Starting phenix.real_space_refine on Mon Mar 11 15:10:20 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7scg_25034/03_2024/7scg_25034_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7scg_25034/03_2024/7scg_25034.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7scg_25034/03_2024/7scg_25034.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7scg_25034/03_2024/7scg_25034.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7scg_25034/03_2024/7scg_25034_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7scg_25034/03_2024/7scg_25034_updated.pdb" } resolution = 3.0 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= 1.000 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 64 5.16 5 C 5460 2.51 5 N 1454 2.21 5 O 1561 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B ARG 8": "NH1" <-> "NH2" Residue "B GLU 10": "OE1" <-> "OE2" Residue "B ARG 19": "NH1" <-> "NH2" Residue "B ASP 20": "OD1" <-> "OD2" Residue "B ARG 46": "NH1" <-> "NH2" Residue "B TYR 59": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 66": "OD1" <-> "OD2" Residue "B ARG 68": "NH1" <-> "NH2" Residue "B ASP 76": "OD1" <-> "OD2" Residue "B ASP 83": "OD1" <-> "OD2" Residue "B ARG 96": "NH1" <-> "NH2" Residue "B TYR 111": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 124": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 137": "NH1" <-> "NH2" Residue "B TYR 145": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 154": "OD1" <-> "OD2" Residue "B PHE 180": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 256": "NH1" <-> "NH2" Residue "B GLU 260": "OE1" <-> "OE2" Residue "B TYR 289": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 322": "OD1" <-> "OD2" Residue "B ASP 333": "OD1" <-> "OD2" Residue "C ARG 13": "NH1" <-> "NH2" Residue "C ASP 36": "OD1" <-> "OD2" Residue "C TYR 40": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 42": "OE1" <-> "OE2" Residue "C PHE 61": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 123": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 128": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 135": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 149": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 263": "NH1" <-> "NH2" Residue "D TYR 299": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 320": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 336": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 341": "OE1" <-> "OE2" Residue "D PHE 347": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 20": "OD1" <-> "OD2" Residue "A PHE 196": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 223": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 287": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 307": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 320": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 323": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 337": "OD1" <-> "OD2" Residue "A ASP 341": "OD1" <-> "OD2" Residue "A PHE 354": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 62": "OD1" <-> "OD2" Residue "E PHE 68": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 102": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 109": "OD1" <-> "OD2" Residue "E ARG 148": "NH1" <-> "NH2" Residue "E TYR 163": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 191": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 211": "OD1" <-> "OD2" Residue "E PHE 227": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 8539 Number of models: 1 Model: "" Number of chains: 6 Chain: "B" Number of atoms: 2547 Number of conformers: 1 Conformer: "" Number of residues, atoms: 336, 2547 Classifications: {'peptide': 336} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PTRANS': 5, 'TRANS': 330} Unresolved non-hydrogen bonds: 37 Unresolved non-hydrogen angles: 46 Unresolved non-hydrogen dihedrals: 28 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 1, 'ASN:plan1': 2, 'ARG:plan': 1, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 32 Chain: "C" Number of atoms: 381 Number of conformers: 1 Conformer: "" Number of residues, atoms: 53, 381 Classifications: {'peptide': 53} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 4, 'TRANS': 48} Unresolved non-hydrogen bonds: 26 Unresolved non-hydrogen angles: 31 Unresolved non-hydrogen dihedrals: 21 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 2, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 18 Chain: "D" Number of atoms: 2158 Number of conformers: 1 Conformer: "" Number of residues, atoms: 283, 2158 Classifications: {'peptide': 283} Incomplete info: {'truncation_to_alanine': 28} Link IDs: {'PTRANS': 10, 'TRANS': 272} Unresolved non-hydrogen bonds: 124 Unresolved non-hydrogen angles: 153 Unresolved non-hydrogen dihedrals: 114 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 2, 'TRP:plan': 1, 'HIS:plan': 1, 'PHE:plan': 2, 'GLU:plan': 1, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 68 Chain: "A" Number of atoms: 1675 Number of conformers: 1 Conformer: "" Number of residues, atoms: 217, 1675 Classifications: {'peptide': 217} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 22} Link IDs: {'PTRANS': 2, 'TRANS': 214} Chain breaks: 2 Unresolved non-hydrogen bonds: 76 Unresolved non-hydrogen angles: 94 Unresolved non-hydrogen dihedrals: 58 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLU:plan': 8, 'ASP:plan': 6} Unresolved non-hydrogen planarities: 50 Chain: "E" Number of atoms: 1748 Number of conformers: 1 Conformer: "" Number of residues, atoms: 232, 1748 Classifications: {'peptide': 232} Incomplete info: {'truncation_to_alanine': 13} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 221} Chain breaks: 1 Unresolved non-hydrogen bonds: 35 Unresolved non-hydrogen angles: 43 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 5, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 26 Chain: "D" Number of atoms: 30 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 30 Unusual residues: {'8RI': 1} Classifications: {'undetermined': 1, 'water': 2} Link IDs: {None: 2} Time building chain proxies: 5.17, per 1000 atoms: 0.61 Number of scatterers: 8539 At special positions: 0 Unit cell: (103.244, 122.332, 111.92, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 64 16.00 O 1561 8.00 N 1454 7.00 C 5460 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS D 140 " - pdb=" SG CYS D 217 " distance=2.03 Simple disulfide: pdb=" SG CYS E 22 " - pdb=" SG CYS E 96 " distance=2.04 Simple disulfide: pdb=" SG CYS E 147 " - pdb=" SG CYS E 217 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.25 Conformation dependent library (CDL) restraints added in 1.8 seconds 2210 Ramachandran restraints generated. 