Starting phenix.real_space_refine on Sun Sep 13 13:22:28 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7nvx_12616/09_2026/7nvx_12616.cif Found real_map, /net/cci-nas-00/data/ceres_data/7nvx_12616/09_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/7nvx_12616/09_2026/7nvx_12616.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7nvx_12616/09_2026/7nvx_12616.map" restraint_files = "/net/cci-nas-00/data/ceres_data/7nvx_12616/09_2026/7nvx_12616.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7nvx_12616/09_2026/7nvx_12616.cif" model { file = "/net/cci-nas-00/data/ceres_data/7nvx_12616/09_2026/7nvx_12616.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7nvx_12616/09_2026/7nvx_12616.cif" } 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): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 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: 4.95, per 1000 atoms: 0.21 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: 1.95 Conformation dependent library (CDL) restraints added in 1.1 seconds 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: 2.74 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: 4.80 Time building geometry restraints manager: 2.62 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: 8.350 Set stop_for_unknowns flag: 0.010 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.020 Extract box with map and model: 0.430 Check model and map are aligned: 0.090 Set scattering table: 0.060 Process input model: 29.930 Find NCS groups from input model: 0.140 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.190 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 40.280 ------------------------------------------------------------------------------- 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= 0.404 Angle : 0.553 14.213 33049 Z= 0.320 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 0.51199 / 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 : 0.841 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: 0.5122 (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: 0.7497 (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: 0.6712 (t60) REVERT: 7 488 LEU cc_start: 0.8187 (mt) cc_final: 0.7795 (mm) REVERT: 7 541 PHE cc_start: 0.5946 (t80) cc_final: 0.4891 (t80) outliers start: 0 outliers final: 0 residues processed: 689 average time/residue: 0.1767 time to fit residues: 185.7750 Evaluate side-chains 417 residues out of total 2487 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 417 time to evaluate : 0.872 ------------------------------------------------------------------------------- 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 = 0.174612 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.4149 r_free = 0.4149 target = 0.151326 restraints weight = 44500.962| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.4175 r_free = 0.4175 target = 0.154248 restraints weight = 92975.062| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4179 r_free = 0.4179 target = 0.154737 restraints weight = 42963.286| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.4181 r_free = 0.4181 target = 0.154988 restraints weight = 34611.203| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.4186 r_free = 0.4186 target = 0.155435 restraints weight = 28702.056| |-----------------------------------------------------------------------------| r_work (final): 0.4188 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6505 moved from start: 0.2695 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.104 24275 Z= 0.206 Angle : 0.800 20.410 33049 Z= 0.394 Chirality : 0.046 0.298 3724 Planarity : 0.005 0.080 4029 Dihedral : 12.681 100.186 3602 Min Nonbonded Distance : 1.974 Molprobity Statistics. All-atom Clashscore : 10.74 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.51 % Favored : 95.46 % Rotamer: Outliers : 2.29 % Allowed : 11.90 % Favored : 85.81 % 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: 1368 sheet: -1.36 (0.32), residues: 284 loop : -0.84 (0.19), residues: 1100 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG 0 636 TYR 0.037 0.002 TYR 0 410 PHE 0.025 0.002 PHE 1 307 TRP 0.030 0.002 TRP 2 96 HIS 0.013 0.002 HIS 7 187 Details of bonding type rmsd/Z covalent geometry : bond 0.00466 / 0.21 (24242) covalent geometry : angle 0.74493 / 0.39 (33001) hydrogen bonds : bond 0.06602 / 4.39 ( 1110) hydrogen bonds : angle 5.55231 / 4.02 ( 3200) metal coordination : bond 0.01671 / 1.03 ( 32) metal coordination : angle 7.68982 / 4.86 ( 48) Misc. bond : bond 0.00354 / 0.19 ( 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: 57 poor density : 458 time to evaluate : 0.935 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: 0.8218 (OUTLIER) cc_final: 0.7992 (ttm110) REVERT: 0 87 LEU cc_start: 0.7683 (tt) cc_final: 0.7272 (tp) REVERT: 0 438 MET cc_start: 0.6553 (ptp) cc_final: 0.6077 (ttm) REVERT: 0 545 MET cc_start: 0.8010 (ttp) cc_final: 0.7731 (tmm) REVERT: 1 309 HIS cc_start: 0.6365 (m170) cc_final: 0.5890 (m90) REVERT: 1 499 ARG cc_start: 0.6439 (mtt180) cc_final: 0.5295 (mtt180) REVERT: 1 534 ASN cc_start: 0.6806 (m110) cc_final: 0.6523 (t0) REVERT: 2 109 ILE cc_start: 0.8940 (tt) cc_final: 0.8474 (tp) REVERT: 2 156 TRP cc_start: 0.8624 (t-100) cc_final: 0.8354 (t-100) REVERT: 2 318 TYR cc_start: 0.7696 (m-10) cc_final: 0.7330 (m-10) REVERT: 4 56 LYS cc_start: 0.7615 (mmtp) cc_final: 0.7310 (ttmm) REVERT: 6 349 GLN cc_start: 0.7874 (mm110) cc_final: 0.6491 (tm-30) REVERT: 7 103 ILE cc_start: 0.7801 (pt) cc_final: 0.7107 (tp) REVERT: 7 341 PRO cc_start: 0.9051 (Cg_exo) cc_final: 0.8781 (Cg_endo) REVERT: 7 348 LEU cc_start: 0.8102 (OUTLIER) cc_final: 0.7740 (mt) REVERT: 7 488 LEU cc_start: 0.8173 (mt) cc_final: 0.7863 (mm) REVERT: 7 636 GLU cc_start: 0.8687 (tp30) cc_final: 0.8184 (tp30) outliers start: 57 outliers final: 31 residues processed: 484 average time/residue: 0.1498 time to fit residues: 115.8618 Evaluate side-chains 381 residues out of total 2487 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 348 time to evaluate : 0.905 ------------------------------------------------------------------------------- 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 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 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: 10.0000 chunk 143 optimal weight: 0.2980 chunk 173 optimal