Starting phenix.real_space_refine on Mon Sep 14 04:58:44 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6gh5_0001/09_2026/6gh5_0001.cif Found real_map, /net/cci-nas-00/data/ceres_data/6gh5_0001/09_2026/6gh5_0001.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/6gh5_0001/09_2026/6gh5_0001.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6gh5_0001/09_2026/6gh5_0001.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6gh5_0001/09_2026/6gh5_0001.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6gh5_0001/09_2026/6gh5_0001.map" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } 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= 0.008 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 92 5.49 5 S 97 5.16 5 C 17442 2.51 5 N 5014 2.21 5 O 5671 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 69 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 28316 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 2302 Number of conformers: 1 Conformer: "" Number of residues, atoms: 309, 2302 Classifications: {'peptide': 309} Incomplete info: {'truncation_to_alanine': 25} Link IDs: {'PTRANS': 14, 'TRANS': 294} Chain breaks: 1 Unresolved non-hydrogen bonds: 107 Unresolved non-hydrogen angles: 128 Unresolved non-hydrogen dihedrals: 90 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'ARG:plan': 5, 'GLU:plan': 6, 'GLN:plan1': 1, 'PHE:plan': 1, 'ASP:plan': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 67 Chain: "B" Number of atoms: 1733 Number of conformers: 1 Conformer: "" Number of residues, atoms: 235, 1733 Classifications: {'peptide': 235} Incomplete info: {'truncation_to_alanine': 20} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 225} Unresolved non-hydrogen bonds: 95 Unresolved non-hydrogen angles: 118 Unresolved non-hydrogen dihedrals: 79 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'HIS:plan': 2, 'GLU:plan': 5, 'TYR:plan': 1, 'ASP:plan': 3, 'ASN:plan1': 1, 'ARG:plan': 6} Unresolved non-hydrogen planarities: 79 Chain: "C" Number of atoms: 10034 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1341, 10034 Classifications: {'peptide': 1341} Incomplete info: {'truncation_to_alanine': 127} Link IDs: {'PCIS': 1, 'PTRANS': 55, 'TRANS': 1284} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 557 Unresolved non-hydrogen angles: 674 Unresolved non-hydrogen dihedrals: 478 Unresolved non-hydrogen chiralities: 14 Planarities with less than four sites: {'TYR:plan': 4, 'GLU:plan': 27, 'ARG:plan': 19, 'ASP:plan': 12, 'PHE:plan': 7, 'ASN:plan1': 2, 'GLN:plan1': 7, 'HIS:plan': 2, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 362 Chain: "D" Number of atoms: 9790 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1345, 9790 Classifications: {'peptide': 1345} Incomplete info: {'truncation_to_alanine': 163} Link IDs: {'CIS': 1, 'PCIS': 2, 'PTRANS': 51, 'TRANS': 1290} Chain breaks: 4 Unresolved non-hydrogen bonds: 699 Unresolved non-hydrogen angles: 851 Unresolved non-hydrogen dihedrals: 604 Unresolved non-hydrogen chiralities: 18 Planarities with less than four sites: {'GLN:plan1': 13, 'TYR:plan': 5, 'ARG:plan': 25, 'PHE:plan': 12, 'GLU:plan': 25, 'ASP:plan': 15, 'HIS:plan': 2, 'ASN:plan1': 3, 'TRP:plan': 2} Unresolved non-hydrogen planarities: 466 Chain: "E" Number of atoms: 565 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 565 Classifications: {'peptide': 75} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 2, 'TRANS': 72} Unresolved non-hydrogen bonds: 34 Unresolved non-hydrogen angles: 41 Unresolved non-hydrogen dihedrals: 27 Planarities with less than four sites: {'ASP:plan': 1, 'GLU:plan': 3, 'GLN:plan1': 3} Unresolved non-hydrogen planarities: 27 Chain: "M" Number of atoms: 1003 Number of conformers: 1 Conformer: "" Number of residues, atoms: 152, 1003 Classifications: {'peptide': 152} Incomplete info: {'truncation_to_alanine': 51} Link IDs: {'PTRANS': 4, 'TRANS': 147} Unresolved non-hydrogen bonds: 223 Unresolved non-hydrogen angles: 279 Unresolved non-hydrogen dihedrals: 188 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'ASP:plan': 10, 'GLU:plan': 10, 'TYR:plan': 2, 'GLN:plan1': 3, 'ARG:plan': 7, 'PHE:plan': 2, 'TRP:plan': 1, 'HIS:plan': 2, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 165 Chain: "M" Number of atoms: 618 Number of conformers: 1 Conformer: "" Number of residues, atoms: 111, 618 Classifications: {'peptide': 111} Incomplete info: {'truncation_to_alanine': 80} Link IDs: {'PTRANS': 2, 'TRANS': 108} Chain breaks: 1 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 249 Unresolved non-hydrogen angles: 328 Unresolved non-hydrogen dihedrals: 185 Unresolved non-hydrogen chiralities: 9 Planarities with less than four sites: {'UNK:plan-1': 34, 'ARG:plan': 6, 'ASN:plan1': 2, 'GLN:plan1': 5, 'GLU:plan': 8, 'TRP:plan': 1, 'ASP:plan': 2, 'PHE:plan': 2, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 156 Chain: "M" Number of atoms: 381 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 381 Classifications: {'peptide': 75} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 61} Link IDs: {'PTRANS': 4, 'TRANS': 70} Chain breaks: 1 Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 180 Unresolved non-hydrogen angles: 230 Unresolved non-hydrogen dihedrals: 136 Unresolved non-hydrogen chiralities: 15 Planarities with less than four sites: {'UNK:plan-1': 16, 'ARG:plan': 5, 'GLU:plan': 3, 'ASN:plan1': 2, 'ASP:plan': 1, 'GLN:plan1': 2, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 77 Chain: "F" Number of atoms: 944 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 944 Classifications: {'DNA': 46} Link IDs: {'rna3p': 45} Chain: "G" Number of atoms: 946 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 946 Classifications: {'DNA': 46} Link IDs: {'rna3p': 45} Residues with excluded nonbonded symmetry interactions: 4 residue: pdb=" N GLY M 166 " occ=0.20 ... (2 atoms not shown) pdb=" O GLY M 166 " occ=0.20 residue: pdb=" N ASP M 168 " occ=0.20 ... (3 atoms not shown) pdb=" CB ASP M 168 " occ=0.20 residue: pdb=" N GLU M 169 " occ=0.20 ... (3 atoms not shown) pdb=" CB GLU M 169 " occ=0.20 residue: pdb=" N GLY M 171 " occ=0.20 ... (2 atoms not shown) pdb=" O GLY M 171 " occ=0.20 Time building chain proxies: 6.02, per 1000 atoms: 0.21 Number of scatterers: 28316 At special positions: 0 Unit cell: (140.98, 167.48, 160.06, 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 97 16.00 P 92 15.00 O 5671 8.00 N 5014 7.00 C 17442 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 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 Links applied TRANS " UNK M 259 " - " ASP M 257 " Time building additional restraints: 2.66 Conformation dependent library (CDL) restraints added in 1.2 seconds 7134 Ramachandran restraints generated. 3567 Oldfield, 0 Emsley, 3567 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6768 Finding SS restraints... Secondary structure from input PDB file: 123 helices and 38 sheets defined 38.7% alpha, 10.7% beta 29 base pairs and 69 stacking pairs defined. Time for finding SS restraints: 3.45 Creating SS restraints... Processing helix chain 'A' and resid 34 through 50 removed outlier: 3.743A pdb=" N THR A 38 " --> pdb=" O GLY A 34 " (cutoff:3.500A) Processing helix chain 'A' and resid 77 through 87 removed outlier: 3.696A pdb=" N GLY A 87 " --> pdb=" O LEU A 83 " (cutoff:3.500A) Processing helix chain 'A' and resid 113 through 115 No H-bonds generated for 'chain 'A' and resid 113 through 115' Processing helix chain 'A' and resid 157 through 162 removed outlier: 3.714A pdb=" N SER A 161 " --> pdb=" O ARG A 158 " (cutoff:3.500A) Processing helix chain 'A' and resid 212 through 228 Processing helix chain 'A' and resid 256 through 261 removed outlier: 3.569A pdb=" N ASP A 259 " --> pdb=" O PRO A 256 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N GLU A 261 " --> pdb=" O ASP A 258 " (cutoff:3.500A) Processing helix chain 'A' and resid 264 through 272 Processing helix chain 'A' and resid 278 through 283 Processing helix chain 'A' and resid 285 through 290 Processing helix chain 'A' and resid 295 through 307 removed outlier: 3.617A pdb=" N SER A 299 " --> pdb=" O LEU A 295 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N LEU A 300 " --> pdb=" O GLY A 296 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N THR A 301 " --> pdb=" O LYS A 297 " (cutoff:3.500A) Processing helix chain 'B' and resid 34 through 50 removed outlier: 3.628A pdb=" N THR B 38 " --> pdb=" O GLY B 34 " (cutoff:3.500A) Processing helix chain 'B' and resid 70 through 74 Processing helix chain 'B' and resid 77 through 85 Processing helix chain 'B' and resid 160 through 164 removed outlier: 3.883A pdb=" N GLU B 163 " --> pdb=" O HIS B 160 " (cutoff:3.500A) Processing helix chain 'B' and resid 212 through 228 Processing helix chain 'B' and resid 229 through 231 No H-bonds generated for 'chain 'B' and resid 229 through 231' Processing helix chain 'C' and resid 5 through 10 removed outlier: 4.006A pdb=" N ARG C 10 " --> pdb=" O THR C 6 " (cutoff:3.500A) Processing helix chain 'C' and resid 29 through 39 removed outlier: 3.625A pdb=" N SER C 34 " --> pdb=" O ILE C 30 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N PHE C 35 " --> pdb=" O GLN C 31 " (cutoff:3.500A) Processing helix chain 'C' and resid 48 through 55 removed outlier: 3.734A pdb=" N ALA C 52 " --> pdb=" O GLY C 48 " (cutoff:3.500A) Processing helix chain 'C' and resid 81 through 89 Processing helix chain 'C' and resid 159 through 163 removed outlier: 3.877A pdb=" N GLY C 162 " --> pdb=" O SER C 159 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N LYS C 163 " --> pdb=" O ASP C 160 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 159 through 163' Processing helix chain 'C' and resid 206 through 212 removed outlier: 4.047A pdb=" N LEU C 210 " --> pdb=" O ALA C 206 " (cutoff:3.500A) Processing helix chain 'C' and resid 216 through 225 Processing helix chain 'C' and resid 270 through 280 removed outlier: 3.844A pdb=" N ASP C 280 " --> pdb=" O GLN C 276 " (cutoff:3.500A) Processing helix chain 'C' and resid 288 through 295 removed outlier: 3.551A pdb=" N TYR C 291 " --> pdb=" O PRO C 288 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N ALA C 293 " --> pdb=" O GLU C 290 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N GLY C 294 " --> pdb=" O TYR C 291 " (cutoff:3.500A) Processing helix chain 'C' and resid 318 through 329 removed outlier: 3.521A pdb=" N LEU C 322 " --> pdb=" O SER C 318 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N ALA C 323 " --> pdb=" O LEU C 319 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N LYS C 324 " --> pdb=" O ASP C 320 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N GLY C 329 " --> pdb=" O LEU C 325 " (cutoff:3.500A) Processing helix chain 'C' and resid 347 through 354 Processing helix chain 'C' and resid 358 through 371 removed outlier: 4.168A pdb=" N ARG C 371 " --> pdb=" O TYR C 367 " (cutoff:3.500A) Processing helix chain 'C' and resid 378 through 389 removed outlier: 3.551A pdb=" N GLU C 382 " --> pdb=" O ARG C 378 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N GLU C 386 " --> pdb=" O GLU C 382 " (cutoff:3.500A) removed outlier: 4.091A pdb=" N PHE C 389 " --> pdb=" O PHE C 385 " (cutoff:3.500A) Processing helix chain 'C' and resid 397 through 409 Processing helix chain 'C' and resid 421 through 437 Processing helix chain 'C' and resid 447 through 449 No H-bonds generated for 'chain 'C' and resid 447 through 449' Processing helix chain 'C' and resid 455 through 476 removed outlier: 4.053A pdb=" N ALA C 474 " --> pdb=" O ARG C 470 " (cutoff:3.500A) Processing helix chain 'C' and resid 487 through 492 removed outlier: 4.031A pdb=" N ASP C 491 " --> pdb=" O LEU C 487 " (cutoff:3.500A) Processing helix chain 'C' and resid 495 through 506 Processing helix chain 'C' and resid 519 through 528 removed outlier: 3.593A pdb=" N GLU C 523 " --> pdb=" O ASN C 519 " (cutoff:3.500A) Processing helix chain 'C' and resid 608 through 612 removed outlier: 3.821A pdb=" N GLY C 612 " --> pdb=" O ALA C 608 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 608 through 612' Processing helix chain 'C' and resid 656 through 660 removed outlier: 4.157A pdb=" N VAL C 660 " --> pdb=" O THR C 657 " (cutoff:3.500A) Processing helix chain 'C' and resid 662 through 667 removed outlier: 3.598A pdb=" N LEU C 667 " --> pdb=" O VAL C 663 " (cutoff:3.500A) Processing helix chain 'C' and resid 670 through 674 Processing helix chain 'C' and resid 675 through 686 removed outlier: 3.603A pdb=" N ASN C 684 " --> pdb=" O LEU C 680 " (cutoff:3.500A) Processing helix chain 'C' and resid 704 through 713 removed outlier: 3.782A pdb=" N GLY C 713 " --> pdb=" O ALA C 709 " (cutoff:3.500A) Processing helix chain 'C' and resid 820 through 825 Processing helix chain 'C' and resid 858 through 863 removed outlier: 3.786A pdb=" N LEU C 862 " --> pdb=" O GLY C 858 " (cutoff:3.500A) Processing helix chain 'C' and resid 896 through 906 Processing helix chain 'C' and resid 907 through 911 removed outlier: 4.245A pdb=" N ALA C 910 " --> pdb=" O GLY C 907 " (cutoff:3.500A) Processing helix chain 'C' and resid 946 through 979 removed outlier: 3.694A pdb=" N GLU C 962 " --> pdb=" O LYS C 958 " (cutoff:3.500A) removed outlier: 4.545A pdb=" N GLU C 963 " --> pdb=" O ASP C 959 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N LEU C 964 " --> pdb=" O LEU C 960 " (cutoff:3.500A) Processing helix chain 'C' and resid 986 through 991 Processing helix chain 'C' and resid 993 through 1000 removed outlier: 3.675A pdb=" N LEU C1000 " --> pdb=" O TRP C 997 " (cutoff:3.500A) Processing helix chain 'C' and resid 1003 through 1037 Processing helix chain 'C' and resid 1081 through 1085 Processing helix chain 'C' and resid 1099 through 1101 No H-bonds generated for 'chain 'C' and resid 1099 through 1101' Processing helix chain 'C' and resid 1102 through 1107 Processing helix chain 'C' and resid 1109 through 1134 removed outlier: 3.636A pdb=" N ILE C1124 " --> pdb=" O ALA C1120 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N GLY C1125 " --> pdb=" O ALA C1121 " (cutoff:3.500A) Processing helix chain 'C' and resid 1137 through 1150 Processing