Starting phenix.real_space_refine on Fri Aug 7 04:30:10 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9q96_52919/08_2026/9q96_52919.cif Found real_map, /net/cci-nas-00/data/ceres_data/9q96_52919/08_2026/9q96_52919.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9q96_52919/08_2026/9q96_52919.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9q96_52919/08_2026/9q96_52919.map" model { file = "/net/cci-nas-00/data/ceres_data/9q96_52919/08_2026/9q96_52919.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9q96_52919/08_2026/9q96_52919.cif" } resolution = 4.6 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= 0.002 sd= 0.010 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians P 87 5.49 5 C 11447 2.51 5 N 3959 2.21 5 O 4140 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 19633 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 1526 Number of conformers: 1 Conformer: "" Number of residues, atoms: 309, 1526 Classifications: {'peptide': 309} Incomplete info: {'truncation_to_alanine': 269} Link IDs: {'PTRANS': 14, 'TRANS': 294} Chain breaks: 1 Unresolved chain link angles: 14 Unresolved non-hydrogen bonds: 914 Unresolved non-hydrogen angles: 1172 Unresolved non-hydrogen dihedrals: 716 Unresolved non-hydrogen chiralities: 109 Planarities with less than four sites: {'GLU:plan': 32, 'PHE:plan': 4, 'ARG:plan': 22, 'ASP:plan': 20, 'GLN:plan1': 8, 'HIS:plan': 8, 'ASN:plan1': 9, 'TYR:plan': 5, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 465 Chain: "B" Number of atoms: 1160 Number of conformers: 1 Conformer: "" Number of residues, atoms: 235, 1160 Classifications: {'peptide': 235} Incomplete info: {'truncation_to_alanine': 203} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 225} Unresolved chain link angles: 9 Unresolved non-hydrogen bonds: 688 Unresolved non-hydrogen angles: 882 Unresolved non-hydrogen dihedrals: 535 Unresolved non-hydrogen chiralities: 82 Planarities with less than four sites: {'GLU:plan': 25, 'PHE:plan': 3, 'ARG:plan': 18, 'ASP:plan': 15, 'GLN:plan1': 7, 'HIS:plan': 7, 'ASN:plan1': 6, 'TYR:plan': 4} Unresolved non-hydrogen planarities: 362 Chain: "C" Number of atoms: 6599 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1341, 6599 Classifications: {'peptide': 1341} Incomplete info: {'truncation_to_alanine': 1156} Link IDs: {'PCIS': 1, 'PTRANS': 55, 'TRANS': 1284} Unresolved chain link angles: 56 Unresolved non-hydrogen bonds: 4146 Unresolved non-hydrogen angles: 5269 Unresolved non-hydrogen dihedrals: 3362 Unresolved non-hydrogen chiralities: 380 Planarities with less than four sites: {'TYR:plan': 43, 'GLU:plan': 121, 'ARG:plan': 90, 'ASP:plan': 92, 'PHE:plan': 44, 'GLN:plan1': 58, 'ASN:plan1': 51, 'HIS:plan': 19, 'TRP:plan': 4} Unresolved non-hydrogen planarities: 2291 Chain: "D" Number of atoms: 6619 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1345, 6619 Classifications: {'peptide': 1345} Incomplete info: {'truncation_to_alanine': 1124} Link IDs: {'CIS': 1, 'PCIS': 2, 'PTRANS': 51, 'TRANS': 1290} Chain breaks: 4 Unresolved chain link angles: 53 Unresolved non-hydrogen bonds: 4008 Unresolved non-hydrogen angles: 5092 Unresolved non-hydrogen dihedrals: 3254 Unresolved non-hydrogen chiralities: 400 Planarities with less than four sites: {'PHE:plan': 35, 'GLN:plan1': 49, 'GLU:plan': 103, 'ASP:plan': 75, 'ARG:plan': 99, 'TRP:plan': 9, 'ASN:plan1': 46, 'TYR:plan': 34, 'HIS:plan': 21} Unresolved non-hydrogen planarities: 2100 Chain: "E" Number of atoms: 371 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 371 Classifications: {'peptide': 75} Incomplete info: {'truncation_to_alanine': 65} Link IDs: {'PTRANS': 2, 'TRANS': 72} Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 231 Unresolved non-hydrogen angles: 292 Unresolved non-hydrogen dihedrals: 174 Unresolved non-hydrogen chiralities: 23 Planarities with less than four sites: {'ARG:plan': 8, 'GLN:plan1': 8, 'ASP:plan': 5, 'GLU:plan': 9, 'ASN:plan1': 4, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 141 Chain: "M" Number of atoms: 1570 Number of conformers: 1 Conformer: "" Number of residues, atoms: 316, 1570 Classifications: {'peptide': 316} Incomplete info: {'truncation_to_alanine': 283} Link IDs: {'PTRANS': 14, 'TRANS': 301} Chain breaks: 2 Unresolved chain link angles: 14 Unresolved non-hydrogen bonds: 991 Unresolved non-hydrogen angles: 1270 Unresolved non-hydrogen dihedrals: 797 Unresolved non-hydrogen chiralities: 103 Planarities with less than four sites: {'ASP:plan': 23, 'GLU:plan': 28, 'TYR:plan': 8, 'GLN:plan1': 19, 'TRP:plan': 3, 'PHE:plan': 9, 'ARG:plan': 21, 'HIS:plan': 4, 'ASN:plan1': 6} Unresolved non-hydrogen planarities: 537 Chain: "N" Number of atoms: 946 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 946 Classifications: {'DNA': 46} Link IDs: {'rna3p': 45} Chain: "T" Number of atoms: 842 Number of conformers: 1 Conformer: "" Number of residues, atoms: 41, 842 Classifications: {'DNA': 41} Link IDs: {'rna3p': 40} Chain breaks: 1 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: 5.30, per 1000 atoms: 0.27 Number of scatterers: 19633 At special positions: 0 Unit cell: (139.7, 166.1, 159.5, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) P 87 15.00 O 4140 8.00 N 3959 7.00 C 11447 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 Time building additional restraints: 1.95 Conformation dependent library (CDL) restraints added in 1.3 seconds 7190 Ramachandran restraints generated. 