Starting phenix.real_space_refine on Wed Feb 14 01:29:13 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8iw7_35763/02_2024/8iw7_35763_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8iw7_35763/02_2024/8iw7_35763.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.97 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8iw7_35763/02_2024/8iw7_35763.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8iw7_35763/02_2024/8iw7_35763.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8iw7_35763/02_2024/8iw7_35763_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8iw7_35763/02_2024/8iw7_35763_updated.pdb" } resolution = 2.97 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= 0.005 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 48 5.16 5 C 5310 2.51 5 N 1415 2.21 5 O 1532 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "R PHE 107": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R ASP 112": "OD1" <-> "OD2" Residue "R GLU 232": "OE1" <-> "OE2" Residue "R ASP 281": "OD1" <-> "OD2" Residue "B GLU 226": "OE1" <-> "OE2" Residue "A GLU 309": "OE1" <-> "OE2" Residue "A TYR 318": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 327": "OE1" <-> "OE2" Residue "A GLU 344": "OE1" <-> "OE2" Residue "S GLU 6": "OE1" <-> "OE2" Residue "Y GLU 22": "OE1" <-> "OE2" Residue "Y GLU 58": "OE1" <-> "OE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 8305 Number of models: 1 Model: "" Number of chains: 6 Chain: "R" Number of atoms: 1971 Number of conformers: 1 Conformer: "" Number of residues, atoms: 271, 1971 Classifications: {'peptide': 271} Incomplete info: {'truncation_to_alanine': 43} Link IDs: {'PTRANS': 10, 'TRANS': 260} Chain breaks: 1 Unresolved non-hydrogen bonds: 206 Unresolved non-hydrogen angles: 269 Unresolved non-hydrogen dihedrals: 186 Unresolved non-hydrogen chiralities: 10 Planarities with less than four sites: {'GLN:plan1': 3, 'TYR:plan': 4, 'ASN:plan1': 2, 'TRP:plan': 3, 'ASP:plan': 2, 'PHE:plan': 5, 'GLU:plan': 7, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 147 Chain: "B" Number of atoms: 2437 Number of conformers: 1 Conformer: "" Number of residues, atoms: 337, 2437 Classifications: {'peptide': 337} Incomplete info: {'truncation_to_alanine': 44} Link IDs: {'PTRANS': 5, 'TRANS': 331} Unresolved non-hydrogen bonds: 155 Unresolved non-hydrogen angles: 190 Unresolved non-hydrogen dihedrals: 122 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'GLN:plan1': 4, 'ASP:plan': 10, 'ASN:plan1': 1, 'HIS:plan': 1, 'GLU:plan': 4, 'ARG:plan': 8} Unresolved non-hydrogen planarities: 110 Chain: "A" Number of atoms: 1839 Number of conformers: 1 Conformer: "" Number of residues, atoms: 234, 1839 Classifications: {'peptide': 234} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 26} Link IDs: {'PTRANS': 6, 'TRANS': 227} Chain breaks: 1 Unresolved non-hydrogen bonds: 103 Unresolved non-hydrogen angles: 127 Unresolved non-hydrogen dihedrals: 84 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 1, 'ASN:plan1': 3, 'ASP:plan': 3, 'PHE:plan': 1, 'GLU:plan': 6, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 74 Chain: "S" Number of atoms: 1680 Number of conformers: 1 Conformer: "" Number of residues, atoms: 231, 1680 Classifications: {'peptide': 231} Incomplete info: {'truncation_to_alanine': 24} Link IDs: {'PTRANS': 10, 'TRANS': 220} Chain breaks: 3 Unresolved non-hydrogen bonds: 97 Unresolved non-hydrogen angles: 119 Unresolved non-hydrogen dihedrals: 81 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'GLN:plan1': 3, 'GLU:plan': 4, 'ARG:plan': 3, 'TYR:plan': 2} Unresolved non-hydrogen planarities: 57 Chain: "Y" Number of atoms: 369 Number of conformers: 1 Conformer: "" Number of residues, atoms: 56, 369 Classifications: {'peptide': 56} Incomplete info: {'truncation_to_alanine': 18} Link IDs: {'PTRANS': 4, 'TRANS': 51} Unresolved non-hydrogen bonds: 64 Unresolved non-hydrogen angles: 74 Unresolved non-hydrogen dihedrals: 54 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 2, 'ARG:plan': 2, 'ASN:plan1': 1, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 34 Chain: "R" Number of atoms: 9 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 9 Unusual residues: {'PEA': 1} Classifications: {'undetermined': 1} Time building chain proxies: 5.06, per 1000 atoms: 0.61 Number of scatterers: 8305 At special positions: 0 Unit cell: (105.448, 101.144, 120.512, 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 48 16.00 O 1532 8.00 N 1415 7.00 C 5310 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS R 105 " - pdb=" SG CYS R 190 " distance=2.03 Simple disulfide: pdb=" SG CYS S 22 " - pdb=" SG CYS S 96 " 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: 3.31 Conformation dependent library (CDL) restraints added in 2.1 seconds 2218 Ramachandran restraints generated. 1109 Oldfield, 0 Emsley, 1109 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2114 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 29 helices and 11 sheets defined 32.7% alpha, 17.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.59 Creating SS restraints... Processing helix chain 'R' and resid 38 through 58 removed outlier: 4.501A pdb=" N ASN R 50 " --> pdb=" O ALA R 46 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N LEU R 52 " --> pdb=" O PHE R 48 " (cutoff:3.500A) removed outlier: 4.818A pdb=" N VAL R 53 " --> pdb=" O GLY R 49 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N ILE R 57 " --> pdb=" O VAL R 53 " (cutoff:3.500A) removed outlier: 4.127A pdb=" N LEU R 58 " --> pdb=" O ILE R 54 " (cutoff:3.500A) Processing helix chain 'R' and resid 61 through 63 No H-bonds generated for 'chain 'R' and resid 61 through 63' Processing helix chain 'R' and resid 66 through 83 removed outlier: 4.017A pdb=" N LEU R 70 " --> pdb=" O PRO R 66 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N VAL R 71 " --> pdb=" O THR R 67 " (cutoff:3.500A) Processing helix chain 'R' and resid 85 through 95 removed outlier: 3.835A pdb=" N VAL R 91 " --> pdb=" O PRO R 87 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N ARG R 92 " --> pdb=" O PHE R 88 " (cutoff:3.500A) Processing helix chain 'R' and resid 103 through 115 removed outlier: 4.517A pdb=" N CYS R 110 " --> pdb=" O LYS R 106 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N PHE R 111 " --> pdb=" O PHE R 107 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N ASP R 112 " --> pdb=" O HIS R 108 " (cutoff:3.500A) Processing helix chain 'R' and resid 118 through 135 removed outlier: 3.644A pdb=" N HIS R 122 " --> pdb=" O ALA R 118 " (cutoff:3.500A) Processing helix chain 'R' and resid 137 through 143 removed outlier: 3.960A pdb=" N TYR R 140 " --> pdb=" O PRO R 137 " (cutoff:3.500A) Proline residue: R 141 - end of helix No H-bonds generated