Starting phenix.real_space_refine on Tue Jun 17 03:37:21 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9q96_52919/06_2025/9q96_52919.cif Found real_map, /net/cci-nas-00/data/ceres_data/9q96_52919/06_2025/9q96_52919.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9q96_52919/06_2025/9q96_52919.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9q96_52919/06_2025/9q96_52919.map" model { file = "/net/cci-nas-00/data/ceres_data/9q96_52919/06_2025/9q96_52919.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9q96_52919/06_2025/9q96_52919.cif" } resolution = 4.6 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 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-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: {'GLN:plan1': 8, 'ASP:plan': 20, 'TYR:plan': 5, 'ASN:plan1': 9, 'TRP:plan': 1, 'HIS:plan': 8, 'PHE:plan': 4, 'GLU:plan': 32, 'ARG:plan': 22} 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: {'GLN:plan1': 7, 'ASP:plan': 15, 'TYR:plan': 4, 'ASN:plan1': 6, 'HIS:plan': 7, 'PHE:plan': 3, 'GLU:plan': 25, 'ARG:plan': 18} 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: {'GLN:plan1': 58, 'HIS:plan': 19, 'TYR:plan': 43, 'ASN:plan1': 51, 'TRP:plan': 4, 'ASP:plan': 92, 'PHE:plan': 44, 'GLU:plan': 121, 'ARG:plan': 90} 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: {'GLN:plan1': 49, 'HIS:plan': 21, 'TYR:plan': 34, 'ASN:plan1': 46, 'TRP:plan': 9, 'ASP:plan': 75, 'PHE:plan': 35, 'GLU:plan': 103, 'ARG:plan': 99} 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: {'GLN:plan1': 8, 'ASN:plan1': 4, 'ASP:plan': 5, 'PHE:plan': 1, 'GLU:plan': 9, 'ARG:plan': 8} 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: {'GLN:plan1': 19, 'HIS:plan': 4, 'TYR:plan': 8, 'ASN:plan1': 6, 'TRP:plan': 3, 'ASP:plan': 23, 'PHE:plan': 9, 'GLU:plan': 28, 'ARG:plan': 21} 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: 12.47, per 1000 atoms: 0.64 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: 5.46 Conformation dependent library (CDL) restraints added in 3.4 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: 6.96 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: 10.87 Time building geometry restraints manager: 6.35 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: 26009 5.40 - 10.80: 1684 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: 0.560 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.810 Check model and map are aligned: 0.150 Set scattering table: 0.210 Process input model: 56.350 Find NCS groups from input model: 0.540 Set up NCS constraints: 0.100 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.930 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 61.680 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6903 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= 2.396 Angle : 2.833 26.993 27876 Z= 1.975 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -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 TRP 0.000 0.000 TRP A 321 PHE 0.000 0.000 PHE A 8 TYR 0.000 0.000 TYR A 68 Details of bonding type rmsd hydrogen bonds : bond 0.16615 ( 1101) hydrogen bonds : angle 9.39267 ( 3064) covalent geometry : bond 0.03116 (19837) covalent geometry : angle 2.83317 (27876) *********************** 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 : 2.126 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 87 average time/residue: 0.1764 time to fit residues: 32.0015 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 : 2.003 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 367 random chunks: chunk 309 optimal weight: 6.9990 chunk 278 optimal weight: 6.9990 chunk 154 optimal weight: 20.0000 chunk 95 optimal weight: 5.9990 chunk 187 optimal weight: 5.9990 chunk 148 optimal weight: 20.0000 chunk 287 optimal weight: 40.0000 chunk 111 optimal weight: 5.9990 chunk 174 optimal weight: 6.9990 chunk 214 optimal weight: 7.9990 chunk 333 optimal weight: 9.9990 overall best weight: 6.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3992 r_free = 0.3992 target = 0.127331 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3566 r_free = 0.3566 target = 0.101449 restraints weight = 91288.698| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3532 r_free = 0.3532 target = 0.098802 restraints weight = 211562.105| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3529 r_free = 0.3529 target = 0.098361 restraints weight = 204963.784| |-----------------------------------------------------------------------------| r_work (final): 0.3450 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3450 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3450 r_free = 0.3450 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3449 r_free = 0.3449 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| r_final: 0.3449 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6892 moved from start: 0.2774 