1105 Oldfield, 0 Emsley, 1105 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2102 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 26 helices and 14 sheets defined 33.9% alpha, 22.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.70 Creating SS restraints... Processing helix chain 'B' and resid 6 through 23 removed outlier: 4.110A pdb=" N GLU B 10 " --> pdb=" O GLN B 6 " (cutoff:3.500A) removed outlier: 4.413A pdb=" N ALA B 11 " --> pdb=" O LEU B 7 " (cutoff:3.500A) removed outlier: 4.585A pdb=" N GLU B 12 " --> pdb=" O ARG B 8 " (cutoff:3.500A) Processing helix chain 'B' and resid 30 through 32 No H-bonds generated for 'chain 'B' and resid 30 through 32' Processing helix chain 'C' and resid 10 through 22 Processing helix chain 'C' and resid 30 through 43 Processing helix chain 'D' and resid 67 through 96 removed outlier: 4.002A pdb=" N VAL D 94 " --> pdb=" O MET D 90 " (cutoff:3.500A) Processing helix chain 'D' and resid 102 through 130 removed outlier: 4.375A pdb=" N THR D 120 " --> pdb=" O LEU D 116 " (cutoff:3.500A) removed outlier: 5.145A pdb=" N LEU D 121 " --> pdb=" O ALA D 117 " (cutoff:3.500A) Proline residue: D 122 - end of helix Processing helix chain 'D' and resid 137 through 170 removed outlier: 4.212A pdb=" N LYS D 141 " --> pdb=" O ASN D 137 " (cutoff:3.500A) removed outlier: 4.932A pdb=" N ILE D 142 " --> pdb=" O ILE D 138 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N SER D 145 " --> pdb=" O LYS D 141 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N MET D 151 " --> pdb=" O ASP D 147 " (cutoff:3.500A) removed outlier: 4.078A pdb=" N PHE D 152 " --> pdb=" O TYR D 148 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N THR D 153 " --> pdb=" O TYR D 149 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N SER D 154 " --> pdb=" O ASN D 150 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N THR D 157 " --> pdb=" O THR D 153 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N LEU D 158 " --> pdb=" O SER D 154 " (cutoff:3.500A) Processing helix chain 'D' and resid 174 through 178 removed outlier: 3.565A pdb=" N PHE D 178 " --> pdb=" O ALA D 175 " (cutoff:3.500A) Processing helix chain 'D' and resid 181 through 205 removed outlier: 3.621A pdb=" N TRP D 192 " --> pdb=" O ASN D 188 " (cutoff:3.500A) removed outlier: 4.436A pdb=" N ALA D 197 " --> pdb=" O ILE D 193 " (cutoff:3.500A) removed outlier: 4.578A pdb=" N ILE D 198 " --> pdb=" O LEU D 194 " (cutoff:3.500A) Proline residue: D 201 - end of helix Processing helix chain 'D' and resid 225 through 240 Processing helix chain 'D' and resid 242 through 260 removed outlier: 3.923A pdb=" N LYS D 260 " --> pdb=" O ILE D 256 " (cutoff:3.500A) Processing helix chain 'D' and resid 263 through 265 No H-bonds generated for 'chain 'D' and resid 263 through 265' Processing helix chain 'D' and resid 270 through 303 Proline residue: D 295 - end of helix Processing helix chain 'D' and resid 312 through 336 removed outlier: 3.636A pdb=" N ALA D 323 " --> pdb=" O HIS D 319 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N ASN D 328 " --> pdb=" O LEU D 324 " (cutoff:3.500A) removed outlier: 4.407A pdb=" N SER D 329 " --> pdb=" O GLY D 325 " (cutoff:3.500A) Proline residue: D 333 - end of helix Processing helix chain 'D' and resid 341 through 346 Processing helix chain 'A' and resid 9 through 32 removed outlier: 4.060A pdb=" N ARG A 32 " --> pdb=" O GLU A 28 " (cutoff:3.500A) Processing helix chain 'A' and resid 46 through 52 removed outlier: 3.773A pdb=" N VAL A 50 " --> pdb=" O LYS A 46 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N LYS A 51 " --> pdb=" O SER A 47 " (cutoff:3.500A) Processing helix chain 'A' and resid 208 through 210 No H-bonds generated for 'chain 'A' and resid 208 through 210' Processing helix chain 'A' and resid 212 through 215 removed outlier: 3.576A pdb=" N PHE A 215 " --> pdb=" O ILE A 212 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 212 through 215' Processing helix chain 'A' and resid 242 through 254 Processing helix chain 'A' and resid 271 through 280 removed outlier: 4.297A pdb=" N LYS A 279 " --> pdb=" O GLU A 275 " (cutoff:3.500A) removed outlier: 4.148A pdb=" N LYS A 280 " --> pdb=" O GLU A 276 " (cutoff:3.500A) Processing helix chain 'A' and resid 283 through 285 No H-bonds generated for 'chain 'A' and resid 283 through 285' Processing helix chain 'A' and resid 296 through 310 removed outlier: 4.196A pdb=" N ALA A 301 " --> pdb=" O GLU A 297 " (cutoff:3.500A) removed outlier: 4.288A pdb=" N LEU A 310 " --> pdb=" O GLN A 306 " (cutoff:3.500A) Processing helix chain 'A' and resid 331 through 351 Processing helix chain 'E' and resid 29 through 31 No H-bonds generated for 'chain 'E' and resid 29 through 31' Processing helix chain 'E' and resid 88 through 90 No H-bonds generated for 'chain 'E' and resid 88 through 90' Processing sheet with id= A, first strand: chain 'B' and resid 58 through 63 removed outlier: 6.900A pdb=" N ALA B 73 " --> pdb=" O TYR B 59 " (cutoff:3.500A) removed outlier: 4.428A pdb=" N MET B 61 " --> pdb=" O VAL B 71 " (cutoff:3.500A) removed outlier: 6.696A pdb=" N VAL B 71 " --> pdb=" O MET B 61 " (cutoff:3.500A) removed outlier: 5.213A pdb=" N TRP B 63 " --> pdb=" O LEU B 69 " (cutoff:3.500A) removed outlier: 7.450A pdb=" N LEU B 69 " --> pdb=" O TRP B 63 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N SER B 72 " --> pdb=" O ILE B 80 " (cutoff:3.500A) removed outlier: 4.231A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N HIS B 91 " --> pdb=" O ILE B 81 " (cutoff:3.500A) removed outlier: 6.582A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 6.110A pdb=" N LYS B 89 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'B' and resid 100 through 105 removed outlier: 7.097A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.750A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.683A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 5.145A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 7.324A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N GLY B 116 " --> pdb=" O ILE B 120 " (cutoff:3.500A) removed outlier: 4.908A pdb=" N ILE B 120 " --> pdb=" O