Starting phenix.real_space_refine on Sat Jul 4 21:33:50 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7nvx_12616/07_2026/7nvx_12616.cif Found real_map, /net/cci-nas-00/data/ceres_data/7nvx_12616/07_2026/7nvx_12616.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/cci-nas-00/data/ceres_data/7nvx_12616/07_2026/7nvx_12616.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7nvx_12616/07_2026/7nvx_12616.cif" model { file = "/net/cci-nas-00/data/ceres_data/7nvx_12616/07_2026/7nvx_12616.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7nvx_12616/07_2026/7nvx_12616.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7nvx_12616/07_2026/7nvx_12616.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7nvx_12616/07_2026/7nvx_12616.map" } resolution = 3.9 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.002 sd= 0.963 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: 10 Type Number sf(0) Gaussians Fe 4 7.16 5 Zn 7 6.06 5 P 52 5.49 5 Mg 1 5.21 5 S 146 5.16 5 Be 1 3.05 5 C 14929 2.51 5 N 4094 2.21 5 O 4426 1.98 5 F 3 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 13 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 23663 Number of models: 1 Model: "" Number of chains: 18 Chain: "0" Number of atoms: 5751 Number of conformers: 1 Conformer: "" Number of residues, atoms: 714, 5751 Classifications: {'peptide': 714} Link IDs: {'PTRANS': 32, 'TRANS': 681} Chain breaks: 1 Chain: "1" Number of atoms: 2167 Number of conformers: 1 Conformer: "" Number of residues, atoms: 265, 2167 Classifications: {'peptide': 265} Link IDs: {'PTRANS': 11, 'TRANS': 253} Chain breaks: 5 Chain: "2" Number of atoms: 3158 Number of conformers: 1 Conformer: "" Number of residues, atoms: 390, 3158 Classifications: {'peptide': 390} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 369} Chain breaks: 4 Chain: "3" Number of atoms: 1225 Number of conformers: 1 Conformer: "" Number of residues, atoms: 149, 1225 Classifications: {'peptide': 149} Link IDs: {'PTRANS': 6, 'TRANS': 142} Chain: "4" Number of atoms: 2066 Number of conformers: 1 Conformer: "" Number of residues, atoms: 263, 2066 Classifications: {'peptide': 263} Link IDs: {'PTRANS': 9, 'TRANS': 253} Chain breaks: 1 Chain: "5" Number of atoms: 523 Number of conformers: 1 Conformer: "" Number of residues, atoms: 66, 523 Classifications: {'peptide': 66} Link IDs: {'PTRANS': 1, 'TRANS': 64} Chain: "6" Number of atoms: 2567 Number of conformers: 1 Conformer: "" Number of residues, atoms: 329, 2567 Classifications: {'peptide': 329} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 310} Chain breaks: 1 Chain: "7" Number of atoms: 4890 Number of conformers: 1 Conformer: "" Number of residues, atoms: 605, 4890 Classifications: {'peptide': 605} Link IDs: {'PTRANS': 24, 'TRANS': 580} Chain breaks: 1 Chain: "N" Number of atoms: 515 Number of conformers: 1 Conformer: "" Number of residues, atoms: 25, 515 Classifications: {'DNA': 25} Link IDs: {'rna3p': 24} Chain: "T" Number of atoms: 510 Number of conformers: 1 Conformer: "" Number of residues, atoms: 25, 510 Classifications: {'DNA': 25} Link IDs: {'rna3p': 24} Chain: "W" Number of atoms: 124 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 124 Classifications: {'peptide': 15} Link IDs: {'PTRANS': 1, 'TRANS': 13} Chain: "Y" Number of atoms: 40 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 40 Classifications: {'peptide': 8} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'UNK:plan-1': 8} Unresolved non-hydrogen planarities: 8 Chain: "Z" Number of atoms: 80 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 80 Classifications: {'peptide': 16} Incomplete info: {'truncation_to_alanine': 16} Link IDs: {'TRANS': 15} Unresolved non-hydrogen bonds: 32 Unresolved non-hydrogen angles: 48 Unresolved non-hydrogen dihedrals: 16 Planarities with less than four sites: {'UNK:plan-1': 16} Unresolved non-hydrogen planarities: 16 Chain: "0" Number of atoms: 8 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 8 Unusual residues: {'SF4': 1} Classifications: {'undetermined': 1} Chain: "3" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "4" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "6" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' ZN': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "7" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 32 Unusual residues: {' MG': 1, 'ADP': 1, 'BEF': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 1541 SG CYS 0 190 74.263 145.452 47.690 1.00 68.30 S ATOM 943 SG CYS 0 116 72.378 141.599 52.690 1.00 64.04 S ATOM 1083 SG CYS 0 134 68.335 142.945 48.031 1.00 54.22 S ATOM 1252 SG CYS 0 155 70.584 147.759 51.866 1.00 69.31 S ATOM 11119 SG CYS 3 6 21.227 127.727 50.470 1.00 69.65 S ATOM 11143 SG CYS 3 9 18.861 125.041 51.640 1.00 70.46 S ATOM 11315 SG CYS 3 31 20.904 124.607 48.427 1.00 69.70 S ATOM 11336 SG CYS 3 34 17.694 127.507 48.703 1.00 72.86 S ATOM 11280 SG CYS 3 26 20.767 137.691 43.295 1.00 63.49 S ATOM 11423 SG CYS 3 46 18.137 135.484 45.366 1.00 78.25 S ATOM 11445 SG CYS 3 49 19.533 138.727 46.595 1.00 76.89 S ATOM 14188 SG CYS 4 268 124.048 111.046 82.106 1.00 40.34 S ATOM 14207 SG CYS 4 271 127.151 110.811 79.826 1.00 42.66 S ATOM 14292 SG CYS 4 282 126.742 113.773 82.690 1.00 55.77 S ATOM 14312 SG CYS 4 285 124.509 113.626 79.171 1.00 50.77 S ATOM 14080 SG CYS 4 255 135.555 108.283 91.056 1.00 50.63 S ATOM 14097 SG CYS 4 257 135.030 111.991 89.311 1.00 53.68 S ATOM 14246 SG CYS 4 276 134.331 111.257 93.474 1.00 52.99 S ATOM 17135 SG CYS 6 345 131.364 83.832 59.631 1.00 33.62 S ATOM 17157 SG CYS 6 348 130.075 80.763 61.401 1.00 23.04 S ATOM 17314 SG CYS 6 368 127.737 82.971 59.433 1.00 31.55 S ATOM 17335 SG CYS 6 371 129.314 84.158 62.702 1.00 23.68 S ATOM 17255 SG CYS 6 360 132.282 95.212 61.839 1.00 49.29 S ATOM 17273 SG CYS 6 363 135.757 93.973 61.746 1.00 64.00 S ATOM 17422 SG CYS 6 382 132.882 92.831 64.382 1.00 38.31 S ATOM 17439 SG CYS 6 385 135.059 96.688 64.767 1.00 55.53 S ATOM 16699 SG CYS 6 291 120.278 101.540 101.547 1.00 33.57 S ATOM 16721 SG CYS 6 294 116.649 101.502 102.661 1.00 37.35 S ATOM 16810 SG CYS 6 305 117.496 102.193 99.050 1.00 45.15 S ATOM 16833 SG CYS 6 308 117.736 104.564 102.097 1.00 38.84 S Time building chain proxies: 4.43, per 1000 atoms: 0.19 Number of scatterers: 23663 At special positions: 0 Unit cell: (172.2, 170.1, 137.55, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 10 Type Number sf(0) Zn 7 29.99 Fe 4 26.01 S 146 16.00 P 52 15.00 Mg 1 11.99 F 3 9.00 O 4426 8.00 N 4094 7.00 C 14929 6.00 Be 1 4.00 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=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 1.77 Conformation dependent library (CDL) restraints added in 824.2 milliseconds Dynamic metal coordination Iron sulfur cluster coordination pdb=" SF4 01000 " pdb="FE1 SF4 01000 " - pdb=" SG CYS 0 190 " pdb="FE4 SF4 01000 " - pdb=" SG CYS 0 155 " pdb="FE3 SF4 01000 " - pdb=" SG CYS 0 134 " pdb="FE2 SF4 01000 " - pdb=" SG CYS 0 116 " Number of angles added : 12 Zn2+ tetrahedral coordination pdb=" ZN 3 400 " pdb="ZN ZN 3 400 " - pdb=" SG CYS 3 6 " pdb="ZN ZN 3 400 " - pdb=" SG CYS 3 9 " pdb="ZN ZN 3 400 " - pdb=" SG CYS 3 31 " pdb="ZN ZN 3 400 " - pdb=" SG CYS 3 34 " pdb=" ZN 3 401 " pdb="ZN ZN 3 401 " - pdb=" NE2 HIS 3 28 " pdb="ZN ZN 3 401 " - pdb=" SG CYS 3 49 " pdb="ZN ZN 3 401 " - pdb=" SG CYS 3 46 " pdb="ZN ZN 3 401 " - pdb=" SG CYS 3 26 " pdb=" ZN 4 401 " pdb="ZN ZN 4 401 " - pdb=" SG CYS 4 268 " pdb="ZN ZN 4 401 " - pdb=" SG CYS 4 271 " pdb="ZN ZN 4 401 " - pdb=" SG CYS 4 285 " pdb="ZN ZN 4 401 " - pdb=" SG CYS 4 282 " pdb=" ZN 4 402 " pdb="ZN ZN 4 402 " - pdb=" NE2 HIS 4 258 " pdb="ZN ZN 4 402 " - pdb=" SG CYS 4 276 " pdb="ZN ZN 4 402 " - pdb=" SG CYS 4 255 " pdb="ZN ZN 4 402 " - pdb=" SG CYS 4 257 " pdb=" ZN 6 401 " pdb="ZN ZN 6 401 " - pdb=" SG CYS 6 345 " pdb="ZN ZN 6 401 " - pdb=" SG CYS 6 348 " pdb="ZN ZN 6 401 " - pdb=" SG CYS 6 371 " pdb="ZN ZN 6 401 " - pdb=" SG CYS 6 368 " pdb=" ZN 6 402 " pdb="ZN ZN 6 402 " - pdb=" SG CYS 6 360 " pdb="ZN ZN 6 402 " - pdb=" SG CYS 6 363 " pdb="ZN ZN 6 402 " - pdb=" SG CYS 6 382 " pdb="ZN ZN 6 402 " - pdb=" SG CYS 6 385 " pdb=" ZN 6 403 " pdb="ZN ZN 6 403 " - pdb=" SG CYS 6 294 " pdb="ZN ZN 6 403 " - pdb=" SG CYS 6 308 " pdb="ZN ZN 6 403 " - pdb=" SG CYS 6 305 " pdb="ZN ZN 6 403 " - pdb=" SG CYS 6 291 " Number of angles added : 36 5504 Ramachandran restraints generated. 2752 Oldfield, 0 Emsley, 2752 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5384 Finding SS restraints... Secondary structure from input PDB file: 129 helices and 21 sheets defined 54.9% alpha, 10.1% beta 25 base pairs and 39 stacking pairs defined. Time for finding SS restraints: 2.58 Creating SS restraints... Processing helix chain '0' and resid 18 through 35 removed outlier: 3.556A pdb=" N PHE 0 22 " --> pdb=" O TYR 0 18 " (cutoff:3.500A) Processing helix chain '0' and resid 47 through 63 removed outlier: 3.516A pdb=" N ILE 0 56 " --> pdb=" O LEU 0 52 " (cutoff:3.500A) Processing helix chain '0' and resid 76 through 99 removed outlier: 4.051A pdb=" N LYS 0 82 " --> pdb=" O PRO 0 78 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N GLU 0 85 " --> pdb=" O GLU 0 81 " (cutoff:3.500A) Processing helix chain '0' and resid 126 through 138 Processing helix chain '0' and resid 139 through 149 removed outlier: 3.590A pdb=" N HIS 0 148 " --> pdb=" O ALA 0 144 " (cutoff:3.500A) Processing helix chain '0' and resid 155 through 166 removed outlier: 3.560A pdb=" N GLU 0 159 " --> pdb=" O CYS 0 155 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N ALA 0 163 " --> pdb=" O GLU 0 159 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N ARG 0 166 " --> pdb=" O ASP 0 162 " (cutoff:3.500A) Processing helix chain '0' and resid 176 through 188 Processing helix chain '0' and resid 190 through 199 removed outlier: 3.572A pdb=" N ALA 0 195 " --> pdb=" O PRO 0 191 " (cutoff:3.500A) Processing helix chain '0' and resid 200 through 202 No H-bonds generated for 'chain '0' and resid 200 through 202' Processing helix chain '0' and resid 208 through 212 Processing helix chain '0' and resid 217 through 222 removed outlier: 3.538A pdb=" N VAL 0 221 " --> pdb=" O ILE 0 217 " (cutoff:3.500A) Processing helix chain '0' and resid 235 through 237 No H-bonds generated for 'chain '0' and resid 235 through 237' Processing helix chain '0' and resid 238 through 248 removed outlier: 3.841A pdb=" N MET 0 247 " --> pdb=" O CYS 0 243 " (cutoff:3.500A) Processing helix chain '0' and resid 253 through 277 Processing helix chain '0' and resid 278 through 291 removed outlier: 4.422A pdb=" N GLU 0 284 " --> pdb=" O ARG 0 280 " (cutoff:3.500A) removed outlier: 4.347A pdb=" N TYR 0 285 " --> pdb=" O LEU 0 281 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N ARG 0 286 " --> pdb=" O ARG 0 282 " (cutoff:3.500A) Processing helix chain '0' and resid 325 through 346 Processing helix chain '0' and resid 355 through 366 Processing helix chain '0' and resid 368 through 374 removed outlier: 3.930A pdb=" N PHE 0 374 " --> pdb=" O LYS 0 370 " (cutoff:3.500A) Processing helix chain '0' and resid 374 through 386 Processing helix chain '0' and resid 394 through 410 Processing helix chain '0' and resid 440 through 451 Proline residue: 0 446 - end of helix Processing helix chain '0' and resid 465 through 471 removed outlier: 3.862A pdb=" N LYS 0 469 " --> pdb=" O ASP 0 465 " (cutoff:3.500A) Processing helix chain '0' and resid 513 through 531 removed outlier: 3.605A pdb=" N VAL 0 530 " --> pdb=" O GLU 0 526 " (cutoff:3.500A) Processing helix chain '0' and resid 541 through 555 Processing helix chain '0' and resid 556 through 565 Processing helix chain '0' and resid 573 through 590 Processing helix chain '0' and resid 602 through 608 removed outlier: 3.812A pdb=" N GLU 0 606 " --> pdb=" O GLY 0 602 " (cutoff:3.500A) Processing helix chain '0' and resid 630 through 643 Processing helix chain '0' and resid 647 through 665 Processing helix chain '0' and resid 666 through 669 Processing helix chain '0' and resid 681 through 685 Processing helix chain '0' and resid 686 through 693 Processing helix chain '0' and resid 694 through 701 removed outlier: 3.599A pdb=" N HIS 0 700 " --> pdb=" O TRP 0 696 " (cutoff:3.500A) Processing helix chain '0' and resid 709 through 726 Processing helix chain '1' and resid 108 through 120 removed outlier: 4.335A pdb=" N GLN 1 119 " --> pdb=" O ASN 1 115 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N GLU 1 120 " --> pdb=" O ARG 1 116 " (cutoff:3.500A) Processing helix chain '1' and resid 121 through 134 removed outlier: 3.822A pdb=" N PHE 1 125 " --> pdb=" O ASP 1 121 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N LEU 1 127 " --> pdb=" O VAL 1 123 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N TYR 1 128 " --> pdb=" O LEU 1 124 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N VAL 1 132 " --> pdb=" O TYR 1 128 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N SER 1 134 " --> pdb=" O ASP 1 130 " (cutoff:3.500A) Processing helix chain '1' and resid 139 through 146 removed outlier: 3.887A pdb=" N TRP 1 143 " --> pdb=" O ALA 1 139 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N ARG 1 146 " --> pdb=" O PHE 1 142 " (cutoff:3.500A) Processing helix chain '1' and resid 191 through 200 Processing helix chain '1' and resid 200 through 210 Processing helix chain '1' and resid 216 through 226 removed outlier: 3.537A pdb=" N PHE 1 224 " --> pdb=" O PHE 1 220 " (cutoff:3.500A) removed outlier: 4.328A pdb=" N PHE 1 225 " --> pdb=" O TRP 1 221 " (cutoff:3.500A) removed outlier: 4.213A pdb=" N GLN 1 226 " --> pdb=" O THR 1 222 " (cutoff:3.500A) Processing helix chain '1' and resid 298 through 318 removed outlier: 3.539A pdb=" N ALA 1 302 " --> pdb=" O ASN 1 298 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N ILE 1 303 " --> pdb=" O SER 1 299 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N ILE 1 304 " --> pdb=" O ASN 1 300 " (cutoff:3.500A) Processing helix chain '1' and resid 379 through 384 removed outlier: 3.845A pdb=" N TYR 1 383 " --> pdb=" O SER 1 379 " (cutoff:3.500A) Processing helix chain '1' and resid 397 through 409 removed outlier: 3.512A pdb=" N ILE 1 401 " --> pdb=" O SER 1 397 " (cutoff:3.500A) Processing helix chain '1' and resid 423 through 435 Processing helix chain '1' and resid 455 through 479 removed outlier: 3.858A pdb=" N SER 1 459 " --> pdb=" O ASN 1 455 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N GLU 1 460 " --> pdb=" O ASP 1 456 " (cutoff:3.500A) removed outlier: 4.144A pdb=" N HIS 1 474 " --> pdb=" O GLU 1 470 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N CYS 1 478 " --> pdb=" O HIS 1 474 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N PHE 1 479 " --> pdb=" O PHE 1 475 " (cutoff:3.500A) Processing helix chain '1' and resid 485 through 515 removed outlier: 3.751A pdb=" N VAL 1 491 " --> pdb=" O GLU 1 487 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N LYS 1 492 " --> pdb=" O GLU 1 488 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N PHE 1 500 " --> pdb=" O ASN 1 496 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N LEU 1 505 " --> pdb=" O GLN 1 501 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N CYS 1 506 " --> pdb=" O VAL 1 502 " (cutoff:3.500A) Proline residue: 1 507 - end of helix Processing helix chain '1' and resid 523 through 547 removed outlier: 3.608A pdb=" N MET 1 528 " --> pdb=" O HIS 1 524 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N LEU 1 529 " --> pdb=" O ILE 1 525 " (cutoff:3.500A) Processing helix chain '2' and resid 19 through 25 Processing helix chain '2' and resid 27 through 35 Processing helix chain '2' and resid 37 through 47 removed outlier: 4.044A pdb=" N CYS 2 41 " --> pdb=" O HIS 2 37 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N GLU 2 47 " --> pdb=" O ALA 2 43 " (cutoff:3.500A) Processing helix chain '2' and resid 51 through 59 Processing helix chain '2' and resid 67 through 73 removed outlier: 3.899A pdb=" N VAL 2 71 " --> pdb=" O PRO 2 67 " (cutoff:3.500A) Processing helix chain '2' and resid 79 through 94 removed outlier: 3.931A pdb=" N GLN 2 83 " --> pdb=" O PHE 2 79 " (cutoff:3.500A) Processing helix chain '2' and resid 111 through 122 Processing helix chain '2' and resid 146 through 164 removed outlier: 3.532A pdb=" N LYS 2 150 " --> pdb=" O PRO 2 146 " (cutoff:3.500A) Processing helix chain '2' and resid 172 through 182 Processing helix chain '2' and resid 197 through 206 removed outlier: 3.743A pdb=" N GLN 2 202 " --> pdb=" O SER 2 198 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N LEU 2 205 " --> pdb=" O PHE 2 201 " (cutoff:3.500A) Processing helix chain '2' and resid 207 through 227 removed outlier: 3.780A pdb=" N GLN 2 224 " --> pdb=" O LEU 2 220 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N SER 2 225 " --> pdb=" O GLN 2 221 " (cutoff:3.500A) Processing helix chain '2' and resid 229 through 241 removed outlier: 3.690A pdb=" N ILE 2 233 " --> pdb=" O ASP 2 229 " (cutoff:3.500A) Processing helix chain '2' and resid 256 through 268 Processing helix chain '2' and resid 284 through 289 removed outlier: 3.826A pdb=" N ILE 2 288 " --> pdb=" O THR 2 284 " (cutoff:3.500A) removed outlier: 4.354A pdb=" N ASN 2 289 " --> pdb=" O ARG 2 285 " (cutoff:3.500A) No H-bonds generated for 'chain '2' and resid 284 through 289' Processing helix chain '2' and resid 321 through 329 removed outlier: 3.635A pdb=" N ILE 2 325 " --> pdb=" O SER 2 321 " (cutoff:3.500A) Processing helix chain '2' and resid 347 through 358 Processing helix chain '2' and resid 360 through 371 Processing helix chain '2' and resid 373 through 379 removed outlier: 3.910A pdb=" N LYS 2 378 " --> pdb=" O PRO 2 374 " (cutoff:3.500A) removed outlier: 4.396A pdb=" N GLN 2 379 " --> pdb=" O VAL 2 375 " (cutoff:3.500A) Processing helix chain '2' and resid 384 through 399 removed outlier: 3.781A pdb=" N ARG 2 398 " --> pdb=" O TRP 2 394 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N ASP 2 399 " --> pdb=" O GLU 2 395 " (cutoff:3.500A) Processing helix chain '2' and resid 414 through 428 removed outlier: 3.713A pdb=" N GLU 2 419 " --> pdb=" O GLN 2 415 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N LEU 2 420 " --> pdb=" O VAL 2 416 " (cutoff:3.500A) Processing helix chain '2' and resid 447 through 458 Processing helix chain '3' and resid 11 through 16 Processing helix chain '3' and resid 31 through 41 removed outlier: 3.635A pdb=" N LEU 3 37 " --> pdb=" O SER 3 33 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N ARG 3 41 " --> pdb=" O LEU 3 37 " (cutoff:3.500A) Processing helix chain '3' and resid 65 through 80 removed outlier: 3.519A pdb=" N LYS 3 70 " --> pdb=" O PRO 3 66 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N LYS 3 77 " --> pdb=" O GLU 3 73 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N LYS 3 80 " --> pdb=" O LYS 3 76 " (cutoff:3.500A) Processing helix chain '3' and resid 85 through 89 Processing helix chain '3' and resid 93 through 111 removed outlier: 3.698A pdb=" N ASP 3 97 " --> pdb=" O ARG 3 93 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N PHE 3 98 " --> pdb=" O GLU 3 94 " (cutoff:3.500A) removed outlier: 4.524A pdb=" N LEU 3 99 " --> pdb=" O TYR 3 95 " (cutoff:3.500A) Processing helix chain '3' and resid 113 through 129 removed outlier: 4.443A pdb=" N ASN 3 117 " --> pdb=" O VAL 3 113 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N LYS 3 127 " --> pdb=" O GLU 3 123 " (cutoff:3.500A) Processing helix chain '3' and resid 131 through 149 removed outlier: 4.177A pdb=" N THR 3 141 " --> pdb=" O LYS 3 137 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N ARG 3 142 " --> pdb=" O LEU 3 138 " (cutoff:3.500A) Processing helix chain '4' and resid 18 through 29 Processing helix chain '4' and resid 33 through 52 removed outlier: 3.946A pdb=" N ASN 4 52 " --> pdb=" O HIS 4 48 " (cutoff:3.500A) Processing helix chain '4' and resid 101 through 121 Processing helix chain '4' and resid 133 through 151 Processing helix chain '4' and resid 170 through 172 No H-bonds generated for 'chain '4' and resid 170 through 172' Processing helix chain '4' and resid 173 through 188 removed outlier: 3.556A pdb=" N VAL 4 180 " --> pdb=" O ASN 4 176 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N PHE 4 182 " --> pdb=" O MET 4 178 " (cutoff:3.500A) Processing helix chain '4' and resid 200 through 210 removed outlier: 3.750A pdb=" N ASP 4 208 " --> pdb=" O GLN 4 204 " (cutoff:3.500A) Processing helix chain '4' and resid 219 through 221 No H-bonds generated for 'chain '4' and resid 219 through 221' Processing helix chain '4' and resid 222 through 231 removed outlier: 3.736A pdb=" N TYR 4 226 " --> pdb=" O SER 4 222 " (cutoff:3.500A) Processing helix chain '4' and resid 234 through 239 removed outlier: 3.774A pdb=" N SER 4 239 " --> pdb=" O GLN 4 235 " (cutoff:3.500A) Processing helix chain '5' and resid 13 through 27 removed outlier: 3.545A pdb=" N GLN 5 18 " --> pdb=" O PRO 5 14 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N PHE 5 19 " --> pdb=" O ALA 5 15 " (cutoff:3.500A) Processing helix chain '5' and resid 49 through 64 Processing helix chain '6' and resid 68 through 73 Processing helix chain '6' and resid 79 through 98 removed outlier: 3.654A pdb=" N TYR 6 90 " --> pdb=" O LYS 6 86 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N PHE 6 96 " --> pdb=" O VAL 6 92 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ASP 6 97 " --> pdb=" O GLU 6 93 " (cutoff:3.500A) Processing helix chain '6' and resid 123 through 135 removed outlier: 3.538A pdb=" N HIS 6 127 " --> pdb=" O ASN 6 123 " (cutoff:3.500A) Processing helix chain '6' and resid 144 through 158 removed outlier: 4.198A pdb=" N HIS 6 158 " --> pdb=" O GLN 6 154 " (cutoff:3.500A) Processing helix chain '6' and resid 182 through 192 Processing helix chain '6' and resid 205 through 216 Processing helix chain '6' and resid 224 through 237 removed outlier: 3.694A pdb=" N GLU 6 230 " --> pdb=" O SER 6 226 " (cutoff:3.500A) removed outlier: 4.182A pdb=" N SER 6 237 " --> pdb=" O THR 6 233 " (cutoff:3.500A) Processing helix chain '6' and resid 314 through 321 removed outlier: 3.760A pdb=" N LEU 6 318 " --> pdb=" O SER 6 314 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N SER 6 321 " --> pdb=" O HIS 6 317 " (cutoff:3.500A) Processing helix chain '6' and resid 321 through 326 removed outlier: 3.913A pdb=" N LEU 6 325 " --> pdb=" O SER 6 321 " (cutoff:3.500A) Processing helix chain '6' and resid 368 through 378 Processing helix chain '6' and resid 383 through 387 Processing helix chain '7' and resid 92 through 104 removed outlier: 3.557A pdb=" N ASP 7 98 " --> pdb=" O LYS 7 94 " (cutoff:3.500A) Processing helix chain '7' and resid 119 through 130 removed outlier: 3.672A pdb=" N ALA 7 126 " --> pdb=" O SER 7 122 " (cutoff:3.500A) Processing helix chain '7' and resid 132 through 144 Processing helix chain '7' and resid 149 through 159 Processing helix chain '7' and resid 181 through 191 removed outlier: 3.683A pdb=" N ILE 7 185 " --> pdb=" O HIS 7 181 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N ASP 7 191 " --> pdb=" O HIS 7 187 " (cutoff:3.500A) Processing helix chain '7' and resid 191 through 197 Processing helix chain '7' and resid 273 through 275 No H-bonds generated for 'chain '7' and resid 273 through 275' Processing helix chain '7' and resid 276 through 287 Processing helix chain '7' and resid 296 through 300 Processing helix chain '7' and resid 317 through 328 Processing helix chain '7' and resid 345 through 358 Processing helix chain '7' and resid 367 through 382 Processing helix chain '7' and resid 410 through 415 Processing helix chain '7' and resid 420 through 432 removed outlier: 3.771A pdb=" N VAL 7 426 " --> pdb=" O GLU 7 422 " (cutoff:3.500A) Processing helix chain '7' and resid 443 through 446 Processing helix chain '7' and resid 452 through 458 removed outlier: 4.234A pdb=" N THR 7 456 " --> pdb=" O ARG 7 452 " (cutoff:3.500A) Processing helix chain '7' and resid 475 through 478 removed outlier: 3.833A pdb=" N VAL 7 478 " --> pdb=" O ASP 7 475 " (cutoff:3.500A) No H-bonds generated for 'chain '7' and resid 475 through 478' Processing helix chain '7' and resid 479 through 484 Processing helix chain '7' and resid 492 through 499 Processing helix chain '7' and resid 515 through 525 removed outlier: 3.644A pdb=" N GLU 7 521 " --> pdb=" O GLU 7 517 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N ALA 7 524 " --> pdb=" O ARG 7 520 " (cutoff:3.500A) Processing helix chain '7' and resid 529 through 536 Processing helix chain '7' and resid 537 through 553 Processing helix chain '7' and resid 564 through 576 Processing helix chain '7' and resid 585 through 599 Processing helix chain '7' and resid 608 through 613 removed outlier: 3.698A pdb=" N ASP 7 612 " --> pdb=" O LYS 7 609 " (cutoff:3.500A) removed outlier: 4.384A pdb=" N THR 7 613 " --> pdb=" O VAL 7 610 " (cutoff:3.500A) Processing helix chain '7' and resid 632 through 642 removed outlier: 3.770A pdb=" N ARG 7 642 " --> pdb=" O GLN 7 638 " (cutoff:3.500A) Processing helix chain '7' and resid 643 through 645 No H-bonds generated for 'chain '7' and resid 643 through 645' Processing helix chain '7' and resid 667 through 677 removed outlier: 4.140A pdb=" N ALA 7 671 " --> pdb=" O THR 7 667 " (cutoff:3.500A) Processing helix chain '7' and resid 677 through 683 Processing helix chain '7' and resid 705 through 720 removed outlier: 3.721A pdb=" N THR 7 720 " --> pdb=" O VAL 7 716 " (cutoff:3.500A) Processing helix chain 'W' and resid 278 through 283 Processing sheet with id=AA1, first strand: chain '0' and resid 3 through 4 Processing sheet with id=AA2, first strand: chain '0' and resid 173 through 175 removed outlier: 4.124A pdb=" N ALA 0 108 " --> pdb=" O TYR 0 175 " (cutoff:3.500A) removed outlier: 6.354A pdb=" N LEU 0 105 " --> pdb=" O VAL 0 204 " (cutoff:3.500A) removed outlier: 8.065A pdb=" N VAL 0 206 " --> pdb=" O LEU 0 105 " (cutoff:3.500A) removed outlier: 6.679A pdb=" N LEU 0 107 " --> pdb=" O VAL 0 206 " (cutoff:3.500A) removed outlier: 6.015A pdb=" N LEU 0 70 " --> pdb=" O VAL 0 205 " (cutoff:3.500A) removed outlier: 6.131A pdb=" N ILE 0 71 " --> pdb=" O VAL 0 232 " (cutoff:3.500A) removed outlier: 6.868A pdb=" N VAL 0 231 " --> pdb=" O ILE 0 455 " (cutoff:3.500A) removed outlier: 7.258A pdb=" N THR 0 457 " --> pdb=" O VAL 0 231 " (cutoff:3.500A) removed outlier: 5.323A pdb=" N PHE 0 233 " --> pdb=" O THR 0 457 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N ALA 0 479 " --> pdb=" O VAL 0 39 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain '0' and resid 250 through 252 removed outlier: 3.538A pdb=" N ILE 0 432 " --> pdb=" O GLU 0 419 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain '0' and resid 490 through 494 removed outlier: 6.255A pdb=" N CYS 0 491 " --> pdb=" O MET 0 677 " (cutoff:3.500A) removed outlier: 7.827A pdb=" N PHE 0 679 " --> pdb=" O CYS 0 491 " (cutoff:3.500A) removed outlier: 6.905A pdb=" N MET 0 493 " --> pdb=" O PHE 0 679 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N VAL 0 536 " --> pdb=" O ALA 0 617 " (cutoff:3.500A) removed outlier: 6.987A pdb=" N LEU 0 566 " --> pdb=" O ILE 0 595 " (cutoff:3.500A) removed outlier: 7.611A pdb=" N LEU 0 597 " --> pdb=" O LEU 0 566 " (cutoff:3.500A) removed outlier: 6.519A pdb=" N PHE 0 568 " --> pdb=" O LEU 0 597 " (cutoff:3.500A) removed outlier: 8.673A pdb=" N VAL 0 599 " --> pdb=" O PHE 0 568 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain '2' and resid 96 through 97 Processing sheet with id=AA6, first strand: chain '2' and resid 185 through 186 removed outlier: 3.529A pdb=" N LYS 2 186 " --> pdb=" O CYS 2 195 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain '2' and resid 271 through 272 Processing sheet with id=AA8, first strand: chain '2' and resid 307 through 309 removed outlier: 6.988A pdb=" N MET 2 341 " --> pdb=" O ARG 2 337 " (cutoff:3.500A) removed outlier: 5.003A pdb=" N ARG 2 337 " --> pdb=" O MET 2 341 " (cutoff:3.500A) removed outlier: 6.532A pdb=" N VAL 2 343 " --> pdb=" O LEU 2 335 " (cutoff:3.500A) removed outlier: 8.868A pdb=" N LYS 7 59 " --> pdb=" O GLU 2 333 " (cutoff:3.500A) removed outlier: 7.156A pdb=" N LEU 2 335 " --> pdb=" O LYS 7 59 " (cutoff:3.500A) removed outlier: 4.118A pdb=" N LYS 7 52 " --> pdb=" O ASP 7 60 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain '2' and resid 431 through 435 removed