Starting phenix.real_space_refine on Fri Aug 7 14:05:10 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8gwb_34308/08_2026/8gwb_34308.cif Found real_map, /net/cci-nas-00/data/ceres_data/8gwb_34308/08_2026/8gwb_34308.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.75 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/cci-nas-00/data/ceres_data/8gwb_34308/08_2026/8gwb_34308.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8gwb_34308/08_2026/8gwb_34308.cif" model { file = "/net/cci-nas-00/data/ceres_data/8gwb_34308/08_2026/8gwb_34308.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8gwb_34308/08_2026/8gwb_34308.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8gwb_34308/08_2026/8gwb_34308.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8gwb_34308/08_2026/8gwb_34308.map" } resolution = 2.75 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= -0.000 sd= 0.053 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: 7 Type Number sf(0) Gaussians Mn 2 7.51 5 Zn 8 6.06 5 P 54 5.49 5 S 157 5.16 5 C 13689 2.51 5 N 3681 2.21 5 O 4288 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 23 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 21879 Number of models: 1 Model: "" Number of chains: 16 Chain: "A" Number of atoms: 7458 Number of conformers: 1 Conformer: "" Number of residues, atoms: 926, 7458 Classifications: {'peptide': 926} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 29, 'TRANS': 895} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "B" Number of atoms: 1396 Number of conformers: 1 Conformer: "" Number of residues, atoms: 187, 1396 Classifications: {'peptide': 187} Incomplete info: {'truncation_to_alanine': 15} Link IDs: {'PTRANS': 6, 'TRANS': 180} Unresolved non-hydrogen bonds: 58 Unresolved non-hydrogen angles: 71 Unresolved non-hydrogen dihedrals: 50 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 2, 'TYR:plan': 1, 'GLN:plan1': 1, 'ASN:plan1': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 34 Chain: "C" Number of atoms: 553 Number of conformers: 1 Conformer: "" Number of residues, atoms: 72, 553 Classifications: {'peptide': 72} Link IDs: {'TRANS': 71} Chain: "D" Number of atoms: 1414 Number of conformers: 1 Conformer: "" Number of residues, atoms: 186, 1414 Classifications: {'peptide': 186} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 6, 'TRANS': 179} Unresolved non-hydrogen bonds: 31 Unresolved non-hydrogen angles: 38 Unresolved non-hydrogen dihedrals: 26 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 2, 'GLN:plan1': 1, 'ASN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 24 Chain: "I" Number of atoms: 545 Number of conformers: 1 Conformer: "" Number of residues, atoms: 25, 545 Classifications: {'RNAv2': 25} Modifications used: {'rna2p_pur': 1, 'rna3p_pur': 16, 'rna3p_pyr': 8} Link IDs: {'rna3p': 24} Chain: "J" Number of atoms: 565 Number of conformers: 1 Conformer: "" Number of residues, atoms: 27, 565 Classifications: {'RNAv2': 27} Modifications used: {'rna2p_pur': 1, 'rna3p_pur': 9, 'rna3p_pyr': 17} Link IDs: {'rna2p': 1, 'rna3p': 25} Chain: "F" Number of atoms: 4508 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 585, 4500 Classifications: {'peptide': 585} Incomplete info: {'truncation_to_alanine': 14} Link IDs: {'PTRANS': 30, 'TRANS': 554} Chain breaks: 2 Unresolved non-hydrogen bonds: 62 Unresolved non-hydrogen angles: 71 Unresolved non-hydrogen dihedrals: 53 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASP:plan': 1, 'ASN:plan1': 1, 'ARG:plan': 5, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 35 Conformer: "B" Number of residues, atoms: 585, 4500 Classifications: {'peptide': 585} Incomplete info: {'truncation_to_alanine': 14} Link IDs: {'PTRANS': 30, 'TRANS': 554} Chain breaks: 2 Unresolved non-hydrogen bonds: 62 Unresolved non-hydrogen angles: 71 Unresolved non-hydrogen dihedrals: 53 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASP:plan': 1, 'ASN:plan1': 1, 'ARG:plan': 5, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 35 bond proxies already assigned to first conformer: 4593 Chain: "E" Number of atoms: 4513 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 586, 4505 Classifications: {'peptide': 586} Incomplete info: {'truncation_to_alanine': 14} Link IDs: {'PTRANS': 30, 'TRANS': 555} Chain breaks: 2 Unresolved non-hydrogen bonds: 62 Unresolved non-hydrogen angles: 71 Unresolved non-hydrogen dihedrals: 53 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASP:plan': 1, 'ASN:plan1': 1, 'ARG:plan': 5, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 35 Conformer: "B" Number of residues, atoms: 586, 4505 Classifications: {'peptide': 586} Incomplete info: {'truncation_to_alanine': 14} Link IDs: {'PTRANS': 30, 'TRANS': 555} Chain breaks: 2 Unresolved non-hydrogen bonds: 62 Unresolved non-hydrogen angles: 71 Unresolved non-hydrogen dihedrals: 53 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASP:plan': 1, 'ASN:plan1': 1, 'ARG:plan': 5, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 35 bond proxies already assigned to first conformer: 4598 Chain: "G" Number of atoms: 868 Number of conformers: 1 Conformer: "" Number of residues, atoms: 113, 868 Classifications: {'peptide': 113} Link IDs: {'PTRANS': 6, 'TRANS': 106} Chain: "M" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 42 Classifications: {'RNAv2': 2} Modifications used: {'rna2p_pyr': 1, 'rna3p_pur': 1} Link IDs: {'rna3p': 1} Chain: "A" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Unusual residues: {' MN': 2, ' ZN': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "F" 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: "E" 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: "A" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Chain: "G" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "M" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 2446 SG CYS A 301 88.954 57.320 63.002 1.00 31.45 S ATOM 2487 SG CYS A 306 89.585 59.411 60.028 1.00 42.65 S ATOM 2519 SG CYS A 310 87.261 56.343 60.075 1.00 52.03 S ATOM 3927 SG CYS A 487 90.091 69.817 80.117 1.00 35.69 S ATOM 5180 SG CYS A 645 91.497 71.748 77.082 1.00 53.57 S ATOM 5186 SG CYS A 646 91.811 67.874 77.373 1.00 53.06 S ATOM 12035 SG CYS F 16 60.647 69.650 134.275 1.00180.59 S ATOM 12050 SG CYS F 19 58.927 66.440 135.640 1.00182.13 S ATOM 11953 SG CYS F 5 49.538 76.179 131.797 1.00182.59 S ATOM 11974 SG CYS F 8 49.445 78.126 135.000 1.00190.86 S ATOM 12112 SG CYS F 26 51.642 79.419 132.284 1.00188.57 S ATOM 12129 SG CYS F 29 52.777 76.427 134.031 1.00193.40 S ATOM 12294 SG CYS F 50 76.363 76.882 122.167 1.00163.85 S ATOM 12324 SG CYS F 55 78.347 74.790 124.518 1.00172.84 S ATOM 12457 SG CYS F 72 77.087 77.874 125.773 1.00160.49 S ATOM 16548 SG CYS E 16 105.825 65.355 121.422 1.00161.69 S ATOM 16563 SG CYS E 19 105.603 61.610 122.172 1.00168.49 S ATOM 16466 SG CYS E 5 94.156 63.654 128.424 1.00189.90 S ATOM 16487 SG CYS E 8 94.606 65.241 131.846 1.00200.92 S ATOM 16625 SG CYS E 26 93.566 67.468 129.032 1.00189.25 S ATOM 16642 SG CYS E 29 97.161 66.024 129.368 1.00195.34 S ATOM 16807 SG CYS E 50 105.717 81.183 109.224 1.00167.63 S ATOM 16837 SG CYS E 55 109.424 80.949 108.484 1.00154.77 S ATOM 16970 SG CYS E 72 108.277 83.165 111.358 1.00188.61 S Residues with excluded nonbonded symmetry interactions: 2 residue: pdb=" N AMET F 474 " occ=0.41 ... (14 atoms not shown) pdb=" CE BMET F 474 " occ=0.59 residue: pdb=" N AMET E 474 " occ=0.41 ... (14 atoms not shown) pdb=" CE BMET E 474 " occ=0.59 Time building chain proxies: 6.59, per 1000 atoms: 0.30 Number of scatterers: 21879 At special positions: 0 Unit cell: (151.7, 141.04, 180.4, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 8 29.99 Mn 2 24.99 S 157 16.00 P 54 15.00 O 4288 8.00 N 3681 7.00 C 13689 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.61 Conformation dependent library (CDL) restraints added in 1.5 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A1001 " pdb="ZN ZN A1001 " - pdb=" NE2 HIS A 295 " pdb="ZN ZN A1001 " - pdb=" SG CYS A 301 " pdb="ZN ZN A1001 " - pdb=" SG CYS A 306 " pdb="ZN ZN A1001 " - pdb=" SG CYS A 310 " pdb=" ZN A1002 " pdb="ZN ZN A1002 " - pdb=" ND1 HIS A 642 " pdb="ZN ZN A1002 " - pdb=" SG CYS A 487 " pdb="ZN ZN A1002 " - pdb=" SG CYS A 646 " pdb="ZN ZN A1002 " - pdb=" SG CYS A 645 " pdb=" ZN E 701 " pdb="ZN ZN E 701 " - pdb=" ND1 HIS E 39 " pdb="ZN ZN E 701 " - pdb=" NE2 HIS E 33 " pdb="ZN ZN E 701 " - pdb=" SG CYS E 16 " pdb="ZN ZN E 701 " - pdb=" SG CYS E 19 " pdb=" ZN E 702 " pdb="ZN ZN E 702 " - pdb=" SG CYS E 8 " pdb="ZN ZN E 702 " - pdb=" SG CYS E 29 " pdb="ZN ZN E 702 " - pdb=" SG CYS E 26 " pdb="ZN ZN E 702 " - pdb=" SG CYS E 5 " pdb=" ZN E 703 " pdb="ZN ZN E 703 " - pdb=" ND1 HIS E 75 " pdb="ZN ZN E 703 " - pdb=" SG CYS E 55 " pdb="ZN ZN E 703 " - pdb=" SG CYS E 72 " pdb="ZN ZN E 703 " - pdb=" SG CYS E 50 " pdb=" ZN F 701 " pdb="ZN ZN F 701 " - pdb=" NE2 HIS F 33 " pdb="ZN ZN F 701 " - pdb=" ND1 HIS F 39 " pdb="ZN ZN F 701 " - pdb=" SG CYS F 16 " pdb="ZN ZN F 701 " - pdb=" SG CYS F 19 " pdb=" ZN F 702 " pdb="ZN ZN F 702 " - pdb=" SG CYS F 26 " pdb="ZN ZN F 702 " - pdb=" SG CYS F 8 " pdb="ZN ZN F 702 " - pdb=" SG CYS F 29 " pdb="ZN ZN F 702 " - pdb=" SG CYS F 5 " pdb=" ZN F 703 " pdb="ZN ZN F 703 " - pdb=" ND1 HIS F 75 " pdb="ZN ZN F 703 " - pdb=" SG CYS F 50 " pdb="ZN ZN F 703 " - pdb=" SG CYS F 55 " pdb="ZN ZN F 703 " - pdb=" SG CYS F 72 " Number of angles added : 27 5278 Ramachandran restraints generated. 2639 Oldfield, 0 Emsley, 2639 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5068 Finding SS restraints... Secondary structure from input PDB file: 91 helices and 35 sheets defined 39.6% alpha, 13.0% beta 20 base pairs and 39 stacking pairs defined. Time for finding SS restraints: 3.27 Creating SS restraints... Processing helix chain 'A' and resid 5 through 12 removed outlier: 3.935A pdb=" N ASN A 9 " --> pdb=" O GLN A 5 " (cutoff:3.500A) Processing helix chain 'A' and resid 76 through 91 removed outlier: 3.638A pdb=" N TYR A 80 " --> pdb=" O THR A 76 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N GLN A 81 " --> pdb=" O PHE A 77 " (cutoff:3.500A) Processing helix chain 'A' and resid 123 through 133 Processing helix chain 'A' and resid 140 through 149 removed outlier: 3.636A pdb=" N TYR A 149 " --> pdb=" O ILE A 145 " (cutoff:3.500A) Processing helix chain 'A' and resid 153 through 159 Processing helix chain 'A' and resid 169 through 176 removed outlier: 4.144A pdb=" N ARG A 173 " --> pdb=" O PRO A 169 " (cutoff:3.500A) Processing helix chain 'A' and resid 178 through 200 Processing helix chain 'A' and resid 206 through 210 removed outlier: 3.526A pdb=" N GLN A 210 " --> pdb=" O LEU A 207 " (cutoff:3.500A) Processing helix chain 'A' and resid 235 through 248 Proline residue: A 243 - end of helix removed outlier: 4.255A pdb=" N THR A 246 " --> pdb=" O MET A 242 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N LEU A 247 " --> pdb=" O PRO A 243 " (cutoff:3.500A) Processing helix chain 'A' and resid 251 through 255 removed outlier: 3.520A pdb=" N SER A 255 " --> pdb=" O THR A 252 " (cutoff:3.500A) Processing helix chain 'A' and resid 275 through 287 removed outlier: 3.509A pdb=" N LEU A 280 " --> pdb=" O THR A 276 " (cutoff:3.500A) Processing helix chain 'A' and resid 297 through 301 Processing helix chain 'A' and resid 303 through 318 removed outlier: 3.523A pdb=" N PHE A 313 " --> pdb=" O HIS A 309 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N LEU A 316 " --> pdb=" O ASN A 312 " (cutoff:3.500A) Processing helix chain 'A' and resid 322 through 326 removed outlier: 3.942A pdb=" N PHE A 326 " --> pdb=" O PRO A 323 " (cutoff:3.500A) Processing helix chain 'A' and resid 368 through 377 Processing helix chain 'A' and resid 377 through 384 removed outlier: 4.399A pdb=" N HIS A 381 " --> pdb=" O ASP A 377 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 426 Processing helix chain 'A' and resid 448 through 454 Processing helix chain 'A' and resid 455 through 459 Processing helix chain 'A' and resid 465 through 480 removed outlier: 4.216A pdb=" N PHE A 471 " --> pdb=" O ARG A 467 " (cutoff:3.500A) removed outlier: 4.512A pdb=" N GLU A 474 " --> pdb=" O LEU A 470 " (cutoff:3.500A) Processing helix chain 'A' and resid 489 through 493 removed outlier: 3.724A pdb=" N VAL A 493 " --> pdb=" O ALA A 490 " (cutoff:3.500A) Processing helix chain 'A' and resid 505 through 509 Processing helix chain 'A' and resid 511 through 518 removed outlier: 3.807A pdb=" N TYR A 515 " --> pdb=" O LYS A 511 " (cutoff:3.500A) Processing helix chain 'A' and resid 520 through 531 removed outlier: 3.594A pdb=" N THR A 531 " --> pdb=" O LEU A 527 " (cutoff:3.500A) Processing helix chain 'A' and resid 561 through 580 removed outlier: 3.559A pdb=" N THR A 567 " --> pdb=" O CYS A 563 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N GLN A 570 " --> pdb=" O MET A 566 " (cutoff:3.500A) removed outlier: 5.960A pdb=" N LYS A 574 " --> pdb=" O GLN A 570 " (cutoff:3.500A) removed outlier: 6.061A pdb=" N LEU A 575 " --> pdb=" O PHE A 571 " (cutoff:3.500A) Processing helix chain 'A' and resid 596 through 606 Processing helix chain 'A' and resid 621 through 626 removed outlier: 3.685A pdb=" N MET A 626 " --> pdb=" O CYS A 622 " (cutoff:3.500A) Processing helix chain 'A' and resid 627 through 639 Processing helix chain 'A' and resid 647 through 663 Processing helix chain 'A' and resid 686 through 709 Processing helix chain 'A' and resid 711 through 715 Processing helix chain 'A' and resid 719 through 733 Processing helix chain 'A' and resid 738 through 752 Processing helix chain 'A' and resid 768 through 772 Processing helix chain 'A' and resid 779 through 790 Processing helix chain 'A' and resid 833 through 842 Processing helix chain 'A' and