helix chain 'C' and resid 1168 through 1176 Processing helix chain 'C' and resid 1191 through 1201 removed outlier: 3.618A pdb=" N LEU C1201 " --> pdb=" O GLU C1197 " (cutoff:3.500A) Processing helix chain 'C' and resid 1238 through 1243 Processing helix chain 'C' and resid 1271 through 1282 Processing helix chain 'C' and resid 1283 through 1292 removed outlier: 3.686A pdb=" N LEU C1287 " --> pdb=" O ALA C1283 " (cutoff:3.500A) Processing helix chain 'C' and resid 1297 through 1310 Processing helix chain 'C' and resid 1320 through 1332 removed outlier: 3.852A pdb=" N ASN C1324 " --> pdb=" O PRO C1320 " (cutoff:3.500A) Processing helix chain 'D' and resid 26 through 34 Processing helix chain 'D' and resid 96 through 100 Processing helix chain 'D' and resid 122 through 128 Processing helix chain 'D' and resid 131 through 140 removed outlier: 4.776A pdb=" N TYR D 140 " --> pdb=" O GLU D 136 " (cutoff:3.500A) Processing helix chain 'D' and resid 161 through 172 Processing helix chain 'D' and resid 182 through 191 Processing helix chain 'D' and resid 193 through 207 removed outlier: 3.657A pdb=" N GLU D 197 " --> pdb=" O ASP D 193 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N GLU D 207 " --> pdb=" O GLU D 203 " (cutoff:3.500A) Processing helix chain 'D' and resid 212 through 231 removed outlier: 3.914A pdb=" N LYS D 216 " --> pdb=" O THR D 212 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N LEU D 217 " --> pdb=" O LYS D 213 " (cutoff:3.500A) removed outlier: 4.248A pdb=" N THR D 218 " --> pdb=" O ARG D 214 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N ALA D 226 " --> pdb=" O LYS D 222 " (cutoff:3.500A) Processing helix chain 'D' and resid 233 through 237 Processing helix chain 'D' and resid 246 through 250 removed outlier: 3.555A pdb=" N LEU D 249 " --> pdb=" O PRO D 246 " (cutoff:3.500A) Processing helix chain 'D' and resid 263 through 285 removed outlier: 3.820A pdb=" N ASP D 267 " --> pdb=" O SER D 263 " (cutoff:3.500A) removed outlier: 4.132A pdb=" N LEU D 268 " --> pdb=" O ASP D 264 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N TYR D 269 " --> pdb=" O LEU D 265 " (cutoff:3.500A) Processing helix chain 'D' and resid 288 through 308 removed outlier: 3.648A pdb=" N VAL D 292 " --> pdb=" O PRO D 288 " (cutoff:3.500A) Processing helix chain 'D' and resid 377 through 389 Processing helix chain 'D' and resid 393 through 404 Processing helix chain 'D' and resid 406 through 417 removed outlier: 3.854A pdb=" N ASP D 410 " --> pdb=" O ALA D 406 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N GLU D 414 " --> pdb=" O ASP D 410 " (cutoff:3.500A) Processing helix chain 'D' and resid 430 through 432 No H-bonds generated for 'chain 'D' and resid 430 through 432' Processing helix chain 'D' and resid 450 through 452 No H-bonds generated for 'chain 'D' and resid 450 through 452' Processing helix chain 'D' and resid 453 through 458 Processing helix chain 'D' and resid 474 through 482 Processing helix chain 'D' and resid 504 through 514 Processing helix chain 'D' and resid 532 through 537 Processing helix chain 'D' and resid 573 through 580 Processing helix chain 'D' and resid 581 through 583 No H-bonds generated for 'chain 'D' and resid 581 through 583' Processing helix chain 'D' and resid 597 through 613 Processing helix chain 'D' and resid 613 through 635 removed outlier: 3.814A pdb=" N THR D 617 " --> pdb=" O GLY D 613 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N ILE D 619 " --> pdb=" O LYS D 615 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N ASP D 622 " --> pdb=" O VAL D 618 " (cutoff:3.500A) Processing helix chain 'D' and resid 640 through 644 Processing helix chain 'D' and resid 649 through 670 Processing helix chain 'D' and resid 674 through 702 removed outlier: 4.178A pdb=" N ASN D 680 " --> pdb=" O GLY D 676 " (cutoff:3.500A) Processing helix chain 'D' and resid 720 through 729 removed outlier: 3.554A pdb=" N GLY D 729 " --> pdb=" O MET D 725 " (cutoff:3.500A) Processing helix chain 'D' and resid 733 through 741 removed outlier: 3.555A pdb=" N GLN D 739 " --> pdb=" O ALA D 735 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N LEU D 740 " --> pdb=" O GLN D 736 " (cutoff:3.500A) Processing helix chain 'D' and resid 768 through 805 removed outlier: 3.968A pdb=" N HIS D 777 " --> pdb=" O PHE D 773 " (cutoff:3.500A) removed outlier: 4.087A pdb=" N GLY D 778 " --> pdb=" O ILE D 774 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N ASP D 785 " --> pdb=" O LYS D 781 " (cutoff:3.500A) removed outlier: 4.328A pdb=" N THR D 786 " --> pdb=" O GLY D 782 " (cutoff:3.500A) removed outlier: 4.351A pdb=" N ALA D 787 " --> pdb=" O LEU D 783 " (cutoff:3.500A) removed outlier: 4.347A pdb=" N LEU D 788 " --> pdb=" O ALA D 784 " (cutoff:3.500A) Processing helix chain 'D' and resid 834 through 840 removed outlier: 3.740A pdb=" N ARG D 838 " --> pdb=" O PRO D 834 " (cutoff:3.500A) Processing helix chain 'D' and resid 865 through 875 removed outlier: 3.524A pdb=" N ASN D 875 " --> pdb=" O LEU D 871 " (cutoff:3.500A) Processing helix chain 'D' and resid 915 through 925 Processing helix chain 'D' and resid 1137 through 1146 Processing helix chain 'D' and resid 1216 through 1223 Processing helix chain 'D' and resid 1225 through 1244 removed outlier: 3.570A pdb=" N VAL D1229 " --> pdb=" O GLY D1225 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N VAL D1240 " --> pdb=" O GLU D1236 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N GLN D1244 " --> pdb=" O VAL D1240 " (cutoff:3.500A) Processing helix chain 'D' and resid 1249 through 1260 removed outlier: 4.472A pdb=" N ILE D1253 " --> pdb=" O ASN D1249 " (cutoff:3.500A) Processing helix chain 'D' and resid 1279 through 1293 Processing helix chain 'D' and resid 1309 through 1315 removed outlier: 3.564A pdb=" N SER D1313 " --> pdb=" O ILE D1309 " (cutoff:3.500A) Processing helix chain 'D' and resid 1328 through 1339 Processing helix chain 'D' and resid 1346 through 1354 removed outlier: 3.618A pdb=" N ASN D1350 " --> pdb=" O GLY D1346 " (cutoff:3.500A) Processing helix chain 'D' and resid 1360 through 1376 removed outlier: 3.822A pdb=" N ALA D1364 " --> pdb=" O GLY D1360 " (cutoff:3.500A) removed outlier: 4.277A pdb=" N TYR D1365 " --> pdb=" O THR D1361 " (cutoff:3.500A) Processing helix chain 'E' and resid 6 through 13 removed outlier: 3.801A pdb=" N LYS E 12 " --> pdb=" O ASP E 8 " (cutoff:3.500A) Processing helix chain 'E' and resid 15 through 33 removed outlier: 3.749A pdb=" N LEU E 19 " --> pdb=" O ASN E 15 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N LEU E 21 " --> pdb=" O PHE E 17 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N GLN E 29 " --> pdb=" O ARG E 25 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N MET E 30 " --> pdb=" O ARG E 26 " (cutoff:3.500A) Processing helix chain 'E' and resid 45 through 56 Processing helix chain 'E' and resid 60 through 75 Processing helix chain 'M' and resid 119 through 130 removed outlier: 3.524A pdb=" N LEU M 130 " --> pdb=" O TRP M 126 " (cutoff:3.500A) Processing helix chain 'M' and resid 134 through 146 removed outlier: 3.508A pdb=" N ALA M 139 " --> pdb=" O ASP M 135 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N ASP M 146 " --> pdb=" O THR M 142 " (cutoff:3.500A) Processing helix chain 'M' and resid 158 through 164 Processing helix chain 'M' and resid 171 through 184 removed outlier: 3.823A pdb=" N VAL M 175 " --> pdb=" O GLY M 171 " (cutoff:3.500A) Processing helix chain 'M' and resid 195 through 203 Processing helix chain 'M' and resid 212 through 223 removed outlier: 3.774A pdb=" N ALA M 216 " --> pdb=" O TRP M 212 " (cutoff:3.500A) Processing helix chain 'M' and resid 233 through 239 removed outlier: 3.915A pdb=" N ARG M 237 " --> pdb=" O ARG M 233 " (cutoff:3.500A) Processing helix chain 'M' and resid 243 through 255 removed outlier: 4.118A pdb=" N LYS M 247 " --> pdb=" O GLU M 243 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N ALA M 249 " --> pdb=" O VAL M 245 " (cutoff:3.500A) Processing helix chain 'M' and resid 321 through 355 removed outlier: 3.518A pdb=" N LEU M 329 " --> pdb=" O GLU M 325 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N ASP M 338 " --> pdb=" O GLU M 334 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N THR M 339 " --> pdb=" O SER M 335 " (cutoff:3.500A) removed outlier: 4.102A pdb=" N LEU M 341 " --> pdb=" O ASN M 337 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N ARG M 342 " --> pdb=" O ASP M 338 " (cutoff:3.500A) Processing helix chain 'M' and resid 366 through 374 removed outlier: 4.156A pdb=" N ILE M 370 " --> pdb=" O VAL M 366 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N VAL M 374 " --> pdb=" O ILE M 370 " (cutoff:3.500A) Processing helix chain 'M' and resid 377 through 388 Processing helix chain 'M' and resid 416 through 430 removed outlier: 3.815A pdb=" N ALA M 430 " --> pdb=" O LYS M 426 " (cutoff:3.500A) Processing helix chain 'M' and resid 438 through 449 removed outlier: 3.738A pdb=" N LEU M 442 " --> pdb=" O SER M 438 " (cutoff:3.500A) Processing helix chain 'M' and resid 456 through 464 Processing sheet with id=AA1, first strand: chain 'A' and resid 13 through 18 removed outlier: 9.340A pdb=" N LEU A 13 " --> pdb=" O GLU A 29 " (cutoff:3.500A) removed outlier: 7.581A pdb=" N GLU A 29 " --> pdb=" O LEU A 13 " (cutoff:3.500A) removed outlier: 5.099A pdb=" N ASP A 15 " --> pdb=" O THR A 27 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N THR A 27 " --> pdb=" O ASP A 15 " (cutoff:3.500A) removed outlier: 6.755A pdb=" N ASP A 199 " --> pdb=" O PRO A 30 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N ARG A 182 " --> pdb=" O GLU A 206 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 99 through 105 removed outlier: 3.581A pdb=" N GLU A 58 " --> pdb=" O LYS A 145 " (cutoff:3.500A) removed outlier: 6.197A pdb=" N GLN A 147 " --> pdb=" O VAL A 56 " (cutoff:3.500A) removed outlier: 5.466A pdb=" N VAL A 56 " --> pdb=" O GLN A 147 " (cutoff:3.500A) removed outlier: 7.084A pdb=" N GLY A 149 " --> pdb=" O CYS A 54 " (cutoff:3.500A) removed outlier: 5.349A pdb=" N CYS A 54 " --> pdb=" O GLY A 149 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 90 through 91 Processing sheet with id=AA4, first strand: chain 'A' and resid 108 through 111 removed outlier: 6.902A pdb=" N GLY A 108 " --> pdb=" O HIS A 132 " (cutoff:3.500A) removed outlier: 5.163A pdb=" N HIS A 132 " --> pdb=" O GLY A 108 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N VAL A 110 " --> pdb=" O ILE A 130 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 15 through 19 Processing sheet with id=AA6, first strand: chain 'B' and resid 52 through 61 removed outlier: 7.155A pdb=" N LYS B 145 " --> pdb=" O THR B 57 " (cutoff:3.500A) removed outlier: 4.727A pdb=" N VAL B 59 " --> pdb=" O ARG B 143 " (cutoff:3.500A) removed outlier: 6.593A pdb=" N ARG B 143 " --> pdb=" O VAL B 59 " (cutoff:3.500A) removed outlier: 5.505A pdb=" N ILE B 61 " --> pdb=" O SER B 141 " (cutoff:3.500A) removed outlier: 8.333A pdb=" N SER B 141 " --> pdb=" O ILE B 61 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 90 through 91 Processing sheet with id=AA8, first strand: chain 'B' and resid 152 through 153 Processing sheet with id=AA9, first strand: chain 'C' and resid 13 through 14 removed outlier: 5.882A pdb=" N LYS C 13 " --> pdb=" O ALA C1183 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'C' and resid 67 through 71 removed outlier: 4.006A pdb=" N LYS C 99 " --> pdb=" O VAL C 71 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 67 through 71 removed outlier: 4.006A pdb=" N LYS C 99 " --> pdb=" O VAL C 71 " (cutoff:3.500A) removed outlier: 5.368A pdb=" N ALA C 94 " --> pdb=" O GLU C 126 " (cutoff:3.500A) removed outlier: 4.374A pdb=" N GLU C 126 " --> pdb=" O ALA C 94 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N LEU C 96 " --> pdb=" O MET C 124 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 451 through 454 Processing sheet with id=AB4, first strand: chain 'C' and resid 154 through 158 removed outlier: 3.979A pdb=" N LEU C 184 " --> pdb=" O ILE C 176 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 230 through 231 Processing sheet with id=AB6, first strand: chain 'C' and resid 238 through 239 removed outlier: 3.621A pdb=" N ILE C 285 " --> pdb=" O MET C 239 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 255 through 256 Processing sheet with id=AB8, first strand: chain 'C' and resid 580 through 581 removed outlier: 5.229A pdb=" N GLU C 602 " --> pdb=" O LYS C 593 " (cutoff:3.500A) removed outlier: 6.712A pdb=" N THR C 595 " --> pdb=" O THR C 600 " (cutoff:3.500A) removed outlier: 5.880A pdb=" N THR C 600 " --> pdb=" O THR C 595 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 633 through 637 Processing sheet with id=AC1, first strand: chain 'C' and resid 716 through 717 removed outlier: 6.359A pdb=" N ALA C 716 " --> pdb=" O LEU C 783 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 722 through 726 removed outlier: 7.011A pdb=" N VAL C 733 " --> pdb=" O GLN C 725 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 757 through 758 Processing sheet with id=AC4, first strand: chain 'C' and resid 789 through 790 Processing sheet with id=AC5, first strand: chain 'C' and resid 1066 through 1068 removed outlier: 4.224A pdb=" N THR C1226 " --> pdb=" O PHE C 804 " (cutoff:3.500A) removed outlier: 8.303A pdb=" N ILE C1096 " --> pdb=" O ASN C 799 " (cutoff:3.500A) removed outlier: 5.788A pdb=" N ARG C 801 " --> pdb=" O ILE C1096 " (cutoff:3.500A) removed outlier: 7.379A pdb=" N LEU C1098 " --> pdb=" O ARG C 801 " (cutoff:3.500A) removed outlier: 6.122A pdb=" N ALA C 803 " --> pdb=" O LEU C1098 " (cutoff:3.500A) removed outlier: 7.308A pdb=" N ILE C 816 " --> pdb=" O SER C1077 " (cutoff:3.500A) removed outlier: 6.944A pdb=" N ILE C1079 " --> pdb=" O ILE C 816 " (cutoff:3.500A) removed outlier: 6.849A pdb=" N VAL C 818 " --> pdb=" O ILE C1079 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'C' and resid 1066 through 1068 Processing sheet with id=AC7, first strand: chain 'C' and resid 830 through 840 removed outlier: 3.938A pdb=" N ASP C 930 " --> pdb=" O TYR C1053 " (cutoff:3.500A) removed outlier: 6.807A pdb=" N ALA C1055 " --> pdb=" O VAL C 928 " (cutoff:3.500A) removed outlier: 6.107A pdb=" N VAL C 928 " --> pdb=" O ALA C1055 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'C' and resid 1269 through 1270 Processing sheet with id=AC9, first strand: chain 'C' and resid 1335 through 1339 Processing sheet with id=AD1, first strand: chain 'D' and resid 104 through 111 removed outlier: 6.348A pdb=" N THR D 240 " --> pdb=" O LEU D 107 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'D' and resid 350 through 357 Processing sheet with id=AD3, first strand: chain 'D' and resid 526 through 528 removed outlier: 3.542A pdb=" N LEU D 527 " --> pdb=" O LYS D 549 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'D' and resid 748 through 749 removed outlier: 3.525A pdb=" N SER D 753 " --> pdb=" O LYS D 749 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'D' and resid 820 through 822 Processing sheet with id=AD6, first strand: chain 'D' and resid 959 through 961 Processing sheet with id=AD7, first strand: chain 'D' and resid 966 through 967 Processing sheet with id=AD8, first strand: chain 'D' and resid 1002 through 1003 Processing sheet with id=AD9, first strand: chain 'D' and resid 1059 through 1060 Processing sheet with id=AE1, first strand: chain 'D' and resid 1277 through 1278 Processing sheet with id=AE2, first strand: chain 'M' and resid 287 through 288 removed outlier: 5.956A pdb=" N UNK M 277 " --> pdb=" O HIS M 391 " (cutoff:3.500A) 1032 hydrogen bonds defined for protein. 