GLY B 116 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N ARG B 137 " --> pdb=" O ILE B 123 " (cutoff:3.500A) removed outlier: 6.102A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 6.050A pdb=" N VAL B 135 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'B' and resid 146 through 151 removed outlier: 6.692A pdb=" N SER B 160 " --> pdb=" O SER B 147 " (cutoff:3.500A) removed outlier: 4.556A pdb=" N CYS B 149 " --> pdb=" O VAL B 158 " (cutoff:3.500A) removed outlier: 6.898A pdb=" N VAL B 158 " --> pdb=" O CYS B 149 " (cutoff:3.500A) removed outlier: 5.002A pdb=" N PHE B 151 " --> pdb=" O GLN B 156 " (cutoff:3.500A) removed outlier: 7.522A pdb=" N GLN B 156 " --> pdb=" O PHE B 151 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N ILE B 157 " --> pdb=" O TRP B 169 " (cutoff:3.500A) removed outlier: 6.687A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 6.206A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 187 through 192 removed outlier: 6.850A pdb=" N GLY B 202 " --> pdb=" O MET B 188 " (cutoff:3.500A) removed outlier: 4.448A pdb=" N LEU B 190 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 6.750A pdb=" N VAL B 200 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 5.720A pdb=" N LEU B 192 " --> pdb=" O LEU B 198 " (cutoff:3.500A) removed outlier: 7.449A pdb=" N LEU B 198 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 4.400A pdb=" N SER B 207 " --> pdb=" O ALA B 203 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) removed outlier: 7.055A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.580A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.548A pdb=" N GLY B 244 " --> pdb=" O ASN B 230 " (cutoff:3.500A) removed outlier: 4.222A pdb=" N ILE B 232 " --> pdb=" O ALA B 242 " (cutoff:3.500A) removed outlier: 6.585A pdb=" N ALA B 242 " --> pdb=" O ILE B 232 " (cutoff:3.500A) removed outlier: 4.724A pdb=" N PHE B 234 " --> pdb=" O ALA B 240 " (cutoff:3.500A) removed outlier: 7.029A pdb=" N ALA B 240 " --> pdb=" O PHE B 234 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N CYS B 250 " --> pdb=" O TYR B 264 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N MET B 262 " --> pdb=" O LEU B 252 " (cutoff:3.500A) removed outlier: 5.761A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 6.019A pdb=" N GLU B 260 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 273 through 277 removed outlier: 6.552A pdb=" N GLY B 288 " --> pdb=" O THR B 274 " (cutoff:3.500A) removed outlier: 4.812A pdb=" N VAL B 276 " --> pdb=" O LEU B 286 " (cutoff:3.500A) removed outlier: 6.937A pdb=" N LEU B 286 " --> pdb=" O VAL B 276 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N GLY B 306 " --> pdb=" O VAL B 296 " (cutoff:3.500A) removed outlier: 5.903A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.407A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'B' and resid 47 through 51 removed outlier: 6.635A pdb=" N ILE B 338 " --> pdb=" O ARG B 48 " (cutoff:3.500A) removed outlier: 4.793A pdb=" N THR B 50 " --> pdb=" O LEU B 336 " (cutoff:3.500A) removed outlier: 6.793A pdb=" N LEU B 336 " --> pdb=" O THR B 50 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N CYS B 317 " --> pdb=" O GLY B 330 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'D' and resid 206 through 210 removed outlier: 3.724A pdb=" N THR D 218 " --> pdb=" O THR D 207 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N LYS D 209 " --> pdb=" O ASP D 216 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N ASP D 216 " --> pdb=" O LYS D 209 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'A' and resid 319 through 322 removed outlier: 6.592A pdb=" N ILE A 264 " --> pdb=" O TYR A 320 " (cutoff:3.500A) removed outlier: 8.203A pdb=" N HIS A 322 " --> pdb=" O ILE A 264 " (cutoff:3.500A) removed outlier: 6.834A pdb=" N LEU A 266 " --> pdb=" O HIS A 322 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N ALA A 220 " --> pdb=" O LYS A 35 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N CYS A 224 " --> pdb=" O LEU A 39 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N PHE A 189 " --> pdb=" O PHE A 196 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'E' and resid 4 through 7 Processing sheet with id= K, first strand: chain 'E' and resid 10 through 12 removed outlier: 3.502A pdb=" N THR E 118 " --> pdb=" O GLY E 10 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N ALA E 49 " --> pdb=" O TRP E 36 " (cutoff:3.500A) removed outlier: 5.823A pdb=" N ARG E 38 " --> pdb=" O TRP E 47 " (cutoff:3.500A) removed outlier: 5.231A pdb=" N TRP E 47 " --> pdb=" O ARG E 38 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'E' and resid 134 through 136 removed outlier: 6.793A pdb=" N LYS E 232 " --> pdb=" O VAL E 135 " (cutoff:3.500A) No H-bonds generated for sheet with id= L Processing sheet with id= M, first strand: chain 'E' and resid 142 through 147 removed outlier: 3.618A pdb=" N PHE E 200 " --> pdb=" O CYS E 147 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'E' and resid 213 through 219 removed outlier: 3.540A pdb=" N ILE E 177 " --> pdb=" O TRP E 164 " (cutoff:3.500A) removed outlier: 6.129A pdb=" N LEU E 166 " --> pdb=" O LEU E 175 " (cutoff:3.500A) removed outlier: 5.570A pdb=" N LEU E 175 " --> pdb=" O LEU E 166 " (cutoff:3.500A) 368 hydrogen bonds defined for protein. 1071 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.43 Time building geometry restraints manager: 3.52 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 1351 1.31 - 1.44: 2431 1.44 - 1.56: 4842 1.56 - 1.69: 1 1.69 - 1.81: 91 Bond restraints: 8716 Sorted by residual: bond pdb=" C01 8RI D 401 " pdb=" N01 8RI D 401 " ideal model delta sigma weight residual 1.341 1.469 -0.128 2.00e-02 2.50e+03 4.09e+01 bond pdb=" C03 8RI D 401 " pdb=" C04 8RI D 401 " ideal model delta sigma weight residual 1.464 1.568 -0.104 2.00e-02 2.50e+03 2.68e+01 bond pdb=" C01 8RI D 401 " pdb=" C02 8RI D 401 " ideal model delta sigma weight residual 1.485 1.547 -0.062 2.00e-02 2.50e+03 9.55e+00 bond pdb=" C22 8RI D 401 " pdb=" O02 8RI D 401 " ideal model delta sigma weight residual 1.350 1.400 -0.050 2.00e-02 2.50e+03 6.26e+00 bond pdb=" N SER B 74 " pdb=" CA SER B 74 " ideal model delta sigma weight residual 1.455 1.485 -0.031 1.32e-02 5.74e+03 5.42e+00 ... (remaining 8711 not shown) Histogram of bond angle deviations from ideal: 99.90 - 106.73: 192 106.73 - 113.57: 4827 113.57 - 120.40: 3291 120.40 - 127.23: 