for 'chain 'R' and resid 137 through 143' Processing helix chain 'R' and resid 146 through 162 removed outlier: 3.696A pdb=" N ILE R 153 " --> pdb=" O SER R 149 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ALA R 154 " --> pdb=" O GLY R 150 " (cutoff:3.500A) removed outlier: 4.263A pdb=" N SER R 160 " --> pdb=" O SER R 156 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N VAL R 161 " --> pdb=" O TRP R 157 " (cutoff:3.500A) Processing helix chain 'R' and resid 165 through 168 No H-bonds generated for 'chain 'R' and resid 165 through 168' Processing helix chain 'R' and resid 178 through 184 removed outlier: 3.788A pdb=" N VAL R 182 " --> pdb=" O GLU R 178 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N ALA R 183 " --> pdb=" O GLU R 179 " (cutoff:3.500A) Processing helix chain 'R' and resid 196 through 231 removed outlier: 3.805A pdb=" N LEU R 200 " --> pdb=" O GLN R 196 " (cutoff:3.500A) removed outlier: 4.615A pdb=" N LEU R 201 " --> pdb=" O ASN R 197 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N PHE R 206 " --> pdb=" O CYS R 202 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N LEU R 208 " --> pdb=" O LEU R 204 " (cutoff:3.500A) Proline residue: R 209 - end of helix removed outlier: 4.176A pdb=" N MET R 213 " --> pdb=" O PRO R 209 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N ILE R 220 " --> pdb=" O LEU R 216 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N ALA R 228 " --> pdb=" O ALA R 224 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N ILE R 231 " --> pdb=" O GLN R 227 " (cutoff:3.500A) Processing helix chain 'R' and resid 254 through 268 removed outlier: 3.714A pdb=" N LYS R 258 " --> pdb=" O ARG R 254 " (cutoff:3.500A) removed outlier: 4.570A pdb=" N PHE R 267 " --> pdb=" O ALA R 263 " (cutoff:3.500A) Processing helix chain 'R' and resid 271 through 282 removed outlier: 3.582A pdb=" N ILE R 280 " --> pdb=" O ILE R 276 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N ASP R 281 " --> pdb=" O ASP R 277 " (cutoff:3.500A) removed outlier: 5.376A pdb=" N ALA R 282 " --> pdb=" O ALA R 278 " (cutoff:3.500A) Processing helix chain 'R' and resid 290 through 292 No H-bonds generated for 'chain 'R' and resid 290 through 292' Processing helix chain 'R' and resid 294 through 310 removed outlier: 4.065A pdb=" N VAL R 300 " --> pdb=" O LEU R 296 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N TYR R 301 " --> pdb=" O VAL R 297 " (cutoff:3.500A) Proline residue: R 308 - end of helix Processing helix chain 'R' and resid 316 through 325 removed outlier: 3.609A pdb=" N ALA R 321 " --> pdb=" O TRP R 317 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N LEU R 324 " --> pdb=" O LYS R 320 " (cutoff:3.500A) removed outlier: 5.343A pdb=" N ILE R 325 " --> pdb=" O ALA R 321 " (cutoff:3.500A) Processing helix chain 'B' and resid 5 through 25 removed outlier: 4.481A pdb=" N GLN B 9 " --> pdb=" O ASP B 5 " (cutoff:3.500A) removed outlier: 4.592A pdb=" N GLU B 10 " --> pdb=" O GLN B 6 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N GLN B 13 " --> pdb=" O GLN B 9 " (cutoff:3.500A) Processing helix chain 'B' and resid 30 through 33 No H-bonds generated for 'chain 'B' and resid 30 through 33' Processing helix chain 'A' and resid 7 through 38 removed outlier: 3.920A pdb=" N ALA A 11 " --> pdb=" O ALA A 7 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N GLN A 35 " --> pdb=" O GLN A 31 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N VAL A 36 " --> pdb=" O LYS A 32 " (cutoff:3.500A) Processing helix chain 'A' and resid 53 through 62 Processing helix chain 'A' and resid 254 through 277 removed outlier: 4.141A pdb=" N GLU A 268 " --> pdb=" O ASN A 254 " (cutoff:3.500A) Processing helix chain 'A' and resid 294 through 303 Processing helix chain 'A' and resid 332 through 349 removed outlier: 3.601A pdb=" N ARG A 342 " --> pdb=" O LYS A 338 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N ILE A 348 " --> pdb=" O GLU A 344 " (cutoff:3.500A) Processing helix chain 'A' and resid 372 through 390 Processing helix chain 'S' and resid 29 through 31 No H-bonds generated for 'chain 'S' and resid 29 through 31' Processing helix chain 'S' and resid 53 through 55 No H-bonds generated for 'chain 'S' and resid 53 through 55' Processing helix chain 'Y' and resid 11 through 23 Processing helix chain 'Y' and resid 30 through 43 Processing helix chain 'Y' and resid 45 through 47 No H-bonds generated for 'chain 'Y' and resid 45 through 47' Processing sheet with id= A, first strand: chain 'B' and resid 58 through 63 removed outlier: 7.039A pdb=" N ALA B 73 " --> pdb=" O TYR B 59 " (cutoff:3.500A) removed outlier: 4.337A pdb=" N MET B 61 " --> pdb=" O VAL B 71 " (cutoff:3.500A) removed outlier: 6.569A pdb=" N VAL B 71 " --> pdb=" O MET B 61 " (cutoff:3.500A) removed outlier: 5.061A pdb=" N TRP B 63 " --> pdb=" O LEU B 69 " (cutoff:3.500A) removed outlier: 7.277A pdb=" N LEU B 69 " --> pdb=" O TRP B 63 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N LEU B 70 " --> pdb=" O TRP B 82 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 6.550A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 6.156A 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: 7.154A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.262A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.512A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 4.851A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 7.059A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N ARG B 137 " --> pdb=" O ILE B 123 " (cutoff:3.500A) removed outlier: 6.233A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 6.544A pdb=" N VAL B 135 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'B' and resid 178 through 180 Processing sheet with id= D, first strand: chain 'B' and resid 187 through 191 removed outlier: 6.842A pdb=" N GLY B 202 " --> pdb=" O MET B 188 " (cutoff:3.500A) removed outlier: 4.476A pdb=" N LEU B 190 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 6.654A pdb=" N VAL B 200 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 4.578A pdb=" N SER B 207 " --> pdb=" O ALA B 203 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 249 through 254 removed outlier: 4.311A pdb=" N THR B 249 " --> pdb=" O SER B 245 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 275 through 278 removed outlier: 3.582A pdb=" N SER B 275 " --> pdb=" O GLY B 288 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'B' and resid 47 through 51 removed outlier: 6.990A pdb=" N ILE B 338 " --> pdb=" O ARG B 48 " (cutoff:3.500A) removed outlier: 4.511A pdb=" N THR B 50 " --> pdb=" O LEU B 336 " (cutoff:3.500A) removed outlier: 6.611A pdb=" N LEU B 336 " --> pdb=" O THR B 50 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N