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.089 19837 Z= 0.212 Angle : 0.698 8.830 27876 Z= 0.413 Chirality : 0.046 0.180 3709 Planarity : 0.004 0.023 3695 Dihedral : 17.707 179.294 4541 Min Nonbonded Distance : 2.310 Molprobity Statistics. All-atom Clashscore : 3.65 Ramachandran Plot: Outliers : 1.08 % Allowed : 7.43 % Favored : 91.49 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.26 (0.13), residues: 3595 helix: -0.37 (0.14), residues: 1278 sheet: -0.90 (0.27), residues: 318 loop : -2.47 (0.12), residues: 1999 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.000 0.000 TRP A 321 PHE 0.000 0.000 PHE A 8 TYR 0.000 0.000 TYR A 68 Details of bonding type rmsd hydrogen bonds : bond 0.05243 ( 1101) hydrogen bonds : angle 5.20565 ( 3064) covalent geometry : bond 0.00347 (19837) covalent geometry : angle 0.69841 (27876) *********************** 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 : 2.986 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 87 average time/residue: 0.2024 time to fit residues: 39.0620 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 : 2.182 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 367 random chunks: chunk 85 optimal weight: 0.9980 chunk 361 optimal weight: 20.0000 chunk 281 optimal weight: 50.0000 chunk 277 optimal weight: 20.0000 chunk 45 optimal weight: 50.0000 chunk 215 optimal weight: 50.0000 chunk 187 optimal weight: 50.0000 chunk 119 optimal weight: 8.9990 chunk 236 optimal weight: 9.9990 chunk 311 optimal weight: 20.0000 chunk 247 optimal weight: 20.0000 overall best weight: 11.9992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3848 r_free = 0.3848 target = 0.119972 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.090532 restraints weight = 87646.090| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3307 r_free = 0.3307 target = 0.087793 restraints weight = 214454.145| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3293 r_free = 0.3293 target = 0.086707 restraints weight = 194279.422| |-----------------------------------------------------------------------------| r_work (final): 0.3213 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3213 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3213 r_free = 0.3213 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3213 r_free = 0.3213 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.3213 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7263 moved from start: 0.5165 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.068 19837 Z= 0.300 Angle : 0.769 9.066 27876 Z= 0.464 Chirality : 0.048 0.219 3709 Planarity : 0.004 0.023 3695 Dihedral : 17.909 177.739 4541 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 5.01 Ramachandran Plot: Outliers : 1.17 % Allowed : 10.82 % Favored : 88.01 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.11 (0.13), residues: 3595 helix: 0.01 (0.14), residues: 1275 sheet: -0.99 (0.28), residues: 335 loop : -2.56 (0.13), residues: 1985 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.000 0.000 TRP A 321 PHE 0.000 0.000 PHE A 8 TYR 0.000 0.000 TYR A 68 Details of bonding type rmsd hydrogen bonds : bond 0.05990 ( 1101) hydrogen bonds : angle 5.75436 ( 3064) covalent geometry : bond 0.00459 (19837) covalent geometry : angle 0.76931 (27876) *********************** 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 : 1.730 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 87 average time/residue: 0.1879 time to fit residues: 34.0799 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 : 1.941 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 367 random chunks: chunk 249 optimal weight: 20.0000 chunk 161 optimal weight: 3.9990 chunk 283 optimal weight: 50.0000 chunk 132 optimal weight: 20.0000 chunk 13 optimal weight: 40.0000 chunk 129 optimal weight: 30.0000 chunk 224 optimal weight: 20.0000 chunk 46 optimal weight: 40.0000 chunk 52 optimal weight: 30.0000 chunk 51 optimal weight: 7.9990 chunk 323 optimal weight: 30.0000 overall best weight: 14.3996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3680 r_free = 0.3680 target = 0.104636 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.089685 restraints weight = 94933.825| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.089605 restraints weight = 258897.749| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3382 r_free = 0.3382 target = 0.089403 restraints weight = 227898.230| |-----------------------------------------------------------------------------| r_work (final): 0.3372 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3372 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3372 r_free = 0.3372 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3372 r_free = 0.3372 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 10 | |-----------------------------------------------------------------------------| r_final: 0.3372 