3445 127.23 - 134.07: 87 Bond angle restraints: 11842 Sorted by residual: angle pdb=" C ASN D 150 " pdb=" CA ASN D 150 " pdb=" CB ASN D 150 " ideal model delta sigma weight residual 110.37 117.34 -6.97 1.78e+00 3.16e-01 1.53e+01 angle pdb=" N THR B 164 " pdb=" CA THR B 164 " pdb=" CB THR B 164 " ideal model delta sigma weight residual 114.17 109.91 4.26 1.14e+00 7.69e-01 1.39e+01 angle pdb=" N ASN D 150 " pdb=" CA ASN D 150 " pdb=" C ASN D 150 " ideal model delta sigma weight residual 113.02 109.14 3.88 1.20e+00 6.94e-01 1.05e+01 angle pdb=" N ASP B 76 " pdb=" CA ASP B 76 " pdb=" C ASP B 76 " ideal model delta sigma weight residual 113.20 109.72 3.48 1.21e+00 6.83e-01 8.27e+00 angle pdb=" C THR B 29 " pdb=" N LEU B 30 " pdb=" CA LEU B 30 " ideal model delta sigma weight residual 121.54 126.98 -5.44 1.91e+00 2.74e-01 8.12e+00 ... (remaining 11837 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.70: 4684 17.70 - 35.40: 394 35.40 - 53.11: 52 53.11 - 70.81: 5 70.81 - 88.51: 4 Dihedral angle restraints: 5139 sinusoidal: 1883 harmonic: 3256 Sorted by residual: dihedral pdb=" CB CYS D 140 " pdb=" SG CYS D 140 " pdb=" SG CYS D 217 " pdb=" CB CYS D 217 " ideal model delta sinusoidal sigma weight residual 93.00 -179.48 -87.52 1 1.00e+01 1.00e-02 9.19e+01 dihedral pdb=" CA LEU B 95 " pdb=" C LEU B 95 " pdb=" N ARG B 96 " pdb=" CA ARG B 96 " ideal model delta harmonic sigma weight residual 180.00 -158.65 -21.35 0 5.00e+00 4.00e-02 1.82e+01 dihedral pdb=" CA TYR E 101 " pdb=" C TYR E 101 " pdb=" N TYR E 102 " pdb=" CA TYR E 102 " ideal model delta harmonic sigma weight residual 180.00 159.93 20.07 0 5.00e+00 4.00e-02 1.61e+01 ... (remaining 5136 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.049: 1078 0.049 - 0.098: 239 0.098 - 0.147: 59 0.147 - 0.196: 2 0.196 - 0.245: 1 Chirality restraints: 1379 Sorted by residual: chirality pdb=" CA ASN D 150 " pdb=" N ASN D 150 " pdb=" C ASN D 150 " pdb=" CB ASN D 150 " both_signs ideal model delta sigma weight residual False 2.51 2.26 0.25 2.00e-01 2.50e+01 1.51e+00 chirality pdb=" CA MET D 151 " pdb=" N MET D 151 " pdb=" C MET D 151 " pdb=" CB MET D 151 " both_signs ideal model delta sigma weight residual False 2.51 2.69 -0.18 2.00e-01 2.50e+01 8.30e-01 chirality pdb=" CA ILE B 232 " pdb=" N ILE B 232 " pdb=" C ILE B 232 " pdb=" CB ILE B 232 " both_signs ideal model delta sigma weight residual False 2.43 2.60 -0.16 2.00e-01 2.50e+01 6.54e-01 ... (remaining 1376 not shown) Planarity restraints: 1486 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA TYR D 149 " -0.015 2.00e-02 2.50e+03 3.02e-02 9.13e+00 pdb=" C TYR D 149 " 0.052 2.00e-02 2.50e+03 pdb=" O TYR D 149 " -0.019 2.00e-02 2.50e+03 pdb=" N ASN D 150 " -0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR B 164 " 0.009 2.00e-02 2.50e+03 1.74e-02 3.04e+00 pdb=" C THR B 164 " -0.030 2.00e-02 2.50e+03 pdb=" O THR B 164 " 0.011 2.00e-02 2.50e+03 pdb=" N THR B 165 " 0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LEU D 200 " 0.025 5.00e-02 4.00e+02 3.83e-02 2.34e+00 pdb=" N PRO D 201 " -0.066 5.00e-02 4.00e+02 pdb=" CA PRO D 201 " 0.019 5.00e-02 4.00e+02 pdb=" CD PRO D 201 " 0.022 5.00e-02 4.00e+02 ... (remaining 1483 not shown) Histogram of nonbonded interaction distances: 2.27 - 2.80: 2217 2.80 - 3.32: 7542 3.32 - 3.85: 12950 3.85 - 4.37: 15214 4.37 - 4.90: 28558 Nonbonded interactions: 66481 Sorted by model distance: nonbonded pdb=" O SER E 52 " pdb=" NH1 ARG E 72 " model vdw 2.274 2.520 nonbonded pdb=" O SER B 334 " pdb=" OG SER B 334 " model vdw 2.280 2.440 nonbonded pdb=" O THR B 86 " pdb=" OG1 THR B 87 " model vdw 2.286 2.440 nonbonded pdb=" OE2 GLU A 308 " pdb=" OG1 THR A 321 " model vdw 2.295 2.440 nonbonded pdb=" OG1 THR D 101 " pdb=" OD1 ASN D 104 " model vdw 2.304 2.440 ... (remaining 66476 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.150 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: 0.000 Extract box with map and model: 3.940 Check model and map are aligned: 0.140 Set scattering table: 0.080 Process input model: 27.620 Find NCS groups from input model: 0.260 Set up NCS constraints: 0.030 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:13.300 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 46.520 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8468 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 : 0.005 0.128 8716 Z= 0.326 Angle : 0.610 8.129 11842 Z= 0.340 Chirality : 0.043 0.245 1379 Planarity : 0.004 0.038 1486 Dihedral : 12.870 88.509 3028 Min Nonbonded Distance : 2.274 Molprobity Statistics. All-atom Clashscore : 9.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.43 % Favored : 95.57 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % 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: -0.30 (0.26), residues: 1105 helix: 1.82 (0.28), residues: 371 sheet: -0.93 (0.31), residues: 294 loop : -1.41 (0.28), residues: 440 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP B 82 HIS 0.004 0.001 HIS E 35 PHE 0.013 0.001 PHE B 151 TYR 0.011 0.002 TYR E 50 ARG 0.005 0.000 ARG E 98 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2210 Ramachandran restraints generated. 1105 Oldfield, 0 Emsley, 1105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2210 Ramachandran restraints generated. 1105 Oldfield, 0 Emsley, 1105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 969 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 116 time to evaluate : 1.047 Fit side-chains REVERT: B 247 ASP cc_start: 0.7577 (t0) cc_final: 0.7377 (t0) outliers start: 0 outliers final: 0 residues processed: 116 average time/residue: 1.3258 time to fit residues: 163.0407 Evaluate side-chains 100 residues out of total 969 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 100 time to evaluate : 1.004 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 92 optimal weight: 3.9990 chunk 83 optimal weight: 0.9990 chunk 46 optimal weight: 0.9980 chunk 28 optimal weight: 0.9990 chunk 56 optimal weight: 3.9990 chunk 44 optimal weight: 0.9990 chunk 86 optimal weight: 3.9990 chunk 33 optimal weight: 0.9980 chunk 52 optimal weight: 30.0000 chunk 64 optimal weight: 5.9990 chunk 99 optimal weight: 1.9990 overall best weight: 0.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 17 GLN D 109 ASN D 188 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8436 moved from start: 0.0954 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 8716 Z= 0.189 Angle : 0.555 8.464 11842 Z= 0.287 Chirality : 0.042 0.151 1379 Planarity : 0.003 0.033 1486 Dihedral : 4.784 36.055 1222 Min Nonbonded Distance : 2.072 Molprobity Statistics. All-atom Clashscore : 5.