue "C PHE 180": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 212": "OD1" <-> "OD2" Residue "C PHE 253": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 256": "NH1" <-> "NH2" Residue "C TYR 264": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 289": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 322": "OD1" <-> "OD2" Residue "C ASP 323": "OD1" <-> "OD2" Residue "D PHE 61": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R ARG 55": "NH1" <-> "NH2" Residue "R PHE 75": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R PHE 104": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R TYR 106": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R PHE 107": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R PHE 186": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R TYR 215": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R PHE 225": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R PHE 232": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R PHE 239": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R PHE 250": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R PHE 259": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R PHE 274": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 59": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 60": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 62": "OD1" <-> "OD2" Residue "E PHE 68": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 74": "OD1" <-> "OD2" Residue "E ASP 90": "OD1" <-> "OD2" Residue "E TYR 103": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 108": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 148": "NH1" <-> "NH2" Residue "E TYR 161": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 163": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 165": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 215": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 216": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 227": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/chem_data/mon_lib" Total number of atoms: 8350 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 124 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 124 Classifications: {'peptide': 13} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 1, 'TRANS': 11} 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: "B" Number of atoms: 1704 Number of conformers: 1 Conformer: "" Number of residues, atoms: 221, 1704 Classifications: {'peptide': 221} Incomplete info: {'truncation_to_alanine': 26} Link IDs: {'PTRANS': 6, 'TRANS': 214} Chain breaks: 2 Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 102 Unresolved non-hydrogen angles: 124 Unresolved non-hydrogen dihedrals: 84 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 5, 'ARG:plan': 4, 'ASP:plan': 7} Unresolved non-hydrogen planarities: 67 Chain: "C" Number of atoms: 2480 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 2480 Classifications: {'peptide': 338} Incomplete info: {'truncation_to_alanine': 33} Link IDs: {'PTRANS': 5, 'TRANS': 332} Unresolved non-hydrogen bonds: 120 Unresolved non-hydrogen angles: 147 Unresolved non-hydrogen dihedrals: 93 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLN:plan1': 4, 'GLU:plan': 5, 'ARG:plan': 7, 'ASN:plan1': 1, 'ASP:plan': 6} Unresolved non-hydrogen planarities: 92 Chain: "D" Number of atoms: 350 Number of conformers: 1 Conformer: "" Number of residues, atoms: 51, 350 Classifications: {'peptide': 51} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PTRANS': 4, 'TRANS': 46} Unresolved non-hydrogen bonds: 44 Unresolved non-hydrogen angles: 52 Unresolved non-hydrogen dihedrals: 36 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 2, 'ARG:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 23 Chain: "R" Number of atoms: 1937 Number of conformers: 1 Conformer: "" Number of residues, atoms: 247, 1937 Classifications: {'peptide': 247} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 6, 'TRANS': 240} Chain breaks: 1 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 34 Unresolved non-hydrogen angles: 41 Unresolved non-hydrogen dihedrals: 28 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 8 Chain: "E" Number of atoms: 1730 Number of conformers: 1 Conformer: "" Number of residues, atoms: 231, 1730 Classifications: {'peptide': 231} Incomplete info: {'truncation_to_alanine': 14} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 220} Chain breaks: 1 Unresolved non-hydrogen bonds: 47 Unresolved non-hydrogen angles: 58 Unresolved non-hydrogen dihedrals: 36 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLU:plan': 6, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 29 Chain: "R" Number of atoms: 25 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 25 Unusual residues: {'U39': 1} Classifications: {'undetermined': 1} Time building chain proxies: 4.98, per 1000 atoms: 0.60 Number of scatterers: 8350 At special positions: 0 Unit cell: (97.68, 116.16, 120.56, 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 57 16.00 O 1516 8.00 N 1421 7.00 C 5356 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS R 23 " - pdb=" SG CYS R 251 " distance=2.03 Simple disulfide: pdb=" SG CYS R 161 " - pdb=" SG CYS R 173 " distance=2.03 Simple disulfide: pdb=" SG CYS E 147 " - pdb=" SG CYS E 217 " distance=2.04 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: 3.16 Conformation dependent library (CDL) restraints added in 1.6 seconds 2162 Ramachandran restraints generated. 1081 Oldfield, 0 Emsley, 1081 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2060 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 27 helices and 12 sheets defined 33.2% alpha, 22.