Starting phenix.real_space_refine on Thu May 29 16:14:56 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8s0b_19620/05_2025/8s0b_19620.cif Found real_map, /net/cci-nas-00/data/ceres_data/8s0b_19620/05_2025/8s0b_19620.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8s0b_19620/05_2025/8s0b_19620.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8s0b_19620/05_2025/8s0b_19620.map" model { file = "/net/cci-nas-00/data/ceres_data/8s0b_19620/05_2025/8s0b_19620.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8s0b_19620/05_2025/8s0b_19620.cif" } resolution = 3.6 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= 0.003 sd= 0.027 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 105 5.49 5 Mg 6 5.21 5 S 191 5.16 5 C 20068 2.51 5 N 5750 2.21 5 O 6299 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 residue(s): 0.09s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 32424 Number of models: 1 Model: "" Number of chains: 15 Chain: "F" Number of atoms: 1341 Number of conformers: 1 Conformer: "" Number of residues, atoms: 175, 1341 Classifications: {'peptide': 175} Link IDs: {'PTRANS': 5, 'TRANS': 169} Chain breaks: 1 Chain: "2" Number of atoms: 5093 Number of conformers: 1 Conformer: "" Number of residues, atoms: 643, 5093 Classifications: {'peptide': 643} Link IDs: {'PTRANS': 29, 'TRANS': 613} Chain breaks: 2 Chain: "3" Number of atoms: 4715 Number of conformers: 1 Conformer: "" Number of residues, atoms: 598, 4715 Classifications: {'peptide': 598} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 20, 'TRANS': 577} Chain breaks: 5 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'GLU:plan': 2} Unresolved non-hydrogen planarities: 8 Chain: "4" Number of atoms: 4969 Number of conformers: 1 Conformer: "" Number of residues, atoms: 623, 4969 Classifications: {'peptide': 623} Link IDs: {'PTRANS': 28, 'TRANS': 594} Chain breaks: 1 Chain: "5" Number of atoms: 4679 Number of conformers: 1 Conformer: "" Number of residues, atoms: 595, 4679 Classifications: {'peptide': 595} Link IDs: {'PTRANS': 25, 'TRANS': 569} Chain breaks: 4 Chain: "6" Number of atoms: 5259 Number of conformers: 1 Conformer: "" Number of residues, atoms: 652, 5259 Classifications: {'peptide': 652} Link IDs: {'PTRANS': 21, 'TRANS': 630} Chain breaks: 5 Chain: "7" Number of atoms: 4338 Number of conformers: 1 Conformer: "" Number of residues, atoms: 548, 4338 Classifications: {'peptide': 548} Link IDs: {'PTRANS': 25, 'TRANS': 522} Chain breaks: 8 Chain: "X" Number of atoms: 921 Number of conformers: 1 Conformer: "" Number of residues, atoms: 45, 921 Classifications: {'DNA': 45} Link IDs: {'rna3p': 44} Chain: "Y" Number of atoms: 924 Number of conformers: 1 Conformer: "" Number of residues, atoms: 45, 924 Classifications: {'DNA': 45} Link IDs: {'rna3p': 44} Chain: "2" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {' MG': 1, ' ZN': 1, 'AGS': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "3" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "4" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' ZN': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "5" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 29 Unusual residues: {' MG': 1, ' ZN': 1, 'ADP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "6" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {' MG': 1, ' ZN': 1, 'AGS': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "7" Number of atoms: 34 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 34 Unusual residues: {' MG': 2, ' ZN': 1, 'AGS': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 2557 SG CYS 2 329 112.947 35.988 67.665 1.00 65.06 S ATOM 2580 SG CYS 2 332 114.338 32.943 66.695 1.00 73.56 S ATOM 2731 SG CYS 2 352 115.830 34.362 70.055 1.00 79.31 S ATOM 2753 SG CYS 2 355 116.625 35.977 66.940 1.00 84.13 S ATOM 12432 SG CYS 4 306 134.093 77.790 90.065 1.00 57.77 S ATOM 12454 SG CYS 4 309 136.428 79.271 92.609 1.00 60.67 S ATOM 12600 SG CYS 4 328 136.874 80.238 88.970 1.00 63.48 S ATOM 12621 SG CYS 4 331 137.551 76.709 89.710 1.00 72.53 S ATOM 17265 SG CYS 5 172 115.482 48.290 47.433 1.00123.88 S ATOM 17288 SG CYS 5 175 116.997 45.833 45.415 1.00127.77 S ATOM 17459 SG CYS 5 197 117.033 45.405 49.177 1.00142.68 S ATOM 21965 SG CYS 6 158 129.206 61.549 85.221 1.00 87.76 S ATOM 21987 SG CYS 6 161 132.916 60.782 86.331 1.00 92.86 S ATOM 22148 SG CYS 6 180 131.347 63.905 86.939 1.00 99.34 S ATOM 22187 SG CYS 6 185 132.385 62.259 83.249 1.00105.97 S ATOM 27397 SG CYS 7 184 132.337 89.444 63.685 1.00137.60 S ATOM 27420 SG CYS 7 187 133.847 91.326 61.010 1.00145.03 S ATOM 27566 SG CYS 7 206 131.342 88.273 60.416 1.00135.17 S ATOM 27603 SG CYS 7 211 134.965 87.669 61.589 1.00136.56 S Time building chain proxies: 19.50, per 1000 atoms: 0.60 Number of scatterers: 32424 At special positions: 0 Unit cell: (179.28, 149.04, 143.64, 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 191 16.00 P 105 15.00 Mg 6 11.99 O 6299 8.00 N 5750 7.00 C 20068 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: 7.58 Conformation dependent library (CDL) restraints added in 3.8 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN 21003 " pdb="ZN ZN 21003 " - pdb=" SG CYS 2 355 " pdb="ZN ZN 21003 " - pdb=" SG CYS 2 332 " pdb="ZN ZN 21003 " - pdb=" SG CYS 2 329 " pdb="ZN ZN 21003 " - pdb=" SG CYS 2 352 " pdb=" ZN 4 901 " pdb="ZN ZN 4 901 " - pdb=" SG CYS 4 306 " pdb="ZN ZN 4 901 " - pdb=" SG CYS 4 328 " pdb="ZN ZN 4 901 " - pdb=" SG CYS 4 331 " pdb="ZN ZN 4 901 " - pdb=" SG CYS 4 309 " pdb=" ZN 5 803 " pdb="ZN ZN 5 803 " - pdb=" SG CYS 5 172 " pdb="ZN ZN 5 803 " - pdb=" SG CYS 5 175 " pdb="ZN ZN 5 803 " - pdb=" SG CYS 5 197 " pdb=" ZN 6 903 " pdb="ZN ZN 6 903 " - pdb=" SG CYS 6 180 " pdb="ZN ZN 6 903 " - pdb=" SG CYS 6 161 " pdb="ZN ZN 6 903 " - pdb=" SG CYS 6 185 " pdb="ZN ZN 6 903 " - pdb=" SG CYS 6 158 " pdb=" ZN 7 804 " pdb="ZN ZN 7 804 " - pdb=" SG CYS 7 184 " pdb="ZN ZN 7 804 " - pdb=" SG CYS 7 187 " pdb="ZN ZN 7 804 " - pdb=" SG CYS 7 206 " pdb="ZN ZN 7 804 " - pdb=" SG CYS 7 211 " Number of angles added : 24 7536 Ramachandran restraints generated. 