Starting phenix.real_space_refine on Fri Sep 19 05:59:59 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7nvx_12616/09_2025/7nvx_12616.cif Found real_map, /net/cci-nas-00/data/ceres_data/7nvx_12616/09_2025/7nvx_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_2025/7nvx_12616.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7nvx_12616/09_2025/7nvx_12616.map" model { file = "/net/cci-nas-00/data/ceres_data/7nvx_12616/09_2025/7nvx_12616.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7nvx_12616/09_2025/7nvx_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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/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: 4.47, per 1000 atoms: 0.19 Number of scatterers: 23663 At special positions: 0 Unit cell: (172.2, 170.1, 137.55, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 10 Type Number sf(0) Zn 7 29.99 Fe 4 26.01 S 146 16.00 P 52 15.00 Mg 1 11.99 F 3 9.00 O 4426 8.00 N 4094 7.00 C 14929 6.00 Be 1 4.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 1.59 Conformation dependent library (CDL) restraints added in 1.0 seconds Enol-peptide restraints added in 715.3 nanoseconds 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: 2.90 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: 4.55 Time building geometry restraints manager: 2.07 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: 32784 2.29 - 4.58: 200 4.58 - 6.87: 9 6.87 - 9.16: 4 9.16 - 11.45: 4 Bond angle restraints: 33001 Sorted by residual: angle pdb=" PA ADP 7 901 " pdb=" O3A ADP 7 901 " pdb=" PB ADP 7 901 " ideal model delta sigma weight residual 120.50 131.95 -11.45 3.00e+00 1.11e-01 1.46e+01 angle pdb=" C2' ADP 7 901 " pdb=" C3' ADP 7 901 " pdb=" C4' ADP 7 901 " ideal model delta sigma weight residual 111.00 100.09 10.91 3.00e+00 1.11e-01 1.32e+01 angle pdb=" C1' ADP 7 901 " pdb=" C2' ADP 7 901 " pdb=" C3' ADP 7 901 " ideal model delta sigma weight residual 111.00 100.13 10.87 3.00e+00 1.11e-01 1.31e+01 angle pdb=" N ILE 5 35 " pdb=" CA ILE 5 35 " pdb=" C ILE 5 35 " ideal model delta sigma weight residual 111.90 109.21 2.69 8.10e-01 1.52e+00 1.10e+01 angle pdb=" C SER 0 462 " pdb=" CA SER 0 462 " pdb=" CB SER 0 462 " ideal model delta sigma weight residual 109.51 115.52 -6.01 1.85e+00 2.92e-01 1.06e+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: 2989 0.041 - 0.081: 506 0.081 - 0.122: 215 0.122 - 0.162: 13 0.162 - 0.203: 1 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=" CA ILE 7 580 " pdb=" N ILE 7 580 " pdb=" C ILE 7 580 " pdb=" CB ILE 7 580 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.54e-01 chirality pdb=" CA VAL 1 211 " pdb=" N VAL 1 211 " pdb=" C VAL 1 211 " pdb=" CB VAL 1 211 " both_signs ideal model delta sigma weight residual False 2.44 2.58 -0.13 2.00e-01 2.50e+01 4.54e-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: 7.230 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.270 Check model and map are aligned: 0.070 Set scattering table: 0.060 Process input model: 27.330 Find NCS groups from input model: 0.130 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.400 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.550 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6395 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= 0.378 Angle : 0.534 14.213 33049 Z= 0.278 Chirality : 0.037 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 aren 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 covalent geometry : bond 0.00272 (24242) covalent geometry : angle 0.49198 (33001) hydrogen bonds : bond 0.24945 ( 1110) hydrogen bonds : angle 7.26933 ( 3200) metal coordination : bond 0.14592 ( 32) metal coordination : angle 5.47538 ( 48) Misc. bond : bond 0.46374 ( 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 : 0.908 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 0 365 VAL cc_start: 0.7821 (p) cc_final: 0.7495 (t) REVERT: 0 438 MET cc_start: 0.6887 (ptp) cc_final: 0.5184 (ttm) REVERT: 1 499 ARG cc_start: 0.6071 (mtt180) cc_final: 0.5123 (mtt180) REVERT: 1 534 ASN cc_start: 0.6570 (m110) cc_final: 0.6307 (t0) REVERT: 1 545 MET cc_start: 0.4405 (ttt) cc_final: 0.3833 (ptt) REVERT: 2 85 GLU cc_start: 0.7152 (pp20) cc_final: 0.6900 (mt-10) REVERT: 2 109 ILE cc_start: 0.8822 (tt) cc_final: 0.8476 (tp) REVERT: 2 225 SER cc_start: 0.8787 (m) cc_final: 0.8286 (t) REVERT: 2 310 GLU cc_start: 0.7724 (mm-30) cc_final: 0.7495 (mm-30) REVERT: 2 318 TYR cc_start: 0.7498 (m-10) cc_final: 0.7292 (m-10) REVERT: 2 322 GLU cc_start: 0.7833 (tp30) cc_final: 0.7560 (tm-30) REVERT: 4 56 LYS cc_start: 0.7698 (mmtp) cc_final: 0.7469 (ttmm) REVERT: 4 277 ASN cc_start: 0.5202 (t0) cc_final: 0.4886 (m-40) REVERT: 6 233 THR cc_start: 0.8713 (m) cc_final: 0.8485 (p) REVERT: 6 236 VAL cc_start: 0.8724 (t) cc_final: 0.8438 (t) REVERT: 7 289 TYR cc_start: 0.5305 (m-80) cc_final: 0.5018 (m-80) REVERT: 7 421 TRP cc_start: 0.6963 (t60) cc_final: 0.6705 (t60) REVERT: 7 488 LEU cc_start: 0.8187 (mt) cc_final: 0.7793 (mm) REVERT: 7 541 PHE cc_start: 0.5945 (t80) cc_final: 0.4892 (t80) REVERT: 7 634 ARG cc_start: 0.8482 (ttp80) cc_final: 0.8106 (ttp80) outliers start: 0 outliers final: 0 residues processed: 689 average time/residue: 0.1666 time to fit residues: 173.8047 Evaluate side-chains 418 residues out of total 2487 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 418 time to evaluate : 0.734 ------------------------------------------------------------------------------- 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: 4.9990 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... Flipped N/Q/H residues before XYZ refinement: 0 328 HIS 0 384 HIS 0 402 ASN 0 649 ASN 1 537 HIS ** 2 37 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 2 211 GLN 2 224 GLN 2 289 ASN 2 390 GLN 3 24 ASN ** 4 63 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 4 176 ASN ** 4 258 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 7 459 GLN 7 481 ASN ** 7 497 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 7 506 GLN 7 564 ASN 7 595 ASN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4442 r_free = 0.4442 target = 0.174857 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.4156 r_free = 0.4156 target = 0.151967 restraints weight = 44668.927| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.4185 r_free = 0.4185 target = 0.155139 restraints weight = 90155.525| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4183 r_free = 0.4183 target = 0.155204 restraints weight = 40750.722| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.4188 r_free = 0.4188 target = 0.155670 restraints weight = 32741.823| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.4191 r_free = 0.4191 target = 0.156007 restraints weight = 27478.809| |-----------------------------------------------------------------------------| r_work (final): 0.4194 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6487 moved from start: 0.2937 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.069 24275 Z= 0.182 Angle : 0.752 20.705 33049 Z= 0.361 Chirality : 0.045 0.285 3724 Planarity : 0.005 0.081 4029 Dihedral : 12.674 92.442 3602 Min Nonbonded Distance : 1.939 Molprobity Statistics. All-atom Clashscore : 10.10 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.40 % Favored : 95.57 % Rotamer: Outliers : 2.53 % Allowed : 12.26 % Favored : 85.