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.92 Creating SS restraints... Processing helix chain 'B' and resid 7 through 32 removed outlier: 3.536A pdb=" N ALA B 11 " --> pdb=" O ALA B 7 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N ALA B 12 " --> pdb=" O GLU B 8 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N LYS B 29 " --> pdb=" O GLU B 25 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N ARG B 32 " --> pdb=" O GLU B 28 " (cutoff:3.500A) Processing helix chain 'B' and resid 46 through 48 No H-bonds generated for 'chain 'B' and resid 46 through 48' Processing helix chain 'B' and resid 96 through 98 No H-bonds generated for 'chain 'B' and resid 96 through 98' Processing helix chain 'B' and resid 115 through 129 removed outlier: 3.582A pdb=" N LEU B 118 " --> pdb=" O TYR B 115 " (cutoff:3.500A) removed outlier: 5.048A pdb=" N GLN B 119 " --> pdb=" O ASN B 116 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N ASP B 124 " --> pdb=" O ALA B 121 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N PHE B 125 " --> pdb=" O LEU B 122 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N SER B 127 " --> pdb=" O ASP B 124 " (cutoff:3.500A) Processing helix chain 'B' and resid 132 through 134 No H-bonds generated for 'chain 'B' and resid 132 through 134' Processing helix chain 'B' and resid 146 through 154 removed outlier: 3.637A pdb=" N GLU B 151 " --> pdb=" O ASP B 147 " (cutoff:3.500A) Processing helix chain 'B' and resid 160 through 163 No H-bonds generated for 'chain 'B' and resid 160 through 163' Processing helix chain 'B' and resid 165 through 167 No H-bonds generated for 'chain 'B' and resid 165 through 167' Processing helix chain 'B' and resid 184 through 203 removed outlier: 3.574A pdb=" N ALA B 189 " --> pdb=" O ARG B 185 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N ARG B 194 " --> pdb=" O LYS B 190 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N PHE B 197 " --> pdb=" O ILE B 193 " (cutoff:3.500A) removed outlier: 4.128A pdb=" N ILE B 200 " --> pdb=" O GLU B 196 " (cutoff:3.500A) Processing helix chain 'B' and resid 223 through 242 Processing helix chain 'C' and resid 4 through 24 Processing helix chain 'C' and resid 30 through 36 removed outlier: 3.626A pdb=" N ASN C 35 " --> pdb=" O SER C 31 " (cutoff:3.500A) removed outlier: 4.997A pdb=" N ASN C 36 " --> pdb=" O GLN C 32 " (cutoff:3.500A) Processing helix chain 'D' and resid 13 through 23 Processing helix chain 'D' and resid 30 through 43 Processing helix chain 'R' and resid 24 through 52 removed outlier: 3.904A pdb=" N LEU R 28 " --> pdb=" O TYR R 24 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N SER R 29 " --> pdb=" O LYS R 25 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N VAL R 47 " --> pdb=" O THR R 43 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N VAL R 48 " --> pdb=" O GLY R 44 " (cutoff:3.500A) Processing helix chain 'R' and resid 60 through 87 removed outlier: 3.754A pdb=" N TYR R 64 " --> pdb=" O ALA R 60 " (cutoff:3.500A) Processing helix chain 'R' and resid 93 through 97 removed outlier: 3.561A pdb=" N ILE R 97 " --> pdb=" O THR R 93 " (cutoff:3.500A) No H-bonds generated for 'chain 'R' and resid 93 through 97' Processing helix chain 'R' and resid 99 through 125 removed outlier: 4.801A pdb=" N PHE R 104 " --> pdb=" O PRO R 100 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N VAL R 124 " --> pdb=" O ARG R 120 " (cutoff:3.500A) Processing helix chain 'R' and resid 127 through 132 Processing helix chain 'R' and resid 138 through 160 Processing helix chain 'R' and resid 171 through 203 Processing helix chain 'R' and resid 212 through 228 Processing helix chain 'R' and resid 231 through 238 removed outlier: 6.192A pdb=" N PHE R 236 " --> pdb=" O PHE R 232 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N PHE R 237 " --> pdb=" O GLY R 233 " (cutoff:3.500A) Processing helix chain 'R' and resid 246 through 251 removed outlier: 3.899A pdb=" N PHE R 250 " --> pdb=" O ARG R 246 " (cutoff:3.500A) Processing helix chain 'R' and resid 254 through 272 Proline residue: R 269 - end of helix Processing helix chain 'E' and resid 29 through 31 No H-bonds generated for 'chain 'E' and resid 29 through 31' Processing helix chain 'E' and resid 88 through 90 No H-bonds generated for 'chain 'E' and resid 88 through 90' Processing sheet with id= A, first strand: chain 'B' and resid 211 through 215 removed outlier: 6.830A pdb=" N VAL B 139 " --> pdb=" O TYR B 212 " (cutoff:3.500A) removed outlier: 7.886A pdb=" N HIS B 214 " --> pdb=" O VAL B 139 " (cutoff:3.500A) removed outlier: 6.338A pdb=" N LEU B 141 " --> pdb=" O HIS B 214 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N ALA B 105 " --> pdb=" O ARG B 35 " (cutoff:3.500A) removed outlier: 6.758A pdb=" N ASN B 80 " --> pdb=" O LEU B 34 " (cutoff:3.500A) removed outlier: 7.935A pdb=" N LEU B 36 " --> pdb=" O ASN B 80 " (cutoff:3.500A) removed outlier: 6.333A pdb=" N HIS B 82 " --> pdb=" O LEU B 36 " (cutoff:3.500A) removed outlier: 7.391A pdb=" N LEU B 38 " --> pdb=" O HIS B 82 " (cutoff:3.500A) removed outlier: 6.358A pdb=" N PHE B 84 " --> pdb=" O LEU B 38 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'C' and resid 58 through 63 removed outlier: 6.867A pdb=" N ALA C 73 " --> pdb=" O TYR C 59 " (cutoff:3.500A) removed outlier: 4.339A pdb=" N MET C 61 " --> pdb=" O VAL C 71 " (cutoff:3.500A) removed outlier: 6.587A pdb=" N VAL C 71 " --> pdb=" O MET C 61 " (cutoff:3.500A) removed outlier: 5.022A pdb=" N TRP C 63 " --> pdb=" O LEU C 69 " (cutoff:3.500A) removed outlier: 7.223A