Starting phenix.real_space_refine on Sat Feb 7 17:17:40 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8xmb_38470/02_2026/8xmb_38470.cif Found real_map, /net/cci-nas-00/data/ceres_data/8xmb_38470/02_2026/8xmb_38470.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8xmb_38470/02_2026/8xmb_38470.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8xmb_38470/02_2026/8xmb_38470.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8xmb_38470/02_2026/8xmb_38470.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8xmb_38470/02_2026/8xmb_38470.map" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.003 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 Zn 9 6.06 5 P 56 5.49 5 Mg 2 5.21 5 S 220 5.16 5 C 22313 2.51 5 N 6175 2.21 5 O 6524 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 12 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 35299 Number of models: 1 Model: "" Number of chains: 23 Chain: "A" Number of atoms: 8582 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1159, 8582 Classifications: {'peptide': 1159} Incomplete info: {'truncation_to_alanine': 142} Link IDs: {'PCIS': 1, 'PTRANS': 52, 'TRANS': 1105} Chain breaks: 6 Unresolved non-hydrogen bonds: 503 Unresolved non-hydrogen angles: 617 Unresolved non-hydrogen dihedrals: 405 Unresolved non-hydrogen chiralities: 24 Planarities with less than four sites: {'GLU:plan': 25, 'ASN:plan1': 7, 'ASP:plan': 26, 'ARG:plan': 10, 'PHE:plan': 3, 'GLN:plan1': 6, 'TYR:plan': 2, 'HIS:plan': 2} Unresolved non-hydrogen planarities: 315 Chain: "B" Number of atoms: 8080 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1064, 8080 Classifications: {'peptide': 1064} Incomplete info: {'truncation_to_alanine': 111} Link IDs: {'PCIS': 1, 'PTRANS': 40, 'TRANS': 1022} Chain breaks: 8 Unresolved non-hydrogen bonds: 393 Unresolved non-hydrogen angles: 477 Unresolved non-hydrogen dihedrals: 317 Unresolved non-hydrogen chiralities: 9 Planarities with less than four sites: {'ASN:plan1': 5, 'GLU:plan': 34, 'ASP:plan': 21, 'GLN:plan1': 5, 'TYR:plan': 2, 'ARG:plan': 2, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 263 Chain: "C" Number of atoms: 2148 Number of conformers: 1 Conformer: "" Number of residues, atoms: 291, 2148 Classifications: {'peptide': 291} Incomplete info: {'truncation_to_alanine': 39} Link IDs: {'PTRANS': 12, 'TRANS': 278} Chain breaks: 1 Unresolved non-hydrogen bonds: 137 Unresolved non-hydrogen angles: 174 Unresolved non-hydrogen dihedrals: 104 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLU:plan': 11, 'ASP:plan': 17, 'ASN:plan1': 1, 'PHE:plan': 1, 'HIS:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 114 Chain: "D" Number of atoms: 869 Number of conformers: 1 Conformer: "" Number of residues, atoms: 113, 869 Classifications: {'peptide': 113} Link IDs: {'PTRANS': 6, 'TRANS': 106} Chain: "E" Number of atoms: 1505 Number of conformers: 1 Conformer: "" Number of residues, atoms: 198, 1505 Classifications: {'peptide': 198} Incomplete info: {'truncation_to_alanine': 41} Link IDs: {'PTRANS': 6, 'TRANS': 191} Chain breaks: 1 Unresolved non-hydrogen bonds: 155 Unresolved non-hydrogen angles: 188 Unresolved non-hydrogen dihedrals: 127 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 10, 'ASP:plan': 7, 'GLN:plan1': 3, 'ARG:plan': 3, 'HIS:plan': 1, 'ASN:plan1': 3, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 109 Chain: "F" Number of atoms: 568 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 568 Classifications: {'peptide': 76} Incomplete info: {'truncation_to_alanine': 15} Link IDs: {'PTRANS': 4, 'TRANS': 71} Unresolved non-hydrogen bonds: 57 Unresolved non-hydrogen angles: 69 Unresolved non-hydrogen dihedrals: 45 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'ARG:plan': 2, 'GLU:plan': 6, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 37 Chain: "G" Number of atoms: 1096 Number of conformers: 1 Conformer: "" Number of residues, atoms: 174, 1096 Classifications: {'peptide': 174} Incomplete info: {'truncation_to_alanine': 77} Link IDs: {'PTRANS': 9, 'TRANS': 164} Unresolved chain link angles: 4 Unresolved non-hydrogen bonds: 318 Unresolved non-hydrogen angles: 395 Unresolved non-hydrogen dihedrals: 278 Unresolved non-hydrogen chiralities: 14 Planarities with less than four sites: {'PHE:plan': 7, 'ASP:plan': 8, 'GLU:plan': 9, 'ARG:plan': 6, 'GLN:plan1': 2, 'HIS:plan': 3, 'TYR:plan': 2, 'ASN:plan1': 3, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 187 Chain: "H" Number of atoms: 949 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 949 Classifications: {'peptide': 126} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 22} Link IDs: {'PTRANS': 5, 'TRANS': 120} Chain breaks: 2 Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 75 Unresolved non-hydrogen angles: 97 Unresolved non-hydrogen dihedrals: 61 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'ASP:plan': 7, 'HIS:plan': 3, 'GLU:plan': 3} Unresolved non-hydrogen planarities: 48 Chain: "I" Number of atoms: 823 Number of conformers: 1 Conformer: "" Number of residues, atoms: 113, 823 Classifications: {'peptide': 113} Incomplete info: {'truncation_to_alanine': 23} Link IDs: {'PTRANS': 4, 'TRANS': 108} Unresolved non-hydrogen bonds: 93 Unresolved non-hydrogen angles: 117 Unresolved non-hydrogen dihedrals: 74 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'TYR:plan': 1, 'GLU:plan': 5, 'ASP:plan': 3, 'GLN:plan1': 2, 'ASN:plan1': 1, 'HIS:plan': 1, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 67 Chain: "J" Number of atoms: 476 Number of conformers: 1 Conformer: "" Number of residues, atoms: 62, 476 Classifications: {'peptide': 62} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 1, 'TRANS': 60} Unresolved non-hydrogen bonds: 34 Unresolved non-hydrogen angles: 44 Unresolved non-hydrogen dihedrals: 27 Planarities with less than four sites: {'ASP:plan': 5, 'GLN:plan1': 1, 'GLU:plan': 1, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 30 Chain: "K" Number of atoms: 715 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 715 Classifications: {'peptide': 94} Incomplete info: {'truncation_to_alanine': 17} Link IDs: {'PTRANS': 3, 'TRANS': 90} Unresolved non-hydrogen bonds: 55 Unresolved non-hydrogen angles: 67 Unresolved non-hydrogen dihedrals: 43 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASP:plan': 4, 'ARG:plan': 1, 'GLU:plan': 5, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 41 Chain: "L" Number of atoms: 312 Number of conformers: 1 Conformer: "" Number of residues, atoms: 42, 312 Classifications: {'peptide': 42} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'TRANS': 41} Unresolved non-hydrogen bonds: 28 Unresolved non-hydrogen angles: 35 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'ASN:plan1': 1, 'ASP:plan': 1, 'ARG:plan': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 15 Chain: "M" Number of atoms: 8044 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1052, 8044 Classifications: {'peptide': 1052} Incomplete info: {'truncation_to_alanine': 113} Link IDs: {'PTRANS': 40, 'TRANS': 1011} Chain breaks: 3 Unresolved non-hydrogen bonds: 422 Unresolved non-hydrogen angles: 525 Unresolved non-hydrogen dihedrals: 342 Unresolved non-hydrogen chiralities: 25 Planarities with less than four sites: {'GLU:plan': 19, 'ASP:plan': 12, 'ARG:plan': 11, 'ASN:plan1': 5, 'GLN:plan1': 8, 'PHE:plan': 3, 'TYR:plan': 5, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 272 Chain: "N" Number of atoms: 351 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 351 Classifications: {'DNA': 17} Link IDs: {'rna3p': 16} Chain: "O" Number of atoms: 197 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 197 Classifications: {'RNA': 9} Modifications used: {'rna3p_pur': 6, 'rna3p_pyr': 2} Link IDs: {'rna3p': 8} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "Q" Number of atoms: 541 Number of conformers: 1 Conformer: "" Number of residues, atoms: 27, 541 Classifications: {'DNA': 27} Link IDs: {'rna3p': 26} Chain: "A" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 5 Unusual residues: {' MG': 2, ' ZN': 3} Classifications: {'undetermined': 5} Link IDs: {None: 4} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "I" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "J" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "L" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "Q" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 32 Unusual residues: {'GTP': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 326 SG CYS A 56 45.664 67.409 129.217 1.00316.46 S ATOM 344 SG CYS A 59 45.302 70.093 129.019 1.00321.96 S ATOM 391 SG CYS A 67 46.544 70.181 126.810 1.00321.03 S ATOM 6898 SG CYS A1031 138.411 70.682 86.426 1.00449.67 S ATOM 6967 SG CYS A1044 136.133 72.053 88.878 1.00403.21 S ATOM 613 SG CYS A 97 97.775 65.087 145.914 1.00441.80 S ATOM 630 SG CYS A 100 98.844 65.665 149.687 1.00473.94 S ATOM 661 SG CYS A 118 100.458 62.613 147.923 1.00439.82 S ATOM 690 SG CYS A 121 101.365 64.784 146.563 1.00418.07 S ATOM 16284 SG CYS B1108 55.537 82.911 139.563 1.00495.20 S ATOM 16306 SG CYS B1111 58.077 81.279 140.105 1.00470.52 S ATOM 16376 SG CYS B1133 55.296 78.805 140.053 1.00463.23 S ATOM 16400 SG CYS B1136 55.175 80.392 143.008 1.00470.57 S ATOM 17329 SG CYS C 90 14.518 83.163 70.154 1.00240.38 S ATOM 17345 SG CYS C 93 12.790 80.175 70.182 1.00236.72 S ATOM 17378 SG CYS C 99 13.964 79.384 68.189 1.00190.87 S ATOM 17400 SG CYS C 102 16.935 80.226 69.000 1.00184.01 S ATOM 24331 SG CYS I 76 109.050 104.735 69.091 1.00110.02 S ATOM 24352 SG CYS I 79 105.541 104.332 68.147 1.00113.85 S ATOM 24530 SG CYS I 103 106.592 101.749 70.371 1.00114.98 S ATOM 24565 SG CYS I 108 107.410 102.412 66.512 1.00114.35 S ATOM 23844 SG CYS I 7 130.730 41.089 89.830 1.00222.06 S ATOM 23870 SG CYS I 10 129.019 37.942 91.824 1.00246.01 S ATOM 23997 SG CYS I 29 131.334 41.006 93.589 1.00267.67 S ATOM 24022 SG CYS I 32 132.068 38.408 92.856 1.00281.22 S ATOM 24672 SG CYS J 7 45.067 77.506 55.451 1.00 86.05 S ATOM 24696 SG CYS J 10 44.064 80.760 53.342 1.00 86.03 S ATOM 24953 SG CYS J 44 47.590 80.144 54.112 1.00 85.10 S ATOM 24959 SG CYS J 45 45.247 77.831 52.377 1.00 84.54 S ATOM 25843 SG CYS L 12 38.389 39.385 79.445 1.00154.43 S ATOM 25861 SG CYS L 15 36.557 36.587 76.836 1.00177.41 S ATOM 25945 SG CYS L 29 36.465 37.162 80.889 1.00164.29 S ATOM 25961 SG CYS L 32 39.644 36.031 78.981 1.00161.28 S Time building chain proxies: 7.77, per 1000 atoms: 0.22 Number of scatterers: 35299 At special positions: 0 Unit cell: (176, 169.4, 195.8, 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 9 29.99 S 220 16.00 P 56 15.00 Mg 2 11.99 O 6524 8.00 N 6175 7.00 C 22313 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=2, symmetry=0 Number of additional bonds: simple=2, symmetry=0 Coordination: Other bonds: Time building additional restraints: 2.81 Conformation dependent library (CDL) restraints added in 1.4 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A1501 " pdb="ZN ZN A1501 " - pdb=" SG CYS A 59 " pdb="ZN ZN A1501 " - pdb=" ND1 HIS A 70 " pdb="ZN ZN A1501 " - pdb=" SG CYS A 67 " pdb="ZN ZN A1501 " - pdb=" SG CYS A 56 " pdb=" ZN A1503 " pdb="ZN ZN A1503 " - pdb=" NE2 HIS A 985 " pdb="ZN ZN A1503 " - pdb=" ND1 HIS A 983 " pdb="ZN ZN A1503 " - pdb=" SG CYS A1044 " pdb="ZN ZN A1503 " - pdb=" SG CYS A1031 " pdb=" ZN A1504 " pdb="ZN ZN A1504 " - pdb=" SG CYS A 121 " pdb="ZN ZN A1504 " - pdb=" SG CYS A 118 " pdb="ZN ZN A1504 " - pdb=" SG CYS A 100 " pdb="ZN ZN A1504 " - pdb=" SG CYS A 97 " pdb=" ZN B2001 " pdb="ZN ZN B2001 " - pdb=" SG CYS B1111 " pdb="ZN ZN B2001 " - pdb=" SG CYS B1133 " pdb="ZN ZN B2001 " - pdb=" SG CYS B1108 " pdb="ZN ZN B2001 " - pdb=" SG CYS B1136 " pdb=" ZN C 401 " pdb="ZN ZN C 401 " - pdb=" SG CYS C 102 " pdb="ZN ZN C 401 " - pdb=" SG CYS C 93 " pdb="ZN ZN C 401 " - pdb=" SG CYS C 90 " pdb="ZN ZN C 401 " - pdb=" SG CYS C 99 " pdb=" ZN I 201 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 79 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 103 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 76 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 108 " pdb=" ZN I 202 " pdb="ZN ZN I 202 " - pdb=" SG CYS I 32 " pdb="ZN ZN I 202 " - pdb=" SG CYS I 29 " pdb="ZN ZN I 202 " - pdb=" SG CYS I 10 " pdb="ZN ZN I 202 " - pdb=" SG CYS I 7 " pdb=" ZN J 200 " pdb="ZN ZN J 200 " - pdb=" SG CYS J 10 " pdb="ZN ZN J 200 " - pdb=" SG CYS J 44 " pdb="ZN ZN J 200 " - pdb=" SG CYS J 7 " pdb="ZN ZN J 200 " - pdb=" SG CYS J 45 " pdb=" ZN L 101 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 12 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 32 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 29 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 15 " Number of angles added : 46 8992 Ramachandran restraints generated. 4496 Oldfield, 0 Emsley, 4496 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8612 Finding SS restraints... Secondary structure from input PDB file: 159 helices and 51 sheets defined 37.1% alpha, 17.1% beta 25 base pairs and 39 stacking pairs defined. Time for finding SS restraints: 4.29 Creating SS restraints... Processing helix chain 'A' and resid 24 through 32 Processing helix chain 'A' and resid 85 through 96 removed outlier: 3.544A pdb=" N LYS A 95 " --> pdb=" O ALA A 91 " (cutoff:3.500A) Processing helix chain 'A' and resid 122 through 126 removed outlier: 3.627A pdb=" N THR A 125 " --> pdb=" O THR A 122 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N GLY A 126 " --> pdb=" O LEU A 123 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 122 through 126' Processing helix chain 'A' and resid 150 through 160 Processing helix chain 'A' and resid 166 through 171 removed outlier: 4.450A pdb=" N TRP A 170 " --> pdb=" O PRO A 167 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N SER A 171 " --> pdb=" O ASP A 168 " (cutoff:3.500A) Processing helix chain 'A' and resid 192 through 201 removed outlier: 3.778A pdb=" N TYR A 197 " --> pdb=" O HIS A 193 " (cutoff:3.500A) Processing helix chain 'A' and resid 204 through 212 Processing helix chain 'A' and resid 215 through 217 No H-bonds generated for 'chain 'A' and resid 215 through 217' Processing helix chain 'A' and resid 250 through 257 Processing helix chain 'A' and resid 262 through 275 removed outlier: 3.585A pdb=" N LEU A 266 " --> pdb=" O ASN A 262 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N SER A 267 " --> pdb=" O THR A 263 " (cutoff:3.500A) removed outlier: 4.076A pdb=" N SER A 268 " --> pdb=" O LEU A 264 " (cutoff:3.500A) Processing helix chain 'A' and resid 305 through 313 Processing helix chain 'A' and resid 341 through 347 removed outlier: 4.011A pdb=" N ARG A 346 " --> pdb=" O SER A 342 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 420 removed outlier: 3.565A pdb=" N LEU A 420 " --> pdb=" O GLN A 417 " (cutoff:3.500A) Processing helix chain 'A' and resid 437 through 439 No H-bonds generated for 'chain 'A' and resid 437 through 439' Processing helix chain 'A' and resid 440 through 445 removed outlier: 4.177A pdb=" N PHE A 444 " --> pdb=" O CYS A 440 " (cutoff:3.500A) Processing helix chain 'A' and resid 460 through 471 removed outlier: 3.603A pdb=" N ASP A 468 " --> pdb=" O LYS A 464 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N GLU A 469 " --> pdb=" O VAL A 465 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N LEU A 470 " --> pdb=" O GLU A 466 " (cutoff:3.500A) Processing helix chain 'A' and resid 472 through 476 Processing helix chain 'A' and resid 491 through 503 Processing helix chain 'A' and resid 509 through 518 removed outlier: 3.668A pdb=" N MET A 518 " --> pdb=" O GLN A 514 " (cutoff:3.500A) Processing helix chain 'A' and resid 542 through 548 removed outlier: 3.629A pdb=" N LEU A 546 " --> pdb=" O THR A 542 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N PHE A 547 " --> pdb=" O GLY A 543 " (cutoff:3.500A) Processing helix chain 'A' and resid 549 through 551 No H-bonds generated for 'chain 'A' and resid 549 through 551' Processing helix chain 'A' and resid 587 through 596 Processing helix chain 'A' and resid 599 through 619 Processing helix chain 'A' and resid 623 through 629 removed outlier: 3.732A pdb=" N LEU A 627 " --> pdb=" O SER A 623 " (cutoff:3.500A) Processing helix chain 'A' and resid 632 through 658 Processing helix chain 'A' and resid 659 through 660 No H-bonds generated for 'chain 'A' and resid 659 through 660' Processing helix chain 'A' and resid 661 through 663 No H-bonds generated for 'chain 'A' and resid 661 through 663' Processing helix chain 'A' and resid 664 through 669 Processing helix chain 'A' and resid 675 through 682 removed outlier: 3.618A pdb=" N SER A 679 " --> pdb=" O LYS A 675 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N VAL A 680 " --> pdb=" O GLU A 676 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N ASP A 682 " --> pdb=" O ASP A 678 " (cutoff:3.500A) Processing helix chain 