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7018 moved from start: 0.6915 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.065 19837 Z= 0.330 Angle : 0.800 9.944 27876 Z= 0.484 Chirality : 0.049 0.212 3709 Planarity : 0.005 0.025 3695 Dihedral : 18.129 179.327 4541 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 6.44 Ramachandran Plot: Outliers : 1.08 % Allowed : 12.32 % Favored : 86.59 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.42 (0.13), residues: 3595 helix: -0.12 (0.14), residues: 1256 sheet: -0.82 (0.30), residues: 300 loop : -2.86 (0.13), residues: 2039 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.000 0.000 TRP A 321 PHE 0.000 0.000 PHE A 8 TYR 0.000 0.000 TYR A 68 Details of bonding type rmsd hydrogen bonds : bond 0.06340 ( 1101) hydrogen bonds : angle 6.07742 ( 3064) covalent geometry : bond 0.00501 (19837) covalent geometry : angle 0.79982 (27876) *********************** 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 : 2.005 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 87 average time/residue: 0.1737 time to fit residues: 31.1618 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 : 1.928 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 367 random chunks: chunk 74 optimal weight: 20.0000 chunk 217 optimal weight: 40.0000 chunk 2 optimal weight: 50.0000 chunk 366 optimal weight: 30.0000 chunk 51 optimal weight: 30.0000 chunk 239 optimal weight: 20.0000 chunk 29 optimal weight: 50.0000 chunk 16 optimal weight: 20.0000 chunk 127 optimal weight: 0.2980 chunk 11 optimal weight: 3.9990 chunk 116 optimal weight: 50.0000 overall best weight: 12.8594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3776 r_free = 0.3776 target = 0.115697 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3219 r_free = 0.3219 target = 0.080485 restraints weight = 88668.769| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3123 r_free = 0.3123 target = 0.075786 restraints weight = 102576.512| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3125 r_free = 0.3125 target = 0.075902 restraints weight = 127474.295| |-----------------------------------------------------------------------------| r_work (final): 0.3022 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3024 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3024 r_free = 0.3024 target_work(ls_wunit_k1) = 0.071 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 10 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3024 r_free = 0.3024 target_work(ls_wunit_k1) = 0.071 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 15 | |-----------------------------------------------------------------------------| r_final: 0.3024 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7656 moved from start: 0.7573 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 19837 Z= 0.290 Angle : 0.725 8.982 27876 Z= 0.437 Chirality : 0.047 0.217 3709 Planarity : 0.004 0.034 3695 Dihedral : 17.851 178.736 4541 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 5.81 Ramachandran Plot: Outliers : 1.06 % Allowed : 13.21 % Favored : 85.73 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.40 (0.14), residues: 3595 helix: 0.06 (0.14), residues: 1277 sheet: -1.32 (0.28), residues: 329 loop : -2.93 (0.13), residues: 1989 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.000 0.000 TRP A 321 PHE 0.000 0.000 PHE A 8 TYR 0.000 0.000 TYR A 68 Details of bonding type rmsd hydrogen bonds : bond 0.05695 ( 1101) hydrogen bonds : angle 5.84753 ( 3064) covalent geometry : bond 0.00445 (19837) covalent geometry : angle 0.72453 (27876) *********************** 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 : 2.122 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 87 average time/residue: 0.1834 time to fit residues: 33.2432 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 : 2.105 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 367 random chunks: chunk 209 optimal weight: 40.0000 chunk 83 optimal weight: 50.0000 chunk 213 optimal weight: 60.0000 chunk 63 optimal weight: 50.0000 chunk 307 optimal weight: 20.0000 chunk 156 optimal weight: 10.0000 chunk 276 optimal weight: 40.0000 chunk 301 optimal weight: 50.0000 chunk 115 optimal weight: 20.0000 chunk 214 optimal weight: 8.9990 chunk 65 optimal weight: 50.0000 overall best weight: 19.7998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3618 r_free = 0.3618 target = 0.101173 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3311 r_free = 0.3311 target = 0.085739 restraints weight = 94570.035| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.085709 restraints weight = 281343.465| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3300 r_free = 0.3300 target = 0.085314 restraints weight = 221949.633| |-----------------------------------------------------------------------------| r_work (final): 0.3286 