2910 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 77 hydrogen bonds 154 hydrogen bond angles 0 basepair planarities 29 basepair parallelities 69 stacking parallelities Total time for adding SS restraints: 7.79 Time building geometry restraints manager: 3.36 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.03 - 1.22: 776 1.22 - 1.41: 10342 1.41 - 1.60: 17155 1.60 - 1.79: 514 1.79 - 1.98: 104 Bond restraints: 28891 Sorted by residual: bond pdb=" C HIS C 526 " pdb=" O HIS C 526 " ideal model delta sigma weight residual 1.237 1.026 0.211 1.19e-02 7.06e+03 3.14e+02 bond pdb=" C TYR C 555 " pdb=" O TYR C 555 " ideal model delta sigma weight residual 1.236 1.436 -0.200 1.15e-02 7.56e+03 3.01e+02 bond pdb=" C VAL C1225 " pdb=" O VAL C1225 " ideal model delta sigma weight residual 1.236 1.410 -0.175 1.01e-02 9.80e+03 2.99e+02 bond pdb=" N GLY D 333 " pdb=" CA GLY D 333 " ideal model delta sigma weight residual 1.449 1.698 -0.248 1.45e-02 4.76e+03 2.93e+02 bond pdb=" CZ ARG D 99 " pdb=" NH1 ARG D 99 " ideal model delta sigma weight residual 1.323 1.560 -0.237 1.40e-02 5.10e+03 2.86e+02 ... (remaining 28886 not shown) Histogram of bond angle deviations from ideal: 0.00 - 7.81: 38253 7.81 - 15.63: 1296 15.63 - 23.44: 110 23.44 - 31.25: 22 31.25 - 39.07: 7 Bond angle restraints: 39688 Sorted by residual: angle pdb=" N ASP D 462 " pdb=" CA ASP D 462 " pdb=" C ASP D 462 " ideal model delta sigma weight residual 113.02 86.00 27.02 1.49e+00 4.50e-01 3.29e+02 angle pdb=" C GLU D 765 " pdb=" N GLY D 766 " pdb=" CA GLY D 766 " ideal model delta sigma weight residual 120.64 100.22 20.42 1.26e+00 6.30e-01 2.63e+02 angle pdb=" CB ILE A 61 " pdb=" CG1 ILE A 61 " pdb=" CD1 ILE A 61 " ideal model delta sigma weight residual 113.80 79.98 33.82 2.10e+00 2.27e-01 2.59e+02 angle pdb=" CG MET C 805 " pdb=" SD MET C 805 " pdb=" CE MET C 805 " ideal model delta sigma weight residual 100.90 65.55 35.35 2.20e+00 2.07e-01 2.58e+02 angle pdb=" N ASP M 186 " pdb=" CA ASP M 186 " pdb=" CB ASP M 186 " ideal model delta sigma weight residual 110.42 129.15 -18.73 1.18e+00 7.18e-01 2.52e+02 ... (remaining 39683 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.30: 16659 35.30 - 70.60: 639 70.60 - 105.90: 26 105.90 - 141.20: 3 141.20 - 176.50: 7 Dihedral angle restraints: 17334 sinusoidal: 6859 harmonic: 10475 Sorted by residual: dihedral pdb=" N TYR C 555 " pdb=" C TYR C 555 " pdb=" CA TYR C 555 " pdb=" CB TYR C 555 " ideal model delta harmonic sigma weight residual 122.80 159.58 -36.78 0 2.50e+00 1.60e-01 2.16e+02 dihedral pdb=" C TYR C 555 " pdb=" N TYR C 555 " pdb=" CA TYR C 555 " pdb=" CB TYR C 555 " ideal model delta harmonic sigma weight residual -122.60 -159.21 36.61 0 2.50e+00 1.60e-01 2.14e+02 dihedral pdb=" N GLU D 534 " pdb=" C GLU D 534 " pdb=" CA GLU D 534 " pdb=" CB GLU D 534 " ideal model delta harmonic sigma weight residual 122.80 159.04 -36.24 0 2.50e+00 1.60e-01 2.10e+02 ... (remaining 17331 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.615: 4665 0.615 - 1.230: 98 1.230 - 1.844: 10 1.844 - 2.459: 0 2.459 - 3.074: 1 Chirality restraints: 4774 Sorted by residual: chirality pdb=" CG LEU C 699 " pdb=" CB LEU C 699 " pdb=" CD1 LEU C 699 " pdb=" CD2 LEU C 699 " both_signs ideal model delta sigma weight residual False -2.59 0.48 -3.07 2.00e-01 2.50e+01 2.36e+02 chirality pdb=" CA GLU D 534 " pdb=" N GLU D 534 " pdb=" C GLU D 534 " pdb=" CB GLU D 534 " both_signs ideal model delta sigma weight residual False 2.51 0.87 1.64 2.00e-01 2.50e+01 6.71e+01 chirality pdb=" CA TYR C 555 " pdb=" N TYR C 555 " pdb=" C TYR C 555 " pdb=" CB TYR C 555 " both_signs ideal model delta sigma weight residual False 2.51 0.88 1.63 2.00e-01 2.50e+01 6.67e+01 ... (remaining 4771 not shown) Planarity restraints: 4889 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP C1276 " 0.018 2.00e-02 2.50e+03 1.06e-01 2.80e+02 pdb=" CG TRP C1276 " -0.057 2.00e-02 2.50e+03 pdb=" CD1 TRP C1276 " 0.123 2.00e-02 2.50e+03 pdb=" CD2 TRP C1276 " -0.181 2.00e-02 2.50e+03 pdb=" NE1 TRP C1276 " 0.111 2.00e-02 2.50e+03 pdb=" CE2 TRP C1276 " -0.127 2.00e-02 2.50e+03 pdb=" CE3 TRP C1276 " 0.047 2.00e-02 2.50e+03 pdb=" CZ2 TRP C1276 " -0.112 2.00e-02 2.50e+03 pdb=" CZ3 TRP C1276 " 0.065 2.00e-02 2.50e+03 pdb=" CH2 TRP C1276 " 0.113 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE D 380 " -0.071 2.00e-02 2.50e+03 1.10e-01 2.11e+02 pdb=" CG PHE D 380 " 0.097 2.00e-02 2.50e+03 pdb=" CD1 PHE D 380 " -0.007 2.00e-02 2.50e+03 pdb=" CD2 PHE D 380 " 0.104 2.00e-02 2.50e+03 pdb=" CE1 PHE D 380 " -0.066 2.00e-02 2.50e+03 pdb=" CE2 PHE D 380 " -0.191 2.00e-02 2.50e+03 pdb=" CZ PHE D 380 " 0.135 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP D 115 " 0.128 2.00e-02 2.50e+03 7.03e-02 1.23e+02 pdb=" CG TRP D 115 " -0.046 2.00e-02 2.50e+03 pdb=" CD1 TRP D 115 " -0.029 2.00e-02 2.50e+03 pdb=" CD2 TRP D 115 " -0.076 2.00e-02 2.50e+03 pdb=" NE1 TRP D 115 " -0.009 2.00e-02 2.50e+03 pdb=" CE2 TRP D 115 " 0.059 2.00e-02 2.50e+03 pdb=" CE3 TRP D 115 " -0.116 2.00e-02 2.50e+03 pdb=" CZ2 TRP D 115 " -0.020 2.00e-02 2.50e+03 pdb=" CZ3 TRP D 115 " 0.032 2.00e-02 2.50e+03 pdb=" CH2 TRP D 115 " 0.077 2.00e-02 2.50e+03 ... (remaining 4886 not shown) Histogram of nonbonded interaction distances: 1.85 - 2.46: 177 2.46 - 3.07: 19488 3.07 - 3.68: 41568 3.68 - 4.29: 62237 4.29 - 4.90: 96609 Nonbonded interactions: 220079 Sorted by model distance: nonbonded pdb=" CD1 ILE D 316 " pdb=" N THR D 317 " model vdw 1.847 3.540 nonbonded pdb=" O GLY C1260 " pdb=" NH1 ARG D 346 " model vdw 1.882 3.120 nonbonded pdb=" CA GLY C1260 " pdb=" NH1 ARG D 346 " model vdw 1.994 3.520 nonbonded pdb=" O HIS D 113 " pdb=" CB HIS D 113 " model vdw 2.030 2.752 nonbonded pdb=" CD1 ILE D 316 " pdb=" O THR D 317 " model vdw 2.049 3.460 ... (remaining 220074 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 ========== 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=0.20 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.210 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: 0.520 Check model and map are aligned: 0.090 Set scattering table: 0.070 Process input model: 30.960 Find NCS groups from input model: 0.200 Set up NCS constraints: 0.040 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:1.540 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.650 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8785 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 : 0.033 0.383 28892 Z= 2.188 Angle : 3.295 39.068 39691 Z= 1.968 Chirality : 0.221 3.074 4774 Planarity : 0.019 0.160 4888 Dihedral : 17.387 176.499 10563 Min Nonbonded Distance : 1.847 Molprobity Statistics. All-atom Clashscore : 24.47 Ramachandran Plot: Outliers : 2.30 % Allowed : 11.02 % Favored : 86.68 % Rotamer: Outliers : 4.29 % Allowed : 8.51 % Favored : 87.20 % Cbeta Deviations : 9.84 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.03 % Twisted Proline : 2.08 % Twisted General : 0.55 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.34 (0.11), residues: 3567 helix: -3.21 (0.10), residues: 1267 sheet: -1.73 (0.27), residues: 316 loop : -2.91 (0.11), residues: 1984 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.160 0.008 ARG C 12 TYR 0.125 0.022 TYR D 899 PHE 0.191 0.024 PHE D 380 TRP 0.181 0.030 TRP C1276 HIS 0.103 0.017 HIS C1116 Details of bonding type rmsd/Z covalent geometry : bond 0.03344 / 2.19 (28891) covalent geometry : angle 3.29459 / 1.97 (39688) hydrogen bonds : bond 0.16484 / 11.18 ( 1102) hydrogen bonds : angle 9.60729 / 6.75 ( 3064) link_TRANS : bond 0.00025 / 0.01 ( 1) link_TRANS : angle 1.95568 / 0.91 ( 3) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7134 Ramachandran restraints generated. 3567 Oldfield, 0 Emsley, 3567 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7134 Ramachandran restraints generated. 3567 Oldfield, 0 Emsley, 3567 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 726 residues out of total 3073 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 111 poor density : 615 time to evaluate : 1.058 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: A 147 GLN cc_start: 0.9315 (pt0) cc_final: 0.8782 (pt0) REVERT: A 201 LEU cc_start: 0.9423 (tp) cc_final: 0.9201 (tt) REVERT: B 18 GLN cc_start: 0.9418 (pm20) cc_final: 0.9113 (pm20) REVERT: B 51 MET cc_start: 0.9284 (tpp) cc_final: 0.9033 (mmm) REVERT: B 125 LYS cc_start: 0.9340 (pttt) cc_final: 0.9092 (pttp) REVERT: C 5 TYR cc_start: 0.8403 (m-80) cc_final: 0.7951 (m-10) REVERT: C 80 PHE cc_start: 0.9296 (m-10) cc_final: 0.9010 (m-10) REVERT: C 88 ARG cc_start: 0.9238 (mtt180) cc_final: 0.7678 (tpt-90) REVERT: C 149 LEU cc_start: 0.9454 (OUTLIER) cc_final: 0.9173 (tp) REVERT: C 165 HIS cc_start: 0.9116 (t70) cc_final: 0.8541 (t-90) REVERT: C 200 ARG cc_start: 0.9391 (tpp-160) cc_final: 0.9007 (mmm160) REVERT: C 369 MET cc_start: 0.8967 (tpt) cc_final: 0.8713 (tpp) REVERT: C 370 MET cc_start: 0.8603 (mmm) cc_final: 0.8310 (mmm) REVERT: C 464 PHE cc_start: 0.9513 (t80) cc_final: 0.9213 (t80) REVERT: C 564 PRO cc_start: 0.9677 (OUTLIER) cc_final: 0.9426 (Cg_endo) REVERT: C 603 ILE cc_start: 0.9706 (pt) cc_final: 0.9421 (mm) REVERT: C 696 ASP cc_start: 0.9371 (t0) cc_final: 0.9061 (t0) REVERT: C 697 LYS cc_start: 0.9257 (OUTLIER) cc_final: 0.9037 (ptpp) REVERT: C 765 ILE cc_start: 0.9259 (pp) cc_final: 0.8919 (mp) REVERT: C 821 ARG cc_start: 0.9518 (OUTLIER) cc_final: 0.9251 (tpp80) REVERT: C 929 ILE cc_start: 0.9647 (OUTLIER) cc_final: 0.9322 (tt) REVERT: C 1029 LEU cc_start: 0.9124 (tt) cc_final: 0.8897 (tt) REVERT: C 1030 GLU cc_start: 0.9457 (mm-30) cc_final: 0.9239 (tp30) REVERT: C 1050 VAL cc_start: 0.9376 (OUTLIER) cc_final: 0.9066 (t) REVERT: C 1268 GLN cc_start: 0.9287 (OUTLIER) cc_final: 0.9038 (mm-40) REVERT: C 1290 MET cc_start: 0.9765 (mmt) cc_final: 0.9439 (mmt) REVERT: C 1319 MET cc_start: 0.9538 (OUTLIER) cc_final: 0.9309 (tpp) REVERT: D 15 GLU cc_start: 0.9149 (pt0) cc_final: 0.8786 (pm20) REVERT: D 43 THR cc_start: 0.9378 (p) cc_final: 0.9133 (p) REVERT: D 68 TYR cc_start: 0.9474 (m-80) cc_final: 0.9230 (m-80) REVERT: D 80 HIS cc_start: 0.8012 (p90) cc_final: 0.7533 (p90) REVERT: D 93 THR cc_start: 0.9328 (OUTLIER) cc_final: 0.9037 (t) REVERT: D 192 MET cc_start: 0.9447 (tpp) cc_final: 0.9244 (tpp) REVERT: D 253 VAL cc_start: 0.9417 (m) cc_final: 0.9092 (p) REVERT: D 262 THR cc_start: 0.9234 (m) cc_final: 0.9012 (t) REVERT: D 339 ARG cc_start: 0.9436 (tpp-160) cc_final: 0.9062 (ttm170) REVERT: D 394 ILE cc_start: 0.9692 (OUTLIER) cc_final: 0.9471 (tp) REVERT: D 462 ASP cc_start: 0.8993 (p0) cc_final: 0.7998 (p0) REVERT: D 490 ILE cc_start: 0.9389 (pt) cc_final: 0.8814 (mt) REVERT: D 605 LEU cc_start: 0.9758 (mt) cc_final: 0.9556 (mm) REVERT: D 619 ILE cc_start: 0.9098 (tt) cc_final: 0.8671 (pt) REVERT: D 625 MET cc_start: 0.9664 (ttp) cc_final: 0.9458 (ttp) REVERT: D 644 MET cc_start: 0.9618 (OUTLIER) cc_final: 0.9298 (mpp) REVERT: D 668 PHE cc_start: 0.7898 (t80) cc_final: 0.7581 (t80) REVERT: D 716 GLN cc_start: 0.8512 (tt0) cc_final: 0.8247 (pt0) REVERT: D 719 PHE cc_start: 0.7659 (m-80) cc_final: 0.7170 (m-80) REVERT: D 826 ILE cc_start: 0.9349 (pt) cc_final: 0.8886 (mt) REVERT: D 833 GLU cc_start: 0.9308 (mt-10) cc_final: 0.8914 (mt-10) REVERT: D 848 VAL cc_start: 0.9348 (m) cc_final: 0.8945 (p) REVERT: D 1040 MET cc_start: 0.8273 (mtp) cc_final: 0.7876 (mmm) REVERT: D 1250 ASP cc_start: 0.9465 (m-30) cc_final: 0.9143 (m-30) REVERT: D 1263 LYS cc_start: 0.9406 (OUTLIER) cc_final: 0.8989 (mmmt) REVERT: D 1325 PHE cc_start: 0.9386 (t80) cc_final: 0.9080 (t80) REVERT: E 30 MET cc_start: 0.9213 (mtm) cc_final: 0.8898 (mtp) REVERT: E 41 GLU cc_start: 0.9539 (mt-10) cc_final: 0.9331 (tt0) REVERT: E 42 GLU cc_start: 0.9455 (mm-30) cc_final: 0.9199 (mp0) REVERT: E 44 ASP cc_start: 0.9230 (p0) cc_final: 0.8778 (p0) REVERT: E 48 VAL cc_start: 0.9508 (t) cc_final: 0.9048 (m) REVERT: E 71 GLU cc_start: 0.9381 (mm-30) cc_final: 0.9154 (pp20) REVERT: M 121 GLN cc_start: 0.9553 (mp10) cc_final: 0.9257 (mt0) outliers start: 111 outliers final: 27 residues processed: 697 average time/residue: 0.2162 time to fit residues: 233.5476 Evaluate side-chains 380 residues out of total 3073 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 341 time to evaluate : 1.060 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 98 VAL Chi-restraints excluded: chain C residue 149 LEU Chi-restraints excluded: chain C residue 184 LEU Chi-restraints excluded: chain C residue 388 LEU Chi-restraints excluded: chain C residue 445 ILE Chi-restraints excluded: chain C residue 521 LEU Chi-restraints excluded: chain C residue 564 PRO Chi-restraints excluded: chain C residue 690 VAL Chi-restraints excluded: chain C