3595 Oldfield, 0 Emsley, 3595 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6722 Finding SS restraints... Secondary structure from input PDB file: 125 helices and 38 sheets defined 38.5% alpha, 10.6% beta 28 base pairs and 65 stacking pairs defined. Time for finding SS restraints: 2.37 Creating SS restraints... Processing helix chain 'A' and resid 34 through 50 removed outlier: 3.744A pdb=" N THR A 38 " --> pdb=" O GLY A 34 " (cutoff:3.500A) Processing helix chain 'A' and resid 77 through 87 removed outlier: 3.697A 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: 3.664A 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: 3.618A 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: 3.624A pdb=" N SER C 34 " --> pdb=" O ILE C 30 " (cutoff:3.500A) removed outlier: 3.522A 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: 3.585A 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: 3.845A 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: 3.655A 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: 3.522A pdb=" N GLU C 386 " --> pdb=" O GLU C 382 " (cutoff:3.500A) removed outlier: 4.090A 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: 4.054A 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: 3.592A pdb=" N GLU C 523 " --> pdb=" O ASN C 519 " (cutoff:3.500A) Processing helix chain 'C' and resid 608 through 612 removed outlier: 3.823A 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: 4.156A 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: 3.602A 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: 4.546A pdb=" N GLU C 963 " --> pdb=" O ASP C 959 " (cutoff:3.500A) removed outlier: 3.514A 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: 3.674A 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: 3.685A 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 173 Processing helix chain 'D' and resid 182 through 191 Processing helix chain 'D' and resid 193 through 208 Processing helix chain 'D' and resid 212 through 231 removed outlier: 3.886A 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: 4.249A pdb=" N THR D 218 " --> pdb=" O ARG D 214 " (cutoff:3.500A) removed outlier: 3.569A 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: 3.554A pdb=" N LEU D 249 " --> pdb=" O PRO D 246 " (cutoff:3.500A) Processing helix chain 'D' and resid 263 through 285 removed outlier: 3.821A pdb=" N ASP D 267 " --> pdb=" O SER D 263 " (cutoff:3.500A) removed outlier: 4.131A 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: 3.647A pdb=" N VAL D 292 " --> pdb=" O PRO D 288 " (cutoff:3.500A) Processing helix chain 'D' and resid 336 through 341 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: 3.653A 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: 3.791A 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: 3.877A pdb=" N LEU D 740 " --> pdb=" O GLN D 736 " (cutoff:3.500A) Processing helix chain 'D' and resid 768 through 805 removed outlier: 3.970A 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: 3.847A 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: 3.523A 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: 3.567A pdb=" N VAL D1240 " --> pdb=" O GLU D1236 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N GLN D1244 " --> pdb=" O VAL D1240 " (cutoff:3.500A) Processing helix chain 'D' and resid 1249 through 1260 removed outlier: 4.471A 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: 3.563A 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: 3.619A pdb=" N ASN D1350 " --> pdb=" O GLY D1346 " (cutoff:3.500A) Processing helix chain 'D' and resid 1360 through 1376 removed outlier: 3.821A 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: 3.830A 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: 3.509A 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: 3.822A 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: 3.773A 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 334 through 355 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: 3.666A 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 432 removed outlier: 3.816A pdb=" N ALA M 430 " --> pdb=" O LYS M 426 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N ASN M 432 " --> pdb=" O ILE M 428 " (cutoff:3.500A) Processing helix chain 'M' and resid 438 through 450 Processing helix chain 'M' and resid 456 through 464 Processing helix chain 'M' and resid 467 through 472 removed outlier: 4.632A pdb=" N ASN M 471 " --> pdb=" O ILE M 467 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 13 through 18 removed outlier: 9.339A pdb=" N LEU A 13 " --> pdb=" O GLU A 29 " (cutoff:3.500A) removed outlier: 7.582A 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: 6.756A 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: 5.465A 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: 5.350A 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: 7.154A pdb=" N LYS B 145 " --> pdb=" O THR B 57 " (cutoff:3.500A) removed outlier: 4.728A 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: 5.506A pdb=" N ILE B 61 " --> pdb=" O SER B 141 " (cutoff:3.500A) removed outlier: 8.332A 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: 4.005A 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: 4.005A 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: 6.711A 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: 4.225A pdb=" N THR C1226 " --> pdb=" O PHE C 804 " (cutoff:3.500A) removed outlier: 8.302A 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: 7.378A pdb=" N LEU C1098 " --> pdb=" O ARG C 801 " (cutoff:3.500A) removed outlier: 6.121A pdb=" N ALA C 803 " --> pdb=" O LEU C1098 " (cutoff:3.500A) removed outlier: 7.310A 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: 6.346A 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: 5.540A pdb=" N VAL M 277 " --> pdb=" O HIS M 391 " (cutoff:3.500A) 1034 hydrogen bonds defined for protein. 2916 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 74 hydrogen bonds 148 hydrogen bond angles 0 basepair planarities 28 basepair parallelities 65 stacking parallelities Total time for adding SS restraints: 5.16 Time building geometry restraints manager: 2.55 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.03 - 1.17: 129 1.17 - 1.31: 3761 1.31 - 1.45: 5586 1.45 - 1.59: 9944 1.59 - 1.73: 417 Bond restraints: 19837 Sorted by residual: bond pdb=" C HIS C 526 " pdb=" O HIS C 526 " ideal model delta sigma weight residual 1.237 1.027 0.210 1.19e-02 7.06e+03 3.12e+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 -0.174 1.01e-02 9.80e+03 2.98e+02 bond pdb=" C GLU C 813 " pdb=" O GLU C 813 " ideal model delta sigma weight residual 1.239 1.391 -0.152 9.60e-03 1.09e+04 2.50e+02 bond pdb=" N ARG C 827 " pdb=" CA ARG C 827 " ideal model delta sigma weight residual 1.456 1.649 -0.194 1.25e-02 6.40e+03 2.40e+02 ... (remaining 19832 not shown) Histogram of bond angle deviations from ideal: 0.00 - 5.40: 26013 5.40 - 10.80: 1680 10.80 - 16.20: 158 16.20 - 21.59: 23 21.59 - 26.99: 2 Bond angle restraints: 27876 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 