CYS B 317 " --> pdb=" O GLY B 330 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'A' and resid 286 through 292 removed outlier: 4.257A pdb=" N ALA A 243 " --> pdb=" O ARG A 42 " (cutoff:3.500A) removed outlier: 6.843A pdb=" N ASN A 218 " --> pdb=" O HIS A 41 " (cutoff:3.500A) removed outlier: 7.968A pdb=" N LEU A 43 " --> pdb=" O ASN A 218 " (cutoff:3.500A) removed outlier: 6.257A pdb=" N HIS A 220 " --> pdb=" O LEU A 43 " (cutoff:3.500A) removed outlier: 7.333A pdb=" N LEU A 45 " --> pdb=" O HIS A 220 " (cutoff:3.500A) removed outlier: 6.716A pdb=" N PHE A 222 " --> pdb=" O LEU A 45 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N VAL A 217 " --> pdb=" O VAL A 214 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'S' and resid 5 through 7 Processing sheet with id= J, first strand: chain 'S' and resid 92 through 99 removed outlier: 4.941A pdb=" N ARG S 38 " --> pdb=" O TRP S 47 " (cutoff:3.500A) removed outlier: 5.121A pdb=" N TRP S 47 " --> pdb=" O ARG S 38 " (cutoff:3.500A) removed outlier: 6.847A pdb=" N ALA S 40 " --> pdb=" O LEU S 45 " (cutoff:3.500A) removed outlier: 6.378A pdb=" N LEU S 45 " --> pdb=" O ALA S 40 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'S' and resid 226 through 232 removed outlier: 6.174A pdb=" N LEU S 179 " --> pdb=" O LEU S 188 " (cutoff:3.500A) removed outlier: 5.575A pdb=" N LEU S 188 " --> pdb=" O LEU S 179 " (cutoff:3.500A) 317 hydrogen bonds defined for protein. 930 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: 2.65 Time building geometry restraints manager: 3.35 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2676 1.34 - 1.46: 1598 1.46 - 1.58: 4147 1.58 - 1.70: 0 1.70 - 1.81: 64 Bond restraints: 8485 Sorted by residual: bond pdb=" N GLN A 390 " pdb=" CA GLN A 390 " ideal model delta sigma weight residual 1.459 1.488 -0.029 1.23e-02 6.61e+03 5.66e+00 bond pdb=" N ARG A 385 " pdb=" CA ARG A 385 " ideal model delta sigma weight residual 1.458 1.485 -0.027 1.30e-02 5.92e+03 4.27e+00 bond pdb=" CA ASN R 307 " pdb=" C ASN R 307 " ideal model delta sigma weight residual 1.524 1.545 -0.022 1.26e-02 6.30e+03 2.91e+00 bond pdb=" N PEA R 401 " pdb=" C1 PEA R 401 " ideal model delta sigma weight residual 1.486 1.452 0.034 2.00e-02 2.50e+03 2.89e+00 bond pdb=" C ASP A 381 " pdb=" O ASP A 381 " ideal model delta sigma weight residual 1.237 1.218 0.019 1.19e-02 7.06e+03 2.42e+00 ... (remaining 8480 not shown) Histogram of bond angle deviations from ideal: 98.41 - 105.53: 129 105.53 - 112.65: 4475 112.65 - 119.77: 2661 119.77 - 126.89: 4195 126.89 - 134.01: 108 Bond angle restraints: 11568 Sorted by residual: angle pdb=" N GLN B 17 " pdb=" CA GLN B 17 " pdb=" C GLN B 17 " ideal model delta sigma weight residual 111.14 103.58 7.56 1.08e+00 8.57e-01 4.90e+01 angle pdb=" N ILE A 308 " pdb=" CA ILE A 308 " pdb=" C ILE A 308 " ideal model delta sigma weight residual 111.90 107.50 4.40 8.10e-01 1.52e+00 2.95e+01 angle pdb=" N ASP R 112 " pdb=" CA ASP R 112 " pdb=" C ASP R 112 " ideal model delta sigma weight residual 111.03 105.07 5.96 1.11e+00 8.12e-01 2.88e+01 angle pdb=" N TYR R 301 " pdb=" CA TYR R 301 " pdb=" C TYR R 301 " ideal model delta sigma weight residual 112.23 107.14 5.09 1.26e+00 6.30e-01 1.63e+01 angle pdb=" N LEU Y 50 " pdb=" CA LEU Y 50 " pdb=" C LEU Y 50 " ideal model delta sigma weight residual 114.04 109.03 5.01 1.24e+00 6.50e-01 1.63e+01 ... (remaining 11563 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.73: 4396 17.73 - 35.47: 433 35.47 - 53.20: 88 53.20 - 70.94: 20 70.94 - 88.67: 5 Dihedral angle restraints: 4942 sinusoidal: 1667 harmonic: 3275 Sorted by residual: dihedral pdb=" CA PHE R 115 " pdb=" C PHE R 115 " pdb=" N CYS R 116 " pdb=" CA CYS R 116 " ideal model delta harmonic sigma weight residual 180.00 157.73 22.27 0 5.00e+00 4.00e-02 1.98e+01 dihedral pdb=" CA LEU R 205 " pdb=" C LEU R 205 " pdb=" N PHE R 206 " pdb=" CA PHE R 206 " ideal model delta harmonic sigma weight residual 180.00 160.28 19.72 0 5.00e+00 4.00e-02 1.56e+01 dihedral pdb=" CB CYS R 105 " pdb=" SG CYS R 105 " pdb=" SG CYS R 190 " pdb=" CB CYS R 190 " ideal model delta sinusoidal sigma weight residual 93.00 124.40 -31.40 1 1.00e+01 1.00e-02 1.41e+01 ... (remaining 4939 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.038: 924 0.038 - 0.077: 308 0.077 - 0.115: 103 0.115 - 0.153: 15 0.153 - 0.191: 4 Chirality restraints: 1354 Sorted by residual: chirality pdb=" CA SER A 352 " pdb=" N SER A 352 " pdb=" C SER A 352 " pdb=" CB SER A 352 " both_signs ideal model delta sigma weight residual False 2.51 2.32 0.19 2.00e-01 2.50e+01 9.16e-01 chirality pdb=" CG LEU Y 37 " pdb=" CB LEU Y 37 " pdb=" CD1 LEU Y 37 " pdb=" CD2 LEU Y 37 " both_signs ideal model delta sigma weight residual False -2.59 -2.40 -0.19 2.00e-01 2.50e+01 8.94e-01 chirality pdb=" CA ARG A 356 " pdb=" N ARG A 356 " pdb=" C ARG A 356 " pdb=" CB ARG A 356 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.16 2.00e-01 2.50e+01 6.54e-01 ... (remaining 1351 not shown) Planarity restraints: 1471 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASP S 74 " -0.047 5.00e-02 4.00e+02 7.02e-02 7.88e+00 pdb=" N PRO S 75 " 0.121 5.00e-02 4.00e+02 pdb=" CA PRO S 75 " -0.034 5.00e-02 4.00e+02 pdb=" CD PRO S 75 " -0.040 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ASN B 16 " 0.011 2.00e-02 2.50e+03 2.30e-02 5.29e+00 pdb=" C ASN B 16 " -0.040 2.00e-02 2.50e+03 pdb=" O ASN B 16 " 0.015 2.00e-02 2.50e+03 pdb=" N GLN B 17 " 0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR B 87 " -0.010 2.00e-02 2.50e+03 1.96e-02 3.83e+00 pdb=" C THR B 87 " 0.034 2.00e-02 2.50e+03 pdb=" O THR B 87 " -0.013 2.00e-02 2.50e+03 pdb=" N ASN B 88 " -0.011 2.00e-02 2.50e+03 ... (remaining 1468 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 1209 2.75 - 3.29: 8073 3.29 - 3.83: 13223 3.83 - 4.36: 15557 4.36 - 4.90: 27081 Nonbonded interactions: 65143 Sorted by model distance: nonbonded pdb=" N GLU B 226 " pdb=" OE1 GLU B 226 " model vdw 2.214 2.520 nonbonded pdb=" N GLU Y 58 " pdb=" OE1 GLU Y 58 " model vdw 2.239 2.520 nonbonded pdb=" OG SER B 245 " pdb=" OD1 ASP B 247 " model vdw 2.257 2.440 nonbonded pdb=" O SER B 334 " pdb=" OG SER B 334 " model vdw 2.258 2.440 nonbonded pdb=" O HIS B 54 " pdb=" OG SER B 334 " model vdw 2.265 2.440 ... (remaining 65138 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.410 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 1.800 Check model and map are aligned: 0.130 Set scattering table: 0.090 Process input model: 28.120 Find NCS groups from input model: 0.390 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: 0.010 Load rotamer database and sin/cos tables:12.660 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 43.650 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7607 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 : 0.004 0.062 8485 Z= 0.269 Angle : 0.705 9.218 11568 Z= 0.409 Chirality : 0.044 0.191 1354 Planarity : 0.004 0.070 1471 Dihedral : 15.117 88.670 2822 Min Nonbonded Distance : 2.214 Molprobity Statistics. All-atom Clashscore : 9.