weight: 0.6980 chunk 93 optimal weight: 0.9980 chunk 6 optimal weight: 0.8980 chunk 24 optimal weight: 0.9980 chunk 82 optimal weight: 0.7980 chunk 180 optimal weight: 0.0050 chunk 100 optimal weight: 0.6980 chunk 9 optimal weight: 3.9990 overall best weight: 0.4194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 1 530 GLN 1 534 ASN 2 37 HIS 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** 7 366 ASN 7 459 GLN 7 481 ASN 7 656 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4435 r_free = 0.4435 target = 0.174324 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4177 r_free = 0.4177 target = 0.152628 restraints weight = 44757.309| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.4139 r_free = 0.4139 target = 0.150238 restraints weight = 67844.939| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.4127 r_free = 0.4127 target = 0.149384 restraints weight = 51568.408| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.4121 r_free = 0.4121 target = 0.149081 restraints weight = 50918.900| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.4121 r_free = 0.4121 target = 0.149166 restraints weight = 42504.608| |-----------------------------------------------------------------------------| r_work (final): 0.4122 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6643 moved from start: 0.3270 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 24275 Z= 0.168 Angle : 0.734 25.556 33049 Z= 0.353 Chirality : 0.043 0.235 3724 Planarity : 0.005 0.072 4029 Dihedral : 12.834 90.948 3602 Min Nonbonded Distance : 1.967 Molprobity Statistics. All-atom Clashscore : 10.89 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.22 % Favored : 95.75 % Rotamer: Outliers : 2.73 % Allowed : 15.32 % Favored : 81.95 % 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: -0.25 (0.16), residues: 2752 helix: 0.82 (0.14), residues: 1388 sheet: -1.51 (0.31), residues: 277 loop : -1.00 (0.19), residues: 1087 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG 7 62 TYR 0.035 0.002 TYR 3 95 PHE 0.019 0.002 PHE 2 261 TRP 0.025 0.001 TRP 2 96 HIS 0.020 0.002 HIS 2 424 Details of bonding type rmsd/Z covalent geometry : bond 0.00360 / 0.17 (24242) covalent geometry : angle 0.67743 / 0.35 (33001) hydrogen bonds : bond 0.05389 / 3.55 ( 1110) hydrogen bonds : angle 5.16068 / 3.74 ( 3200) metal coordination : bond 0.01038 / 0.57 ( 32) metal coordination : angle 7.45321 / 4.44 ( 48) Misc. bond : bond 0.00292 / 0.15 ( 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 473 residues out of total 2487 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 405 time to evaluate : 0.876 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: 0 438 MET cc_start: 0.6535 (ptp) cc_final: 0.6089 (ttm) REVERT: 0 545 MET cc_start: 0.8051 (ttp) cc_final: 0.7797 (tmm) REVERT: 0 657 MET cc_start: 0.7403 (mmp) cc_final: 0.7154 (mmm) REVERT: 1 309 HIS cc_start: 0.6464 (m170) cc_final: 0.6033 (m90) REVERT: 1 499 ARG cc_start: 0.6333 (mtt180) cc_final: 0.5201 (mtt180) REVERT: 2 109 ILE cc_start: 0.8924 (tt) cc_final: 0.8390 (tp) REVERT: 2 310 GLU cc_start: 0.7482 (mm-30) cc_final: 0.6233 (mt-10) REVERT: 2 399 ASP cc_start: 0.7543 (p0) cc_final: 0.7288 (p0) REVERT: 4 56 LYS cc_start: 0.7838 (mmtp) cc_final: 0.7588 (ttmm) REVERT: 5 26 SER cc_start: 0.8006 (m) cc_final: 0.7599 (t) REVERT: 6 184 ASP cc_start: 0.6984 (p0) cc_final: 0.6671 (p0) REVERT: 6 185 LEU cc_start: 0.7871 (tp) cc_final: 0.7648 (tp) REVERT: 6 349 GLN cc_start: 0.8119 (mm110) cc_final: 0.6713 (tm-30) REVERT: 7 103 ILE cc_start: 0.7832 (pt) cc_final: 0.7229 (tp) REVERT: 7 341 PRO cc_start: 0.8990 (Cg_exo) cc_final: 0.8722 (Cg_endo) REVERT: 7 488 LEU cc_start: 0.8057 (mt) cc_final: 0.7721 (mm) REVERT: 7 586 GLN cc_start: 0.8259 (tp40) cc_final: 0.7270 (mp10) REVERT: 7 636 GLU cc_start: 0.8541 (tp30) cc_final: 0.7906 (tp30) REVERT: 7 667 THR cc_start: 0.8563 (OUTLIER) cc_final: 0.8196 (p) outliers start: 68 outliers final: 41 residues processed: 440 average time/residue: 0.1469 time to fit residues: 103.8663 Evaluate side-chains 395 residues out of total 2487 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 353 time to evaluate : 0.761 ------------------------------------------------------------------------------- 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 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 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 2 residue 19 LEU 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 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 221 VAL Chi-restraints excluded: chain 6 residue 258 THR Chi-restraints excluded: chain 6 residue 312 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 366 ASN 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: 1.9990 chunk 69 optimal weight: 1.9990 chunk 16 optimal weight: 0.7980 chunk 148 optimal weight: 5.9990 chunk 274 optimal weight: 9.9990 chunk 67 optimal weight: 2.9990 chunk 236 optimal weight: 1.9990 chunk 173 optimal weight: 0.9990 chunk 216 optimal weight: 0.7980 chunk 44 optimal weight: 4.9990 chunk 29 optimal weight: 8.9990 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 1 530 GLN 2 117 ASN ** 3 28 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 4 55 ASN ** 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** 6 265 GLN 7 97 GLN 7 187 HIS 7 366 ASN 7 459 GLN 7 506 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4397 r_free = 0.4397 target = 0.171007 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4148 r_free = 0.4148 target = 0.150347 restraints weight = 44786.964| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4103 r_free = 0.4103 target = 0.147445 restraints weight = 65710.012| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.4083 r_free = 0.4083 target = 0.146008 restraints weight = 50366.638| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.4069 r_free = 0.4069 target = 0.145165 restraints weight = 52742.729| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.4068 r_free = 0.4068 target = 0.145103 restraints weight = 44165.983| |-----------------------------------------------------------------------------| r_work (final): 0.4069 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6757 moved from start: 0.3568 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.070 24275 Z= 0.240 Angle : 0.770 25.569 33049 Z= 0.371 