'A' and resid 683 through 692 removed outlier: 4.252A pdb=" N CYS A 687 " --> pdb=" O LEU A 683 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N TYR A 688 " --> pdb=" O ALA A 684 " (cutoff:3.500A) Processing helix chain 'A' and resid 694 through 713 removed outlier: 4.423A pdb=" N ASP A 710 " --> pdb=" O ASP A 706 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N VAL A 711 " --> pdb=" O ALA A 707 " (cutoff:3.500A) Processing helix chain 'A' and resid 714 through 719 Processing helix chain 'A' and resid 723 through 731 Processing helix chain 'A' and resid 736 through 745 Processing helix chain 'A' and resid 765 through 770 Processing helix chain 'A' and resid 805 through 817 Processing helix chain 'A' and resid 825 through 840 removed outlier: 3.805A pdb=" N GLY A 829 " --> pdb=" O ALA A 825 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N PHE A 838 " --> pdb=" O ARG A 834 " (cutoff:3.500A) Processing helix chain 'A' and resid 876 through 892 Processing helix chain 'A' and resid 893 through 895 No H-bonds generated for 'chain 'A' and resid 893 through 895' Processing helix chain 'A' and resid 903 through 913 Processing helix chain 'A' and resid 931 through 935 removed outlier: 3.806A pdb=" N SER A 934 " --> pdb=" O GLU A 931 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N LYS A 935 " --> pdb=" O TYR A 932 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 931 through 935' Processing helix chain 'A' and resid 938 through 951 Processing helix chain 'A' and resid 957 through 959 No H-bonds generated for 'chain 'A' and resid 957 through 959' Processing helix chain 'A' and resid 988 through 995 Processing helix chain 'A' and resid 997 through 1012 removed outlier: 3.692A pdb=" N ARG A1012 " --> pdb=" O GLN A1008 " (cutoff:3.500A) Processing helix chain 'A' and resid 1059 through 1073 removed outlier: 4.192A pdb=" N ILE A1063 " --> pdb=" O GLU A1059 " (cutoff:3.500A) removed outlier: 4.170A pdb=" N ILE A1068 " --> pdb=" O ARG A1064 " (cutoff:3.500A) Proline residue: A1069 - end of helix removed outlier: 3.579A pdb=" N LEU A1072 " --> pdb=" O ILE A1068 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N ASP A1073 " --> pdb=" O PRO A1069 " (cutoff:3.500A) Processing helix chain 'A' and resid 1121 through 1130 Processing helix chain 'A' and resid 1147 through 1154 removed outlier: 3.514A pdb=" N CYS A1151 " --> pdb=" O ILE A1147 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N SER A1152 " --> pdb=" O ARG A1148 " (cutoff:3.500A) Processing helix chain 'A' and resid 1155 through 1175 Processing helix chain 'A' and resid 1179 through 1190 removed outlier: 3.827A pdb=" N LEU A1183 " --> pdb=" O LEU A1179 " (cutoff:3.500A) Processing helix chain 'A' and resid 1200 through 1211 removed outlier: 3.503A pdb=" N TRP A1204 " --> pdb=" O ASN A1200 " (cutoff:3.500A) Processing helix chain 'A' and resid 1215 through 1223 Processing helix chain 'A' and resid 1224 through 1236 Processing helix chain 'A' and resid 1243 through 1250 Processing helix chain 'B' and resid 28 through 46 Processing helix chain 'B' and resid 50 through 62 Processing helix chain 'B' and resid 62 through 71 removed outlier: 3.975A pdb=" N ASN B 66 " --> pdb=" O HIS B 62 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N PHE B 71 " --> pdb=" O VAL B 67 " (cutoff:3.500A) Processing helix chain 'B' and resid 117 through 125 Processing helix chain 'B' and resid 191 through 195 Processing helix chain 'B' and resid 279 through 286 Processing helix chain 'B' and resid 290 through 298 Processing helix chain 'B' and resid 304 through 322 removed outlier: 3.624A pdb=" N THR B 308 " --> pdb=" O ASP B 304 " (cutoff:3.500A) Processing helix chain 'B' and resid 329 through 341 Processing helix chain 'B' and resid 349 through 357 removed outlier: 3.816A pdb=" N HIS B 355 " --> pdb=" O ASP B 351 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N LEU B 356 " --> pdb=" O GLU B 352 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N TYR B 357 " --> pdb=" O CYS B 353 " (cutoff:3.500A) Processing helix chain 'B' and resid 366 through 384 Processing helix chain 'B' and resid 394 through 396 No H-bonds generated for 'chain 'B' and resid 394 through 396' Processing helix chain 'B' and resid 405 through 431 removed outlier: 3.645A pdb=" N ARG B 409 " --> pdb=" O GLU B 405 " (cutoff:3.500A) removed outlier: 4.235A pdb=" N GLU B 410 " --> pdb=" O LEU B 406 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N SER B 431 " --> pdb=" O GLN B 427 " (cutoff:3.500A) Processing helix chain 'B' and resid 438 through 443 removed outlier: 4.218A pdb=" N TYR B 442 " --> pdb=" O PRO B 438 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N LEU B 443 " --> pdb=" O ILE B 439 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 438 through 443' Processing helix chain 'B' and resid 446 through 459 Processing helix chain 'B' and resid 482 through 490 removed outlier: 3.652A pdb=" N THR B 486 " --> pdb=" O ASN B 482 " (cutoff:3.500A) Processing helix chain 'B' and resid 510 through 514 removed outlier: 3.527A pdb=" N TRP B 514 " --> pdb=" O PRO B 511 " (cutoff:3.500A) Processing helix chain 'B' and resid 548 through 556 removed outlier: 3.801A pdb=" N GLY B 556 " --> pdb=" O LEU B 552 " (cutoff:3.500A) Processing helix chain 'B' and resid 586 through 600 Processing helix chain 'B' and resid 636 through 641 removed outlier: 3.654A pdb=" N LYS B 641 " --> pdb=" O GLN B 638 " (cutoff:3.500A) Processing helix chain 'B' and resid 649 through 656 Processing helix chain 'B' and resid 664 through 668 removed outlier: 3.881A pdb=" N GLU B 668 " --> pdb=" O ILE B 664 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 664 through 668' Processing helix chain 'B' and resid 675 through 682 removed outlier: 3.779A pdb=" N LEU B 679 " --> pdb=" O GLY B 675 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N LEU B 680 " --> pdb=" O ILE B 676 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N LYS B 681 " --> pdb=" O LYS B 677 " (cutoff:3.500A) Processing helix chain 'B' and resid 692 through 697 removed outlier: 3.558A pdb=" N LEU B 697 " --> pdb=" O SER B 694 " (cutoff:3.500A) Processing helix chain 'B' and resid 698 through 703 removed outlier: 3.918A pdb=" N VAL B 703 " --> pdb=" O VAL B 699 " (cutoff:3.500A) Processing helix chain 'B' and resid 711 through 721 Processing helix chain 'B' and resid 721 through 726 Processing helix chain 'B' and resid 755 through 762 Processing helix chain 'B' and resid 763 through 767 removed outlier: 4.130A pdb=" N LEU B 766 " --> pdb=" O LYS B 763 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N PHE B 767 " --> pdb=" O GLU B 764 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 763 through 767' Processing helix chain 'B' and resid 792 through 797 Processing helix chain 'B' and resid 929 through 933 removed outlier: 3.631A pdb=" N PHE B 933 " --> pdb=" O GLN B 930 " (cutoff:3.500A) Processing helix chain 'B' and resid 949 through 955 removed outlier: 4.100A pdb=" N SER B 953 " --> pdb=" O HIS B 949 " (cutoff:3.500A) Processing helix chain 'B' and resid 958 through 971 Processing helix chain 'B' and resid 990 through 994 removed outlier: 4.024A pdb=" N THR B 994 " --> pdb=" O PRO B 991 " (cutoff:3.500A) Processing helix chain 'B' and resid 996 through 1007 Processing helix chain 'B' and resid 1076 through 1087 Processing helix chain 'B' and resid 1088 through 1097 removed outlier: 3.688A pdb=" N LEU B1092 " --> pdb=" O ALA B1088 " (cutoff:3.500A) Processing helix chain 'B' and resid 1148 through 1162 Processing helix chain 'C' and resid 30 through 44 removed outlier: 3.591A pdb=" N ALA C 34 " --> pdb=" O ASP C 30 " (cutoff:3.500A) Processing helix chain 'C' and resid 63 through 72 Processing helix chain 'C' and resid 86 through 90 Processing helix chain 'C' and resid 129 through 133 removed outlier: 3.686A pdb=" N THR C 133 " --> pdb=" O PRO C 130 " (cutoff:3.500A) Processing helix chain 'C' and resid 205 through 216 removed outlier: 3.661A pdb=" N ILE C 210 " --> pdb=" O ASP C 206 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N SER C 216 " --> pdb=" O LEU C 212 " (cutoff:3.500A) Processing helix chain 'C' and resid 243 through 252 Processing helix chain 'C' and resid 277 through 306 Processing helix chain 'D' and resid 94 through 109 removed outlier: 3.556A pdb=" N LEU D 101 " --> pdb=" O ALA D 97 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N VAL D 109 " --> pdb=" O LYS D 105 " (cutoff:3.500A) Processing helix chain 'D' and resid 119 through 128 removed outlier: 4.440A pdb=" N TYR D 123 " --> pdb=" O ILE D 119 " (cutoff:3.500A) Processing helix chain 'D' and resid 137 through 152 removed outlier: 3.618A pdb=" N SER D 141 " --> pdb=" O THR D 137 " (cutoff:3.500A) Proline residue: D 148 - end of helix Processing helix chain 'D' and resid 155 through 166 Processing helix chain 'D' and resid 169 through 177 removed outlier: 4.178A pdb=" N VAL D 173 " --> pdb=" O SER D 169 " (cutoff:3.500A) Processing helix chain 'D' and resid 178 through 181 Processing helix chain 'D' and resid 187 through 202 removed outlier: 3.692A pdb=" N LEU D 191 " --> pdb=" O ILE D 187 " (cutoff:3.500A) Processing helix chain 'E' and resid 4 through 25 Processing helix chain 'E' and resid 29 through 34 removed outlier: 3.503A pdb=" N LEU E 33 " --> pdb=" O ALA E 29 " (cutoff:3.500A) Processing helix chain 'E' and resid 36 through 45 removed outlier: 3.682A pdb=" N GLY E 45 " --> pdb=" O ILE E 41 " (cutoff:3.500A) Processing helix chain 'E' and resid 78 through 93 removed outlier: 3.894A pdb=" N MET E 82 " --> pdb=" O GLY E 78 " (cutoff:3.500A) Processing helix chain 'E' and resid 106 through 116 removed outlier: 3.524A pdb=" N ILE E 116 " --> pdb=" O CYS E 112 " (cutoff:3.500A) Processing helix chain 'E' and resid 147 through 159 Processing helix chain 'E' and resid 172 through 179 Processing helix chain 'F' and resid 66 through 83 Processing helix chain 'F' and resid 96 through 107 Processing helix chain 'G' and resid 20 through 23 Processing helix chain 'G' and resid 24 through 40 removed outlier: 3.657A pdb=" N GLU G 39 " --> pdb=" O ALA G 35 " (cutoff:3.500A) Processing helix chain 'G' and resid 113 through 117 removed outlier: 3.741A pdb=" N LYS G 116 " --> pdb=" O SER G 113 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N MET G 117 " --> pdb=" O HIS G 114 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 113 through 117' Processing helix chain 'G' and resid 131 through 135 removed outlier: 4.183A pdb=" N TYR G 134 " --> pdb=" O MET G 131 " (cutoff:3.500A) Processing helix chain 'J' and resid 17 through 27 Processing helix chain 'J' and resid 30 through 38 Processing helix chain 'J' and resid 42 through 52 removed outlier: 3.746A pdb=" N HIS J 52 " --> pdb=" O MET J 48 " (cutoff:3.500A) Processing helix chain 'J' and resid 55 through 62 Processing helix chain 'K' and resid 39 through 51 removed outlier: 4.368A pdb=" N ILE K 45 " --> pdb=" O THR K 41 " (cutoff:3.500A) Processing helix chain 'K' and resid 82 through 110 Processing helix chain 'M' and resid 22 through 34 Processing helix chain 'M' and resid 63 through 76 Processing helix chain 'M' and resid 246 through 252 removed outlier: 3.946A pdb=" N ILE M 250 " --> pdb=" O THR M 246 " (cutoff:3.500A) Processing helix chain 'M' and resid 292 through 305 Processing helix chain 'M' and resid 309 through 314 Processing helix chain 'M' and resid 315 through 324 removed outlier: 3.826A pdb=" N ILE M 319 " --> pdb=" O ASP M 315 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N GLY M 324 " --> pdb=" O LYS M 320 " (cutoff:3.500A) Processing helix chain 'M' and resid 326 through 340 removed outlier: 3.740A pdb=" N GLN M 340 " --> pdb=" O LYS M 336 " (cutoff:3.500A) Processing helix chain 'M' and resid 346 through 355 removed outlier: 3.750A pdb=" N PHE M 350 " --> pdb=" O ASP M 346 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N MET M 355 " --> pdb=" O VAL M 351 " (cutoff:3.500A) Processing helix chain 'M' and resid 368 through 377 Processing helix chain 'M' and resid 403 through 408 removed outlier: 3.823A pdb=" N ASN M 407 " --> pdb=" O TYR M 403 " (cutoff:3.500A) Processing helix chain 'M' and resid 429 through 433 Processing helix chain 'M' and resid 448 through 461 removed outlier: 3.512A pdb=" N ASN M 452 " --> pdb=" O THR M 448 " (cutoff:3.500A) Processing helix chain 'M' and resid 475 through 482 removed outlier: 3.797A pdb=" N ARG M 480 " --> pdb=" O ALA M 476 " (cutoff:3.500A) Processing helix chain 'M' and resid 494 through 503 removed outlier: 3.611A pdb=" N GLY M 503 " --> pdb=" O ARG M 499 " (cutoff:3.500A) Processing helix chain 'M' and resid 510 through 520 Processing helix chain 'M' and resid 561 through 569 Processing helix chain 'M' and resid 632 through 639 Processing helix chain 'M' and resid 645 through 662 removed outlier: 4.321A pdb=" N PHE M 649 " --> pdb=" O GLU M 645 " (cutoff:3.500A) Processing helix chain 'M' and resid 666 through 675 removed outlier: 3.530A pdb=" N ALA M 670 " --> pdb=" O ASP M 666 " (cutoff:3.500A) Processing helix chain 'M' and resid 684 through 692 removed outlier: 3.727A pdb=" N LEU M 691 " --> pdb=" O VAL M 687 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N GLN M 692 " --> pdb=" O LYS M 688 " (cutoff:3.500A) Processing helix chain 'M' and resid 699 through 720 removed outlier: 3.611A pdb=" N MET M 705 " --> pdb=" O TYR M 701 " (cutoff:3.500A) Processing helix chain 'M' and resid 753 through 759 Processing helix chain 'M' and resid 788 through 792 removed outlier: 3.501A pdb=" N ILE M 792 " --> pdb=" O PRO M 789 " (cutoff:3.500A) Processing helix chain 'M' and resid 800 through 806 removed outlier: 3.672A pdb=" N LYS M 806 " --> pdb=" O HIS M 802 " (cutoff:3.500A) Processing helix chain 'M' and resid 821 through 826 Processing helix chain 'M' and resid 870 through 879 Processing helix chain 'M' and resid 884 through 899 removed outlier: 4.185A pdb=" N SER M 889 " --> pdb=" O LEU M 885 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N THR M 890 " --> pdb=" O GLY M 886 " (cutoff:3.500A) Processing helix chain 'M' and resid 905 through 920 Processing helix chain 'M' and resid 955 through 969 Processing helix chain 'M' and resid 999 through 1018 Processing helix chain 'M' and resid 1021 through 1027 removed outlier: 3.769A pdb=" N ILE M1025 " --> pdb=" O ASN M1021 " (cutoff:3.500A) Processing helix chain 'M' and resid 1040 through 1071 removed outlier: 4.239A pdb=" N TYR M1044 " --> pdb=" O ASP M1040 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N CYS M1070 " --> pdb=" O PHE M1066 " (cutoff:3.500A) Processing helix chain 'M' and resid 1072 through 1089 Processing helix chain 'M' and resid 1090 through 1093 removed outlier: 3.617A pdb=" N ARG M1093 " --> pdb=" O PRO M1090 " (cutoff:3.500A) No H-bonds generated for 'chain 'M' and resid 1090 through 1093' Processing sheet with id=AA1, first strand: chain 'A' and resid 1238 through 1239 removed outlier: 5.023A pdb=" N SER A 17 " --> pdb=" O ASP B1168 " (cutoff:3.500A) removed outlier: 4.249A pdb=" N ASP B1168 " --> pdb=" O SER A 17 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 72 through 81 removed outlier: 3.807A pdb=" N GLY A 72 " --> pdb=" O VAL A 225 " (cutoff:3.500A) removed outlier: 7.832A pdb=" N THR A 221 " --> pdb=" O PHE A 76 " (cutoff:3.500A) removed outlier: 10.382A pdb=" N TYR A 78 " --> pdb=" O GLY A 219 " (cutoff:3.500A) removed outlier: 8.990A pdb=" N GLY A 219 " --> pdb=" O TYR A 78 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 130 through 135 removed outlier: 3.931A pdb=" N GLY A 144 " --> pdb=" O THR A 135 " (cutoff:3.500A) removed outlier: 4.714A pdb=" N ILE A 145 " --> pdb=" O ILE A 191 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 316 through 318 removed outlier: 3.575A pdb=" N SER A 318 " --> pdb=" O ILE B1073 " (cutoff:3.500A) removed outlier: 4.372A pdb=" N ILE B1073 " --> pdb=" O SER A 318 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 1049 through 1051 removed outlier: 8.275A pdb=" N VAL A 434 " --> pdb=" O ARG A 323 " (cutoff:3.500A) removed outlier: 6.346A pdb=" N VAL A 325 " --> pdb=" O VAL A 434 " (cutoff:3.500A) removed outlier: 8.008A pdb=" N LEU A 436 " --> pdb=" O VAL A 325 " (cutoff:3.500A) removed outlier: 6.495A pdb=" N VAL A 327 " --> pdb=" O LEU A 436 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 348 through 349 Processing sheet with id=AA7, first strand: chain 'A' and resid 557 through 559 removed outlier: 6.560A pdb=" N VAL A 565 " --> pdb=" O LEU A 572 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 748 through 751 removed outlier: 3.513A pdb=" N GLY A 748 " --> pdb=" O ILE A 796 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 842 through 844 removed outlier: 6.573A pdb=" N ASN A 852 " --> pdb=" O LEU A 858 " (cutoff:3.500A) removed outlier: 6.345A pdb=" N LEU A 858 " --> pdb=" O ASN A 852 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 