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.79 % Favored : 96.21 % Rotamer: Outliers : 1.85 % Allowed : 23.24 % Favored : 74.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.84 (0.24), residues: 1109 helix: -1.07 (0.26), residues: 369 sheet: -0.50 (0.34), residues: 246 loop : -1.61 (0.26), residues: 494 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP B 339 HIS 0.005 0.001 HIS A 357 PHE 0.026 0.002 PHE R 159 TYR 0.020 0.001 TYR S 228 ARG 0.005 0.000 ARG S 181 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2218 Ramachandran restraints generated. 1109 Oldfield, 0 Emsley, 1109 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2218 Ramachandran restraints generated. 1109 Oldfield, 0 Emsley, 1109 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 964 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 134 time to evaluate : 1.036 Fit side-chains outliers start: 15 outliers final: 11 residues processed: 147 average time/residue: 0.9270 time to fit residues: 147.3806 Evaluate side-chains 126 residues out of total 964 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 115 time to evaluate : 0.967 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 57 ILE Chi-restraints excluded: chain R residue 96 SER Chi-restraints excluded: chain R residue 135 THR Chi-restraints excluded: chain R residue 138 LEU Chi-restraints excluded: chain R residue 163 TYR Chi-restraints excluded: chain R residue 167 ILE Chi-restraints excluded: chain R residue 204 LEU Chi-restraints excluded: chain R residue 325 ILE Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain A residue 323 ASP Chi-restraints excluded: chain S residue 146 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 93 optimal weight: 0.0170 chunk 84 optimal weight: 9.9990 chunk 46 optimal weight: 0.0980 chunk 28 optimal weight: 5.9990 chunk 56 optimal weight: 3.9990 chunk 44 optimal weight: 6.9990 chunk 87 optimal weight: 0.0970 chunk 33 optimal weight: 0.3980 chunk 52 optimal weight: 0.5980 chunk 64 optimal weight: 0.9990 chunk 100 optimal weight: 3.9990 overall best weight: 0.2416 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 307 ASN B 75 GLN B 268 ASN A 239 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7525 moved from start: 0.1350 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 8485 Z= 0.132 Angle : 0.527 9.394 11568 Z= 0.270 Chirality : 0.040 0.250 1354 Planarity : 0.004 0.053 1471 Dihedral : 4.962 59.123 1227 Min Nonbonded Distance : 2.210 Molprobity Statistics. All-atom Clashscore : 6.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer: Outliers : 3.83 % Allowed : 22.74 % Favored : 73.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.03 (0.25), residues: 1109 helix: 0.25 (0.28), residues: 362 sheet: -0.34 (0.33), residues: 258 loop : -1.55 (0.27), residues: 489 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 82 HIS 0.003 0.001 HIS S 35 PHE 0.018 0.001 PHE R 159 TYR 0.014 0.001 TYR S 191 ARG 0.005 0.000 ARG R 92 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2218 Ramachandran restraints generated. 1109 Oldfield, 0 Emsley, 1109 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2218 Ramachandran restraints generated. 1109 Oldfield, 0 Emsley, 1109 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 964 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 134 time to evaluate : 0.897 Fit side-chains revert: symmetry clash REVERT: R 127 SER cc_start: 0.8296 (m) cc_final: 0.7959 (p) REVERT: R 163 TYR cc_start: 0.7488 (OUTLIER) cc_final: 0.6491 (t80) REVERT: B 10 GLU cc_start: 0.7388 (pp20) cc_final: 0.7185 (pp20) REVERT: B 75 GLN cc_start: 0.8455 (OUTLIER) cc_final: 0.7727 (mp-120) REVERT: B 226 GLU cc_start: 0.8259 (pm20) cc_final: 0.7875 (pm20) REVERT: A 392 GLU cc_start: 0.8532 (tt0) cc_final: 0.8261 (mt-10) outliers start: 31 outliers final: 10 residues processed: 152 average time/residue: 0.8801 time to fit residues: 144.9680 Evaluate side-chains 130 residues out of total 964 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 118 time to evaluate : 0.994 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 91 VAL Chi-restraints excluded: chain R residue 105 CYS Chi-restraints excluded: chain R residue 160 SER Chi-restraints excluded: chain R residue 161 VAL Chi-restraints excluded: chain R residue 163 TYR Chi-restraints excluded: chain R residue 325 ILE Chi-restraints excluded: chain B residue 75 GLN Chi-restraints excluded: chain B residue 165 THR Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 205 ASP Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain S residue 227 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 56 optimal weight: 7.9990 chunk 31 optimal weight: 6.9990 chunk 83 optimal weight: 4.9990 chunk 68 optimal weight: 0.7980 chunk 27 optimal weight: 0.7980 chunk 100 optimal weight: 0.6980 chunk 109 optimal weight: 9.9990 chunk 89 optimal weight: 9.9990 chunk 34 optimal weight: 0.9990 chunk 81 optimal weight: 1.9990 chunk 99 optimal weight: 4.9990 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 75 GLN A 239 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7552 moved from start: 0.1479 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 8485 Z= 0.160 Angle : 0.520 7.994 11568 Z= 0.264 Chirality : 0.040 0.278 1354 Planarity : 0.003 0.055 1471 Dihedral : 4.583 57.551 1214 Min Nonbonded Distance : 2.229 Molprobity Statistics. All-atom Clashscore : 6.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % Rotamer: Outliers : 4.20 % Allowed : 24.47 % Favored : 71.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.76 (0.25), residues: 1109 helix: 0.57 (0.29), residues: 365 sheet: -0.23 (0.33), residues: 259 loop : -1.47 (0.27), residues: 485 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 82 HIS 0.004 0.001 HIS A 357 PHE 0.013 0.001 PHE R 144 TYR 0.016 0.001 TYR B 59 ARG 0.004 0.000 ARG R 92 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2218 Ramachandran restraints generated. 1109 Oldfield, 0 Emsley, 1109 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2218 Ramachandran restraints generated. 