Chirality : 0.045 0.328 3724 Planarity : 0.005 0.062 4029 Dihedral : 13.141 74.681 3602 Min Nonbonded Distance : 1.884 Molprobity Statistics. All-atom Clashscore : 13.24 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.01 % Favored : 94.95 % Rotamer: Outliers : 3.66 % Allowed : 16.65 % Favored : 79.69 % 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: -0.56 (0.16), residues: 2752 helix: 0.61 (0.14), residues: 1389 sheet: -1.89 (0.32), residues: 261 loop : -1.16 (0.18), residues: 1102 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG 7 74 TYR 0.031 0.002 TYR 1 414 PHE 0.037 0.002 PHE 2 261 TRP 0.028 0.002 TRP 2 96 HIS 0.020 0.002 HIS 3 28 Details of bonding type rmsd/Z covalent geometry : bond 0.00543 / 0.24 (24242) covalent geometry : angle 0.71224 / 0.37 (33001) hydrogen bonds : bond 0.05092 / 3.38 ( 1110) hydrogen bonds : angle 5.19227 / 3.76 ( 3200) metal coordination : bond 0.01362 / 0.68 ( 32) metal coordination : angle 7.69654 / 4.58 ( 48) Misc. bond : bond 0.00004 / 0.00 ( 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 456 residues out of total 2487 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 365 time to evaluate : 0.704 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: 0 438 MET cc_start: 0.6585 (ptp) cc_final: 0.6093 (ttm) REVERT: 1 309 HIS cc_start: 0.6550 (m170) cc_final: 0.6268 (m90) REVERT: 1 499 ARG cc_start: 0.6344 (mtt180) cc_final: 0.5199 (mtt180) REVERT: 2 109 ILE cc_start: 0.8980 (tt) cc_final: 0.8549 (tp) REVERT: 2 393 LEU cc_start: 0.9273 (OUTLIER) cc_final: 0.8953 (mm) REVERT: 4 56 LYS cc_start: 0.8147 (mmtp) cc_final: 0.7819 (ttmm) REVERT: 4 261 LEU cc_start: 0.7689 (mp) cc_final: 0.7235 (tt) REVERT: 5 17 LYS cc_start: 0.6162 (tmtt) cc_final: 0.5946 (tmtt) REVERT: 6 146 TYR cc_start: 0.7383 (t80) cc_final: 0.7130 (t80) REVERT: 6 184 ASP cc_start: 0.6948 (p0) cc_final: 0.6677 (p0) REVERT: 6 236 VAL cc_start: 0.8794 (OUTLIER) cc_final: 0.8551 (t) REVERT: 7 56 TYR cc_start: 0.7776 (OUTLIER) cc_final: 0.7359 (m-80) REVERT: 7 103 ILE cc_start: 0.7827 (pt) cc_final: 0.7156 (tp) REVERT: 7 341 PRO cc_start: 0.8978 (Cg_exo) cc_final: 0.8677 (Cg_endo) REVERT: 7 488 LEU cc_start: 0.8269 (mt) cc_final: 0.7916 (mm) REVERT: 7 586 GLN cc_start: 0.8000 (tp40) cc_final: 0.7343 (mp10) REVERT: 7 636 GLU cc_start: 0.8661 (tp30) cc_final: 0.8249 (tp30) outliers start: 91 outliers final: 54 residues processed: 425 average time/residue: 0.1454 time to fit residues: 99.4021 Evaluate side-chains 386 residues out of total 2487 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 329 time to evaluate : 0.853 ------------------------------------------------------------------------------- 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 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 526 GLU Chi-restraints excluded: chain 0 residue 560 ASN Chi-restraints excluded: chain 0 residue 604 VAL Chi-restraints excluded: chain 0 residue 619 ILE Chi-restraints excluded: chain 0 residue 626 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 51 LEU 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 4 residue 11 LEU 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 192 ASP Chi-restraints excluded: chain 4 residue 257 CYS 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 318 LEU Chi-restraints excluded: chain 6 residue 336 LEU Chi-restraints excluded: chain 6 residue 366 VAL 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 366 ASN 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 280 random chunks: chunk 53 optimal weight: 0.0970 chunk 65 optimal weight: 2.9990 chunk 233 optimal weight: 1.9990 chunk 258 optimal weight: 0.1980 chunk 259 optimal weight: 0.5980 chunk 163 optimal weight: 0.7980 chunk 13 optimal weight: 0.7980 chunk 228 optimal weight: 4.9990 chunk 230 optimal weight: 0.6980 chunk 57 optimal weight: 4.9990 chunk 185 optimal weight: 0.7980 overall best weight: 0.4778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 3 28 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 3 111 ASN ** 4 46 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 4 55 ASN ** 4 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 145 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 4 205 GLN ** 5 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 6 376 HIS 7 459 GLN 7 506 GLN 7 621 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4423 r_free = 0.4423 target = 0.173409 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.4165 r_free = 0.4165 target = 0.151816 restraints weight = 44643.682| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.4127 r_free = 0.4127 target = 0.149342 restraints weight = 68131.215| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.4104 r_free = 0.4104 target = 0.147740 restraints weight = 55525.917| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.4102 r_free = 0.4102 target = 0.147629 restraints weight = 52971.183| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.4101 r_free = 0.4101 target = 0.147642 restraints weight = 43551.315| |-----------------------------------------------------------------------------| r_work (final): 0.4098 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6699 moved from start: 0.3825 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.089 24275 Z= 0.158 Angle : 0.731 26.850 33049 Z= 0.342 Chirality : 0.043 0.275 3724 Planarity : 0.004 0.063 4029 Dihedral : 13.232 68.168 3602 Min Nonbonded Distance : 1.962 Molprobity Statistics. All-atom Clashscore : 12.73 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.76 % Favored : 95.20 % Rotamer: Outliers : 2.94 % Allowed : 18.21 % Favored : 78.85 % 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: -0.51 (0.16), residues: 2752 helix: 0.65 (0.14), residues: 1386 sheet: -1.78 (0.33), residues: 251 loop : -1.17 (0.18), residues: 1115 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG 0 30 TYR 0.027 0.002 TYR 7 581 PHE 0.029 0.002 PHE 2 261 TRP 0.023 0.001 TRP 0 552 HIS 0.018 0.001 HIS 0 237 Details of bonding type rmsd/Z covalent geometry : bond 0.00348 / 0.16 (24242) covalent geometry : angle 0.66281 / 0.34 (33001) hydrogen bonds : bond 0.04563 / 3.02 ( 1110) hydrogen bonds : angle 4.93798 / 3.59 ( 3200) metal coordination : bond 0.01733 / 0.75 ( 32) metal coordination : angle 8.13189 / 4.63 ( 48) Misc. bond : bond 0.00031 / 0.02 ( 