Starting phenix.real_space_refine on Fri Jan 19 23:43:04 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hps_34942/01_2024/8hps_34942_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hps_34942/01_2024/8hps_34942.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.51 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hps_34942/01_2024/8hps_34942.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hps_34942/01_2024/8hps_34942.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hps_34942/01_2024/8hps_34942_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hps_34942/01_2024/8hps_34942_updated.pdb" } resolution = 3.51 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.016 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: 6 Type Number sf(0) Gaussians P 6 5.49 5 Mg 2 5.21 5 S 34 5.16 5 C 8310 2.51 5 N 2194 2.21 5 O 2438 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 21": "NH1" <-> "NH2" Residue "A ARG 22": "NH1" <-> "NH2" Residue "A ARG 110": "NH1" <-> "NH2" Residue "A ARG 119": "NH1" <-> "NH2" Residue "A GLU 173": "OE1" <-> "OE2" Residue "A ARG 210": "NH1" <-> "NH2" Residue "A ARG 230": "NH1" <-> "NH2" Residue "A ARG 236": "NH1" <-> "NH2" Residue "B ARG 8": "NH1" <-> "NH2" Residue "B ARG 9": "NH1" <-> "NH2" Residue "B ARG 97": "NH1" <-> "NH2" Residue "B ARG 130": "NH1" <-> "NH2" Residue "B ARG 162": "NH1" <-> "NH2" Residue "B GLU 163": "OE1" <-> "OE2" Residue "B ARG 221": "NH1" <-> "NH2" Residue "B ARG 265": "NH1" <-> "NH2" Residue "B ARG 266": "NH1" <-> "NH2" Residue "C ARG 8": "NH1" <-> "NH2" Residue "C ARG 21": "NH1" <-> "NH2" Residue "C ARG 66": "NH1" <-> "NH2" Residue "C ARG 71": "NH1" <-> "NH2" Residue "C ARG 80": "NH1" <-> "NH2" Residue "C ARG 98": "NH1" <-> "NH2" Residue "C ARG 134": "NH1" <-> "NH2" Residue "C ARG 144": "NH1" <-> "NH2" Residue "C ARG 151": "NH1" <-> "NH2" Residue "C ARG 155": "NH1" <-> "NH2" Residue "C ARG 174": "NH1" <-> "NH2" Residue "C ARG 178": "NH1" <-> "NH2" Residue "C ARG 183": "NH1" <-> "NH2" Residue "C ARG 187": "NH1" <-> "NH2" Residue "C ARG 208": "NH1" <-> "NH2" Residue "C ARG 251": "NH1" <-> "NH2" Residue "C ARG 257": "NH1" <-> "NH2" Residue "C ARG 278": "NH1" <-> "NH2" Residue "C ARG 304": "NH1" <-> "NH2" Residue "C ARG 355": "NH1" <-> "NH2" Residue "C ARG 361": "NH1" <-> "NH2" Residue "C ARG 363": "NH1" <-> "NH2" Residue "D ARG 8": "NH1" <-> "NH2" Residue "D ARG 21": "NH1" <-> "NH2" Residue "D ARG 66": "NH1" <-> "NH2" Residue "D ARG 71": "NH1" <-> "NH2" Residue "D ARG 80": "NH1" <-> "NH2" Residue "D ARG 98": "NH1" <-> "NH2" Residue "D ARG 134": "NH1" <-> "NH2" Residue "D ARG 144": "NH1" <-> "NH2" Residue "D ARG 146": "NH1" <-> "NH2" Residue "D ARG 151": "NH1" <-> "NH2" Residue "D ARG 155": "NH1" <-> "NH2" Residue "D ARG 174": "NH1" <-> "NH2" Residue "D ARG 178": "NH1" <-> "NH2" Residue "D ARG 183": "NH1" <-> "NH2" Residue "D ARG 187": "NH1" <-> "NH2" Residue "D ARG 208": "NH1" <-> "NH2" Residue "D GLU 225": "OE1" <-> "OE2" Residue "D ARG 251": "NH1" <-> "NH2" Residue "D ARG 257": "NH1" <-> "NH2" Residue "D ARG 278": "NH1" <-> "NH2" Residue "D ARG 304": "NH1" <-> "NH2" Residue "D ARG 311": "NH1" <-> "NH2" Residue "D PHE 326": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 355": "NH1" <-> "NH2" Residue "D ARG 361": "NH1" <-> "NH2" Residue "D ARG 363": "NH1" <-> "NH2" Residue "D ARG 390": "NH1" <-> "NH2" Residue "E ARG 50": "NH1" <-> "NH2" Residue "E ARG 58": "NH1" <-> "NH2" Residue "E ARG 64": "NH1" <-> "NH2" Residue "E ARG 74": "NH1" <-> "NH2" Residue "E ARG 79": "NH1" <-> "NH2" Residue "E ARG 80": "NH1" <-> "NH2" Residue "E ARG 135": "NH1" <-> "NH2" Residue "E ARG 155": "NH1" <-> "NH2" Residue "E ARG 175": "NH1" <-> "NH2" Residue "E ARG 178": "NH1" <-> "NH2" Residue "E ARG 227": "NH1" <-> "NH2" Residue "E ARG 235": "NH1" <-> "NH2" Residue "E ARG 259": "NH1" <-> "NH2" Residue "E PHE 328": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 343": "NH1" <-> "NH2" Residue "E ARG 368": "NH1" <-> "NH2" Residue "E ARG 371": "NH1" <-> "NH2" Residue "E ARG 377": "NH1" <-> "NH2" Residue "E ARG 389": "NH1" <-> "NH2" Residue "E ARG 409": "NH1" <-> "NH2" Residue "E ARG 418": "NH1" <-> "NH2" Residue "E ARG 430": "NH1" <-> "NH2" Residue "E ARG 445": "NH1" <-> "NH2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/chem_data/mon_lib" Total number of atoms: 12984 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 2153 Number of conformers: 1 Conformer: "" Number of residues, atoms: 285, 2153 Classifications: {'peptide': 285} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 14, 'TRANS': 270} Unresolved non-hydrogen bonds: 28 Unresolved non-hydrogen angles: 36 Unresolved non-hydrogen dihedrals: 20 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "B" Number of atoms: 1994 Number of conformers: 1 Conformer: "" Number of residues, atoms: 264, 1994 Classifications: {'peptide': 264} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 16, 'TRANS': 247} Unresolved non-hydrogen bonds: 23 Unresolved non-hydrogen angles: 30 Unresolved non-hydrogen dihedrals: 16 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "C" Number of atoms: 2684 Number of conformers: 1 Conformer: "" Number of residues, atoms: 368, 2684 Classifications: {'peptide': 368} Incomplete info: {'truncation_to_alanine': 37} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 350} Chain breaks: 2 Unresolved non-hydrogen bonds: 138 Unresolved non-hydrogen angles: 172 Unresolved non-hydrogen dihedrals: 108 Unresolved non-hydrogen chiralities: 13 Planarities with less than four sites: {'GLN:plan1': 1, 'HIS:plan': 1, 'ASN:plan1': 2, 'ASP:plan': 4, 'PHE:plan': 1, 'GLU:plan': 5, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 78 Chain: "D" Number of atoms: 2725 Number of conformers: 1 Conformer: "" Number of residues, atoms: 368, 2725 Classifications: {'peptide': 368} Incomplete info: {'truncation_to_alanine': 27} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 350} Chain breaks: 2 Unresolved non-hydrogen bonds: 97 Unresolved non-hydrogen angles: 122 Unresolved non-hydrogen dihedrals: 76 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'GLN:plan1': 1, 'HIS:plan': 2, 'ASN:plan1': 2, 'ASP:plan': 2, 'GLU:plan': 6, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 60 Chain: "E" Number of atoms: 3341 Number of conformers: 1 Conformer: "" Number of residues, atoms: 437, 3341 Classifications: {'peptide': 437} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 30, 'TRANS': 405} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 4 Planarities with less than four sites: {'ASN:plan1': 2} Unresolved non-hydrogen planarities: 6 Chain: "H" Number of atoms: 23 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 23 Unusual residues: {'GLC': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Chain: "C" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 7.38, per 1000 atoms: 0.57 Number of scatterers: 12984 At special positions: 0 Unit cell: (86.1, 86.1, 168.1, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 34 16.00 P 6 15.00 Mg 2 11.99 O 2438 8.00 N 2194 7.00 C 8310 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 Links applied ALPHA1-1 " GLC H 1 " - " GLC H 2 " Time building additional restraints: 5.46 Conformation dependent library (CDL) restraints added in 2.5 seconds 3408 Ramachandran restraints generated. 1704 Oldfield, 0 Emsley, 1704 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3198 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 81 helices and 15 sheets defined 48.3% alpha, 11.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.55 Creating SS restraints... Processing helix chain 'A' and resid 16 through 27 Processing helix chain 'A' and resid 29 through 51 removed outlier: 3.699A pdb=" N VAL A 38 " --> pdb=" O LEU A 34 " (cutoff:3.500A) removed outlier: 5.077A pdb=" N TYR A 41 " --> pdb=" O ALA A 37 " (cutoff:3.500A) Proline residue: A 42 - end of helix removed outlier: 3.785A pdb=" N SER A 50 " --> pdb=" O ALA A 46 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N LEU A 51 " --> pdb=" O VAL A 47 " (cutoff:3.500A) Processing helix chain 'A' and resid 66 through 74 removed outlier: 4.454A pdb=" N ASN A 69 " --> pdb=" O GLY A 66 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N VAL A 71 " --> pdb=" O ALA A 68 " (cutoff:3.500A) removed outlier: 4.175A pdb=" N THR A 72 " --> pdb=" O ASN A 69 " (cutoff:3.500A) Processing helix chain 'A' and resid 77 through 110 removed outlier: 3.569A pdb=" N ALA A 103 " --> pdb=" O ALA A 99 " (cutoff:3.500A) Processing helix chain 'A' and resid 116 through 121 Processing helix chain 'A' and resid 130 through 141 Processing helix chain 'A' and resid 149 through 151 No H-bonds generated for 'chain 'A' and resid 149 through 151' Processing helix chain 'A' and resid 158 through 160 No H-bonds generated for 'chain 'A' and resid 158 through 160' Processing helix chain 'A' and resid 162 through 191 removed outlier: 4.010A pdb=" N LYS A 176 " --> pdb=" O ALA A 172 " (cutoff:3.500A) Proline residue: A 179 - end of helix removed outlier: 4.204A pdb=" N LEU A 191 " --> pdb=" O ALA A 187 " (cutoff:3.500A) Processing helix chain 'A' and resid 194 through 202 Processing helix chain 'A' and resid 209 through 213 removed outlier: 3.518A pdb=" N LYS A 213 " --> pdb=" O LYS A 209 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 209 through 213' Processing helix chain 'A' and resid 215 through 