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.64 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.19 (0.16), residues: 2752 helix: 1.26 (0.14), residues: 1385 sheet: -1.39 (0.31), residues: 296 loop : -0.86 (0.19), residues: 1071 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG 0 282 TYR 0.034 0.002 TYR 0 410 PHE 0.031 0.002 PHE 0 332 TRP 0.032 0.002 TRP 2 96 HIS 0.010 0.002 HIS 7 187 Details of bonding type rmsd covalent geometry : bond 0.00412 (24242) covalent geometry : angle 0.69653 (33001) hydrogen bonds : bond 0.05476 ( 1110) hydrogen bonds : angle 5.23315 ( 3200) metal coordination : bond 0.01507 ( 32) metal coordination : angle 7.49410 ( 48) Misc. bond : bond 0.00103 ( 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 517 residues out of total 2487 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 454 time to evaluate : 0.905 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: 0 75 ARG cc_start: 0.8112 (OUTLIER) cc_final: 0.7909 (ttm110) REVERT: 0 87 LEU cc_start: 0.7715 (tt) cc_final: 0.7372 (tp) REVERT: 0 212 LEU cc_start: 0.7925 (tp) cc_final: 0.7702 (tp) REVERT: 0 438 MET cc_start: 0.6532 (ptp) cc_final: 0.5975 (ttm) REVERT: 0 677 MET cc_start: 0.8318 (pmm) cc_final: 0.7998 (pmm) REVERT: 1 309 HIS cc_start: 0.6438 (m170) cc_final: 0.5913 (m90) REVERT: 1 499 ARG cc_start: 0.6386 (mtt180) cc_final: 0.5261 (mtt180) REVERT: 1 534 ASN cc_start: 0.6688 (m110) cc_final: 0.6471 (t0) REVERT: 2 109 ILE cc_start: 0.8945 (tt) cc_final: 0.8535 (tp) REVERT: 2 156 TRP cc_start: 0.8580 (t-100) cc_final: 0.8371 (t-100) REVERT: 2 318 TYR cc_start: 0.7758 (m-10) cc_final: 0.7483 (m-10) REVERT: 4 56 LYS cc_start: 0.7604 (mmtp) cc_final: 0.7242 (ttmm) REVERT: 7 103 ILE cc_start: 0.7970 (pt) cc_final: 0.7274 (tp) REVERT: 7 341 PRO cc_start: 0.9020 (Cg_exo) cc_final: 0.8759 (Cg_endo) REVERT: 7 348 LEU cc_start: 0.7984 (OUTLIER) cc_final: 0.7711 (mt) REVERT: 7 488 LEU cc_start: 0.8241 (mt) cc_final: 0.7909 (mm) REVERT: 7 575 LEU cc_start: 0.8139 (mp) cc_final: 0.7792 (mp) REVERT: 7 636 GLU cc_start: 0.8661 (tp30) cc_final: 0.8201 (tp30) outliers start: 63 outliers final: 31 residues processed: 486 average time/residue: 0.1459 time to fit residues: 112.5988 Evaluate side-chains 388 residues out of total 2487 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 355 time to evaluate : 0.885 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 75 ARG Chi-restraints excluded: chain 0 residue 83 VAL Chi-restraints excluded: chain 0 residue 309 VAL Chi-restraints excluded: chain 0 residue 330 LEU Chi-restraints excluded: chain 0 residue 359 SER 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 547 SER Chi-restraints excluded: chain 0 residue 604 VAL Chi-restraints excluded: chain 0 residue 678 VAL Chi-restraints excluded: chain 1 residue 461 LEU Chi-restraints excluded: chain 2 residue 19 LEU Chi-restraints excluded: chain 2 residue 68 GLN Chi-restraints excluded: chain 2 residue 89 LEU Chi-restraints excluded: chain 2 residue 260 ASN Chi-restraints excluded: chain 3 residue 35 VAL Chi-restraints excluded: chain 3 residue 109 LEU Chi-restraints excluded: chain 4 residue 35 SER Chi-restraints excluded: chain 4 residue 57 LEU Chi-restraints excluded: chain 5 residue 57 VAL Chi-restraints excluded: chain 6 residue 182 ILE Chi-restraints excluded: chain 6 residue 218 THR Chi-restraints excluded: chain 6 residue 258 THR Chi-restraints excluded: chain 6 residue 312 LEU Chi-restraints excluded: chain 6 residue 318 LEU Chi-restraints excluded: chain 6 residue 336 LEU Chi-restraints excluded: chain 7 residue 72 THR Chi-restraints excluded: chain 7 residue 119 THR Chi-restraints excluded: chain 7 residue 189 LEU 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: 0.5980 chunk 80 optimal weight: 10.0000 chunk 143 optimal weight: 1.9990 chunk 173 optimal weight: 3.9990 chunk 93 optimal weight: 5.9990 chunk 6 optimal weight: 0.9980 chunk 24 optimal weight: 0.9980 chunk 82 optimal weight: 0.7980 chunk 180 optimal weight: 4.9990 chunk 100 optimal weight: 0.9990 chunk 9 optimal weight: 2.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 0 187 GLN 0 555 GLN 0 705 ASN 1 530 GLN 1 534 ASN 2 68 GLN 2 424 HIS 3 111 ASN ** 4 145 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 7 97 GLN 7 366 ASN 7 459 GLN 7 481 ASN 7 506 GLN 7 545 GLN 7 621 ASN 7 656 ASN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4408 r_free = 0.4408 target = 0.172035 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4168 r_free = 0.4168 target = 0.151917 restraints weight = 44806.826| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.4127 r_free = 0.4127 target = 0.149247 restraints weight = 62675.787| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.4109 r_free = 0.4109 target = 0.147728 restraints weight = 48948.120| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.4103 r_free = 0.4103 target = 0.147544 restraints weight = 50074.499| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.4091 r_free = 0.4091 target = 0.146603 restraints weight = 46949.776| |-----------------------------------------------------------------------------| r_work (final): 0.4095 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6692 moved from start: 0.3613 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 24275 Z= 0.189 Angle : 0.737 27.345 33049 Z= 0.345 Chirality : 0.043 0.257 3724 Planarity : 0.005 0.062 4029 Dihedral : 12.984 69.462 3602 Min Nonbonded Distance : 1.904 Molprobity Statistics. All-atom Clashscore : 11.81 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.58 % Favored : 95.39 % Rotamer: Outliers : 3.06 % Allowed : 14.92 % Favored : 82.03 % 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 aren not related in a simple way. whole: -0.24 (0.16), residues: 2752 helix: 0.86 (0.14), residues: 1395 sheet: -1.67 (0.32), residues: 261 loop : -1.03 (0.19), residues: 1096 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG 7 62 TYR 0.030 0.002 TYR 3 95 PHE 0.020 0.002 PHE 2 261 TRP 0.030 0.002 TRP 2 96 HIS 0.023 0.002 HIS 2 424 Details of bonding type rmsd covalent geometry : bond 0.00431 (24242) covalent geometry : angle 0.66929 (33001) hydrogen bonds : bond 0.04685 ( 1110) hydrogen bonds : angle 5.02959 ( 3200) metal coordination : bond 0.01021 ( 32) metal coordination : angle 8.13295 ( 48) Misc. bond : bond 0.00028 ( 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 462 residues out of total 2487 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 386 time to evaluate : 0.943 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: 0 75 ARG cc_start: 0.8209 (OUTLIER) cc_final: 0.7943 (ttm110) REVERT: 0 212 LEU cc_start: 0.8146 (tp) cc_final: 0.7897 (tp) REVERT: 0 438 MET cc_start: 0.6494 (ptp) cc_final: 0.6013 (ttm) REVERT: 1 499 ARG cc_start: 0.6206 (mtt180) cc_final: 0.5118 (mtt180) REVERT: 1 545 MET cc_start: 0.2086 (ptt) cc_final: 0.0517 (tmm) REVERT: 2 109 ILE cc_start: 0.8888 (tt) cc_final: 0.8419 (tp) REVERT: 2 225 SER cc_start: 0.8804 (m) cc_final: 0.8499 (t) REVERT: 2 288 ILE cc_start: 0.8362 (OUTLIER) cc_final: 0.8141 (mt) REVERT: 2 393 LEU cc_start: 0.9228 (OUTLIER) cc_final: 0.8972 (mm) REVERT: 2 399 ASP cc_start: 0.7391 (p0) cc_final: 0.7137 (p0) REVERT: 4 56 LYS cc_start: 0.8105 (mmtp) cc_final: 0.7730 (ttmm) REVERT: 4 192 ASP cc_start: 0.8603 (OUTLIER) cc_final: 0.8067 (m-30) REVERT: 7 93 TYR cc_start: 0.7124 (t80) cc_final: 0.5180 (p90) REVERT: 7 103 ILE cc_start: 0.7845 (pt) cc_final: 0.7223 (tp) REVERT: 7 289 TYR cc_start: 0.5400 (m-10) cc_final: 0.5198 (m-80) REVERT: 7 341 PRO cc_start: 0.8948 (Cg_exo) cc_final: 0.8663 (Cg_endo) REVERT: 7 488 LEU cc_start: 0.8212 (mt) cc_final: 0.7893 (mm) REVERT: 7 494 MET cc_start: 0.7465 (mmm) cc_final: 0.7220 (mpp) REVERT: 7 634 ARG cc_start: 0.8697 (ttp80) cc_final: 0.8258 (ttp80) REVERT: 7 636 GLU cc_start: 0.8603 (tp30) cc_final: 0.8237 (tp30) outliers start: 76 outliers final: 46 residues processed: 435 average time/residue: 0.1621 time to fit residues: 111.7707 Evaluate side-chains 382 residues out of total 2487 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 332 time to evaluate : 0.908 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 75 ARG Chi-restraints excluded: chain 0 residue 83 VAL Chi-restraints excluded: chain 0 residue 266 LEU 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 367 ILE 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 547 SER 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 668 ILE 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 89 LEU Chi-restraints excluded: chain 2 residue 158 VAL Chi-restraints excluded: chain 2 residue 260 ASN Chi-restraints excluded: chain 2 residue 288 ILE Chi-restraints excluded: chain 2 residue 393 LEU Chi-restraints excluded: chain 2 residue 401 LEU Chi-restraints excluded: chain 3 residue 35 VAL Chi-restraints excluded: chain 4 residue 11 LEU Chi-restraints excluded: chain 4 residue 57 LEU Chi-restraints excluded: chain 4 residue 176 ASN Chi-restraints excluded: chain 4 residue 192 ASP Chi-restraints excluded: chain 4 residue 196 LEU Chi-restraints excluded: chain 4 residue 257 CYS 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 258 THR Chi-restraints excluded: chain 6 residue 318 LEU 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 284 CYS Chi-restraints excluded: chain 7 residue 361 CYS Chi-restraints excluded: chain 7 residue 548 ILE Chi-restraints excluded: chain 7 residue 666 ASP Chi-restraints excluded: chain 7 residue 667 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 280 random chunks: chunk 109 optimal weight: 3.9990 chunk 69 