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.53 % Favored : 96.47 % Rotamer: Outliers : 1.58 % Allowed : 8.00 % Favored : 90.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % 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: 0.04 (0.26), residues: 1105 helix: 2.05 (0.28), residues: 372 sheet: -0.45 (0.31), residues: 293 loop : -1.40 (0.27), residues: 440 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 169 HIS 0.003 0.001 HIS B 225 PHE 0.012 0.001 PHE A 189 TYR 0.010 0.001 TYR E 178 ARG 0.004 0.000 ARG E 98 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2210 Ramachandran restraints generated. 1105 Oldfield, 0 Emsley, 1105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2210 Ramachandran restraints generated. 1105 Oldfield, 0 Emsley, 1105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 969 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 113 time to evaluate : 1.015 Fit side-chains REVERT: B 23 LYS cc_start: 0.8334 (tppt) cc_final: 0.7886 (tmmt) REVERT: B 247 ASP cc_start: 0.7336 (t0) cc_final: 0.7136 (t0) outliers start: 14 outliers final: 4 residues processed: 119 average time/residue: 1.2370 time to fit residues: 156.8386 Evaluate side-chains 109 residues out of total 969 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 105 time to evaluate : 0.977 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 95 LEU Chi-restraints excluded: chain B residue 205 ASP Chi-restraints excluded: chain C residue 57 SER Chi-restraints excluded: chain A residue 21 ARG Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 55 optimal weight: 2.9990 chunk 31 optimal weight: 0.6980 chunk 83 optimal weight: 0.0970 chunk 68 optimal weight: 0.0000 chunk 27 optimal weight: 0.8980 chunk 100 optimal weight: 20.0000 chunk 108 optimal weight: 0.5980 chunk 89 optimal weight: 0.6980 chunk 99 optimal weight: 1.9990 chunk 34 optimal weight: 6.9990 chunk 80 optimal weight: 10.0000 overall best weight: 0.4182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 17 GLN B 75 GLN D 86 ASN ** D 150 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 183 ASN D 297 HIS A 269 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8361 moved from start: 0.1579 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 8716 Z= 0.119 Angle : 0.467 6.605 11842 Z= 0.244 Chirality : 0.040 0.148 1379 Planarity : 0.003 0.032 1486 Dihedral : 4.216 30.701 1222 Min Nonbonded Distance : 2.126 Molprobity Statistics. All-atom Clashscore : 4.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.71 % Favored : 97.29 % Rotamer: Outliers : 1.35 % Allowed : 9.80 % Favored : 88.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % 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 (0.26), residues: 1105 helix: 2.30 (0.28), residues: 372 sheet: -0.22 (0.31), residues: 294 loop : -1.19 (0.27), residues: 439 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 169 HIS 0.002 0.000 HIS B 225 PHE 0.010 0.001 PHE A 189 TYR 0.009 0.001 TYR A 230 ARG 0.003 0.000 ARG B 46 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2210 Ramachandran restraints generated. 1105 Oldfield, 0 Emsley, 1105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2210 Ramachandran restraints generated. 1105 Oldfield, 0 Emsley, 1105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 969 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 117 time to evaluate : 0.946 Fit side-chains REVERT: B 44 GLN cc_start: 0.8507 (OUTLIER) cc_final: 0.8200 (mt0) outliers start: 12 outliers final: 7 residues processed: 120 average time/residue: 1.1752 time to fit residues: 150.7484 Evaluate side-chains 119 residues out of total 969 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 111 time to evaluate : 1.004 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 44 GLN Chi-restraints excluded: chain B residue 95 LEU Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 205 ASP Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 232 ILE Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain A residue 21 ARG Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 98 optimal weight: 2.9990 chunk 75 optimal weight: 5.9990 chunk 51 optimal weight: 9.9990 chunk 11 optimal weight: 0.9990 chunk 47 optimal weight: 3.9990 chunk 67 optimal weight: 1.9990 chunk 100 optimal weight: 10.0000 chunk 106 optimal weight: 6.9990 chunk 52 optimal weight: 0.0470 chunk 95 optimal weight: 5.9990 chunk 28 optimal weight: 1.9990 overall best weight: 1.6086 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 17 GLN ** D 150 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 188 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8459 moved from start: 0.1380 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 8716 Z= 0.260 Angle : 0.568 8.639 11842 Z= 0.291 Chirality : 0.043 0.161 1379 Planarity : 0.003 0.034 1486 Dihedral : 4.806 45.470 1222 Min Nonbonded Distance : 2.047 Molprobity Statistics. All-atom Clashscore : 4.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.80 % Favored : 96.20 % Rotamer: Outliers : 2.25 % Allowed : 12.39 % Favored : 85.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % 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: 0.46 (0.26), residues: 1105 helix: 2.29 (0.28), residues: 372 sheet: -0.10 (0.31), residues: 291 loop : -1.16 (0.27), residues: 442 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 82 HIS 0.005 0.001 HIS E 35 PHE 0.012 0.001 PHE A 189 TYR 0.014 0.001 TYR B 105 ARG 0.006 0.000 ARG E 98 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2210 Ramachandran restraints generated. 1105 Oldfield, 0 Emsley, 1105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2210 Ramachandran restraints generated. 