86.03 26.99 1.49e+00 4.50e-01 3.28e+02 angle pdb=" C GLU D 765 " pdb=" N GLY D 766 " pdb=" CA GLY D 766 " ideal model delta sigma weight residual 120.64 100.29 20.35 1.26e+00 6.30e-01 2.61e+02 angle pdb=" N ASP M 186 " pdb=" CA ASP M 186 " pdb=" CB ASP M 186 " ideal model delta sigma weight residual 110.42 129.11 -18.69 1.18e+00 7.18e-01 2.51e+02 angle pdb=" C GLY D 358 " pdb=" N PRO D 359 " pdb=" CA PRO D 359 " ideal model delta sigma weight residual 119.84 102.21 17.63 1.25e+00 6.40e-01 1.99e+02 angle pdb=" C GLY C 786 " pdb=" N PRO C 787 " pdb=" CA PRO C 787 " ideal model delta sigma weight residual 120.66 105.34 15.32 1.09e+00 8.42e-01 1.98e+02 ... (remaining 27871 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.31: 10885 35.31 - 70.62: 362 70.62 - 105.93: 9 105.93 - 141.23: 2 141.23 - 176.54: 5 Dihedral angle restraints: 11263 sinusoidal: 933 harmonic: 10330 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 122.80 159.61 -36.81 0 2.50e+00 1.60e-01 2.17e+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 -159.23 36.63 0 2.50e+00 1.60e-01 2.15e+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 11260 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.328: 3387 0.328 - 0.656: 278 0.656 - 0.983: 36 0.983 - 1.311: 5 1.311 - 1.639: 3 Chirality restraints: 3709 Sorted by residual: 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 1.64 2.00e-01 2.50e+01 6.68e+01 chirality pdb=" CA ASP M 186 " pdb=" N ASP M 186 " pdb=" C ASP M 186 " pdb=" CB ASP M 186 " both_signs ideal model delta sigma weight residual False 2.51 1.18 1.33 2.00e-01 2.50e+01 4.42e+01 ... (remaining 3706 not shown) Planarity restraints: 3695 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' DC T -2 " 0.083 2.00e-02 2.50e+03 5.54e-02 6.91e+01 pdb=" N1 DC T -2 " -0.011 2.00e-02 2.50e+03 pdb=" C2 DC T -2 " 0.014 2.00e-02 2.50e+03 pdb=" O2 DC T -2 " -0.083 2.00e-02 2.50e+03 pdb=" N3 DC T -2 " 0.069 2.00e-02 2.50e+03 pdb=" C4 DC T -2 " 0.011 2.00e-02 2.50e+03 pdb=" N4 DC T -2 " -0.004 2.00e-02 2.50e+03 pdb=" C5 DC T -2 " 0.012 2.00e-02 2.50e+03 pdb=" C6 DC T -2 " -0.092 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLY C1266 " -0.042 2.00e-02 2.50e+03 7.97e-02 6.35e+01 pdb=" C GLY C1266 " 0.138 2.00e-02 2.50e+03 pdb=" O GLY C1266 " -0.047 2.00e-02 2.50e+03 pdb=" N GLY C1267 " -0.048 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PRO D 369 " -0.039 2.00e-02 2.50e+03 7.92e-02 6.27e+01 pdb=" C PRO D 369 " 0.137 2.00e-02 2.50e+03 pdb=" O PRO D 369 " -0.051 2.00e-02 2.50e+03 pdb=" N LYS D 370 " -0.046 2.00e-02 2.50e+03 ... (remaining 3692 not shown) Histogram of nonbonded interaction distances: 1.50 - 2.18: 12 2.18 - 2.86: 7479 2.86 - 3.54: 26298 3.54 - 4.22: 37019 4.22 - 4.90: 56939 Nonbonded interactions: 127747 Sorted by model distance: nonbonded pdb=" N LEU M 367 " pdb=" OP2 DT N -17 " model vdw 1.495 3.120 nonbonded pdb=" N SER M 379 " pdb=" C7 DT N -15 " model vdw 1.511 3.540 nonbonded pdb=" CB SER M 379 " pdb=" C7 DT N -15 " model vdw 1.838 3.860 nonbonded pdb=" CA SER M 379 " pdb=" C7 DT N -15 " model vdw 1.862 3.890 nonbonded pdb=" C VAL M 366 " pdb=" OP2 DT N -17 " model vdw 1.925 3.270 ... (remaining 127742 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.710 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: 0.020 Extract box with map and model: 0.360 Check model and map are aligned: 0.060 Set scattering table: 0.050 Process input model: 23.840 Find NCS groups from input model: 0.310 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.320 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.720 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7074 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 : 0.031 0.210 19837 Z= 2.401 Angle : 2.830 26.993 27876 Z= 1.976 Chirality : 0.201 1.639 3709 Planarity : 0.016 0.080 3695 Dihedral : 18.141 176.544 4541 Min Nonbonded Distance : 1.495 Molprobity Statistics. All-atom Clashscore : 10.09 Ramachandran Plot: Outliers : 2.50 % Allowed : 10.82 % Favored : 86.68 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 9.70 % Peptide Plane: Cis-proline : 2.70 % Cis-general : 0.03 % Twisted Proline : 2.03 % Twisted General : 0.52 % 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: -4.05 (0.11), residues: 3595 helix: -2.75 (0.11), residues: 1266 sheet: -1.80 (0.26), residues: 327 loop : -2.88 (0.11), residues: 2002 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.000 0.000 TYR A 68 PHE 0.000 0.000 PHE A 8 TRP 0.000 0.000 TRP A 321 Details of bonding type rmsd/Z covalent geometry : bond 0.03115 / 2.40 (19837) covalent geometry : angle 2.83013 / 1.98 (27876) hydrogen bonds : bond 0.16615 / 12.84 ( 1101) hydrogen bonds : angle 9.39267 / 7.01 ( 3064) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7190 Ramachandran restraints generated. 3595 Oldfield, 0 Emsley, 3595 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7190 Ramachandran restraints generated. 3595 Oldfield, 0 Emsley, 3595 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 3100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 87 time to evaluate : 0.577 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 87 average time/residue: 0.0797 time to fit residues: 13.8618 Evaluate side-chains 87 residues out of total 3100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 87 time to evaluate : 0.649 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 367 random chunks: chunk 197 optimal weight: 7.9990 chunk 215 optimal weight: 9.9990 chunk 20 optimal weight: 5.9990 chunk 132 optimal weight: 5.9990 chunk 261 optimal weight: 5.9990 chunk 248 optimal weight: 10.0000 chunk 207 optimal weight: 40.0000 chunk 155 optimal weight: 5.9990 chunk 244 optimal weight: 8.9990 chunk 183 optimal weight: 10.0000 chunk 298 optimal weight: 5.9990 overall best weight: 5.