residue 697 LYS Chi-restraints excluded: chain C residue 821 ARG Chi-restraints excluded: chain C residue 827 ARG Chi-restraints excluded: chain C residue 929 ILE Chi-restraints excluded: chain C residue 1050 VAL Chi-restraints excluded: chain C residue 1070 HIS Chi-restraints excluded: chain C residue 1096 ILE Chi-restraints excluded: chain C residue 1151 LEU Chi-restraints excluded: chain C residue 1159 VAL Chi-restraints excluded: chain C residue 1243 MET Chi-restraints excluded: chain C residue 1268 GLN Chi-restraints excluded: chain C residue 1319 MET Chi-restraints excluded: chain D residue 78 LEU Chi-restraints excluded: chain D residue 93 THR Chi-restraints excluded: chain D residue 132 LEU Chi-restraints excluded: chain D residue 316 ILE Chi-restraints excluded: chain D residue 394 ILE Chi-restraints excluded: chain D residue 434 ILE Chi-restraints excluded: chain D residue 472 LEU Chi-restraints excluded: chain D residue 505 ASP Chi-restraints excluded: chain D residue 527 LEU Chi-restraints excluded: chain D residue 641 ILE Chi-restraints excluded: chain D residue 644 MET Chi-restraints excluded: chain D residue 788 LEU Chi-restraints excluded: chain D residue 835 LEU Chi-restraints excluded: chain D residue 1263 LYS Chi-restraints excluded: chain D residue 1309 ILE Chi-restraints excluded: chain D residue 1347 LEU Chi-restraints excluded: chain D residue 1353 VAL Chi-restraints excluded: chain E residue 6 VAL Chi-restraints excluded: chain M residue 156 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 351 random chunks: chunk 197 optimal weight: 6.9990 chunk 215 optimal weight: 3.9990 chunk 20 optimal weight: 1.9990 chunk 132 optimal weight: 1.9990 chunk 261 optimal weight: 6.9990 chunk 248 optimal weight: 0.7980 chunk 207 optimal weight: 6.9990 chunk 155 optimal weight: 7.9990 chunk 244 optimal weight: 1.9990 chunk 183 optimal weight: 0.9980 chunk 298 optimal weight: 0.8980 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 132 HIS ** C 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 165 HIS C 193 ASN ** C 519 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 526 HIS C 604 HIS ** C 618 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 686 GLN C 799 ASN C 856 ASN C1080 ASN C1116 HIS C1136 GLN ** C1244 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1257 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1268 GLN D 157 GLN D 435 GLN D 560 ASN ** D 716 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 861 ASN D 897 HIS D1249 ASN M 127 GLN M 157 GLN Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4004 r_free = 0.4004 target = 0.129493 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3214 r_free = 0.3214 target = 0.083814 restraints weight = 67121.891| |-----------------------------------------------------------------------------| r_work (start): 0.3137 rms_B_bonded: 3.28 r_work: 0.2952 rms_B_bonded: 4.02 restraints_weight: 0.5000 r_work (final): 0.2952 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2958 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2958 r_free = 0.2958 target_work(ls_wunit_k1) = 0.070 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2954 r_free = 0.2954 target_work(ls_wunit_k1) = 0.070 | | occupancies: max = 1.00 min = 0.08 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 6 (10 function evaluations) r_final: 0.2954 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8491 moved from start: 0.2548 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 28892 Z= 0.196 Angle : 0.916 14.485 39691 Z= 0.475 Chirality : 0.052 0.355 4774 Planarity : 0.007 0.164 4888 Dihedral : 18.185 179.103 4963 Min Nonbonded Distance : 2.207 Molprobity Statistics. All-atom Clashscore : 13.34 Ramachandran Plot: Outliers : 1.15 % Allowed : 8.10 % Favored : 90.75 % Rotamer: Outliers : 3.02 % Allowed : 13.19 % Favored : 83.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.03 % Twisted Proline : 0.69 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.78 (0.12), residues: 3567 helix: -1.23 (0.13), residues: 1265 sheet: -0.97 (0.28), residues: 287 loop : -2.47 (0.12), residues: 2015 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG D 346 TYR 0.024 0.003 TYR C 73 PHE 0.023 0.003 PHE D 461 TRP 0.022 0.003 TRP D 115 HIS 0.009 0.002 HIS C 832 Details of bonding type rmsd/Z covalent geometry : bond 0.00416 / 0.20 (28891) covalent geometry : angle 0.91592 / 0.47 (39688) hydrogen bonds : bond 0.05028 / 3.46 ( 1102) hydrogen bonds : angle 6.02109 / 4.21 ( 3064) link_TRANS : bond 0.00009 / 0.00 ( 1) link_TRANS : angle 0.69931 / 0.32 ( 3) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7134 Ramachandran restraints generated. 3567 Oldfield, 0 Emsley, 3567 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7134 Ramachandran restraints generated. 3567 Oldfield, 0 Emsley, 3567 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 453 residues out of total 3073 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 375 time to evaluate : 0.780 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: A 62 ASP cc_start: 0.7923 (p0) cc_final: 0.7612 (p0) REVERT: A 95 LYS cc_start: 0.8155 (ttpt) cc_final: 0.7639 (ptpt) REVERT: A 262 LEU cc_start: 0.8692 (OUTLIER) cc_final: 0.8236 (tt) REVERT: B 18 GLN cc_start: 0.9149 (pm20) cc_final: 0.8811 (pm20) REVERT: C 77 GLU cc_start: 0.8927 (OUTLIER) cc_final: 0.8675 (mp0) REVERT: C 88 ARG cc_start: 0.8911 (mtt180) cc_final: 0.8006 (ttt90) REVERT: C 165 HIS cc_start: 0.8418 (t-90) cc_final: 0.7998 (t-90) REVERT: C 958 LYS cc_start: 0.9055 (tttt) cc_final: 0.8749 (mtpt) REVERT: C 1030 GLU cc_start: 0.9200 (mm-30) cc_final: 0.8537 (tp30) REVERT: D 5 LEU cc_start: 0.8991 (tp) cc_final: 0.8316 (pp) REVERT: D 130 MET cc_start: 0.8458 (mtt) cc_final: 0.8078 (ttm) REVERT: D 180 MET cc_start: 0.7634 (tmm) cc_final: 0.7426 (tmm) REVERT: D 298 MET cc_start: 0.9061 (tpp) cc_final: 0.8845 (mtm) REVERT: D 339 ARG cc_start: 0.8273 (tpp-160) cc_final: 0.7904 (mtt180) REVERT: D 490 ILE cc_start: 0.9217 (pt) cc_final: 0.8804 (mt) REVERT: D 497 GLU cc_start: 0.8566 (mm-30) cc_final: 0.8302 (mm-30) REVERT: D 525 MET cc_start: 0.8896 (mtp) cc_final: 0.8686 (mtp) REVERT: D 747 MET cc_start: 0.8611 (mmm) cc_final: 0.8298 (mmp) REVERT: D 818 GLU cc_start: 0.8813 (mp0) cc_final: 0.8467 (mp0) REVERT: D 981 GLU cc_start: 0.8547 (mm-30) cc_final: 0.7345 (pm20) REVERT: D 1040 MET cc_start: 0.1581 (mtp) cc_final: 0.0936 (mmm) REVERT: E 6 VAL cc_start: 0.9321 (p) cc_final: 0.9109 (t) REVERT: E 15 ASN cc_start: 0.9141 (p0) cc_final: 0.8835 (p0) REVERT: E 30 MET cc_start: 0.9017 (mtm) cc_final: 0.8816 (mtp) REVERT: E 63 ILE cc_start: 0.8981 (mt) cc_final: 0.8747 (mp) REVERT: M 203 LEU cc_start: 0.9351 (tt) cc_final: 0.9015 (pp) REVERT: M 376 MET cc_start: 0.6376 (mmm) cc_final: 0.5675 (mmm) outliers start: 78 outliers final: 27 residues processed: 435 average time/residue: 0.1861 time to fit residues: 130.0220 Evaluate side-chains 300 residues out of total 3073 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 271 time to evaluate : 1.082 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 LEU Chi-restraints excluded: chain A residue 137 ASN Chi-restraints excluded: chain A residue 157 THR Chi-restraints excluded: chain A residue 168 ILE Chi-restraints excluded: chain A residue 262 LEU Chi-restraints excluded: chain B residue 59 VAL Chi-restraints excluded: chain B residue 172 LEU Chi-restraints excluded: chain C residue 77 GLU Chi-restraints excluded: chain C residue 442 VAL Chi-restraints excluded: chain C residue 445 ILE Chi-restraints excluded: chain C residue 469 VAL Chi-restraints excluded: chain C residue 471 VAL Chi-restraints excluded: chain C residue 690 VAL Chi-restraints excluded: chain C residue 699 LEU Chi-restraints excluded: chain C residue 719 LYS Chi-restraints excluded: chain C residue 1042 LEU Chi-restraints excluded: chain C residue 1049 ILE Chi-restraints excluded: chain C residue 1165 SER Chi-restraints excluded: chain C residue 1239 VAL Chi-restraints excluded: chain D residue 75 TYR Chi-restraints excluded: chain D residue 309 ASN Chi-restraints excluded: chain D residue 527 LEU Chi-restraints excluded: chain D residue 641 ILE Chi-restraints excluded: chain D residue 645 VAL Chi-restraints excluded: chain D residue 913 GLU Chi-restraints excluded: chain D residue 1159 ILE Chi-restraints excluded: chain D residue 1309 ILE Chi-restraints excluded: chain E residue 65 ASP Chi-restraints excluded: chain M residue 195 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 351 random chunks: chunk 26 optimal weight: 6.9990 chunk 28 optimal weight: 0.0870 chunk 201 optimal weight: 20.0000 chunk 328 optimal weight: 0.0060 chunk 169 optimal weight: 10.0000 chunk 281 optimal weight: 20.0000 chunk 200 optimal weight: 6.9990 chunk 84 optimal weight: 0.8980 chunk 134 optimal weight: 1.9990 chunk 317 optimal weight: 7.9990 chunk 316 optimal weight: 0.9980 overall best weight: 0.7976 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 510 GLN C 618 GLN C1257 GLN ** C1264 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 113 HIS D 157 GLN D 861 ASN ** D 910 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D1295 ASN E 31 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4004 r_free = 0.4004 target = 0.129190 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3213 r_free = 0.3213 target = 0.083800 restraints weight = 66890.693| |-----------------------------------------------------------------------------| r_work (start): 0.3136 rms_B_bonded: 3.29 r_work: 0.2953 rms_B_bonded: 4.09 restraints_weight: 0.5000 r_work (final): 0.2953 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2957 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2957 r_free = 0.2957 target_work(ls_wunit_k1) = 0.070 | | occupancies: max = 1.00 min = 0.08 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2957 r_free = 0.2957 target_work(ls_wunit_k1) = 0.070 | | occupancies: max = 1.00 min = 0.02 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2957 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8492 moved from start: 0.3114 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 28892 Z= 0.151 Angle : 0.788 14.876 39691 Z= 0.407 Chirality : 0.048 0.400 4774 Planarity : 0.005 0.092 4888 Dihedral : 17.905 179.205 4888 Min Nonbonded Distance : 2.266 Molprobity Statistics. All-atom Clashscore : 11.52 Ramachandran Plot: Outliers : 0.98 % Allowed : 8.63 % Favored : 90.38 % Rotamer: Outliers : 3.17 % Allowed : 14.19 % Favored : 82.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.03 % Twisted Proline : 0.69 % Twisted General : 0.09 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.99 (0.13), residues: 3567 helix: -0.22 (0.14), residues: 1269 sheet: -0.90 (0.28), residues: 300 loop : -2.21 (0.13), residues: 1998 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 33 TYR 0.022 0.002 TYR C 123 PHE 0.020 0.002 PHE D 338 TRP 0.012 0.001 TRP D 115 HIS 0.004 0.001 HIS C 673 Details of bonding type rmsd/Z covalent geometry : bond 0.00312 / 0.15 (28891) covalent geometry : angle 0.78763 / 0.41 (39688) hydrogen bonds : bond 0.04022 / 2.77 ( 1102) hydrogen bonds : angle 5.28603 / 3.67 ( 3064) link_TRANS : bond 0.00125 / 0.07 ( 1) link_TRANS : angle 0.47178 / 0.22 ( 3) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7134 Ramachandran restraints generated. 3567 Oldfield, 0 Emsley, 3567 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7134 Ramachandran restraints generated. 3567 Oldfield, 0 Emsley, 3567 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 401 residues out of total 3073 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 319 time to evaluate : 1.057 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: A 62 ASP cc_start: 0.8048 (p0) cc_final: 0.7662 (p0) REVERT: A 95 LYS cc_start: 0.8257 (ttpt) cc_final: 0.8034 (ptpt) REVERT: A 262 LEU cc_start: 0.8737 (OUTLIER) cc_final: 0.8159 (tt) REVERT: B 18 GLN cc_start: 0.9116 (pm20) cc_final: 0.8859 (pm20) REVERT: C 77 GLU cc_start: 0.8874 (OUTLIER) cc_final: 0.8653 (mp0) REVERT: C 88 ARG cc_start: 0.8903 (mtt180) cc_final: 0.8027 (ttt90) REVERT: C 165 HIS cc_start: 0.8381 (t-90) cc_final: 0.7990 (t-90) REVERT: C 768 MET cc_start: 0.8925 (mtp) cc_final: 0.8719 (mtt) REVERT: C 868 SER cc_start: 0.8658 (t) cc_final: 0.8405 (p) REVERT: C 958 LYS cc_start: 0.9038 (tttt) cc_final: 0.8743 (mtpt) REVERT: C 1030 GLU cc_start: 0.9217 (mm-30) cc_final: 0.8665 (tp30) REVERT: C 1047 LEU cc_start: 0.8989 (OUTLIER) cc_final: 0.8776 (mt) REVERT: D 130 MET cc_start: 0.8468 (mtt) cc_final: 0.8113 (ttm) REVERT: D 192 MET cc_start: 0.8973 (tpp) cc_final: 0.8669 (ttm) REVERT: D 298 MET cc_start: 0.9126 (tpp) cc_final: 0.8833 (mtm) REVERT: D 410 ASP cc_start: 0.9026 (t70) cc_final: 0.8792 (t0) REVERT: D 490 ILE cc_start: 0.9204 (pt) cc_final: 0.8755 (mt) REVERT: D 818 GLU cc_start: 0.8868 (mp0) cc_final: 0.8617 (mp0) REVERT: D 981 GLU cc_start: 0.8554 (mm-30) cc_final: 0.7389 (pm20) REVERT: D 1040 MET cc_start: 0.1358 (mtp) cc_final: 0.0759 (mmm) REVERT: E 3 ARG cc_start: 0.8704 (mmm-85) cc_final: 0.8499 (mmp80) REVERT: E 63 ILE cc_start: 0.8933 (mt) cc_final: 0.8618 (mp) REVERT: M 157 GLN cc_start: 0.8741 (tp-100) cc_final: 0.8495 (tp40) REVERT: M 181 ARG cc_start: 0.8546 (mtp180) cc_final: 0.8306 (mtp180) REVERT: M 376 MET cc_start: 0.6446 (mmm) cc_final: 0.6122 (mmm) outliers start: 82 outliers final: 30 residues processed: 381 average time/residue: 0.1728 time to fit residues: 107.1066 Evaluate side-chains 314 residues out of total 3073 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 281 time to evaluate : 0.964 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 LEU Chi-restraints excluded: chain A residue 102 LEU Chi-restraints excluded: chain A residue 137 ASN Chi-restraints excluded: chain A residue 157 THR Chi-restraints excluded: chain A residue 262 LEU Chi-restraints excluded: chain B residue 172 LEU Chi-restraints excluded: chain C residue 77 GLU Chi-restraints excluded: chain C residue 82 VAL Chi-restraints excluded: chain C residue 155 VAL Chi-restraints excluded: chain C residue 170 VAL Chi-restraints excluded: chain C residue 187 GLU Chi-restraints excluded: chain C residue 445 ILE Chi-restraints excluded: chain C residue 469 VAL Chi-restraints excluded: chain C residue 471 VAL Chi-restraints excluded: chain C residue 733 VAL Chi-restraints excluded: chain C residue 1042 LEU Chi-restraints excluded: chain C residue 1047 LEU Chi-restraints excluded: chain C residue 1049 ILE Chi-restraints excluded: chain C residue 1165 SER Chi-restraints excluded: chain C residue 1303 LYS Chi-restraints excluded: chain D residue 18 ASP Chi-restraints excluded: chain D residue 75 TYR Chi-restraints excluded: chain D residue 119 SER Chi-restraints excluded: chain D residue 309 ASN Chi-restraints excluded: chain D residue 527 LEU Chi-restraints excluded: chain D residue 560 ASN Chi-restraints excluded: chain D residue 641 ILE Chi-restraints excluded: chain D residue 645 VAL Chi-restraints excluded: chain D residue 664 ILE Chi-restraints excluded: chain D residue 913 GLU Chi-restraints excluded: chain D residue 1250 ASP Chi-restraints excluded: chain D residue 1309 ILE Chi-restraints excluded: chain E residue 65 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 351 random chunks: chunk 230 optimal weight: 0.6980 chunk 44 optimal weight: 10.0000 chunk 38 optimal weight: 9.9990 chunk 2 optimal weight: 6.9990 chunk 236 optimal weight: 0.9990 chunk 346 optimal weight: 50.0000 chunk 214 optimal weight: 8.9990 chunk 56 optimal weight: 6.9990 chunk 159 optimal weight: 2.9990 chunk 132 optimal weight: 5.9990 chunk 336 optimal weight: 10.0000 overall best weight: 3.