Starting phenix.real_space_refine on Thu Jun 19 05:10:52 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8gwb_34308/06_2025/8gwb_34308.cif Found real_map, /net/cci-nas-00/data/ceres_data/8gwb_34308/06_2025/8gwb_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8gwb_34308/06_2025/8gwb_34308.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8gwb_34308/06_2025/8gwb_34308.map" model { file = "/net/cci-nas-00/data/ceres_data/8gwb_34308/06_2025/8gwb_34308.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8gwb_34308/06_2025/8gwb_34308.cif" } resolution = 2.75 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 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): 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: {'GLN:plan1': 1, 'TYR:plan': 1, 'ASN:plan1': 2, 'ASP:plan': 1, 'PHE:plan': 1, 'GLU:plan': 2} 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, 'ASN:plan1': 1, 'GLN: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: {'RNA': 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: {'RNA': 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: {'ARG:plan': 5, 'ASN:plan1': 1, 'GLU:plan': 1, 'ASP: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: {'ARG:plan': 5, 'ASN:plan1': 1, 'GLU:plan': 1, 'ASP: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: {'ARG:plan': 5, 'ASN:plan1': 1, 'GLU:plan': 1, 'ASP: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: {'ARG:plan': 5, 'ASN:plan1': 1, 'GLU:plan': 1, 'ASP: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: {'RNA': 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: 18.07, per 1000 atoms: 0.83 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: 5.73 Conformation dependent library (CDL) restraints added in 3.6 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: 8.19 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: 8.78 Time building geometry restraints manager: 6.70 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=" N PRO E 284 " pdb=" CD PRO E 284 " ideal model delta sigma weight residual 1.473 1.556 -0.083 1.40e-02 5.10e+03 3.55e+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: 12446 25.85 - 51.70: 909 51.70 - 77.56: 151 77.56 - 103.41: 10 103.41 - 129.26: 2 Dihedral angle restraints: 13518 sinusoidal: 5662 harmonic: 7856 Sorted by residual: dihedral pdb=" CA TRP B 182 " pdb=" C TRP B 182 " pdb=" N PRO B 183 " pdb=" CA PRO B 183 " ideal model delta harmonic sigma weight residual 180.00 142.48 37.52 0 5.00e+00 4.00e-02 5.63e+01 dihedral pdb=" C5' U M 2 " pdb=" C4' U M 2 " pdb=" C3' U M 2 " pdb=" O3' U M 2 " ideal model delta sinusoidal sigma weight residual 147.00 96.10 50.90 1 8.00e+00 1.56e-02 5.54e+01 dihedral pdb=" O4' U M 2 " pdb=" C4' U M 2 " pdb=" C3' U M 2 " pdb=" C2' U M 2 " ideal model delta sinusoidal sigma weight residual 24.00 -26.74 50.74 1 8.00e+00 1.56e-02 5.51e+01 ... (remaining 13515 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.100: 3430 0.100 - 0.201: 134 0.201 - 0.301: 4 0.301 - 0.402: 2 0.402 - 0.502: 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 2.41 -2.91 -0.50 2.00e-01 2.50e+01 6.31e+00 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 -2.48 -2.08 -0.39 2.00e-01 2.50e+01 3.87e+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 593 or resid 701 throug \ h 703)) selection = (chain 'F' and (resid 2 through 473 or resid 475 through 593 or resid 701 throug \ h 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: 5.400 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.950 Check model and map are aligned: 0.160 Set scattering table: 0.200 Process input model: 66.630 Find NCS groups from input model: 0.650 Set up NCS constraints: 0.110 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:14.150 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 88.280 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.0099 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= 0.327 Angle : 1.077 96.004 30796 Z= 0.566 Chirality : 0.046 0.502 3571 Planarity : 0.007 0.142 3732 Dihedral : 17.301 129.259 8450 Min Nonbonded Distance : 1.556 Molprobity Statistics. All-atom Clashscore : 16.84 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.40 (0.15), 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 TRP 0.037 0.002 TRP D 182 HIS 0.020 0.002 HIS A 295 PHE 0.028 0.002 PHE E 357 TYR 0.032 0.002 TYR E 185 ARG 0.008 0.001 ARG F 427 Details of bonding type rmsd hydrogen bonds : bond 0.20231 ( 822) hydrogen bonds : angle 7.29691 ( 2247) metal coordination : bond 0.05501 ( 32) metal coordination : angle 5.52929 ( 27) covalent geometry : bond 0.00945 (22446) covalent geometry : angle 1.06516 (30769) *********************** 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 : 2.217 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: 1.0490 time to fit residues: 352.3837 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 : 2.559 ------------------------------------------------------------------------------- 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 224 optimal weight: 5.9990 chunk 201 optimal weight: 10.0000 chunk 111 optimal weight: 0.6980 chunk 68 optimal weight: 4.9990 chunk 135 optimal weight: 9.9990 chunk 107 optimal weight: 0.0870 chunk 208 optimal weight: 7.9990 chunk 80 optimal weight: 5.9990 chunk 126 optimal weight: 4.9990 chunk 155 optimal weight: 0.0770 chunk 241 optimal weight: 0.9980 overall best weight: 1.3718 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 52 ASN A 88 ASN ** A 177 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 295 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 573 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 725 HIS ** A 752 HIS ** 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 815 GLN A 898 HIS B 176 ASN C 18 GLN F 9 ASN ** F 381 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 388 ASN F 404 GLN F 489 ASN F 518 GLN F 537 GLN ** 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 75 HIS E 220 ASN ** E 492 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 519 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 531 GLN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5253 r_free = 0.5253 target = 0.262624 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.5111 r_free = 0.5111 target = 0.244995 restraints weight = 81995.278| |-----------------------------------------------------------------------------| r_work (start): 0.5071 rms_B_bonded: 3.49 r_work: 0.4823 rms_B_bonded: 4.60 restraints_weight: 0.5000 r_work (final): 0.4823 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4783 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4783 r_free = 0.4783 target_work(ls_wunit_k1) = 0.214 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4783 r_free = 0.4783 target_work(ls_wunit_k1) = 0.214 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| r_final: 0.4783 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.0716 moved from start: 0.2876 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.015 2.167 22478 Z= 0.314 Angle : 0.775 13.036 30796 Z= 0.395 Chirality : 0.046 0.232 3571 Planarity : 0.006 0.109 3732 Dihedral : 12.658 123.229 3751 Min Nonbonded Distance : 2.043 Molprobity Statistics. All-atom Clashscore : 15.51 Ramachandran Plot: Outliers : 0.08 % Allowed : 8.20 % Favored : 91.72 % Rotamer: Outliers : 4.63 % Allowed : 22.28 % Favored : 73.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.93 % Cis-general : 0.00 % Twisted Proline : 0.93 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.29 (0.15), residues: 2639 helix: -0.54 (0.16), residues: 952 sheet: -1.89 (0.32), residues: 229 loop : -2.19 (0.15), residues: 1458 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP D 182 HIS 0.013 0.002 HIS A 816 PHE 0.021 0.002 PHE A 287 TYR 0.030 0.002 TYR A 453 ARG 0.007 0.001 ARG A 132 Details of bonding type rmsd hydrogen bonds : bond 0.05254 ( 822) hydrogen bonds : angle 5.34502 ( 2247) metal coordination : bond 0.38428 ( 32) metal coordination : angle 4.12453 ( 27) covalent geometry : bond 0.00392 (22446) covalent geometry : angle 0.76525 (30769) *********************** 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 284 residues out of total 2316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 103 poor density : 181 time to evaluate : 2.318 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 215 ASN cc_start: 0.2891 (m-40) cc_final: 0.2324 (m-40) REVERT: A 266 ILE cc_start: -0.1506 (OUTLIER) cc_final: -0.2776 (tt) REVERT: A 438 LYS cc_start: 0.0058 (OUTLIER) cc_final: -0.0197 (mmtp) REVERT: A 463 MET cc_start: -0.1054 (ttt) cc_final: -0.1718 (ttt) REVERT: A 501 SER cc_start: 0.1743 (t) cc_final: 0.1279 (p) REVERT: A 555 ARG cc_start: -0.0088 (tpt170) cc_final: -0.0429 (mmt180) REVERT: A 601 MET cc_start: 0.1237 (mtm) cc_final: 0.0829 (ppp) REVERT: A 615 MET cc_start: -0.0339 (ppp) cc_final: -0.0559 (pmt) REVERT: A 629 MET cc_start: 0.3372 (mmm) cc_final: 0.2685 (pmm) REVERT: A 657 ASN cc_start: -0.0096 (OUTLIER) cc_final: -0.1431 (m-40) REVERT: A 658 GLU cc_start: 