236 Proline residue: A 221 - end of helix removed outlier: 4.052A pdb=" N VAL A 225 " --> pdb=" O PRO A 221 " (cutoff:3.500A) removed outlier: 4.312A pdb=" N ARG A 236 " --> pdb=" O LEU A 232 " (cutoff:3.500A) Processing helix chain 'A' and resid 239 through 242 No H-bonds generated for 'chain 'A' and resid 239 through 242' Processing helix chain 'A' and resid 254 through 262 Processing helix chain 'A' and resid 268 through 271 No H-bonds generated for 'chain 'A' and resid 268 through 271' Processing helix chain 'A' and resid 273 through 293 removed outlier: 3.977A pdb=" N ILE A 278 " --> pdb=" O ILE A 274 " (cutoff:3.500A) Processing helix chain 'B' and resid 7 through 36 Proline residue: B 27 - end of helix Processing helix chain 'B' and resid 55 through 61 Processing helix chain 'B' and resid 65 through 97 removed outlier: 3.629A pdb=" N ALA B 69 " --> pdb=" O ALA B 65 " (cutoff:3.500A) Processing helix chain 'B' and resid 104 through 115 removed outlier: 3.780A pdb=" N ALA B 114 " --> pdb=" O ALA B 110 " (cutoff:3.500A) Processing helix chain 'B' and resid 118 through 132 removed outlier: 5.206A pdb=" N THR B 123 " --> pdb=" O ILE B 119 " (cutoff:3.500A) Proline residue: B 124 - end of helix removed outlier: 3.646A pdb=" N GLY B 131 " --> pdb=" O ASN B 127 " (cutoff:3.500A) Processing helix chain 'B' and resid 138 through 163 Proline residue: B 144 - end of helix Proline residue: B 151 - end of helix removed outlier: 5.016A pdb=" N GLU B 163 " --> pdb=" O ALA B 159 " (cutoff:3.500A) Processing helix chain 'B' and resid 166 through 174 Processing helix chain 'B' and resid 179 through 185 Processing helix chain 'B' and resid 187 through 190 No H-bonds generated for 'chain 'B' and resid 187 through 190' Processing helix chain 'B' and resid 192 through 208 removed outlier: 3.611A pdb=" N ASN B 208 " --> pdb=" O ILE B 204 " (cutoff:3.500A) Processing helix chain 'B' and resid 211 through 215 removed outlier: 3.607A pdb=" N SER B 215 " --> pdb=" O LEU B 211 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 211 through 215' Processing helix chain 'B' and resid 225 through 228 No H-bonds generated for 'chain 'B' and resid 225 through 228' Processing helix chain 'B' and resid 242 through 252 Processing helix chain 'B' and resid 254 through 266 removed outlier: 4.007A pdb=" N VAL B 260 " --> pdb=" O ILE B 256 " (cutoff:3.500A) removed outlier: 4.476A pdb=" N ARG B 265 " --> pdb=" O LEU B 261 " (cutoff:3.500A) removed outlier: 4.921A pdb=" N ARG B 266 " --> pdb=" O ILE B 262 " (cutoff:3.500A) Processing helix chain 'C' and resid 47 through 55 Processing helix chain 'C' and resid 77 through 80 No H-bonds generated for 'chain 'C' and resid 77 through 80' Processing helix chain 'C' and resid 97 through 101 Processing helix chain 'C' and resid 103 through 107 Processing helix chain 'C' and resid 112 through 125 Processing helix chain 'C' and resid 136 through 138 No H-bonds generated for 'chain 'C' and resid 136 through 138' Processing helix chain 'C' and resid 141 through 155 removed outlier: 3.757A pdb=" N GLY C 150 " --> pdb=" O ARG C 146 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N ARG C 151 " --> pdb=" O VAL C 147 " (cutoff:3.500A) removed outlier: 4.229A pdb=" N ALA C 152 " --> pdb=" O ALA C 148 " (cutoff:3.500A) removed outlier: 4.405A pdb=" N ARG C 155 " --> pdb=" O ARG C 151 " (cutoff:3.500A) Processing helix chain 'C' and resid 171 through 187 removed outlier: 4.335A pdb=" N GLN C 176 " --> pdb=" O LYS C 172 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N ALA C 179 " --> pdb=" O VAL C 175 " (cutoff:3.500A) Processing helix chain 'C' and resid 199 through 205 removed outlier: 3.738A pdb=" N THR C 204 " --> pdb=" O THR C 200 " (cutoff:3.500A) Processing helix chain 'C' and resid 223 through 228 Processing helix chain 'C' and resid 233 through 236 No H-bonds generated for 'chain 'C' and resid 233 through 236' Processing helix chain 'C' and resid 267 through 275 Processing helix chain 'C' and resid 288 through 290 No H-bonds generated for 'chain 'C' and resid 288 through 290' Processing helix chain 'C' and resid 294 through 296 No H-bonds generated for 'chain 'C' and resid 294 through 296' Processing helix chain 'C' and resid 299 through 304 removed outlier: 3.983A pdb=" N ILE C 303 " --> pdb=" O GLY C 299 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N ARG C 304 " --> pdb=" O TYR C 300 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 299 through 304' Processing helix chain 'D' and resid 47 through 55 Processing helix chain 'D' and resid 77 through 80 No H-bonds generated for 'chain 'D' and resid 77 through 80' Processing helix chain 'D' and resid 97 through 107 Proline residue: D 104 - end of helix Processing helix chain 'D' and resid 112 through 125 removed outlier: 3.934A pdb=" N LYS D 124 " --> pdb=" O GLU D 120 " (cutoff:3.500A) Processing helix chain 'D' and resid 136 through 138 No H-bonds generated for 'chain 'D' and resid 136 through 138' Processing helix chain 'D' and resid 141 through 155 removed outlier: 4.287A pdb=" N ARG D 146 " --> pdb=" O GLY D 142 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N ALA D 152 " --> pdb=" O ALA D 148 " (cutoff:3.500A) removed outlier: 4.154A pdb=" N ARG D 155 " --> pdb=" O ARG D 151 " (cutoff:3.500A) Processing helix chain 'D' and resid 171 through 187 Processing helix chain 'D' and resid 199 through 205 removed outlier: 3.982A pdb=" N THR D 204 " --> pdb=" O THR D 200 " (cutoff:3.500A) Processing helix chain 'D' and resid 223 through 228 Processing helix chain 'D' and resid 233 through 238 Processing helix chain 'D' and resid 267 through 275 Processing helix chain 'D' and resid 288 through 290 No H-bonds generated for 'chain 'D' and resid 288 through 290' Processing helix chain 'D' and resid 299 through 302 No H-bonds generated for 'chain 'D' and resid 299 through 302' Processing helix chain 'D' and resid 374 through 376 No H-bonds generated for 'chain 'D' and resid 374 through 376' Processing helix chain 'E' and resid 38 through 54 removed outlier: 3.855A pdb=" N GLU E 41 " --> pdb=" O ALA E 38 " (cutoff:3.500A) removed outlier: 4.761A pdb=" N ALA E 42 " --> pdb=" O ASN E 39 " (cutoff:3.500A) removed outlier: 5.017A pdb=" N LYS E 45 " --> pdb=" O ALA E 42 " (cutoff:3.500A) Processing helix chain 'E' and resid 70 through 82 removed outlier: 3.997A pdb=" N LEU E 75 " --> pdb=" O ASP E 71 " (cutoff:3.500A) Processing helix chain 'E' and resid 95 through 103 removed outlier: 3.909A pdb=" N THR E 98 " --> pdb=" O VAL E 95 " (cutoff:3.500A) removed outlier: 4.405A pdb=" N ALA E 99 " --> pdb=" O VAL E 96 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N ALA E 102 " --> pdb=" O ALA E 99 " (cutoff:3.500A) Processing helix chain 'E' and resid 110 through 112 No H-bonds generated for 'chain 'E' and resid 110 through 112' Processing helix chain 'E' and resid 118 through 121 No H-bonds generated for 'chain 'E' and resid 118 through 121' Processing helix chain 'E' and resid 128 through 134 Processing helix chain 'E' and resid 166 through 179 Processing helix chain 'E' and resid 193 through 205 Processing helix chain 'E' and resid 224 through 242 Processing helix chain 'E' and resid 250 through 252 No H-bonds generated for 'chain 'E' and resid 250 through 252' Processing helix chain 'E' and resid 255 through 263 Processing helix chain 'E' and resid 274 through 286 removed outlier: 3.667A pdb=" N LEU E 277 " --> pdb=" O PRO E 274 " (cutoff:3.500A) Proline residue: E 278 - end of helix removed outlier: 3.814A pdb=" N VAL E 285 " --> pdb=" O GLU E 282 " (cutoff:3.500A) Processing helix chain 'E' and resid 294 through 296 No H-bonds generated for 'chain 'E' and resid 294 through 296' Processing helix chain 'E' and resid 314 through 326 removed outlier: 3.538A pdb=" N LYS E 326 " --> pdb=" O ASP E 322 " (cutoff:3.500A) Processing helix chain 'E' and resid 360 through 370 Processing helix chain 'E' and resid 373 through 381 Processing helix chain 'E' and resid 390 through 394 Processing helix chain 'E' and resid 396 through 401 Processing helix chain 'E' and resid 405 through 413 Processing helix chain 'E' and resid 424 through 435 Processing helix chain 'E' and resid 438 through 440 No H-bonds generated for 'chain 'E' and resid 438 through 440' Processing helix chain 'E' and resid 443 through 459 Processing sheet with id= A, first strand: chain 'C' and resid 29 through 31 Processing sheet with id= B, first strand: chain 'C' and resid 216 through 221 removed outlier: 6.937A pdb=" N VAL C 211 " --> pdb=" O GLN C 218 " (cutoff:3.500A) removed outlier: 4.507A pdb=" N ILE C 220 " --> pdb=" O VAL C 209 " (cutoff:3.500A) removed outlier: 6.726A pdb=" N VAL C 209 " --> pdb=" O ILE C 220 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N ARG C 208 " --> pdb=" O PHE C 36 " (cutoff:3.500A) removed outlier: 6.338A pdb=" N THR C 192 " --> pdb=" O ILE C 37 " (cutoff:3.500A) removed outlier: 7.484A pdb=" N LEU C 39 " --> pdb=" O THR C 192 " (cutoff:3.500A) removed outlier: 6.632A pdb=" N TYR C 194 " --> pdb=" O LEU C 39 " (cutoff:3.500A) removed outlier: 8.897A pdb=" N GLY C 41 " --> pdb=" O TYR C 194 " (cutoff:3.500A) removed outlier: 6.087A pdb=" N PHE C 160 " --> pdb=" O VAL C 193 " (cutoff:3.500A) removed outlier: 8.057A pdb=" N VAL C 195 " --> pdb=" O PHE C 160 " (cutoff:3.500A) removed outlier: 6.892A pdb=" N MET C 162 " --> pdb=" O VAL C 195 " (cutoff:3.500A) removed outlier: 6.121A pdb=" N ALA C 83 " --> pdb=" O LEU C 161 " (cutoff:3.500A) removed outlier: 7.902A pdb=" N ASP C 163 " --> pdb=" O ALA C 83 " (cutoff:3.500A) removed outlier: 6.450A pdb=" N VAL C 85 " --> pdb=" O ASP C 163 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'C' and resid 261 through 264 Processing sheet with id= D, first strand: chain 'C' and resid 291 through 293 Processing sheet with id= E, first strand: chain 'C' and resid 352 through 357 Processing sheet with id= F, first strand: chain 'C' and resid 11 through 13 removed outlier: 6.737A pdb=" N TYR C 13 " --> pdb=" O ALA C 22 " (cutoff:3.500A) removed outlier: 5.495A pdb=" N ALA C 22 " --> pdb=" O TYR C 13 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'D' and resid 29 through 31 Processing sheet with id= H, first strand: chain 'D' and resid 216 through 221 removed outlier: 6.878A pdb=" N VAL D 211 " --> pdb=" O GLN D 218 " (cutoff:3.500A) removed outlier: 4.436A pdb=" N ILE D 220 " --> pdb=" O VAL D 209 " (cutoff:3.500A) removed outlier: 6.688A pdb=" N VAL D 209 " --> pdb=" O ILE D 220 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ARG D 208 " --> pdb=" O PHE D 36 " (cutoff:3.500A) removed outlier: 6.358A pdb=" N THR D 192 " --> pdb=" O ILE D 37 " (cutoff:3.500A) removed outlier: 7.418A pdb=" N LEU D 39 " --> pdb=" O THR D 192 " (cutoff:3.500A) removed outlier: 6.505A pdb=" N TYR D 194 " --> pdb=" O LEU D 39 " (cutoff:3.500A) removed outlier: 8.722A pdb=" N GLY D 41 " --> pdb=" O TYR D 194 " (cutoff:3.500A) removed outlier: 6.296A pdb=" N ALA D 83 " --> pdb=" O LEU D 161 " (cutoff:3.500A) removed outlier: 7.858A pdb=" N ASP D 163 " --> pdb=" O ALA D 83 " (cutoff:3.500A) removed outlier: 6.503A pdb=" N VAL D 85 " --> pdb=" O ASP D 163 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'D' and resid 261 through 264 Processing sheet with id= J, first strand: chain 'D' and resid 291 through 293 removed outlier: 3.701A pdb=" N LEU D 306 " --> pdb=" O ILE D 372 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'D' and resid 321 through 326 Processing sheet with id= L, first strand: chain 'D' and resid 11 through 13 removed outlier: 6.834A pdb=" N TYR D 13 " --> pdb=" O ALA D 22 " (cutoff:3.500A) removed outlier: 5.440A pdb=" N ALA D 22 " --> pdb=" O TYR D 13 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'E' and resid 30 through 36 Processing sheet with id= N, first strand: chain 'E' and resid 90 through 94 removed outlier: 5.665A pdb=" N LEU E 351 " --> pdb=" O PRO E 144 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'E' and resid 329 through 331 removed outlier: 8.210A pdb=" N TRP E 184 " --> pdb=" O ALA E 268 " (cutoff:3.500A) removed outlier: 6.283A pdb=" N GLU E 270 " --> pdb=" O TRP E 184 " (cutoff:3.500A) removed outlier: 6.422A pdb=" N ALA E 186 " --> pdb=" O GLU E 270 " (cutoff:3.500A) removed outlier: 5.720A pdb=" N ASN E 272 " --> pdb=" O ALA E 186 " (cutoff:3.500A) 577 hydrogen bonds defined for protein. 1584 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: 3.86 Time building geometry restraints manager: 5.81 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 3007 1.33 - 1.45: 2612 1.45 - 1.58: 7553 1.58 - 1.70: 10 1.70 - 1.82: 64 Bond restraints: 13246 Sorted by residual: bond pdb=" C4 ATP D 501 " pdb=" C5 ATP D 501 " ideal model delta sigma weight residual 1.388 1.472 -0.084 1.00e-02 1.00e+04 7.01e+01 bond pdb=" C4 ATP C 501 " pdb=" C5 ATP C 501 " ideal model delta sigma weight residual 1.388 1.471 -0.083 1.00e-02 1.00e+04 6.87e+01 bond pdb=" C5 ATP D 501 " pdb=" C6 ATP D 501 " ideal model delta sigma weight residual 1.409 1.482 -0.073 1.00e-02 1.00e+04 5.40e+01 bond pdb=" C5 ATP C 501 " pdb=" C6 ATP C 501 " ideal model delta sigma weight residual 1.409 1.482 -0.073 1.00e-02 1.00e+04 5.30e+01 bond pdb=" C5 GLC H 1 " pdb=" O5 GLC H 1 " ideal model delta sigma weight residual 1.410 1.548 -0.138 2.00e-02 2.50e+03 4.77e+01 ... (remaining 13241 not shown) Histogram of bond angle deviations from ideal: 94.30 - 102.67: 113 102.67 - 111.04: 4066 111.04 - 119.41: 6841 119.41 - 127.78: 6971 127.78 - 136.15: 96 Bond angle restraints: 18087 Sorted by residual: angle pdb=" PB ATP C 501 " pdb=" O3B ATP C 501 " pdb=" PG ATP C 501 " ideal model delta sigma weight residual 139.87 120.28 19.59 1.00e+00 1.00e+00 3.84e+02 angle pdb=" PB ATP D 501 " pdb=" O3B ATP D 501 " pdb=" PG ATP D 501 " ideal model delta sigma weight residual 139.87 120.36 19.51 1.00e+00 1.00e+00 3.81e+02 angle pdb=" PA ATP C 501 " pdb=" O3A ATP C 501 " pdb=" PB ATP C 501 " ideal model delta sigma weight residual 136.83 120.33 16.50 1.00e+00 1.00e+00 2.72e+02 angle pdb=" PA ATP D 501 " pdb=" O3A ATP D 501 " pdb=" PB ATP D 501 " ideal model delta sigma weight residual 136.83 120.51 16.32 1.00e+00 1.00e+00 2.66e+02 angle pdb=" C5 ATP C 501 " pdb=" C4 ATP C 501 " pdb=" N3 ATP C 501 " ideal model delta sigma weight residual 126.80 118.65 8.15 1.00e+00 1.00e+00 6.65e+01 ... (remaining 18082 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.82: 7397 17.82 - 35.63: 434 35.63 - 53.45: 83 53.45 - 71.27: 31 71.27 - 89.08: 8 Dihedral angle restraints: 7953 sinusoidal: 2997 harmonic: 4956 Sorted by residual: dihedral pdb=" CA SER C 129 " pdb=" C SER C 129 " pdb=" N GLU C 130 " pdb=" CA GLU C 130 " ideal model delta harmonic sigma weight residual 180.00 151.19 28.81 0 5.00e+00 4.00e-02 3.32e+01 dihedral pdb=" CA ASP A 161 " pdb=" C ASP A 161 " pdb=" N GLN A 162 " pdb=" CA GLN A 162 " ideal model delta harmonic sigma weight residual 180.00 -151.72 -28.28 0 5.00e+00 4.00e-02 3.20e+01 dihedral pdb=" CA THR C 328 " pdb=" C THR C 328 " pdb=" N GLU C 329 " pdb=" CA GLU C 329 " ideal model delta harmonic sigma weight residual 180.00 151.81 28.19 0 5.00e+00 4.00e-02 3.18e+01 ... (remaining 7950 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.930: 2149 0.930 - 1.861: 0 1.861 - 2.791: 0 2.791 - 3.721: 0 3.721 - 4.651: 1 Chirality restraints: 2150 Sorted by residual: chirality pdb=" C1 GLC H 2 " pdb=" C2 GLC H 2 " pdb=" O1 GLC H 2 " pdb=" O5 GLC H 2 " both_signs ideal model delta sigma weight residual False 2.33 -2.32 4.65 2.00e-01 2.50e+01 5.41e+02 chirality pdb=" C1 GLC H 1 " pdb=" C2 GLC H 1 " pdb=" O5 GLC H 1 " pdb=" O1 GLC H 2 " both_signs ideal model delta sigma weight residual False 2.40 2.30 0.10 2.00e-02 2.50e+03 2.31e+01 chirality pdb=" CA THR A 130 " pdb=" N THR A 130 " pdb=" C THR A 130 " pdb=" CB THR A 130 " both_signs ideal model delta sigma weight residual False 2.53 2.06 0.47 2.00e-01 2.50e+01 5.47e+00 ... (remaining 2147 not shown) Planarity restraints: 2313 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP E 153 " 0.130 2.00e-02 2.50e+03 6.54e-02 1.07e+02 pdb=" CG TRP E 153 " -0.030 2.00e-02 2.50e+03 pdb=" CD1 TRP E 153 " -0.041 2.00e-02 2.50e+03 pdb=" CD2 TRP E 153 " -0.054 2.00e-02 2.50e+03 pdb=" NE1 TRP E 153 " -0.039 2.00e-02 2.50e+03 pdb=" CE2 TRP E 153 " -0.003 2.00e-02 2.50e+03 pdb=" CE3 TRP E 153 " -0.077 2.00e-02 2.50e+03 pdb=" CZ2 TRP E 153 " 0.086 2.00e-02 2.50e+03 pdb=" CZ3 TRP E 153 " -0.037 2.00e-02 2.50e+03 pdb=" CH2 TRP E 153 " 0.064 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR E 333 " -0.116 2.00e-02 2.50e+03 6.15e-02 7.56e+01 pdb=" CG TYR E 333 " 0.045 2.00e-02 2.50e+03 pdb=" CD1 TYR E 333 " 0.043 2.00e-02 2.50e+03 pdb=" CD2 TYR E 333 " 0.063 2.00e-02 2.50e+03 pdb=" CE1 TYR E 333 " 0.033 2.00e-02 2.50e+03 pdb=" CE2 TYR E 333 " 0.017 2.00e-02 2.50e+03 pdb=" CZ TYR E 333 " 0.003 2.00e-02 2.50e+03 pdb=" OH TYR E 333 " -0.087 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR E 424 " -0.113 2.00e-02 2.50e+03 6.04e-02 7.30e+01 pdb=" CG TYR E 424 " 0.044 2.00e-02 2.50e+03 pdb=" CD1 TYR E 424 " 0.055 2.00e-02 2.50e+03 pdb=" CD2 TYR E 424 " 0.039 2.00e-02 2.50e+03 pdb=" CE1 TYR E 424 " 0.023 2.00e-02 2.50e+03 pdb=" CE2 TYR E 424 " 0.038 2.00e-02 2.50e+03 pdb=" CZ TYR E 424 " 0.001 2.00e-02 2.50e+03 pdb=" OH TYR E 424 " -0.089 2.00e-02 2.50e+03 ... (remaining 2310 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 513 2.75 - 3.29: 14102 3.29 - 3.82: 20108 3.82 - 4.36: 26014 4.36 - 4.90: 42815 Nonbonded interactions: 103552 Sorted by model distance: nonbonded pdb=" O ASP A 250 " pdb=" OD1 ASP A 250 " model vdw 2.209 3.040 nonbonded pdb=" OE1 GLN D 87 " pdb="MG MG D 502 " model vdw 2.248 2.170 nonbonded pdb=" NH1 ARG E 80 " pdb=" OD2 ASP E 85 " model vdw 2.255 2.520 nonbonded pdb=" CE2 PHE C 36 " pdb=" CB LEU C 205 " model vdw 2.267 3.740 nonbonded pdb=" OE1 GLN C 87 " pdb="MG MG C 502 " model vdw 2.275 2.170 ... (remaining 103547 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'C' and (resid 2 through 28 or (resid 29 and (name N or name CA or name C \ or name O or name CB )) or resid 30 through 125 or (resid 126 through 128 and ( \ name N or name CA or name C or name O or name CB )) or resid 129 or (resid 130 t \ hrough 132 and (name N or name CA or name C or name O or name CB )) or resid 133 \ through 179 or (resid 180 and (name N or name CA or name C or name O or name CB \ )) or resid 181 through 196 or (resid 197 and (name N or name CA or name C or n \ ame O or name CB )) or resid 198 through 359 or (resid 360 and (name N or name C \ A or name C or name O or name CB )) or resid 361 through 391 or resid 501 throug \ h 502)) selection = (chain 'D' and (resid 2 through 77 or (resid 78 and (name N or name CA or name C \ or