Starting phenix.real_space_refine on Thu Dec 26 06:54:52 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8dr6_27672/12_2024/8dr6_27672_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/8dr6_27672/12_2024/8dr6_27672.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.39 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8dr6_27672/12_2024/8dr6_27672.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8dr6_27672/12_2024/8dr6_27672.map" model { file = "/net/cci-nas-00/data/ceres_data/8dr6_27672/12_2024/8dr6_27672_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8dr6_27672/12_2024/8dr6_27672_trim.cif" } resolution = 2.39 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 sd= 0.043 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: 7 Type Number sf(0) Gaussians P 77 5.49 5 Mg 4 5.21 5 S 101 5.16 5 C 13683 2.51 5 N 3753 2.21 5 O 4380 1.98 5 H 21632 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 116 residue(s): 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/chem_data/mon_lib" Total number of atoms: 43630 Number of models: 1 Model: "" Number of chains: 20 Chain: "A" Number of atoms: 7845 Number of conformers: 1 Conformer: "" Number of residues, atoms: 493, 7845 Classifications: {'peptide': 493} Link IDs: {'PTRANS': 19, 'TRANS': 473} Chain breaks: 1 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 7 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'HIS:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "B" Number of atoms: 5084 Number of conformers: 1 Conformer: "" Number of residues, atoms: 318, 5084 Classifications: {'peptide': 318} Link IDs: {'PTRANS': 9, 'TRANS': 308} Chain: "C" Number of atoms: 5263 Number of conformers: 1 Conformer: "" Number of residues, atoms: 330, 5263 Classifications: {'peptide': 330} Link IDs: {'PTRANS': 12, 'TRANS': 317} Chain: "D" Number of atoms: 5457 Number of conformers: 1 Conformer: "" Number of residues, atoms: 343, 5457 Classifications: {'peptide': 343} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 12, 'TRANS': 330} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "E" Number of atoms: 5698 Number of conformers: 1 Conformer: "" Number of residues, atoms: 354, 5698 Classifications: {'peptide': 354} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 14, 'TRANS': 339} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 3 Chain: "F" Number of atoms: 4055 Number of conformers: 1 Conformer: "" Number of residues, atoms: 258, 4055 Classifications: {'peptide': 258} Link IDs: {'PTRANS': 8, 'TRANS': 249} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Chain: "G" Number of atoms: 4047 Number of conformers: 1 Conformer: "" Number of residues, atoms: 257, 4047 Classifications: {'peptide': 257} Link IDs: {'PTRANS': 8, 'TRANS': 248} Chain: "H" Number of atoms: 4023 Number of conformers: 1 Conformer: "" Number of residues, atoms: 255, 4023 Classifications: {'peptide': 255} Link IDs: {'PTRANS': 8, 'TRANS': 246} Chain: "I" Number of atoms: 1012 Number of conformers: 1 Conformer: "" Number of residues, atoms: 32, 1012 Classifications: {'DNA': 32} Modifications used: {'3*END': 1} Link IDs: {'rna3p': 31} Chain: "J" Number of atoms: 553 Number of conformers: 1 Conformer: "" Number of residues, atoms: 18, 553 Classifications: {'DNA': 18} Modifications used: {'3*END': 1} Link IDs: {'rna3p': 17} Chain: "K" Number of atoms: 426 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 426 Classifications: {'DNA': 13} Modifications used: {'3*END': 1} Link IDs: {'rna3p': 12} Chain: "A" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'AGS': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'AGS': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'AGS': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'AGS': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "A" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Chain: "C" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Chain: "D" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Time building chain proxies: 20.63, per 1000 atoms: 0.47 Number of scatterers: 43630 At special positions: 0 Unit cell: (132.986, 119.77, 144.55, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) S 101 16.00 P 77 15.00 Mg 4 11.99 O 4380 8.00 N 3753 7.00 C 13683 6.00 H 21632 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 12.38 Conformation dependent library (CDL) restraints added in 3.8 seconds 5180 Ramachandran restraints generated. 2590 Oldfield, 0 Emsley, 2590 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4960 Finding SS restraints... Secondary structure from input PDB file: 135 helices and 15 sheets defined 54.9% alpha, 15.5% beta 20 base pairs and 46 stacking pairs defined. Time for finding SS restraints: 22.65 Creating SS restraints... Processing helix chain 'A' and resid 292 through 296 Processing helix chain 'A' and resid 297 through 302 Processing helix chain 'A' and resid 306 through 310 removed outlier: 3.669A pdb=" N VAL A 310 " --> pdb=" O LEU A 307 " (cutoff:3.500A) Processing helix chain 'A' and resid 313 through 326 Processing helix chain 'A' and resid 326 through 333 Processing helix chain 'A' and resid 342 through 346 removed outlier: 4.294A pdb=" N VAL A 345 " --> pdb=" O GLY A 342 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N PHE A 346 " --> pdb=" O SER A 343 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 342 through 346' Processing helix chain 'A' and resid 358 through 370 Processing helix chain 'A' and resid 384 through 391 Processing helix chain 'A' and resid 391 through 396 removed outlier: 3.650A pdb=" N ALA A 395 " --> pdb=" O GLY A 391 " (cutoff:3.500A) Processing helix chain 'A' and resid 400 through 406 Processing helix chain 'A' and resid 425 through 429 Processing helix chain 'A' and resid 436 through 447 Processing helix chain 'A' and resid 460 through 467 Proline residue: A 465 - end of helix Processing helix chain 'A' and resid 479 through 495 removed outlier: 3.668A pdb=" N ILE A 483 " --> pdb=" O ASP A 479 " (cutoff:3.500A) removed outlier: 4.289A pdb=" N SER A 485 " --> pdb=" O ASN A 481 " (cutoff:3.500A) removed outlier: 5.172A pdb=" N ARG A 486 " --> pdb=" O SER A 482 " (cutoff:3.500A) Processing helix chain 'A' and resid 502 through 510 Processing helix chain 'A' and resid 513 through 526 removed outlier: 3.686A pdb=" N THR A 526 " --> pdb=" O SER A 522 " (cutoff:3.500A) Processing helix chain 'A' and resid 535 through 543 Processing helix chain 'A' and resid 550 through 559 Processing helix chain 'A' and resid 561 through 564 Processing helix chain 'A' and resid 565 through 572 Processing helix chain 'A' and resid 573 through 583 Processing helix chain 'A' and resid 587 through 596 Processing helix chain 'A' and resid 609 through 632 Processing helix chain 'A' and resid 637 through 639 No H-bonds generated for 'chain 'A' and resid 637 through 639' Processing helix chain 'A' and resid 640 through 649 Processing helix chain 'A' and resid 649 through 657 removed outlier: 3.504A pdb=" N VAL A 656 " --> pdb=" O PRO A 652 " (cutoff:3.500A) Processing helix chain 'A' and resid 668 through 690 Processing helix chain 'A' and resid 697 through 704 Processing helix chain 'A' and resid 704 through 714 removed outlier: 3.960A pdb=" N THR A 708 " --> pdb=" O ASP A 704 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N LYS A 711 " --> pdb=" O PRO A 707 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N ARG A 712 " --> pdb=" O THR A 708 " (cutoff:3.500A) Processing helix chain 'A' and resid 714 through 721 removed outlier: 3.698A pdb=" N LEU A 718 " --> pdb=" O LEU A 714 " (cutoff:3.500A) Processing helix chain 'A' and resid 724 through 735 Processing