optimal weight: 5.9990 chunk 16 optimal weight: 3.9990 chunk 148 optimal weight: 3.9990 chunk 274 optimal weight: 4.9990 chunk 67 optimal weight: 0.6980 chunk 236 optimal weight: 0.5980 chunk 173 optimal weight: 7.9990 chunk 216 optimal weight: 0.5980 chunk 44 optimal weight: 2.9990 chunk 29 optimal weight: 7.9990 overall best weight: 1.7784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 0 238 ASN 1 530 GLN 2 37 HIS 2 68 GLN 2 362 GLN ** 4 55 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 4 63 HIS ** 4 145 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 4 248 HIS 6 162 HIS 7 173 ASN 7 187 HIS 7 459 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4351 r_free = 0.4351 target = 0.167202 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4112 r_free = 0.4112 target = 0.147461 restraints weight = 44712.031| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.4061 r_free = 0.4061 target = 0.144096 restraints weight = 61941.460| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.4033 r_free = 0.4033 target = 0.141820 restraints weight = 53682.773| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.4024 r_free = 0.4024 target = 0.141470 restraints weight = 57065.759| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.4011 r_free = 0.4011 target = 0.140371 restraints weight = 49468.439| |-----------------------------------------------------------------------------| r_work (final): 0.4013 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6865 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 : 0.007 0.072 24275 Z= 0.301 Angle : 0.835 28.501 33049 Z= 0.396 Chirality : 0.046 0.191 3724 Planarity : 0.005 0.051 4029 Dihedral : 13.624 68.394 3602 Min Nonbonded Distance : 1.857 Molprobity Statistics. All-atom Clashscore : 15.07 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.85 % Favored : 94.11 % Rotamer: Outliers : 4.42 % Allowed : 16.61 % Favored : 78.97 % 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 aren not related in a simple way. whole: -0.86 (0.16), residues: 2752 helix: 0.41 (0.13), residues: 1394 sheet: -2.05 (0.32), residues: 257 loop : -1.39 (0.18), residues: 1101 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG 2 58 TYR 0.032 0.002 TYR 4 71 PHE 0.033 0.003 PHE 2 261 TRP 0.030 0.002 TRP 2 96 HIS 0.017 0.002 HIS 2 424 Details of bonding type rmsd covalent geometry : bond 0.00686 (24242) covalent geometry : angle 0.76343 (33001) hydrogen bonds : bond 0.04870 ( 1110) hydrogen bonds : angle 5.25867 ( 3200) metal coordination : bond 0.02084 ( 32) metal coordination : angle 8.88766 ( 48) Misc. bond : bond 0.00015 ( 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 462 residues out of total 2487 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 110 poor density : 352 time to evaluate : 0.816 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: 0 212 LEU cc_start: 0.8211 (tp) cc_final: 0.7952 (tp) REVERT: 0 438 MET cc_start: 0.6645 (ptp) cc_final: 0.6092 (mtm) REVERT: 0 677 MET cc_start: 0.8337 (pmm) cc_final: 0.8033 (pmm) REVERT: 1 499 ARG cc_start: 0.6307 (mtt180) cc_final: 0.5189 (mtt180) REVERT: 1 545 MET cc_start: 0.2017 (ptt) cc_final: 0.0456 (tmm) REVERT: 2 109 ILE cc_start: 0.8859 (tt) cc_final: 0.8491 (tp) REVERT: 2 225 SER cc_start: 0.8932 (m) cc_final: 0.8612 (t) REVERT: 2 310 GLU cc_start: 0.7747 (mm-30) cc_final: 0.7083 (mm-30) REVERT: 2 393 LEU cc_start: 0.9397 (OUTLIER) cc_final: 0.9087 (mm) REVERT: 3 134 GLN cc_start: 0.6561 (mp10) cc_final: 0.6208 (mp10) REVERT: 4 157 MET cc_start: 0.7854 (OUTLIER) cc_final: 0.7641 (ttt) REVERT: 6 150 SER cc_start: 0.7703 (p) cc_final: 0.7382 (t) REVERT: 6 265 GLN cc_start: 0.7415 (mm110) cc_final: 0.7181 (mm-40) REVERT: 7 103 ILE cc_start: 0.7842 (pt) cc_final: 0.7189 (tp) REVERT: 7 341 PRO cc_start: 0.8970 (Cg_exo) cc_final: 0.8717 (Cg_endo) REVERT: 7 442 GLU cc_start: 0.7716 (mm-30) cc_final: 0.7263 (mp0) REVERT: 7 494 MET cc_start: 0.7511 (mmm) cc_final: 0.7212 (mmm) REVERT: 7 634 ARG cc_start: 0.8707 (ttp80) cc_final: 0.8247 (ttp80) outliers start: 110 outliers final: 66 residues processed: 430 average time/residue: 0.1613 time to fit residues: 111.8160 Evaluate side-chains 383 residues out of total 2487 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 315 time to evaluate : 0.886 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 83 VAL Chi-restraints excluded: chain 0 residue 92 ASN 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 547 SER Chi-restraints excluded: chain 0 residue 560 ASN Chi-restraints excluded: chain 0 residue 569 ILE Chi-restraints excluded: chain 0 residue 619 ILE Chi-restraints excluded: chain 0 residue 626 VAL Chi-restraints excluded: chain 0 residue 663 CYS Chi-restraints excluded: chain 0 residue 668 ILE Chi-restraints excluded: chain 0 residue 678 VAL Chi-restraints excluded: chain 1 residue 376 LEU Chi-restraints excluded: chain 1 residue 529 LEU Chi-restraints excluded: chain 2 residue 19 LEU Chi-restraints excluded: chain 2 residue 44 VAL 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 401 LEU Chi-restraints excluded: chain 3 residue 21 LEU Chi-restraints excluded: chain 3 residue 35 VAL Chi-restraints excluded: chain 3 residue 82 TYR 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 157 MET Chi-restraints excluded: chain 4 residue 176 ASN Chi-restraints excluded: chain 4 residue 192 ASP Chi-restraints excluded: chain 4 residue 196 LEU Chi-restraints excluded: chain 4 residue 257 CYS Chi-restraints excluded: chain 5 residue 26 SER Chi-restraints excluded: chain 6 residue 84 THR Chi-restraints excluded: chain 6 residue 87 LEU Chi-restraints excluded: chain 6 residue 123 ASN Chi-restraints excluded: chain 6 residue 174 LEU Chi-restraints excluded: chain 6 residue 182 ILE Chi-restraints excluded: chain 6 residue 214 GLU Chi-restraints excluded: chain 6 residue 218 THR Chi-restraints excluded: chain 6 residue 221 VAL Chi-restraints excluded: chain 6 residue 258 THR Chi-restraints excluded: chain 6 residue 284 LEU Chi-restraints excluded: chain 6 residue 307 ILE Chi-restraints excluded: chain 6 residue 318 LEU Chi-restraints excluded: chain 6 residue 357 VAL Chi-restraints excluded: chain 6 residue 366 VAL Chi-restraints excluded: chain 6 residue 385 CYS Chi-restraints excluded: chain 7 residue 72 THR Chi-restraints excluded: chain 7 residue 119 THR Chi-restraints excluded: chain 7 residue 189 LEU Chi-restraints excluded: chain 7 residue 361 CYS Chi-restraints excluded: chain 7 residue 385 ASP Chi-restraints excluded: chain 7 residue 470 LEU Chi-restraints excluded: chain 7 residue 477 ILE Chi-restraints excluded: chain 7 residue 505 VAL Chi-restraints excluded: chain 7 residue 548 ILE Chi-restraints excluded: chain 7 residue 604 THR 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: 0.4980 chunk 65 optimal weight: 0.8980 chunk 233 optimal weight: 2.9990 chunk 258 optimal weight: 0.5980 chunk 259 optimal weight: 0.7980 chunk 163 optimal weight: 0.8980 chunk 13 optimal weight: 10.0000 chunk 228 optimal weight: 0.9980 chunk 230 optimal weight: 1.9990 chunk 57 optimal weight: 3.9990 chunk 185 optimal weight: 0.9980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 0 135 HIS 0 519 ASN 2 37 HIS ** 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** ** 4 145 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 7 187 HIS 7 459 GLN ** 7 545 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 = 0.4387 r_free = 0.4387 target = 0.170421 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4164 r_free = 0.4164 target = 0.151616 restraints weight = 44266.457| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.4110 r_free = 0.4110 target = 0.147870 restraints weight = 54094.697| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.4081 r_free = 0.4081 target = 0.145624 restraints weight = 48413.169| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.4069 r_free = 0.4069 target = 0.145099 restraints weight = 50066.242| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.4060 r_free = 0.4060 target = 0.144293 restraints weight = 40705.638| |-----------------------------------------------------------------------------| r_work (final): 0.4062 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6771 moved from start: 0.4415 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.198 24275 Z= 0.167 Angle : 0.727 27.514 33049 Z= 0.335 Chirality : 0.043 0.269 3724 Planarity : 0.004 0.055 4029 Dihedral : 13.391 68.320 3602 Min Nonbonded