name O or name CB )) or resid 79 through 106 or (resid 107 through 108 and ( \ name N or name CA or name C or name O or name CB )) or resid 109 through 111 or \ (resid 112 through 113 and (name N or name CA or name C or name O or name CB )) \ or resid 114 through 120 or (resid 121 and (name N or name CA or name C or name \ O or name CB )) or resid 122 through 124 or (resid 125 through 128 and (name N o \ r name CA or name C or name O or name CB )) or resid 129 through 145 or (resid 1 \ 46 and (name N or name CA or name C or name O or name CB )) or resid 147 through \ 225 or (resid 226 and (name N or name CA or name C or name O or name CB )) or r \ esid 227 through 237 or (resid 238 and (name N or name CA or name C or name O or \ name CB )) or resid 239 through 251 or (resid 252 and (name N or name CA or nam \ e C or name O or name CB )) or resid 253 through 263 or (resid 264 and (name N o \ r name CA or name C or name O or name CB )) or resid 265 through 268 or (resid 2 \ 69 and (name N or name CA or name C or name O or name CB )) or resid 270 through \ 295 or (resid 296 and (name N or name CA or name C or name O or name CB )) or r \ esid 297 or (resid 298 and (name N or name CA or name C or name O or name CB )) \ or resid 299 through 302 or (resid 303 and (name N or name CA or name C or name \ O or name CB )) or resid 304 through 305 or (resid 306 and (name N or name CA or \ name C or name O or name CB )) or resid 307 through 310 or (resid 311 through 3 \ 12 and (name N or name CA or name C or name O or name CB )) or resid 313 through \ 378 or (resid 379 and (name N or name CA or name C or name O or name CB )) or r \ esid 380 through 389 or (resid 390 and (name N or name CA or name C or name O or \ name CB )) or resid 391 or resid 501 through 502)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.540 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 12.210 Check model and map are aligned: 0.190 Set scattering table: 0.110 Process input model: 37.050 Find NCS groups from input model: 0.550 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:2.790 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 55.530 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8005 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 : 0.012 0.138 13246 Z= 0.819 Angle : 1.769 19.594 18087 Z= 1.214 Chirality : 0.140 4.651 2150 Planarity : 0.012 0.110 2313 Dihedral : 13.102 89.082 4755 Min Nonbonded Distance : 2.209 Molprobity Statistics. All-atom Clashscore : 4.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.93 % Favored : 96.07 % Rotamer: Outliers : 0.38 % Allowed : 5.20 % Favored : 94.42 % Cbeta Deviations : 0.38 % Peptide Plane: Cis-proline : 3.16 % 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 (0.18), residues: 1704 helix: -1.33 (0.15), residues: 824 sheet: 0.53 (0.47), residues: 112 loop : -0.99 (0.20), residues: 768 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.130 0.020 TRP E 153 HIS 0.012 0.003 HIS C 197 PHE 0.057 0.012 PHE C 234 TYR 0.116 0.018 TYR E 333 ARG 0.007 0.001 ARG A 119 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3408 Ramachandran restraints generated. 1704 Oldfield, 0 Emsley, 1704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3408 Ramachandran restraints generated. 1704 Oldfield, 0 Emsley, 1704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 341 residues out of total 1390 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 336 time to evaluate : 1.550 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 110 ARG cc_start: 0.7567 (mmt90) cc_final: 0.7366 (mmm160) REVERT: A 289 TYR cc_start: 0.7904 (m-10) cc_final: 0.7559 (m-80) REVERT: B 12 TRP cc_start: 0.8446 (t-100) cc_final: 0.8234 (t60) REVERT: B 125 ILE cc_start: 0.8887 (mm) cc_final: 0.8485 (mm) REVERT: C 100 ASN cc_start: 0.8153 (m-40) cc_final: 0.7312 (t0) REVERT: C 220 ILE cc_start: 0.9030 (mt) cc_final: 0.8580 (mp) REVERT: C 260 PHE cc_start: 0.6833 (p90) cc_final: 0.6374 (p90) REVERT: C 308 PHE cc_start: 0.3849 (p90) cc_final: 0.3457 (p90) REVERT: D 36 PHE cc_start: 0.7907 (t80) cc_final: 0.7685 (t80) REVERT: D 84 MET cc_start: 0.8802 (ttt) cc_final: 0.8555 (ttm) REVERT: D 199 GLN cc_start: 0.8361 (pp30) cc_final: 0.8085 (pp30) REVERT: E 54 GLN cc_start: 0.7459 (mt0) cc_final: 0.7090 (mt0) outliers start: 5 outliers final: 3 residues processed: 338 average time/residue: 0.2779 time to fit residues: 130.4584 Evaluate side-chains 228 residues out of total 1390 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 225 time to evaluate : 1.500 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 130 THR Chi-restraints excluded: chain B residue 118 HIS Chi-restraints excluded: chain B residue 238 PHE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 169 random chunks: chunk 142 optimal weight: 0.6980 chunk 128 optimal weight: 2.9990 chunk 71 optimal weight: 0.7980 chunk 43 optimal weight: 0.9980 chunk 86 optimal weight: 7.9990 chunk 68 optimal weight: 0.8980 chunk 132 optimal weight: 0.7980 chunk 51 optimal weight: 0.0010 chunk 80 optimal weight: 5.9990 chunk 98 optimal weight: 0.0770 chunk 153 optimal weight: 2.9990 overall best weight: 0.4744 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 150 ASN A 261 ASN ** C 219 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 325 HIS E 39 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8008 moved from start: 0.2492 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 13246 Z= 0.194 Angle : 0.670 8.173 18087 Z= 0.350 Chirality : 0.045 0.189 2150 Planarity : 0.005 0.037 2313 Dihedral : 7.694 72.352 1931 Min Nonbonded Distance : 2.077 Molprobity Statistics. All-atom Clashscore : 6.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer: Outliers : 2.60 % Allowed : 11.47 % Favored : 85.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.16 % 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: -0.13 (0.20), residues: 1704 helix: 0.19 (0.17), residues: 845 sheet: 0.20 (0.39), residues: 160 loop : -0.32 (0.23), residues: 699 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP A 80 HIS 0.004 0.001 HIS E 359 PHE 0.020 0.002 PHE C 234 TYR 0.023 0.002 TYR E 192 ARG 0.005 0.001 ARG E 418 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3408 Ramachandran restraints generated. 1704 Oldfield, 0 Emsley, 1704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3408 Ramachandran restraints generated. 1704 Oldfield, 0 Emsley, 1704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 292 residues out of total 1390 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 258 time to evaluate : 1.598 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 110 ARG cc_start: 0.7623 (mmt90) cc_final: 0.7388 (mmm160) REVERT: B 158 SER cc_start: 0.9350 (t) cc_final: 0.9014 (m) REVERT: C 4 ILE cc_start: 0.8949 (mp) cc_final: 0.8707 (tt) REVERT: C 100 ASN cc_start: 0.7967 (m-40) cc_final: 0.7524 (t0) REVERT: C 219 GLN cc_start: 0.7511 (tp40) cc_final: 0.7249 (tp40) REVERT: C 244 MET cc_start: 0.3867 (ttm) cc_final: 0.3651 (ttp) REVERT: C 260 PHE cc_start: 0.6581 (p90) cc_final: 0.5987 (p90) REVERT: D 158 LYS cc_start: 0.8232 (mttt) cc_final: 0.7445 (tptt) REVERT: D 199 GLN cc_start: 0.8291 (pp30) cc_final: 0.7993 (pp30) REVERT: E 263 GLU cc_start: 0.7638 (OUTLIER) cc_final: 0.7199 (tp30) REVERT: E 378 TYR cc_start: 0.7989 (t80) cc_final: 0.7689 (t80) outliers start: 34 outliers final: 17 residues processed: 273 average time/residue: 0.2286 time to fit residues: 93.4912 Evaluate side-chains 221 residues out of total 1390 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 203 time to evaluate : 1.440 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 ASP Chi-restraints excluded: chain A residue 33 LEU Chi-restraints excluded: chain B residue 74 ILE Chi-restraints excluded: chain B residue 112 LEU Chi-restraints excluded: chain B residue 155 TYR Chi-restraints excluded: chain B residue 236 SER Chi-restraints excluded: chain B residue 238 PHE Chi-restraints excluded: chain B residue 267 ILE Chi-restraints excluded: chain C residue 213 LEU Chi-restraints excluded: chain C residue 250 THR Chi-restraints excluded: chain C residue 273 LEU Chi-restraints excluded: chain C residue 377 LEU Chi-restraints excluded: chain D residue 169 LEU Chi-restraints excluded: chain D residue 205 LEU Chi-restraints excluded: chain D residue 235 VAL Chi-restraints excluded: chain E residue 254 ASP Chi-restraints excluded: chain E residue 263 GLU Chi-restraints excluded: chain E residue 289 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 169 random chunks: chunk 85 optimal weight: 10.0000 chunk 47 optimal weight: 0.5980 chunk 127 optimal weight: 0.8980 chunk 104 optimal weight: 0.9980 chunk 42 optimal weight: 4.9990 chunk 153 optimal weight: 0.0000 chunk 166 optimal weight: 1.9990 chunk 136 optimal weight: 0.7980 chunk 152 optimal weight: 0.9980 chunk 52 optimal weight: 3.9990 chunk 123 optimal weight: 6.9990 overall best weight: 0.6584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 150 ASN C 99 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8025 moved from start: 0.2998 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 13246 Z= 0.177 Angle : 0.590 8.884 18087 Z= 0.301 Chirality : 0.043 0.215 2150 Planarity : 0.004 0.041 2313 Dihedral : 7.100 70.225 1928 Min Nonbonded Distance : 2.070 Molprobity Statistics. All-atom Clashscore : 6.