Starting phenix.real_space_refine on Sat Mar 16 02:16:06 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jhh_22337/03_2024/7jhh_22337_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jhh_22337/03_2024/7jhh_22337.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.92 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jhh_22337/03_2024/7jhh_22337.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jhh_22337/03_2024/7jhh_22337.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jhh_22337/03_2024/7jhh_22337_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jhh_22337/03_2024/7jhh_22337_updated.pdb" } resolution = 3.92 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= 0.002 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: 5 Type Number sf(0) Gaussians P 6 5.49 5 S 51 5.16 5 C 8559 2.51 5 N 2253 2.21 5 O 2549 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 438": "NH1" <-> "NH2" Residue "A TYR 446": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 201": "NH1" <-> "NH2" Residue "G ARG 70": "NH1" <-> "NH2" Residue "G ARG 152": "NH1" <-> "NH2" Residue "G ARG 224": "NH1" <-> "NH2" Residue "G ARG 299": "NH1" <-> "NH2" Residue "L TYR 50": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 193": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N ARG 36": "NH1" <-> "NH2" Residue "N ARG 40": "NH1" <-> "NH2" Residue "N ARG 54": "NH1" <-> "NH2" Residue "N ARG 61": "NH1" <-> "NH2" Residue "N ARG 62": "NH1" <-> "NH2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 13418 Number of models: 1 Model: "" Number of chains: 9 Chain: "A" Number of atoms: 3074 Number of conformers: 1 Conformer: "" Number of residues, atoms: 379, 3074 Classifications: {'peptide': 379} Link IDs: {'PTRANS': 19, 'TRANS': 359} Chain breaks: 1 Chain: "B" Number of atoms: 736 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 736 Classifications: {'peptide': 93} Link IDs: {'PTRANS': 11, 'TRANS': 81} Chain: "G" Number of atoms: 2421 Number of conformers: 1 Conformer: "" Number of residues, atoms: 300, 2421 Classifications: {'peptide': 300} Link IDs: {'PTRANS': 10, 'TRANS': 289} Chain: "M" Number of atoms: 2834 Number of conformers: 1 Conformer: "" Number of residues, atoms: 367, 2834 Classifications: {'peptide': 367} Link IDs: {'PTRANS': 21, 'TRANS': 345} Chain: "L" Number of atoms: 1601 Number of conformers: 1 Conformer: "" Number of residues, atoms: 211, 1601 Classifications: {'peptide': 211} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 199} Chain: "H" Number of atoms: 1723 Number of conformers: 1 Conformer: "" Number of residues, atoms: 228, 1723 Classifications: {'peptide': 228} Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 214} Chain: "N" Number of atoms: 925 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 925 Classifications: {'peptide': 120} Link IDs: {'PTRANS': 3, 'TRANS': 116} Chain: "C" Number of atoms: 23 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 23 Unusual residues: {'GLC': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "G" Number of atoms: 81 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 81 Unusual residues: {'ADP': 1, 'ATP': 1} Classifications: {'RNA': 1, 'undetermined': 2} Modifications used: {'rna2p': 1} Link IDs: {None: 2} Time building chain proxies: 7.70, per 1000 atoms: 0.57 Number of scatterers: 13418 At special positions: 0 Unit cell: (103.929, 129.654, 163.611, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 51 16.00 P 6 15.00 O 2549 8.00 N 2253 7.00 C 8559 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=5, symmetry=0 Simple disulfide: pdb=" SG CYS L 24 " - pdb=" SG CYS L 89 " distance=2.03 Simple disulfide: pdb=" SG CYS L 135 " - pdb=" SG CYS L 195 " distance=2.04 Simple disulfide: pdb=" SG CYS H 25 " - pdb=" SG CYS H 99 " distance=2.03 Simple disulfide: pdb=" SG CYS H 156 " - pdb=" SG CYS H 212 " distance=2.03 Simple disulfide: pdb=" SG CYS N 31 " - pdb=" SG CYS N 105 " 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 Links applied ALPHA1-4 " GLC C 1 " - " GLC C 2 " Time building additional restraints: 5.19 Conformation dependent library (CDL) restraints added in 2.4 seconds 3364 Ramachandran restraints generated. 1682 Oldfield, 0 Emsley, 1682 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3182 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 49 helices and 23 sheets defined 25.7% alpha, 18.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.48 Creating SS restraints... Processing helix chain 'A' and resid 51 through 54 No H-bonds generated for 'chain 'A' and resid 51 through 54' Processing helix chain 'A' and resid 60 through 70 Processing helix chain 'A' and resid 103 through 110 Processing helix chain 'A' and resid 115 through 134 removed outlier: 3.561A pdb=" N ARG A 120 " --> pdb=" O LYS A 116 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N GLN A 124 " --> pdb=" O ARG A 120 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N TYR A 131 " --> pdb=" O SER A 127 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N CYS A 132 " --> pdb=" O GLY A 128 " (cutoff:3.500A) Processing helix chain 'A' and resid 161 through 169 removed outlier: 3.639A pdb=" N MET A 165 " --> pdb=" O GLY A 161 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N MET A 166 " --> pdb=" O LEU A 162 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N ASP A 168 " --> pdb=" O ASN A 164 " (cutoff:3.500A) Processing helix chain 'A' and resid 171 through 177 Processing helix chain 'A' and resid 184 through 188 Processing helix chain 'A' and resid 194 through 211 removed outlier: 3.666A pdb=" N VAL A 197 " --> pdb=" O GLY A 194 " (cutoff:3.500A) removed outlier: 4.112A pdb=" N ILE A 199 " --> pdb=" O GLU A 196 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ILE A 205 " --> pdb=" O SER A 202 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N CYS A 211 " --> pdb=" O ALA A 208 " (cutoff:3.500A) Processing helix chain 'A' and resid 221 through 229 Processing helix chain 'A' and resid 241 through 250 removed outlier: 3.954A pdb=" N SER A 245 " --> pdb=" O PRO A 241 " (cutoff:3.500A) removed outlier: 4.392A pdb=" N LEU A 246 " --> pdb=" O SER A 242 " (cutoff:3.500A) Processing helix chain 'A' and resid 261 through 265 Processing helix chain 'A' and resid 408 through 421 removed outlier: 3.697A pdb=" N MET A 412 " --> pdb=" O PRO A 408 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N ALA A 413 " --> pdb=" O ASN A 409 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N GLN A 421 " --> pdb=" O ARG A 417 " (cutoff:3.500A) Processing helix chain 'A' and resid 534 through 548 removed outlier: 3.585A pdb=" N CYS A 541 " --> pdb=" O PHE A 537 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N ASN A 543 " --> pdb=" O GLU A 539 " (cutoff:3.500A) removed outlier: 4.816A pdb=" N LEU A 544 " --> pdb=" O MET A 540 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N LYS A 546 " --> pdb=" O ALA A 542 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N ILE A 547 " --> pdb=" O ASN A 543 " (cutoff:3.500A) Processing helix chain 'B' and resid 210 through 215 Processing helix chain 'G' and resid 27 through 35 removed outlier: 3.670A pdb=" N SER G 31 " --> pdb=" O SER G 27 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N PHE G 32 " --> pdb=" O VAL G 28 " (cutoff:3.500A) Processing helix chain 'G' and resid 38 through 40 No H-bonds generated for 'chain 'G' and resid 38 through 40' Processing helix chain 'G' and resid 57 through 67 removed outlier: 3.960A pdb=" N PHE G 61 " --> pdb=" O VAL G 57 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N PHE G 62 " --> pdb=" O LYS G 58 " (cutoff:3.500A) Processing helix chain 'G' and resid 88 through 97 Processing helix chain 'G' and resid 107 through 111 Processing helix chain 'G' and resid 114 through 121 removed outlier: 3.578A pdb=" N GLU G 119 " --> pdb=" O GLU G 115 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N VAL G 120 " --> pdb=" O THR G 116 " (cutoff:3.500A) Processing helix chain 'G' and resid 138 through 147 removed outlier: 3.648A pdb=" N ARG G 147 " --> pdb=" O SER G 143 " (cutoff:3.500A) Processing helix chain 'G' and resid 169 through 177 Processing helix chain 'G' and resid 193 through 196 No H-bonds generated for 'chain 'G' and resid 193 through 196' Processing helix chain 'G' and resid 213 through 222 Processing helix chain 'G' and resid 244 through 251 removed outlier: 3.599A pdb=" N ASN G 248 " --> pdb=" O ASP G 245 " (cutoff:3.500A) Processing helix chain 'G' and resid 262 through 266 Processing helix chain 'G' and resid 285 through 294 removed outlier: 3.575A pdb=" N GLU G 294 " --> pdb=" O ASN G 290 " (cutoff:3.500A) Processing helix chain 'G' and resid 315 through 323 removed outlier: 3.708A pdb=" N GLN G 320 " --> pdb=" O SER G 316 " (cutoff:3.500A) Processing helix chain 'M' and resid 17 through 31 removed outlier: 3.694A pdb=" N ASP M 30 " --> pdb=" O LYS M 26 " (cutoff:3.500A) Processing helix chain 'M' and resid 43 through 51 Proline residue: M 48 - end of helix Processing helix chain 'M' and resid 67 through 72 Processing helix chain 'M' and resid 83 through 87 Processing helix chain 'M' and resid 91 through 97 removed outlier: 3.779A pdb=" N VAL M 97 " --> pdb=" O THR M 93 " (cutoff:3.500A) Processing helix chain 'M' and resid 131 through 142 removed outlier: 3.693A pdb=" N GLU M 138 " --> pdb=" O ALA M 134 " (cutoff:3.500A) removed outlier: 4.074A pdb=" N ALA M 141 " --> pdb=" O LYS M 137 