resid 856 through 865 Processing helix chain 'A' and resid 866 through 872 Processing helix chain 'A' and resid 874 through 902 removed outlier: 4.010A pdb=" N ALA A 878 " --> pdb=" O ASN A 874 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N PHE A 881 " --> pdb=" O TYR A 877 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N GLY A 897 " --> pdb=" O ASP A 893 " (cutoff:3.500A) Processing helix chain 'A' and resid 917 through 922 removed outlier: 4.454A pdb=" N TYR A 921 " --> pdb=" O GLU A 917 " (cutoff:3.500A) Processing helix chain 'A' and resid 923 through 926 removed outlier: 3.809A pdb=" N THR A 926 " --> pdb=" O ALA A 923 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 923 through 926' Processing helix chain 'B' and resid 9 through 29 removed outlier: 4.159A pdb=" N ALA B 13 " --> pdb=" O LEU B 9 " (cutoff:3.500A) removed outlier: 4.098A pdb=" N ALA B 14 " --> pdb=" O PRO B 10 " (cutoff:3.500A) Processing helix chain 'B' and resid 31 through 95 removed outlier: 3.653A pdb=" N ASN B 43 " --> pdb=" O LYS B 39 " (cutoff:3.500A) removed outlier: 4.696A pdb=" N ARG B 51 " --> pdb=" O SER B 47 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N ASP B 52 " --> pdb=" O GLU B 48 " (cutoff:3.500A) removed outlier: 4.696A pdb=" N ALA B 54 " --> pdb=" O ASP B 50 " (cutoff:3.500A) removed outlier: 4.513A pdb=" N GLN B 56 " --> pdb=" O ASP B 52 " (cutoff:3.500A) removed outlier: 5.119A pdb=" N ARG B 57 " --> pdb=" O ALA B 53 " (cutoff:3.500A) removed outlier: 4.647A pdb=" N LYS B 58 " --> pdb=" O ALA B 54 " (cutoff:3.500A) removed outlier: 4.249A pdb=" N LYS B 61 " --> pdb=" O ARG B 57 " (cutoff:3.500A) Processing helix chain 'B' and resid 96 through 98 No H-bonds generated for 'chain 'B' and resid 96 through 98' Processing helix chain 'B' and resid 101 through 108 removed outlier: 3.526A pdb=" N ASN B 108 " --> pdb=" O ASN B 104 " (cutoff:3.500A) Processing helix chain 'B' and resid 119 through 124 Processing helix chain 'B' and resid 134 through 142 removed outlier: 4.142A pdb=" N ASN B 140 " --> pdb=" O ASN B 136 " (cutoff:3.500A) Processing helix chain 'B' and resid 168 through 172 Processing helix chain 'B' and resid 176 through 180 Processing helix chain 'C' and resid 3 through 20 Processing helix chain 'C' and resid 21 through 24 Processing helix chain 'C' and resid 25 through 40 Processing helix chain 'C' and resid 46 through 61 removed outlier: 3.693A pdb=" N VAL C 58 " --> pdb=" O SER C 54 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N LEU C 59 " --> pdb=" O LEU C 55 " (cutoff:3.500A) Processing helix chain 'D' and resid 9 through 29 Processing helix chain 'D' and resid 31 through 48 removed outlier: 4.007A pdb=" N LEU D 38 " --> pdb=" O VAL D 34 " (cutoff:3.500A) removed outlier: 5.244A pdb=" N LEU D 42 " --> pdb=" O LEU D 38 " (cutoff:3.500A) removed outlier: 4.093A pdb=" N VAL D 44 " --> pdb=" O LYS D 40 " (cutoff:3.500A) removed outlier: 4.674A pdb=" N ALA D 45 " --> pdb=" O SER D 41 " (cutoff:3.500A) Processing helix chain 'D' and resid 51 through 80 removed outlier: 4.074A pdb=" N ARG D 57 " --> pdb=" O ALA D 53 " (cutoff:3.500A) Processing helix chain 'D' and resid 82 through 99 removed outlier: 3.969A pdb=" N GLN D 88 " --> pdb=" O THR D 84 " (cutoff:3.500A) Processing helix chain 'D' and resid 100 through 113 Processing helix chain 'D' and resid 134 through 141 removed outlier: 3.754A pdb=" N TYR D 138 " --> pdb=" O ASP D 134 " (cutoff:3.500A) Processing helix chain 'F' and resid 26 through 36 removed outlier: 3.905A pdb=" N SER F 36 " --> pdb=" O ASP F 32 " (cutoff:3.500A) Processing helix chain 'F' and resid 74 through 76 No H-bonds generated for 'chain 'F' and resid 74 through 76' Processing helix chain 'F' and resid 103 through 111 removed outlier: 3.571A pdb=" N THR F 111 " --> pdb=" O ASN F 107 " (cutoff:3.500A) Processing helix chain 'F' and resid 116 through 125 removed outlier: 3.644A pdb=" N TYR F 120 " --> pdb=" O ASN F 116 " (cutoff:3.500A) Processing helix chain 'F' and resid 127 through 147 removed outlier: 3.663A pdb=" N LEU F 147 " --> pdb=" O GLU F 143 " (cutoff:3.500A) Processing helix chain 'F' and resid 265 through 273 removed outlier: 4.164A pdb=" N LYS F 271 " --> pdb=" O ALA F 267 " (cutoff:3.500A) Processing helix chain 'F' and resid 287 through 299 removed outlier: 3.733A pdb=" N ALA F 292 " --> pdb=" O LYS F 288 " (cutoff:3.500A) removed outlier: 4.084A pdb=" N ILE F 293 " --> pdb=" O SER F 289 " (cutoff:3.500A) Processing helix chain 'F' and resid 310 through 325 removed outlier: 4.758A pdb=" N ALA F 316 " --> pdb=" O ALA F 312 " (cutoff:3.500A) removed outlier: 4.889A pdb=" N LEU F 317 " --> pdb=" O ALA F 313 " (cutoff:3.500A) removed outlier: 4.111A pdb=" N LYS F 320 " --> pdb=" O ALA F 316 " (cutoff:3.500A) removed outlier: 4.453A pdb=" N LEU F 322 " --> pdb=" O CYS F 318 " (cutoff:3.500A) removed outlier: 4.741A pdb=" N LYS F 323 " --> pdb=" O GLU F 319 " (cutoff:3.500A) Processing helix chain 'F' and resid 380 through 391 removed outlier: 4.318A pdb=" N VAL F 387 " --> pdb=" O ASP F 383 " (cutoff:3.500A) removed outlier: 4.581A pdb=" N ASN F 388 " --> pdb=" O LEU F 384 " (cutoff:3.500A) Processing helix chain 'F' and resid 418 through 423 removed outlier: 3.764A pdb=" N PHE F 422 " --> pdb=" O PRO F 419 " (cutoff:3.500A) removed outlier: 4.254A pdb=" N ASN F 423 " --> pdb=" O GLU F 420 " (cutoff:3.500A) Processing helix chain 'F' and resid 427 through 432 Processing helix chain 'F' and resid 445 through 454 removed outlier: 3.555A pdb=" N ASP F 450 " --> pdb=" O ALA F 446 " (cutoff:3.500A) removed outlier: 4.141A pdb=" N THR F 451 " --> pdb=" O GLU F 447 " (cutoff:3.500A) Processing helix chain 'F' and resid 489 through 503 Processing helix chain 'F' and resid 504 through 507 removed outlier: 3.637A pdb=" N ARG F 507 " --> pdb=" O PRO F 504 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 504 through 507' Processing helix chain 'F' and resid 515 through 523 removed outlier: 4.144A pdb=" N ASN F 519 " --> pdb=" O TYR F 515 " (cutoff:3.500A) Processing helix chain 'F' and resid 561 through 566 removed outlier: 3.600A pdb=" N THR F 566 " --> pdb=" O ASN F 562 " (cutoff:3.500A) Processing helix chain 'E' and resid 26 through 36 removed outlier: 3.919A pdb=" N SER E 36 " --> pdb=" O ASP E 32 " (cutoff:3.500A) Processing helix chain 'E' and resid 103 through 112 Processing helix chain 'E' and resid 116 through 125 removed outlier: 4.207A pdb=" N TYR E 120 " --> pdb=" O ASN E 116 " (cutoff:3.500A) Processing helix chain 'E' and resid 127 through 147 Processing helix chain 'E' and resid 177 through 181 Processing helix chain 'E' and resid 265 through 273 Processing helix chain 'E' and resid 287 through 299 removed outlier: 4.528A pdb=" N ALA E 292 " --> pdb=" O LYS E 288 " (cutoff:3.500A) removed outlier: 5.259A pdb=" N ILE E 293 " --> pdb=" O SER E 289 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N LEU E 297 " --> pdb=" O ILE E 293 " (cutoff:3.500A) Processing helix chain 'E' and resid 314 through 320 removed outlier: 4.831A pdb=" N LYS E 320 " --> pdb=" O ALA E 316 " (cutoff:3.500A) Processing helix chain 'E' and resid 380 through 390 removed outlier: 3.581A pdb=" N LEU E 384 " --> pdb=" O THR E 380 " (cutoff:3.500A) Processing helix chain 'E' and resid 418 through 422 Processing helix chain 'E' and resid 423 through 429 removed outlier: 3.537A pdb=" N ARG E 427 " --> pdb=" O ASN E 423 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N LEU E 428 " --> pdb=" O SER E 424 " (cutoff:3.500A) Processing helix chain 'E' and resid 445 through 456 removed outlier: 3.634A pdb=" N VAL E 449 " --> pdb=" O PRO E 445 " (cutoff:3.500A) Processing helix chain 'E' and resid 489 through 501 removed outlier: 3.763A pdb=" N VAL E 495 " --> pdb=" O PRO E 491 " (cutoff:3.500A) removed outlier: 4.409A pdb=" N ARG E 497 " --> pdb=" O ILE E 493 " (cutoff:3.500A) Processing helix chain 'E' and resid 502 through 507 removed outlier: 7.008A pdb=" N ALA E 505 " --> pdb=" O ARG E 502 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N ARG E 507 " --> pdb=" O PRO E 504 " (cutoff:3.500A) Processing helix chain 'E' and resid 516 through 524 removed outlier: 3.946A pdb=" N LYS E 524 " --> pdb=" O ALA E 520 " (cutoff:3.500A) Processing helix chain 'G' and resid 95 through 110 Processing sheet with id=AA1, first strand: chain 'A' and resid 19 through 21 removed outlier: 3.789A pdb=" N GLN A 57 " --> pdb=" O THR A 20 " (cutoff:3.500A) removed outlier: 5.074A pdb=" N SER A 68 " --> pdb=" O GLU A 58 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N PHE A 102 " --> pdb=" O HIS A 113 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 31 through 35 Processing sheet with id=AA3, first strand: chain 'A' and resid 38 through 39 removed outlier: 3.893A pdb=" N VAL A 42 " --> pdb=" O ASN A 39 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 223 through 224 removed outlier: 7.074A pdb=" N VAL A 233 " --> pdb=" O ILE A 201 " (cutoff:3.500A) removed outlier: 6.922A pdb=" N GLY A 203 " --> pdb=" O VAL A 233 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 352 through 355 removed outlier: 3.548A pdb=" N VAL A 342 " --> pdb=" O ARG A 331 " (cutoff:3.500A) removed outlier: 6.311A pdb=" N LEU A 329 " --> pdb=" O THR A 344 " (cutoff:3.500A) removed outlier: 4.578A pdb=" N TYR A 346 " --> pdb=" O GLY A 327 " (cutoff:3.500A) removed outlier: 6.453A pdb=" N GLY A 327 " --> pdb=" O TYR A 346 " (cutoff:3.500A) removed outlier: 9.842A pdb=" N SER A 363 " --> pdb=" O LYS A 332 " (cutoff:3.500A) removed outlier: 6.785A pdb=" N PHE A 334 " --> pdb=" O SER A 363 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 352 through 355 removed outlier: 3.548A pdb=" N VAL A 342 " --> pdb=" O ARG A 331 " (cutoff:3.500A) removed outlier: 6.311A pdb=" N LEU A 329 " --> pdb=" O THR A 344 " (cutoff:3.500A) removed outlier: 4.578A pdb=" N TYR A 346 " --> pdb=" O GLY A 327 " (cutoff:3.500A) removed outlier: 6.453A pdb=" N GLY A 327 " --> pdb=" O TYR A 346 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 556 through 560 removed outlier: 7.051A pdb=" N THR A 540 " --> pdb=" O MET A 668 " (cutoff:3.500A) removed outlier: 6.908A pdb=" N LEU A 673 " --> pdb=" O VAL A 398 " (cutoff:3.500A) removed outlier: 4.680A pdb=" N VAL A 398 " --> pdb=" O LEU A 388 " (cutoff:3.500A) removed outlier: 4.187A pdb=" N LEU A 388 " --> pdb=" O VAL A 398 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N GLN B 158 " --> pdb=" O THR B 187 " (cutoff:3.500A) removed outlier: 6.478A pdb=" N LEU B 189 " --> pdb=" O ILE B 156 " (cutoff:3.500A) removed outlier: 5.815A pdb=" N ILE B 156 " --> pdb=" O LEU B 189 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 414 through 415 Processing sheet with id=AA9, first strand: chain 'A' and resid 753 through 757 Processing sheet with id=AB1, first strand: chain 'A' and resid 816 through 822 Processing sheet with id=AB2, first strand: chain 'D' and resid 127 through 129 removed outlier: 3.556A pdb=" N ALA D 188 " --> pdb=" O LEU D 128 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N VAL D 160 " --> pdb=" O ILE D 185 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N GLN D 158 " --> pdb=" O THR D 187 " (cutoff:3.500A) removed outlier: 6.938A pdb=" N LEU D 189 " --> pdb=" O ILE D 156 " (cutoff:3.500A) removed outlier: 5.819A pdb=" N ILE D 156 " --> pdb=" O LEU D 189 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 127 through 129 removed outlier: 3.556A pdb=" N ALA D 188 " --> pdb=" O LEU D 128 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N VAL D 160 " --> pdb=" O ILE D 185 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N GLN D 158 " --> pdb=" O THR D 187 " (cutoff:3.500A) removed outlier: 6.938A pdb=" N LEU D 189 " --> pdb=" O ILE D 156 " (cutoff:3.500A) removed outlier: 5.819A pdb=" N ILE D 156 " --> pdb=" O LEU D 189 " (cutoff:3.500A) removed outlier: 4.284A pdb=" N VAL D 159 " --> pdb=" O VAL D 167 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'F' and resid 3 through 4 Processing sheet with id=AB5, first strand: chain 'F' and resid 24 through 25 removed outlier: 4.210A pdb=" N LEU F 14 " --> pdb=" O LEU F 25 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'F' and resid 63 through 65 Processing sheet with id=AB7, first strand: chain 'F' and resid 84 through 85 removed outlier: 3.619A pdb=" N ALA F 85 " --> pdb=" O GLN F 88 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'F' and resid 163 through 166 removed outlier: 7.170A pdb=" N HIS F 164 " --> pdb=" O ARG F 155 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'F' and resid 182 through 187 removed outlier: 6.711A pdb=" N PHE F 182 " --> pdb=" O GLU F 197 " (cutoff:3.500A) removed outlier: 4.365A pdb=" N GLU F 197 " --> pdb=" O PHE F 182 " (cutoff:3.500A) removed outlier: 6.584A pdb=" N GLY F 184 " --> pdb=" O ILE F 195 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N ILE F 195 " --> pdb=" O GLY F 184 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'F' and resid 200 through 201 Processing sheet with id=AC2, first strand: chain 'F' and resid 330 through 332 removed outlier: 5.913A pdb=" N SER F 331 " --> pdb=" O PHE F 357 " (cutoff:3.500A) removed outlier: 6.056A pdb=" N VAL F 305 " --> pdb=" O VAL F 372 " (cutoff:3.500A) removed outlier: 5.248A pdb=" N VAL F 371 " --> pdb=" O VAL F 397 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'F' and resid 544 through 545 removed outlier: 6.937A pdb=" N VAL F 544 " --> pdb=" O LEU F 573 " (cutoff:3.500A) removed outlier: 8.582A pdb=" N ILE F 575 " --> pdb=" O VAL F 544 " (cutoff:3.500A) removed outlier: 6.665A pdb=" N PHE F 472 " --> pdb=" O CYS F 574 " (cutoff:3.500A) removed outlier: 7.430A pdb=" N MET F 576 " --> pdb=" O PHE F 472 " (cutoff:3.500A) removed outlier: 6.563A pdb=" N AMET F 