Distance : 1.959 Molprobity Statistics. All-atom Clashscore : 13.02 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.80 % Favored : 95.17 % Rotamer: Outliers : 3.74 % Allowed : 19.10 % Favored : 77.16 % 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 aren not related in a simple way. whole: -0.75 (0.16), residues: 2752 helix: 0.54 (0.14), residues: 1383 sheet: -1.97 (0.32), residues: 250 loop : -1.41 (0.18), residues: 1119 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG 7 62 TYR 0.030 0.002 TYR 0 674 PHE 0.035 0.002 PHE 2 261 TRP 0.039 0.002 TRP 0 552 HIS 0.021 0.001 HIS 3 28 Details of bonding type rmsd covalent geometry : bond 0.00380 (24242) covalent geometry : angle 0.65523 (33001) hydrogen bonds : bond 0.04092 ( 1110) hydrogen bonds : angle 4.89814 ( 3200) metal coordination : bond 0.03680 ( 32) metal coordination : angle 8.27189 ( 48) Misc. bond : bond 0.00014 ( 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 453 residues out of total 2487 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 360 time to evaluate : 0.931 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: 0 212 LEU cc_start: 0.8136 (tp) cc_final: 0.7871 (tp) REVERT: 0 438 MET cc_start: 0.6565 (ptp) cc_final: 0.6143 (mtm) REVERT: 0 620 MET cc_start: 0.6123 (tpp) cc_final: 0.5908 (ttt) REVERT: 1 499 ARG cc_start: 0.6279 (mtt180) cc_final: 0.5112 (mtt180) REVERT: 1 545 MET cc_start: 0.1984 (ptt) cc_final: 0.0532 (tmm) REVERT: 2 109 ILE cc_start: 0.8844 (tt) cc_final: 0.8487 (tp) REVERT: 2 225 SER cc_start: 0.8897 (m) cc_final: 0.8619 (t) REVERT: 2 393 LEU cc_start: 0.9310 (OUTLIER) cc_final: 0.8980 (mm) REVERT: 4 56 LYS cc_start: 0.8247 (mmtp) cc_final: 0.7918 (ttmm) REVERT: 6 150 SER cc_start: 0.7722 (p) cc_final: 0.7434 (t) REVERT: 7 103 ILE cc_start: 0.7865 (pt) cc_final: 0.7297 (tp) REVERT: 7 341 PRO cc_start: 0.8855 (Cg_exo) cc_final: 0.8596 (Cg_endo) outliers start: 93 outliers final: 64 residues processed: 428 average time/residue: 0.1552 time to fit residues: 107.2967 Evaluate side-chains 383 residues out of total 2487 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 318 time to evaluate : 0.874 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 83 VAL Chi-restraints excluded: chain 0 residue 135 HIS 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 315 LEU 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 547 SER 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 668 ILE Chi-restraints excluded: chain 0 residue 678 VAL 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 1 residue 534 ASN Chi-restraints excluded: chain 2 residue 19 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 359 ILE Chi-restraints excluded: chain 2 residue 383 LEU Chi-restraints excluded: chain 2 residue 393 LEU Chi-restraints excluded: chain 2 residue 401 LEU Chi-restraints excluded: chain 2 residue 440 LEU Chi-restraints excluded: chain 3 residue 23 VAL Chi-restraints excluded: chain 3 residue 35 VAL Chi-restraints excluded: chain 3 residue 81 ILE 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 132 LEU 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 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 123 ASN Chi-restraints excluded: chain 6 residue 145 LEU Chi-restraints excluded: chain 6 residue 174 LEU Chi-restraints excluded: chain 6 residue 182 ILE Chi-restraints excluded: chain 6 residue 214 GLU Chi-restraints excluded: chain 6 residue 218 THR Chi-restraints excluded: chain 6 residue 221 VAL Chi-restraints excluded: chain 6 residue 258 THR Chi-restraints excluded: chain 6 residue 284 LEU Chi-restraints excluded: chain 6 residue 312 LEU Chi-restraints excluded: chain 6 residue 318 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 284 CYS Chi-restraints excluded: chain 7 residue 361 CYS Chi-restraints excluded: chain 7 residue 385 ASP Chi-restraints excluded: chain 7 residue 484 ILE Chi-restraints excluded: chain 7 residue 502 ILE Chi-restraints excluded: chain 7 residue 667 THR Chi-restraints excluded: chain 7 residue 686 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 280 random chunks: chunk 166 optimal weight: 0.5980 chunk 213 optimal weight: 1.9990 chunk 195 optimal weight: 0.9990 chunk 118 optimal weight: 0.9980 chunk 153 optimal weight: 0.6980 chunk 204 optimal weight: 0.7980 chunk 24 optimal weight: 2.9990 chunk 196 optimal weight: 0.1980 chunk 125 optimal weight: 0.6980 chunk 269 optimal weight: 0.4980 chunk 1 optimal weight: 0.9990 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 0 145 GLN 0 262 ASN 0 307 ASN 2 20 GLN ** 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** ** 4 145 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 4 248 HIS 7 187 HIS 7 459 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4397 r_free = 0.4397 target = 0.171208 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.4160 r_free = 0.4160 target = 0.151355 restraints weight = 44525.987| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.4114 r_free = 0.4114 target = 0.148238 restraints weight = 61900.080| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.4093 r_free = 0.4093 target = 0.146676 restraints weight = 49075.144| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.4088 r_free = 0.4088 target = 0.146508 restraints weight = 47818.104| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.4075 r_free = 0.4075 target = 0.145453 restraints weight = 44146.694| |-----------------------------------------------------------------------------| r_work (final): 0.4081 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6739 moved from start: 0.4620 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.134 24275 Z= 0.151 Angle : 0.716 25.707 33049 Z= 0.331 Chirality : 0.042 0.235 3724 Planarity : 0.004 0.057 4029 Dihedral : 13.302 68.582 3602 Min Nonbonded Distance : 2.010 Molprobity Statistics. All-atom Clashscore : 12.85 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.94 % Favored : 95.02 % Rotamer: Outliers : 3.66 % Allowed : 20.06 % Favored : 76.28 % 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 aren not related in a simple way. whole: -0.70 (0.16), residues: 2752 helix: 0.58 (0.14), residues: 1386 sheet: -1.84 (0.32), residues: 252 loop : -1.41 (0.18), residues: 1114 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG 7 62 TYR 0.028 0.002 TYR 0 674 PHE 0.018 0.002 PHE 4 50 TRP 0.049 0.001 TRP 0 552 HIS 0.018 0.001 HIS 0 135 Details of bonding type rmsd covalent geometry : bond 0.00343 (24242) covalent geometry : angle 0.64734 (33001) hydrogen bonds : bond 0.03903 ( 1110) hydrogen bonds : angle 4.79203 ( 3200) metal coordination : bond 0.02972 ( 32) metal coordination : angle 8.07657 ( 48) Misc. bond : bond 0.00035 ( 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 452 residues out of total 2487 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 361 time to evaluate : 0.982 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: 0.6403 (ptp) cc_final: 0.5484 (ttm) REVERT: 1 499 ARG cc_start: 0.6053 (mtt180) cc_final: 0.5024 (mtt180) REVERT: 1 533 TYR cc_start: 0.6236 (OUTLIER) cc_final: 0.5746 (m-10) REVERT: 1 545 MET cc_start: 0.2385 (ptt) cc_final: 0.0923 (tmm) REVERT: 2 109 ILE cc_start: 0.8830 (tt) cc_final: 0.8365 (tp) REVERT: 2 156 TRP cc_start: 0.8602 (t-100) cc_final: 0.8209 (t-100) REVERT: 2 225 SER cc_start: 0.8836 (m) cc_final: 0.8574 (t) REVERT: 2 261 PHE cc_start: 0.8757 (t80) cc_final: 0.8458 (t80) REVERT: 2 310 GLU cc_start: 0.7486 (mm-30) cc_final: 0.6589 (mm-30) REVERT: 2 393 LEU cc_start: 0.9274 (OUTLIER) cc_final: 0.8970 (mm) REVERT: 4 56 LYS cc_start: 0.8156 (mmtp) cc_final: 0.7917 (ttmm) REVERT: 6 150 SER cc_start: 0.7658 (p) cc_final: 0.7321 (t) REVERT: 6 236 VAL cc_start: 0.8748 (OUTLIER) cc_final: 0.8474 (t) REVERT: 7 93 TYR cc_start: 0.6701 (t80) cc_final: 0.4924 (p90) REVERT: 7 103 ILE cc_start: 0.7805 (pt) cc_final: 0.7180 (tp) REVERT: 7 341 PRO cc_start: 0.8799 (Cg_exo) cc_final: 0.8473 (Cg_endo) outliers start: 91 outliers final: 71 residues processed: 425 average time/residue: 0.1585 time to fit residues: 108.3064 Evaluate side-chains 404 residues out of total 2487 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 330 time to evaluate : 0.926 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 315 LEU Chi-restraints excluded: chain 0 residue 325 THR 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 547 SER 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 663 CYS Chi-restraints excluded: chain 