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3951 r_free = 0.3951 target = 0.122368 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3690 r_free = 0.3690 target = 0.107055 restraints weight = 92956.807| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3676 r_free = 0.3676 target = 0.106180 restraints weight = 197024.499| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3659 r_free = 0.3659 target = 0.105247 restraints weight = 214615.161| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3653 r_free = 0.3653 target = 0.104894 restraints weight = 190479.459| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3647 r_free = 0.3647 target = 0.104553 restraints weight = 185371.191| |-----------------------------------------------------------------------------| r_work (final): 0.3636 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3636 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3636 r_free = 0.3636 target_work(ls_wunit_k1) = 0.104 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3635 r_free = 0.3635 target_work(ls_wunit_k1) = 0.104 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 10 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 7 (12 function evaluations) r_final: 0.3635 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6659 moved from start: 0.1907 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 19837 Z= 0.216 Angle : 0.747 11.325 27876 Z= 0.442 Chirality : 0.049 0.357 3709 Planarity : 0.004 0.019 3695 Dihedral : 17.666 177.989 4541 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 3.27 Ramachandran Plot: Outliers : 1.08 % Allowed : 7.57 % Favored : 91.35 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % Cis-general : 0.03 % Twisted Proline : 0.00 % 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: -2.36 (0.13), residues: 3595 helix: -0.56 (0.13), residues: 1298 sheet: -1.09 (0.26), residues: 335 loop : -2.45 (0.12), residues: 1962 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.000 0.000 TYR A 68 PHE 0.000 0.000 PHE A 8 TRP 0.000 0.000 TRP A 321 Details of bonding type rmsd/Z covalent geometry : bond 0.00300 / 0.22 (19837) covalent geometry : angle 0.74704 / 0.44 (27876) hydrogen bonds : bond 0.05366 / 4.08 ( 1101) hydrogen bonds : angle 5.41019 / 4.07 ( 3064) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7190 Ramachandran restraints generated. 3595 Oldfield, 0 Emsley, 3595 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7190 Ramachandran restraints generated. 3595 Oldfield, 0 Emsley, 3595 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 3100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 87 time to evaluate : 0.675 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 87 average time/residue: 0.0769 time to fit residues: 13.5178 Evaluate side-chains 87 residues out of total 3100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 87 time to evaluate : 0.551 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 367 random chunks: chunk 8 optimal weight: 50.0000 chunk 134 optimal weight: 20.0000 chunk 260 optimal weight: 20.0000 chunk 170 optimal weight: 20.0000 chunk 90 optimal weight: 40.0000 chunk 337 optimal weight: 6.9990 chunk 158 optimal weight: 20.0000 chunk 296 optimal weight: 50.0000 chunk 328 optimal weight: 30.0000 chunk 232 optimal weight: 20.0000 chunk 310 optimal weight: 50.0000 overall best weight: 17.3998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3845 r_free = 0.3845 target = 0.120025 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3337 r_free = 0.3337 target = 0.090288 restraints weight = 88169.728| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.087289 restraints weight = 221865.794| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3286 r_free = 0.3286 target = 0.085832 restraints weight = 187810.394| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3253 r_free = 0.3253 target = 0.084135 restraints weight = 170029.784| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3252 r_free = 0.3252 target = 0.083951 restraints weight = 167871.849| |-----------------------------------------------------------------------------| r_work (final): 0.3159 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3159 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3159 r_free = 0.3159 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 10 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3159 r_free = 0.3159 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (10 function evaluations) r_final: 0.3159 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7488 moved from start: 0.4674 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.087 19837 Z= 0.370 Angle : 0.946 13.250 27876 Z= 0.573 Chirality : 0.054 0.414 3709 Planarity : 0.006 0.027 3695 Dihedral : 18.289 176.622 4541 Min Nonbonded Distance : 2.401 Molprobity Statistics. All-atom Clashscore : 6.40 Ramachandran Plot: Outliers : 1.08 % Allowed : 12.02 % Favored : 86.90 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % Cis-general : 0.03 % Twisted Proline : 0.00 % 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: -2.78 (0.13), residues: 3595 helix: -0.94 (0.13), residues: 1275 sheet: -1.04 (0.26), residues: 367 loop : -2.74 (0.13), residues: 1953 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.000 0.000 TYR A 68 PHE 0.000 0.000 PHE A 8 TRP 0.000 0.000 TRP A 321 Details of bonding type rmsd/Z covalent geometry : bond 0.00527 / 0.37 (19837) covalent geometry : angle 0.94565 / 0.57 (27876) hydrogen bonds : bond 0.08273 / 6.36 ( 1101) hydrogen bonds : angle 6.59952 / 4.93 ( 3064) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7190 Ramachandran restraints generated. 3595 Oldfield, 0 Emsley, 3595 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7190 Ramachandran restraints generated. 