Starting phenix.real_space_refine on Sun May 25 07:38:44 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8cro_16809/05_2025/8cro_16809.cif Found real_map, /net/cci-nas-00/data/ceres_data/8cro_16809/05_2025/8cro_16809.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8cro_16809/05_2025/8cro_16809.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8cro_16809/05_2025/8cro_16809.map" model { file = "/net/cci-nas-00/data/ceres_data/8cro_16809/05_2025/8cro_16809.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8cro_16809/05_2025/8cro_16809.cif" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.005 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 5 6.06 5 P 39 5.49 5 Mg 1 5.21 5 S 110 5.16 5 C 17149 2.51 5 N 4730 2.21 5 O 5135 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 57 residue(s): 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 27169 Number of models: 1 Model: "" Number of chains: 18 Chain: "A" Number of atoms: 7189 Number of conformers: 1 Conformer: "" Number of residues, atoms: 900, 7189 Classifications: {'peptide': 900} Link IDs: {'PTRANS': 52, 'TRANS': 847} Chain: "B" Number of atoms: 8802 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1098, 8802 Classifications: {'peptide': 1098} Link IDs: {'PTRANS': 61, 'TRANS': 1036} Chain breaks: 1 Chain: "C" Number of atoms: 3057 Number of conformers: 1 Conformer: "" Number of residues, atoms: 390, 3057 Classifications: {'peptide': 390} Link IDs: {'PTRANS': 16, 'TRANS': 373} Chain: "D" Number of atoms: 2086 Number of conformers: 1 Conformer: "" Number of residues, atoms: 258, 2086 Classifications: {'peptide': 258} Link IDs: {'PTRANS': 15, 'TRANS': 242} Chain: "E" Number of atoms: 1528 Number of conformers: 1 Conformer: "" Number of residues, atoms: 189, 1528 Classifications: {'peptide': 189} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 8, 'TRANS': 180} Chain: "F" Number of atoms: 946 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 946 Classifications: {'peptide': 116} Link IDs: {'PTRANS': 4, 'TRANS': 111} Chain: "L" Number of atoms: 777 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 777 Classifications: {'peptide': 94} Link IDs: {'PTRANS': 4, 'TRANS': 89} Chain: "H" Number of atoms: 609 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 609 Classifications: {'peptide': 76} Link IDs: {'PTRANS': 5, 'TRANS': 70} Chain: "N" Number of atoms: 543 Number of conformers: 1 Conformer: "" Number of residues, atoms: 65, 543 Classifications: {'peptide': 65} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 62} Chain: "K" Number of atoms: 424 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 424 Classifications: {'peptide': 55} Link IDs: {'PTRANS': 6, 'TRANS': 48} Chain: "P" Number of atoms: 393 Number of conformers: 1 Conformer: "" Number of residues, atoms: 48, 393 Classifications: {'peptide': 48} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 43} Chain: "X" Number of atoms: 414 Number of conformers: 1 Conformer: "" Number of residues, atoms: 20, 414 Classifications: {'DNA': 20} Link IDs: {'rna3p': 19} Chain: "Y" Number of atoms: 199 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 199 Classifications: {'DNA': 10} Link IDs: {'rna3p': 9} Chain: "Z" Number of atoms: 196 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 196 Classifications: {'RNA': 9} Modifications used: {'rna2p_pur': 1, 'rna3p_pur': 5, 'rna3p_pyr': 3} Link IDs: {'rna2p': 1, 'rna3p': 7} Chain: "A" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' MG': 1, ' ZN': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} 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: "N" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "P" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 426 SG CYS A 57 86.898 74.748 73.746 1.00 0.73 S ATOM 448 SG CYS A 60 83.241 74.070 74.733 1.00 30.00 S ATOM 491 SG CYS A 67 84.206 77.486 73.297 1.00 0.77 S ATOM 728 SG CYS A 97 84.716 85.508 121.002 1.00 0.80 S ATOM 754 SG CYS A 100 82.869 82.385 120.734 1.00 0.73 S ATOM 1130 SG CYS A 144 81.681 85.097 123.261 1.00 0.72 S ATOM 1153 SG CYS A 147 84.771 82.935 123.920 1.00 0.78 S ATOM 15523 SG CYS B1059 73.253 69.879 87.302 1.00 0.85 S ATOM 15546 SG CYS B1062 75.279 70.618 90.517 1.00 0.85 S ATOM 15676 SG CYS B1077 77.014 70.451 86.964 1.00 0.84 S ATOM 15696 SG CYS B1080 75.704 67.542 89.129 1.00 0.68 S ATOM 25048 SG CYS N 7 64.441 132.617 35.220 1.00 0.59 S ATOM 25072 SG CYS N 10 61.431 132.848 32.821 1.00 30.00 S ATOM 25352 SG CYS N 44 61.506 134.856 36.140 1.00 0.60 S ATOM 25358 SG CYS N 45 63.526 135.714 33.041 1.00 0.60 S ATOM 26018 SG CYS P 8 105.211 116.168 38.679 1.00 86.83 S ATOM 26044 SG CYS P 11 106.104 117.983 35.582 1.00 84.70 S ATOM 26173 SG CYS P 27 108.321 114.976 36.949 1.00 79.74 S ATOM 26198 SG CYS P 30 108.358 118.342 38.643 1.00 82.76 S Time building chain proxies: 14.33, per 1000 atoms: 0.53 Number of scatterers: 27169 At special positions: 0 Unit cell: (148.89, 176.541, 143.573, 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 5 29.99 S 110 16.00 P 39 15.00 Mg 1 11.99 O 5135 8.00 N 4730 7.00 C 17149 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 7.21 Conformation dependent library (CDL) restraints added in 3.6 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A1000 " pdb="ZN ZN A1000 " - pdb=" NE2 HIS A 70 " pdb="ZN ZN A1000 " - pdb=" SG CYS A 60 " pdb="ZN ZN A1000 " - pdb=" SG CYS A 67 " pdb="ZN ZN A1000 " - pdb=" SG CYS A 57 " pdb=" ZN A1001 " pdb="ZN ZN A1001 " - pdb=" SG CYS A 100 " pdb="ZN ZN A1001 " - pdb=" SG CYS A 97 " pdb="ZN ZN A1001 " - pdb=" SG CYS A 147 " pdb="ZN ZN A1001 " - pdb=" SG CYS A 144 " pdb=" ZN B1201 " pdb="ZN ZN B1201 " - pdb=" SG CYS B1080 " pdb="ZN ZN B1201 " - pdb=" SG CYS B1062 " pdb="ZN ZN B1201 " - pdb=" SG CYS B1059 " pdb="ZN ZN B1201 " - pdb=" SG CYS B1077 " pdb=" ZN N 101 " pdb="ZN ZN N 101 " - pdb=" SG CYS N 45 " pdb="ZN ZN N 101 " - pdb=" SG CYS N 10 " pdb="ZN ZN N 101 " - pdb=" SG CYS N 44 " pdb="ZN ZN N 101 " - pdb=" SG CYS N 7 " pdb=" ZN P 101 " pdb="ZN ZN P 101 " - pdb=" SG CYS P 8 " pdb="ZN ZN P 101 " - pdb=" SG CYS P 11 " pdb="ZN ZN P 101 " - pdb=" SG CYS P 30 " pdb="ZN ZN P 101 " - pdb=" SG CYS P 27 " Number of angles added : 27 6530 Ramachandran restraints generated. 3265 Oldfield, 0 Emsley, 3265 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6106 Finding SS restraints... Secondary structure from input PDB file: 126 helices and 42 sheets defined 42.8% alpha, 20.5% beta 19 base pairs and 27 stacking pairs defined. Time for finding SS restraints: 9.95 Creating SS restraints... Processing helix chain 'A' and resid 14 through 22 Processing helix chain 'A' and resid 45 through 49 Processing helix chain 'A' and resid 85 through 96 Processing helix chain 'A' and resid 106 through 119 Processing helix chain 'A' and resid 123 through 141 removed outlier: 3.741A pdb=" N PHE A 127 " --> pdb=" O ARG A 123 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N ARG A 141 " --> pdb=" O LYS A 137 " (cutoff:3.500A) Processing helix chain 'A' and resid 179 through 189 Processing helix chain 'A' and resid 195 through 199 Processing helix chain 'A' and resid 206 through 209 Processing helix chain 'A' and resid 219 through 223 Processing helix chain 'A' and resid 236 through 259 Processing helix chain 'A' and resid 261 through 281 Processing helix chain 'A' and resid 300 through 306 Processing helix chain 'A' and resid 310 through 316 Processing helix chain 'A' and resid 344 through 350 Processing helix chain 'A' and resid 360 through 371 Processing helix chain 'A' and resid 395 through 402 Processing helix chain 'A' and resid 428 through 430 No H-bonds generated for 'chain 'A' and resid 428 through 430' Processing helix chain 'A' and resid 451 through 456 removed outlier: 3.758A pdb=" N TYR A 455 " --> pdb=" O VAL A 451 " (cutoff:3.500A) Processing helix chain 'A' and resid 471 through 482 Processing helix chain 'A' and resid 502 through 513 Processing helix chain 'A' and resid 520 through 531 Processing helix chain 'A' and resid 553 through 559 Processing helix chain 'A' and resid 576 through 591 removed outlier: 3.867A pdb=" N CYS A 580 " --> pdb=" O GLU A 576 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N GLU A 589 " --> pdb=" O LYS A 585 " (cutoff:3.500A) removed outlier: 4.521A pdb=" N LYS A 590 " --> pdb=" O LEU A 586 " (cutoff:3.500A) Processing helix chain 'A' and resid 594 through 601 Processing helix chain 'A' and resid 629 through 639 Processing helix chain 'A' and resid 641 through 663 Processing helix chain 'A' and resid 667 through 672 Processing helix chain 'A' and resid 674 through 701 Processing helix chain 'A' and resid 711 through 740 removed outlier: 4.055A pdb=" N GLY A 740 " --> pdb=" O GLU A 736 " (cutoff:3.500A) Processing helix chain 'A' and resid 743 through 751 Processing helix chain 'A' and resid 756 through 765 removed outlier: 3.642A pdb=" N ILE A 760 " --> pdb=" O LYS A 756 " (cutoff:3.500A) Processing helix chain 'A' and resid 796 through 799 Processing helix chain 'A' and resid 811 through 848 removed outlier: 4.010A pdb=" N ALA A 830 " --> pdb=" O LEU A 826 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N VAL A 831 " --> pdb=" O VAL A 827 " (cutoff:3.500A) Processing helix chain 'A' and resid 869 through 873 removed outlier: 3.505A pdb=" N ASP A 873 " --> pdb=" O TYR A 870 " (cutoff:3.500A) Processing helix chain 'A' and resid 887 through 901 Processing helix chain 'B' and resid 10 through 25 removed outlier: 3.947A pdb=" N ILE B 16 " --> pdb=" O ASP B 12 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N VAL B 17 " --> pdb=" O ASP B 13 " (cutoff:3.500A) Processing helix chain 'B' and resid 28 through 41 Processing helix chain 'B' and resid 41 through 50 Processing helix chain 'B' and resid 85 through 92 Processing helix chain 'B' and resid 138 through 145 Processing helix chain 'B' and resid 225 through 232 Processing helix chain 'B' and resid 236 through 245 Processing helix chain 'B' and resid 247 through 263 removed outlier: 4.069A pdb=" N ASP B 260 " --> pdb=" O ASP B 256 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N ALA B 261 " --> pdb=" O ASN B 257 " (cutoff:3.500A) Processing helix chain 'B' and resid 266 through 279 removed outlier: 4.269A pdb=" N LEU B 271 " --> pdb=" O GLN B 267 " (cutoff:3.500A) removed outlier: 4.119A pdb=" N GLU B 272 " --> pdb=" O GLN B 268 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N LEU B 277 " --> pdb=" O PHE B 273 " (cutoff:3.500A) Processing helix chain 'B' and resid 283 through 297 Processing helix chain 'B' and resid 300 through 304 Processing helix chain 'B' and resid 306 through 308 No H-bonds generated for 'chain 'B' and resid 306 through 308' Processing helix chain 'B' and resid 309 through 329 Processing helix chain 'B' and resid 347 through 379 Processing helix chain 'B' and resid 386 through 394 removed outlier: 3.559A pdb=" N PHE B 390 " --> pdb=" O ASN B 386 " (cutoff:3.500A) Processing helix chain 'B' and resid 397 through 411 removed outlier: 3.873A pdb=" N THR B 401 " --> pdb=" O PRO B 397 " (cutoff:3.500A) Processing helix chain 'B' and resid 428 through 437 Processing helix chain 'B' and resid 456 through 460 removed outlier: 3.591A pdb=" N TRP B 460 " --> pdb=" O GLY B 457 " (cutoff:3.500A) Processing helix chain 'B' and resid 491 through 502 removed outlier: 3.683A pdb=" N ILE B 495 " --> pdb=" O PRO B 491 " (cutoff:3.500A) Processing helix chain 'B' and resid 531 through 545 Processing helix chain 'B' and resid 587 through 596 Processing helix chain 'B' and resid 600 through 607 Processing helix chain 'B' and resid 614 through 620 removed outlier: 3.897A pdb=" N ASN B 620 " --> pdb=" O GLU B 616 " (cutoff:3.500A) Processing helix chain 'B' and resid 626 through 630 Processing helix chain 'B' and resid 640 through 645 removed outlier: 3.501A pdb=" N ILE B 644 " --> pdb=" O PRO B 641 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N LEU B 645 " --> pdb=" O ALA B 642 " (cutoff:3.500A) Processing helix chain 'B' and resid 646 through 652 removed outlier: 3.895A pdb=" N VAL B 652 " --> pdb=" O PRO B 648 " (cutoff:3.500A) Processing helix chain 'B' and resid 654 through 658 removed outlier: 3.525A pdb=" N ASN B 658 " --> pdb=" O PRO B 655 " (cutoff:3.500A) Processing helix chain 'B' and resid 659 through 670 Processing helix chain 'B' and resid 671 through 673 No H-bonds generated for 'chain 'B' and resid 671 through 673' Processing helix chain 'B' and resid 702 through 709 removed outlier: 3.755A pdb=" N LYS B 706 " --> pdb=" O SER B 702 " (cutoff:3.500A) Processing helix chain 'B' and resid 710 through 713 Processing helix chain 'B' and resid 739 through 744 Processing helix chain 'B' and resid 762 through 766 removed outlier: 3.671A pdb=" N GLY B 765 " --> pdb=" O TYR B 762 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N GLN B 766 " --> pdb=" O LEU B 763 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 762 through 766' Processing helix chain 'B' and resid 891 through 895 Processing helix chain 'B' and resid 910 through 913 Processing helix chain 'B' and resid 918 through 935 removed outlier: 3.944A pdb=" N LEU B 922 " --> pdb=" O THR B 918 " (cutoff:3.500A) Processing helix chain 'B' and resid 947 through 958 Processing helix chain 'B' and resid 994 through 998 Processing helix chain 'B' and resid 1017 through 1021 removed outlier: 3.810A pdb=" N GLU B1021 " --> pdb=" O ARG B1018 " (cutoff:3.500A) Processing helix chain 'B' and resid 1027 through 1037 Processing helix chain 'B' and resid 1039 through 1048 removed outlier: 3.643A pdb=" N LEU B1043 " --> pdb=" O ALA B1039 " (cutoff:3.500A) Processing helix chain 'B' and resid 1093 through 1104 Processing helix chain 'B' and resid 1105 through 1107 No H-bonds generated for 'chain 'B' and resid 1105 through 1107' Processing helix chain 'C' and resid 3 through 15 removed outlier: 3.525A pdb=" N ILE C 7 " --> pdb=" O SER C 3 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N LYS C 8 " --> pdb=" O LEU C 4 " (cutoff:3.500A) Processing helix chain 'C' and resid 19 through 37 Processing helix chain 'C' and resid 40 through 58 Processing helix chain 'C' and resid 65 through 76 Processing helix chain 'C' and resid 77 through 81 Processing helix chain 'C' and resid 99 through 108 Processing helix chain 'C' and resid 129 through 141 removed outlier: 3.803A pdb=" N GLU C 135 " --> pdb=" O ALA C 131 " (cutoff:3.500A) removed outlier: 4.247A pdb=" N VAL C 136 " --> pdb=" O LYS C 132 " (cutoff:3.500A) Processing helix chain 'C' and resid 145 through 148 No H-bonds generated for 'chain 'C' and resid 145 through 148' Processing helix chain 'C' and resid 166 through 172 Processing helix chain 'C' and resid 176 through 188 removed outlier: 4.204A pdb=" N LYS C 183 " --> pdb=" O LYS C 179 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N LEU C 184 " --> pdb=" O VAL C 180 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N SER C 186 " --> pdb=" O LYS C 182 " (cutoff:3.500A) Processing helix chain 'C' and resid 209 through 223 Processing helix chain 'C' and resid 251 through 258 Processing helix chain 'C' and resid 270 through 279 Processing helix chain 'C' and resid 279 through 298 removed outlier: 3.696A pdb=" N GLN C 298 " --> pdb=" O THR C 294 " (cutoff:3.500A) Processing helix chain 'C' and resid 303 through 315 removed outlier: 3.869A pdb=" N ILE C 307 " --> pdb=" O ASP C 303 " (cutoff:3.500A) Processing helix chain 'C' and resid 334 through 341 removed outlier: 3.553A pdb=" N PHE C 341 " --> pdb=" O ALA C 337 " (cutoff:3.500A) Processing helix chain 'C' and resid 344 through 355 Processing helix chain 'C' and resid 363 through 370 Processing helix chain 'C' and resid 375 through 380 removed outlier: 3.564A pdb=" N VAL C 380 " --> pdb=" O THR C 377 " (cutoff:3.500A) Processing helix chain 'D' and resid 24 through 38 Processing helix chain 'D' and resid 57 through 68 Processing helix chain 'D' and resid 104 through 106 No H-bonds generated for 'chain 'D' and resid 104 through 106' Processing helix chain 'D' and resid 145 through 149 Processing helix chain 'D' and resid 169 through 181 removed outlier: 3.973A pdb=" N LEU D 173 " --> pdb=" O GLU D 169 " (cutoff:3.500A) Processing helix chain 'D' and resid 203 through 209 removed outlier: 4.271A pdb=" N GLU D 207 " --> pdb=" O ASP D 204 " (cutoff:3.500A) Processing helix chain 'D' and resid 233 through 260 Processing helix chain 'E' and resid 14 through 18 Processing helix chain 'E' and resid 21 through 34 Processing helix chain 'E' and resid 111 through 113 No H-bonds generated for 'chain 'E' and resid 111 through 113' Processing helix chain 'E' and resid 173 through 189 Processing helix chain 'F' and resid 13 through 32 Processing helix chain 'F' and resid 38 through 51 removed outlier: 3.521A pdb=" N PHE F 51 " --> pdb=" O HIS F 47 " (cutoff:3.500A) Processing helix chain 'F' and resid 55 through 70 removed outlier: 3.563A pdb=" N PHE F 70 " --> pdb=" O LEU F 66 " (cutoff:3.500A) Processing helix chain 'F' and resid 74 through 85 Processing helix chain 'F' and resid 88 through 96 