0 residue 668 ILE Chi-restraints excluded: chain 0 residue 678 VAL Chi-restraints excluded: chain 1 residue 457 ILE Chi-restraints excluded: chain 1 residue 461 LEU Chi-restraints excluded: chain 1 residue 533 TYR Chi-restraints excluded: chain 2 residue 19 LEU Chi-restraints excluded: chain 2 residue 44 VAL Chi-restraints excluded: chain 2 residue 158 VAL Chi-restraints excluded: chain 2 residue 260 ASN Chi-restraints excluded: chain 2 residue 341 MET Chi-restraints excluded: chain 2 residue 359 ILE Chi-restraints excluded: chain 2 residue 393 LEU Chi-restraints excluded: chain 2 residue 401 LEU Chi-restraints excluded: chain 2 residue 440 LEU Chi-restraints excluded: chain 3 residue 23 VAL Chi-restraints excluded: chain 3 residue 34 CYS Chi-restraints excluded: chain 3 residue 35 VAL Chi-restraints excluded: chain 3 residue 81 ILE Chi-restraints excluded: chain 4 residue 35 SER Chi-restraints excluded: chain 4 residue 50 PHE Chi-restraints excluded: chain 4 residue 57 LEU Chi-restraints excluded: chain 4 residue 132 LEU Chi-restraints excluded: chain 4 residue 176 ASN Chi-restraints excluded: chain 4 residue 196 LEU Chi-restraints excluded: chain 4 residue 257 CYS Chi-restraints excluded: chain 5 residue 5 LEU Chi-restraints excluded: chain 5 residue 26 SER 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 117 LEU Chi-restraints excluded: chain 6 residue 123 ASN Chi-restraints excluded: chain 6 residue 145 LEU Chi-restraints excluded: chain 6 residue 174 LEU Chi-restraints excluded: chain 6 residue 182 ILE Chi-restraints excluded: chain 6 residue 214 GLU Chi-restraints excluded: chain 6 residue 218 THR Chi-restraints excluded: chain 6 residue 221 VAL Chi-restraints excluded: chain 6 residue 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 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 284 CYS Chi-restraints excluded: chain 7 residue 308 ILE Chi-restraints excluded: chain 7 residue 361 CYS Chi-restraints excluded: chain 7 residue 385 ASP Chi-restraints excluded: chain 7 residue 484 ILE Chi-restraints excluded: chain 7 residue 667 THR Chi-restraints excluded: chain 7 residue 686 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 280 random chunks: chunk 38 optimal weight: 0.9980 chunk 0 optimal weight: 9.9990 chunk 23 optimal weight: 2.9990 chunk 68 optimal weight: 5.9990 chunk 173 optimal weight: 6.9990 chunk 266 optimal weight: 0.7980 chunk 31 optimal weight: 0.9990 chunk 36 optimal weight: 0.9990 chunk 106 optimal weight: 1.9990 chunk 208 optimal weight: 0.0980 chunk 90 optimal weight: 0.5980 overall best weight: 0.6982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 0 135 HIS 0 307 ASN ** 3 28 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 48 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 6 364 GLN 7 459 GLN 7 537 ASN ** 7 545 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 = 0.4391 r_free = 0.4391 target = 0.170787 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.4149 r_free = 0.4149 target = 0.150468 restraints weight = 44410.699| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.4107 r_free = 0.4107 target = 0.147696 restraints weight = 60539.491| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.4078 r_free = 0.4078 target = 0.145394 restraints weight = 49516.976| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.4065 r_free = 0.4065 target = 0.144718 restraints weight = 51259.409| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.4059 r_free = 0.4059 target = 0.144205 restraints weight = 41452.237| |-----------------------------------------------------------------------------| r_work (final): 0.4063 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6771 moved from start: 0.4824 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.128 24275 Z= 0.163 Angle : 0.729 26.032 33049 Z= 0.338 Chirality : 0.044 0.294 3724 Planarity : 0.004 0.057 4029 Dihedral : 13.317 68.992 3602 Min Nonbonded Distance : 1.923 Molprobity Statistics. All-atom Clashscore : 13.07 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.94 % Favored : 95.02 % Rotamer: Outliers : 3.94 % Allowed : 20.71 % Favored : 75.35 % 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 aren not related in a simple way. whole: -0.70 (0.16), residues: 2752 helix: 0.57 (0.14), residues: 1394 sheet: -1.82 (0.33), residues: 249 loop : -1.42 (0.18), residues: 1109 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG 0 616 TYR 0.039 0.002 TYR 0 674 PHE 0.025 0.002 PHE 2 162 TRP 0.052 0.002 TRP 0 552 HIS 0.014 0.001 HIS 3 28 Details of bonding type rmsd covalent geometry : bond 0.00373 (24242) covalent geometry : angle 0.66356 (33001) hydrogen bonds : bond 0.03901 ( 1110) hydrogen bonds : angle 4.77282 ( 3200) metal coordination : bond 0.02695 ( 32) metal coordination : angle 7.93388 ( 48) Misc. bond : bond 0.00033 ( 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 448 residues out of total 2487 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 350 time to evaluate : 1.040 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: 0 212 LEU cc_start: 0.8130 (tp) cc_final: 0.7876 (tp) REVERT: 0 438 MET cc_start: 0.6308 (ptp) cc_final: 0.5849 (ttm) REVERT: 1 499 ARG cc_start: 0.6117 (mtt180) cc_final: 0.5084 (mtt180) REVERT: 1 533 TYR cc_start: 0.6317 (OUTLIER) cc_final: 0.5865 (m-10) REVERT: 1 545 MET cc_start: 0.2363 (ptt) cc_final: 0.0952 (tmm) REVERT: 2 109 ILE cc_start: 0.8830 (tt) cc_final: 0.8369 (tp) REVERT: 2 225 SER cc_start: 0.8818 (m) cc_final: 0.8614 (t) REVERT: 2 261 PHE cc_start: 0.8742 (t80) cc_final: 0.8395 (t80) REVERT: 2 310 GLU cc_start: 0.7657 (mm-30) cc_final: 0.6654 (mm-30) REVERT: 2 393 LEU cc_start: 0.9277 (OUTLIER) cc_final: 0.8946 (mm) REVERT: 5 18 GLN cc_start: 0.7227 (mp10) cc_final: 0.6695 (mp10) REVERT: 6 150 SER cc_start: 0.7633 (p) cc_final: 0.7317 (t) REVERT: 6 171 PHE cc_start: 0.7215 (t80) cc_final: 0.6952 (t80) REVERT: 6 236 VAL cc_start: 0.8833 (OUTLIER) cc_final: 0.8557 (t) REVERT: 7 93 TYR cc_start: 0.6810 (t80) cc_final: 0.5042 (p90) REVERT: 7 103 ILE cc_start: 0.7841 (pt) cc_final: 0.7230 (tp) REVERT: 7 289 TYR cc_start: 0.5421 (m-10) cc_final: 0.5213 (m-80) REVERT: 7 341 PRO cc_start: 0.8797 (Cg_exo) cc_final: 0.8491 (Cg_endo) REVERT: 7 545 GLN cc_start: 0.7301 (mt0) cc_final: 0.6993 (mt0) REVERT: 7 634 ARG cc_start: 0.8750 (ttp80) cc_final: 0.8292 (ttp80) outliers start: 98 outliers final: 76 residues processed: 415 average time/residue: 0.1557 time to fit residues: 104.2090 Evaluate side-chains 409 residues out of total 2487 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 330 time to evaluate : 0.929 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 307 ASN Chi-restraints excluded: chain 0 residue 309 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 483 MET 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 663 CYS Chi-restraints excluded: chain 0 residue 668 ILE Chi-restraints excluded: chain 0 residue 678 VAL Chi-restraints excluded: chain 1 residue 127 LEU Chi-restraints excluded: chain 1 residue 411 MET Chi-restraints excluded: chain 1 residue 457 ILE Chi-restraints excluded: chain 1 residue 461 LEU Chi-restraints excluded: chain 1 residue 533 TYR Chi-restraints excluded: chain 2 residue 19 LEU Chi-restraints excluded: chain 2 residue 44 VAL Chi-restraints excluded: chain 2 residue 158 VAL Chi-restraints excluded: chain 2 residue 260 ASN Chi-restraints excluded: chain 2 residue 341 MET Chi-restraints excluded: chain 2 residue 359 ILE Chi-restraints excluded: chain 2 residue 383 LEU Chi-restraints excluded: chain 2 residue 393 LEU Chi-restraints excluded: chain 2 residue 401 LEU Chi-restraints excluded: chain 2 residue 440 LEU Chi-restraints excluded: chain 3 residue 34 CYS Chi-restraints excluded: chain 3 residue 35 VAL Chi-restraints excluded: chain 3 residue 81 ILE Chi-restraints excluded: chain 4 residue 32 PHE Chi-restraints excluded: chain 4 residue 50 PHE Chi-restraints excluded: chain 4 residue 57 LEU Chi-restraints excluded: chain 4 residue 132 LEU Chi-restraints excluded: chain 4 residue 151 VAL Chi-restraints excluded: chain 4 residue 176 ASN Chi-restraints excluded: chain 4 residue 190 LEU Chi-restraints excluded: chain 4 residue 196 LEU Chi-restraints excluded: chain 4 residue 202 LEU Chi-restraints excluded: chain 4 residue 257 CYS Chi-restraints excluded: chain 5 residue 5 LEU Chi-restraints excluded: chain 5 residue 26 SER 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 123 ASN Chi-restraints excluded: chain 6 residue 145 LEU Chi-restraints excluded: chain 6 residue 174 LEU Chi-restraints excluded: chain 6 residue 182 ILE Chi-restraints excluded: chain 6 residue 214 GLU Chi-restraints excluded: chain 6 residue 218 THR Chi-restraints excluded: chain 6 residue 221 VAL Chi-restraints excluded: chain 6 residue 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 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 284 CYS Chi-restraints excluded: chain 7 residue 308 ILE Chi-restraints excluded: chain 7 residue 361 CYS 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 Chi-restraints excluded: chain 7 residue 686 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 280 random chunks: chunk 205 optimal weight: 1.9990 chunk 196 optimal weight: 1.9990 chunk 260 optimal weight: 1.9990 chunk 176 optimal weight: 2.9990 chunk 208 optimal weight: 0.5980 chunk 141 optimal weight: 6.9990 chunk 237 optimal weight: 4.9990 chunk 7 optimal weight: 4.9990 chunk 74 optimal weight: 1.9990 chunk 103 optimal weight: 3.9990 chunk 36 optimal weight: 0.9990 overall best weight: 1.