3768 Oldfield, 0 Emsley, 3768 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7304 Finding SS restraints... Secondary structure from input PDB file: 162 helices and 39 sheets defined 48.1% alpha, 14.1% beta 45 base pairs and 78 stacking pairs defined. Time for finding SS restraints: 11.13 Creating SS restraints... Processing helix chain 'F' and resid 2 through 14 removed outlier: 3.860A pdb=" N ILE F 6 " --> pdb=" O GLY F 2 " (cutoff:3.500A) Proline residue: F 11 - end of helix Processing helix chain 'F' and resid 17 through 35 removed outlier: 3.570A pdb=" N LEU F 21 " --> pdb=" O GLU F 17 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N GLU F 26 " --> pdb=" O ARG F 22 " (cutoff:3.500A) Processing helix chain 'F' and resid 35 through 42 Processing helix chain 'F' and resid 44 through 59 removed outlier: 3.637A pdb=" N ALA F 48 " --> pdb=" O GLU F 44 " (cutoff:3.500A) Processing helix chain 'F' and resid 64 through 73 Processing helix chain 'F' and resid 75 through 91 Processing helix chain 'F' and resid 97 through 104 removed outlier: 3.661A pdb=" N LEU F 101 " --> pdb=" O GLY F 97 " (cutoff:3.500A) Processing helix chain 'F' and resid 109 through 123 removed outlier: 4.042A pdb=" N MET F 113 " --> pdb=" O GLU F 109 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N LYS F 119 " --> pdb=" O SER F 115 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N SER F 120 " --> pdb=" O LYS F 116 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N SER F 123 " --> pdb=" O LYS F 119 " (cutoff:3.500A) Processing helix chain 'F' and resid 128 through 133 removed outlier: 4.303A pdb=" N ASP F 132 " --> pdb=" O THR F 128 " (cutoff:3.500A) Processing helix chain 'F' and resid 137 through 151 removed outlier: 3.686A pdb=" N THR F 141 " --> pdb=" O ARG F 137 " (cutoff:3.500A) Processing helix chain 'F' and resid 159 through 166 Processing helix chain 'F' and resid 168 through 182 removed outlier: 3.700A pdb=" N GLN F 178 " --> pdb=" O ARG F 174 " (cutoff:3.500A) Processing helix chain '2' and resid 182 through 188 removed outlier: 3.704A pdb=" N MET 2 188 " --> pdb=" O GLU 2 184 " (cutoff:3.500A) Processing helix chain '2' and resid 188 through 206 Processing helix chain '2' and resid 213 through 225 removed outlier: 3.608A pdb=" N GLU 2 217 " --> pdb=" O ASN 2 213 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N GLU 2 225 " --> pdb=" O ASP 2 221 " (cutoff:3.500A) Processing helix chain '2' and resid 233 through 241 Processing helix chain '2' and resid 242 through 248 Processing helix chain '2' and resid 251 through 271 removed outlier: 3.808A pdb=" N LEU 2 255 " --> pdb=" O ALA 2 251 " (cutoff:3.500A) Processing helix chain '2' and resid 273 through 278 removed outlier: 3.771A pdb=" N ILE 2 277 " --> pdb=" O LYS 2 273 " (cutoff:3.500A) Processing helix chain '2' and resid 293 through 297 removed outlier: 3.802A pdb=" N LEU 2 297 " --> pdb=" O LEU 2 294 " (cutoff:3.500A) Processing helix chain '2' and resid 298 through 302 removed outlier: 3.515A pdb=" N LEU 2 302 " --> pdb=" O GLN 2 299 " (cutoff:3.500A) Processing helix chain '2' and resid 401 through 403 No H-bonds generated for 'chain '2' and resid 401 through 403' Processing helix chain '2' and resid 459 through 469 Processing helix chain '2' and resid 472 through 481 Processing helix chain '2' and resid 488 through 501 Processing helix chain '2' and resid 529 through 540 removed outlier: 3.638A pdb=" N LEU 2 533 " --> pdb=" O LYS 2 529 " (cutoff:3.500A) Processing helix chain '2' and resid 574 through 579 Processing helix chain '2' and resid 588 through 592 removed outlier: 4.142A pdb=" N MET 2 592 " --> pdb=" O PHE 2 589 " (cutoff:3.500A) Processing helix chain '2' and resid 593 through 606 Processing helix chain '2' and resid 642 through 647 Processing helix chain '2' and resid 650 through 657 removed outlier: 3.649A pdb=" N ARG 2 656 " --> pdb=" O PRO 2 652 " (cutoff:3.500A) removed outlier: 4.421A pdb=" N PHE 2 657 " --> pdb=" O ILE 2 653 " (cutoff:3.500A) Processing helix chain '2' and resid 668 through 686 Processing helix chain '2' and resid 716 through 730 Processing helix chain '2' and resid 739 through 758 removed outlier: 3.682A pdb=" N VAL 2 743 " --> pdb=" O ASP 2 739 " (cutoff:3.500A) Processing helix chain '2' and resid 763 through 781 removed outlier: 3.988A pdb=" N ILE 2 767 " --> pdb=" O THR 2 763 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N HIS 2 781 " --> pdb=" O HIS 2 777 " (cutoff:3.500A) Processing helix chain '2' and resid 787 through 806 removed outlier: 3.610A pdb=" N VAL 2 791 " --> pdb=" O ILE 2 787 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N GLN 2 806 " --> pdb=" O PHE 2 802 " (cutoff:3.500A) Processing helix chain '2' and resid 807 through 818 Processing helix chain '2' and resid 818 through 823 Processing helix chain '2' and resid 827 through 851 Processing helix chain '3' and resid 11 through 24 Processing helix chain '3' and resid 25 through 29 removed outlier: 3.516A pdb=" N GLN 3 29 " --> pdb=" O GLU 3 26 " (cutoff:3.500A) Processing helix chain '3' and resid 31 through 42 Processing helix chain '3' and resid 51 through 58 Processing helix chain '3' and resid 58 through 68 Processing helix chain '3' and resid 69 through 88 Processing helix chain '3' and resid 88 through 93 Processing helix chain '3' and resid 117 through 121 Processing helix chain '3' and resid 224 through 226 No H-bonds generated for 'chain '3' and resid 224 through 226' Processing helix chain '3' and resid 279 through 291 removed outlier: 4.237A pdb=" N LYS 3 283 " --> pdb=" O GLU 3 279 " (cutoff:3.500A) Processing helix chain '3' and resid 294 through 302 Processing helix chain '3' and resid 310 through 323 Processing helix chain '3' and resid 351 through 362 Processing helix chain '3' and resid 374 through 379 Processing helix chain '3' and resid 396 through 401 Processing helix chain '3' and resid 410 through 414 Processing helix chain '3' and resid 415 through 429 removed outlier: 4.154A pdb=" N GLU 3 424 " --> pdb=" O THR 3 420 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N VAL 3 425 " --> pdb=" O ALA 3 421 " (cutoff:3.500A) Processing helix chain '3' and resid 464 through 470 Processing helix chain '3' and resid 472 through 479 Processing helix chain '3' and resid 490 through 507 Processing helix chain '3' and resid 555 through 559 removed outlier: 3.999A pdb=" N LYS 3 559 " --> pdb=" O LYS 3 556 " (cutoff:3.500A) Processing helix chain '3' and resid 564 through 578 Processing helix chain '3' and resid 583 through 600 removed outlier: 4.100A pdb=" N ALA 3 587 " --> pdb=" O THR 3 583 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N THR 3 588 " --> pdb=" O GLN 3 584 " (cutoff:3.500A) Processing helix chain '3' and resid 601 through 604 removed outlier: 3.931A pdb=" N SER 3 604 " --> pdb=" O ASP 3 601 " (cutoff:3.500A) No H-bonds generated for 'chain '3' and resid 601 through 604' Processing helix chain '3' and resid 615 through 632 removed outlier: 3.761A pdb=" N GLU 3 619 " --> pdb=" O ALA 3 615 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N ARG 3 632 " --> pdb=" O HIS 3 628 " (cutoff:3.500A) Processing helix chain '3' and resid 638 through 653 removed outlier: 3.528A pdb=" N ALA 3 642 " --> pdb=" O ASP 3 638 " (cutoff:3.500A) Processing helix chain '4' and resid 158 through 173 removed outlier: 3.552A pdb=" N GLN 4 171 " --> pdb=" O GLN 4 167 " (cutoff:3.500A) Processing helix chain '4' and resid 191 through 204 Processing helix chain '4' and resid 212 through 219 Processing helix chain '4' and resid 220 through 229 Processing helix chain '4' and resid 229 through 249 Proline residue: 4 235 - end of helix Processing helix chain '4' and resid 270 through 274 Processing helix chain '4' and resid 275 through 279 Processing helix chain '4' and resid 377 through 379 No H-bonds generated for 'chain '4' and resid 377 through 379' Processing helix chain '4' and resid 431 through 436 Processing helix chain '4' and resid 442 through 455 removed outlier: 3.731A pdb=" N LYS 4 455 " --> pdb=" O GLU 4 451 " (cutoff:3.500A) Processing helix chain '4' and resid 457 through 466 Processing helix chain '4' and resid 473 through 486 Processing helix chain '4' and resid 516 through 525 Processing helix chain '4' and resid 536 through 538 No H-bonds generated for 'chain '4' and resid 536 through 538' Processing helix chain '4' and resid 561 through 566 Processing helix chain '4' and resid 580 through 594 removed outlier: 3.905A pdb=" N VAL 4 586 " --> pdb=" O SER 4 582 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N LEU 4 587 " --> pdb=" O THR 4 583 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N GLU 4 589 " --> pdb=" O SER 4 585 " (cutoff:3.500A) removed outlier: 4.466A pdb=" N GLU 4 592 " --> pdb=" O HIS 4 588 " (cutoff:3.500A) Processing helix chain '4' and resid 629 through 635 Processing helix chain '4' and resid 637 through 642 Processing helix chain '4' and resid 655 through 670 removed outlier: 3.790A pdb=" N TYR 4 670 " --> pdb=" O LEU 4 666 " (cutoff:3.500A) Processing helix chain '4' and resid 683 through 698 removed outlier: 3.742A pdb=" N ILE 4 698 " --> pdb=" O ALA 4 694 " (cutoff:3.500A) Processing helix chain '4' and resid 703 through 722 Processing helix chain '4' and resid 730 through 748 removed outlier: 4.073A pdb=" N LEU 4 734 " --> pdb=" O TYR 4 730 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N GLU 4 735 " --> pdb=" O PRO 4 731 " (cutoff:3.500A) Processing helix chain '4' and resid 754 through 769 removed outlier: 3.616A pdb=" N VAL 4 758 " --> pdb=" O GLU 4 754 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N LEU 4 769 " --> pdb=" O HIS 4 765 " (cutoff:3.500A) Processing helix chain '5' and resid 27 through 42 Processing helix chain '5' and resid 53 through 66 Processing helix chain '5' and resid 74 through 81 Processing helix chain '5' and resid 81 through 89 removed outlier: 3.857A pdb=" N ALA 5 85 " --> pdb=" O ASP 5 81 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N TYR 5 89 " --> pdb=" O ALA 5 85 " (cutoff:3.500A) Processing helix chain '5' and resid 91 through 111 removed outlier: 3.817A pdb=" N HIS 5 95 " --> pdb=" O GLN 5 91 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N GLN 5 97 " --> pdb=" O ALA 5 93 " (cutoff:3.500A) Processing helix chain '5' and resid 136 through 140 removed outlier: 3.955A pdb=" N LEU 5 140 " --> pdb=" O ILE 5 137 " (cutoff:3.500A) Processing helix chain '5' and resid 141 through 145 Processing helix chain '5' and resid 216 through 219 removed outlier: 3.644A pdb=" N CYS 5 219 " --> pdb=" O PRO 5 216 " (cutoff:3.500A) No H-bonds generated for 'chain '5' and resid 216 through 219' Processing helix chain '5' and resid 252 through 254 No H-bonds generated for 'chain '5' and resid 252 through 254' Processing helix chain '5' and resid 317 through 328 removed outlier: 3.616A pdb=" N LEU 5 328 " --> pdb=" O ARG 5 324 " (cutoff:3.500A) Processing helix chain '5' and resid 330 through 339 Processing helix chain '5' and resid 346 through 359 Processing helix chain '5' and resid 387 through 398 Processing helix chain '5' and resid 432 through 437 Processing helix chain '5' and resid 446 through 450 removed outlier: 3.702A pdb=" N LYS 5 449 " --> pdb=" O GLU 5 446 " (cutoff:3.500A) removed outlier: 4.162A pdb=" N MET 5 450 " --> pdb=" O PHE 5 447 " (cutoff:3.500A) No H-bonds generated for 'chain '5' and resid 446 through 450' Processing helix chain '5' and resid 451 through 464 removed outlier: 3.686A pdb=" N HIS 5 459 " --> pdb=" O ARG 5 455 " (cutoff:3.500A) removed outlier: 4.138A pdb=" N GLU 5 460 " --> pdb=" O VAL 5 456 " (cutoff:3.500A) Processing helix chain '5' and resid 507 through 512 Processing helix chain '5' and resid 525 through 543 removed outlier: 3.569A pdb=" N VAL 5 530 " --> pdb=" O GLU 5 526 " (cutoff:3.500A) Processing helix chain '5' and resid 555 through 570 removed outlier: 3.711A pdb=" N CYS 5 570 " --> pdb=" O CYS 5 566 " (cutoff:3.500A) Processing helix chain '5' and resid 575 through 601 Processing helix chain '5' and resid 609 through 627 removed outlier: 3.631A pdb=" N LEU 5 613 " --> pdb=" O THR 5 609 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N LYS 5 627 " --> pdb=" O LEU 5 623 " (cutoff:3.500A) Processing helix chain '5' and resid 633 through 654 removed outlier: 4.107A pdb=" N ASP 5 650 " --> pdb=" O VAL 5 646 " (cutoff:3.500A) Processing helix chain '6' and resid 20 through 37 Processing helix chain '6' and resid 44 through 52 removed outlier: 3.839A pdb=" N GLN 6 48 " --> pdb=" O ILE 6 44 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N GLU 6 52 " --> pdb=" O GLN 6 48 " (cutoff:3.500A) Processing helix chain '6' and resid 53 through 55 No H-bonds generated for 'chain '6' and resid 53 through 55' Processing helix chain '6' and resid 64 through 70 Processing helix chain '6' and resid 72 through 82 Processing helix chain '6' and resid 82 through 102 Proline residue: 6 88 - end of helix Processing helix chain '6' and resid 122 through 126 Processing helix chain '6' and resid 127 through 131 Processing helix chain '6' and resid 195 through 198 Processing helix chain '6' and resid 211 through 215 removed outlier: 3.641A pdb=" N GLU 6 214 " --> pdb=" O THR 6 211 " (cutoff:3.500A) Processing helix chain '6' and resid 231 through 234 Processing helix chain '6' and resid 322 through 329 Processing helix chain '6' and resid 330 through 342 Processing helix chain '6' and resid 345 through 355 removed outlier: 4.216A pdb=" N CYS 6 351 " --> pdb=" O TYR 6 347 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N PHE 6 355 " --> pdb=" O CYS 6 351 " (cutoff:3.500A) Processing helix chain '6' and resid 361 through 