helix chain 'A' and resid 738 through 747 Processing helix chain 'A' and resid 750 through 754 Processing helix chain 'A' and resid 755 through 762 removed outlier: 3.573A pdb=" N ILE A 762 " --> pdb=" O ILE A 758 " (cutoff:3.500A) Processing helix chain 'A' and resid 763 through 776 Processing helix chain 'B' and resid 10 through 15 Processing helix chain 'B' and resid 19 through 23 Processing helix chain 'B' and resid 26 through 40 Processing helix chain 'B' and resid 54 through 68 Processing helix chain 'B' and resid 70 through 74 Processing helix chain 'B' and resid 85 through 99 removed outlier: 3.761A pdb=" N ILE B 93 " --> pdb=" O VAL B 89 " (cutoff:3.500A) removed outlier: 4.792A pdb=" N LYS B 94 " --> pdb=" O ARG B 90 " (cutoff:3.500A) Processing helix chain 'B' and resid 116 through 119 Processing helix chain 'B' and resid 120 through 134 removed outlier: 3.569A pdb=" N ARG B 128 " --> pdb=" O GLN B 124 " (cutoff:3.500A) removed outlier: 4.573A pdb=" N ARG B 129 " --> pdb=" O GLN B 125 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N THR B 130 " --> pdb=" O ALA B 126 " (cutoff:3.500A) Processing helix chain 'B' and resid 146 through 150 Processing helix chain 'B' and resid 151 through 157 removed outlier: 3.519A pdb=" N ARG B 157 " --> pdb=" O PRO B 153 " (cutoff:3.500A) Processing helix chain 'B' and resid 167 through 183 Processing helix chain 'B' and resid 187 through 199 Processing helix chain 'B' and resid 201 through 216 Processing helix chain 'B' and resid 220 through 228 Processing helix chain 'B' and resid 231 through 241 removed outlier: 3.572A pdb=" N ILE B 235 " --> pdb=" O PRO B 231 " (cutoff:3.500A) Processing helix chain 'B' and resid 244 through 256 Processing helix chain 'B' and resid 262 through 276 removed outlier: 3.521A pdb=" N ASN B 276 " --> pdb=" O ARG B 272 " (cutoff:3.500A) Processing helix chain 'B' and resid 281 through 301 Processing helix chain 'B' and resid 305 through 320 removed outlier: 3.577A pdb=" N LEU B 309 " --> pdb=" O THR B 305 " (cutoff:3.500A) Processing helix chain 'C' and resid 9 through 13 Processing helix chain 'C' and resid 14 through 19 Processing helix chain 'C' and resid 23 through 27 removed outlier: 3.518A pdb=" N VAL C 27 " --> pdb=" O LEU C 24 " (cutoff:3.500A) Processing helix chain 'C' and resid 30 through 43 Processing helix chain 'C' and resid 58 through 72 Processing helix chain 'C' and resid 74 through 77 Processing helix chain 'C' and resid 89 through 103 removed outlier: 4.044A pdb=" N ILE C 97 " --> pdb=" O VAL C 93 " (cutoff:3.500A) removed outlier: 4.691A pdb=" N LYS C 98 " --> pdb=" O ARG C 94 " (cutoff:3.500A) Processing helix chain 'C' and resid 118 through 122 Processing helix chain 'C' and resid 123 through 137 removed outlier: 4.530A pdb=" N ARG C 132 " --> pdb=" O ASN C 128 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N VAL C 133 " --> pdb=" O ALA C 129 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N TYR C 137 " --> pdb=" O VAL C 133 " (cutoff:3.500A) Processing helix chain 'C' and resid 149 through 153 removed outlier: 3.652A pdb=" N LYS C 152 " --> pdb=" O TYR C 149 " (cutoff:3.500A) Processing helix chain 'C' and resid 154 through 160 removed outlier: 3.543A pdb=" N ARG C 160 " --> pdb=" O ALA C 156 " (cutoff:3.500A) Processing helix chain 'C' and resid 170 through 186 Processing helix chain 'C' and resid 190 through 202 removed outlier: 3.970A pdb=" N ASN C 202 " --> pdb=" O ILE C 198 " (cutoff:3.500A) Processing helix chain 'C' and resid 204 through 219 Processing helix chain 'C' and resid 228 through 237 Processing helix chain 'C' and resid 240 through 254 Processing helix chain 'C' and resid 255 through 270 removed outlier: 4.243A pdb=" N LYS C 270 " --> pdb=" O VAL C 266 " (cutoff:3.500A) Processing helix chain 'C' and resid 273 through 286 Processing helix chain 'C' and resid 292 through 312 removed outlier: 3.996A pdb=" N ARG C 296 " --> pdb=" O ASN C 292 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N LYS C 312 " --> pdb=" O TYR C 308 " (cutoff:3.500A) Processing helix chain 'C' and resid 315 through 331 Processing helix chain 'C' and resid 332 through 335 removed outlier: 3.825A pdb=" N THR C 335 " --> pdb=" O GLU C 332 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 332 through 335' Processing helix chain 'D' and resid 17 through 24 removed outlier: 3.623A pdb=" N GLN D 24 " --> pdb=" O GLN D 20 " (cutoff:3.500A) Processing helix chain 'D' and resid 26 through 31 Processing helix chain 'D' and resid 35 through 39 removed outlier: 3.508A pdb=" N VAL D 39 " --> pdb=" O LEU D 36 " (cutoff:3.500A) Processing helix chain 'D' and resid 42 through 56 removed outlier: 4.435A pdb=" N VAL D 48 " --> pdb=" O HIS D 44 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N LEU D 53 " --> pdb=" O LEU D 49 " (cutoff:3.500A) removed outlier: 4.290A pdb=" N LYS D 54 " --> pdb=" O LYS D 50 " (cutoff:3.500A) Processing helix chain 'D' and resid 70 through 91 Proline residue: D 85 - end of helix removed outlier: 5.053A pdb=" N LYS D 89 " --> pdb=" O PRO D 85 " (cutoff:3.500A) removed outlier: 4.995A pdb=" N SER D 90 " --> pdb=" O ASP D 86 " (cutoff:3.500A) Processing helix chain 'D' and resid 102 through 116 removed outlier: 3.822A pdb=" N VAL D 110 " --> pdb=" O VAL D 106 " (cutoff:3.500A) removed outlier: 4.686A pdb=" N LYS D 111 " --> pdb=" O ARG D 107 " (cutoff:3.500A) Processing helix chain 'D' and resid 122 through 129 Processing helix chain 'D' and resid 142 through 145 Processing helix chain 'D' and resid 146 through 153 Processing helix chain 'D' and resid 153 through 160 removed outlier: 3.620A pdb=" N GLU D 158 " --> pdb=" O ARG D 154 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N TYR D 160 " --> pdb=" O THR D 156 " (cutoff:3.500A) Processing helix chain 'D' and resid 172 through 176 Processing helix chain 'D' and resid 177 through 184 Processing helix chain 'D' and resid 197 through 208 Processing helix chain 'D' and resid 215 through 225 Processing helix chain 'D' and resid 227 through 246 Processing helix chain 'D' and resid 252 through 261 Processing helix chain 'D' and resid 264 through 278 Processing helix chain 'D' and resid 279 through 292 removed outlier: 3.788A pdb=" N LYS D 292 " --> pdb=" O ASN D 288 " (cutoff:3.500A) Processing helix chain 'D' and resid 296 through 310 removed outlier: 3.515A pdb=" N THR D 310 " --> pdb=" O GLU D 306 " (cutoff:3.500A) Processing helix chain 'D' and resid 315 through 334 removed outlier: 3.507A pdb=" N TRP D 324 " --> pdb=" O ASN D 320 " (cutoff:3.500A) Processing helix chain 'D' and resid 338 through 352 Processing helix chain 'E' and resid 3 through 8 Processing helix chain 'E' and resid 12 through 16 Processing helix chain 'E' and resid 19 through 32 removed outlier: 4.429A pdb=" N GLN E 32 " --> pdb=" O SER E 28 " (cutoff:3.500A) Processing helix chain 'E' and resid 33 through 36 Processing helix chain 'E' and resid 48 through 62 Processing helix chain 'E' and resid 63 through 67 Processing helix chain 'E' and resid 97 through 103 removed outlier: 6.870A pdb=" N ASN E 103 " --> pdb=" O ASP E 100 " (cutoff:3.500A) Processing helix chain 'E' and resid 104 through 111 removed outlier: 3.874A pdb=" N VAL E 108 " --> pdb=" O ASN E 104 " (cutoff:3.500A) Processing helix chain 'E' and resid 111 through 118 Processing helix chain 'E' and resid 143 through 146 Processing helix chain 'E' and resid 147 through 161 removed outlier: 4.562A pdb=" N ARG E 156 " --> pdb=" O ALA E 152 " (cutoff:3.500A) removed outlier: 4.294A pdb=" N THR E 157 " --> pdb=" O ALA E 153 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N GLU E 159 " --> pdb=" O ARG E 155 " (cutoff:3.500A) Processing helix chain 'E' and resid 178 through 184 Processing helix chain 'E' and resid 194 through 210 Processing helix chain 'E' and resid 216 through 227 removed outlier: 3.693A pdb=" N ASN E 227 " --> pdb=" O ALA E 223 " (cutoff:3.500A) Processing helix chain 'E' and resid 229 through 243 Processing helix chain 'E' and resid 257 through 273 Processing helix chain 'E' and resid 275 through 291 removed outlier: 3.515A pdb=" N ALA E 284 " --> pdb=" O ILE E 280 " (cutoff:3.500A) Processing helix chain 'E' and resid 295 through 308 Processing helix chain 'E' and resid 314 through 334 Processing helix chain 'E' and resid 337 through 354 removed outlier: 3.956A pdb=" N HIS E 341 " --> pdb=" O LYS E 337 " (cutoff:3.500A) Processing helix chain 'F' and resid 9 through 20 removed outlier: 3.895A pdb=" N PHE F 19 " --> pdb=" O ILE F 15 " (cutoff:3.500A) Processing helix chain 'F' and resid 55 through 57 No H-bonds generated for 'chain 'F' and resid 55 through 57' Processing helix chain 'F' and resid 72 through 80 Processing helix chain 'F' and resid 141 through 155 removed outlier: 3.754A pdb=" N GLN F 153 " --> pdb=" O ARG F 149 " (cutoff:3.500A) removed outlier: 4.181A pdb=" N LEU F 154 " --> pdb=" O ASP F 150 " (cutoff:3.500A) Processing helix chain 'F' and resid 190 through 194 Processing helix chain 'F' and resid 209 through 216 Processing helix chain 'F' and resid 217 through 221 removed outlier: 4.029A pdb=" N SER F 220 " --> pdb=" O LYS F 217 " (cutoff:3.500A) Processing helix chain 'G' and resid 9 through 19 removed outlier: 3.902A pdb=" N PHE G 19 " --> pdb=" O ILE G 15 " (cutoff:3.500A) Processing helix chain 'G' and resid 55 through 57 No H-bonds generated for 'chain 'G' and resid 55 through 57' Processing helix chain 'G' and resid 72 through 80 Processing helix chain 'G' and resid 141 through 155 removed outlier: 3.555A pdb=" N GLN G 153 " --> pdb=" O ARG G 149 " (cutoff:3.500A) removed outlier: 4.277A pdb=" N LEU G 154 " --> pdb=" O ASP G 150 " (cutoff:3.500A) Processing helix chain 'G' and resid 190 through 194 removed outlier: 3.581A pdb=" N SER G 194 " --> pdb=" O PRO G 191 " (cutoff:3.500A) Processing helix chain 'G' and resid 209 through 216 Processing helix chain 'G' and resid 217 through 221 removed outlier: 3.990A pdb=" N SER G 220 " --> pdb=" O LYS G 217 " (cutoff:3.500A) Processing helix chain 'H' and resid 9 through 20 removed outlier: 3.872A pdb=" N PHE H 19 " --> pdb=" O ILE H 15 " (cutoff:3.500A) Processing helix chain 'H' and resid 72 through 80 Processing helix chain 'H' and resid 141 through 152 Processing helix chain 'H' and resid 209 through 217 removed outlier: 3.788A pdb=" N LYS H 217 " --> pdb=" O LEU H 213 " (cutoff:3.500A) Processing helix chain 'H' and resid 218 through 221 Processing sheet with id=AA1, first strand: chain 'A' and resid 373 through 377 removed outlier: 6.562A pdb=" N ASP A 373 " --> pdb=" O VAL A 420 " (cutoff:3.500A) removed outlier: 7.155A pdb=" N ILE A 422 " --> pdb=" O ASP A 373 " (cutoff:3.500A) removed outlier: 6.308A pdb=" N LEU A 375 " --> pdb=" O ILE A 422 " (cutoff:3.500A) removed outlier: 8.000A pdb=" N ILE A 452 " --> pdb=" O PHE A 419 " (cutoff:3.500A) removed outlier: 6.409A pdb=" N ILE A 421 " --> pdb=" O ILE A 452 " (cutoff:3.500A) removed outlier: 7.819A pdb=" N ILE A 454 " --> pdb=" O ILE A 421 " (cutoff:3.500A) removed outlier: 6.875A pdb=" N MET A 423 " --> pdb=" O ILE A 454 " (cutoff:3.500A) removed outlier: 7.267A pdb=" N ALA A 348 " --> pdb=" O LEU A 471 " (cutoff:3.500A) removed outlier: 7.966A pdb=" N ILE A 473 " --> pdb=" O ALA A 348 " (cutoff:3.500A) removed outlier: 6.144A pdb=" N MET A 350 " --> pdb=" O ILE A 473 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 497 through 498 removed outlier: 6.755A pdb=" N LYS A 497 " --> pdb=" O ILE A 531 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'A' and resid 599 through 601 Processing sheet with id=AA4, first strand: chain 'B' and resid 75 through 78 removed outlier: 6.354A pdb=" N LYS B 109 " --> pdb=" O ARG B 139 " (cutoff:3.500A) removed outlier: 7.588A pdb=" N ALA B 141 " --> pdb=" O LYS B 109 " (cutoff:3.500A) removed outlier: 6.341A pdb=" N VAL B 111 " --> pdb=" O ALA B 141 " (cutoff:3.500A) removed outlier: 7.635A pdb=" N ALA B 143 " --> pdb=" O VAL B 111 " (cutoff:3.500A) removed outlier: 6.667A pdb=" N LEU B 113 " --> pdb=" O ALA B 143 " (cutoff:3.500A) removed outlier: 6.310A pdb=" N ILE B 46 " --> pdb=" O LEU B 161 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 79 through 82 removed outlier: 6.687A pdb=" N LEU C 49 " --> pdb=" O VAL C 145 " (cutoff:3.500A) removed outlier: 8.071A pdb=" N ALA C 147 " --> pdb=" O LEU C 49 " (cutoff:3.500A) removed outlier: 6.262A pdb=" N PHE C 51 " --> pdb=" O ALA C 147 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 188 through 189 removed outlier: 7.156A pdb=" N LYS C 188 " --> pdb=" O ILE C 227 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'D' and resid 92 through 95 removed outlier: 6.610A pdb=" N MET D 61 " --> pdb=" O LEU D 168 " (cutoff:3.500A) removed outlier: 8.011A pdb=" N CYS D 170 " --> pdb=" O MET D 61 " (cutoff:3.500A) removed outlier: 6.280A pdb=" N PHE D 63 " --> pdb=" O CYS D 170 " (cutoff:3.500A) removed outlier: 6.226A pdb=" N LEU D 62 " --> pdb=" O PHE D 187 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'E' and resid 69 through 76 removed outlier: 6.283A pdb=" N LYS E 136 " --> pdb=" O ARG E 166 " (cutoff:3.500A) removed outlier: 7.650A pdb=" N ILE E 168 " --> pdb=" O LYS E 136 " (cutoff:3.500A) removed outlier: 6.193A pdb=" N VAL E 138 " --> pdb=" O ILE E 168 " (cutoff:3.500A) removed outlier: 7.462A pdb=" N VAL E 170 " --> pdb=" O VAL E 138 " (cutoff:3.500A) removed outlier: 6.750A pdb=" N ILE E 140 " --> pdb=" O VAL E 170 " (cutoff:3.500A) removed outlier: 6.579A pdb=" N LEU E 39 " --> pdb=" O MET E 169 " (cutoff:3.500A) removed outlier: 7.844A pdb=" N CYS E 171 " --> pdb=" O LEU E 39 " (cutoff:3.500A) removed outlier: 6.033A pdb=" N LEU E 41 " --> pdb=" O CYS E 171 " (cutoff:3.500A) removed outlier: 6.370A pdb=" N LEU E 40 " --> pdb=" O ILE E 188 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'E' and resid 212 through 213 removed outlier: 6.354A pdb=" N GLN E 212 " --> pdb=" O LEU E 248 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'F' and resid 59 through 62 removed outlier: 3.817A pdb=" N GLU F 59 " --> pdb=" O LYS F 5 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N ILE F 111 " --> pdb=" O ILE H 181 " (cutoff:3.500A) removed outlier: 4.740A pdb=" N ASP H 172 " --> pdb=" O SER H 157 " (cutoff:3.500A) removed outlier: 6.163A pdb=" N SER H 157 " --> pdb=" O ASP H 172 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'F' and resid 66 through 71 removed outlier: 6.616A pdb=" N LEU F 25 " --> pdb=" O VAL F 40 " (cutoff:3.500A) removed outlier: 5.813A pdb=" N VAL F 40 " --> pdb=" O LEU F 25 " (cutoff:3.500A) removed outlier: 4.396A pdb=" N ASN F 27 " --> pdb=" O GLN F 38 " (cutoff:3.500A) removed outlier: 4.196A pdb=" N GLN F 38 " --> pdb=" O ASN F 27 " (cutoff:3.500A) removed outlier: 5.340A pdb=" N SER F 230 " --> pdb=" O PRO F 234 " (cutoff:3.500A) removed outlier: 4.748A pdb=" N ASP F 240 " --> pdb=" O ARG F 224 " (cutoff:3.500A) removed outlier: 6.791A pdb=" N ARG F 224 " --> pdb=" O ASP F 240 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'F' and resid 203 through 208 removed outlier: 6.065A pdb=" N SER F 157 " --> pdb=" O ASP F 172 " (cutoff:3.500A) removed outlier: 4.733A pdb=" N ASP F 172 " --> pdb=" O SER F 157 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N ILE G 111 " --> pdb=" O ILE F 181 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N