954 through 955 removed outlier: 6.720A pdb=" N LEU A 954 " --> pdb=" O VAL A1076 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 1023 through 1028 removed outlier: 3.630A pdb=" N THR A 962 " --> pdb=" O HIS A 985 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N TYR I 44 " --> pdb=" O ILE A 965 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 1082 through 1087 removed outlier: 6.942A pdb=" N THR A1112 " --> pdb=" O LYS A1083 " (cutoff:3.500A) removed outlier: 4.560A pdb=" N VAL A1085 " --> pdb=" O LYS A1110 " (cutoff:3.500A) removed outlier: 6.780A pdb=" N LYS A1110 " --> pdb=" O VAL A1085 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 1261 through 1264 Processing sheet with id=AB5, first strand: chain 'B' and resid 100 through 102 removed outlier: 5.714A pdb=" N ALA B 130 " --> pdb=" O SER B 175 " (cutoff:3.500A) removed outlier: 4.468A pdb=" N SER B 175 " --> pdb=" O ALA B 130 " (cutoff:3.500A) removed outlier: 7.145A pdb=" N ILE B 132 " --> pdb=" O ILE B 173 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N VAL B 134 " --> pdb=" O ILE B 171 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 107 through 108 Processing sheet with id=AB7, first strand: chain 'B' and resid 208 through 209 Processing sheet with id=AB8, first strand: chain 'B' and resid 398 through 401 removed outlier: 3.739A pdb=" N GLN B 220 " --> pdb=" O GLU B 401 " (cutoff:3.500A) removed outlier: 6.132A pdb=" N ALA B 219 " --> pdb=" O ARG B 494 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 229 through 231 removed outlier: 4.192A pdb=" N TRP B 235 " --> pdb=" O LEU B 252 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 539 through 540 removed outlier: 3.563A pdb=" N ARG B 629 " --> pdb=" O ILE B 662 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N GLU B 660 " --> pdb=" O LEU B 631 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 539 through 540 Processing sheet with id=AC3, first strand: chain 'B' and resid 558 through 559 removed outlier: 7.238A pdb=" N VAL B 574 " --> pdb=" O VAL B 581 " (cutoff:3.500A) removed outlier: 4.634A pdb=" N LEU B 583 " --> pdb=" O HIS B 572 " (cutoff:3.500A) removed outlier: 6.523A pdb=" N HIS B 572 " --> pdb=" O LEU B 583 " (cutoff:3.500A) removed outlier: 6.121A pdb=" N LYS B 573 " --> pdb=" O VAL B 618 " (cutoff:3.500A) removed outlier: 7.387A pdb=" N ILE B 620 " --> pdb=" O LYS B 573 " (cutoff:3.500A) removed outlier: 6.151A pdb=" N LEU B 575 " --> pdb=" O ILE B 620 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N GLU B 617 " --> pdb=" O ASP B 612 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N ASP B 612 " --> pdb=" O GLU B 617 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 742 through 745 removed outlier: 3.739A pdb=" N SER B 802 " --> pdb=" O ARG B 906 " (cutoff:3.500A) removed outlier: 4.099A pdb=" N LYS B 885 " --> pdb=" O SER B 901 " (cutoff:3.500A) removed outlier: 6.194A pdb=" N ARG B 903 " --> pdb=" O VAL B 883 " (cutoff:3.500A) removed outlier: 5.676A pdb=" N VAL B 883 " --> pdb=" O ARG B 903 " (cutoff:3.500A) removed outlier: 8.994A pdb=" N VAL B 905 " --> pdb=" O GLY B 881 " (cutoff:3.500A) removed outlier: 9.490A pdb=" N GLY B 881 " --> pdb=" O VAL B 905 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 742 through 745 removed outlier: 3.739A pdb=" N SER B 802 " --> pdb=" O ARG B 906 " (cutoff:3.500A) removed outlier: 4.099A pdb=" N LYS B 885 " --> pdb=" O SER B 901 " (cutoff:3.500A) removed outlier: 6.194A pdb=" N ARG B 903 " --> pdb=" O VAL B 883 " (cutoff:3.500A) removed outlier: 5.676A pdb=" N VAL B 883 " --> pdb=" O ARG B 903 " (cutoff:3.500A) removed outlier: 8.994A pdb=" N VAL B 905 " --> pdb=" O GLY B 881 " (cutoff:3.500A) removed outlier: 9.490A pdb=" N GLY B 881 " --> pdb=" O VAL B 905 " (cutoff:3.500A) removed outlier: 5.258A pdb=" N VAL B 886 " --> pdb=" O LYS L 39 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 1014 through 1015 removed outlier: 7.163A pdb=" N ILE B 788 " --> pdb=" O GLY B 925 " (cutoff:3.500A) removed outlier: 6.563A pdb=" N LEU B 927 " --> pdb=" O ILE B 788 " (cutoff:3.500A) removed outlier: 7.175A pdb=" N MET B 790 " --> pdb=" O LEU B 927 " (cutoff:3.500A) removed outlier: 4.582A pdb=" N PHE B1031 " --> pdb=" O VAL B 776 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 859 through 861 removed outlier: 3.612A pdb=" N ILE B 861 " --> pdb=" O ILE B 873 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 1105 through 1108 Processing sheet with id=AC9, first strand: chain 'C' and resid 11 through 17 removed outlier: 6.748A pdb=" N LYS C 23 " --> pdb=" O ARG C 15 " (cutoff:3.500A) removed outlier: 4.441A pdb=" N LEU C 17 " --> pdb=" O TYR C 21 " (cutoff:3.500A) removed outlier: 6.804A pdb=" N TYR C 21 " --> pdb=" O LEU C 17 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N ILE C 267 " --> pdb=" O MET C 189 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'C' and resid 126 through 127 removed outlier: 5.251A pdb=" N CYS C 112 " --> pdb=" O GLN C 161 " (cutoff:3.500A) removed outlier: 5.268A pdb=" N GLN C 161 " --> pdb=" O CYS C 112 " (cutoff:3.500A) removed outlier: 7.419A pdb=" N GLU C 162 " --> pdb=" O ASN C 58 " (cutoff:3.500A) removed outlier: 4.163A pdb=" N ASN C 58 " --> pdb=" O GLU C 162 " (cutoff:3.500A) removed outlier: 6.813A pdb=" N LYS C 164 " --> pdb=" O GLU C 56 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N GLU C 56 " --> pdb=" O LYS C 164 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N LEU C 52 " --> pdb=" O ILE C 168 " (cutoff:3.500A) removed outlier: 6.587A pdb=" N ARG C 170 " --> pdb=" O ILE C 50 " (cutoff:3.500A) removed outlier: 5.645A pdb=" N ILE C 50 " --> pdb=" O ARG C 170 " (cutoff:3.500A) removed outlier: 7.002A pdb=" N GLY C 172 " --> pdb=" O VAL C 48 " (cutoff:3.500A) removed outlier: 5.478A pdb=" N VAL C 48 " --> pdb=" O GLY C 172 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'C' and resid 118 through 120 removed outlier: 3.539A pdb=" N VAL C 155 " --> pdb=" O VAL C 120 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'C' and resid 193 through 196 removed outlier: 3.856A pdb=" N ASP C 193 " --> pdb=" O SER C 260 " (cutoff:3.500A) removed outlier: 4.111A pdb=" N SER C 260 " --> pdb=" O ASP C 193 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'C' and resid 221 through 224 Processing sheet with id=AD5, first strand: chain 'E' and resid 56 through 58 removed outlier: 4.077A pdb=" N ARG E 96 " --> pdb=" O GLN E 66 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N VAL E 100 " --> pdb=" O PHE E 70 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N ALA E 97 " --> pdb=" O HIS E 121 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'E' and resid 142 through 145 removed outlier: 3.704A pdb=" N GLU E 142 " --> pdb=" O ILE E 189 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N ARG E 190 " --> pdb=" O TYR E 198 " (cutoff:3.500A) removed outlier: 4.533A pdb=" N TYR E 198 " --> pdb=" O ARG E 190 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'G' and resid 6 through 14 removed outlier: 3.870A pdb=" N PHE G 75 " --> pdb=" O LEU G 7 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N VAL G 11 " --> pdb=" O PHE G 71 " (cutoff:3.500A) removed outlier: 7.021A pdb=" N ASN G 76 " --> pdb=" O LEU G 54 " (cutoff:3.500A) removed outlier: 5.871A pdb=" N LEU G 54 " --> pdb=" O ASN G 76 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'G' and resid 6 through 14 removed outlier: 3.870A pdb=" N PHE G 75 " --> pdb=" O LEU G 7 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N VAL G 11 " --> pdb=" O PHE G 71 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N GLU G 68 " --> pdb=" O LYS G 63 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'G' and resid 87 through 92 removed outlier: 7.038A pdb=" N TYR G 111 " --> pdb=" O ALA G 164 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N SER G 165 " --> pdb=" O VAL G 147 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'H' and resid 8 through 17 removed outlier: 7.038A pdb=" N GLU H 31 " --> pdb=" O ASP H 15 " (cutoff:3.500A) removed outlier: 4.776A pdb=" N LEU H 17 " --> pdb=" O ARG H 29 " (cutoff:3.500A) removed outlier: 6.953A pdb=" N ARG H 29 " --> pdb=" O LEU H 17 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N ASP H 44 " --> pdb=" O LEU H 120 " (cutoff:3.500A) removed outlier: 6.490A pdb=" N LEU H 120 " --> pdb=" O ASP H 44 " (cutoff:3.500A) removed outlier: 7.061A pdb=" N TYR H 113 " --> pdb=" O TYR H 98 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N GLN H 137 " --> pdb=" O LEU H 97 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N PHE H 8 " --> pdb=" O MET H 62 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'I' and resid 15 through 18 Processing sheet with id=AE3, first strand: chain 'I' and resid 70 through 71 removed outlier: 3.512A pdb=" N PHE I 87 " --> pdb=" O PHE I 100 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'K' and resid 19 through 23 removed outlier: 6.783A pdb=" N ILE K 72 " --> pdb=" O TYR K 61 " (cutoff:3.500A) removed outlier: 4.356A pdb=" N TYR K 61 " --> pdb=" O ILE K 72 " (cutoff:3.500A) removed outlier: 6.937A pdb=" N ARG K 74 " --> pdb=" O ALA K 59 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N ALA K 59 " --> pdb=" O ARG K 74 " (cutoff:3.500A) removed outlier: 6.503A pdb=" N HIS K 76 " --> pdb=" O LEU K 57 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'M' and resid 39 through 43 removed outlier: 3.548A pdb=" N ALA M 57 " --> pdb=" O ILE M 14 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'M' and resid 218 through 221 removed outlier: 3.866A pdb=" N MET M 218 " --> pdb=" O VAL M 195 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N LYS M 155 " --> pdb=" O PHE M 192 " (cutoff:3.500A) removed outlier: 5.837A pdb=" N CYS M 153 " --> pdb=" O ARG M 194 " (cutoff:3.500A) removed outlier: 5.565A pdb=" N TRP M 148 " --> pdb=" O GLY M 131 " (cutoff:3.500A) removed outlier: 7.642A pdb=" N GLY M 131 " --> pdb=" O TRP M 148 " (cutoff:3.500A) removed outlier: 4.076A pdb=" N GLU M 127 " --> pdb=" O VAL M 113 " (cutoff:3.500A) removed outlier: 5.357A pdb=" N ILE M 109 " --> pdb=" O GLY M 131 " (cutoff:3.500A) removed outlier: 6.884A pdb=" N ARG M 133 " --> pdb=" O ASP M 107 " (cutoff:3.500A) removed outlier: 7.030A pdb=" N ASP M 107 " --> pdb=" O ARG M 133 " (cutoff:3.500A) removed outlier: 7.332A pdb=" N TRP M 135 " --> pdb=" O ARG M 105 " (cutoff:3.500A) removed outlier: 7.486A pdb=" N ARG M 105 " --> pdb=" O TRP M 135 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N VAL M 110 " --> pdb=" O GLU M 240 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N GLU M 165 " --> pdb=" O LYS M 184 " (cutoff:3.500A) removed outlier: 7.873A pdb=" N ARG M 258 " --> pdb=" O ILE M 164 " (cutoff:3.500A) removed outlier: 6.791A pdb=" N THR M 166 " --> pdb=" O ARG M 258 " (cutoff:3.500A) removed outlier: 6.780A pdb=" N ASP M 260 " --> pdb=" O THR M 166 " (cutoff:3.500A) removed outlier: 4.550A pdb=" N SER M 168 " --> pdb=" O ASP M 260 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'M' and resid 123 through 125 removed outlier: 3.522A pdb=" N ALA M 125 " --> pdb=" O VAL M 267 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'M' and resid 391 through 400 removed outlier: 6.636A pdb=" N ARG M 383 " --> pdb=" O LEU M 394 " (cutoff:3.500A) removed outlier: 5.294A pdb=" N CYS M 381 " --> pdb=" O PRO M 396 " (cutoff:3.500A) removed outlier: 4.600A pdb=" N LEU M 398 " --> pdb=" O MET M 379 " (cutoff:3.500A) removed outlier: 6.820A pdb=" N MET M 379 " --> pdb=" O LEU M 398 " (cutoff:3.500A) removed outlier: 6.853A pdb=" N PHE M 415 " --> pdb=" O SER M 380 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N GLN M 382 " --> pdb=" O PHE M 415 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'M' and resid 438 through 439 removed outlier: 3.685A pdb=" N GLU M 439 " --> pdb=" O PHE M 442 " (cutoff:3.500A) removed outlier: 4.141A pdb=" N PHE M 442 " --> pdb=" O GLU M 439 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE9 Processing sheet with id=AF1, first strand: chain 'M' and resid 526 through 527 removed outlier: 3.545A pdb=" N VAL M 620 " --> pdb=" O ARG M 526 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N ASN M 619 " --> pdb=" O ARG M 584 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N ARG M 584 " --> pdb=" O ASN M 619 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'M' and resid 543 through 546 Processing sheet with id=AF3, first strand: chain 'M' and resid 627 through 631 removed outlier: 4.516A pdb=" N MET M 627 " --> pdb=" O ILE M 730 " (cutoff:3.500A) removed outlier: 6.319A pdb=" N GLY M 728 " --> pdb=" O CYS M 629 " (cutoff:3.500A) removed outlier: 11.549A pdb=" N LEU M 631 " --> pdb=" O PRO M 726 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'M' and resid 733 through 735 removed outlier: 6.837A pdb=" N CYS M 734 " --> pdb=" O PHE M 814 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF4 Processing sheet with id=AF5, first strand: chain 'M' and resid 745 through 746 removed outlier: 3.647A pdb=" N VAL M 746 " --> pdb=" O ASP M 796 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'M' and resid 749 through 751 removed outlier: 3.738A pdb=" N VAL M 750 " --> pdb=" O SER M 773 " (cutoff:3.500A) 1406 hydrogen bonds defined for protein. 3984 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 61 hydrogen bonds 122 hydrogen bond angles 0 basepair planarities 25 basepair parallelities 39 stacking parallelities Total time for adding SS restraints: 9.37 Time building geometry restraints manager: 3.55 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 11248 1.34 - 1.46: 5451 1.46 - 1.58: 18928 1.58 - 1.70: 108 1.70 - 1.82: 334 Bond restraints: 36069 Sorted by residual: bond pdb=" CA THR H 71 " pdb=" CB THR H 71 " ideal model delta sigma weight residual 1.522 1.531 -0.009 7.00e-03 2.04e+04 1.48e+00 bond pdb=" C3' DG Q 13 " pdb=" C2' DG Q 13 " ideal model delta sigma weight residual 1.525 1.545 -0.020 2.00e-02 2.50e+03 9.68e-01 bond pdb=" C LEU A 49 " pdb=" N PRO A 50 " ideal model delta sigma weight residual 1.334 1.356 -0.022 2.34e-02 1.83e+03 9.21e-01 bond pdb=" C3' DA Q 18 " pdb=" O3' DA Q 18 " ideal model delta sigma weight residual 1.422 1.448 -0.026 3.00e-02 1.11e+03 7.55e-01 bond pdb=" CA THR H 71 " pdb=" C THR H 71 " ideal model delta sigma weight residual 1.531 1.525 0.006 7.40e-03 1.83e+04 7.52e-01 ... (remaining 36064 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.31: 48519 1.31 - 2.62: 448 2.62 - 3.93: 140 3.93 - 5.24: 23 5.24 - 6.55: 10 Bond angle restraints: 49140 Sorted by residual: angle pdb=" N ILE M 776 " pdb=" CA ILE M 776 " pdb=" C ILE M 776 " ideal model delta sigma weight residual 113.20 109.35 3.85 9.60e-01 1.09e+00 1.61e+01 angle pdb=" C GLY A 490 " pdb=" N GLN A 491 " pdb=" CA GLN A 491 " ideal model delta sigma weight residual 121.54 127.30 -5.76 1.91e+00 2.74e-01 9.08e+00 angle pdb=" C LYS M 82 " pdb=" N THR M 83 " pdb=" CA THR M 83 " ideal model delta sigma weight residual 121.54 126.19 -4.65 1.91e+00 2.74e-01 5.92e+00 angle pdb=" C3' DA N 39 " pdb=" C2' DA N 39 " pdb=" C1' DA N 39 " ideal model delta sigma weight residual 101.60 98.02 3.58 1.50e+00 4.44e-01 5.68e+00 angle pdb=" C GLN F 107 " pdb=" N ARG F 108 " pdb=" CA ARG F 108 " ideal model delta sigma weight residual 121.54 125.70 -4.16 1.91e+00 2.74e-01 4.75e+00 ... (remaining 49135 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 25.35: 21087 25.35 - 50.70: 387 50.70 - 76.05: 124 76.05 - 101.41: 8 101.41 - 126.76: 2 Dihedral angle restraints: 21608 sinusoidal: 8330 harmonic: 13278 Sorted by residual: dihedral pdb=" C5' GTP Q 101 " pdb=" O5' GTP Q 101 " pdb=" PA GTP Q 101 " pdb=" O3A GTP Q 101 " ideal model delta sinusoidal sigma weight residual 69.27 -168.90 -121.83 1 2.00e+01 2.50e-03 3.67e+01 dihedral pdb=" C8 GTP Q 101 " pdb=" C1' GTP Q 101 " pdb=" N9 GTP Q 101 " pdb=" O4' GTP Q 101 " ideal model delta sinusoidal sigma weight residual 104.59 13.98 90.61 1 2.00e+01 2.50e-03 2.43e+01 dihedral pdb=" C4' DA Q 15 " pdb=" C3' DA Q 15 " pdb=" O3' DA Q 15 " pdb=" P DC Q 16 " ideal model delta sinusoidal sigma weight residual 220.00 93.24 126.76 1 3.50e+01 8.16e-04 1.25e+01 ... (remaining 21605 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.042: 4554 0.042 - 0.085: 761 0.085 - 0.127: 391 0.127 - 0.170: 3 0.170 - 0.212: 1 Chirality restraints: 5710 Sorted by residual: chirality pdb=" C1' GTP Q 101 " pdb=" C2' GTP Q 101 " pdb=" N9 GTP Q 101 " pdb=" O4' GTP Q 101 " both_signs ideal model delta sigma weight residual False 2.44 2.65 -0.21 2.00e-01 2.50e+01 1.13e+00 chirality pdb=" CA ILE A 529 " pdb=" N ILE A 529 " pdb=" C ILE A 529 " pdb=" CB ILE A 529 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.53e-01 chirality pdb=" CA ILE B 176 " pdb=" N ILE B 176 " pdb=" C ILE B 176 " pdb=" CB ILE B 176 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.31e-01 ... (remaining 5707 not shown) Planarity restraints: 6094 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLN A 491 " 0.013 2.00e-02 2.50e+03 2.60e-02 6.75e+00 pdb=" C GLN A 491 " -0.045 2.00e-02 2.50e+03 pdb=" O GLN A 491 " 0.017 2.00e-02 2.50e+03 pdb=" N ASP A 492 " 0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PHE M 939 " -0.021 5.00e-02 4.00e+02 3.15e-02 1.58e+00 pdb=" N PRO M 940 " 0.054 5.00e-02 4.00e+02 pdb=" CA PRO M 940 " -0.016 5.00e-02 4.00e+02 pdb=" CD PRO M 940 " -0.017 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO A 525 " -0.019 5.00e-02 4.00e+02 2.92e-02 1.37e+00 pdb=" N PRO A 526 " 0.051 5.00e-02 4.00e+02 pdb=" CA PRO A 526 " -0.015 5.00e-02 4.00e+02 pdb=" CD PRO A 526 " -0.016 5.00e-02 4.00e+02 ... (remaining 6091 not shown) Histogram of nonbonded interaction distances: 2.01 - 2.59: 194 2.59 - 3.17: 27521 3.17 - 3.74: 52059 3.74 - 4.32: 69468 4.32 - 4.90: 118276 Nonbonded interactions: 267518 Sorted by model distance: nonbonded pdb=" OD1 ASP A 449 " pdb="MG MG A1502 " model vdw 2.009 2.170 nonbonded pdb=" OD1 ASP A 447 " pdb="MG MG A1502 " model vdw 2.014 2.170 nonbonded pdb=" OD2 ASP A 447 " pdb="MG MG A1505 " model vdw 2.188 2.170 nonbonded pdb=" OD2 ASP A 447 " pdb="MG MG A1502 " model vdw 2.196 2.170 nonbonded pdb=" OD2 ASP B 786 " pdb="MG MG A1505 " model vdw 2.197 2.170 ... (remaining 267513 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 1.230 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.570 Check model and map are aligned: 0.110 Set scattering table: 0.060 Process input model: 39.670 Find NCS groups from input model: 0.390 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.200 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 43.330 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7064 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 : 0.003 0.261 36107 Z= 0.108 Angle : 0.720 45.382 49186 Z= 0.235 Chirality : 0.038 0.212 5710 Planarity : 0.003 0.031 6094 Dihedral : 10.613 126.757 12996 Min Nonbonded Distance : 2.009 Molprobity Statistics. All-atom Clashscore : 4.