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 0 114 ASN 0 135 HIS 0 307 ASN ** 0 499 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 0 501 GLN 2 83 GLN ** 3 28 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 55 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 145 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 4 179 ASN ** 5 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 6 340 ASN 6 376 HIS 7 173 ASN ** 7 545 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 7 710 GLN 7 714 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4353 r_free = 0.4353 target = 0.167143 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.4066 r_free = 0.4066 target = 0.143808 restraints weight = 44069.372| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4046 r_free = 0.4046 target = 0.142916 restraints weight = 71082.882| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.4030 r_free = 0.4030 target = 0.141825 restraints weight = 49358.461| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.4021 r_free = 0.4021 target = 0.141152 restraints weight = 49940.598| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.4022 r_free = 0.4022 target = 0.141359 restraints weight = 40038.309| |-----------------------------------------------------------------------------| r_work (final): 0.4022 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6850 moved from start: 0.5080 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.114 24275 Z= 0.262 Angle : 0.822 26.625 33049 Z= 0.387 Chirality : 0.046 0.261 3724 Planarity : 0.005 0.056 4029 Dihedral : 13.564 68.670 3602 Min Nonbonded Distance : 1.866 Molprobity Statistics. All-atom Clashscore : 16.22 Ramachandran Plot: Outliers : 0.04 % Allowed : 6.29 % Favored : 93.68 % Rotamer: Outliers : 4.22 % Allowed : 21.71 % Favored : 74.07 % 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 aren not related in a simple way. whole: -1.03 (0.16), residues: 2752 helix: 0.34 (0.14), residues: 1376 sheet: -1.97 (0.34), residues: 228 loop : -1.63 (0.18), residues: 1148 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG 7 62 TYR 0.036 0.002 TYR 0 674 PHE 0.030 0.002 PHE 4 50 TRP 0.057 0.002 TRP 0 552 HIS 0.012 0.002 HIS 3 28 Details of bonding type rmsd covalent geometry : bond 0.00604 (24242) covalent geometry : angle 0.75474 (33001) hydrogen bonds : bond 0.04381 ( 1110) hydrogen bonds : angle 5.12031 ( 3200) metal coordination : bond 0.02553 ( 32) metal coordination : angle 8.55977 ( 48) Misc. bond : bond 0.00079 ( 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 437 residues out of total 2487 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 105 poor density : 332 time to evaluate : 0.949 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: 0 212 LEU cc_start: 0.8264 (tp) cc_final: 0.8000 (tp) REVERT: 0 438 MET cc_start: 0.6560 (ptp) cc_final: 0.6159 (ttm) REVERT: 1 499 ARG cc_start: 0.6247 (mtt180) cc_final: 0.5189 (mtt180) REVERT: 1 533 TYR cc_start: 0.6373 (OUTLIER) cc_final: 0.5935 (m-10) REVERT: 1 545 MET cc_start: 0.2424 (ptt) cc_final: 0.0938 (tmm) REVERT: 2 83 GLN cc_start: 0.7522 (OUTLIER) cc_final: 0.6769 (tp-100) REVERT: 2 109 ILE cc_start: 0.8813 (tt) cc_final: 0.8387 (tp) REVERT: 2 110 LEU cc_start: 0.8547 (mt) cc_final: 0.8063 (mp) REVERT: 2 149 ASP cc_start: 0.6492 (p0) cc_final: 0.6267 (m-30) REVERT: 2 261 PHE cc_start: 0.8842 (t80) cc_final: 0.8585 (t80) REVERT: 2 310 GLU cc_start: 0.7660 (mm-30) cc_final: 0.6788 (mm-30) REVERT: 2 393 LEU cc_start: 0.9352 (OUTLIER) cc_final: 0.9021 (mm) REVERT: 5 21 LEU cc_start: 0.7526 (mt) cc_final: 0.7151 (mt) REVERT: 6 150 SER cc_start: 0.7659 (p) cc_final: 0.7344 (t) REVERT: 7 93 TYR cc_start: 0.6931 (t80) cc_final: 0.5060 (p90) REVERT: 7 103 ILE cc_start: 0.7852 (pt) cc_final: 0.7253 (tp) REVERT: 7 341 PRO cc_start: 0.8852 (Cg_exo) cc_final: 0.8561 (Cg_endo) outliers start: 105 outliers final: 80 residues processed: 407 average time/residue: 0.1554 time to fit residues: 103.2487 Evaluate side-chains 392 residues out of total 2487 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 309 time to evaluate : 0.859 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 454 VAL Chi-restraints excluded: chain 0 residue 471 LEU Chi-restraints excluded: chain 0 residue 483 MET Chi-restraints excluded: chain 0 residue 490 LEU Chi-restraints excluded: chain 0 residue 560 ASN Chi-restraints excluded: chain 0 residue 567 LEU Chi-restraints excluded: chain 0 residue 604 VAL Chi-restraints excluded: chain 0 residue 619 ILE Chi-restraints excluded: chain 0 residue 663 CYS Chi-restraints excluded: chain 0 residue 668 ILE Chi-restraints excluded: chain 0 residue 672 THR Chi-restraints excluded: chain 0 residue 678 VAL Chi-restraints excluded: chain 1 residue 411 MET Chi-restraints excluded: chain 1 residue 457 ILE Chi-restraints excluded: chain 1 residue 461 LEU Chi-restraints excluded: chain 1 residue 529 LEU Chi-restraints excluded: chain 1 residue 533 TYR Chi-restraints excluded: chain 2 residue 19 LEU Chi-restraints excluded: chain 2 residue 44 VAL Chi-restraints excluded: chain 2 residue 83 GLN Chi-restraints excluded: chain 2 residue 158 VAL Chi-restraints excluded: chain 2 residue 260 ASN Chi-restraints excluded: chain 2 residue 341 MET Chi-restraints excluded: chain 2 residue 359 ILE Chi-restraints excluded: chain 2 residue 383 LEU Chi-restraints excluded: chain 2 residue 393 LEU Chi-restraints excluded: chain 2 residue 401 LEU Chi-restraints excluded: chain 2 residue 440 LEU Chi-restraints excluded: chain 3 residue 34 CYS Chi-restraints excluded: chain 3 residue 35 VAL Chi-restraints excluded: chain 3 residue 81 ILE Chi-restraints excluded: chain 4 residue 32 PHE Chi-restraints excluded: chain 4 residue 34 LEU Chi-restraints excluded: chain 4 residue 57 LEU Chi-restraints excluded: chain 4 residue 63 HIS Chi-restraints excluded: chain 4 residue 132 LEU Chi-restraints excluded: chain 4 residue 151 VAL 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 5 LEU Chi-restraints excluded: chain 5 residue 26 SER Chi-restraints excluded: chain 6 residue 84 THR Chi-restraints excluded: chain 6 residue 87 LEU Chi-restraints excluded: chain 6 residue 117 LEU Chi-restraints excluded: chain 6 residue 123 ASN Chi-restraints excluded: chain 6 residue 174 LEU Chi-restraints excluded: chain 6 residue 182 ILE Chi-restraints excluded: chain 6 residue 214 GLU Chi-restraints excluded: chain 6 residue 218 THR Chi-restraints excluded: chain 6 residue 221 VAL Chi-restraints excluded: chain 6 residue 258 THR Chi-restraints excluded: chain 6 residue 284 LEU Chi-restraints excluded: chain 6 residue 307 ILE Chi-restraints excluded: chain 6 residue 357 VAL Chi-restraints excluded: chain 6 residue 366 VAL Chi-restraints excluded: chain 6 residue 370 ASP 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 280 LEU Chi-restraints excluded: chain 7 residue 284 CYS Chi-restraints excluded: chain 7 residue 308 ILE Chi-restraints excluded: chain 7 residue 361 CYS Chi-restraints excluded: chain 7 residue 385 ASP Chi-restraints excluded: chain 7 residue 417 THR Chi-restraints excluded: chain 7 residue 502 ILE Chi-restraints excluded: chain 7 residue 505 VAL Chi-restraints excluded: chain 7 residue 604 THR Chi-restraints excluded: chain 7 residue 666 ASP Chi-restraints excluded: chain 7 residue 667 THR Chi-restraints excluded: chain 7 residue 686 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 280 random chunks: chunk 198 optimal weight: 0.7980 chunk 188 optimal weight: 0.3980 chunk 138 optimal weight: 4.9990 chunk 147 optimal weight: 2.9990 chunk 83 optimal weight: 0.7980 chunk 21 optimal weight: 0.9990 chunk 223 optimal weight: 0.8980 chunk 14 optimal weight: 2.9990 chunk 192 optimal weight: 0.7980 chunk 28 optimal weight: 1.9990 chunk 229 optimal weight: 2.