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3286 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3286 r_free = 0.3286 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 15 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3286 r_free = 0.3286 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 15 | |-----------------------------------------------------------------------------| r_final: 0.3286 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7143 moved from start: 0.8603 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.083 19837 Z= 0.440 Angle : 0.926 11.823 27876 Z= 0.565 Chirality : 0.051 0.254 3709 Planarity : 0.005 0.026 3695 Dihedral : 18.384 179.700 4541 Min Nonbonded Distance : 2.421 Molprobity Statistics. All-atom Clashscore : 9.05 Ramachandran Plot: Outliers : 1.20 % Allowed : 17.39 % Favored : 81.42 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % Cis-general : 0.03 % Twisted Proline : 0.68 % Twisted General : 0.17 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.42 (0.13), residues: 3595 helix: -0.92 (0.14), residues: 1269 sheet: -2.05 (0.27), residues: 325 loop : -3.39 (0.12), residues: 2001 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.000 0.000 TRP A 321 PHE 0.000 0.000 PHE A 8 TYR 0.000 0.000 TYR A 68 Details of bonding type rmsd hydrogen bonds : bond 0.08328 ( 1101) hydrogen bonds : angle 6.97503 ( 3064) covalent geometry : bond 0.00672 (19837) covalent geometry : angle 0.92568 (27876) *********************** 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 : 1.956 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 87 average time/residue: 0.1753 time to fit residues: 31.5569 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 : 2.139 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 367 random chunks: chunk 74 optimal weight: 20.0000 chunk 213 optimal weight: 60.0000 chunk 127 optimal weight: 0.5980 chunk 41 optimal weight: 50.0000 chunk 137 optimal weight: 50.0000 chunk 79 optimal weight: 50.0000 chunk 0 optimal weight: 20.0000 chunk 85 optimal weight: 50.0000 chunk 87 optimal weight: 50.0000 chunk 42 optimal weight: 20.0000 chunk 336 optimal weight: 50.0000 overall best weight: 22.1196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3601 r_free = 0.3601 target = 0.100106 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3300 r_free = 0.3300 target = 0.085038 restraints weight = 94775.400| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.084858 restraints weight = 259668.800| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3288 r_free = 0.3288 target = 0.084584 restraints weight = 245522.877| |-----------------------------------------------------------------------------| r_work (final): 0.3278 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3278 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3278 r_free = 0.3278 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 15 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3278 r_free = 0.3278 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 10 | |-----------------------------------------------------------------------------| r_final: 0.3278 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7157 moved from start: 0.9323 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.093 19837 Z= 0.467 Angle : 0.948 11.921 27876 Z= 0.579 Chirality : 0.052 0.247 3709 Planarity : 0.005 0.027 3695 Dihedral : 18.656 179.867 4541 Min Nonbonded Distance : 2.375 Molprobity Statistics. All-atom Clashscore : 9.37 Ramachandran Plot: Outliers : 1.11 % Allowed : 18.83 % Favored : 80.06 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.88 (0.12), residues: 3595 helix: -1.22 (0.13), residues: 1249 sheet: -2.38 (0.27), residues: 319 loop : -3.70 (0.12), residues: 2027 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.000 0.000 TRP A 321 PHE 0.000 0.000 PHE A 8 TYR 0.000 0.000 TYR A 68 Details of bonding type rmsd hydrogen bonds : bond 0.07902 ( 1101) hydrogen bonds : angle 7.12103 ( 3064) covalent geometry : bond 0.00709 (19837) covalent geometry : angle 0.94811 (27876) *********************** 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 : 2.236 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 87 average time/residue: 0.1778 time to fit residues: 32.4115 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 : 2.187 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 367 random chunks: chunk 164 optimal weight: 6.9990 chunk 58 optimal weight: 50.0000 chunk 163 optimal weight: 5.9990 chunk 283 optimal weight: 50.0000 chunk 242 optimal weight: 0.2980 chunk 143 optimal weight: 10.0000 chunk 61 optimal weight: 2.9990 chunk 135 optimal weight: 7.9990 chunk 320 optimal weight: 30.0000 chunk 67 optimal weight: 5.9990 chunk 237 optimal weight: 20.0000 overall best weight: 4.4588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3672 