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N LYS M 142 " --> pdb=" O GLU M 138 " (cutoff:3.500A) Processing helix chain 'M' and resid 154 through 164 Proline residue: M 159 - end of helix removed outlier: 5.064A pdb=" N ASP M 164 " --> pdb=" O LEU M 160 " (cutoff:3.500A) Processing helix chain 'M' and resid 186 through 200 removed outlier: 3.692A pdb=" N ILE M 199 " --> pdb=" O LEU M 195 " (cutoff:3.500A) Processing helix chain 'M' and resid 210 through 218 Processing helix chain 'M' and resid 229 through 237 removed outlier: 4.116A pdb=" N SER M 233 " --> pdb=" O TRP M 230 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N THR M 237 " --> pdb=" O ASN M 234 " (cutoff:3.500A) Processing helix chain 'M' and resid 273 through 283 Processing helix chain 'M' and resid 287 through 296 removed outlier: 3.876A pdb=" N GLU M 291 " --> pdb=" O ASP M 287 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N ALA M 292 " --> pdb=" O GLU M 288 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N VAL M 293 " --> pdb=" O GLY M 289 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N ASP M 296 " --> pdb=" O ALA M 292 " (cutoff:3.500A) Processing helix chain 'M' and resid 305 through 313 removed outlier: 3.867A pdb=" N GLU M 310 " --> pdb=" O SER M 306 " (cutoff:3.500A) removed outlier: 5.097A pdb=" N LYS M 313 " --> pdb=" O GLU M 309 " (cutoff:3.500A) Processing helix chain 'M' and resid 315 through 325 Processing helix chain 'M' and resid 334 through 351 removed outlier: 4.082A pdb=" N TRP M 340 " --> pdb=" O SER M 337 " (cutoff:3.500A) removed outlier: 4.147A pdb=" N TYR M 341 " --> pdb=" O ALA M 338 " (cutoff:3.500A) Processing helix chain 'M' and resid 357 through 366 Processing helix chain 'L' and resid 123 through 127 removed outlier: 3.626A pdb=" N LYS L 127 " --> pdb=" O ASP L 123 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 123 through 127' Processing helix chain 'L' and resid 151 through 153 No H-bonds generated for 'chain 'L' and resid 151 through 153' Processing helix chain 'H' and resid 65 through 67 No H-bonds generated for 'chain 'H' and resid 65 through 67' Processing helix chain 'H' and resid 202 through 204 No H-bonds generated for 'chain 'H' and resid 202 through 204' Processing helix chain 'N' and resid 97 through 99 No H-bonds generated for 'chain 'N' and resid 97 through 99' Processing sheet with id= A, first strand: chain 'A' and resid 18 through 20 Processing sheet with id= B, first strand: chain 'A' and resid 402 through 404 Processing sheet with id= C, first strand: chain 'A' and resid 23 through 26 removed outlier: 7.259A pdb=" N VAL A 32 " --> pdb=" O LEU A 24 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 250 through 255 removed outlier: 3.533A pdb=" N LYS B 270 " --> pdb=" O MET B 251 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'G' and resid 50 through 52 removed outlier: 7.547A pdb=" N PHE G 51 " --> pdb=" O ALA G 71 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N GLY G 84 " --> pdb=" O LEU G 74 " (cutoff:3.500A) removed outlier: 6.641A pdb=" N ASP G 76 " --> pdb=" O PHE G 82 " (cutoff:3.500A) removed outlier: 6.130A pdb=" N PHE G 82 " --> pdb=" O ASP G 76 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'G' and resid 278 through 280 removed outlier: 8.269A pdb=" N CYS G 279 " --> pdb=" O ARG G 299 " (cutoff:3.500A) removed outlier: 6.357A pdb=" N VAL G 301 " --> pdb=" O CYS G 279 " (cutoff:3.500A) removed outlier: 4.140A pdb=" N GLY G 311 " --> pdb=" O VAL G 302 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'M' and resid 7 through 10 Processing sheet with id= H, first strand: chain 'M' and resid 59 through 63 removed outlier: 5.918A pdb=" N ALA M 264 " --> pdb=" O PRO M 107 " (cutoff:3.500A) removed outlier: 8.072A pdb=" N ILE M 266 " --> pdb=" O ALA M 105 " (cutoff:3.500A) removed outlier: 7.749A pdb=" N ALA M 105 " --> pdb=" O ILE M 266 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'M' and resid 224 through 227 removed outlier: 3.908A pdb=" N ASN M 227 " --> pdb=" O SER M 114 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N SER M 114 " --> pdb=" O ASN M 227 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'L' and resid 12 through 14 removed outlier: 4.156A pdb=" N GLU L 106 " --> pdb=" O LEU L 12 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'L' and resid 20 through 25 removed outlier: 3.522A pdb=" N VAL L 20 " --> pdb=" O ILE L 76 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'L' and resid 86 through 91 removed outlier: 3.866A pdb=" N ILE L 49 " --> pdb=" O TRP L 36 " (cutoff:3.500A) removed outlier: 6.103A pdb=" N GLN L 38 " --> pdb=" O LEU L 47 " (cutoff:3.500A) removed outlier: 5.170A pdb=" N LEU L 47 " --> pdb=" O GLN L 38 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'L' and resid 115 through 119 removed outlier: 4.207A pdb=" N VAL L 134 " --> pdb=" O PHE L 119 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N CYS L 135 " --> pdb=" O SER L 178 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N SER L 178 " --> pdb=" O CYS L 135 " (cutoff:3.500A) removed outlier: 5.502A pdb=" N TYR L 174 " --> pdb=" O ASN L 139 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'L' and resid 145 through 149 removed outlier: 3.581A pdb=" N LYS L 146 " --> pdb=" O THR L 198 " (cutoff:3.500A) removed outlier: 4.422A pdb=" N TYR L 193 " --> pdb=" O PHE L 210 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N PHE L 210 " --> pdb=" O TYR L 193 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N CYS L 195 " --> pdb=" O LYS L 208 " (cutoff:3.500A) removed outlier: 4.166A pdb=" N LYS L 208 " --> pdb=" O CYS L 195 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N VAL L 197 " --> pdb=" O VAL L 206 " (cutoff:3.500A) removed outlier: 4.259A pdb=" N VAL L 206 " --> pdb=" O VAL L 197 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'H' and resid 6 through 10 removed outlier: 3.596A pdb=" N SER H 28 " --> pdb=" O GLN H 6 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N VAL H 8 " --> pdb=" O ALA H 26 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'H' and resid 13 through 15 removed outlier: 3.512A pdb=" N ALA H 95 " --> pdb=" O VAL H 125 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'H' and resid 21 through 23 removed outlier: 3.675A pdb=" N LEU H 23 " --> pdb=" O LEU H 84 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'H' and resid 60 through 63 removed outlier: 3.530A pdb=" N SER H 53 " --> pdb=" O SER H 62 " (cutoff:3.500A) removed outlier: 6.945A pdb=" N TRP H 39 " --> pdb=" O VAL H 51 " (cutoff:3.500A) removed outlier: 4.595A pdb=" N SER H 53 " --> pdb=" O ILE H 37 " (cutoff:3.500A) removed outlier: 7.161A pdb=" N ILE H 37 " --> pdb=" O SER H 53 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'H' and resid 136 through 140 removed outlier: 3.524A pdb=" N LYS H 159 " --> pdb=" O SER H 136 " (cutoff:3.500A) removed outlier: 4.459A pdb=" N GLY H 155 " --> pdb=" O LEU H 140 " (cutoff:3.500A) removed outlier: 5.976A pdb=" N TYR H 192 " --> pdb=" O ASP H 160 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'H' and resid 166 through 169 removed outlier: 4.864A pdb=" N TYR H 210 " --> pdb=" O VAL H 227 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'N' and resid 14 through 17 removed outlier: 3.585A pdb=" N CYS N 31 " --> pdb=" O VAL N 88 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'N' and resid 123 through 126 removed outlier: 3.562A pdb=" N VAL N 102 " --> pdb=" O GLN N 48 " (cutoff:3.500A) removed outlier: 4.206A pdb=" N SER N 44 " --> pdb=" O ALA N 106 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N MET N 43 " --> pdb=" O ALA N 60 " (cutoff:3.500A) removed outlier: 5.299A pdb=" N ARG N 47 " --> pdb=" O PHE N 56 " (cutoff:3.500A) removed outlier: 4.807A pdb=" N PHE N 56 " --> pdb=" O ARG N 47 " (cutoff:3.500A) Processing sheet with id= W, first strand: chain 'N' and resid 106 through 108 removed outlier: 3.772A pdb=" N TYR N 119 " --> pdb=" O ILE N 107 " (cutoff:3.500A) 366 hydrogen bonds defined for protein. 