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Rotamer: Outliers : 2.91 % Allowed : 13.07 % Favored : 84.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.16 % 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: 0.21 (0.20), residues: 1704 helix: 0.55 (0.18), residues: 842 sheet: 0.06 (0.36), residues: 192 loop : -0.18 (0.24), residues: 670 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 80 HIS 0.005 0.001 HIS E 359 PHE 0.015 0.001 PHE B 183 TYR 0.031 0.001 TYR E 192 ARG 0.017 0.000 ARG D 178 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3408 Ramachandran restraints generated. 1704 Oldfield, 0 Emsley, 1704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3408 Ramachandran restraints generated. 1704 Oldfield, 0 Emsley, 1704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 261 residues out of total 1390 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 223 time to evaluate : 1.412 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 110 ARG cc_start: 0.7614 (mmt90) cc_final: 0.7182 (mmm160) REVERT: B 239 GLU cc_start: 0.6627 (tm-30) cc_final: 0.6409 (tm-30) REVERT: C 4 ILE cc_start: 0.8935 (mp) cc_final: 0.8622 (tt) REVERT: C 100 ASN cc_start: 0.7911 (m-40) cc_final: 0.7508 (t0) REVERT: C 153 ILE cc_start: 0.8298 (mm) cc_final: 0.8000 (tp) REVERT: C 219 GLN cc_start: 0.7552 (tp40) cc_final: 0.7244 (tp40) REVERT: C 244 MET cc_start: 0.3695 (ttm) cc_final: 0.3445 (ttp) REVERT: C 260 PHE cc_start: 0.6640 (p90) cc_final: 0.5992 (p90) REVERT: D 138 GLN cc_start: 0.7990 (mp10) cc_final: 0.7566 (mt0) REVERT: D 151 ARG cc_start: 0.8609 (OUTLIER) cc_final: 0.7205 (mtm110) REVERT: D 158 LYS cc_start: 0.8193 (mttt) cc_final: 0.7453 (tppt) REVERT: E 378 TYR cc_start: 0.8030 (t80) cc_final: 0.7790 (t80) outliers start: 38 outliers final: 27 residues processed: 244 average time/residue: 0.2365 time to fit residues: 85.1925 Evaluate side-chains 219 residues out of total 1390 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 191 time to evaluate : 1.497 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 ASP Chi-restraints excluded: chain A residue 33 LEU Chi-restraints excluded: chain A residue 60 HIS Chi-restraints excluded: chain A residue 102 LEU Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 239 ASP Chi-restraints excluded: chain A residue 244 LEU Chi-restraints excluded: chain B residue 23 TYR Chi-restraints excluded: chain B residue 26 ILE Chi-restraints excluded: chain B residue 112 LEU Chi-restraints excluded: chain B residue 197 THR Chi-restraints excluded: chain B residue 229 ILE Chi-restraints excluded: chain B residue 238 PHE Chi-restraints excluded: chain B residue 267 ILE Chi-restraints excluded: chain C residue 60 ILE Chi-restraints excluded: chain C residue 213 LEU Chi-restraints excluded: chain C residue 250 THR Chi-restraints excluded: chain C residue 377 LEU Chi-restraints excluded: chain D residue 151 ARG Chi-restraints excluded: chain D residue 205 LEU Chi-restraints excluded: chain D residue 235 VAL Chi-restraints excluded: chain E residue 95 VAL Chi-restraints excluded: chain E residue 201 THR Chi-restraints excluded: chain E residue 254 ASP Chi-restraints excluded: chain E residue 289 VAL Chi-restraints excluded: chain E residue 339 ASP Chi-restraints excluded: chain E residue 428 SER Chi-restraints excluded: chain E residue 450 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 169 random chunks: chunk 151 optimal weight: 0.0870 chunk 115 optimal weight: 0.2980 chunk 79 optimal weight: 5.9990 chunk 17 optimal weight: 0.9980 chunk 73 optimal weight: 2.9990 chunk 103 optimal weight: 0.2980 chunk 154 optimal weight: 4.9990 chunk 163 optimal weight: 0.7980 chunk 80 optimal weight: 5.9990 chunk 146 optimal weight: 0.8980 chunk 44 optimal weight: 3.9990 overall best weight: 0.4758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 127 ASN D 99 GLN E 411 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8009 moved from start: 0.3363 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 13246 Z= 0.159 Angle : 0.566 8.142 18087 Z= 0.284 Chirality : 0.042 0.163 2150 Planarity : 0.004 0.052 2313 Dihedral : 6.720 67.407 1928 Min Nonbonded Distance : 2.063 Molprobity Statistics. All-atom Clashscore : 7.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 2.68 % Allowed : 13.99 % Favored : 83.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.16 % 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: 0.40 (0.20), residues: 1704 helix: 0.83 (0.18), residues: 840 sheet: 0.15 (0.36), residues: 192 loop : -0.27 (0.23), residues: 672 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 80 HIS 0.003 0.001 HIS E 359 PHE 0.018 0.001 PHE E 59 TYR 0.023 0.001 TYR E 192 ARG 0.023 0.000 ARG D 178 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3408 Ramachandran restraints generated. 1704 Oldfield, 0 Emsley, 1704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3408 Ramachandran restraints generated. 1704 Oldfield, 0 Emsley, 1704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 252 residues out of total 1390 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 217 time to evaluate : 1.764 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 45 TYR cc_start: 0.8540 (t80) cc_final: 0.8320 (t80) REVERT: A 110 ARG cc_start: 0.7587 (mmt90) cc_final: 0.7227 (mmm160) REVERT: C 4 ILE cc_start: 0.8947 (mp) cc_final: 0.8591 (tt) REVERT: C 100 ASN cc_start: 0.7868 (m-40) cc_final: 0.7474 (t0) REVERT: C 153 ILE cc_start: 0.8231 (mm) cc_final: 0.7993 (tp) REVERT: C 244 MET cc_start: 0.3678 (ttm) cc_final: 0.3419 (ttp) REVERT: C 260 PHE cc_start: 0.6688 (p90) cc_final: 0.6161 (p90) REVERT: D 21 ARG cc_start: 0.6803 (ptt-90) cc_final: 0.6549 (ptt180) REVERT: D 151 ARG cc_start: 0.8550 (OUTLIER) cc_final: 0.7189 (mtm110) REVERT: D 158 LYS cc_start: 0.8224 (mttt) cc_final: 0.7449 (tppt) outliers start: 35 outliers final: 24 residues processed: 237 average time/residue: 0.2336 time to fit residues: 83.9627 Evaluate side-chains 221 residues out of total 1390 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 196 time to evaluate : 1.658 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 LEU Chi-restraints excluded: chain A residue 60 HIS Chi-restraints excluded: chain A residue 67 LEU Chi-restraints excluded: chain A residue 106 LEU Chi-restraints excluded: chain A residue 191 LEU Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 244 LEU Chi-restraints excluded: chain B residue 23 TYR Chi-restraints excluded: chain B residue 26 ILE Chi-restraints excluded: chain B residue 78 LEU Chi-restraints excluded: chain B residue 168 LEU Chi-restraints excluded: chain B residue 197 THR Chi-restraints excluded: chain B residue 229 ILE Chi-restraints excluded: chain B residue 238 PHE Chi-restraints excluded: chain C residue 213 LEU Chi-restraints excluded: chain C residue 250 THR Chi-restraints excluded: chain D residue 151 ARG Chi-restraints excluded: chain D residue 205 LEU Chi-restraints excluded: chain D residue 235 VAL Chi-restraints excluded: chain E residue 95 VAL Chi-restraints excluded: chain E residue 289 VAL Chi-restraints excluded: chain E residue 339 ASP Chi-restraints excluded: chain E residue 428 SER Chi-restraints excluded: chain E residue 450 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 169 random chunks: chunk 136 optimal weight: 0.9990 chunk 92 optimal weight: 1.9990 chunk 2 optimal weight: 3.9990 chunk 121 optimal weight: 2.9990 chunk 67 optimal weight: 0.0670 chunk 139 optimal weight: 0.3980 chunk 112 optimal weight: 10.0000 chunk 0 optimal weight: 7.9990 chunk 83 optimal weight: 5.9990 chunk 146 optimal weight: 3.9990 chunk 41 optimal weight: 3.9990 overall best weight: 1.2924 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 56 ASN C 99 GLN D 367 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8066 moved from start: 0.3531 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 13246 Z= 0.219 Angle : 0.572 8.051 18087 Z= 0.286 Chirality : 0.042 0.166 2150 Planarity : 0.004 0.042 2313 Dihedral : 6.484 67.595 1928 Min Nonbonded Distance : 2.024 Molprobity Statistics. All-atom Clashscore : 8.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer: Outliers : 3.21 % Allowed : 14.14 % Favored : 82.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.16 % 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: 0.54 (0.20), residues: 1704 helix: 0.97 (0.18), residues: 832 sheet: 0.19 (0.37), residues: 192 loop : -0.24 (0.23), residues: 680 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 80 HIS 0.004 0.001 HIS E 359 PHE 0.016 0.001 PHE B 183 TYR 0.018 0.001 TYR E 192 ARG 0.011 0.000 ARG D 178 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3408 Ramachandran restraints generated. 1704 Oldfield, 0 Emsley, 1704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3408 Ramachandran restraints generated. 