474 " --> pdb=" O MET F 576 " (cutoff:3.500A) removed outlier: 7.531A pdb=" N LYS F 473 " --> pdb=" O LEU F 590 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC3 Processing sheet with id=AC4, first strand: chain 'F' and resid 481 through 482 removed outlier: 4.050A pdb=" N THR F 481 " --> pdb=" O ILE F 488 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N ILE F 488 " --> pdb=" O THR F 481 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC4 Processing sheet with id=AC5, first strand: chain 'F' and resid 511 through 512 removed outlier: 6.130A pdb=" N PHE F 511 " --> pdb=" O GLN F 531 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC5 Processing sheet with id=AC6, first strand: chain 'E' and resid 3 through 4 Processing sheet with id=AC7, first strand: chain 'E' and resid 15 through 16 Processing sheet with id=AC8, first strand: chain 'E' and resid 69 through 71 Processing sheet with id=AC9, first strand: chain 'E' and resid 153 through 159 removed outlier: 3.713A pdb=" N ARG E 155 " --> pdb=" O HIS E 164 " (cutoff:3.500A) removed outlier: 7.931A pdb=" N HIS E 164 " --> pdb=" O ARG E 155 " (cutoff:3.500A) removed outlier: 7.004A pdb=" N VAL E 157 " --> pdb=" O GLU E 162 " (cutoff:3.500A) removed outlier: 9.300A pdb=" N GLU E 162 " --> pdb=" O VAL E 157 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'E' and resid 185 through 187 Processing sheet with id=AD2, first strand: chain 'E' and resid 200 through 201 Processing sheet with id=AD3, first strand: chain 'E' and resid 330 through 332 removed outlier: 6.526A pdb=" N SER E 331 " --> pdb=" O PHE E 357 " (cutoff:3.500A) removed outlier: 8.721A pdb=" N THR E 359 " --> pdb=" O SER E 331 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N VAL E 356 " --> pdb=" O ILE E 304 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N CYS E 358 " --> pdb=" O TYR E 306 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ALA E 308 " --> pdb=" O CYS E 358 " (cutoff:3.500A) removed outlier: 5.834A pdb=" N VAL E 305 " --> pdb=" O VAL E 372 " (cutoff:3.500A) removed outlier: 7.242A pdb=" N ASP E 374 " --> pdb=" O VAL E 305 " (cutoff:3.500A) removed outlier: 6.681A pdb=" N THR E 307 " --> pdb=" O ASP E 374 " (cutoff:3.500A) removed outlier: 5.627A pdb=" N VAL E 371 " --> pdb=" O VAL E 397 " (cutoff:3.500A) removed outlier: 7.315A pdb=" N ILE E 399 " --> pdb=" O VAL E 371 " (cutoff:3.500A) removed outlier: 5.950A pdb=" N PHE E 373 " --> pdb=" O ILE E 399 " (cutoff:3.500A) removed outlier: 6.327A pdb=" N SER E 278 " --> pdb=" O TYR E 398 " (cutoff:3.500A) removed outlier: 7.790A pdb=" N GLY E 400 " --> pdb=" O SER E 278 " (cutoff:3.500A) removed outlier: 5.135A pdb=" N LEU E 280 " --> pdb=" O GLY E 400 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'E' and resid 366 through 367 removed outlier: 7.094A pdb=" N THR E 366 " --> pdb=" O ARG E 392 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD4 Processing sheet with id=AD5, first strand: chain 'E' and resid 481 through 482 Processing sheet with id=AD6, first strand: chain 'E' and resid 530 through 532 removed outlier: 6.121A pdb=" N PHE E 511 " --> pdb=" O GLN E 531 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'G' and resid 11 through 12 removed outlier: 6.272A pdb=" N TYR G 31 " --> pdb=" O LEU G 42 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N THR G 35 " --> pdb=" O GLY G 38 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'G' and resid 16 through 17 removed outlier: 3.576A pdb=" N PHE G 56 " --> pdb=" O ILE G 65 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N ILE G 65 " --> pdb=" O PHE G 56 " (cutoff:3.500A) 786 hydrogen bonds defined for protein. 2157 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 49 hydrogen bonds 90 hydrogen bond angles 0 basepair planarities 20 basepair parallelities 39 stacking parallelities Total time for adding SS restraints: 5.42 Time building geometry restraints manager: 2.08 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.90 - 1.23: 508 1.23 - 1.56: 21606 1.56 - 1.89: 331 1.89 - 2.22: 0 2.22 - 2.55: 1 Bond restraints: 22446 Sorted by residual: bond pdb=" CB PRO E 284 " pdb=" CG PRO E 284 " ideal model delta sigma weight residual 1.492 2.547 -1.055 5.00e-02 4.00e+02 4.45e+02 bond pdb=" CG PRO E 284 " pdb=" CD PRO E 284 " ideal model delta sigma weight residual 1.503 0.904 0.599 3.40e-02 8.65e+02 3.11e+02 bond pdb=" C ASN A 52 " pdb=" N CYS A 53 " ideal model delta sigma weight residual 1.333 1.092 0.240 1.38e-02 5.25e+03 3.03e+02 bond pdb=" C THR A 51 " pdb=" N ASN A 52 " ideal model delta sigma weight residual 1.330 1.135 0.195 1.36e-02 5.41e+03 2.05e+02 bond pdb=" O3' A M 1 " pdb=" P U M 2 " ideal model delta sigma weight residual 1.607 1.531 0.076 1.20e-02 6.94e+03 4.00e+01 ... (remaining 22441 not shown) Histogram of bond angle deviations from ideal: 0.00 - 19.20: 30765 19.20 - 38.40: 3 38.40 - 57.60: 0 57.60 - 76.80: 0 76.80 - 96.00: 1 Bond angle restraints: 30769 Sorted by residual: angle pdb=" CB PRO E 284 " pdb=" CG PRO E 284 " pdb=" CD PRO E 284 " ideal model delta sigma weight residual 106.10 10.10 96.00 3.20e+00 9.77e-02 9.00e+02 angle pdb=" O ASN A 52 " pdb=" C ASN A 52 " pdb=" N CYS A 53 " ideal model delta sigma weight residual 121.83 96.89 24.94 1.33e+00 5.65e-01 3.52e+02 angle pdb=" N PRO E 284 " pdb=" CA PRO E 284 " pdb=" CB PRO E 284 " ideal model delta sigma weight residual 103.25 88.58 14.67 1.05e+00 9.07e-01 1.95e+02 angle pdb=" CA ASN A 52 " pdb=" C ASN A 52 " pdb=" N CYS A 53 " ideal model delta sigma weight residual 116.19 135.61 -19.42 1.66e+00 3.63e-01 1.37e+02 angle pdb=" CA PRO E 284 " pdb=" N PRO E 284 " pdb=" CD PRO E 284 " ideal model delta sigma weight residual 112.00 96.57 15.43 1.40e+00 5.10e-01 1.21e+02 ... (remaining 30764 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 25.85: 12323 25.85 - 51.70: 902 51.70 - 77.56: 81 77.56 - 103.41: 10 103.41 - 129.26: 2 Dihedral angle restraints: 13318 sinusoidal: 5462 harmonic: 7856 Sorted by residual: dihedral pdb=" C4' G I 33 " pdb=" C3' G I 33 " pdb=" C2' G I 33 " pdb=" C1' G I 33 " ideal model delta sinusoidal sigma weight residual 36.34 -35.75 72.10 1 3.10e+00 1.04e-01 6.92e+02 dihedral pdb=" C4' G J 25 " pdb=" C3' G J 25 " pdb=" C2' G J 25 " pdb=" C1' G J 25 " ideal model delta sinusoidal sigma weight residual 36.35 -35.03 71.37 1 3.10e+00 1.04e-01 6.80e+02 dihedral pdb=" O4' G I 33 " pdb=" C4' G I 33 " pdb=" C3' G I 33 " pdb=" C2' G I 33 " ideal model delta sinusoidal sigma weight residual -35.15 24.51 -59.66 1 4.00e+00 6.25e-02 2.97e+02 ... (remaining 13315 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.148: 3490 0.148 - 0.296: 78 0.296 - 0.444: 2 0.444 - 0.592: 0 0.592 - 0.739: 1 Chirality restraints: 3571 Sorted by residual: chirality pdb=" P A M 1 " pdb=" OP1 A M 1 " pdb=" OP2 A M 1 " pdb=" O5' A M 1 " both_signs ideal model delta sigma weight residual True 2.17 -2.91 -0.74 2.00e-01 2.50e+01 1.37e+01 chirality pdb=" C3' A M 1 " pdb=" C4' A M 1 " pdb=" O3' A M 1 " pdb=" C2' A M 1 " both_signs ideal model delta sigma weight residual False -2.50 -2.08 -0.41 2.00e-01 2.50e+01 4.30e+00 chirality pdb=" CA PRO E 284 " pdb=" N PRO E 284 " pdb=" C PRO E 284 " pdb=" CB PRO E 284 " both_signs ideal model delta sigma weight residual False 2.72 2.39 0.33 2.00e-01 2.50e+01 2.75e+00 ... (remaining 3568 not shown) Planarity restraints: 3732 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASN A 52 " 0.046 2.00e-02 2.50e+03 7.97e-02 6.36e+01 pdb=" C ASN A 52 " -0.138 2.00e-02 2.50e+03 pdb=" O ASN A 52 " 0.038 2.00e-02 2.50e+03 pdb=" N CYS A 53 " 0.055 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASN G 1 " 0.026 2.00e-02 2.50e+03 6.25e-02 3.91e+01 pdb=" C ASN G 1 " -0.108 2.00e-02 2.50e+03 pdb=" O ASN G 1 " 0.045 2.00e-02 2.50e+03 pdb=" N ASN G 2 " 0.037 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C TRP B 182 " -0.092 5.00e-02 4.00e+02 1.42e-01 3.22e+01 pdb=" N PRO B 183 " 0.245 5.00e-02 4.00e+02 pdb=" CA PRO B 183 " -0.079 5.00e-02 4.00e+02 pdb=" CD PRO B 183 " -0.074 5.00e-02 4.00e+02 ... (remaining 3729 not shown) Histogram of nonbonded interaction distances: 1.56 - 2.23: 20 2.23 - 2.89: 8875 2.89 - 3.56: 31700 3.56 - 4.23: 52281 4.23 - 4.90: 85658 Nonbonded interactions: 178534 Sorted by model distance: nonbonded pdb=" N ASN G 1 " pdb=" P A M 1 " model vdw 1.556 3.480 nonbonded pdb="MN MN A1003 " pdb=" O HOH M 102 " model vdw 2.106 2.320 nonbonded pdb="MN MN A1004 " pdb=" O HOH A1103 " model vdw 2.134 2.320 nonbonded pdb=" N2 G I 11 " pdb=" O2 C J 49 " model vdw 2.135 2.496 nonbonded pdb=" O PHE F 145 " pdb=" OG SER F 148 " model vdw 2.141 3.040 ... (remaining 178529 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 Found NCS groups: ncs_group { reference = (chain 'B' and ((resid 6 through 8 and (name N or name CA or name C or name O or \ name CB )) or resid 9 through 22 or (resid 23 through 28 and (name N or name CA \ or name C or name O or name CB )) or resid 29 through 191)) selection = (chain 'D' and (resid 6 through 21 or (resid 22 through 28 and (name N or name C \ A or name C or name O or name CB )) or resid 29 through 31 or (resid 32 and (nam \ e N or name CA or name C or name O or name CB )) or resid 33 through 34 or (resi \ d 35 through 37 and (name N or name CA or name C or name O or name CB )) or resi \ d 38 or (resid 39 through 40 and (name N or name CA or name C or name O or name \ CB )) or resid 41 through 42 or (resid 43 and (name N or name CA or name C or na \ me O or name CB )) or resid 44 through 46 or (resid 47 and (name N or name CA or \ name C or name O or name CB )) or resid 48 through 191)) } ncs_group { reference = (chain 'E' and (resid 2 through 473 or resid 475 through 703)) selection = (chain 'F' and (resid 2 through 473 or resid 475 through 703)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.41 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 8.740 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: 0.030 Extract box with map and model: 0.460 Check model and map are aligned: 0.050 Set scattering table: 0.050 Process input model: 29.370 Find NCS groups from input model: 0.340 Set up NCS constraints: 0.070 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:9.730 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 48.850 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.0119 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 : 0.010 1.055 22478 Z= 0.329 Angle : 1.095 96.004 30796 Z= 0.567 Chirality : 0.055 0.739 3571 Planarity : 0.007 0.142 3732 Dihedral : 16.442 129.259 8250 Min Nonbonded Distance : 1.556 Molprobity Statistics. All-atom Clashscore : 16.82 Ramachandran Plot: Outliers : 0.19 % Allowed : 7.52 % Favored : 92.29 % Rotamer: Outliers : 2.25 % Allowed : 24.39 % Favored : 73.36 % Cbeta Deviations : 0.04 % Peptide Plane: Cis-proline : 0.93 % Cis-general : 0.00 % Twisted Proline : 0.93 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.40 (0.15), residues: 2639 helix: -0.53 (0.17), residues: 946 sheet: -2.16 (0.34), residues: 199 loop : -2.30 (0.15), residues: 1494 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG F 427 TYR 0.032 0.002 TYR E 185 PHE 0.028 0.002 PHE E 357 TRP 0.037 0.002 TRP D 182 HIS 0.020 0.002 HIS A 295 Details of bonding type rmsd/Z covalent geometry : bond 0.00946 / 0.33 (22446) covalent geometry : angle 1.08270 / 0.57 (30769) hydrogen bonds : bond 0.20231 / 13.58 ( 822) hydrogen bonds : angle 7.29691 / 5.12 ( 2247) metal coordination : bond 0.05501 / 3.05 ( 32) metal coordination : angle 5.52929 / 3.84 ( 27) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5278 Ramachandran restraints generated. 2639 Oldfield, 0 Emsley, 2639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5278 Ramachandran restraints generated. 2639 Oldfield, 0 Emsley, 2639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 290 residues out of total 2316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 241 time to evaluate : 0.883 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: A 109 ASP cc_start: -0.1464 (OUTLIER) cc_final: -0.1999 (m-30) REVERT: A 218 ASP cc_start: 0.3787 (t0) cc_final: 0.2627 (m-30) REVERT: A 463 MET cc_start: -0.3071 (ttt) cc_final: -0.3522 (ptp) REVERT: A 818 MET cc_start: 0.0061 (ptp) cc_final: -0.1004 (mmt) REVERT: A 845 ASP cc_start: -0.0259 (OUTLIER) cc_final: -0.0874 (m-30) REVERT: A 894 GLU cc_start: 0.0660 (OUTLIER) cc_final: -0.0281 (tt0) REVERT: D 94 MET cc_start: -0.0991 (mtp) cc_final: -0.1327 (mmm) REVERT: D 174 MET cc_start: -0.0180 (mmp) cc_final: -0.0983 (tpt) REVERT: E 9 ASN cc_start: 0.5105 (t0) cc_final: 0.4445 (p0) REVERT: E 65 LEU cc_start: -0.2314 (OUTLIER) cc_final: -0.2620 (mp) REVERT: E 274 MET cc_start: 0.2893 (tpp) cc_final: 0.2675 (ptm) outliers start: 49 outliers final: 5 residues processed: 285 average time/residue: 0.5055 time to fit residues: 169.7368 Evaluate side-chains 154 residues out of total 2316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 145 time to evaluate : 0.798 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 109 ASP Chi-restraints excluded: chain A residue 295 HIS Chi-restraints excluded: chain A residue 618 ASP Chi-restraints excluded: chain A residue 776 VAL Chi-restraints excluded: chain A residue 845 ASP Chi-restraints excluded: chain A residue 885 LEU Chi-restraints excluded: chain A residue 894 GLU Chi-restraints excluded: chain D residue 122 LEU Chi-restraints excluded: chain E residue 65 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 266 random chunks: chunk 197 optimal weight: 5.9990 chunk 215 optimal weight: 8.9990 chunk 20 optimal weight: 0.6980 chunk 132 optimal weight: 0.7980 chunk 261 optimal weight: 8.9990 chunk 248 optimal weight: 0.2980 chunk 207 optimal weight: 5.9990 chunk 155 optimal weight: 0.0770 chunk 244 optimal weight: 0.0270 chunk 183 optimal weight: 0.9980 chunk 111 optimal weight: 0.6980 overall best weight: 0.3596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 52 ASN A 88 ASN A 168 ASN ** A 177 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 295 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 439 HIS ** A 573 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 176 ASN C 18 GLN F 9 ASN F 281 GLN ** F 381 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 404 GLN F 489 ASN F 518 GLN F 537 GLN ** F 548 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 220 ASN ** E 519 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 531 GLN ** G 1 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5248 r_free = 0.5248 target = 0.262135 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.5098 r_free = 0.5098 target = 0.244700 restraints weight = 85627.643| |-----------------------------------------------------------------------------| r_work (start): 0.5065 rms_B_bonded: 4.64 r_work (final): 0.5065 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.5066 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.5066 r_free = 0.5066 target_work(ls_wunit_k1) = 0.242 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.5066 r_free = 0.5066 target_work(ls_wunit_k1) = 0.242 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.5066 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.0207 moved from start: 0.2131 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.086 22478 Z= 0.142 Angle : 0.741 12.372 30796 Z= 0.365 Chirality : 0.046 0.322 3571 Planarity : 0.005 0.100 3732 Dihedral : 8.528 123.358 3551 Min Nonbonded Distance : 2.077 Molprobity Statistics. All-atom Clashscore : 13.82 Ramachandran Plot: Outliers : 0.08 % Allowed : 7.67 % Favored : 92.25 % Rotamer: Outliers : 3.71 % Allowed : 22.63 % Favored : 73.