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 0 135 HIS 0 307 ASN ** 2 324 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 28 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4387 r_free = 0.4387 target = 0.170229 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4136 r_free = 0.4136 target = 0.149319 restraints weight = 44667.433| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.4092 r_free = 0.4092 target = 0.146557 restraints weight = 67169.033| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.4077 r_free = 0.4077 target = 0.145478 restraints weight = 56537.082| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.4074 r_free = 0.4074 target = 0.145457 restraints weight = 52074.883| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.4070 r_free = 0.4070 target = 0.145212 restraints weight = 45558.659| |-----------------------------------------------------------------------------| r_work (final): 0.4068 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6759 moved from start: 0.5224 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.116 24275 Z= 0.170 Angle : 0.765 26.396 33049 Z= 0.355 Chirality : 0.044 0.389 3724 Planarity : 0.004 0.057 4029 Dihedral : 13.430 68.557 3602 Min Nonbonded Distance : 1.979 Molprobity Statistics. All-atom Clashscore : 14.22 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.38 % Favored : 94.59 % Rotamer: Outliers : 3.70 % Allowed : 22.44 % Favored : 73.86 % 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 aren not related in a simple way. whole: -0.89 (0.16), residues: 2752 helix: 0.44 (0.14), residues: 1383 sheet: -1.81 (0.34), residues: 228 loop : -1.57 (0.18), residues: 1141 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG 7 62 TYR 0.036 0.002 TYR 0 674 PHE 0.018 0.002 PHE 2 367 TRP 0.058 0.002 TRP 0 552 HIS 0.012 0.001 HIS 3 28 Details of bonding type rmsd covalent geometry : bond 0.00389 (24242) covalent geometry : angle 0.69911 (33001) hydrogen bonds : bond 0.03889 ( 1110) hydrogen bonds : angle 4.91845 ( 3200) metal coordination : bond 0.02504 ( 32) metal coordination : angle 8.19333 ( 48) Misc. bond : bond 0.00064 ( 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 422 residues out of total 2487 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 330 time to evaluate : 1.056 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: 0 212 LEU cc_start: 0.8166 (tp) cc_final: 0.7903 (tp) REVERT: 0 438 MET cc_start: 0.6384 (ptp) cc_final: 0.5928 (mtm) REVERT: 0 554 GLU cc_start: 0.6785 (OUTLIER) cc_final: 0.6494 (pp20) REVERT: 0 677 MET cc_start: 0.8159 (pmm) cc_final: 0.7936 (pmm) REVERT: 1 499 ARG cc_start: 0.6087 (mtt180) cc_final: 0.5049 (mtt180) REVERT: 1 533 TYR cc_start: 0.6264 (OUTLIER) cc_final: 0.5908 (m-10) REVERT: 1 545 MET cc_start: 0.2256 (ptt) cc_final: 0.0913 (tmm) REVERT: 2 109 ILE cc_start: 0.8772 (tt) cc_final: 0.8373 (tp) REVERT: 2 110 LEU cc_start: 0.8491 (mt) cc_final: 0.7983 (mp) REVERT: 2 149 ASP cc_start: 0.6482 (p0) cc_final: 0.6232 (m-30) REVERT: 2 261 PHE cc_start: 0.8817 (t80) cc_final: 0.8565 (t80) REVERT: 2 310 GLU cc_start: 0.7611 (mm-30) cc_final: 0.6785 (mm-30) REVERT: 2 334 MET cc_start: 0.8842 (mmt) cc_final: 0.8579 (mmt) REVERT: 2 393 LEU cc_start: 0.9222 (OUTLIER) cc_final: 0.8888 (mm) REVERT: 5 18 GLN cc_start: 0.7011 (mp10) cc_final: 0.6562 (mp10) REVERT: 5 49 LEU cc_start: 0.7106 (tp) cc_final: 0.6718 (tp) REVERT: 6 150 SER cc_start: 0.7603 (p) cc_final: 0.7238 (t) REVERT: 6 372 ASP cc_start: 0.6871 (t0) cc_final: 0.6587 (t0) REVERT: 7 93 TYR cc_start: 0.6850 (t80) cc_final: 0.5033 (p90) REVERT: 7 103 ILE cc_start: 0.7806 (pt) cc_final: 0.7225 (tp) REVERT: 7 276 MET cc_start: 0.7182 (mmp) cc_final: 0.6923 (mmp) REVERT: 7 341 PRO cc_start: 0.8840 (Cg_exo) cc_final: 0.8560 (Cg_endo) REVERT: 7 545 GLN cc_start: 0.7171 (mt0) cc_final: 0.6920 (mt0) outliers start: 92 outliers final: 75 residues processed: 392 average time/residue: 0.1521 time to fit residues: 97.3836 Evaluate side-chains 392 residues out of total 2487 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 314 time to evaluate : 0.982 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 83 VAL Chi-restraints excluded: chain 0 residue 92 ASN Chi-restraints excluded: chain 0 residue 135 HIS Chi-restraints excluded: chain 0 residue 168 VAL Chi-restraints excluded: chain 0 residue 309 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 471 LEU Chi-restraints excluded: chain 0 residue 483 MET Chi-restraints excluded: chain 0 residue 490 LEU Chi-restraints excluded: chain 0 residue 554 GLU 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 663 CYS Chi-restraints excluded: chain 0 residue 668 ILE Chi-restraints excluded: chain 0 residue 678 VAL Chi-restraints excluded: chain 1 residue 127 LEU Chi-restraints excluded: chain 1 residue 411 MET Chi-restraints excluded: chain 1 residue 457 ILE Chi-restraints excluded: chain 1 residue 461 LEU Chi-restraints excluded: chain 1 residue 533 TYR Chi-restraints excluded: chain 2 residue 19 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 359 ILE 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 34 CYS Chi-restraints excluded: chain 3 residue 35 VAL Chi-restraints excluded: chain 3 residue 81 ILE Chi-restraints excluded: chain 4 residue 32 PHE Chi-restraints excluded: chain 4 residue 57 LEU Chi-restraints excluded: chain 4 residue 63 HIS Chi-restraints excluded: chain 4 residue 132 LEU Chi-restraints excluded: chain 4 residue 151 VAL 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 26 SER Chi-restraints excluded: chain 6 residue 84 THR Chi-restraints excluded: chain 6 residue 87 LEU Chi-restraints excluded: chain 6 residue 117 LEU Chi-restraints excluded: chain 6 residue 123 ASN Chi-restraints excluded: chain 6 residue 145 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 359 VAL Chi-restraints excluded: chain 6 residue 366 VAL Chi-restraints excluded: chain 6 residue 370 ASP Chi-restraints excluded: chain 7 residue 72 THR Chi-restraints excluded: chain 7 residue 119 THR Chi-restraints excluded: chain 7 residue 189 LEU Chi-restraints excluded: chain 7 residue 193 VAL Chi-restraints excluded: chain 7 residue 267 THR Chi-restraints excluded: chain 7 residue 284 CYS Chi-restraints excluded: chain 7 residue 308 ILE Chi-restraints excluded: chain 7 residue 361 CYS Chi-restraints excluded: chain 7 residue 385 ASP Chi-restraints excluded: chain 7 residue 417 THR Chi-restraints excluded: chain 7 residue 523 VAL Chi-restraints excluded: chain 7 residue 590 MET Chi-restraints excluded: chain 7 residue 604 THR Chi-restraints excluded: chain 7 residue 666 ASP Chi-restraints excluded: chain 7 residue 667 THR Chi-restraints excluded: chain 7 residue 686 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 280 random chunks: chunk 243 optimal weight: 0.8980 chunk 21 optimal weight: 0.5980 chunk 149 optimal weight: 7.9990 chunk 110 optimal weight: 1.9990 chunk 176 optimal weight: 2.9990 chunk 259 optimal weight: 0.5980 chunk 175 optimal weight: 0.8980 chunk 23 optimal weight: 0.7980 chunk 227 optimal weight: 3.9990 chunk 111 optimal weight: 0.6980 chunk 180 optimal weight: 0.4980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 0 135 HIS 0 238 ASN 0 307 ASN 2 324 GLN ** 3 28 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 4 179 ASN 5 63 GLN 7 187 HIS ** 7 545 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4390 r_free = 0.4390 target = 0.170487 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.4128 r_free = 0.4128 target = 0.148759 restraints weight = 44209.186| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.4099 r_free = 0.4099 target = 0.147185 restraints weight = 66711.980| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.4090 r_free = 0.4090 target = 0.146597 restraints weight = 47946.079| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.4089 r_free = 0.4089 target = 0.146479 restraints weight = 43923.750| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.4089 r_free = 0.4089 target = 0.146553 restraints