1704 Oldfield, 0 Emsley, 1704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 252 residues out of total 1390 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 210 time to evaluate : 1.469 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 34 LEU cc_start: 0.9267 (tp) cc_final: 0.9002 (tt) REVERT: A 45 TYR cc_start: 0.8577 (t80) cc_final: 0.8367 (t80) REVERT: A 110 ARG cc_start: 0.7600 (mmt90) cc_final: 0.7138 (mmm160) REVERT: A 173 GLU cc_start: 0.7752 (mt-10) cc_final: 0.7453 (mt-10) REVERT: C 100 ASN cc_start: 0.7935 (m-40) cc_final: 0.7595 (t0) REVERT: C 244 MET cc_start: 0.3615 (ttm) cc_final: 0.3349 (ttp) REVERT: C 260 PHE cc_start: 0.6620 (p90) cc_final: 0.6107 (p90) REVERT: C 283 ILE cc_start: 0.8664 (mm) cc_final: 0.8231 (pt) REVERT: D 151 ARG cc_start: 0.8660 (OUTLIER) cc_final: 0.7228 (mtm110) REVERT: D 158 LYS cc_start: 0.8165 (mttt) cc_final: 0.7486 (tppt) outliers start: 42 outliers final: 38 residues processed: 234 average time/residue: 0.2258 time to fit residues: 79.4045 Evaluate side-chains 235 residues out of total 1390 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 196 time to evaluate : 1.446 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 ASP Chi-restraints excluded: chain A residue 33 LEU Chi-restraints excluded: chain A residue 60 HIS Chi-restraints excluded: chain A residue 67 LEU Chi-restraints excluded: chain A residue 90 THR Chi-restraints excluded: chain A residue 106 LEU Chi-restraints excluded: chain A residue 191 LEU Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 239 ASP Chi-restraints excluded: chain A residue 244 LEU Chi-restraints excluded: chain B residue 23 TYR Chi-restraints excluded: chain B residue 26 ILE Chi-restraints excluded: chain B residue 78 LEU Chi-restraints excluded: chain B residue 112 LEU Chi-restraints excluded: chain B residue 158 SER Chi-restraints excluded: chain B residue 168 LEU Chi-restraints excluded: chain B residue 197 THR Chi-restraints excluded: chain B residue 229 ILE Chi-restraints excluded: chain B residue 236 SER Chi-restraints excluded: chain B residue 238 PHE Chi-restraints excluded: chain B residue 267 ILE Chi-restraints excluded: chain C residue 60 ILE Chi-restraints excluded: chain C residue 213 LEU Chi-restraints excluded: chain C residue 250 THR Chi-restraints excluded: chain D residue 151 ARG Chi-restraints excluded: chain D residue 169 LEU Chi-restraints excluded: chain D residue 205 LEU Chi-restraints excluded: chain D residue 235 VAL Chi-restraints excluded: chain D residue 256 VAL Chi-restraints excluded: chain E residue 89 ASP Chi-restraints excluded: chain E residue 95 VAL Chi-restraints excluded: chain E residue 167 ASP Chi-restraints excluded: chain E residue 201 THR Chi-restraints excluded: chain E residue 254 ASP Chi-restraints excluded: chain E residue 289 VAL Chi-restraints excluded: chain E residue 339 ASP Chi-restraints excluded: chain E residue 428 SER Chi-restraints excluded: chain E residue 450 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 169 random chunks: chunk 54 optimal weight: 9.9990 chunk 147 optimal weight: 4.9990 chunk 32 optimal weight: 0.0070 chunk 95 optimal weight: 10.0000 chunk 40 optimal weight: 3.9990 chunk 163 optimal weight: 3.9990 chunk 135 optimal weight: 0.8980 chunk 75 optimal weight: 2.9990 chunk 13 optimal weight: 0.8980 chunk 85 optimal weight: 6.9990 chunk 157 optimal weight: 3.9990 overall best weight: 1.7602 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 87 GLN C 164 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8106 moved from start: 0.3702 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 13246 Z= 0.263 Angle : 0.594 8.658 18087 Z= 0.297 Chirality : 0.043 0.230 2150 Planarity : 0.004 0.043 2313 Dihedral : 6.355 67.449 1928 Min Nonbonded Distance : 1.949 Molprobity Statistics. All-atom Clashscore : 8.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer: Outliers : 3.90 % Allowed : 14.98 % Favored : 81.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.16 % 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: 0.57 (0.20), residues: 1704 helix: 1.02 (0.18), residues: 829 sheet: 0.14 (0.35), residues: 201 loop : -0.21 (0.24), residues: 674 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP B 166 HIS 0.003 0.001 HIS E 359 PHE 0.028 0.002 PHE C 234 TYR 0.027 0.002 TYR D 89 ARG 0.009 0.000 ARG D 178 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3408 Ramachandran restraints generated. 1704 Oldfield, 0 Emsley, 1704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3408 Ramachandran restraints generated. 1704 Oldfield, 0 Emsley, 1704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 253 residues out of total 1390 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 202 time to evaluate : 1.623 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 45 TYR cc_start: 0.8564 (t80) cc_final: 0.8346 (t80) REVERT: A 110 ARG cc_start: 0.7624 (mmt90) cc_final: 0.7192 (mmm160) REVERT: B 58 LYS cc_start: 0.8869 (OUTLIER) cc_final: 0.8514 (mtmm) REVERT: B 174 MET cc_start: 0.8518 (mmt) cc_final: 0.8083 (mmt) REVERT: B 216 LEU cc_start: 0.8714 (OUTLIER) cc_final: 0.8504 (mt) REVERT: C 100 ASN cc_start: 0.7933 (m-40) cc_final: 0.7682 (t0) REVERT: C 153 ILE cc_start: 0.8327 (mm) cc_final: 0.8001 (tp) REVERT: C 244 MET cc_start: 0.3675 (ttm) cc_final: 0.3397 (ttp) REVERT: C 283 ILE cc_start: 0.8633 (mm) cc_final: 0.8201 (pt) REVERT: D 138 GLN cc_start: 0.8175 (mp10) cc_final: 0.7909 (pm20) REVERT: D 151 ARG cc_start: 0.8836 (OUTLIER) cc_final: 0.7378 (mtm110) REVERT: D 158 LYS cc_start: 0.8186 (mttt) cc_final: 0.7465 (tppt) REVERT: D 205 LEU cc_start: 0.7335 (OUTLIER) cc_final: 0.7011 (mp) REVERT: E 345 THR cc_start: 0.8727 (m) cc_final: 0.8416 (p) outliers start: 51 outliers final: 42 residues processed: 232 average time/residue: 0.2376 time to fit residues: 81.8006 Evaluate side-chains 236 residues out of total 1390 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 190 time to evaluate : 1.530 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 ASP Chi-restraints excluded: chain A residue 33 LEU Chi-restraints excluded: chain A residue 34 LEU Chi-restraints excluded: chain A residue 60 HIS Chi-restraints excluded: chain A residue 67 LEU Chi-restraints excluded: chain A residue 90 THR Chi-restraints excluded: chain A residue 106 LEU Chi-restraints excluded: chain A residue 178 THR Chi-restraints excluded: chain A residue 191 LEU Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 239 ASP Chi-restraints excluded: chain A residue 244 LEU Chi-restraints excluded: chain A residue 251 THR Chi-restraints excluded: chain B residue 23 TYR Chi-restraints excluded: chain B residue 26 ILE Chi-restraints excluded: chain B residue 58 LYS Chi-restraints excluded: chain B residue 78 LEU Chi-restraints excluded: chain B residue 112 LEU Chi-restraints excluded: chain B residue 158 SER Chi-restraints excluded: chain B residue 168 LEU Chi-restraints excluded: chain B residue 197 THR Chi-restraints excluded: chain B residue 216 LEU Chi-restraints excluded: chain B residue 229 ILE Chi-restraints excluded: chain B residue 236 SER Chi-restraints excluded: chain B residue 238 PHE Chi-restraints excluded: chain B residue 267 ILE Chi-restraints excluded: chain C residue 60 ILE Chi-restraints excluded: chain C residue 213 LEU Chi-restraints excluded: chain C residue 250 THR Chi-restraints excluded: chain C residue 273 LEU Chi-restraints excluded: chain D residue 151 ARG Chi-restraints excluded: chain D residue 169 LEU Chi-restraints excluded: chain D residue 205 LEU Chi-restraints excluded: chain D residue 235 VAL Chi-restraints excluded: chain D residue 256 VAL Chi-restraints excluded: chain E residue 63 GLN Chi-restraints excluded: chain E residue 89 ASP Chi-restraints excluded: chain E residue 95 VAL Chi-restraints excluded: chain E residue 167 ASP Chi-restraints excluded: chain E residue 201 THR Chi-restraints excluded: chain E residue 254 ASP Chi-restraints excluded: chain E residue 289 VAL Chi-restraints excluded: chain E residue 339 ASP Chi-restraints excluded: chain E residue 428 SER Chi-restraints excluded: chain E residue 450 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 169 random chunks: chunk 18 optimal weight: 2.9990 chunk 93 optimal weight: 0.9980 chunk 119 optimal weight: 20.0000 chunk 92 optimal weight: 10.0000 chunk 137 optimal weight: 6.9990 chunk 91 optimal weight: 0.9980 chunk 162 optimal weight: 0.9990 chunk 101 optimal weight: 1.9990 chunk 99 optimal weight: 0.9980 chunk 75 optimal weight: 4.9990 chunk 100 optimal weight: 0.0060 overall best weight: 0.7998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 164 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8066 moved from start: 0.3853 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 13246 Z= 0.173 Angle : 0.558 8.302 18087 Z= 0.277 Chirality : 0.042 0.180 2150 Planarity : 0.004 0.042 2313 Dihedral : 6.050 63.792 1928 Min Nonbonded Distance : 2.027 Molprobity Statistics. All-atom Clashscore : 8.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % Rotamer: Outliers : 3.52 % Allowed : 15.37 % Favored : 81.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.16 % 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: 0.68 (0.20), residues: 1704 helix: 1.14 (0.19), residues: 822 sheet: 0.31 (0.37), residues: 183 loop : -0.24 (0.23), residues: 699 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 80 HIS 0.003 0.001 HIS E 359 PHE 0.008 0.001 PHE C 234 TYR 0.027 0.001 TYR D 89 ARG 0.006 0.000 ARG D 178 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3408 Ramachandran restraints generated. 1704 Oldfield, 0 Emsley, 1704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3408 Ramachandran restraints generated. 