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 449 residues out of total 2487 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 376 time to evaluate : 0.961 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: 0 438 MET cc_start: 0.6585 (ptp) cc_final: 0.6153 (ttm) REVERT: 0 677 MET cc_start: 0.8123 (pmm) cc_final: 0.7894 (pmm) REVERT: 1 309 HIS cc_start: 0.6493 (m170) cc_final: 0.6293 (m90) REVERT: 1 499 ARG cc_start: 0.6264 (mtt180) cc_final: 0.5170 (mtt180) REVERT: 1 528 MET cc_start: 0.6434 (mpp) cc_final: 0.6184 (mpp) REVERT: 2 109 ILE cc_start: 0.8932 (tt) cc_final: 0.8463 (tp) REVERT: 4 56 LYS cc_start: 0.7954 (mmtp) cc_final: 0.7670 (ttmm) REVERT: 4 261 LEU cc_start: 0.7838 (mp) cc_final: 0.7409 (tt) REVERT: 5 21 LEU cc_start: 0.7471 (mt) cc_final: 0.7209 (mt) REVERT: 6 146 TYR cc_start: 0.7303 (t80) cc_final: 0.7045 (t80) REVERT: 6 150 SER cc_start: 0.7630 (p) cc_final: 0.7213 (t) REVERT: 6 184 ASP cc_start: 0.6932 (p0) cc_final: 0.6608 (p0) REVERT: 6 236 VAL cc_start: 0.8726 (OUTLIER) cc_final: 0.8388 (t) REVERT: 7 93 TYR cc_start: 0.7052 (t80) cc_final: 0.5141 (p90) REVERT: 7 103 ILE cc_start: 0.7860 (pt) cc_final: 0.7237 (tp) REVERT: 7 341 PRO cc_start: 0.8936 (Cg_exo) cc_final: 0.8625 (Cg_endo) REVERT: 7 488 LEU cc_start: 0.8179 (mt) cc_final: 0.7809 (mm) REVERT: 7 586 GLN cc_start: 0.8200 (tp40) cc_final: 0.7361 (mp10) REVERT: 7 636 GLU cc_start: 0.8470 (tp30) cc_final: 0.7948 (tp30) outliers start: 73 outliers final: 48 residues processed: 424 average time/residue: 0.1449 time to fit residues: 99.7618 Evaluate side-chains 383 residues out of total 2487 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 334 time to evaluate : 0.718 ------------------------------------------------------------------------------- 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 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 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 663 CYS 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 341 MET Chi-restraints excluded: chain 3 residue 1 MET Chi-restraints excluded: chain 3 residue 82 TYR 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 205 GLN 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 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 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 523 VAL Chi-restraints excluded: chain 7 residue 666 ASP Chi-restraints excluded: chain 7 residue 667 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 280 random chunks: chunk 166 optimal weight: 0.5980 chunk 213 optimal weight: 0.9980 chunk 195 optimal weight: 2.9990 chunk 118 optimal weight: 0.0980 chunk 153 optimal weight: 0.5980 chunk 204 optimal weight: 10.0000 chunk 24 optimal weight: 0.8980 chunk 196 optimal weight: 2.9990 chunk 125 optimal weight: 0.7980 chunk 269 optimal weight: 0.6980 chunk 1 optimal weight: 4.9990 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 3 28 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 46 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 145 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 5 63 GLN ** 6 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 7 366 ASN 7 459 GLN ** 7 497 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4427 r_free = 0.4427 target = 0.173606 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4187 r_free = 0.4187 target = 0.153353 restraints weight = 45131.132| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.4140 r_free = 0.4140 target = 0.150154 restraints weight = 63279.129| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.4120 r_free = 0.4120 target = 0.148602 restraints weight = 55806.750| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.4115 r_free = 0.4115 target = 0.148492 restraints weight = 54794.079| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.4104 r_free = 0.4104 target = 0.147602 restraints weight = 48314.786| |-----------------------------------------------------------------------------| r_work (final): 0.4102 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6703 moved from start: 0.4016 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.068 24275 Z= 0.159 Angle : 0.741 25.001 33049 Z= 0.345 Chirality : 0.043 0.285 3724 Planarity : 0.004 0.058 4029 Dihedral : 13.349 68.533 3602 Min Nonbonded Distance : 1.935 Molprobity Statistics. All-atom Clashscore : 12.94 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.83 % Favored : 95.13 % Rotamer: Outliers : 3.50 % Allowed : 18.90 % Favored : 77.60 % 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: -0.57 (0.16), residues: 2752 helix: 0.58 (0.14), residues: 1386 sheet: -1.69 (0.33), residues: 245 loop : -1.22 (0.18), residues: 1121 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG 2 33 TYR 0.021 0.002 TYR 7 581 PHE 0.031 0.002 PHE 2 261 TRP 0.017 0.001 TRP 2 96 HIS 0.017 0.001 HIS 0 237 Details of bonding type rmsd/Z covalent geometry : bond 0.00353 / 0.16 (24242) covalent geometry : angle 0.67622 / 0.34 (33001) hydrogen bonds : bond 0.04377 / 2.89 ( 1110) hydrogen bonds : angle 4.90227 / 3.57 ( 3200) metal coordination : bond 0.02046 / 1.27 ( 32) metal coordination : angle 7.98009 / 4.69 ( 48) Misc. bond : bond 0.00003 / 0.00 ( 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 443 residues out of total 2487 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 356 time to evaluate : 0.826 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: 0 438 MET cc_start: 0.6455 (ptp) cc_final: 0.6016 (ttm) REVERT: 1 499 ARG cc_start: 0.6127 (mtt180) cc_final: 0.4986 (mtt180) REVERT: 1 545 MET cc_start: 0.2073 (ptt) cc_final: 0.0406 (tmm) REVERT: 2 109 ILE cc_start: 0.8893 (tt) cc_final: 0.8458 (tp) REVERT: 2 376 MET cc_start: 0.7807 (OUTLIER) cc_final: 0.7438 (mtp) REVERT: 4 56 LYS cc_start: 0.8065 (mmtp) cc_final: 0.7746 (ttmm) REVERT: 4 261 LEU cc_start: 0.7919 (mp) cc_final: 0.7468 (tt) REVERT: 6 150 SER cc_start: 0.7642 (p) cc_final: 0.7261 (t) REVERT: 6 214 GLU cc_start: 0.7272 (pp20) cc_final: 0.6856 (pp20) REVERT: 7 103 ILE cc_start: 0.7763 (pt) cc_final: 0.7196 (tp) REVERT: 7 341 PRO cc_start: 0.8812 (Cg_exo) cc_final: 0.8514 (Cg_endo) REVERT: 7 494 MET cc_start: 0.6945 (mmm) cc_final: 0.6698 (mmm) REVERT: 7 586 GLN cc_start: 0.8023 (tp40) cc_final: 0.7428 (mp10) REVERT: 7 590 MET cc_start: 0.7480 (mtp) cc_final: 0.7027 (mtp) REVERT: 7 636 GLU cc_start: 