933 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.59 Time building geometry restraints manager: 5.65 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 4249 1.34 - 1.46: 3141 1.46 - 1.58: 6258 1.58 - 1.70: 9 1.70 - 1.82: 81 Bond restraints: 13738 Sorted by residual: bond pdb=" C4 ATP G 401 " pdb=" C5 ATP G 401 " ideal model delta sigma weight residual 1.388 1.470 -0.082 1.00e-02 1.00e+04 6.77e+01 bond pdb=" C5 ATP G 401 " pdb=" C6 ATP G 401 " ideal model delta sigma weight residual 1.409 1.482 -0.073 1.00e-02 1.00e+04 5.29e+01 bond pdb=" C8 ATP G 401 " pdb=" N7 ATP G 401 " ideal model delta sigma weight residual 1.310 1.357 -0.047 1.00e-02 1.00e+04 2.23e+01 bond pdb=" C5 ATP G 401 " pdb=" N7 ATP G 401 " ideal model delta sigma weight residual 1.387 1.345 0.042 1.00e-02 1.00e+04 1.73e+01 bond pdb=" C4 ATP G 401 " pdb=" N9 ATP G 401 " ideal model delta sigma weight residual 1.374 1.334 0.040 1.00e-02 1.00e+04 1.60e+01 ... (remaining 13733 not shown) Histogram of bond angle deviations from ideal: 99.83 - 107.11: 501 107.11 - 114.39: 7899 114.39 - 121.68: 6994 121.68 - 128.96: 3167 128.96 - 136.24: 98 Bond angle restraints: 18659 Sorted by residual: angle pdb=" PB ATP G 401 " pdb=" O3B ATP G 401 " pdb=" PG ATP G 401 " ideal model delta sigma weight residual 139.87 121.07 18.80 1.00e+00 1.00e+00 3.53e+02 angle pdb=" PA ATP G 401 " pdb=" O3A ATP G 401 " pdb=" PB ATP G 401 " ideal model delta sigma weight residual 136.83 121.31 15.52 1.00e+00 1.00e+00 2.41e+02 angle pdb=" C5 ATP G 401 " pdb=" C4 ATP G 401 " pdb=" N3 ATP G 401 " ideal model delta sigma weight residual 126.80 118.69 8.11 1.00e+00 1.00e+00 6.57e+01 angle pdb=" N3 ATP G 401 " pdb=" C4 ATP G 401 " pdb=" N9 ATP G 401 " ideal model delta sigma weight residual 127.04 134.97 -7.93 1.15e+00 7.59e-01 4.77e+01 angle pdb=" N1 ATP G 401 " pdb=" C2 ATP G 401 " pdb=" N3 ATP G 401 " ideal model delta sigma weight residual 128.69 123.59 5.10 1.00e+00 1.00e+00 2.60e+01 ... (remaining 18654 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.71: 8142 23.71 - 47.41: 127 47.41 - 71.12: 10 71.12 - 94.82: 5 94.82 - 118.53: 1 Dihedral angle restraints: 8285 sinusoidal: 3327 harmonic: 4958 Sorted by residual: dihedral pdb=" CB CYS L 135 " pdb=" SG CYS L 135 " pdb=" SG CYS L 195 " pdb=" CB CYS L 195 " ideal model delta sinusoidal sigma weight residual 93.00 19.66 73.34 1 1.00e+01 1.00e-02 6.85e+01 dihedral pdb=" C5' AMP G 403 " pdb=" O5' AMP G 403 " pdb=" P AMP G 403 " pdb=" O3P AMP G 403 " ideal model delta sinusoidal sigma weight residual -60.00 58.53 -118.53 1 2.00e+01 2.50e-03 3.55e+01 dihedral pdb=" CA ASN A 69 " pdb=" C ASN A 69 " pdb=" N LEU A 70 " pdb=" CA LEU A 70 " ideal model delta harmonic sigma weight residual -180.00 -162.23 -17.77 0 5.00e+00 4.00e-02 1.26e+01 ... (remaining 8282 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.079: 1851 0.079 - 0.159: 221 0.159 - 0.238: 12 0.238 - 0.318: 0 0.318 - 0.397: 2 Chirality restraints: 2086 Sorted by residual: chirality pdb=" C1 GLC C 2 " pdb=" O4 GLC C 1 " pdb=" C2 GLC C 2 " pdb=" O5 GLC C 2 " both_signs ideal model delta sigma weight residual False 2.40 2.31 0.09 2.00e-02 2.50e+03 1.88e+01 chirality pdb=" CB ILE G 106 " pdb=" CA ILE G 106 " pdb=" CG1 ILE G 106 " pdb=" CG2 ILE G 106 " both_signs ideal model delta sigma weight residual False 2.64 2.25 0.40 2.00e-01 2.50e+01 3.94e+00 chirality pdb=" C1 GLC C 1 " pdb=" C2 GLC C 1 " pdb=" O1 GLC C 1 " pdb=" O5 GLC C 1 " both_signs ideal model delta sigma weight residual False -2.04 -2.38 0.34 2.00e-01 2.50e+01 2.81e+00 ... (remaining 2083 not shown) Planarity restraints: 2359 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C SER L 8 " 0.040 5.00e-02 4.00e+02 6.05e-02 5.86e+00 pdb=" N PRO L 9 " -0.105 5.00e-02 4.00e+02 pdb=" CA PRO L 9 " 0.032 5.00e-02 4.00e+02 pdb=" CD PRO L 9 " 0.033 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASN A 430 " 0.037 5.00e-02 4.00e+02 5.61e-02 5.04e+00 pdb=" N PRO A 431 " -0.097 5.00e-02 4.00e+02 pdb=" CA PRO A 431 " 0.029 5.00e-02 4.00e+02 pdb=" CD PRO A 431 " 0.031 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS A 143 " 0.033 5.00e-02 4.00e+02 5.06e-02 4.09e+00 pdb=" N PRO A 144 " -0.087 5.00e-02 4.00e+02 pdb=" CA PRO A 144 " 0.026 5.00e-02 4.00e+02 pdb=" CD PRO A 144 " 0.028 5.00e-02 4.00e+02 ... (remaining 2356 not shown) Histogram of nonbonded interaction distances: 1.33 - 2.04: 1 2.04 - 2.76: 1332 2.76 - 3.47: 17904 3.47 - 4.19: 31071 4.19 - 4.90: 53499 Nonbonded interactions: 103807 Sorted by model distance: nonbonded pdb=" N VAL A 13 " pdb=" C PHE M 371 " model vdw 1.328 3.350 nonbonded pdb=" N VAL A 13 " pdb=" O PHE M 371 " model vdw 2.252 2.520 nonbonded pdb=" OE1 GLU M 111 " pdb=" O2 GLC C 1 " model vdw 2.300 2.440 nonbonded pdb=" OG SER L 64 " pdb=" OG1 THR L 75 " model vdw 2.310 2.440 nonbonded pdb=" OG1 THR G 89 " pdb=" O1B ADP G 402 " model vdw 2.347 2.440 ... (remaining 103802 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.570 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: 3.590 Check model and map are aligned: 0.210 Set scattering table: 0.130 Process input model: 37.790 Find NCS groups from input model: 0.380 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.810 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 45.540 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7519 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 : 0.003 0.082 13738 Z= 0.226 Angle : 0.772 18.796 18659 Z= 0.441 Chirality : 0.051 0.397 2086 Planarity : 0.007 0.061 2359 Dihedral : 9.112 118.528 5088 Min Nonbonded Distance : 1.328 Molprobity Statistics. All-atom Clashscore : 5.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.97 % Favored : 97.03 % Rotamer: Outliers : 0.00 % Allowed : 1.71 % Favored : 98.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % 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: -3.32 (0.17), residues: 1682 helix: -2.88 (0.16), residues: 434 sheet: -1.80 (0.27), residues: 327 loop : -1.98 (0.18), residues: 921 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP H 119 HIS 0.006 0.001 HIS G 36 PHE 0.029 0.002 PHE A 225 TYR 0.016 0.002 TYR H 102 ARG 0.012 0.001 ARG A 435 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3364 Ramachandran restraints generated. 1682 Oldfield, 0 Emsley, 1682 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3364 Ramachandran restraints generated. 1682 Oldfield, 0 Emsley, 1682 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 460 residues out of total 1464 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 460 time to evaluate : 1.501 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 69 ASN cc_start: 0.7035 (t0) cc_final: 0.6476 (t0) REVERT: A 99 SER cc_start: 0.8405 (m) cc_final: 0.8102 (t) REVERT: A 222 PRO cc_start: 0.9282 (Cg_exo) cc_final: 0.8975 (Cg_endo) REVERT: B 192 GLU cc_start: 0.6717 (pt0) cc_final: 0.6341 (tt0) REVERT: B 193 MET cc_start: 0.7938 (mtt) cc_final: 0.7571 (mpp) REVERT: B 252 VAL cc_start: 0.8328 (t) cc_final: 0.7904 (t) REVERT: G 75 TRP cc_start: 0.7190 (t-100) cc_final: 0.6902 (t-100) REVERT: G 143 SER cc_start: 0.8540 (t) cc_final: 0.8225 (p) REVERT: G 169 HIS cc_start: 0.7884 (m-70) cc_final: 0.7384 (m170) REVERT: G 189 MET cc_start: 0.9024 (mmt) cc_final: 0.8783 (mmt) REVERT: G 319 LEU cc_start: 0.9056 (mt) cc_final: 0.8336 (tp) REVERT: M 67 PHE cc_start: 0.8835 (m-10) cc_final: 0.8088 (m-80) REVERT: M 94 TRP cc_start: 0.7809 (m100) cc_final: 0.7489 (m100) REVERT: M 113 LEU cc_start: 0.8276 (mt) cc_final: 0.7944 (mt) REVERT: M 365 GLN cc_start: 0.8581 (tp40) cc_final: 0.8214 (tp40) REVERT: L 83 ASP cc_start: 0.7388 (m-30) cc_final: 0.6407 (m-30) REVERT: L 97 ILE cc_start: 0.9073 (mt) cc_final: 0.8865 (mm) REVERT: L 203 SER cc_start: 0.7023 (t) cc_final: 0.5981 (p) REVERT: H 213 ASN cc_start: 0.8350 (m110) cc_final: 0.7655 (m-40) REVERT: N 45 TRP cc_start: 0.7203 (m100) cc_final: 0.6799 (m100) REVERT: N 82 ASP cc_start: 0.7148 (t70) cc_final: 0.6780 (t70) outliers start: 0 outliers final: 0 residues processed: 460 average time/residue: 0.2835 time to fit residues: 179.5153 Evaluate side-chains 238 residues out of total 1464 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 238 time to evaluate : 1.600 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 167 random chunks: chunk 141 optimal weight: 7.9990 chunk 126 optimal weight: 0.9980 chunk 70 optimal weight: 3.9990 chunk 43 optimal weight: 10.0000 chunk 85 optimal weight: 8.9990 chunk 67 optimal weight: 2.9990 chunk 130 optimal weight: 4.9990 chunk 50 optimal weight: 5.9990 chunk 79 optimal weight: 0.0570 chunk 97 optimal weight: 10.0000 chunk 151 optimal weight: 0.4980 overall best weight: 1.7102 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 135 HIS A 146 ASN ** A 220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 222 ASN G 112 HIS G 223 HIS ** G 248 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 290 ASN M 64 HIS M 86 GLN M 365 GLN ** L 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 12 GLN N 86 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7808 moved from start: 0.3484 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 13738 Z= 0.241 Angle : 0.662 10.471 18659 Z= 0.336 Chirality : 0.043 0.196 2086 Planarity : 0.005 0.055 2359 Dihedral : 5.827 88.798 1937 Min Nonbonded Distance : 2.120 Molprobity Statistics. All-atom Clashscore : 15.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.63 % Favored : 96.37 % Rotamer: Outliers : 2.66 % Allowed : 12.57 % Favored : 84.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % 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: -2.15 (0.19), residues: 1682 helix: -1.45 (0.21), residues: 435 sheet: -1.25 (0.27), residues: 330 loop : -1.43 (0.19), residues: 917 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP M 10 HIS 0.006 0.001 HIS B 211 PHE 0.029 0.002 PHE M 279 TYR 0.024 0.001 TYR H 109 ARG 0.006 0.001 ARG L 25 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3364 Ramachandran restraints generated. 1682 Oldfield, 0 Emsley, 1682 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3364 Ramachandran restraints generated. 