removed outlier: 3.719A pdb=" N LEU F 92 " --> pdb=" O ASP F 88 " (cutoff:3.500A) Processing helix chain 'F' and resid 104 through 117 Processing helix chain 'L' and resid 21 through 34 removed outlier: 3.683A pdb=" N LEU L 27 " --> pdb=" O THR L 23 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N GLU L 34 " --> pdb=" O GLU L 30 " (cutoff:3.500A) Processing helix chain 'L' and resid 66 through 94 Processing helix chain 'H' and resid 8 through 12 Processing helix chain 'H' and resid 22 through 34 Processing helix chain 'H' and resid 36 through 40 Processing helix chain 'H' and resid 47 through 52 Processing helix chain 'N' and resid 16 through 27 removed outlier: 4.344A pdb=" N GLU N 20 " --> pdb=" O ASP N 16 " (cutoff:3.500A) Processing helix chain 'N' and resid 30 through 39 Processing helix chain 'N' and resid 42 through 51 removed outlier: 3.517A pdb=" N MET N 48 " --> pdb=" O CYS N 44 " (cutoff:3.500A) Processing helix chain 'N' and resid 55 through 60 Processing helix chain 'K' and resid 5 through 22 Processing helix chain 'K' and resid 35 through 47 Processing sheet with id=AA1, first strand: chain 'B' and resid 1108 through 1115 removed outlier: 6.251A pdb=" N ARG B1108 " --> pdb=" O PHE A 10 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N PHE A 10 " --> pdb=" O ARG B1108 " (cutoff:3.500A) removed outlier: 6.231A pdb=" N LYS B1110 " --> pdb=" O ILE A 8 " (cutoff:3.500A) removed outlier: 4.306A pdb=" N ILE A 8 " --> pdb=" O LYS B1110 " (cutoff:3.500A) removed outlier: 6.677A pdb=" N ASN B1112 " --> pdb=" O GLY A 6 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 24 through 25 removed outlier: 6.650A pdb=" N VAL A 24 " --> pdb=" O HIS A 73 " (cutoff:3.500A) removed outlier: 7.722A pdb=" N GLU A 75 " --> pdb=" O VAL A 24 " (cutoff:3.500A) removed outlier: 6.890A pdb=" N THR A 213 " --> pdb=" O LEU A 76 " (cutoff:3.500A) removed outlier: 10.636A pdb=" N ARG A 78 " --> pdb=" O VAL A 211 " (cutoff:3.500A) removed outlier: 10.506A pdb=" N VAL A 211 " --> pdb=" O ARG A 78 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 154 through 157 removed outlier: 4.524A pdb=" N ILE A 161 " --> pdb=" O GLU A 157 " (cutoff:3.500A) removed outlier: 6.991A pdb=" N ASN A 172 " --> pdb=" O ASP A 168 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 226 through 227 Processing sheet with id=AA5, first strand: chain 'A' and resid 319 through 321 removed outlier: 3.823A pdb=" N LEU B1024 " --> pdb=" O VAL A 321 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 1000 through 1002 removed outlier: 3.822A pdb=" N THR A 327 " --> pdb=" O MET A 464 " (cutoff:3.500A) removed outlier: 5.984A pdb=" N VAL A 340 " --> pdb=" O ARG A 438 " (cutoff:3.500A) removed outlier: 6.672A pdb=" N MET A 440 " --> pdb=" O VAL A 340 " (cutoff:3.500A) removed outlier: 5.786A pdb=" N VAL A 342 " --> pdb=" O MET A 440 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 351 through 355 removed outlier: 3.834A pdb=" N TYR A 380 " --> pdb=" O GLU A 410 " (cutoff:3.500A) removed outlier: 6.336A pdb=" N HIS A 412 " --> pdb=" O ALA A 378 " (cutoff:3.500A) removed outlier: 7.034A pdb=" N ALA A 378 " --> pdb=" O HIS A 412 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 517 through 519 Processing sheet with id=AA9, first strand: chain 'A' and resid 567 through 570 removed outlier: 6.471A pdb=" N TYR A 608 " --> pdb=" O LEU A 615 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 768 through 769 Processing sheet with id=AB2, first strand: chain 'A' and resid 771 through 772 Processing sheet with id=AB3, first strand: chain 'A' and resid 851 through 852 removed outlier: 4.133A pdb=" N LYS A 851 " --> pdb=" O ARG A 859 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 60 through 69 removed outlier: 5.475A pdb=" N GLU B 103 " --> pdb=" O GLY B 65 " (cutoff:3.500A) removed outlier: 4.317A pdb=" N ILE B 67 " --> pdb=" O TYR B 101 " (cutoff:3.500A) removed outlier: 6.594A pdb=" N TYR B 101 " --> pdb=" O ILE B 67 " (cutoff:3.500A) removed outlier: 4.518A pdb=" N VAL B 69 " --> pdb=" O PRO B 99 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 60 through 69 removed outlier: 5.475A pdb=" N GLU B 103 " --> pdb=" O GLY B 65 " (cutoff:3.500A) removed outlier: 4.317A pdb=" N ILE B 67 " --> pdb=" O TYR B 101 " (cutoff:3.500A) removed outlier: 6.594A pdb=" N TYR B 101 " --> pdb=" O ILE B 67 " (cutoff:3.500A) removed outlier: 4.518A pdb=" N VAL B 69 " --> pdb=" O PRO B 99 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N GLY B 121 " --> pdb=" O LEU B 100 " (cutoff:3.500A) removed outlier: 6.658A pdb=" N LEU B 102 " --> pdb=" O ARG B 119 " (cutoff:3.500A) removed outlier: 5.557A pdb=" N ARG B 119 " --> pdb=" O LEU B 102 " (cutoff:3.500A) removed outlier: 7.080A pdb=" N MET B 104 " --> pdb=" O GLU B 117 " (cutoff:3.500A) removed outlier: 5.946A pdb=" N GLU B 117 " --> pdb=" O MET B 104 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 73 through 75 Processing sheet with id=AB7, first strand: chain 'B' and resid 156 through 158 Processing sheet with id=AB8, first strand: chain 'B' and resid 343 through 346 removed outlier: 3.648A pdb=" N SER B 167 " --> pdb=" O ARG B 438 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 177 through 180 Processing sheet with id=AC1, first strand: chain 'B' and resid 485 through 486 Processing sheet with id=AC2, first strand: chain 'B' and resid 583 through 584 Processing sheet with id=AC3, first strand: chain 'B' and resid 505 through 506 removed outlier: 7.315A pdb=" N VAL B 519 " --> pdb=" O ILE B 526 " (cutoff:3.500A) removed outlier: 4.541A pdb=" N THR B 528 " --> pdb=" O TRP B 517 " (cutoff:3.500A) removed outlier: 6.583A pdb=" N TRP B 517 " --> pdb=" O THR B 528 " (cutoff:3.500A) removed outlier: 6.381A pdb=" N ARG B 518 " --> pdb=" O VAL B 563 " (cutoff:3.500A) removed outlier: 7.671A pdb=" N VAL B 565 " --> pdb=" O ARG B 518 " (cutoff:3.500A) removed outlier: 6.382A pdb=" N TYR B 520 " --> pdb=" O VAL B 565 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 688 through 692 removed outlier: 6.446A pdb=" N ARG B 865 " --> pdb=" O VAL B 845 " (cutoff:3.500A) removed outlier: 5.482A pdb=" N VAL B 845 " --> pdb=" O ARG B 865 " (cutoff:3.500A) removed outlier: 7.633A pdb=" N LEU B 867 " --> pdb=" O GLY B 843 " (cutoff:3.500A) removed outlier: 8.032A pdb=" N GLY B 843 " --> pdb=" O LEU B 867 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 688 through 692 removed outlier: 6.446A pdb=" N ARG B 865 " --> pdb=" O VAL B 845 " (cutoff:3.500A) removed outlier: 5.482A pdb=" N VAL B 845 " --> pdb=" O ARG B 865 " (cutoff:3.500A) removed outlier: 7.633A pdb=" N LEU B 867 " --> pdb=" O GLY B 843 " (cutoff:3.500A) removed outlier: 8.032A pdb=" N GLY B 843 " --> pdb=" O LEU B 867 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N LEU P 17 " --> pdb=" O ALA P 4 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 700 through 701 Processing sheet with id=AC7, first strand: chain 'B' and resid 965 through 966 removed outlier: 6.842A pdb=" N ILE B 735 " --> pdb=" O GLY B 887 " (cutoff:3.500A) removed outlier: 6.121A pdb=" N ILE B 889 " --> pdb=" O ILE B 735 " (cutoff:3.500A) removed outlier: 6.717A pdb=" N ILE B 737 " --> pdb=" O ILE B 889 " (cutoff:3.500A) removed outlier: 4.553A pdb=" N PHE B 982 " --> pdb=" O VAL B 723 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 769 through 770 Processing sheet with id=AC9, first strand: chain 'B' and resid 806 through 808 removed outlier: 6.867A pdb=" N VAL B 835 " --> pdb=" O LEU B 807 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 897 through 898 Processing sheet with id=AD2, first strand: chain 'B' and resid 1053 through 1059 Processing sheet with id=AD3, first strand: chain 'B' and resid 1067 through 1069 Processing sheet with id=AD4, first strand: chain 'C' and resid 118 through 120 removed outlier: 3.508A pdb=" N MET C 118 " --> pdb=" O THR C 247 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'C' and resid 143 through 144 removed outlier: 6.972A pdb=" N THR C 143 " --> pdb=" O LEU C 225 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 149 through 155 Processing sheet with id=AD7, first strand: chain 'E' and resid 38 through 39 removed outlier: 5.701A pdb=" N ILE E 45 " --> pdb=" O TRP E 77 " (cutoff:3.500A) removed outlier: 6.867A pdb=" N TRP E 77 " --> pdb=" O ILE E 45 " (cutoff:3.500A) removed outlier: 6.737A pdb=" N ASP E 73 " --> pdb=" O LEU E 49 " (cutoff:3.500A) removed outlier: 4.528A pdb=" N VAL E 51 " --> pdb=" O VAL E 71 " (cutoff:3.500A) removed outlier: 6.959A pdb=" N VAL E 71 " --> pdb=" O VAL E 51 " (cutoff:3.500A) removed outlier: 6.871A pdb=" N ASP E 53 " --> pdb=" O GLU E 69 " (cutoff:3.500A) removed outlier: 6.880A pdb=" N GLU E 69 " --> pdb=" O ASP E 53 " (cutoff:3.500A) removed outlier: 8.266A pdb=" N TYR E 2 " --> pdb=" O TYR F 11 " (cutoff:3.500A) removed outlier: 5.629A pdb=" N TYR F 11 " --> pdb=" O TYR E 2 " (cutoff:3.500A) removed outlier: 7.080A pdb=" N ILE E 4 " --> pdb=" O GLU F 9 " (cutoff:3.500A) removed outlier: 4.625A pdb=" N GLU F 9 " --> pdb=" O ILE E 4 " (cutoff:3.500A) removed outlier: 6.512A pdb=" N THR E 6 " --> pdb=" O LEU F 7 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'E' and resid 38 through 39 removed outlier: 5.701A pdb=" N ILE E 45 " --> pdb=" O TRP E 77 " (cutoff:3.500A) removed outlier: 6.867A pdb=" N TRP E 77 " --> pdb=" O ILE E 45 " (cutoff:3.500A) removed outlier: 6.737A pdb=" N ASP E 73 " --> pdb=" O LEU E 49 " (cutoff:3.500A) removed outlier: 4.528A pdb=" N VAL E 51 " --> pdb=" O VAL E 71 " (cutoff:3.500A) removed outlier: 6.959A pdb=" N VAL E 71 " --> pdb=" O VAL E 51 " (cutoff:3.500A) removed outlier: 6.871A pdb=" N ASP E 53 " --> pdb=" O GLU E 69 " (cutoff:3.500A) removed outlier: 6.880A pdb=" N GLU E 69 " --> pdb=" O ASP E 53 " (cutoff:3.500A) removed outlier: 4.289A pdb=" N LEU C 382 " --> pdb=" O ILE E 59 " (cutoff:3.500A) removed outlier: 4.627A pdb=" N LYS C 381 " --> pdb=" O ILE K 54 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'D' and resid 5 through 11 removed outlier: 6.637A pdb=" N LYS D 17 " --> pdb=" O LEU D 9 " (cutoff:3.500A) removed outlier: 4.998A pdb=" N LYS D 11 " --> pdb=" O SER D 15 " (cutoff:3.500A) removed outlier: 6.921A pdb=" N SER D 15 " --> pdb=" O LYS D 11 " (cutoff:3.500A) removed outlier: 5.140A pdb=" N TYR D 158 " --> pdb=" O VAL D 218 " (cutoff:3.500A) removed outlier: 9.008A pdb=" N ASN D 220 " --> pdb=" O LYS D 156 " (cutoff:3.500A) removed outlier: 10.688A pdb=" N LYS D 156 " --> pdb=" O ASN D 220 " (cutoff:3.500A) removed outlier: 9.522A pdb=" N TYR D 222 " --> pdb=" O TYR D 154 " (cutoff:3.500A) removed outlier: 10.256A pdb=" N TYR D 154 " --> pdb=" O TYR D 222 " (cutoff:3.500A) removed outlier: 10.221A pdb=" N PHE D 224 " --> pdb=" O PHE D 152 " (cutoff:3.500A) removed outlier: 11.403A pdb=" N PHE D 152 " --> pdb=" O PHE D 224 " (cutoff:3.500A) removed outlier: 4.394A pdb=" N THR D 159 " --> pdb=" O THR D 195 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'D' and resid 89 through 96 removed outlier: 6.877A pdb=" N ARG D 130 " --> pdb=" O ASN D 52 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N ASN D 52 " --> pdb=" O ARG D 130 " (cutoff:3.500A) removed outlier: 6.804A pdb=" N VAL D 132 " --> pdb=" O TYR D 50 " (cutoff:3.500A) removed outlier: 6.518A pdb=" N LYS D 138 " --> pdb=" O VAL D 44 " (cutoff:3.500A) removed outlier: 5.687A pdb=" N VAL D 44 " --> pdb=" O LYS D 138 " (cutoff:3.500A) removed outlier: 7.296A pdb=" N GLY D 140 " --> pdb=" O PHE D 42 " (cutoff:3.500A) removed outlier: 6.105A pdb=" N PHE D 42 " --> pdb=" O GLY D 140 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'D' and resid 99 through 102 removed outlier: 3.591A pdb=" N VAL D 123 " --> pdb=" O VAL D 101 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'E' and resid 171 through 172 removed outlier: 6.989A pdb=" N GLY E 162 " --> pdb=" O ILE E 147 " (cutoff:3.500A) removed outlier: 5.231A pdb=" N ILE E 149 " --> pdb=" O ARG E 160 " (cutoff:3.500A) removed outlier: 7.389A pdb=" N ARG E 160 " --> pdb=" O ILE E 149 " (cutoff:3.500A) removed outlier: 7.024A pdb=" N ASP E 105 " --> pdb=" O ILE E 161 " (cutoff:3.500A) removed outlier: 7.989A pdb=" N LEU E 163 " --> pdb=" O ASP E 105 " (cutoff:3.500A) removed outlier: 6.337A pdb=" N LEU E 107 " --> pdb=" O LEU E 163 " (cutoff:3.500A) removed outlier: 6.983A pdb=" N GLY E 96 " --> pdb=" O VAL E 92 " (cutoff:3.500A) removed outlier: 5.250A pdb=" N VAL E 92 " --> pdb=" O GLY E 96 " (cutoff:3.500A) removed outlier: 7.104A pdb=" N PHE E 98 " --> pdb=" O ALA E 90 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N TYR E 88 " --> pdb=" O ARG E 100 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'E' and resid 118 through 121 Processing sheet with id=AE5, first strand: chain 'L' and resid 3 through 7 removed outlier: 6.443A pdb=" N GLU L 14 " --> pdb=" O ILE L 6 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'H' and resid 17 through 20 removed outlier: 3.846A pdb=" N GLU H 17 " --> pdb=" O LYS H 64 " (cutoff:3.500A) 1255 hydrogen bonds defined for protein. 3468 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 49 hydrogen bonds 98 hydrogen bond angles 0 basepair planarities 19 basepair parallelities 27 stacking parallelities Total time for adding SS restraints: 12.44 Time building geometry restraints manager: 8.09 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: 8705 1.34 - 1.46: 3840 1.46 - 1.58: 14946 1.58 - 1.70: 75 1.70 - 1.82: 194 Bond restraints: 27760 Sorted by residual: bond pdb=" CA ARG B 377 " pdb=" CB ARG B 377 " ideal model delta sigma weight residual 1.532 1.558 -0.026 1.74e-02 3.30e+03 2.22e+00 bond pdb=" CB GLU A 140 " pdb=" CG GLU A 140 " ideal model delta sigma weight residual 1.520 1.556 -0.036 3.00e-02 1.11e+03 1.41e+00 bond pdb=" CB LYS F 53 " pdb=" CG LYS F 53 " ideal model delta sigma weight residual 1.520 1.555 -0.035 3.00e-02 1.11e+03 1.37e+00 bond pdb=" CG LYS H 51 " pdb=" CD LYS H 51 " ideal model delta sigma weight residual 1.520 1.552 -0.032 3.00e-02 1.11e+03 1.13e+00 bond pdb=" CB ASP B 550 " pdb=" CG ASP B 550 " ideal model delta sigma weight residual 1.516 1.542 -0.026 2.50e-02 1.60e+03 1.06e+00 ... (remaining 27755 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.70: 37582 3.70 - 7.40: 63 7.40 - 11.09: 3 11.09 - 14.79: 0 14.79 - 18.49: 1 Bond angle restraints: 37649 Sorted by residual: angle pdb=" O GLY C 230 " pdb=" C GLY C 230 " pdb=" N VAL C 231 " ideal model delta sigma weight residual 122.39 103.90 18.49 1.27e+00 6.20e-01 2.12e+02 angle pdb=" CA GLU B 249 " pdb=" CB GLU B 249 " pdb=" CG GLU B 249 " ideal model delta sigma weight residual 114.10 121.83 -7.73 2.00e+00 2.50e-01 1.49e+01 angle pdb=" CA ARG B 377 " pdb=" CB ARG B 377 " pdb=" CG ARG B 377 " ideal model delta sigma weight residual 114.10 121.19 -7.09 2.00e+00 2.50e-01 1.26e+01 angle pdb=" N PRO A 425 " pdb=" CA PRO A 425 " pdb=" C PRO A 425 " ideal model delta sigma weight residual 112.47 105.70 6.77 2.06e+00 2.36e-01 1.08e+01 angle pdb=" C ARG B 377 " pdb=" CA ARG B 377 " pdb=" CB ARG B 377 " ideal model delta sigma weight residual 110.09 115.15 -5.06 1.67e+00 3.59e-01 9.19e+00 ... (remaining 37644 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 26.93: 15615 26.93 - 53.86: 1187 53.86 - 80.78: 181 80.78 - 107.71: 26 107.71 - 134.64: 2 Dihedral angle restraints: 17011 sinusoidal: 7505 harmonic: 9506 Sorted by residual: dihedral pdb=" CA GLN A 424 " pdb=" C GLN A 424 " pdb=" N PRO A 425 " pdb=" CA PRO A 425 " ideal model delta harmonic sigma weight residual 180.00 126.37 53.63 0 5.00e+00 4.00e-02 1.15e+02 dihedral pdb=" CA LYS A 158 " pdb=" C LYS A 158 " pdb=" N PRO A 159 " pdb=" CA PRO A 159 " ideal model delta harmonic sigma weight residual -180.00 -133.08 -46.92 0 5.00e+00 4.00e-02 8.80e+01 dihedral pdb=" CA ARG A 423 " pdb=" C ARG A 423 " pdb=" N GLN A 424 " pdb=" CA GLN A 424 " ideal model delta harmonic sigma weight residual -180.00 -154.94 -25.06 0 5.00e+00 4.00e-02 2.51e+01 ... (remaining 17008 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.038: 2962 0.038 - 0.076: 815 0.076 - 0.115: 348 0.115 - 0.153: 56 0.153 - 0.191: 5 Chirality restraints: 4186 Sorted by residual: chirality pdb=" CB ILE B 188 " pdb=" CA ILE B 188 " pdb=" CG1 ILE B 188 " pdb=" CG2 ILE B 188 " both_signs ideal model delta sigma weight residual False 2.64 2.45 0.19 2.00e-01 2.50e+01 9.12e-01 chirality pdb=" CA GLN A 424 " pdb=" N GLN A 424 " pdb=" C GLN A 424 " pdb=" CB GLN A 424 " both_signs ideal model delta sigma weight residual False 2.51 2.32 0.19 2.00e-01 2.50e+01 8.91e-01 chirality pdb=" CA ILE B 529 " pdb=" N ILE B 529 " pdb=" C ILE B 529 " pdb=" CB ILE B 529 " both_signs ideal model delta sigma weight residual False 2.43 2.61 -0.18 2.00e-01 2.50e+01 8.23e-01 ... (remaining 4183 not shown) Planarity restraints: 4740 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLY C 230 " 0.079 2.00e-02 2.50e+03 1.40e-01 1.97e+02 pdb=" C GLY C 230 " -0.243 2.00e-02 2.50e+03 pdb=" O GLY C 230 " 0.087 2.00e-02 2.50e+03 pdb=" N VAL C 231 " 0.077 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LYS A 158 " 0.054 5.00e-02 4.00e+02 8.23e-02 1.08e+01 pdb=" N PRO A 159 " -0.142 5.00e-02 4.00e+02 pdb=" CA PRO A 159 " 0.043 5.00e-02 4.00e+02 pdb=" CD PRO A 159 " 0.045 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP A 201 " 0.045 5.00e-02 4.00e+02 6.89e-02 7.60e+00 pdb=" N PRO A 202 " -0.119 5.00e-02 4.00e+02 pdb=" CA PRO A 202 " 0.036 5.00e-02 4.00e+02 pdb=" CD PRO A 202 " 0.038 5.00e-02 4.00e+02 ... (remaining 4737 not shown) Histogram of nonbonded interaction distances: 1.92 - 2.52: 174 2.52 - 3.11: 19479 3.11 - 3.71: 43605 3.71 - 4.30: 62235 4.30 - 4.90: 104816 Nonbonded interactions: 230309 Sorted by model distance: nonbonded pdb=" OD1 ASP A 458 " pdb="MG MG A1002 " model vdw 1.922 2.170 nonbonded pdb=" O3' G Z 19 " pdb="MG MG A1002 " model vdw 1.935 2.170 nonbonded pdb=" OD1 ASP A 460 " pdb="MG MG A1002 " model vdw 1.947 2.170 nonbonded pdb=" O ASP P 18 " pdb=" OG1 THR P 22 " model vdw 2.090 3.040 nonbonded pdb=" OD1 ASP A 462 " pdb="MG MG A1002 " model vdw 2.180 2.170 ... (remaining 230304 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: 0.930 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 1.010 Check model and map are aligned: 0.180 Set scattering table: 0.240 Process input model: 72.360 Find NCS groups from input model: 0.250 Set up NCS constraints: 0.100 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:2.730 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 77.840 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6409 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 0.041 27780 Z= 0.126 Angle : 0.571 18.491 37676 Z= 0.302 Chirality : 0.042 0.191 4186 Planarity : 0.005 0.140 4740 Dihedral : 18.211 134.640 10905 Min Nonbonded Distance : 1.922 Molprobity Statistics. All-atom Clashscore : 10.