Starting phenix.real_space_refine on Sat Jul 4 07:55:18 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9q96_52919/07_2026/9q96_52919.cif Found real_map, /net/cci-nas-00/data/ceres_data/9q96_52919/07_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 { model { file = "/net/cci-nas-00/data/ceres_data/9q96_52919/07_2026/9q96_52919.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9q96_52919/07_2026/9q96_52919.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9q96_52919/07_2026/9q96_52919.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9q96_52919/07_2026/9q96_52919.map" } 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-dev-6108/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: 4.98, per 1000 atoms: 0.25 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: 1.90 Conformation dependent library (CDL) restraints added in 1.2 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: 1.99 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: 4.82 Time building geometry restraints manager: 2.42 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: 26012 5.40 - 10.80: 1681 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: 0.500 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.340 Check model and map are aligned: 0.060 Set scattering table: 0.040 Process input model: 22.360 Find NCS groups from input model: 0.170 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.250 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.770 ------------------------------------------------------------------------------- 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= 2.400 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 2.82972 / 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 : 0.773 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 87 average time/residue: 0.0812 time to fit residues: 14.1690 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 : 0.633 ------------------------------------------------------------------------------- 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 = 0.3950 r_free = 0.3950 target = 0.122320 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3686 r_free = 0.3686 target = 0.106869 restraints weight = 92943.991| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3682 r_free = 0.3682 target = 0.106536 restraints weight = 202134.192| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3667 r_free = 0.3667 target = 0.105673 restraints weight = 205372.320| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3663 r_free = 0.3663 target = 0.105482 restraints weight = 177316.379| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3661 r_free = 0.3661 target = 0.105350 restraints weight = 165403.981| |-----------------------------------------------------------------------------| r_work (final): 0.3651 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3651 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3651 r_free = 0.3651 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3650 r_free = 0.3650 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: 0.3650 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6629 moved from start: 0.1915 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= 0.210 Angle : 0.740 11.905 27876 Z= 0.441 Chirality : 0.049 0.323 3709 Planarity : 0.004 0.020 3695 Dihedral : 17.683 177.039 4541 Min Nonbonded Distance : 2.441 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 (0.12), residues: 3595 helix: -0.57 (0.13), residues: 1298 sheet: -1.08 (0.26), residues: 325 loop : -2.44 (0.12), residues: 1972 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 0.00292 / 0.21 (19837) covalent geometry : angle 0.74035 / 0.44 (27876) hydrogen bonds : bond 0.05349 / 4.07 ( 1101) hydrogen bonds : angle 5.40349 / 4.06 ( 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 : 0.641 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 87 average time/residue: 0.0841 time to fit residues: 14.5711 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 : 0.697 ------------------------------------------------------------------------------- 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: 20.0000 chunk 337 optimal weight: 5.9990 chunk 158 optimal weight: 20.0000 chunk 296 optimal weight: 50.0000 chunk 328 optimal weight: 20.0000 chunk 232 optimal weight: 20.0000 chunk 310 optimal weight: 50.0000 overall best weight: 17.1998 ------------------------------------------------------------------------------- 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 = 0.3838 r_free = 0.3838 target = 0.119584 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.089732 restraints weight = 88327.133| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3286 r_free = 0.3286 target = 0.086230 restraints weight = 228906.076| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3270 r_free = 0.3270 target = 0.085057 restraints weight = 195045.288| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3237 r_free = 0.3237 target = 0.083403 restraints weight = 183020.752| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3239 r_free = 0.3239 target = 0.083346 restraints weight = 171238.838| |-----------------------------------------------------------------------------| r_work (final): 0.3148 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3148 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3148 r_free = 0.3148 target_work(ls_wunit_k1) = 0.077 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 10 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3148 r_free = 0.3148 target_work(ls_wunit_k1) = 0.077 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 10 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3148 