GLU G 59 " --> pdb=" O LYS G 5 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'G' and resid 66 through 71 removed outlier: 6.669A pdb=" N LEU G 25 " --> pdb=" O VAL G 40 " (cutoff:3.500A) removed outlier: 5.764A pdb=" N VAL G 40 " --> pdb=" O LEU G 25 " (cutoff:3.500A) removed outlier: 4.479A pdb=" N ASN G 27 " --> pdb=" O GLN G 38 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N GLN G 38 " --> pdb=" O ASN G 27 " (cutoff:3.500A) removed outlier: 4.585A pdb=" N ASP G 240 " --> pdb=" O ARG G 224 " (cutoff:3.500A) removed outlier: 6.706A pdb=" N ARG G 224 " --> pdb=" O ASP G 240 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'G' and resid 203 through 208 removed outlier: 5.553A pdb=" N SER G 157 " --> pdb=" O ASP G 172 " (cutoff:3.500A) removed outlier: 4.476A pdb=" N ASP G 172 " --> pdb=" O SER G 157 " (cutoff:3.500A) removed outlier: 4.376A pdb=" N ILE G 181 " --> pdb=" O ILE H 111 " (cutoff:3.500A) removed outlier: 5.250A pdb=" N ILE H 111 " --> pdb=" O ILE G 181 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N LEU H 102 " --> pdb=" O THR H 89 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'H' and resid 66 through 71 removed outlier: 7.522A pdb=" N LEU H 25 " --> pdb=" O VAL H 40 " (cutoff:3.500A) removed outlier: 6.398A pdb=" N VAL H 40 " --> pdb=" O LEU H 25 " (cutoff:3.500A) removed outlier: 5.342A pdb=" N ASN H 27 " --> pdb=" O GLN H 38 " (cutoff:3.500A) removed outlier: 4.572A pdb=" N GLN H 38 " --> pdb=" O ASN H 27 " (cutoff:3.500A) removed outlier: 4.462A pdb=" N ASP H 240 " --> pdb=" O ARG H 224 " (cutoff:3.500A) removed outlier: 6.553A pdb=" N ARG H 224 " --> pdb=" O ASP H 240 " (cutoff:3.500A) 1150 hydrogen bonds defined for protein. 3234 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 50 hydrogen bonds 100 hydrogen bond angles 0 basepair planarities 20 basepair parallelities 46 stacking parallelities Total time for adding SS restraints: 20.80 Time building geometry restraints manager: 14.49 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.06: 21593 1.06 - 1.28: 3624 1.28 - 1.50: 9407 1.50 - 1.73: 9319 1.73 - 1.95: 159 Bond restraints: 44102 Sorted by residual: bond pdb=" N SER H 0 " pdb=" CA SER H 0 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.90e-02 2.77e+03 3.06e+00 bond pdb=" N ALA G -1 " pdb=" CA ALA G -1 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.90e-02 2.77e+03 3.04e+00 bond pdb=" N ALA F -1 " pdb=" CA ALA F -1 " ideal model delta sigma weight residual 1.458 1.490 -0.032 1.90e-02 2.77e+03 2.77e+00 bond pdb=" CA ASP H 204 " pdb=" CB ASP H 204 " ideal model delta sigma weight residual 1.523 1.544 -0.021 1.35e-02 5.49e+03 2.42e+00 bond pdb=" N ALA F -1 " pdb=" H ALA F -1 " ideal model delta sigma weight residual 0.860 0.890 -0.030 2.00e-02 2.50e+03 2.23e+00 ... (remaining 44097 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.81: 79397 1.81 - 3.63: 577 3.63 - 5.44: 37 5.44 - 7.25: 2 7.25 - 9.07: 1 Bond angle restraints: 80014 Sorted by residual: angle pdb=" N VAL F 45 " pdb=" CA VAL F 45 " pdb=" C VAL F 45 " ideal model delta sigma weight residual 112.96 109.70 3.26 1.00e+00 1.00e+00 1.06e+01 angle pdb=" CB MET H 188 " pdb=" CG MET H 188 " pdb=" SD MET H 188 " ideal model delta sigma weight residual 112.70 121.77 -9.07 3.00e+00 1.11e-01 9.14e+00 angle pdb=" N VAL B 303 " pdb=" CA VAL B 303 " pdb=" C VAL B 303 " ideal model delta sigma weight residual 106.21 109.33 -3.12 1.07e+00 8.73e-01 8.51e+00 angle pdb=" CG MET H 188 " pdb=" SD MET H 188 " pdb=" CE MET H 188 " ideal model delta sigma weight residual 100.90 106.28 -5.38 2.20e+00 2.07e-01 5.98e+00 angle pdb=" C ILE F 215 " pdb=" CA ILE F 215 " pdb=" CB ILE F 215 " ideal model delta sigma weight residual 112.22 108.85 3.37 1.38e+00 5.25e-01 5.95e+00 ... (remaining 80009 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.45: 19410 35.45 - 70.90: 810 70.90 - 106.36: 37 106.36 - 141.81: 1 141.81 - 177.26: 1 Dihedral angle restraints: 20259 sinusoidal: 11624 harmonic: 8635 Sorted by residual: dihedral pdb=" O1B ADP E 401 " pdb=" O3A ADP E 401 " pdb=" PB ADP E 401 " pdb=" PA ADP E 401 " ideal model delta sinusoidal sigma weight residual 300.00 178.58 121.42 1 2.00e+01 2.50e-03 3.65e+01 dihedral pdb=" C4' DT K -1 " pdb=" C3' DT K -1 " pdb=" O3' DT K -1 " pdb=" P DA K 0 " ideal model delta sinusoidal sigma weight residual 220.00 42.74 177.26 1 3.50e+01 8.16e-04 1.57e+01 dihedral pdb=" O1A AGS C 402 " pdb=" O3A AGS C 402 " pdb=" PA AGS C 402 " pdb=" PB AGS C 402 " ideal model delta sinusoidal sigma weight residual -67.73 32.24 -99.97 1 3.00e+01 1.11e-03 1.25e+01 ... (remaining 20256 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.030: 2403 0.030 - 0.060: 757 0.060 - 0.090: 249 0.090 - 0.120: 133 0.120 - 0.150: 27 Chirality restraints: 3569 Sorted by residual: chirality pdb=" CA ILE G 167 " pdb=" N ILE G 167 " pdb=" C ILE G 167 " pdb=" CB ILE G 167 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.64e-01 chirality pdb=" CA ILE A 762 " pdb=" N ILE A 762 " pdb=" C ILE A 762 " pdb=" CB ILE A 762 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.44e-01 chirality pdb=" CA ILE F 111 " pdb=" N ILE F 111 " pdb=" C ILE F 111 " pdb=" CB ILE F 111 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.14 2.00e-01 2.50e+01 5.25e-01 ... (remaining 3566 not shown) Planarity restraints: 6236 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LYS H 183 " -0.035 5.00e-02 4.00e+02 5.28e-02 4.47e+00 pdb=" N PRO H 184 " 0.091 5.00e-02 4.00e+02 pdb=" CA PRO H 184 " -0.027 5.00e-02 4.00e+02 pdb=" CD PRO H 184 " -0.029 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CG GLN A 439 " 0.008 2.00e-02 2.50e+03 1.44e-02 3.10e+00 pdb=" CD GLN A 439 " -0.031 2.00e-02 2.50e+03 pdb=" OE1 GLN A 439 " 0.014 2.00e-02 2.50e+03 pdb=" NE2 GLN A 439 " 0.004 2.00e-02 2.50e+03 pdb="HE21 GLN A 439 " 0.005 2.00e-02 2.50e+03 pdb="HE22 GLN A 439 " -0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 458 " -0.138 9.50e-02 1.11e+02 4.61e-02 2.63e+00 pdb=" NE ARG A 458 " 0.011 2.00e-02 2.50e+03 pdb=" CZ ARG A 458 " -0.009 2.00e-02 2.50e+03 pdb=" NH1 ARG A 458 " -0.000 2.00e-02 2.50e+03 pdb=" NH2 ARG A 458 " -0.000 2.00e-02 2.50e+03 pdb="HH11 ARG A 458 " 0.004 2.00e-02 2.50e+03 pdb="HH12 ARG A 458 " 0.000 2.00e-02 2.50e+03 pdb="HH21 ARG A 458 " -0.000 2.00e-02 2.50e+03 pdb="HH22 ARG A 458 " 0.000 2.00e-02 2.50e+03 ... (remaining 6233 not shown) Histogram of nonbonded interaction distances: 1.49 - 2.12: 798 2.12 - 2.74: 76838 2.74 - 3.36: 125781 3.36 - 3.98: 165065 3.98 - 4.60: 254660 Nonbonded interactions: 623142 Sorted by model distance: nonbonded pdb=" OE1 GLU A 740 " pdb=" H GLU A 740 " model vdw 1.495 2.450 nonbonded pdb=" OE1 GLU G 7 " pdb=" H GLU G 7 " model vdw 1.544 2.450 nonbonded pdb="HE22 GLN H 24 " pdb=" OG1 THR H 73 " model vdw 1.589 2.450 nonbonded pdb=" O GLY C 53 " pdb="HD22 ASN C 148 " model vdw 1.593 2.450 nonbonded pdb=" OE1 GLU H 55 " pdb=" H GLU H 55 " model vdw 1.603 2.450 ... (remaining 623137 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'F' and resid 0 through 254) selection = (chain 'G' and ((resid 0 and (name N or name CA or name C or name O or name CB o \ r name H or name HA )) or resid 1 through 254)) selection = (chain 'H' and ((resid 0 and (name N or name CA or name C or name O or name CB o \ r name H or name HA )) or resid 1 through 254)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 15.580 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.000 Check model and map are aligned: 0.000 Set scattering table: 0.000 Process input model: 108.280 Find NCS groups from input model: 0.920 Set up NCS constraints: 0.150 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:14.280 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 139.220 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8282 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 : 0.002 0.033 22470 Z= 0.150 Angle : 0.521 9.069 30653 Z= 0.298 Chirality : 0.038 0.150 3569 Planarity : 0.003 0.061 3672 Dihedral : 17.898 177.260 8626 Min Nonbonded Distance : 1.996 Molprobity Statistics. All-atom Clashscore : 3.