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.93 % Cis-general : 0.00 % Twisted Proline : 0.93 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.04 (0.16), residues: 2639 helix: -0.21 (0.17), residues: 957 sheet: -1.53 (0.31), residues: 234 loop : -2.19 (0.15), residues: 1448 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 111 TYR 0.020 0.001 TYR E 180 PHE 0.023 0.001 PHE A 157 TRP 0.019 0.001 TRP D 182 HIS 0.007 0.001 HIS E 33 Details of bonding type rmsd/Z covalent geometry : bond 0.00308 / 0.14 (22446) covalent geometry : angle 0.72968 / 0.36 (30769) hydrogen bonds : bond 0.04960 / 3.42 ( 822) hydrogen bonds : angle 5.20554 / 3.67 ( 2247) metal coordination : bond 0.02918 / 1.70 ( 32) metal coordination : angle 4.32931 / 3.18 ( 27) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5278 Ramachandran restraints generated. 2639 Oldfield, 0 Emsley, 2639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5278 Ramachandran restraints generated. 2639 Oldfield, 0 Emsley, 2639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 251 residues out of total 2316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 169 time to evaluate : 0.791 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 218 ASP cc_start: 0.4337 (t0) cc_final: 0.3484 (m-30) REVERT: A 463 MET cc_start: -0.2421 (ttt) cc_final: -0.2880 (ttt) REVERT: A 601 MET cc_start: 0.1198 (mtm) cc_final: -0.0912 (ppp) REVERT: A 894 GLU cc_start: 0.0960 (OUTLIER) cc_final: 0.0203 (tt0) REVERT: A 906 MET cc_start: -0.0705 (tmm) cc_final: -0.2545 (ptt) REVERT: A 924 MET cc_start: -0.0126 (mmp) cc_final: -0.1882 (tmm) REVERT: C 13 LEU cc_start: 0.1014 (tp) cc_final: 0.0774 (tp) REVERT: C 19 GLN cc_start: -0.0434 (OUTLIER) cc_final: -0.2808 (tp40) REVERT: D 67 MET cc_start: 0.3008 (mtp) cc_final: 0.2346 (mmt) REVERT: D 70 MET cc_start: -0.0625 (mtm) cc_final: -0.1655 (tpp) REVERT: D 94 MET cc_start: -0.1195 (mtp) cc_final: -0.1511 (mmm) REVERT: D 174 MET cc_start: -0.0515 (mmp) cc_final: -0.0757 (tpt) REVERT: F 341 GLU cc_start: 0.1231 (pt0) cc_final: 0.0214 (tp30) outliers start: 82 outliers final: 17 residues processed: 234 average time/residue: 0.5603 time to fit residues: 153.0246 Evaluate side-chains 152 residues out of total 2316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 133 time to evaluate : 0.768 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 295 HIS Chi-restraints excluded: chain A residue 338 VAL Chi-restraints excluded: chain A residue 633 MET Chi-restraints excluded: chain A residue 714 LYS Chi-restraints excluded: chain A residue 833 ASP Chi-restraints excluded: chain A residue 894 GLU Chi-restraints excluded: chain B residue 94 MET Chi-restraints excluded: chain C residue 6 VAL Chi-restraints excluded: chain C residue 19 GLN Chi-restraints excluded: chain D residue 76 SER Chi-restraints excluded: chain D residue 130 VAL Chi-restraints excluded: chain D residue 153 LEU Chi-restraints excluded: chain F residue 90 PHE Chi-restraints excluded: chain E residue 26 CYS Chi-restraints excluded: chain E residue 185 TYR Chi-restraints excluded: chain E residue 223 ASP Chi-restraints excluded: chain E residue 284 PRO Chi-restraints excluded: chain E residue 510 VAL Chi-restraints excluded: chain G residue 18 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 266 random chunks: chunk 114 optimal weight: 0.9980 chunk 78 optimal weight: 2.9990 chunk 24 optimal weight: 2.9990 chunk 190 optimal weight: 0.8980 chunk 242 optimal weight: 8.9990 chunk 47 optimal weight: 3.9990 chunk 192 optimal weight: 9.9990 chunk 27 optimal weight: 2.9990 chunk 200 optimal weight: 1.9990 chunk 20 optimal weight: 0.5980 chunk 235 optimal weight: 10.0000 overall best weight: 1.4984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 113 HIS ** A 177 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 295 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 381 HIS ** A 439 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 573 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 695 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 725 HIS ** A 767 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 790 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 815 GLN A 898 HIS B 118 ASN ** C 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 157 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 245 HIS ** F 381 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 548 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 559 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 88 GLN ** E 492 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 519 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5269 r_free = 0.5269 target = 0.264869 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.5084 r_free = 0.5084 target = 0.241832 restraints weight = 100505.605| |-----------------------------------------------------------------------------| r_work (start): 0.5012 rms_B_bonded: 4.32 r_work: 0.4877 rms_B_bonded: 4.36 restraints_weight: 0.5000 r_work (final): 0.4877 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4852 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4852 r_free = 0.4852 target_work(ls_wunit_k1) = 0.219 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4852 r_free = 0.4852 target_work(ls_wunit_k1) = 0.219 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 16 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.4852 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.0951 moved from start: 0.3855 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.089 22478 Z= 0.181 Angle : 0.783 12.191 30796 Z= 0.391 Chirality : 0.049 0.415 3571 Planarity : 0.006 0.079 3732 Dihedral : 8.403 118.876 3538 Min Nonbonded Distance : 2.130 Molprobity Statistics. All-atom Clashscore : 15.40 Ramachandran Plot: Outliers : 0.08 % Allowed : 7.94 % Favored : 91.99 % Rotamer: Outliers : 4.46 % Allowed : 23.20 % Favored : 72.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.93 % Cis-general : 0.00 % Twisted Proline : 0.93 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.25 (0.15), residues: 2639 helix: -0.47 (0.16), residues: 942 sheet: -1.70 (0.31), residues: 244 loop : -2.23 (0.15), residues: 1453 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG A 654 TYR 0.038 0.002 TYR A 453 PHE 0.027 0.002 PHE A 134 TRP 0.020 0.003 TRP A 800 HIS 0.018 0.002 HIS A 816 Details of bonding type rmsd/Z covalent geometry : bond 0.00396 / 0.18 (22446) covalent geometry : angle 0.77479 / 0.39 (30769) hydrogen bonds : bond 0.05043 / 3.51 ( 822) hydrogen bonds : angle 5.34788 / 3.72 ( 2247) metal coordination : bond 0.02647 / 1.59 ( 32) metal coordination : angle 3.97538 / 2.77 ( 27) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5278 Ramachandran restraints generated. 2639 Oldfield, 0 Emsley, 2639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5278 Ramachandran restraints generated. 2639 Oldfield, 0 Emsley, 2639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 277 residues out of total 2316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 99 poor density : 178 time to evaluate : 0.718 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 124 MET cc_start: 0.0208 (OUTLIER) cc_final: -0.1397 (mmm) REVERT: A 463 MET cc_start: -0.1001 (ttt) cc_final: -0.1561 (ttt) REVERT: A 501 SER cc_start: 0.3220 (t) cc_final: 0.2995 (m) REVERT: A 519 MET cc_start: 0.0903 (ptt) cc_final: -0.0256 (mpp) REVERT: A 601 MET cc_start: 0.1315 (mtm) cc_final: 0.0512 (ppp) REVERT: A 629 MET cc_start: 0.4011 (OUTLIER) cc_final: 0.2268 (pmm) REVERT: A 658 GLU cc_start: 0.0934 (OUTLIER) cc_final: -0.0096 (tt0) REVERT: A 672 SER cc_start: 0.3947 (p) cc_final: 0.3746 (m) REVERT: A 894 GLU cc_start: 0.0563 (OUTLIER) cc_final: 0.0182 (tt0) REVERT: A 924 MET cc_start: 0.0741 (mmp) cc_final: -0.1391 (tmm) REVERT: B 51 ARG cc_start: 0.3515 (tpp80) cc_final: 0.3292 (tpm170) REVERT: B 55 MET cc_start: 0.5634 (ptt) cc_final: 0.5223 (ptt) REVERT: B 75 ARG cc_start: 0.0476 (ttp80) cc_final: 0.0083 (mmt180) REVERT: B 103 LEU cc_start: -0.2680 (OUTLIER) cc_final: -0.2895 (tt) REVERT: B 105 ASN cc_start: -0.0282 (OUTLIER) cc_final: -0.1969 (m-40) REVERT: C 13 LEU cc_start: 0.0485 (tp) cc_final: 0.0230 (tp) REVERT: C 19 GLN cc_start: -0.0520 (OUTLIER) cc_final: -0.2413 (mm110) REVERT: D 67 MET cc_start: 0.3108 (mtp) cc_final: 0.2367 (mmt) REVERT: D 79 LYS cc_start: -0.1210 (OUTLIER) cc_final: -0.1455 (ttmm) REVERT: D 91 LEU cc_start: -0.2443 (OUTLIER) cc_final: -0.3330 (tp) REVERT: D 94 MET cc_start: -0.1338 (mtp) cc_final: -0.1928 (mmm) REVERT: D 174 MET cc_start: -0.0196 (mmp) cc_final: -0.1165 (tpt) REVERT: F 165 LEU cc_start: 0.0271 (OUTLIER) cc_final: -0.0053 (mt) REVERT: F 274 MET cc_start: 0.1975 (mmp) cc_final: 0.0610 (mtp) REVERT: F 341 GLU cc_start: 0.1594 (pt0) cc_final: 0.1189 (pp20) REVERT: E 223 ASP cc_start: 0.0551 (OUTLIER) cc_final: -0.0462 (m-30) REVERT: E 274 MET cc_start: 0.2951 (ptm) cc_final: 0.1985 (pmm) REVERT: E 436 MET cc_start: -0.1501 (OUTLIER) cc_final: -0.2116 (mpt) REVERT: E 503 ASN cc_start: 0.4644 (p0) cc_final: 0.3941 (t0) outliers start: 99 outliers final: 26 residues processed: 253 average time/residue: 0.5438 time to fit residues: 160.9017 Evaluate side-chains 187 residues out of total 2316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 149 time to evaluate : 0.768 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 ASP Chi-restraints excluded: chain A residue 124 MET Chi-restraints excluded: chain A residue 163 TYR Chi-restraints excluded: chain A residue 205 LEU Chi-restraints excluded: chain A residue 242 MET Chi-restraints excluded: chain A residue 299 VAL Chi-restraints excluded: chain A residue 338 VAL Chi-restraints excluded: chain A residue 553 ARG Chi-restraints excluded: chain A residue 569 ARG Chi-restraints excluded: chain A residue 629 MET Chi-restraints excluded: chain A residue 633 MET Chi-restraints excluded: chain A residue 658 GLU Chi-restraints excluded: chain A residue 760 ASP Chi-restraints excluded: chain A residue 833 ASP Chi-restraints excluded: chain A residue 894 GLU Chi-restraints excluded: chain A residue 906 MET Chi-restraints excluded: chain B residue 103 LEU Chi-restraints excluded: chain B residue 105 ASN Chi-restraints excluded: chain C residue 6 VAL Chi-restraints excluded: chain C residue 19 GLN Chi-restraints excluded: chain D residue 76 SER Chi-restraints excluded: chain D residue 79 LYS Chi-restraints excluded: chain D residue 83 VAL Chi-restraints excluded: chain D residue 91 LEU Chi-restraints excluded: chain D residue 98 LEU Chi-restraints excluded: chain D residue 130 VAL Chi-restraints excluded: chain F residue 68 MET Chi-restraints excluded: chain F residue 165 LEU Chi-restraints excluded: chain F residue 181 VAL Chi-restraints excluded: chain E residue 26 CYS Chi-restraints excluded: chain E residue 185 TYR Chi-restraints excluded: chain E residue 223 ASP Chi-restraints excluded: chain E residue 231 THR Chi-restraints excluded: chain E residue 284 PRO Chi-restraints excluded: chain E residue 436 MET Chi-restraints excluded: chain E residue 510 VAL Chi-restraints excluded: chain E residue 523 SER Chi-restraints excluded: chain G residue 76 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 266 random chunks: chunk 79 optimal weight: 0.5980 chunk 5 optimal weight: 0.6980 chunk 56 optimal weight: 0.9990 chunk 245 optimal weight: 7.9990 chunk 100 optimal weight: 5.9990 chunk 116 optimal weight: 10.0000 chunk 161 optimal weight: 0.0060 chunk 38 optimal weight: 1.9990 chunk 85 optimal weight: 0.9980 chunk 125 optimal weight: 0.9990 chunk 82 optimal weight: 1.9990 overall best weight: 0.6598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 168 ASN A 177 ASN A 210 GLN A 215 ASN ** A 295 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 439 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 573 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 695 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 752 HIS ** A 767 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 791 ASN B 118 ASN ** C 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 39 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 381 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 559 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 492 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 518 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 519 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 11 GLN G 98 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5272 r_free = 0.5272 target = 0.264547 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.5150 r_free = 0.5150 target = 0.246099 restraints weight = 86990.719| |-----------------------------------------------------------------------------| r_work (start): 0.5076 rms_B_bonded: 3.40 r_work: 0.4925 rms_B_bonded: 3.95 restraints_weight: 0.5000 r_work (final): 0.4925 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4884 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4884 r_free = 0.4884 target_work(ls_wunit_k1) = 0.222 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 16 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4884 r_free = 0.4884 target_work(ls_wunit_k1) = 0.222 | | occupancies: max = 1.00 min = 0.03 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (6 function evaluations) r_final: 0.4884 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.0874 moved from start: 0.4343 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 22478 Z= 0.129 Angle : 0.692 15.122 30796 Z= 0.335 Chirality : 0.045 0.272 3571 Planarity : 0.005 0.062 3732 Dihedral : 7.967 118.307 3536 Min Nonbonded Distance : 2.079 Molprobity Statistics. All-atom Clashscore : 13.47 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.42 % Favored : 93.51 % Rotamer: Outliers : 2.87 % Allowed : 25.72 % Favored : 71.