0.0745 (OUTLIER) cc_final: -0.1635 (pp20) REVERT: A 780 LYS cc_start: 0.0208 (OUTLIER) cc_final: -0.0228 (pttm) REVERT: A 894 GLU cc_start: 0.1486 (OUTLIER) cc_final: 0.0691 (tt0) REVERT: B 51 ARG cc_start: 0.3243 (tpp80) cc_final: 0.2842 (tpm170) REVERT: B 55 MET cc_start: 0.5720 (ptt) cc_final: 0.5286 (ptt) REVERT: B 75 ARG cc_start: 0.0450 (ttp80) cc_final: 0.0119 (mmm-85) REVERT: C 19 GLN cc_start: -0.0219 (OUTLIER) cc_final: -0.2317 (mm-40) REVERT: D 67 MET cc_start: 0.3000 (mtp) cc_final: 0.2260 (mmt) REVERT: D 70 MET cc_start: -0.0915 (mtm) cc_final: -0.1360 (tpp) REVERT: D 91 LEU cc_start: -0.2044 (OUTLIER) cc_final: -0.2650 (pp) REVERT: D 94 MET cc_start: -0.1689 (mtp) cc_final: -0.2145 (mmm) REVERT: D 112 ASP cc_start: 0.5359 (OUTLIER) cc_final: 0.4838 (p0) REVERT: D 153 LEU cc_start: 0.3196 (OUTLIER) cc_final: 0.2965 (pp) REVERT: D 174 MET cc_start: -0.0360 (mmp) cc_final: -0.1148 (tpt) REVERT: F 201 GLU cc_start: -0.0610 (OUTLIER) cc_final: -0.1271 (tm-30) REVERT: E 223 ASP cc_start: 0.1924 (OUTLIER) cc_final: 0.0328 (m-30) REVERT: E 231 THR cc_start: 0.6481 (p) cc_final: 0.6113 (m) REVERT: E 409 ARG cc_start: 0.2435 (mtt90) cc_final: 0.1578 (mmp-170) outliers start: 103 outliers final: 19 residues processed: 263 average time/residue: 1.1523 time to fit residues: 355.1851 Evaluate side-chains 180 residues out of total 2316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 149 time to evaluate : 2.056 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 438 LYS Chi-restraints excluded: chain A residue 527 LEU Chi-restraints excluded: chain A residue 586 THR Chi-restraints excluded: chain A residue 633 MET Chi-restraints excluded: chain A residue 657 ASN Chi-restraints excluded: chain A residue 658 GLU Chi-restraints excluded: chain A residue 714 LYS Chi-restraints excluded: chain A residue 760 ASP Chi-restraints excluded: chain A residue 780 LYS Chi-restraints excluded: chain A residue 831 TYR Chi-restraints excluded: chain A residue 833 ASP Chi-restraints excluded: chain A residue 894 GLU 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 83 VAL Chi-restraints excluded: chain D residue 91 LEU Chi-restraints excluded: chain D residue 112 ASP Chi-restraints excluded: chain D residue 130 VAL Chi-restraints excluded: chain D residue 153 LEU Chi-restraints excluded: chain F residue 201 GLU 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 Chi-restraints excluded: chain G residue 76 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 266 random chunks: chunk 196 optimal weight: 5.9990 chunk 248 optimal weight: 8.9990 chunk 139 optimal weight: 1.9990 chunk 58 optimal weight: 5.9990 chunk 130 optimal weight: 10.0000 chunk 156 optimal weight: 7.9990 chunk 40 optimal weight: 7.9990 chunk 91 optimal weight: 0.5980 chunk 48 optimal weight: 0.9990 chunk 148 optimal weight: 4.9990 chunk 222 optimal weight: 0.0970 overall best weight: 1.7384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 5 GLN A 9 ASN ** A 295 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 381 HIS A 524 GLN A 570 GLN A 573 GLN ** A 611 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 695 ASN A 703 ASN ** A 767 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 791 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 886 GLN B 118 ASN ** D 157 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 245 HIS F 270 GLN ** 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 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 88 GLN ** E 245 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 492 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5274 r_free = 0.5274 target = 0.268695 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.5142 r_free = 0.5142 target = 0.248019 restraints weight = 89997.721| |-----------------------------------------------------------------------------| r_work (start): 0.5043 rms_B_bonded: 3.85 r_work: 0.4917 rms_B_bonded: 3.75 restraints_weight: 0.5000 r_work (final): 0.4917 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4891 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4891 r_free = 0.4891 target_work(ls_wunit_k1) = 0.223 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4891 r_free = 0.4891 target_work(ls_wunit_k1) = 0.223 | | occupancies: max = 1.00 min = 0.13 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.4891 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1148 moved from start: 0.4583 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.241 22478 Z= 0.191 Angle : 0.783 14.098 30796 Z= 0.399 Chirality : 0.047 0.226 3571 Planarity : 0.006 0.084 3732 Dihedral : 12.577 122.158 3738 Min Nonbonded Distance : 1.993 Molprobity Statistics. All-atom Clashscore : 17.24 Ramachandran Plot: Outliers : 0.08 % Allowed : 8.24 % Favored : 91.68 % Rotamer: Outliers : 4.98 % Allowed : 23.03 % Favored : 71.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.93 % Cis-general : 0.00 % Twisted Proline : 0.93 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.36 (0.15), residues: 2639 helix: -0.63 (0.17), residues: 921 sheet: -1.78 (0.31), residues: 229 loop : -2.22 (0.15), residues: 1489 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.003 TRP B 182 HIS 0.020 0.002 HIS E 75 PHE 0.037 0.002 PHE A 287 TYR 0.041 0.002 TYR A 156 ARG 0.021 0.001 ARG F 390 Details of bonding type rmsd hydrogen bonds : bond 0.05226 ( 822) hydrogen bonds : angle 5.51149 ( 2247) metal coordination : bond 0.05073 ( 32) metal coordination : angle 5.06541 ( 27) covalent geometry : bond 0.00418 (22446) covalent geometry : angle 0.76911 (30769) *********************** 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 287 residues out of total 2316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 111 poor density : 176 time to evaluate : 2.480 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 119 LEU cc_start: 0.1505 (OUTLIER) cc_final: 0.1231 (mt) REVERT: A 156 TYR cc_start: 0.1848 (OUTLIER) cc_final: 0.1167 (m-10) REVERT: A 204 VAL cc_start: 0.4455 (p) cc_final: 0.4252 (t) REVERT: A 254 GLU cc_start: 0.2343 (OUTLIER) cc_final: 0.2128 (tp30) REVERT: A 266 ILE cc_start: -0.1305 (OUTLIER) cc_final: -0.2379 (tt) REVERT: A 419 PHE cc_start: -0.1110 (t80) cc_final: -0.1821 (t80) REVERT: A 555 ARG cc_start: 0.0511 (tpt170) cc_final: 0.0071 (mmt180) REVERT: A 601 MET cc_start: 0.1108 (mtm) cc_final: 0.0579 (ppp) REVERT: A 629 MET cc_start: 0.2917 (mmm) cc_final: 0.2169 (pmm) REVERT: A 658 GLU cc_start: 0.1375 (OUTLIER) cc_final: 0.0546 (mm-30) REVERT: A 666 MET cc_start: 0.3227 (ttp) cc_final: 0.2973 (ttp) REVERT: A 674 TYR cc_start: 0.3241 (m-80) cc_final: 0.0619 (m-80) REVERT: B 51 ARG cc_start: 0.3670 (tpp80) cc_final: 0.3445 (tpm170) REVERT: B 55 MET cc_start: 0.5585 (ptt) cc_final: 0.5180 (ptt) REVERT: B 75 ARG cc_start: 0.0528 (ttp80) cc_final: 0.0207 (mmm-85) REVERT: B 105 ASN cc_start: 0.0083 (OUTLIER) cc_final: -0.1852 (m-40) REVERT: C 13 LEU cc_start: 0.0004 (tp) cc_final: -0.0595 (tt) REVERT: C 19 GLN cc_start: -0.0457 (OUTLIER) cc_final: -0.2565 (mm-40) REVERT: D 67 MET cc_start: 0.3001 (mtp) cc_final: 0.2261 (mmt) REVERT: D 91 LEU cc_start: -0.2105 (OUTLIER) cc_final: -0.2704 (tt) REVERT: D 94 MET cc_start: -0.1464 (mtp) cc_final: -0.2064 (mmt) REVERT: D 174 MET cc_start: -0.0122 (mmp) cc_final: -0.1257 (tpt) REVERT: F 165 LEU cc_start: 0.0423 (OUTLIER) cc_final: 0.0108 (mt) REVERT: F 201 GLU cc_start: -0.0704 (OUTLIER) cc_final: -0.1335 (tm-30) REVERT: F 274 MET cc_start: 0.2155 (OUTLIER) cc_final: 0.0951 (mtm) REVERT: F 341 GLU cc_start: 0.1712 (pt0) cc_final: 0.1257 (pp20) REVERT: E 223 ASP cc_start: 0.0654 (OUTLIER) cc_final: -0.0222 (m-30) REVERT: E 274 MET cc_start: 0.2999 (ptm) cc_final: 0.2128 (pmm) REVERT: E 378 MET cc_start: 0.1956 (tmm) cc_final: 0.1562 (tmm) REVERT: E 409 ARG cc_start: 0.2476 (mtt90) cc_final: 0.1386 (mmp-170) REVERT: E 429 MET cc_start: 0.0955 (OUTLIER) cc_final: 0.0662 (mmp) REVERT: E 503 ASN cc_start: 0.4761 (p0) cc_final: 0.3927 (t0) REVERT: E 544 VAL cc_start: 0.0416 (OUTLIER) cc_final: 0.0088 (t) outliers start: 111 outliers final: 40 residues processed: 259 average time/residue: 1.3262 time to fit residues: 403.8912 Evaluate side-chains 204 residues out of total 2316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 150 time to evaluate : 2.472 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 LYS Chi-restraints excluded: chain A residue 92 ASP Chi-restraints excluded: chain A residue 119 LEU Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 140 ASP Chi-restraints excluded: chain A residue 156 TYR Chi-restraints excluded: chain A residue 163 TYR Chi-restraints excluded: chain A residue 254 GLU Chi-restraints excluded: chain A residue 260 ASP Chi-restraints excluded: chain A residue 262 THR Chi-restraints excluded: chain A residue 266 ILE Chi-restraints excluded: chain A residue 294 TYR Chi-restraints excluded: chain A residue 299 VAL Chi-restraints excluded: chain A residue 338 VAL Chi-restraints excluded: chain A residue 533 ARG Chi-restraints