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.27 % Favored : 98.73 % Rotamer: Outliers : 0.95 % Allowed : 18.00 % Favored : 81.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.01 (0.17), residues: 2590 helix: 2.11 (0.16), residues: 1227 sheet: 0.97 (0.22), residues: 521 loop : 0.53 (0.23), residues: 842 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 742 HIS 0.003 0.000 HIS C 260 PHE 0.011 0.001 PHE H 245 TYR 0.011 0.001 TYR H 211 ARG 0.009 0.000 ARG A 458 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5180 Ramachandran restraints generated. 2590 Oldfield, 0 Emsley, 2590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5180 Ramachandran restraints generated. 2590 Oldfield, 0 Emsley, 2590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue MET 1 is missing expected H atoms. Skipping. Residue SER 0 is missing expected H atoms. Skipping. Evaluate side-chains 311 residues out of total 2316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 289 time to evaluate : 3.821 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: H 122 ASP cc_start: 0.7072 (p0) cc_final: 0.6853 (p0) outliers start: 22 outliers final: 17 residues processed: 309 average time/residue: 3.4160 time to fit residues: 1191.4911 Evaluate side-chains 224 residues out of total 2316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 207 time to evaluate : 3.542 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 341 ASP Chi-restraints excluded: chain A residue 723 ASP Chi-restraints excluded: chain B residue 4 THR Chi-restraints excluded: chain B residue 248 SER Chi-restraints excluded: chain C residue 76 SER Chi-restraints excluded: chain C residue 235 CYS Chi-restraints excluded: chain E residue 2 SER Chi-restraints excluded: chain E residue 17 SER Chi-restraints excluded: chain E residue 90 SER Chi-restraints excluded: chain E residue 206 VAL Chi-restraints excluded: chain F residue 185 PHE Chi-restraints excluded: chain G residue 166 THR Chi-restraints excluded: chain H residue 30 CYS Chi-restraints excluded: chain H residue 51 GLU Chi-restraints excluded: chain H residue 81 CYS Chi-restraints excluded: chain H residue 152 SER Chi-restraints excluded: chain H residue 194 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 262 random chunks: chunk 221 optimal weight: 1.9990 chunk 198 optimal weight: 2.9990 chunk 110 optimal weight: 1.9990 chunk 67 optimal weight: 3.9990 chunk 133 optimal weight: 0.4980 chunk 106 optimal weight: 2.9990 chunk 205 optimal weight: 0.9990 chunk 79 optimal weight: 1.9990 chunk 124 optimal weight: 0.9990 chunk 152 optimal weight: 1.9990 chunk 237 optimal weight: 8.9990 overall best weight: 1.2988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 389 ASN B 317 HIS B 321 ASN D 317 ASN E 212 GLN F 84 ASN G 29 GLN G 159 ASN G 255 ASN H 84 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8360 moved from start: 0.1482 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 22470 Z= 0.238 Angle : 0.542 6.227 30653 Z= 0.294 Chirality : 0.040 0.169 3569 Planarity : 0.004 0.050 3672 Dihedral : 15.203 177.449 3532 Min Nonbonded Distance : 1.684 Molprobity Statistics. All-atom Clashscore : 2.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.43 % Favored : 98.57 % Rotamer: Outliers : 1.56 % Allowed : 17.87 % Favored : 80.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.74 (0.17), residues: 2590 helix: 1.82 (0.15), residues: 1256 sheet: 0.99 (0.22), residues: 516 loop : 0.34 (0.22), residues: 818 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 638 HIS 0.005 0.001 HIS C 260 PHE 0.014 0.001 PHE E 328 TYR 0.010 0.001 TYR H 211 ARG 0.006 0.001 ARG A 663 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5180 Ramachandran restraints generated. 2590 Oldfield, 0 Emsley, 2590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5180 Ramachandran restraints generated. 2590 Oldfield, 0 Emsley, 2590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue MET 1 is missing expected H atoms. Skipping. Residue SER 0 is missing expected H atoms. Skipping. Evaluate side-chains 249 residues out of total 2316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 213 time to evaluate : 3.760 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 outliers start: 36 outliers final: 17 residues processed: 241 average time/residue: 3.4230 time to fit residues: 933.6281 Evaluate side-chains 214 residues out of total 2316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 197 time to evaluate : 3.520 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 4 THR Chi-restraints excluded: chain C residue 74 ASN Chi-restraints excluded: chain C residue 76 SER Chi-restraints excluded: chain C residue 91 ASP Chi-restraints excluded: chain C residue 235 CYS Chi-restraints excluded: chain D residue 277 SER Chi-restraints excluded: chain E residue 2 SER Chi-restraints excluded: chain E residue 17 SER Chi-restraints excluded: chain E residue 90 SER Chi-restraints excluded: chain E residue 145 SER Chi-restraints excluded: chain E residue 206 VAL Chi-restraints excluded: chain F residue 83 ASN Chi-restraints excluded: chain F residue 185 PHE Chi-restraints excluded: chain G residue 166 THR Chi-restraints excluded: chain G residue 179 SER Chi-restraints excluded: chain H residue 30 CYS Chi-restraints excluded: chain H residue 51 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 262 random chunks: chunk 132 optimal weight: 2.9990 chunk 73 optimal weight: 1.9990 chunk 198 optimal weight: 0.6980 chunk 162 optimal weight: 2.9990 chunk 65 optimal weight: 0.5980 chunk 238 optimal weight: 7.9990 chunk 257 optimal weight: 10.0000 chunk 212 optimal weight: 3.9990 chunk 236 optimal weight: 0.0370 chunk 81 optimal weight: 1.9990 chunk 191 optimal weight: 1.9990 overall best weight: 1.0662 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 389 ASN B 146 GLN H 84 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8373 moved from start: 0.1747 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 22470 Z= 0.192 Angle : 0.505 7.084 30653 Z= 0.271 Chirality : 0.039 0.160 3569 Planarity : 0.003 0.040 3672 Dihedral : 15.221 176.784 3524 Min Nonbonded Distance : 1.769 Molprobity Statistics. All-atom Clashscore : 2.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.51 % Favored : 98.49 % Rotamer: Outliers : 1.17 % Allowed : 17.70 % Favored : 81.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.77 (0.17), residues: 2590 helix: 1.90 (0.15), residues: 1245 sheet: 0.93 (0.22), residues: 519 loop : 0.34 (0.22), residues: 826 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 638 HIS 0.004 0.001 HIS C 260 PHE 0.011 0.001 PHE E 328 TYR 0.009 0.001 TYR H 211 ARG 0.004 0.000 ARG E 81 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5180 Ramachandran restraints generated. 2590 Oldfield, 0 Emsley, 2590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5180 Ramachandran restraints generated. 