1105 Oldfield, 0 Emsley, 1105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 969 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 106 time to evaluate : 1.078 Fit side-chains REVERT: B 44 GLN cc_start: 0.8540 (OUTLIER) cc_final: 0.8230 (mt0) REVERT: B 153 ASP cc_start: 0.7612 (OUTLIER) cc_final: 0.7319 (m-30) outliers start: 20 outliers final: 10 residues processed: 117 average time/residue: 1.2156 time to fit residues: 151.6478 Evaluate side-chains 117 residues out of total 969 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 105 time to evaluate : 0.981 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 44 GLN Chi-restraints excluded: chain B residue 153 ASP Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 205 ASP Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 232 ILE Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 323 ASP Chi-restraints excluded: chain C residue 57 SER Chi-restraints excluded: chain D residue 331 LEU Chi-restraints excluded: chain A residue 9 ASP Chi-restraints excluded: chain A residue 21 ARG Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 88 optimal weight: 0.2980 chunk 60 optimal weight: 0.0870 chunk 1 optimal weight: 2.9990 chunk 79 optimal weight: 3.9990 chunk 43 optimal weight: 9.9990 chunk 90 optimal weight: 1.9990 chunk 73 optimal weight: 2.9990 chunk 0 optimal weight: 5.9990 chunk 54 optimal weight: 6.9990 chunk 95 optimal weight: 0.9990 chunk 26 optimal weight: 0.9980 overall best weight: 0.8762 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 17 GLN ** D 150 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 294 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8417 moved from start: 0.1560 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 8716 Z= 0.161 Angle : 0.501 7.178 11842 Z= 0.261 Chirality : 0.041 0.150 1379 Planarity : 0.003 0.033 1486 Dihedral : 4.639 50.714 1222 Min Nonbonded Distance : 2.090 Molprobity Statistics. All-atom Clashscore : 4.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer: Outliers : 2.25 % Allowed : 13.40 % Favored : 84.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % 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 (0.26), residues: 1105 helix: 2.36 (0.28), residues: 375 sheet: -0.05 (0.30), residues: 294 loop : -1.10 (0.27), residues: 436 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 82 HIS 0.003 0.001 HIS B 225 PHE 0.011 0.001 PHE A 189 TYR 0.009 0.001 TYR E 178 ARG 0.004 0.000 ARG E 98 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2210 Ramachandran restraints generated. 1105 Oldfield, 0 Emsley, 1105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2210 Ramachandran restraints generated. 1105 Oldfield, 0 Emsley, 1105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 969 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 109 time to evaluate : 1.103 Fit side-chains REVERT: B 44 GLN cc_start: 0.8509 (OUTLIER) cc_final: 0.8183 (mt0) REVERT: B 58 ILE cc_start: 0.8451 (OUTLIER) cc_final: 0.8163 (pt) outliers start: 20 outliers final: 10 residues processed: 121 average time/residue: 1.1864 time to fit residues: 153.3557 Evaluate side-chains 121 residues out of total 969 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 109 time to evaluate : 1.021 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 44 GLN Chi-restraints excluded: chain B residue 58 ILE Chi-restraints excluded: chain B residue 95 LEU Chi-restraints excluded: chain B residue 153 ASP Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 205 ASP Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 232 ILE Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain D residue 74 LEU Chi-restraints excluded: chain D residue 331 LEU Chi-restraints excluded: chain A residue 21 ARG Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 35 optimal weight: 2.9990 chunk 95 optimal weight: 0.9990 chunk 21 optimal weight: 0.4980 chunk 62 optimal weight: 5.9990 chunk 26 optimal weight: 0.3980 chunk 106 optimal weight: 0.5980 chunk 88 optimal weight: 0.1980 chunk 49 optimal weight: 8.9990 chunk 8 optimal weight: 0.9980 chunk 55 optimal weight: 0.9990 chunk 102 optimal weight: 2.9990 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 17 GLN ** D 150 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 188 HIS A 294 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8378 moved from start: 0.1808 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 8716 Z= 0.127 Angle : 0.466 6.588 11842 Z= 0.243 Chirality : 0.040 0.153 1379 Planarity : 0.003 0.032 1486 Dihedral : 4.487 55.285 1222 Min Nonbonded Distance : 2.117 Molprobity Statistics. All-atom Clashscore : 4.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 2.14 % Allowed : 13.85 % Favored : 84.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.78 (0.26), residues: 1105 helix: 2.60 (0.28), residues: 369 sheet: 0.08 (0.31), residues: 294 loop : -0.99 (0.27), residues: 442 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 169 HIS 0.002 0.001 HIS B 225 PHE 0.010 0.001 PHE A 189 TYR 0.008 0.001 TYR E 178 ARG 0.003 0.000 ARG E 98 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2210 Ramachandran restraints generated. 1105 Oldfield, 0 Emsley, 1105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2210 Ramachandran restraints generated. 1105 Oldfield, 0 Emsley, 1105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 969 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 111 time to evaluate : 1.178 Fit side-chains REVERT: B 44 GLN cc_start: 0.8493 (OUTLIER) cc_final: 0.8168 (mt0) REVERT: B 95 LEU cc_start: 0.8420 (OUTLIER) cc_final: 0.7805 (mt) REVERT: B 262 MET cc_start: 0.8658 (tpp) cc_final: 0.8438 (ttt) outliers start: 19 outliers final: 11 residues processed: 123 average time/residue: 1.1929 time to fit residues: 156.8364 Evaluate side-chains 119 residues out of total 969 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 106 time to evaluate : 1.024 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 44 GLN Chi-restraints excluded: chain B residue 95 LEU Chi-restraints excluded: chain B residue 153 ASP Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 205 ASP Chi-restraints excluded: chain B residue 232 ILE Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 284 LEU Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain D residue 74 LEU Chi-restraints excluded: chain D residue 331 LEU Chi-restraints excluded: chain A residue 9 ASP Chi-restraints excluded: chain A residue 21 ARG Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 11 optimal weight: 0.9980 chunk 60 optimal weight: 0.8980 chunk 77 optimal weight: 4.9990 chunk 89 optimal weight: 3.9990 chunk 59 optimal weight: 1.9990 chunk 106 optimal weight: 0.0170 chunk 66 optimal weight: 0.9980 chunk 64 optimal weight: 0.9990 chunk 48 optimal weight: 1.9990 chunk 65 optimal weight: 7.9990 chunk 42 optimal weight: 6.9990 overall best weight: 0.7820 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 150 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 294 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8396 moved from start: 0.1793 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 8716 Z= 0.150 Angle : 0.483 6.843 11842 Z= 0.251 Chirality : 0.041 0.152 1379 Planarity : 0.003 0.031 1486 Dihedral : 4.570 57.398 1222 Min Nonbonded Distance : 2.103 Molprobity Statistics. All-atom Clashscore : 4.