0.8512 (tp30) cc_final: 0.7972 (tp30) outliers start: 87 outliers final: 63 residues processed: 416 average time/residue: 0.1428 time to fit residues: 97.2470 Evaluate side-chains 398 residues out of total 2487 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 334 time to evaluate : 0.909 ------------------------------------------------------------------------------- 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 330 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 490 LEU Chi-restraints excluded: chain 0 residue 560 ASN Chi-restraints excluded: chain 0 residue 567 LEU Chi-restraints excluded: chain 0 residue 604 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 1 residue 534 ASN 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 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 376 MET Chi-restraints excluded: chain 2 residue 383 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 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 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 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 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 366 ASN Chi-restraints excluded: chain 7 residue 385 ASP 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 Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 280 random chunks: chunk 38 optimal weight: 0.6980 chunk 0 optimal weight: 9.9990 chunk 23 optimal weight: 0.7980 chunk 68 optimal weight: 0.5980 chunk 173 optimal weight: 0.1980 chunk 266 optimal weight: 0.5980 chunk 31 optimal weight: 4.9990 chunk 36 optimal weight: 4.9990 chunk 106 optimal weight: 1.9990 chunk 208 optimal weight: 3.9990 chunk 90 optimal weight: 0.3980 overall best weight: 0.4980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 0 237 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 28 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 48 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 5 64 ASN ** 6 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 6 364 GLN ** 7 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 7 187 HIS 7 366 ASN 7 459 GLN ** 7 497 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4426 r_free = 0.4426 target = 0.173514 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.4151 r_free = 0.4151 target = 0.150587 restraints weight = 44657.782| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.4140 r_free = 0.4140 target = 0.150463 restraints weight = 74834.191| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4137 r_free = 0.4137 target = 0.150439 restraints weight = 53214.610| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.4124 r_free = 0.4124 target = 0.149489 restraints weight = 50509.859| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.4128 r_free = 0.4128 target = 0.149852 restraints weight = 42858.585| |-----------------------------------------------------------------------------| r_work (final): 0.4131 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6641 moved from start: 0.4173 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 24275 Z= 0.153 Angle : 0.735 24.328 33049 Z= 0.344 Chirality : 0.043 0.345 3724 Planarity : 0.004 0.059 4029 Dihedral : 13.403 68.766 3602 Min Nonbonded Distance : 1.944 Molprobity Statistics. All-atom Clashscore : 12.87 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.65 % Favored : 95.31 % Rotamer: Outliers : 3.42 % Allowed : 19.54 % Favored : 77.04 % 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: -0.58 (0.16), residues: 2752 helix: 0.57 (0.14), residues: 1386 sheet: -1.70 (0.33), residues: 245 loop : -1.23 (0.18), residues: 1121 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG 7 62 TYR 0.020 0.001 TYR 7 175 PHE 0.034 0.002 PHE 2 261 TRP 0.045 0.002 TRP 0 552 HIS 0.023 0.001 HIS 7 187 Details of bonding type rmsd/Z covalent geometry : bond 0.00339 / 0.15 (24242) covalent geometry : angle 0.67740 / 0.34 (33001) hydrogen bonds : bond 0.04198 / 2.76 ( 1110) hydrogen bonds : angle 4.83061 / 3.52 ( 3200) metal coordination : bond 0.01741 / 1.06 ( 32) metal coordination : angle 7.53510 / 4.33 ( 48) Misc. bond : bond 0.00000 / 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 445 residues out of total 2487 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 360 time to evaluate : 0.898 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: 0.3903 (mtp) cc_final: 0.2999 (mtp) REVERT: 1 441 MET cc_start: 0.6747 (tpp) cc_final: 0.6526 (tpt) REVERT: 1 499 ARG cc_start: 0.6090 (mtt180) cc_final: 0.5037 (mtt180) REVERT: 1 545 MET cc_start: 0.1947 (ptt) cc_final: 0.0282 (tmm) REVERT: 2 109 ILE cc_start: 0.8832 (tt) cc_final: 0.8321 (tp) REVERT: 2 393 LEU cc_start: 0.9219 (OUTLIER) cc_final: 0.8889 (mm) REVERT: 4 56 LYS cc_start: 0.7826 (mmtp) cc_final: 0.7437 (ttmm) REVERT: 4 261 LEU cc_start: 0.7835 (mp) cc_final: 0.7477 (tt) REVERT: 6 150 SER cc_start: 0.7644 (p) cc_final: 0.7269 (t) REVERT: 7 103 ILE cc_start: 0.7873 (pt) cc_final: 0.7298 (tp) REVERT: 7 341 PRO cc_start: 0.8774 (Cg_exo) cc_final: 0.8461 (Cg_endo) REVERT: 7 494 MET cc_start: 0.6949 (mmm) cc_final: 0.6712 (mmm) REVERT: 7 586 GLN cc_start: 0.7913 (tp40) cc_final: 0.7431 (mp10) REVERT: 7 590 MET cc_start: 0.7379 (mtp) cc_final: 0.6954 (mtp) REVERT: 7 636 GLU cc_start: 0.8527 (tp30) cc_final: 0.7996 (tp30) outliers start: 85 outliers final: 63 residues processed: 420 average time/residue: 0.1420 time to fit residues: 97.0859 Evaluate side-chains 390 residues out of total 2487 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 326 time to evaluate : 0.828 ------------------------------------------------------------------------------- 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 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 567 LEU 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 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 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 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 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 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 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 366 VAL Chi-restraints excluded: chain 7 residue 119 THR Chi-restraints excluded: chain 7 residue 187 HIS 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 280 random chunks: chunk 205 optimal weight: 0.5980 chunk 196 