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer: Outliers : 0.38 % Allowed : 2.62 % Favored : 97.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.58 (0.12), residues: 4496 helix: 1.21 (0.14), residues: 1487 sheet: -0.17 (0.20), residues: 724 loop : -1.59 (0.12), residues: 2285 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 714 TYR 0.009 0.001 TYR M 451 PHE 0.007 0.001 PHE M 210 TRP 0.006 0.001 TRP B 119 HIS 0.003 0.000 HIS A 416 Details of bonding type rmsd covalent geometry : bond 0.00143 (36069) covalent geometry : angle 0.39205 (49140) hydrogen bonds : bond 0.19861 ( 1439) hydrogen bonds : angle 6.73860 ( 4106) metal coordination : bond 0.07693 ( 36) metal coordination : angle 19.73828 ( 46) Misc. bond : bond 0.00075 ( 2) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8992 Ramachandran restraints generated. 4496 Oldfield, 0 Emsley, 4496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8992 Ramachandran restraints generated. 4496 Oldfield, 0 Emsley, 4496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 778 residues out of total 4048 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 765 time to evaluate : 1.417 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 192 THR cc_start: 0.8069 (p) cc_final: 0.7830 (p) REVERT: A 269 ARG cc_start: 0.6731 (mmt180) cc_final: 0.6476 (mmt90) REVERT: A 276 TYR cc_start: 0.7840 (m-80) cc_final: 0.7454 (m-80) REVERT: A 426 ARG cc_start: 0.7542 (tpp80) cc_final: 0.7269 (tpp-160) REVERT: A 549 MET cc_start: 0.8098 (mtm) cc_final: 0.7847 (mtp) REVERT: A 616 LEU cc_start: 0.8654 (tp) cc_final: 0.8402 (tp) REVERT: A 708 TYR cc_start: 0.6929 (t80) cc_final: 0.6724 (t80) REVERT: A 1057 VAL cc_start: 0.7117 (OUTLIER) cc_final: 0.6901 (t) REVERT: B 244 LYS cc_start: 0.7387 (tptt) cc_final: 0.7163 (tmtt) REVERT: B 440 GLU cc_start: 0.8845 (mt-10) cc_final: 0.8416 (mp0) REVERT: B 692 ASP cc_start: 0.8662 (t0) cc_final: 0.8347 (t0) REVERT: B 732 THR cc_start: 0.8453 (p) cc_final: 0.8192 (p) REVERT: B 756 LEU cc_start: 0.8908 (tt) cc_final: 0.8616 (tt) REVERT: B 1107 ILE cc_start: 0.6868 (mm) cc_final: 0.6612 (mm) REVERT: B 1167 PHE cc_start: 0.7807 (m-80) cc_final: 0.7579 (m-80) REVERT: C 105 GLU cc_start: 0.8820 (tt0) cc_final: 0.8100 (tt0) REVERT: C 208 GLU cc_start: 0.8927 (mt-10) cc_final: 0.8614 (mt-10) REVERT: C 211 ASP cc_start: 0.8512 (m-30) cc_final: 0.8184 (m-30) REVERT: D 92 MET cc_start: 0.0937 (pmm) cc_final: -0.0193 (mtt) REVERT: E 14 GLN cc_start: 0.8408 (tm-30) cc_final: 0.8095 (tm-30) REVERT: E 76 LYS cc_start: 0.9147 (ptpt) cc_final: 0.8431 (tmtt) REVERT: E 96 ARG cc_start: 0.8127 (mtt180) cc_final: 0.7771 (mmm-85) REVERT: E 102 GLN cc_start: 0.8354 (mt0) cc_final: 0.7753 (mp10) REVERT: E 112 CYS cc_start: 0.8855 (t) cc_final: 0.8413 (p) REVERT: E 126 GLN cc_start: 0.7003 (mm110) cc_final: 0.6700 (mm-40) REVERT: E 127 GLU cc_start: 0.8321 (mt-10) cc_final: 0.8084 (mt-10) REVERT: E 129 GLU cc_start: 0.8910 (mt-10) cc_final: 0.8690 (tt0) REVERT: E 161 LYS cc_start: 0.8232 (mttt) cc_final: 0.7983 (mtpp) REVERT: E 189 ILE cc_start: 0.8557 (mp) cc_final: 0.8356 (mp) REVERT: F 69 GLU cc_start: 0.8435 (mt-10) cc_final: 0.8053 (mt-10) REVERT: F 114 ILE cc_start: 0.7867 (mt) cc_final: 0.7662 (mm) REVERT: F 130 GLU cc_start: 0.8480 (mt-10) cc_final: 0.8179 (mt-10) REVERT: G 24 LEU cc_start: 0.4708 (pp) cc_final: 0.4372 (mt) REVERT: G 115 MET cc_start: -0.0488 (mmm) cc_final: -0.1706 (pmm) REVERT: H 7 MET cc_start: 0.8746 (mtt) cc_final: 0.8530 (mtp) REVERT: H 48 GLU cc_start: 0.8633 (tp30) cc_final: 0.8347 (mm-30) REVERT: I 45 ARG cc_start: 0.7742 (ttt-90) cc_final: 0.7338 (ttm-80) REVERT: I 72 LYS cc_start: 0.9201 (mttt) cc_final: 0.8979 (mttm) REVERT: I 97 MET cc_start: 0.8912 (mmt) cc_final: 0.7924 (mmt) REVERT: I 104 CYS cc_start: 0.8488 (m) cc_final: 0.8175 (m) REVERT: K 89 GLN cc_start: 0.7113 (tp-100) cc_final: 0.6908 (tp-100) REVERT: L 38 TYR cc_start: 0.8090 (m-80) cc_final: 0.7835 (m-80) REVERT: M 43 GLU cc_start: 0.8552 (tt0) cc_final: 0.8275 (tt0) REVERT: M 497 ASP cc_start: 0.8797 (t0) cc_final: 0.8339 (m-30) REVERT: M 814 PHE cc_start: 0.8001 (m-80) cc_final: 0.7262 (m-80) REVERT: M 878 ASP cc_start: 0.8255 (m-30) cc_final: 0.7929 (m-30) REVERT: M 920 ASP cc_start: 0.8201 (m-30) cc_final: 0.7995 (t0) REVERT: M 951 TYR cc_start: 0.8282 (t80) cc_final: 0.7874 (t80) REVERT: M 954 GLU cc_start: 0.8634 (mt-10) cc_final: 0.7925 (tm-30) REVERT: M 1085 TYR cc_start: 0.5445 (t80) cc_final: 0.4684 (m-10) outliers start: 13 outliers final: 3 residues processed: 774 average time/residue: 0.2495 time to fit residues: 300.9180 Evaluate side-chains 441 residues out of total 4048 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 437 time to evaluate : 1.435 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 471 VAL Chi-restraints excluded: chain A residue 1057 VAL Chi-restraints excluded: chain B residue 184 LEU Chi-restraints excluded: chain E residue 168 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 454 random chunks: chunk 432 optimal weight: 9.9990 chunk 197 optimal weight: 7.9990 chunk 388 optimal weight: 6.9990 chunk 215 optimal weight: 7.9990 chunk 20 optimal weight: 8.9990 chunk 132 optimal weight: 1.9990 chunk 261 optimal weight: 8.9990 chunk 248 optimal weight: 7.9990 chunk 207 optimal weight: 5.9990 chunk 401 optimal weight: 0.9980 chunk 424 optimal weight: 8.9990 overall best weight: 4.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 41 GLN ** A 70 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 476 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 562 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 634 GLN A 658 GLN A 742 GLN A 857 GLN A1006 ASN A1008 GLN A1149 GLN A1182 HIS A1227 GLN B 66 ASN B 220 GLN B 222 GLN B 450 ASN B 477 ASN B 495 GLN B 513 HIS B 543 GLN B 600 GLN B 688 HIS B 711 HIS B 724 GLN B 749 GLN B 771 ASN B 779 HIS B 949 HIS B1042 HIS B1052 ASN ** B1091 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1106 HIS C 197 ASN D 140 GLN E 126 GLN H 94 HIS I 80 GLN I 81 HIS K 89 GLN K 104 GLN L 17 GLN L 47 GLN M 84 HIS M 298 GLN M 300 ASN M 304 HIS M 306 GLN M 340 GLN M 376 GLN M 377 ASN M 478 GLN M 567 GLN ** M 822 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 873 HIS M1059 HIS Total number of N/Q/H flips: 51 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3755 r_free = 0.3755 target = 0.113950 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3080 r_free = 0.3080 target = 0.076475 restraints weight = 85049.234| |-----------------------------------------------------------------------------| r_work (start): 0.3036 rms_B_bonded: 2.99 r_work: 0.2910 rms_B_bonded: 3.46 restraints_weight: 0.5000 r_work (final): 0.2910 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8364 moved from start: 0.2511 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.103 36107 Z= 0.260 Angle : 0.689 32.326 49186 Z= 0.327 Chirality : 0.045 0.197 5710 Planarity : 0.004 0.042 6094 Dihedral : 11.821 138.697 5529 Min Nonbonded Distance : 1.904 Molprobity Statistics. All-atom Clashscore : 5.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.40 % Favored : 95.60 % Rotamer: Outliers : 2.22 % Allowed : 8.48 % Favored : 89.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.51 (0.12), residues: 4496 helix: 1.24 (0.14), residues: 1521 sheet: -0.34 (0.20), residues: 724 loop : -1.49 (0.12), residues: 2251 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG I 30 TYR 0.027 0.002 TYR B1037 PHE 0.025 0.002 PHE C 66 TRP 0.013 0.002 TRP I 112 HIS 0.007 0.001 HIS C 177 Details of bonding type rmsd covalent geometry : bond 0.00600 (36069) covalent geometry : angle 0.62627 (49140) hydrogen bonds : bond 0.04738 ( 1439) hydrogen bonds : angle 4.90399 ( 4106) metal coordination : bond 0.01996 ( 36) metal coordination : angle 9.39017 ( 46) Misc. bond : bond 0.00346 ( 2) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8992 Ramachandran restraints generated. 4496 Oldfield, 0 Emsley, 4496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8992 Ramachandran restraints generated. 4496 Oldfield, 0 Emsley, 4496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 470 residues out of total 4048 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 394 time to evaluate : 1.445 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 46 ARG cc_start: 0.7863 (OUTLIER) cc_final: 0.7640 (mtp85) REVERT: A 130 MET cc_start: 0.7480 (ptp) cc_final: 0.7158 (mtm) REVERT: A 218 LEU cc_start: 0.8662 (mm) cc_final: 0.8331 (mm) REVERT: A 269 ARG cc_start: 0.7476 (mmt180) cc_final: 0.7042 (mmt90) REVERT: A 409 MET cc_start: 0.8634 (mmm) cc_final: 0.8266 (mmm) REVERT: A 708 TYR cc_start: 0.8456 (t80) cc_final: 0.7938 (t80) REVERT: B 440 GLU cc_start: 0.8857 (mt-10) cc_final: 0.8501 (mp0) REVERT: B 756 LEU cc_start: 0.9300 (tt) cc_final: 0.9047 (tt) REVERT: C 211 ASP cc_start: 0.8628 (m-30) cc_final: 0.8384 (m-30) REVERT: D 92 MET cc_start: 0.0308 (pmm) cc_final: -0.1148 (mtt) REVERT: E 14 GLN cc_start: 0.9045 (tm-30) cc_final: 0.8763 (tm-30) REVERT: E 48 MET cc_start: 0.7869 (mmm) cc_final: 0.7474 (mmm) REVERT: E 76 LYS cc_start: 0.9097 (ptpt) cc_final: 0.8576 (tmtt) REVERT: E 102 GLN cc_start: 0.8466 (mt0) cc_final: 0.8052 (mp10) REVERT: E 126 GLN cc_start: 0.8780 (mm-40) cc_final: 0.8407 (mm-40) REVERT: E 127 GLU cc_start: 0.8598 (mt-10) cc_final: 0.8343 (mt-10) REVERT: F 70 ARG cc_start: 0.9004 (OUTLIER) cc_final: 0.7990 (ttm-80) REVERT: F 130 GLU cc_start: 0.8927 (mt-10) cc_final: 0.8580 (mt-10) REVERT: G 22 LEU cc_start: 0.8291 (mm) cc_final: 0.8031 (tp) REVERT: G 115 MET cc_start: -0.0555 (mmm) cc_final: -0.1787 (pmm) REVERT: L 49 GLU cc_start: 0.8181 (tt0) cc_final: 0.7820 (tm-30) REVERT: M 659 MET cc_start: 0.7409 (ppp) cc_final: 0.7074 (ppp) REVERT: M 814 PHE cc_start: 0.8099 (m-80) cc_final: 0.7534 (m-80) REVERT: M 920 ASP cc_start: 0.8501 (m-30) cc_final: 0.8264 (t0) REVERT: M 937 ARG cc_start: 0.7487 (tpp-160) cc_final: 0.7239 (tpm170) REVERT: M 951 TYR cc_start: 0.8436 (t80) cc_final: 0.7948 (t80) REVERT: M 954 GLU cc_start: 0.8709 (mt-10) cc_final: 0.7991 (tm-30) REVERT: M 1047 MET cc_start: 0.9223 (ttm) cc_final: 0.9002 (ttm) REVERT: M 1060 LYS cc_start: 0.8945 (tmtt) cc_final: 0.8364 (pttt) REVERT: M 1085 TYR cc_start: 0.5019 (t80) cc_final: 0.4274 (m-80) outliers start: 76 outliers final: 50 residues processed: 452 average time/residue: 0.2331 time to fit residues: 170.0031 Evaluate side-chains 407 residues out of total 4048 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 355 time to evaluate : 1.368 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 ARG Chi-restraints excluded: chain A residue 226 THR Chi-restraints excluded: chain A residue 274 MET Chi-restraints excluded: chain A residue 281 SER Chi-restraints excluded: chain A residue 452 CYS Chi-restraints excluded: chain A residue 454 HIS Chi-restraints excluded: chain A residue 464 LYS Chi-restraints excluded: chain A residue 471 VAL Chi-restraints excluded: chain A residue 540 GLN Chi-restraints excluded: chain A residue 916 SER Chi-restraints excluded: chain A residue 1018 LEU Chi-restraints excluded: chain A residue 1020 ILE Chi-restraints excluded: chain A residue 1172 SER Chi-restraints excluded: chain A residue 1265 ILE Chi-restraints excluded: chain B residue 70 SER Chi-restraints excluded: chain B residue 176 ILE Chi-restraints excluded: chain B residue 184 LEU Chi-restraints excluded: chain B residue 202 PHE Chi-restraints excluded: chain B residue 216 VAL Chi-restraints excluded: chain B residue 522 THR Chi-restraints excluded: chain B residue 633 VAL Chi-restraints excluded: chain B residue 654 LEU Chi-restraints excluded: chain B residue 771 ASN Chi-restraints excluded: chain B residue 871 HIS Chi-restraints excluded: chain B residue 889 SER Chi-restraints excluded: chain B residue 895 LYS Chi-restraints excluded: chain B residue 1060 THR Chi-restraints excluded: chain B residue 1096 LEU Chi-restraints excluded: chain B residue 1135 VAL Chi-restraints excluded: chain C residue 41 MET Chi-restraints excluded: chain C residue 173 ILE Chi-restraints excluded: chain C residue 207 GLU Chi-restraints excluded: chain E residue 17 LEU Chi-restraints excluded: chain E residue 79 VAL Chi-restraints excluded: chain E residue 134 ILE Chi-restraints excluded: chain F residue 70 ARG Chi-restraints excluded: chain F residue 113 THR Chi-restraints excluded: chain F residue 129 ASP Chi-restraints excluded: chain G residue 54 LEU Chi-restraints excluded: chain G residue 161 MET Chi-restraints excluded: chain H residue 47 THR Chi-restraints excluded: chain H residue 137 GLN Chi-restraints excluded: chain I residue 26 LEU Chi-restraints excluded: chain I residue 31 ASN Chi-restraints excluded: chain I residue 107 ASN Chi-restraints excluded: chain J residue 2 ILE Chi-restraints excluded: chain J residue 9 THR Chi-restraints excluded: chain K residue 20 SER Chi-restraints excluded: chain M residue 59 VAL Chi-restraints excluded: chain M residue 108 ASP Chi-restraints excluded: chain M residue 239 LEU Chi-restraints excluded: chain M residue 308 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 454 random chunks: chunk 179 optimal weight: 1.9990 chunk 383 optimal weight: 10.0000 chunk 162 optimal weight: 0.9990 chunk 2 optimal weight: 20.0000 chunk 280 optimal weight: 7.9990 chunk 12 optimal weight: 6.9990 chunk 308 optimal weight: 2.9990 chunk 87 optimal weight: 8.9990 chunk 53 optimal weight: 4.9990 chunk 153 optimal weight: 10.0000 chunk 136 optimal weight: 1.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 70 HIS A 228 ASN ** A 476 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 562 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 768 ASN ** B1052 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 99 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 138 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 137 GLN M 377 ASN ** M 822 HIS ** 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 = 0.3759 r_free = 0.3759 target = 0.114257 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3086 r_free = 0.3086 target = 0.076816 restraints weight = 84901.060| |-----------------------------------------------------------------------------| r_work (start): 0.3041 rms_B_bonded: 2.97 r_work: 0.2916 rms_B_bonded: 3.44 restraints_weight: 0.5000 r_work (final): 0.2916 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8354 moved from start: 0.2754 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 1.792 36107 Z= 0.228 Angle : 0.545 13.298 49186 Z= 0.269 Chirality : 0.042 0.174 5710 Planarity : 0.004 0.044 6094 Dihedral : 11.755 137.573 5526 Min Nonbonded Distance : 1.870 Molprobity Statistics. All-atom Clashscore : 5.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.00 % Favored : 96.00 % Rotamer: Outliers : 2.22 % Allowed : 10.15 % Favored : 87.