r_free = 0.3672 target = 0.103958 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.088604 restraints weight = 94322.778| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.087889 restraints weight = 235151.178| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3355 r_free = 0.3355 target = 0.087767 restraints weight = 221854.368| |-----------------------------------------------------------------------------| r_work (final): 0.3346 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3346 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3346 r_free = 0.3346 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 10 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3346 r_free = 0.3346 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 10 | |-----------------------------------------------------------------------------| r_final: 0.3346 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7059 moved from start: 0.9074 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 19837 Z= 0.147 Angle : 0.602 9.469 27876 Z= 0.354 Chirality : 0.044 0.157 3709 Planarity : 0.002 0.018 3695 Dihedral : 17.856 179.720 4541 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 3.90 Ramachandran Plot: Outliers : 1.03 % Allowed : 11.63 % Favored : 87.34 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.54 (0.14), residues: 3595 helix: 0.52 (0.15), residues: 1264 sheet: -2.05 (0.28), residues: 295 loop : -3.30 (0.13), residues: 2036 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.000 0.000 TRP A 321 PHE 0.000 0.000 PHE A 8 TYR 0.000 0.000 TYR A 68 Details of bonding type rmsd hydrogen bonds : bond 0.03965 ( 1101) hydrogen bonds : angle 5.26638 ( 3064) covalent geometry : bond 0.00239 (19837) covalent geometry : angle 0.60201 (27876) *********************** 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 : 2.135 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 87 average time/residue: 0.1801 time to fit residues: 32.5533 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 : 1.947 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 367 random chunks: chunk 57 optimal weight: 30.0000 chunk 247 optimal weight: 30.0000 chunk 263 optimal weight: 30.0000 chunk 358 optimal weight: 20.0000 chunk 87 optimal weight: 0.5980 chunk 322 optimal weight: 30.0000 chunk 336 optimal weight: 50.0000 chunk 24 optimal weight: 0.2980 chunk 204 optimal weight: 50.0000 chunk 146 optimal weight: 50.0000 chunk 52 optimal weight: 20.0000 overall best weight: 14.1792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3627 r_free = 0.3627 target = 0.101477 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.085852 restraints weight = 95170.570| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.085306 restraints weight = 266098.455| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3307 r_free = 0.3307 target = 0.085479 restraints weight = 219694.565| |-----------------------------------------------------------------------------| r_work (final): 0.3299 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3299 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3299 r_free = 0.3299 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 = 0.3299 r_free = 0.3299 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 15 | |-----------------------------------------------------------------------------| r_final: 0.3299 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7140 moved from start: 0.9363 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.062 19837 Z= 0.315 Angle : 0.749 9.304 27876 Z= 0.453 Chirality : 0.047 0.212 3709 Planarity : 0.004 0.020 3695 Dihedral : 18.098 179.895 4541 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 6.16 Ramachandran Plot: Outliers : 1.00 % Allowed : 17.69 % Favored : 81.31 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.90 (0.14), residues: 3595 helix: 0.05 (0.15), residues: 1276 sheet: -2.11 (0.29), residues: 296 loop : -3.43 (0.13), residues: 2023 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.000 0.000 TRP A 321 PHE 0.000 0.000 PHE A 8 TYR 0.000 0.000 TYR A 68 Details of bonding type rmsd hydrogen bonds : bond 0.06249 ( 1101) hydrogen bonds : angle 6.05861 ( 3064) covalent geometry : bond 0.00486 (19837) covalent geometry : angle 0.74859 (27876) *********************** 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 : 2.098 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 87 average time/residue: 0.1851 time to fit residues: 33.5167 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 : 2.087 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 367 random chunks: chunk 205 optimal weight: 20.0000 chunk 133 optimal weight: 9.9990 chunk 247 optimal weight: 30.0000 chunk 303 optimal weight: 40.0000 chunk 229 optimal weight: 9.9990 chunk 106 optimal weight: 0.5980 chunk 342 optimal weight: 50.0000 chunk 237 optimal weight: 5.9990 chunk 11 optimal weight: 50.0000 chunk 236 optimal weight: 0.8980 chunk 295 optimal weight: 40.0000 overall best weight: 5.