1682 Oldfield, 0 Emsley, 1682 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 294 residues out of total 1464 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 255 time to evaluate : 1.613 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 99 SER cc_start: 0.8425 (m) cc_final: 0.8210 (t) REVERT: A 535 ILE cc_start: 0.9524 (mm) cc_final: 0.9214 (tp) REVERT: B 237 MET cc_start: 0.7703 (ptp) cc_final: 0.7163 (mpp) REVERT: G 159 GLU cc_start: 0.8251 (mt-10) cc_final: 0.7872 (tp30) REVERT: G 169 HIS cc_start: 0.8239 (m-70) cc_final: 0.7776 (m170) REVERT: G 259 ASP cc_start: 0.8567 (OUTLIER) cc_final: 0.8088 (p0) REVERT: G 319 LEU cc_start: 0.9156 (mt) cc_final: 0.8436 (tp) REVERT: G 320 GLN cc_start: 0.8728 (tp40) cc_final: 0.8187 (mm-40) REVERT: M 67 PHE cc_start: 0.8921 (m-10) cc_final: 0.8631 (m-80) REVERT: M 94 TRP cc_start: 0.8041 (m100) cc_final: 0.7484 (m100) REVERT: M 148 MET cc_start: 0.7608 (tpp) cc_final: 0.6996 (tpp) REVERT: M 224 MET cc_start: 0.8528 (mtm) cc_final: 0.8298 (ptp) REVERT: M 321 MET cc_start: 0.9012 (mmm) cc_final: 0.8626 (mmp) REVERT: L 34 VAL cc_start: 0.9261 (t) cc_final: 0.8928 (p) REVERT: L 97 ILE cc_start: 0.9168 (mt) cc_final: 0.8917 (mm) REVERT: L 136 LEU cc_start: 0.9232 (tp) cc_final: 0.8994 (tt) REVERT: L 138 ASN cc_start: 0.8387 (t0) cc_final: 0.8084 (t0) REVERT: H 71 PHE cc_start: 0.7045 (m-10) cc_final: 0.6749 (m-10) REVERT: N 45 TRP cc_start: 0.6983 (m100) cc_final: 0.6396 (m100) outliers start: 39 outliers final: 25 residues processed: 283 average time/residue: 0.2636 time to fit residues: 107.1990 Evaluate side-chains 212 residues out of total 1464 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 186 time to evaluate : 1.541 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 VAL Chi-restraints excluded: chain A residue 127 SER Chi-restraints excluded: chain A residue 197 VAL Chi-restraints excluded: chain A residue 202 SER Chi-restraints excluded: chain A residue 204 VAL Chi-restraints excluded: chain A residue 205 ILE Chi-restraints excluded: chain A residue 251 LEU Chi-restraints excluded: chain B residue 216 ILE Chi-restraints excluded: chain G residue 38 CYS Chi-restraints excluded: chain G residue 56 GLN Chi-restraints excluded: chain G residue 240 ILE Chi-restraints excluded: chain G residue 259 ASP Chi-restraints excluded: chain G residue 301 VAL Chi-restraints excluded: chain M residue 61 PHE Chi-restraints excluded: chain M residue 115 LEU Chi-restraints excluded: chain M residue 255 SER Chi-restraints excluded: chain M residue 366 THR Chi-restraints excluded: chain L residue 48 LEU Chi-restraints excluded: chain L residue 49 ILE Chi-restraints excluded: chain L residue 64 SER Chi-restraints excluded: chain L residue 98 THR Chi-restraints excluded: chain H residue 14 LEU Chi-restraints excluded: chain N residue 12 GLN Chi-restraints excluded: chain N residue 31 CYS Chi-restraints excluded: chain N residue 95 LEU Chi-restraints excluded: chain N residue 124 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 167 random chunks: chunk 84 optimal weight: 10.0000 chunk 47 optimal weight: 9.9990 chunk 126 optimal weight: 7.9990 chunk 103 optimal weight: 7.9990 chunk 41 optimal weight: 20.0000 chunk 151 optimal weight: 1.9990 chunk 164 optimal weight: 20.0000 chunk 135 optimal weight: 0.8980 chunk 150 optimal weight: 9.9990 chunk 51 optimal weight: 0.9990 chunk 121 optimal weight: 3.9990 overall best weight: 3.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 67 ASN G 105 GLN ** G 248 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 86 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8007 moved from start: 0.4868 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.106 13738 Z= 0.367 Angle : 0.715 9.107 18659 Z= 0.361 Chirality : 0.043 0.148 2086 Planarity : 0.005 0.046 2359 Dihedral : 6.131 80.513 1937 Min Nonbonded Distance : 2.139 Molprobity Statistics. All-atom Clashscore : 19.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.10 % Favored : 95.90 % Rotamer: Outliers : 3.76 % Allowed : 14.28 % Favored : 81.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % 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: -1.51 (0.20), residues: 1682 helix: -0.72 (0.24), residues: 416 sheet: -1.29 (0.26), residues: 357 loop : -0.92 (0.21), residues: 909 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP M 10 HIS 0.007 0.001 HIS G 223 PHE 0.024 0.002 PHE M 279 TYR 0.030 0.002 TYR B 242 ARG 0.011 0.001 ARG A 134 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3364 Ramachandran restraints generated. 1682 Oldfield, 0 Emsley, 1682 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3364 Ramachandran restraints generated. 1682 Oldfield, 0 Emsley, 1682 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 262 residues out of total 1464 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 207 time to evaluate : 1.533 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 105 ASP cc_start: 0.8726 (m-30) cc_final: 0.7837 (m-30) REVERT: A 535 ILE cc_start: 0.9410 (mm) cc_final: 0.9203 (tp) REVERT: B 258 ARG cc_start: 0.8303 (tpt-90) cc_final: 0.7481 (tpt-90) REVERT: G 33 MET cc_start: 0.8584 (mtm) cc_final: 0.8336 (ttp) REVERT: G 98 TYR cc_start: 0.7910 (m-10) cc_final: 0.7547 (m-80) REVERT: G 105 GLN cc_start: 0.8282 (OUTLIER) cc_final: 0.7939 (tm-30) REVERT: G 159 GLU cc_start: 0.8373 (mt-10) cc_final: 0.7935 (tp30) REVERT: G 230 VAL cc_start: 0.9070 (m) cc_final: 0.8864 (p) REVERT: G 259 ASP cc_start: 0.8684 (OUTLIER) cc_final: 0.8280 (p0) REVERT: M 67 PHE cc_start: 0.8987 (m-10) cc_final: 0.8517 (m-80) REVERT: M 94 TRP cc_start: 0.8119 (m100) cc_final: 0.7611 (m100) REVERT: M 321 MET cc_start: 0.9029 (mmm) cc_final: 0.8806 (mmm) REVERT: L 97 ILE cc_start: 0.9294 (mt) cc_final: 0.9030 (mm) REVERT: L 140 PHE cc_start: 0.8865 (p90) cc_final: 0.8580 (p90) REVERT: H 113 MET cc_start: 0.8062 (tmm) cc_final: 0.7850 (tmm) REVERT: N 12 GLN cc_start: 0.6043 (OUTLIER) cc_final: 0.4597 (pp30) REVERT: N 41 TYR cc_start: 0.6888 (m-80) cc_final: 0.6286 (m-80) outliers start: 55 outliers final: 35 residues processed: 248 average time/residue: 0.2402 time to fit residues: 87.8880 Evaluate side-chains 215 residues out of total 1464 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 177 time to evaluate : 1.462 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 VAL Chi-restraints excluded: chain A residue 34 VAL Chi-restraints excluded: chain A residue 98 VAL Chi-restraints excluded: chain A residue 107 ILE Chi-restraints excluded: chain A residue 127 SER Chi-restraints excluded: chain A residue 148 LEU Chi-restraints excluded: chain A residue 191 LEU Chi-restraints excluded: chain A residue 202 SER Chi-restraints excluded: chain A residue 204 VAL Chi-restraints excluded: chain A residue 205 ILE Chi-restraints excluded: chain A residue 224 LEU Chi-restraints excluded: chain A residue 251 LEU Chi-restraints excluded: chain A residue 456 VAL Chi-restraints excluded: chain B residue 216 ILE Chi-restraints excluded: chain G residue 38 CYS Chi-restraints excluded: chain G residue 56 GLN Chi-restraints excluded: chain G residue 105 GLN Chi-restraints excluded: chain G residue 213 VAL Chi-restraints excluded: chain G residue 228 LEU Chi-restraints excluded: chain G residue 240 ILE Chi-restraints excluded: chain G residue 259 ASP Chi-restraints excluded: chain G residue 301 VAL Chi-restraints excluded: chain M residue 61 PHE Chi-restraints excluded: chain M residue 209 ASP Chi-restraints excluded: chain M residue 255 SER Chi-restraints excluded: chain M residue 366 THR Chi-restraints excluded: chain L residue 48 LEU Chi-restraints excluded: chain L residue 49 ILE Chi-restraints excluded: chain L residue 64 SER Chi-restraints excluded: chain L residue 98 THR Chi-restraints excluded: chain H residue 32 ILE Chi-restraints excluded: chain H residue 180 HIS Chi-restraints excluded: chain N residue 12 GLN Chi-restraints excluded: chain N residue 13 LEU Chi-restraints excluded: chain N residue 31 CYS Chi-restraints excluded: chain N residue 47 ARG Chi-restraints excluded: chain N residue 95 LEU Chi-restraints excluded: chain N residue 100 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 167 random chunks: chunk 150 optimal weight: 0.6980 chunk 114 optimal weight: 8.9990 chunk 78 optimal weight: 9.9990 chunk 16 optimal weight: 10.0000 chunk 72 optimal weight: 1.9990 chunk 102 optimal weight: 3.9990 chunk 152 optimal weight: 6.9990 chunk 161 optimal weight: 5.9990 chunk 79 optimal weight: 8.9990 chunk 144 optimal weight: 0.9980 chunk 43 optimal weight: 4.9990 overall best weight: 2.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 222 ASN G 67 ASN ** G 248 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 290 ASN ** M 203 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 139 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 180 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8034 moved from start: 0.5377 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.072 13738 Z= 0.285 Angle : 0.656 8.877 18659 Z= 0.328 Chirality : 0.042 0.140 2086 Planarity : 0.004 0.046 2359 Dihedral : 5.995 82.532 1937 Min Nonbonded Distance : 2.165 Molprobity Statistics. All-atom Clashscore : 18.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.98 % Favored : 96.02 % Rotamer: Outliers : 3.35 % Allowed : 16.33 % Favored : 80.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % 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: -1.26 (0.20), residues: 1682 helix: -0.52 (0.24), residues: 430 sheet: -1.05 (0.26), residues: 370 loop : -0.80 (0.22), residues: 882 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP N 45 HIS 0.005 0.001 HIS A 220 PHE 0.020 0.002 PHE M 279 TYR 0.020 0.002 TYR H 109 ARG 0.006 0.001 ARG B 258 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3364 Ramachandran restraints generated. 1682 Oldfield, 0 Emsley, 1682 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3364 Ramachandran restraints generated. 