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.32 (0.13), residues: 4496 helix: 1.56 (0.14), residues: 1523 sheet: -0.29 (0.20), residues: 720 loop : -1.49 (0.12), residues: 2253 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B1061 TYR 0.019 0.001 TYR I 27 PHE 0.019 0.001 PHE C 66 TRP 0.008 0.001 TRP I 112 HIS 0.004 0.001 HIS C 177 Details of bonding type rmsd covalent geometry : bond 0.00352 (36069) covalent geometry : angle 0.51831 (49140) hydrogen bonds : bond 0.03849 ( 1439) hydrogen bonds : angle 4.56894 ( 4106) metal coordination : bond 0.29880 ( 36) metal coordination : angle 5.50995 ( 46) Misc. bond : bond 0.00201 ( 2) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8992 Ramachandran restraints generated. 4496 Oldfield, 0 Emsley, 4496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8992 Ramachandran restraints generated. 4496 Oldfield, 0 Emsley, 4496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 450 residues out of total 4048 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 374 time to evaluate : 1.365 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 46 ARG cc_start: 0.7908 (OUTLIER) cc_final: 0.7689 (mtp85) REVERT: A 269 ARG cc_start: 0.7376 (mmt180) cc_final: 0.6929 (mmt90) REVERT: A 311 ASP cc_start: 0.8543 (m-30) cc_final: 0.8334 (m-30) REVERT: A 409 MET cc_start: 0.8477 (mmm) cc_final: 0.8266 (mmm) REVERT: A 708 TYR cc_start: 0.8424 (t80) cc_final: 0.7895 (t80) REVERT: A 776 LEU cc_start: 0.9465 (mt) cc_final: 0.9254 (mt) REVERT: B 557 MET cc_start: 0.8783 (ttp) cc_final: 0.8138 (ttp) REVERT: B 756 LEU cc_start: 0.9315 (tt) cc_final: 0.9058 (tt) REVERT: C 201 MET cc_start: 0.8277 (mmm) cc_final: 0.8010 (tmm) REVERT: C 211 ASP cc_start: 0.8641 (m-30) cc_final: 0.8310 (m-30) REVERT: D 92 MET cc_start: 0.0629 (pmm) cc_final: -0.0820 (mtt) REVERT: E 14 GLN cc_start: 0.9070 (tm-30) cc_final: 0.8764 (tm-30) REVERT: E 48 MET cc_start: 0.7873 (mmm) cc_final: 0.7533 (mmt) REVERT: E 76 LYS cc_start: 0.9023 (ptpt) cc_final: 0.8576 (tmtt) REVERT: E 102 GLN cc_start: 0.8499 (mt0) cc_final: 0.8058 (mp10) REVERT: E 126 GLN cc_start: 0.8741 (mm-40) cc_final: 0.8358 (mm-40) REVERT: E 127 GLU cc_start: 0.8647 (mt-10) cc_final: 0.8340 (mt-10) REVERT: G 1 MET cc_start: 0.2174 (mpp) cc_final: 0.1238 (ptp) REVERT: G 115 MET cc_start: -0.0399 (mmm) cc_final: -0.1693 (pmm) REVERT: L 49 GLU cc_start: 0.8224 (tt0) cc_final: 0.7827 (tm-30) REVERT: M 486 MET cc_start: 0.8716 (OUTLIER) cc_final: 0.8292 (tpp) REVERT: M 814 PHE cc_start: 0.8020 (m-80) cc_final: 0.7472 (m-80) REVERT: M 920 ASP cc_start: 0.8500 (m-30) cc_final: 0.8291 (t0) REVERT: M 937 ARG cc_start: 0.7502 (tpp-160) cc_final: 0.7220 (tpm170) REVERT: M 951 TYR cc_start: 0.8501 (t80) cc_final: 0.8037 (t80) REVERT: M 954 GLU cc_start: 0.8652 (mt-10) cc_final: 0.7912 (tm-30) REVERT: M 1060 LYS cc_start: 0.8885 (tmtt) cc_final: 0.8323 (pttt) REVERT: M 1085 TYR cc_start: 0.5129 (t80) cc_final: 0.4334 (m-80) outliers start: 76 outliers final: 53 residues processed: 422 average time/residue: 0.2145 time to fit residues: 149.7977 Evaluate side-chains 410 residues out of total 4048 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 355 time to evaluate : 1.419 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 ARG Chi-restraints excluded: chain A residue 226 THR Chi-restraints excluded: chain A residue 274 MET Chi-restraints excluded: chain A residue 281 SER Chi-restraints excluded: chain A residue 452 CYS Chi-restraints excluded: chain A residue 464 LYS Chi-restraints excluded: chain A residue 471 VAL Chi-restraints excluded: chain A residue 502 VAL Chi-restraints excluded: chain A residue 533 SER Chi-restraints excluded: chain A residue 540 GLN Chi-restraints excluded: chain A residue 853 SER Chi-restraints excluded: chain A residue 916 SER Chi-restraints excluded: chain A residue 1018 LEU Chi-restraints excluded: chain A residue 1020 ILE Chi-restraints excluded: chain A residue 1172 SER Chi-restraints excluded: chain B residue 70 SER Chi-restraints excluded: chain B residue 176 ILE Chi-restraints excluded: chain B residue 184 LEU Chi-restraints excluded: chain B residue 202 PHE Chi-restraints excluded: chain B residue 247 ARG Chi-restraints excluded: chain B residue 289 SER Chi-restraints excluded: chain B residue 522 THR Chi-restraints excluded: chain B residue 633 VAL Chi-restraints excluded: chain B residue 732 THR Chi-restraints excluded: chain B residue 771 ASN Chi-restraints excluded: chain B residue 780 LEU Chi-restraints excluded: chain B residue 871 HIS Chi-restraints excluded: chain B residue 889 SER Chi-restraints excluded: chain B residue 1096 LEU Chi-restraints excluded: chain C residue 41 MET Chi-restraints excluded: chain C residue 44 GLU Chi-restraints excluded: chain D residue 93 MET Chi-restraints excluded: chain E residue 7 LEU Chi-restraints excluded: chain E residue 17 LEU Chi-restraints excluded: chain E residue 20 MET Chi-restraints excluded: chain E residue 35 MET Chi-restraints excluded: chain E residue 134 ILE Chi-restraints excluded: chain F residue 83 MET Chi-restraints excluded: chain F residue 110 ILE Chi-restraints excluded: chain F residue 113 THR Chi-restraints excluded: chain G residue 54 LEU Chi-restraints excluded: chain G residue 161 MET Chi-restraints excluded: chain H residue 20 ASP Chi-restraints excluded: chain H residue 47 THR Chi-restraints excluded: chain I residue 26 LEU Chi-restraints excluded: chain I residue 37 VAL Chi-restraints excluded: chain K residue 20 SER Chi-restraints excluded: chain M residue 22 VAL Chi-restraints excluded: chain M residue 59 VAL Chi-restraints excluded: chain M residue 239 LEU Chi-restraints excluded: chain M residue 486 MET Chi-restraints excluded: chain M residue 608 MET Chi-restraints excluded: chain M residue 631 LEU Chi-restraints excluded: chain M residue 872 ILE Chi-restraints excluded: chain M residue 1029 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 454 random chunks: chunk 104 optimal weight: 6.9990 chunk 76 optimal weight: 7.9990 chunk 166 optimal weight: 7.9990 chunk 379 optimal weight: 0.0570 chunk 409 optimal weight: 6.9990 chunk 93 optimal weight: 3.9990 chunk 286 optimal weight: 6.9990 chunk 50 optimal weight: 3.9990 chunk 430 optimal weight: 9.9990 chunk 139 optimal weight: 10.0000 chunk 292 optimal weight: 20.0000 overall best weight: 4.4106 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 70 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 476 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 562 ASN A 910 ASN B 771 ASN B1052 ASN ** B1091 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 284 ASN ** D 99 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 138 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 76 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 478 GLN ** M 822 HIS ** 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 = 0.3741 r_free = 0.3741 target = 0.112740 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3071 r_free = 0.3071 target = 0.075806 restraints weight = 82157.127| |-----------------------------------------------------------------------------| r_work (start): 0.3018 rms_B_bonded: 2.87 r_work: 0.2893 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work (final): 0.2893 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8406 moved from start: 0.3340 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.329 36107 Z= 0.241 Angle : 0.613 11.961 49186 Z= 0.306 Chirality : 0.044 0.185 5710 Planarity : 0.004 0.043 6094 Dihedral : 11.833 138.600 5526 Min Nonbonded Distance : 1.662 Molprobity Statistics. All-atom Clashscore : 5.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.98 % Favored : 95.02 % Rotamer: Outliers : 3.12 % Allowed : 10.35 % Favored : 86.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.38 (0.13), residues: 4496 helix: 1.52 (0.14), residues: 1525 sheet: -0.41 (0.19), residues: 757 loop : -1.51 (0.12), residues: 2214 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG E 88 TYR 0.019 0.001 TYR H 91 PHE 0.026 0.002 PHE G 36 TRP 0.011 0.001 TRP I 112 HIS 0.026 0.001 HIS A 70 Details of bonding type rmsd covalent geometry : bond 0.00559 (36069) covalent geometry : angle 0.58839 (49140) hydrogen bonds : bond 0.04180 ( 1439) hydrogen bonds : angle 4.55653 ( 4106) metal coordination : bond 0.05652 ( 36) metal coordination : angle 5.70962 ( 46) Misc. bond : bond 0.00239 ( 2) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8992 Ramachandran restraints generated. 4496 Oldfield, 0 Emsley, 4496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8992 Ramachandran restraints generated. 4496 Oldfield, 0 Emsley, 4496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 473 residues out of total 4048 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 107 poor density : 366 time to evaluate : 1.446 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 46 ARG cc_start: 0.7930 (OUTLIER) cc_final: 0.7703 (mtp85) REVERT: A 130 MET cc_start: 0.7781 (ptp) cc_final: 0.7340 (mtm) REVERT: A 218 LEU cc_start: 0.8573 (mm) cc_final: 0.8222 (mm) REVERT: A 269 ARG cc_start: 0.7534 (mmt180) cc_final: 0.6976 (mmt90) REVERT: A 311 ASP cc_start: 0.8513 (m-30) cc_final: 0.8287 (m-30) REVERT: A 409 MET cc_start: 0.8779 (mmm) cc_final: 0.8533 (mmm) REVERT: A 708 TYR cc_start: 0.8480 (t80) cc_final: 0.7911 (t80) REVERT: A 964 MET cc_start: 0.8468 (OUTLIER) cc_final: 0.8189 (ptm) REVERT: B 184 LEU cc_start: 0.9425 (OUTLIER) cc_final: 0.9109 (pp) REVERT: B 441 HIS cc_start: 0.7756 (t-90) cc_final: 0.7466 (t-170) REVERT: B 557 MET cc_start: 0.8856 (ttp) cc_final: 0.8320 (ttp) REVERT: B 756 LEU cc_start: 0.9378 (tt) cc_final: 0.9152 (tt) REVERT: C 211 ASP cc_start: 0.8691 (m-30) cc_final: 0.8418 (m-30) REVERT: D 92 MET cc_start: 0.0149 (pmm) cc_final: -0.0675 (mtt) REVERT: D 191 LEU cc_start: 0.5958 (tt) cc_final: 0.5507 (mp) REVERT: E 14 GLN cc_start: 0.9100 (tm-30) cc_final: 0.8721 (tm-30) REVERT: E 76 LYS cc_start: 0.9045 (ptpt) cc_final: 0.8564 (tmtt) REVERT: E 126 GLN cc_start: 0.8866 (mm-40) cc_final: 0.8373 (mm-40) REVERT: F 70 ARG cc_start: 0.8949 (OUTLIER) cc_final: 0.7857 (ttm-80) REVERT: F 130 GLU cc_start: 0.8914 (mt-10) cc_final: 0.8546 (mt-10) REVERT: G 1 MET cc_start: 0.2313 (mpp) cc_final: 0.1442 (ptp) REVERT: G 115 MET cc_start: -0.0166 (mmm) cc_final: -0.1615 (pmm) REVERT: H 24 PHE cc_start: 0.7750 (m-80) cc_final: 0.7449 (m-80) REVERT: L 49 GLU cc_start: 0.8301 (tt0) cc_final: 0.7971 (tm-30) REVERT: M 216 ASP cc_start: 0.8396 (m-30) cc_final: 0.7972 (p0) REVERT: M 378 ILE cc_start: 0.8646 (mm) cc_final: 0.8274 (mp) REVERT: M 416 MET cc_start: 0.8569 (ttp) cc_final: 0.8164 (ttm) REVERT: M 486 MET cc_start: 0.8624 (OUTLIER) cc_final: 0.8337 (tpp) REVERT: M 617 MET cc_start: 0.8691 (tpp) cc_final: 0.8488 (tpp) REVERT: M 814 PHE cc_start: 0.8058 (m-80) cc_final: 0.7672 (m-80) REVERT: M 954 GLU cc_start: 0.8737 (mt-10) cc_final: 0.7905 (tm-30) outliers start: 107 outliers final: 71 residues processed: 435 average time/residue: 0.2196 time to fit residues: 157.7848 Evaluate side-chains 407 residues out of total 4048 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 331 time to evaluate : 1.206 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 ARG Chi-restraints excluded: chain A residue 81 ILE Chi-restraints excluded: chain A residue 226 THR Chi-restraints excluded: chain A residue 271 MET Chi-restraints excluded: chain A residue 274 MET Chi-restraints excluded: chain A residue 281 SER Chi-restraints excluded: chain A residue 314 LEU Chi-restraints excluded: chain A residue 452 CYS Chi-restraints excluded: chain A residue 454 HIS Chi-restraints excluded: chain A residue 464 LYS Chi-restraints excluded: chain A residue 471 VAL Chi-restraints excluded: chain A residue 502 VAL Chi-restraints excluded: chain A residue 533 SER Chi-restraints excluded: chain A residue 540 GLN Chi-restraints excluded: chain A residue 853 SER Chi-restraints excluded: chain A residue 916 SER Chi-restraints excluded: chain A residue 960 VAL Chi-restraints excluded: chain A residue 964 MET Chi-restraints excluded: chain A residue 1018 LEU Chi-restraints excluded: chain A residue 1057 VAL Chi-restraints excluded: chain A residue 1071 LEU Chi-restraints excluded: chain A residue 1172 SER Chi-restraints excluded: chain B residue 70 SER Chi-restraints excluded: chain B residue 176 ILE Chi-restraints excluded: chain B residue 184 LEU Chi-restraints excluded: chain B residue 202 PHE Chi-restraints excluded: chain B residue 247 ARG Chi-restraints excluded: chain B residue 289 SER Chi-restraints excluded: chain B residue 295 MET Chi-restraints excluded: chain B residue 568 LEU Chi-restraints excluded: chain B residue 633 VAL Chi-restraints excluded: chain B residue 732 THR Chi-restraints excluded: chain B residue 771 ASN Chi-restraints excluded: chain B residue 780 LEU Chi-restraints excluded: chain B residue 871 HIS Chi-restraints excluded: chain B residue 889 SER Chi-restraints excluded: chain B residue 1052 ASN Chi-restraints excluded: chain B residue 1060 THR Chi-restraints excluded: chain B residue 1096 LEU Chi-restraints excluded: chain C residue 41 MET Chi-restraints excluded: chain C residue 44 GLU Chi-restraints excluded: chain C residue 173 ILE Chi-restraints excluded: chain C residue 185 THR Chi-restraints excluded: chain C residue 207 GLU Chi-restraints excluded: chain C residue 226 VAL Chi-restraints excluded: chain E residue 7 LEU Chi-restraints excluded: chain E residue 20 MET Chi-restraints excluded: chain E residue 35 MET Chi-restraints excluded: chain E residue 53 LEU Chi-restraints excluded: chain E residue 134 ILE Chi-restraints excluded: chain F residue 70 ARG Chi-restraints excluded: chain F residue 95 THR Chi-restraints excluded: chain G residue 32 LEU Chi-restraints excluded: chain G residue 33 LEU Chi-restraints excluded: chain G residue 48 LEU Chi-restraints excluded: chain G residue 54 LEU Chi-restraints excluded: chain G residue 147 VAL Chi-restraints excluded: chain G residue 161 MET Chi-restraints excluded: chain H residue 47 THR Chi-restraints excluded: chain I residue 26 LEU Chi-restraints excluded: chain I residue 37 VAL Chi-restraints excluded: chain I residue 77 SER Chi-restraints excluded: chain I residue 98 THR Chi-restraints excluded: chain I residue 107 ASN Chi-restraints excluded: chain J residue 2 ILE Chi-restraints excluded: chain J residue 9 THR Chi-restraints excluded: chain K residue 20 SER Chi-restraints excluded: chain M residue 59 VAL Chi-restraints excluded: chain M residue 108 ASP Chi-restraints excluded: chain M residue 130 ASP Chi-restraints excluded: chain M residue 446 SER Chi-restraints excluded: chain M residue 486 MET Chi-restraints excluded: chain M residue 544 VAL Chi-restraints excluded: chain M residue 608 MET Chi-restraints excluded: chain M residue 872 ILE Chi-restraints excluded: chain M residue 1029 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 454 random chunks: chunk 367 optimal weight: 9.9990 chunk 27 optimal weight: 1.9990 chunk 52 optimal weight: 0.8980 chunk 213 optimal weight: 3.9990 chunk 35 optimal weight: 6.9990 chunk 294 optimal weight: 0.8980 chunk 45 optimal weight: 5.9990 chunk 442 optimal weight: 20.0000 chunk 200 optimal weight: 0.1980 chunk 413 optimal weight: 10.0000 chunk 268 optimal weight: 2.9990 overall best weight: 1.3984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 70 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 476 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 381 ASN B 724 GLN B1052 ASN ** D 138 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 300 ASN ** M 822 HIS ** 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 = 0.3778 r_free = 0.3778 target = 0.114316 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3122 r_free = 0.3122 target = 0.077398 restraints weight = 83455.614| |-----------------------------------------------------------------------------| r_work (start): 0.3071 rms_B_bonded: 2.84 r_work: 0.2946 rms_B_bonded: 3.32 restraints_weight: 0.5000 r_work (final): 0.2946 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8394 moved from start: 0.3341 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.255 36107 Z= 0.113 Angle : 0.520 9.945 49186 Z= 0.259 Chirality : 0.041 0.197 5710 Planarity : 0.003 0.036 6094 Dihedral : 11.742 137.965 5526 Min Nonbonded Distance : 1.838 Molprobity Statistics. All-atom Clashscore : 5.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.00 % Favored : 96.00 % Rotamer: Outliers : 2.48 % Allowed : 11.55 % Favored : 85.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.18 (0.13), residues: 4496 helix: 1.71 (0.14), residues: 1535 sheet: -0.21 (0.19), residues: 728 loop : -1.46 (0.12), residues: 2233 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 445 TYR 0.014 0.001 TYR J 43 PHE 0.018 0.001 PHE G 36 TRP 0.007 0.001 TRP B 119 HIS 0.015 0.001 HIS A 70 Details of bonding type rmsd covalent geometry : bond 0.00248 (36069) covalent geometry : angle 0.50076 (49140) hydrogen bonds : bond 0.03328 ( 1439) hydrogen bonds : angle 4.33092 ( 4106) metal coordination : bond 0.04324 ( 36) metal coordination : angle 4.62243 ( 46) Misc. bond : bond 0.00152 ( 2) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8992 Ramachandran restraints generated. 