1109 Oldfield, 0 Emsley, 1109 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 964 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 125 time to evaluate : 1.065 Fit side-chains revert: symmetry clash REVERT: R 127 SER cc_start: 0.8383 (m) cc_final: 0.8119 (p) REVERT: B 226 GLU cc_start: 0.8350 (pm20) cc_final: 0.7951 (pm20) REVERT: S 180 GLN cc_start: 0.8816 (OUTLIER) cc_final: 0.8084 (tm-30) REVERT: S 181 ARG cc_start: 0.8303 (mmt90) cc_final: 0.7695 (tpp-160) outliers start: 34 outliers final: 16 residues processed: 151 average time/residue: 0.8758 time to fit residues: 143.8475 Evaluate side-chains 136 residues out of total 964 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 119 time to evaluate : 1.013 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 91 VAL Chi-restraints excluded: chain R residue 105 CYS Chi-restraints excluded: chain R residue 160 SER Chi-restraints excluded: chain R residue 161 VAL Chi-restraints excluded: chain R residue 163 TYR Chi-restraints excluded: chain R residue 167 ILE Chi-restraints excluded: chain R residue 325 ILE Chi-restraints excluded: chain B residue 165 THR Chi-restraints excluded: chain B residue 205 ASP Chi-restraints excluded: chain B residue 247 ASP Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain A residue 237 CYS Chi-restraints excluded: chain A residue 320 THR Chi-restraints excluded: chain S residue 57 THR Chi-restraints excluded: chain S residue 146 SER Chi-restraints excluded: chain S residue 180 GLN Chi-restraints excluded: chain S residue 227 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 75 optimal weight: 0.0870 chunk 52 optimal weight: 2.9990 chunk 11 optimal weight: 1.9990 chunk 48 optimal weight: 6.9990 chunk 67 optimal weight: 9.9990 chunk 101 optimal weight: 0.2980 chunk 107 optimal weight: 0.9990 chunk 96 optimal weight: 20.0000 chunk 28 optimal weight: 5.9990 chunk 89 optimal weight: 9.9990 chunk 60 optimal weight: 6.9990 overall best weight: 1.2764 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 307 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 239 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7562 moved from start: 0.1638 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 8485 Z= 0.170 Angle : 0.525 8.297 11568 Z= 0.263 Chirality : 0.040 0.291 1354 Planarity : 0.003 0.053 1471 Dihedral : 4.519 55.359 1214 Min Nonbonded Distance : 2.235 Molprobity Statistics. All-atom Clashscore : 7.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.07 % Favored : 96.93 % Rotamer: Outliers : 4.20 % Allowed : 24.47 % Favored : 71.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.64 (0.26), residues: 1109 helix: 0.83 (0.29), residues: 360 sheet: -0.23 (0.32), residues: 260 loop : -1.49 (0.27), residues: 489 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 82 HIS 0.004 0.001 HIS A 357 PHE 0.030 0.001 PHE A 376 TYR 0.010 0.001 TYR B 59 ARG 0.003 0.000 ARG R 92 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2218 Ramachandran restraints generated. 1109 Oldfield, 0 Emsley, 1109 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2218 Ramachandran restraints generated. 1109 Oldfield, 0 Emsley, 1109 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 964 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 129 time to evaluate : 0.951 Fit side-chains revert: symmetry clash REVERT: R 127 SER cc_start: 0.8332 (m) cc_final: 0.8125 (p) REVERT: B 10 GLU cc_start: 0.7412 (pp20) cc_final: 0.7134 (pp20) REVERT: B 226 GLU cc_start: 0.8356 (pm20) cc_final: 0.7997 (pm20) REVERT: S 4 LEU cc_start: 0.7374 (OUTLIER) cc_final: 0.7139 (pp) REVERT: S 180 GLN cc_start: 0.8812 (OUTLIER) cc_final: 0.8276 (tm-30) outliers start: 34 outliers final: 18 residues processed: 152 average time/residue: 0.9750 time to fit residues: 160.4497 Evaluate side-chains 135 residues out of total 964 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 115 time to evaluate : 0.895 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 91 VAL Chi-restraints excluded: chain R residue 105 CYS Chi-restraints excluded: chain R residue 146 VAL Chi-restraints excluded: chain R residue 160 SER Chi-restraints excluded: chain R residue 161 VAL Chi-restraints excluded: chain R residue 163 TYR Chi-restraints excluded: chain R residue 167 ILE Chi-restraints excluded: chain R residue 325 ILE Chi-restraints excluded: chain B residue 36 ASN Chi-restraints excluded: chain B residue 205 ASP Chi-restraints excluded: chain B residue 247 ASP Chi-restraints excluded: chain B residue 267 ASP Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain A residue 237 CYS Chi-restraints excluded: chain A residue 320 THR Chi-restraints excluded: chain S residue 4 LEU Chi-restraints excluded: chain S residue 57 THR Chi-restraints excluded: chain S residue 140 VAL Chi-restraints excluded: chain S residue 180 GLN Chi-restraints excluded: chain S residue 227 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 1 optimal weight: 5.9990 chunk 79 optimal weight: 0.0020 chunk 44 optimal weight: 6.9990 chunk 91 optimal weight: 20.0000 chunk 74 optimal weight: 5.9990 chunk 0 optimal weight: 20.0000 chunk 54 optimal weight: 4.9990 chunk 96 optimal weight: 20.0000 chunk 27 optimal weight: 0.9990 chunk 36 optimal weight: 0.3980 chunk 21 optimal weight: 7.9990 overall best weight: 2.4794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 307 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 239 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7613 moved from start: 0.1674 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 8485 Z= 0.271 Angle : 0.577 8.357 11568 Z= 0.295 Chirality : 0.042 0.285 1354 Planarity : 0.004 0.052 1471 Dihedral : 4.819 52.771 1214 Min Nonbonded Distance : 2.210 Molprobity Statistics. All-atom Clashscore : 7.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.33 % Favored : 95.67 % Rotamer: Outliers : 5.19 % Allowed : 24.47 % Favored : 70.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.77 (0.25), residues: 1109 helix: 0.71 (0.29), residues: 360 sheet: -0.24 (0.32), residues: 260 loop : -1.59 (0.27), residues: 489 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP S 47 HIS 0.005 0.001 HIS A 357 PHE 0.023 0.002 PHE A 376 TYR 0.013 0.001 TYR S 228 ARG 0.009 0.001 ARG A 389 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2218 Ramachandran restraints generated. 1109 Oldfield, 0 Emsley, 1109 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2218 Ramachandran restraints generated. 