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.93 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.89 (0.16), residues: 2639 helix: -0.11 (0.17), residues: 953 sheet: -1.55 (0.32), residues: 237 loop : -2.05 (0.15), residues: 1449 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG E 303 TYR 0.017 0.001 TYR E 277 PHE 0.022 0.001 PHE A 504 TRP 0.012 0.001 TRP B 182 HIS 0.008 0.001 HIS A 816 Details of bonding type rmsd/Z covalent geometry : bond 0.00280 / 0.13 (22446) covalent geometry : angle 0.67452 / 0.33 (30769) hydrogen bonds : bond 0.04205 / 3.00 ( 822) hydrogen bonds : angle 4.90367 / 3.45 ( 2247) metal coordination : bond 0.02434 / 1.42 ( 32) metal coordination : angle 5.24396 / 3.46 ( 27) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5278 Ramachandran restraints generated. 2639 Oldfield, 0 Emsley, 2639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5278 Ramachandran restraints generated. 2639 Oldfield, 0 Emsley, 2639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 221 residues out of total 2316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 158 time to evaluate : 0.800 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 124 MET cc_start: 0.0380 (OUTLIER) cc_final: -0.1215 (mmm) REVERT: A 419 PHE cc_start: -0.1184 (t80) cc_final: -0.2867 (t80) REVERT: A 463 MET cc_start: -0.1295 (ttt) cc_final: -0.1802 (ttt) REVERT: A 519 MET cc_start: 0.0770 (ptt) cc_final: -0.0565 (mpp) REVERT: A 601 MET cc_start: 0.1165 (mtm) cc_final: 0.0492 (ppp) REVERT: A 629 MET cc_start: 0.3467 (tpt) cc_final: 0.1910 (pmm) REVERT: A 674 TYR cc_start: 0.3285 (m-80) cc_final: 0.0674 (m-80) REVERT: A 883 LEU cc_start: 0.2292 (OUTLIER) cc_final: 0.1611 (tt) REVERT: B 51 ARG cc_start: 0.3816 (tpp80) cc_final: 0.3591 (tpm170) REVERT: B 55 MET cc_start: 0.5606 (ptt) cc_final: 0.5108 (ptt) REVERT: B 75 ARG cc_start: 0.0503 (ttp80) cc_final: 0.0155 (mmm-85) REVERT: C 13 LEU cc_start: 0.0370 (tp) cc_final: 0.0156 (tp) REVERT: C 19 GLN cc_start: -0.0099 (OUTLIER) cc_final: -0.2175 (mm110) REVERT: D 67 MET cc_start: 0.3064 (mtp) cc_final: 0.2416 (mmt) REVERT: D 91 LEU cc_start: -0.2078 (OUTLIER) cc_final: -0.2615 (pp) REVERT: D 94 MET cc_start: -0.0522 (mtp) cc_final: -0.1438 (mmm) REVERT: D 174 MET cc_start: 0.0030 (mmp) cc_final: -0.1005 (tpt) REVERT: F 164 HIS cc_start: 0.0721 (OUTLIER) cc_final: 0.0212 (t70) REVERT: F 165 LEU cc_start: 0.0293 (tp) cc_final: 0.0086 (mt) REVERT: F 274 MET cc_start: 0.1651 (mmp) cc_final: 0.0451 (mtp) REVERT: F 322 LEU cc_start: -0.0387 (mt) cc_final: -0.0838 (pp) REVERT: F 341 GLU cc_start: 0.1433 (pt0) cc_final: 0.1151 (pp20) REVERT: F 518 GLN cc_start: -0.1084 (OUTLIER) cc_final: -0.1548 (mt0) REVERT: E 223 ASP cc_start: 0.0957 (OUTLIER) cc_final: 0.0672 (t0) REVERT: E 436 MET cc_start: -0.1074 (OUTLIER) cc_final: -0.1368 (mpt) REVERT: E 503 ASN cc_start: 0.4659 (p0) cc_final: 0.3729 (t0) REVERT: G 11 GLN cc_start: -0.1323 (OUTLIER) cc_final: -0.2797 (pm20) outliers start: 63 outliers final: 31 residues processed: 205 average time/residue: 0.5569 time to fit residues: 133.6523 Evaluate side-chains 183 residues out of total 2316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 143 time to evaluate : 0.788 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 VAL Chi-restraints excluded: chain A residue 92 ASP Chi-restraints excluded: chain A residue 124 MET Chi-restraints excluded: chain A residue 140 ASP Chi-restraints excluded: chain A residue 151 CYS Chi-restraints excluded: chain A residue 205 LEU Chi-restraints excluded: chain A residue 270 LEU Chi-restraints excluded: chain A residue 338 VAL Chi-restraints excluded: chain A residue 408 GLN Chi-restraints excluded: chain A residue 533 ARG Chi-restraints excluded: chain A residue 553 ARG Chi-restraints excluded: chain A residue 569 ARG Chi-restraints excluded: chain A residue 633 MET Chi-restraints excluded: chain A residue 794 MET Chi-restraints excluded: chain A residue 833 ASP Chi-restraints excluded: chain A residue 883 LEU Chi-restraints excluded: chain A residue 906 MET Chi-restraints excluded: chain B residue 148 THR Chi-restraints excluded: chain B residue 187 THR Chi-restraints excluded: chain C residue 18 GLN Chi-restraints excluded: chain C residue 19 GLN Chi-restraints excluded: chain D residue 76 SER Chi-restraints excluded: chain D residue 83 VAL Chi-restraints excluded: chain D residue 91 LEU Chi-restraints excluded: chain D residue 114 CYS Chi-restraints excluded: chain D residue 187 THR Chi-restraints excluded: chain F residue 68 MET Chi-restraints excluded: chain F residue 90 PHE Chi-restraints excluded: chain F residue 164 HIS Chi-restraints excluded: chain F residue 181 VAL Chi-restraints excluded: chain F residue 277 TYR Chi-restraints excluded: chain F residue 518 GLN Chi-restraints excluded: chain E residue 26 CYS Chi-restraints excluded: chain E residue 185 TYR Chi-restraints excluded: chain E residue 223 ASP Chi-restraints excluded: chain E residue 284 PRO Chi-restraints excluded: chain E residue 436 MET Chi-restraints excluded: chain E residue 510 VAL Chi-restraints excluded: chain G residue 11 GLN Chi-restraints excluded: chain G residue 18 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 266 random chunks: chunk 195 optimal weight: 5.9990 chunk 14 optimal weight: 0.5980 chunk 28 optimal weight: 0.5980 chunk 215 optimal weight: 8.9990 chunk 222 optimal weight: 0.0970 chunk 226 optimal weight: 8.9990 chunk 113 optimal weight: 0.8980 chunk 101 optimal weight: 3.9990 chunk 188 optimal weight: 0.0010 chunk 21 optimal weight: 4.9990 chunk 186 optimal weight: 0.0060 overall best weight: 0.2600 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 177 ASN ** A 295 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 447 ASN ** A 767 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 39 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 381 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 245 HIS ** E 492 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 518 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5284 r_free = 0.5284 target = 0.274544 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.5136 r_free = 0.5136 target = 0.254741 restraints weight = 110027.049| |-----------------------------------------------------------------------------| r_work (start): 0.5081 rms_B_bonded: 5.89 r_work (final): 0.5081 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.5080 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.5080 r_free = 0.5080 target_work(ls_wunit_k1) = 0.245 | | occupancies: max = 1.00 min = 0.03 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.5080 r_free = 0.5080 target_work(ls_wunit_k1) = 0.245 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.5080 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.0672 moved from start: 0.4575 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.124 22478 Z= 0.117 Angle : 0.665 22.688 30796 Z= 0.317 Chirality : 0.044 0.299 3571 Planarity : 0.005 0.057 3732 Dihedral : 7.730 119.524 3533 Min Nonbonded Distance : 1.743 Molprobity Statistics. All-atom Clashscore : 11.84 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.42 % Favored : 93.51 % Rotamer: Outliers : 3.13 % Allowed : 25.28 % Favored : 71.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.93 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.62 (0.16), residues: 2639 helix: 0.20 (0.17), residues: 948 sheet: -1.14 (0.34), residues: 223 loop : -2.01 (0.15), residues: 1468 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 303 TYR 0.017 0.001 TYR F 277 PHE 0.020 0.001 PHE A 504 TRP 0.008 0.001 TRP F 167 HIS 0.004 0.001 HIS E 33 Details of bonding type rmsd/Z covalent geometry : bond 0.00251 / 0.11 (22446) covalent geometry : angle 0.63864 / 0.31 (30769) hydrogen bonds : bond 0.03982 / 2.86 ( 822) hydrogen bonds : angle 4.67493 / 3.29 ( 2247) metal coordination : bond 0.02886 / 1.61 ( 32) metal coordination : angle 6.25350 / 3.87 ( 27) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5278 Ramachandran restraints generated. 2639 Oldfield, 0 Emsley, 2639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5278 Ramachandran restraints generated. 2639 Oldfield, 0 Emsley, 2639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 228 residues out of total 2316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 159 time to evaluate : 0.782 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 74 ARG cc_start: 0.2159 (OUTLIER) cc_final: 0.1797 (pmm150) REVERT: A 124 MET cc_start: 0.0428 (OUTLIER) cc_final: -0.0230 (mmm) REVERT: A 419 PHE cc_start: -0.0854 (t80) cc_final: -0.2434 (t80) REVERT: A 463 MET cc_start: -0.1587 (ttt) cc_final: -0.1844 (ttt) REVERT: A 519 MET cc_start: 0.0542 (ptt) cc_final: -0.0612 (mpp) REVERT: A 555 ARG cc_start: 0.2357 (tpt170) cc_final: 0.2134 (mmt180) REVERT: A 601 MET cc_start: 0.1337 (mtm) cc_final: 0.0445 (ppp) REVERT: A 924 MET cc_start: -0.0526 (OUTLIER) cc_final: -0.1435 (mmp) REVERT: B 75 ARG cc_start: 0.0855 (ttp80) cc_final: 0.0292 (mmm-85) REVERT: C 13 LEU cc_start: 0.0773 (tp) cc_final: 0.0444 (tp) REVERT: C 19 GLN cc_start: 0.0204 (OUTLIER) cc_final: -0.1809 (mm-40) REVERT: D 67 MET cc_start: 0.3056 (mtp) cc_final: 0.2583 (mmt) REVERT: D 70 MET cc_start: -0.0474 (mtm) cc_final: -0.1722 (tpp) REVERT: D 91 LEU cc_start: -0.1302 (OUTLIER) cc_final: -0.2254 (tp) REVERT: D 94 MET cc_start: 0.0029 (mtp) cc_final: -0.1112 (mmm) REVERT: D 174 MET cc_start: -0.0024 (mmp) cc_final: -0.0485 (tpt) REVERT: F 164 HIS cc_start: 0.2144 (OUTLIER) cc_final: 0.1285 (t70) REVERT: F 165 LEU cc_start: 0.0197 (tp) cc_final: -0.0356 (mp) REVERT: F 277 TYR cc_start: 0.3392 (p90) cc_final: 0.3095 (p90) REVERT: F 518 GLN cc_start: 0.1223 (OUTLIER) cc_final: 0.0049 (mt0) REVERT: E 223 ASP cc_start: 0.2936 (OUTLIER) cc_final: 0.2419 (t0) REVERT: E 274 MET cc_start: 0.3242 (ppp) cc_final: 0.2474 (pmm) REVERT: E 436 MET cc_start: 0.2229 (OUTLIER) cc_final: 0.1657 (mpt) REVERT: E 511 PHE cc_start: 0.1127 (OUTLIER) cc_final: 0.0916 (t80) REVERT: G 11 GLN cc_start: -0.0866 (OUTLIER) cc_final: -0.2762 (pm20) outliers start: 69 outliers final: 26 residues processed: 210 average time/residue: 0.5895 time to fit residues: 143.7579 Evaluate side-chains 178 residues out of total 2316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 141 time to evaluate : 0.822 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 ARG Chi-restraints excluded: chain A residue 92 ASP Chi-restraints excluded: chain A residue 124 MET Chi-restraints excluded: chain A residue 151 CYS Chi-restraints excluded: chain A residue 177 ASN Chi-restraints excluded: chain A residue 205 LEU Chi-restraints excluded: chain A residue 270 LEU Chi-restraints excluded: chain A residue 295 HIS Chi-restraints excluded: chain A residue 338 VAL Chi-restraints excluded: chain A residue 533 ARG Chi-restraints excluded: chain A residue 553 ARG Chi-restraints excluded: chain A residue 569 ARG Chi-restraints excluded: chain A residue 633 MET Chi-restraints excluded: chain A residue 794 MET Chi-restraints excluded: chain A residue 833 ASP Chi-restraints excluded: chain A residue 883 LEU Chi-restraints excluded: chain A residue 906 MET Chi-restraints excluded: chain A residue 924 MET Chi-restraints excluded: chain B residue 148 THR Chi-restraints excluded: chain B residue 171 GLU Chi-restraints excluded: chain C residue 18 GLN Chi-restraints excluded: chain C residue 19 GLN Chi-restraints excluded: chain D residue 83 VAL Chi-restraints excluded: chain D residue 91 LEU Chi-restraints excluded: chain D residue 182 TRP Chi-restraints excluded: chain F residue 68 MET Chi-restraints excluded: chain F residue 90 PHE Chi-restraints excluded: chain F residue 164 HIS Chi-restraints excluded: chain F residue 181 VAL Chi-restraints excluded: chain F residue 518 GLN Chi-restraints excluded: chain E residue 223 ASP Chi-restraints excluded: chain E residue 284 PRO Chi-restraints excluded: chain E residue 436 MET Chi-restraints excluded: chain E residue 510 VAL Chi-restraints excluded: chain E residue 511 PHE Chi-restraints excluded: chain G residue 11 GLN Chi-restraints excluded: chain G residue 18 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 266 random chunks: chunk 175 optimal weight: 3.9990 chunk 245 optimal weight: 6.9990 chunk 121 optimal weight: 9.9990 chunk 167 optimal weight: 10.0000 chunk 27 optimal weight: 0.7980 chunk 219 optimal weight: 20.0000 chunk 103 optimal weight: 0.7980 chunk 65 optimal weight: 3.9990 chunk 60 optimal weight: 3.9990 chunk 227 optimal weight: 20.0000 chunk 252 optimal weight: 0.8980 overall best weight: 2.