4496 Oldfield, 0 Emsley, 4496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8992 Ramachandran restraints generated. 4496 Oldfield, 0 Emsley, 4496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 447 residues out of total 4048 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 362 time to evaluate : 1.523 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 46 ARG cc_start: 0.8263 (OUTLIER) cc_final: 0.7917 (mtp85) REVERT: A 130 MET cc_start: 0.7694 (ptp) cc_final: 0.7085 (mtm) REVERT: A 218 LEU cc_start: 0.8552 (mm) cc_final: 0.8174 (mm) REVERT: A 269 ARG cc_start: 0.7556 (mmt180) cc_final: 0.6975 (mmt90) REVERT: A 311 ASP cc_start: 0.8488 (m-30) cc_final: 0.8270 (m-30) REVERT: A 466 GLU cc_start: 0.8811 (pt0) cc_final: 0.8450 (tm-30) REVERT: A 568 ASN cc_start: 0.8884 (t0) cc_final: 0.8634 (t0) REVERT: A 708 TYR cc_start: 0.8433 (t80) cc_final: 0.7952 (t80) REVERT: A 964 MET cc_start: 0.8443 (OUTLIER) cc_final: 0.8211 (ptm) REVERT: A 1217 PHE cc_start: 0.8270 (OUTLIER) cc_final: 0.7994 (m-80) REVERT: A 1261 GLN cc_start: 0.9338 (OUTLIER) cc_final: 0.7625 (pm20) REVERT: B 184 LEU cc_start: 0.9305 (OUTLIER) cc_final: 0.9026 (pp) REVERT: B 557 MET cc_start: 0.8785 (ttp) cc_final: 0.8232 (ttp) REVERT: B 1083 LEU cc_start: 0.9303 (OUTLIER) cc_final: 0.8907 (mt) REVERT: C 201 MET cc_start: 0.7670 (tmm) cc_final: 0.7446 (tmm) REVERT: C 211 ASP cc_start: 0.8671 (m-30) cc_final: 0.8388 (m-30) REVERT: D 92 MET cc_start: 0.0194 (pmm) cc_final: -0.0548 (mtt) REVERT: D 191 LEU cc_start: 0.5841 (tt) cc_final: 0.5546 (mp) REVERT: E 14 GLN cc_start: 0.9066 (tm-30) cc_final: 0.8682 (tm-30) REVERT: E 48 MET cc_start: 0.7638 (mmm) cc_final: 0.6960 (mmm) REVERT: E 76 LYS cc_start: 0.9013 (ptpt) cc_final: 0.8594 (tmtt) REVERT: E 126 GLN cc_start: 0.8778 (mm-40) cc_final: 0.8315 (mm-40) REVERT: F 70 ARG cc_start: 0.8972 (OUTLIER) cc_final: 0.7900 (ttm-80) REVERT: F 130 GLU cc_start: 0.8890 (mt-10) cc_final: 0.8545 (mt-10) REVERT: G 1 MET cc_start: 0.2128 (mpp) cc_final: 0.1198 (ptp) REVERT: G 115 MET cc_start: -0.0310 (mmm) cc_final: -0.1601 (pmm) REVERT: H 24 PHE cc_start: 0.7679 (m-80) cc_final: 0.7442 (m-80) REVERT: L 49 GLU cc_start: 0.7992 (tt0) cc_final: 0.7668 (tm-30) REVERT: M 325 MET cc_start: 0.6923 (ptm) cc_final: 0.6673 (ptm) REVERT: M 378 ILE cc_start: 0.8677 (mm) cc_final: 0.8243 (mp) REVERT: M 486 MET cc_start: 0.8688 (OUTLIER) cc_final: 0.7969 (tpp) REVERT: M 814 PHE cc_start: 0.7990 (m-80) cc_final: 0.7598 (m-80) REVERT: M 954 GLU cc_start: 0.8688 (mt-10) cc_final: 0.7856 (tm-30) REVERT: M 1060 LYS cc_start: 0.9078 (tmtt) cc_final: 0.8583 (ttpt) outliers start: 85 outliers final: 55 residues processed: 416 average time/residue: 0.2231 time to fit residues: 151.9797 Evaluate side-chains 410 residues out of total 4048 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 347 time to evaluate : 1.367 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 ARG Chi-restraints excluded: chain A residue 81 ILE Chi-restraints excluded: chain A residue 271 MET Chi-restraints excluded: chain A residue 274 MET Chi-restraints excluded: chain A residue 314 LEU Chi-restraints excluded: chain A residue 454 HIS Chi-restraints excluded: chain A residue 464 LYS Chi-restraints excluded: chain A residue 471 VAL Chi-restraints excluded: chain A residue 533 SER Chi-restraints excluded: chain A residue 540 GLN Chi-restraints excluded: chain A residue 853 SER Chi-restraints excluded: chain A residue 916 SER Chi-restraints excluded: chain A residue 964 MET Chi-restraints excluded: chain A residue 1018 LEU Chi-restraints excluded: chain A residue 1217 PHE Chi-restraints excluded: chain A residue 1261 GLN Chi-restraints excluded: chain B residue 176 ILE Chi-restraints excluded: chain B residue 184 LEU Chi-restraints excluded: chain B residue 202 PHE Chi-restraints excluded: chain B residue 247 ARG Chi-restraints excluded: chain B residue 277 ILE Chi-restraints excluded: chain B residue 522 THR Chi-restraints excluded: chain B residue 568 LEU Chi-restraints excluded: chain B residue 633 VAL Chi-restraints excluded: chain B residue 771 ASN Chi-restraints excluded: chain B residue 871 HIS Chi-restraints excluded: chain B residue 889 SER Chi-restraints excluded: chain B residue 1052 ASN Chi-restraints excluded: chain B residue 1077 GLU Chi-restraints excluded: chain B residue 1083 LEU Chi-restraints excluded: chain B residue 1089 SER Chi-restraints excluded: chain B residue 1096 LEU Chi-restraints excluded: chain B residue 1113 THR Chi-restraints excluded: chain B residue 1161 MET Chi-restraints excluded: chain C residue 41 MET Chi-restraints excluded: chain C residue 44 GLU Chi-restraints excluded: chain C residue 226 VAL Chi-restraints excluded: chain D residue 93 MET Chi-restraints excluded: chain E residue 7 LEU Chi-restraints excluded: chain E residue 35 MET Chi-restraints excluded: chain E residue 118 SER Chi-restraints excluded: chain F residue 70 ARG Chi-restraints excluded: chain F residue 113 THR Chi-restraints excluded: chain G residue 32 LEU Chi-restraints excluded: chain G residue 33 LEU Chi-restraints excluded: chain G residue 147 VAL Chi-restraints excluded: chain G residue 161 MET Chi-restraints excluded: chain H residue 20 ASP Chi-restraints excluded: chain I residue 26 LEU Chi-restraints excluded: chain I residue 37 VAL Chi-restraints excluded: chain J residue 2 ILE Chi-restraints excluded: chain J residue 9 THR Chi-restraints excluded: chain K residue 20 SER Chi-restraints excluded: chain M residue 22 VAL Chi-restraints excluded: chain M residue 59 VAL Chi-restraints excluded: chain M residue 108 ASP Chi-restraints excluded: chain M residue 130 ASP Chi-restraints excluded: chain M residue 239 LEU Chi-restraints excluded: chain M residue 446 SER Chi-restraints excluded: chain M residue 486 MET Chi-restraints excluded: chain M residue 544 VAL Chi-restraints excluded: chain M residue 872 ILE Chi-restraints excluded: chain M residue 1029 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 454 random chunks: chunk 97 optimal weight: 6.9990 chunk 420 optimal weight: 50.0000 chunk 110 optimal weight: 10.0000 chunk 248 optimal weight: 7.9990 chunk 136 optimal weight: 9.9990 chunk 112 optimal weight: 2.9990 chunk 440 optimal weight: 30.0000 chunk 42 optimal weight: 0.0870 chunk 173 optimal weight: 7.9990 chunk 156 optimal weight: 6.9990 chunk 87 optimal weight: 3.9990 overall best weight: 4.2166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 70 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 476 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 381 ASN B 652 HIS B 656 HIS B 771 ASN B1052 ASN ** C 229 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 138 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 76 HIS M 482 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3757 r_free = 0.3757 target = 0.112693 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3089 r_free = 0.3089 target = 0.075597 restraints weight = 83419.855| |-----------------------------------------------------------------------------| r_work (start): 0.3046 rms_B_bonded: 2.84 r_work: 0.2922 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.2922 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8466 moved from start: 0.3686 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.198 36107 Z= 0.229 Angle : 0.599 9.270 49186 Z= 0.299 Chirality : 0.044 0.192 5710 Planarity : 0.004 0.039 6094 Dihedral : 11.803 139.181 5526 Min Nonbonded Distance : 1.888 Molprobity Statistics. All-atom Clashscore : 6.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.14 % Favored : 94.86 % Rotamer: Outliers : 2.65 % Allowed : 11.66 % Favored : 85.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.27 (0.13), residues: 4496 helix: 1.63 (0.14), residues: 1535 sheet: -0.38 (0.19), residues: 749 loop : -1.45 (0.12), residues: 2212 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 954 TYR 0.016 0.001 TYR H 91 PHE 0.025 0.002 PHE G 36 TRP 0.010 0.001 TRP I 112 HIS 0.012 0.001 HIS A 70 Details of bonding type rmsd covalent geometry : bond 0.00531 (36069) covalent geometry : angle 0.58013 (49140) hydrogen bonds : bond 0.03938 ( 1439) hydrogen bonds : angle 4.44026 ( 4106) metal coordination : bond 0.03415 ( 36) metal coordination : angle 4.93043 ( 46) Misc. bond : bond 0.00222 ( 2) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8992 Ramachandran restraints generated. 4496 Oldfield, 0 Emsley, 4496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8992 Ramachandran restraints generated. 4496 Oldfield, 0 Emsley, 4496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 423 residues out of total 4048 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 332 time to evaluate : 1.425 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 46 ARG cc_start: 0.8238 (OUTLIER) cc_final: 0.8011 (mtp85) REVERT: A 71 PHE cc_start: 0.7566 (OUTLIER) cc_final: 0.5424 (m-80) REVERT: A 218 LEU cc_start: 0.8461 (mm) cc_final: 0.8078 (mm) REVERT: A 269 ARG cc_start: 0.7664 (mmt180) cc_final: 0.7136 (mmt90) REVERT: A 311 ASP cc_start: 0.8494 (m-30) cc_final: 0.8289 (m-30) REVERT: A 462 GLN cc_start: 0.9014 (OUTLIER) cc_final: 0.8601 (mp10) REVERT: A 518 MET cc_start: 0.9188 (mtp) cc_final: 0.8824 (mtt) REVERT: A 568 ASN cc_start: 0.8921 (t0) cc_final: 0.8714 (t0) REVERT: A 708 TYR cc_start: 0.8565 (t80) cc_final: 0.8051 (t80) REVERT: A 964 MET cc_start: 0.8412 (OUTLIER) cc_final: 0.8196 (ptm) REVERT: A 1099 ASN cc_start: 0.8562 (m-40) cc_final: 0.8332 (p0) REVERT: A 1261 GLN cc_start: 0.9389 (OUTLIER) cc_final: 0.7711 (pm20) REVERT: B 184 LEU cc_start: 0.9371 (OUTLIER) cc_final: 0.9080 (pp) REVERT: B 557 MET cc_start: 0.8818 (ttp) cc_final: 0.8304 (ttp) REVERT: C 197 ASN cc_start: 0.8784 (OUTLIER) cc_final: 0.8556 (t0) REVERT: D 92 MET cc_start: 0.0193 (pmm) cc_final: -0.0504 (mtt) REVERT: D 191 LEU cc_start: 0.5987 (tt) cc_final: 0.5680 (mp) REVERT: E 14 GLN cc_start: 0.9031 (tm-30) cc_final: 0.8630 (tm-30) REVERT: E 76 LYS cc_start: 0.9044 (ptpt) cc_final: 0.8630 (tmtt) REVERT: E 126 GLN cc_start: 0.8889 (mm-40) cc_final: 0.8528 (mm-40) REVERT: F 70 ARG cc_start: 0.9027 (OUTLIER) cc_final: 0.7924 (ttm-80) REVERT: F 102 MET cc_start: 0.8693 (tpp) cc_final: 0.8466 (mmm) REVERT: F 130 GLU cc_start: 0.8882 (mt-10) cc_final: 0.8548 (mt-10) REVERT: G 1 MET cc_start: 0.2010 (mpp) cc_final: 0.1150 (ptp) REVERT: G 115 MET cc_start: -0.0101 (mmm) cc_final: -0.1488 (pmm) REVERT: L 49 GLU cc_start: 0.8065 (tt0) cc_final: 0.7791 (tm-30) REVERT: M 378 ILE cc_start: 0.8727 (mm) cc_final: 0.8287 (mp) REVERT: M 416 MET cc_start: 0.8630 (ttp) cc_final: 0.8159 (ttm) REVERT: M 486 MET cc_start: 0.8586 (OUTLIER) cc_final: 0.8007 (tpp) REVERT: M 814 PHE cc_start: 0.7980 (m-80) cc_final: 0.7615 (m-80) REVERT: M 954 GLU cc_start: 0.8740 (mt-10) cc_final: 0.7704 (tm-30) REVERT: M 1060 LYS cc_start: 0.9045 (tmtt) cc_final: 0.8518 (pttt) outliers start: 91 outliers final: 71 residues processed: 399 average time/residue: 0.2186 time to fit residues: 143.4887 Evaluate side-chains 406 residues out of total 4048 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 326 time to evaluate : 1.390 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 46 ARG Chi-restraints excluded: chain A residue 71 PHE Chi-restraints excluded: chain A residue 81 ILE Chi-restraints excluded: chain A residue 226 THR Chi-restraints excluded: chain A residue 271 MET Chi-restraints excluded: chain A residue 274 MET Chi-restraints excluded: chain A residue 281 SER Chi-restraints excluded: chain A residue 314 LEU Chi-restraints excluded: chain A residue 452 CYS Chi-restraints excluded: chain A residue 454 HIS Chi-restraints excluded: chain A residue 462 GLN Chi-restraints excluded: chain A residue 464 LYS Chi-restraints excluded: chain A residue 471 VAL Chi-restraints excluded: chain A residue 502 VAL Chi-restraints excluded: chain A residue 540 GLN Chi-restraints excluded: chain A residue 853 SER Chi-restraints excluded: chain A residue 916 SER Chi-restraints excluded: chain A residue 964 MET Chi-restraints excluded: chain A residue 1018 LEU Chi-restraints excluded: chain A residue 1057 VAL Chi-restraints excluded: chain A residue 1071 LEU Chi-restraints excluded: chain A residue 1172 SER Chi-restraints excluded: chain A residue 1261 GLN Chi-restraints excluded: chain B residue 70 SER Chi-restraints excluded: chain B residue 176 ILE Chi-restraints excluded: chain B residue 184 LEU Chi-restraints excluded: chain B residue 202 PHE Chi-restraints excluded: chain B residue 247 ARG Chi-restraints excluded: chain B residue 289 SER Chi-restraints excluded: chain B residue 295 MET Chi-restraints excluded: chain B residue 522 THR Chi-restraints excluded: chain B residue 568 LEU Chi-restraints excluded: chain B residue 633 VAL Chi-restraints excluded: chain B residue 771 ASN Chi-restraints excluded: chain B residue 780 LEU Chi-restraints excluded: chain B residue 871 HIS Chi-restraints excluded: chain B residue 889 SER Chi-restraints excluded: chain B residue 1060 THR Chi-restraints excluded: chain B residue 1096 LEU Chi-restraints excluded: chain B residue 1113 THR Chi-restraints excluded: chain C residue 41 MET Chi-restraints excluded: chain C residue 44 GLU Chi-restraints excluded: chain C residue 173 ILE Chi-restraints excluded: chain C residue 185 THR Chi-restraints excluded: chain C residue 197 ASN Chi-restraints excluded: chain C residue 226 VAL Chi-restraints excluded: chain D residue 93 MET Chi-restraints excluded: chain E residue 7 LEU Chi-restraints excluded: chain E residue 35 MET Chi-restraints excluded: chain E residue 118 SER Chi-restraints excluded: chain E residue 134 ILE Chi-restraints excluded: chain F residue 70 ARG Chi-restraints excluded: chain F residue 82 SER Chi-restraints excluded: chain F residue 113 THR Chi-restraints excluded: chain G residue 32 LEU Chi-restraints excluded: chain G residue 33 LEU Chi-restraints excluded: chain G residue 54 LEU Chi-restraints excluded: chain G residue 68 GLU Chi-restraints excluded: chain G residue 147 VAL Chi-restraints excluded: chain G residue 161 MET Chi-restraints excluded: chain H residue 47 THR Chi-restraints excluded: chain I residue 26 LEU Chi-restraints excluded: chain I residue 37 VAL Chi-restraints excluded: chain I residue 77 SER Chi-restraints excluded: chain J residue 2 ILE Chi-restraints excluded: chain J residue 9 THR Chi-restraints excluded: chain K residue 20 SER Chi-restraints excluded: chain M residue 22 VAL Chi-restraints excluded: chain M residue 59 VAL Chi-restraints excluded: chain M residue 108 ASP Chi-restraints excluded: chain M residue 130 ASP Chi-restraints excluded: chain M residue 446 SER Chi-restraints excluded: chain M residue 486 MET Chi-restraints excluded: chain M residue 544 VAL Chi-restraints excluded: chain M residue 631 LEU Chi-restraints excluded: chain M residue 658 SER Chi-restraints excluded: chain M residue 663 MET Chi-restraints excluded: chain M residue 872 ILE Chi-restraints excluded: chain M residue 1029 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 454 random chunks: chunk 10 optimal weight: 7.9990 chunk 238 optimal weight: 0.9980 chunk 13 optimal weight: 7.9990 chunk 156 optimal weight: 0.8980 chunk 367 optimal weight: 20.0000 chunk 365 optimal weight: 9.9990 chunk 86 optimal weight: 5.9990 chunk 227 optimal weight: 0.9990 chunk 22 optimal weight: 20.0000 chunk 66 optimal weight: 0.9990 chunk 418 optimal weight: 30.0000 overall best weight: 1.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 70 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 476 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 441 HIS B 656 HIS B1052 ASN ** D 138 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 76 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3778 r_free = 0.3778 target = 0.113977 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3121 r_free = 0.3121 target = 0.077044 restraints weight = 82998.965| |-----------------------------------------------------------------------------| r_work (start): 0.3080 rms_B_bonded: 2.83 r_work: 0.2955 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work (final): 0.2955 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8432 moved from start: 0.3688 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.149 36107 Z= 0.128 Angle : 0.541 18.694 49186 Z= 0.268 Chirality : 0.041 0.183 5710 Planarity : 0.003 0.037 6094 Dihedral : 11.758 138.799 5526 Min Nonbonded Distance : 1.975 Molprobity Statistics. All-atom Clashscore : 5.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.47 % Favored : 95.53 % Rotamer: Outliers : 2.42 % Allowed : 12.39 % Favored : 85.