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 147 GLN B 23 HIS C 437 ASN ** C 447 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1264 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 430 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 450 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 861 ASN ** D 910 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1218 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3951 r_free = 0.3951 target = 0.125524 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3119 r_free = 0.3119 target = 0.079543 restraints weight = 66967.192| |-----------------------------------------------------------------------------| r_work (start): 0.3049 rms_B_bonded: 3.16 r_work: 0.2869 rms_B_bonded: 3.92 restraints_weight: 0.5000 r_work (final): 0.2869 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2874 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2874 r_free = 0.2874 target_work(ls_wunit_k1) = 0.066 | | occupancies: max = 1.00 min = 0.02 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2874 r_free = 0.2874 target_work(ls_wunit_k1) = 0.066 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2874 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8592 moved from start: 0.3427 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.100 28892 Z= 0.236 Angle : 0.795 17.842 39691 Z= 0.410 Chirality : 0.049 0.382 4774 Planarity : 0.005 0.080 4888 Dihedral : 17.847 176.353 4887 Min Nonbonded Distance : 2.381 Molprobity Statistics. All-atom Clashscore : 11.23 Ramachandran Plot: Outliers : 1.01 % Allowed : 8.86 % Favored : 90.13 % Rotamer: Outliers : 2.90 % Allowed : 15.89 % Favored : 81.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.03 % Twisted Proline : 0.69 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.66 (0.13), residues: 3567 helix: 0.15 (0.14), residues: 1289 sheet: -0.67 (0.28), residues: 301 loop : -2.12 (0.13), residues: 1977 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG M 181 TYR 0.022 0.002 TYR B 185 PHE 0.022 0.002 PHE D1325 TRP 0.013 0.002 TRP D 115 HIS 0.006 0.001 HIS C1116 Details of bonding type rmsd/Z covalent geometry : bond 0.00539 / 0.24 (28891) covalent geometry : angle 0.79480 / 0.41 (39688) hydrogen bonds : bond 0.04252 / 2.91 ( 1102) hydrogen bonds : angle 4.98058 / 3.45 ( 3064) link_TRANS : bond 0.00069 / 0.04 ( 1) link_TRANS : angle 0.22339 / 0.10 ( 3) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7134 Ramachandran restraints generated. 3567 Oldfield, 0 Emsley, 3567 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7134 Ramachandran restraints generated. 3567 Oldfield, 0 Emsley, 3567 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 365 residues out of total 3073 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 290 time to evaluate : 1.069 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 62 ASP cc_start: 0.8192 (p0) cc_final: 0.7807 (p0) REVERT: A 95 LYS cc_start: 0.8436 (ttpt) cc_final: 0.8201 (ptpt) REVERT: A 262 LEU cc_start: 0.8787 (OUTLIER) cc_final: 0.8175 (tt) REVERT: B 18 GLN cc_start: 0.9156 (pm20) cc_final: 0.8918 (pm20) REVERT: B 125 LYS cc_start: 0.9024 (pttp) cc_final: 0.8565 (pptt) REVERT: C 84 GLU cc_start: 0.9122 (mt-10) cc_final: 0.8910 (mp0) REVERT: C 88 ARG cc_start: 0.8939 (mtt180) cc_final: 0.7387 (tpt170) REVERT: C 161 LYS cc_start: 0.9284 (mptt) cc_final: 0.8976 (mmtm) REVERT: C 165 HIS cc_start: 0.8406 (t-90) cc_final: 0.8017 (t-90) REVERT: C 395 TYR cc_start: 0.7560 (t80) cc_final: 0.7242 (t80) REVERT: C 685 MET cc_start: 0.8942 (mtt) cc_final: 0.8730 (mtt) REVERT: C 958 LYS cc_start: 0.9067 (tttt) cc_final: 0.8742 (mtpt) REVERT: C 1030 GLU cc_start: 0.9235 (mm-30) cc_final: 0.8660 (tp30) REVERT: D 130 MET cc_start: 0.8540 (mtt) cc_final: 0.8222 (ttm) REVERT: D 298 MET cc_start: 0.9142 (tpp) cc_final: 0.8813 (mtm) REVERT: D 410 ASP cc_start: 0.9000 (t70) cc_final: 0.8747 (t0) REVERT: D 490 ILE cc_start: 0.9267 (pt) cc_final: 0.8888 (mt) REVERT: D 818 GLU cc_start: 0.8927 (mp0) cc_final: 0.8621 (mp0) REVERT: D 981 GLU cc_start: 0.8558 (mm-30) cc_final: 0.7208 (pm20) REVERT: D 1040 MET cc_start: 0.1623 (mtp) cc_final: 0.0910 (mmm) REVERT: D 1279 GLN cc_start: 0.8308 (mm110) cc_final: 0.8082 (mm110) REVERT: D 1370 MET cc_start: 0.8325 (ttm) cc_final: 0.8056 (tmm) REVERT: E 42 GLU cc_start: 0.9139 (mm-30) cc_final: 0.8669 (mp0) REVERT: E 63 ILE cc_start: 0.9066 (mt) cc_final: 0.8708 (mp) REVERT: M 181 ARG cc_start: 0.8667 (mtp180) cc_final: 0.8430 (mtp180) outliers start: 75 outliers final: 40 residues processed: 347 average time/residue: 0.1831 time to fit residues: 102.3848 Evaluate side-chains 305 residues out of total 3073 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 264 time to evaluate : 0.922 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 LYS Chi-restraints excluded: chain A residue 13 LEU Chi-restraints excluded: chain A residue 102 LEU Chi-restraints excluded: chain A residue 137 ASN Chi-restraints excluded: chain A residue 157 THR Chi-restraints excluded: chain A residue 262 LEU Chi-restraints excluded: chain B residue 49 SER Chi-restraints excluded: chain B residue 153 VAL Chi-restraints excluded: chain B residue 171 LEU Chi-restraints excluded: chain B residue 172 LEU Chi-restraints excluded: chain C residue 144 VAL Chi-restraints excluded: chain C residue 170 VAL Chi-restraints excluded: chain C residue 187 GLU Chi-restraints excluded: chain C residue 269 ILE Chi-restraints excluded: chain C residue 397 LEU Chi-restraints excluded: chain C residue 442 VAL Chi-restraints excluded: chain C residue 445 ILE Chi-restraints excluded: chain C residue 469 VAL Chi-restraints excluded: chain C residue 1037 THR Chi-restraints excluded: chain C residue 1042 LEU Chi-restraints excluded: chain C residue 1303 LYS Chi-restraints excluded: chain D residue 7 PHE Chi-restraints excluded: chain D residue 75 TYR Chi-restraints excluded: chain D residue 119 SER Chi-restraints excluded: chain D residue 189 LEU Chi-restraints excluded: chain D residue 343 LEU Chi-restraints excluded: chain D residue 527 LEU Chi-restraints excluded: chain D residue 560 ASN Chi-restraints excluded: chain D residue 641 ILE Chi-restraints excluded: chain D residue 645 VAL Chi-restraints excluded: chain D residue 717 VAL Chi-restraints excluded: chain D residue 913 GLU Chi-restraints excluded: chain D residue 1159 ILE Chi-restraints excluded: chain D residue 1250 ASP Chi-restraints excluded: chain D residue 1306 LEU Chi-restraints excluded: chain D residue 1309 ILE Chi-restraints excluded: chain D residue 1320 ILE Chi-restraints excluded: chain E residue 61 ASN Chi-restraints excluded: chain E residue 65 ASP Chi-restraints excluded: chain M residue 195 LEU Chi-restraints excluded: chain M residue 203 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 351 random chunks: chunk 19 optimal weight: 8.9990 chunk 45 optimal weight: 8.9990 chunk 9 optimal weight: 2.9990 chunk 230 optimal weight: 0.9990 chunk 286 optimal weight: 30.0000 chunk 130 optimal weight: 3.9990 chunk 307 optimal weight: 5.9990 chunk 162 optimal weight: 0.7980 chunk 56 optimal weight: 5.9990 chunk 148 optimal weight: 8.9990 chunk 47 optimal weight: 7.9990 overall best weight: 2.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 447 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1264 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 335 GLN ** D 450 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 861 ASN D1218 HIS M 157 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3948 r_free = 0.3948 target = 0.125352 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3111 r_free = 0.3111 target = 0.078753 restraints weight = 68161.222| |-----------------------------------------------------------------------------| r_work (start): 0.3044 rms_B_bonded: 3.25 r_work: 0.2862 rms_B_bonded: 3.99 restraints_weight: 0.5000 r_work (final): 0.2862 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2866 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2866 r_free = 0.2866 target_work(ls_wunit_k1) = 0.066 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2866 r_free = 0.2866 target_work(ls_wunit_k1) = 0.066 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2866 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8588 moved from start: 0.3733 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.064 28892 Z= 0.201 Angle : 0.755 16.638 39691 Z= 0.389 Chirality : 0.048 0.382 4774 Planarity : 0.005 0.081 4888 Dihedral : 17.746 175.313 4887 Min Nonbonded Distance : 2.354 Molprobity Statistics. All-atom Clashscore : 10.47 Ramachandran Plot: Outliers : 1.07 % Allowed : 8.61 % Favored : 90.33 % Rotamer: Outliers : 3.05 % Allowed : 16.86 % Favored : 80.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.03 % Twisted Proline : 0.69 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.43 (0.14), residues: 3567 helix: 0.48 (0.15), residues: 1283 sheet: -0.59 (0.28), residues: 307 loop : -2.09 (0.13), residues: 1977 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG M 181 TYR 0.018 0.002 TYR C 123 PHE 0.018 0.002 PHE C 156 TRP 0.009 0.001 TRP D 115 HIS 0.006 0.001 HIS C1116 Details of bonding type rmsd/Z covalent geometry : bond 0.00454 / 0.20 (28891) covalent geometry : angle 0.75519 / 0.39 (39688) hydrogen bonds : bond 0.03829 / 2.61 ( 1102) hydrogen bonds : angle 4.83014 / 3.33 ( 3064) link_TRANS : bond 0.00000 / 0.00 ( 1) link_TRANS : angle 0.16572 / 0.09 ( 3) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7134 Ramachandran restraints generated. 3567 Oldfield, 0 Emsley, 3567 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7134 Ramachandran restraints generated. 3567 Oldfield, 0 Emsley, 3567 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 361 residues out of total 3073 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 282 time to evaluate : 1.076 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 95 LYS cc_start: 0.8468 (ttpt) cc_final: 0.8004 (ptpt) REVERT: B 18 GLN cc_start: 0.9152 (pm20) cc_final: 0.8762 (pm20) REVERT: B 125 LYS cc_start: 0.8999 (pttp) cc_final: 0.8544 (pptt) REVERT: C 84 GLU cc_start: 0.9129 (mt-10) cc_final: 0.8916 (mp0) REVERT: C 88 ARG cc_start: 0.8989 (mtt180) cc_final: 0.7403 (tpt170) REVERT: C 165 HIS cc_start: 0.8423 (t-90) cc_final: 0.8029 (t-90) REVERT: C 395 TYR cc_start: 0.7559 (t80) cc_final: 0.7213 (t80) REVERT: C 548 ARG cc_start: 0.8424 (OUTLIER) cc_final: 0.7943 (mmt180) REVERT: C 958 LYS cc_start: 0.9147 (tttt) cc_final: 0.8843 (mtpt) REVERT: C 1030 GLU cc_start: 0.9242 (mm-30) cc_final: 0.8657 (tp30) REVERT: D 113 HIS cc_start: 0.7859 (t70) cc_final: 0.7438 (t70) REVERT: D 130 MET cc_start: 0.8601 (mtt) cc_final: 0.8288 (ttm) REVERT: D 298 MET cc_start: 0.9182 (tpp) cc_final: 0.8742 (mtm) REVERT: D 410 ASP cc_start: 0.8992 (t70) cc_final: 0.8700 (t0) REVERT: D 443 GLU cc_start: 0.8494 (pm20) cc_final: 0.8272 (pm20) REVERT: D 490 ILE cc_start: 0.9274 (pt) cc_final: 0.8844 (mt) REVERT: D 551 ARG cc_start: 0.9389 (OUTLIER) cc_final: 0.8877 (ptp-170) REVERT: D 818 GLU cc_start: 0.8970 (mp0) cc_final: 0.8653 (mp0) REVERT: D 981 GLU cc_start: 0.8579 (mm-30) cc_final: 0.8149 (tp30) REVERT: D 1040 MET cc_start: 0.2012 (mtp) cc_final: 0.1186 (mmm) REVERT: D 1149 ARG cc_start: 0.8571 (mmt90) cc_final: 0.8152 (mmt90) REVERT: D 1279 GLN cc_start: 0.8355 (mm110) cc_final: 0.7904 (mm110) REVERT: D 1370 MET cc_start: 0.8337 (ttm) cc_final: 0.8066 (tmm) REVERT: E 63 ILE cc_start: 0.9036 (mt) cc_final: 0.8643 (mp) REVERT: M 181 ARG cc_start: 0.8697 (mtp180) cc_final: 0.8259 (mmm-85) outliers start: 79 outliers final: 51 residues processed: 342 average time/residue: 0.1809 time to fit residues: 99.4529 Evaluate side-chains 317 residues out of total 3073 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 264 time to evaluate : 1.062 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 LYS Chi-restraints excluded: chain A residue 13 LEU Chi-restraints excluded: chain A residue 101 THR Chi-restraints excluded: chain A residue 102 LEU Chi-restraints excluded: chain A residue 137 ASN Chi-restraints excluded: chain A residue 262 LEU Chi-restraints excluded: chain B residue 26 VAL Chi-restraints excluded: chain B residue 49 SER Chi-restraints excluded: chain B residue 172 LEU Chi-restraints excluded: chain C residue 144 VAL Chi-restraints excluded: chain C residue 155 VAL Chi-restraints excluded: chain C residue 170 VAL Chi-restraints excluded: chain C residue 187 GLU Chi-restraints excluded: chain C residue 269 ILE Chi-restraints excluded: chain C residue 316 GLU Chi-restraints excluded: chain C residue 397 LEU Chi-restraints excluded: chain C residue 442 VAL Chi-restraints excluded: chain C residue 445 ILE Chi-restraints excluded: chain C residue 448 LEU Chi-restraints excluded: chain C residue 469 VAL Chi-restraints excluded: chain C residue 548 ARG Chi-restraints excluded: chain C residue 733 VAL Chi-restraints excluded: chain C residue 736 VAL Chi-restraints excluded: chain C residue 772 SER Chi-restraints excluded: chain C residue 856 ASN Chi-restraints excluded: chain C residue 857 VAL Chi-restraints excluded: chain C residue 1042 LEU Chi-restraints excluded: chain C residue 1165 SER Chi-restraints excluded: chain C residue 1303 LYS Chi-restraints excluded: chain D residue 7 PHE Chi-restraints excluded: chain D residue 18 ASP Chi-restraints excluded: chain D residue 75 TYR Chi-restraints excluded: chain D residue 126 LEU Chi-restraints excluded: chain D residue 189 LEU Chi-restraints excluded: chain D residue 283 LEU Chi-restraints excluded: chain D residue 416 ILE Chi-restraints excluded: chain D residue 527 LEU Chi-restraints excluded: chain D residue 551 ARG Chi-restraints excluded: chain D residue 560 ASN Chi-restraints excluded: chain D residue 641 ILE Chi-restraints excluded: chain D residue 645 VAL Chi-restraints excluded: chain D residue 717 VAL Chi-restraints excluded: chain D residue 788 LEU Chi-restraints excluded: chain D residue 905 ARG Chi-restraints excluded: chain D residue 928 THR Chi-restraints excluded: chain D residue 1159 ILE Chi-restraints excluded: chain D residue 1196 LEU Chi-restraints excluded: chain D residue 1250 ASP Chi-restraints excluded: chain D residue 1309 ILE Chi-restraints excluded: chain E residue 61 ASN Chi-restraints excluded: chain E residue 65 ASP Chi-restraints excluded: chain M residue 195 LEU Chi-restraints excluded: chain M residue 203 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 351 random chunks: chunk 343 optimal weight: 50.0000 chunk 303 optimal weight: 0.0870 chunk 201 optimal weight: 8.9990 chunk 113 optimal weight: 9.9990 chunk 332 optimal weight: 8.9990 chunk 63 optimal weight: 20.0000 chunk 207 optimal weight: 9.9990 chunk 66 optimal weight: 3.9990 chunk 334 optimal weight: 8.9990 chunk 90 optimal weight: 20.0000 chunk 245 optimal weight: 0.1980 overall best weight: 4.4564 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 447 HIS C 513 GLN C 526 HIS C 686 GLN D 364 HIS ** D 450 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 861 ASN ** D 910 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3915 r_free = 0.3915 target = 0.123172 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3058 r_free = 0.3058 target = 0.075793 restraints weight = 68028.206| |-----------------------------------------------------------------------------| r_work (start): 0.2998 rms_B_bonded: 2.94 r_work: 0.2833 rms_B_bonded: 3.71 restraints_weight: 0.5000 r_work (final): 0.2833 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2833 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2833 r_free = 0.2833 target_work(ls_wunit_k1) = 0.064 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2833 r_free = 0.2833 target_work(ls_wunit_k1) = 0.064 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2833 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8627 moved from start: 0.3974 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.119 28892 Z= 0.288 Angle : 0.795 17.828 39691 Z= 0.410 Chirality : 0.049 0.392 4774 Planarity : 0.005 0.082 4888 Dihedral : 17.732 176.709 4887 Min Nonbonded Distance : 2.342 Molprobity Statistics. All-atom Clashscore : 11.23 Ramachandran Plot: Outliers : 1.01 % Allowed : 9.45 % Favored : 89.54 % Rotamer: Outliers : 3.56 % Allowed : 17.29 % Favored : 79.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.03 % Twisted Proline : 0.69 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.39 (0.14), residues: 3567 helix: 0.55 (0.15), residues: 1284 sheet: -0.49 (0.29), residues: 302 loop : -2.10 (0.13), residues: 1981 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG E 67 TYR 0.021 0.002 TYR C 123 PHE 0.027 0.002 PHE C 230 TRP 0.012 0.001 TRP D 115 HIS 0.007 0.002 HIS D 113 Details of bonding type rmsd/Z covalent geometry : bond 0.00668 / 0.29 (28891) covalent geometry : angle 0.79544 / 0.41 (39688) hydrogen bonds : bond 0.04244 / 2.89 ( 1102) hydrogen bonds : angle 4.81468 / 3.33 ( 3064) link_TRANS : bond 0.00080 / 0.04 ( 1) link_TRANS : angle 0.34866 / 0.20 ( 3) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7134 Ramachandran restraints generated. 3567 Oldfield, 0 Emsley, 3567 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7134 Ramachandran restraints generated. 3567 Oldfield, 0 Emsley, 3567 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 354 residues out of total 3073 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 262 time to evaluate : 1.277 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 95 LYS cc_start: 0.8539 (ttpt) cc_final: 0.8096 (ptpt) REVERT: B 125 LYS cc_start: 0.8997 (pttp) cc_final: 0.8573 (pptt) REVERT: C 165 HIS cc_start: 0.8361 (t-90) cc_final: 0.8109 (t-90) REVERT: C 302 ILE cc_start: 0.7408 (OUTLIER) cc_final: 0.7179 (pp) REVERT: C 395 TYR cc_start: 0.7473 (t80) cc_final: 0.7087 (t80) REVERT: C 548 ARG cc_start: 0.8432 (OUTLIER) cc_final: 0.7936 (mmt180) REVERT: C 958 LYS cc_start: 0.9177 (tttt) cc_final: 0.8845 (mtpt) REVERT: C 1030 GLU cc_start: 0.9265 (mm-30) cc_final: 0.8658 (tp30) REVERT: D 130 MET cc_start: 0.8610 (mtt) cc_final: 0.8307 (ttm) REVERT: D 298 MET cc_start: 0.9153 (tpp) cc_final: 0.8631 (mtm) REVERT: D 340 GLN cc_start: 0.8432 (mp10) cc_final: 0.7891 (mp10) REVERT: D 410 ASP cc_start: 0.8983 (t70) cc_final: 0.8696 (t0) REVERT: D 490 ILE cc_start: 0.9267 (pt) cc_final: 0.8884 (mt) REVERT: D 527 LEU cc_start: 0.9301 (OUTLIER) cc_final: 0.8862 (pp) REVERT: D 818 GLU cc_start: 0.8965 (mp0) cc_final: 0.8679 (mp0) REVERT: E 10 VAL cc_start: 0.9266 (t) cc_final: 0.9060 (p) REVERT: E 42 GLU cc_start: 0.9211 (mm-30) cc_final: 0.8827 (mp0) REVERT: E 63 ILE cc_start: 0.9030 (OUTLIER) cc_final: 0.8648 (mp) REVERT: M 181 ARG cc_start: 0.8754 (mtp180) cc_final: 0.8320 (mmm-85) REVERT: M 350 GLN cc_start: 0.8795 (mm-40) cc_final: 0.8591 (mm-40) outliers start: 92 outliers final: 64 residues processed: 334 average time/residue: 0.1873 time to fit residues: 100.5899 Evaluate side-chains 316 residues out of total 3073 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 248 time to evaluate : 0.865 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 LYS Chi-restraints excluded: chain A residue 13 LEU Chi-restraints excluded: chain A residue 101 THR Chi-restraints excluded: chain A residue 102 LEU Chi-restraints excluded: chain A residue 137 ASN Chi-restraints excluded: chain A residue 262 LEU Chi-restraints excluded: chain B residue 26 VAL Chi-restraints excluded: chain B residue 48 LEU Chi-restraints excluded: chain B residue 49 SER Chi-restraints excluded: chain B residue 153 VAL Chi-restraints excluded: chain B residue 172 LEU Chi-restraints excluded: chain B residue 205 MET Chi-restraints excluded: chain C residue 144 VAL Chi-restraints excluded: chain C residue 170 VAL Chi-restraints excluded: chain C residue 187 GLU Chi-restraints excluded: chain C residue 220 ILE Chi-restraints excluded: chain C residue 221 LEU Chi-restraints excluded: chain C residue 269 ILE Chi-restraints excluded: chain C residue 302 ILE Chi-restraints excluded: chain C residue 316 GLU Chi-restraints excluded: chain C residue 397 LEU Chi-restraints excluded: chain C residue 442 VAL Chi-restraints excluded: chain C residue 445 ILE Chi-restraints excluded: chain C residue 448 LEU Chi-restraints excluded: chain C residue 469 VAL Chi-restraints excluded: chain C residue 513 GLN Chi-restraints excluded: chain C residue 548 ARG Chi-restraints excluded: chain C residue 563 THR Chi-restraints excluded: chain C residue 714 VAL Chi-restraints excluded: chain C residue 733 VAL Chi-restraints excluded: chain C residue 736 VAL Chi-restraints excluded: chain C residue 772 SER Chi-restraints excluded: chain C residue 857 VAL Chi-restraints excluded: chain C residue 882 ILE Chi-restraints excluded: chain C residue 920 VAL Chi-restraints excluded: chain C residue 1037 THR Chi-restraints excluded: chain C residue 1042 LEU Chi-restraints excluded: chain C residue 1165 SER Chi-restraints excluded: chain C residue 1243 MET Chi-restraints excluded: chain C residue 1303 LYS Chi-restraints excluded: chain D residue 7 PHE Chi-restraints excluded: chain D residue 18 ASP Chi-restraints excluded: chain D residue 75 TYR Chi-restraints excluded: chain D residue 92 VAL Chi-restraints excluded: chain D residue 119 SER Chi-restraints excluded: chain D residue 126 LEU Chi-restraints excluded: chain D residue 189 LEU Chi-restraints excluded: chain D residue 227 PHE Chi-restraints excluded: chain D residue 416 ILE Chi-restraints excluded: chain D residue 434 ILE Chi-restraints excluded: chain D residue 527 LEU Chi-restraints excluded: chain D residue 560 ASN Chi-restraints excluded: chain D residue 641 ILE Chi-restraints excluded: chain D residue 645 VAL Chi-restraints excluded: chain D residue 717 VAL Chi-restraints excluded: chain D residue 722 ILE Chi-restraints excluded: chain D residue 861 ASN Chi-restraints excluded: chain D residue 905 ARG Chi-restraints excluded: chain D residue 1159 ILE Chi-restraints excluded: chain D residue 1196 LEU Chi-restraints excluded: chain D residue 1250 ASP Chi-restraints excluded: chain D residue 1306 LEU Chi-restraints excluded: chain D residue 1309 ILE Chi-restraints excluded: chain E residue 63 ILE Chi-restraints excluded: chain E residue 65 ASP Chi-restraints excluded: chain M residue 144 ILE Chi-restraints excluded: chain M residue 195 LEU Chi-restraints excluded: chain M residue 203 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 351 random chunks: chunk 248 optimal weight: 0.9980 chunk 267 optimal weight: 1.9990 chunk 16 optimal weight: 0.8980 chunk 251 optimal weight: 7.9990 chunk 32 optimal weight: 2.9990 chunk 160 optimal weight: 0.9980 chunk 25 optimal weight: 8.9990 chunk 322 optimal weight: 0.8980 chunk 85 optimal weight: 20.0000 chunk 21 optimal weight: 0.8980 chunk 245 optimal weight: 1.9990 overall best weight: 0.9380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 513 GLN ** C1264 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 450 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 910 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3951 r_free = 0.3951 target = 0.125495 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3138 r_free = 0.3138 target = 0.079983 restraints weight = 66543.189| |-----------------------------------------------------------------------------| r_work (start): 0.3071 rms_B_bonded: 3.21 r_work: 0.2873 rms_B_bonded: 4.07 restraints_weight: 0.5000 r_work (final): 0.2873 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2874 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2874 r_free = 0.2874 target_work(ls_wunit_k1) = 0.066 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2874 r_free = 0.2874 target_work(ls_wunit_k1) = 0.066 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2874 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8580 moved from start: 0.4120 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 28892 Z= 0.135 Angle : 0.727 15.632 39691 Z= 0.371 Chirality : 0.045 0.360 4774 Planarity : 0.005 0.083 4888 Dihedral : 17.636 176.616 4887 Min Nonbonded Distance : 2.342 Molprobity Statistics. All-atom Clashscore : 10.11 Ramachandran Plot: Outliers : 0.95 % Allowed : 8.75 % Favored : 90.30 % Rotamer: Outliers : 3.17 % Allowed : 17.71 % Favored : 79.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.03 % Twisted Proline : 0.69 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.16 (0.14), residues: 3567 helix: 0.84 (0.15), residues: 1282 sheet: -0.47 (0.29), residues: 307 loop : -2.02 (0.13), residues: 1978 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG C 88 TYR 0.014 0.001 TYR B 185 PHE 0.020 0.001 PHE D1325 TRP 0.009 0.001 TRP D 580 HIS 0.005 0.001 HIS D 430 Details of bonding type rmsd/Z covalent geometry : bond 0.00278 / 0.13 (28891) covalent geometry : angle 0.72728 / 0.37 (39688) hydrogen bonds : bond 0.03483 / 2.36 ( 1102) hydrogen bonds : angle 4.62582 / 3.19 ( 3064) link_TRANS : bond 0.00052 / 0.03 ( 1) link_TRANS : angle 0.22254 / 0.12 ( 3) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7134 Ramachandran restraints generated. 3567 Oldfield, 0 Emsley, 3567 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7134 Ramachandran restraints generated. 