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 5 GLN A 9 ASN ** A 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 99 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 213 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 295 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 408 GLN A 447 ASN A 650 HIS ** A 695 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 767 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 790 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 886 GLN B 118 ASN D 157 GLN ** F 381 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 559 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 562 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 492 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 11 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5277 r_free = 0.5277 target = 0.264852 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.5162 r_free = 0.5162 target = 0.251738 restraints weight = 127513.440| |-----------------------------------------------------------------------------| r_work (start): 0.5116 rms_B_bonded: 4.73 r_work (final): 0.5116 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.5120 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.5120 r_free = 0.5120 target_work(ls_wunit_k1) = 0.248 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.5120 r_free = 0.5120 target_work(ls_wunit_k1) = 0.248 | | occupancies: max = 1.00 min = 0.06 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (7 function evaluations) r_final: 0.5120 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1113 moved from start: 0.5745 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.151 22478 Z= 0.204 Angle : 0.820 19.818 30796 Z= 0.403 Chirality : 0.050 0.467 3571 Planarity : 0.006 0.072 3732 Dihedral : 8.305 116.728 3533 Min Nonbonded Distance : 1.890 Molprobity Statistics. All-atom Clashscore : 17.24 Ramachandran Plot: Outliers : 0.08 % Allowed : 8.51 % Favored : 91.42 % Rotamer: Outliers : 4.59 % Allowed : 24.13 % Favored : 71.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.93 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.06 (0.15), residues: 2639 helix: -0.38 (0.16), residues: 943 sheet: -1.29 (0.33), residues: 240 loop : -2.12 (0.15), residues: 1456 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A 132 TYR 0.026 0.002 TYR A 156 PHE 0.043 0.003 PHE A 287 TRP 0.028 0.003 TRP B 154 HIS 0.018 0.002 HIS A 816 Details of bonding type rmsd/Z covalent geometry : bond 0.00453 / 0.20 (22446) covalent geometry : angle 0.80350 / 0.40 (30769) hydrogen bonds : bond 0.04989 / 3.48 ( 822) hydrogen bonds : angle 5.40883 / 3.78 ( 2247) metal coordination : bond 0.03377 / 1.87 ( 32) metal coordination : angle 5.65619 / 3.51 ( 27) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5278 Ramachandran restraints generated. 2639 Oldfield, 0 Emsley, 2639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5278 Ramachandran restraints generated. 2639 Oldfield, 0 Emsley, 2639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 257 residues out of total 2316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 102 poor density : 155 time to evaluate : 0.823 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 74 ARG cc_start: 0.2797 (OUTLIER) cc_final: 0.2537 (pmm150) REVERT: A 98 LYS cc_start: 0.3289 (tttt) cc_final: 0.1239 (mppt) REVERT: A 156 TYR cc_start: 0.1592 (OUTLIER) cc_final: 0.1340 (m-10) REVERT: A 266 ILE cc_start: 0.0104 (OUTLIER) cc_final: -0.1144 (tt) REVERT: A 269 ASP cc_start: 0.2068 (p0) cc_final: 0.1736 (t0) REVERT: A 519 MET cc_start: 0.0575 (ptt) cc_final: -0.0561 (mpp) REVERT: A 601 MET cc_start: 0.1174 (mtm) cc_final: 0.0734 (ppp) REVERT: A 629 MET cc_start: 0.3817 (OUTLIER) cc_final: 0.2184 (pmm) REVERT: A 674 TYR cc_start: 0.3172 (m-80) cc_final: 0.0505 (m-80) REVERT: A 924 MET cc_start: 0.1064 (OUTLIER) cc_final: -0.0166 (mmp) REVERT: B 75 ARG cc_start: 0.1155 (ttp80) cc_final: 0.0184 (mmt180) REVERT: C 13 LEU cc_start: 0.1008 (tp) cc_final: 0.0594 (tt) REVERT: C 19 GLN cc_start: 0.0471 (OUTLIER) cc_final: -0.1804 (mm-40) REVERT: D 67 MET cc_start: 0.3566 (mtp) cc_final: 0.3024 (mmt) REVERT: D 79 LYS cc_start: -0.0622 (OUTLIER) cc_final: -0.0995 (tttp) REVERT: D 91 LEU cc_start: -0.1003 (OUTLIER) cc_final: -0.2022 (tp) REVERT: D 94 MET cc_start: 0.0533 (mtp) cc_final: -0.0972 (mmm) REVERT: D 174 MET cc_start: 0.0076 (mmp) cc_final: -0.0470 (mmt) REVERT: F 68 MET cc_start: -0.0331 (OUTLIER) cc_final: -0.0950 (pp-130) REVERT: F 164 HIS cc_start: 0.2575 (OUTLIER) cc_final: 0.1701 (t70) REVERT: F 230 HIS cc_start: -0.1539 (p-80) cc_final: -0.2365 (t70) REVERT: F 436 MET cc_start: -0.0452 (OUTLIER) cc_final: -0.0656 (tmm) REVERT: F 518 GLN cc_start: 0.1517 (OUTLIER) cc_final: 0.0404 (mt0) REVERT: E 70 TYR cc_start: -0.2800 (OUTLIER) cc_final: -0.3107 (m-10) REVERT: E 223 ASP cc_start: 0.3521 (OUTLIER) cc_final: 0.3152 (t0) REVERT: E 274 MET cc_start: 0.3544 (ppp) cc_final: 0.2639 (pmm) REVERT: E 436 MET cc_start: 0.2785 (OUTLIER) cc_final: 0.2250 (mpt) REVERT: E 511 PHE cc_start: 0.1254 (OUTLIER) cc_final: 0.0962 (t80) outliers start: 102 outliers final: 37 residues processed: 233 average time/residue: 0.5292 time to fit residues: 145.0583 Evaluate side-chains 197 residues out of total 2316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 144 time to evaluate : 0.725 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 ARG Chi-restraints excluded: chain A residue 92 ASP Chi-restraints excluded: chain A residue 140 ASP Chi-restraints excluded: chain A residue 151 CYS Chi-restraints excluded: chain A residue 156 TYR Chi-restraints excluded: chain A residue 233 VAL Chi-restraints excluded: chain A residue 262 THR Chi-restraints excluded: chain A residue 266 ILE Chi-restraints excluded: chain A residue 295 HIS Chi-restraints excluded: chain A residue 338 VAL Chi-restraints excluded: chain A residue 482 CYS Chi-restraints excluded: chain A residue 533 ARG Chi-restraints excluded: chain A residue 553 ARG Chi-restraints excluded: chain A residue 569 ARG Chi-restraints excluded: chain A residue 629 MET Chi-restraints excluded: chain A residue 760 ASP Chi-restraints excluded: chain A residue 792 VAL Chi-restraints excluded: chain A residue 806 THR Chi-restraints excluded: chain A residue 924 MET Chi-restraints excluded: chain B residue 148 THR Chi-restraints excluded: chain B residue 171 GLU Chi-restraints excluded: chain B residue 187 THR Chi-restraints excluded: chain C residue 6 VAL Chi-restraints excluded: chain C residue 18 GLN Chi-restraints excluded: chain C residue 19 GLN Chi-restraints excluded: chain D residue 76 SER Chi-restraints excluded: chain D residue 79 LYS Chi-restraints excluded: chain D residue 83 VAL Chi-restraints excluded: chain D residue 91 LEU Chi-restraints excluded: chain D residue 114 CYS Chi-restraints excluded: chain D residue 182 TRP Chi-restraints excluded: chain D residue 187 THR Chi-restraints excluded: chain F residue 68 MET Chi-restraints excluded: chain F residue 164 HIS Chi-restraints excluded: chain F residue 181 VAL Chi-restraints excluded: chain F residue 210 VAL Chi-restraints excluded: chain F residue 258 ILE Chi-restraints excluded: chain F residue 277 TYR Chi-restraints excluded: chain F residue 356 VAL Chi-restraints excluded: chain F residue 436 MET Chi-restraints excluded: chain F residue 518 GLN Chi-restraints excluded: chain E residue 26 CYS Chi-restraints excluded: chain E residue 70 TYR Chi-restraints excluded: chain E residue 185 TYR Chi-restraints excluded: chain E residue 223 ASP Chi-restraints excluded: chain E residue 231 THR Chi-restraints excluded: chain E residue 284 PRO Chi-restraints excluded: chain E residue 436 MET Chi-restraints excluded: chain E residue 510 VAL Chi-restraints excluded: chain E residue 511 PHE Chi-restraints excluded: chain E residue 523 SER Chi-restraints excluded: chain G residue 18 THR Chi-restraints excluded: chain G residue 76 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 266 random chunks: chunk 251 optimal weight: 8.9990 chunk 116 optimal weight: 0.9980 chunk 0 optimal weight: 4.9990 chunk 249 optimal weight: 10.0000 chunk 15 optimal weight: 0.8980 chunk 188 optimal weight: 0.1980 chunk 66 optimal weight: 0.8980 chunk 67 optimal weight: 0.8980 chunk 133 optimal weight: 4.9990 chunk 102 optimal weight: 0.9980 chunk 71 optimal weight: 4.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 81 GLN ** A 99 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 177 ASN A 210 GLN ** A 295 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 439 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 570 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 695 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 767 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 790 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 104 ASN B 118 ASN ** F 381 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 559 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 562 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 179 ASN ** E 492 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 11 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5276 r_free = 0.5276 target = 0.263830 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.5154 r_free = 0.5154 target = 0.249067 restraints weight = 95541.099| |-----------------------------------------------------------------------------| r_work (start): 0.5110 rms_B_bonded: 3.40 r_work: 0.4894 rms_B_bonded: 4.44 restraints_weight: 0.5000 r_work (final): 0.4894 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4873 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4873 r_free = 0.4873 target_work(ls_wunit_k1) = 0.221 | | occupancies: max = 1.00 min = 0.06 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4873 r_free = 0.4873 target_work(ls_wunit_k1) = 0.221 | | occupancies: max = 1.00 min = 0.08 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.4873 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1260 moved from start: 0.5877 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.132 22478 Z= 0.132 Angle : 0.699 22.908 30796 Z= 0.336 Chirality : 0.045 0.273 3571 Planarity : 0.005 0.067 3732 Dihedral : 7.913 117.858 3533 Min Nonbonded Distance : 1.892 Molprobity Statistics. All-atom Clashscore : 14.27 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.76 % Favored : 93.16 % Rotamer: Outliers : 3.26 % Allowed : 25.72 % Favored : 71.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.93 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.79 (0.16), residues: 2639 helix: -0.10 (0.17), residues: 942 sheet: -1.26 (0.33), residues: 236 loop : -1.98 (0.16), residues: 1461 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 631 TYR 0.034 0.002 TYR F 277 PHE 0.046 0.002 PHE A 157 TRP 0.009 0.001 TRP B 154 HIS 0.006 0.001 HIS A 725 Details of bonding type rmsd/Z covalent geometry : bond 0.00287 / 0.13 (22446) covalent geometry : angle 0.67692 / 0.33 (30769) hydrogen bonds : bond 0.04235 / 3.04 ( 822) hydrogen bonds : angle 4.95584 / 3.47 ( 2247) metal coordination : bond 0.02916 / 1.61 ( 32) metal coordination : angle 5.97383 / 3.53 ( 27) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5278 Ramachandran restraints generated. 2639 Oldfield, 0 Emsley, 2639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5278 Ramachandran restraints generated. 