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.72 % Favored : 98.28 % Rotamer: Outliers : 0.42 % Allowed : 22.35 % Favored : 77.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.13 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.71 (0.15), residues: 3265 helix: 1.40 (0.15), residues: 1269 sheet: -0.36 (0.24), residues: 484 loop : 0.07 (0.16), residues: 1512 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP A 163 HIS 0.004 0.001 HIS B 302 PHE 0.024 0.001 PHE B 225 TYR 0.015 0.001 TYR P 36 ARG 0.008 0.000 ARG B 377 Details of bonding type rmsd hydrogen bonds : bond 0.16599 ( 1274) hydrogen bonds : angle 6.81991 ( 3566) metal coordination : bond 0.00454 ( 20) metal coordination : angle 4.67276 ( 27) covalent geometry : bond 0.00282 (27760) covalent geometry : angle 0.55716 (37649) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6530 Ramachandran restraints generated. 3265 Oldfield, 0 Emsley, 3265 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6530 Ramachandran restraints generated. 3265 Oldfield, 0 Emsley, 3265 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1053 residues out of total 2854 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 1041 time to evaluate : 2.973 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 40 LYS cc_start: 0.8145 (mmtt) cc_final: 0.7598 (mmtt) REVERT: F 57 ASP cc_start: 0.7478 (p0) cc_final: 0.6906 (p0) REVERT: F 117 LYS cc_start: 0.7866 (ptpt) cc_final: 0.6948 (pttt) outliers start: 12 outliers final: 4 residues processed: 1043 average time/residue: 0.4336 time to fit residues: 677.5415 Evaluate side-chains 850 residues out of total 2854 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 846 time to evaluate : 2.916 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 564 ASP Chi-restraints excluded: chain B residue 139 ASP Chi-restraints excluded: chain B residue 687 THR Chi-restraints excluded: chain B residue 851 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 326 random chunks: chunk 275 optimal weight: 10.0000 chunk 247 optimal weight: 5.9990 chunk 137 optimal weight: 0.9990 chunk 84 optimal weight: 7.9990 chunk 166 optimal weight: 8.9990 chunk 132 optimal weight: 0.9990 chunk 255 optimal weight: 1.9990 chunk 98 optimal weight: 6.9990 chunk 155 optimal weight: 1.9990 chunk 190 optimal weight: 2.9990 chunk 296 optimal weight: 5.9990 overall best weight: 1.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 128 ASN ** A 370 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 424 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 485 GLN A 546 ASN A 744 HIS B 368 GLN B 590 HIS B 663 ASN ** B1037 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 296 GLN ** C 366 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 371 GLN D 7 GLN D 134 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3570 r_free = 0.3570 target = 0.119539 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3090 r_free = 0.3090 target = 0.092355 restraints weight = 63880.951| |-----------------------------------------------------------------------------| r_work (start): 0.3022 rms_B_bonded: 3.53 r_work: 0.2864 rms_B_bonded: 4.18 restraints_weight: 0.5000 r_work (final): 0.2864 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8034 moved from start: 0.1952 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 27780 Z= 0.167 Angle : 0.652 14.926 37676 Z= 0.332 Chirality : 0.046 0.335 4186 Planarity : 0.005 0.078 4740 Dihedral : 11.000 135.372 4111 Min Nonbonded Distance : 1.921 Molprobity Statistics. All-atom Clashscore : 10.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.96 % Favored : 98.04 % Rotamer: Outliers : 2.98 % Allowed : 24.04 % Favored : 72.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.13 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.80 (0.15), residues: 3265 helix: 1.44 (0.15), residues: 1298 sheet: -0.45 (0.24), residues: 476 loop : 0.20 (0.17), residues: 1491 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A 163 HIS 0.018 0.001 HIS F 47 PHE 0.023 0.002 PHE C 341 TYR 0.031 0.001 TYR E 134 ARG 0.010 0.001 ARG F 42 Details of bonding type rmsd hydrogen bonds : bond 0.04488 ( 1274) hydrogen bonds : angle 5.23573 ( 3566) metal coordination : bond 0.00858 ( 20) metal coordination : angle 4.84217 ( 27) covalent geometry : bond 0.00377 (27760) covalent geometry : angle 0.63966 (37649) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6530 Ramachandran restraints generated. 3265 Oldfield, 0 Emsley, 3265 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6530 Ramachandran restraints generated. 3265 Oldfield, 0 Emsley, 3265 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1003 residues out of total 2854 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 918 time to evaluate : 2.928 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 94 GLU cc_start: 0.8734 (pt0) cc_final: 0.8491 (pt0) REVERT: A 128 ASN cc_start: 0.9441 (m-40) cc_final: 0.9228 (m110) REVERT: A 237 ASP cc_start: 0.9407 (m-30) cc_final: 0.9194 (m-30) REVERT: A 464 MET cc_start: 0.9452 (mtp) cc_final: 0.9219 (mtp) REVERT: A 524 GLU cc_start: 0.8753 (mt-10) cc_final: 0.8498 (mt-10) REVERT: A 563 GLU cc_start: 0.8288 (tp30) cc_final: 0.8055 (tp30) REVERT: A 633 ASP cc_start: 0.9142 (t0) cc_final: 0.8922 (t0) REVERT: B 33 ASP cc_start: 0.9211 (m-30) cc_final: 0.8982 (m-30) REVERT: B 74 PHE cc_start: 0.7887 (t80) cc_final: 0.7609 (t80) REVERT: B 155 TYR cc_start: 0.9351 (p90) cc_final: 0.8766 (p90) REVERT: B 169 GLU cc_start: 0.8824 (tt0) cc_final: 0.8543 (tt0) REVERT: B 212 LEU cc_start: 0.9270 (mm) cc_final: 0.9012 (mm) REVERT: B 326 GLU cc_start: 0.8991 (tp30) cc_final: 0.8108 (tp30) REVERT: B 444 ASP cc_start: 0.8541 (t0) cc_final: 0.8108 (t0) REVERT: B 447 GLN cc_start: 0.8165 (mp10) cc_final: 0.7048 (mp10) REVERT: B 478 LYS cc_start: 0.8916 (mttp) cc_final: 0.8709 (mttp) REVERT: B 500 MET cc_start: 0.8982 (mmt) cc_final: 0.8495 (mmt) REVERT: B 541 GLN cc_start: 0.9356 (OUTLIER) cc_final: 0.8982 (tm-30) REVERT: B 562 GLU cc_start: 0.9010 (mt-10) cc_final: 0.8705 (mm-30) REVERT: B 663 ASN cc_start: 0.9372 (m-40) cc_final: 0.9126 (m110) REVERT: B 743 GLU cc_start: 0.9127 (mt-10) cc_final: 0.8917 (mt-10) REVERT: B 760 LYS cc_start: 0.8532 (mtmm) cc_final: 0.8300 (mtmm) REVERT: B 804 LYS cc_start: 0.8234 (tptp) cc_final: 0.7975 (tptp) REVERT: B 994 MET cc_start: 0.9451 (mtm) cc_final: 0.9212 (mtt) REVERT: B 1052 ASP cc_start: 0.8843 (p0) cc_final: 0.8186 (p0) REVERT: B 1060 GLU cc_start: 0.9169 (mt-10) cc_final: 0.8928 (mp0) REVERT: B 1092 SER cc_start: 0.9685 (p) cc_final: 0.9464 (p) REVERT: B 1103 LYS cc_start: 0.9005 (mtmm) cc_final: 0.8781 (mtmm) REVERT: C 94 ILE cc_start: 0.8810 (OUTLIER) cc_final: 0.8604 (tp) REVERT: C 188 PHE cc_start: 0.8210 (m-80) cc_final: 0.7966 (m-10) REVERT: C 198 TYR cc_start: 0.8884 (m-10) cc_final: 0.8432 (m-10) REVERT: C 248 GLU cc_start: 0.8980 (tt0) cc_final: 0.8635 (tm-30) REVERT: C 300 LEU cc_start: 0.9460 (mt) cc_final: 0.9165 (mp) REVERT: C 303 ASP cc_start: 0.8859 (t0) cc_final: 0.8490 (t0) REVERT: D 117 ASN cc_start: 0.8664 (t0) cc_final: 0.8246 (t0) REVERT: D 206 GLU cc_start: 0.9015 (pp20) cc_final: 0.8368 (mt-10) REVERT: D 209 GLU cc_start: 0.9197 (mt-10) cc_final: 0.8658 (mt-10) REVERT: E 38 TYR cc_start: 0.9101 (t80) cc_final: 0.8829 (t80) REVERT: E 127 PHE cc_start: 0.8271 (m-80) cc_final: 0.7935 (t80) REVERT: E 163 LEU cc_start: 0.7477 (tt) cc_final: 0.7219 (tt) REVERT: F 57 ASP cc_start: 0.9176 (p0) cc_final: 0.8784 (p0) REVERT: F 73 MET cc_start: 0.8762 (ppp) cc_final: 0.7659 (ppp) REVERT: L 39 LYS cc_start: 0.9383 (mtmm) cc_final: 0.9064 (mtmm) REVERT: L 53 ARG cc_start: 0.9186 (tpp80) cc_final: 0.8975 (tpp80) REVERT: L 56 ARG cc_start: 0.9270 (ttt180) cc_final: 0.8882 (ttt180) REVERT: L 73 GLU cc_start: 0.8922 (tt0) cc_final: 0.8326 (tp30) REVERT: L 77 LYS cc_start: 0.9232 (OUTLIER) cc_final: 0.8960 (tppp) REVERT: H 66 LYS cc_start: 0.9506 (ttmm) cc_final: 0.9167 (tptp) REVERT: N 32 GLU cc_start: 0.8677 (pp20) cc_final: 0.8206 (pp20) REVERT: K 11 ARG cc_start: 0.8902 (tpt90) cc_final: 0.8635 (tpt170) REVERT: K 38 GLU cc_start: 0.9239 (mt-10) cc_final: 0.9035 (mt-10) REVERT: P 3 GLU cc_start: 0.8352 (tp30) cc_final: 0.8123 (tp30) REVERT: P 14 GLU cc_start: 0.8006 (tm-30) cc_final: 0.7768 (tm-30) REVERT: P 17 LEU cc_start: 0.8239 (OUTLIER) cc_final: 0.7868 (pt) outliers start: 85 outliers final: 40 residues processed: 957 average time/residue: 0.4165 time to fit residues: 603.7391 Evaluate side-chains 880 residues out of total 2854 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 836 time to evaluate : 2.884 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 437 VAL Chi-restraints excluded: chain A residue 501 ILE Chi-restraints excluded: chain A residue 523 VAL Chi-restraints excluded: chain A residue 619 ILE Chi-restraints excluded: chain A residue 767 LEU Chi-restraints excluded: chain A residue 787 SER Chi-restraints excluded: chain B residue 67 ILE Chi-restraints excluded: chain B residue 116 VAL Chi-restraints excluded: chain B residue 391 ILE Chi-restraints excluded: chain B residue 466 THR Chi-restraints excluded: chain B residue 507 ILE Chi-restraints excluded: chain B residue 541 GLN Chi-restraints excluded: chain B residue 733 ASP Chi-restraints excluded: chain B residue 756 GLU Chi-restraints excluded: chain B residue 801 VAL Chi-restraints excluded: chain B residue 849 ILE Chi-restraints excluded: chain B residue 1116 ARG Chi-restraints excluded: chain C residue 30 LEU Chi-restraints excluded: chain C residue 73 SER Chi-restraints excluded: chain C residue 78 SER Chi-restraints excluded: chain C residue 80 GLN Chi-restraints excluded: chain C residue 94 ILE Chi-restraints excluded: chain C residue 96 VAL Chi-restraints excluded: chain C residue 273 GLU Chi-restraints excluded: chain C residue 353 GLU Chi-restraints excluded: chain D residue 15 SER Chi-restraints excluded: chain D residue 59 GLU Chi-restraints excluded: chain D residue 184 VAL Chi-restraints excluded: chain E residue 74 VAL Chi-restraints excluded: chain E residue 89 VAL Chi-restraints excluded: chain E residue 146 ILE Chi-restraints excluded: chain L residue 8 LYS Chi-restraints excluded: chain L residue 41 THR Chi-restraints excluded: chain L residue 77 LYS Chi-restraints excluded: chain H residue 9 ILE Chi-restraints excluded: chain N residue 3 VAL Chi-restraints excluded: chain N residue 60 MET Chi-restraints excluded: chain K residue 48 VAL Chi-restraints excluded: chain P residue 17 LEU Chi-restraints excluded: chain P residue 20 SER Chi-restraints excluded: chain P residue 24 ASP Chi-restraints excluded: chain P residue 29 TYR Chi-restraints excluded: chain P residue 42 VAL Chi-restraints excluded: chain P residue 47 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 326 random chunks: chunk 212 optimal weight: 8.9990 chunk 305 optimal weight: 9.9990 chunk 173 optimal weight: 5.9990 chunk 48 optimal weight: 4.9990 chunk 194 optimal weight: 6.9990 chunk 150 optimal weight: 0.8980 chunk 39 optimal weight: 0.6980 chunk 190 optimal weight: 10.0000 chunk 66 optimal weight: 4.9990 chunk 60 optimal weight: 6.9990 chunk 99 optimal weight: 1.9990 overall best weight: 2.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 424 GLN A 759 ASN B 75 GLN ** B 992 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1008 GLN ** B1037 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 72 GLN ** C 366 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 371 GLN D 7 GLN L 22 HIS K 19 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3552 r_free = 0.3552 target = 0.117801 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3072 r_free = 0.3072 target = 0.090815 restraints weight = 64358.684| |-----------------------------------------------------------------------------| r_work (start): 0.3040 rms_B_bonded: 3.52 r_work: 0.2876 rms_B_bonded: 4.21 restraints_weight: 0.5000 r_work (final): 0.2876 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8109 moved from start: 0.2389 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 27780 Z= 0.192 Angle : 0.628 14.535 37676 Z= 0.318 Chirality : 0.045 0.211 4186 Planarity : 0.005 0.078 4740 Dihedral : 10.883 135.009 4105 Min Nonbonded Distance : 1.908 Molprobity Statistics. All-atom Clashscore : 10.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.75 % Favored : 98.25 % Rotamer: Outliers : 4.10 % Allowed : 23.51 % Favored : 72.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.13 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.82 (0.15), residues: 3265 helix: 1.51 (0.15), residues: 1293 sheet: -0.57 (0.24), residues: 477 loop : 0.20 (0.16), residues: 1495 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 163 HIS 0.017 0.001 HIS F 47 PHE 0.018 0.001 PHE E 173 TYR 0.030 0.001 TYR E 134 ARG 0.007 0.001 ARG P 39 Details of bonding type rmsd hydrogen bonds : bond 0.04153 ( 1274) hydrogen bonds : angle 4.98628 ( 3566) metal coordination : bond 0.00920 ( 20) metal coordination : angle 4.49158 ( 27) covalent geometry : bond 0.00437 (27760) covalent geometry : angle 0.61691 (37649) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6530 Ramachandran restraints generated. 3265 Oldfield, 0 Emsley, 3265 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6530 Ramachandran restraints generated. 