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7496 moved from start: 0.4863 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.109 19837 Z= 0.379 Angle : 0.965 13.900 27876 Z= 0.586 Chirality : 0.054 0.401 3709 Planarity : 0.006 0.028 3695 Dihedral : 18.357 177.829 4541 Min Nonbonded Distance : 2.405 Molprobity Statistics. All-atom Clashscore : 6.55 Ramachandran Plot: Outliers : 1.08 % Allowed : 12.10 % Favored : 86.82 % 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: -0.92 (0.13), residues: 1273 sheet: -1.04 (0.27), residues: 355 loop : -2.75 (0.13), residues: 1967 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 0.00544 / 0.38 (19837) covalent geometry : angle 0.96465 / 0.59 (27876) hydrogen bonds : bond 0.08256 / 6.35 ( 1101) hydrogen bonds : angle 6.66411 / 4.98 ( 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 : 0.690 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 87 average time/residue: 0.0760 time to fit residues: 13.5346 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 : 0.556 ------------------------------------------------------------------------------- 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: 40.0000 chunk 40 optimal weight: 50.0000 chunk 168 optimal weight: 30.0000 chunk 135 optimal weight: 6.9990 chunk 184 optimal weight: 30.0000 chunk 257 optimal weight: 50.0000 chunk 297 optimal weight: 30.0000 chunk 11 optimal weight: 50.0000 chunk 271 optimal weight: 50.0000 chunk 351 optimal weight: 50.0000 chunk 227 optimal weight: 10.0000 overall best weight: 21.3998 ------------------------------------------------------------------------------- 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 = 0.3673 r_free = 0.3673 target = 0.104087 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3427 r_free = 0.3427 target = 0.091430 restraints weight = 95074.160| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3420 r_free = 0.3420 target = 0.091154 restraints weight = 260374.623| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.090622 restraints weight = 226840.799| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.089879 restraints weight = 245208.316| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.089860 restraints weight = 203761.793| |-----------------------------------------------------------------------------| r_work (final): 0.3372 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3371 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3371 r_free = 0.3371 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 10 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3371 r_free = 0.3371 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 10 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3371 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7112 moved from start: 0.6288 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.090 19837 Z= 0.432 Angle : 0.954 11.707 27876 Z= 0.578 Chirality : 0.054 0.523 3709 Planarity : 0.006 0.056 3695 Dihedral : 18.500 175.816 4541 Min Nonbonded Distance : 2.372 Molprobity Statistics. All-atom Clashscore : 7.45 Ramachandran Plot: Outliers : 1.11 % Allowed : 14.80 % Favored : 84.09 % 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 : 0.12 % 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: -3.28 (0.13), residues: 3595 helix: -1.21 (0.13), residues: 1259 sheet: -1.32 (0.28), residues: 326 loop : -3.12 (0.12), 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 0.00611 / 0.43 (19837) covalent geometry : angle 0.95430 / 0.58 (27876) hydrogen bonds : bond 0.07954 / 6.08 ( 1101) hydrogen bonds : angle 6.81697 / 5.11 ( 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 : 0.635 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 87 average time/residue: 0.0776 time to fit residues: 13.3631 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 : 0.690 ------------------------------------------------------------------------------- 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: 40.0000 chunk 20 optimal weight: 9.9990 chunk 23 optimal weight: 0.2980 chunk 213 optimal weight: 30.0000 chunk 241 optimal weight: 40.0000 chunk 346 optimal weight: 50.0000 chunk 147 optimal weight: 3.9990 chunk 289 optimal weight: 0.0980 chunk 246 optimal weight: 9.9990 chunk 10 optimal weight: 40.0000 overall best weight: 4.8786 ------------------------------------------------------------------------------- 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 = 0.3722 r_free = 0.3722 target = 0.106573 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3524 r_free = 0.3524 target = 0.096278 restraints weight = 96312.826| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3517 r_free = 0.3517 target = 0.095926 restraints weight = 244739.140| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3502 r_free = 0.3502 target = 0.095278 restraints weight = 221587.847| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3496 r_free = 0.3496 target = 0.094982 restraints weight = 208518.418| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3495 r_free = 0.3495 target = 0.094925 restraints weight = 185211.904| |-----------------------------------------------------------------------------| r_work (final): 0.3475 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3475 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3475 r_free = 0.3475 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 10 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3475 r_free = 0.3475 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 10 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3475 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6922 moved from start: 