excluded: chain A residue 569 ARG Chi-restraints excluded: chain A residue 586 THR Chi-restraints excluded: chain A residue 658 GLU Chi-restraints excluded: chain A residue 667 VAL Chi-restraints excluded: chain A residue 756 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 906 MET Chi-restraints excluded: chain A residue 924 MET Chi-restraints excluded: chain B residue 90 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 C residue 54 SER 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 122 LEU Chi-restraints excluded: chain D residue 187 THR Chi-restraints excluded: chain F residue 69 SER Chi-restraints excluded: chain F residue 90 PHE Chi-restraints excluded: chain F residue 165 LEU Chi-restraints excluded: chain F residue 201 GLU Chi-restraints excluded: chain F residue 210 VAL Chi-restraints excluded: chain F residue 274 MET Chi-restraints excluded: chain E residue 26 CYS Chi-restraints excluded: chain E residue 45 VAL 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 429 MET Chi-restraints excluded: chain E residue 523 SER Chi-restraints excluded: chain E residue 544 VAL 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 172 optimal weight: 0.0980 chunk 31 optimal weight: 0.7980 chunk 108 optimal weight: 2.9990 chunk 177 optimal weight: 10.0000 chunk 265 optimal weight: 10.0000 chunk 192 optimal weight: 5.9990 chunk 139 optimal weight: 1.9990 chunk 239 optimal weight: 0.4980 chunk 22 optimal weight: 9.9990 chunk 54 optimal weight: 1.9990 chunk 115 optimal weight: 0.6980 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 210 GLN A 573 GLN A 752 HIS ** A 767 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 791 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 118 ASN ** C 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 157 GLN ** 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 75 HIS ** 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 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5295 r_free = 0.5295 target = 0.264211 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.5192 r_free = 0.5192 target = 0.250560 restraints weight = 91897.303| |-----------------------------------------------------------------------------| r_work (start): 0.5131 rms_B_bonded: 2.73 r_work: 0.4965 rms_B_bonded: 3.53 restraints_weight: 0.5000 r_work (final): 0.4965 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4920 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4920 r_free = 0.4920 target_work(ls_wunit_k1) = 0.224 | | occupancies: max = 1.00 min = 0.13 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4920 r_free = 0.4920 target_work(ls_wunit_k1) = 0.224 | | occupancies: max = 1.00 min = 0.15 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.4920 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1140 moved from start: 0.4962 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.142 22478 Z= 0.133 Angle : 0.673 11.691 30796 Z= 0.338 Chirality : 0.042 0.222 3571 Planarity : 0.005 0.068 3732 Dihedral : 12.260 121.117 3733 Min Nonbonded Distance : 2.087 Molprobity Statistics. All-atom Clashscore : 14.71 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.87 % Favored : 93.05 % Rotamer: Outliers : 3.66 % Allowed : 25.14 % Favored : 71.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.93 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.05 (0.16), residues: 2639 helix: -0.41 (0.17), residues: 945 sheet: -1.52 (0.32), residues: 221 loop : -2.04 (0.16), residues: 1473 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP F 167 HIS 0.014 0.001 HIS E 75 PHE 0.017 0.002 PHE E 499 TYR 0.024 0.002 TYR A 32 ARG 0.004 0.000 ARG A 631 Details of bonding type rmsd hydrogen bonds : bond 0.04414 ( 822) hydrogen bonds : angle 5.09281 ( 2247) metal coordination : bond 0.03157 ( 32) metal coordination : angle 4.54994 ( 27) covalent geometry : bond 0.00290 (22446) covalent geometry : angle 0.65972 (30769) *********************** 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 233 residues out of total 2316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 152 time to evaluate : 2.189 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 266 ILE cc_start: -0.1217 (OUTLIER) cc_final: -0.2190 (tt) REVERT: A 369 LYS cc_start: -0.1060 (OUTLIER) cc_final: -0.1320 (tppt) REVERT: A 408 GLN cc_start: -0.0580 (OUTLIER) cc_final: -0.1332 (pm20) REVERT: A 419 PHE cc_start: -0.1196 (t80) cc_final: -0.2370 (t80) REVERT: A 555 ARG cc_start: 0.0554 (tpt170) cc_final: 0.0175 (mmt180) REVERT: A 566 MET cc_start: 0.1577 (OUTLIER) cc_final: 0.1317 (ttm) REVERT: A 601 MET cc_start: 0.1133 (mtm) cc_final: 0.0455 (ppp) REVERT: A 626 MET cc_start: 0.1423 (mmt) cc_final: 0.1191 (mmp) REVERT: A 674 TYR cc_start: 0.3226 (m-80) cc_final: 0.0798 (m-80) REVERT: A 924 MET cc_start: 0.1151 (OUTLIER) cc_final: -0.0307 (mmp) REVERT: B 55 MET cc_start: 0.5660 (ptt) cc_final: 0.5162 (ptt) REVERT: B 75 ARG cc_start: 0.0689 (ttp80) cc_final: 0.0240 (mmm-85) REVERT: C 19 GLN cc_start: -0.0145 (OUTLIER) cc_final: -0.2335 (mm110) REVERT: D 67 MET cc_start: 0.3081 (mtp) cc_final: 0.2334 (mmt) REVERT: D 91 LEU cc_start: -0.1912 (OUTLIER) cc_final: -0.2535 (tt) REVERT: D 94 MET cc_start: -0.1565 (mtp) cc_final: -0.2026 (mmt) REVERT: D 174 MET cc_start: 0.0233 (mmp) cc_final: -0.0928 (tpt) REVERT: F 164 HIS cc_start: 0.0486 (OUTLIER) cc_final: -0.0028 (t70) REVERT: F 165 LEU cc_start: 0.0463 (tp) cc_final: 0.0202 (mt) REVERT: F 201 GLU cc_start: -0.0869 (OUTLIER) cc_final: -0.1458 (tm-30) REVERT: F 274 MET cc_start: 0.1986 (OUTLIER) cc_final: 0.0948 (mtm) REVERT: F 322 LEU cc_start: -0.0323 (mt) cc_final: -0.0748 (pp) REVERT: F 518 GLN cc_start: -0.1677 (OUTLIER) cc_final: -0.1900 (mt0) REVERT: E 223 ASP cc_start: 0.0952 (OUTLIER) cc_final: 0.0152 (m-30) REVERT: E 303 ARG cc_start: 0.2200 (OUTLIER) cc_final: 0.1936 (mmt180) REVERT: E 409 ARG cc_start: 0.2222 (mtt90) cc_final: 0.1583 (mmt180) REVERT: E 418 GLU cc_start: 0.2426 (OUTLIER) cc_final: 0.2175 (mt-10) REVERT: E 429 MET cc_start: 0.1104 (OUTLIER) cc_final: 0.0805 (mmp) REVERT: E 503 ASN cc_start: 0.4722 (p0) cc_final: 0.3799 (t0) REVERT: G 11 GLN cc_start: -0.0877 (OUTLIER) cc_final: -0.2563 (pm20) outliers start: 81 outliers final: 31 residues processed: 210 average time/residue: 1.1751 time to fit residues: 287.1963 Evaluate side-chains 190 residues out of total 2316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 143 time to evaluate : 2.142 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 ASP Chi-restraints excluded: chain A residue 140 ASP Chi-restraints excluded: chain A residue 171 ILE Chi-restraints excluded: chain A residue 242 MET Chi-restraints excluded: chain A residue 262 THR Chi-restraints excluded: chain A residue 266 ILE Chi-restraints excluded: chain A residue 338 VAL Chi-restraints excluded: chain A residue 369 LYS Chi-restraints excluded: chain A residue 408 GLN Chi-restraints excluded: chain A residue 482 CYS Chi-restraints excluded: chain A residue 501 SER Chi-restraints excluded: chain A residue 533 ARG Chi-restraints excluded: chain A residue 566 MET Chi-restraints excluded: chain A residue 569 ARG Chi-restraints excluded: chain A residue 724 GLN Chi-restraints excluded: chain A residue 760 ASP Chi-restraints excluded: chain A residue 794 MET Chi-restraints excluded: chain A residue 820 VAL Chi-restraints excluded: chain A residue 889 ARG Chi-restraints excluded: chain A residue 906 MET Chi-restraints excluded: chain A residue 924 MET Chi-restraints excluded: chain B residue 105 ASN Chi-restraints excluded: chain B residue 148 THR Chi-restraints excluded: chain C residue 6 VAL Chi-restraints excluded: chain C residue 19 GLN Chi-restraints excluded: chain D residue 70 MET 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 153 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 201 GLU Chi-restraints excluded: chain F residue 258 ILE Chi-restraints excluded: chain F residue 274 MET 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 223 ASP Chi-restraints excluded: chain E residue 284 PRO Chi-restraints excluded: chain E residue 303 ARG Chi-restraints excluded: chain E residue 418 GLU Chi-restraints excluded: chain E residue 429 MET Chi-restraints excluded: chain E residue 510 VAL Chi-restraints excluded: chain G residue 11 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 266 random chunks: chunk 51 optimal weight: 8.9990 chunk 57 optimal weight: 0.8980 chunk 242 optimal weight: 6.9990 chunk 58 optimal weight: 0.9980 chunk 54 optimal weight: 0.3980 chunk 104 optimal weight: 0.6980 chunk 189 optimal weight: 1.9990 chunk 81 optimal weight: 0.0470 chunk 108 optimal weight: 2.9990 chunk 154 optimal weight: 7.9990 chunk 76 optimal weight: 0.5980 overall best weight: 0.5278 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 295 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 767 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 791 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 157 GLN ** 