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 2.03 % Allowed : 14.64 % Favored : 83.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % 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: 0.85 (0.26), residues: 1105 helix: 2.66 (0.28), residues: 369 sheet: 0.13 (0.31), residues: 289 loop : -0.95 (0.28), residues: 447 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 169 HIS 0.003 0.001 HIS E 35 PHE 0.011 0.001 PHE A 189 TYR 0.009 0.001 TYR E 178 ARG 0.003 0.000 ARG E 98 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2210 Ramachandran restraints generated. 1105 Oldfield, 0 Emsley, 1105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2210 Ramachandran restraints generated. 1105 Oldfield, 0 Emsley, 1105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 969 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 110 time to evaluate : 1.018 Fit side-chains REVERT: B 44 GLN cc_start: 0.8486 (OUTLIER) cc_final: 0.8153 (mt0) REVERT: B 58 ILE cc_start: 0.8428 (OUTLIER) cc_final: 0.8127 (pt) REVERT: B 262 MET cc_start: 0.8662 (tpp) cc_final: 0.8443 (ttm) outliers start: 18 outliers final: 14 residues processed: 119 average time/residue: 1.1627 time to fit residues: 147.9681 Evaluate side-chains 125 residues out of total 969 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 109 time to evaluate : 1.028 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 44 GLN Chi-restraints excluded: chain B residue 58 ILE Chi-restraints excluded: chain B residue 95 LEU Chi-restraints excluded: chain B residue 153 ASP Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 205 ASP Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 232 ILE Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 284 LEU Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain C residue 57 SER Chi-restraints excluded: chain D residue 74 LEU Chi-restraints excluded: chain D residue 331 LEU Chi-restraints excluded: chain A residue 9 ASP Chi-restraints excluded: chain A residue 21 ARG Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 63 optimal weight: 5.9990 chunk 31 optimal weight: 1.9990 chunk 20 optimal weight: 0.9980 chunk 67 optimal weight: 0.8980 chunk 72 optimal weight: 3.9990 chunk 52 optimal weight: 30.0000 chunk 9 optimal weight: 0.9990 chunk 83 optimal weight: 3.9990 chunk 96 optimal weight: 2.9990 chunk 101 optimal weight: 6.9990 chunk 92 optimal weight: 0.7980 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 150 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 188 HIS A 294 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8425 moved from start: 0.1720 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 8716 Z= 0.192 Angle : 0.515 7.363 11842 Z= 0.267 Chirality : 0.042 0.155 1379 Planarity : 0.003 0.032 1486 Dihedral : 4.744 59.855 1222 Min Nonbonded Distance : 2.081 Molprobity Statistics. All-atom Clashscore : 4.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.35 % Favored : 96.65 % Rotamer: Outliers : 2.03 % Allowed : 14.75 % Favored : 83.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.84 (0.26), residues: 1105 helix: 2.65 (0.27), residues: 369 sheet: 0.13 (0.31), residues: 289 loop : -0.95 (0.28), residues: 447 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 211 HIS 0.004 0.001 HIS E 35 PHE 0.011 0.001 PHE A 189 TYR 0.009 0.001 TYR E 178 ARG 0.004 0.000 ARG E 98 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2210 Ramachandran restraints generated. 1105 Oldfield, 0 Emsley, 1105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2210 Ramachandran restraints generated. 1105 Oldfield, 0 Emsley, 1105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 969 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 108 time to evaluate : 1.058 Fit side-chains REVERT: B 44 GLN cc_start: 0.8493 (OUTLIER) cc_final: 0.8170 (mt0) REVERT: B 58 ILE cc_start: 0.8522 (OUTLIER) cc_final: 0.8232 (pt) REVERT: B 247 ASP cc_start: 0.7216 (t0) cc_final: 0.6961 (t0) outliers start: 18 outliers final: 14 residues processed: 119 average time/residue: 1.2226 time to fit residues: 155.7570 Evaluate side-chains 122 residues out of total 969 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 106 time to evaluate : 1.019 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 44 GLN Chi-restraints excluded: chain B residue 58 ILE Chi-restraints excluded: chain B residue 95 LEU Chi-restraints excluded: chain B residue 153 ASP Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 205 ASP Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 232 ILE Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 284 LEU Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain C residue 57 SER Chi-restraints excluded: chain D residue 74 LEU Chi-restraints excluded: chain D residue 331 LEU Chi-restraints excluded: chain A residue 9 ASP Chi-restraints excluded: chain A residue 21 ARG Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 98 optimal weight: 3.9990 chunk 101 optimal weight: 6.9990 chunk 59 optimal weight: 3.9990 chunk 43 optimal weight: 10.0000 chunk 77 optimal weight: 2.9990 chunk 30 optimal weight: 0.0470 chunk 89 optimal weight: 0.8980 chunk 93 optimal weight: 4.9990 chunk 64 optimal weight: 4.9990 chunk 104 optimal weight: 2.9990 chunk 63 optimal weight: 1.9990 overall best weight: 1.7884 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 13 GLN ** D 150 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 294 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8464 moved from start: 0.1589 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 8716 Z= 0.279 Angle : 0.573 8.494 11842 Z= 0.295 Chirality : 0.043 0.161 1379 Planarity : 0.003 0.033 1486 Dihedral : 5.072 62.664 1222 Min Nonbonded Distance : 2.054 Molprobity Statistics. All-atom Clashscore : 4.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.89 % Favored : 96.11 % Rotamer: Outliers : 2.48 % Allowed : 14.86 % Favored : 82.