1109 Oldfield, 0 Emsley, 1109 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 964 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 120 time to evaluate : 1.096 Fit side-chains revert: symmetry clash REVERT: R 127 SER cc_start: 0.8433 (m) cc_final: 0.8166 (p) REVERT: R 281 ASP cc_start: 0.7292 (OUTLIER) cc_final: 0.7004 (t0) REVERT: B 124 TYR cc_start: 0.8145 (m-80) cc_final: 0.7839 (m-80) REVERT: B 226 GLU cc_start: 0.8373 (pm20) cc_final: 0.8134 (pm20) REVERT: S 4 LEU cc_start: 0.7552 (OUTLIER) cc_final: 0.7297 (pp) REVERT: S 180 GLN cc_start: 0.8773 (OUTLIER) cc_final: 0.8446 (tm-30) outliers start: 42 outliers final: 21 residues processed: 153 average time/residue: 0.8399 time to fit residues: 140.0293 Evaluate side-chains 138 residues out of total 964 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 114 time to evaluate : 0.965 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 91 VAL Chi-restraints excluded: chain R residue 105 CYS Chi-restraints excluded: chain R residue 146 VAL Chi-restraints excluded: chain R residue 160 SER Chi-restraints excluded: chain R residue 161 VAL Chi-restraints excluded: chain R residue 163 TYR Chi-restraints excluded: chain R residue 167 ILE Chi-restraints excluded: chain R residue 281 ASP Chi-restraints excluded: chain R residue 325 ILE Chi-restraints excluded: chain B residue 36 ASN Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 205 ASP Chi-restraints excluded: chain B residue 247 ASP Chi-restraints excluded: chain B residue 267 ASP Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 237 CYS Chi-restraints excluded: chain A residue 320 THR Chi-restraints excluded: chain S residue 4 LEU Chi-restraints excluded: chain S residue 57 THR Chi-restraints excluded: chain S residue 140 VAL Chi-restraints excluded: chain S residue 146 SER Chi-restraints excluded: chain S residue 180 GLN Chi-restraints excluded: chain S residue 227 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 62 optimal weight: 5.9990 chunk 26 optimal weight: 5.9990 chunk 107 optimal weight: 5.9990 chunk 89 optimal weight: 10.0000 chunk 49 optimal weight: 0.9990 chunk 8 optimal weight: 0.7980 chunk 35 optimal weight: 0.0870 chunk 56 optimal weight: 6.9990 chunk 103 optimal weight: 0.5980 chunk 12 optimal weight: 10.0000 chunk 61 optimal weight: 0.8980 overall best weight: 0.6760 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 307 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 75 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7551 moved from start: 0.1940 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 8485 Z= 0.140 Angle : 0.531 8.974 11568 Z= 0.264 Chirality : 0.040 0.297 1354 Planarity : 0.003 0.050 1471 Dihedral : 4.434 51.555 1214 Min Nonbonded Distance : 2.216 Molprobity Statistics. All-atom Clashscore : 6.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % Rotamer: Outliers : 3.34 % Allowed : 26.82 % Favored : 69.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 (0.25), residues: 1109 helix: 0.95 (0.29), residues: 360 sheet: -0.13 (0.33), residues: 245 loop : -1.49 (0.27), residues: 504 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 82 HIS 0.003 0.001 HIS S 35 PHE 0.024 0.001 PHE A 376 TYR 0.009 0.001 TYR R 274 ARG 0.006 0.000 ARG S 181 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2218 Ramachandran restraints generated. 1109 Oldfield, 0 Emsley, 1109 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2218 Ramachandran restraints generated. 1109 Oldfield, 0 Emsley, 1109 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 964 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 130 time to evaluate : 0.951 Fit side-chains revert: symmetry clash REVERT: R 100 PHE cc_start: 0.8497 (m-10) cc_final: 0.7638 (p90) REVERT: R 127 SER cc_start: 0.8376 (m) cc_final: 0.8136 (p) REVERT: R 281 ASP cc_start: 0.7148 (OUTLIER) cc_final: 0.6922 (t0) REVERT: B 10 GLU cc_start: 0.7344 (pp20) cc_final: 0.7056 (pp20) REVERT: B 124 TYR cc_start: 0.8067 (m-80) cc_final: 0.7825 (m-80) REVERT: B 226 GLU cc_start: 0.8313 (pm20) cc_final: 0.8078 (pm20) REVERT: S 180 GLN cc_start: 0.8681 (OUTLIER) cc_final: 0.8153 (tm-30) outliers start: 27 outliers final: 15 residues processed: 153 average time/residue: 0.8331 time to fit residues: 139.1069 Evaluate side-chains 138 residues out of total 964 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 121 time to evaluate : 0.954 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 91 VAL Chi-restraints excluded: chain R residue 105 CYS Chi-restraints excluded: chain R residue 109 THR Chi-restraints excluded: chain R residue 160 SER Chi-restraints excluded: chain R residue 161 VAL Chi-restraints excluded: chain R residue 163 TYR Chi-restraints excluded: chain R residue 281 ASP Chi-restraints excluded: chain R residue 325 ILE Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 205 ASP Chi-restraints excluded: chain B residue 247 ASP Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain A residue 320 THR Chi-restraints excluded: chain S residue 140 VAL Chi-restraints excluded: chain S residue 146 SER Chi-restraints excluded: chain S residue 180 GLN Chi-restraints excluded: chain S residue 227 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 78 optimal weight: 7.9990 chunk 60 optimal weight: 7.9990 chunk 90 optimal weight: 0.8980 chunk 59 optimal weight: 10.0000 chunk 106 optimal weight: 10.0000 chunk 66 optimal weight: 0.9980 chunk 65 optimal weight: 10.0000 chunk 49 optimal weight: 0.8980 chunk 42 optimal weight: 0.1980 chunk 63 optimal weight: 1.9990 chunk 32 optimal weight: 10.0000 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 307 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 75 GLN B 340 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7555 moved from start: 0.2002 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 8485 Z= 0.159 Angle : 0.541 9.881 11568 Z= 0.267 Chirality : 0.041 0.326 1354 Planarity : 0.003 0.049 1471 Dihedral : 4.381 50.617 1214 Min Nonbonded Distance : 2.211 Molprobity Statistics. All-atom Clashscore : 6.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.52 % Favored : 96.48 % Rotamer: Outliers : 3.96 % Allowed : 26.70 % Favored : 69.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1109 helix: 0.89 (0.29), residues: 366 sheet: -0.14 (0.31), residues: 260 loop : -1.51 (0.28), residues: 483 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP S 47 HIS 0.004 0.001 HIS A 357 PHE 0.022 0.001 PHE A 376 TYR 0.008 0.001 TYR R 274 ARG 0.006 0.000 ARG S 181 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2218 Ramachandran restraints generated. 1109 Oldfield, 0 Emsley, 1109 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2218 Ramachandran restraints generated. 