3595 Oldfield, 0 Emsley, 3595 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 3100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 87 time to evaluate : 0.856 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 87 average time/residue: 0.0768 time to fit residues: 13.5122 Evaluate side-chains 87 residues out of total 3100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 87 time to evaluate : 0.475 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 367 random chunks: chunk 86 optimal weight: 50.0000 chunk 40 optimal weight: 50.0000 chunk 168 optimal weight: 9.9990 chunk 135 optimal weight: 1.9990 chunk 184 optimal weight: 30.0000 chunk 257 optimal weight: 8.9990 chunk 297 optimal weight: 20.0000 chunk 11 optimal weight: 50.0000 chunk 271 optimal weight: 50.0000 chunk 351 optimal weight: 20.0000 chunk 227 optimal weight: 8.9990 overall best weight: 9.9992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3746 r_free = 0.3746 target = 0.107984 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3528 r_free = 0.3528 target = 0.096644 restraints weight = 96569.111| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3526 r_free = 0.3526 target = 0.096468 restraints weight = 239407.434| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3512 r_free = 0.3512 target = 0.095849 restraints weight = 215024.959| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3508 r_free = 0.3508 target = 0.095642 restraints weight = 192605.450| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3502 r_free = 0.3502 target = 0.095355 restraints weight = 189577.625| |-----------------------------------------------------------------------------| r_work (final): 0.3484 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3484 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3484 r_free = 0.3484 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3484 r_free = 0.3484 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3484 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6915 moved from start: 0.5104 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 19837 Z= 0.224 Angle : 0.687 9.781 27876 Z= 0.408 Chirality : 0.048 0.382 3709 Planarity : 0.003 0.020 3695 Dihedral : 17.903 177.789 4541 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 3.83 Ramachandran Plot: Outliers : 1.03 % Allowed : 10.18 % Favored : 88.79 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % Cis-general : 0.03 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: -2.09 (0.14), residues: 3595 helix: 0.11 (0.14), residues: 1269 sheet: -0.84 (0.29), residues: 315 loop : -2.61 (0.13), residues: 2011 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.000 0.000 TYR A 68 PHE 0.000 0.000 PHE A 8 TRP 0.000 0.000 TRP A 321 Details of bonding type rmsd/Z covalent geometry : bond 0.00310 / 0.22 (19837) covalent geometry : angle 0.68698 / 0.41 (27876) hydrogen bonds : bond 0.04796 / 3.64 ( 1101) hydrogen bonds : angle 5.45772 / 4.10 ( 3064) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7190 Ramachandran restraints generated. 3595 Oldfield, 0 Emsley, 3595 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7190 Ramachandran restraints generated. 3595 Oldfield, 0 Emsley, 3595 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 3100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 87 time to evaluate : 0.541 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 87 average time/residue: 0.0708 time to fit residues: 12.1666 Evaluate side-chains 87 residues out of total 3100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 87 time to evaluate : 0.638 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 367 random chunks: chunk 112 optimal weight: 50.0000 chunk 292 optimal weight: 20.0000 chunk 20 optimal weight: 30.0000 chunk 23 optimal weight: 0.9980 chunk 213 optimal weight: 40.0000 chunk 241 optimal weight: 50.0000 chunk 346 optimal weight: 50.0000 chunk 147 optimal weight: 1.9990 chunk 289 optimal weight: 40.0000 chunk 246 optimal weight: 20.0000 chunk 10 optimal weight: 40.0000 overall best weight: 14.5994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3690 r_free = 0.3690 target = 0.104945 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3484 r_free = 0.3484 target = 0.094445 restraints weight = 96406.335| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3478 r_free = 0.3478 target = 0.094171 restraints weight = 247809.603| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3467 r_free = 0.3467 target = 0.093692 restraints weight = 241139.008| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.093209 restraints weight = 230700.064| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3455 r_free = 0.3455 target = 0.093147 restraints weight = 202851.792| |-----------------------------------------------------------------------------| r_work (final): 0.3431 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3431 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3431 r_free = 0.3431 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3431 r_free = 0.3431 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3431 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7001 moved from start: 0.6217 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.073 19837 Z= 0.325 Angle : 0.803 10.190 27876 Z= 0.484 Chirality : 0.051 0.459 3709 Planarity : 0.004 0.023 3695 Dihedral : 18.016 179.211 4541 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 5.64 Ramachandran Plot: Outliers : 1.03 % Allowed : 14.08 % Favored : 84.90 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % Cis-general : 0.03 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: -2.47 (0.13), residues: 3595 helix: -0.22 (0.14), residues: 1244 sheet: -1.14 (0.28), residues: 341 loop : -2.81 (0.13), residues: 2010 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.000 0.000 TYR A 68 PHE 0.000 0.000 PHE A 8 TRP 0.000 0.000 TRP A 321 Details of bonding type rmsd/Z covalent geometry : bond 0.00461 / 0.32 (19837) covalent geometry : angle 0.80349 / 0.48 (27876) hydrogen bonds : bond 0.06685 / 5.11 ( 1101) hydrogen bonds : angle 6.02217 / 4.52 ( 3064) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7190 Ramachandran restraints generated. 3595 Oldfield, 0 Emsley, 3595 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7190 Ramachandran restraints generated. 