pdb=" N LEU C 69 " --> pdb=" O TRP C 63 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N SER C 74 " --> pdb=" O LYS C 78 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N LYS C 78 " --> pdb=" O SER C 74 " (cutoff:3.500A) removed outlier: 6.180A pdb=" N ASP C 83 " --> pdb=" O LYS C 89 " (cutoff:3.500A) removed outlier: 5.979A pdb=" N LYS C 89 " --> pdb=" O ASP C 83 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'C' and resid 100 through 105 removed outlier: 6.967A pdb=" N GLY C 115 " --> pdb=" O MET C 101 " (cutoff:3.500A) removed outlier: 4.569A pdb=" N CYS C 103 " --> pdb=" O ALA C 113 " (cutoff:3.500A) removed outlier: 6.385A pdb=" N ALA C 113 " --> pdb=" O CYS C 103 " (cutoff:3.500A) removed outlier: 4.904A pdb=" N TYR C 105 " --> pdb=" O TYR C 111 " (cutoff:3.500A) removed outlier: 7.117A pdb=" N TYR C 111 " --> pdb=" O TYR C 105 " (cutoff:3.500A) removed outlier: 5.911A pdb=" N ASN C 125 " --> pdb=" O VAL C 135 " (cutoff:3.500A) removed outlier: 6.206A pdb=" N VAL C 135 " --> pdb=" O ASN C 125 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'C' and resid 146 through 151 removed outlier: 6.806A pdb=" N SER C 160 " --> pdb=" O SER C 147 " (cutoff:3.500A) removed outlier: 4.324A pdb=" N CYS C 149 " --> pdb=" O VAL C 158 " (cutoff:3.500A) removed outlier: 6.659A pdb=" N VAL C 158 " --> pdb=" O CYS C 149 " (cutoff:3.500A) removed outlier: 4.905A pdb=" N PHE C 151 " --> pdb=" O GLN C 156 " (cutoff:3.500A) removed outlier: 7.507A pdb=" N GLN C 156 " --> pdb=" O PHE C 151 " (cutoff:3.500A) removed outlier: 4.265A pdb=" N THR C 165 " --> pdb=" O SER C 161 " (cutoff:3.500A) removed outlier: 6.346A pdb=" N ASP C 170 " --> pdb=" O GLN C 176 " (cutoff:3.500A) removed outlier: 5.959A pdb=" N GLN C 176 " --> pdb=" O ASP C 170 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'C' and resid 187 through 192 removed outlier: 6.822A pdb=" N GLY C 202 " --> pdb=" O MET C 188 " (cutoff:3.500A) removed outlier: 4.430A pdb=" N LEU C 190 " --> pdb=" O VAL C 200 " (cutoff:3.500A) removed outlier: 6.695A pdb=" N VAL C 200 " --> pdb=" O LEU C 190 " (cutoff:3.500A) removed outlier: 5.262A pdb=" N LEU C 192 " --> pdb=" O LEU C 198 " (cutoff:3.500A) removed outlier: 7.439A pdb=" N LEU C 198 " --> pdb=" O LEU C 192 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N GLN C 220 " --> pdb=" O LEU C 210 " (cutoff:3.500A) removed outlier: 6.738A pdb=" N ASP C 212 " --> pdb=" O CYS C 218 " (cutoff:3.500A) removed outlier: 6.235A pdb=" N CYS C 218 " --> pdb=" O ASP C 212 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'C' and resid 229 through 234 removed outlier: 6.632A pdb=" N GLY C 244 " --> pdb=" O ASN C 230 " (cutoff:3.500A) removed outlier: 4.321A pdb=" N ILE C 232 " --> pdb=" O ALA C 242 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N ALA C 242 " --> pdb=" O ILE C 232 " (cutoff:3.500A) removed outlier: 4.744A pdb=" N PHE C 234 " --> pdb=" O ALA C 240 " (cutoff:3.500A) removed outlier: 7.191A pdb=" N ALA C 240 " --> pdb=" O PHE C 234 " (cutoff:3.500A) removed outlier: 5.947A pdb=" N ASP C 254 " --> pdb=" O GLU C 260 " (cutoff:3.500A) removed outlier: 5.763A pdb=" N GLU C 260 " --> pdb=" O ASP C 254 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'C' and resid 273 through 278 removed outlier: 6.514A pdb=" N GLY C 288 " --> pdb=" O THR C 274 " (cutoff:3.500A) removed outlier: 4.301A pdb=" N VAL C 276 " --> pdb=" O LEU C 286 " (cutoff:3.500A) removed outlier: 6.731A pdb=" N LEU C 286 " --> pdb=" O VAL C 276 " (cutoff:3.500A) removed outlier: 4.472A pdb=" N PHE C 278 " --> pdb=" O LEU C 284 " (cutoff:3.500A) removed outlier: 6.685A pdb=" N LEU C 284 " --> pdb=" O PHE C 278 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N GLY C 306 " --> pdb=" O VAL C 296 " (cutoff:3.500A) removed outlier: 5.903A pdb=" N ASP C 298 " --> pdb=" O ARG C 304 " (cutoff:3.500A) removed outlier: 6.412A pdb=" N ARG C 304 " --> pdb=" O ASP C 298 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'C' and resid 46 through 51 removed outlier: 6.393A pdb=" N ILE C 338 " --> pdb=" O ARG C 48 " (cutoff:3.500A) removed outlier: 4.287A pdb=" N THR C 50 " --> pdb=" O LEU C 336 " (cutoff:3.500A) removed outlier: 6.460A pdb=" N LEU C 336 " --> pdb=" O THR C 50 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'E' and resid 3 through 7 Processing sheet with id= J, first strand: chain 'E' and resid 10 through 12 removed outlier: 6.223A pdb=" N ARG E 38 " --> pdb=" O TRP E 47 " (cutoff:3.500A) removed outlier: 4.950A pdb=" N TRP E 47 " --> pdb=" O ARG E 38 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'E' and resid 134 through 136 removed outlier: 6.297A pdb=" N LYS E 232 " --> pdb=" O VAL E 135 " (cutoff:3.500A) removed outlier: 6.261A pdb=" N LEU E 166 " --> pdb=" O LEU E 175 " (cutoff:3.500A) removed outlier: 5.581A pdb=" N LEU E 175 " --> pdb=" O LEU E 166 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'E' and resid 143 through 147 378 hydrogen bonds defined for protein. 