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3770 r_free = 0.3770 target = 0.115234 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3225 r_free = 0.3225 target = 0.080921 restraints weight = 88426.311| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3158 r_free = 0.3158 target = 0.077654 restraints weight = 94961.653| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3158 r_free = 0.3158 target = 0.077660 restraints weight = 97287.287| |-----------------------------------------------------------------------------| r_work (final): 0.3055 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3055 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3055 r_free = 0.3055 target_work(ls_wunit_k1) = 0.072 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 15 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3055 r_free = 0.3055 target_work(ls_wunit_k1) = 0.072 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 15 | |-----------------------------------------------------------------------------| r_final: 0.3055 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7613 moved from start: 0.9274 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 19837 Z= 0.150 Angle : 0.579 9.469 27876 Z= 0.341 Chirality : 0.044 0.157 3709 Planarity : 0.002 0.018 3695 Dihedral : 17.734 179.701 4541 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 3.76 Ramachandran Plot: Outliers : 0.95 % Allowed : 11.91 % Favored : 87.15 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.15 (0.14), residues: 3595 helix: 1.01 (0.15), residues: 1276 sheet: -2.05 (0.28), residues: 309 loop : -3.17 (0.13), residues: 2010 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.000 0.000 TRP A 321 PHE 0.000 0.000 PHE A 8 TYR 0.000 0.000 TYR A 68 Details of bonding type rmsd hydrogen bonds : bond 0.03905 ( 1101) hydrogen bonds : angle 5.08063 ( 3064) covalent geometry : bond 0.00246 (19837) covalent geometry : angle 0.57883 (27876) ********************** 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 : 2.036 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 87 average time/residue: 0.1737 time to fit residues: 31.4189 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 : 2.122 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 367 random chunks: chunk 79 optimal weight: 40.0000 chunk 36 optimal weight: 40.0000 chunk 73 optimal weight: 50.0000 chunk 188 optimal weight: 50.0000 chunk 365 optimal weight: 30.0000 chunk 359 optimal weight: 30.0000 chunk 22 optimal weight: 30.0000 chunk 179 optimal weight: 20.0000 chunk 280 optimal weight: 40.0000 chunk 330 optimal weight: 40.0000 chunk 6 optimal weight: 4.9990 overall best weight: 22.9998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3588 r_free = 0.3588 target = 0.099472 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3287 r_free = 0.3287 target = 0.084456 restraints weight = 95429.939| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.084099 restraints weight = 249489.918| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.083647 restraints weight = 231186.588| |-----------------------------------------------------------------------------| r_work (final): 0.3262 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3262 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3262 r_free = 0.3262 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 15 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3262 r_free = 0.3262 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 15 | |-----------------------------------------------------------------------------| r_final: 0.3262 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7191 moved from start: 0.9888 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.093 19837 Z= 0.503 Angle : 0.964 12.878 27876 Z= 0.592 Chirality : 0.053 0.277 3709 Planarity : 0.005 0.029 3695 Dihedral : 18.548 179.695 4541 Min Nonbonded Distance : 2.411 Molprobity Statistics. All-atom Clashscore : 9.54 Ramachandran Plot: Outliers : 1.31 % Allowed : 20.56 % Favored : 78.14 % 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 : 0.12 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.56 (0.13), residues: 3595 helix: -0.77 (0.14), residues: 1278 sheet: -2.41 (0.28), residues: 319 loop : -3.63 (0.13), residues: 1998 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.000 0.000 TRP A 321 PHE 0.000 0.000 PHE A 8 TYR 0.000 0.000 TYR A 68 Details of bonding type rmsd hydrogen bonds : bond 0.08577 ( 1101) hydrogen bonds : angle 7.09699 ( 3064) covalent geometry : bond 0.00764 (19837) covalent geometry : angle 0.96393 (27876) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5093.49 seconds wall clock time: 89 minutes 17.09 seconds (5357.09 seconds total)