1682 Oldfield, 0 Emsley, 1682 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 248 residues out of total 1464 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 199 time to evaluate : 1.529 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 398 TRP cc_start: 0.6913 (OUTLIER) cc_final: 0.6662 (m-10) REVERT: A 535 ILE cc_start: 0.9427 (mm) cc_final: 0.9049 (tp) REVERT: B 237 MET cc_start: 0.7619 (ptp) cc_final: 0.7082 (mpp) REVERT: B 242 TYR cc_start: 0.7351 (m-80) cc_final: 0.6611 (m-80) REVERT: G 33 MET cc_start: 0.8564 (mtm) cc_final: 0.8282 (ttp) REVERT: G 75 TRP cc_start: 0.7648 (t-100) cc_final: 0.7218 (t-100) REVERT: G 98 TYR cc_start: 0.8126 (m-10) cc_final: 0.7840 (m-80) REVERT: G 159 GLU cc_start: 0.8414 (mt-10) cc_final: 0.7960 (tp30) REVERT: G 259 ASP cc_start: 0.8709 (OUTLIER) cc_final: 0.8420 (p0) REVERT: G 317 ASP cc_start: 0.8586 (OUTLIER) cc_final: 0.8099 (p0) REVERT: G 320 GLN cc_start: 0.8682 (tp40) cc_final: 0.8304 (mm110) REVERT: M 42 LYS cc_start: 0.9025 (mmtm) cc_final: 0.8429 (mmmt) REVERT: M 67 PHE cc_start: 0.8997 (m-10) cc_final: 0.8526 (m-80) REVERT: M 94 TRP cc_start: 0.8261 (m100) cc_final: 0.7620 (m100) REVERT: M 148 MET cc_start: 0.8204 (tpp) cc_final: 0.7837 (tpp) REVERT: M 204 MET cc_start: 0.6589 (tpt) cc_final: 0.6273 (tpt) REVERT: M 344 ARG cc_start: 0.8958 (ttp-170) cc_final: 0.8757 (ttp-170) REVERT: L 83 ASP cc_start: 0.8093 (m-30) cc_final: 0.7826 (t70) REVERT: L 97 ILE cc_start: 0.9290 (mt) cc_final: 0.9033 (mm) REVERT: L 138 ASN cc_start: 0.8782 (t0) cc_final: 0.8458 (t0) REVERT: H 110 TYR cc_start: 0.8268 (p90) cc_final: 0.8047 (p90) REVERT: H 113 MET cc_start: 0.8066 (tmm) cc_final: 0.7735 (tmm) REVERT: N 41 TYR cc_start: 0.7120 (m-80) cc_final: 0.6877 (m-80) REVERT: N 45 TRP cc_start: 0.6482 (m100) cc_final: 0.6195 (m100) REVERT: N 91 GLN cc_start: 0.8004 (tp-100) cc_final: 0.7607 (tm-30) outliers start: 49 outliers final: 31 residues processed: 232 average time/residue: 0.2333 time to fit residues: 80.5502 Evaluate side-chains 207 residues out of total 1464 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 173 time to evaluate : 1.574 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 VAL Chi-restraints excluded: chain A residue 98 VAL Chi-restraints excluded: chain A residue 107 ILE Chi-restraints excluded: chain A residue 191 LEU Chi-restraints excluded: chain A residue 202 SER Chi-restraints excluded: chain A residue 204 VAL Chi-restraints excluded: chain A residue 205 ILE Chi-restraints excluded: chain A residue 224 LEU Chi-restraints excluded: chain A residue 251 LEU Chi-restraints excluded: chain A residue 398 TRP Chi-restraints excluded: chain A residue 422 LEU Chi-restraints excluded: chain A residue 456 VAL Chi-restraints excluded: chain B residue 256 THR Chi-restraints excluded: chain B residue 264 VAL Chi-restraints excluded: chain G residue 83 VAL Chi-restraints excluded: chain G residue 173 LEU Chi-restraints excluded: chain G residue 228 LEU Chi-restraints excluded: chain G residue 240 ILE Chi-restraints excluded: chain G residue 258 LEU Chi-restraints excluded: chain G residue 259 ASP Chi-restraints excluded: chain G residue 301 VAL Chi-restraints excluded: chain G residue 317 ASP Chi-restraints excluded: chain M residue 61 PHE Chi-restraints excluded: chain M residue 366 THR Chi-restraints excluded: chain L residue 48 LEU Chi-restraints excluded: chain L residue 49 ILE Chi-restraints excluded: chain L residue 103 THR Chi-restraints excluded: chain H residue 137 VAL Chi-restraints excluded: chain H residue 180 HIS Chi-restraints excluded: chain N residue 13 LEU Chi-restraints excluded: chain N residue 31 CYS Chi-restraints excluded: chain N residue 47 ARG Chi-restraints excluded: chain N residue 95 LEU Chi-restraints excluded: chain N residue 100 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 167 random chunks: chunk 134 optimal weight: 6.9990 chunk 91 optimal weight: 7.9990 chunk 2 optimal weight: 2.9990 chunk 120 optimal weight: 1.9990 chunk 66 optimal weight: 0.0050 chunk 137 optimal weight: 0.5980 chunk 111 optimal weight: 0.9980 chunk 0 optimal weight: 0.6980 chunk 82 optimal weight: 6.9990 chunk 144 optimal weight: 0.7980 chunk 40 optimal weight: 0.0270 overall best weight: 0.4252 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 220 HIS ** G 248 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 201 ASN M 323 ASN ** L 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 139 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 200 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 213 ASN ** N 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 86 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7964 moved from start: 0.5456 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 13738 Z= 0.162 Angle : 0.607 8.063 18659 Z= 0.297 Chirality : 0.042 0.154 2086 Planarity : 0.004 0.039 2359 Dihedral : 5.650 69.739 1937 Min Nonbonded Distance : 2.106 Molprobity Statistics. All-atom Clashscore : 14.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.15 % Favored : 96.85 % Rotamer: Outliers : 2.25 % Allowed : 17.55 % Favored : 80.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % 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: -1.07 (0.20), residues: 1682 helix: -0.35 (0.25), residues: 427 sheet: -0.86 (0.26), residues: 369 loop : -0.72 (0.22), residues: 886 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP N 45 HIS 0.005 0.001 HIS A 77 PHE 0.018 0.001 PHE M 279 TYR 0.015 0.001 TYR L 50 ARG 0.006 0.000 ARG L 19 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3364 Ramachandran restraints generated. 1682 Oldfield, 0 Emsley, 1682 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3364 Ramachandran restraints generated. 1682 Oldfield, 0 Emsley, 1682 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 239 residues out of total 1464 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 206 time to evaluate : 1.677 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 192 GLU cc_start: 0.3741 (OUTLIER) cc_final: 0.3471 (tp30) REVERT: B 193 MET cc_start: 0.6813 (ppp) cc_final: 0.6497 (ppp) REVERT: G 33 MET cc_start: 0.8620 (mtm) cc_final: 0.8265 (ttp) REVERT: G 75 TRP cc_start: 0.7485 (t-100) cc_final: 0.6987 (t-100) REVERT: G 159 GLU cc_start: 0.8329 (mt-10) cc_final: 0.7937 (tp30) REVERT: G 320 GLN cc_start: 0.8615 (tp40) cc_final: 0.8344 (mm110) REVERT: M 41 ASP cc_start: 0.8331 (t0) cc_final: 0.7930 (p0) REVERT: M 67 PHE cc_start: 0.8911 (m-10) cc_final: 0.8387 (m-80) REVERT: M 94 TRP cc_start: 0.8112 (m100) cc_final: 0.7617 (m100) REVERT: M 148 MET cc_start: 0.8102 (tpp) cc_final: 0.7810 (tpp) REVERT: M 204 MET cc_start: 0.6521 (tpt) cc_final: 0.6233 (tpt) REVERT: M 321 MET cc_start: 0.9000 (mmm) cc_final: 0.8729 (mmm) REVERT: L 97 ILE cc_start: 0.9249 (mt) cc_final: 0.8997 (mm) REVERT: L 138 ASN cc_start: 0.8701 (t0) cc_final: 0.7640 (t0) REVERT: L 139 ASN cc_start: 0.8630 (m110) cc_final: 0.7890 (m110) REVERT: H 110 TYR cc_start: 0.8146 (p90) cc_final: 0.7831 (p90) REVERT: N 36 ARG cc_start: 0.4148 (ptm-80) cc_final: 0.3227 (ptm160) REVERT: N 41 TYR cc_start: 0.7202 (m-80) cc_final: 0.6859 (m-80) REVERT: N 45 TRP cc_start: 0.6279 (m100) cc_final: 0.6022 (m100) REVERT: N 53 GLU cc_start: 0.8274 (pm20) cc_final: 0.7903 (pm20) outliers start: 33 outliers final: 20 residues processed: 226 average time/residue: 0.2401 time to fit residues: 80.3425 Evaluate side-chains 200 residues out of total 1464 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 179 time to evaluate : 1.572 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 98 VAL Chi-restraints excluded: chain A residue 191 LEU Chi-restraints excluded: chain A residue 202 SER Chi-restraints excluded: chain A residue 204 VAL Chi-restraints excluded: chain A residue 205 ILE Chi-restraints excluded: chain A residue 210 LEU Chi-restraints excluded: chain A residue 422 LEU Chi-restraints excluded: chain B residue 192 GLU Chi-restraints excluded: chain G residue 83 VAL Chi-restraints excluded: chain G residue 176 LEU Chi-restraints excluded: chain G residue 228 LEU Chi-restraints excluded: chain G residue 301 VAL Chi-restraints excluded: chain L residue 48 LEU Chi-restraints excluded: chain L residue 103 THR Chi-restraints excluded: chain H residue 65 ASP Chi-restraints excluded: chain H residue 137 VAL Chi-restraints excluded: chain N residue 31 CYS Chi-restraints excluded: chain N residue 47 ARG Chi-restraints excluded: chain N residue 100 THR Chi-restraints excluded: chain N residue 105 CYS Chi-restraints excluded: chain N residue 128 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 167 random chunks: chunk 54 optimal weight: 0.4980 chunk 145 optimal weight: 2.9990 chunk 31 optimal weight: 6.9990 chunk 94 optimal weight: 0.9990 chunk 39 optimal weight: 7.9990 chunk 161 optimal weight: 9.9990 chunk 134 optimal weight: 6.9990 chunk 74 optimal weight: 0.9980 chunk 13 optimal weight: 5.9990 chunk 53 optimal weight: 2.9990 chunk 84 optimal weight: 3.9990 overall best weight: 1.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 17 HIS ** G 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 248 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 200 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8013 moved from start: 0.5726 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 13738 Z= 0.224 Angle : 0.627 9.308 18659 Z= 0.308 Chirality : 0.042 0.158 2086 Planarity : 0.004 0.039 2359 Dihedral : 5.604 62.966 1937 Min Nonbonded Distance : 2.016 Molprobity Statistics. All-atom Clashscore : 16.