3265 Oldfield, 0 Emsley, 3265 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 991 residues out of total 2854 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 117 poor density : 874 time to evaluate : 3.219 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 128 ASN cc_start: 0.9515 (m-40) cc_final: 0.9306 (m110) REVERT: A 179 MET cc_start: 0.9001 (mmp) cc_final: 0.8537 (mmp) REVERT: A 235 GLU cc_start: 0.8825 (mm-30) cc_final: 0.8594 (mm-30) REVERT: A 392 MET cc_start: 0.9233 (ppp) cc_final: 0.8889 (ppp) REVERT: A 430 MET cc_start: 0.9460 (mpp) cc_final: 0.8772 (mpp) REVERT: A 483 GLU cc_start: 0.9145 (tt0) cc_final: 0.8894 (tt0) REVERT: A 485 GLN cc_start: 0.9298 (mt0) cc_final: 0.8919 (mt0) REVERT: A 563 GLU cc_start: 0.8425 (tp30) cc_final: 0.8091 (tp30) REVERT: A 585 LYS cc_start: 0.9568 (tmtt) cc_final: 0.9256 (tptm) REVERT: A 592 MET cc_start: 0.9119 (mtp) cc_final: 0.8714 (mpp) REVERT: A 700 LYS cc_start: 0.9564 (mtmt) cc_final: 0.9363 (mtmm) REVERT: A 828 ASP cc_start: 0.9014 (t0) cc_final: 0.8718 (t0) REVERT: B 74 PHE cc_start: 0.7912 (t80) cc_final: 0.7659 (t80) REVERT: B 126 MET cc_start: 0.9210 (ttm) cc_final: 0.8991 (ttp) REVERT: B 155 TYR cc_start: 0.9333 (p90) cc_final: 0.8700 (p90) REVERT: B 169 GLU cc_start: 0.8754 (tt0) cc_final: 0.8437 (tt0) REVERT: B 326 GLU cc_start: 0.9039 (tp30) cc_final: 0.8184 (tp30) REVERT: B 352 LEU cc_start: 0.9539 (OUTLIER) cc_final: 0.9199 (mm) REVERT: B 444 ASP cc_start: 0.8747 (t0) cc_final: 0.8304 (t0) REVERT: B 447 GLN cc_start: 0.8436 (mp10) cc_final: 0.7295 (mp10) REVERT: B 541 GLN cc_start: 0.9368 (OUTLIER) cc_final: 0.8950 (tm-30) REVERT: B 726 TYR cc_start: 0.9317 (t80) cc_final: 0.8619 (t80) REVERT: B 760 LYS cc_start: 0.8583 (mtmm) cc_final: 0.8019 (mtmm) REVERT: B 800 LYS cc_start: 0.9378 (mtmm) cc_final: 0.9167 (mttm) REVERT: B 804 LYS cc_start: 0.8318 (tptp) cc_final: 0.8017 (tptp) REVERT: B 954 GLU cc_start: 0.9089 (mp0) cc_final: 0.8780 (mm-30) REVERT: B 994 MET cc_start: 0.9446 (mtm) cc_final: 0.9180 (mtt) REVERT: B 1052 ASP cc_start: 0.8910 (p0) cc_final: 0.8201 (p0) REVERT: B 1060 GLU cc_start: 0.9191 (mt-10) cc_final: 0.8935 (mp0) REVERT: B 1091 MET cc_start: 0.8996 (ptm) cc_final: 0.8652 (ptm) REVERT: C 81 MET cc_start: 0.8502 (tpp) cc_final: 0.8207 (tpp) REVERT: C 161 PHE cc_start: 0.8644 (t80) cc_final: 0.8393 (t80) REVERT: C 248 GLU cc_start: 0.9019 (tt0) cc_final: 0.8618 (tm-30) REVERT: C 303 ASP cc_start: 0.9020 (t0) cc_final: 0.8579 (t0) REVERT: D 10 GLU cc_start: 0.8901 (tp30) cc_final: 0.8692 (tm-30) REVERT: D 87 TYR cc_start: 0.9024 (t80) cc_final: 0.8787 (t80) REVERT: D 117 ASN cc_start: 0.8694 (t0) cc_final: 0.8210 (t0) REVERT: D 206 GLU cc_start: 0.9013 (pp20) cc_final: 0.8389 (mt-10) REVERT: D 209 GLU cc_start: 0.9226 (mt-10) cc_final: 0.8686 (mt-10) REVERT: E 38 TYR cc_start: 0.9097 (t80) cc_final: 0.8882 (t80) REVERT: E 163 LEU cc_start: 0.7699 (OUTLIER) cc_final: 0.7412 (tt) REVERT: F 37 LEU cc_start: 0.9121 (OUTLIER) cc_final: 0.8904 (mt) REVERT: F 42 ARG cc_start: 0.9423 (mtm-85) cc_final: 0.9087 (mtm-85) REVERT: F 73 MET cc_start: 0.8783 (ppp) cc_final: 0.8190 (ppp) REVERT: L 39 LYS cc_start: 0.9398 (mtmm) cc_final: 0.9060 (mtmm) REVERT: L 46 GLU cc_start: 0.8961 (mp0) cc_final: 0.8752 (mp0) REVERT: L 53 ARG cc_start: 0.9232 (tpp80) cc_final: 0.8944 (tpp80) REVERT: L 73 GLU cc_start: 0.8954 (tt0) cc_final: 0.8541 (tp30) REVERT: H 17 GLU cc_start: 0.8287 (tm-30) cc_final: 0.7746 (tm-30) REVERT: H 24 GLU cc_start: 0.9369 (tp30) cc_final: 0.9163 (tp30) REVERT: H 66 LYS cc_start: 0.9507 (ttmm) cc_final: 0.9226 (tptp) REVERT: N 32 GLU cc_start: 0.8828 (pp20) cc_final: 0.8492 (pp20) REVERT: N 33 LYS cc_start: 0.9597 (ttmm) cc_final: 0.9319 (mmmm) REVERT: K 38 GLU cc_start: 0.9246 (mt-10) cc_final: 0.9008 (mt-10) REVERT: P 45 ARG cc_start: 0.8890 (tpp-160) cc_final: 0.8648 (tpp-160) outliers start: 117 outliers final: 69 residues processed: 933 average time/residue: 0.4151 time to fit residues: 590.8449 Evaluate side-chains 898 residues out of total 2854 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 825 time to evaluate : 2.897 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 163 TRP Chi-restraints excluded: chain A residue 252 LEU Chi-restraints excluded: chain A residue 306 LYS Chi-restraints excluded: chain A residue 421 PHE Chi-restraints excluded: chain A residue 437 VAL Chi-restraints excluded: chain A residue 501 ILE Chi-restraints excluded: chain A residue 523 VAL Chi-restraints excluded: chain A residue 619 ILE Chi-restraints excluded: chain A residue 767 LEU Chi-restraints excluded: chain A residue 787 SER Chi-restraints excluded: chain A residue 891 ILE Chi-restraints excluded: chain B residue 67 ILE Chi-restraints excluded: chain B residue 116 VAL Chi-restraints excluded: chain B residue 125 ILE Chi-restraints excluded: chain B residue 143 ILE Chi-restraints excluded: chain B residue 164 VAL Chi-restraints excluded: chain B residue 234 LEU Chi-restraints excluded: chain B residue 305 VAL Chi-restraints excluded: chain B residue 340 TYR Chi-restraints excluded: chain B residue 347 LEU Chi-restraints excluded: chain B residue 352 LEU Chi-restraints excluded: chain B residue 366 ASP Chi-restraints excluded: chain B residue 391 ILE Chi-restraints excluded: chain B residue 405 GLU Chi-restraints excluded: chain B residue 466 THR Chi-restraints excluded: chain B residue 468 THR Chi-restraints excluded: chain B residue 507 ILE Chi-restraints excluded: chain B residue 541 GLN Chi-restraints excluded: chain B residue 673 SER Chi-restraints excluded: chain B residue 687 THR Chi-restraints excluded: chain B residue 733 ASP Chi-restraints excluded: chain B residue 756 GLU Chi-restraints excluded: chain B residue 763 LEU Chi-restraints excluded: chain B residue 801 VAL Chi-restraints excluded: chain B residue 849 ILE Chi-restraints excluded: chain B residue 978 GLU Chi-restraints excluded: chain B residue 1044 ILE Chi-restraints excluded: chain B residue 1116 ARG Chi-restraints excluded: chain C residue 37 TYR Chi-restraints excluded: chain C residue 50 ASP Chi-restraints excluded: chain C residue 59 LEU Chi-restraints excluded: chain C residue 73 SER Chi-restraints excluded: chain C residue 80 GLN Chi-restraints excluded: chain C residue 96 VAL Chi-restraints excluded: chain C residue 118 MET Chi-restraints excluded: chain C residue 136 VAL Chi-restraints excluded: chain C residue 145 LEU Chi-restraints excluded: chain C residue 233 LYS Chi-restraints excluded: chain C residue 265 ARG Chi-restraints excluded: chain C residue 273 GLU Chi-restraints excluded: chain C residue 353 GLU Chi-restraints excluded: chain C residue 386 LEU Chi-restraints excluded: chain D residue 15 SER Chi-restraints excluded: chain D residue 59 GLU Chi-restraints excluded: chain D residue 184 VAL Chi-restraints excluded: chain E residue 56 ASP Chi-restraints excluded: chain E residue 74 VAL Chi-restraints excluded: chain E residue 146 ILE Chi-restraints excluded: chain E residue 163 LEU Chi-restraints excluded: chain F residue 21 LEU Chi-restraints excluded: chain F residue 37 LEU Chi-restraints excluded: chain L residue 8 LYS Chi-restraints excluded: chain L residue 41 THR Chi-restraints excluded: chain L residue 50 THR Chi-restraints excluded: chain L residue 94 LYS Chi-restraints excluded: chain H residue 9 ILE Chi-restraints excluded: chain N residue 3 VAL Chi-restraints excluded: chain N residue 60 MET Chi-restraints excluded: chain K residue 21 SER Chi-restraints excluded: chain K residue 48 VAL Chi-restraints excluded: chain P residue 24 ASP Chi-restraints excluded: chain P residue 42 VAL Chi-restraints excluded: chain P residue 47 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 326 random chunks: chunk 189 optimal weight: 1.9990 chunk 114 optimal weight: 4.9990 chunk 262 optimal weight: 2.9990 chunk 187 optimal weight: 9.9990 chunk 22 optimal weight: 10.0000 chunk 223 optimal weight: 9.9990 chunk 247 optimal weight: 9.9990 chunk 180 optimal weight: 0.9990 chunk 228 optimal weight: 5.9990 chunk 56 optimal weight: 2.9990 chunk 257 optimal weight: 0.1980 overall best weight: 1.8388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 254 GLN A 759 ASN B1008 GLN ** B1037 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 72 GLN C 371 GLN D 7 GLN L 22 HIS K 19 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3562 r_free = 0.3562 target = 0.118330 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3087 r_free = 0.3087 target = 0.091385 restraints weight = 64504.965| |-----------------------------------------------------------------------------| r_work (start): 0.3019 rms_B_bonded: 3.55 r_work: 0.2857 rms_B_bonded: 4.24 restraints_weight: 0.5000 r_work (final): 0.2857 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8079 moved from start: 0.2619 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 27780 Z= 0.153 Angle : 0.608 14.444 37676 Z= 0.307 Chirality : 0.044 0.186 4186 Planarity : 0.004 0.074 4740 Dihedral : 10.798 134.710 4105 Min Nonbonded Distance : 1.913 Molprobity Statistics. All-atom Clashscore : 10.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.02 % Favored : 97.98 % Rotamer: Outliers : 3.68 % Allowed : 24.84 % Favored : 71.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.13 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.86 (0.15), residues: 3265 helix: 1.52 (0.15), residues: 1293 sheet: -0.44 (0.23), residues: 469 loop : 0.21 (0.17), residues: 1503 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 163 HIS 0.008 0.001 HIS F 47 PHE 0.028 0.001 PHE C 193 TYR 0.026 0.001 TYR E 134 ARG 0.007 0.000 ARG C 267 Details of bonding type rmsd hydrogen bonds : bond 0.03799 ( 1274) hydrogen bonds : angle 4.81122 ( 3566) metal coordination : bond 0.00779 ( 20) metal coordination : angle 4.45667 ( 27) covalent geometry : bond 0.00351 (27760) covalent geometry : angle 0.59634 (37649) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6530 Ramachandran restraints generated. 3265 Oldfield, 0 Emsley, 3265 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6530 Ramachandran restraints generated. 3265 Oldfield, 0 Emsley, 3265 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 967 residues out of total 2854 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 105 poor density : 862 time to evaluate : 3.055 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 128 ASN cc_start: 0.9571 (m-40) cc_final: 0.9336 (m110) REVERT: A 179 MET cc_start: 0.8953 (mmp) cc_final: 0.8735 (mmp) REVERT: A 392 MET cc_start: 0.9211 (ppp) cc_final: 0.8936 (ppp) REVERT: A 485 GLN cc_start: 0.9272 (mt0) cc_final: 0.8987 (mt0) REVERT: A 563 GLU cc_start: 0.8387 (tp30) cc_final: 0.8028 (tp30) REVERT: A 585 LYS cc_start: 0.9543 (tmtt) cc_final: 0.9207 (tptm) REVERT: A 592 MET cc_start: 0.9151 (mtp) cc_final: 0.8722 (mpp) REVERT: A 700 LYS cc_start: 0.9565 (mtmt) cc_final: 0.9356 (mtmm) REVERT: A 828 ASP cc_start: 0.8910 (t0) cc_final: 0.8623 (t0) REVERT: A 860 SER cc_start: 0.8530 (OUTLIER) cc_final: 0.8274 (p) REVERT: A 864 ILE cc_start: 0.9477 (mt) cc_final: 0.9252 (mp) REVERT: B 74 PHE cc_start: 0.7948 (t80) cc_final: 0.7688 (t80) REVERT: B 126 MET cc_start: 0.9216 (ttm) cc_final: 0.8998 (ttp) REVERT: B 155 TYR cc_start: 0.9324 (p90) cc_final: 0.8722 (p90) REVERT: B 169 GLU cc_start: 0.8769 (tt0) cc_final: 0.8568 (tt0) REVERT: B 326 GLU cc_start: 0.9009 (tp30) cc_final: 0.8187 (tp30) REVERT: B 352 LEU cc_start: 0.9510 (OUTLIER) cc_final: 0.9196 (mm) REVERT: B 362 GLN cc_start: 0.9110 (OUTLIER) cc_final: 0.8717 (tm-30) REVERT: B 444 ASP cc_start: 0.8729 (t0) cc_final: 0.8344 (t0) REVERT: B 447 GLN cc_start: 0.8415 (mp10) cc_final: 0.7322 (mp10) REVERT: B 541 GLN cc_start: 0.9394 (OUTLIER) cc_final: 0.8984 (tm-30) REVERT: B 562 GLU cc_start: 0.9152 (mt-10) cc_final: 0.8814 (mm-30) REVERT: B 726 TYR cc_start: 0.9276 (t80) cc_final: 0.8570 (t80) REVERT: B 760 LYS cc_start: 0.8618 (mtmm) cc_final: 0.8282 (mtmm) REVERT: B 804 LYS cc_start: 0.8344 (tptp) cc_final: 0.8016 (tptp) REVERT: B 895 MET cc_start: 0.9533 (tpp) cc_final: 0.9272 (tpp) REVERT: B 1052 ASP cc_start: 0.8808 (p0) cc_final: 0.8166 (p0) REVERT: B 1060 GLU cc_start: 0.9185 (mt-10) cc_final: 0.8937 (mp0) REVERT: B 1091 MET cc_start: 0.8999 (ptm) cc_final: 0.8474 (ptm) REVERT: C 59 LEU cc_start: 0.9503 (OUTLIER) cc_final: 0.9151 (mt) REVERT: C 83 LEU cc_start: 0.7623 (OUTLIER) cc_final: 0.7375 (tt) REVERT: C 141 GLU cc_start: 0.8980 (tt0) cc_final: 0.8658 (pt0) REVERT: C 248 GLU cc_start: 0.9011 (tt0) cc_final: 0.8802 (tt0) REVERT: C 265 ARG cc_start: 0.9069 (OUTLIER) cc_final: 0.8545 (mtm180) REVERT: C 276 GLU cc_start: 0.9003 (mt-10) cc_final: 0.8764 (mt-10) REVERT: C 296 GLN cc_start: 0.9035 (tm-30) cc_final: 0.8736 (pp30) REVERT: C 303 ASP cc_start: 0.9070 (t0) cc_final: 0.8551 (t0) REVERT: D 10 GLU cc_start: 0.8896 (tp30) cc_final: 0.8464 (tm-30) REVERT: D 87 TYR cc_start: 0.9095 (t80) cc_final: 0.8809 (t80) REVERT: D 117 ASN cc_start: 0.8766 (t0) cc_final: 0.8349 (t0) REVERT: D 206 GLU cc_start: 0.9009 (pp20) cc_final: 0.8411 (mt-10) REVERT: D 209 GLU cc_start: 0.9242 (mt-10) cc_final: 0.8651 (mt-10) REVERT: E 38 TYR cc_start: 0.9096 (t80) cc_final: 0.8888 (t80) REVERT: E 158 GLU cc_start: 0.9519 (mm-30) cc_final: 0.9265 (mm-30) REVERT: E 164 THR cc_start: 0.7756 (OUTLIER) cc_final: 0.7334 (t) REVERT: F 76 ARG cc_start: 0.8850 (tmm-80) cc_final: 0.8586 (ptm-80) REVERT: L 39 LYS cc_start: 0.9381 (mtmm) cc_final: 0.9009 (mtmm) REVERT: L 46 GLU cc_start: 0.9045 (mp0) cc_final: 0.8820 (mp0) REVERT: L 56 ARG cc_start: 0.9275 (ttt180) cc_final: 0.8891 (ttt180) REVERT: L 73 GLU cc_start: 0.8970 (tt0) cc_final: 0.8554 (tp30) REVERT: H 17 GLU cc_start: 0.8309 (tm-30) cc_final: 0.7765 (tm-30) REVERT: H 51 LYS cc_start: 0.9590 (mmmm) cc_final: 0.9332 (mmmm) REVERT: H 66 LYS cc_start: 0.9496 (ttmm) cc_final: 0.9219 (tptp) REVERT: N 32 GLU cc_start: 0.8790 (pp20) cc_final: 0.8396 (pp20) REVERT: N 33 LYS cc_start: 0.9608 (ttmm) cc_final: 0.9324 (mmmm) REVERT: P 3 GLU cc_start: 0.8284 (tp30) cc_final: 0.8013 (tp30) outliers start: 105 outliers final: 73 residues processed: 911 average time/residue: 0.4139 time to fit residues: 573.7152 Evaluate side-chains 906 residues out of total 2854 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 825 time to evaluate : 3.267 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 163 TRP Chi-restraints excluded: chain A residue 252 LEU Chi-restraints excluded: chain A residue 306 LYS Chi-restraints excluded: chain A residue 421 PHE Chi-restraints excluded: chain A residue 487 HIS Chi-restraints excluded: chain A residue 501 ILE Chi-restraints excluded: chain A residue 519 THR Chi-restraints excluded: chain A residue 523 VAL Chi-restraints excluded: chain A residue 641 VAL Chi-restraints excluded: chain A residue 714 ASP Chi-restraints excluded: chain A residue 767 LEU Chi-restraints excluded: chain A residue 787 SER Chi-restraints excluded: chain A residue 860 SER Chi-restraints excluded: chain A residue 878 MET Chi-restraints excluded: chain A residue 891 ILE Chi-restraints excluded: chain B residue 67 ILE Chi-restraints excluded: chain B residue 116 VAL Chi-restraints excluded: chain B residue 143 ILE Chi-restraints excluded: chain B residue 234 LEU Chi-restraints excluded: chain B residue 258 LEU Chi-restraints excluded: chain B residue 265 THR Chi-restraints excluded: chain B residue 305 VAL Chi-restraints excluded: chain B residue 340 TYR Chi-restraints excluded: chain B residue 347 LEU Chi-restraints excluded: chain B residue 352 LEU Chi-restraints excluded: chain B residue 362 GLN Chi-restraints excluded: chain B residue 364 VAL Chi-restraints excluded: chain B residue 366 ASP Chi-restraints excluded: chain B residue 391 ILE Chi-restraints excluded: chain B residue 405 GLU Chi-restraints excluded: chain B residue 466 THR Chi-restraints excluded: chain B residue 468 THR Chi-restraints excluded: chain B residue 482 LEU Chi-restraints excluded: chain B residue 507 ILE Chi-restraints excluded: chain B residue 541 GLN Chi-restraints excluded: chain B residue 673 SER Chi-restraints excluded: chain B residue 687 THR Chi-restraints excluded: chain B residue 733 ASP Chi-restraints excluded: chain B residue 756 GLU Chi-restraints excluded: chain B residue 801 VAL Chi-restraints excluded: chain B residue 849 ILE Chi-restraints excluded: chain B residue 1044 ILE Chi-restraints excluded: chain C residue 30 LEU Chi-restraints excluded: chain C residue 37 TYR Chi-restraints excluded: chain C residue 59 LEU Chi-restraints excluded: chain C residue 74 ILE Chi-restraints excluded: chain C residue 80 GLN Chi-restraints excluded: chain C residue 83 LEU Chi-restraints excluded: chain C residue 96 VAL Chi-restraints excluded: chain C residue 136 VAL Chi-restraints excluded: chain C residue 145 LEU Chi-restraints excluded: chain C residue 170 LEU Chi-restraints excluded: chain C residue 233 LYS Chi-restraints excluded: chain C residue 265 ARG Chi-restraints excluded: chain C residue 273 GLU Chi-restraints excluded: chain C residue 353 GLU Chi-restraints excluded: chain C residue 386 LEU Chi-restraints excluded: chain D residue 15 SER Chi-restraints excluded: chain D residue 59 GLU Chi-restraints excluded: chain D residue 100 ILE Chi-restraints excluded: chain D residue 184 VAL Chi-restraints excluded: chain E residue 56 ASP Chi-restraints excluded: chain E residue 74 VAL Chi-restraints excluded: chain E residue 130 LYS Chi-restraints excluded: chain E residue 146 ILE Chi-restraints excluded: chain E residue 164 THR Chi-restraints excluded: chain L residue 8 LYS Chi-restraints excluded: chain L residue 41 THR Chi-restraints excluded: chain L residue 94 LYS Chi-restraints excluded: chain H residue 9 ILE Chi-restraints excluded: chain H residue 32 LYS Chi-restraints excluded: chain H residue 56 LYS Chi-restraints excluded: chain N residue 3 VAL Chi-restraints excluded: chain N residue 13 VAL Chi-restraints excluded: chain N residue 49 LEU Chi-restraints excluded: chain N residue 60 MET Chi-restraints excluded: chain K residue 48 VAL Chi-restraints excluded: chain P residue 20 SER Chi-restraints excluded: chain P residue 24 ASP Chi-restraints excluded: chain P residue 42 VAL Chi-restraints excluded: chain P residue 47 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 326 random chunks: chunk 21 optimal weight: 0.9980 chunk 211 optimal weight: 9.9990 chunk 267 optimal weight: 7.9990 chunk 210 optimal weight: 3.9990 chunk 60 optimal weight: 7.9990 chunk 36 optimal weight: 6.9990 chunk 199 optimal weight: 9.9990 chunk 79 optimal weight: 2.9990 chunk 124 optimal weight: 0.9990 chunk 75 optimal weight: 9.9990 chunk 271 optimal weight: 6.9990 overall best weight: 3.