2639 Oldfield, 0 Emsley, 2639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 214 residues out of total 2316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 142 time to evaluate : 0.659 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 124 MET cc_start: 0.1216 (ptm) cc_final: -0.0037 (tpt) REVERT: A 156 TYR cc_start: 0.1650 (OUTLIER) cc_final: 0.0356 (m-10) REVERT: A 266 ILE cc_start: -0.0246 (OUTLIER) cc_final: -0.1380 (tt) REVERT: A 269 ASP cc_start: 0.2428 (p0) cc_final: 0.1897 (t0) REVERT: A 519 MET cc_start: 0.0868 (ptt) cc_final: -0.0302 (mpp) REVERT: A 601 MET cc_start: 0.1679 (mtm) cc_final: 0.0854 (ppp) REVERT: A 674 TYR cc_start: 0.3349 (m-80) cc_final: 0.0582 (m-80) REVERT: A 924 MET cc_start: 0.1651 (OUTLIER) cc_final: 0.0164 (mmp) REVERT: B 67 MET cc_start: 0.2410 (ttt) cc_final: 0.0919 (mpm) REVERT: B 75 ARG cc_start: 0.0833 (ttp80) cc_final: 0.0111 (mmt180) REVERT: B 105 ASN cc_start: 0.0112 (OUTLIER) cc_final: -0.0223 (t0) REVERT: C 19 GLN cc_start: 0.0330 (OUTLIER) cc_final: -0.1873 (mm-40) REVERT: D 67 MET cc_start: 0.3482 (mtp) cc_final: 0.2817 (mmt) REVERT: D 91 LEU cc_start: -0.1279 (OUTLIER) cc_final: -0.2213 (pp) REVERT: D 94 MET cc_start: 0.0535 (mtp) cc_final: -0.1335 (mmm) REVERT: D 134 ASP cc_start: 0.0462 (OUTLIER) cc_final: -0.0042 (t0) REVERT: D 174 MET cc_start: 0.0432 (mmp) cc_final: -0.0817 (tpt) REVERT: F 164 HIS cc_start: 0.1296 (OUTLIER) cc_final: 0.0679 (t70) REVERT: F 230 HIS cc_start: -0.1984 (p-80) cc_final: -0.2629 (t70) REVERT: F 518 GLN cc_start: -0.0909 (OUTLIER) cc_final: -0.1294 (mt0) REVERT: E 274 MET cc_start: 0.2825 (ppp) cc_final: 0.1842 (pmm) REVERT: E 436 MET cc_start: -0.0366 (OUTLIER) cc_final: -0.0778 (mpt) REVERT: E 511 PHE cc_start: 0.1249 (OUTLIER) cc_final: 0.1019 (t80) REVERT: G 11 GLN cc_start: -0.0798 (OUTLIER) cc_final: -0.2482 (pm20) outliers start: 72 outliers final: 34 residues processed: 198 average time/residue: 0.5092 time to fit residues: 119.2092 Evaluate side-chains 183 residues out of total 2316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 137 time to evaluate : 0.621 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 ASP Chi-restraints excluded: chain A residue 151 CYS Chi-restraints excluded: chain A residue 156 TYR Chi-restraints excluded: chain A residue 233 VAL Chi-restraints excluded: chain A residue 262 THR Chi-restraints excluded: chain A residue 266 ILE Chi-restraints excluded: chain A residue 295 HIS Chi-restraints excluded: chain A residue 338 VAL Chi-restraints excluded: chain A residue 354 VAL Chi-restraints excluded: chain A residue 533 ARG Chi-restraints excluded: chain A residue 757 ILE Chi-restraints excluded: chain A residue 924 MET Chi-restraints excluded: chain A residue 928 HIS Chi-restraints excluded: chain B residue 94 MET Chi-restraints excluded: chain B residue 105 ASN Chi-restraints excluded: chain B residue 148 THR Chi-restraints excluded: chain B residue 171 GLU Chi-restraints excluded: chain B residue 187 THR Chi-restraints excluded: chain C residue 6 VAL Chi-restraints excluded: chain C residue 18 GLN Chi-restraints excluded: chain C residue 19 GLN Chi-restraints excluded: chain D residue 76 SER Chi-restraints excluded: chain D residue 83 VAL Chi-restraints excluded: chain D residue 91 LEU Chi-restraints excluded: chain D residue 114 CYS Chi-restraints excluded: chain D residue 134 ASP Chi-restraints excluded: chain D residue 182 TRP Chi-restraints excluded: chain D residue 187 THR Chi-restraints excluded: chain F residue 20 ILE Chi-restraints excluded: chain F residue 68 MET Chi-restraints excluded: chain F residue 90 PHE Chi-restraints excluded: chain F residue 164 HIS Chi-restraints excluded: chain F residue 181 VAL Chi-restraints excluded: chain F residue 210 VAL Chi-restraints excluded: chain F residue 216 THR Chi-restraints excluded: chain F residue 518 GLN Chi-restraints excluded: chain E residue 10 SER Chi-restraints excluded: chain E residue 26 CYS Chi-restraints excluded: chain E residue 185 TYR Chi-restraints excluded: chain E residue 231 THR Chi-restraints excluded: chain E residue 284 PRO Chi-restraints excluded: chain E residue 436 MET Chi-restraints excluded: chain E residue 510 VAL Chi-restraints excluded: chain E residue 511 PHE Chi-restraints excluded: chain G residue 11 GLN Chi-restraints excluded: chain G residue 76 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 266 random chunks: chunk 157 optimal weight: 1.9990 chunk 219 optimal weight: 3.9990 chunk 89 optimal weight: 4.9990 chunk 49 optimal weight: 0.9990 chunk 83 optimal weight: 0.2980 chunk 153 optimal weight: 10.0000 chunk 21 optimal weight: 0.0980 chunk 43 optimal weight: 1.9990 chunk 151 optimal weight: 0.0870 chunk 39 optimal weight: 7.9990 chunk 54 optimal weight: 0.9980 overall best weight: 0.4960 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 295 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 695 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 767 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 381 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 492 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5278 r_free = 0.5278 target = 0.264151 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.5153 r_free = 0.5153 target = 0.249258 restraints weight = 100026.953| |-----------------------------------------------------------------------------| r_work (start): 0.5111 rms_B_bonded: 3.86 r_work: 0.4882 rms_B_bonded: 4.90 restraints_weight: 0.5000 r_work (final): 0.4882 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4860 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4860 r_free = 0.4860 target_work(ls_wunit_k1) = 0.220 | | occupancies: max = 1.00 min = 0.08 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4860 r_free = 0.4860 target_work(ls_wunit_k1) = 0.220 | | occupancies: max = 1.00 min = 0.08 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.4860 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1207 moved from start: 0.6043 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.127 22478 Z= 0.122 Angle : 0.682 19.329 30796 Z= 0.328 Chirality : 0.044 0.276 3571 Planarity : 0.005 0.064 3732 Dihedral : 7.728 119.297 3533 Min Nonbonded Distance : 1.879 Molprobity Statistics. All-atom Clashscore : 13.26 Ramachandran Plot: Outliers : 0.08 % Allowed : 7.10 % Favored : 92.82 % Rotamer: Outliers : 2.87 % Allowed : 26.38 % Favored : 70.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.93 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.58 (0.16), residues: 2639 helix: 0.04 (0.17), residues: 947 sheet: -1.04 (0.35), residues: 226 loop : -1.84 (0.16), residues: 1466 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 181 TYR 0.015 0.001 TYR F 298 PHE 0.029 0.001 PHE A 415 TRP 0.010 0.001 TRP E 506 HIS 0.006 0.001 HIS A 816 Details of bonding type rmsd/Z covalent geometry : bond 0.00266 / 0.12 (22446) covalent geometry : angle 0.66386 / 0.33 (30769) hydrogen bonds : bond 0.04041 / 2.92 ( 822) hydrogen bonds : angle 4.76199 / 3.34 ( 2247) metal coordination : bond 0.02789 / 1.53 ( 32) metal coordination : angle 5.34908 / 3.23 ( 27) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5278 Ramachandran restraints generated. 2639 Oldfield, 0 Emsley, 2639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5278 Ramachandran restraints generated. 2639 Oldfield, 0 Emsley, 2639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 199 residues out of total 2316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 136 time to evaluate : 0.709 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 156 TYR cc_start: 0.1230 (OUTLIER) cc_final: 0.0883 (m-10) REVERT: A 266 ILE cc_start: -0.0482 (OUTLIER) cc_final: -0.1518 (tt) REVERT: A 269 ASP cc_start: 0.2406 (p0) cc_final: 0.1841 (t0) REVERT: A 519 MET cc_start: 0.0781 (ptt) cc_final: -0.0515 (mpp) REVERT: A 601 MET cc_start: 0.1753 (mtm) cc_final: 0.0858 (ppp) REVERT: A 629 MET cc_start: 0.2512 (tpt) cc_final: 0.1018 (mpt) REVERT: A 924 MET cc_start: 0.1745 (OUTLIER) cc_final: 0.0115 (mmp) REVERT: B 62 MET cc_start: -0.0170 (mmm) cc_final: -0.0877 (mmp) REVERT: B 67 MET cc_start: 0.2338 (ttt) cc_final: 0.0964 (mpm) REVERT: B 75 ARG cc_start: 0.0880 (ttp80) cc_final: 0.0136 (mmt90) REVERT: B 105 ASN cc_start: 0.0019 (OUTLIER) cc_final: -0.0340 (t0) REVERT: C 19 GLN cc_start: 0.0223 (OUTLIER) cc_final: -0.1884 (mm110) REVERT: D 67 MET cc_start: 0.3407 (mtp) cc_final: 0.2817 (mmt) REVERT: D 94 MET cc_start: 0.0426 (mtp) cc_final: -0.1235 (mmt) REVERT: D 134 ASP cc_start: 0.0334 (OUTLIER) cc_final: -0.0129 (t0) REVERT: D 174 MET cc_start: 0.0472 (mmp) cc_final: -0.0920 (tpt) REVERT: F 164 HIS cc_start: 0.1087 (OUTLIER) cc_final: 0.0528 (t70) REVERT: F 165 LEU cc_start: -0.0915 (OUTLIER) cc_final: -0.1462 (pt) REVERT: F 230 HIS cc_start: -0.1837 (p-80) cc_final: -0.2566 (t70) REVERT: F 240 LEU cc_start: 0.1824 (mm) cc_final: 0.1397 (tt) REVERT: F 518 GLN cc_start: -0.0972 (OUTLIER) cc_final: -0.1319 (mt0) REVERT: E 274 MET cc_start: 0.2903 (ppp) cc_final: 0.1905 (pmm) REVERT: E 436 MET cc_start: -0.0547 (OUTLIER) cc_final: -0.0965 (mpt) outliers start: 63 outliers final: 33 residues processed: 183 average time/residue: 0.5119 time to fit residues: 111.3257 Evaluate side-chains 175 residues out of total 2316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 132 time to evaluate : 0.831 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 ILE Chi-restraints excluded: chain A residue 92 ASP Chi-restraints excluded: chain A residue 151 CYS Chi-restraints excluded: chain A residue 156 TYR Chi-restraints excluded: chain A residue 171 ILE Chi-restraints excluded: chain A residue 262 THR Chi-restraints excluded: chain A residue 266 ILE Chi-restraints excluded: chain A residue 295 HIS Chi-restraints excluded: chain A residue 338 VAL Chi-restraints excluded: chain A residue 533 ARG Chi-restraints excluded: chain A residue 633 MET Chi-restraints excluded: chain A residue 757 ILE Chi-restraints excluded: chain A residue 778 SER Chi-restraints excluded: chain A residue 820 VAL Chi-restraints excluded: chain A residue 924 MET Chi-restraints excluded: chain A residue 928 HIS Chi-restraints excluded: chain B residue 94 MET Chi-restraints excluded: chain B residue 105 ASN Chi-restraints excluded: chain B residue 148 THR Chi-restraints excluded: chain B residue 171 GLU Chi-restraints excluded: chain B residue 187 THR Chi-restraints excluded: chain C residue 6 VAL Chi-restraints excluded: chain C residue 19 GLN Chi-restraints excluded: chain D residue 83 VAL Chi-restraints excluded: chain D residue 114 CYS Chi-restraints excluded: chain D residue 134 ASP Chi-restraints excluded: chain D residue 182 TRP Chi-restraints excluded: chain F residue 20 ILE Chi-restraints excluded: chain F residue 68 MET Chi-restraints excluded: chain F residue 164 HIS Chi-restraints excluded: chain F residue 165 LEU Chi-restraints excluded: chain F residue 181 VAL Chi-restraints excluded: chain F residue 210 VAL Chi-restraints excluded: chain F residue 216 THR Chi-restraints excluded: chain F residue 233 MET Chi-restraints excluded: chain F residue 518 GLN Chi-restraints excluded: chain F residue 544 VAL Chi-restraints excluded: chain E residue 10 SER Chi-restraints excluded: chain E residue 231 THR Chi-restraints excluded: chain E residue 284 PRO Chi-restraints excluded: chain E residue 436 MET Chi-restraints excluded: chain E residue 510 VAL Chi-restraints excluded: chain E residue 523 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 266 random chunks: chunk 82 optimal weight: 1.9990 chunk 31 optimal weight: 0.6980 chunk 138 optimal weight: 9.9990 chunk 14 optimal weight: 0.0370 chunk 44 optimal weight: 0.0270 chunk 46 optimal weight: 2.9990 chunk 9 optimal weight: 0.7980 chunk 181 optimal weight: 5.9990 chunk 172 optimal weight: 5.9990 chunk 27 optimal weight: 0.6980 chunk 98 optimal weight: 5.9990 overall best weight: 0.4516 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 295 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 695 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 724 GLN ** A 767 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 43 ASN ** F 39 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 381 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 492 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 518 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 1 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 11 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5280 r_free = 0.5280 target = 0.264291 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.5156 r_free = 0.5156 target = 0.250243 restraints weight = 117977.159| |-----------------------------------------------------------------------------| r_work (start): 0.5128 rms_B_bonded: 4.46 r_work (final): 0.5128 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.5129 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.5129 r_free = 0.5129 target_work(ls_wunit_k1) = 0.249 | | occupancies: max = 1.00 min = 0.08 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.5129 r_free = 0.5129 target_work(ls_wunit_k1) = 0.249 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 16 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.5129 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.0913 moved from start: 0.6266 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.122 22478 Z= 0.117 Angle : 0.667 16.638 30796 Z= 0.320 Chirality : 0.044 0.276 3571 Planarity : 0.005 0.067 3732 Dihedral : 7.598 120.128 3533 Min Nonbonded Distance : 1.886 Molprobity Statistics. All-atom Clashscore : 12.99 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.68 % Favored : 93.24 % Rotamer: Outliers : 2.38 % Allowed : 27.04 % Favored : 70.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.93 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.47 (0.16), residues: 2639 helix: 0.16 (0.17), residues: 954 sheet: -0.92 (0.35), residues: 235 loop : -1.83 (0.16), residues: 1450 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG G 39 TYR 0.027 0.001 TYR F 277 PHE 0.042 0.001 PHE A 157 TRP 0.009 0.001 TRP E 506 HIS 0.005 0.001 HIS A 816 Details of bonding type rmsd/Z covalent geometry : bond 0.00254 / 0.11 (22446) covalent geometry : angle 0.65135 / 0.32 (30769) hydrogen bonds : bond 0.03937 / 2.86 ( 822) hydrogen bonds : angle 4.60106 / 3.23 ( 2247) metal coordination : bond 0.02724 / 1.49 ( 32) metal coordination : angle 4.93921 / 3.02 ( 27) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5278 Ramachandran restraints generated. 2639 Oldfield, 0 Emsley, 2639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5278 Ramachandran restraints generated. 