1704 Oldfield, 0 Emsley, 1704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 251 residues out of total 1390 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 205 time to evaluate : 1.461 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 27 LEU cc_start: 0.9069 (OUTLIER) cc_final: 0.8745 (mp) REVERT: A 34 LEU cc_start: 0.9231 (OUTLIER) cc_final: 0.8966 (tt) REVERT: A 110 ARG cc_start: 0.7594 (mmt90) cc_final: 0.7100 (mmm160) REVERT: A 237 ILE cc_start: 0.8965 (tp) cc_final: 0.8710 (tt) REVERT: B 216 LEU cc_start: 0.8713 (OUTLIER) cc_final: 0.8466 (mt) REVERT: C 100 ASN cc_start: 0.7918 (m-40) cc_final: 0.7644 (t0) REVERT: C 153 ILE cc_start: 0.8279 (mm) cc_final: 0.7970 (tp) REVERT: C 244 MET cc_start: 0.3636 (ttm) cc_final: 0.3371 (ttp) REVERT: D 138 GLN cc_start: 0.8051 (mp10) cc_final: 0.7848 (mp10) REVERT: D 151 ARG cc_start: 0.8741 (OUTLIER) cc_final: 0.7391 (mtm110) REVERT: D 158 LYS cc_start: 0.8166 (mttt) cc_final: 0.7464 (tptt) REVERT: D 162 MET cc_start: 0.7691 (mtt) cc_final: 0.7326 (mtt) REVERT: E 44 PHE cc_start: 0.8578 (m-80) cc_final: 0.8285 (m-10) REVERT: E 345 THR cc_start: 0.8699 (m) cc_final: 0.8367 (p) outliers start: 46 outliers final: 35 residues processed: 235 average time/residue: 0.2159 time to fit residues: 76.6679 Evaluate side-chains 228 residues out of total 1390 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 189 time to evaluate : 1.467 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 ASP Chi-restraints excluded: chain A residue 27 LEU Chi-restraints excluded: chain A residue 33 LEU Chi-restraints excluded: chain A residue 34 LEU Chi-restraints excluded: chain A residue 60 HIS Chi-restraints excluded: chain A residue 67 LEU Chi-restraints excluded: chain A residue 106 LEU Chi-restraints excluded: chain A residue 178 THR Chi-restraints excluded: chain A residue 191 LEU Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 223 ILE Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 239 ASP Chi-restraints excluded: chain A residue 244 LEU Chi-restraints excluded: chain B residue 23 TYR Chi-restraints excluded: chain B residue 26 ILE Chi-restraints excluded: chain B residue 78 LEU Chi-restraints excluded: chain B residue 112 LEU Chi-restraints excluded: chain B residue 158 SER Chi-restraints excluded: chain B residue 216 LEU Chi-restraints excluded: chain B residue 229 ILE Chi-restraints excluded: chain B residue 236 SER Chi-restraints excluded: chain B residue 238 PHE Chi-restraints excluded: chain C residue 60 ILE Chi-restraints excluded: chain C residue 213 LEU Chi-restraints excluded: chain C residue 250 THR Chi-restraints excluded: chain D residue 151 ARG Chi-restraints excluded: chain D residue 169 LEU Chi-restraints excluded: chain D residue 235 VAL Chi-restraints excluded: chain D residue 256 VAL Chi-restraints excluded: chain E residue 63 GLN Chi-restraints excluded: chain E residue 89 ASP Chi-restraints excluded: chain E residue 95 VAL Chi-restraints excluded: chain E residue 167 ASP Chi-restraints excluded: chain E residue 254 ASP Chi-restraints excluded: chain E residue 289 VAL Chi-restraints excluded: chain E residue 339 ASP Chi-restraints excluded: chain E residue 428 SER Chi-restraints excluded: chain E residue 450 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 169 random chunks: chunk 65 optimal weight: 4.9990 chunk 97 optimal weight: 8.9990 chunk 49 optimal weight: 2.9990 chunk 32 optimal weight: 0.2980 chunk 31 optimal weight: 3.9990 chunk 103 optimal weight: 2.9990 chunk 110 optimal weight: 7.9990 chunk 80 optimal weight: 10.0000 chunk 15 optimal weight: 2.9990 chunk 128 optimal weight: 0.1980 chunk 148 optimal weight: 3.9990 overall best weight: 1.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 164 GLN E 455 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8121 moved from start: 0.3963 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 13246 Z= 0.281 Angle : 0.607 8.351 18087 Z= 0.303 Chirality : 0.043 0.167 2150 Planarity : 0.004 0.043 2313 Dihedral : 6.094 63.117 1928 Min Nonbonded Distance : 1.920 Molprobity Statistics. All-atom Clashscore : 9.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.64 % Favored : 96.36 % Rotamer: Outliers : 3.75 % Allowed : 15.90 % Favored : 80.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.16 % 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: 0.67 (0.21), residues: 1704 helix: 1.14 (0.19), residues: 810 sheet: 0.31 (0.38), residues: 183 loop : -0.24 (0.23), residues: 711 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 129 HIS 0.005 0.001 HIS E 359 PHE 0.015 0.002 PHE E 59 TYR 0.029 0.002 TYR D 89 ARG 0.006 0.000 ARG D 178 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3408 Ramachandran restraints generated. 1704 Oldfield, 0 Emsley, 1704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3408 Ramachandran restraints generated. 1704 Oldfield, 0 Emsley, 1704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 243 residues out of total 1390 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 194 time to evaluate : 1.399 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 27 LEU cc_start: 0.9088 (OUTLIER) cc_final: 0.8810 (mp) REVERT: A 110 ARG cc_start: 0.7627 (mmt90) cc_final: 0.7167 (mmm160) REVERT: A 237 ILE cc_start: 0.9081 (tp) cc_final: 0.8833 (tt) REVERT: B 216 LEU cc_start: 0.8813 (OUTLIER) cc_final: 0.8596 (mt) REVERT: C 100 ASN cc_start: 0.7862 (m-40) cc_final: 0.7623 (t0) REVERT: C 244 MET cc_start: 0.3644 (ttm) cc_final: 0.3386 (ttp) REVERT: D 151 ARG cc_start: 0.8853 (OUTLIER) cc_final: 0.7370 (mtm110) REVERT: D 158 LYS cc_start: 0.8177 (mttt) cc_final: 0.7450 (tppt) outliers start: 49 outliers final: 41 residues processed: 226 average time/residue: 0.2211 time to fit residues: 75.2262 Evaluate side-chains 228 residues out of total 1390 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 184 time to evaluate : 1.526 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 ASP Chi-restraints excluded: chain A residue 27 LEU Chi-restraints excluded: chain A residue 33 LEU Chi-restraints excluded: chain A residue 34 LEU Chi-restraints excluded: chain A residue 60 HIS Chi-restraints excluded: chain A residue 67 LEU Chi-restraints excluded: chain A residue 106 LEU Chi-restraints excluded: chain A residue 178 THR Chi-restraints excluded: chain A residue 191 LEU Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 223 ILE Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 239 ASP Chi-restraints excluded: chain A residue 244 LEU Chi-restraints excluded: chain B residue 23 TYR Chi-restraints excluded: chain B residue 26 ILE Chi-restraints excluded: chain B residue 78 LEU Chi-restraints excluded: chain B residue 112 LEU Chi-restraints excluded: chain B residue 113 ILE Chi-restraints excluded: chain B residue 158 SER Chi-restraints excluded: chain B residue 197 THR Chi-restraints excluded: chain B residue 216 LEU Chi-restraints excluded: chain B residue 229 ILE Chi-restraints excluded: chain B residue 236 SER Chi-restraints excluded: chain B residue 238 PHE Chi-restraints excluded: chain B residue 267 ILE Chi-restraints excluded: chain C residue 60 ILE Chi-restraints excluded: chain C residue 213 LEU Chi-restraints excluded: chain C residue 250 THR Chi-restraints excluded: chain C residue 273 LEU Chi-restraints excluded: chain D residue 151 ARG Chi-restraints excluded: chain D residue 169 LEU Chi-restraints excluded: chain D residue 235 VAL Chi-restraints excluded: chain D residue 256 VAL Chi-restraints excluded: chain E residue 63 GLN Chi-restraints excluded: chain E residue 89 ASP Chi-restraints excluded: chain E residue 95 VAL Chi-restraints excluded: chain E residue 167 ASP Chi-restraints excluded: chain E residue 201 THR Chi-restraints excluded: chain E residue 254 ASP Chi-restraints excluded: chain E residue 289 VAL Chi-restraints excluded: chain E residue 339 ASP Chi-restraints excluded: chain E residue 428 SER Chi-restraints excluded: chain E residue 450 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 169 random chunks: chunk 156 optimal weight: 2.9990 chunk 142 optimal weight: 0.6980 chunk 151 optimal weight: 0.0980 chunk 91 optimal weight: 0.9990 chunk 66 optimal weight: 4.9990 chunk 119 optimal weight: 3.9990 chunk 46 optimal weight: 0.9980 chunk 137 optimal weight: 4.9990 chunk 143 optimal weight: 0.7980 chunk 99 optimal weight: 0.9980 chunk 160 optimal weight: 0.8980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 164 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8064 moved from start: 0.4111 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 13246 Z= 0.172 Angle : 0.572 8.759 18087 Z= 0.284 Chirality : 0.042 0.164 2150 Planarity : 0.004 0.042 2313 Dihedral : 5.810 63.255 1928 Min Nonbonded Distance : 2.014 Molprobity Statistics. All-atom Clashscore : 9.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer: Outliers : 3.29 % Allowed : 16.59 % Favored : 80.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.16 % 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: 0.67 (0.20), residues: 1704 helix: 1.13 (0.19), residues: 821 sheet: 0.31 (0.37), residues: 183 loop : -0.24 (0.23), residues: 700 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 80 HIS 0.004 0.001 HIS E 359 PHE 0.009 0.001 PHE A 180 TYR 0.027 0.001 TYR D 89 ARG 0.005 0.000 ARG D 178 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3408 Ramachandran restraints generated. 1704 Oldfield, 0 Emsley, 1704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3408 Ramachandran restraints generated. 