2590 Oldfield, 0 Emsley, 2590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue MET 1 is missing expected H atoms. Skipping. Residue SER 0 is missing expected H atoms. Skipping. Evaluate side-chains 238 residues out of total 2316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 211 time to evaluate : 3.960 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 outliers start: 27 outliers final: 14 residues processed: 232 average time/residue: 3.6096 time to fit residues: 952.4932 Evaluate side-chains 211 residues out of total 2316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 197 time to evaluate : 3.641 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 76 SER Chi-restraints excluded: chain C residue 91 ASP Chi-restraints excluded: chain C residue 235 CYS Chi-restraints excluded: chain D residue 277 SER Chi-restraints excluded: chain E residue 2 SER Chi-restraints excluded: chain E residue 17 SER Chi-restraints excluded: chain E residue 90 SER Chi-restraints excluded: chain E residue 145 SER Chi-restraints excluded: chain E residue 206 VAL Chi-restraints excluded: chain F residue 83 ASN Chi-restraints excluded: chain F residue 185 PHE Chi-restraints excluded: chain G residue 166 THR Chi-restraints excluded: chain H residue 30 CYS Chi-restraints excluded: chain H residue 51 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 262 random chunks: chunk 235 optimal weight: 7.9990 chunk 179 optimal weight: 1.9990 chunk 123 optimal weight: 2.9990 chunk 26 optimal weight: 3.9990 chunk 113 optimal weight: 8.9990 chunk 160 optimal weight: 3.9990 chunk 239 optimal weight: 5.9990 chunk 253 optimal weight: 4.9990 chunk 124 optimal weight: 0.8980 chunk 226 optimal weight: 1.9990 chunk 68 optimal weight: 3.9990 overall best weight: 2.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 389 ASN E 212 GLN F 159 ASN H 84 ASN H 153 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8442 moved from start: 0.2117 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 22470 Z= 0.345 Angle : 0.546 6.518 30653 Z= 0.296 Chirality : 0.042 0.170 3569 Planarity : 0.004 0.058 3672 Dihedral : 15.381 177.795 3523 Min Nonbonded Distance : 1.695 Molprobity Statistics. All-atom Clashscore : 2.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.70 % Favored : 98.30 % Rotamer: Outliers : 1.17 % Allowed : 17.14 % Favored : 81.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.52 (0.17), residues: 2590 helix: 1.69 (0.15), residues: 1248 sheet: 0.81 (0.22), residues: 522 loop : 0.21 (0.22), residues: 820 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 638 HIS 0.008 0.001 HIS B 232 PHE 0.015 0.001 PHE E 328 TYR 0.012 0.001 TYR A 688 ARG 0.003 0.000 ARG H 110 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5180 Ramachandran restraints generated. 2590 Oldfield, 0 Emsley, 2590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5180 Ramachandran restraints generated. 2590 Oldfield, 0 Emsley, 2590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue MET 1 is missing expected H atoms. Skipping. Residue SER 0 is missing expected H atoms. Skipping. Evaluate side-chains 223 residues out of total 2316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 196 time to evaluate : 3.609 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: H 109 ASP cc_start: 0.7890 (p0) cc_final: 0.7641 (p0) outliers start: 27 outliers final: 17 residues processed: 217 average time/residue: 3.7189 time to fit residues: 907.2271 Evaluate side-chains 208 residues out of total 2316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 191 time to evaluate : 3.884 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 91 ASP Chi-restraints excluded: chain C residue 235 CYS Chi-restraints excluded: chain D residue 277 SER Chi-restraints excluded: chain E residue 2 SER Chi-restraints excluded: chain E residue 45 ASN Chi-restraints excluded: chain E residue 90 SER Chi-restraints excluded: chain E residue 206 VAL Chi-restraints excluded: chain F residue 83 ASN Chi-restraints excluded: chain F residue 165 GLU Chi-restraints excluded: chain F residue 185 PHE Chi-restraints excluded: chain G residue 131 LEU Chi-restraints excluded: chain G residue 141 SER Chi-restraints excluded: chain G residue 145 SER Chi-restraints excluded: chain G residue 166 THR Chi-restraints excluded: chain H residue 26 VAL Chi-restraints excluded: chain H residue 30 CYS Chi-restraints excluded: chain H residue 51 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 262 random chunks: chunk 210 optimal weight: 0.6980 chunk 143 optimal weight: 1.9990 chunk 3 optimal weight: 4.9990 chunk 188 optimal weight: 3.9990 chunk 104 optimal weight: 2.9990 chunk 216 optimal weight: 2.9990 chunk 175 optimal weight: 2.9990 chunk 0 optimal weight: 4.9990 chunk 129 optimal weight: 0.9990 chunk 227 optimal weight: 1.9990 chunk 63 optimal weight: 0.9990 overall best weight: 1.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 389 ASN H 84 ASN H 153 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8423 moved from start: 0.2199 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 22470 Z= 0.216 Angle : 0.507 8.823 30653 Z= 0.274 Chirality : 0.040 0.161 3569 Planarity : 0.004 0.041 3672 Dihedral : 15.358 177.900 3521 Min Nonbonded Distance : 1.748 Molprobity Statistics. All-atom Clashscore : 2.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.70 % Favored : 98.30 % Rotamer: Outliers : 1.13 % Allowed : 17.31 % Favored : 81.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.62 (0.17), residues: 2590 helix: 1.82 (0.15), residues: 1239 sheet: 0.79 (0.22), residues: 521 loop : 0.25 (0.22), residues: 830 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 638 HIS 0.006 0.001 HIS B 232 PHE 0.012 0.001 PHE E 328 TYR 0.009 0.001 TYR A 688 ARG 0.007 0.000 ARG G 80 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5180 Ramachandran restraints generated. 2590 Oldfield, 0 Emsley, 2590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5180 Ramachandran restraints generated. 2590 Oldfield, 0 Emsley, 2590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue MET 1 is missing expected H atoms. Skipping. Residue SER 0 is missing expected H atoms. Skipping. Evaluate side-chains 225 residues out of total 2316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 199 time to evaluate : 3.680 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: G 125 PHE cc_start: 0.7707 (OUTLIER) cc_final: 0.7225 (t80) outliers start: 26 outliers final: 13 residues processed: 217 average time/residue: 3.6341 time to fit residues: 886.6615 Evaluate side-chains 207 residues out of total 2316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 193 time to evaluate : 4.006 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 91 ASP Chi-restraints excluded: chain C residue 235 CYS Chi-restraints excluded: chain D residue 277 SER Chi-restraints excluded: chain E residue 2 SER Chi-restraints excluded: chain E residue 45 ASN Chi-restraints excluded: chain E residue 90 SER Chi-restraints excluded: chain E residue 206 VAL Chi-restraints excluded: chain F residue 83 ASN Chi-restraints excluded: chain F residue 185 PHE Chi-restraints excluded: chain G residue 125 PHE Chi-restraints excluded: chain G residue 166 THR Chi-restraints excluded: chain H residue 26 VAL Chi-restraints excluded: chain H residue 30 CYS Chi-restraints excluded: chain H residue 51 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 262 random chunks: chunk 85 optimal weight: 0.5980 chunk 228 optimal weight: 2.9990 chunk 50 optimal weight: 1.9990 chunk 148 optimal weight: 0.9980 chunk 62 optimal weight: 2.9990 chunk 253 optimal weight: 3.9990 chunk 210 optimal weight: 0.0050 chunk 117 optimal weight: 0.0770 chunk 21 optimal weight: 4.9990 chunk 83 optimal weight: 1.9990 chunk 133 optimal weight: 3.9990 overall best weight: 0.7354 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 212 GLN H 84 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8401 moved from start: 0.2270 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 22470 Z= 0.163 Angle : 0.496 6.679 30653 Z= 0.266 Chirality : 0.039 0.161 3569 Planarity : 0.004 0.087 3672 Dihedral : 15.279 177.789 3521 Min Nonbonded Distance : 1.790 Molprobity Statistics. All-atom Clashscore : 2.