1059 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: 2.60 Time building geometry restraints manager: 3.41 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2668 1.34 - 1.46: 1972 1.46 - 1.58: 3819 1.58 - 1.69: 1 1.69 - 1.81: 77 Bond restraints: 8537 Sorted by residual: bond pdb=" C1 U39 R 401 " pdb=" N1 U39 R 401 " ideal model delta sigma weight residual 1.463 1.354 0.109 2.00e-02 2.50e+03 2.95e+01 bond pdb=" N2 U39 R 401 " pdb=" S1 U39 R 401 " ideal model delta sigma weight residual 1.724 1.627 0.097 2.00e-02 2.50e+03 2.34e+01 bond pdb=" C11 U39 R 401 " pdb=" N2 U39 R 401 " ideal model delta sigma weight residual 1.473 1.379 0.094 2.00e-02 2.50e+03 2.19e+01 bond pdb=" C12 U39 R 401 " pdb=" S1 U39 R 401 " ideal model delta sigma weight residual 1.832 1.754 0.078 2.00e-02 2.50e+03 1.52e+01 bond pdb=" C2 U39 R 401 " pdb=" N1 U39 R 401 " ideal model delta sigma weight residual 1.471 1.413 0.058 2.00e-02 2.50e+03 8.53e+00 ... (remaining 8532 not shown) Histogram of bond angle deviations from ideal: 59.96 - 74.79: 3 74.79 - 89.61: 0 89.61 - 104.44: 88 104.44 - 119.27: 6893 119.27 - 134.10: 4635 Bond angle restraints: 11619 Sorted by residual: angle pdb=" O3 U39 R 401 " pdb=" S1 U39 R 401 " pdb=" O4 U39 R 401 " ideal model delta sigma weight residual 101.20 119.19 -17.99 3.00e+00 1.11e-01 3.59e+01 angle pdb=" N MET E 180 " pdb=" CA MET E 180 " pdb=" CB MET E 180 " ideal model delta sigma weight residual 114.17 108.46 5.71 1.14e+00 7.69e-01 2.51e+01 angle pdb=" N LEU R 230 " pdb=" CA LEU R 230 " pdb=" C LEU R 230 " ideal model delta sigma weight residual 109.81 116.34 -6.53 2.21e+00 2.05e-01 8.72e+00 angle pdb=" C HIS R 243 " pdb=" N VAL R 244 " pdb=" CA VAL R 244 " ideal model delta sigma weight residual 122.97 120.08 2.89 9.80e-01 1.04e+00 8.72e+00 angle pdb=" C THR B 216 " pdb=" N CYS B 217 " pdb=" CA CYS B 217 " ideal model delta sigma weight residual 121.54 116.12 5.42 1.91e+00 2.74e-01 8.06e+00 ... (remaining 11614 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.46: 4564 17.46 - 34.92: 330 34.92 - 52.37: 59 52.37 - 69.83: 5 69.83 - 87.29: 4 Dihedral angle restraints: 4962 sinusoidal: 1772 harmonic: 3190 Sorted by residual: dihedral pdb=" CB CYS E 147 " pdb=" SG CYS E 147 " pdb=" SG CYS E 217 " pdb=" CB CYS E 217 " ideal model delta sinusoidal sigma weight residual 93.00 141.76 -48.76 1 1.00e+01 1.00e-02 3.27e+01 dihedral pdb=" CA MET E 128 " pdb=" C MET E 128 " pdb=" N THR E 129 " pdb=" CA THR E 129 " ideal model delta harmonic sigma weight residual -180.00 -156.77 -23.23 0 5.00e+00 4.00e-02 2.16e+01 dihedral pdb=" CA PHE C 234 " pdb=" C PHE C 234 " pdb=" N PHE C 235 " pdb=" CA PHE C 235 " ideal model delta harmonic sigma weight residual 180.00 158.89 21.11 0 5.00e+00 4.00e-02 1.78e+01 ... (remaining 4959 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.073: 1208 0.073 - 0.147: 132 0.147 - 0.220: 4 0.220 - 0.294: 0 0.294 - 0.367: 1 Chirality restraints: 1345 Sorted by residual: chirality pdb=" C12 U39 R 401 " pdb=" C13 U39 R 401 " pdb=" C14 U39 R 401 " pdb=" S1 U39 R 401 " both_signs ideal model delta sigma weight residual True 3.22 -2.86 0.37 2.00e-01 2.50e+01 3.37e+00 chirality pdb=" CG LEU B 143 " pdb=" CB LEU B 143 " pdb=" CD1 LEU B 143 " pdb=" CD2 LEU B 143 " both_signs ideal model delta sigma weight residual False -2.59 -2.39 -0.20 2.00e-01 2.50e+01 1.03e+00 chirality pdb=" CB THR C 223 " pdb=" CA THR C 223 " pdb=" OG1 THR C 223 " pdb=" CG2 THR C 223 " both_signs ideal model delta sigma weight residual False 2.55 2.38 0.17 2.00e-01 2.50e+01 7.06e-01 ... (remaining 1342 not shown) Planarity restraints: 1456 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1 U39 R 401 " -0.058 2.00e-02 2.50e+03 9.95e-02 1.24e+02 pdb=" C10 U39 R 401 " 0.094 2.00e-02 2.50e+03 pdb=" C2 U39 R 401 " 0.119 2.00e-02 2.50e+03 pdb=" N1 U39 R 401 " -0.152 2.00e-02 2.50e+03 pdb=" O1 U39 R 401 " -0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASP D 48 " -0.037 5.00e-02 4.00e+02 5.63e-02 5.08e+00 pdb=" N PRO D 49 " 0.097 5.00e-02 4.00e+02 pdb=" CA PRO D 49 " -0.029 5.00e-02 4.00e+02 pdb=" CD PRO D 49 " -0.031 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ASP D 48 " -0.010 2.00e-02 2.50e+03 1.99e-02 3.96e+00 pdb=" C ASP D 48 " 0.034 2.00e-02 2.50e+03 pdb=" O ASP D 48 " -0.013 2.00e-02 2.50e+03 pdb=" N PRO D 49 " -0.012 2.00e-02 2.50e+03 ... (remaining 1453 not shown) Histogram of nonbonded interaction distances: 2.11 - 2.66: 131 2.66 - 3.22: 7698 3.22 - 3.78: 12701 3.78 - 4.34: 18186 4.34 - 4.90: 30422 Nonbonded interactions: 69138 Sorted by model distance: nonbonded pdb=" OH TYR R 106 " pdb=" O PHE R 232 " model vdw 2.106 2.440 nonbonded pdb=" OG SER C 281 " pdb=" OD2 ASP D 48 " model vdw 2.177 2.440 nonbonded pdb=" OH TYR B 243 " pdb=" OH TYR R 130 " model vdw 2.177 2.440 nonbonded pdb=" OE2 GLU B 25 " pdb=" NZ LYS B 29 " model vdw 2.199 2.520 nonbonded pdb=" O TYR B 170 " pdb=" NH1 ARG B 188 " model vdw 2.227 2.520 ... (remaining 69133 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: 0.930 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: 5.130 Check model and map are aligned: 0.130 Set scattering table: 0.080 Process input model: 26.940 Find NCS groups from input model: 0.280 Set up NCS constraints: 0.040 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:13.420 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 46.970 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7756 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 : 0.006 0.109 8537 Z= 0.418 Angle : 0.639 17.986 11619 Z= 0.349 Chirality : 0.046 0.367 1345 Planarity : 0.005 0.100 1456 Dihedral : 12.609 87.290 2893 Min Nonbonded Distance : 2.106 Molprobity Statistics. All-atom Clashscore : 6.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.53 % Favored : 95.47 % Rotamer: Outliers : 0.00 % Allowed : 0.23 % Favored : 99.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: -1.14 (0.25), residues: 1081 helix: -1.23 (0.24), residues: 367 sheet: 0.27 (0.31), residues: 281 loop : -0.85 (0.30), residues: 433 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP C 339 HIS 0.013 0.001 HIS B 82 PHE 0.012 0.002 PHE R 225 TYR 0.016 0.002 TYR C 59 ARG 0.009 0.000 ARG C 49 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2162 Ramachandran restraints generated. 