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 479 ASN ** B 992 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1008 GLN ** B1037 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 72 GLN C 269 ASN C 371 GLN ** D 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 22 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3544 r_free = 0.3544 target = 0.116936 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3062 r_free = 0.3062 target = 0.089998 restraints weight = 64586.811| |-----------------------------------------------------------------------------| r_work (start): 0.2995 rms_B_bonded: 3.54 r_work: 0.2830 rms_B_bonded: 4.22 restraints_weight: 0.5000 r_work (final): 0.2830 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8142 moved from start: 0.2813 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 27780 Z= 0.217 Angle : 0.628 13.844 37676 Z= 0.319 Chirality : 0.045 0.198 4186 Planarity : 0.004 0.073 4740 Dihedral : 10.786 135.115 4105 Min Nonbonded Distance : 1.890 Molprobity Statistics. All-atom Clashscore : 10.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.99 % Favored : 98.01 % Rotamer: Outliers : 4.20 % Allowed : 24.42 % Favored : 71.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.13 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.81 (0.15), residues: 3265 helix: 1.45 (0.15), residues: 1296 sheet: -0.70 (0.24), residues: 436 loop : 0.26 (0.16), residues: 1533 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 163 HIS 0.009 0.001 HIS F 47 PHE 0.021 0.001 PHE C 161 TYR 0.026 0.001 TYR E 134 ARG 0.011 0.001 ARG F 42 Details of bonding type rmsd hydrogen bonds : bond 0.03893 ( 1274) hydrogen bonds : angle 4.79621 ( 3566) metal coordination : bond 0.01160 ( 20) metal coordination : angle 4.34305 ( 27) covalent geometry : bond 0.00496 (27760) covalent geometry : angle 0.61746 (37649) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6530 Ramachandran restraints generated. 3265 Oldfield, 0 Emsley, 3265 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6530 Ramachandran restraints generated. 3265 Oldfield, 0 Emsley, 3265 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 954 residues out of total 2854 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 120 poor density : 834 time to evaluate : 3.141 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 128 ASN cc_start: 0.9586 (m-40) cc_final: 0.9354 (m110) REVERT: A 235 GLU cc_start: 0.8634 (mm-30) cc_final: 0.8404 (mm-30) REVERT: A 392 MET cc_start: 0.9275 (ppp) cc_final: 0.9043 (ppp) REVERT: A 430 MET cc_start: 0.9461 (mpp) cc_final: 0.8919 (mpp) REVERT: A 464 MET cc_start: 0.9519 (mtp) cc_final: 0.9306 (mtm) REVERT: A 524 GLU cc_start: 0.8936 (OUTLIER) cc_final: 0.8612 (mt-10) REVERT: A 563 GLU cc_start: 0.8453 (tp30) cc_final: 0.8085 (tp30) REVERT: A 585 LYS cc_start: 0.9542 (tmtt) cc_final: 0.9204 (tptm) REVERT: A 592 MET cc_start: 0.9164 (mtp) cc_final: 0.8707 (mpp) REVERT: A 828 ASP cc_start: 0.8939 (t0) cc_final: 0.8647 (t0) REVERT: B 74 PHE cc_start: 0.8008 (t80) cc_final: 0.7760 (t80) REVERT: B 126 MET cc_start: 0.9252 (ttm) cc_final: 0.9014 (ttp) REVERT: B 155 TYR cc_start: 0.9338 (p90) cc_final: 0.8775 (p90) REVERT: B 205 GLU cc_start: 0.8636 (mt-10) cc_final: 0.8054 (mp0) REVERT: B 212 LEU cc_start: 0.9330 (OUTLIER) cc_final: 0.9117 (mm) REVERT: B 319 MET cc_start: 0.8902 (tmm) cc_final: 0.8453 (tmm) REVERT: B 326 GLU cc_start: 0.8988 (tp30) cc_final: 0.8211 (tp30) REVERT: B 352 LEU cc_start: 0.9535 (OUTLIER) cc_final: 0.9210 (mm) REVERT: B 362 GLN cc_start: 0.9122 (OUTLIER) cc_final: 0.8717 (tm-30) REVERT: B 396 ARG cc_start: 0.8426 (ttm-80) cc_final: 0.7925 (mtt90) REVERT: B 444 ASP cc_start: 0.8757 (t0) cc_final: 0.8358 (t0) REVERT: B 447 GLN cc_start: 0.8421 (mp10) cc_final: 0.7314 (mp10) REVERT: B 479 ASN cc_start: 0.8793 (m110) cc_final: 0.8428 (m-40) REVERT: B 541 GLN cc_start: 0.9379 (OUTLIER) cc_final: 0.8962 (tm-30) REVERT: B 562 GLU cc_start: 0.9125 (mt-10) cc_final: 0.8769 (mm-30) REVERT: B 726 TYR cc_start: 0.9319 (t80) cc_final: 0.8623 (t80) REVERT: B 760 LYS cc_start: 0.8685 (mtmm) cc_final: 0.8356 (mtmm) REVERT: B 800 LYS cc_start: 0.9396 (mtmm) cc_final: 0.9185 (mttm) REVERT: B 804 LYS cc_start: 0.8382 (tptp) cc_final: 0.8040 (tptp) REVERT: B 1052 ASP cc_start: 0.8870 (p0) cc_final: 0.8233 (p0) REVERT: B 1091 MET cc_start: 0.9047 (ptm) cc_final: 0.8527 (ptm) REVERT: C 81 MET cc_start: 0.8569 (tpp) cc_final: 0.8235 (tpp) REVERT: C 83 LEU cc_start: 0.7672 (OUTLIER) cc_final: 0.7437 (tt) REVERT: C 106 ILE cc_start: 0.9616 (OUTLIER) cc_final: 0.9387 (mt) REVERT: C 141 GLU cc_start: 0.8992 (tt0) cc_final: 0.8739 (tt0) REVERT: C 276 GLU cc_start: 0.9007 (mt-10) cc_final: 0.8766 (mt-10) REVERT: C 296 GLN cc_start: 0.9078 (tm-30) cc_final: 0.8798 (pp30) REVERT: C 303 ASP cc_start: 0.9184 (t0) cc_final: 0.8728 (t0) REVERT: D 10 GLU cc_start: 0.8888 (tp30) cc_final: 0.8517 (tm-30) REVERT: D 87 TYR cc_start: 0.9089 (t80) cc_final: 0.8859 (t80) REVERT: D 195 THR cc_start: 0.9561 (m) cc_final: 0.8995 (p) REVERT: D 206 GLU cc_start: 0.9019 (pp20) cc_final: 0.8354 (mt-10) REVERT: D 209 GLU cc_start: 0.9247 (mt-10) cc_final: 0.8756 (mt-10) REVERT: D 250 ASP cc_start: 0.9529 (t0) cc_final: 0.9270 (t70) REVERT: E 127 PHE cc_start: 0.8514 (OUTLIER) cc_final: 0.8122 (t80) REVERT: E 158 GLU cc_start: 0.9510 (mm-30) cc_final: 0.9227 (mm-30) REVERT: L 39 LYS cc_start: 0.9363 (mtmm) cc_final: 0.8998 (mtmm) REVERT: L 46 GLU cc_start: 0.9133 (mp0) cc_final: 0.8846 (mp0) REVERT: L 56 ARG cc_start: 0.9311 (ttt180) cc_final: 0.8864 (ttt180) REVERT: L 73 GLU cc_start: 0.9012 (tt0) cc_final: 0.8576 (tp30) REVERT: H 17 GLU cc_start: 0.8403 (tm-30) cc_final: 0.7819 (tm-30) REVERT: H 51 LYS cc_start: 0.9593 (mmmm) cc_final: 0.9356 (mmmm) REVERT: H 66 LYS cc_start: 0.9501 (ttmm) cc_final: 0.9258 (tptp) REVERT: N 32 GLU cc_start: 0.8778 (pp20) cc_final: 0.8369 (pp20) REVERT: N 33 LYS cc_start: 0.9630 (ttmm) cc_final: 0.9415 (mmmm) REVERT: P 3 GLU cc_start: 0.8420 (tp30) cc_final: 0.8048 (tp30) outliers start: 120 outliers final: 79 residues processed: 898 average time/residue: 0.4207 time to fit residues: 578.0250 Evaluate side-chains 891 residues out of total 2854 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 804 time to evaluate : 3.028 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 163 TRP Chi-restraints excluded: chain A residue 252 LEU Chi-restraints excluded: chain A residue 501 ILE Chi-restraints excluded: chain A residue 519 THR Chi-restraints excluded: chain A residue 523 VAL Chi-restraints excluded: chain A residue 524 GLU Chi-restraints excluded: chain A residue 641 VAL Chi-restraints excluded: chain A residue 713 GLU Chi-restraints excluded: chain A residue 721 MET Chi-restraints excluded: chain A residue 767 LEU Chi-restraints excluded: chain A residue 787 SER Chi-restraints excluded: chain A residue 878 MET Chi-restraints excluded: chain A residue 891 ILE Chi-restraints excluded: chain B residue 67 ILE Chi-restraints excluded: chain B residue 116 VAL Chi-restraints excluded: chain B residue 125 ILE Chi-restraints excluded: chain B residue 212 LEU Chi-restraints excluded: chain B residue 234 LEU Chi-restraints excluded: chain B residue 258 LEU Chi-restraints excluded: chain B residue 265 THR Chi-restraints excluded: chain B residue 305 VAL Chi-restraints excluded: chain B residue 338 ASP Chi-restraints excluded: chain B residue 340 TYR Chi-restraints excluded: chain B residue 347 LEU Chi-restraints excluded: chain B residue 352 LEU Chi-restraints excluded: chain B residue 362 GLN Chi-restraints excluded: chain B residue 364 VAL Chi-restraints excluded: chain B residue 366 ASP Chi-restraints excluded: chain B residue 391 ILE Chi-restraints excluded: chain B residue 405 GLU Chi-restraints excluded: chain B residue 468 THR Chi-restraints excluded: chain B residue 482 LEU Chi-restraints excluded: chain B residue 507 ILE Chi-restraints excluded: chain B residue 541 GLN Chi-restraints excluded: chain B residue 673 SER Chi-restraints excluded: chain B residue 687 THR Chi-restraints excluded: chain B residue 733 ASP Chi-restraints excluded: chain B residue 756 GLU Chi-restraints excluded: chain B residue 763 LEU Chi-restraints excluded: chain B residue 801 VAL Chi-restraints excluded: chain B residue 849 ILE Chi-restraints excluded: chain B residue 978 GLU Chi-restraints excluded: chain B residue 1044 ILE Chi-restraints excluded: chain B residue 1092 SER Chi-restraints excluded: chain B residue 1105 MET Chi-restraints excluded: chain C residue 37 TYR Chi-restraints excluded: chain C residue 50 ASP Chi-restraints excluded: chain C residue 73 SER Chi-restraints excluded: chain C residue 80 GLN Chi-restraints excluded: chain C residue 83 LEU Chi-restraints excluded: chain C residue 96 VAL Chi-restraints excluded: chain C residue 106 ILE Chi-restraints excluded: chain C residue 118 MET Chi-restraints excluded: chain C residue 119 THR Chi-restraints excluded: chain C residue 136 VAL Chi-restraints excluded: chain C residue 170 LEU Chi-restraints excluded: chain C residue 233 LYS Chi-restraints excluded: chain C residue 247 THR Chi-restraints excluded: chain C residue 265 ARG Chi-restraints excluded: chain C residue 273 GLU Chi-restraints excluded: chain C residue 353 GLU Chi-restraints excluded: chain C residue 386 LEU Chi-restraints excluded: chain D residue 15 SER Chi-restraints excluded: chain D residue 100 ILE Chi-restraints excluded: chain D residue 184 VAL Chi-restraints excluded: chain E residue 56 ASP Chi-restraints excluded: chain E residue 74 VAL Chi-restraints excluded: chain E residue 81 ILE Chi-restraints excluded: chain E residue 127 PHE Chi-restraints excluded: chain E residue 130 LYS Chi-restraints excluded: chain E residue 146 ILE Chi-restraints excluded: chain F residue 21 LEU Chi-restraints excluded: chain L residue 8 LYS Chi-restraints excluded: chain L residue 41 THR Chi-restraints excluded: chain L residue 94 LYS Chi-restraints excluded: chain H residue 9 ILE Chi-restraints excluded: chain H residue 32 LYS Chi-restraints excluded: chain H residue 56 LYS Chi-restraints excluded: chain N residue 3 VAL Chi-restraints excluded: chain N residue 13 VAL Chi-restraints excluded: chain N residue 49 LEU Chi-restraints excluded: chain N residue 60 MET Chi-restraints excluded: chain K residue 48 VAL Chi-restraints excluded: chain P residue 20 SER Chi-restraints excluded: chain P residue 24 ASP Chi-restraints excluded: chain P residue 42 VAL Chi-restraints excluded: chain P residue 47 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 326 random chunks: chunk 149 optimal weight: 5.9990 chunk 183 optimal weight: 6.9990 chunk 291 optimal weight: 20.0000 chunk 175 optimal weight: 5.9990 chunk 284 optimal weight: 20.0000 chunk 193 optimal weight: 2.9990 chunk 59 optimal weight: 5.9990 chunk 191 optimal weight: 0.9980 chunk 287 optimal weight: 10.0000 chunk 162 optimal weight: 5.9990 chunk 172 optimal weight: 2.9990 overall best weight: 3.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 992 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1008 GLN ** B1037 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 371 GLN ** D 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 29 ASN ** E 126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 22 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3522 r_free = 0.3522 target = 0.115011 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3035 r_free = 0.3035 target = 0.088200 restraints weight = 65360.261| |-----------------------------------------------------------------------------| r_work (start): 0.3033 rms_B_bonded: 3.43 r_work: 0.2871 rms_B_bonded: 4.08 restraints_weight: 0.5000 r_work (final): 0.2871 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8186 moved from start: 0.2958 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.072 27780 Z= 0.246 Angle : 0.652 13.402 37676 Z= 0.330 Chirality : 0.046 0.286 4186 Planarity : 0.004 0.073 4740 Dihedral : 10.785 135.012 4105 Min Nonbonded Distance : 1.877 Molprobity Statistics. All-atom Clashscore : 11.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer: Outliers : 3.92 % Allowed : 25.96 % Favored : 70.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.13 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.75 (0.15), residues: 3265 helix: 1.41 (0.15), residues: 1294 sheet: -0.74 (0.24), residues: 433 loop : 0.21 (0.16), residues: 1538 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 163 HIS 0.009 0.001 HIS F 47 PHE 0.030 0.002 PHE C 193 TYR 0.027 0.001 TYR E 134 ARG 0.009 0.001 ARG P 39 Details of bonding type rmsd hydrogen bonds : bond 0.04010 ( 1274) hydrogen bonds : angle 4.81109 ( 3566) metal coordination : bond 0.01294 ( 20) metal coordination : angle 4.32868 ( 27) covalent geometry : bond 0.00560 (27760) covalent geometry : angle 0.64204 (37649) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6530 Ramachandran restraints generated. 3265 Oldfield, 0 Emsley, 3265 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6530 Ramachandran restraints generated. 3265 Oldfield, 0 Emsley, 3265 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 937 residues out of total 2854 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 112 poor density : 825 time to evaluate : 2.868 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 128 ASN cc_start: 0.9599 (m-40) cc_final: 0.9384 (m110) REVERT: A 235 GLU cc_start: 0.8706 (mm-30) cc_final: 0.8445 (mm-30) REVERT: A 392 MET cc_start: 0.9234 (ppp) cc_final: 0.9019 (ppp) REVERT: A 414 MET cc_start: 0.8780 (ptp) cc_final: 0.8578 (ptp) REVERT: A 430 MET cc_start: 0.9497 (mpp) cc_final: 0.8768 (mpp) REVERT: A 524 GLU cc_start: 0.8909 (OUTLIER) cc_final: 0.8585 (mt-10) REVERT: A 563 GLU cc_start: 0.8495 (tp30) cc_final: 0.8168 (tp30) REVERT: A 585 LYS cc_start: 0.9544 (tmtt) cc_final: 0.9203 (tptm) REVERT: A 592 MET cc_start: 0.9131 (mtp) cc_final: 0.8683 (mpp) REVERT: A 828 ASP cc_start: 0.8972 (t0) cc_final: 0.8686 (t0) REVERT: A 842 ARG cc_start: 0.9552 (mtm-85) cc_final: 0.8731 (mtm-85) REVERT: B 74 PHE cc_start: 0.8048 (t80) cc_final: 0.7831 (t80) REVERT: B 126 MET cc_start: 0.9256 (ttm) cc_final: 0.9013 (ttp) REVERT: B 155 TYR cc_start: 0.9308 (p90) cc_final: 0.8801 (p90) REVERT: B 169 GLU cc_start: 0.8668 (tt0) cc_final: 0.8375 (tt0) REVERT: B 205 GLU cc_start: 0.8632 (mt-10) cc_final: 0.8162 (mp0) REVERT: B 212 LEU cc_start: 0.9342 (OUTLIER) cc_final: 0.9111 (mm) REVERT: B 326 GLU cc_start: 0.9027 (tp30) cc_final: 0.8271 (tp30) REVERT: B 352 LEU cc_start: 0.9546 (OUTLIER) cc_final: 0.9207 (mm) REVERT: B 362 GLN cc_start: 0.9131 (OUTLIER) cc_final: 0.8713 (tm-30) REVERT: B 425 ASP cc_start: 0.9131 (t0) cc_final: 0.8584 (t0) REVERT: B 444 ASP cc_start: 0.8736 (t0) cc_final: 0.8312 (t0) REVERT: B 447 GLN cc_start: 0.8480 (mp10) cc_final: 0.7330 (mp10) REVERT: B 541 GLN cc_start: 0.9383 (OUTLIER) cc_final: 0.8979 (tm-30) REVERT: B 562 GLU cc_start: 0.9044 (mt-10) cc_final: 0.8720 (mm-30) REVERT: B 726 TYR cc_start: 0.9324 (t80) cc_final: 0.8641 (t80) REVERT: B 760 LYS cc_start: 0.8729 (mtmm) cc_final: 0.8375 (mtmm) REVERT: B 804 LYS cc_start: 0.8539 (tptp) cc_final: 0.8132 (tptp) REVERT: B 929 LYS cc_start: 0.9429 (ttpt) cc_final: 0.9215 (ttpt) REVERT: B 1052 ASP cc_start: 0.8879 (p0) cc_final: 0.8234 (p0) REVERT: B 1060 GLU cc_start: 0.9184 (mt-10) cc_final: 0.8955 (mp0) REVERT: C 141 GLU cc_start: 0.8954 (tt0) cc_final: 0.8682 (tt0) REVERT: C 265 ARG cc_start: 0.9169 (OUTLIER) cc_final: 0.8678 (mtm180) REVERT: C 276 GLU cc_start: 0.9013 (mt-10) cc_final: 0.8767 (mt-10) REVERT: C 303 ASP cc_start: 0.9129 (t0) cc_final: 0.8757 (t0) REVERT: D 7 GLN cc_start: 0.8300 (mm-40) cc_final: 0.8092 (mp10) REVERT: D 10 GLU cc_start: 0.8869 (tp30) cc_final: 0.8472 (tm-30) REVERT: D 87 TYR cc_start: 0.9082 (t80) cc_final: 0.8872 (t80) REVERT: D 195 THR cc_start: 0.9572 (m) cc_final: 0.9007 (p) REVERT: D 206 GLU cc_start: 0.9016 (pp20) cc_final: 0.8358 (mt-10) REVERT: D 209 GLU cc_start: 0.9220 (mt-10) cc_final: 0.8744 (mt-10) REVERT: D 250 ASP cc_start: 0.9534 (t0) cc_final: 0.9253 (t70) REVERT: D 251 ARG cc_start: 0.9461 (tpp80) cc_final: 0.9216 (tpp80) REVERT: E 32 GLU cc_start: 0.8915 (mp0) cc_final: 0.8565 (mp0) REVERT: E 38 TYR cc_start: 0.9082 (t80) cc_final: 0.8796 (t80) REVERT: E 127 PHE cc_start: 0.8424 (OUTLIER) cc_final: 0.8142 (t80) REVERT: E 158 GLU cc_start: 0.9520 (mm-30) cc_final: 0.9234 (mm-30) REVERT: E 170 LEU cc_start: 0.7733 (mt) cc_final: 0.7063 (tt) REVERT: F 76 ARG cc_start: 0.9161 (tmm-80) cc_final: 0.8933 (ptm-80) REVERT: L 39 LYS cc_start: 0.9353 (mtmm) cc_final: 0.9117 (mtmm) REVERT: L 46 GLU cc_start: 0.9188 (mp0) cc_final: 0.8845 (mp0) REVERT: L 56 ARG cc_start: 0.9344 (ttt180) cc_final: 0.8878 (ttt180) REVERT: L 73 GLU cc_start: 0.9013 (tt0) cc_final: 0.8588 (tp30) REVERT: H 17 GLU cc_start: 0.8419 (tm-30) cc_final: 0.7814 (tm-30) REVERT: H 27 LYS cc_start: 0.9346 (mtmm) cc_final: 0.8977 (mtmm) REVERT: H 66 LYS cc_start: 0.9458 (ttmm) cc_final: 0.9255 (tptp) REVERT: N 32 GLU cc_start: 0.8795 (pp20) cc_final: 0.8360 (pp20) REVERT: N 33 LYS cc_start: 0.9618 (ttmm) cc_final: 0.9368 (mmmm) outliers start: 112 outliers final: 83 residues processed: 880 average time/residue: 0.4104 time to fit residues: 550.3609 Evaluate side-chains 897 residues out of total 2854 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 807 time to evaluate : 3.325 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 163 TRP