374 Processing helix chain '6' and resid 402 through 413 removed outlier: 4.339A pdb=" N LEU 6 406 " --> pdb=" O LYS 6 402 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N LYS 6 407 " --> pdb=" O SER 6 403 " (cutoff:3.500A) Processing helix chain '6' and resid 422 through 424 No H-bonds generated for 'chain '6' and resid 422 through 424' Processing helix chain '6' and resid 447 through 452 Processing helix chain '6' and resid 466 through 480 Processing helix chain '6' and resid 515 through 519 Processing helix chain '6' and resid 523 through 530 removed outlier: 3.671A pdb=" N PHE 6 530 " --> pdb=" O ILE 6 526 " (cutoff:3.500A) Processing helix chain '6' and resid 541 through 558 Processing helix chain '6' and resid 568 through 580 Processing helix chain '6' and resid 587 through 604 removed outlier: 4.085A pdb=" N GLU 6 591 " --> pdb=" O SER 6 587 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N ASP 6 592 " --> pdb=" O LYS 6 588 " (cutoff:3.500A) Processing helix chain '6' and resid 617 through 635 removed outlier: 3.877A pdb=" N LEU 6 621 " --> pdb=" O THR 6 617 " (cutoff:3.500A) Processing helix chain '6' and resid 641 through 655 Processing helix chain '6' and resid 718 through 734 Processing helix chain '6' and resid 744 through 756 Processing helix chain '6' and resid 764 through 783 Processing helix chain '7' and resid 5 through 18 removed outlier: 4.087A pdb=" N GLU 7 9 " --> pdb=" O ASP 7 5 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N GLN 7 18 " --> pdb=" O LYS 7 14 " (cutoff:3.500A) Processing helix chain '7' and resid 31 through 42 Processing helix chain '7' and resid 52 through 56 Processing helix chain '7' and resid 59 through 69 removed outlier: 3.968A pdb=" N VAL 7 63 " --> pdb=" O ASP 7 59 " (cutoff:3.500A) Processing helix chain '7' and resid 69 through 89 Proline residue: 7 86 - end of helix removed outlier: 3.678A pdb=" N LYS 7 89 " --> pdb=" O LEU 7 85 " (cutoff:3.500A) Processing helix chain '7' and resid 97 through 109 Processing helix chain '7' and resid 127 through 132 removed outlier: 3.585A pdb=" N MET 7 131 " --> pdb=" O PRO 7 127 " (cutoff:3.500A) Processing helix chain '7' and resid 148 through 152 removed outlier: 3.840A pdb=" N VAL 7 152 " --> pdb=" O ILE 7 149 " (cutoff:3.500A) Processing helix chain '7' and resid 153 through 157 Processing helix chain '7' and resid 208 through 214 Processing helix chain '7' and resid 260 through 262 No H-bonds generated for 'chain '7' and resid 260 through 262' Processing helix chain '7' and resid 347 through 360 removed outlier: 3.647A pdb=" N LYS 7 352 " --> pdb=" O GLU 7 348 " (cutoff:3.500A) removed outlier: 4.671A pdb=" N ALA 7 353 " --> pdb=" O ASP 7 349 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N LEU 7 354 " --> pdb=" O VAL 7 350 " (cutoff:3.500A) Processing helix chain '7' and resid 387 through 398 Processing helix chain '7' and resid 406 through 414 removed outlier: 3.729A pdb=" N SER 7 410 " --> pdb=" O ARG 7 407 " (cutoff:3.500A) removed outlier: 7.605A pdb=" N GLY 7 411 " --> pdb=" O GLY 7 408 " (cutoff:3.500A) removed outlier: 6.108A pdb=" N VAL 7 412 " --> pdb=" O SER 7 409 " (cutoff:3.500A) Processing helix chain '7' and resid 432 through 437 Processing helix chain '7' and resid 447 through 450 Processing helix chain '7' and resid 451 through 465 Processing helix chain '7' and resid 508 through 515 removed outlier: 3.908A pdb=" N LEU 7 512 " --> pdb=" O PRO 7 508 " (cutoff:3.500A) Processing helix chain '7' and resid 526 through 544 Processing helix chain '7' and resid 555 through 568 removed outlier: 3.713A pdb=" N GLU 7 568 " --> pdb=" O ALA 7 564 " (cutoff:3.500A) Processing helix chain '7' and resid 577 through 595 removed outlier: 4.176A pdb=" N ALA 7 583 " --> pdb=" O ASP 7 579 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N MET 7 588 " --> pdb=" O ALA 7 584 " (cutoff:3.500A) Processing helix chain '7' and resid 602 through 621 removed outlier: 3.826A pdb=" N LEU 7 606 " --> pdb=" O SER 7 602 " (cutoff:3.500A) Processing helix chain '7' and resid 626 through 642 removed outlier: 3.711A pdb=" N VAL 7 630 " --> pdb=" O GLU 7 626 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain '2' and resid 229 through 232 removed outlier: 6.219A pdb=" N LEU 2 230 " --> pdb=" O ARG 2 284 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain '2' and resid 319 through 323 removed outlier: 9.711A pdb=" N ILE 2 439 " --> pdb=" O SER 2 393 " (cutoff:3.500A) removed outlier: 6.750A pdb=" N ASP 2 395 " --> pdb=" O ILE 2 439 " (cutoff:3.500A) removed outlier: 7.409A pdb=" N ALA 2 441 " --> pdb=" O ASP 2 395 " (cutoff:3.500A) removed outlier: 6.132A pdb=" N ILE 2 397 " --> pdb=" O ALA 2 441 " (cutoff:3.500A) removed outlier: 7.391A pdb=" N HIS 2 443 " --> pdb=" O ILE 2 397 " (cutoff:3.500A) removed outlier: 9.263A pdb=" N LEU 2 399 " --> pdb=" O HIS 2 443 " (cutoff:3.500A) removed outlier: 12.594A pdb=" N ALA 2 445 " --> pdb=" O LEU 2 399 " (cutoff:3.500A) removed outlier: 6.779A pdb=" N THR 2 415 " --> pdb=" O ASN 2 442 " (cutoff:3.500A) removed outlier: 4.206A pdb=" N VAL 2 444 " --> pdb=" O GLU 2 413 " (cutoff:3.500A) removed outlier: 6.403A pdb=" N GLU 2 413 " --> pdb=" O VAL 2 444 " (cutoff:3.500A) removed outlier: 6.800A pdb=" N ARG 2 377 " --> pdb=" O THR 2 313 " (cutoff:3.500A) removed outlier: 4.623A pdb=" N CYS 2 315 " --> pdb=" O ARG 2 375 " (cutoff:3.500A) removed outlier: 7.145A pdb=" N ARG 2 375 " --> pdb=" O CYS 2 315 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain '2' and resid 327 through 328 Processing sheet with id=AA4, first strand: chain '2' and resid 543 through 547 removed outlier: 6.665A pdb=" N VAL 2 519 " --> pdb=" O ALA 2 628 " (cutoff:3.500A) removed outlier: 8.193A pdb=" N ALA 2 630 " --> pdb=" O VAL 2 519 " (cutoff:3.500A) removed outlier: 6.225A pdb=" N LEU 2 521 " --> pdb=" O ALA 2 630 " (cutoff:3.500A) removed outlier: 6.535A pdb=" N LEU 2 520 " --> pdb=" O CYS 2 661 " (cutoff:3.500A) removed outlier: 7.720A pdb=" N VAL 2 663 " --> pdb=" O LEU 2 520 " (cutoff:3.500A) removed outlier: 6.675A pdb=" N CYS 2 522 " --> pdb=" O VAL 2 663 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain '2' and resid 559 through 562 Processing sheet with id=AA6, first strand: chain '2' and resid 608 through 613 Processing sheet with id=AA7, first strand: chain '3' and resid 46 through 50 removed outlier: 3.615A pdb=" N LEU 3 47 " --> pdb=" O TYR 3 99 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain '3' and resid 124 through 133 WARNING: can't find start of bonding for strands! previous: chain '3' and resid 124 through 