3567 Oldfield, 0 Emsley, 3567 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 355 residues out of total 3073 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 273 time to evaluate : 1.042 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: A 95 LYS cc_start: 0.8445 (ttpt) cc_final: 0.8055 (ptpt) REVERT: B 125 LYS cc_start: 0.8943 (pttp) cc_final: 0.8549 (pptt) REVERT: B 152 TYR cc_start: 0.9075 (t80) cc_final: 0.8864 (t80) REVERT: C 165 HIS cc_start: 0.8467 (t-90) cc_final: 0.8237 (t70) REVERT: C 302 ILE cc_start: 0.7343 (OUTLIER) cc_final: 0.7111 (pp) REVERT: C 395 TYR cc_start: 0.7460 (t80) cc_final: 0.7158 (t80) REVERT: C 958 LYS cc_start: 0.9180 (tttt) cc_final: 0.8859 (mtpt) REVERT: C 1030 GLU cc_start: 0.9280 (mm-30) cc_final: 0.8656 (tp30) REVERT: D 130 MET cc_start: 0.8623 (mtt) cc_final: 0.8368 (ttt) REVERT: D 298 MET cc_start: 0.9160 (tpp) cc_final: 0.8658 (mtm) REVERT: D 410 ASP cc_start: 0.8938 (t70) cc_final: 0.8632 (t0) REVERT: D 422 LEU cc_start: 0.9458 (OUTLIER) cc_final: 0.9148 (pp) REVERT: D 490 ILE cc_start: 0.9230 (pt) cc_final: 0.8785 (mt) REVERT: D 551 ARG cc_start: 0.9374 (OUTLIER) cc_final: 0.9154 (ptm160) REVERT: D 818 GLU cc_start: 0.9006 (mp0) cc_final: 0.8714 (mp0) REVERT: D 1040 MET cc_start: 0.2930 (OUTLIER) cc_final: 0.1264 (mmm) REVERT: D 1370 MET cc_start: 0.8245 (tmm) cc_final: 0.7861 (tmm) REVERT: E 42 GLU cc_start: 0.9161 (mm-30) cc_final: 0.8822 (mp0) REVERT: E 63 ILE cc_start: 0.9023 (OUTLIER) cc_final: 0.8628 (mp) REVERT: E 72 GLN cc_start: 0.9151 (tp40) cc_final: 0.8781 (pp30) REVERT: M 157 GLN cc_start: 0.8817 (tp-100) cc_final: 0.8574 (tm-30) REVERT: M 181 ARG cc_start: 0.8667 (mtp180) cc_final: 0.8225 (mmm-85) REVERT: M 350 GLN cc_start: 0.8795 (mm-40) cc_final: 0.8594 (mm-40) outliers start: 82 outliers final: 56 residues processed: 335 average time/residue: 0.1814 time to fit residues: 98.7048 Evaluate side-chains 316 residues out of total 3073 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 255 time to evaluate : 1.059 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 LYS Chi-restraints excluded: chain A residue 13 LEU Chi-restraints excluded: chain A residue 67 GLU Chi-restraints excluded: chain A residue 102 LEU Chi-restraints excluded: chain A residue 137 ASN Chi-restraints excluded: chain A residue 262 LEU Chi-restraints excluded: chain B residue 26 VAL Chi-restraints excluded: chain B residue 49 SER Chi-restraints excluded: chain B residue 153 VAL Chi-restraints excluded: chain B residue 172 LEU Chi-restraints excluded: chain C residue 144 VAL Chi-restraints excluded: chain C residue 170 VAL Chi-restraints excluded: chain C residue 187 GLU Chi-restraints excluded: chain C residue 220 ILE Chi-restraints excluded: chain C residue 221 LEU Chi-restraints excluded: chain C residue 269 ILE Chi-restraints excluded: chain C residue 302 ILE Chi-restraints excluded: chain C residue 397 LEU Chi-restraints excluded: chain C residue 442 VAL Chi-restraints excluded: chain C residue 445 ILE Chi-restraints excluded: chain C residue 448 LEU Chi-restraints excluded: chain C residue 469 VAL Chi-restraints excluded: chain C residue 714 VAL Chi-restraints excluded: chain C residue 733 VAL Chi-restraints excluded: chain C residue 736 VAL Chi-restraints excluded: chain C residue 856 ASN Chi-restraints excluded: chain C residue 857 VAL Chi-restraints excluded: chain C residue 920 VAL Chi-restraints excluded: chain C residue 1042 LEU Chi-restraints excluded: chain C residue 1159 VAL Chi-restraints excluded: chain C residue 1165 SER Chi-restraints excluded: chain C residue 1303 LYS Chi-restraints excluded: chain D residue 7 PHE Chi-restraints excluded: chain D residue 18 ASP Chi-restraints excluded: chain D residue 119 SER Chi-restraints excluded: chain D residue 126 LEU Chi-restraints excluded: chain D residue 189 LEU Chi-restraints excluded: chain D residue 227 PHE Chi-restraints excluded: chain D residue 416 ILE Chi-restraints excluded: chain D residue 422 LEU Chi-restraints excluded: chain D residue 434 ILE Chi-restraints excluded: chain D residue 527 LEU Chi-restraints excluded: chain D residue 551 ARG Chi-restraints excluded: chain D residue 560 ASN Chi-restraints excluded: chain D residue 645 VAL Chi-restraints excluded: chain D residue 706 VAL Chi-restraints excluded: chain D residue 717 VAL Chi-restraints excluded: chain D residue 905 ARG Chi-restraints excluded: chain D residue 913 GLU Chi-restraints excluded: chain D residue 1040 MET Chi-restraints excluded: chain D residue 1159 ILE Chi-restraints excluded: chain D residue 1209 VAL Chi-restraints excluded: chain D residue 1250 ASP Chi-restraints excluded: chain D residue 1306 LEU Chi-restraints excluded: chain D residue 1320 ILE Chi-restraints excluded: chain E residue 61 ASN Chi-restraints excluded: chain E residue 63 ILE Chi-restraints excluded: chain E residue 65 ASP Chi-restraints excluded: chain M residue 185 PHE Chi-restraints excluded: chain M residue 195 LEU Chi-restraints excluded: chain M residue 203 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 351 random chunks: chunk 337 optimal weight: 0.9980 chunk 28 optimal weight: 0.0970 chunk 127 optimal weight: 7.9990 chunk 179 optimal weight: 5.9990 chunk 148 optimal weight: 8.9990 chunk 35 optimal weight: 20.0000 chunk 227 optimal weight: 6.9990 chunk 272 optimal weight: 2.9990 chunk 8 optimal weight: 4.9990 chunk 338 optimal weight: 1.9990 chunk 326 optimal weight: 5.9990 overall best weight: 2.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 513 GLN ** D 450 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 504 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 910 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D1218 HIS D1279 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3942 r_free = 0.3942 target = 0.124836 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3121 r_free = 0.3121 target = 0.078814 restraints weight = 67918.324| |-----------------------------------------------------------------------------| r_work (start): 0.3049 rms_B_bonded: 3.23 r_work: 0.2849 rms_B_bonded: 4.09 restraints_weight: 0.5000 r_work (final): 0.2849 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2851 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2851 r_free = 0.2851 target_work(ls_wunit_k1) = 0.065 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2851 r_free = 0.2851 target_work(ls_wunit_k1) = 0.065 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2851 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8610 moved from start: 0.4236 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 28892 Z= 0.172 Angle : 0.725 16.310 39691 Z= 0.370 Chirality : 0.045 0.361 4774 Planarity : 0.005 0.081 4888 Dihedral : 17.559 177.576 4883 Min Nonbonded Distance : 2.347 Molprobity Statistics. All-atom Clashscore : 10.36 Ramachandran Plot: Outliers : 0.90 % Allowed : 9.11 % Favored : 89.99 % Rotamer: Outliers : 2.51 % Allowed : 18.72 % Favored : 78.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.03 % Twisted Proline : 0.69 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.10 (0.14), residues: 3567 helix: 0.92 (0.15), residues: 1286 sheet: -0.42 (0.29), residues: 300 loop : -2.01 (0.13), residues: 1981 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG D 339 TYR 0.014 0.001 TYR C 123 PHE 0.021 0.001 PHE D1325 TRP 0.009 0.001 TRP D 115 HIS 0.005 0.001 HIS D 450 Details of bonding type rmsd/Z covalent geometry : bond 0.00387 / 0.17 (28891) covalent geometry : angle 0.72499 / 0.37 (39688) hydrogen bonds : bond 0.03555 / 2.42 ( 1102) hydrogen bonds : angle 4.56644 / 3.14 ( 3064) link_TRANS : bond 0.00011 / 0.01 ( 1) link_TRANS : angle 0.26281 / 0.14 ( 3) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7134 Ramachandran restraints generated. 3567 Oldfield, 0 Emsley, 3567 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7134 Ramachandran restraints generated. 3567 Oldfield, 0 Emsley, 3567 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 329 residues out of total 3073 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 264 time to evaluate : 1.136 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: A 95 LYS cc_start: 0.8493 (ttpt) cc_final: 0.8144 (ptpt) REVERT: B 12 ARG cc_start: 0.7926 (mmm160) cc_final: 0.7513 (mmp-170) REVERT: B 125 LYS cc_start: 0.8954 (pttp) cc_final: 0.8532 (pptt) REVERT: B 152 TYR cc_start: 0.9088 (t80) cc_final: 0.8863 (t80) REVERT: C 165 HIS cc_start: 0.8455 (t-90) cc_final: 0.8222 (t70) REVERT: C 302 ILE cc_start: 0.7338 (OUTLIER) cc_final: 0.7104 (pp) REVERT: C 395 TYR cc_start: 0.7507 (t80) cc_final: 0.7130 (t80) REVERT: C 958 LYS cc_start: 0.9175 (tttt) cc_final: 0.8859 (mtpt) REVERT: C 1030 GLU cc_start: 0.9286 (mm-30) cc_final: 0.8665 (tp30) REVERT: D 130 MET cc_start: 0.8669 (mtt) cc_final: 0.8275 (ttt) REVERT: D 298 MET cc_start: 0.9131 (tpp) cc_final: 0.8570 (mtm) REVERT: D 410 ASP cc_start: 0.8943 (t70) cc_final: 0.8640 (t0) REVERT: D 422 LEU cc_start: 0.9541 (OUTLIER) cc_final: 0.9198 (pp) REVERT: D 490 ILE cc_start: 0.9244 (pt) cc_final: 0.8848 (mt) REVERT: D 551 ARG cc_start: 0.9418 (OUTLIER) cc_final: 0.9013 (ptp-170) REVERT: D 698 MET cc_start: 0.9162 (tpp) cc_final: 0.8757 (mmm) REVERT: D 818 GLU cc_start: 0.8998 (mp0) cc_final: 0.8734 (mp0) REVERT: D 1040 MET cc_start: 0.3004 (mtt) cc_final: 0.1588 (mmm) REVERT: D 1365 TYR cc_start: 0.8790 (t80) cc_final: 0.8365 (t80) REVERT: E 42 GLU cc_start: 0.9169 (mm-30) cc_final: 0.8911 (mp0) REVERT: E 63 ILE cc_start: 0.8990 (OUTLIER) cc_final: 0.8588 (mp) REVERT: M 181 ARG cc_start: 0.8735 (mtp180) cc_final: 0.8315 (mmm-85) REVERT: M 350 GLN cc_start: 0.8761 (mm-40) cc_final: 0.8400 (mm-40) outliers start: 65 outliers final: 52 residues processed: 315 average time/residue: 0.1827 time to fit residues: 93.3508 Evaluate side-chains 311 residues out of total 3073 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 255 time to evaluate : 1.008 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 LYS Chi-restraints excluded: chain A residue 67 GLU Chi-restraints excluded: chain A residue 101 THR Chi-restraints excluded: chain A residue 102 LEU Chi-restraints excluded: chain A residue 137 ASN Chi-restraints excluded: chain A residue 262 LEU Chi-restraints excluded: chain B residue 26 VAL Chi-restraints excluded: chain B residue 48 LEU Chi-restraints excluded: chain B residue 49 SER Chi-restraints excluded: chain B residue 153 VAL Chi-restraints excluded: chain B residue 171 LEU Chi-restraints excluded: chain B residue 172 LEU Chi-restraints excluded: chain B residue 205 MET Chi-restraints excluded: chain C residue 144 VAL Chi-restraints excluded: chain C residue 170 VAL Chi-restraints excluded: chain C residue 187 GLU Chi-restraints excluded: chain C residue 221 LEU Chi-restraints excluded: chain C residue 269 ILE Chi-restraints excluded: chain C residue 302 ILE Chi-restraints excluded: chain C residue 397 LEU Chi-restraints excluded: chain C residue 442 VAL Chi-restraints excluded: chain C residue 445 ILE Chi-restraints excluded: chain C residue 448 LEU Chi-restraints excluded: chain C residue 469 VAL Chi-restraints excluded: chain C residue 714 VAL Chi-restraints excluded: chain C residue 733 VAL Chi-restraints excluded: chain C residue 736 VAL Chi-restraints excluded: chain C residue 920 VAL Chi-restraints excluded: chain C residue 1042 LEU Chi-restraints excluded: chain C residue 1159 VAL Chi-restraints excluded: chain C residue 1165 SER Chi-restraints excluded: chain C residue 1303 LYS Chi-restraints excluded: chain D residue 7 PHE Chi-restraints excluded: chain D residue 18 ASP Chi-restraints excluded: chain D residue 119 SER Chi-restraints excluded: chain D residue 189 LEU Chi-restraints excluded: chain D residue 227 PHE Chi-restraints excluded: chain D residue 416 ILE Chi-restraints excluded: chain D residue 422 LEU Chi-restraints excluded: chain D residue 434 ILE Chi-restraints excluded: chain D residue 527 LEU Chi-restraints excluded: chain D residue 551 ARG Chi-restraints excluded: chain D residue 560 ASN Chi-restraints excluded: chain D residue 645 VAL Chi-restraints excluded: chain D residue 706 VAL Chi-restraints excluded: chain D residue 717 VAL Chi-restraints excluded: chain D residue 905 ARG Chi-restraints excluded: chain D residue 913 GLU Chi-restraints excluded: chain D residue 1159 ILE Chi-restraints excluded: chain D residue 1209 VAL Chi-restraints excluded: chain D residue 1250 ASP Chi-restraints excluded: chain E residue 63 ILE Chi-restraints excluded: chain E residue 65 ASP Chi-restraints excluded: chain M residue 144 ILE Chi-restraints excluded: chain M residue 185 PHE Chi-restraints excluded: chain M residue 195 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 351 random chunks: chunk 231 optimal weight: 3.9990 chunk 219 optimal weight: 0.0370 chunk 337 optimal weight: 3.9990 chunk 140 optimal weight: 6.9990 chunk 21 optimal weight: 6.9990 chunk 178 optimal weight: 0.9980 chunk 164 optimal weight: 2.9990 chunk 211 optimal weight: 0.0470 chunk 68 optimal weight: 0.9980 chunk 14 optimal weight: 10.0000 chunk 208 optimal weight: 10.0000 overall best weight: 1.0158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C1264 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 450 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 504 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 712 GLN D 739 GLN ** D 910 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3958 r_free = 0.3958 target = 0.126008 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3126 r_free = 0.3126 target = 0.079717 restraints weight = 67880.954| |-----------------------------------------------------------------------------| r_work (start): 0.3059 rms_B_bonded: 3.34 r_work: 0.2875 rms_B_bonded: 4.10 restraints_weight: 0.5000 r_work (final): 0.2875 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2881 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2881 r_free = 0.2881 target_work(ls_wunit_k1) = 0.066 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2881 r_free = 0.2881 target_work(ls_wunit_k1) = 0.066 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2881 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8584 moved from start: 0.4347 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 28892 Z= 0.133 Angle : 0.721 15.507 39691 Z= 0.366 Chirality : 0.045 0.350 4774 Planarity : 0.004 0.083 4888 Dihedral : 17.509 178.315 4883 Min Nonbonded Distance : 2.251 Molprobity Statistics. All-atom Clashscore : 10.24 Ramachandran Plot: Outliers : 0.87 % Allowed : 8.61 % Favored : 90.52 % Rotamer: Outliers : 2.32 % Allowed : 19.22 % Favored : 78.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.03 % Twisted Proline : 0.69 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.98 (0.14), residues: 3567 helix: 1.04 (0.15), residues: 1284 sheet: -0.37 (0.29), residues: 300 loop : -1.96 (0.13), residues: 1983 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG E 67 TYR 0.013 0.001 TYR B 185 PHE 0.018 0.001 PHE D1325 TRP 0.008 0.001 TRP D 580 HIS 0.004 0.001 HIS D 430 Details of bonding type rmsd/Z covalent geometry : bond 0.00279 / 0.13 (28891) covalent geometry : angle 0.72152 / 0.37 (39688) hydrogen bonds : bond 0.03298 / 2.24 ( 1102) hydrogen bonds : angle 4.47419 / 3.07 ( 3064) link_TRANS : bond 0.00052 / 0.03 ( 1) link_TRANS : angle 0.23449 / 0.12 ( 3) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7134 Ramachandran restraints generated. 3567 Oldfield, 0 Emsley, 3567 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7134 Ramachandran restraints generated. 