Chi-restraints excluded: chain A residue 187 LEU Chi-restraints excluded: chain A residue 252 LEU Chi-restraints excluded: chain A residue 487 HIS Chi-restraints excluded: chain A residue 501 ILE Chi-restraints excluded: chain A residue 519 THR Chi-restraints excluded: chain A residue 523 VAL Chi-restraints excluded: chain A residue 524 GLU Chi-restraints excluded: chain A residue 641 VAL Chi-restraints excluded: chain A residue 713 GLU Chi-restraints excluded: chain A residue 721 MET Chi-restraints excluded: chain A residue 767 LEU Chi-restraints excluded: chain A residue 787 SER Chi-restraints excluded: chain A residue 878 MET Chi-restraints excluded: chain A residue 891 ILE Chi-restraints excluded: chain B residue 67 ILE Chi-restraints excluded: chain B residue 116 VAL Chi-restraints excluded: chain B residue 125 ILE Chi-restraints excluded: chain B residue 164 VAL Chi-restraints excluded: chain B residue 204 VAL Chi-restraints excluded: chain B residue 212 LEU Chi-restraints excluded: chain B residue 234 LEU Chi-restraints excluded: chain B residue 258 LEU Chi-restraints excluded: chain B residue 265 THR Chi-restraints excluded: chain B residue 338 ASP Chi-restraints excluded: chain B residue 340 TYR Chi-restraints excluded: chain B residue 352 LEU Chi-restraints excluded: chain B residue 362 GLN Chi-restraints excluded: chain B residue 364 VAL Chi-restraints excluded: chain B residue 366 ASP Chi-restraints excluded: chain B residue 391 ILE Chi-restraints excluded: chain B residue 405 GLU Chi-restraints excluded: chain B residue 468 THR Chi-restraints excluded: chain B residue 482 LEU Chi-restraints excluded: chain B residue 505 VAL Chi-restraints excluded: chain B residue 507 ILE Chi-restraints excluded: chain B residue 541 GLN Chi-restraints excluded: chain B residue 673 SER Chi-restraints excluded: chain B residue 687 THR Chi-restraints excluded: chain B residue 733 ASP Chi-restraints excluded: chain B residue 742 ILE Chi-restraints excluded: chain B residue 756 GLU Chi-restraints excluded: chain B residue 801 VAL Chi-restraints excluded: chain B residue 849 ILE Chi-restraints excluded: chain B residue 978 GLU Chi-restraints excluded: chain B residue 1044 ILE Chi-restraints excluded: chain B residue 1092 SER Chi-restraints excluded: chain B residue 1105 MET Chi-restraints excluded: chain C residue 37 TYR Chi-restraints excluded: chain C residue 73 SER Chi-restraints excluded: chain C residue 80 GLN Chi-restraints excluded: chain C residue 96 VAL Chi-restraints excluded: chain C residue 118 MET Chi-restraints excluded: chain C residue 119 THR Chi-restraints excluded: chain C residue 136 VAL Chi-restraints excluded: chain C residue 145 LEU Chi-restraints excluded: chain C residue 170 LEU Chi-restraints excluded: chain C residue 179 LYS Chi-restraints excluded: chain C residue 233 LYS Chi-restraints excluded: chain C residue 247 THR Chi-restraints excluded: chain C residue 265 ARG Chi-restraints excluded: chain C residue 273 GLU Chi-restraints excluded: chain C residue 353 GLU Chi-restraints excluded: chain C residue 386 LEU Chi-restraints excluded: chain D residue 15 SER Chi-restraints excluded: chain D residue 100 ILE Chi-restraints excluded: chain D residue 184 VAL Chi-restraints excluded: chain E residue 74 VAL Chi-restraints excluded: chain E residue 81 ILE Chi-restraints excluded: chain E residue 127 PHE Chi-restraints excluded: chain E residue 130 LYS Chi-restraints excluded: chain E residue 146 ILE Chi-restraints excluded: chain E residue 163 LEU Chi-restraints excluded: chain F residue 21 LEU Chi-restraints excluded: chain L residue 8 LYS Chi-restraints excluded: chain L residue 41 THR Chi-restraints excluded: chain L residue 61 THR Chi-restraints excluded: chain L residue 94 LYS Chi-restraints excluded: chain H residue 9 ILE Chi-restraints excluded: chain H residue 29 LEU Chi-restraints excluded: chain H residue 32 LYS Chi-restraints excluded: chain H residue 56 LYS Chi-restraints excluded: chain N residue 3 VAL Chi-restraints excluded: chain N residue 49 LEU Chi-restraints excluded: chain N residue 60 MET Chi-restraints excluded: chain K residue 41 ILE Chi-restraints excluded: chain K residue 48 VAL Chi-restraints excluded: chain P residue 20 SER Chi-restraints excluded: chain P residue 24 ASP Chi-restraints excluded: chain P residue 47 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 326 random chunks: chunk 186 optimal weight: 0.8980 chunk 18 optimal weight: 0.9990 chunk 150 optimal weight: 0.5980 chunk 244 optimal weight: 1.9990 chunk 249 optimal weight: 4.9990 chunk 215 optimal weight: 7.9990 chunk 179 optimal weight: 1.9990 chunk 156 optimal weight: 4.9990 chunk 232 optimal weight: 7.9990 chunk 151 optimal weight: 0.9980 chunk 277 optimal weight: 20.0000 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 370 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 762 GLN ** B 992 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1008 GLN ** B1037 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 371 GLN D 7 GLN ** E 126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 22 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3571 r_free = 0.3571 target = 0.118449 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3098 r_free = 0.3098 target = 0.091618 restraints weight = 64129.487| |-----------------------------------------------------------------------------| r_work (start): 0.3033 rms_B_bonded: 3.55 r_work: 0.2872 rms_B_bonded: 4.24 restraints_weight: 0.5000 r_work (final): 0.2872 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8129 moved from start: 0.3114 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 27780 Z= 0.130 Angle : 0.638 12.938 37676 Z= 0.319 Chirality : 0.045 0.290 4186 Planarity : 0.004 0.066 4740 Dihedral : 10.666 135.033 4105 Min Nonbonded Distance : 1.943 Molprobity Statistics. All-atom Clashscore : 10.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.96 % Favored : 98.04 % Rotamer: Outliers : 3.47 % Allowed : 26.94 % Favored : 69.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.13 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.81 (0.15), residues: 3265 helix: 1.48 (0.15), residues: 1294 sheet: -0.54 (0.23), residues: 462 loop : 0.20 (0.17), residues: 1509 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 163 HIS 0.008 0.001 HIS F 47 PHE 0.026 0.001 PHE C 193 TYR 0.028 0.001 TYR P 6 ARG 0.013 0.001 ARG C 267 Details of bonding type rmsd hydrogen bonds : bond 0.03549 ( 1274) hydrogen bonds : angle 4.64158 ( 3566) metal coordination : bond 0.00616 ( 20) metal coordination : angle 4.09702 ( 27) covalent geometry : bond 0.00301 (27760) covalent geometry : angle 0.62863 (37649) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6530 Ramachandran restraints generated. 3265 Oldfield, 0 Emsley, 3265 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6530 Ramachandran restraints generated. 3265 Oldfield, 0 Emsley, 3265 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 947 residues out of total 2854 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 99 poor density : 848 time to evaluate : 3.062 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 9 GLU cc_start: 0.8751 (mt-10) cc_final: 0.8524 (mt-10) REVERT: A 39 ILE cc_start: 0.9201 (OUTLIER) cc_final: 0.8899 (mm) REVERT: A 128 ASN cc_start: 0.9579 (m-40) cc_final: 0.9355 (m110) REVERT: A 235 GLU cc_start: 0.8728 (mm-30) cc_final: 0.8484 (mm-30) REVERT: A 392 MET cc_start: 0.9200 (ppp) cc_final: 0.8980 (ppp) REVERT: A 428 HIS cc_start: 0.9221 (OUTLIER) cc_final: 0.8860 (p90) REVERT: A 430 MET cc_start: 0.9482 (mpp) cc_final: 0.8662 (mpp) REVERT: A 483 GLU cc_start: 0.9296 (tt0) cc_final: 0.8808 (tt0) REVERT: A 485 GLN cc_start: 0.9274 (mt0) cc_final: 0.8774 (mp10) REVERT: A 524 GLU cc_start: 0.8861 (OUTLIER) cc_final: 0.8471 (mp0) REVERT: A 548 ASN cc_start: 0.9622 (m-40) cc_final: 0.9386 (m-40) REVERT: A 563 GLU cc_start: 0.8466 (tp30) cc_final: 0.8097 (tp30) REVERT: A 585 LYS cc_start: 0.9524 (tmtt) cc_final: 0.9181 (tptm) REVERT: A 592 MET cc_start: 0.9132 (mtp) cc_final: 0.8659 (mpp) REVERT: A 842 ARG cc_start: 0.9557 (mtm-85) cc_final: 0.8725 (mtm-85) REVERT: B 33 ASP cc_start: 0.9272 (m-30) cc_final: 0.8964 (m-30) REVERT: B 126 MET cc_start: 0.9231 (ttm) cc_final: 0.8966 (ttp) REVERT: B 155 TYR cc_start: 0.9271 (p90) cc_final: 0.8748 (p90) REVERT: B 169 GLU cc_start: 0.8666 (tt0) cc_final: 0.8414 (tt0) REVERT: B 205 GLU cc_start: 0.8660 (mt-10) cc_final: 0.8064 (mp0) REVERT: B 212 LEU cc_start: 0.9318 (OUTLIER) cc_final: 0.9077 (mm) REVERT: B 326 GLU cc_start: 0.9054 (tp30) cc_final: 0.8254 (tp30) REVERT: B 352 LEU cc_start: 0.9515 (OUTLIER) cc_final: 0.9230 (mm) REVERT: B 362 GLN cc_start: 0.9133 (OUTLIER) cc_final: 0.8720 (tm-30) REVERT: B 371 MET cc_start: 0.8437 (mtm) cc_final: 0.8202 (ptm) REVERT: B 396 ARG cc_start: 0.8414 (ttm-80) cc_final: 0.7807 (mtt90) REVERT: B 425 ASP cc_start: 0.9132 (t0) cc_final: 0.8614 (t0) REVERT: B 444 ASP cc_start: 0.8719 (t0) cc_final: 0.8358 (t0) REVERT: B 447 GLN cc_start: 0.8436 (mp10) cc_final: 0.7393 (mp10) REVERT: B 562 GLU cc_start: 0.9127 (mt-10) cc_final: 0.8774 (mm-30) REVERT: B 726 TYR cc_start: 0.9240 (t80) cc_final: 0.8680 (t80) REVERT: B 760 LYS cc_start: 0.8740 (mtmm) cc_final: 0.8391 (mtmm) REVERT: B 804 LYS cc_start: 0.8525 (tptp) cc_final: 0.8087 (tptp) REVERT: B 1046 ARG cc_start: 0.9359 (tpp-160) cc_final: 0.9132 (tpp-160) REVERT: B 1052 ASP cc_start: 0.8887 (p0) cc_final: 0.8319 (p0) REVERT: B 1060 GLU cc_start: 0.9210 (mt-10) cc_final: 0.8956 (mp0) REVERT: B 1091 MET cc_start: 0.8887 (ptm) cc_final: 0.8470 (ptm) REVERT: C 81 MET cc_start: 0.8538 (tpp) cc_final: 0.8292 (tpp) REVERT: C 141 GLU cc_start: 0.8980 (tt0) cc_final: 0.8736 (pt0) REVERT: C 265 ARG cc_start: 0.9108 (OUTLIER) cc_final: 0.8324 (mtm180) REVERT: C 276 GLU cc_start: 0.8994 (mt-10) cc_final: 0.8721 (mt-10) REVERT: C 296 GLN cc_start: 0.9149 (OUTLIER) cc_final: 0.8929 (pp30) REVERT: C 303 ASP cc_start: 0.9095 (t0) cc_final: 0.8617 (t0) REVERT: D 10 GLU cc_start: 0.8796 (tp30) cc_final: 0.8506 (tm-30) REVERT: D 50 TYR cc_start: 0.9161 (m-10) cc_final: 0.8955 (m-10) REVERT: D 58 ASP cc_start: 0.9377 (m-30) cc_final: 0.9060 (m-30) REVERT: D 87 TYR cc_start: 0.9065 (t80) cc_final: 0.8838 (t80) REVERT: D 195 THR cc_start: 0.9567 (m) cc_final: 0.8984 (p) REVERT: D 206 GLU cc_start: 0.8990 (pp20) cc_final: 0.8688 (pp20) REVERT: D 209 GLU cc_start: 0.9215 (mt-10) cc_final: 0.8829 (mt-10) REVERT: D 250 ASP cc_start: 0.9507 (t0) cc_final: 0.9240 (t70) REVERT: E 38 TYR cc_start: 0.9066 (t80) cc_final: 0.8772 (t80) REVERT: E 127 PHE cc_start: 0.8282 (OUTLIER) cc_final: 0.8009 (t80) REVERT: E 158 GLU cc_start: 0.9546 (mm-30) cc_final: 0.9291 (mm-30) REVERT: E 170 LEU cc_start: 0.7443 (mt) cc_final: 0.7130 (tt) REVERT: F 67 MET cc_start: 0.9099 (mmm) cc_final: 0.8838 (mmm) REVERT: L 39 LYS cc_start: 0.9350 (mtmm) cc_final: 0.9090 (mtmm) REVERT: L 46 GLU cc_start: 0.9197 (mp0) cc_final: 0.8800 (mp0) REVERT: L 54 LYS cc_start: 0.9311 (mttm) cc_final: 0.8642 (mtpp) REVERT: L 56 ARG cc_start: 0.9346 (ttt180) cc_final: 0.8872 (ttt180) REVERT: L 73 GLU cc_start: 0.9010 (tt0) cc_final: 0.8544 (tp30) REVERT: H 27 LYS cc_start: 0.9343 (mtmm) cc_final: 0.8757 (pttm) REVERT: N 32 GLU cc_start: 0.8766 (pp20) cc_final: 0.8173 (pp20) REVERT: N 33 LYS cc_start: 0.9608 (ttmm) cc_final: 0.9374 (mmmm) REVERT: N 36 ASP cc_start: 0.9149 (m-30) cc_final: 0.8941 (m-30) REVERT: N 47 ARG cc_start: 0.9412 (ttp-170) cc_final: 0.9211 (ptt-90) REVERT: P 45 ARG cc_start: 0.8864 (tpp-160) cc_final: 0.8395 (tpp-160) outliers start: 99 outliers final: 61 residues processed: 897 average time/residue: 0.4109 time to fit residues: 562.2770 Evaluate side-chains 885 residues out of total 2854 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 815 time to evaluate : 3.340 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 ILE Chi-restraints excluded: chain A residue 66 GLU Chi-restraints excluded: chain A residue 163 TRP Chi-restraints excluded: chain A residue 252 LEU Chi-restraints excluded: chain A residue 306 LYS Chi-restraints excluded: chain A residue 428 HIS Chi-restraints excluded: chain A residue 444 THR Chi-restraints excluded: chain A residue 501 ILE Chi-restraints excluded: chain A residue 519 THR Chi-restraints excluded: chain A residue 524 GLU Chi-restraints excluded: chain A residue 713 GLU Chi-restraints excluded: chain A residue 721 MET Chi-restraints excluded: chain A residue 878 MET Chi-restraints excluded: chain A residue 891 ILE Chi-restraints excluded: chain B residue 67 ILE Chi-restraints excluded: chain B residue 212 LEU Chi-restraints excluded: chain B residue 234 LEU Chi-restraints excluded: chain B residue 265 THR Chi-restraints excluded: chain B residue 340 TYR Chi-restraints excluded: chain B residue 352 LEU Chi-restraints excluded: chain B residue 362 GLN Chi-restraints excluded: chain B residue 364 VAL Chi-restraints excluded: chain B residue 366 ASP Chi-restraints excluded: chain B residue 405 GLU Chi-restraints excluded: chain B residue 482 LEU Chi-restraints excluded: chain B residue 505 VAL Chi-restraints excluded: chain B residue 507 ILE Chi-restraints excluded: chain B residue 687 THR Chi-restraints excluded: chain B residue 733 ASP Chi-restraints excluded: chain B residue 742 ILE Chi-restraints excluded: chain B residue 756 GLU Chi-restraints excluded: chain B residue 801 VAL Chi-restraints excluded: chain B residue 833 THR Chi-restraints excluded: chain B residue 1044 ILE Chi-restraints excluded: chain B residue 1092 SER Chi-restraints excluded: chain C residue 30 LEU Chi-restraints excluded: chain C residue 37 TYR Chi-restraints excluded: chain C residue 73 SER Chi-restraints excluded: chain C residue 80 GLN Chi-restraints excluded: chain C residue 118 MET Chi-restraints excluded: chain C residue 119 THR Chi-restraints excluded: chain C residue 170 LEU Chi-restraints excluded: chain C residue 233 LYS Chi-restraints excluded: chain C residue 265 ARG Chi-restraints excluded: chain C residue 273 GLU Chi-restraints excluded: chain C residue 291 ILE Chi-restraints excluded: chain C residue 296 GLN Chi-restraints excluded: chain C residue 353 GLU Chi-restraints excluded: chain C residue 386 LEU Chi-restraints excluded: chain D residue 184 VAL Chi-restraints excluded: chain E residue 74 VAL Chi-restraints excluded: chain E residue 81 ILE Chi-restraints excluded: chain E residue 89 VAL Chi-restraints excluded: chain E residue 99 ILE Chi-restraints excluded: chain E residue 127 PHE Chi-restraints excluded: chain E residue 146 ILE Chi-restraints excluded: chain F residue 21 LEU Chi-restraints excluded: chain L residue 50 THR Chi-restraints excluded: chain L residue 61 THR Chi-restraints excluded: chain L residue 94 LYS Chi-restraints excluded: chain H residue 9 ILE Chi-restraints excluded: chain H residue 32 LYS Chi-restraints excluded: chain N residue 3 VAL Chi-restraints excluded: chain N residue 49 LEU Chi-restraints excluded: chain N residue 60 MET Chi-restraints excluded: chain K residue 35 THR Chi-restraints excluded: chain K residue 48 VAL Chi-restraints excluded: chain P residue 20 SER Chi-restraints excluded: chain P residue 24 ASP Chi-restraints excluded: chain P residue 47 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 326 random chunks: chunk 322 optimal weight: 1.9990 chunk 49 optimal weight: 8.9990 chunk 44 optimal weight: 6.9990 chunk 155 optimal weight: 3.9990 chunk 307 optimal weight: 5.9990 chunk 112 optimal weight: 8.9990 chunk 57 optimal weight: 0.9990 chunk 268 optimal weight: 10.0000 chunk 204 optimal weight: 5.9990 chunk 15 optimal weight: 0.9990 chunk 244 optimal weight: 3.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 759 ASN B 962 HIS ** B 992 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1008 GLN ** B1037 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 371 GLN D 7 GLN L 22 HIS K 19 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3542 r_free = 0.3542 target = 0.116595 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3066 r_free = 0.3066 target = 0.089832 restraints weight = 64091.591| |-----------------------------------------------------------------------------| r_work (start): 0.3065 rms_B_bonded: 3.54 r_work: 0.2893 rms_B_bonded: 4.22 restraints_weight: 0.5000 r_work (final): 0.2893 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8166 moved from start: 0.3221 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 27780 Z= 0.179 Angle : 0.651 12.181 37676 Z= 0.327 Chirality : 0.046 0.246 4186 Planarity : 0.004 0.067 4740 Dihedral : 10.629 135.738 4105 Min Nonbonded Distance : 1.920 Molprobity Statistics. All-atom Clashscore : 10.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 3.33 % Allowed : 26.91 % Favored : 69.