outlier: 3.735A pdb=" N PHE 2 433 " --> pdb=" O VAL 2 442 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N MET 2 441 " --> pdb=" O TYR 2 409 " (cutoff:3.500A) removed outlier: 8.363A pdb=" N HIS 5 42 " --> pdb=" O ASP 5 37 " (cutoff:3.500A) removed outlier: 6.513A pdb=" N ASP 5 37 " --> pdb=" O HIS 5 42 " (cutoff:3.500A) removed outlier: 7.892A pdb=" N PHE 5 44 " --> pdb=" O ILE 5 35 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N ILE 5 35 " --> pdb=" O PHE 5 44 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain '3' and resid 22 through 23 removed outlier: 3.591A pdb=" N ARG 3 59 " --> pdb=" O VAL 3 23 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain '4' and resid 56 through 60 removed outlier: 5.785A pdb=" N ASN 4 9 " --> pdb=" O LYS 4 56 " (cutoff:3.500A) removed outlier: 7.755A pdb=" N ALA 4 58 " --> pdb=" O ASN 4 9 " (cutoff:3.500A) removed outlier: 6.386A pdb=" N LEU 4 11 " --> pdb=" O ALA 4 58 " (cutoff:3.500A) removed outlier: 7.962A pdb=" N ILE 4 60 " --> pdb=" O LEU 4 11 " (cutoff:3.500A) removed outlier: 6.021A pdb=" N ILE 4 13 " --> pdb=" O ILE 4 60 " (cutoff:3.500A) removed outlier: 5.896A pdb=" N LEU 4 10 " --> pdb=" O ARG 4 160 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N LEU 4 190 " --> pdb=" O SER 4 159 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain '4' and resid 264 through 268 removed outlier: 4.134A pdb=" N THR 6 311 " --> pdb=" O ARG 6 251 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain '6' and resid 113 through 116 removed outlier: 5.972A pdb=" N HIS 6 60 " --> pdb=" O GLU 6 166 " (cutoff:3.500A) removed outlier: 7.454A pdb=" N LEU 6 168 " --> pdb=" O HIS 6 60 " (cutoff:3.500A) removed outlier: 6.043A pdb=" N TYR 6 62 " --> pdb=" O LEU 6 168 " (cutoff:3.500A) removed outlier: 7.050A pdb=" N ILE 6 170 " --> pdb=" O TYR 6 62 " (cutoff:3.500A) removed outlier: 7.036A pdb=" N VAL 6 64 " --> pdb=" O ILE 6 170 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain '6' and resid 113 through 116 removed outlier: 5.972A pdb=" N HIS 6 60 " --> pdb=" O GLU 6 166 " (cutoff:3.500A) removed outlier: 7.454A pdb=" N LEU 6 168 " --> pdb=" O HIS 6 60 " (cutoff:3.500A) removed outlier: 6.043A pdb=" N TYR 6 62 " --> pdb=" O LEU 6 168 " (cutoff:3.500A) removed outlier: 7.050A pdb=" N ILE 6 170 " --> pdb=" O TYR 6 62 " (cutoff:3.500A) removed outlier: 7.036A pdb=" N VAL 6 64 " --> pdb=" O ILE 6 170 " (cutoff:3.500A) removed outlier: 7.307A pdb=" N ILE 6 199 " --> pdb=" O VAL 6 167 " (cutoff:3.500A) removed outlier: 6.378A pdb=" N ILE 6 169 " --> pdb=" O ILE 6 199 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain '6' and resid 257 through 258 removed outlier: 3.917A pdb=" N THR 6 258 " --> pdb=" O GLY 6 288 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain '6' and resid 332 through 333 removed outlier: 3.611A pdb=" N GLN 6 332 " --> pdb=" O VAL 6 359 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N VAL 6 359 " --> pdb=" O GLN 6 332 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB7 Processing sheet with id=AB8, first strand: chain '7' and resid 84 through 87 removed outlier: 6.071A pdb=" N LYS 7 117 " --> pdb=" O PRO 7 106 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain '7' and resid 268 through 272 removed outlier: 3.638A pdb=" N SER 7 179 " --> pdb=" O VAL 7 268 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N PHE 7 270 " --> pdb=" O VAL 7 177 " (cutoff:3.500A) removed outlier: 4.179A pdb=" N TYR 7 175 " --> pdb=" O VAL 7 272 " (cutoff:3.500A) removed outlier: 7.878A pdb=" N VAL 7 166 " --> pdb=" O LEU 7 292 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain '7' and resid 389 through 392 removed outlier: 4.325A pdb=" N THR 7 409 " --> pdb=" O PHE 7 392 " (cutoff:3.500A) removed outlier: 8.530A pdb=" N TRP 7 435 " --> pdb=" O HIS 7 461 " (cutoff:3.500A) removed outlier: 7.114A pdb=" N LYS 7 463 " --> pdb=" O TRP 7 435 " (cutoff:3.500A) removed outlier: 8.551A pdb=" N LEU 7 437 " --> pdb=" O LYS 7 463 " (cutoff:3.500A) removed outlier: 9.487A pdb=" N GLY 7 465 " --> pdb=" O LEU 7 437 " (cutoff:3.500A) removed outlier: 8.579A pdb=" N ILE 7 439 " --> pdb=" O GLY 7 465 " (cutoff:3.500A) removed outlier: 9.748A pdb=" N THR 7 467 " --> pdb=" O ILE 7 439 " (cutoff:3.500A) removed outlier: 9.198A pdb=" N ASP 7 441 " --> pdb=" O THR 7 467 " (cutoff:3.500A) removed outlier: 6.093A pdb=" N VAL 7 337 " --> pdb=" O LYS 7 487 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N TYR 7 489 " --> pdb=" O VAL 7 337 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain '7' and resid 604 through 607 removed outlier: 6.850A pdb=" N ILE 7 558 " --> pdb=" O ILE 7 605 " (cutoff:3.500A) removed outlier: 8.090A pdb=" N ILE 7 607 " --> pdb=" O ILE 7 558 " (cutoff:3.500A) removed outlier: 6.271A pdb=" N VAL 7 560 " --> pdb=" O ILE 7 607 " (cutoff:3.500A) removed outlier: 6.219A pdb=" N ILE 7 559 " --> pdb=" O ILE 7 624 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N PHE 7 659 " --> pdb=" O GLN 7 506 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N VAL 7 510 " --> pdb=" O SER 7 661 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain '7' and resid 604 through 607 removed outlier: 6.850A pdb=" N ILE 7 558 " --> pdb=" O ILE 7 605 " (cutoff:3.500A) removed outlier: 8.090A pdb=" N ILE 7 607 " --> pdb=" O ILE 7 558 " (cutoff:3.500A) removed outlier: 6.271A pdb=" N VAL 7 560 " --> pdb=" O ILE 7 607 " (cutoff:3.500A) removed outlier: 6.219A pdb=" N ILE 7 559 " --> pdb=" O ILE 7 624 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N PHE 7 659 " --> pdb=" O GLN 7 506 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N VAL 7 510 " --> pdb=" O SER 7 661 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N LYS 7 688 " --> pdb=" O CYS 7 507 " (cutoff:3.500A) 1060 hydrogen bonds defined for protein. 3066 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 67 hydrogen bonds 134 hydrogen bond angles 0 basepair planarities 25 basepair parallelities 39 stacking parallelities Total time for adding SS restraints: 4.59 Time building geometry restraints manager: 2.35 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.43: 10168 1.43 - 1.64: 13848 1.64 - 1.86: 214 1.86 - 2.07: 0 2.07 - 2.28: 12 Bond restraints: 24242 Sorted by residual: bond pdb=" C4 ADP 7 901 " pdb=" C5 ADP 7 901 " ideal model delta sigma weight residual 1.490 1.381 0.109 2.00e-02 2.50e+03 2.97e+01 bond pdb=" F2 BEF 7 903 " pdb="BE BEF 7 903 " ideal model delta sigma weight residual 1.476 1.561 -0.085 2.00e-02 2.50e+03 1.80e+01 bond pdb=" C5 ADP 7 901 " pdb=" C6 ADP 7 901 " ideal model delta sigma weight residual 1.490 1.409 0.081 2.00e-02 2.50e+03 1.65e+01 bond pdb=" F3 BEF 7 903 " pdb="BE BEF 7 903 " ideal model delta sigma weight residual 1.476 1.547 -0.071 2.00e-02 2.50e+03 1.25e+01 bond pdb=" F1 BEF 7 903 " pdb="BE BEF 7 903 " ideal model delta sigma weight residual 1.476 1.532 -0.056 2.00e-02 2.50e+03 7.88e+00 ... (remaining 24237 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.29: 32737 2.29 - 4.58: 247 4.58 - 6.87: 9 6.87 - 9.16: 4 9.16 - 11.45: 4 Bond angle restraints: 33001 Sorted by residual: angle pdb=" N3 DT T -63 " pdb=" C4 DT T -63 " pdb=" O4 DT T -63 " ideal model delta sigma weight residual 119.90 122.49 -2.59 6.00e-01 2.78e+00 1.86e+01 angle pdb=" N3 DT N 51 " pdb=" C4 DT N 51 " pdb=" O4 DT N 51 " ideal model delta sigma weight residual 119.90 122.45 -2.55 6.00e-01 2.78e+00 1.80e+01 angle pdb=" N3 DT N 53 " pdb=" C4 DT N 53 " pdb=" O4 DT N 53 " ideal model delta sigma weight residual 119.90 122.42 -2.52 6.00e-01 2.78e+00 1.76e+01 angle pdb=" N3 DT T -57 " pdb=" C4 DT T -57 " pdb=" O4 DT T -57 " ideal model delta sigma weight residual 119.90 122.41 -2.51 6.00e-01 2.78e+00 1.75e+01 angle pdb=" N3 DT N 66 " pdb=" C4 DT N 66 " pdb=" O4 DT N 66 " ideal model delta sigma weight residual 119.90 122.41 -2.51 6.00e-01 2.78e+00 1.74e+01 ... (remaining 32996 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.09: 13469 24.09 - 48.18: 941 48.18 - 72.27: 135 72.27 - 96.36: 18 96.36 - 120.45: 1 Dihedral angle restraints: 14564 sinusoidal: 6279 harmonic: 8285 Sorted by residual: dihedral pdb=" C5' ADP 7 901 " pdb=" O5' ADP 7 901 " pdb=" PA ADP 7 901 " pdb=" O2A ADP 7 901 " ideal model delta sinusoidal sigma weight residual 300.00 179.55 120.45 1 2.00e+01 2.50e-03 3.62e+01 dihedral pdb=" CA GLY 3 27 " pdb=" C GLY 3 27 " pdb=" N HIS 3 28 " pdb=" CA HIS 3 28 " ideal model delta harmonic sigma weight residual 180.00 -151.80 -28.20 0 5.00e+00 4.00e-02 3.18e+01 dihedral pdb=" CA SER 0 462 " pdb=" C SER 0 462 " pdb=" N PRO 0 463 " pdb=" CA PRO 0 463 " ideal model delta harmonic sigma weight residual 180.00 -153.25 -26.75 0 5.00e+00 4.00e-02 2.86e+01 ... (remaining 14561 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.041: 2979 0.041 - 0.081: 474 0.081 - 0.122: 208 0.122 - 0.162: 58 0.162 - 0.203: 5 Chirality restraints: 3724 Sorted by residual: chirality pdb=" C3' ADP 7 901 " pdb=" C2' ADP 7 901 " pdb=" C4' ADP 7 901 " pdb=" O3' ADP 7 901 " both_signs ideal model delta sigma weight residual False -2.51 -2.71 0.20 2.00e-01 2.50e+01 1.03e+00 chirality pdb=" C3' DG N 58 " pdb=" C4' DG N 58 " pdb=" O3' DG N 58 " pdb=" C2' DG N 58 " both_signs ideal model delta sigma weight residual False -2.73 -2.55 -0.18 2.00e-01 2.50e+01 7.93e-01 chirality pdb=" C3' DG N 60 " pdb=" C4' DG N 60 " pdb=" O3' DG N 60 " pdb=" C2' DG N 60 " both_signs ideal model delta sigma weight residual False -2.73 -2.55 -0.18 2.00e-01 2.50e+01 7.87e-01 ... (remaining 3721 not shown) Planarity restraints: 4029 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C SER 0 462 " -0.039 5.00e-02 4.00e+02 5.81e-02 5.39e+00 pdb=" N PRO 0 463 " 0.100 5.00e-02 4.00e+02 pdb=" CA PRO 0 463 " -0.030 5.00e-02 4.00e+02 pdb=" CD PRO 0 463 " -0.032 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE 2 338 " 0.030 5.00e-02 4.00e+02 4.54e-02 3.29e+00 pdb=" N PRO 2 339 " -0.078 5.00e-02 4.00e+02 pdb=" CA PRO 2 339 " 0.023 5.00e-02 4.00e+02 pdb=" CD PRO 2 339 " 0.026 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TRP 2 96 " 0.011 2.00e-02 2.50e+03 8.87e-03 1.97e+00 pdb=" CG TRP 2 96 " -0.024 2.00e-02 2.50e+03 pdb=" CD1 TRP 2 96 " 0.008 2.00e-02 2.50e+03 pdb=" CD2 TRP 2 96 " -0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP 2 96 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 TRP 2 96 " 0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP 2 96 " 0.002 2.00e-02 2.50e+03 pdb=" CZ2 TRP 2 96 " 0.002 2.00e-02 2.50e+03 pdb=" CZ3 TRP 2 96 " 0.001 2.00e-02 2.50e+03 pdb=" CH2 TRP 2 96 " -0.000 2.00e-02 2.50e+03 ... (remaining 4026 not shown) Histogram of nonbonded interaction distances: 1.97 - 2.56: 208 2.56 - 3.14: 20236 3.14 - 3.73: 38179 3.73 - 4.31: 51711 4.31 - 4.90: 85046 Nonbonded interactions: 195380 Sorted by model distance: nonbonded pdb=" OE2 GLU 7 442 " pdb=" OG SER 7 614 " model vdw 1.971 3.040 nonbonded pdb=" O GLU 1 527 " pdb=" OG1 THR 1 531 " model vdw 1.990 3.040 nonbonded pdb=" O2B ADP 7 901 " pdb="MG MG 7 902 " model vdw 2.001 2.170 nonbonded pdb=" O PHE 7 378 " pdb=" OG SER 7 382 " model vdw 2.011 3.040 nonbonded pdb=" OG SER 2 172 " pdb=" OD1 ASP 2 174 " model vdw 2.013 3.040 ... (remaining 195375 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=1.00 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: 6.180 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.340 Check model and map are aligned: 0.070 Set scattering table: 0.060 Process input model: 26.590 Find NCS groups from input model: 0.100 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.000 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.390 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6415 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 : 0.007 0.464 24275 Z= 0.403 Angle : 0.552 14.213 33049 Z= 0.319 Chirality : 0.039 0.203 3724 Planarity : 0.003 0.058 4029 Dihedral : 15.663 120.451 9180 Min Nonbonded Distance : 1.971 Molprobity Statistics. All-atom Clashscore : 6.59 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.47 % Favored : 95.49 % Rotamer: Outliers : 0.00 % Allowed : 0.20 % Favored : 99.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.64 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.85 (0.17), residues: 2752 helix: 2.06 (0.15), residues: 1293 sheet: -1.28 (0.31), residues: 311 loop : -0.61 (0.18), residues: 1148 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG 7 62 TYR 0.015 0.001 TYR 7 581 PHE 0.007 0.001 PHE 4 50 TRP 0.024 0.001 TRP 2 96 HIS 0.013 0.001 HIS 4 258 Details of bonding type rmsd/Z covalent geometry : bond 0.00303 / 0.20 (24242) covalent geometry : angle 0.51154 / 0.32 (33001) hydrogen bonds : bond 0.24945 / 16.70 ( 1110) hydrogen bonds : angle 7.26933 / 5.24 ( 3200) metal coordination : bond 0.14592 / 8.50 ( 32) metal coordination : angle 5.47538 / 3.51 ( 48) Misc. bond : bond 0.46374 / 24.41 ( 1) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5504 Ramachandran restraints generated. 2752 Oldfield, 0 Emsley, 2752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5504 Ramachandran restraints generated. 