1081 Oldfield, 0 Emsley, 1081 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2162 Ramachandran restraints generated. 1081 Oldfield, 0 Emsley, 1081 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 950 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 186 time to evaluate : 0.970 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 186 average time/residue: 1.0974 time to fit residues: 218.1184 Evaluate side-chains 179 residues out of total 950 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 179 time to evaluate : 0.975 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.0920 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 91 optimal weight: 1.9990 chunk 81 optimal weight: 0.5980 chunk 45 optimal weight: 1.9990 chunk 27 optimal weight: 0.8980 chunk 55 optimal weight: 0.9990 chunk 43 optimal weight: 0.5980 chunk 84 optimal weight: 0.5980 chunk 32 optimal weight: 0.7980 chunk 51 optimal weight: 0.7980 chunk 63 optimal weight: 0.8980 chunk 98 optimal weight: 0.0770 overall best weight: 0.5338 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 22 ASN B 80 ASN B 82 HIS B 101 ASN B 144 ASN ** B 223 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 220 GLN ** C 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 268 ASN C 340 ASN E 39 GLN E 82 GLN E 167 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7723 moved from start: 0.1137 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 8537 Z= 0.214 Angle : 0.544 6.130 11619 Z= 0.293 Chirality : 0.042 0.138 1345 Planarity : 0.004 0.042 1456 Dihedral : 5.084 54.497 1188 Min Nonbonded Distance : 2.090 Molprobity Statistics. All-atom Clashscore : 5.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.79 % Favored : 96.21 % Rotamer: Outliers : 1.17 % Allowed : 9.72 % Favored : 89.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: 0.18 (0.26), residues: 1081 helix: 0.95 (0.27), residues: 363 sheet: 0.51 (0.30), residues: 286 loop : -0.80 (0.31), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP C 169 HIS 0.013 0.001 HIS B 82 PHE 0.018 0.002 PHE R 104 TYR 0.014 0.001 TYR E 178 ARG 0.005 0.000 ARG C 49 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2162 Ramachandran restraints generated. 1081 Oldfield, 0 Emsley, 1081 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2162 Ramachandran restraints generated. 1081 Oldfield, 0 Emsley, 1081 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 950 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 180 time to evaluate : 0.884 Fit side-chains outliers start: 10 outliers final: 3 residues processed: 183 average time/residue: 1.2060 time to fit residues: 234.2995 Evaluate side-chains 176 residues out of total 950 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 173 time to evaluate : 0.964 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 1 residues processed: 2 average time/residue: 0.0785 time to fit residues: 1.4605 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 54 optimal weight: 1.9990 chunk 30 optimal weight: 0.9980 chunk 81 optimal weight: 0.9990 chunk 66 optimal weight: 0.6980 chunk 27 optimal weight: 3.9990 chunk 98 optimal weight: 1.9990 chunk 106 optimal weight: 0.6980 chunk 87 optimal weight: 1.9990 chunk 97 optimal weight: 0.9980 chunk 33 optimal weight: 0.4980 chunk 78 optimal weight: 2.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 22 ASN B 101 ASN B 144 ASN ** B 223 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 176 GLN C 220 GLN C 237 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7740 moved from start: 0.1319 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 8537 Z= 0.266 Angle : 0.555 11.089 11619 Z= 0.293 Chirality : 0.043 0.155 1345 Planarity : 0.004 0.036 1456 Dihedral : 5.098 55.553 1188 Min Nonbonded Distance : 2.085 Molprobity Statistics. All-atom Clashscore : 6.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.44 % Favored : 95.56 % Rotamer: Outliers : 3.04 % Allowed : 12.18 % Favored : 84.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: 0.59 (0.26), residues: 1081 helix: 1.70 (0.27), residues: 358 sheet: 0.48 (0.29), residues: 292 loop : -0.75 (0.31), residues: 431 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP C 82 HIS 0.006 0.001 HIS B 209 PHE 0.018 0.002 PHE C 234 TYR 0.015 0.002 TYR C 105 ARG 0.008 0.000 ARG C 134 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2162 Ramachandran restraints generated. 1081 Oldfield, 0 Emsley, 1081 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2162 Ramachandran restraints generated. 1081 Oldfield, 0 Emsley, 1081 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 950 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 168 time to evaluate : 0.984 Fit side-chains outliers start: 26 outliers final: 10 residues processed: 177 average time/residue: 1.2349 time to fit residues: 232.1326 Evaluate side-chains 175 residues out of total 950 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 165 time to evaluate : 0.947 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 5 residues processed: 5 average time/residue: 0.3385 time to fit residues: 3.2933 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 97 optimal weight: 0.8980 chunk 73 optimal weight: 0.9990 chunk 50 optimal weight: 0.0980 chunk 10 optimal weight: 0.9980 chunk 46 optimal weight: 0.9980 chunk 65 optimal weight: 1.9990 chunk 98 optimal weight: 3.9990 chunk 104 optimal weight: 1.9990 chunk 51 optimal weight: 0.5980 chunk 93 optimal weight: 2.9990 chunk 28 optimal weight: 0.0050 overall best weight: 0.5194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 22 ASN B 101 ASN ** B 223 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 220 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7723 moved from start: 0.1577 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 8537 Z= 0.196 Angle : 0.504 7.308 11619 Z= 0.269 Chirality : 0.041 0.137 1345 Planarity : 0.004 0.033 1456 Dihedral : 4.873 55.153 1188 Min Nonbonded Distance : 2.104 Molprobity Statistics. All-atom Clashscore : 5.