optimal weight: 0.9990 chunk 260 optimal weight: 0.0010 chunk 176 optimal weight: 0.9990 chunk 208 optimal weight: 0.2980 chunk 141 optimal weight: 6.9990 chunk 237 optimal weight: 0.5980 chunk 7 optimal weight: 3.9990 chunk 74 optimal weight: 5.9990 chunk 103 optimal weight: 3.9990 chunk 36 optimal weight: 0.6980 overall best weight: 0.4386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 ** 4 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 6 265 GLN 7 366 ASN 7 459 GLN ** 7 497 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4432 r_free = 0.4432 target = 0.174014 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4178 r_free = 0.4178 target = 0.152516 restraints weight = 44662.569| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.4136 r_free = 0.4136 target = 0.149837 restraints weight = 69939.673| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.4119 r_free = 0.4119 target = 0.148524 restraints weight = 51950.423| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.4110 r_free = 0.4110 target = 0.148003 restraints weight = 52479.301| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.4108 r_free = 0.4108 target = 0.147892 restraints weight = 45821.083| |-----------------------------------------------------------------------------| r_work (final): 0.4105 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6696 moved from start: 0.4302 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 24275 Z= 0.148 Angle : 0.740 23.941 33049 Z= 0.347 Chirality : 0.044 0.400 3724 Planarity : 0.004 0.059 4029 Dihedral : 13.425 68.946 3602 Min Nonbonded Distance : 1.953 Molprobity Statistics. All-atom Clashscore : 12.79 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.69 % Favored : 95.28 % Rotamer: Outliers : 3.42 % Allowed : 19.94 % Favored : 76.64 % 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: -0.58 (0.16), residues: 2752 helix: 0.57 (0.14), residues: 1385 sheet: -1.68 (0.33), residues: 245 loop : -1.22 (0.18), residues: 1122 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG 7 62 TYR 0.019 0.001 TYR 7 175 PHE 0.044 0.002 PHE 2 261 TRP 0.051 0.002 TRP 0 552 HIS 0.024 0.001 HIS 7 187 Details of bonding type rmsd/Z covalent geometry : bond 0.00330 / 0.15 (24242) covalent geometry : angle 0.68531 / 0.34 (33001) hydrogen bonds : bond 0.04135 / 2.72 ( 1110) hydrogen bonds : angle 4.82827 / 3.53 ( 3200) metal coordination : bond 0.01570 / 0.96 ( 32) metal coordination : angle 7.35780 / 4.19 ( 48) Misc. bond : bond 0.00000 / 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 431 residues out of total 2487 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 346 time to evaluate : 0.879 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: 0.3851 (mtp) cc_final: 0.2929 (mtp) REVERT: 0 438 MET cc_start: 0.6371 (ptp) cc_final: 0.5812 (ttm) REVERT: 0 709 THR cc_start: 0.7714 (OUTLIER) cc_final: 0.7405 (p) REVERT: 1 441 MET cc_start: 0.6833 (tpp) cc_final: 0.6615 (tpt) REVERT: 1 499 ARG cc_start: 0.6104 (mtt180) cc_final: 0.5009 (mtt180) REVERT: 1 545 MET cc_start: 0.1819 (ptt) cc_final: 0.0270 (tmm) REVERT: 2 109 ILE cc_start: 0.8817 (tt) cc_final: 0.8311 (tp) REVERT: 2 393 LEU cc_start: 0.9181 (OUTLIER) cc_final: 0.8827 (mm) REVERT: 4 56 LYS cc_start: 0.8118 (mmtp) cc_final: 0.7755 (ttmm) REVERT: 4 261 LEU cc_start: 0.7810 (mp) cc_final: 0.7415 (tt) REVERT: 6 150 SER cc_start: 0.7733 (p) cc_final: 0.7387 (t) REVERT: 7 103 ILE cc_start: 0.7819 (pt) cc_final: 0.7244 (tp) REVERT: 7 341 PRO cc_start: 0.8776 (Cg_exo) cc_final: 0.8470 (Cg_endo) REVERT: 7 494 MET cc_start: 0.7047 (mmm) cc_final: 0.6811 (mmm) REVERT: 7 586 GLN cc_start: 0.7918 (tp40) cc_final: 0.7660 (mp10) REVERT: 7 590 MET cc_start: 0.7455 (mtp) cc_final: 0.7050 (mtp) REVERT: 7 636 GLU cc_start: 0.8455 (tp30) cc_final: 0.7989 (tp30) outliers start: 85 outliers final: 68 residues processed: 405 average time/residue: 0.1408 time to fit residues: 92.6566 Evaluate side-chains 405 residues out of total 2487 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 335 time to evaluate : 0.617 ------------------------------------------------------------------------------- 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 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 361 LEU 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 567 LEU Chi-restraints excluded: chain 0 residue 604 VAL Chi-restraints excluded: chain 0 residue 619 ILE 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 1 residue 534 ASN 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 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 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 176 ASN Chi-restraints excluded: chain 4 residue 196 LEU Chi-restraints excluded: chain 4 residue 202 LEU Chi-restraints excluded: chain 4 residue 223 LEU Chi-restraints excluded: chain 4 residue 257 CYS 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 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 265 GLN 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 193 VAL Chi-restraints excluded: chain 7 residue 267 THR Chi-restraints excluded: chain 7 residue 361 CYS Chi-restraints excluded: chain 7 residue 366 ASN 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 280 random chunks: chunk 198 optimal weight: 1.9990 chunk 188 optimal weight: 0.5980 chunk 138 optimal weight: 3.9990 chunk 147 optimal weight: 6.9990 chunk 83 optimal weight: 0.8980 chunk 21 optimal weight: 0.4980 chunk 223 optimal weight: 0.3980 chunk 14 optimal weight: 5.9990 chunk 192 optimal weight: 0.1980 chunk 28 optimal weight: 2.9990 chunk 229 optimal weight: 0.5980 overall best weight: 0.4580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 46 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 4 48 HIS ** 4 108 ASN ** 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** 7 187 HIS 7 366 ASN 7 459 GLN ** 7 497 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4434 r_free = 0.4434 target = 0.174395 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4174 r_free = 0.4174 target = 0.152374 restraints weight = 44924.380| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.4132 r_free = 0.4132 target = 0.149655 restraints weight = 68502.700| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.4112 r_free = 0.4112 target = 0.148211 restraints weight = 