2639 Oldfield, 0 Emsley, 2639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 2316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 133 time to evaluate : 0.753 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: A 266 ILE cc_start: -0.0174 (OUTLIER) cc_final: -0.1120 (tt) REVERT: A 269 ASP cc_start: 0.2252 (p0) cc_final: 0.1924 (t0) REVERT: A 380 MET cc_start: 0.1318 (OUTLIER) cc_final: -0.0036 (ptt) REVERT: A 417 LYS cc_start: -0.0699 (OUTLIER) cc_final: -0.1598 (pttm) REVERT: A 553 ARG cc_start: 0.1048 (OUTLIER) cc_final: 0.0540 (mmt180) REVERT: A 601 MET cc_start: 0.1055 (mtm) cc_final: -0.0019 (ppp) REVERT: A 629 MET cc_start: 0.2685 (tpt) cc_final: 0.1168 (mpt) REVERT: A 924 MET cc_start: 0.0690 (mmp) cc_final: -0.0638 (mmp) REVERT: B 67 MET cc_start: 0.2494 (ttt) cc_final: 0.0732 (mpm) REVERT: B 75 ARG cc_start: 0.0815 (ttp80) cc_final: -0.0095 (mmt90) REVERT: C 19 GLN cc_start: 0.0653 (OUTLIER) cc_final: -0.1517 (mm-40) REVERT: C 62 MET cc_start: 0.0437 (mpt) cc_final: -0.0119 (mpt) REVERT: D 67 MET cc_start: 0.3488 (mtp) cc_final: 0.2994 (mmt) REVERT: D 94 MET cc_start: 0.0577 (mtp) cc_final: -0.1081 (mmm) REVERT: D 174 MET cc_start: 0.0442 (mmp) cc_final: -0.0190 (mmt) REVERT: D 187 THR cc_start: 0.5544 (OUTLIER) cc_final: 0.4061 (p) REVERT: F 164 HIS cc_start: 0.2276 (OUTLIER) cc_final: 0.1413 (t70) REVERT: F 230 HIS cc_start: -0.1594 (p-80) cc_final: -0.2282 (t70) REVERT: E 274 MET cc_start: 0.3273 (ppp) cc_final: 0.2579 (pmm) REVERT: E 436 MET cc_start: 0.2996 (OUTLIER) cc_final: 0.2265 (mpt) outliers start: 52 outliers final: 33 residues processed: 171 average time/residue: 0.4888 time to fit residues: 98.9803 Evaluate side-chains 173 residues out of total 2316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 132 time to evaluate : 0.865 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 ILE Chi-restraints excluded: chain A residue 92 ASP Chi-restraints excluded: chain A residue 151 CYS Chi-restraints excluded: chain A residue 262 THR Chi-restraints excluded: chain A residue 266 ILE Chi-restraints excluded: chain A residue 295 HIS Chi-restraints excluded: chain A residue 338 VAL Chi-restraints excluded: chain A residue 380 MET Chi-restraints excluded: chain A residue 417 LYS Chi-restraints excluded: chain A residue 488 ILE Chi-restraints excluded: chain A residue 533 ARG Chi-restraints excluded: chain A residue 553 ARG Chi-restraints excluded: chain A residue 633 MET Chi-restraints excluded: chain A residue 778 SER Chi-restraints excluded: chain B residue 94 MET Chi-restraints excluded: chain B residue 148 THR Chi-restraints excluded: chain B residue 171 GLU Chi-restraints excluded: chain B residue 187 THR Chi-restraints excluded: chain C residue 6 VAL Chi-restraints excluded: chain C residue 18 GLN Chi-restraints excluded: chain C residue 19 GLN Chi-restraints excluded: chain C residue 54 SER Chi-restraints excluded: chain D residue 83 VAL Chi-restraints excluded: chain D residue 114 CYS Chi-restraints excluded: chain D residue 182 TRP Chi-restraints excluded: chain D residue 187 THR Chi-restraints excluded: chain F residue 20 ILE Chi-restraints excluded: chain F residue 68 MET Chi-restraints excluded: chain F residue 164 HIS Chi-restraints excluded: chain F residue 181 VAL Chi-restraints excluded: chain F residue 216 THR Chi-restraints excluded: chain F residue 277 TYR Chi-restraints excluded: chain F residue 544 VAL Chi-restraints excluded: chain E residue 10 SER Chi-restraints excluded: chain E residue 26 CYS Chi-restraints excluded: chain E residue 185 TYR Chi-restraints excluded: chain E residue 231 THR Chi-restraints excluded: chain E residue 284 PRO Chi-restraints excluded: chain E residue 436 MET Chi-restraints excluded: chain E residue 510 VAL Chi-restraints excluded: chain E residue 523 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 266 random chunks: chunk 201 optimal weight: 0.8980 chunk 108 optimal weight: 3.9990 chunk 43 optimal weight: 2.9990 chunk 91 optimal weight: 0.7980 chunk 208 optimal weight: 0.0980 chunk 5 optimal weight: 4.9990 chunk 75 optimal weight: 0.7980 chunk 234 optimal weight: 8.9990 chunk 241 optimal weight: 9.9990 chunk 205 optimal weight: 3.9990 chunk 152 optimal weight: 3.9990 overall best weight: 1.1182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 184 GLN ** A 295 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 439 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 524 GLN ** A 695 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 767 ASN ** A 790 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 39 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 381 ASN F 559 ASN F 562 ASN ** E 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 492 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 503 ASN ** E 519 ASN ** 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 = 0.5275 r_free = 0.5275 target = 0.264634 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.5153 r_free = 0.5153 target = 0.248661 restraints weight = 105189.267| |-----------------------------------------------------------------------------| r_work (start): 0.5110 rms_B_bonded: 3.99 r_work: 0.4897 rms_B_bonded: 4.91 restraints_weight: 0.5000 r_work (final): 0.4897 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4872 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4872 r_free = 0.4872 target_work(ls_wunit_k1) = 0.221 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 16 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4872 r_free = 0.4872 target_work(ls_wunit_k1) = 0.221 | | occupancies: max = 1.00 min = 0.08 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 5 (11 function evaluations) r_final: 0.4872 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1425 moved from start: 0.6818 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.117 22478 Z= 0.145 Angle : 0.730 15.672 30796 Z= 0.354 Chirality : 0.046 0.322 3571 Planarity : 0.006 0.130 3732 Dihedral : 7.832 119.105 3533 Min Nonbonded Distance : 1.941 Molprobity Statistics. All-atom Clashscore : 14.48 Ramachandran Plot: Outliers : 0.08 % Allowed : 7.94 % Favored : 91.99 % Rotamer: Outliers : 2.65 % Allowed : 26.64 % Favored : 70.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.93 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.55 (0.16), residues: 2639 helix: 0.05 (0.17), residues: 929 sheet: -0.80 (0.34), residues: 239 loop : -1.85 (0.16), residues: 1471 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 183 TYR 0.026 0.002 TYR F 277 PHE 0.030 0.002 PHE A 287 TRP 0.020 0.002 TRP B 154 HIS 0.008 0.001 HIS A 816 Details of bonding type rmsd/Z covalent geometry : bond 0.00319 / 0.14 (22446) covalent geometry : angle 0.71736 / 0.35 (30769) hydrogen bonds : bond 0.04265 / 3.05 ( 822) hydrogen bonds : angle 4.91136 / 3.45 ( 2247) metal coordination : bond 0.02667 / 1.47 ( 32) metal coordination : angle 4.64722 / 2.86 ( 27) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5278 Ramachandran restraints generated. 2639 Oldfield, 0 Emsley, 2639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5278 Ramachandran restraints generated. 2639 Oldfield, 0 Emsley, 2639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 196 residues out of total 2316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 138 time to evaluate : 0.795 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: A 266 ILE cc_start: -0.0272 (OUTLIER) cc_final: -0.1471 (tt) REVERT: A 269 ASP cc_start: 0.2512 (p0) cc_final: 0.1903 (t0) REVERT: A 380 MET cc_start: 0.1561 (OUTLIER) cc_final: 0.0227 (ptt) REVERT: A 519 MET cc_start: 0.0280 (ptt) cc_final: -0.0909 (mpp) REVERT: A 601 MET cc_start: 0.1547 (mtm) cc_final: 0.0661 (ppp) REVERT: A 629 MET cc_start: 0.2568 (OUTLIER) cc_final: 0.0991 (mpt) REVERT: B 67 MET cc_start: 0.2373 (ttt) cc_final: 0.1080 (mpm) REVERT: B 75 ARG cc_start: 0.1031 (ttp80) cc_final: 0.0059 (mmm-85) REVERT: B 128 LEU cc_start: -0.1062 (OUTLIER) cc_final: -0.2660 (tp) REVERT: C 19 GLN cc_start: 0.0203 (OUTLIER) cc_final: -0.1940 (mm-40) REVERT: D 67 MET cc_start: 0.3718 (mtp) cc_final: 0.3095 (mmt) REVERT: D 94 MET cc_start: 0.0538 (mtp) cc_final: -0.1323 (mmm) REVERT: D 174 MET cc_start: 0.0543 (mmp) cc_final: -0.0932 (mmt) REVERT: D 187 THR cc_start: 0.4239 (OUTLIER) cc_final: 0.2916 (p) REVERT: F 68 MET cc_start: -0.0225 (OUTLIER) cc_final: -0.0710 (pp-130) REVERT: F 165 LEU cc_start: 0.2443 (OUTLIER) cc_final: 0.1609 (tt) REVERT: F 518 GLN cc_start: -0.0924 (OUTLIER) cc_final: -0.1147 (mt0) REVERT: E 274 MET cc_start: 0.2619 (ppp) cc_final: 0.1863 (pmm) REVERT: E 277 TYR cc_start: 0.1848 (p90) cc_final: 0.1344 (p90) REVERT: E 280 LEU cc_start: 0.1050 (OUTLIER) cc_final: 0.0715 (tm) outliers start: 58 outliers final: 36 residues processed: 183 average time/residue: 0.5134 time to fit residues: 111.2420 Evaluate side-chains 180 residues out of total 2316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 134 time to evaluate : 0.774 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 ILE Chi-restraints excluded: chain A residue 92 ASP Chi-restraints excluded: chain A residue 124 MET Chi-restraints excluded: chain A residue 151 CYS Chi-restraints excluded: chain A residue 171 ILE Chi-restraints excluded: chain A residue 262 THR Chi-restraints excluded: chain A residue 265 TYR Chi-restraints excluded: chain A residue 266 ILE Chi-restraints excluded: chain A residue 295 HIS Chi-restraints excluded: chain A residue 338 VAL Chi-restraints excluded: chain A residue 380 MET Chi-restraints excluded: chain A residue 488 ILE Chi-restraints excluded: chain A residue 533 ARG Chi-restraints excluded: chain A residue 567 THR Chi-restraints excluded: chain A residue 629 MET Chi-restraints excluded: chain A residue 778 SER Chi-restraints excluded: chain A residue 792 VAL Chi-restraints excluded: chain B residue 94 MET Chi-restraints excluded: chain B residue 128 LEU Chi-restraints excluded: chain B residue 148 THR Chi-restraints excluded: chain B residue 171 GLU Chi-restraints excluded: chain B residue 187 THR Chi-restraints excluded: chain C residue 6 VAL Chi-restraints excluded: chain C residue 18 GLN Chi-restraints excluded: chain C residue 19 GLN Chi-restraints excluded: chain D residue 83 VAL Chi-restraints excluded: chain D residue 114 CYS Chi-restraints excluded: chain D residue 149 TYR Chi-restraints excluded: chain D residue 182 TRP Chi-restraints excluded: chain D residue 187 THR Chi-restraints excluded: chain F residue 20 ILE Chi-restraints excluded: chain F residue 68 MET Chi-restraints excluded: chain F residue 165 LEU Chi-restraints excluded: chain F residue 210 VAL Chi-restraints excluded: chain F residue 216 THR Chi-restraints excluded: chain F residue 277 TYR Chi-restraints excluded: chain F residue 518 GLN Chi-restraints excluded: chain F residue 544 VAL Chi-restraints excluded: chain E residue 10 SER Chi-restraints excluded: chain E residue 26 CYS Chi-restraints excluded: chain E residue 185 TYR Chi-restraints excluded: chain E residue 231 THR Chi-restraints excluded: chain E residue 280 LEU Chi-restraints excluded: chain E residue 284 PRO Chi-restraints excluded: chain E residue 510 VAL Chi-restraints excluded: chain E residue 523 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 266 random chunks: chunk 136 optimal weight: 8.9990 chunk 22 optimal weight: 0.9990 chunk 80 optimal weight: 0.5980 chunk 113 optimal weight: 0.5980 chunk 122 optimal weight: 0.3980 chunk 108 optimal weight: 3.9990 chunk 154 optimal weight: 1.9990 chunk 111 optimal weight: 6.9990 chunk 244 optimal weight: 0.9980 chunk 37 optimal weight: 0.0970 chunk 212 optimal weight: 0.7980 overall best weight: 0.4978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 295 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 439 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 613 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 695 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 19 GLN ** C 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 39 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 381 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 492 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 503 ASN ** E 519 ASN ** 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 = 0.5283 r_free = 0.5283 target = 0.264573 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.5159 r_free = 0.5159 target = 0.249942 restraints weight = 106654.487| |-----------------------------------------------------------------------------| r_work (start): 0.5118 rms_B_bonded: 3.65 r_work: 0.4909 rms_B_bonded: 4.69 restraints_weight: 0.5000 r_work (final): 0.4909 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4887 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4887 r_free = 0.4887 target_work(ls_wunit_k1) = 0.222 | | occupancies: max = 1.00 min = 0.08 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4887 r_free = 0.4887 target_work(ls_wunit_k1) = 0.222 | | occupancies: max = 1.00 min = 0.09 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.4887 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1282 moved from start: 0.6886 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.123 22478 Z= 0.118 Angle : 0.675 15.566 30796 Z= 0.326 Chirality : 0.044 0.273 3571 Planarity : 0.005 0.062 3732 Dihedral : 7.618 119.964 3533 Min Nonbonded Distance : 1.914 Molprobity Statistics. All-atom Clashscore : 12.65 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.42 % Favored : 93.51 % Rotamer: Outliers : 2.07 % Allowed : 27.44 % Favored : 70.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.93 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.37 (0.16), residues: 2639 helix: 0.24 (0.17), residues: 927 sheet: -0.75 (0.34), residues: 240 loop : -1.76 (0.16), residues: 1472 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG G 39 TYR 0.030 0.001 TYR F 277 PHE 0.026 0.001 PHE A 812 TRP 0.010 0.001 TRP A 617 HIS 0.004 0.001 HIS A 725 Details of bonding type rmsd/Z covalent geometry : bond 0.00255 / 0.12 (22446) covalent geometry : angle 0.66040 / 0.32 (30769) hydrogen bonds : bond 0.03946 / 2.87 ( 822) hydrogen bonds : angle 4.69023 / 3.30 ( 2247) metal coordination : bond 0.02689 / 1.47 ( 32) metal coordination : angle 4.73938 / 2.91 ( 27) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8791.39 seconds wall clock time: 150 minutes 33.18 seconds (9033.18 seconds total)