3595 Oldfield, 0 Emsley, 3595 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 3100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 87 time to evaluate : 0.413 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 87 average time/residue: 0.0728 time to fit residues: 12.8315 Evaluate side-chains 87 residues out of total 3100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 87 time to evaluate : 0.416 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 367 random chunks: chunk 279 optimal weight: 10.0000 chunk 168 optimal weight: 30.0000 chunk 203 optimal weight: 20.0000 chunk 22 optimal weight: 20.0000 chunk 192 optimal weight: 40.0000 chunk 154 optimal weight: 9.9990 chunk 51 optimal weight: 5.9990 chunk 180 optimal weight: 6.9990 chunk 224 optimal weight: 20.0000 chunk 60 optimal weight: 9.9990 chunk 306 optimal weight: 30.0000 overall best weight: 8.5992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3708 r_free = 0.3708 target = 0.105883 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3495 r_free = 0.3495 target = 0.094999 restraints weight = 95544.033| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3481 r_free = 0.3481 target = 0.094355 restraints weight = 269812.967| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3478 r_free = 0.3478 target = 0.094220 restraints weight = 246435.455| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3475 r_free = 0.3475 target = 0.094099 restraints weight = 190633.146| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3476 r_free = 0.3476 target = 0.094165 restraints weight = 172176.606| |-----------------------------------------------------------------------------| r_work (final): 0.3455 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3455 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3455 r_free = 0.3455 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3455 r_free = 0.3455 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (11 function evaluations) r_final: 0.3455 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6954 moved from start: 0.6431 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 19837 Z= 0.197 Angle : 0.641 9.017 27876 Z= 0.380 Chirality : 0.047 0.320 3709 Planarity : 0.003 0.018 3695 Dihedral : 17.680 178.124 4541 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 4.07 Ramachandran Plot: Outliers : 1.00 % Allowed : 11.13 % Favored : 87.87 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % Cis-general : 0.03 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: -2.04 (0.14), residues: 3595 helix: 0.44 (0.15), residues: 1267 sheet: -1.26 (0.29), residues: 325 loop : -2.73 (0.13), residues: 2003 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.000 0.000 TYR A 68 PHE 0.000 0.000 PHE A 8 TRP 0.000 0.000 TRP A 321 Details of bonding type rmsd/Z covalent geometry : bond 0.00272 / 0.20 (19837) covalent geometry : angle 0.64064 / 0.38 (27876) hydrogen bonds : bond 0.04571 / 3.48 ( 1101) hydrogen bonds : angle 5.34428 / 4.02 ( 3064) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7190 Ramachandran restraints generated. 3595 Oldfield, 0 Emsley, 3595 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7190 Ramachandran restraints generated. 3595 Oldfield, 0 Emsley, 3595 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 3100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 87 time to evaluate : 0.596 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 87 average time/residue: 0.0774 time to fit residues: 13.4788 Evaluate side-chains 87 residues out of total 3100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 87 time to evaluate : 0.598 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 367 random chunks: chunk 296 optimal weight: 40.0000 chunk 132 optimal weight: 20.0000 chunk 102 optimal weight: 50.0000 chunk 276 optimal weight: 30.0000 chunk 9 optimal weight: 6.9990 chunk 200 optimal weight: 40.0000 chunk 173 optimal weight: 20.0000 chunk 278 optimal weight: 6.9990 chunk 266 optimal weight: 30.0000 chunk 89 optimal weight: 50.0000 chunk 7 optimal weight: 40.0000 overall best weight: 16.7996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3650 r_free = 0.3650 target = 0.102866 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.087017 restraints weight = 94748.810| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3325 r_free = 0.3325 target = 0.086606 restraints weight = 271015.662| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3324 r_free = 0.3324 target = 0.086555 restraints weight = 245344.192| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3322 r_free = 0.3322 target = 0.086479 restraints weight = 175712.659| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.086862 restraints weight = 150273.640| |-----------------------------------------------------------------------------| r_work (final): 0.3312 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3312 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3312 r_free = 0.3312 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3312 r_free = 0.3312 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 15 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (12 function evaluations) r_final: 0.3312 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7217 moved from start: 0.7309 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.083 19837 Z= 0.348 Angle : 0.845 10.301 27876 Z= 0.513 Chirality : 0.051 0.342 3709 Planarity : 0.005 0.024 3695 Dihedral : 18.030 178.480 4541 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 7.42 Ramachandran Plot: Outliers : 1.03 % Allowed : 16.94 % Favored : 82.03 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % Cis-general : 0.03 % Twisted Proline : 0.00 % 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: -2.90 (0.13), residues: 3595 helix: -0.47 (0.14), residues: 1265 sheet: -1.65 (0.29), residues: 309 loop : -3.10 (0.13), residues: 2021 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.000 0.000 TYR A 68 PHE 0.000 0.000 PHE A 8 TRP 0.000 0.000 TRP A 321 Details of bonding type rmsd/Z covalent geometry : bond 0.00492 / 0.35 (19837) covalent geometry : angle 0.84513 / 0.51 (27876) hydrogen bonds : bond 0.07565 / 5.78 ( 1101) hydrogen bonds : angle 6.42645 / 4.83 ( 3064) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7190 Ramachandran restraints generated. 3595 Oldfield, 0 Emsley, 3595 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7190 Ramachandran restraints generated. 