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.51 % Favored : 96.49 % Rotamer: Outliers : 2.32 % Allowed : 18.24 % Favored : 79.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % 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: -0.89 (0.21), residues: 1682 helix: -0.12 (0.25), residues: 424 sheet: -0.74 (0.26), residues: 368 loop : -0.66 (0.22), residues: 890 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A 269 HIS 0.004 0.001 HIS B 240 PHE 0.018 0.001 PHE L 140 TYR 0.019 0.001 TYR L 50 ARG 0.007 0.000 ARG N 28 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3364 Ramachandran restraints generated. 1682 Oldfield, 0 Emsley, 1682 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3364 Ramachandran restraints generated. 1682 Oldfield, 0 Emsley, 1682 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 217 residues out of total 1464 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 183 time to evaluate : 1.569 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 224 LEU cc_start: 0.8937 (mt) cc_final: 0.8714 (mt) REVERT: A 398 TRP cc_start: 0.7014 (OUTLIER) cc_final: 0.6686 (m-10) REVERT: B 193 MET cc_start: 0.6578 (ppp) cc_final: 0.6331 (ppp) REVERT: B 251 MET cc_start: 0.7973 (tpp) cc_final: 0.7611 (tpp) REVERT: B 261 LYS cc_start: 0.8635 (tppt) cc_final: 0.8222 (mttp) REVERT: G 33 MET cc_start: 0.8574 (mtm) cc_final: 0.8309 (ttp) REVERT: G 159 GLU cc_start: 0.8380 (mt-10) cc_final: 0.7953 (tp30) REVERT: G 320 GLN cc_start: 0.8642 (tp40) cc_final: 0.8344 (mm110) REVERT: M 67 PHE cc_start: 0.8948 (m-10) cc_final: 0.8492 (m-80) REVERT: M 94 TRP cc_start: 0.8289 (m100) cc_final: 0.7637 (m100) REVERT: M 148 MET cc_start: 0.8101 (tpp) cc_final: 0.7774 (tpp) REVERT: M 204 MET cc_start: 0.6569 (tpt) cc_final: 0.6280 (tpt) REVERT: M 321 MET cc_start: 0.9014 (mmm) cc_final: 0.8660 (mmp) REVERT: L 97 ILE cc_start: 0.9250 (mt) cc_final: 0.8983 (mm) REVERT: L 106 GLU cc_start: 0.7084 (tp30) cc_final: 0.6850 (tp30) REVERT: L 138 ASN cc_start: 0.8679 (t0) cc_final: 0.8411 (t0) REVERT: H 110 TYR cc_start: 0.8183 (p90) cc_final: 0.7877 (p90) REVERT: N 36 ARG cc_start: 0.4224 (ptm-80) cc_final: 0.3305 (ptm160) REVERT: N 41 TYR cc_start: 0.7281 (m-80) cc_final: 0.7017 (m-80) REVERT: N 45 TRP cc_start: 0.6397 (m100) cc_final: 0.6098 (m100) REVERT: N 53 GLU cc_start: 0.8094 (pm20) cc_final: 0.7739 (pm20) REVERT: N 55 GLU cc_start: 0.8316 (mm-30) cc_final: 0.7574 (mm-30) REVERT: N 91 GLN cc_start: 0.7970 (tp-100) cc_final: 0.7469 (tm-30) REVERT: N 93 ASN cc_start: 0.8612 (m-40) cc_final: 0.7727 (m-40) outliers start: 34 outliers final: 27 residues processed: 206 average time/residue: 0.2281 time to fit residues: 70.8151 Evaluate side-chains 202 residues out of total 1464 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 174 time to evaluate : 1.474 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 VAL Chi-restraints excluded: chain A residue 98 VAL Chi-restraints excluded: chain A residue 127 SER Chi-restraints excluded: chain A residue 191 LEU Chi-restraints excluded: chain A residue 202 SER Chi-restraints excluded: chain A residue 204 VAL Chi-restraints excluded: chain A residue 205 ILE Chi-restraints excluded: chain A residue 210 LEU Chi-restraints excluded: chain A residue 398 TRP Chi-restraints excluded: chain A residue 422 LEU Chi-restraints excluded: chain A residue 456 VAL Chi-restraints excluded: chain B residue 197 ARG Chi-restraints excluded: chain B residue 264 VAL Chi-restraints excluded: chain G residue 83 VAL Chi-restraints excluded: chain G residue 176 LEU Chi-restraints excluded: chain G residue 228 LEU Chi-restraints excluded: chain G residue 301 VAL Chi-restraints excluded: chain G residue 317 ASP Chi-restraints excluded: chain L residue 48 LEU Chi-restraints excluded: chain L residue 49 ILE Chi-restraints excluded: chain L residue 103 THR Chi-restraints excluded: chain L residue 206 VAL Chi-restraints excluded: chain H residue 65 ASP Chi-restraints excluded: chain H residue 137 VAL Chi-restraints excluded: chain N residue 31 CYS Chi-restraints excluded: chain N residue 47 ARG Chi-restraints excluded: chain N residue 100 THR Chi-restraints excluded: chain N residue 128 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 167 random chunks: chunk 155 optimal weight: 20.0000 chunk 18 optimal weight: 0.6980 chunk 92 optimal weight: 8.9990 chunk 117 optimal weight: 1.9990 chunk 91 optimal weight: 0.9990 chunk 136 optimal weight: 4.9990 chunk 90 optimal weight: 8.9990 chunk 160 optimal weight: 0.8980 chunk 100 optimal weight: 7.9990 chunk 98 optimal weight: 7.9990 chunk 74 optimal weight: 0.6980 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 26 ASN ** G 112 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 248 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 139 ASN ** L 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 200 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 12 GLN ** N 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 86 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7995 moved from start: 0.5840 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 13738 Z= 0.179 Angle : 0.611 8.598 18659 Z= 0.297 Chirality : 0.041 0.145 2086 Planarity : 0.004 0.037 2359 Dihedral : 5.510 57.872 1937 Min Nonbonded Distance : 2.005 Molprobity Statistics. All-atom Clashscore : 15.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer: Outliers : 2.46 % Allowed : 18.78 % Favored : 78.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % 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: -0.74 (0.21), residues: 1682 helix: -0.03 (0.25), residues: 425 sheet: -0.58 (0.26), residues: 376 loop : -0.58 (0.22), residues: 881 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP G 75 HIS 0.003 0.001 HIS G 169 PHE 0.022 0.001 PHE N 46 TYR 0.016 0.001 TYR L 50 ARG 0.009 0.000 ARG N 28 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3364 Ramachandran restraints generated. 1682 Oldfield, 0 Emsley, 1682 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3364 Ramachandran restraints generated. 1682 Oldfield, 0 Emsley, 1682 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 221 residues out of total 1464 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 185 time to evaluate : 1.612 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 224 LEU cc_start: 0.8878 (mt) cc_final: 0.8655 (mt) REVERT: A 256 MET cc_start: 0.8504 (mmm) cc_final: 0.8217 (tpp) REVERT: A 398 TRP cc_start: 0.6869 (OUTLIER) cc_final: 0.6517 (m-10) REVERT: B 193 MET cc_start: 0.6332 (ppp) cc_final: 0.6036 (ppp) REVERT: B 237 MET cc_start: 0.7959 (ptp) cc_final: 0.7552 (mpp) REVERT: B 242 TYR cc_start: 0.6802 (m-80) cc_final: 0.6039 (m-80) REVERT: B 251 MET cc_start: 0.7935 (tpp) cc_final: 0.7591 (tpp) REVERT: G 159 GLU cc_start: 0.8407 (mt-10) cc_final: 0.7963 (tp30) REVERT: G 319 LEU cc_start: 0.9074 (mm) cc_final: 0.8858 (mm) REVERT: G 320 GLN cc_start: 0.8620 (tp40) cc_final: 0.8333 (mm110) REVERT: M 67 PHE cc_start: 0.8925 (m-10) cc_final: 0.8512 (m-80) REVERT: M 94 TRP cc_start: 0.8266 (m100) cc_final: 0.7640 (m100) REVERT: M 148 MET cc_start: 0.8056 (tpp) cc_final: 0.7742 (tpp) REVERT: M 204 MET cc_start: 0.6527 (tpt) cc_final: 0.6217 (tpt) REVERT: M 321 MET cc_start: 0.9020 (mmm) cc_final: 0.8657 (mmp) REVERT: L 97 ILE cc_start: 0.9247 (mt) cc_final: 0.8978 (mm) REVERT: L 138 ASN cc_start: 0.8645 (t0) cc_final: 0.8348 (t0) REVERT: L 140 PHE cc_start: 0.9020 (p90) cc_final: 0.8635 (p90) REVERT: H 110 TYR cc_start: 0.8089 (p90) cc_final: 0.7769 (p90) REVERT: N 12 GLN cc_start: 0.6651 (OUTLIER) cc_final: 0.4701 (tp40) REVERT: N 36 ARG cc_start: 0.4526 (ptm-80) cc_final: 0.3801 (ptm160) REVERT: N 41 TYR cc_start: 0.7335 (m-80) cc_final: 0.6948 (m-80) REVERT: N 45 TRP cc_start: 0.6109 (m100) cc_final: 0.5851 (m100) REVERT: N 53 GLU cc_start: 0.8008 (pm20) cc_final: 0.7718 (pm20) REVERT: N 55 GLU cc_start: 0.8698 (mm-30) cc_final: 0.7675 (mm-30) REVERT: N 74 GLN cc_start: 0.8263 (pm20) cc_final: 0.7846 (pm20) outliers start: 36 outliers final: 27 residues processed: 210 average time/residue: 0.2283 time to fit residues: 72.1957 Evaluate side-chains 200 residues out of total 1464 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 171 time to evaluate : 1.459 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 VAL Chi-restraints excluded: chain A residue 98 VAL Chi-restraints excluded: chain A residue 191 LEU Chi-restraints excluded: chain A residue 202 SER Chi-restraints excluded: chain A residue 204 VAL Chi-restraints excluded: chain A residue 205 ILE Chi-restraints excluded: chain A residue 210 LEU Chi-restraints excluded: chain A residue 398 TRP Chi-restraints excluded: chain A residue 422 LEU Chi-restraints excluded: chain A residue 456 VAL Chi-restraints excluded: chain B residue 264 VAL Chi-restraints excluded: chain G residue 83 VAL Chi-restraints excluded: chain G residue 176 LEU Chi-restraints excluded: chain G residue 228 LEU Chi-restraints excluded: chain G residue 258 LEU Chi-restraints excluded: chain G residue 301 VAL Chi-restraints excluded: chain L residue 48 LEU Chi-restraints excluded: chain L residue 49 ILE Chi-restraints excluded: chain L residue 59 VAL Chi-restraints excluded: chain L residue 103 THR Chi-restraints excluded: chain L residue 206 VAL Chi-restraints excluded: chain H residue 65 ASP Chi-restraints excluded: chain H residue 137 VAL Chi-restraints excluded: chain N residue 12 GLN Chi-restraints excluded: chain N residue 31 CYS