133 current: chain '3' and resid 153 through 158 WARNING: can't find start of bonding for strands! previous: chain '3' and resid 153 through 158 current: chain '3' and resid 216 through 222 WARNING: can't find start of bonding for strands! previous: chain '3' and resid 216 through 222 current: chain '3' and resid 255 through 267 WARNING: can't find start of bonding for strands! previous: chain '3' and resid 255 through 267 current: chain '5' and resid 178 through 183 WARNING: can't find start of bonding for strands! previous: chain '5' and resid 178 through 183 current: chain '5' and resid 244 through 250 WARNING: can't find start of bonding for strands! previous: chain '5' and resid 244 through 250 current: chain '5' and resid 292 through 301 No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain '3' and resid 251 through 252 Processing sheet with id=AB1, first strand: chain '3' and resid 327 through 328 Processing sheet with id=AB2, first strand: chain '3' and resid 365 through 368 removed outlier: 6.928A pdb=" N ILE 3 341 " --> pdb=" O ALA 3 450 " (cutoff:3.500A) removed outlier: 8.310A pdb=" N ALA 3 452 " --> pdb=" O ILE 3 341 " (cutoff:3.500A) removed outlier: 6.373A pdb=" N LEU 3 343 " --> pdb=" O ALA 3 452 " (cutoff:3.500A) removed outlier: 6.505A pdb=" N LEU 3 342 " --> pdb=" O PHE 3 483 " (cutoff:3.500A) removed outlier: 7.891A pdb=" N MET 3 485 " --> pdb=" O LEU 3 342 " (cutoff:3.500A) removed outlier: 6.562A pdb=" N ILE 3 344 " --> pdb=" O MET 3 485 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain '3' and resid 381 through 382 Processing sheet with id=AB4, first strand: chain '3' and resid 430 through 435 Processing sheet with id=AB5, first strand: chain '3' and resid 608 through 609 Processing sheet with id=AB6, first strand: chain '4' and resid 207 through 211 Processing sheet with id=AB7, first strand: chain '4' and resid 312 through 316 removed outlier: 7.806A pdb=" N PHE 4 346 " --> pdb=" O PRO 4 297 " (cutoff:3.500A) removed outlier: 8.945A pdb=" N MET 4 299 " --> pdb=" O SER 4 344 " (cutoff:3.500A) removed outlier: 10.274A pdb=" N SER 4 344 " --> pdb=" O MET 4 299 " (cutoff:3.500A) removed outlier: 10.468A pdb=" N GLU 4 301 " --> pdb=" O ASN 4 342 " (cutoff:3.500A) removed outlier: 8.328A pdb=" N ASN 4 342 " --> pdb=" O GLU 4 301 " (cutoff:3.500A) removed outlier: 4.271A pdb=" N PHE 4 303 " --> pdb=" O ILE 4 340 " (cutoff:3.500A) removed outlier: 11.187A pdb=" N THR 4 369 " --> pdb=" O THR 4 414 " (cutoff:3.500A) removed outlier: 9.455A pdb=" N ILE 4 416 " --> pdb=" O THR 4 369 " (cutoff:3.500A) removed outlier: 6.547A pdb=" N ILE 4 371 " --> pdb=" O ILE 4 416 " (cutoff:3.500A) removed outlier: 7.479A pdb=" N VAL 4 418 " --> pdb=" O ILE 4 371 " (cutoff:3.500A) removed outlier: 7.243A pdb=" N PHE 4 373 " --> pdb=" O VAL 4 418 " (cutoff:3.500A) removed outlier: 8.334A pdb=" N HIS 4 420 " --> pdb=" O PHE 4 373 " (cutoff:3.500A) removed outlier: 10.957A pdb=" N HIS 4 375 " --> pdb=" O HIS 4 420 " (cutoff:3.500A) removed outlier: 13.733A pdb=" N ARG 4 422 " --> pdb=" O HIS 4 375 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N HIS 4 415 " --> pdb=" O ARG 4 395 " (cutoff:3.500A) removed outlier: 6.765A pdb=" N THR 4 391 " --> pdb=" O ILE 4 419 " (cutoff:3.500A) removed outlier: 4.392A pdb=" N TYR 4 421 " --> pdb=" O ASN 4 389 " (cutoff:3.500A) removed outlier: 6.573A pdb=" N ASN 4 389 " --> pdb=" O TYR 4 421 " (cutoff:3.500A) removed outlier: 6.890A pdb=" N LYS 4 353 " --> pdb=" O ILE 4 290 " (cutoff:3.500A) removed outlier: 4.669A pdb=" N THR 4 292 " --> pdb=" O MET 4 351 " (cutoff:3.500A) removed outlier: 7.110A pdb=" N MET 4 351 " --> pdb=" O THR 4 292 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain '4' and resid 400 through 402 removed outlier: 8.105A pdb=" N ASN 4 407 " --> pdb=" O VAL 4 401 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain '4' and resid 530 through 534 removed outlier: 6.457A pdb=" N GLN 4 531 " --> pdb=" O CYS 4 572 " (cutoff:3.500A) removed outlier: 7.804A pdb=" N ASP 4 574 " --> pdb=" O GLN 4 531 " (cutoff:3.500A) removed outlier: 6.694A pdb=" N THR 4 533 " --> pdb=" O ASP 4 574 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N SER 4 612 " --> pdb=" O GLY 4 569 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N GLY 4 510 " --> pdb=" O ALA 4 617 " (cutoff:3.500A) removed outlier: 6.805A pdb=" N LEU 4 507 " --> pdb=" O PHE 4 648 " (cutoff:3.500A) removed outlier: 7.594A pdb=" N MET 4 650 " --> pdb=" O LEU 4 507 " (cutoff:3.500A) removed outlier: 6.466A pdb=" N CYS 4 509 " --> pdb=" O MET 4 650 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain '4' and resid 545 through 549 Processing sheet with id=AC2, first strand: chain '4' and resid 595 through 600 Processing sheet with id=AC3, first strand: chain '4' and resid 701 through 702 removed outlier: 6.859A pdb=" N ARG 4 701 " --> pdb=" O VAL 4 753 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC3 Processing sheet with id=AC4, first strand: chain '5' and resid 69 through 73 Processing sheet with id=AC5, first strand: chain '5' and resid 363 through 364 removed outlier: 3.640A pdb=" N LYS 5 363 " --> pdb=" O ARG 5 371 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain '5' and resid 401 through 403 removed outlier: 6.281A pdb=" N VAL 5 402 " --> pdb=" O CYS 5 443 " (cutoff:3.500A) removed outlier: 6.761A pdb=" N LEU 5 378 " --> pdb=" O PHE 5 518 " (cutoff:3.500A) removed outlier: 8.054A pdb=" N VAL 5 520 " --> pdb=" O LEU 5 378 " (cutoff:3.500A) removed outlier: 6.632A pdb=" N LEU 5 380 " --> pdb=" O VAL 5 520 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain '5' and resid 417 through 420 Processing sheet with id=AC8, first strand: chain '5' and resid 466 through 471 Processing sheet with id=AC9, first strand: chain '6' and resid 60 through 63 Processing sheet with id=AD1, first strand: chain '6' and resid 134 through 143 WARNING: can't find start of bonding for strands! previous: chain '6' and resid 134 through 143 current: chain '6' and resid 199 through 209 removed outlier: 3.613A pdb=" N GLN 6 204 " --> pdb=" O LEU 6 228 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain '6' and resid 223 through 229 current: chain '6' and resid 294 through 299 Processing sheet with id=AD2, first strand: chain '6' and resid 164 through 165 Processing sheet with id=AD3, first strand: chain '6' and resid 378 through 379 removed outlier: 3.702A pdb=" N LYS 6 378 " --> pdb=" O LEU 6 386 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain '6' and resid 416 through 420 removed outlier: 6.091A pdb=" N VAL 6 417 " --> pdb=" O