0.6223 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 19837 Z= 0.153 Angle : 0.618 8.470 27876 Z= 0.365 Chirality : 0.046 0.305 3709 Planarity : 0.002 0.020 3695 Dihedral : 17.731 175.875 4541 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 4.00 Ramachandran Plot: Outliers : 1.00 % Allowed : 10.46 % Favored : 88.54 % 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: -2.13 (0.14), residues: 3595 helix: 0.36 (0.15), residues: 1259 sheet: -1.20 (0.29), residues: 315 loop : -2.78 (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 0.00208 / 0.15 (19837) covalent geometry : angle 0.61849 / 0.37 (27876) hydrogen bonds : bond 0.04131 / 3.15 ( 1101) hydrogen bonds : angle 5.32816 / 3.99 ( 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 : 0.692 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 87 average time/residue: 0.0786 time to fit residues: 13.7951 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 : 0.668 ------------------------------------------------------------------------------- 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: 20.0000 chunk 168 optimal weight: 0.0020 chunk 203 optimal weight: 30.0000 chunk 22 optimal weight: 30.0000 chunk 192 optimal weight: 40.0000 chunk 154 optimal weight: 9.9990 chunk 51 optimal weight: 30.0000 chunk 180 optimal weight: 20.0000 chunk 224 optimal weight: 20.0000 chunk 60 optimal weight: 6.9990 chunk 306 optimal weight: 40.0000 overall best weight: 11.4000 ------------------------------------------------------------------------------- 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 = 0.3685 r_free = 0.3685 target = 0.104563 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.092652 restraints weight = 95787.122| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3437 r_free = 0.3437 target = 0.092061 restraints weight = 267893.961| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3434 r_free = 0.3434 target = 0.091882 restraints weight = 241327.202| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.091690 restraints weight = 190440.792| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3430 r_free = 0.3430 target = 0.091710 restraints weight = 182949.992| |-----------------------------------------------------------------------------| r_work (final): 0.3406 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3406 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3406 r_free = 0.3406 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 10 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3406 r_free = 0.3406 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 10 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3406 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7043 moved from start: 0.6695 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 19837 Z= 0.243 Angle : 0.690 8.933 27876 Z= 0.413 Chirality : 0.048 0.304 3709 Planarity : 0.003 0.019 3695 Dihedral : 17.787 177.018 4541 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 4.80 Ramachandran Plot: Outliers : 1.00 % Allowed : 14.02 % Favored : 84.98 % 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: -2.35 (0.14), residues: 3595 helix: 0.17 (0.15), residues: 1266 sheet: -1.50 (0.28), residues: 337 loop : -2.89 (0.13), residues: 1992 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 0.00342 / 0.24 (19837) covalent geometry : angle 0.69026 / 0.41 (27876) hydrogen bonds : bond 0.05589 / 4.26 ( 1101) hydrogen bonds : angle 5.66632 / 4.25 ( 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 : 0.699 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 87 average time/residue: 0.0814 time to fit residues: 14.2255 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 : 0.582 ------------------------------------------------------------------------------- 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: 50.0000 chunk 132 optimal weight: 20.0000 chunk 102 optimal weight: 40.0000 chunk 276 optimal weight: 30.0000 chunk 9 optimal weight: 9.9990 chunk 200 optimal weight: 40.0000 chunk 173 optimal weight: 9.9990 chunk 278 optimal weight: 20.0000 chunk 266 optimal weight: 30.0000 chunk 89 optimal weight: 50.0000 chunk 7 optimal weight: 40.0000 overall best weight: 17.9996 ------------------------------------------------------------------------------- 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 = 0.3631 r_free = 0.3631 target = 0.101772 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3323 r_free = 0.3323 target = 0.086300 restraints weight = 95004.036| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3313 r_free = 0.3313 target = 0.085952 restraints weight = 266581.940| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3312 r_free = 0.3312 target = 0.085904 restraints weight = 235709.417| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3307 r_free = 0.3307 target = 0.085687 restraints weight = 179572.630| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3308 r_free = 0.3308 target = 0.085743 restraints weight = 170984.493| |-----------------------------------------------------------------------------| r_work (final): 0.3293 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3293 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3293 r_free = 0.3293 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 = 0.3293 r_free = 0.3293 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: 0.3293 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7242 moved from start: 0.7839 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.090 19837 Z= 0.387 Angle : 0.912 11.943 27876 Z= 0.555 Chirality : 0.052 0.373 3709 Planarity : 0.005 0.026 3695 Dihedral : 18.349 178.050 4541 Min Nonbonded