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.89 % Favored : 96.11 % Rotamer: Outliers : 2.22 % Allowed : 14.40 % Favored : 83.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: 0.77 (0.26), residues: 1081 helix: 2.02 (0.28), residues: 363 sheet: 0.44 (0.29), residues: 293 loop : -0.75 (0.31), residues: 425 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP C 82 HIS 0.005 0.001 HIS B 209 PHE 0.015 0.001 PHE R 104 TYR 0.013 0.001 TYR E 178 ARG 0.008 0.000 ARG B 185 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2162 Ramachandran restraints generated. 1081 Oldfield, 0 Emsley, 1081 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2162 Ramachandran restraints generated. 1081 Oldfield, 0 Emsley, 1081 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 950 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 169 time to evaluate : 0.936 Fit side-chains outliers start: 19 outliers final: 11 residues processed: 178 average time/residue: 1.2437 time to fit residues: 234.9707 Evaluate side-chains 179 residues out of total 950 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 168 time to evaluate : 1.008 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 7 residues processed: 5 average time/residue: 0.1441 time to fit residues: 2.3730 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 86 optimal weight: 1.9990 chunk 59 optimal weight: 0.8980 chunk 1 optimal weight: 5.9990 chunk 77 optimal weight: 0.0980 chunk 43 optimal weight: 0.3980 chunk 89 optimal weight: 0.6980 chunk 72 optimal weight: 0.9980 chunk 0 optimal weight: 3.9990 chunk 53 optimal weight: 4.9990 chunk 93 optimal weight: 0.6980 chunk 26 optimal weight: 3.9990 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 22 ASN B 101 ASN ** B 223 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 220 GLN C 237 ASN C 259 GLN E 130 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7726 moved from start: 0.1632 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 8537 Z= 0.206 Angle : 0.516 11.306 11619 Z= 0.272 Chirality : 0.042 0.225 1345 Planarity : 0.004 0.033 1456 Dihedral : 4.810 55.447 1188 Min Nonbonded Distance : 2.103 Molprobity Statistics. All-atom Clashscore : 5.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.98 % Favored : 96.02 % Rotamer: Outliers : 2.22 % Allowed : 15.93 % Favored : 81.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: 0.84 (0.26), residues: 1081 helix: 2.15 (0.28), residues: 362 sheet: 0.44 (0.29), residues: 292 loop : -0.74 (0.31), residues: 427 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP C 82 HIS 0.004 0.001 HIS B 209 PHE 0.014 0.001 PHE R 104 TYR 0.015 0.001 TYR C 105 ARG 0.008 0.000 ARG B 185 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2162 Ramachandran restraints generated. 1081 Oldfield, 0 Emsley, 1081 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2162 Ramachandran restraints generated. 1081 Oldfield, 0 Emsley, 1081 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 950 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 167 time to evaluate : 0.961 Fit side-chains outliers start: 19 outliers final: 13 residues processed: 179 average time/residue: 1.2468 time to fit residues: 236.7394 Evaluate side-chains 179 residues out of total 950 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 166 time to evaluate : 0.950 Switching outliers to nearest non-outliers outliers start: 13 outliers final: 8 residues processed: 6 average time/residue: 0.3402 time to fit residues: 3.7392 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 35 optimal weight: 0.0070 chunk 94 optimal weight: 0.9980 chunk 20 optimal weight: 3.9990 chunk 61 optimal weight: 2.9990 chunk 25 optimal weight: 2.9990 chunk 104 optimal weight: 2.9990 chunk 86 optimal weight: 0.7980 chunk 48 optimal weight: 0.3980 chunk 8 optimal weight: 0.0980 chunk 34 optimal weight: 0.4980 chunk 54 optimal weight: 1.9990 overall best weight: 0.3598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 22 ASN B 101 ASN ** B 223 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 220 GLN C 259 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7709 moved from start: 0.1813 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 8537 Z= 0.160 Angle : 0.492 11.498 11619 Z= 0.259 Chirality : 0.041 0.168 1345 Planarity : 0.003 0.033 1456 Dihedral : 4.620 54.056 1188 Min Nonbonded Distance : 2.126 Molprobity Statistics. All-atom Clashscore : 6.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.89 % Favored : 96.11 % Rotamer: Outliers : 2.58 % Allowed : 16.51 % Favored : 80.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: 0.92 (0.26), residues: 1081 helix: 2.28 (0.28), residues: 362 sheet: 0.43 (0.29), residues: 292 loop : -0.72 (0.31), residues: 427 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP C 82 HIS 0.004 0.001 HIS B 209 PHE 0.014 0.001 PHE R 104 TYR 0.012 0.001 TYR E 178 ARG 0.009 0.000 ARG B 185 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2162 Ramachandran restraints generated. 1081 Oldfield, 0 Emsley, 1081 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2162 Ramachandran restraints generated. 