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 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 245 HIS ** E 492 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 11 GLN G 98 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5299 r_free = 0.5299 target = 0.264698 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.5202 r_free = 0.5202 target = 0.250807 restraints weight = 87179.367| |-----------------------------------------------------------------------------| r_work (start): 0.5128 rms_B_bonded: 2.46 r_work: 0.4981 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work (final): 0.4981 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4935 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4935 r_free = 0.4935 target_work(ls_wunit_k1) = 0.225 | | occupancies: max = 1.00 min = 0.15 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4935 r_free = 0.4935 target_work(ls_wunit_k1) = 0.225 | | occupancies: max = 1.00 min = 0.15 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.4935 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1110 moved from start: 0.5208 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= 0.124 Angle : 0.649 11.785 30796 Z= 0.323 Chirality : 0.042 0.221 3571 Planarity : 0.005 0.060 3732 Dihedral : 12.092 121.600 3733 Min Nonbonded Distance : 1.780 Molprobity Statistics. All-atom Clashscore : 13.47 Ramachandran Plot: Outliers : 0.08 % Allowed : 7.29 % Favored : 92.63 % Rotamer: Outliers : 3.93 % Allowed : 24.70 % Favored : 71.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.93 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.82 (0.16), residues: 2639 helix: -0.13 (0.17), residues: 936 sheet: -1.25 (0.32), residues: 236 loop : -1.98 (0.16), residues: 1467 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 617 HIS 0.011 0.001 HIS E 75 PHE 0.016 0.001 PHE E 499 TYR 0.032 0.001 TYR F 277 ARG 0.004 0.000 ARG D 111 Details of bonding type rmsd hydrogen bonds : bond 0.04194 ( 822) hydrogen bonds : angle 4.87655 ( 2247) metal coordination : bond 0.03155 ( 32) metal coordination : angle 4.37261 ( 27) covalent geometry : bond 0.00262 (22446) covalent geometry : angle 0.63597 (30769) *********************** 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 240 residues out of total 2316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 153 time to evaluate : 2.125 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 266 ILE cc_start: -0.1256 (OUTLIER) cc_final: -0.2110 (tt) REVERT: A 269 ASP cc_start: 0.1819 (p0) cc_final: 0.1521 (t0) REVERT: A 408 GLN cc_start: -0.0524 (OUTLIER) cc_final: -0.1242 (pm20) REVERT: A 419 PHE cc_start: -0.1190 (t80) cc_final: -0.2456 (t80) REVERT: A 519 MET cc_start: 0.0158 (OUTLIER) cc_final: -0.0056 (pmt) REVERT: A 555 ARG cc_start: 0.0777 (tpt170) cc_final: 0.0386 (mmt180) REVERT: A 566 MET cc_start: 0.1697 (OUTLIER) cc_final: 0.1321 (ttm) REVERT: A 601 MET cc_start: 0.1253 (mtm) cc_final: 0.0439 (ppp) REVERT: A 629 MET cc_start: 0.2746 (mmm) cc_final: 0.0996 (mpt) REVERT: A 657 ASN cc_start: -0.0196 (OUTLIER) cc_final: -0.0977 (t0) REVERT: A 924 MET cc_start: 0.1211 (OUTLIER) cc_final: -0.0478 (mmp) REVERT: B 75 ARG cc_start: 0.0657 (ttp80) cc_final: 0.0142 (mmt90) REVERT: C 19 GLN cc_start: -0.0362 (OUTLIER) cc_final: -0.2344 (mm-40) REVERT: D 67 MET cc_start: 0.3055 (mtp) cc_final: 0.2377 (mmt) REVERT: D 91 LEU cc_start: -0.2030 (OUTLIER) cc_final: -0.2699 (pp) REVERT: D 112 ASP cc_start: 0.4328 (OUTLIER) cc_final: 0.4047 (p0) REVERT: D 134 ASP cc_start: 0.0260 (OUTLIER) cc_final: -0.0169 (t0) REVERT: D 174 MET cc_start: 0.0389 (mmp) cc_final: -0.0812 (tpt) REVERT: F 164 HIS cc_start: 0.0496 (OUTLIER) cc_final: -0.0074 (t70) REVERT: F 165 LEU cc_start: 0.0453 (tp) cc_final: 0.0233 (mt) REVERT: F 201 GLU cc_start: -0.0926 (OUTLIER) cc_final: -0.1490 (tm-30) REVERT: F 230 HIS cc_start: -0.1685 (p-80) cc_final: -0.2662 (t70) REVERT: F 274 MET cc_start: 0.1798 (OUTLIER) cc_final: 0.0840 (ttm) REVERT: F 322 LEU cc_start: -0.0246 (mt) cc_final: -0.0698 (pp) REVERT: F 341 GLU cc_start: 0.1162 (pt0) cc_final: 0.0873 (pp20) REVERT: F 518 GLN cc_start: -0.1626 (OUTLIER) cc_final: -0.1869 (mt0) REVERT: E 223 ASP cc_start: 0.0765 (OUTLIER) cc_final: -0.0006 (m-30) REVERT: E 274 MET cc_start: 0.3018 (ppp) cc_final: 0.2250 (pmm) REVERT: E 409 ARG cc_start: 0.2346 (mtt90) cc_final: 0.1696 (mmt180) REVERT: E 503 ASN cc_start: 0.4648 (p0) cc_final: 0.3695 (t0) REVERT: G 11 GLN cc_start: -0.0997 (OUTLIER) cc_final: -0.2623 (pm20) outliers start: 87 outliers final: 36 residues processed: 215 average time/residue: 1.1373 time to fit residues: 287.1458 Evaluate side-chains 194 residues out of total 2316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 142 time to evaluate : 2.131 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 ASP Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 140 ASP Chi-restraints excluded: chain A residue 171 ILE Chi-restraints excluded: chain A residue 242 MET 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 408 GLN Chi-restraints excluded: chain A residue 450 ILE Chi-restraints excluded: chain A residue 501 SER Chi-restraints excluded: chain A residue 519 MET Chi-restraints excluded: chain A residue 566 MET Chi-restraints excluded: chain A residue 657 ASN Chi-restraints excluded: chain A residue 760 ASP Chi-restraints excluded: chain A residue 794 MET Chi-restraints excluded: chain A residue 806 THR Chi-restraints excluded: chain A residue 894 GLU Chi-restraints excluded: chain A residue 906 MET Chi-restraints excluded: chain A residue 924 MET 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 C residue 54 SER Chi-restraints excluded: chain D residue 70 MET 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 112 ASP Chi-restraints excluded: chain D residue 114 CYS Chi-restraints excluded: chain D residue 134 ASP Chi-restraints excluded: chain D residue 153 LEU Chi-restraints excluded: chain D residue 182 TRP Chi-restraints excluded: chain D residue 187 THR Chi-restraints excluded: chain F residue 90 PHE Chi-restraints excluded: chain F residue 164 HIS Chi-restraints excluded: chain F residue 201 GLU Chi-restraints excluded: chain F residue 210 VAL Chi-restraints excluded: chain F residue 274 MET Chi-restraints excluded: chain F residue 518 GLN 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 11 GLN Chi-restraints excluded: chain G residue 18 THR Chi-restraints excluded: chain G residue 101 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 266 random chunks: chunk 186 optimal weight: 20.0000 chunk 187 optimal weight: 4.9990 chunk 86 optimal weight: 3.9990 chunk 196 optimal weight: 7.9990 chunk 141 optimal weight: 20.0000 chunk 83 optimal weight: 0.6980 chunk 111 optimal weight: 0.9980 chunk 36 optimal weight: 2.9990 chunk 79 optimal weight: 0.7980 chunk 175 optimal weight: 0.9990 chunk 154 optimal weight: 0.0060 overall best weight: 0.6998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 213 ASN ** A 295 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 724 GLN ** A 767 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 791 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 886 GLN B 19 GLN ** C 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 157 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 75 HIS ** 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** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5289 r_free = 0.5289 target = 0.274393 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.5143 r_free = 0.5143 target = 0.253262 restraints weight = 86156.962| |-----------------------------------------------------------------------------| r_work (start): 0.5059 rms_B_bonded: 4.05 r_work: 0.4877 rms_B_bonded: 4.11 restraints_weight: 0.5000 r_work (final): 0.4877 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4861 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4861 r_free = 0.4861 target_work(ls_wunit_k1) = 0.220 | | occupancies: max = 1.00 min = 0.15 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4861 r_free = 0.4861 target_work(ls_wunit_k1) = 0.220 | | occupancies: max = 1.00 min = 0.15 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.4861 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1188 moved from start: 0.5550 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.147 22478 Z= 0.124 Angle : 0.641 11.768 30796 Z= 0.318 Chirality : 0.042 0.221 3571 Planarity : 0.005 0.058 3732 Dihedral : 12.038 121.641 3733 Min Nonbonded Distance : 1.809 Molprobity Statistics. All-atom Clashscore : 13.12 Ramachandran Plot: Outliers : 0.08 % Allowed : 7.14 % Favored : 92.78 % Rotamer: Outliers : 4.15 % Allowed : 25.01 % Favored : 70.