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.70 (0.26), residues: 1105 helix: 2.44 (0.27), residues: 375 sheet: 0.16 (0.30), residues: 293 loop : -1.09 (0.28), residues: 437 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 211 HIS 0.005 0.001 HIS E 35 PHE 0.013 0.001 PHE B 151 TYR 0.011 0.001 TYR B 105 ARG 0.005 0.000 ARG E 98 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2210 Ramachandran restraints generated. 1105 Oldfield, 0 Emsley, 1105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2210 Ramachandran restraints generated. 1105 Oldfield, 0 Emsley, 1105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 969 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 103 time to evaluate : 1.065 Fit side-chains REVERT: B 44 GLN cc_start: 0.8501 (OUTLIER) cc_final: 0.8202 (mt0) outliers start: 22 outliers final: 15 residues processed: 115 average time/residue: 1.2728 time to fit residues: 155.8719 Evaluate side-chains 119 residues out of total 969 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 103 time to evaluate : 0.897 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 44 GLN Chi-restraints excluded: chain B residue 95 LEU Chi-restraints excluded: chain B residue 153 ASP Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 205 ASP Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 232 ILE Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 284 LEU Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain C residue 57 SER Chi-restraints excluded: chain D residue 74 LEU Chi-restraints excluded: chain D residue 331 LEU Chi-restraints excluded: chain A residue 9 ASP Chi-restraints excluded: chain A residue 21 ARG Chi-restraints excluded: chain A residue 276 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 49 optimal weight: 5.9990 chunk 72 optimal weight: 2.9990 chunk 109 optimal weight: 1.9990 chunk 100 optimal weight: 6.9990 chunk 87 optimal weight: 1.9990 chunk 9 optimal weight: 1.9990 chunk 67 optimal weight: 1.9990 chunk 53 optimal weight: 0.0370 chunk 69 optimal weight: 0.9990 chunk 92 optimal weight: 0.0670 chunk 26 optimal weight: 3.9990 overall best weight: 1.0202 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 150 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 294 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8425 moved from start: 0.1708 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 8716 Z= 0.182 Angle : 0.510 7.037 11842 Z= 0.266 Chirality : 0.041 0.152 1379 Planarity : 0.003 0.033 1486 Dihedral : 4.901 66.331 1222 Min Nonbonded Distance : 2.088 Molprobity Statistics. All-atom Clashscore : 4.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer: Outliers : 2.25 % Allowed : 15.20 % Favored : 82.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % 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: 0.79 (0.26), residues: 1105 helix: 2.50 (0.27), residues: 375 sheet: 0.22 (0.31), residues: 282 loop : -1.01 (0.27), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 211 HIS 0.003 0.001 HIS E 35 PHE 0.012 0.001 PHE A 189 TYR 0.009 0.001 TYR E 178 ARG 0.004 0.000 ARG E 148 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2210 Ramachandran restraints generated. 1105 Oldfield, 0 Emsley, 1105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2210 Ramachandran restraints generated. 1105 Oldfield, 0 Emsley, 1105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 969 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 107 time to evaluate : 1.017 Fit side-chains REVERT: B 44 GLN cc_start: 0.8468 (OUTLIER) cc_final: 0.8143 (mt0) REVERT: B 247 ASP cc_start: 0.7258 (t0) cc_final: 0.7010 (t0) outliers start: 20 outliers final: 15 residues processed: 119 average time/residue: 1.2592 time to fit residues: 159.5136 Evaluate side-chains 121 residues out of total 969 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 105 time to evaluate : 1.019 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 44 GLN Chi-restraints excluded: chain B residue 95 LEU Chi-restraints excluded: chain B residue 153 ASP Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 205 ASP Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 232 ILE Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 284 LEU Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain C residue 57 SER Chi-restraints excluded: chain D residue 74 LEU Chi-restraints excluded: chain D residue 331 LEU Chi-restraints excluded: chain A residue 9 ASP Chi-restraints excluded: chain A residue 21 ARG Chi-restraints excluded: chain A residue 276 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 80 optimal weight: 0.9980 chunk 12 optimal weight: 0.0170 chunk 24 optimal weight: 0.8980 chunk 87 optimal weight: 0.2980 chunk 36 optimal weight: 0.9990 chunk 89 optimal weight: 0.7980 chunk 11 optimal weight: 3.9990 chunk 16 optimal weight: 2.9990 chunk 76 optimal weight: 3.9990 chunk 4 optimal weight: 3.9990 chunk 63 optimal weight: 0.9990 overall best weight: 0.6018 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 150 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3802 r_free = 0.3802 target = 0.141844 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3245 r_free = 0.3245 target = 0.097792 restraints weight = 10649.674| |-----------------------------------------------------------------------------| r_work (start): 0.3306 rms_B_bonded: 2.29 r_work: 0.3165 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.3023 rms_B_bonded: 4.31 restraints_weight: 0.2500 r_work (final): 0.3023 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8595 moved from start: 0.1897 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 8716 Z= 0.134 Angle : 0.471 6.624 11842 Z= 0.247 Chirality : 0.040 0.153 1379 Planarity : 0.003 0.032 1486 Dihedral : 4.593 61.678 1222 Min Nonbonded Distance : 2.119 Molprobity Statistics. All-atom Clashscore : 4.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 2.03 % Allowed : 15.32 % Favored : 82.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % 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: 0.94 (0.26), residues: 1105 helix: 2.70 (0.27), residues: 369 sheet: 0.23 (0.31), residues: 289 loop : -0.89 (0.28), residues: 447 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 169 HIS 0.003 0.001 HIS B 225 PHE 0.010 0.001 PHE A 189 TYR 0.008 0.001 TYR E 178 ARG 0.004 0.000 ARG E 148 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3242.77 seconds wall clock time: 58 minutes 18.66 seconds (3498.66 seconds total)