2752 Oldfield, 0 Emsley, 2752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 689 residues out of total 2487 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 689 time to evaluate : 0.717 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 0 365 VAL cc_start: 0.7821 (p) cc_final: 0.7495 (t) REVERT: 0 438 MET cc_start: 0.6887 (ptp) cc_final: 0.5184 (ttm) REVERT: 1 499 ARG cc_start: 0.6071 (mtt180) cc_final: 0.5123 (mtt180) REVERT: 1 534 ASN cc_start: 0.6570 (m110) cc_final: 0.6307 (t0) REVERT: 1 545 MET cc_start: 0.4405 (ttt) cc_final: 0.3833 (ptt) REVERT: 2 85 GLU cc_start: 0.7152 (pp20) cc_final: 0.6900 (mt-10) REVERT: 2 109 ILE cc_start: 0.8822 (tt) cc_final: 0.8476 (tp) REVERT: 2 225 SER cc_start: 0.8787 (m) cc_final: 0.8286 (t) REVERT: 2 310 GLU cc_start: 0.7724 (mm-30) cc_final: 0.7495 (mm-30) REVERT: 2 318 TYR cc_start: 0.7498 (m-10) cc_final: 0.7292 (m-10) REVERT: 2 322 GLU cc_start: 0.7833 (tp30) cc_final: 0.7560 (tm-30) REVERT: 4 56 LYS cc_start: 0.7698 (mmtp) cc_final: 0.7469 (ttmm) REVERT: 4 277 ASN cc_start: 0.5202 (t0) cc_final: 0.4886 (m-40) REVERT: 6 233 THR cc_start: 0.8713 (m) cc_final: 0.8485 (p) REVERT: 6 236 VAL cc_start: 0.8724 (t) cc_final: 0.8438 (t) REVERT: 7 289 TYR cc_start: 0.5305 (m-80) cc_final: 0.5018 (m-80) REVERT: 7 421 TRP cc_start: 0.6963 (t60) cc_final: 0.6705 (t60) REVERT: 7 488 LEU cc_start: 0.8187 (mt) cc_final: 0.7793 (mm) REVERT: 7 541 PHE cc_start: 0.5946 (t80) cc_final: 0.4892 (t80) REVERT: 7 634 ARG cc_start: 0.8482 (ttp80) cc_final: 0.8106 (ttp80) outliers start: 0 outliers final: 0 residues processed: 689 average time/residue: 0.1635 time to fit residues: 171.8700 Evaluate side-chains 418 residues out of total 2487 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 418 time to evaluate : 0.896 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 280 random chunks: chunk 197 optimal weight: 0.9980 chunk 215 optimal weight: 0.0970 chunk 20 optimal weight: 2.9990 chunk 132 optimal weight: 6.9990 chunk 261 optimal weight: 2.9990 chunk 248 optimal weight: 4.9990 chunk 207 optimal weight: 0.9990 chunk 155 optimal weight: 0.0870 chunk 244 optimal weight: 3.9990 chunk 183 optimal weight: 0.9980 chunk 111 optimal weight: 1.9990 overall best weight: 0.6358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 0 328 HIS 0 384 HIS 0 402 ASN 0 555 GLN 0 649 ASN ** 2 37 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 117 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 2 211 GLN 2 224 GLN ** 2 363 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 2 390 GLN 3 24 ASN 4 63 HIS ** 4 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 145 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 4 176 ASN 4 205 GLN ** 4 258 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 5 63 GLN 7 459 GLN 7 481 ASN 7 497 GLN 7 564 ASN 7 595 ASN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4440 r_free = 0.4440 target = 0.174650 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4146 r_free = 0.4146 target = 0.151160 restraints weight = 44516.115| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.4180 r_free = 0.4180 target = 0.154685 restraints weight = 87965.948| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4176 r_free = 0.4176 target = 0.154432 restraints weight = 41374.725| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.4182 r_free = 0.4182 target = 0.155023 restraints weight = 33339.542| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.4184 r_free = 0.4184 target = 0.155290 restraints weight = 27795.721| |-----------------------------------------------------------------------------| r_work (final): 0.4187 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6508 moved from start: 0.2701 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.084 24275 Z= 0.205 Angle : 0.804 21.008 33049 Z= 0.396 Chirality : 0.046 0.293 3724 Planarity : 0.006 0.083 4029 Dihedral : 12.681 100.806 3602 Min Nonbonded Distance : 1.973 Molprobity Statistics. All-atom Clashscore : 10.72 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.51 % Favored : 95.46 % Rotamer: Outliers : 2.33 % Allowed : 11.90 % Favored : 85.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.64 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.07 (0.16), residues: 2752 helix: 1.11 (0.14), residues: 1371 sheet: -1.36 (0.32), residues: 284 loop : -0.86 (0.19), residues: 1097 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG 3 93 TYR 0.034 0.002 TYR 0 410 PHE 0.025 0.002 PHE 1 307 TRP 0.031 0.002 TRP 2 96 HIS 0.013 0.002 HIS 7 187 Details of bonding type rmsd/Z covalent geometry : bond 0.00459 / 0.20 (24242) covalent geometry : angle 0.74820 / 0.39 (33001) hydrogen bonds : bond 0.06641 / 4.42 ( 1110) hydrogen bonds : angle 5.54794 / 4.02 ( 3200) metal coordination : bond 0.01598 / 0.93 ( 32) metal coordination : angle 7.76495 / 4.90 ( 48) Misc. bond : bond 0.00547 / 0.29 ( 1) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5504 Ramachandran restraints generated. 2752 Oldfield, 0 Emsley, 2752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5504 Ramachandran restraints generated. 2752 Oldfield, 0 Emsley, 2752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 515 residues out of total 2487 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 457 time to evaluate : 0.937 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 0 75 ARG cc_start: 0.8221 (OUTLIER) cc_final: 0.7993 (ttm110) REVERT: 0 87 LEU cc_start: 0.7679 (tt) cc_final: 0.7265 (tp) REVERT: 0 410 TYR cc_start: 0.5678 (OUTLIER) cc_final: 0.5388 (p90) REVERT: 0 545 MET cc_start: 0.8009 (ttp) cc_final: 0.7731 (tmm) REVERT: 1 309 HIS cc_start: 0.6378 (m170) cc_final: 0.5909 (m90) REVERT: 1 499 ARG cc_start: 0.6433 (mtt180) cc_final: 0.5281 (mtt180) REVERT: 1 534 ASN cc_start: 0.6805 (m110) cc_final: 0.6513 (t0) REVERT: 2 109 ILE cc_start: 0.8944 (tt) cc_final: 0.8485 (tp) REVERT: 2 156 TRP cc_start: 0.8619 (t-100) cc_final: 0.8388 (t-100) REVERT: 2 318 TYR cc_start: 0.7708 (m-10) cc_final: 0.7348 (m-10) REVERT: 4 56 LYS cc_start: 0.7612 (mmtp) cc_final: 0.7305 (ttmm) REVERT: 6 349 GLN cc_start: 0.7878 (mm110) cc_final: 0.6489 (tm-30) REVERT: 7 103 ILE cc_start: 0.7823 (pt) cc_final: 0.7120 (tp) REVERT: 7 341 PRO cc_start: 0.9054 (Cg_exo) cc_final: 0.8777 (Cg_endo) REVERT: 7 348 LEU cc_start: 0.8097 (OUTLIER) cc_final: 0.7734 (mt) REVERT: 7 488 LEU cc_start: 0.8196 (mt) cc_final: 0.7847 (mm) REVERT: 7 636 GLU cc_start: 0.8703 (tp30) cc_final: 0.8178 (tp30) outliers start: 58 outliers final: 32 residues processed: 484 average time/residue: 0.1460 time to fit residues: 112.9396 Evaluate side-chains 385 residues out of total 2487 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 350 time to evaluate : 0.867 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 75 ARG Chi-restraints excluded: chain 0 residue 242 VAL Chi-restraints excluded: chain 0 residue 309 VAL Chi-restraints excluded: chain 0 residue 330 LEU Chi-restraints excluded: chain 0 residue 361 LEU Chi-restraints excluded: chain 0 residue 410 TYR Chi-restraints excluded: chain 0 residue 471 LEU Chi-restraints excluded: chain 0 residue 483 MET Chi-restraints excluded: chain 0 residue 490 LEU Chi-restraints excluded: chain 0 residue 526 GLU Chi-restraints excluded: chain 0 residue 547 SER Chi-restraints excluded: chain 0 residue 604 VAL Chi-restraints excluded: chain 0 residue 619 ILE Chi-restraints excluded: chain 0 residue 678 VAL Chi-restraints excluded: chain 2 residue 19 LEU Chi-restraints excluded: chain 2 residue 68 GLN Chi-restraints excluded: chain 2 residue 89 LEU Chi-restraints excluded: chain 2 residue 198 SER Chi-restraints excluded: chain 2 residue 260 ASN Chi-restraints excluded: chain 3 residue 67 THR Chi-restraints excluded: chain 3 residue 109 LEU Chi-restraints excluded: chain 4 residue 57 LEU Chi-restraints excluded: chain 4 residue 257 CYS Chi-restraints excluded: chain 5 residue 5 LEU Chi-restraints excluded: chain 5 residue 57 VAL Chi-restraints excluded: chain 6 residue 258 THR Chi-restraints excluded: chain 6 residue 336 LEU Chi-restraints excluded: chain 7 residue 72 THR Chi-restraints excluded: chain 7 residue 119 THR Chi-restraints excluded: chain 7 residue 189 LEU Chi-restraints excluded: chain 7 residue 272 VAL Chi-restraints excluded: chain 7 residue 348 LEU Chi-restraints excluded: chain 7 residue 361 CYS Chi-restraints excluded: chain 7 residue 417 THR Chi-restraints excluded: chain 7 residue 666 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 280 random chunks: chunk 270 optimal weight: 0.3980 chunk 80 optimal weight: 9.9990 chunk 143 optimal weight: 0.9990 chunk 173 optimal weight: 0.7980 chunk 93 optimal weight: 0.9990 chunk 6 optimal weight: 0.7980 chunk 24 optimal weight: 0.6980 chunk 82 optimal weight: 0.2980 chunk 180 optimal weight: 0.2980 chunk 100 optimal weight: 0.8980 chunk 9 optimal weight: 2.9990 overall best weight: 0.4980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 1 530 GLN 1 534 ASN 2 68 GLN 2 117 ASN 2 289 ASN 2 424 HIS ** 3 28 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 3 144 GLN ** 4 145 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 4 205 GLN ** 6 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 376 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 7 459 GLN 7 481 ASN 7 656 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4433 r_free = 0.4433 target = 0.174203 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.4164 r_free = 0.4164 target = 0.152574 restraints weight = 44745.872| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.4191 r_free = 0.4191 target = 0.155693 restraints weight = 87240.756| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4181 r_free = 0.4181 target = 0.154901 restraints weight = 40831.665| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.4188 r_free = 0.4188 target = 0.155602 restraints weight = 34616.042| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.4189 r_free = 0.4189 target = 0.155694 restraints weight = 27821.730| |-----------------------------------------------------------------------------| r_work (final): 0.4193 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6484 moved from start: 0.3285 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.072 24275 Z= 0.169 Angle : 0.737 26.916 33049 Z= 0.353 Chirality : 0.043 0.249 3724 Planarity : 0.005 0.072 4029 Dihedral : 12.873 89.045 3602 Min Nonbonded Distance : 1.957 Molprobity Statistics. All-atom Clashscore : 10.66 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.25 % Favored : 95.71 % Rotamer: Outliers : 2.81 % Allowed : 15.20 % Favored : 81.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.64 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.30 (0.16), residues: 2752 helix: 0.79 (0.14), residues: 1388 sheet: -1.61 (0.31), residues: 279 loop : -1.01 (0.19), residues: 1085 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG 3 93 TYR 0.032 0.002 TYR 0 410 PHE 0.025 0.002 PHE 2 261 TRP 0.027 0.002 TRP 2 96 HIS 0.022 0.002 HIS 2 424 Details of bonding type rmsd/Z covalent geometry : bond 0.00366 / 0.17 (24242) covalent geometry : angle 0.67737 / 0.35 (33001) hydrogen bonds : bond 0.05301 / 3.49 ( 1110) hydrogen bonds : angle 5.12562 / 3.71 ( 3200) metal coordination : bond 0.01039 / 0.57 ( 32) metal coordination : angle 7.65260 / 4.53 ( 48) Misc. bond : bond 0.00184 / 0.10 ( 1) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5504 Ramachandran restraints generated. 2752 Oldfield, 0 Emsley, 2752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5504 Ramachandran restraints generated. 2752 Oldfield, 0 Emsley, 2752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 477 residues out of total 2487 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 407 time to evaluate : 0.755 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 0 545 MET cc_start: 0.7951 (ttp) cc_final: 0.7707 (tmm) REVERT: 1 309 HIS cc_start: 0.6467 (m170) cc_final: 0.6045 (m90) REVERT: 1 499 ARG cc_start: 0.6188 (mtt180) cc_final: 0.5133 (mtt180) REVERT: 2 109 ILE cc_start: 0.8946 (tt) cc_final: 0.8500 (tp) REVERT: 2 310 GLU cc_start: 0.7409 (mm-30) cc_final: 0.6176 (mt-10) REVERT: 4 56 LYS cc_start: 0.7553 (mmtp) cc_final: 0.7175 (ttmm) REVERT: 5 26 SER cc_start: 0.7929 (m) cc_final: 0.7533 (t) REVERT: 5 46 ILE cc_start: 0.5311 (pt) cc_final: 0.5011 (pt) REVERT: 6 184 ASP cc_start: 0.6836 (p0) cc_final: 0.6553 (p0) REVERT: 6 185 LEU cc_start: 0.7711 (tp) cc_final: 0.7509 (tp) REVERT: 6 236 VAL cc_start: 0.8761 (OUTLIER) cc_final: 0.8330 (t) REVERT: 7 103 ILE cc_start: 0.7903 (pt) cc_final: 0.7270 (tp) REVERT: 7 341 PRO cc_start: 0.8999 (Cg_exo) cc_final: 0.8723 (Cg_endo) REVERT: 7 488 LEU cc_start: 0.8108 (mt) cc_final: 0.7822 (mm) REVERT: 7 636 GLU cc_start: 0.8671 (tp30) cc_final: 0.8065 (tp30) REVERT: 7 650 MET cc_start: 0.2628 (ptm) cc_final: 0.2090 (mtm) outliers start: 70 outliers final: 45 residues processed: 445 average time/residue: 0.1443 time to fit residues: 103.2483 Evaluate side-chains 396 residues out of total 2487 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 350 time to evaluate : 0.806 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 81 GLU Chi-restraints excluded: chain 0 residue 83 VAL Chi-restraints excluded: chain 0 residue 309 VAL Chi-restraints excluded: chain 0 residue 359 SER Chi-restraints excluded: chain 0 residue 361 LEU Chi-restraints excluded: chain 0 residue 438 MET Chi-restraints excluded: chain 0 residue 454 VAL Chi-restraints excluded: chain 0 residue 471 LEU Chi-restraints excluded: chain 0 residue 472 ASP Chi-restraints excluded: chain 0 residue 483 MET Chi-restraints excluded: chain 0 residue 490 LEU Chi-restraints excluded: chain 0 residue 526 GLU Chi-restraints excluded: chain 0 residue 604 VAL Chi-restraints excluded: chain 0 residue 626 VAL Chi-restraints excluded: chain 0 residue 678 VAL Chi-restraints excluded: chain 2 residue 19 LEU Chi-restraints excluded: chain 2 residue 50 SER Chi-restraints excluded: chain 2 residue 89 LEU Chi-restraints excluded: chain 2 residue 158 VAL Chi-restraints excluded: chain 2 residue 260 ASN Chi-restraints excluded: chain 3 residue 1 MET Chi-restraints excluded: chain 3 residue 67 THR Chi-restraints excluded: chain 3 residue 109 LEU Chi-restraints excluded: chain 3 residue 144 GLN Chi-restraints excluded: chain 4 residue 35 SER Chi-restraints excluded: chain 4 residue 57 LEU Chi-restraints excluded: chain 4 residue 63 HIS Chi-restraints excluded: chain 4 residue 272 LEU Chi-restraints excluded: chain 5 residue 68 LEU Chi-restraints excluded: chain 6 residue 84 THR Chi-restraints excluded: chain 6 residue 85 LEU Chi-restraints excluded: chain 6 residue 174 LEU Chi-restraints excluded: chain 6 residue 182 ILE Chi-restraints excluded: chain 6 residue 218 THR Chi-restraints excluded: chain 6 residue 221 VAL Chi-restraints excluded: chain 6 residue 236 VAL Chi-restraints excluded: chain 6 residue 258 THR Chi-restraints excluded: chain 6 residue 312 LEU Chi-restraints excluded: chain 6 residue 318 LEU Chi-restraints excluded: chain 6 residue 336 LEU Chi-restraints excluded: chain 7 residue 119 THR Chi-restraints excluded: chain 7 residue 189 LEU Chi-restraints excluded: chain 7 residue 361 CYS Chi-restraints excluded: chain 7 residue 548 ILE Chi-restraints excluded: chain 7 residue 666 ASP Chi-restraints excluded: chain 7 residue 667 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 280 random chunks: chunk 109 optimal weight: 0.8980 chunk 69 optimal weight: 0.0770 chunk 16 optimal weight: 4.9990 chunk 148 optimal weight: 0.2980 chunk 274 optimal weight: 10.0000 chunk 67 optimal weight: 5.9990 chunk 236 optimal weight: 1.9990 chunk 173 optimal weight: 0.5980 chunk 216 optimal weight: 0.8980 chunk 44 optimal weight: 4.9990 chunk 29 optimal weight: 10.0000 overall best weight: 0.5538 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 1 530 GLN ** 3 28 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 145 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 6 265 GLN ** 7 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 7 187 HIS 7 459 GLN 7 621 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4432 r_free = 0.4432 target = 0.174127 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.4192 r_free = 0.4192 target = 0.153830 restraints weight = 44848.785| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.4153 r_free = 0.4153 target = 0.151326 restraints weight = 62304.647| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.4127 r_free = 0.4127 target = 0.149389 restraints weight = 46525.233| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.4116 r_free = 0.4116 target = 0.148802 restraints weight = 48755.501| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.4112 r_free = 0.4112 target = 0.148586 restraints weight = 42440.801| |-----------------------------------------------------------------------------| r_work (final): 0.4112 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6672 moved from start: 0.3564 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 24275 Z= 0.162 Angle : 0.719 24.835 33049 Z= 0.344 Chirality : 0.043 0.311 3724 Planarity : 0.004 0.059 4029 Dihedral : 13.032 76.834 3602 Min Nonbonded Distance : 1.948 Molprobity Statistics. All-atom Clashscore : 11.49 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.47 % Favored : 95.49 % Rotamer: Outliers : 3.38 % Allowed : 16.28 % Favored : 80.