weight = 35986.523| |-----------------------------------------------------------------------------| r_work (final): 0.4088 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6721 moved from start: 0.5328 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.110 24275 Z= 0.162 Angle : 0.799 29.039 33049 Z= 0.361 Chirality : 0.044 0.368 3724 Planarity : 0.004 0.056 4029 Dihedral : 13.373 69.170 3602 Min Nonbonded Distance : 1.962 Molprobity Statistics. All-atom Clashscore : 13.86 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.31 % Favored : 94.66 % Rotamer: Outliers : 3.26 % Allowed : 23.32 % Favored : 73.42 % 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 aren not related in a simple way. whole: -0.87 (0.16), residues: 2752 helix: 0.46 (0.14), residues: 1383 sheet: -1.85 (0.34), residues: 225 loop : -1.55 (0.18), residues: 1144 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG 7 62 TYR 0.035 0.002 TYR 0 674 PHE 0.016 0.002 PHE 2 367 TRP 0.054 0.002 TRP 0 552 HIS 0.022 0.002 HIS 0 135 Details of bonding type rmsd covalent geometry : bond 0.00373 (24242) covalent geometry : angle 0.70708 (33001) hydrogen bonds : bond 0.03886 ( 1110) hydrogen bonds : angle 4.87094 ( 3200) metal coordination : bond 0.02448 ( 32) metal coordination : angle 9.78903 ( 48) Misc. bond : bond 0.00069 ( 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 408 residues out of total 2487 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 327 time to evaluate : 0.997 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: 0 131 ASP cc_start: 0.6560 (t0) cc_final: 0.5769 (t70) REVERT: 0 212 LEU cc_start: 0.8150 (tp) cc_final: 0.7879 (tp) REVERT: 0 438 MET cc_start: 0.6335 (ptp) cc_final: 0.5909 (mtm) REVERT: 0 677 MET cc_start: 0.8121 (pmm) cc_final: 0.7910 (pmm) REVERT: 1 499 ARG cc_start: 0.6053 (mtt180) cc_final: 0.5083 (mtt180) REVERT: 1 533 TYR cc_start: 0.6255 (OUTLIER) cc_final: 0.5893 (m-10) REVERT: 1 545 MET cc_start: 0.2136 (ptt) cc_final: 0.0848 (tmm) REVERT: 2 109 ILE cc_start: 0.8805 (tt) cc_final: 0.8381 (tp) REVERT: 2 110 LEU cc_start: 0.8561 (mt) cc_final: 0.8037 (mp) REVERT: 2 149 ASP cc_start: 0.6491 (p0) cc_final: 0.6245 (m-30) REVERT: 2 261 PHE cc_start: 0.8870 (t80) cc_final: 0.8556 (t80) REVERT: 2 310 GLU cc_start: 0.7596 (mm-30) cc_final: 0.6716 (mm-30) REVERT: 2 393 LEU cc_start: 0.9207 (OUTLIER) cc_final: 0.8880 (mm) REVERT: 5 18 GLN cc_start: 0.6927 (mp10) cc_final: 0.6549 (mp10) REVERT: 5 34 ILE cc_start: 0.6803 (OUTLIER) cc_final: 0.6335 (mt) REVERT: 5 49 LEU cc_start: 0.7069 (tp) cc_final: 0.6729 (tp) REVERT: 6 150 SER cc_start: 0.7646 (p) cc_final: 0.7250 (t) REVERT: 6 236 VAL cc_start: 0.9012 (OUTLIER) cc_final: 0.8740 (t) REVERT: 6 265 GLN cc_start: 0.7638 (mm-40) cc_final: 0.7243 (mm-40) REVERT: 7 93 TYR cc_start: 0.6832 (t80) cc_final: 0.4996 (p90) REVERT: 7 103 ILE cc_start: 0.7855 (pt) cc_final: 0.7253 (tp) REVERT: 7 341 PRO cc_start: 0.8820 (Cg_exo) cc_final: 0.8542 (Cg_endo) REVERT: 7 545 GLN cc_start: 0.7208 (mt0) cc_final: 0.6928 (mt0) outliers start: 81 outliers final: 72 residues processed: 382 average time/residue: 0.1511 time to fit residues: 95.1782 Evaluate side-chains 390 residues out of total 2487 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 314 time to evaluate : 1.538 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 471 LEU Chi-restraints excluded: chain 0 residue 483 MET Chi-restraints excluded: chain 0 residue 490 LEU Chi-restraints excluded: chain 0 residue 560 ASN Chi-restraints excluded: chain 0 residue 567 LEU Chi-restraints excluded: chain 0 residue 604 VAL Chi-restraints excluded: chain 0 residue 619 ILE Chi-restraints excluded: chain 0 residue 663 CYS Chi-restraints excluded: chain 0 residue 668 ILE Chi-restraints excluded: chain 0 residue 678 VAL Chi-restraints excluded: chain 1 residue 127 LEU Chi-restraints excluded: chain 1 residue 411 MET Chi-restraints excluded: chain 1 residue 457 ILE Chi-restraints excluded: chain 1 residue 461 LEU Chi-restraints excluded: chain 1 residue 533 TYR Chi-restraints excluded: chain 2 residue 19 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 359 ILE Chi-restraints excluded: chain 2 residue 393 LEU Chi-restraints excluded: chain 2 residue 401 LEU Chi-restraints excluded: chain 2 residue 440 LEU Chi-restraints excluded: chain 3 residue 34 CYS Chi-restraints excluded: chain 3 residue 35 VAL Chi-restraints excluded: chain 3 residue 81 ILE Chi-restraints excluded: chain 4 residue 32 PHE Chi-restraints excluded: chain 4 residue 57 LEU Chi-restraints excluded: chain 4 residue 63 HIS Chi-restraints excluded: chain 4 residue 132 LEU Chi-restraints excluded: chain 4 residue 151 VAL Chi-restraints excluded: chain 4 residue 176 ASN Chi-restraints excluded: chain 4 residue 179 ASN Chi-restraints excluded: chain 4 residue 190 LEU 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 26 SER Chi-restraints excluded: chain 5 residue 34 ILE Chi-restraints excluded: chain 6 residue 84 THR Chi-restraints excluded: chain 6 residue 87 LEU Chi-restraints excluded: chain 6 residue 117 LEU Chi-restraints excluded: chain 6 residue 123 ASN 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 366 VAL Chi-restraints excluded: chain 7 residue 72 THR Chi-restraints excluded: chain 7 residue 119 THR Chi-restraints excluded: chain 7 residue 139 TYR 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 284 CYS Chi-restraints excluded: chain 7 residue 308 ILE 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 590 MET Chi-restraints excluded: chain 7 residue 604 THR Chi-restraints excluded: chain 7 residue 667 THR Chi-restraints excluded: chain 7 residue 686 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 280 random chunks: chunk 100 optimal weight: 0.0970 chunk 55 optimal weight: 0.6980 chunk 7 optimal weight: 0.6980 chunk 67 optimal weight: 4.9990 chunk 70 optimal weight: 3.9990 chunk 119 optimal weight: 0.7980 chunk 95 optimal weight: 0.8980 chunk 21 optimal weight: 0.6980 chunk 81 optimal weight: 0.9980 chunk 61 optimal weight: 1.9990 chunk 125 optimal weight: 0.5980 overall best weight: 0.5578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 0 135 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 0 307 ASN ** 3 28 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 4 179 ASN 6 376 HIS 7 187 HIS ** 7 545 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 = 0.4397 r_free = 0.4397 target = 0.171098 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4140 r_free = 0.4140 target = 0.149612 restraints weight = 44299.958| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.4106 r_free = 0.4106 target = 0.147634 restraints weight = 67834.576| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.4085 r_free = 0.4085 target = 0.145985 restraints weight = 50343.734| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.4067 r_free = 0.4067 target = 0.144828 restraints weight = 52053.244| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.4062 r_free = 0.4062 target = 0.144486 restraints weight = 46698.366| |-----------------------------------------------------------------------------| r_work (final): 0.4058 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6779 moved from start: 0.5406 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.105 24275 Z= 0.157 Angle : 0.798 29.690 33049 Z= 0.362 Chirality : 0.044 0.363 3724 Planarity : 0.004 0.055 4029 Dihedral : 13.347 69.557 3602 Min Nonbonded Distance : 1.994 Molprobity Statistics. All-atom Clashscore : 13.66 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.09 % Favored : 94.88 % Rotamer: Outliers : 3.30 % Allowed : 23.56 % Favored : 73.14 % 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 aren not related in a simple way. whole: -0.87 (0.16), residues: 2752 helix: 0.48 (0.14), residues: 1382 sheet: -1.81 (0.34), residues: 226 loop : -1.59 (0.18), residues: 1144 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG 2 94 TYR 0.034 0.002 TYR 0 674 PHE 0.038 0.002 PHE 7 615 TRP 0.055 0.002 TRP 4 229 HIS 0.035 0.002 HIS 7 187 Details of bonding type rmsd covalent geometry : bond 0.00362 (24242) covalent geometry : angle 0.70931 (33001) hydrogen bonds : bond 0.03812 ( 1110) hydrogen bonds : angle 4.85158 ( 3200) metal coordination : bond 0.02359 ( 32) metal coordination : angle 9.61365 ( 48) Misc. bond : bond 0.00068 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4086.02 seconds wall clock time: 71 minutes 49.81 seconds (4309.81 seconds total)