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.13 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.80 (0.15), residues: 3265 helix: 1.48 (0.15), residues: 1294 sheet: -0.65 (0.23), residues: 482 loop : 0.24 (0.17), residues: 1489 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 163 HIS 0.008 0.001 HIS F 47 PHE 0.026 0.002 PHE C 193 TYR 0.026 0.001 TYR D 154 ARG 0.011 0.001 ARG C 267 Details of bonding type rmsd hydrogen bonds : bond 0.03721 ( 1274) hydrogen bonds : angle 4.67715 ( 3566) metal coordination : bond 0.00959 ( 20) metal coordination : angle 4.10046 ( 27) covalent geometry : bond 0.00416 (27760) covalent geometry : angle 0.64241 (37649) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6530 Ramachandran restraints generated. 3265 Oldfield, 0 Emsley, 3265 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6530 Ramachandran restraints generated. 3265 Oldfield, 0 Emsley, 3265 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 924 residues out of total 2854 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 829 time to evaluate : 2.960 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 39 ILE cc_start: 0.9217 (OUTLIER) cc_final: 0.8917 (mm) REVERT: A 123 ARG cc_start: 0.8300 (mtm180) cc_final: 0.7912 (mpp-170) REVERT: A 128 ASN cc_start: 0.9585 (m-40) cc_final: 0.9361 (m110) REVERT: A 223 ARG cc_start: 0.9044 (ptt90) cc_final: 0.8773 (ptt90) REVERT: A 235 GLU cc_start: 0.8767 (mm-30) cc_final: 0.8551 (mm-30) REVERT: A 392 MET cc_start: 0.9226 (ppp) cc_final: 0.9010 (ppp) REVERT: A 430 MET cc_start: 0.9492 (mpp) cc_final: 0.8672 (mpp) REVERT: A 485 GLN cc_start: 0.9290 (mt0) cc_final: 0.8840 (mp10) REVERT: A 524 GLU cc_start: 0.8905 (OUTLIER) cc_final: 0.8546 (mt-10) REVERT: A 563 GLU cc_start: 0.8490 (tp30) cc_final: 0.8171 (tp30) REVERT: A 585 LYS cc_start: 0.9532 (tmtt) cc_final: 0.9193 (tptm) REVERT: A 592 MET cc_start: 0.9122 (mtp) cc_final: 0.8643 (mpp) REVERT: B 33 ASP cc_start: 0.9257 (m-30) cc_final: 0.8940 (m-30) REVERT: B 45 GLU cc_start: 0.8678 (mt-10) cc_final: 0.8353 (mt-10) REVERT: B 104 MET cc_start: 0.9273 (mmt) cc_final: 0.8997 (mmm) REVERT: B 126 MET cc_start: 0.9251 (ttm) cc_final: 0.8999 (ttp) REVERT: B 155 TYR cc_start: 0.9287 (p90) cc_final: 0.8777 (p90) REVERT: B 205 GLU cc_start: 0.8698 (mt-10) cc_final: 0.8168 (mp0) REVERT: B 212 LEU cc_start: 0.9324 (OUTLIER) cc_final: 0.9097 (mm) REVERT: B 326 GLU cc_start: 0.9020 (tp30) cc_final: 0.8262 (tp30) REVERT: B 352 LEU cc_start: 0.9543 (OUTLIER) cc_final: 0.9231 (mm) REVERT: B 362 GLN cc_start: 0.9161 (OUTLIER) cc_final: 0.8769 (tm-30) REVERT: B 371 MET cc_start: 0.8462 (mtm) cc_final: 0.8252 (ptm) REVERT: B 396 ARG cc_start: 0.8541 (ttm-80) cc_final: 0.7983 (mtt90) REVERT: B 425 ASP cc_start: 0.9137 (t0) cc_final: 0.8549 (t0) REVERT: B 444 ASP cc_start: 0.8720 (t0) cc_final: 0.8361 (t0) REVERT: B 447 GLN cc_start: 0.8402 (mp10) cc_final: 0.7327 (mp10) REVERT: B 562 GLU cc_start: 0.9101 (mt-10) cc_final: 0.8735 (mm-30) REVERT: B 726 TYR cc_start: 0.9256 (t80) cc_final: 0.8679 (t80) REVERT: B 760 LYS cc_start: 0.8743 (mtmm) cc_final: 0.8400 (mtmm) REVERT: B 804 LYS cc_start: 0.8613 (tptp) cc_final: 0.8222 (tptp) REVERT: B 1052 ASP cc_start: 0.8860 (p0) cc_final: 0.8277 (p0) REVERT: B 1060 GLU cc_start: 0.9223 (mt-10) cc_final: 0.8958 (mp0) REVERT: C 81 MET cc_start: 0.8544 (tpp) cc_final: 0.8265 (tpp) REVERT: C 141 GLU cc_start: 0.8968 (tt0) cc_final: 0.8738 (pt0) REVERT: C 265 ARG cc_start: 0.9173 (OUTLIER) cc_final: 0.8366 (mtm180) REVERT: C 276 GLU cc_start: 0.9019 (mt-10) cc_final: 0.8756 (mt-10) REVERT: C 303 ASP cc_start: 0.9065 (t0) cc_final: 0.8659 (t0) REVERT: C 341 PHE cc_start: 0.9526 (t80) cc_final: 0.9232 (t80) REVERT: D 10 GLU cc_start: 0.8780 (tp30) cc_final: 0.8499 (tm-30) REVERT: D 195 THR cc_start: 0.9556 (m) cc_final: 0.8947 (p) REVERT: D 206 GLU cc_start: 0.9016 (pp20) cc_final: 0.8687 (pp20) REVERT: D 209 GLU cc_start: 0.9303 (mt-10) cc_final: 0.8864 (mt-10) REVERT: D 250 ASP cc_start: 0.9482 (t0) cc_final: 0.9231 (t70) REVERT: E 38 TYR cc_start: 0.9108 (t80) cc_final: 0.8814 (t80) REVERT: E 127 PHE cc_start: 0.8261 (OUTLIER) cc_final: 0.8036 (t80) REVERT: E 133 LYS cc_start: 0.8793 (tptp) cc_final: 0.8409 (tppt) REVERT: E 158 GLU cc_start: 0.9561 (mm-30) cc_final: 0.9303 (mm-30) REVERT: L 18 GLU cc_start: 0.9112 (tp30) cc_final: 0.8822 (mm-30) REVERT: L 39 LYS cc_start: 0.9359 (mtmm) cc_final: 0.9102 (mtmm) REVERT: L 46 GLU cc_start: 0.9214 (mp0) cc_final: 0.8802 (mp0) REVERT: L 54 LYS cc_start: 0.9138 (mttm) cc_final: 0.8837 (mtpp) REVERT: L 56 ARG cc_start: 0.9333 (ttt180) cc_final: 0.8815 (ttt180) REVERT: L 73 GLU cc_start: 0.9074 (tt0) cc_final: 0.8551 (tp30) REVERT: N 32 GLU cc_start: 0.8779 (pp20) cc_final: 0.8184 (pp20) REVERT: N 33 LYS cc_start: 0.9602 (ttmm) cc_final: 0.9366 (mmmm) REVERT: N 36 ASP cc_start: 0.9131 (m-30) cc_final: 0.8931 (m-30) REVERT: P 45 ARG cc_start: 0.8787 (tpp-160) cc_final: 0.8519 (tpp-160) outliers start: 95 outliers final: 72 residues processed: 878 average time/residue: 0.4001 time to fit residues: 538.0955 Evaluate side-chains 888 residues out of total 2854 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 809 time to evaluate : 4.556 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 ILE Chi-restraints excluded: chain A residue 66 GLU Chi-restraints excluded: chain A residue 163 TRP Chi-restraints excluded: chain A residue 252 LEU Chi-restraints excluded: chain A residue 414 MET Chi-restraints excluded: chain A residue 444 THR Chi-restraints excluded: chain A residue 501 ILE Chi-restraints excluded: chain A residue 503 ASP Chi-restraints excluded: chain A residue 519 THR Chi-restraints excluded: chain A residue 524 GLU Chi-restraints excluded: chain A residue 641 VAL Chi-restraints excluded: chain A residue 713 GLU Chi-restraints excluded: chain A residue 721 MET Chi-restraints excluded: chain A residue 787 SER Chi-restraints excluded: chain A residue 878 MET Chi-restraints excluded: chain A residue 891 ILE Chi-restraints excluded: chain B residue 67 ILE Chi-restraints excluded: chain B residue 164 VAL Chi-restraints excluded: chain B residue 212 LEU Chi-restraints excluded: chain B residue 234 LEU Chi-restraints excluded: chain B residue 265 THR Chi-restraints excluded: chain B residue 340 TYR Chi-restraints excluded: chain B residue 352 LEU Chi-restraints excluded: chain B residue 362 GLN Chi-restraints excluded: chain B residue 364 VAL Chi-restraints excluded: chain B residue 366 ASP Chi-restraints excluded: chain B residue 405 GLU Chi-restraints excluded: chain B residue 468 THR Chi-restraints excluded: chain B residue 482 LEU Chi-restraints excluded: chain B residue 505 VAL Chi-restraints excluded: chain B residue 507 ILE Chi-restraints excluded: chain B residue 687 THR Chi-restraints excluded: chain B residue 733 ASP Chi-restraints excluded: chain B residue 742 ILE Chi-restraints excluded: chain B residue 749 SER Chi-restraints excluded: chain B residue 756 GLU Chi-restraints excluded: chain B residue 801 VAL Chi-restraints excluded: chain B residue 833 THR Chi-restraints excluded: chain B residue 938 VAL Chi-restraints excluded: chain B residue 978 GLU Chi-restraints excluded: chain B residue 1044 ILE Chi-restraints excluded: chain B residue 1092 SER Chi-restraints excluded: chain C residue 37 TYR Chi-restraints excluded: chain C residue 73 SER Chi-restraints excluded: chain C residue 80 GLN Chi-restraints excluded: chain C residue 96 VAL Chi-restraints excluded: chain C residue 118 MET Chi-restraints excluded: chain C residue 119 THR Chi-restraints excluded: chain C residue 136 VAL Chi-restraints excluded: chain C residue 179 LYS Chi-restraints excluded: chain C residue 233 LYS Chi-restraints excluded: chain C residue 250 SER Chi-restraints excluded: chain C residue 265 ARG Chi-restraints excluded: chain C residue 273 GLU Chi-restraints excluded: chain C residue 323 ILE Chi-restraints excluded: chain C residue 353 GLU Chi-restraints excluded: chain C residue 386 LEU Chi-restraints excluded: chain D residue 15 SER Chi-restraints excluded: chain D residue 184 VAL Chi-restraints excluded: chain E residue 74 VAL Chi-restraints excluded: chain E residue 81 ILE Chi-restraints excluded: chain E residue 89 VAL Chi-restraints excluded: chain E residue 99 ILE Chi-restraints excluded: chain E residue 127 PHE Chi-restraints excluded: chain E residue 146 ILE Chi-restraints excluded: chain L residue 61 THR Chi-restraints excluded: chain L residue 94 LYS Chi-restraints excluded: chain H residue 9 ILE Chi-restraints excluded: chain H residue 32 LYS Chi-restraints excluded: chain N residue 3 VAL Chi-restraints excluded: chain N residue 13 VAL Chi-restraints excluded: chain N residue 49 LEU Chi-restraints excluded: chain N residue 53 VAL Chi-restraints excluded: chain N residue 60 MET Chi-restraints excluded: chain K residue 35 THR Chi-restraints excluded: chain K residue 48 VAL Chi-restraints excluded: chain P residue 20 SER Chi-restraints excluded: chain P residue 24 ASP Chi-restraints excluded: chain P residue 47 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 326 random chunks: chunk 173 optimal weight: 10.0000 chunk 130 optimal weight: 0.0870 chunk 167 optimal weight: 4.9990 chunk 108 optimal weight: 8.9990 chunk 232 optimal weight: 3.9990 chunk 68 optimal weight: 0.8980 chunk 237 optimal weight: 3.9990 chunk 196 optimal weight: 6.9990 chunk 305 optimal weight: 4.9990 chunk 221 optimal weight: 8.9990 chunk 242 optimal weight: 5.9990 overall best weight: 2.7964 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 992 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1008 GLN ** B1037 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 366 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 371 GLN ** E 126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 22 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3542 r_free = 0.3542 target = 0.116339 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3065 r_free = 0.3065 target = 0.089653 restraints weight = 64499.040| |-----------------------------------------------------------------------------| r_work (start): 0.3011 rms_B_bonded: 3.54 r_work: 0.2839 rms_B_bonded: 4.28 restraints_weight: 0.5000 r_work (final): 0.2839 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8158 moved from start: 0.3314 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.072 27780 Z= 0.196 Angle : 0.674 12.198 37676 Z= 0.336 Chirality : 0.046 0.229 4186 Planarity : 0.004 0.065 4740 Dihedral : 10.590 135.419 4105 Min Nonbonded Distance : 1.914 Molprobity Statistics. All-atom Clashscore : 11.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.02 % Favored : 97.98 % Rotamer: Outliers : 3.43 % Allowed : 27.26 % Favored : 69.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.13 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.80 (0.15), residues: 3265 helix: 1.48 (0.15), residues: 1292 sheet: -0.65 (0.24), residues: 443 loop : 0.22 (0.17), residues: 1530 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 163 HIS 0.007 0.001 HIS F 47 PHE 0.029 0.001 PHE A 421 TYR 0.027 0.001 TYR E 134 ARG 0.009 0.001 ARG C 267 Details of bonding type rmsd hydrogen bonds : bond 0.03728 ( 1274) hydrogen bonds : angle 4.67994 ( 3566) metal coordination : bond 0.00959 ( 20) metal coordination : angle 4.05142 ( 27) covalent geometry : bond 0.00454 (27760) covalent geometry : angle 0.66543 (37649) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6530 Ramachandran restraints generated. 3265 Oldfield, 0 Emsley, 3265 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6530 Ramachandran restraints generated. 3265 Oldfield, 0 Emsley, 3265 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 913 residues out of total 2854 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 815 time to evaluate : 2.989 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 39 ILE cc_start: 0.9192 (OUTLIER) cc_final: 0.8892 (mm) REVERT: A 123 ARG cc_start: 0.8301 (mtm180) cc_final: 0.7905 (mpp-170) REVERT: A 128 ASN cc_start: 0.9589 (m-40) cc_final: 0.9368 (m110) REVERT: A 235 GLU cc_start: 0.8790 (mm-30) cc_final: 0.8538 (mm-30) REVERT: A 311 ARG cc_start: 0.9362 (tpp-160) cc_final: 0.9077 (tpp80) REVERT: A 392 MET cc_start: 0.9240 (ppp) cc_final: 0.9026 (ppp) REVERT: A 430 MET cc_start: 0.9498 (mpp) cc_final: 0.8662 (mpp) REVERT: A 485 GLN cc_start: 0.9308 (OUTLIER) cc_final: 0.8867 (mp10) REVERT: A 524 GLU cc_start: 0.8925 (OUTLIER) cc_final: 0.8544 (mt-10) REVERT: A 563 GLU cc_start: 0.8491 (tp30) cc_final: 0.8173 (tp30) REVERT: A 585 LYS cc_start: 0.9525 (tmtt) cc_final: 0.9191 (tptm) REVERT: A 592 MET cc_start: 0.9131 (mtp) cc_final: 0.8628 (mpp) REVERT: A 842 ARG cc_start: 0.9558 (mtm-85) cc_final: 0.8628 (mtm-85) REVERT: B 33 ASP cc_start: 0.9291 (m-30) cc_final: 0.8981 (m-30) REVERT: B 45 GLU cc_start: 0.8678 (mt-10) cc_final: 0.8366 (mt-10) REVERT: B 104 MET cc_start: 0.9294 (mmt) cc_final: 0.9009 (mmm) REVERT: B 119 ARG cc_start: 0.8597 (ttp80) cc_final: 0.8269 (ttp-110) REVERT: B 126 MET cc_start: 0.9240 (ttm) cc_final: 0.8936 (ttp) REVERT: B 155 TYR cc_start: 0.9301 (p90) cc_final: 0.8802 (p90) REVERT: B 205 GLU cc_start: 0.8696 (mt-10) cc_final: 0.8141 (mp0) REVERT: B 212 LEU cc_start: 0.9326 (OUTLIER) cc_final: 0.9105 (mm) REVERT: B 229 MET cc_start: 0.8955 (tpt) cc_final: 0.8716 (mtp) REVERT: B 326 GLU cc_start: 0.9001 (tp30) cc_final: 0.8275 (tp30) REVERT: B 352 LEU cc_start: 0.9524 (OUTLIER) cc_final: 0.9217 (mm) REVERT: B 362 GLN cc_start: 0.9151 (OUTLIER) cc_final: 0.8771 (tm-30) REVERT: B 371 MET cc_start: 0.8445 (mtm) cc_final: 0.8224 (ptm) REVERT: B 396 ARG cc_start: 0.8519 (ttm-80) cc_final: 0.7964 (mtt90) REVERT: B 425 ASP cc_start: 0.9121 (t0) cc_final: 0.8514 (t0) REVERT: B 444 ASP cc_start: 0.8728 (t0) cc_final: 0.8341 (t0) REVERT: B 447 GLN cc_start: 0.8439 (mp10) cc_final: 0.7309 (mp10) REVERT: B 562 GLU cc_start: 0.9163 (mt-10) cc_final: 0.8762 (mm-30) REVERT: B 726 TYR cc_start: 0.9243 (t80) cc_final: 0.8647 (t80) REVERT: B 760 LYS cc_start: 0.8769 (mtmm) cc_final: 0.8432 (mtmm) REVERT: B 800 LYS cc_start: 0.9416 (mtmm) cc_final: 0.9214 (mttm) REVERT: B 804 LYS cc_start: 0.8601 (tptp) cc_final: 0.8249 (tptt) REVERT: B 1052 ASP cc_start: 0.8908 (p0) cc_final: 0.8329 (p0) REVERT: B 1103 LYS cc_start: 0.8982 (mtmm) cc_final: 0.8756 (mtmm) REVERT: C 59 LEU cc_start: 0.9567 (mt) cc_final: 0.9137 (mt) REVERT: C 81 MET cc_start: 0.8621 (tpp) cc_final: 0.8355 (tpp) REVERT: C 141 GLU cc_start: 0.9003 (tt0) cc_final: 0.8760 (pt0) REVERT: C 265 ARG cc_start: 0.9136 (OUTLIER) cc_final: 0.8244 (mtm180) REVERT: C 276 GLU cc_start: 0.9051 (mt-10) cc_final: 0.8777 (mt-10) REVERT: C 303 ASP cc_start: 0.9110 (t0) cc_final: 0.8685 (t0) REVERT: C 341 PHE cc_start: 0.9505 (t80) cc_final: 0.9210 (t80) REVERT: D 10 GLU cc_start: 0.8815 (tp30) cc_final: 0.8522 (tm-30) REVERT: D 195 THR cc_start: 0.9545 (m) cc_final: 0.9028 (p) REVERT: D 206 GLU cc_start: 0.9027 (pp20) cc_final: 0.8696 (pp20) REVERT: D 209 GLU cc_start: 0.9298 (mt-10) cc_final: 0.8856 (mt-10) REVERT: D 250 ASP cc_start: 0.9510 (t0) cc_final: 0.9234 (t70) REVERT: E 38 TYR cc_start: 0.9053 (t80) cc_final: 0.8736 (t80) REVERT: E 127 PHE cc_start: 0.8224 (OUTLIER) cc_final: 0.7992 (t80) REVERT: E 133 LYS cc_start: 0.8824 (tptp) cc_final: 0.8458 (tppt) REVERT: E 158 GLU cc_start: 0.9566 (mm-30) cc_final: 0.9319 (mm-30) REVERT: L 39 LYS cc_start: 0.9350 (mtmm) cc_final: 0.9086 (mtmm) REVERT: L 46 GLU cc_start: 0.9238 (mp0) cc_final: 0.8805 (mp0) REVERT: L 56 ARG cc_start: 0.9354 (ttt180) cc_final: 0.8841 (ttt180) REVERT: H 27 LYS cc_start: 0.9240 (pptt) cc_final: 0.9039 (ptpp) REVERT: N 9 THR cc_start: 0.9540 (m) cc_final: 0.9053 (p) REVERT: N 20 GLU cc_start: 0.8799 (tp30) cc_final: 0.8472 (tp30) REVERT: N 32 GLU cc_start: 0.8775 (pp20) cc_final: 0.8181 (pp20) REVERT: N 33 LYS cc_start: 0.9602 (ttmm) cc_final: 0.9362 (mmmm) REVERT: N 36 ASP cc_start: 0.9175 (m-30) cc_final: 0.8971 (m-30) REVERT: P 45 ARG cc_start: 0.8895 (tpp-160) cc_final: 0.8450 (tpp-160) outliers start: 98 outliers final: 78 residues processed: 866 average time/residue: 0.4508 time to fit residues: 595.9444 Evaluate side-chains 887 residues out of total 2854 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 801 time to evaluate : 2.960 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 ILE Chi-restraints excluded: chain A residue 66 GLU Chi-restraints excluded: chain A residue 163 TRP Chi-restraints excluded: chain A residue 187 LEU Chi-restraints excluded: chain A residue 252 LEU Chi-restraints excluded: chain A residue 267 ASP Chi-restraints excluded: chain A residue 414 MET Chi-restraints excluded: chain A residue 444 THR Chi-restraints excluded: chain A residue 485 GLN Chi-restraints excluded: chain A residue 501 ILE Chi-restraints excluded: chain A residue 503 ASP Chi-restraints excluded: chain A residue 519 THR Chi-restraints excluded: chain A residue 523 VAL Chi-restraints excluded: chain A residue 524 GLU Chi-restraints excluded: chain A residue 641 VAL Chi-restraints excluded: chain A residue 668 ILE Chi-restraints excluded: chain A residue 713 GLU Chi-restraints excluded: chain A residue 721 MET Chi-restraints excluded: chain A residue 878 MET Chi-restraints excluded: chain A residue 891 ILE Chi-restraints excluded: chain B residue 67 ILE Chi-restraints excluded: chain B residue 116 VAL Chi-restraints