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.64 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.40 (0.16), residues: 2752 helix: 0.69 (0.14), residues: 1390 sheet: -1.64 (0.33), residues: 255 loop : -1.08 (0.18), residues: 1107 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG 7 74 TYR 0.028 0.002 TYR 4 266 PHE 0.039 0.002 PHE 2 261 TRP 0.022 0.001 TRP 2 96 HIS 0.019 0.002 HIS 3 28 Details of bonding type rmsd/Z covalent geometry : bond 0.00359 / 0.16 (24242) covalent geometry : angle 0.66185 / 0.34 (33001) hydrogen bonds : bond 0.04781 / 3.16 ( 1110) hydrogen bonds : angle 4.98229 / 3.62 ( 3200) metal coordination : bond 0.01036 / 0.52 ( 32) metal coordination : angle 7.42997 / 4.34 ( 48) Misc. bond : bond 0.00154 / 0.08 ( 1) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5504 Ramachandran restraints generated. 2752 Oldfield, 0 Emsley, 2752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5504 Ramachandran restraints generated. 2752 Oldfield, 0 Emsley, 2752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 464 residues out of total 2487 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 380 time to evaluate : 0.918 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 1 309 HIS cc_start: 0.6503 (m170) cc_final: 0.6231 (m90) REVERT: 1 499 ARG cc_start: 0.6335 (mtt180) cc_final: 0.5206 (mtt180) REVERT: 1 545 MET cc_start: 0.1964 (ptt) cc_final: 0.0056 (tmm) REVERT: 2 109 ILE cc_start: 0.8952 (tt) cc_final: 0.8482 (tp) REVERT: 4 56 LYS cc_start: 0.7838 (mmtp) cc_final: 0.7505 (ttmm) REVERT: 4 261 LEU cc_start: 0.7546 (mp) cc_final: 0.7092 (tt) REVERT: 5 17 LYS cc_start: 0.6051 (tmtt) cc_final: 0.5841 (tmtt) REVERT: 6 184 ASP cc_start: 0.6846 (p0) cc_final: 0.6581 (p0) REVERT: 7 56 TYR cc_start: 0.7716 (OUTLIER) cc_final: 0.7394 (m-80) REVERT: 7 103 ILE cc_start: 0.7801 (pt) cc_final: 0.7226 (tp) REVERT: 7 341 PRO cc_start: 0.8927 (Cg_exo) cc_final: 0.8644 (Cg_endo) REVERT: 7 488 LEU cc_start: 0.8091 (mt) cc_final: 0.7761 (mm) REVERT: 7 586 GLN cc_start: 0.8007 (tp40) cc_final: 0.7242 (mp10) REVERT: 7 636 GLU cc_start: 0.8490 (tp30) cc_final: 0.8143 (tp30) outliers start: 84 outliers final: 48 residues processed: 428 average time/residue: 0.1401 time to fit residues: 96.8188 Evaluate side-chains 390 residues out of total 2487 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 341 time to evaluate : 0.844 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 83 VAL Chi-restraints excluded: chain 0 residue 309 VAL Chi-restraints excluded: chain 0 residue 361 LEU Chi-restraints excluded: chain 0 residue 367 ILE Chi-restraints excluded: chain 0 residue 454 VAL Chi-restraints excluded: chain 0 residue 471 LEU Chi-restraints excluded: chain 0 residue 483 MET Chi-restraints excluded: chain 0 residue 490 LEU Chi-restraints excluded: chain 0 residue 526 GLU Chi-restraints excluded: chain 0 residue 560 ASN Chi-restraints excluded: chain 0 residue 604 VAL Chi-restraints excluded: chain 0 residue 626 VAL Chi-restraints excluded: chain 0 residue 678 VAL Chi-restraints excluded: chain 0 residue 706 LEU Chi-restraints excluded: chain 1 residue 461 LEU Chi-restraints excluded: chain 2 residue 19 LEU Chi-restraints excluded: chain 2 residue 44 VAL Chi-restraints excluded: chain 2 residue 50 SER Chi-restraints excluded: chain 2 residue 51 LEU Chi-restraints excluded: chain 2 residue 89 LEU Chi-restraints excluded: chain 2 residue 158 VAL Chi-restraints excluded: chain 3 residue 1 MET Chi-restraints excluded: chain 4 residue 35 SER Chi-restraints excluded: chain 4 residue 50 PHE Chi-restraints excluded: chain 4 residue 57 LEU Chi-restraints excluded: chain 4 residue 63 HIS Chi-restraints excluded: chain 4 residue 176 ASN Chi-restraints excluded: chain 4 residue 272 LEU Chi-restraints excluded: chain 5 residue 68 LEU Chi-restraints excluded: chain 6 residue 84 THR Chi-restraints excluded: chain 6 residue 85 LEU Chi-restraints excluded: chain 6 residue 174 LEU Chi-restraints excluded: chain 6 residue 182 ILE Chi-restraints excluded: chain 6 residue 218 THR Chi-restraints excluded: chain 6 residue 221 VAL Chi-restraints excluded: chain 6 residue 258 THR Chi-restraints excluded: chain 6 residue 312 LEU Chi-restraints excluded: chain 6 residue 318 LEU Chi-restraints excluded: chain 6 residue 336 LEU Chi-restraints excluded: chain 7 residue 56 TYR Chi-restraints excluded: chain 7 residue 72 THR Chi-restraints excluded: chain 7 residue 119 THR Chi-restraints excluded: chain 7 residue 189 LEU Chi-restraints excluded: chain 7 residue 291 LEU Chi-restraints excluded: chain 7 residue 361 CYS Chi-restraints excluded: chain 7 residue 505 VAL Chi-restraints excluded: chain 7 residue 523 VAL Chi-restraints excluded: chain 7 residue 666 ASP Chi-restraints excluded: chain 7 residue 667 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 280 random chunks: chunk 53 optimal weight: 0.6980 chunk 65 optimal weight: 5.9990 chunk 233 optimal weight: 2.9990 chunk 258 optimal weight: 0.9980 chunk 259 optimal weight: 0.7980 chunk 163 optimal weight: 0.5980 chunk 13 optimal weight: 10.0000 chunk 228 optimal weight: 4.9990 chunk 230 optimal weight: 0.5980 chunk 57 optimal weight: 5.9990 chunk 185 optimal weight: 0.5980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 0 135 HIS ** 0 164 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 3 111 ASN ** 4 46 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 145 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 237 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 6 376 HIS 7 97 GLN 7 187 HIS 7 459 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4426 r_free = 0.4426 target = 0.173672 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4175 r_free = 0.4175 target = 0.152645 restraints weight = 44582.901| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.4136 r_free = 0.4136 target = 0.150190 restraints weight = 63483.713| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4126 r_free = 0.4126 target = 0.149434 restraints weight = 43738.823| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.4124 r_free = 0.4124 target = 0.149393 restraints weight = 40395.466| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.4120 r_free = 0.4120 target = 0.149116 restraints weight = 36543.522| |-----------------------------------------------------------------------------| r_work (final): 0.4116 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6661 moved from start: 0.3807 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.077 24275 Z= 0.165 Angle : 0.720 24.565 33049 Z= 0.339 Chirality : 0.043 0.265 3724 Planarity : 0.004 0.069 4029 Dihedral : 13.202 68.348 3602 Min Nonbonded Distance : 1.926 Molprobity Statistics. All-atom Clashscore : 12.75 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.65 % Favored : 95.31 % Rotamer: Outliers : 3.54 % Allowed : 17.77 % Favored : 78.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.64 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.47 (0.16), residues: 2752 helix: 0.65 (0.14), residues: 1388 sheet: -1.72 (0.32), residues: 253 loop : -1.11 (0.18), residues: 1111 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG 2 94 TYR 0.040 0.002 TYR 4 266 PHE 0.033 0.002 PHE 2 261 TRP 0.038 0.002 TRP 0 552 HIS 0.018 0.002 HIS 0 237 Details of bonding type rmsd/Z covalent geometry : bond 0.00367 / 0.16 (24242) covalent geometry : angle 0.65875 / 0.34 (33001) hydrogen bonds : bond 0.04532 / 3.00 ( 1110) hydrogen bonds : angle 4.92430 / 3.58 ( 3200) metal coordination : bond 0.01531 / 0.69 ( 32) metal coordination : angle 7.64594 / 4.34 ( 48) Misc. bond : bond 0.00247 / 0.13 ( 1) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5504 Ramachandran restraints generated. 2752 Oldfield, 0 Emsley, 2752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5504 Ramachandran restraints generated. 2752 Oldfield, 0 Emsley, 2752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 457 residues out of total 2487 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 369 time to evaluate : 0.899 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 1 499 ARG cc_start: 0.6079 (mtt180) cc_final: 0.5047 (mtt180) REVERT: 1 545 MET cc_start: 0.1899 (ptt) cc_final: 0.0252 (tmm) REVERT: 2 109 ILE cc_start: 0.8931 (tt) cc_final: 0.8452 (tp) REVERT: 2 393 LEU cc_start: 0.9205 (OUTLIER) cc_final: 0.8824 (mm) REVERT: 4 56 LYS cc_start: 0.7858 (mmtp) cc_final: 0.7549 (ttmm) REVERT: 4 261 LEU cc_start: 0.7772 (mp) cc_final: 0.7351 (tt) REVERT: 6 150 SER cc_start: 0.7642 (p) cc_final: 0.7248 (t) REVERT: 6 184 ASP cc_start: 0.6880 (p0) cc_final: 0.6551 (p0) REVERT: 7 97 GLN cc_start: 0.8358 (OUTLIER) cc_final: 0.7823 (tm-30) REVERT: 7 103 ILE cc_start: 0.7850 (pt) cc_final: 0.7334 (tp) REVERT: 7 341 PRO cc_start: 0.8952 (Cg_exo) cc_final: 0.8640 (Cg_endo) REVERT: 7 442 GLU cc_start: 0.7609 (mm-30) cc_final: 0.7223 (mp0) REVERT: 7 488 LEU cc_start: 0.8147 (mt) cc_final: 0.7855 (mm) REVERT: 7 494 MET cc_start: 0.7380 (mmm) cc_final: 0.6925 (mmm) REVERT: 7 586 GLN cc_start: 0.8132 (tp40) cc_final: 0.7652 (mp10) REVERT: 7 636 GLU cc_start: 0.8519 (tp30) cc_final: 0.8260 (tp30) outliers start: 88 outliers final: 52 residues processed: 427 average time/residue: 0.1355 time to fit residues: 93.6584 Evaluate side-chains 385 residues out of total 2487 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 331 time to evaluate : 0.676 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 83 VAL Chi-restraints excluded: chain 0 residue 237 HIS Chi-restraints excluded: chain 0 residue 309 VAL Chi-restraints excluded: chain 0 residue 361 LEU Chi-restraints excluded: chain 0 residue 438 MET Chi-restraints excluded: chain 0 residue 454 VAL Chi-restraints excluded: chain 0 residue 471 LEU Chi-restraints excluded: chain 0 residue 483 MET Chi-restraints excluded: chain 0 residue 490 LEU Chi-restraints excluded: chain 0 residue 560 ASN Chi-restraints excluded: chain 0 residue 604 VAL Chi-restraints excluded: chain 0 residue 678 VAL Chi-restraints excluded: chain 1 residue 461 LEU Chi-restraints excluded: chain 2 residue 19 LEU Chi-restraints excluded: chain 2 residue 44 VAL Chi-restraints excluded: chain 2 residue 50 SER Chi-restraints excluded: chain 2 residue 89 LEU Chi-restraints excluded: chain 2 residue 158 VAL Chi-restraints excluded: chain 2 residue 260 ASN Chi-restraints excluded: chain 2 residue 393 LEU Chi-restraints excluded: chain 3 residue 1 MET Chi-restraints excluded: chain 3 residue 34 CYS Chi-restraints excluded: chain 3 residue 35 VAL Chi-restraints excluded: chain 4 residue 35 SER Chi-restraints excluded: chain 4 residue 50 PHE Chi-restraints excluded: chain 4 residue 57 LEU Chi-restraints excluded: chain 4 residue 63 HIS Chi-restraints excluded: chain 4 residue 176 ASN Chi-restraints excluded: chain 4 residue 196 LEU Chi-restraints excluded: chain 4 residue 257 CYS Chi-restraints excluded: chain 4 residue 272 LEU Chi-restraints excluded: chain 6 residue 84 THR Chi-restraints excluded: chain 6 residue 85 LEU Chi-restraints excluded: chain 6 residue 174 LEU Chi-restraints excluded: chain 6 residue 182 ILE Chi-restraints excluded: chain 6 residue 218 THR Chi-restraints excluded: chain 6 residue 221 VAL Chi-restraints excluded: chain 6 residue 258 THR Chi-restraints excluded: chain 6 residue 284 LEU Chi-restraints excluded: chain 6 residue 318 LEU Chi-restraints excluded: chain 6 residue 336 LEU Chi-restraints excluded: chain 6 residue 366 VAL Chi-restraints excluded: chain 7 residue 72 THR Chi-restraints excluded: chain 7 residue 97 GLN Chi-restraints excluded: chain 7 residue 119 THR Chi-restraints excluded: chain 7 residue 189 LEU Chi-restraints excluded: chain 7 residue 361 CYS Chi-restraints excluded: chain 7 residue 385 ASP Chi-restraints excluded: chain 7 residue 505 VAL Chi-restraints excluded: chain 7 residue 523 VAL Chi-restraints excluded: chain 7 residue 548 ILE Chi-restraints excluded: chain 7 residue 666 ASP Chi-restraints excluded: chain 7 residue 667 THR Chi-restraints excluded: chain 7 residue 686 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 280 random chunks: chunk 166 optimal weight: 0.7980 chunk 213 optimal weight: 0.7980 chunk 195 optimal weight: 0.9990 chunk 118 optimal weight: 0.6980 chunk 153 optimal weight: 0.5980 chunk 204 optimal weight: 8.9990 chunk 24 optimal weight: 0.9980 chunk 196 optimal weight: 0.5980 chunk 125 optimal weight: 0.5980 chunk 269 optimal weight: 0.9980 chunk 1 optimal weight: 3.