Chi-restraints excluded: chain N residue 47 ARG Chi-restraints excluded: chain N residue 88 VAL Chi-restraints excluded: chain N residue 100 THR Chi-restraints excluded: chain N residue 128 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 167 random chunks: chunk 99 optimal weight: 10.0000 chunk 64 optimal weight: 3.9990 chunk 96 optimal weight: 20.0000 chunk 48 optimal weight: 10.0000 chunk 31 optimal weight: 2.9990 chunk 102 optimal weight: 10.0000 chunk 109 optimal weight: 0.9990 chunk 79 optimal weight: 4.9990 chunk 15 optimal weight: 5.9990 chunk 126 optimal weight: 7.9990 chunk 146 optimal weight: 10.0000 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 77 HIS A 164 ASN B 222 ASN ** G 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 169 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 248 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 290 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 203 HIS ** L 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 139 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 200 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 180 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 213 ASN ** N 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8131 moved from start: 0.6555 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.089 13738 Z= 0.403 Angle : 0.746 12.726 18659 Z= 0.370 Chirality : 0.043 0.150 2086 Planarity : 0.005 0.058 2359 Dihedral : 6.122 63.905 1937 Min Nonbonded Distance : 1.985 Molprobity Statistics. All-atom Clashscore : 22.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.29 % Favored : 94.71 % Rotamer: Outliers : 2.94 % Allowed : 18.65 % Favored : 78.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % 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 (0.21), residues: 1682 helix: -0.04 (0.25), residues: 416 sheet: -0.80 (0.26), residues: 367 loop : -0.53 (0.22), residues: 899 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP G 117 HIS 0.006 0.001 HIS A 220 PHE 0.018 0.002 PHE A 279 TYR 0.026 0.002 TYR H 97 ARG 0.007 0.001 ARG G 70 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3364 Ramachandran restraints generated. 1682 Oldfield, 0 Emsley, 1682 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3364 Ramachandran restraints generated. 1682 Oldfield, 0 Emsley, 1682 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 225 residues out of total 1464 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 182 time to evaluate : 1.621 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 224 LEU cc_start: 0.8891 (mt) cc_final: 0.8637 (mt) REVERT: A 256 MET cc_start: 0.8473 (mmm) cc_final: 0.8244 (mmm) REVERT: A 446 TYR cc_start: 0.7608 (OUTLIER) cc_final: 0.7374 (p90) REVERT: B 193 MET cc_start: 0.6212 (ppp) cc_final: 0.5978 (ppp) REVERT: B 263 TYR cc_start: 0.7164 (m-10) cc_final: 0.6955 (m-10) REVERT: G 159 GLU cc_start: 0.8463 (mt-10) cc_final: 0.7990 (tp30) REVERT: G 320 GLN cc_start: 0.8693 (tp40) cc_final: 0.8330 (mm110) REVERT: M 67 PHE cc_start: 0.9016 (m-10) cc_final: 0.8603 (m-80) REVERT: M 148 MET cc_start: 0.8148 (tpp) cc_final: 0.7745 (tpp) REVERT: L 5 MET cc_start: 0.6803 (ttp) cc_final: 0.6602 (ttp) REVERT: L 97 ILE cc_start: 0.9301 (mt) cc_final: 0.9035 (mm) REVERT: H 110 TYR cc_start: 0.8340 (p90) cc_final: 0.8066 (p90) REVERT: H 113 MET cc_start: 0.8459 (tmm) cc_final: 0.7257 (tmm) REVERT: H 194 LEU cc_start: 0.9446 (tp) cc_final: 0.9193 (tt) REVERT: N 36 ARG cc_start: 0.4777 (ptm-80) cc_final: 0.3868 (ptm160) REVERT: N 45 TRP cc_start: 0.5934 (m100) cc_final: 0.5705 (m100) REVERT: N 53 GLU cc_start: 0.8252 (pm20) cc_final: 0.7822 (pm20) REVERT: N 55 GLU cc_start: 0.8882 (mm-30) cc_final: 0.7943 (mm-30) REVERT: N 81 ARG cc_start: 0.7795 (OUTLIER) cc_final: 0.7039 (ttt180) REVERT: N 93 ASN cc_start: 0.8562 (m-40) cc_final: 0.7571 (p0) outliers start: 43 outliers final: 33 residues processed: 214 average time/residue: 0.2415 time to fit residues: 76.4152 Evaluate side-chains 199 residues out of total 1464 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 164 time to evaluate : 1.608 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 VAL Chi-restraints excluded: chain A residue 107 ILE Chi-restraints excluded: chain A residue 137 VAL Chi-restraints excluded: chain A residue 153 MET Chi-restraints excluded: chain A residue 191 LEU Chi-restraints excluded: chain A residue 202 SER Chi-restraints excluded: chain A residue 204 VAL Chi-restraints excluded: chain A residue 205 ILE Chi-restraints excluded: chain A residue 210 LEU Chi-restraints excluded: chain A residue 398 TRP Chi-restraints excluded: chain A residue 446 TYR Chi-restraints excluded: chain A residue 456 VAL Chi-restraints excluded: chain A residue 535 ILE Chi-restraints excluded: chain G residue 83 VAL Chi-restraints excluded: chain G residue 105 GLN Chi-restraints excluded: chain G residue 166 ILE Chi-restraints excluded: chain G residue 176 LEU Chi-restraints excluded: chain G residue 228 LEU Chi-restraints excluded: chain G residue 301 VAL Chi-restraints excluded: chain G residue 317 ASP Chi-restraints excluded: chain M residue 209 ASP Chi-restraints excluded: chain L residue 48 LEU Chi-restraints excluded: chain L residue 49 ILE Chi-restraints excluded: chain L residue 59 VAL Chi-restraints excluded: chain L residue 82 GLU Chi-restraints excluded: chain L residue 103 THR Chi-restraints excluded: chain L residue 118 ILE Chi-restraints excluded: chain L residue 206 VAL Chi-restraints excluded: chain H residue 32 ILE Chi-restraints excluded: chain H residue 137 VAL Chi-restraints excluded: chain N residue 31 CYS Chi-restraints excluded: chain N residue 81 ARG Chi-restraints excluded: chain N residue 88 VAL Chi-restraints excluded: chain N residue 100 THR Chi-restraints excluded: chain N residue 128 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 167 random chunks: chunk 154 optimal weight: 3.9990 chunk 140 optimal weight: 0.0060 chunk 149 optimal weight: 0.9990 chunk 90 optimal weight: 0.9990 chunk 65 optimal weight: 0.9990 chunk 117 optimal weight: 0.0970 chunk 46 optimal weight: 20.0000 chunk 135 optimal weight: 5.9990 chunk 141 optimal weight: 1.9990 chunk 98 optimal weight: 0.9990 chunk 158 optimal weight: 0.9980 overall best weight: 0.6198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 222 ASN ** G 112 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 169 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 218 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 200 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 180 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 12 GLN ** N 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8031 moved from start: 0.6465 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 13738 Z= 0.179 Angle : 0.648 10.053 18659 Z= 0.313 Chirality : 0.043 0.150 2086 Planarity : 0.004 0.038 2359 Dihedral : 5.720 62.111 1937 Min Nonbonded Distance : 2.029 Molprobity Statistics. All-atom Clashscore : 16.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.27 % Favored : 96.73 % Rotamer: Outliers : 2.05 % Allowed : 20.42 % Favored : 77.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % 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: -0.62 (0.21), residues: 1682 helix: 0.09 (0.26), residues: 428 sheet: -0.56 (0.26), residues: 377 loop : -0.49 (0.22), residues: 877 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP H 50 HIS 0.005 0.001 HIS B 240 PHE 0.017 0.001 PHE M 279 TYR 0.019 0.001 TYR H 161 ARG 0.006 0.000 ARG L 19 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3364 Ramachandran restraints generated. 1682 Oldfield, 0 Emsley, 1682 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3364 Ramachandran restraints generated. 1682 Oldfield, 0 Emsley, 1682 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 220 residues out of total 1464 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 190 time to evaluate : 1.733 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 224 LEU cc_start: 0.8878 (mt) cc_final: 0.8610 (mt) REVERT: A 398 TRP cc_start: 0.6976 (OUTLIER) cc_final: 0.6634 (m-10) REVERT: A 446 TYR cc_start: 0.7434 (OUTLIER) cc_final: 0.7209 (p90) REVERT: B 193 MET cc_start: 0.6206 (ppp) cc_final: 0.5918 (ppp) REVERT: B 222 ASN cc_start: 0.1847 (OUTLIER) cc_final: 0.0411 (t0) REVERT: B 237 MET cc_start: 0.7949 (ptp) cc_final: 0.7546 (mpp) REVERT: B 251 MET cc_start: 0.7935 (tpp) cc_final: 0.7619 (tpp) REVERT: B 261 LYS cc_start: 0.8780 (tppt) cc_final: 0.8301 (mttt) REVERT: G 159 GLU cc_start: 0.8447 (mt-10) cc_final: 0.7956 (tp30) REVERT: G 320 GLN cc_start: 0.8653 (tp40) cc_final: 0.8312 (mm110) REVERT: M 67 PHE cc_start: 0.8934 (m-10) cc_final: 0.8526 (m-80) REVERT: M 148 MET cc_start: 0.8087 (tpp) cc_final: 0.7692 (tpp) REVERT: M 321 MET cc_start: 0.8953 (mmm) cc_final: 0.8589 (mmp) REVERT: L 97 ILE cc_start: 0.9270 (mt) cc_final: 0.8958 (mm) REVERT: H 54 ILE cc_start: 0.9263 (tt) cc_final: 0.8904 (pt) REVERT: H 110 TYR cc_start: 0.8169 (p90) cc_final: 0.7849 (p90) REVERT: H 194 LEU cc_start: 0.9280 (tp) cc_final: 0.9030 (tt) REVERT: N 12 GLN cc_start: 0.6698 (OUTLIER) cc_final: 0.5345 (tp40) REVERT: N 36 ARG cc_start: 0.4317 (ptm-80) cc_final: 0.3705 (ptm160) REVERT: N 53 GLU cc_start: 0.8152 (pm20) cc_final: 0.7695 (pm20) REVERT: N 55 GLU cc_start: 0.8756 (mm-30) cc_final: 0.7878 (mm-30) REVERT: N 74 GLN cc_start: 0.8235 (pm20) cc_final: 0.7927 (pm20) REVERT: N 