3567 Oldfield, 0 Emsley, 3567 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 333 residues out of total 3073 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 273 time to evaluate : 1.135 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: A 95 LYS cc_start: 0.8471 (ttpt) cc_final: 0.8267 (ptpt) REVERT: B 125 LYS cc_start: 0.8948 (pttp) cc_final: 0.8658 (pptt) REVERT: B 152 TYR cc_start: 0.9089 (t80) cc_final: 0.8862 (t80) REVERT: C 165 HIS cc_start: 0.8463 (t-90) cc_final: 0.8232 (t70) REVERT: C 302 ILE cc_start: 0.7324 (OUTLIER) cc_final: 0.7088 (pp) REVERT: C 395 TYR cc_start: 0.7382 (t80) cc_final: 0.7110 (t80) REVERT: C 958 LYS cc_start: 0.9161 (tttt) cc_final: 0.8850 (mtpt) REVERT: C 1030 GLU cc_start: 0.9285 (mm-30) cc_final: 0.8649 (tp30) REVERT: C 1033 ARG cc_start: 0.8037 (tpt90) cc_final: 0.7575 (tpm170) REVERT: D 130 MET cc_start: 0.8627 (mtt) cc_final: 0.8270 (ttm) REVERT: D 229 GLN cc_start: 0.8986 (OUTLIER) cc_final: 0.8775 (mp10) REVERT: D 298 MET cc_start: 0.9129 (tpp) cc_final: 0.8603 (mtm) REVERT: D 410 ASP cc_start: 0.8871 (t70) cc_final: 0.8561 (t0) REVERT: D 422 LEU cc_start: 0.9479 (OUTLIER) cc_final: 0.9165 (pp) REVERT: D 490 ILE cc_start: 0.9225 (pt) cc_final: 0.8779 (mt) REVERT: D 551 ARG cc_start: 0.9401 (OUTLIER) cc_final: 0.9200 (ptm160) REVERT: D 698 MET cc_start: 0.9138 (tpp) cc_final: 0.8713 (mmm) REVERT: D 818 GLU cc_start: 0.9023 (mp0) cc_final: 0.8762 (mp0) REVERT: D 1040 MET cc_start: 0.3017 (mtt) cc_final: 0.1627 (mmt) REVERT: E 63 ILE cc_start: 0.8936 (OUTLIER) cc_final: 0.8545 (mp) REVERT: M 181 ARG cc_start: 0.8731 (mtp180) cc_final: 0.8319 (mmm-85) REVERT: M 350 GLN cc_start: 0.8769 (mm-40) cc_final: 0.8416 (mm-40) outliers start: 60 outliers final: 48 residues processed: 321 average time/residue: 0.1816 time to fit residues: 94.8993 Evaluate side-chains 308 residues out of total 3073 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 255 time to evaluate : 1.104 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 LYS Chi-restraints excluded: chain A residue 67 GLU Chi-restraints excluded: chain A residue 102 LEU Chi-restraints excluded: chain A residue 137 ASN Chi-restraints excluded: chain A residue 262 LEU Chi-restraints excluded: chain B residue 26 VAL Chi-restraints excluded: chain B residue 48 LEU Chi-restraints excluded: chain B residue 49 SER Chi-restraints excluded: chain B residue 153 VAL Chi-restraints excluded: chain B residue 172 LEU Chi-restraints excluded: chain B residue 205 MET Chi-restraints excluded: chain C residue 144 VAL Chi-restraints excluded: chain C residue 170 VAL Chi-restraints excluded: chain C residue 187 GLU Chi-restraints excluded: chain C residue 221 LEU Chi-restraints excluded: chain C residue 269 ILE Chi-restraints excluded: chain C residue 302 ILE Chi-restraints excluded: chain C residue 316 GLU Chi-restraints excluded: chain C residue 397 LEU Chi-restraints excluded: chain C residue 442 VAL Chi-restraints excluded: chain C residue 445 ILE Chi-restraints excluded: chain C residue 448 LEU Chi-restraints excluded: chain C residue 469 VAL Chi-restraints excluded: chain C residue 714 VAL Chi-restraints excluded: chain C residue 733 VAL Chi-restraints excluded: chain C residue 736 VAL Chi-restraints excluded: chain C residue 920 VAL Chi-restraints excluded: chain C residue 1042 LEU Chi-restraints excluded: chain C residue 1159 VAL Chi-restraints excluded: chain D residue 7 PHE Chi-restraints excluded: chain D residue 18 ASP Chi-restraints excluded: chain D residue 119 SER Chi-restraints excluded: chain D residue 227 PHE Chi-restraints excluded: chain D residue 229 GLN Chi-restraints excluded: chain D residue 416 ILE Chi-restraints excluded: chain D residue 422 LEU Chi-restraints excluded: chain D residue 434 ILE Chi-restraints excluded: chain D residue 527 LEU Chi-restraints excluded: chain D residue 551 ARG Chi-restraints excluded: chain D residue 560 ASN Chi-restraints excluded: chain D residue 645 VAL Chi-restraints excluded: chain D residue 706 VAL Chi-restraints excluded: chain D residue 717 VAL Chi-restraints excluded: chain D residue 905 ARG Chi-restraints excluded: chain D residue 913 GLU Chi-restraints excluded: chain D residue 1156 LEU Chi-restraints excluded: chain D residue 1159 ILE Chi-restraints excluded: chain D residue 1209 VAL Chi-restraints excluded: chain D residue 1250 ASP Chi-restraints excluded: chain E residue 63 ILE Chi-restraints excluded: chain M residue 144 ILE Chi-restraints excluded: chain M residue 185 PHE Chi-restraints excluded: chain M residue 195 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 351 random chunks: chunk 44 optimal weight: 10.0000 chunk 286 optimal weight: 40.0000 chunk 271 optimal weight: 5.9990 chunk 121 optimal weight: 0.7980 chunk 281 optimal weight: 8.9990 chunk 138 optimal weight: 6.9990 chunk 220 optimal weight: 3.9990 chunk 174 optimal weight: 5.9990 chunk 40 optimal weight: 20.0000 chunk 330 optimal weight: 2.9990 chunk 226 optimal weight: 0.5980 overall best weight: 2.8786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** D 450 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 504 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 910 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3934 r_free = 0.3934 target = 0.124377 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3084 r_free = 0.3084 target = 0.077654 restraints weight = 67786.904| |-----------------------------------------------------------------------------| r_work (start): 0.3013 rms_B_bonded: 3.26 r_work: 0.2837 rms_B_bonded: 4.01 restraints_weight: 0.5000 r_work (final): 0.2837 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2839 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2839 r_free = 0.2839 target_work(ls_wunit_k1) = 0.064 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2839 r_free = 0.2839 target_work(ls_wunit_k1) = 0.064 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2839 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8623 moved from start: 0.4437 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.084 28892 Z= 0.203 Angle : 0.755 16.450 39691 Z= 0.384 Chirality : 0.046 0.367 4774 Planarity : 0.005 0.081 4888 Dihedral : 17.510 179.140 4883 Min Nonbonded Distance : 2.314 Molprobity Statistics. All-atom Clashscore : 10.73 Ramachandran Plot: Outliers : 0.95 % Allowed : 9.00 % Favored : 90.05 % Rotamer: Outliers : 2.24 % Allowed : 19.53 % Favored : 78.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.03 % Twisted Proline : 0.69 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.06 (0.14), residues: 3567 helix: 0.94 (0.15), residues: 1296 sheet: -0.31 (0.29), residues: 298 loop : -2.01 (0.13), residues: 1973 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG E 69 TYR 0.044 0.002 TYR C 26 PHE 0.021 0.002 PHE D1325 TRP 0.011 0.001 TRP D 115 HIS 0.005 0.001 HIS D 450 Details of bonding type rmsd/Z covalent geometry : bond 0.00463 / 0.20 (28891) covalent geometry : angle 0.75546 / 0.38 (39688) hydrogen bonds : bond 0.03602 / 2.45 ( 1102) hydrogen bonds : angle 4.48569 / 3.08 ( 3064) link_TRANS : bond 0.00033 / 0.02 ( 1) link_TRANS : angle 0.32100 / 0.17 ( 3) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7134 Ramachandran restraints generated. 3567 Oldfield, 0 Emsley, 3567 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7134 Ramachandran restraints generated. 3567 Oldfield, 0 Emsley, 3567 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 310 residues out of total 3073 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 252 time to evaluate : 0.764 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 95 LYS cc_start: 0.8503 (ttpt) cc_final: 0.8126 (ptpt) REVERT: B 125 LYS cc_start: 0.9026 (pttp) cc_final: 0.8594 (pptt) REVERT: C 165 HIS cc_start: 0.8450 (t-90) cc_final: 0.8222 (t70) REVERT: C 302 ILE cc_start: 0.7427 (OUTLIER) cc_final: 0.7190 (pp) REVERT: C 395 TYR cc_start: 0.7513 (t80) cc_final: 0.7146 (t80) REVERT: C 958 LYS cc_start: 0.9162 (tttt) cc_final: 0.8845 (mtpt) REVERT: C 1030 GLU cc_start: 0.9303 (mm-30) cc_final: 0.8675 (tp30) REVERT: D 130 MET cc_start: 0.8656 (mtt) cc_final: 0.8319 (ttm) REVERT: D 229 GLN cc_start: 0.8990 (OUTLIER) cc_final: 0.8756 (mp10) REVERT: D 298 MET cc_start: 0.9141 (tpp) cc_final: 0.8609 (mtm) REVERT: D 410 ASP cc_start: 0.8947 (t70) cc_final: 0.8632 (t0) REVERT: D 422 LEU cc_start: 0.9589 (OUTLIER) cc_final: 0.9260 (pp) REVERT: D 551 ARG cc_start: 0.9428 (OUTLIER) cc_final: 0.9028 (ptp-170) REVERT: D 818 GLU cc_start: 0.8993 (mp0) cc_final: 0.8742 (mp0) REVERT: D 1040 MET cc_start: 0.3081 (mtt) cc_final: 0.1716 (mmt) REVERT: D 1365 TYR cc_start: 0.8804 (t80) cc_final: 0.8361 (t80) REVERT: M 181 ARG cc_start: 0.8777 (mtp180) cc_final: 0.8350 (mmm-85) REVERT: M 350 GLN cc_start: 0.8769 (mm-40) cc_final: 0.8390 (mm-40) outliers start: 58 outliers final: 49 residues processed: 299 average time/residue: 0.1707 time to fit residues: 82.9420 Evaluate side-chains 299 residues out of total 3073 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 246 time to evaluate : 0.706 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 LYS Chi-restraints excluded: chain A residue 67 GLU Chi-restraints excluded: chain A residue 102 LEU Chi-restraints excluded: chain B residue 26 VAL Chi-restraints excluded: chain B residue 48 LEU Chi-restraints excluded: chain B residue 49 SER Chi-restraints excluded: chain B residue 153 VAL Chi-restraints excluded: chain B residue 172 LEU Chi-restraints excluded: chain B residue 205 MET Chi-restraints excluded: chain C residue 144 VAL Chi-restraints excluded: chain C residue 170 VAL Chi-restraints excluded: chain C residue 187 GLU Chi-restraints excluded: chain C residue 221 LEU Chi-restraints excluded: chain C residue 269 ILE Chi-restraints excluded: chain C residue 302 ILE Chi-restraints excluded: chain C residue 316 GLU Chi-restraints excluded: chain C residue 397 LEU Chi-restraints excluded: chain C residue 442 VAL Chi-restraints excluded: chain C residue 445 ILE Chi-restraints excluded: chain C residue 448 LEU Chi-restraints excluded: chain C residue 469 VAL Chi-restraints excluded: chain C residue 589 THR Chi-restraints excluded: chain C residue 714 VAL Chi-restraints excluded: chain C residue 733 VAL Chi-restraints excluded: chain C residue 736 VAL Chi-restraints excluded: chain C residue 920 VAL Chi-restraints excluded: chain C residue 1042 LEU Chi-restraints excluded: chain C residue 1159 VAL Chi-restraints excluded: chain C residue 1165 SER Chi-restraints excluded: chain C residue 1303 LYS Chi-restraints excluded: chain D residue 7 PHE Chi-restraints excluded: chain D residue 18 ASP Chi-restraints excluded: chain D residue 119 SER Chi-restraints excluded: chain D residue 227 PHE Chi-restraints excluded: chain D residue 229 GLN Chi-restraints excluded: chain D residue 416 ILE Chi-restraints excluded: chain D residue 422 LEU Chi-restraints excluded: chain D residue 434 ILE Chi-restraints excluded: chain D residue 527 LEU Chi-restraints excluded: chain D residue 551 ARG Chi-restraints excluded: chain D residue 560 ASN Chi-restraints excluded: chain D residue 645 VAL Chi-restraints excluded: chain D residue 706 VAL Chi-restraints excluded: chain D residue 717 VAL Chi-restraints excluded: chain D residue 905 ARG Chi-restraints excluded: chain D residue 1156 LEU Chi-restraints excluded: chain D residue 1159 ILE Chi-restraints excluded: chain D residue 1209 VAL Chi-restraints excluded: chain D residue 1250 ASP Chi-restraints excluded: chain E residue 65 ASP Chi-restraints excluded: chain M residue 144 ILE Chi-restraints excluded: chain M residue 185 PHE Chi-restraints excluded: chain M residue 195 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 351 random chunks: chunk 76 optimal weight: 50.0000 chunk 92 optimal weight: 10.0000 chunk 221 optimal weight: 0.0020 chunk 178 optimal weight: 0.6980 chunk 2 optimal weight: 8.9990 chunk 242 optimal weight: 2.9990 chunk 328 optimal weight: 0.0370 chunk 153 optimal weight: 30.0000 chunk 169 optimal weight: 2.9990 chunk 9 optimal weight: 4.9990 chunk 287 optimal weight: 5.9990 overall best weight: 1.3470 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** D 450 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 504 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 910 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3953 r_free = 0.3953 target = 0.125654 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3118 r_free = 0.3118 target = 0.079315 restraints weight = 67772.015| |-----------------------------------------------------------------------------| r_work (start): 0.3052 rms_B_bonded: 3.29 r_work: 0.2866 rms_B_bonded: 4.08 restraints_weight: 0.5000 r_work (final): 0.2866 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2870 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2870 r_free = 0.2870 target_work(ls_wunit_k1) = 0.066 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2870 r_free = 0.2870 target_work(ls_wunit_k1) = 0.066 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2870 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8593 moved from start: 0.4525 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 28892 Z= 0.140 Angle : 0.734 15.566 39691 Z= 0.372 Chirality : 0.045 0.357 4774 Planarity : 0.005 0.083 4888 Dihedral : 17.469 179.960 4883 Min Nonbonded Distance : 2.261 Molprobity Statistics. All-atom Clashscore : 10.29 Ramachandran Plot: Outliers : 0.98 % Allowed : 8.61 % Favored : 90.41 % Rotamer: Outliers : 2.13 % Allowed : 19.80 % Favored : 78.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.03 % Twisted Proline : 0.69 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.97 (0.14), residues: 3567 helix: 1.04 (0.15), residues: 1291 sheet: -0.30 (0.29), residues: 300 loop : -1.97 (0.13), residues: 1976 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.001 ARG C1033 TYR 0.032 0.001 TYR C 26 PHE 0.018 0.001 PHE D1325 TRP 0.009 0.001 TRP D 115 HIS 0.004 0.001 HIS C 447 Details of bonding type rmsd/Z covalent geometry : bond 0.00302 / 0.14 (28891) covalent geometry : angle 0.73425 / 0.37 (39688) hydrogen bonds : bond 0.03271 / 2.22 ( 1102) hydrogen bonds : angle 4.40660 / 3.02 ( 3064) link_TRANS : bond 0.00024 / 0.01 ( 1) link_TRANS : angle 0.24282 / 0.13 ( 3) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7420.64 seconds wall clock time: 127 minutes 27.07 seconds (7647.07 seconds total)