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.78 % Favored : 98.22 % Rotamer: Outliers : 0.87 % Allowed : 17.57 % Favored : 81.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.77 (0.17), residues: 2590 helix: 1.96 (0.15), residues: 1240 sheet: 0.79 (0.22), residues: 521 loop : 0.34 (0.22), residues: 829 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP E 259 HIS 0.013 0.001 HIS H 190 PHE 0.009 0.001 PHE E 328 TYR 0.008 0.001 TYR D 286 ARG 0.006 0.000 ARG E 34 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5180 Ramachandran restraints generated. 2590 Oldfield, 0 Emsley, 2590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5180 Ramachandran restraints generated. 2590 Oldfield, 0 Emsley, 2590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue MET 1 is missing expected H atoms. Skipping. Residue SER 0 is missing expected H atoms. Skipping. Evaluate side-chains 226 residues out of total 2316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 206 time to evaluate : 3.677 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 outliers start: 20 outliers final: 13 residues processed: 219 average time/residue: 3.8745 time to fit residues: 950.3614 Evaluate side-chains 202 residues out of total 2316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 189 time to evaluate : 3.551 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 490 ILE Chi-restraints excluded: chain B residue 267 VAL Chi-restraints excluded: chain C residue 91 ASP Chi-restraints excluded: chain C residue 235 CYS Chi-restraints excluded: chain D residue 212 CYS Chi-restraints excluded: chain D residue 277 SER Chi-restraints excluded: chain E residue 2 SER Chi-restraints excluded: chain E residue 90 SER Chi-restraints excluded: chain F residue 83 ASN Chi-restraints excluded: chain F residue 185 PHE Chi-restraints excluded: chain G residue 166 THR Chi-restraints excluded: chain H residue 30 CYS Chi-restraints excluded: chain H residue 51 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 262 random chunks: chunk 244 optimal weight: 7.9990 chunk 28 optimal weight: 1.9990 chunk 144 optimal weight: 0.9990 chunk 185 optimal weight: 2.9990 chunk 143 optimal weight: 0.9990 chunk 213 optimal weight: 0.5980 chunk 141 optimal weight: 3.9990 chunk 252 optimal weight: 2.9990 chunk 158 optimal weight: 3.9990 chunk 153 optimal weight: 2.9990 chunk 116 optimal weight: 2.9990 overall best weight: 1.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 84 ASN H 153 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8429 moved from start: 0.2380 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 22470 Z= 0.244 Angle : 0.515 6.924 30653 Z= 0.276 Chirality : 0.040 0.154 3569 Planarity : 0.004 0.110 3672 Dihedral : 15.306 178.019 3520 Min Nonbonded Distance : 1.704 Molprobity Statistics. All-atom Clashscore : 2.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.74 % Favored : 98.26 % Rotamer: Outliers : 0.82 % Allowed : 17.61 % Favored : 81.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.75 (0.17), residues: 2590 helix: 1.94 (0.15), residues: 1240 sheet: 0.77 (0.22), residues: 531 loop : 0.33 (0.22), residues: 819 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 638 HIS 0.006 0.001 HIS G 190 PHE 0.012 0.001 PHE E 328 TYR 0.009 0.001 TYR D 286 ARG 0.011 0.000 ARG E 34 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5180 Ramachandran restraints generated. 2590 Oldfield, 0 Emsley, 2590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5180 Ramachandran restraints generated. 2590 Oldfield, 0 Emsley, 2590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue MET 1 is missing expected H atoms. Skipping. Residue SER 0 is missing expected H atoms. Skipping. Evaluate side-chains 212 residues out of total 2316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 193 time to evaluate : 3.389 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: H 109 ASP cc_start: 0.7836 (p0) cc_final: 0.7549 (p0) outliers start: 19 outliers final: 15 residues processed: 208 average time/residue: 3.7655 time to fit residues: 889.0457 Evaluate side-chains 198 residues out of total 2316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 183 time to evaluate : 3.727 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 490 ILE Chi-restraints excluded: chain B residue 267 VAL Chi-restraints excluded: chain C residue 76 SER Chi-restraints excluded: chain C residue 91 ASP Chi-restraints excluded: chain C residue 235 CYS Chi-restraints excluded: chain D residue 212 CYS Chi-restraints excluded: chain D residue 277 SER Chi-restraints excluded: chain E residue 2 SER Chi-restraints excluded: chain E residue 90 SER Chi-restraints excluded: chain E residue 206 VAL Chi-restraints excluded: chain F residue 83 ASN Chi-restraints excluded: chain F residue 185 PHE Chi-restraints excluded: chain G residue 166 THR Chi-restraints excluded: chain H residue 30 CYS Chi-restraints excluded: chain H residue 199 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 262 random chunks: chunk 156 optimal weight: 0.6980 chunk 100 optimal weight: 0.0980 chunk 150 optimal weight: 2.9990 chunk 76 optimal weight: 2.9990 chunk 49 optimal weight: 2.9990 chunk 48 optimal weight: 7.9990 chunk 160 optimal weight: 0.6980 chunk 172 optimal weight: 2.9990 chunk 124 optimal weight: 0.6980 chunk 23 optimal weight: 9.9990 chunk 198 optimal weight: 0.4980 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 212 GLN H 84 ASN H 153 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8395 moved from start: 0.2421 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.052 22470 Z= 0.155 Angle : 0.500 7.499 30653 Z= 0.267 Chirality : 0.039 0.161 3569 Planarity : 0.004 0.072 3672 Dihedral : 15.190 177.886 3517 Min Nonbonded Distance : 1.828 Molprobity Statistics. All-atom Clashscore : 2.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.81 % Favored : 98.19 % Rotamer: Outliers : 0.74 % Allowed : 17.78 % Favored : 81.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.89 (0.17), residues: 2590 helix: 2.07 (0.15), residues: 1240 sheet: 0.78 (0.22), residues: 529 loop : 0.43 (0.22), residues: 821 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP E 259 HIS 0.005 0.001 HIS G 190 PHE 0.008 0.001 PHE E 328 TYR 0.007 0.001 TYR D 286 ARG 0.007 0.000 ARG G 80 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5180 Ramachandran restraints generated. 2590 Oldfield, 0 Emsley, 2590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5180 Ramachandran restraints generated. 2590 Oldfield, 0 Emsley, 2590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue MET 1 is missing expected H atoms. Skipping. Residue SER 0 is missing expected H atoms. Skipping. Evaluate side-chains 211 residues out of total 2316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 194 time to evaluate : 3.629 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: H 109 ASP cc_start: 0.7775 (p0) cc_final: 0.7542 (p0) outliers start: 17 outliers final: 9 residues processed: 203 average time/residue: 3.7499 time to fit residues: 853.1935 Evaluate side-chains 193 residues out of total 2316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 184 time to evaluate : 3.818 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 267 VAL Chi-restraints excluded: chain C residue 91 ASP Chi-restraints excluded: chain C residue 235 CYS Chi-restraints excluded: chain D residue 212 CYS Chi-restraints excluded: chain E residue 90 SER Chi-restraints excluded: chain F residue 83 ASN Chi-restraints excluded: chain F residue 185 PHE Chi-restraints excluded: chain G residue 166 THR Chi-restraints excluded: chain H residue 30 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 262 random chunks: chunk 229 optimal weight: 4.9990 chunk 241 optimal weight: 3.9990 chunk 220 optimal weight: 0.9980 chunk 235 optimal weight: 9.9990 chunk 141 optimal weight: 3.9990 chunk 102 optimal weight: 2.9990 chunk 184 optimal weight: 2.9990 chunk 72 optimal weight: 2.9990 chunk 212 optimal weight: 1.9990 chunk 222 optimal weight: 5.9990 chunk 234 optimal weight: 4.9990 overall best weight: 2.