81 ARG cc_start: 0.7783 (OUTLIER) cc_final: 0.6989 (ttt180) REVERT: N 93 ASN cc_start: 0.8609 (m-40) cc_final: 0.7594 (p0) outliers start: 30 outliers final: 22 residues processed: 214 average time/residue: 0.2296 time to fit residues: 74.1565 Evaluate side-chains 200 residues out of total 1464 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 173 time to evaluate : 1.592 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 VAL Chi-restraints excluded: chain A residue 98 VAL Chi-restraints excluded: chain A residue 191 LEU Chi-restraints excluded: chain A residue 202 SER Chi-restraints excluded: chain A residue 204 VAL Chi-restraints excluded: chain A residue 205 ILE Chi-restraints excluded: chain A residue 210 LEU Chi-restraints excluded: chain A residue 398 TRP Chi-restraints excluded: chain A residue 446 TYR Chi-restraints excluded: chain A residue 456 VAL Chi-restraints excluded: chain A residue 535 ILE Chi-restraints excluded: chain B residue 222 ASN Chi-restraints excluded: chain G residue 112 HIS Chi-restraints excluded: chain G residue 258 LEU Chi-restraints excluded: chain G residue 301 VAL Chi-restraints excluded: chain L residue 48 LEU Chi-restraints excluded: chain L residue 59 VAL Chi-restraints excluded: chain L residue 103 THR Chi-restraints excluded: chain L residue 206 VAL Chi-restraints excluded: chain H residue 65 ASP Chi-restraints excluded: chain H residue 137 VAL Chi-restraints excluded: chain N residue 12 GLN Chi-restraints excluded: chain N residue 31 CYS Chi-restraints excluded: chain N residue 81 ARG Chi-restraints excluded: chain N residue 88 VAL Chi-restraints excluded: chain N residue 100 THR Chi-restraints excluded: chain N residue 128 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 167 random chunks: chunk 96 optimal weight: 10.0000 chunk 75 optimal weight: 0.7980 chunk 110 optimal weight: 0.8980 chunk 166 optimal weight: 5.9990 chunk 153 optimal weight: 6.9990 chunk 132 optimal weight: 4.9990 chunk 13 optimal weight: 0.8980 chunk 102 optimal weight: 0.0570 chunk 81 optimal weight: 7.9990 chunk 105 optimal weight: 0.9990 chunk 141 optimal weight: 0.6980 overall best weight: 0.6698 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 112 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 169 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 218 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 139 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 200 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 180 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8034 moved from start: 0.6495 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.205 13738 Z= 0.346 Angle : 0.992 59.200 18659 Z= 0.569 Chirality : 0.047 0.670 2086 Planarity : 0.004 0.063 2359 Dihedral : 5.755 62.068 1937 Min Nonbonded Distance : 1.933 Molprobity Statistics. All-atom Clashscore : 18.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer: Outliers : 2.05 % Allowed : 21.24 % Favored : 76.71 % Cbeta Deviations : 0.13 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: -0.61 (0.21), residues: 1682 helix: 0.10 (0.26), residues: 428 sheet: -0.55 (0.26), residues: 377 loop : -0.48 (0.22), residues: 877 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP N 45 HIS 0.004 0.001 HIS G 112 PHE 0.016 0.001 PHE M 279 TYR 0.049 0.001 TYR B 263 ARG 0.044 0.001 ARG H 41 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3364 Ramachandran restraints generated. 1682 Oldfield, 0 Emsley, 1682 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3364 Ramachandran restraints generated. 1682 Oldfield, 0 Emsley, 1682 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 203 residues out of total 1464 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 173 time to evaluate : 1.701 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 224 LEU cc_start: 0.8878 (mt) cc_final: 0.8608 (mt) REVERT: A 398 TRP cc_start: 0.6977 (OUTLIER) cc_final: 0.6635 (m-10) REVERT: A 446 TYR cc_start: 0.7434 (OUTLIER) cc_final: 0.7210 (p90) REVERT: B 193 MET cc_start: 0.6197 (ppp) cc_final: 0.5917 (ppp) REVERT: B 236 VAL cc_start: 0.8626 (m) cc_final: 0.8326 (m) REVERT: B 237 MET cc_start: 0.7986 (ptp) cc_final: 0.7532 (mpp) REVERT: B 251 MET cc_start: 0.7938 (tpp) cc_final: 0.7632 (tpp) REVERT: B 261 LYS cc_start: 0.8782 (tppt) cc_final: 0.8300 (mttt) REVERT: G 159 GLU cc_start: 0.8451 (mt-10) cc_final: 0.7956 (tp30) REVERT: G 317 ASP cc_start: 0.8411 (OUTLIER) cc_final: 0.8164 (p0) REVERT: G 320 GLN cc_start: 0.8654 (tp40) cc_final: 0.8313 (mm110) REVERT: M 67 PHE cc_start: 0.8926 (m-10) cc_final: 0.8524 (m-80) REVERT: M 148 MET cc_start: 0.8086 (tpp) cc_final: 0.7692 (tpp) REVERT: M 321 MET cc_start: 0.8954 (mmm) cc_final: 0.8583 (mmp) REVERT: L 97 ILE cc_start: 0.9270 (mt) cc_final: 0.8962 (mm) REVERT: H 54 ILE cc_start: 0.9244 (tt) cc_final: 0.8901 (pt) REVERT: H 110 TYR cc_start: 0.8170 (p90) cc_final: 0.7848 (p90) REVERT: H 194 LEU cc_start: 0.9275 (tp) cc_final: 0.9030 (tt) REVERT: N 36 ARG cc_start: 0.4321 (ptm-80) cc_final: 0.3704 (ptm160) REVERT: N 53 GLU cc_start: 0.8149 (pm20) cc_final: 0.7695 (pm20) REVERT: N 55 GLU cc_start: 0.8756 (mm-30) cc_final: 0.7880 (mm-30) REVERT: N 74 GLN cc_start: 0.8231 (pm20) cc_final: 0.7929 (pm20) REVERT: N 81 ARG cc_start: 0.7780 (OUTLIER) cc_final: 0.6990 (ttt180) REVERT: N 93 ASN cc_start: 0.8609 (m-40) cc_final: 0.7594 (p0) outliers start: 30 outliers final: 24 residues processed: 195 average time/residue: 0.2225 time to fit residues: 66.4017 Evaluate side-chains 199 residues out of total 1464 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 171 time to evaluate : 1.610 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 VAL Chi-restraints excluded: chain A residue 98 VAL Chi-restraints excluded: chain A residue 191 LEU Chi-restraints excluded: chain A residue 202 SER Chi-restraints excluded: chain A residue 204 VAL Chi-restraints excluded: chain A residue 205 ILE Chi-restraints excluded: chain A residue 210 LEU Chi-restraints excluded: chain A residue 398 TRP Chi-restraints excluded: chain A residue 423 ASP Chi-restraints excluded: chain A residue 446 TYR Chi-restraints excluded: chain A residue 456 VAL Chi-restraints excluded: chain A residue 535 ILE Chi-restraints excluded: chain G residue 112 HIS Chi-restraints excluded: chain G residue 247 ILE Chi-restraints excluded: chain G residue 258 LEU Chi-restraints excluded: chain G residue 301 VAL Chi-restraints excluded: chain G residue 317 ASP Chi-restraints excluded: chain L residue 48 LEU Chi-restraints excluded: chain L residue 103 THR Chi-restraints excluded: chain L residue 206 VAL Chi-restraints excluded: chain H residue 65 ASP Chi-restraints excluded: chain H residue 137 VAL Chi-restraints excluded: chain H residue 145 LYS Chi-restraints excluded: chain N residue 31 CYS Chi-restraints excluded: chain N residue 81 ARG Chi-restraints excluded: chain N residue 88 VAL Chi-restraints excluded: chain N residue 100 THR Chi-restraints excluded: chain N residue 128 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 167 random chunks: chunk 40 optimal weight: 0.5980 chunk 122 optimal weight: 5.9990 chunk 19 optimal weight: 1.9990 chunk 36 optimal weight: 0.8980 chunk 132 optimal weight: 9.9990 chunk 55 optimal weight: 0.8980 chunk 136 optimal weight: 0.5980 chunk 16 optimal weight: 9.9990 chunk 24 optimal weight: 2.9990 chunk 116 optimal weight: 0.8980 chunk 7 optimal weight: 5.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 222 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 112 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 169 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 218 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 139 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 200 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 180 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 22 GLN ** 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 = 0.3771 r_free = 0.3771 target = 0.084170 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3324 r_free = 0.3324 target = 0.064581 restraints weight = 56589.560| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3320 r_free = 0.3320 target = 0.065083 restraints weight = 40903.956| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3331 r_free = 0.3331 target = 0.065622 restraints weight = 33518.498| |-----------------------------------------------------------------------------| r_work (final): 0.3316 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8021 moved from start: 0.6493 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.205 13738 Z= 0.346 Angle : 0.992 59.200 18659 Z= 0.569 Chirality : 0.047 0.670 2086 Planarity : 0.004 0.063 2359 Dihedral : 5.755 62.068 1937 Min Nonbonded Distance : 1.584 Molprobity Statistics. All-atom Clashscore : 19.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer: Outliers : 1.91 % Allowed : 21.45 % Favored : 76.64 % Cbeta Deviations : 0.13 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: -0.61 (0.21), residues: 1682 helix: 0.10 (0.26), residues: 428 sheet: -0.55 (0.26), residues: 377 loop : -0.48 (0.22), residues: 877 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP N 45 HIS 0.004 0.001 HIS G 112 PHE 0.016 0.001 PHE M 279 TYR 0.049 0.001 TYR B 263 ARG 0.044 0.001 ARG H 41 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2703.07 seconds wall clock time: 52 minutes 1.75 seconds (3121.75 seconds total)