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.15 (0.13), residues: 4496 helix: 1.72 (0.14), residues: 1537 sheet: -0.23 (0.20), residues: 721 loop : -1.41 (0.12), residues: 2238 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 445 TYR 0.013 0.001 TYR A 793 PHE 0.019 0.001 PHE G 36 TRP 0.007 0.001 TRP B 119 HIS 0.009 0.001 HIS A 70 Details of bonding type rmsd covalent geometry : bond 0.00291 (36069) covalent geometry : angle 0.52601 (49140) hydrogen bonds : bond 0.03359 ( 1439) hydrogen bonds : angle 4.30857 ( 4106) metal coordination : bond 0.02572 ( 36) metal coordination : angle 4.10951 ( 46) Misc. bond : bond 0.00173 ( 2) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8992 Ramachandran restraints generated. 4496 Oldfield, 0 Emsley, 4496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8992 Ramachandran restraints generated. 4496 Oldfield, 0 Emsley, 4496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 423 residues out of total 4048 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 340 time to evaluate : 1.467 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 71 PHE cc_start: 0.7576 (OUTLIER) cc_final: 0.5405 (m-80) REVERT: A 218 LEU cc_start: 0.8481 (mm) cc_final: 0.8089 (mm) REVERT: A 269 ARG cc_start: 0.7623 (mmt180) cc_final: 0.7059 (mmt90) REVERT: A 462 GLN cc_start: 0.8965 (OUTLIER) cc_final: 0.8639 (mp10) REVERT: A 466 GLU cc_start: 0.8740 (pt0) cc_final: 0.8409 (tm-30) REVERT: A 568 ASN cc_start: 0.8943 (t0) cc_final: 0.8734 (t0) REVERT: A 708 TYR cc_start: 0.8440 (t80) cc_final: 0.7960 (t80) REVERT: A 1113 MET cc_start: 0.8613 (mtp) cc_final: 0.8179 (mtm) REVERT: A 1261 GLN cc_start: 0.9360 (OUTLIER) cc_final: 0.7640 (pm20) REVERT: B 184 LEU cc_start: 0.9314 (OUTLIER) cc_final: 0.9079 (pp) REVERT: B 557 MET cc_start: 0.8780 (ttp) cc_final: 0.8291 (ttp) REVERT: C 201 MET cc_start: 0.7860 (tmm) cc_final: 0.7510 (tmm) REVERT: D 92 MET cc_start: -0.0182 (pmm) cc_final: -0.0688 (mtt) REVERT: E 14 GLN cc_start: 0.9019 (tm-30) cc_final: 0.8596 (tm-30) REVERT: E 76 LYS cc_start: 0.9044 (ptpt) cc_final: 0.8640 (tmtt) REVERT: E 126 GLN cc_start: 0.8865 (mm-40) cc_final: 0.8471 (mm-40) REVERT: F 70 ARG cc_start: 0.9013 (OUTLIER) cc_final: 0.7918 (ttm-80) REVERT: F 102 MET cc_start: 0.8653 (tpp) cc_final: 0.8448 (mmm) REVERT: F 130 GLU cc_start: 0.8855 (mt-10) cc_final: 0.8529 (mt-10) REVERT: G 1 MET cc_start: 0.2110 (mpp) cc_final: 0.1202 (ptp) REVERT: G 63 LYS cc_start: 0.8216 (mtmm) cc_final: 0.7961 (ptpt) REVERT: G 103 LYS cc_start: 0.6099 (mmtm) cc_final: 0.5394 (tttm) REVERT: G 115 MET cc_start: -0.0232 (mmm) cc_final: -0.1549 (pmm) REVERT: L 49 GLU cc_start: 0.8050 (tt0) cc_final: 0.7741 (tm-30) REVERT: M 378 ILE cc_start: 0.8692 (mm) cc_final: 0.8317 (mp) REVERT: M 416 MET cc_start: 0.8585 (ttp) cc_final: 0.8111 (ttm) REVERT: M 486 MET cc_start: 0.8666 (OUTLIER) cc_final: 0.8054 (tpp) REVERT: M 814 PHE cc_start: 0.7955 (m-80) cc_final: 0.7417 (m-80) REVERT: M 954 GLU cc_start: 0.8750 (mt-10) cc_final: 0.7717 (tm-30) outliers start: 83 outliers final: 66 residues processed: 401 average time/residue: 0.2323 time to fit residues: 152.6545 Evaluate side-chains 403 residues out of total 4048 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 331 time to evaluate : 1.530 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 71 PHE Chi-restraints excluded: chain A residue 81 ILE Chi-restraints excluded: chain A residue 226 THR Chi-restraints excluded: chain A residue 271 MET Chi-restraints excluded: chain A residue 274 MET Chi-restraints excluded: chain A residue 314 LEU Chi-restraints excluded: chain A residue 452 CYS Chi-restraints excluded: chain A residue 454 HIS Chi-restraints excluded: chain A residue 462 GLN Chi-restraints excluded: chain A residue 464 LYS Chi-restraints excluded: chain A residue 471 VAL Chi-restraints excluded: chain A residue 502 VAL Chi-restraints excluded: chain A residue 533 SER Chi-restraints excluded: chain A residue 540 GLN Chi-restraints excluded: chain A residue 654 CYS Chi-restraints excluded: chain A residue 853 SER Chi-restraints excluded: chain A residue 916 SER Chi-restraints excluded: chain A residue 960 VAL Chi-restraints excluded: chain A residue 1018 LEU Chi-restraints excluded: chain A residue 1172 SER Chi-restraints excluded: chain A residue 1261 GLN Chi-restraints excluded: chain B residue 70 SER Chi-restraints excluded: chain B residue 176 ILE Chi-restraints excluded: chain B residue 184 LEU Chi-restraints excluded: chain B residue 202 PHE Chi-restraints excluded: chain B residue 247 ARG Chi-restraints excluded: chain B residue 277 ILE Chi-restraints excluded: chain B residue 522 THR Chi-restraints excluded: chain B residue 568 LEU Chi-restraints excluded: chain B residue 633 VAL Chi-restraints excluded: chain B residue 771 ASN Chi-restraints excluded: chain B residue 780 LEU Chi-restraints excluded: chain B residue 871 HIS Chi-restraints excluded: chain B residue 889 SER Chi-restraints excluded: chain B residue 924 LEU Chi-restraints excluded: chain B residue 1060 THR Chi-restraints excluded: chain B residue 1089 SER Chi-restraints excluded: chain B residue 1096 LEU Chi-restraints excluded: chain B residue 1113 THR Chi-restraints excluded: chain C residue 41 MET Chi-restraints excluded: chain C residue 44 GLU Chi-restraints excluded: chain C residue 226 VAL Chi-restraints excluded: chain D residue 93 MET Chi-restraints excluded: chain E residue 7 LEU Chi-restraints excluded: chain E residue 35 MET Chi-restraints excluded: chain E residue 118 SER Chi-restraints excluded: chain F residue 70 ARG Chi-restraints excluded: chain F residue 113 THR Chi-restraints excluded: chain G residue 11 VAL Chi-restraints excluded: chain G residue 32 LEU Chi-restraints excluded: chain G residue 33 LEU Chi-restraints excluded: chain G residue 54 LEU Chi-restraints excluded: chain G residue 64 GLU Chi-restraints excluded: chain G residue 147 VAL Chi-restraints excluded: chain G residue 161 MET Chi-restraints excluded: chain I residue 26 LEU Chi-restraints excluded: chain I residue 37 VAL Chi-restraints excluded: chain J residue 2 ILE Chi-restraints excluded: chain J residue 9 THR Chi-restraints excluded: chain K residue 20 SER Chi-restraints excluded: chain M residue 22 VAL Chi-restraints excluded: chain M residue 59 VAL Chi-restraints excluded: chain M residue 108 ASP Chi-restraints excluded: chain M residue 130 ASP Chi-restraints excluded: chain M residue 446 SER Chi-restraints excluded: chain M residue 486 MET Chi-restraints excluded: chain M residue 544 VAL Chi-restraints excluded: chain M residue 663 MET Chi-restraints excluded: chain M residue 782 THR Chi-restraints excluded: chain M residue 872 ILE Chi-restraints excluded: chain M residue 1029 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 454 random chunks: chunk 181 optimal weight: 5.9990 chunk 425 optimal weight: 30.0000 chunk 207 optimal weight: 4.9990 chunk 26 optimal weight: 0.2980 chunk 297 optimal weight: 0.7980 chunk 419 optimal weight: 50.0000 chunk 37 optimal weight: 7.9990 chunk 34 optimal weight: 0.9980 chunk 374 optimal weight: 9.9990 chunk 55 optimal weight: 8.9990 chunk 191 optimal weight: 5.9990 overall best weight: 2.6184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 70 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 476 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1099 ASN B 771 ASN ** D 138 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 76 HIS M 788 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3769 r_free = 0.3769 target = 0.113416 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3109 r_free = 0.3109 target = 0.076515 restraints weight = 82976.160| |-----------------------------------------------------------------------------| r_work (start): 0.3070 rms_B_bonded: 2.82 r_work: 0.2941 rms_B_bonded: 3.32 restraints_weight: 0.5000 r_work (final): 0.2941 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8459 moved from start: 0.3804 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.137 36107 Z= 0.154 Angle : 0.553 12.664 49186 Z= 0.275 Chirality : 0.042 0.167 5710 Planarity : 0.003 0.036 6094 Dihedral : 11.752 139.099 5526 Min Nonbonded Distance : 1.955 Molprobity Statistics. All-atom Clashscore : 5.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.98 % Favored : 95.02 % Rotamer: Outliers : 2.39 % Allowed : 12.57 % Favored : 85.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.16 (0.13), residues: 4496 helix: 1.71 (0.14), residues: 1538 sheet: -0.36 (0.19), residues: 753 loop : -1.38 (0.13), residues: 2205 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG M 323 TYR 0.015 0.001 TYR A 793 PHE 0.029 0.001 PHE G 36 TRP 0.008 0.001 TRP I 112 HIS 0.008 0.001 HIS A 70 Details of bonding type rmsd covalent geometry : bond 0.00357 (36069) covalent geometry : angle 0.53972 (49140) hydrogen bonds : bond 0.03450 ( 1439) hydrogen bonds : angle 4.30594 ( 4106) metal coordination : bond 0.02381 ( 36) metal coordination : angle 4.00189 ( 46) Misc. bond : bond 0.00176 ( 2) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8992 Ramachandran restraints generated. 4496 Oldfield, 0 Emsley, 4496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8992 Ramachandran restraints generated. 4496 Oldfield, 0 Emsley, 4496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 420 residues out of total 4048 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 338 time to evaluate : 1.482 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 46 ARG cc_start: 0.8382 (OUTLIER) cc_final: 0.8179 (mtp85) REVERT: A 71 PHE cc_start: 0.7584 (OUTLIER) cc_final: 0.5416 (m-80) REVERT: A 218 LEU cc_start: 0.8490 (mm) cc_final: 0.8082 (mm) REVERT: A 269 ARG cc_start: 0.7589 (mmt180) cc_final: 0.7073 (mmt90) REVERT: A 462 GLN cc_start: 0.8972 (OUTLIER) cc_final: 0.8620 (mp10) REVERT: A 568 ASN cc_start: 0.8952 (t0) cc_final: 0.8749 (t0) REVERT: A 708 TYR cc_start: 0.8458 (t80) cc_final: 0.7960 (t80) REVERT: A 1099 ASN cc_start: 0.8534 (m-40) cc_final: 0.8265 (p0) REVERT: A 1261 GLN cc_start: 0.9370 (OUTLIER) cc_final: 0.7651 (pm20) REVERT: B 184 LEU cc_start: 0.9321 (OUTLIER) cc_final: 0.9109 (pp) REVERT: B 411 ILE cc_start: 0.9165 (OUTLIER) cc_final: 0.8828 (tp) REVERT: B 557 MET cc_start: 0.8794 (ttp) cc_final: 0.8301 (ttp) REVERT: C 201 MET cc_start: 0.7802 (tmm) cc_final: 0.7469 (tmm) REVERT: D 92 MET cc_start: -0.0175 (pmm) cc_final: -0.0673 (mtt) REVERT: E 14 GLN cc_start: 0.9032 (tm-30) cc_final: 0.8599 (tm-30) REVERT: E 76 LYS cc_start: 0.9048 (ptpt) cc_final: 0.8639 (tmtt) REVERT: E 102 GLN cc_start: 0.8617 (mt0) cc_final: 0.8348 (mp10) REVERT: F 70 ARG cc_start: 0.9027 (OUTLIER) cc_final: 0.7934 (ttm-80) REVERT: F 102 MET cc_start: 0.8616 (tpp) cc_final: 0.8403 (mmm) REVERT: F 130 GLU cc_start: 0.8831 (mt-10) cc_final: 0.8515 (mt-10) REVERT: G 1 MET cc_start: 0.2319 (mpp) cc_final: 0.1526 (ptp) REVERT: G 63 LYS cc_start: 0.8222 (mtmm) cc_final: 0.7977 (ptpt) REVERT: G 103 LYS cc_start: 0.6095 (mmtm) cc_final: 0.5446 (tttm) REVERT: G 115 MET cc_start: -0.0174 (mmm) cc_final: -0.1517 (pmm) REVERT: L 49 GLU cc_start: 0.7890 (tt0) cc_final: 0.7665 (tm-30) REVERT: M 378 ILE cc_start: 0.8692 (mm) cc_final: 0.8315 (mp) REVERT: M 416 MET cc_start: 0.8611 (ttp) cc_final: 0.8073 (ttm) REVERT: M 814 PHE cc_start: 0.7954 (m-80) cc_final: 0.7403 (m-80) REVERT: M 954 GLU cc_start: 0.8755 (mt-10) cc_final: 0.7721 (tm-30) outliers start: 82 outliers final: 68 residues processed: 399 average time/residue: 0.2238 time to fit residues: 147.4404 Evaluate side-chains 407 residues out of total 4048 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 332 time to evaluate : 1.393 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 ILE Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 46 ARG Chi-restraints excluded: chain A residue 71 PHE Chi-restraints excluded: chain A residue 81 ILE Chi-restraints excluded: chain A residue 226 THR Chi-restraints excluded: chain A residue 271 MET Chi-restraints excluded: chain A residue 274 MET Chi-restraints excluded: chain A residue 314 LEU Chi-restraints excluded: chain A residue 452 CYS Chi-restraints excluded: chain A residue 454 HIS Chi-restraints excluded: chain A residue 462 GLN Chi-restraints excluded: chain A residue 464 LYS Chi-restraints excluded: chain A residue 471 VAL Chi-restraints excluded: chain A residue 502 VAL Chi-restraints excluded: chain A residue 533 SER Chi-restraints excluded: chain A residue 540 GLN Chi-restraints excluded: chain A residue 654 CYS Chi-restraints excluded: chain A residue 853 SER Chi-restraints excluded: chain A residue 916 SER Chi-restraints excluded: chain A residue 960 VAL Chi-restraints excluded: chain A residue 1018 LEU Chi-restraints excluded: chain A residue 1071 LEU Chi-restraints excluded: chain A residue 1172 SER Chi-restraints excluded: chain A residue 1261 GLN Chi-restraints excluded: chain B residue 70 SER Chi-restraints excluded: chain B residue 176 ILE Chi-restraints excluded: chain B residue 184 LEU Chi-restraints excluded: chain B residue 202 PHE Chi-restraints excluded: chain B residue 277 ILE Chi-restraints excluded: chain B residue 411 ILE Chi-restraints excluded: chain B residue 522 THR Chi-restraints excluded: chain B residue 568 LEU Chi-restraints excluded: chain B residue 633 VAL Chi-restraints excluded: chain B residue 771 ASN Chi-restraints excluded: chain B residue 780 LEU Chi-restraints excluded: chain B residue 871 HIS Chi-restraints excluded: chain B residue 889 SER Chi-restraints excluded: chain B residue 924 LEU Chi-restraints excluded: chain B residue 1060 THR Chi-restraints excluded: chain B residue 1089 SER Chi-restraints excluded: chain B residue 1096 LEU Chi-restraints excluded: chain B residue 1113 THR Chi-restraints excluded: chain C residue 41 MET Chi-restraints excluded: chain C residue 44 GLU Chi-restraints excluded: chain C residue 226 VAL Chi-restraints excluded: chain D residue 93 MET Chi-restraints excluded: chain D residue 182 THR Chi-restraints excluded: chain E residue 7 LEU Chi-restraints excluded: chain E residue 35 MET Chi-restraints excluded: chain E residue 118 SER Chi-restraints excluded: chain F residue 70 ARG Chi-restraints excluded: chain F residue 113 THR Chi-restraints excluded: chain G residue 11 VAL Chi-restraints excluded: chain G residue 32 LEU Chi-restraints excluded: chain G residue 54 LEU Chi-restraints excluded: chain G residue 64 GLU Chi-restraints excluded: chain G residue 147 VAL Chi-restraints excluded: chain G residue 161 MET Chi-restraints excluded: chain I residue 26 LEU Chi-restraints excluded: chain I residue 37 VAL Chi-restraints excluded: chain J residue 2 ILE Chi-restraints excluded: chain J residue 9 THR Chi-restraints excluded: chain M residue 22 VAL Chi-restraints excluded: chain M residue 59 VAL Chi-restraints excluded: chain M residue 108 ASP Chi-restraints excluded: chain M residue 130 ASP Chi-restraints excluded: chain M residue 446 SER Chi-restraints excluded: chain M residue 544 VAL Chi-restraints excluded: chain M residue 658 SER Chi-restraints excluded: chain M residue 663 MET Chi-restraints excluded: chain M residue 782 THR Chi-restraints excluded: chain M residue 792 ILE Chi-restraints excluded: chain M residue 872 ILE Chi-restraints excluded: chain M residue 1029 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 454 random chunks: chunk 59 optimal weight: 10.0000 chunk 406 optimal weight: 2.9990 chunk 101 optimal weight: 6.9990 chunk 325 optimal weight: 6.9990 chunk 421 optimal weight: 0.0370 chunk 104 optimal weight: 3.9990 chunk 28 optimal weight: 8.9990 chunk 57 optimal weight: 8.9990 chunk 436 optimal weight: 0.4980 chunk 420 optimal weight: 40.0000 chunk 340 optimal weight: 1.9990 overall best weight: 1.9064 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 70 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 476 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 441 HIS ** D 138 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3778 r_free = 0.3778 target = 0.113963 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3129 r_free = 0.3129 target = 0.077385 restraints weight = 82371.578| |-----------------------------------------------------------------------------| r_work (start): 0.3086 rms_B_bonded: 2.81 r_work: 0.2956 rms_B_bonded: 3.30 restraints_weight: 0.5000 r_work (final): 0.2956 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8440 moved from start: 0.3832 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.120 36107 Z= 0.125 Angle : 0.538 13.264 49186 Z= 0.269 Chirality : 0.041 0.174 5710 Planarity : 0.003 0.037 6094 Dihedral : 11.731 138.920 5526 Min Nonbonded Distance : 1.975 Molprobity Statistics. All-atom Clashscore : 5.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.54 % Favored : 95.46 % Rotamer: Outliers : 2.33 % Allowed : 12.74 % Favored : 84.