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 0 164 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 28 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 46 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 237 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 5 63 GLN ** 6 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 7 97 GLN 7 459 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4430 r_free = 0.4430 target = 0.174237 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4206 r_free = 0.4206 target = 0.155107 restraints weight = 44834.441| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.4159 r_free = 0.4159 target = 0.151966 restraints weight = 55552.131| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.4119 r_free = 0.4119 target = 0.148697 restraints weight = 49954.120| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.4114 r_free = 0.4114 target = 0.148799 restraints weight = 51760.706| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.4101 r_free = 0.4101 target = 0.147655 restraints weight = 43255.837| |-----------------------------------------------------------------------------| r_work (final): 0.4094 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6717 moved from start: 0.3999 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 24275 Z= 0.167 Angle : 0.743 24.193 33049 Z= 0.349 Chirality : 0.043 0.304 3724 Planarity : 0.004 0.063 4029 Dihedral : 13.344 68.693 3602 Min Nonbonded Distance : 1.929 Molprobity Statistics. All-atom Clashscore : 12.64 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.65 % Favored : 95.31 % Rotamer: Outliers : 3.34 % Allowed : 18.86 % Favored : 77.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.64 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.57 (0.16), residues: 2752 helix: 0.57 (0.14), residues: 1387 sheet: -1.68 (0.33), residues: 240 loop : -1.20 (0.18), residues: 1125 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG 2 33 TYR 0.032 0.002 TYR 4 266 PHE 0.034 0.002 PHE 2 261 TRP 0.040 0.002 TRP 0 552 HIS 0.017 0.001 HIS 0 237 Details of bonding type rmsd/Z covalent geometry : bond 0.00373 / 0.17 (24242) covalent geometry : angle 0.68383 / 0.35 (33001) hydrogen bonds : bond 0.04376 / 2.87 ( 1110) hydrogen bonds : angle 4.88269 / 3.55 ( 3200) metal coordination : bond 0.01859 / 1.18 ( 32) metal coordination : angle 7.68415 / 4.49 ( 48) Misc. bond : bond 0.00047 / 0.02 ( 1) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5504 Ramachandran restraints generated. 2752 Oldfield, 0 Emsley, 2752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5504 Ramachandran restraints generated. 2752 Oldfield, 0 Emsley, 2752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 442 residues out of total 2487 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 359 time to evaluate : 0.756 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 1 441 MET cc_start: 0.6911 (tpp) cc_final: 0.6699 (tpt) REVERT: 1 499 ARG cc_start: 0.6254 (mtt180) cc_final: 0.5133 (mtt180) REVERT: 1 545 MET cc_start: 0.2108 (ptt) cc_final: 0.0420 (tmm) REVERT: 2 109 ILE cc_start: 0.8899 (tt) cc_final: 0.8463 (tp) REVERT: 2 393 LEU cc_start: 0.9197 (OUTLIER) cc_final: 0.8845 (mm) REVERT: 4 56 LYS cc_start: 0.8011 (mmtp) cc_final: 0.7616 (ttmm) REVERT: 4 261 LEU cc_start: 0.7852 (mp) cc_final: 0.7400 (tt) REVERT: 6 150 SER cc_start: 0.7652 (p) cc_final: 0.7206 (t) REVERT: 7 93 TYR cc_start: 0.6863 (t80) cc_final: 0.5119 (p90) REVERT: 7 103 ILE cc_start: 0.7747 (pt) cc_final: 0.7178 (tp) REVERT: 7 341 PRO cc_start: 0.8880 (Cg_exo) cc_final: 0.8583 (Cg_endo) REVERT: 7 442 GLU cc_start: 0.7561 (mm-30) cc_final: 0.7184 (mp0) REVERT: 7 494 MET cc_start: 0.7242 (mmm) cc_final: 0.7019 (mmm) REVERT: 7 586 GLN cc_start: 0.8065 (tp40) cc_final: 0.7634 (mp10) REVERT: 7 636 GLU cc_start: 0.8711 (tp30) cc_final: 0.8491 (tp30) outliers start: 83 outliers final: 61 residues processed: 411 average time/residue: 0.1294 time to fit residues: 87.0385 Evaluate side-chains 395 residues out of total 2487 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 333 time to evaluate : 0.940 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 39 VAL Chi-restraints excluded: chain 0 residue 83 VAL Chi-restraints excluded: chain 0 residue 168 VAL Chi-restraints excluded: chain 0 residue 237 HIS Chi-restraints excluded: chain 0 residue 266 LEU Chi-restraints excluded: chain 0 residue 309 VAL Chi-restraints excluded: chain 0 residue 337 LEU Chi-restraints excluded: chain 0 residue 359 SER Chi-restraints excluded: chain 0 residue 361 LEU Chi-restraints excluded: chain 0 residue 454 VAL Chi-restraints excluded: chain 0 residue 471 LEU Chi-restraints excluded: chain 0 residue 483 MET Chi-restraints excluded: chain 0 residue 490 LEU Chi-restraints excluded: chain 0 residue 560 ASN Chi-restraints excluded: chain 0 residue 604 VAL Chi-restraints excluded: chain 0 residue 626 VAL Chi-restraints excluded: chain 0 residue 678 VAL Chi-restraints excluded: chain 1 residue 376 LEU Chi-restraints excluded: chain 1 residue 461 LEU Chi-restraints excluded: chain 2 residue 19 LEU Chi-restraints excluded: chain 2 residue 44 VAL Chi-restraints excluded: chain 2 residue 50 SER Chi-restraints excluded: chain 2 residue 84 GLU Chi-restraints excluded: chain 2 residue 89 LEU Chi-restraints excluded: chain 2 residue 158 VAL Chi-restraints excluded: chain 2 residue 260 ASN Chi-restraints excluded: chain 2 residue 341 MET Chi-restraints excluded: chain 2 residue 393 LEU Chi-restraints excluded: chain 3 residue 1 MET Chi-restraints excluded: chain 3 residue 34 CYS Chi-restraints excluded: chain 3 residue 81 ILE Chi-restraints excluded: chain 4 residue 35 SER Chi-restraints excluded: chain 4 residue 50 PHE Chi-restraints excluded: chain 4 residue 57 LEU Chi-restraints excluded: chain 4 residue 176 ASN Chi-restraints excluded: chain 4 residue 196 LEU Chi-restraints excluded: chain 4 residue 257 CYS Chi-restraints excluded: chain 4 residue 272 LEU Chi-restraints excluded: chain 5 residue 68 LEU Chi-restraints excluded: chain 6 residue 84 THR Chi-restraints excluded: chain 6 residue 85 LEU Chi-restraints excluded: chain 6 residue 87 LEU Chi-restraints excluded: chain 6 residue 174 LEU Chi-restraints excluded: chain 6 residue 182 ILE Chi-restraints excluded: chain 6 residue 218 THR Chi-restraints excluded: chain 6 residue 221 VAL Chi-restraints excluded: chain 6 residue 258 THR Chi-restraints excluded: chain 6 residue 284 LEU Chi-restraints excluded: chain 6 residue 318 LEU Chi-restraints excluded: chain 6 residue 336 LEU Chi-restraints excluded: chain 6 residue 357 VAL Chi-restraints excluded: chain 6 residue 366 VAL Chi-restraints excluded: chain 7 residue 72 THR Chi-restraints excluded: chain 7 residue 119 THR Chi-restraints excluded: chain 7 residue 189 LEU Chi-restraints excluded: chain 7 residue 361 CYS Chi-restraints excluded: chain 7 residue 385 ASP Chi-restraints excluded: chain 7 residue 505 VAL Chi-restraints excluded: chain 7 residue 523 VAL Chi-restraints excluded: chain 7 residue 666 ASP Chi-restraints excluded: chain 7 residue 667 THR Chi-restraints excluded: chain 7 residue 686 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 280 random chunks: chunk 38 optimal weight: 0.5980 chunk 0 optimal weight: 9.9990 chunk 23 optimal weight: 1.9990 chunk 68 optimal weight: 0.7980 chunk 173 optimal weight: 0.6980 chunk 266 optimal weight: 0.4980 chunk 31 optimal weight: 4.9990 chunk 36 optimal weight: 6.9990 chunk 106 optimal weight: 0.0020 chunk 208 optimal weight: 0.6980 chunk 90 optimal weight: 0.5980 overall best weight: 0.4788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 0 164 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0 237 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 28 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 3 144 GLN ** 4 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 237 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 6 364 GLN 7 459 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4437 r_free = 0.4437 target = 0.174946 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4195 r_free = 0.4195 target = 0.154486 restraints weight = 44715.607| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.4156 r_free = 0.4156 target = 0.151892 restraints weight = 66526.191| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.4141 r_free = 0.4141 target = 0.150963 restraints weight = 46109.271| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.4122 r_free = 0.4122 target = 0.149515 restraints weight = 50748.037| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.4120 r_free = 0.4120 target = 0.149462 restraints weight = 48038.119| |-----------------------------------------------------------------------------| r_work (final): 0.4113 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6678 moved from start: 0.4199 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 24275 Z= 0.149 Angle : 0.728 23.819 33049 Z= 0.341 Chirality : 0.043 0.343 3724 Planarity : 0.004 0.057 4029 Dihedral : 13.400 68.948 3602 Min Nonbonded Distance : 1.950 Molprobity Statistics. All-atom Clashscore : 12.13 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.54 % Favored : 95.42 % Rotamer: Outliers : 3.02 % Allowed : 19.70 % Favored : 77.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.64 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.50 (0.16), residues: 2752 helix: 0.65 (0.14), residues: 1387 sheet: -1.62 (0.33), residues: 242 loop : -1.21 (0.18), residues: 1123 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG 7 62 TYR 0.019 0.001 TYR 4 266 PHE 0.046 0.002 PHE 2 261 TRP 0.047 0.002 TRP 0 552 HIS 0.017 0.001 HIS 0 237 Details of bonding type rmsd/Z covalent geometry : bond 0.00332 / 0.15 (24242) covalent geometry : angle 0.67100 / 0.34 (33001) hydrogen bonds : bond 0.04155 / 2.72 ( 1110) hydrogen bonds : angle 4.75708 / 3.46 ( 3200) metal coordination : bond 0.01812 / 1.11 ( 32) metal coordination : angle 7.41305 / 4.24 ( 48) Misc. bond : bond 0.00006 / 0.00 ( 1) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5504 Ramachandran restraints generated. 2752 Oldfield, 0 Emsley, 2752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5504 Ramachandran restraints generated. 2752 Oldfield, 0 Emsley, 2752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 432 residues out of total 2487 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 357 time to evaluate : 0.718 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 0 1 MET cc_start: 0.3457 (mtp) cc_final: 0.3000 (mtm) REVERT: 0 709 THR cc_start: 0.7709 (OUTLIER) cc_final: 0.7382 (p) REVERT: 1 499 ARG cc_start: 0.6216 (mtt180) cc_final: 0.5092 (mtt180) REVERT: 1 545 MET cc_start: 0.1860 (ptt) cc_final: 0.0165 (tmm) REVERT: 2 109 ILE cc_start: 0.8855 (tt) cc_final: 0.8323 (tp) REVERT: 2 376 MET cc_start: 0.7923 (OUTLIER) cc_final: 0.7624 (mtp) REVERT: 2 393 LEU cc_start: 0.9180 (OUTLIER) cc_final: 0.8902 (mm) REVERT: 4 56 LYS cc_start: 0.8006 (mmtp) cc_final: 0.7574 (ttmm) REVERT: 4 261 LEU cc_start: 0.7797 (mp) cc_final: 0.7454 (tt) REVERT: 6 146 TYR cc_start: 0.7030 (t80) cc_final: 0.6794 (t80) REVERT: 6 150 SER cc_start: 0.7614 (p) cc_final: 0.7237 (t) REVERT: 7 103 ILE cc_start: 0.7764 (pt) cc_final: 0.7213 (tp) REVERT: 7 341 PRO cc_start: 0.8792 (Cg_exo) cc_final: 0.8491 (Cg_endo) REVERT: 7 442 GLU cc_start: 0.7546 (mm-30) cc_final: 0.7210 (mp0) REVERT: 7 494 MET cc_start: 0.7263 (mmm) cc_final: 0.6938 (mmm) REVERT: 7 586 GLN cc_start: 0.8039 (tp40) cc_final: 0.7701 (mp10) REVERT: 7 590 MET cc_start: 0.7459 (mtp) cc_final: 0.7065 (mtp) REVERT: 7 636 GLU cc_start: 0.8449 (tp30) cc_final: 0.8102 (tp30) outliers start: 75 outliers final: 58 residues processed: 407 average time/residue: 0.1341 time to fit residues: 88.7405 Evaluate side-chains 390 residues out of total 2487 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 329 time to evaluate : 0.801 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 39 VAL Chi-restraints excluded: chain 0 residue 83 VAL Chi-restraints excluded: chain 0 residue 92 ASN Chi-restraints excluded: chain 0 residue 168 VAL Chi-restraints excluded: chain 0 residue 237 HIS Chi-restraints excluded: chain 0 residue 266 LEU Chi-restraints excluded: chain 0 residue 309 VAL Chi-restraints excluded: chain 0 residue 333 LEU Chi-restraints excluded: chain 0 residue 337 LEU Chi-restraints excluded: chain 0 residue 359 SER Chi-restraints excluded: chain 0 residue 361 LEU Chi-restraints excluded: chain 0 residue 471 LEU Chi-restraints excluded: chain 0 residue 490 LEU Chi-restraints excluded: chain 0 residue 560 ASN Chi-restraints excluded: chain 0 residue 604 VAL Chi-restraints excluded: chain 0 residue 626 VAL Chi-restraints excluded: chain 0 residue 678 VAL Chi-restraints excluded: chain 0 residue 709 THR Chi-restraints excluded: chain 1 residue 376 LEU Chi-restraints excluded: chain 1 residue 461 LEU Chi-restraints excluded: chain 2 residue 19 LEU Chi-restraints excluded: chain 2 residue 23 LEU Chi-restraints excluded: chain 2 residue 44 VAL Chi-restraints excluded: chain 2 residue 50 SER Chi-restraints excluded: chain 2 residue 84 GLU Chi-restraints excluded: chain 2 residue 158 VAL Chi-restraints excluded: chain 2 residue 260 ASN Chi-restraints excluded: chain 2 residue 341 MET Chi-restraints excluded: chain 2 residue 376 MET Chi-restraints excluded: chain 2 residue 383 LEU Chi-restraints excluded: chain 2 residue 393 LEU Chi-restraints excluded: chain 3 residue 1 MET Chi-restraints excluded: chain 3 residue 35 VAL Chi-restraints excluded: chain 3 residue 81 ILE Chi-restraints excluded: chain 4 residue 35 SER Chi-restraints excluded: chain 4 residue 50 PHE Chi-restraints excluded: chain 4 residue 57 LEU Chi-restraints excluded: chain 4 residue 63 HIS Chi-restraints excluded: chain 4 residue 196 LEU Chi-restraints excluded: chain 4 residue 257 CYS Chi-restraints excluded: chain 4 residue 272 LEU Chi-restraints excluded: chain 5 residue 68 LEU Chi-restraints excluded: chain 6 residue 84 THR Chi-restraints excluded: chain 6 residue 87 LEU Chi-restraints excluded: chain 6 residue 174 LEU Chi-restraints excluded: chain 6 residue 182 ILE Chi-restraints excluded: chain 6 residue 214 GLU Chi-restraints excluded: chain 6 residue 218 THR Chi-restraints excluded: chain 6 residue 221 VAL Chi-restraints excluded: chain 6 residue 258 THR Chi-restraints excluded: chain 6 residue 284 LEU Chi-restraints excluded: chain 6 residue 318 LEU Chi-restraints excluded: chain 6 residue 336 LEU Chi-restraints excluded: chain 6 residue 357 VAL Chi-restraints excluded: chain 6 residue 366 VAL Chi-restraints excluded: chain 7 residue 119 THR Chi-restraints excluded: chain 7 residue 189 LEU Chi-restraints excluded: chain 7 residue 361 CYS Chi-restraints excluded: chain 7 residue 385 ASP Chi-restraints excluded: chain 7 residue 666 ASP Chi-restraints excluded: chain 7 residue 667 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 280 random chunks: chunk 205 optimal weight: 0.8980 chunk 196 optimal weight: 0.8980 chunk 260 optimal weight: 1.9990 chunk 176 optimal weight: 1.9990 chunk 208 optimal weight: 1.9990 chunk 141 optimal weight: 10.0000 chunk 237 optimal weight: 0.6980 chunk 7 optimal weight: 0.7980 chunk 74 optimal weight: 0.9990 chunk 103 optimal weight: 3.9990 chunk 36 optimal weight: 0.