3595 Oldfield, 0 Emsley, 3595 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 3100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 87 time to evaluate : 0.629 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 87 average time/residue: 0.0776 time to fit residues: 13.4507 Evaluate side-chains 87 residues out of total 3100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 87 time to evaluate : 0.693 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 367 random chunks: chunk 86 optimal weight: 40.0000 chunk 294 optimal weight: 6.9990 chunk 224 optimal weight: 20.0000 chunk 211 optimal weight: 40.0000 chunk 165 optimal weight: 20.0000 chunk 315 optimal weight: 20.0000 chunk 164 optimal weight: 5.9990 chunk 125 optimal weight: 50.0000 chunk 35 optimal weight: 50.0000 chunk 260 optimal weight: 30.0000 chunk 215 optimal weight: 50.0000 overall best weight: 14.5996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3656 r_free = 0.3656 target = 0.103096 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3360 r_free = 0.3360 target = 0.088013 restraints weight = 94692.356| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.087813 restraints weight = 271174.031| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3347 r_free = 0.3347 target = 0.087513 restraints weight = 230199.215| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3345 r_free = 0.3345 target = 0.087466 restraints weight = 164503.878| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3347 r_free = 0.3347 target = 0.087531 restraints weight = 146456.393| |-----------------------------------------------------------------------------| r_work (final): 0.3330 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3332 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3332 r_free = 0.3332 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 15 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3332 r_free = 0.3332 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 10 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3332 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7177 moved from start: 0.7752 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 19837 Z= 0.299 Angle : 0.750 9.211 27876 Z= 0.452 Chirality : 0.049 0.319 3709 Planarity : 0.004 0.020 3695 Dihedral : 17.897 179.942 4541 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 5.92 Ramachandran Plot: Outliers : 0.97 % Allowed : 15.10 % Favored : 83.92 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % Cis-general : 0.03 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: -2.80 (0.13), residues: 3595 helix: -0.17 (0.14), residues: 1269 sheet: -1.81 (0.29), residues: 299 loop : -3.17 (0.13), residues: 2027 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.000 0.000 TYR A 68 PHE 0.000 0.000 PHE A 8 TRP 0.000 0.000 TRP A 321 Details of bonding type rmsd/Z covalent geometry : bond 0.00419 / 0.30 (19837) covalent geometry : angle 0.75046 / 0.45 (27876) hydrogen bonds : bond 0.05816 / 4.43 ( 1101) hydrogen bonds : angle 6.01579 / 4.53 ( 3064) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7190 Ramachandran restraints generated. 3595 Oldfield, 0 Emsley, 3595 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7190 Ramachandran restraints generated. 3595 Oldfield, 0 Emsley, 3595 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 3100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 87 time to evaluate : 0.579 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 87 average time/residue: 0.0734 time to fit residues: 12.8085 Evaluate side-chains 87 residues out of total 3100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 87 time to evaluate : 0.608 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 367 random chunks: chunk 133 optimal weight: 2.9990 chunk 18 optimal weight: 30.0000 chunk 125 optimal weight: 40.0000 chunk 190 optimal weight: 40.0000 chunk 357 optimal weight: 50.0000 chunk 284 optimal weight: 6.9990 chunk 335 optimal weight: 50.0000 chunk 13 optimal weight: 40.0000 chunk 123 optimal weight: 10.0000 chunk 35 optimal weight: 50.0000 chunk 28 optimal weight: 10.0000 overall best weight: 11.9996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3652 r_free = 0.3652 target = 0.102710 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3350 r_free = 0.3350 target = 0.087327 restraints weight = 93812.812| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.086640 restraints weight = 270865.997| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3330 r_free = 0.3330 target = 0.086528 restraints weight = 255090.960| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.086437 restraints weight = 179164.512| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.086473 restraints weight = 175068.496| |-----------------------------------------------------------------------------| r_work (final): 0.3311 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3311 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3311 r_free = 0.3311 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 10 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3311 r_free = 0.3311 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 15 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3311 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7205 moved from start: 0.8039 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 19837 Z= 0.265 Angle : 0.713 8.673 27876 Z= 0.428 Chirality : 0.048 0.322 3709 Planarity : 0.003 0.020 3695 Dihedral : 17.770 178.455 4541 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 5.68 Ramachandran Plot: Outliers : 0.95 % Allowed : 16.38 % Favored : 82.67 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % Cis-general : 0.03 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: -2.71 (0.14), residues: 3595 helix: 0.07 (0.15), residues: 1260 sheet: -1.91 (0.28), residues: 312 loop : -3.20 (0.13), residues: 2023 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.000 0.000 TYR A 68 PHE 0.000 0.000 PHE A 8 TRP 0.000 0.000 TRP A 321 Details of bonding type rmsd/Z covalent geometry : bond 0.00371 / 0.26 (19837) covalent geometry : angle 0.71297 / 0.43 (27876) hydrogen bonds : bond 0.05759 / 4.39 ( 1101) hydrogen bonds : angle 5.88409 / 4.43 ( 3064) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7190 Ramachandran restraints generated. 3595 Oldfield, 0 Emsley, 3595 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7190 Ramachandran restraints generated. 