57930.309| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.4108 r_free = 0.4108 target = 0.148043 restraints weight = 53955.428| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.4103 r_free = 0.4103 target = 0.147801 restraints weight = 44709.989| |-----------------------------------------------------------------------------| r_work (final): 0.4100 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6706 moved from start: 0.4403 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 24275 Z= 0.151 Angle : 0.750 23.378 33049 Z= 0.353 Chirality : 0.044 0.412 3724 Planarity : 0.004 0.059 4029 Dihedral : 13.446 69.072 3602 Min Nonbonded Distance : 1.950 Molprobity Statistics. All-atom Clashscore : 12.92 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.76 % Favored : 95.20 % Rotamer: Outliers : 3.14 % Allowed : 20.59 % Favored : 76.28 % 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: -0.59 (0.16), residues: 2752 helix: 0.56 (0.14), residues: 1385 sheet: -1.68 (0.33), residues: 245 loop : -1.24 (0.18), residues: 1122 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG 7 62 TYR 0.019 0.001 TYR 7 534 PHE 0.041 0.002 PHE 2 261 TRP 0.054 0.002 TRP 0 552 HIS 0.024 0.001 HIS 7 187 Details of bonding type rmsd/Z covalent geometry : bond 0.00336 / 0.15 (24242) covalent geometry : angle 0.69841 / 0.35 (33001) hydrogen bonds : bond 0.04015 / 2.65 ( 1110) hydrogen bonds : angle 4.82177 / 3.53 ( 3200) metal coordination : bond 0.01495 / 0.92 ( 32) metal coordination : angle 7.20622 / 4.07 ( 48) Misc. bond : bond 0.00004 / 0.00 ( 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 424 residues out of total 2487 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 346 time to evaluate : 0.979 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: 0 1 MET cc_start: 0.3713 (mtp) cc_final: 0.2897 (mtp) REVERT: 0 329 PHE cc_start: 0.7538 (t80) cc_final: 0.7256 (t80) REVERT: 0 438 MET cc_start: 0.6151 (ptp) cc_final: 0.5836 (ttm) REVERT: 0 709 THR cc_start: 0.7717 (OUTLIER) cc_final: 0.7406 (p) REVERT: 1 441 MET cc_start: 0.6928 (tpp) cc_final: 0.6709 (tpt) REVERT: 1 499 ARG cc_start: 0.6087 (mtt180) cc_final: 0.4965 (mtt180) REVERT: 1 545 MET cc_start: 0.1765 (ptt) cc_final: 0.0241 (tmm) REVERT: 2 109 ILE cc_start: 0.8843 (tt) cc_final: 0.8335 (tp) REVERT: 2 393 LEU cc_start: 0.9195 (OUTLIER) cc_final: 0.8838 (mm) REVERT: 4 56 LYS cc_start: 0.7987 (mmtp) cc_final: 0.7646 (ttmm) REVERT: 4 261 LEU cc_start: 0.8109 (mp) cc_final: 0.7751 (tt) REVERT: 6 150 SER cc_start: 0.7699 (p) cc_final: 0.7321 (t) REVERT: 6 331 PHE cc_start: 0.4813 (m-80) cc_final: 0.4461 (m-80) REVERT: 7 103 ILE cc_start: 0.7768 (pt) cc_final: 0.7226 (tp) REVERT: 7 341 PRO cc_start: 0.8774 (Cg_exo) cc_final: 0.8423 (Cg_endo) REVERT: 7 366 ASN cc_start: 0.7629 (OUTLIER) cc_final: 0.7339 (t0) REVERT: 7 421 TRP cc_start: 0.7328 (t-100) cc_final: 0.7101 (t-100) REVERT: 7 442 GLU cc_start: 0.7550 (mm-30) cc_final: 0.7288 (mp0) REVERT: 7 494 MET cc_start: 0.6938 (mmm) cc_final: 0.6725 (mmm) REVERT: 7 590 MET cc_start: 0.7424 (mtp) cc_final: 0.7005 (mtp) REVERT: 7 636 GLU cc_start: 0.8476 (tp30) cc_final: 0.7981 (tp30) outliers start: 78 outliers final: 67 residues processed: 399 average time/residue: 0.1380 time to fit residues: 89.3158 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 : 0.986 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 25 MET 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 361 LEU 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 567 LEU 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 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 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 176 ASN Chi-restraints excluded: chain 4 residue 196 LEU Chi-restraints excluded: chain 4 residue 202 LEU Chi-restraints excluded: chain 4 residue 223 LEU Chi-restraints excluded: chain 4 residue 257 CYS 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 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 187 HIS 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 366 ASN Chi-restraints excluded: chain 7 residue 385 ASP Chi-restraints excluded: chain 7 residue 604 THR 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: 0.4980 chunk 21 optimal weight: 1.9990 chunk 149 optimal weight: 6.9990 chunk 110 optimal weight: 1.9990 chunk 176 optimal weight: 0.9980 chunk 259 optimal weight: 0.5980 chunk 175 optimal weight: 4.9990 chunk 23 optimal weight: 4.9990 chunk 227 optimal weight: 0.6980 chunk 111 optimal weight: 0.0570 chunk 180 optimal weight: 7.9990 overall best weight: 0.5698 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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** ** 3 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 4 48 HIS ** 4 108 ASN ** 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** 6 265 GLN 7 187 HIS 7 366 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4430 r_free = 0.4430 target = 0.173946 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4183 r_free = 0.4183 target = 0.153028 restraints weight = 44578.277| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4147 r_free = 0.4147 target = 0.150796 restraints weight = 65326.028| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.4132 r_free = 0.4132 target = 0.149626 restraints weight = 47449.106| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.4129 r_free = 0.4129 target = 0.149504 restraints weight = 42355.694| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.4121 r_free = 0.4121 target = 0.148914 restraints weight = 39646.208| |-----------------------------------------------------------------------------| r_work (final): 0.4118 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6680 moved from start: 0.4507 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 24275 Z= 0.160 Angle : 0.763 23.402 33049 Z= 0.359 Chirality : 0.044 0.396 3724 Planarity : 0.004 0.077 4029 Dihedral : 13.479 69.177 3602 Min Nonbonded Distance : 1.937 Molprobity Statistics. All-atom Clashscore : 13.45 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.91 % Favored : 95.06 % Rotamer: Outliers : 3.26 % Allowed : 20.75 % Favored : 76.00 % 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: -0.67 (0.16), residues: 2752 helix: 0.51 (0.14), residues: 1391 sheet: -1.75 (0.33), residues: 248 loop : -1.29 (0.18), residues: 1113 