Distance : 2.387 Molprobity Statistics. All-atom Clashscore : 8.53 Ramachandran Plot: Outliers : 1.03 % Allowed : 18.61 % Favored : 80.36 % 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: -3.39 (0.13), residues: 3595 helix: -0.92 (0.14), residues: 1248 sheet: -2.03 (0.28), residues: 316 loop : -3.33 (0.12), residues: 2031 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 0.00549 / 0.39 (19837) covalent geometry : angle 0.91235 / 0.56 (27876) hydrogen bonds : bond 0.08371 / 6.40 ( 1101) hydrogen bonds : angle 6.92266 / 5.20 ( 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 : 0.758 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 87 average time/residue: 0.0780 time to fit residues: 13.7109 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 : 0.681 ------------------------------------------------------------------------------- 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: 50.0000 chunk 294 optimal weight: 0.0270 chunk 224 optimal weight: 0.5980 chunk 211 optimal weight: 7.9990 chunk 165 optimal weight: 8.9990 chunk 315 optimal weight: 8.9990 chunk 164 optimal weight: 6.9990 chunk 125 optimal weight: 50.0000 chunk 35 optimal weight: 50.0000 chunk 260 optimal weight: 20.0000 chunk 215 optimal weight: 50.0000 overall best weight: 4.9244 ------------------------------------------------------------------------------- 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 = 0.3684 r_free = 0.3684 target = 0.104530 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3470 r_free = 0.3470 target = 0.093637 restraints weight = 95934.792| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3461 r_free = 0.3461 target = 0.093224 restraints weight = 274900.410| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3461 r_free = 0.3461 target = 0.093249 restraints weight = 224471.229| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3453 r_free = 0.3453 target = 0.092889 restraints weight = 191452.008| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3454 r_free = 0.3454 target = 0.092934 restraints weight = 186593.562| |-----------------------------------------------------------------------------| 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: 15 | |-----------------------------------------------------------------------------| |-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: 15 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3431 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6992 moved from start: 0.7669 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 19837 Z= 0.156 Angle : 0.613 9.336 27876 Z= 0.364 Chirality : 0.046 0.300 3709 Planarity : 0.002 0.018 3695 Dihedral : 17.694 178.842 4541 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 4.35 Ramachandran Plot: Outliers : 0.95 % Allowed : 12.24 % Favored : 86.82 % 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: -2.37 (0.14), residues: 3595 helix: 0.44 (0.15), residues: 1282 sheet: -1.90 (0.28), residues: 316 loop : -3.07 (0.13), residues: 1997 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 0.00211 / 0.16 (19837) covalent geometry : angle 0.61349 / 0.36 (27876) hydrogen bonds : bond 0.04233 / 3.23 ( 1101) hydrogen bonds : angle 5.41207 / 4.06 ( 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 : 0.624 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 87 average time/residue: 0.0820 time to fit residues: 14.3001 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 : 0.733 ------------------------------------------------------------------------------- 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: 10.0000 chunk 18 optimal weight: 40.0000 chunk 125 optimal weight: 50.0000 chunk 190 optimal weight: 50.0000 chunk 357 optimal weight: 50.0000 chunk 284 optimal weight: 8.9990 chunk 335 optimal weight: 50.0000 chunk 13 optimal weight: 50.0000 chunk 123 optimal weight: 20.0000 chunk 35 optimal weight: 50.0000 chunk 28 optimal weight: 3.9990 overall best weight: 16.5996 ------------------------------------------------------------------------------- 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 = 0.3637 r_free = 0.3637 target = 0.102035 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3342 r_free = 0.3342 target = 0.087069 restraints weight = 94102.791| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3339 r_free = 0.3339 target = 0.087048 restraints weight = 254221.384| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3330 r_free = 0.3330 target = 0.086628 restraints weight = 212766.681| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3326 r_free = 0.3326 target = 0.086417 restraints weight = 174053.240| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3324 r_free = 0.3324 target = 0.086329 restraints weight = 162745.275| |-----------------------------------------------------------------------------| r_work (final): 0.3347 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3346 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3346 r_free = 0.3346 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 15 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3345 r_free = 0.3345 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 10 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (9 function evaluations) r_final: 0.3345 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7206 moved from start: 0.8099 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.072 19837 Z= 0.340 Angle : 0.805 9.593 27876 Z= 0.488 Chirality : 0.050 0.309 3709 Planarity : 0.004 0.021 3695 Dihedral : 18.009 178.702 4541 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 7.07 Ramachandran Plot: Outliers : 0.97 % Allowed : 18.25 % Favored : 80.78 % 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: -3.03 (0.13), residues: 3595 helix: -0.31 (0.14), residues: 1267 sheet: -2.14 (0.28), residues: 323 loop : -3.31 (0.13), residues: 2005 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 0.00481 / 0.34 (19837) covalent geometry : angle 0.80476 / 0.49 (27876) hydrogen bonds : bond 0.07084 / 5.41 ( 1101) hydrogen bonds : angle 6.34674 / 4.77 ( 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 : 0.747 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 87 average time/residue: 0.0799 time to fit residues: 13.9781 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 : 0.631 ------------------------------------------------------------------------------- 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: 50.0000 chunk 114 optimal weight: 40.0000 chunk 357 optimal weight: 50.0000 chunk 229 optimal weight: 9.9990 chunk 201 optimal weight: 50.0000 chunk 24 optimal weight: 50.0000 chunk 290 optimal weight: 20.0000 overall best weight: 27.9998 ------------------------------------------------------------------------------- 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 = 0.3586 r_free = 0.3586 target = 0.099374 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3288 r_free = 0.3288 target = 0.084411 restraints weight = 94789.853| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3287 r_free = 0.3287 target = 0.084440 restraints weight = 249748.967| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3270 r_free = 0.3270 target = 0.083765 restraints weight = 221530.181| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3255 r_free = 0.3255 target = 0.083105 restraints weight = 230464.972| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3252 r_free = 0.3252 target = 0.082994 restraints weight = 186319.876| |-----------------------------------------------------------------------------| r_work (final): 0.3238 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3238 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3238 r_free = 0.3238 target_work(ls_wunit_k1) = 0.082 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 10 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3237 r_free = 0.3237 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: 0.3237 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7313 moved from start: 0.9001 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.135 19837 Z= 0.576 Angle : 1.142 15.340 27876 Z= 0.699 Chirality : 0.059 0.470 3709 Planarity : 0.007 0.033 3695 Dihedral : 18.885 177.588 4541 Min Nonbonded Distance : 2.338 Molprobity Statistics. All-atom Clashscore : 12.92 Ramachandran Plot: Outliers : 1.14 % Allowed : 22.48 % Favored : 76.38 % 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 : 1.35 % Twisted General : 0.23 % 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: -4.41 (0.12), residues: 3595 helix: -1.77 (0.13), residues: 1257 sheet: -2.77 (0.25), residues: 343 loop : -3.93 (0.12), residues: 1995 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 0.00819 / 0.58 (19837) covalent geometry : angle 1.14227 / 0.70 (27876) hydrogen bonds : bond 0.10363 / 7.94 ( 1101) hydrogen bonds : angle 7.88317 / 5.90 ( 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 : 0.697 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 87 average time/residue: 0.0766 time to fit residues: 13.2744 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 : 0.772 ------------------------------------------------------------------------------- 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: 30.0000 chunk 284 optimal weight: 50.0000 chunk 19 optimal weight: 50.0000 chunk 10 optimal weight: 50.0000 chunk 154 optimal weight: 8.9990 chunk 165 optimal weight: 7.9990 chunk 365 optimal weight: 50.0000 chunk 254 optimal weight: 50.0000 chunk 311 optimal weight: 30.0000 chunk 212 optimal weight: 40.0000 overall best weight: 19.3996 ------------------------------------------------------------------------------- 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 = 0.3607 r_free = 0.3607 target = 0.100251 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3325 r_free = 0.3325 target = 0.086053 restraints weight = 94761.301| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.085811 restraints weight = 238055.909| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.085383 restraints weight = 217128.433| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.085014 restraints weight = 199707.043| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3300 r_free = 0.3300 target = 0.084920 restraints weight = 185193.024| |-----------------------------------------------------------------------------| r_work (final): 0.3289 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7236 moved from start: 0.9093 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.075 19837 Z= 0.408 Angle : 0.892 11.227 27876 Z= 0.541 Chirality : 0.052 0.301 3709 Planarity : 0.005 0.022 3695 Dihedral : 18.561 173.691 4541 Min Nonbonded Distance : 2.368 Molprobity Statistics. All-atom Clashscore : 8.15 Ramachandran Plot: Outliers : 1.03 % Allowed : 20.08 % Favored : 78.89 % 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: -4.06 (0.13), residues: 3595 helix: -1.25 (0.14), residues: 1266 sheet: -2.68 (0.27), residues: 316 loop : -3.87 (0.12), residues: 2013 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 0.00573 / 0.41 (19837) covalent geometry : angle 0.89196 / 0.54 (27876) hydrogen bonds : bond 0.07408 / 5.66 ( 1101) hydrogen bonds : angle 6.95874 / 5.22 ( 3064) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2150.04 seconds wall clock time: 37 minutes 33.69 seconds (2253.69 seconds total)