CYS 6 458 " (cutoff:3.500A) removed outlier: 7.718A pdb=" N ASP 6 460 " --> pdb=" O VAL 6 417 " (cutoff:3.500A) removed outlier: 6.545A pdb=" N THR 6 419 " --> pdb=" O ASP 6 460 " (cutoff:3.500A) removed outlier: 6.100A pdb=" N CYS 6 457 " --> pdb=" O LEU 6 500 " (cutoff:3.500A) removed outlier: 7.996A pdb=" N ALA 6 502 " --> pdb=" O CYS 6 457 " (cutoff:3.500A) removed outlier: 6.993A pdb=" N ILE 6 459 " --> pdb=" O ALA 6 502 " (cutoff:3.500A) removed outlier: 6.668A pdb=" N VAL 6 392 " --> pdb=" O ALA 6 501 " (cutoff:3.500A) removed outlier: 8.223A pdb=" N ALA 6 503 " --> pdb=" O VAL 6 392 " (cutoff:3.500A) removed outlier: 6.346A pdb=" N ILE 6 394 " --> pdb=" O ALA 6 503 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain '6' and resid 431 through 435 Processing sheet with id=AD6, first strand: chain '6' and resid 481 through 486 Processing sheet with id=AD7, first strand: chain '6' and resid 585 through 586 removed outlier: 7.164A pdb=" N LYS 6 585 " --> pdb=" O VAL 6 640 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD7 Processing sheet with id=AD8, first strand: chain '7' and resid 48 through 51 removed outlier: 6.171A pdb=" N LEU 7 48 " --> pdb=" O TYR 7 137 " (cutoff:3.500A) removed outlier: 7.484A pdb=" N GLN 7 139 " --> pdb=" O LEU 7 48 " (cutoff:3.500A) removed outlier: 6.623A pdb=" N VAL 7 50 " --> pdb=" O GLN 7 139 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD8 Processing sheet with id=AD9, first strand: chain '7' and resid 160 through 170 WARNING: can't find start of bonding for strands! previous: chain '7' and resid 160 through 170 current: chain '7' and resid 190 through 194 WARNING: can't find start of bonding for strands! previous: chain '7' and resid 190 through 194 current: chain '7' and resid 252 through 258 WARNING: can't find start of bonding for strands! previous: chain '7' and resid 252 through 258 current: chain '7' and resid 295 through 305 No H-bonds generated for sheet with id=AD9 Processing sheet with id=AE1, first strand: chain '7' and resid 401 through 404 removed outlier: 6.683A pdb=" N GLN 7 402 " --> pdb=" O CYS 7 443 " (cutoff:3.500A) removed outlier: 7.912A pdb=" N ASP 7 445 " --> pdb=" O GLN 7 402 " (cutoff:3.500A) removed outlier: 6.600A pdb=" N THR 7 404 " --> pdb=" O ASP 7 445 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N SER 7 483 " --> pdb=" O GLY 7 440 " (cutoff:3.500A) removed outlier: 6.534A pdb=" N ILE 7 377 " --> pdb=" O ALA 7 486 " (cutoff:3.500A) removed outlier: 8.241A pdb=" N ALA 7 488 " --> pdb=" O ILE 7 377 " (cutoff:3.500A) removed outlier: 6.243A pdb=" N LEU 7 379 " --> pdb=" O ALA 7 488 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain '7' and resid 416 through 418 Processing sheet with id=AE3, first strand: chain '7' and resid 466 through 471 1309 hydrogen bonds defined for protein. 3771 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 113 hydrogen bonds 226 hydrogen bond angles 0 basepair planarities 45 basepair parallelities 78 stacking parallelities Total time for adding SS restraints: 14.05 Time building geometry restraints manager: 8.86 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.36: 10811 1.36 - 1.51: 8708 1.51 - 1.65: 13322 1.65 - 1.80: 205 1.80 - 1.95: 92 Bond restraints: 33138 Sorted by residual: bond pdb=" C LEU F 38 " pdb=" O LEU F 38 " ideal model delta sigma weight residual 1.237 1.253 -0.016 1.19e-02 7.06e+03 1.86e+00 bond pdb=" CD GLN 7 389 " pdb=" NE2 GLN 7 389 " ideal model delta sigma weight residual 1.328 1.301 0.027 2.10e-02 2.27e+03 1.61e+00 bond pdb=" CD GLN 2 374 " pdb=" NE2 GLN 2 374 " ideal model delta sigma weight residual 1.328 1.302 0.026 2.10e-02 2.27e+03 1.53e+00 bond pdb=" CD GLN 2 806 " pdb=" NE2 GLN 2 806 " ideal model delta sigma weight residual 1.328 1.302 0.026 2.10e-02 2.27e+03 1.50e+00 bond pdb=" C ILE 2 477 " pdb=" O ILE 2 477 " ideal model delta sigma weight residual 1.237 1.250 -0.014 1.12e-02 7.97e+03 1.49e+00 ... (remaining 33133 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.41: 44193 1.41 - 2.82: 800 2.82 - 4.23: 104 4.23 - 5.64: 30 5.64 - 7.06: 6 Bond angle restraints: 45133 Sorted by residual: angle pdb=" C ARG F 41 " pdb=" N THR F 42 " pdb=" CA THR F 42 " ideal model delta sigma weight residual 122.56 118.10 4.46 1.50e+00 4.44e-01 8.82e+00 angle pdb=" N HIS 5 524 " pdb=" CA HIS 5 524 " pdb=" C HIS 5 524 " ideal model delta sigma weight residual 108.41 112.48 -4.07 1.61e+00 3.86e-01 6.40e+00 angle pdb=" N ILE 5 510 " pdb=" CA ILE 5 510 " pdb=" C ILE 5 510 " ideal model delta sigma weight residual 113.16 109.91 3.25 1.49e+00 4.50e-01 4.76e+00 angle pdb=" C ARG 4 172 " pdb=" N PHE 4 173 " pdb=" CA PHE 4 173 " ideal model delta sigma weight residual 122.77 119.99 2.78 1.33e+00 5.65e-01 4.38e+00 angle pdb=" O3' DA Y 21 " pdb=" P DT Y 22 " pdb=" OP1 DT Y 22 " ideal model delta sigma weight residual 108.00 114.20 -6.20 3.00e+00 1.11e-01 4.27e+00 ... (remaining 45128 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 32.96: 19280 32.96 - 65.93: 847 65.93 - 98.89: 61 98.89 - 131.85: 4 131.85 - 164.82: 1 Dihedral angle restraints: 20193 sinusoidal: 8965 harmonic: 11228 Sorted by residual: dihedral pdb=" C5' ADP 3 901 " pdb=" O5' ADP 3 901 " pdb=" PA ADP 3 901 " pdb=" O2A ADP 3 901 " ideal model delta sinusoidal sigma weight residual 300.00 176.34 123.66 1 2.00e+01 2.50e-03 3.73e+01 dihedral pdb=" CA ASP 5 448 " pdb=" C ASP 5 448 " pdb=" N LYS 5 449 " pdb=" CA LYS 5 449 " ideal model delta harmonic sigma weight residual -180.00 -157.96 -22.04 0 5.00e+00 4.00e-02 1.94e+01 dihedral pdb=" C5' ADP 4 902 " pdb=" O5' ADP 4 902 " pdb=" PA ADP 4 902 " pdb=" O2A ADP 4 902 " ideal model delta sinusoidal sigma weight residual -60.00 -135.23 75.23 1 2.00e+01 2.50e-03 1.79e+01 ... (remaining 20190 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.056: 4443 0.056 - 0.113: 620 0.113 - 0.169: 80 0.169 - 0.225: 0 0.225 - 0.281: 1 Chirality restraints: 5144 Sorted by residual: chirality pdb=" P DA X 26 " pdb=" OP1 DA X 26 " pdb=" OP2 DA X 26 " pdb=" O5' DA X 26 " both_signs ideal model delta sigma weight residual True 2.35 -2.63 -0.28 2.00e-01 2.50e+01 1.98e+00 chirality pdb=" P DT Y 22 " pdb=" OP1 DT Y 22 " pdb=" OP2 DT Y 22 " pdb=" O5' DT Y 22 " both_signs ideal model delta sigma weight residual True 2.35 -2.50 -0.16 2.00e-01 2.50e+01 6.11e-01 chirality pdb=" CA ILE 4 285 " pdb=" N ILE 4 285 " pdb=" C ILE 4 285 " pdb=" CB ILE 4 285 " both_signs ideal model delta sigma weight residual False 2.43 2.59 -0.16 2.00e-01 2.50e+01 6.08e-01 ... (remaining 5141 not shown) Planarity restraints: 5476 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA VAL 4 590 " 0.015 2.00e-02 2.50e+03 3.08e-02 9.49e+00 pdb=" C VAL 4 590 " -0.053 2.00e-02 2.50e+03 pdb=" O VAL 4 590 " 0.020 2.00e-02 2.50e+03 pdb=" N MET 4 591 " 0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU 6 346 " 0.013 2.00e-02 2.50e+03 2.69e-02 7.26e+00 pdb=" C LEU 6 346 " -0.047 2.00e-02 2.50e+03 pdb=" O LEU 6 346 " 0.017 2.00e-02 2.50e+03 pdb=" N TYR 6 347 " 0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PRO 4 191 " 0.013 2.00e-02 2.50e+03 2.63e-02 6.90e+00 pdb=" C PRO 4 191 " -0.045 2.00e-02 2.50e+03 pdb=" O PRO 4 191 " 0.017 2.00e-02 2.50e+03 pdb=" N LEU 4 192 " 0.015 2.00e-02 2.50e+03 ... (remaining 5473 not shown) Histogram of nonbonded interaction distances: 1.85 - 2.46: 95 2.46 - 3.07: 20321 3.07 - 3.68: 45830 3.68 - 4.29: 65129 4.29 - 4.90: 110632 Nonbonded interactions: 242007 Sorted by model distance: nonbonded pdb=" O2G AGS 21001 " pdb="MG MG 21002 " model vdw 1.851 2.170 nonbonded pdb=" OG SER 2 530 " pdb="MG MG 21002 " model vdw 1.884 2.170 nonbonded pdb=" O1B AGS 21001 " pdb="MG MG 21002 " model vdw 1.938 2.170 nonbonded pdb=" O2G AGS 6 901 " pdb="MG MG 6 902 " model vdw 1.942 2.170 nonbonded pdb=" OG SER 6 403 " pdb="MG MG 6 902 " model vdw 2.060 2.170 ... (remaining 242002 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.650 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: 1.320 Check model and map are aligned: 0.250 Set scattering table: 0.330 Process input model: 83.510 Find NCS groups from input model: 1.130 Set up NCS constraints: 0.130 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: 0.000 Load rotamer database and sin/cos tables:2.780 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 94.130 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7108 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 0.034 33157 Z= 0.131 Angle : 0.525 19.935 45157 Z= 0.272 Chirality : 0.040 0.281 5144 Planarity : 0.004 0.060 5476 Dihedral : 16.898 164.816 12889 Min Nonbonded Distance : 1.851 Molprobity Statistics. All-atom Clashscore : 3.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer: Outliers : 0.00 % Allowed : 0.03 % Favored : 99.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.23 (0.14), residues: 3768 helix: 1.99 (0.13), residues: 1609 sheet: 0.29 (0.20), residues: 698 loop : -0.17 (0.16), residues: 1461 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP 6 614 HIS 0.012 0.001 HIS 5 524 PHE 0.034 0.001 PHE F 86 TYR 0.015 0.001 TYR 7 182 ARG 0.003 0.000 ARG 5 138 Details of bonding type rmsd hydrogen bonds : bond 0.10316 ( 1422) hydrogen bonds : angle 4.75864 ( 3997) metal coordination : bond 0.01279 ( 19) metal coordination : angle 8.01855 ( 24) covalent geometry : bond 0.00276 (33138) covalent geometry : angle 0.49182 (45133) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7536 Ramachandran restraints generated. 3768 Oldfield, 0 Emsley, 3768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7536 Ramachandran restraints generated. 3768 Oldfield, 0 Emsley, 3768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 709 residues out of total 3358 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 709 time to evaluate : 3.673 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: F 50 MET cc_start: 0.6469 (mtt) cc_final: 0.6108 (mtp) REVERT: F 59 MET cc_start: 0.7004 (mmm) cc_final: 0.6767 (mmm) REVERT: F 82 CYS cc_start: 0.8448 (m) cc_final: 0.8168 (t) REVERT: F 159 ASN cc_start: 0.7684 (m-40) cc_final: 0.7448 (m-40) REVERT: 2 222 MET cc_start: 0.7297 (tmm) cc_final: 0.7046 (tmm) REVERT: 2 328 ASN cc_start: 0.8268 (t0) cc_final: 0.7988 (t0) REVERT: 3 547 LYS cc_start: 0.7485 (mptt) cc_final: 0.7267 (tmtt) REVERT: 4 186 ILE cc_start: 0.8544 (mm) cc_final: 0.8340 (mm) REVERT: 4 192 LEU cc_start: 0.7355 (tp) cc_final: 0.6758 (tp) REVERT: 4 207 PHE cc_start: 0.6889 (m-80) cc_final: 0.6626 (m-80) REVERT: 4 403 PRO cc_start: 0.8162 (Cg_exo) cc_final: 0.7589 (Cg_endo) REVERT: 4 650 MET cc_start: 0.8617 (mtp) cc_final: 0.8322 (mtt) REVERT: 5 184 MET cc_start: 0.8039 (mmm) cc_final: 0.7756 (mmt) REVERT: 6 527 MET cc_start: 0.7710 (mmm) cc_final: 0.7341 (ttp) REVERT: 6 769 LYS cc_start: 0.8829 (tptt) cc_final: 0.8451 (ptpp) REVERT: 7 306 MET cc_start: 0.5686 (mmm) cc_final: 0.5340 (mmt) REVERT: 7 540 VAL cc_start: 0.7321 (t) cc_final: 0.7069 (t) outliers start: 0 outliers final: 0 residues processed: 709 average time/residue: 0.5086 time to fit residues: 543.9998 Evaluate side-chains 313 residues out of total 3358 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 313 time to evaluate : 3.456 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 388 random chunks: chunk 327 optimal weight: 1.9990 chunk 294 optimal weight: 2.9990 chunk 163 optimal weight: 2.9990 chunk 100 optimal weight: 0.8980 chunk 198 optimal weight: 2.9990 chunk 157 optimal weight: 20.0000 chunk 304 optimal weight: 2.9990 chunk 117 optimal weight: 6.9990 chunk 184 optimal weight: 0.9990 chunk 226 optimal weight: 0.7980 chunk 352 optimal weight: 0.4980 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 2 531 GLN 2 606 GLN 2 671 GLN ** 2 687 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 2 781 HIS 3 236 GLN 3 298 GLN 3 573 HIS 4 225 GLN 4 342 ASN 4 521 GLN ** 4 531 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 5 32 GLN 7 212 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4254 r_free = 0.4254 target = 0.147938 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3793 r_free = 0.3793 target = 0.114694 restraints weight = 64249.973| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3847 r_free = 0.3847 target = 0.118778 restraints weight = 38176.617| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3855 r_free = 0.3855 target = 0.119516 restraints weight = 24930.405| |-----------------------------------------------------------------------------| r_work (final): 0.3867 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7214 moved from start: 0.2120 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 33157 Z= 0.138 Angle : 0.590 12.070 45157 Z= 0.300 Chirality : 0.041 0.181 5144 Planarity : 0.004 0.062 5476 Dihedral : 16.358 169.053 5274 Min Nonbonded Distance : 1.912 Molprobity Statistics. All-atom Clashscore : 5.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.03 % Favored : 96.97 % Rotamer: Outliers : 1.28 % Allowed : 8.52 % Favored : 90.