1109 Oldfield, 0 Emsley, 1109 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 964 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 124 time to evaluate : 0.873 Fit side-chains revert: symmetry clash REVERT: R 100 PHE cc_start: 0.8463 (m-10) cc_final: 0.7679 (p90) REVERT: R 106 LYS cc_start: 0.7877 (tppp) cc_final: 0.7617 (tppp) REVERT: R 127 SER cc_start: 0.8373 (m) cc_final: 0.8121 (p) REVERT: B 10 GLU cc_start: 0.7478 (pp20) cc_final: 0.7120 (pp20) REVERT: B 124 TYR cc_start: 0.8063 (m-80) cc_final: 0.7838 (m-80) REVERT: B 226 GLU cc_start: 0.8340 (pm20) cc_final: 0.8087 (pm20) REVERT: S 180 GLN cc_start: 0.8687 (OUTLIER) cc_final: 0.8118 (tm-30) outliers start: 32 outliers final: 21 residues processed: 150 average time/residue: 0.8926 time to fit residues: 145.3434 Evaluate side-chains 141 residues out of total 964 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 119 time to evaluate : 0.991 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 91 VAL Chi-restraints excluded: chain R residue 105 CYS Chi-restraints excluded: chain R residue 109 THR Chi-restraints excluded: chain R residue 135 THR Chi-restraints excluded: chain R residue 146 VAL Chi-restraints excluded: chain R residue 160 SER Chi-restraints excluded: chain R residue 161 VAL Chi-restraints excluded: chain R residue 163 TYR Chi-restraints excluded: chain R residue 325 ILE Chi-restraints excluded: chain B residue 36 ASN Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 205 ASP Chi-restraints excluded: chain B residue 247 ASP Chi-restraints excluded: chain B residue 267 ASP Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 237 CYS Chi-restraints excluded: chain A residue 320 THR Chi-restraints excluded: chain S residue 140 VAL Chi-restraints excluded: chain S residue 146 SER Chi-restraints excluded: chain S residue 180 GLN Chi-restraints excluded: chain S residue 227 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 21 optimal weight: 6.9990 chunk 20 optimal weight: 3.9990 chunk 68 optimal weight: 6.9990 chunk 72 optimal weight: 3.9990 chunk 52 optimal weight: 3.9990 chunk 9 optimal weight: 2.9990 chunk 84 optimal weight: 20.0000 chunk 97 optimal weight: 9.9990 chunk 102 optimal weight: 5.9990 chunk 93 optimal weight: 1.9990 chunk 99 optimal weight: 3.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 307 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 75 GLN ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7634 moved from start: 0.1916 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 8485 Z= 0.351 Angle : 0.629 9.667 11568 Z= 0.319 Chirality : 0.044 0.319 1354 Planarity : 0.004 0.049 1471 Dihedral : 4.989 51.251 1214 Min Nonbonded Distance : 2.191 Molprobity Statistics. All-atom Clashscore : 8.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.87 % Favored : 95.13 % Rotamer: Outliers : 4.33 % Allowed : 26.95 % Favored : 68.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.83 (0.25), residues: 1109 helix: 0.62 (0.29), residues: 363 sheet: -0.20 (0.32), residues: 262 loop : -1.65 (0.27), residues: 484 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP S 47 HIS 0.007 0.001 HIS A 357 PHE 0.021 0.002 PHE A 376 TYR 0.013 0.002 TYR B 59 ARG 0.011 0.001 ARG A 389 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2218 Ramachandran restraints generated. 1109 Oldfield, 0 Emsley, 1109 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2218 Ramachandran restraints generated. 1109 Oldfield, 0 Emsley, 1109 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 964 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 117 time to evaluate : 0.874 Fit side-chains REVERT: R 100 PHE cc_start: 0.8504 (m-10) cc_final: 0.7679 (p90) REVERT: R 127 SER cc_start: 0.8397 (m) cc_final: 0.8179 (p) REVERT: R 186 CYS cc_start: 0.9062 (m) cc_final: 0.8582 (p) REVERT: B 124 TYR cc_start: 0.8206 (m-80) cc_final: 0.7908 (m-80) REVERT: B 226 GLU cc_start: 0.8372 (pm20) cc_final: 0.8109 (pm20) REVERT: B 338 ILE cc_start: 0.8858 (OUTLIER) cc_final: 0.8273 (mp) REVERT: S 180 GLN cc_start: 0.8725 (OUTLIER) cc_final: 0.8116 (tm-30) outliers start: 35 outliers final: 22 residues processed: 146 average time/residue: 0.8372 time to fit residues: 133.2948 Evaluate side-chains 140 residues out of total 964 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 116 time to evaluate : 0.942 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 91 VAL Chi-restraints excluded: chain R residue 109 THR Chi-restraints excluded: chain R residue 135 THR Chi-restraints excluded: chain R residue 146 VAL Chi-restraints excluded: chain R residue 160 SER Chi-restraints excluded: chain R residue 161 VAL Chi-restraints excluded: chain R residue 163 TYR Chi-restraints excluded: chain R residue 167 ILE Chi-restraints excluded: chain R residue 205 LEU Chi-restraints excluded: chain R residue 325 ILE Chi-restraints excluded: chain B residue 36 ASN Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 205 ASP Chi-restraints excluded: chain B residue 247 ASP Chi-restraints excluded: chain B residue 267 ASP Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 338 ILE Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 237 CYS Chi-restraints excluded: chain A residue 320 THR Chi-restraints excluded: chain A residue 323 ASP Chi-restraints excluded: chain S residue 57 THR Chi-restraints excluded: chain S residue 140 VAL Chi-restraints excluded: chain S residue 180 GLN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 102 optimal weight: 9.9990 chunk 60 optimal weight: 1.9990 chunk 43 optimal weight: 0.0370 chunk 78 optimal weight: 2.9990 chunk 30 optimal weight: 0.8980 chunk 90 optimal weight: 6.9990 chunk 94 optimal weight: 7.9990 chunk 99 optimal weight: 2.9990 chunk 65 optimal weight: 5.9990 chunk 105 optimal weight: 10.0000 chunk 64 optimal weight: 2.9990 overall best weight: 1.7864 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 307 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 44 GLN B 75 GLN ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7602 moved from start: 0.1980 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 8485 Z= 0.219 Angle : 0.585 11.419 11568 Z= 0.292 Chirality : 0.042 0.346 1354 Planarity : 0.004 0.049 1471 Dihedral : 4.771 50.881 1214 Min Nonbonded Distance : 2.201 Molprobity Statistics. All-atom Clashscore : 7.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.70 % Favored : 96.30 % Rotamer: Outliers : 4.08 % Allowed : 27.07 % Favored : 68.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.81 (0.25), residues: 1109 helix: 0.58 (0.28), residues: 369 sheet: -0.17 (0.32), residues: 262 loop : -1.62 (0.27), residues: 478 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP S 47 HIS 0.005 0.001 HIS A 357 PHE 0.021 0.001 PHE A 376 TYR 0.013 0.001 TYR B 59 ARG 0.010 0.000 ARG A 389 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2218 Ramachandran restraints generated. 1109 Oldfield, 0 Emsley, 1109 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2218 Ramachandran restraints generated. 