3595 Oldfield, 0 Emsley, 3595 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 3100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 87 time to evaluate : 0.606 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 87 average time/residue: 0.0770 time to fit residues: 13.4469 Evaluate side-chains 87 residues out of total 3100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 87 time to evaluate : 0.520 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 367 random chunks: chunk 158 optimal weight: 30.0000 chunk 213 optimal weight: 40.0000 chunk 262 optimal weight: 40.0000 chunk 206 optimal weight: 50.0000 chunk 195 optimal weight: 40.0000 chunk 114 optimal weight: 50.0000 chunk 357 optimal weight: 50.0000 chunk 229 optimal weight: 10.0000 chunk 201 optimal weight: 50.0000 chunk 24 optimal weight: 50.0000 chunk 290 optimal weight: 40.0000 overall best weight: 32.0000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3584 r_free = 0.3584 target = 0.099318 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3287 r_free = 0.3287 target = 0.084424 restraints weight = 95058.917| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3285 r_free = 0.3285 target = 0.084389 restraints weight = 255590.813| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.083778 restraints weight = 218845.912| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3254 r_free = 0.3254 target = 0.083094 restraints weight = 224290.745| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3248 r_free = 0.3248 target = 0.082875 restraints weight = 187657.933| |-----------------------------------------------------------------------------| r_work (final): 0.3233 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3233 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3233 r_free = 0.3233 target_work(ls_wunit_k1) = 0.082 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 15 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3233 r_free = 0.3233 target_work(ls_wunit_k1) = 0.082 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 15 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3233 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7318 moved from start: 0.8854 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.145 19837 Z= 0.633 Angle : 1.192 15.773 27876 Z= 0.733 Chirality : 0.060 0.445 3709 Planarity : 0.007 0.035 3695 Dihedral : 18.738 176.232 4541 Min Nonbonded Distance : 2.329 Molprobity Statistics. All-atom Clashscore : 13.20 Ramachandran Plot: Outliers : 1.20 % Allowed : 21.78 % Favored : 77.02 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % Cis-general : 0.03 % Twisted Proline : 0.68 % Twisted General : 0.14 % 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: -4.28 (0.12), residues: 3595 helix: -1.70 (0.13), residues: 1278 sheet: -2.64 (0.26), residues: 342 loop : -3.85 (0.12), residues: 1975 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.000 0.000 TYR A 68 PHE 0.000 0.000 PHE A 8 TRP 0.000 0.000 TRP A 321 Details of bonding type rmsd/Z covalent geometry : bond 0.00902 / 0.63 (19837) covalent geometry : angle 1.19226 / 0.73 (27876) hydrogen bonds : bond 0.10601 / 8.12 ( 1101) hydrogen bonds : angle 7.92071 / 5.94 ( 3064) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7190 Ramachandran restraints generated. 3595 Oldfield, 0 Emsley, 3595 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7190 Ramachandran restraints generated. 3595 Oldfield, 0 Emsley, 3595 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 3100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 87 time to evaluate : 0.670 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 87 average time/residue: 0.0734 time to fit residues: 12.8364 Evaluate side-chains 87 residues out of total 3100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 87 time to evaluate : 0.678 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 367 random chunks: chunk 20 optimal weight: 20.0000 chunk 80 optimal weight: 40.0000 chunk 284 optimal weight: 50.0000 chunk 19 optimal weight: 50.0000 chunk 10 optimal weight: 50.0000 chunk 154 optimal weight: 9.9990 chunk 165 optimal weight: 8.9990 chunk 365 optimal weight: 50.0000 chunk 254 optimal weight: 40.0000 chunk 311 optimal weight: 20.0000 chunk 212 optimal weight: 40.0000 overall best weight: 19.7996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3610 r_free = 0.3610 target = 0.100451 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.086502 restraints weight = 94856.889| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.086346 restraints weight = 251971.765| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3315 r_free = 0.3315 target = 0.085833 restraints weight = 216030.950| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3300 r_free = 0.3300 target = 0.085128 restraints weight = 223241.048| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3298 r_free = 0.3298 target = 0.085090 restraints weight = 191055.227| |-----------------------------------------------------------------------------| r_work (final): 0.3281 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3281 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3281 r_free = 0.3281 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 15 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3281 r_free = 0.3281 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 15 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3281 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7244 moved from start: 0.9000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.079 19837 Z= 0.415 Angle : 0.896 11.509 27876 Z= 0.544 Chirality : 0.052 0.317 3709 Planarity : 0.005 0.022 3695 Dihedral : 18.444 178.717 4541 Min Nonbonded Distance : 2.379 Molprobity Statistics. All-atom Clashscore : 7.76 Ramachandran Plot: Outliers : 1.11 % Allowed : 19.47 % Favored : 79.42 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % Cis-general : 0.03 % Twisted Proline : 0.68 % 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: -3.96 (0.13), residues: 3595 helix: -1.18 (0.14), residues: 1260 sheet: -2.55 (0.27), residues: 312 loop : -3.82 (0.12), residues: 2023 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.000 0.000 TYR A 68 PHE 0.000 0.000 PHE A 8 TRP 0.000 0.000 TRP A 321 Details of bonding type rmsd/Z covalent geometry : bond 0.00583 / 0.41 (19837) covalent geometry : angle 0.89574 / 0.54 (27876) hydrogen bonds : bond 0.07281 / 5.57 ( 1101) hydrogen bonds : angle 6.94037 / 5.22 ( 3064) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2112.07 seconds wall clock time: 36 minutes 48.71 seconds (2208.71 seconds total)