excluded: chain B residue 164 VAL Chi-restraints excluded: chain B residue 212 LEU Chi-restraints excluded: chain B residue 234 LEU Chi-restraints excluded: chain B residue 265 THR Chi-restraints excluded: chain B residue 338 ASP Chi-restraints excluded: chain B residue 340 TYR Chi-restraints excluded: chain B residue 352 LEU Chi-restraints excluded: chain B residue 362 GLN Chi-restraints excluded: chain B residue 364 VAL Chi-restraints excluded: chain B residue 366 ASP Chi-restraints excluded: chain B residue 405 GLU Chi-restraints excluded: chain B residue 467 GLU Chi-restraints excluded: chain B residue 468 THR Chi-restraints excluded: chain B residue 482 LEU Chi-restraints excluded: chain B residue 505 VAL Chi-restraints excluded: chain B residue 507 ILE Chi-restraints excluded: chain B residue 687 THR Chi-restraints excluded: chain B residue 733 ASP Chi-restraints excluded: chain B residue 742 ILE Chi-restraints excluded: chain B residue 749 SER Chi-restraints excluded: chain B residue 756 GLU Chi-restraints excluded: chain B residue 801 VAL Chi-restraints excluded: chain B residue 833 THR Chi-restraints excluded: chain B residue 849 ILE Chi-restraints excluded: chain B residue 938 VAL Chi-restraints excluded: chain B residue 978 GLU Chi-restraints excluded: chain B residue 1044 ILE Chi-restraints excluded: chain B residue 1092 SER Chi-restraints excluded: chain B residue 1105 MET Chi-restraints excluded: chain C residue 37 TYR Chi-restraints excluded: chain C residue 73 SER Chi-restraints excluded: chain C residue 80 GLN Chi-restraints excluded: chain C residue 96 VAL Chi-restraints excluded: chain C residue 118 MET Chi-restraints excluded: chain C residue 119 THR Chi-restraints excluded: chain C residue 136 VAL Chi-restraints excluded: chain C residue 179 LYS Chi-restraints excluded: chain C residue 233 LYS Chi-restraints excluded: chain C residue 265 ARG Chi-restraints excluded: chain C residue 273 GLU Chi-restraints excluded: chain C residue 323 ILE Chi-restraints excluded: chain C residue 350 GLU Chi-restraints excluded: chain C residue 353 GLU Chi-restraints excluded: chain C residue 386 LEU Chi-restraints excluded: chain D residue 15 SER Chi-restraints excluded: chain D residue 184 VAL Chi-restraints excluded: chain E residue 56 ASP Chi-restraints excluded: chain E residue 74 VAL Chi-restraints excluded: chain E residue 81 ILE Chi-restraints excluded: chain E residue 89 VAL Chi-restraints excluded: chain E residue 99 ILE Chi-restraints excluded: chain E residue 127 PHE Chi-restraints excluded: chain E residue 146 ILE Chi-restraints excluded: chain F residue 21 LEU Chi-restraints excluded: chain L residue 61 THR Chi-restraints excluded: chain L residue 94 LYS Chi-restraints excluded: chain H residue 9 ILE Chi-restraints excluded: chain H residue 32 LYS Chi-restraints excluded: chain N residue 3 VAL Chi-restraints excluded: chain N residue 60 MET Chi-restraints excluded: chain K residue 35 THR Chi-restraints excluded: chain K residue 48 VAL Chi-restraints excluded: chain P residue 20 SER Chi-restraints excluded: chain P residue 24 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 326 random chunks: chunk 174 optimal weight: 4.9990 chunk 82 optimal weight: 5.9990 chunk 31 optimal weight: 5.9990 chunk 312 optimal weight: 0.4980 chunk 292 optimal weight: 5.9990 chunk 163 optimal weight: 3.9990 chunk 225 optimal weight: 8.9990 chunk 283 optimal weight: 5.9990 chunk 33 optimal weight: 1.9990 chunk 27 optimal weight: 4.9990 chunk 191 optimal weight: 4.9990 overall best weight: 3.2988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 759 ASN A 804 ASN ** B 992 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1008 GLN ** B1037 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 366 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 371 GLN D 29 ASN ** E 126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 22 HIS K 19 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3539 r_free = 0.3539 target = 0.116006 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3062 r_free = 0.3062 target = 0.089421 restraints weight = 64633.448| |-----------------------------------------------------------------------------| r_work (start): 0.2995 rms_B_bonded: 3.51 r_work: 0.2830 rms_B_bonded: 4.21 restraints_weight: 0.5000 r_work (final): 0.2830 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8176 moved from start: 0.3381 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.073 27780 Z= 0.224 Angle : 0.698 12.155 37676 Z= 0.349 Chirality : 0.046 0.231 4186 Planarity : 0.004 0.065 4740 Dihedral : 10.588 135.801 4105 Min Nonbonded Distance : 1.903 Molprobity Statistics. All-atom Clashscore : 11.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Rotamer: Outliers : 3.26 % Allowed : 27.54 % Favored : 69.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.13 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.77 (0.15), residues: 3265 helix: 1.47 (0.15), residues: 1287 sheet: -0.74 (0.23), residues: 444 loop : 0.21 (0.17), residues: 1534 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A 163 HIS 0.007 0.001 HIS F 47 PHE 0.036 0.002 PHE A 421 TYR 0.029 0.001 TYR D 154 ARG 0.009 0.001 ARG C 267 Details of bonding type rmsd hydrogen bonds : bond 0.03862 ( 1274) hydrogen bonds : angle 4.74512 ( 3566) metal coordination : bond 0.01179 ( 20) metal coordination : angle 4.05410 ( 27) covalent geometry : bond 0.00517 (27760) covalent geometry : angle 0.69026 (37649) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6530 Ramachandran restraints generated. 3265 Oldfield, 0 Emsley, 3265 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6530 Ramachandran restraints generated. 3265 Oldfield, 0 Emsley, 3265 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 903 residues out of total 2854 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 810 time to evaluate : 2.935 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 39 ILE cc_start: 0.9201 (OUTLIER) cc_final: 0.8898 (mm) REVERT: A 123 ARG cc_start: 0.8341 (mtm180) cc_final: 0.7927 (mtm-85) REVERT: A 128 ASN cc_start: 0.9601 (m-40) cc_final: 0.9376 (m110) REVERT: A 235 GLU cc_start: 0.8774 (mm-30) cc_final: 0.8516 (mm-30) REVERT: A 237 ASP cc_start: 0.9303 (m-30) cc_final: 0.9044 (m-30) REVERT: A 392 MET cc_start: 0.9231 (ppp) cc_final: 0.9028 (ppp) REVERT: A 430 MET cc_start: 0.9501 (mpp) cc_final: 0.8658 (mpp) REVERT: A 485 GLN cc_start: 0.9309 (OUTLIER) cc_final: 0.8858 (mp10) REVERT: A 524 GLU cc_start: 0.8920 (OUTLIER) cc_final: 0.8536 (mt-10) REVERT: A 563 GLU cc_start: 0.8533 (tp30) cc_final: 0.8234 (tp30) REVERT: A 585 LYS cc_start: 0.9527 (tmtt) cc_final: 0.9194 (tptm) REVERT: A 592 MET cc_start: 0.9124 (mtp) cc_final: 0.8626 (mpp) REVERT: A 828 ASP cc_start: 0.8925 (t0) cc_final: 0.8712 (t0) REVERT: A 842 ARG cc_start: 0.9560 (mtm-85) cc_final: 0.8652 (mtm-85) REVERT: B 33 ASP cc_start: 0.9295 (m-30) cc_final: 0.8984 (m-30) REVERT: B 45 GLU cc_start: 0.8638 (mt-10) cc_final: 0.8320 (mt-10) REVERT: B 104 MET cc_start: 0.9284 (mmt) cc_final: 0.9004 (mmm) REVERT: B 126 MET cc_start: 0.9303 (ttm) cc_final: 0.8996 (ttp) REVERT: B 155 TYR cc_start: 0.9315 (p90) cc_final: 0.8812 (p90) REVERT: B 205 GLU cc_start: 0.8669 (mt-10) cc_final: 0.8158 (mp0) REVERT: B 326 GLU cc_start: 0.9051 (tp30) cc_final: 0.8279 (tp30) REVERT: B 352 LEU cc_start: 0.9536 (OUTLIER) cc_final: 0.9218 (mm) REVERT: B 362 GLN cc_start: 0.9131 (OUTLIER) cc_final: 0.8733 (tm-30) REVERT: B 371 MET cc_start: 0.8471 (mtm) cc_final: 0.8225 (ptm) REVERT: B 425 ASP cc_start: 0.9156 (t0) cc_final: 0.8577 (t0) REVERT: B 444 ASP cc_start: 0.8732 (t0) cc_final: 0.8340 (t0) REVERT: B 447 GLN cc_start: 0.8413 (mp10) cc_final: 0.7299 (mp10) REVERT: B 541 GLN cc_start: 0.9376 (OUTLIER) cc_final: 0.8968 (tm-30) REVERT: B 562 GLU cc_start: 0.9136 (mt-10) cc_final: 0.8800 (mm-30) REVERT: B 568 ASP cc_start: 0.8988 (p0) cc_final: 0.8769 (p0) REVERT: B 616 GLU cc_start: 0.8994 (mt-10) cc_final: 0.8754 (mt-10) REVERT: B 726 TYR cc_start: 0.9221 (t80) cc_final: 0.8589 (t80) REVERT: B 760 LYS cc_start: 0.8781 (mtmm) cc_final: 0.8415 (mtmm) REVERT: B 804 LYS cc_start: 0.8634 (tptp) cc_final: 0.8280 (tptt) REVERT: B 1052 ASP cc_start: 0.8935 (p0) cc_final: 0.8405 (p0) REVERT: B 1103 LYS cc_start: 0.8986 (mtmm) cc_final: 0.8744 (mtmm) REVERT: C 141 GLU cc_start: 0.8985 (tt0) cc_final: 0.8684 (tt0) REVERT: C 265 ARG cc_start: 0.9169 (OUTLIER) cc_final: 0.8298 (mtm180) REVERT: C 276 GLU cc_start: 0.9045 (mt-10) cc_final: 0.8772 (mt-10) REVERT: C 303 ASP cc_start: 0.9091 (t0) cc_final: 0.8668 (t0) REVERT: C 338 ARG cc_start: 0.9460 (mtm-85) cc_final: 0.8970 (mtm-85) REVERT: D 195 THR cc_start: 0.9548 (m) cc_final: 0.9031 (p) REVERT: D 206 GLU cc_start: 0.9040 (pp20) cc_final: 0.8710 (pp20) REVERT: D 209 GLU cc_start: 0.9299 (mt-10) cc_final: 0.8864 (mt-10) REVERT: D 250 ASP cc_start: 0.9514 (t0) cc_final: 0.9222 (t70) REVERT: E 38 TYR cc_start: 0.9074 (t80) cc_final: 0.8756 (t80) REVERT: E 127 PHE cc_start: 0.8237 (OUTLIER) cc_final: 0.8030 (t80) REVERT: E 133 LYS cc_start: 0.8857 (tptp) cc_final: 0.8525 (tppt) REVERT: E 158 GLU cc_start: 0.9556 (mm-30) cc_final: 0.9270 (mm-30) REVERT: L 18 GLU cc_start: 0.9104 (mm-30) cc_final: 0.8760 (mm-30) REVERT: L 39 LYS cc_start: 0.9345 (mtmm) cc_final: 0.9086 (mtmm) REVERT: L 46 GLU cc_start: 0.9235 (mp0) cc_final: 0.8811 (mp0) REVERT: L 56 ARG cc_start: 0.9339 (ttt180) cc_final: 0.8804 (ttt180) REVERT: N 9 THR cc_start: 0.9543 (m) cc_final: 0.9060 (p) REVERT: N 20 GLU cc_start: 0.8818 (tp30) cc_final: 0.8502 (tp30) REVERT: N 32 GLU cc_start: 0.8775 (pp20) cc_final: 0.8183 (pp20) REVERT: N 33 LYS cc_start: 0.9597 (ttmm) cc_final: 0.9372 (mmmm) REVERT: N 36 ASP cc_start: 0.9185 (m-30) cc_final: 0.8985 (m-30) REVERT: P 5 VAL cc_start: 0.9090 (t) cc_final: 0.8790 (p) REVERT: P 45 ARG cc_start: 0.8848 (tpp-160) cc_final: 0.8384 (tpp-160) outliers start: 93 outliers final: 82 residues processed: 855 average time/residue: 0.4020 time to fit residues: 527.4259 Evaluate side-chains 884 residues out of total 2854 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 794 time to evaluate : 3.087 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 ILE Chi-restraints excluded: chain A residue 66 GLU Chi-restraints excluded: chain A residue 163 TRP Chi-restraints excluded: chain A residue 187 LEU Chi-restraints excluded: chain A residue 252 LEU Chi-restraints excluded: chain A residue 267 ASP Chi-restraints excluded: chain A residue 485 GLN Chi-restraints excluded: chain A residue 501 ILE Chi-restraints excluded: chain A residue 503 ASP Chi-restraints excluded: chain A residue 519 THR Chi-restraints excluded: chain A residue 523 VAL Chi-restraints excluded: chain A residue 524 GLU Chi-restraints excluded: chain A residue 641 VAL Chi-restraints excluded: chain A residue 668 ILE Chi-restraints excluded: chain A residue 713 GLU Chi-restraints excluded: chain A residue 721 MET Chi-restraints excluded: chain A residue 878 MET Chi-restraints excluded: chain A residue 891 ILE Chi-restraints excluded: chain B residue 67 ILE Chi-restraints excluded: chain B residue 116 VAL Chi-restraints excluded: chain B residue 143 ILE Chi-restraints excluded: chain B residue 164 VAL Chi-restraints excluded: chain B residue 234 LEU Chi-restraints excluded: chain B residue 265 THR Chi-restraints excluded: chain B residue 338 ASP Chi-restraints excluded: chain B residue 340 TYR Chi-restraints excluded: chain B residue 352 LEU Chi-restraints excluded: chain B residue 362 GLN Chi-restraints excluded: chain B residue 364 VAL Chi-restraints excluded: chain B residue 366 ASP Chi-restraints excluded: chain B residue 405 GLU Chi-restraints excluded: chain B residue 467 GLU Chi-restraints excluded: chain B residue 468 THR Chi-restraints excluded: chain B residue 482 LEU Chi-restraints excluded: chain B residue 505 VAL Chi-restraints excluded: chain B residue 507 ILE Chi-restraints excluded: chain B residue 541 GLN Chi-restraints excluded: chain B residue 673 SER Chi-restraints excluded: chain B residue 687 THR Chi-restraints excluded: chain B residue 733 ASP Chi-restraints excluded: chain B residue 742 ILE Chi-restraints excluded: chain B residue 749 SER Chi-restraints excluded: chain B residue 756 GLU Chi-restraints excluded: chain B residue 801 VAL Chi-restraints excluded: chain B residue 833 THR Chi-restraints excluded: chain B residue 837 VAL Chi-restraints excluded: chain B residue 849 ILE Chi-restraints excluded: chain B residue 938 VAL Chi-restraints excluded: chain B residue 978 GLU Chi-restraints excluded: chain B residue 1044 ILE Chi-restraints excluded: chain B residue 1092 SER Chi-restraints excluded: chain B residue 1105 MET Chi-restraints excluded: chain C residue 37 TYR Chi-restraints excluded: chain C residue 73 SER Chi-restraints excluded: chain C residue 80 GLN Chi-restraints excluded: chain C residue 96 VAL Chi-restraints excluded: chain C residue 118 MET Chi-restraints excluded: chain C residue 119 THR Chi-restraints excluded: chain C residue 136 VAL Chi-restraints excluded: chain C residue 147 ASN Chi-restraints excluded: chain C residue 179 LYS Chi-restraints excluded: chain C residue 233 LYS Chi-restraints excluded: chain C residue 250 SER Chi-restraints excluded: chain C residue 265 ARG Chi-restraints excluded: chain C residue 273 GLU Chi-restraints excluded: chain C residue 323 ILE Chi-restraints excluded: chain C residue 350 GLU Chi-restraints excluded: chain C residue 353 GLU Chi-restraints excluded: chain C residue 386 LEU Chi-restraints excluded: chain D residue 15 SER Chi-restraints excluded: chain D residue 184 VAL Chi-restraints excluded: chain E residue 74 VAL Chi-restraints excluded: chain E residue 81 ILE Chi-restraints excluded: chain E residue 89 VAL Chi-restraints excluded: chain E residue 99 ILE Chi-restraints excluded: chain E residue 127 PHE Chi-restraints excluded: chain E residue 146 ILE Chi-restraints excluded: chain F residue 21 LEU Chi-restraints excluded: chain L residue 41 THR Chi-restraints excluded: chain L residue 61 THR Chi-restraints excluded: chain L residue 94 LYS Chi-restraints excluded: chain H residue 9 ILE Chi-restraints excluded: chain H residue 32 LYS Chi-restraints excluded: chain H residue 35 ILE Chi-restraints excluded: chain N residue 3 VAL Chi-restraints excluded: chain N residue 60 MET Chi-restraints excluded: chain K residue 35 THR Chi-restraints excluded: chain K residue 48 VAL Chi-restraints excluded: chain P residue 24 ASP Chi-restraints excluded: chain P residue 47 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 326 random chunks: chunk 79 optimal weight: 7.9990 chunk 200 optimal weight: 0.0470 chunk 210 optimal weight: 5.9990 chunk 301 optimal weight: 6.9990 chunk 298 optimal weight: 1.9990 chunk 128 optimal weight: 6.9990 chunk 257 optimal weight: 0.8980 chunk 135 optimal weight: 0.9980 chunk 130 optimal weight: 3.9990 chunk 168 optimal weight: 6.9990 chunk 45 optimal weight: 0.9990 overall best weight: 0.9882 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 370 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 992 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1008 GLN ** B1037 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 72 GLN ** C 366 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 371 GLN ** E 126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 22 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3577 r_free = 0.3577 target = 0.118553 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3107 r_free = 0.3107 target = 0.091898 restraints weight = 64276.052| |-----------------------------------------------------------------------------| r_work (start): 0.3043 rms_B_bonded: 3.55 r_work: 0.2883 rms_B_bonded: 4.26 restraints_weight: 0.5000 r_work (final): 0.2883 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8138 moved from start: 0.3501 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 27780 Z= 0.130 Angle : 0.677 13.223 37676 Z= 0.335 Chirality : 0.045 0.208 4186 Planarity : 0.004 0.058 4740 Dihedral : 10.488 135.644 4105 Min Nonbonded Distance : 1.965 Molprobity Statistics. All-atom Clashscore : 10.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer: Outliers : 2.56 % Allowed : 28.56 % Favored : 68.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.13 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.81 (0.15), residues: 3265 helix: 1.49 (0.15), residues: 1287 sheet: -0.59 (0.23), residues: 466 loop : 0.22 (0.17), residues: 1512 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 163 HIS 0.005 0.001 HIS F 47 PHE 0.034 0.001 PHE A 421 TYR 0.030 0.001 TYR P 6 ARG 0.009 0.001 ARG C 267 Details of bonding type rmsd hydrogen bonds : bond 0.03478 ( 1274) hydrogen bonds : angle 4.63400 ( 3566) metal coordination : bond 0.00554 ( 20) metal coordination : angle 3.74679 ( 27) covalent geometry : bond 0.00308 (27760) covalent geometry : angle 0.66962 (37649) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 16586.79 seconds wall clock time: 286 minutes 36.52 seconds (17196.52 seconds total)