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG 7 520 TYR 0.019 0.002 TYR 1 533 PHE 0.045 0.002 PHE 2 261 TRP 0.052 0.002 TRP 0 552 HIS 0.029 0.002 HIS 7 187 Details of bonding type rmsd/Z covalent geometry : bond 0.00362 / 0.16 (24242) covalent geometry : angle 0.71321 / 0.36 (33001) hydrogen bonds : bond 0.03973 / 2.64 ( 1110) hydrogen bonds : angle 4.83370 / 3.53 ( 3200) metal coordination : bond 0.01469 / 0.89 ( 32) metal coordination : angle 7.16390 / 4.02 ( 48) Misc. bond : bond 0.00006 / 0.00 ( 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 424 residues out of total 2487 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 343 time to evaluate : 0.742 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: 0 1 MET cc_start: 0.3446 (mtp) cc_final: 0.2838 (mtp) REVERT: 0 42 MET cc_start: 0.8217 (ppp) cc_final: 0.7548 (ppp) REVERT: 0 438 MET cc_start: 0.6116 (ptp) cc_final: 0.5842 (ttm) REVERT: 0 657 MET cc_start: 0.7401 (mmp) cc_final: 0.7077 (mmm) REVERT: 0 709 THR cc_start: 0.7657 (OUTLIER) cc_final: 0.7333 (p) REVERT: 1 499 ARG cc_start: 0.6192 (mtt180) cc_final: 0.5104 (mtt180) REVERT: 1 545 MET cc_start: 0.1626 (ptt) cc_final: 0.0272 (tmm) REVERT: 2 109 ILE cc_start: 0.8861 (tt) cc_final: 0.8353 (tp) REVERT: 2 393 LEU cc_start: 0.9225 (OUTLIER) cc_final: 0.8861 (mm) REVERT: 4 56 LYS cc_start: 0.8161 (mmtp) cc_final: 0.7831 (ttmm) REVERT: 4 261 LEU cc_start: 0.8100 (mp) cc_final: 0.7714 (tt) REVERT: 6 57 MET cc_start: 0.7469 (mmm) cc_final: 0.7262 (mmm) REVERT: 6 150 SER cc_start: 0.7741 (p) cc_final: 0.7367 (t) REVERT: 7 103 ILE cc_start: 0.7829 (pt) cc_final: 0.7266 (tp) REVERT: 7 341 PRO cc_start: 0.8761 (Cg_exo) cc_final: 0.8438 (Cg_endo) REVERT: 7 366 ASN cc_start: 0.7485 (OUTLIER) cc_final: 0.7196 (t0) REVERT: 7 442 GLU cc_start: 0.7650 (mm-30) cc_final: 0.7272 (mp0) REVERT: 7 494 MET cc_start: 0.6943 (mmm) cc_final: 0.6722 (mmm) REVERT: 7 590 MET cc_start: 0.7475 (mtp) cc_final: 0.7108 (mtp) REVERT: 7 636 GLU cc_start: 0.8531 (tp30) cc_final: 0.8305 (tp30) outliers start: 81 outliers final: 71 residues processed: 395 average time/residue: 0.1391 time to fit residues: 89.4092 Evaluate side-chains 399 residues out of total 2487 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 325 time to evaluate : 0.951 ------------------------------------------------------------------------------- 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 333 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 490 LEU Chi-restraints excluded: chain 0 residue 560 ASN Chi-restraints excluded: chain 0 residue 567 LEU 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 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 81 ILE Chi-restraints excluded: chain 4 residue 34 LEU 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 179 ASN Chi-restraints excluded: chain 4 residue 196 LEU Chi-restraints excluded: chain 4 residue 202 LEU Chi-restraints excluded: chain 4 residue 223 LEU Chi-restraints excluded: chain 4 residue 257 CYS 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 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 265 GLN 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 187 HIS Chi-restraints excluded: chain 7 residue 189 LEU Chi-restraints excluded: chain 7 residue 193 VAL Chi-restraints excluded: chain 7 residue 267 THR Chi-restraints excluded: chain 7 residue 361 CYS Chi-restraints excluded: chain 7 residue 366 ASN Chi-restraints excluded: chain 7 residue 385 ASP Chi-restraints excluded: chain 7 residue 604 THR 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 100 optimal weight: 0.5980 chunk 55 optimal weight: 0.0870 chunk 7 optimal weight: 3.9990 chunk 67 optimal weight: 0.7980 chunk 70 optimal weight: 1.9990 chunk 119 optimal weight: 1.9990 chunk 95 optimal weight: 2.9990 chunk 21 optimal weight: 0.9990 chunk 81 optimal weight: 6.9990 chunk 61 optimal weight: 0.7980 chunk 125 optimal weight: 0.7980 overall best weight: 0.6158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 48 HIS ** 4 108 ASN ** 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** ** 6 265 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 7 366 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4431 r_free = 0.4431 target = 0.174038 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4191 r_free = 0.4191 target = 0.153736 restraints weight = 44544.519| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.4148 r_free = 0.4148 target = 0.150880 restraints weight = 64376.428| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 59)----------------| | r_work = 0.4121 r_free = 0.4121 target = 0.148873 restraints weight = 52941.297| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.4119 r_free = 0.4119 target = 0.148921 restraints weight = 52485.820| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.4115 r_free = 0.4115 target = 0.148632 restraints weight = 40845.225| |-----------------------------------------------------------------------------| r_work (final): 0.4113 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6691 moved from start: 0.4522 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.438 24275 Z= 0.292 Angle : 0.965 59.194 33049 Z= 0.550 Chirality : 0.057 1.790 3724 Planarity : 0.007 0.210 4029 Dihedral : 13.471 69.170 3602 Min Nonbonded Distance : 1.937 Molprobity Statistics. All-atom Clashscore : 15.69 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.94 % Favored : 95.02 % Rotamer: Outliers : 3.10 % Allowed : 21.19 % Favored : 75.71 % Cbeta Deviations : 0.15 % 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: -0.67 (0.16), residues: 2752 helix: 0.51 (0.14), residues: 1391 sheet: -1.75 (0.33), residues: 248 loop : -1.29 (0.18), residues: 1113 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.000 ARG 0 272 TYR 0.017 0.001 TYR 7 534 PHE 0.040 0.002 PHE 2 261 TRP 0.047 0.002 TRP 0 552 HIS 0.280 0.003 HIS 7 187 Details of bonding type rmsd/Z covalent geometry : bond 0.00567 / 0.29 (24242) covalent geometry : angle 0.92648 / 0.55 (33001) hydrogen bonds : bond 0.03999 / 2.66 ( 1110) hydrogen bonds : angle 4.85869 / 3.55 ( 3200) metal coordination : bond 0.01455 / 0.89 ( 32) metal coordination : angle 7.16068 / 4.02 ( 48) Misc. bond : bond 0.00007 / 0.00 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3930.08 seconds wall clock time: 69 minutes 4.00 seconds (4144.00 seconds total)