1109 Oldfield, 0 Emsley, 1109 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 964 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 116 time to evaluate : 1.179 Fit side-chains REVERT: R 100 PHE cc_start: 0.8473 (m-10) cc_final: 0.7628 (p90) REVERT: R 106 LYS cc_start: 0.7971 (tppp) cc_final: 0.7670 (tppp) REVERT: R 127 SER cc_start: 0.8397 (m) cc_final: 0.8147 (p) REVERT: R 186 CYS cc_start: 0.8994 (m) cc_final: 0.8509 (p) REVERT: B 124 TYR cc_start: 0.8123 (m-80) cc_final: 0.7872 (m-80) REVERT: B 226 GLU cc_start: 0.8365 (pm20) cc_final: 0.8106 (pm20) REVERT: S 4 LEU cc_start: 0.7485 (OUTLIER) cc_final: 0.7256 (pp) outliers start: 33 outliers final: 25 residues processed: 142 average time/residue: 0.8594 time to fit residues: 133.1734 Evaluate side-chains 140 residues out of total 964 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 114 time to evaluate : 1.009 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 91 VAL Chi-restraints excluded: chain R residue 109 THR Chi-restraints excluded: chain R residue 135 THR Chi-restraints excluded: chain R residue 146 VAL Chi-restraints excluded: chain R residue 160 SER Chi-restraints excluded: chain R residue 161 VAL Chi-restraints excluded: chain R residue 163 TYR Chi-restraints excluded: chain R residue 167 ILE Chi-restraints excluded: chain R residue 325 ILE Chi-restraints excluded: chain B residue 36 ASN Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 205 ASP Chi-restraints excluded: chain B residue 247 ASP Chi-restraints excluded: chain B residue 267 ASP Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 237 CYS Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 297 LEU Chi-restraints excluded: chain A residue 320 THR Chi-restraints excluded: chain A residue 323 ASP Chi-restraints excluded: chain S residue 4 LEU Chi-restraints excluded: chain S residue 140 VAL Chi-restraints excluded: chain S residue 146 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 50 optimal weight: 0.8980 chunk 73 optimal weight: 3.9990 chunk 110 optimal weight: 6.9990 chunk 101 optimal weight: 3.9990 chunk 88 optimal weight: 0.8980 chunk 9 optimal weight: 1.9990 chunk 68 optimal weight: 4.9990 chunk 53 optimal weight: 0.8980 chunk 69 optimal weight: 1.9990 chunk 93 optimal weight: 0.0770 chunk 26 optimal weight: 0.0470 overall best weight: 0.5636 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 307 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 44 GLN B 75 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7539 moved from start: 0.2255 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 8485 Z= 0.141 Angle : 0.552 11.175 11568 Z= 0.271 Chirality : 0.041 0.328 1354 Planarity : 0.003 0.048 1471 Dihedral : 4.375 49.544 1214 Min Nonbonded Distance : 2.207 Molprobity Statistics. All-atom Clashscore : 7.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.07 % Favored : 96.93 % Rotamer: Outliers : 2.60 % Allowed : 28.43 % Favored : 68.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.60 (0.25), residues: 1109 helix: 0.80 (0.29), residues: 366 sheet: -0.03 (0.33), residues: 245 loop : -1.51 (0.27), residues: 498 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 99 HIS 0.003 0.001 HIS A 357 PHE 0.021 0.001 PHE A 376 TYR 0.010 0.001 TYR S 95 ARG 0.009 0.000 ARG A 389 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2218 Ramachandran restraints generated. 1109 Oldfield, 0 Emsley, 1109 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2218 Ramachandran restraints generated. 1109 Oldfield, 0 Emsley, 1109 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 964 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 126 time to evaluate : 0.859 Fit side-chains REVERT: R 100 PHE cc_start: 0.8482 (m-10) cc_final: 0.7667 (p90) REVERT: R 106 LYS cc_start: 0.7921 (tppp) cc_final: 0.7660 (tppp) REVERT: R 127 SER cc_start: 0.8361 (m) cc_final: 0.8128 (p) REVERT: R 186 CYS cc_start: 0.8979 (m) cc_final: 0.8563 (p) REVERT: B 10 GLU cc_start: 0.7400 (pp20) cc_final: 0.7116 (pp20) REVERT: B 124 TYR cc_start: 0.8071 (m-80) cc_final: 0.7844 (m-80) REVERT: B 226 GLU cc_start: 0.8308 (pm20) cc_final: 0.8056 (pm20) outliers start: 21 outliers final: 19 residues processed: 143 average time/residue: 0.8691 time to fit residues: 135.1211 Evaluate side-chains 138 residues out of total 964 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 119 time to evaluate : 0.944 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 109 THR Chi-restraints excluded: chain R residue 129 ASP Chi-restraints excluded: chain R residue 146 VAL Chi-restraints excluded: chain R residue 160 SER Chi-restraints excluded: chain R residue 161 VAL Chi-restraints excluded: chain R residue 163 TYR Chi-restraints excluded: chain R residue 167 ILE Chi-restraints excluded: chain R residue 325 ILE Chi-restraints excluded: chain B residue 36 ASN Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 205 ASP Chi-restraints excluded: chain B residue 247 ASP Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain A residue 237 CYS Chi-restraints excluded: chain A residue 320 THR Chi-restraints excluded: chain S residue 140 VAL Chi-restraints excluded: chain S residue 146 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 81 optimal weight: 6.9990 chunk 13 optimal weight: 6.9990 chunk 24 optimal weight: 0.6980 chunk 88 optimal weight: 5.9990 chunk 36 optimal weight: 5.9990 chunk 90 optimal weight: 3.9990 chunk 11 optimal weight: 1.9990 chunk 16 optimal weight: 4.9990 chunk 77 optimal weight: 1.9990 chunk 5 optimal weight: 0.9990 chunk 63 optimal weight: 3.9990 overall best weight: 1.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 307 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 75 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3960 r_free = 0.3960 target = 0.139388 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3532 r_free = 0.3532 target = 0.105794 restraints weight = 12120.351| |-----------------------------------------------------------------------------| r_work (start): 0.3523 rms_B_bonded: 2.75 r_work: 0.3404 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work (final): 0.3404 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7570 moved from start: 0.2115 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 8485 Z= 0.227 Angle : 0.574 10.733 11568 Z= 0.288 Chirality : 0.042 0.341 1354 Planarity : 0.003 0.048 1471 Dihedral : 4.600 49.421 1214 Min Nonbonded Distance : 2.209 Molprobity Statistics. All-atom Clashscore : 7.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.79 % Favored : 96.21 % Rotamer: Outliers : 2.97 % Allowed : 28.31 % Favored : 68.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.66 (0.25), residues: 1109 helix: 0.75 (0.29), residues: 365 sheet: -0.09 (0.32), residues: 262 loop : -1.56 (0.27), residues: 482 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP S 47 HIS 0.005 0.001 HIS A 357 PHE 0.020 0.002 PHE A 376 TYR 0.013 0.001 TYR B 59 ARG 0.009 0.000 ARG A 389 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3038.87 seconds wall clock time: 54 minutes 55.62 seconds (3295.62 seconds total)