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.93 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.71 (0.16), residues: 2639 helix: -0.01 (0.17), residues: 937 sheet: -1.14 (0.33), residues: 226 loop : -1.95 (0.16), residues: 1476 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 617 HIS 0.009 0.001 HIS E 75 PHE 0.039 0.002 PHE A 157 TYR 0.016 0.001 TYR F 298 ARG 0.004 0.000 ARG G 39 Details of bonding type rmsd hydrogen bonds : bond 0.04113 ( 822) hydrogen bonds : angle 4.82244 ( 2247) metal coordination : bond 0.03423 ( 32) metal coordination : angle 4.35886 ( 27) covalent geometry : bond 0.00264 (22446) covalent geometry : angle 0.62852 (30769) *********************** 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 246 residues out of total 2316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 154 time to evaluate : 2.397 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 157 PHE cc_start: 0.2848 (t80) cc_final: 0.2418 (m-80) REVERT: A 266 ILE cc_start: -0.1026 (OUTLIER) cc_final: -0.2010 (tt) REVERT: A 269 ASP cc_start: 0.2002 (p0) cc_final: 0.1575 (t0) REVERT: A 408 GLN cc_start: -0.0860 (OUTLIER) cc_final: -0.1444 (pm20) REVERT: A 419 PHE cc_start: -0.0914 (t80) cc_final: -0.2264 (t80) REVERT: A 519 MET cc_start: 0.0135 (OUTLIER) cc_final: -0.0102 (pmt) REVERT: A 555 ARG cc_start: 0.0518 (tpt170) cc_final: 0.0026 (mmt180) REVERT: A 566 MET cc_start: 0.1771 (OUTLIER) cc_final: 0.1411 (ttm) REVERT: A 601 MET cc_start: 0.1574 (mtm) cc_final: 0.0822 (ppp) REVERT: A 629 MET cc_start: 0.2183 (mmm) cc_final: 0.0746 (mpt) REVERT: A 899 MET cc_start: -0.1350 (mtt) cc_final: -0.1564 (mtt) REVERT: A 924 MET cc_start: 0.1442 (OUTLIER) cc_final: -0.0266 (mmp) REVERT: B 62 MET cc_start: -0.0994 (OUTLIER) cc_final: -0.1222 (mmp) REVERT: B 75 ARG cc_start: 0.0574 (ttp80) cc_final: 0.0108 (mmt90) REVERT: C 19 GLN cc_start: -0.0083 (OUTLIER) cc_final: -0.2013 (mm110) REVERT: D 67 MET cc_start: 0.3000 (mtp) cc_final: 0.2459 (mmt) REVERT: D 112 ASP cc_start: 0.4677 (OUTLIER) cc_final: 0.4361 (p0) REVERT: D 134 ASP cc_start: 0.0325 (OUTLIER) cc_final: -0.0124 (t0) REVERT: D 174 MET cc_start: 0.0573 (mmp) cc_final: -0.0861 (mmt) REVERT: F 164 HIS cc_start: 0.0632 (OUTLIER) cc_final: 0.0084 (t70) REVERT: F 165 LEU cc_start: 0.0623 (tp) cc_final: 0.0407 (mt) REVERT: F 201 GLU cc_start: -0.0880 (OUTLIER) cc_final: -0.1180 (mt-10) REVERT: F 230 HIS cc_start: -0.1755 (p-80) cc_final: -0.2584 (t70) REVERT: F 274 MET cc_start: 0.1788 (OUTLIER) cc_final: 0.0877 (ttm) REVERT: F 322 LEU cc_start: -0.0102 (mt) cc_final: -0.0541 (pp) REVERT: F 341 GLU cc_start: 0.1125 (pt0) cc_final: 0.0859 (pp20) REVERT: F 518 GLN cc_start: -0.1430 (OUTLIER) cc_final: -0.1664 (mt0) REVERT: E 274 MET cc_start: 0.2830 (ppp) cc_final: 0.2035 (pmm) REVERT: E 409 ARG cc_start: 0.2502 (mtt90) cc_final: 0.1827 (mmt180) REVERT: E 436 MET cc_start: -0.1252 (OUTLIER) cc_final: -0.1618 (mpt) outliers start: 92 outliers final: 41 residues processed: 221 average time/residue: 1.0851 time to fit residues: 282.6215 Evaluate side-chains 198 residues out of total 2316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 143 time to evaluate : 2.394 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 ASP Chi-restraints excluded: chain A residue 163 TYR Chi-restraints excluded: chain A residue 171 ILE Chi-restraints excluded: chain A residue 233 VAL Chi-restraints excluded: chain A residue 242 MET 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 408 GLN Chi-restraints excluded: chain A residue 457 ARG Chi-restraints excluded: chain A residue 482 CYS Chi-restraints excluded: chain A residue 501 SER Chi-restraints excluded: chain A residue 519 MET Chi-restraints excluded: chain A residue 533 ARG Chi-restraints excluded: chain A residue 566 MET Chi-restraints excluded: chain A residue 760 ASP Chi-restraints excluded: chain A residue 792 VAL Chi-restraints excluded: chain A residue 794 MET Chi-restraints excluded: chain A residue 806 THR Chi-restraints excluded: chain A residue 894 GLU Chi-restraints excluded: chain A residue 906 MET Chi-restraints excluded: chain A residue 924 MET Chi-restraints excluded: chain B residue 62 MET Chi-restraints excluded: chain B residue 94 MET Chi-restraints excluded: chain B residue 105 ASN 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 19 GLN Chi-restraints excluded: chain D residue 76 SER Chi-restraints excluded: chain D residue 83 VAL Chi-restraints excluded: chain D residue 112 ASP Chi-restraints excluded: chain D residue 114 CYS Chi-restraints excluded: chain D residue 134 ASP Chi-restraints excluded: chain D residue 153 LEU 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 90 PHE Chi-restraints excluded: chain F residue 164 HIS Chi-restraints excluded: chain F residue 201 GLU Chi-restraints excluded: chain F residue 274 MET Chi-restraints excluded: chain F residue 355 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 284 PRO Chi-restraints excluded: chain E residue 436 MET Chi-restraints excluded: chain E residue 523 SER Chi-restraints excluded: chain G residue 18 THR Chi-restraints excluded: chain G residue 76 VAL Chi-restraints excluded: chain G residue 101 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 266 random chunks: chunk 129 optimal weight: 0.9990 chunk 115 optimal weight: 2.9990 chunk 56 optimal weight: 0.6980 chunk 60 optimal weight: 0.6980 chunk 101 optimal weight: 5.9990 chunk 228 optimal weight: 8.9990 chunk 124 optimal weight: 0.8980 chunk 196 optimal weight: 0.0570 chunk 40 optimal weight: 3.9990 chunk 261 optimal weight: 9.9990 chunk 133 optimal weight: 0.8980 overall best weight: 0.6498 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 81 GLN ** A 295 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 657 ASN ** A 767 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 791 ASN B 104 ASN ** C 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 157 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 F 562 ASN ** E 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 179 ASN ** E 519 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 11 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5279 r_free = 0.5279 target = 0.264211 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.5149 r_free = 0.5149 target = 0.249490 restraints weight = 110893.496| |-----------------------------------------------------------------------------| r_work (start): 0.5119 rms_B_bonded: 3.87 r_work (final): 0.5119 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.5119 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.5119 r_free = 0.5119 target_work(ls_wunit_k1) = 0.248 | | occupancies: max = 1.00 min = 0.15 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.5119 r_free = 0.5119 target_work(ls_wunit_k1) = 0.248 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| r_final: 0.5119 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.0942 moved from start: 0.5861 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.125 22478 Z= 0.121 Angle : 0.649 11.774 30796 Z= 0.322 Chirality : 0.041 0.220 3571 Planarity : 0.005 0.056 3732 Dihedral : 11.978 121.752 3733 Min Nonbonded Distance : 1.868 Molprobity Statistics. All-atom Clashscore : 13.01 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.68 % Favored : 93.24 % Rotamer: Outliers : 3.31 % Allowed : 26.07 % Favored : 70.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.93 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.60 (0.16), residues: 2639 helix: 0.06 (0.17), residues: 937 sheet: -1.14 (0.34), residues: 229 loop : -1.86 (0.16), residues: 1473 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 617 HIS 0.008 0.001 HIS E 75 PHE 0.027 0.001 PHE A 157 TYR 0.015 0.001 TYR A 515 ARG 0.006 0.000 ARG E 303 Details of bonding type rmsd hydrogen bonds : bond 0.04023 ( 822) hydrogen bonds : angle 4.74051 ( 2247) metal coordination : bond 0.03058 ( 32) metal coordination : angle 4.20530 ( 27) covalent geometry : bond 0.00258 (22446) covalent geometry : angle 0.63739 (30769) *********************** 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 216 residues out of total 2316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 143 time to evaluate : 2.301 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 124 MET cc_start: 0.1008 (ptm) cc_final: -0.1518 (tpp) REVERT: A 266 ILE cc_start: -0.0829 (OUTLIER) cc_final: -0.1491 (tt) REVERT: A 269 ASP cc_start: 0.2015 (p0) cc_final: 0.1768 (t0) REVERT: A 408 GLN cc_start: 0.0335 (OUTLIER) cc_final: -0.0562 (pm20) REVERT: A 555 ARG cc_start: 0.1038 (tpt170) cc_final: 0.0366 (mmt180) REVERT: A 601 MET cc_start: 0.1232 (mtm) cc_final: 0.0330 (ppp) REVERT: A 629 MET cc_start: 0.2409 (mmm) cc_final: 0.0871 (mpt) REVERT: B 75 ARG cc_start: 0.0893 (ttp80) cc_final: 0.0154 (mmt90) REVERT: B 128 LEU cc_start: -0.1151 (OUTLIER) cc_final: -0.2613 (tp) REVERT: C 19 GLN cc_start: 0.0415 (OUTLIER) cc_final: -0.1666 (mm-40) REVERT: D 67 MET cc_start: 0.3270 (mtp) cc_final: 0.2895 (mmt) REVERT: D 91 LEU cc_start: -0.1555 (OUTLIER) cc_final: -0.2326 (tp) REVERT: D 174 MET cc_start: 0.0544 (mmp) cc_final: -0.0154 (mmt) REVERT: F 164 HIS cc_start: 0.2550 (OUTLIER) cc_final: 0.1635 (t70) REVERT: F 201 GLU cc_start: -0.0304 (OUTLIER) cc_final: -0.1414 (pt0) REVERT: F 230 HIS cc_start: -0.1727 (p-80) cc_final: -0.2379 (t70) REVERT: F 518 GLN cc_start: 0.0967 (OUTLIER) cc_final: -0.0058 (mt0) REVERT: E 274 MET cc_start: 0.3312 (ppp) cc_final: 0.2460 (pmm) REVERT: E 436 MET cc_start: 0.2690 (OUTLIER) cc_final: 0.1912 (mpt) REVERT: E 495 VAL cc_start: 0.0506 (OUTLIER) cc_final: 0.0142 (t) REVERT: E 511 PHE cc_start: 0.1412 (OUTLIER) cc_final: 0.1153 (t80) outliers start: 73 outliers final: 39 residues processed: 193 average time/residue: 1.2110 time to fit residues: 273.9366 Evaluate side-chains 187 residues out of total 2316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 137 time to evaluate : 2.397 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 ASP Chi-restraints excluded: chain A residue 163 TYR Chi-restraints excluded: chain A residue 171 ILE Chi-restraints excluded: chain A residue 242 MET 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 408 GLN Chi-restraints excluded: chain A residue 457 ARG Chi-restraints excluded: chain A residue 501 SER Chi-restraints excluded: chain A residue 533 ARG Chi-restraints excluded: chain A residue 622 CYS Chi-restraints excluded: chain A residue 760 ASP Chi-restraints excluded: chain A residue 778 SER Chi-restraints excluded: chain A residue 792 VAL Chi-restraints excluded: chain A residue 806 THR Chi-restraints excluded: chain A residue 818 MET Chi-restraints excluded: chain A residue 894 GLU Chi-restraints excluded: chain A residue 906 MET Chi-restraints excluded: chain B residue 94 MET Chi-restraints excluded: chain B residue 105 ASN 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 19 GLN Chi-restraints excluded: chain C residue 54 SER 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 153 LEU 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 201 GLU Chi-restraints excluded: chain F residue 355 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 284 PRO Chi-restraints excluded: chain E residue 436 MET Chi-restraints excluded: chain E residue 495 VAL Chi-restraints excluded: chain E residue 511 PHE Chi-restraints excluded: chain G residue 76 VAL Chi-restraints excluded: chain G residue 101 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 266 random chunks: chunk 117 optimal weight: 7.9990 chunk 159 optimal weight: 2.9990 chunk 233 optimal weight: 5.9990 chunk 157 optimal weight: 6.9990 chunk 103 optimal weight: 5.9990 chunk 178 optimal weight: 0.6980 chunk 86 optimal weight: 3.9990 chunk 132 optimal weight: 1.9990 chunk 251 optimal weight: 2.9990 chunk 213 optimal weight: 7.9990 chunk 7 optimal weight: 2.9990 overall best weight: 2.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 99 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 133 HIS ** A 210 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 295 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 355 HIS ** A 447 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 767 ASN A 789 GLN ** A 790 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 140 ASN ** D 157 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 381 ASN ** E 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 519 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5280 r_free = 0.5280 target = 0.264907 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.5173 r_free = 0.5173 target = 0.251516 restraints weight = 99681.388| |-----------------------------------------------------------------------------| r_work (start): 0.5113 rms_B_bonded: 2.90 r_work: 0.4937 rms_B_bonded: 3.82 restraints_weight: 0.5000 r_work (final): 0.4937 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4912 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4912 r_free = 0.4912 target_work(ls_wunit_k1) = 0.224 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4912 r_free = 0.4912 target_work(ls_wunit_k1) = 0.224 | | occupancies: max = 1.00 min = 0.01 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| r_final: 0.4912 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1717 moved from start: 0.7003 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.123 22478 Z= 0.214 Angle : 0.831 15.939 30796 Z= 0.424 Chirality : 0.048 0.244 3571 Planarity : 0.006 0.109 3732 Dihedral : 12.564 119.607 3733 Min Nonbonded Distance : 2.042 Molprobity Statistics. All-atom Clashscore : 18.95 Ramachandran Plot: Outliers : 0.08 % Allowed : 9.42 % Favored : 90.51 % Rotamer: Outliers : 4.01 % Allowed : 25.94 % Favored : 70.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.93 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.12 (0.16), residues: 2639 helix: -0.45 (0.16), residues: 904 sheet: -1.23 (0.33), residues: 248 loop : -2.13 (0.15), residues: 1487 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.003 TRP B 154 HIS 0.012 0.002 HIS A 347 PHE 0.049 0.003 PHE A 287 TYR 0.041 0.003 TYR A 515 ARG 0.015 0.001 ARG A 285 Details of bonding type rmsd hydrogen bonds : bond 0.05287 ( 822) hydrogen bonds : angle 5.65051 ( 2247) metal coordination : bond 0.03139 ( 32) metal coordination : angle 4.08234 ( 27) covalent geometry : bond 0.00472 (22446) covalent geometry : angle 0.82206 (30769) *********************** 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 235 residues out of total 2316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 146 time to evaluate : 3.101 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 156 TYR cc_start: 0.3268 (m-10) cc_final: 0.2188 (m-80) REVERT: A 254 GLU cc_start: 0.3582 (OUTLIER) cc_final: 0.3224 (tp30) REVERT: A 266 ILE cc_start: -0.0109 (OUTLIER) cc_final: -0.1069 (tt) REVERT: A 269 ASP cc_start: 0.2636 (p0) cc_final: 0.1904 (t0) REVERT: A 419 PHE cc_start: 0.0028 (t80) cc_final: -0.1090 (t80) REVERT: A 555 ARG cc_start: 0.1418 (tpt170) cc_final: 0.0656 (mmt180) REVERT: A 601 MET cc_start: 0.1537 (mtm) cc_final: 0.0903 (ppp) REVERT: A 629 MET cc_start: 0.2096 (mmm) cc_final: 0.0866 (pmm) REVERT: A 674 TYR cc_start: 0.3624 (m-80) cc_final: 0.1323 (m-80) REVERT: A 794 MET cc_start: 0.4276 (ppp) cc_final: 0.3623 (ptm) REVERT: A 802 GLU cc_start: 0.2659 (tp30) cc_final: -0.0359 (tp30) REVERT: A 831 TYR cc_start: 0.6230 (p90) cc_final: 0.5995 (p90) REVERT: A 853 THR cc_start: -0.0265 (OUTLIER) cc_final: -0.0475 (m) REVERT: A 899 MET cc_start: -0.1043 (mtt) cc_final: -0.1353 (mtt) REVERT: A 906 MET cc_start: -0.0487 (OUTLIER) cc_final: -0.0825 (tmm) REVERT: A 924 MET cc_start: 0.1819 (OUTLIER) cc_final: -0.0102 (pmm) REVERT: B 67 MET cc_start: 0.2295 (ttt) cc_final: 0.1020 (mpm) REVERT: B 75 ARG cc_start: 0.1065 (ttp80) cc_final: 0.0172 (mmm-85) REVERT: B 128 LEU cc_start: -0.0858 (OUTLIER) cc_final: -0.2494 (tp) REVERT: C 19 GLN cc_start: 0.0128 (OUTLIER) cc_final: -0.2027 (mm-40) REVERT: D 67 MET cc_start: 0.3654 (mtp) cc_final: 0.3069 (mmt) REVERT: D 91 LEU cc_start: -0.1626 (OUTLIER) cc_final: -0.2210 (tp) REVERT: D 94 MET cc_start: 0.0914 (OUTLIER) cc_final: -0.0207 (mmt) REVERT: D 174 MET cc_start: 0.0734 (mmp) cc_final: -0.0770 (mmt) REVERT: F 15 ARG cc_start: 0.0607 (mtt180) cc_final: 0.0386 (mtp180) REVERT: F 68 MET cc_start: 0.0036 (OUTLIER) cc_final: -0.1024 (pp-130) REVERT: F 164 HIS cc_start: 0.1228 (OUTLIER) cc_final: 0.0660 (t70) REVERT: F 165 LEU cc_start: -0.0608 (OUTLIER) cc_final: -0.1281 (pt) REVERT: F 201 GLU cc_start: -0.0865 (OUTLIER) cc_final: -0.1313 (pt0) REVERT: E 274 MET cc_start: 0.2760 (ppp) cc_final: 0.1957 (pmm) REVERT: E 436 MET cc_start: -0.0846 (OUTLIER) cc_final: -0.1183 (mpt) REVERT: E 511 PHE cc_start: 0.1676 (OUTLIER) cc_final: 0.1332 (t80) REVERT: G 101 MET cc_start: 0.2067 (OUTLIER) cc_final: 0.1839 (ttt) outliers start: 89 outliers final: 41 residues processed: 216 average time/residue: 1.4640 time to fit residues: 372.2199 Evaluate side-chains 193 residues out of total 2316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 136 time to evaluate : 2.437 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 ASP Chi-restraints excluded: chain A residue 111 VAL Chi-restraints excluded: chain A residue 163 TYR Chi-restraints excluded: chain A residue 171 ILE Chi-restraints excluded: chain A residue 233 VAL Chi-restraints excluded: chain A residue 235 ASP Chi-restraints excluded: chain A residue 254 GLU Chi-restraints excluded: chain A residue 262 THR Chi-restraints excluded: chain A residue 266 ILE Chi-restraints excluded: chain A residue 294 TYR Chi-restraints excluded: chain A residue 295 HIS Chi-restraints excluded: chain A residue 338 VAL Chi-restraints excluded: chain A residue 441 PHE Chi-restraints excluded: chain A residue 457 ARG Chi-restraints excluded: chain A residue 482 CYS Chi-restraints excluded: chain A residue 533 ARG Chi-restraints excluded: chain A residue 622 CYS Chi-restraints excluded: chain A residue 662 VAL Chi-restraints excluded: chain A residue 725 HIS Chi-restraints excluded: chain A residue 760 ASP Chi-restraints excluded: chain A residue 778 SER Chi-restraints excluded: chain A residue 792 VAL Chi-restraints excluded: chain A residue 853 THR Chi-restraints excluded: chain A residue 906 MET Chi-restraints excluded: chain A residue 924 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 