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 0 164 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0 237 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 0 262 ASN ** 3 28 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 55 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 237 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 5 54 GLN ** 6 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 6 265 GLN 7 187 HIS 7 459 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4416 r_free = 0.4416 target = 0.172717 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.4177 r_free = 0.4177 target = 0.152643 restraints weight = 44582.195| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.4139 r_free = 0.4139 target = 0.150221 restraints weight = 63588.783| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.4125 r_free = 0.4125 target = 0.149154 restraints weight = 43520.594| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.4117 r_free = 0.4117 target = 0.148620 restraints weight = 46272.225| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.4109 r_free = 0.4109 target = 0.148055 restraints weight = 42490.812| |-----------------------------------------------------------------------------| r_work (final): 0.4104 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6701 moved from start: 0.4351 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 24275 Z= 0.184 Angle : 0.764 24.246 33049 Z= 0.359 Chirality : 0.044 0.381 3724 Planarity : 0.004 0.060 4029 Dihedral : 13.525 69.101 3602 Min Nonbonded Distance : 1.887 Molprobity Statistics. All-atom Clashscore : 13.81 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.91 % Favored : 95.06 % Rotamer: Outliers : 3.30 % Allowed : 20.10 % Favored : 76.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.64 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.60 (0.16), residues: 2752 helix: 0.59 (0.14), residues: 1390 sheet: -1.76 (0.33), residues: 238 loop : -1.27 (0.18), residues: 1124 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG 7 62 TYR 0.032 0.002 TYR 7 289 PHE 0.039 0.002 PHE 2 261 TRP 0.051 0.002 TRP 0 552 HIS 0.024 0.002 HIS 7 187 Details of bonding type rmsd/Z covalent geometry : bond 0.00419 / 0.18 (24242) covalent geometry : angle 0.71227 / 0.36 (33001) hydrogen bonds : bond 0.04202 / 2.76 ( 1110) hydrogen bonds : angle 4.86631 / 3.55 ( 3200) metal coordination : bond 0.01529 / 0.94 ( 32) metal coordination : angle 7.30337 / 4.06 ( 48) Misc. bond : bond 0.00001 / 0.00 ( 1) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5504 Ramachandran restraints generated. 2752 Oldfield, 0 Emsley, 2752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5504 Ramachandran restraints generated. 2752 Oldfield, 0 Emsley, 2752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 438 residues out of total 2487 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 356 time to evaluate : 0.789 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 0 1 MET cc_start: 0.3422 (mtp) cc_final: 0.2930 (mtm) REVERT: 0 709 THR cc_start: 0.7735 (OUTLIER) cc_final: 0.7422 (p) REVERT: 1 499 ARG cc_start: 0.6074 (mtt180) cc_final: 0.5002 (mtt180) REVERT: 1 545 MET cc_start: 0.1745 (ptt) cc_final: 0.0163 (tmm) REVERT: 2 109 ILE cc_start: 0.8881 (tt) cc_final: 0.8385 (tp) REVERT: 2 376 MET cc_start: 0.8008 (OUTLIER) cc_final: 0.7647 (mtp) REVERT: 2 393 LEU cc_start: 0.9286 (OUTLIER) cc_final: 0.8948 (mm) REVERT: 4 56 LYS cc_start: 0.8083 (mmtp) cc_final: 0.7710 (ttmm) REVERT: 4 261 LEU cc_start: 0.7866 (mp) cc_final: 0.7523 (tt) REVERT: 6 150 SER cc_start: 0.7708 (p) cc_final: 0.7434 (t) REVERT: 7 103 ILE cc_start: 0.7778 (pt) cc_final: 0.7252 (tp) REVERT: 7 341 PRO cc_start: 0.8796 (Cg_exo) cc_final: 0.8459 (Cg_endo) REVERT: 7 442 GLU cc_start: 0.7692 (mm-30) cc_final: 0.7347 (mp0) REVERT: 7 494 MET cc_start: 0.7335 (mmm) cc_final: 0.7052 (mmm) REVERT: 7 586 GLN cc_start: 0.8025 (tp40) cc_final: 0.7653 (mp10) REVERT: 7 590 MET cc_start: 0.7460 (mtp) cc_final: 0.7131 (mtp) REVERT: 7 634 ARG cc_start: 0.8695 (ttp80) cc_final: 0.8323 (ttp80) REVERT: 7 636 GLU cc_start: 0.8587 (tp30) cc_final: 0.8242 (tp30) outliers start: 82 outliers final: 63 residues processed: 410 average time/residue: 0.1321 time to fit residues: 88.1506 Evaluate side-chains 401 residues out of total 2487 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 335 time to evaluate : 0.629 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 25 MET Chi-restraints excluded: chain 0 residue 39 VAL Chi-restraints excluded: chain 0 residue 83 VAL Chi-restraints excluded: chain 0 residue 92 ASN Chi-restraints excluded: chain 0 residue 168 VAL Chi-restraints excluded: chain 0 residue 237 HIS Chi-restraints excluded: chain 0 residue 266 LEU Chi-restraints excluded: chain 0 residue 309 VAL Chi-restraints excluded: chain 0 residue 333 LEU Chi-restraints excluded: chain 0 residue 359 SER Chi-restraints excluded: chain 0 residue 454 VAL Chi-restraints excluded: chain 0 residue 471 LEU Chi-restraints excluded: chain 0 residue 490 LEU Chi-restraints excluded: chain 0 residue 560 ASN Chi-restraints excluded: chain 0 residue 604 VAL Chi-restraints excluded: chain 0 residue 626 VAL Chi-restraints excluded: chain 0 residue 678 VAL Chi-restraints excluded: chain 0 residue 709 THR Chi-restraints excluded: chain 1 residue 376 LEU Chi-restraints excluded: chain 1 residue 457 ILE Chi-restraints excluded: chain 1 residue 461 LEU Chi-restraints excluded: chain 2 residue 19 LEU Chi-restraints excluded: chain 2 residue 44 VAL Chi-restraints excluded: chain 2 residue 50 SER Chi-restraints excluded: chain 2 residue 84 GLU Chi-restraints excluded: chain 2 residue 158 VAL Chi-restraints excluded: chain 2 residue 260 ASN Chi-restraints excluded: chain 2 residue 341 MET Chi-restraints excluded: chain 2 residue 376 MET Chi-restraints excluded: chain 2 residue 383 LEU Chi-restraints excluded: chain 2 residue 393 LEU Chi-restraints excluded: chain 3 residue 1 MET Chi-restraints excluded: chain 3 residue 34 CYS Chi-restraints excluded: chain 3 residue 35 VAL Chi-restraints excluded: chain 3 residue 81 ILE Chi-restraints excluded: chain 4 residue 50 PHE Chi-restraints excluded: chain 4 residue 57 LEU Chi-restraints excluded: chain 4 residue 176 ASN Chi-restraints excluded: chain 4 residue 196 LEU Chi-restraints excluded: chain 4 residue 223 LEU Chi-restraints excluded: chain 4 residue 257 CYS Chi-restraints excluded: chain 4 residue 272 LEU Chi-restraints excluded: chain 5 residue 5 LEU Chi-restraints excluded: chain 5 residue 68 LEU Chi-restraints excluded: chain 6 residue 84 THR Chi-restraints excluded: chain 6 residue 87 LEU Chi-restraints excluded: chain 6 residue 174 LEU Chi-restraints excluded: chain 6 residue 182 ILE Chi-restraints excluded: chain 6 residue 214 GLU Chi-restraints excluded: chain 6 residue 218 THR Chi-restraints excluded: chain 6 residue 221 VAL Chi-restraints excluded: chain 6 residue 250 ILE Chi-restraints excluded: chain 6 residue 258 THR Chi-restraints excluded: chain 6 residue 284 LEU Chi-restraints excluded: chain 6 residue 318 LEU Chi-restraints excluded: chain 6 residue 336 LEU Chi-restraints excluded: chain 6 residue 357 VAL Chi-restraints excluded: chain 6 residue 366 VAL Chi-restraints excluded: chain 7 residue 119 THR Chi-restraints excluded: chain 7 residue 189 LEU Chi-restraints excluded: chain 7 residue 267 THR Chi-restraints excluded: chain 7 residue 361 CYS Chi-restraints excluded: chain 7 residue 385 ASP Chi-restraints excluded: chain 7 residue 666 ASP Chi-restraints excluded: chain 7 residue 667 THR Chi-restraints excluded: chain 7 residue 686 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 280 random chunks: chunk 198 optimal weight: 2.9990 chunk 188 optimal weight: 0.2980 chunk 138 optimal weight: 5.9990 chunk 147 optimal weight: 0.9980 chunk 83 optimal weight: 0.9980 chunk 21 optimal weight: 0.2980 chunk 223 optimal weight: 0.6980 chunk 14 optimal weight: 5.9990 chunk 192 optimal weight: 0.2980 chunk 28 optimal weight: 4.9990 chunk 229 optimal weight: 7.9990 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 0 164 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0 237 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 28 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 48 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 4 179 ASN ** 4 237 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 5 64 ASN ** 6 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4429 r_free = 0.4429 target = 0.174291 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4186 r_free = 0.4186 target = 0.153805 restraints weight = 44717.772| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.4142 r_free = 0.4142 target = 0.150924 restraints weight = 66911.949| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.4125 r_free = 0.4125 target = 0.149775 restraints weight = 49419.825| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.4103 r_free = 0.4103 target = 0.148223 restraints weight = 52137.985| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.4095 r_free = 0.4095 target = 0.147587 restraints weight = 49418.028| |-----------------------------------------------------------------------------| r_work (final): 0.4089 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6728 moved from start: 0.4497 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 24275 Z= 0.155 Angle : 0.757 24.083 33049 Z= 0.354 Chirality : 0.044 0.404 3724 Planarity : 0.004 0.060 4029 Dihedral : 13.519 69.169 3602 Min Nonbonded Distance : 1.961 Molprobity Statistics. All-atom Clashscore : 13.13 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.58 % Favored : 95.39 % Rotamer: Outliers : 3.30 % Allowed : 20.47 % Favored : 76.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.64 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.60 (0.16), residues: 2752 helix: 0.55 (0.14), residues: 1387 sheet: -1.71 (0.33), residues: 242 loop : -1.22 (0.18), residues: 1123 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG 7 283 TYR 0.026 0.002 TYR 6 146 PHE 0.045 0.002 PHE 2 261 TRP 0.056 0.002 TRP 0 552 HIS 0.013 0.001 HIS 0 237 Details of bonding type rmsd/Z covalent geometry : bond 0.00351 / 0.15 (24242) covalent geometry : angle 0.70456 / 0.35 (33001) hydrogen bonds : bond 0.03993 / 2.63 ( 1110) hydrogen bonds : angle 4.81652 / 3.51 ( 3200) metal coordination : bond 0.01582 / 0.98 ( 32) metal coordination : angle 7.32888 / 4.08 ( 48) Misc. bond : bond 0.00015 / 0.01 ( 1) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5504 Ramachandran restraints generated. 2752 Oldfield, 0 Emsley, 2752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5504 Ramachandran restraints generated. 