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.10 (0.13), residues: 4496 helix: 1.75 (0.14), residues: 1538 sheet: -0.27 (0.19), residues: 742 loop : -1.36 (0.13), residues: 2216 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 445 TYR 0.014 0.001 TYR A 793 PHE 0.030 0.001 PHE J 8 TRP 0.007 0.001 TRP B 119 HIS 0.008 0.001 HIS A 70 Details of bonding type rmsd covalent geometry : bond 0.00288 (36069) covalent geometry : angle 0.52628 (49140) hydrogen bonds : bond 0.03222 ( 1439) hydrogen bonds : angle 4.23804 ( 4106) metal coordination : bond 0.02077 ( 36) metal coordination : angle 3.69004 ( 46) Misc. bond : bond 0.00155 ( 2) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8992 Ramachandran restraints generated. 4496 Oldfield, 0 Emsley, 4496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8992 Ramachandran restraints generated. 4496 Oldfield, 0 Emsley, 4496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 427 residues out of total 4048 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 347 time to evaluate : 1.703 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 71 PHE cc_start: 0.7579 (OUTLIER) cc_final: 0.5411 (m-80) REVERT: A 218 LEU cc_start: 0.8456 (mm) cc_final: 0.8052 (mm) REVERT: A 269 ARG cc_start: 0.7521 (mmt180) cc_final: 0.6997 (mmt90) REVERT: A 462 GLN cc_start: 0.8945 (OUTLIER) cc_final: 0.8611 (mp10) REVERT: A 568 ASN cc_start: 0.8949 (t0) cc_final: 0.8746 (t0) REVERT: A 708 TYR cc_start: 0.8443 (t80) cc_final: 0.7951 (t80) REVERT: A 1099 ASN cc_start: 0.8499 (m-40) cc_final: 0.8269 (p0) REVERT: A 1261 GLN cc_start: 0.9341 (OUTLIER) cc_final: 0.7573 (pm20) REVERT: B 557 MET cc_start: 0.8768 (ttp) cc_final: 0.8271 (ttp) REVERT: C 201 MET cc_start: 0.7767 (tmm) cc_final: 0.7460 (tmm) REVERT: D 92 MET cc_start: -0.0177 (pmm) cc_final: -0.0666 (mtt) REVERT: E 14 GLN cc_start: 0.9011 (tm-30) cc_final: 0.8567 (tm-30) REVERT: E 76 LYS cc_start: 0.9043 (ptpt) cc_final: 0.8640 (tmtt) REVERT: E 82 MET cc_start: 0.9303 (mmm) cc_final: 0.8862 (mmm) REVERT: E 130 MET cc_start: 0.9111 (mmp) cc_final: 0.8617 (mmt) REVERT: F 70 ARG cc_start: 0.9016 (OUTLIER) cc_final: 0.7936 (ttm-80) REVERT: F 130 GLU cc_start: 0.8806 (mt-10) cc_final: 0.8490 (mt-10) REVERT: G 1 MET cc_start: 0.2287 (mpp) cc_final: 0.1521 (ptp) REVERT: G 103 LYS cc_start: 0.6324 (mmtm) cc_final: 0.5712 (tttm) REVERT: G 115 MET cc_start: -0.0293 (mmm) cc_final: -0.1585 (pmm) REVERT: H 23 LYS cc_start: 0.9010 (mmtt) cc_final: 0.8728 (mmmt) REVERT: M 378 ILE cc_start: 0.8696 (mm) cc_final: 0.8325 (mp) REVERT: M 416 MET cc_start: 0.8557 (ttp) cc_final: 0.8032 (ttm) REVERT: M 659 MET cc_start: 0.6504 (ppp) cc_final: 0.6151 (ppp) REVERT: M 814 PHE cc_start: 0.7924 (m-80) cc_final: 0.7401 (m-80) REVERT: M 954 GLU cc_start: 0.8725 (mt-10) cc_final: 0.7653 (tm-30) outliers start: 80 outliers final: 69 residues processed: 403 average time/residue: 0.2262 time to fit residues: 149.4686 Evaluate side-chains 405 residues out of total 4048 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 332 time to evaluate : 1.285 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 ILE Chi-restraints excluded: chain A residue 71 PHE Chi-restraints excluded: chain A residue 81 ILE Chi-restraints excluded: chain A residue 226 THR Chi-restraints excluded: chain A residue 271 MET Chi-restraints excluded: chain A residue 274 MET Chi-restraints excluded: chain A residue 314 LEU Chi-restraints excluded: chain A residue 452 CYS Chi-restraints excluded: chain A residue 454 HIS Chi-restraints excluded: chain A residue 462 GLN Chi-restraints excluded: chain A residue 464 LYS Chi-restraints excluded: chain A residue 471 VAL Chi-restraints excluded: chain A residue 502 VAL Chi-restraints excluded: chain A residue 533 SER Chi-restraints excluded: chain A residue 540 GLN Chi-restraints excluded: chain A residue 654 CYS Chi-restraints excluded: chain A residue 853 SER Chi-restraints excluded: chain A residue 916 SER Chi-restraints excluded: chain A residue 960 VAL Chi-restraints excluded: chain A residue 1018 LEU Chi-restraints excluded: chain A residue 1071 LEU Chi-restraints excluded: chain A residue 1172 SER Chi-restraints excluded: chain A residue 1261 GLN Chi-restraints excluded: chain B residue 70 SER Chi-restraints excluded: chain B residue 176 ILE Chi-restraints excluded: chain B residue 202 PHE Chi-restraints excluded: chain B residue 247 ARG Chi-restraints excluded: chain B residue 277 ILE Chi-restraints excluded: chain B residue 522 THR Chi-restraints excluded: chain B residue 568 LEU Chi-restraints excluded: chain B residue 594 LEU Chi-restraints excluded: chain B residue 633 VAL Chi-restraints excluded: chain B residue 771 ASN Chi-restraints excluded: chain B residue 780 LEU Chi-restraints excluded: chain B residue 871 HIS Chi-restraints excluded: chain B residue 889 SER Chi-restraints excluded: chain B residue 924 LEU Chi-restraints excluded: chain B residue 1060 THR Chi-restraints excluded: chain B residue 1089 SER Chi-restraints excluded: chain B residue 1096 LEU Chi-restraints excluded: chain B residue 1113 THR Chi-restraints excluded: chain B residue 1161 MET Chi-restraints excluded: chain C residue 41 MET Chi-restraints excluded: chain C residue 226 VAL Chi-restraints excluded: chain D residue 93 MET Chi-restraints excluded: chain E residue 7 LEU Chi-restraints excluded: chain E residue 35 MET Chi-restraints excluded: chain E residue 118 SER Chi-restraints excluded: chain F residue 70 ARG Chi-restraints excluded: chain F residue 82 SER Chi-restraints excluded: chain F residue 113 THR Chi-restraints excluded: chain G residue 11 VAL Chi-restraints excluded: chain G residue 32 LEU Chi-restraints excluded: chain G residue 54 LEU Chi-restraints excluded: chain G residue 64 GLU Chi-restraints excluded: chain G residue 147 VAL Chi-restraints excluded: chain G residue 161 MET Chi-restraints excluded: chain H residue 47 THR Chi-restraints excluded: chain I residue 26 LEU Chi-restraints excluded: chain I residue 37 VAL Chi-restraints excluded: chain J residue 2 ILE Chi-restraints excluded: chain J residue 9 THR Chi-restraints excluded: chain M residue 22 VAL Chi-restraints excluded: chain M residue 59 VAL Chi-restraints excluded: chain M residue 108 ASP Chi-restraints excluded: chain M residue 130 ASP Chi-restraints excluded: chain M residue 446 SER Chi-restraints excluded: chain M residue 544 VAL Chi-restraints excluded: chain M residue 658 SER Chi-restraints excluded: chain M residue 782 THR Chi-restraints excluded: chain M residue 792 ILE Chi-restraints excluded: chain M residue 872 ILE Chi-restraints excluded: chain M residue 1029 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 454 random chunks: chunk 99 optimal weight: 9.9990 chunk 400 optimal weight: 20.0000 chunk 425 optimal weight: 20.0000 chunk 34 optimal weight: 0.4980 chunk 361 optimal weight: 3.9990 chunk 158 optimal weight: 10.0000 chunk 308 optimal weight: 1.9990 chunk 134 optimal weight: 0.0000 chunk 143 optimal weight: 0.9980 chunk 71 optimal weight: 10.0000 chunk 68 optimal weight: 8.9990 overall best weight: 1.4988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 70 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 476 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 441 HIS B 771 ASN ** D 138 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3786 r_free = 0.3786 target = 0.114373 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3139 r_free = 0.3139 target = 0.077851 restraints weight = 83041.110| |-----------------------------------------------------------------------------| r_work (start): 0.3093 rms_B_bonded: 2.82 r_work: 0.2970 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.2970 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8413 moved from start: 0.3872 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.111 36107 Z= 0.112 Angle : 0.540 12.543 49186 Z= 0.267 Chirality : 0.041 0.192 5710 Planarity : 0.003 0.037 6094 Dihedral : 11.693 138.828 5524 Min Nonbonded Distance : 1.991 Molprobity Statistics. All-atom Clashscore : 5.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.56 % Favored : 95.44 % Rotamer: Outliers : 2.10 % Allowed : 12.89 % Favored : 85.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.04 (0.13), residues: 4496 helix: 1.79 (0.14), residues: 1539 sheet: -0.25 (0.19), residues: 751 loop : -1.31 (0.13), residues: 2206 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG M 898 TYR 0.013 0.001 TYR A 793 PHE 0.018 0.001 PHE G 36 TRP 0.008 0.001 TRP B 119 HIS 0.008 0.001 HIS A 70 Details of bonding type rmsd covalent geometry : bond 0.00255 (36069) covalent geometry : angle 0.52886 (49140) hydrogen bonds : bond 0.03092 ( 1439) hydrogen bonds : angle 4.19757 ( 4106) metal coordination : bond 0.01941 ( 36) metal coordination : angle 3.53121 ( 46) Misc. bond : bond 0.00140 ( 2) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8992 Ramachandran restraints generated. 4496 Oldfield, 0 Emsley, 4496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8992 Ramachandran restraints generated. 4496 Oldfield, 0 Emsley, 4496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 414 residues out of total 4048 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 342 time to evaluate : 1.399 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 71 PHE cc_start: 0.7584 (OUTLIER) cc_final: 0.5422 (m-80) REVERT: A 218 LEU cc_start: 0.8414 (mm) cc_final: 0.8007 (mm) REVERT: A 269 ARG cc_start: 0.7516 (mmt180) cc_final: 0.7037 (mmt90) REVERT: A 397 ILE cc_start: 0.5805 (OUTLIER) cc_final: 0.5477 (mt) REVERT: A 462 GLN cc_start: 0.8898 (OUTLIER) cc_final: 0.8588 (mp10) REVERT: A 568 ASN cc_start: 0.8966 (t0) cc_final: 0.8753 (t0) REVERT: A 708 TYR cc_start: 0.8463 (t80) cc_final: 0.7938 (t80) REVERT: A 1261 GLN cc_start: 0.9318 (OUTLIER) cc_final: 0.7575 (pm20) REVERT: B 411 ILE cc_start: 0.9129 (OUTLIER) cc_final: 0.8791 (tp) REVERT: B 557 MET cc_start: 0.8766 (ttp) cc_final: 0.8252 (ttp) REVERT: C 201 MET cc_start: 0.7726 (tmm) cc_final: 0.7394 (tmm) REVERT: D 92 MET cc_start: -0.0184 (pmm) cc_final: -0.0659 (mtt) REVERT: E 14 GLN cc_start: 0.8988 (tm-30) cc_final: 0.8552 (tm-30) REVERT: E 76 LYS cc_start: 0.9052 (ptpt) cc_final: 0.8641 (tmtt) REVERT: E 82 MET cc_start: 0.9293 (mmm) cc_final: 0.8828 (mmm) REVERT: E 130 MET cc_start: 0.9071 (mmp) cc_final: 0.8638 (mmt) REVERT: F 70 ARG cc_start: 0.8988 (OUTLIER) cc_final: 0.7889 (ttm-80) REVERT: F 130 GLU cc_start: 0.8793 (mt-10) cc_final: 0.8483 (mt-10) REVERT: G 1 MET cc_start: 0.2165 (mpp) cc_final: 0.1503 (ptp) REVERT: G 36 PHE cc_start: 0.7010 (p90) cc_final: 0.5873 (t80) REVERT: G 103 LYS cc_start: 0.6316 (mmtm) cc_final: 0.5672 (tttm) REVERT: G 115 MET cc_start: -0.0140 (mmm) cc_final: -0.1535 (pmm) REVERT: H 23 LYS cc_start: 0.9001 (mmtt) cc_final: 0.8702 (mmmt) REVERT: M 378 ILE cc_start: 0.8727 (mm) cc_final: 0.8294 (mp) REVERT: M 416 MET cc_start: 0.8543 (ttp) cc_final: 0.8006 (ttm) REVERT: M 814 PHE cc_start: 0.7944 (m-80) cc_final: 0.7433 (m-80) REVERT: M 954 GLU cc_start: 0.8737 (mt-10) cc_final: 0.7677 (tm-30) REVERT: M 1060 LYS cc_start: 0.8990 (tptp) cc_final: 0.8452 (pttt) outliers start: 72 outliers final: 59 residues processed: 391 average time/residue: 0.2246 time to fit residues: 143.6712 Evaluate side-chains 398 residues out of total 4048 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 333 time to evaluate : 1.448 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 ILE Chi-restraints excluded: chain A residue 71 PHE Chi-restraints excluded: chain A residue 81 ILE Chi-restraints excluded: chain A residue 226 THR Chi-restraints excluded: chain A residue 271 MET Chi-restraints excluded: chain A residue 314 LEU Chi-restraints excluded: chain A residue 397 ILE Chi-restraints excluded: chain A residue 452 CYS Chi-restraints excluded: chain A residue 454 HIS Chi-restraints excluded: chain A residue 462 GLN Chi-restraints excluded: chain A residue 464 LYS Chi-restraints excluded: chain A residue 471 VAL Chi-restraints excluded: chain A residue 502 VAL Chi-restraints excluded: chain A residue 533 SER Chi-restraints excluded: chain A residue 654 CYS Chi-restraints excluded: chain A residue 853 SER Chi-restraints excluded: chain A residue 916 SER Chi-restraints excluded: chain A residue 1071 LEU Chi-restraints excluded: chain A residue 1261 GLN Chi-restraints excluded: chain B residue 70 SER Chi-restraints excluded: chain B residue 176 ILE Chi-restraints excluded: chain B residue 202 PHE Chi-restraints excluded: chain B residue 277 ILE Chi-restraints excluded: chain B residue 411 ILE Chi-restraints excluded: chain B residue 522 THR Chi-restraints excluded: chain B residue 633 VAL Chi-restraints excluded: chain B residue 871 HIS Chi-restraints excluded: chain B residue 889 SER Chi-restraints excluded: chain B residue 924 LEU Chi-restraints excluded: chain B residue 1060 THR Chi-restraints excluded: chain B residue 1089 SER Chi-restraints excluded: chain B residue 1096 LEU Chi-restraints excluded: chain B residue 1113 THR Chi-restraints excluded: chain B residue 1161 MET Chi-restraints excluded: chain C residue 41 MET Chi-restraints excluded: chain C residue 226 VAL Chi-restraints excluded: chain D residue 93 MET Chi-restraints excluded: chain D residue 182 THR Chi-restraints excluded: chain E residue 7 LEU Chi-restraints excluded: chain E residue 35 MET Chi-restraints excluded: chain E residue 118 SER Chi-restraints excluded: chain F residue 70 ARG Chi-restraints excluded: chain F residue 82 SER Chi-restraints excluded: chain F residue 113 THR Chi-restraints excluded: chain G residue 11 VAL Chi-restraints excluded: chain G residue 32 LEU Chi-restraints excluded: chain G residue 33 LEU Chi-restraints excluded: chain G residue 54 LEU Chi-restraints excluded: chain G residue 64 GLU Chi-restraints excluded: chain G residue 147 VAL Chi-restraints excluded: chain G residue 161 MET Chi-restraints excluded: chain I residue 26 LEU Chi-restraints excluded: chain I residue 37 VAL Chi-restraints excluded: chain J residue 2 ILE Chi-restraints excluded: chain J residue 9 THR Chi-restraints excluded: chain M residue 22 VAL Chi-restraints excluded: chain M residue 59 VAL Chi-restraints excluded: chain M residue 108 ASP Chi-restraints excluded: chain M residue 130 ASP Chi-restraints excluded: chain M residue 446 SER Chi-restraints excluded: chain M residue 544 VAL Chi-restraints excluded: chain M residue 782 THR Chi-restraints excluded: chain M residue 792 ILE Chi-restraints excluded: chain M residue 872 ILE Chi-restraints excluded: chain M residue 1029 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 454 random chunks: chunk 446 optimal weight: 3.9990 chunk 387 optimal weight: 1.9990 chunk 69 optimal weight: 0.9990 chunk 278 optimal weight: 0.6980 chunk 413 optimal weight: 5.9990 chunk 250 optimal weight: 6.9990 chunk 308 optimal weight: 0.0970 chunk 139 optimal weight: 9.9990 chunk 217 optimal weight: 9.9990 chunk 239 optimal weight: 8.9990 chunk 284 optimal weight: 10.0000 overall best weight: 1.5584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 70 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 476 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 441 HIS ** D 138 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3787 r_free = 0.3787 target = 0.114424 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3139 r_free = 0.3139 target = 0.077841 restraints weight = 82589.824| |-----------------------------------------------------------------------------| r_work (start): 0.3095 rms_B_bonded: 2.82 r_work: 0.2971 rms_B_bonded: 3.30 restraints_weight: 0.5000 r_work (final): 0.2971 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8424 moved from start: 0.3900 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.108 36107 Z= 0.112 Angle : 0.536 12.146 49186 Z= 0.265 Chirality : 0.041 0.165 5710 Planarity : 0.003 0.036 6094 Dihedral : 11.670 138.804 5524 Min Nonbonded Distance : 1.995 Molprobity Statistics. All-atom Clashscore : 5.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.43 % Favored : 95.57 % Rotamer: Outliers : 2.01 % Allowed : 13.18 % Favored : 84.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.01 (0.13), residues: 4496 helix: 1.85 (0.14), residues: 1536 sheet: -0.20 (0.19), residues: 761 loop : -1.29 (0.13), residues: 2199 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG M 898 TYR 0.015 0.001 TYR A 793 PHE 0.018 0.001 PHE G 36 TRP 0.008 0.001 TRP B 119 HIS 0.008 0.001 HIS A 70 Details of bonding type rmsd covalent geometry : bond 0.00257 (36069) covalent geometry : angle 0.52510 (49140) hydrogen bonds : bond 0.03038 ( 1439) hydrogen bonds : angle 4.14524 ( 4106) metal coordination : bond 0.01895 ( 36) metal coordination : angle 3.48101 ( 46) Misc. bond : bond 0.00136 ( 2) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9483.65 seconds wall clock time: 163 minutes 0.63 seconds (9780.63 seconds total)