1081 Oldfield, 0 Emsley, 1081 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 950 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 170 time to evaluate : 1.167 Fit side-chains outliers start: 22 outliers final: 11 residues processed: 181 average time/residue: 1.2800 time to fit residues: 245.7581 Evaluate side-chains 177 residues out of total 950 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 166 time to evaluate : 0.992 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 8 residues processed: 4 average time/residue: 0.1073 time to fit residues: 2.0141 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 100 optimal weight: 1.9990 chunk 11 optimal weight: 0.6980 chunk 59 optimal weight: 0.7980 chunk 76 optimal weight: 0.9980 chunk 87 optimal weight: 1.9990 chunk 58 optimal weight: 0.5980 chunk 104 optimal weight: 2.9990 chunk 65 optimal weight: 0.7980 chunk 63 optimal weight: 1.9990 chunk 48 optimal weight: 0.7980 chunk 64 optimal weight: 0.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 22 ASN B 101 ASN ** B 223 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 220 GLN C 259 GLN ** C 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7735 moved from start: 0.1721 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 8537 Z= 0.252 Angle : 0.546 12.147 11619 Z= 0.284 Chirality : 0.043 0.158 1345 Planarity : 0.004 0.035 1456 Dihedral : 4.829 56.158 1188 Min Nonbonded Distance : 2.090 Molprobity Statistics. All-atom Clashscore : 6.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.26 % Favored : 95.74 % Rotamer: Outliers : 2.22 % Allowed : 17.21 % Favored : 80.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: 0.80 (0.26), residues: 1081 helix: 2.11 (0.28), residues: 362 sheet: 0.46 (0.29), residues: 281 loop : -0.75 (0.30), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP R 147 HIS 0.005 0.001 HIS B 209 PHE 0.013 0.002 PHE R 104 TYR 0.018 0.002 TYR C 105 ARG 0.009 0.000 ARG B 185 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2162 Ramachandran restraints generated. 1081 Oldfield, 0 Emsley, 1081 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2162 Ramachandran restraints generated. 1081 Oldfield, 0 Emsley, 1081 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 950 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 171 time to evaluate : 1.081 Fit side-chains outliers start: 19 outliers final: 12 residues processed: 181 average time/residue: 1.2564 time to fit residues: 241.2922 Evaluate side-chains 181 residues out of total 950 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 169 time to evaluate : 1.000 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 7 residues processed: 5 average time/residue: 0.5857 time to fit residues: 4.5737 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 41 optimal weight: 1.9990 chunk 62 optimal weight: 2.9990 chunk 31 optimal weight: 0.8980 chunk 20 optimal weight: 2.9990 chunk 66 optimal weight: 0.9990 chunk 70 optimal weight: 0.6980 chunk 51 optimal weight: 1.9990 chunk 9 optimal weight: 0.9990 chunk 81 optimal weight: 0.4980 chunk 94 optimal weight: 0.5980 chunk 99 optimal weight: 0.6980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 22 ASN B 101 ASN ** B 223 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 220 GLN C 259 GLN ** C 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7731 moved from start: 0.1785 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 8537 Z= 0.237 Angle : 0.545 12.913 11619 Z= 0.283 Chirality : 0.042 0.152 1345 Planarity : 0.004 0.036 1456 Dihedral : 4.840 55.590 1188 Min Nonbonded Distance : 2.101 Molprobity Statistics. All-atom Clashscore : 6.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.07 % Favored : 95.93 % Rotamer: Outliers : 2.34 % Allowed : 17.45 % Favored : 80.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: 0.78 (0.26), residues: 1081 helix: 2.09 (0.28), residues: 362 sheet: 0.42 (0.29), residues: 286 loop : -0.76 (0.30), residues: 433 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP C 82 HIS 0.004 0.001 HIS B 209 PHE 0.016 0.002 PHE B 228 TYR 0.016 0.002 TYR C 105 ARG 0.009 0.000 ARG B 185 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2162 Ramachandran restraints generated. 1081 Oldfield, 0 Emsley, 1081 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2162 Ramachandran restraints generated. 1081 Oldfield, 0 Emsley, 1081 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 950 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 164 time to evaluate : 0.955 Fit side-chains outliers start: 20 outliers final: 13 residues processed: 178 average time/residue: 1.2443 time to fit residues: 235.3989 Evaluate side-chains 178 residues out of total 950 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 165 time to evaluate : 0.938 Switching outliers to nearest non-outliers outliers start: 13 outliers final: 10 residues processed: 4 average time/residue: 0.3965 time to fit residues: 3.1466 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 90 optimal weight: 0.4980 chunk 97 optimal weight: 1.9990 chunk 99 optimal weight: 1.9990 chunk 58 optimal weight: 1.9990 chunk 42 optimal weight: 0.0170 chunk 76 optimal weight: 0.9980 chunk 29 optimal weight: 1.9990 chunk 87 optimal weight: 0.9980 chunk 91 optimal weight: 0.6980 chunk 96 optimal weight: 1.9990 chunk 63 optimal weight: 2.9990 overall best weight: 0.6418 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 22 ASN B 101 ASN ** B 223 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 220 GLN C 259 GLN ** C 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7729 moved from start: 0.1804 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 8537 Z= 0.231 Angle : 0.542 12.167 11619 Z= 0.283 Chirality : 0.042 0.134 1345 Planarity : 0.004 0.049 1456 Dihedral : 4.824 55.483 1188 Min Nonbonded Distance : 2.102 Molprobity Statistics. All-atom Clashscore : 6.