2752 Oldfield, 0 Emsley, 2752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 426 residues out of total 2487 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 344 time to evaluate : 0.786 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 0 1 MET cc_start: 0.3326 (mtp) cc_final: 0.2657 (mtp) REVERT: 0 42 MET cc_start: 0.7994 (ppp) cc_final: 0.7724 (ppp) REVERT: 0 709 THR cc_start: 0.7812 (OUTLIER) cc_final: 0.7469 (p) REVERT: 1 499 ARG cc_start: 0.6063 (mtt180) cc_final: 0.5025 (mtt180) REVERT: 1 545 MET cc_start: 0.1847 (ptt) cc_final: 0.0265 (tmm) REVERT: 2 109 ILE cc_start: 0.8862 (tt) cc_final: 0.8338 (tp) REVERT: 2 376 MET cc_start: 0.7961 (OUTLIER) cc_final: 0.7643 (mtp) REVERT: 2 393 LEU cc_start: 0.9181 (OUTLIER) cc_final: 0.8830 (mm) REVERT: 4 56 LYS cc_start: 0.8034 (mmtp) cc_final: 0.7291 (ttmt) REVERT: 4 261 LEU cc_start: 0.7811 (mp) cc_final: 0.7493 (tt) REVERT: 5 18 GLN cc_start: 0.7617 (mm-40) cc_final: 0.7128 (mp10) REVERT: 6 150 SER cc_start: 0.7694 (p) cc_final: 0.7332 (t) REVERT: 6 215 THR cc_start: 0.8479 (OUTLIER) cc_final: 0.8150 (m) REVERT: 7 103 ILE cc_start: 0.7762 (pt) cc_final: 0.7285 (tp) REVERT: 7 341 PRO cc_start: 0.8743 (Cg_exo) cc_final: 0.8477 (Cg_endo) REVERT: 7 442 GLU cc_start: 0.7698 (mm-30) cc_final: 0.7358 (mp0) REVERT: 7 494 MET cc_start: 0.7273 (mmm) cc_final: 0.6864 (mmm) REVERT: 7 586 GLN cc_start: 0.8003 (tp40) cc_final: 0.7685 (mp10) REVERT: 7 590 MET cc_start: 0.7389 (mtp) cc_final: 0.7056 (mtp) REVERT: 7 636 GLU cc_start: 0.8459 (tp30) cc_final: 0.8175 (tp30) outliers start: 82 outliers final: 66 residues processed: 399 average time/residue: 0.1269 time to fit residues: 82.6872 Evaluate side-chains 402 residues out of total 2487 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 332 time to evaluate : 0.767 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 25 MET Chi-restraints excluded: chain 0 residue 39 VAL Chi-restraints excluded: chain 0 residue 83 VAL Chi-restraints excluded: chain 0 residue 92 ASN Chi-restraints excluded: chain 0 residue 168 VAL Chi-restraints excluded: chain 0 residue 237 HIS Chi-restraints excluded: chain 0 residue 266 LEU Chi-restraints excluded: chain 0 residue 309 VAL Chi-restraints excluded: chain 0 residue 314 VAL Chi-restraints excluded: chain 0 residue 315 LEU Chi-restraints excluded: chain 0 residue 333 LEU Chi-restraints excluded: chain 0 residue 359 SER Chi-restraints excluded: chain 0 residue 454 VAL Chi-restraints excluded: chain 0 residue 471 LEU Chi-restraints excluded: chain 0 residue 490 LEU Chi-restraints excluded: chain 0 residue 522 ASN Chi-restraints excluded: chain 0 residue 560 ASN Chi-restraints excluded: chain 0 residue 604 VAL Chi-restraints excluded: chain 0 residue 626 VAL Chi-restraints excluded: chain 0 residue 678 VAL Chi-restraints excluded: chain 0 residue 709 THR Chi-restraints excluded: chain 1 residue 376 LEU Chi-restraints excluded: chain 1 residue 457 ILE Chi-restraints excluded: chain 1 residue 461 LEU Chi-restraints excluded: chain 2 residue 19 LEU Chi-restraints excluded: chain 2 residue 44 VAL Chi-restraints excluded: chain 2 residue 50 SER Chi-restraints excluded: chain 2 residue 84 GLU Chi-restraints excluded: chain 2 residue 158 VAL Chi-restraints excluded: chain 2 residue 260 ASN Chi-restraints excluded: chain 2 residue 341 MET Chi-restraints excluded: chain 2 residue 359 ILE Chi-restraints excluded: chain 2 residue 376 MET Chi-restraints excluded: chain 2 residue 383 LEU Chi-restraints excluded: chain 2 residue 393 LEU Chi-restraints excluded: chain 2 residue 440 LEU Chi-restraints excluded: chain 3 residue 1 MET Chi-restraints excluded: chain 3 residue 34 CYS Chi-restraints excluded: chain 3 residue 35 VAL Chi-restraints excluded: chain 3 residue 81 ILE Chi-restraints excluded: chain 4 residue 20 ILE Chi-restraints excluded: chain 4 residue 50 PHE Chi-restraints excluded: chain 4 residue 57 LEU Chi-restraints excluded: chain 4 residue 176 ASN Chi-restraints excluded: chain 4 residue 196 LEU Chi-restraints excluded: chain 4 residue 223 LEU Chi-restraints excluded: chain 4 residue 257 CYS Chi-restraints excluded: chain 4 residue 272 LEU Chi-restraints excluded: chain 5 residue 68 LEU Chi-restraints excluded: chain 6 residue 84 THR Chi-restraints excluded: chain 6 residue 87 LEU Chi-restraints excluded: chain 6 residue 174 LEU Chi-restraints excluded: chain 6 residue 215 THR Chi-restraints excluded: chain 6 residue 218 THR Chi-restraints excluded: chain 6 residue 221 VAL Chi-restraints excluded: chain 6 residue 250 ILE Chi-restraints excluded: chain 6 residue 258 THR Chi-restraints excluded: chain 6 residue 284 LEU Chi-restraints excluded: chain 6 residue 318 LEU Chi-restraints excluded: chain 6 residue 336 LEU Chi-restraints excluded: chain 6 residue 357 VAL Chi-restraints excluded: chain 6 residue 366 VAL Chi-restraints excluded: chain 7 residue 72 THR Chi-restraints excluded: chain 7 residue 119 THR Chi-restraints excluded: chain 7 residue 189 LEU Chi-restraints excluded: chain 7 residue 193 VAL Chi-restraints excluded: chain 7 residue 361 CYS Chi-restraints excluded: chain 7 residue 385 ASP Chi-restraints excluded: chain 7 residue 666 ASP Chi-restraints excluded: chain 7 residue 667 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 280 random chunks: chunk 243 optimal weight: 1.9990 chunk 21 optimal weight: 0.0040 chunk 149 optimal weight: 4.9990 chunk 110 optimal weight: 1.9990 chunk 176 optimal weight: 0.9990 chunk 259 optimal weight: 1.9990 chunk 175 optimal weight: 4.9990 chunk 23 optimal weight: 1.9990 chunk 227 optimal weight: 0.8980 chunk 111 optimal weight: 0.7980 chunk 180 optimal weight: 0.9980 overall best weight: 0.7394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 0 164 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 324 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 28 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 4 179 ASN ** 4 237 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 6 340 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4421 r_free = 0.4421 target = 0.173272 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4173 r_free = 0.4173 target = 0.152415 restraints weight = 44491.778| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.4131 r_free = 0.4131 target = 0.149735 restraints weight = 65735.863| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.4118 r_free = 0.4118 target = 0.148781 restraints weight = 49297.678| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.4112 r_free = 0.4112 target = 0.148366 restraints weight = 45359.847| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.4105 r_free = 0.4105 target = 0.147869 restraints weight = 41963.747| |-----------------------------------------------------------------------------| r_work (final): 0.4100 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6712 moved from start: 0.4594 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 24275 Z= 0.173 Angle : 0.768 24.221 33049 Z= 0.361 Chirality : 0.045 0.425 3724 Planarity : 0.004 0.062 4029 Dihedral : 13.574 69.166 3602 Min Nonbonded Distance : 1.914 Molprobity Statistics. All-atom Clashscore : 13.41 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.09 % Favored : 94.88 % Rotamer: Outliers : 3.34 % Allowed : 20.47 % Favored : 76.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.64 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.66 (0.16), residues: 2752 helix: 0.48 (0.14), residues: 1388 sheet: -1.68 (0.32), residues: 247 loop : -1.25 (0.18), residues: 1117 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG 2 94 TYR 0.030 0.002 TYR 6 146 PHE 0.040 0.002 PHE 2 261 TRP 0.064 0.002 TRP 0 552 HIS 0.013 0.001 HIS 0 237 Details of bonding type rmsd/Z covalent geometry : bond 0.00397 / 0.17 (24242) covalent geometry : angle 0.71450 / 0.36 (33001) hydrogen bonds : bond 0.04038 / 2.69 ( 1110) hydrogen bonds : angle 4.87367 / 3.56 ( 3200) metal coordination : bond 0.01549 / 0.95 ( 32) metal coordination : angle 7.41795 / 4.16 ( 48) Misc. bond : bond 0.00055 / 0.03 ( 1) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5504 Ramachandran restraints generated. 2752 Oldfield, 0 Emsley, 2752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5504 Ramachandran restraints generated. 2752 Oldfield, 0 Emsley, 2752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 413 residues out of total 2487 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 330 time to evaluate : 0.705 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 0 1 MET cc_start: 0.3008 (mtp) cc_final: 0.2732 (mtp) REVERT: 0 709 THR cc_start: 0.7758 (OUTLIER) cc_final: 0.7442 (p) REVERT: 1 499 ARG cc_start: 0.5964 (mtt180) cc_final: 0.4968 (mtt180) REVERT: 1 545 MET cc_start: 0.1738 (ptt) cc_final: 0.0263 (tmm) REVERT: 2 109 ILE cc_start: 0.8876 (tt) cc_final: 0.8378 (tp) REVERT: 2 393 LEU cc_start: 0.9245 (OUTLIER) cc_final: 0.8903 (mm) REVERT: 4 56 LYS cc_start: 0.8051 (mmtp) cc_final: 0.7735 (ttmm) REVERT: 4 261 LEU cc_start: 0.7839 (mp) cc_final: 0.7583 (tt) REVERT: 5 18 GLN cc_start: 0.7490 (mm-40) cc_final: 0.7029 (mp10) REVERT: 6 150 SER cc_start: 0.7814 (p) cc_final: 0.7515 (t) REVERT: 7 103 ILE cc_start: 0.7745 (pt) cc_final: 0.7229 (tp) REVERT: 7 341 PRO cc_start: 0.8789 (Cg_exo) cc_final: 0.8501 (Cg_endo) REVERT: 7 442 GLU cc_start: 0.7745 (mm-30) cc_final: 0.7463 (mp0) REVERT: 7 494 MET cc_start: 0.7289 (mmm) cc_final: 0.7007 (mmm) REVERT: 7 586 GLN cc_start: 0.8013 (tp40) cc_final: 0.7692 (mp10) REVERT: 7 590 MET cc_start: 0.7422 (mtp) cc_final: 0.7082 (mtp) REVERT: 7 636 GLU cc_start: 0.8595 (tp30) cc_final: 0.8209 (tp30) outliers start: 83 outliers final: 69 residues processed: 383 average time/residue: 0.1337 time to fit residues: 83.0526 Evaluate side-chains 390 residues out of total 2487 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 319 time to evaluate : 0.670 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 39 VAL Chi-restraints excluded: chain 0 residue 83 VAL Chi-restraints excluded: chain 0 residue 92 ASN Chi-restraints excluded: chain 0 residue 168 VAL Chi-restraints excluded: chain 0 residue 237 HIS Chi-restraints excluded: chain 0 residue 266 LEU Chi-restraints excluded: chain 0 residue 309 VAL Chi-restraints excluded: chain 0 residue 314 VAL Chi-restraints excluded: chain 0 residue 315 LEU Chi-restraints excluded: chain 0 residue 337 LEU Chi-restraints excluded: chain 0 residue 454 VAL Chi-restraints excluded: chain 0 residue 471 LEU Chi-restraints excluded: chain 0 residue 483 MET Chi-restraints excluded: chain 0 residue 490 LEU Chi-restraints excluded: chain 0 residue 522 ASN Chi-restraints excluded: chain 0 residue 560 ASN Chi-restraints excluded: chain 0 residue 604 VAL Chi-restraints excluded: chain 0 residue 626 VAL Chi-restraints excluded: chain 0 residue 663 CYS Chi-restraints excluded: chain 0 residue 678 VAL Chi-restraints excluded: chain 0 residue 709 THR Chi-restraints excluded: chain 1 residue 127 LEU Chi-restraints excluded: chain 1 residue 376 LEU Chi-restraints excluded: chain 1 residue 411 MET Chi-restraints excluded: chain 1 residue 457 ILE Chi-restraints excluded: chain 1 residue 461 LEU Chi-restraints excluded: chain 2 residue 19 LEU Chi-restraints excluded: chain 2 residue 44 VAL Chi-restraints excluded: chain 2 residue 50 SER Chi-restraints excluded: chain 2 residue 158 VAL Chi-restraints excluded: chain 2 residue 260 ASN Chi-restraints excluded: chain 2 residue 341 MET Chi-restraints excluded: chain 2 residue 359 ILE Chi-restraints excluded: chain 2 residue 383 LEU Chi-restraints excluded: chain 2 residue 393 LEU Chi-restraints excluded: chain 3 residue 1 MET Chi-restraints excluded: chain 3 residue 34 CYS Chi-restraints excluded: chain 3 residue 35 VAL Chi-restraints excluded: chain 3 residue 81 ILE Chi-restraints excluded: chain 4 residue 20 ILE Chi-restraints excluded: chain 4 residue 50 PHE Chi-restraints excluded: chain 4 residue 57 LEU Chi-restraints excluded: chain 4 residue 176 ASN Chi-restraints excluded: chain 4 residue 179 ASN Chi-restraints excluded: chain 4 residue 196 LEU Chi-restraints excluded: chain 4 residue 223 LEU Chi-restraints excluded: chain 4 residue 257 CYS Chi-restraints excluded: chain 4 residue 272 LEU Chi-restraints excluded: chain 5 residue 5 LEU Chi-restraints excluded: chain 6 residue 84 THR Chi-restraints excluded: chain 6 residue 87 LEU Chi-restraints excluded: chain 6 residue 174 LEU Chi-restraints excluded: chain 6 residue 218 THR Chi-restraints excluded: chain 6 residue 221 VAL Chi-restraints excluded: chain 6 residue 250 ILE Chi-restraints excluded: chain 6 residue 258 THR Chi-restraints excluded: chain 6 residue 284 LEU Chi-restraints excluded: chain 6 residue 318 LEU Chi-restraints excluded: chain 6 residue 336 LEU Chi-restraints excluded: chain 6 residue 357 VAL Chi-restraints excluded: chain 6 residue 366 VAL Chi-restraints excluded: chain 7 residue 72 THR Chi-restraints excluded: chain 7 residue 119 THR Chi-restraints excluded: chain 7 residue 189 LEU Chi-restraints excluded: chain 7 residue 193 VAL Chi-restraints excluded: chain 7 residue 340 LEU Chi-restraints excluded: chain 7 residue 361 CYS Chi-restraints excluded: chain 7 residue 385 ASP Chi-restraints excluded: chain 7 residue 666 ASP Chi-restraints excluded: chain 7 residue 667 THR Chi-restraints excluded: chain 7 residue 686 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 280 random chunks: chunk 100 optimal weight: 0.3980 chunk 55 optimal weight: 0.1980 chunk 7 optimal weight: 1.9990 chunk 67 optimal weight: 5.9990 chunk 70 optimal weight: 0.0170 chunk 119 optimal weight: 0.1980 chunk 95 optimal weight: 0.9990 chunk 21 optimal weight: 2.9990 chunk 81 optimal weight: 0.0670 chunk 61 optimal weight: 3.9990 chunk 125 optimal weight: 0.6980 overall best weight: 0.1756 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 0 164 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0 237 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 324 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 28 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 4 179 ASN ** 4 237 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4418 r_free = 0.4418 target = 0.172874 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4166 r_free = 0.4166 target = 0.151714 restraints weight = 44068.003| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.4118 r_free = 0.4118 target = 0.148495 restraints weight = 65884.723| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.4102 r_free = 0.4102 target = 0.147315 restraints weight = 50593.613| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.4092 r_free = 0.4092 target = 0.146751 restraints weight = 48655.347| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.4084 r_free = 0.4084 target = 0.146210 restraints weight = 43774.910| |-----------------------------------------------------------------------------| r_work (final): 0.4084 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6743 moved from start: 0.4627 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.362 24275 Z= 0.226 Angle : 0.886 59.174 33049 Z= 0.454 Chirality : 0.056 2.092 3724 Planarity : 0.004 0.064 4029 Dihedral : 13.570 69.196 3602 Min Nonbonded Distance : 1.915 Molprobity Statistics. All-atom Clashscore : 16.56 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.09 % Favored : 94.88 % Rotamer: Outliers : 2.85 % Allowed : 21.11 % Favored : 76.04 % Cbeta Deviations : 0.04 % Peptide Plane: Cis-proline : 1.64 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.66 (0.16), residues: 2752 helix: 0.48 (0.14), residues: 1388 sheet: -1.67 (0.32), residues: 247 loop : -1.24 (0.18), residues: 1117 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG 0 487 TYR 0.040 0.002 TYR 7 501 PHE 0.050 0.002 PHE 6 331 TRP 0.058 0.002 TRP 0 552 HIS 0.013 0.001 HIS 0 237 Details of bonding type rmsd/Z covalent geometry : bond 0.00514 / 0.23 (24242) covalent geometry : angle 0.84074 / 0.45 (33001) hydrogen bonds : bond 0.04065 / 2.71 ( 1110) hydrogen bonds : angle 4.88690 / 3.57 ( 3200) metal coordination : bond 0.01524 / 0.95 ( 32) metal coordination : angle 7.41083 / 4.16 ( 48) Misc. bond : bond 0.00045 / 0.02 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3563.19 seconds wall clock time: 62 minutes 43.74 seconds (3763.74 seconds total)