1704 Oldfield, 0 Emsley, 1704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 242 residues out of total 1390 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 199 time to evaluate : 1.551 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 27 LEU cc_start: 0.9068 (OUTLIER) cc_final: 0.8783 (mp) REVERT: A 34 LEU cc_start: 0.9225 (OUTLIER) cc_final: 0.8982 (tt) REVERT: A 237 ILE cc_start: 0.9056 (tp) cc_final: 0.8794 (tt) REVERT: B 103 LYS cc_start: 0.7021 (tptt) cc_final: 0.6763 (tptt) REVERT: B 216 LEU cc_start: 0.8784 (OUTLIER) cc_final: 0.8496 (mp) REVERT: C 100 ASN cc_start: 0.7867 (m-40) cc_final: 0.7594 (t0) REVERT: C 244 MET cc_start: 0.3516 (ttm) cc_final: 0.3275 (ttp) REVERT: D 151 ARG cc_start: 0.8748 (OUTLIER) cc_final: 0.7349 (mtm110) REVERT: D 158 LYS cc_start: 0.8158 (mttt) cc_final: 0.7467 (tppt) REVERT: E 378 TYR cc_start: 0.7976 (t80) cc_final: 0.7647 (t80) outliers start: 43 outliers final: 34 residues processed: 226 average time/residue: 0.2574 time to fit residues: 87.6364 Evaluate side-chains 223 residues out of total 1390 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 185 time to evaluate : 1.589 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 ASP Chi-restraints excluded: chain A residue 27 LEU Chi-restraints excluded: chain A residue 33 LEU Chi-restraints excluded: chain A residue 34 LEU Chi-restraints excluded: chain A residue 43 ILE Chi-restraints excluded: chain A residue 60 HIS Chi-restraints excluded: chain A residue 67 LEU Chi-restraints excluded: chain A residue 106 LEU Chi-restraints excluded: chain A residue 178 THR Chi-restraints excluded: chain A residue 191 LEU Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 223 ILE Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 239 ASP Chi-restraints excluded: chain A residue 244 LEU Chi-restraints excluded: chain B residue 23 TYR Chi-restraints excluded: chain B residue 26 ILE Chi-restraints excluded: chain B residue 78 LEU Chi-restraints excluded: chain B residue 112 LEU Chi-restraints excluded: chain B residue 216 LEU Chi-restraints excluded: chain B residue 236 SER Chi-restraints excluded: chain B residue 238 PHE Chi-restraints excluded: chain C residue 60 ILE Chi-restraints excluded: chain C residue 213 LEU Chi-restraints excluded: chain C residue 250 THR Chi-restraints excluded: chain C residue 273 LEU Chi-restraints excluded: chain D residue 151 ARG Chi-restraints excluded: chain D residue 169 LEU Chi-restraints excluded: chain D residue 235 VAL Chi-restraints excluded: chain D residue 256 VAL Chi-restraints excluded: chain E residue 63 GLN Chi-restraints excluded: chain E residue 89 ASP Chi-restraints excluded: chain E residue 167 ASP Chi-restraints excluded: chain E residue 254 ASP Chi-restraints excluded: chain E residue 289 VAL Chi-restraints excluded: chain E residue 339 ASP Chi-restraints excluded: chain E residue 428 SER Chi-restraints excluded: chain E residue 450 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 169 random chunks: chunk 97 optimal weight: 0.6980 chunk 76 optimal weight: 0.7980 chunk 111 optimal weight: 7.9990 chunk 168 optimal weight: 1.9990 chunk 154 optimal weight: 0.5980 chunk 134 optimal weight: 0.0870 chunk 13 optimal weight: 2.9990 chunk 103 optimal weight: 3.9990 chunk 82 optimal weight: 6.9990 chunk 106 optimal weight: 0.7980 chunk 142 optimal weight: 1.9990 overall best weight: 0.5958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 164 GLN E 54 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8053 moved from start: 0.4267 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 13246 Z= 0.169 Angle : 0.580 12.084 18087 Z= 0.286 Chirality : 0.042 0.261 2150 Planarity : 0.004 0.042 2313 Dihedral : 5.681 63.067 1928 Min Nonbonded Distance : 1.995 Molprobity Statistics. All-atom Clashscore : 9.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % Rotamer: Outliers : 2.75 % Allowed : 17.81 % Favored : 79.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.16 % 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: 0.69 (0.20), residues: 1704 helix: 1.17 (0.19), residues: 817 sheet: 0.39 (0.37), residues: 183 loop : -0.28 (0.23), residues: 704 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 80 HIS 0.003 0.001 HIS E 359 PHE 0.017 0.001 PHE E 59 TYR 0.025 0.001 TYR D 89 ARG 0.005 0.000 ARG D 8 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3408 Ramachandran restraints generated. 1704 Oldfield, 0 Emsley, 1704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3408 Ramachandran restraints generated. 1704 Oldfield, 0 Emsley, 1704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 230 residues out of total 1390 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 194 time to evaluate : 1.547 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 27 LEU cc_start: 0.9054 (OUTLIER) cc_final: 0.8793 (mp) REVERT: A 34 LEU cc_start: 0.9213 (OUTLIER) cc_final: 0.8966 (tt) REVERT: A 237 ILE cc_start: 0.9059 (tp) cc_final: 0.8793 (tt) REVERT: B 103 LYS cc_start: 0.6973 (tptt) cc_final: 0.6746 (tptt) REVERT: B 216 LEU cc_start: 0.8771 (OUTLIER) cc_final: 0.8464 (mp) REVERT: C 100 ASN cc_start: 0.7820 (m-40) cc_final: 0.7572 (t0) REVERT: C 244 MET cc_start: 0.3467 (ttm) cc_final: 0.3228 (ttp) REVERT: D 151 ARG cc_start: 0.8672 (OUTLIER) cc_final: 0.7252 (mtm110) REVERT: D 158 LYS cc_start: 0.8150 (mttt) cc_final: 0.7488 (tppt) REVERT: E 378 TYR cc_start: 0.7945 (t80) cc_final: 0.7688 (t80) outliers start: 36 outliers final: 29 residues processed: 216 average time/residue: 0.2276 time to fit residues: 73.5314 Evaluate side-chains 217 residues out of total 1390 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 184 time to evaluate : 1.429 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 ASP Chi-restraints excluded: chain A residue 27 LEU Chi-restraints excluded: chain A residue 33 LEU Chi-restraints excluded: chain A residue 34 LEU Chi-restraints excluded: chain A residue 43 ILE Chi-restraints excluded: chain A residue 67 LEU Chi-restraints excluded: chain A residue 106 LEU Chi-restraints excluded: chain A residue 178 THR Chi-restraints excluded: chain A residue 195 ASP Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 223 ILE Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 239 ASP Chi-restraints excluded: chain A residue 244 LEU Chi-restraints excluded: chain B residue 23 TYR Chi-restraints excluded: chain B residue 26 ILE Chi-restraints excluded: chain B residue 112 LEU Chi-restraints excluded: chain B residue 216 LEU Chi-restraints excluded: chain B residue 238 PHE Chi-restraints excluded: chain C residue 213 LEU Chi-restraints excluded: chain C residue 250 THR Chi-restraints excluded: chain D residue 151 ARG Chi-restraints excluded: chain D residue 169 LEU Chi-restraints excluded: chain D residue 235 VAL Chi-restraints excluded: chain D residue 256 VAL Chi-restraints excluded: chain E residue 63 GLN Chi-restraints excluded: chain E residue 89 ASP Chi-restraints excluded: chain E residue 167 ASP Chi-restraints excluded: chain E residue 254 ASP Chi-restraints excluded: chain E residue 289 VAL Chi-restraints excluded: chain E residue 339 ASP Chi-restraints excluded: chain E residue 428 SER Chi-restraints excluded: chain E residue 450 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 169 random chunks: chunk 41 optimal weight: 2.9990 chunk 123 optimal weight: 1.9990 chunk 19 optimal weight: 0.8980 chunk 37 optimal weight: 0.5980 chunk 134 optimal weight: 0.0030 chunk 56 optimal weight: 7.9990 chunk 137 optimal weight: 3.9990 chunk 17 optimal weight: 2.9990 chunk 24 optimal weight: 1.9990 chunk 117 optimal weight: 30.0000 chunk 7 optimal weight: 0.8980 overall best weight: 0.8792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 164 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3993 r_free = 0.3993 target = 0.149004 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3518 r_free = 0.3518 target = 0.111608 restraints weight = 24909.236| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3509 r_free = 0.3509 target = 0.112531 restraints weight = 13381.389| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3565 r_free = 0.3565 target = 0.115919 restraints weight = 8448.373| |-----------------------------------------------------------------------------| r_work (final): 0.3550 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8048 moved from start: 0.4329 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 13246 Z= 0.187 Angle : 0.582 9.803 18087 Z= 0.288 Chirality : 0.042 0.232 2150 Planarity : 0.004 0.042 2313 Dihedral : 5.626 62.963 1928 Min Nonbonded Distance : 1.980 Molprobity Statistics. All-atom Clashscore : 9.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % Rotamer: Outliers : 2.98 % Allowed : 17.43 % Favored : 79.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.16 % 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: 0.73 (0.20), residues: 1704 helix: 1.22 (0.19), residues: 818 sheet: 0.44 (0.37), residues: 183 loop : -0.29 (0.23), residues: 703 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 129 HIS 0.003 0.000 HIS E 359 PHE 0.012 0.001 PHE D 86 TYR 0.026 0.001 TYR D 89 ARG 0.004 0.000 ARG D 178 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2745.49 seconds wall clock time: 50 minutes 49.92 seconds (3049.92 seconds total)