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 389 ASN F 132 GLN H 84 ASN H 153 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8459 moved from start: 0.2559 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.043 22470 Z= 0.362 Angle : 0.545 8.561 30653 Z= 0.292 Chirality : 0.042 0.169 3569 Planarity : 0.004 0.074 3672 Dihedral : 15.331 178.436 3516 Min Nonbonded Distance : 1.687 Molprobity Statistics. All-atom Clashscore : 2.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer: Outliers : 0.69 % Allowed : 18.04 % Favored : 81.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.69 (0.17), residues: 2590 helix: 1.89 (0.15), residues: 1245 sheet: 0.78 (0.22), residues: 530 loop : 0.27 (0.22), residues: 815 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 669 HIS 0.008 0.001 HIS B 232 PHE 0.015 0.001 PHE E 328 TYR 0.011 0.002 TYR A 688 ARG 0.009 0.000 ARG E 210 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5180 Ramachandran restraints generated. 2590 Oldfield, 0 Emsley, 2590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5180 Ramachandran restraints generated. 2590 Oldfield, 0 Emsley, 2590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue MET 1 is missing expected H atoms. Skipping. Residue SER 0 is missing expected H atoms. Skipping. Evaluate side-chains 207 residues out of total 2316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 191 time to evaluate : 3.693 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 16 outliers final: 12 residues processed: 203 average time/residue: 3.7359 time to fit residues: 851.5526 Evaluate side-chains 202 residues out of total 2316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 190 time to evaluate : 3.560 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 267 VAL Chi-restraints excluded: chain C residue 91 ASP Chi-restraints excluded: chain C residue 235 CYS Chi-restraints excluded: chain D residue 212 CYS Chi-restraints excluded: chain E residue 90 SER Chi-restraints excluded: chain E residue 206 VAL Chi-restraints excluded: chain F residue 83 ASN Chi-restraints excluded: chain F residue 185 PHE Chi-restraints excluded: chain G residue 166 THR Chi-restraints excluded: chain H residue 26 VAL Chi-restraints excluded: chain H residue 30 CYS Chi-restraints excluded: chain H residue 199 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 262 random chunks: chunk 154 optimal weight: 3.9990 chunk 248 optimal weight: 3.9990 chunk 151 optimal weight: 0.5980 chunk 118 optimal weight: 0.8980 chunk 172 optimal weight: 0.7980 chunk 261 optimal weight: 10.0000 chunk 240 optimal weight: 8.9990 chunk 207 optimal weight: 3.9990 chunk 21 optimal weight: 4.9990 chunk 160 optimal weight: 1.9990 chunk 127 optimal weight: 0.9980 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 389 ASN E 212 GLN H 84 ASN H 153 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8427 moved from start: 0.2568 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 22470 Z= 0.187 Angle : 0.519 9.960 30653 Z= 0.277 Chirality : 0.039 0.161 3569 Planarity : 0.004 0.072 3672 Dihedral : 15.312 178.425 3516 Min Nonbonded Distance : 1.759 Molprobity Statistics. All-atom Clashscore : 2.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer: Outliers : 0.65 % Allowed : 18.22 % Favored : 81.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.80 (0.17), residues: 2590 helix: 2.00 (0.15), residues: 1238 sheet: 0.81 (0.22), residues: 529 loop : 0.35 (0.22), residues: 823 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 669 HIS 0.005 0.001 HIS B 232 PHE 0.011 0.001 PHE E 328 TYR 0.009 0.001 TYR D 286 ARG 0.011 0.000 ARG E 210 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5180 Ramachandran restraints generated. 2590 Oldfield, 0 Emsley, 2590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5180 Ramachandran restraints generated. 2590 Oldfield, 0 Emsley, 2590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue MET 1 is missing expected H atoms. Skipping. Residue SER 0 is missing expected H atoms. Skipping. Evaluate side-chains 208 residues out of total 2316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 193 time to evaluate : 3.674 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 outliers start: 15 outliers final: 11 residues processed: 204 average time/residue: 3.8179 time to fit residues: 879.7509 Evaluate side-chains 200 residues out of total 2316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 189 time to evaluate : 3.602 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 76 SER Chi-restraints excluded: chain C residue 91 ASP Chi-restraints excluded: chain C residue 235 CYS Chi-restraints excluded: chain D residue 212 CYS Chi-restraints excluded: chain D residue 277 SER Chi-restraints excluded: chain E residue 90 SER Chi-restraints excluded: chain E residue 206 VAL Chi-restraints excluded: chain F residue 185 PHE Chi-restraints excluded: chain G residue 166 THR Chi-restraints excluded: chain H residue 30 CYS Chi-restraints excluded: chain H residue 199 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 262 random chunks: chunk 165 optimal weight: 0.9990 chunk 221 optimal weight: 0.5980 chunk 63 optimal weight: 0.9990 chunk 191 optimal weight: 2.9990 chunk 30 optimal weight: 2.9990 chunk 57 optimal weight: 0.7980 chunk 208 optimal weight: 2.9990 chunk 87 optimal weight: 2.9990 chunk 213 optimal weight: 0.7980 chunk 26 optimal weight: 2.9990 chunk 38 optimal weight: 2.9990 overall best weight: 0.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 132 GLN H 84 ASN H 153 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.099835 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2771 r_free = 0.2771 target = 0.061910 restraints weight = 96057.584| |-----------------------------------------------------------------------------| r_work (start): 0.2721 rms_B_bonded: 2.43 r_work: 0.2577 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.2448 rms_B_bonded: 4.24 restraints_weight: 0.2500 r_work (final): 0.2448 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8505 moved from start: 0.2588 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 22470 Z= 0.179 Angle : 0.511 10.406 30653 Z= 0.272 Chirality : 0.039 0.159 3569 Planarity : 0.004 0.086 3672 Dihedral : 15.260 178.246 3516 Min Nonbonded Distance : 1.783 Molprobity Statistics. All-atom Clashscore : 2.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.89 % Favored : 98.11 % Rotamer: Outliers : 0.56 % Allowed : 18.30 % Favored : 81.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.85 (0.17), residues: 2590 helix: 2.05 (0.15), residues: 1239 sheet: 0.81 (0.22), residues: 520 loop : 0.35 (0.22), residues: 831 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP E 259 HIS 0.005 0.001 HIS G 190 PHE 0.009 0.001 PHE E 328 TYR 0.008 0.001 TYR D 286 ARG 0.012 0.000 ARG E 210 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 15501.90 seconds wall clock time: 277 minutes 35.24 seconds (16655.24 seconds total)