185 ILE Chi-restraints excluded: chain B residue 187 THR Chi-restraints excluded: chain C residue 6 VAL Chi-restraints excluded: chain C residue 11 VAL 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 94 MET Chi-restraints excluded: chain D residue 114 CYS Chi-restraints excluded: chain D residue 149 TYR Chi-restraints excluded: chain D residue 166 ILE 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 69 SER Chi-restraints excluded: chain F residue 90 PHE Chi-restraints excluded: chain F residue 164 HIS Chi-restraints excluded: chain F residue 165 LEU Chi-restraints excluded: chain F residue 201 GLU Chi-restraints excluded: chain F residue 216 THR Chi-restraints excluded: chain F residue 258 ILE Chi-restraints excluded: chain E residue 185 TYR Chi-restraints excluded: chain E residue 284 PRO Chi-restraints excluded: chain E residue 436 MET Chi-restraints excluded: chain E residue 511 PHE Chi-restraints excluded: chain G residue 76 VAL Chi-restraints excluded: chain G residue 101 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 266 random chunks: chunk 186 optimal weight: 0.9990 chunk 25 optimal weight: 0.7980 chunk 22 optimal weight: 5.9990 chunk 2 optimal weight: 0.7980 chunk 199 optimal weight: 6.9990 chunk 48 optimal weight: 9.9990 chunk 79 optimal weight: 2.9990 chunk 228 optimal weight: 0.9980 chunk 161 optimal weight: 7.9990 chunk 206 optimal weight: 0.6980 chunk 93 optimal weight: 7.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 295 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 408 GLN A 713 ASN ** A 790 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 886 GLN B 140 ASN ** C 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 518 GLN ** E 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 519 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5272 r_free = 0.5272 target = 0.264109 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.5150 r_free = 0.5150 target = 0.248607 restraints weight = 97206.888| |-----------------------------------------------------------------------------| r_work (start): 0.5108 rms_B_bonded: 3.20 r_work: 0.4920 rms_B_bonded: 4.30 restraints_weight: 0.5000 r_work (final): 0.4920 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4895 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4895 r_free = 0.4895 target_work(ls_wunit_k1) = 0.223 | | occupancies: max = 1.00 min = 0.01 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4895 r_free = 0.4895 target_work(ls_wunit_k1) = 0.223 | | occupancies: max = 1.00 min = 0.14 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.4895 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1481 moved from start: 0.7076 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= 0.134 Angle : 0.695 12.180 30796 Z= 0.346 Chirality : 0.043 0.218 3571 Planarity : 0.005 0.058 3732 Dihedral : 12.324 120.828 3733 Min Nonbonded Distance : 2.012 Molprobity Statistics. All-atom Clashscore : 15.23 Ramachandran Plot: Outliers : 0.08 % Allowed : 7.41 % Favored : 92.52 % Rotamer: Outliers : 3.09 % Allowed : 27.30 % Favored : 69.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.93 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.88 (0.16), residues: 2639 helix: -0.31 (0.17), residues: 939 sheet: -0.95 (0.33), residues: 255 loop : -2.00 (0.16), residues: 1445 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP B 154 HIS 0.007 0.001 HIS E 75 PHE 0.032 0.002 PHE A 287 TYR 0.030 0.002 TYR A 689 ARG 0.006 0.001 ARG E 303 Details of bonding type rmsd hydrogen bonds : bond 0.04372 ( 822) hydrogen bonds : angle 5.15720 ( 2247) metal coordination : bond 0.02816 ( 32) metal coordination : angle 4.93046 ( 27) covalent geometry : bond 0.00291 (22446) covalent geometry : angle 0.68008 (30769) *********************** 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 204 residues out of total 2316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 136 time to evaluate : 2.385 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 124 MET cc_start: 0.1027 (ptm) cc_final: -0.1660 (tpp) REVERT: A 156 TYR cc_start: 0.3013 (m-10) cc_final: 0.2114 (m-80) REVERT: A 254 GLU cc_start: 0.2832 (OUTLIER) cc_final: 0.2617 (tp30) REVERT: A 266 ILE cc_start: -0.0717 (OUTLIER) cc_final: -0.1433 (tt) REVERT: A 269 ASP cc_start: 0.2582 (p0) cc_final: 0.1949 (t0) REVERT: A 419 PHE cc_start: -0.0303 (t80) cc_final: -0.1757 (t80) REVERT: A 441 PHE cc_start: -0.1148 (OUTLIER) cc_final: -0.1988 (t80) REVERT: A 601 MET cc_start: 0.1502 (mtm) cc_final: 0.0541 (ppp) REVERT: A 615 MET cc_start: -0.0320 (ptm) cc_final: -0.1919 (mmt) REVERT: A 629 MET cc_start: 0.1481 (mmm) cc_final: 0.0712 (pmm) REVERT: A 658 GLU cc_start: 0.2025 (OUTLIER) cc_final: -0.0434 (pp20) REVERT: A 924 MET cc_start: 0.1638 (OUTLIER) cc_final: -0.0249 (pmm) REVERT: B 67 MET cc_start: 0.2179 (ttt) cc_final: 0.1030 (mpm) REVERT: B 75 ARG cc_start: 0.0991 (ttp80) cc_final: 0.0015 (mmt180) REVERT: B 128 LEU cc_start: -0.1107 (OUTLIER) cc_final: -0.2370 (tp) REVERT: C 19 GLN cc_start: 0.0019 (OUTLIER) cc_final: -0.2102 (mm-40) REVERT: D 67 MET cc_start: 0.3676 (mtp) cc_final: 0.3096 (mmt) REVERT: D 94 MET cc_start: 0.0202 (OUTLIER) cc_final: -0.0934 (mmt) REVERT: D 174 MET cc_start: 0.0784 (mmp) cc_final: -0.0765 (mmt) REVERT: F 68 MET cc_start: 0.0236 (OUTLIER) cc_final: -0.0721 (pp-130) REVERT: F 164 HIS cc_start: 0.0487 (OUTLIER) cc_final: 0.0071 (t70) REVERT: F 201 GLU cc_start: -0.0981 (OUTLIER) cc_final: -0.1457 (pt0) REVERT: E 274 MET cc_start: 0.2639 (ppp) cc_final: 0.1852 (pmm) REVERT: E 436 MET cc_start: -0.0719 (OUTLIER) cc_final: -0.1042 (mpt) REVERT: E 511 PHE cc_start: 0.1678 (OUTLIER) cc_final: 0.1307 (t80) REVERT: G 101 MET cc_start: 0.2207 (OUTLIER) cc_final: 0.1988 (ttt) outliers start: 68 outliers final: 33 residues processed: 190 average time/residue: 1.0947 time to fit residues: 245.1045 Evaluate side-chains 177 residues out of total 2316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 130 time to evaluate : 2.016 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 ASP Chi-restraints excluded: chain A residue 111 VAL Chi-restraints excluded: chain A residue 171 ILE Chi-restraints excluded: chain A residue 233 VAL Chi-restraints excluded: chain A residue 235 ASP Chi-restraints excluded: chain A residue 254 GLU 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 441 PHE Chi-restraints excluded: chain A residue 457 ARG Chi-restraints excluded: chain A residue 482 CYS Chi-restraints excluded: chain A residue 533 ARG Chi-restraints excluded: chain A residue 622 CYS Chi-restraints excluded: chain A residue 658 GLU Chi-restraints excluded: chain A residue 662 VAL Chi-restraints excluded: chain A residue 725 HIS Chi-restraints excluded: chain A residue 760 ASP Chi-restraints excluded: chain A residue 778 SER Chi-restraints excluded: chain A residue 792 VAL Chi-restraints excluded: chain A residue 806 THR Chi-restraints excluded: chain A residue 906 MET Chi-restraints excluded: chain A residue 924 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 185 ILE Chi-restraints excluded: chain B residue 187 THR 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 94 MET Chi-restraints excluded: chain D residue 114 CYS Chi-restraints excluded: chain D residue 153 LEU Chi-restraints excluded: chain D residue 166 ILE 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 201 GLU Chi-restraints excluded: chain E residue 284 PRO Chi-restraints excluded: chain E residue 436 MET Chi-restraints excluded: chain E residue 511 PHE Chi-restraints excluded: chain G residue 101 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 266 random chunks: chunk 6 optimal weight: 0.7980 chunk 247 optimal weight: 4.9990 chunk 112 optimal weight: 2.9990 chunk 85 optimal weight: 0.9990 chunk 176 optimal weight: 9.9990 chunk 215 optimal weight: 0.0040 chunk 63 optimal weight: 5.9990 chunk 259 optimal weight: 0.9980 chunk 262 optimal weight: 0.9980 chunk 30 optimal weight: 0.9990 chunk 84 optimal weight: 5.9990 overall best weight: 0.7594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 133 HIS ** A 295 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 408 GLN ** A 790 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** ** E 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 519 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 98 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5288 r_free = 0.5288 target = 0.265578 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.5180 r_free = 0.5180 target = 0.252427 restraints weight = 76913.717| |-----------------------------------------------------------------------------| r_work (start): 0.5116 rms_B_bonded: 2.41 r_work: 0.4954 rms_B_bonded: 3.45 restraints_weight: 0.5000 r_work (final): 0.4954 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4934 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4934 r_free = 0.4934 target_work(ls_wunit_k1) = 0.226 | | occupancies: max = 1.00 min = 0.14 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4934 r_free = 0.4934 target_work(ls_wunit_k1) = 0.226 | | occupancies: max = 1.00 min = 0.15 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.4934 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1469 moved from start: 0.7281 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.113 22478 Z= 0.131 Angle : 0.689 12.452 30796 Z= 0.342 Chirality : 0.042 0.221 3571 Planarity : 0.005 0.058 3732 Dihedral : 12.203 121.935 3733 Min Nonbonded Distance : 1.993 Molprobity Statistics. All-atom Clashscore : 14.83 Ramachandran Plot: Outliers : 0.08 % Allowed : 8.32 % Favored : 91.61 % Rotamer: Outliers : 2.56 % Allowed : 27.92 % Favored : 69.