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.98 % Favored : 96.02 % Rotamer: Outliers : 1.76 % Allowed : 18.15 % Favored : 80.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: 0.78 (0.26), residues: 1081 helix: 2.12 (0.28), residues: 362 sheet: 0.40 (0.29), residues: 286 loop : -0.78 (0.31), residues: 433 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP R 241 HIS 0.004 0.001 HIS B 209 PHE 0.016 0.002 PHE B 228 TYR 0.016 0.002 TYR C 105 ARG 0.009 0.000 ARG B 185 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2162 Ramachandran restraints generated. 1081 Oldfield, 0 Emsley, 1081 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2162 Ramachandran restraints generated. 1081 Oldfield, 0 Emsley, 1081 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 950 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 166 time to evaluate : 1.014 Fit side-chains outliers start: 15 outliers final: 16 residues processed: 176 average time/residue: 1.2503 time to fit residues: 233.7374 Evaluate side-chains 182 residues out of total 950 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 166 time to evaluate : 1.053 Switching outliers to nearest non-outliers outliers start: 16 outliers final: 11 residues processed: 6 average time/residue: 0.3486 time to fit residues: 3.8070 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 102 optimal weight: 0.9990 chunk 62 optimal weight: 0.9990 chunk 48 optimal weight: 0.9990 chunk 71 optimal weight: 0.7980 chunk 107 optimal weight: 0.4980 chunk 99 optimal weight: 0.5980 chunk 85 optimal weight: 2.9990 chunk 8 optimal weight: 0.0770 chunk 66 optimal weight: 0.5980 chunk 52 optimal weight: 2.9990 chunk 68 optimal weight: 1.9990 overall best weight: 0.5138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 22 ASN B 101 ASN ** B 223 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 220 GLN ** C 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7720 moved from start: 0.1921 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 8537 Z= 0.200 Angle : 0.528 11.910 11619 Z= 0.277 Chirality : 0.042 0.137 1345 Planarity : 0.004 0.061 1456 Dihedral : 4.743 54.610 1188 Min Nonbonded Distance : 2.115 Molprobity Statistics. All-atom Clashscore : 6.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.89 % Favored : 96.11 % Rotamer: Outliers : 1.41 % Allowed : 18.38 % Favored : 80.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: 0.81 (0.26), residues: 1081 helix: 2.16 (0.28), residues: 362 sheet: 0.40 (0.29), residues: 286 loop : -0.76 (0.30), residues: 433 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP C 82 HIS 0.004 0.001 HIS B 209 PHE 0.014 0.001 PHE R 104 TYR 0.014 0.001 TYR E 59 ARG 0.009 0.000 ARG B 185 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2162 Ramachandran restraints generated. 1081 Oldfield, 0 Emsley, 1081 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2162 Ramachandran restraints generated. 1081 Oldfield, 0 Emsley, 1081 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 950 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 168 time to evaluate : 1.020 Fit side-chains outliers start: 12 outliers final: 11 residues processed: 178 average time/residue: 1.2707 time to fit residues: 239.8283 Evaluate side-chains 178 residues out of total 950 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 167 time to evaluate : 0.885 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 10 residues processed: 2 average time/residue: 0.6152 time to fit residues: 2.5996 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 91 optimal weight: 1.9990 chunk 26 optimal weight: 2.9990 chunk 79 optimal weight: 3.9990 chunk 12 optimal weight: 1.9990 chunk 23 optimal weight: 0.9980 chunk 85 optimal weight: 3.9990 chunk 35 optimal weight: 2.9990 chunk 88 optimal weight: 0.9980 chunk 10 optimal weight: 0.0980 chunk 15 optimal weight: 0.7980 chunk 75 optimal weight: 3.9990 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 22 ASN B 101 ASN ** B 223 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 220 GLN ** C 340 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 = 0.3458 r_free = 0.3458 target = 0.110271 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3245 r_free = 0.3245 target = 0.096210 restraints weight = 11782.379| |-----------------------------------------------------------------------------| r_work (start): 0.3254 rms_B_bonded: 1.60 r_work: 0.3145 rms_B_bonded: 2.07 restraints_weight: 0.5000 r_work: 0.3004 rms_B_bonded: 3.62 restraints_weight: 0.2500 r_work (final): 0.3004 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8057 moved from start: 0.1779 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 8537 Z= 0.318 Angle : 0.580 12.425 11619 Z= 0.304 Chirality : 0.044 0.137 1345 Planarity : 0.004 0.067 1456 Dihedral : 4.988 56.360 1188 Min Nonbonded Distance : 2.083 Molprobity Statistics. All-atom Clashscore : 6.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.00 % Favored : 95.00 % Rotamer: Outliers : 1.64 % Allowed : 18.74 % Favored : 79.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: 0.70 (0.26), residues: 1081 helix: 1.95 (0.28), residues: 364 sheet: 0.40 (0.29), residues: 287 loop : -0.75 (0.31), residues: 430 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP R 241 HIS 0.006 0.001 HIS E 35 PHE 0.015 0.002 PHE C 234 TYR 0.022 0.002 TYR C 105 ARG 0.009 0.000 ARG B 185 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4150.69 seconds wall clock time: 74 minutes 6.98 seconds (4446.98 seconds total)