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.93 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.75 (0.16), residues: 2639 helix: -0.12 (0.17), residues: 925 sheet: -0.83 (0.34), residues: 255 loop : -1.98 (0.16), residues: 1459 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 154 HIS 0.007 0.001 HIS E 75 PHE 0.031 0.002 PHE A 287 TYR 0.029 0.002 TYR F 277 ARG 0.006 0.001 ARG E 303 Details of bonding type rmsd hydrogen bonds : bond 0.04244 ( 822) hydrogen bonds : angle 5.06514 ( 2247) metal coordination : bond 0.02814 ( 32) metal coordination : angle 4.86048 ( 27) covalent geometry : bond 0.00282 (22446) covalent geometry : angle 0.67446 (30769) ********************** 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 191 residues out of total 2316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 135 time to evaluate : 4.719 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 124 MET cc_start: 0.1204 (ptm) cc_final: -0.1558 (tpp) REVERT: A 156 TYR cc_start: 0.2740 (m-10) cc_final: 0.1728 (m-80) REVERT: A 254 GLU cc_start: 0.2948 (OUTLIER) cc_final: 0.2599 (tp30) REVERT: A 266 ILE cc_start: -0.0784 (OUTLIER) cc_final: -0.1424 (tt) REVERT: A 269 ASP cc_start: 0.2675 (p0) cc_final: 0.2074 (t0) REVERT: A 380 MET cc_start: 0.1408 (OUTLIER) cc_final: 0.0027 (ptt) REVERT: A 419 PHE cc_start: -0.0465 (t80) cc_final: -0.1821 (t80) REVERT: A 441 PHE cc_start: -0.1097 (OUTLIER) cc_final: -0.2043 (t80) REVERT: A 519 MET cc_start: 0.0239 (pmt) cc_final: -0.3076 (mmp) REVERT: A 601 MET cc_start: 0.1414 (mtm) cc_final: 0.0389 (ppp) REVERT: A 615 MET cc_start: -0.0553 (ptm) cc_final: -0.0983 (ptm) REVERT: A 629 MET cc_start: 0.1666 (mmm) cc_final: 0.0854 (pmm) REVERT: A 924 MET cc_start: 0.1835 (OUTLIER) cc_final: -0.0021 (pmm) REVERT: B 67 MET cc_start: 0.2296 (ttt) cc_final: 0.1019 (mpm) REVERT: B 75 ARG cc_start: 0.0745 (ttp80) cc_final: -0.0222 (mmt180) REVERT: B 128 LEU cc_start: -0.1174 (OUTLIER) cc_final: -0.2359 (tp) REVERT: C 19 GLN cc_start: -0.0035 (OUTLIER) cc_final: -0.2111 (mm-40) REVERT: D 67 MET cc_start: 0.3760 (mtp) cc_final: 0.3188 (mmt) REVERT: D 70 MET cc_start: 0.0070 (OUTLIER) cc_final: -0.0797 (mmm) REVERT: D 94 MET cc_start: 0.0716 (OUTLIER) cc_final: -0.0753 (mmt) REVERT: D 174 MET cc_start: 0.0737 (mmp) cc_final: -0.0827 (mmt) REVERT: F 15 ARG cc_start: 0.0483 (mtt180) cc_final: 0.0185 (mtm180) REVERT: F 68 MET cc_start: 0.0469 (OUTLIER) cc_final: -0.0135 (pp-130) REVERT: F 164 HIS cc_start: 0.0625 (OUTLIER) cc_final: 0.0147 (t70) REVERT: F 201 GLU cc_start: -0.0737 (OUTLIER) cc_final: -0.1198 (pt0) REVERT: F 429 MET cc_start: -0.2237 (pmt) cc_final: -0.4047 (ptt) REVERT: E 68 MET cc_start: 0.2157 (mpp) cc_final: 0.0961 (ttp) REVERT: E 274 MET cc_start: 0.2546 (ppp) cc_final: 0.1849 (pmm) REVERT: E 436 MET cc_start: -0.0866 (OUTLIER) cc_final: -0.1157 (mpt) REVERT: E 511 PHE cc_start: 0.1707 (OUTLIER) cc_final: 0.1323 (t80) outliers start: 56 outliers final: 34 residues processed: 175 average time/residue: 1.4262 time to fit residues: 295.4693 Evaluate side-chains 175 residues out of total 2316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 127 time to evaluate : 2.296 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 ASP Chi-restraints excluded: chain A residue 111 VAL Chi-restraints excluded: chain A residue 205 LEU Chi-restraints excluded: chain A residue 233 VAL Chi-restraints excluded: chain A residue 235 ASP Chi-restraints excluded: chain A residue 254 GLU 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 374 TYR Chi-restraints excluded: chain A residue 380 MET Chi-restraints excluded: chain A residue 441 PHE Chi-restraints excluded: chain A residue 457 ARG Chi-restraints excluded: chain A residue 482 CYS Chi-restraints excluded: chain A residue 533 ARG Chi-restraints excluded: chain A residue 622 CYS Chi-restraints excluded: chain A residue 760 ASP Chi-restraints excluded: chain A residue 778 SER Chi-restraints excluded: chain A residue 792 VAL Chi-restraints excluded: chain A residue 806 THR Chi-restraints excluded: chain A residue 894 GLU Chi-restraints excluded: chain A residue 906 MET Chi-restraints excluded: chain A residue 924 MET Chi-restraints excluded: chain B residue 128 LEU Chi-restraints excluded: chain B residue 148 THR Chi-restraints excluded: chain B residue 187 THR Chi-restraints excluded: chain C residue 19 GLN Chi-restraints excluded: chain C residue 54 SER Chi-restraints excluded: chain D residue 70 MET Chi-restraints excluded: chain D residue 83 VAL Chi-restraints excluded: chain D residue 94 MET Chi-restraints excluded: chain D residue 114 CYS Chi-restraints excluded: chain D residue 153 LEU Chi-restraints excluded: chain D residue 166 ILE 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 201 GLU Chi-restraints excluded: chain F residue 216 THR Chi-restraints excluded: chain E residue 284 PRO Chi-restraints excluded: chain E residue 304 ILE Chi-restraints excluded: chain E residue 436 MET Chi-restraints excluded: chain E residue 511 PHE Chi-restraints excluded: chain G residue 101 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 266 random chunks: chunk 216 optimal weight: 0.8980 chunk 40 optimal weight: 7.9990 chunk 127 optimal weight: 5.9990 chunk 154 optimal weight: 40.0000 chunk 167 optimal weight: 4.9990 chunk 259 optimal weight: 7.9990 chunk 235 optimal weight: 0.7980 chunk 45 optimal weight: 0.4980 chunk 147 optimal weight: 20.0000 chunk 76 optimal weight: 5.9990 chunk 118 optimal weight: 9.9990 overall best weight: 2.6384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 57 GLN ** A 99 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 133 HIS ** A 184 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 210 GLN ** A 213 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 295 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 408 GLN ** A 447 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 568 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 790 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 140 ASN B 179 ASN ** D 118 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 519 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 1 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5280 r_free = 0.5280 target = 0.264673 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.5163 r_free = 0.5163 target = 0.250576 restraints weight = 90674.348| |-----------------------------------------------------------------------------| r_work (start): 0.5099 rms_B_bonded: 2.83 r_work: 0.4980 rms_B_bonded: 3.58 restraints_weight: 0.5000 r_work (final): 0.4980 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4964 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4964 r_free = 0.4964 target_work(ls_wunit_k1) = 0.229 | | occupancies: max = 1.00 min = 0.15 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4964 r_free = 0.4964 target_work(ls_wunit_k1) = 0.229 | | occupancies: max = 1.00 min = 0.16 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.4964 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1918 moved from start: 0.8205 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.116 22478 Z= 0.236 Angle : 0.904 15.379 30796 Z= 0.461 Chirality : 0.051 0.344 3571 Planarity : 0.007 0.138 3732 Dihedral : 12.776 120.360 3733 Min Nonbonded Distance : 2.101 Molprobity Statistics. All-atom Clashscore : 22.10 Ramachandran Plot: Outliers : 0.08 % Allowed : 10.10 % Favored : 89.82 % Rotamer: Outliers : 3.04 % Allowed : 27.53 % Favored : 69.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.93 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.38 (0.15), residues: 2639 helix: -0.80 (0.16), residues: 915 sheet: -1.13 (0.34), residues: 237 loop : -2.24 (0.15), residues: 1487 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.042 0.003 TRP B 154 HIS 0.015 0.002 HIS A 572 PHE 0.068 0.003 PHE A 287 TYR 0.105 0.003 TYR A 374 ARG 0.013 0.001 ARG A 285 Details of bonding type rmsd hydrogen bonds : bond 0.05733 ( 822) hydrogen bonds : angle 6.14527 ( 2247) metal coordination : bond 0.02953 ( 32) metal coordination : angle 4.79932 ( 27) covalent geometry : bond 0.00521 (22446) covalent geometry : angle 0.89348 (30769) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 20505.08 seconds wall clock time: 355 minutes 48.88 seconds (21348.88 seconds total)