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.11 (0.14), residues: 3768 helix: 1.89 (0.13), residues: 1622 sheet: 0.22 (0.19), residues: 699 loop : -0.26 (0.16), residues: 1447 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP 7 519 HIS 0.011 0.001 HIS 4 494 PHE 0.015 0.001 PHE 7 77 TYR 0.018 0.001 TYR 4 412 ARG 0.010 0.000 ARG 6 435 Details of bonding type rmsd hydrogen bonds : bond 0.03960 ( 1422) hydrogen bonds : angle 4.18850 ( 3997) metal coordination : bond 0.00829 ( 19) metal coordination : angle 6.09222 ( 24) covalent geometry : bond 0.00316 (33138) covalent geometry : angle 0.57328 (45133) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7536 Ramachandran restraints generated. 3768 Oldfield, 0 Emsley, 3768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7536 Ramachandran restraints generated. 3768 Oldfield, 0 Emsley, 3768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 378 residues out of total 3358 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 335 time to evaluate : 3.402 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: F 20 MET cc_start: 0.6971 (tpp) cc_final: 0.6479 (ttm) REVERT: F 35 CYS cc_start: 0.7855 (m) cc_final: 0.7197 (t) REVERT: F 50 MET cc_start: 0.6553 (mtt) cc_final: 0.6214 (mtp) REVERT: F 59 MET cc_start: 0.7054 (mmm) cc_final: 0.6545 (mmm) REVERT: F 82 CYS cc_start: 0.8598 (m) cc_final: 0.8254 (t) REVERT: F 86 PHE cc_start: 0.7537 (OUTLIER) cc_final: 0.7182 (m-80) REVERT: 2 328 ASN cc_start: 0.8234 (t0) cc_final: 0.7895 (t0) REVERT: 2 683 HIS cc_start: 0.8664 (OUTLIER) cc_final: 0.8447 (t-90) REVERT: 3 70 PHE cc_start: 0.7047 (OUTLIER) cc_final: 0.6618 (m-80) REVERT: 3 485 MET cc_start: 0.7772 (mtt) cc_final: 0.7512 (mtt) REVERT: 3 547 LYS cc_start: 0.7524 (mptt) cc_final: 0.7257 (tmtt) REVERT: 4 650 MET cc_start: 0.8644 (mtp) cc_final: 0.8377 (mtt) REVERT: 4 699 MET cc_start: 0.5944 (mmm) cc_final: 0.5505 (mmm) REVERT: 6 527 MET cc_start: 0.7653 (mmm) cc_final: 0.7210 (ttp) REVERT: 7 108 MET cc_start: 0.5142 (ppp) cc_final: 0.4393 (ppp) REVERT: 7 306 MET cc_start: 0.5890 (mmm) cc_final: 0.5374 (mmt) outliers start: 43 outliers final: 26 residues processed: 360 average time/residue: 0.4463 time to fit residues: 256.1808 Evaluate side-chains 295 residues out of total 3358 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 266 time to evaluate : 3.373 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 86 PHE Chi-restraints excluded: chain F residue 128 THR Chi-restraints excluded: chain F residue 162 VAL Chi-restraints excluded: chain 2 residue 260 ASP Chi-restraints excluded: chain 2 residue 406 CYS Chi-restraints excluded: chain 2 residue 421 ASN Chi-restraints excluded: chain 2 residue 606 GLN Chi-restraints excluded: chain 2 residue 683 HIS Chi-restraints excluded: chain 2 residue 720 LEU Chi-restraints excluded: chain 2 residue 764 VAL Chi-restraints excluded: chain 3 residue 70 PHE Chi-restraints excluded: chain 3 residue 379 THR Chi-restraints excluded: chain 3 residue 456 TYR Chi-restraints excluded: chain 4 residue 239 MET Chi-restraints excluded: chain 4 residue 488 THR Chi-restraints excluded: chain 5 residue 99 LEU Chi-restraints excluded: chain 5 residue 124 ILE Chi-restraints excluded: chain 5 residue 255 ASP Chi-restraints excluded: chain 5 residue 296 VAL Chi-restraints excluded: chain 5 residue 574 LEU Chi-restraints excluded: chain 6 residue 193 LEU Chi-restraints excluded: chain 6 residue 293 SER Chi-restraints excluded: chain 6 residue 346 LEU Chi-restraints excluded: chain 6 residue 651 LEU Chi-restraints excluded: chain 6 residue 782 HIS Chi-restraints excluded: chain 7 residue 16 PHE Chi-restraints excluded: chain 7 residue 21 TYR Chi-restraints excluded: chain 7 residue 52 LEU Chi-restraints excluded: chain 7 residue 177 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 388 random chunks: chunk 225 optimal weight: 2.9990 chunk 200 optimal weight: 3.9990 chunk 346 optimal weight: 0.8980 chunk 377 optimal weight: 2.9990 chunk 44 optimal weight: 0.9980 chunk 345 optimal weight: 6.9990 chunk 236 optimal weight: 3.9990 chunk 295 optimal weight: 0.7980 chunk 363 optimal weight: 3.9990 chunk 247 optimal weight: 3.9990 chunk 281 optimal weight: 0.5980 overall best weight: 1.2582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 2 606 GLN ** 2 687 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 4 638 HIS ** 6 187 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 479 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 7 541 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4235 r_free = 0.4235 target = 0.146455 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3782 r_free = 0.3782 target = 0.113560 restraints weight = 65205.655| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3816 r_free = 0.3816 target = 0.116978 restraints weight = 39285.893| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3830 r_free = 0.3830 target = 0.117937 restraints weight = 26420.199| |-----------------------------------------------------------------------------| r_work (final): 0.3842 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7263 moved from start: 0.2592 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 33157 Z= 0.138 Angle : 0.558 9.933 45157 Z= 0.286 Chirality : 0.041 0.164 5144 Planarity : 0.004 0.060 5476 Dihedral : 16.341 176.158 5274 Min Nonbonded Distance : 1.885 Molprobity Statistics. All-atom Clashscore : 5.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.13 % Favored : 96.87 % Rotamer: Outliers : 1.70 % Allowed : 10.52 % Favored : 87.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.04 (0.14), residues: 3768 helix: 1.92 (0.13), residues: 1614 sheet: 0.15 (0.19), residues: 696 loop : -0.38 (0.16), residues: 1458 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP 6 614 HIS 0.007 0.001 HIS 7 536 PHE 0.019 0.001 PHE 4 207 TYR 0.020 0.001 TYR 4 249 ARG 0.007 0.000 ARG 7 407 Details of bonding type rmsd hydrogen bonds : bond 0.03644 ( 1422) hydrogen bonds : angle 4.03887 ( 3997) metal coordination : bond 0.00791 ( 19) metal coordination : angle 4.63448 ( 24) covalent geometry : bond 0.00319 (33138) covalent geometry : angle 0.54750 (45133) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7536 Ramachandran restraints generated. 3768 Oldfield, 0 Emsley, 3768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7536 Ramachandran restraints generated. 3768 Oldfield, 0 Emsley, 3768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 339 residues out of total 3358 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 282 time to evaluate : 3.430 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 20 MET cc_start: 0.6932 (tpp) cc_final: 0.6508 (ttm) REVERT: F 50 MET cc_start: 0.6780 (mtt) cc_final: 0.6327 (mtp) REVERT: F 59 MET cc_start: 0.7210 (mmm) cc_final: 0.6637 (mmm) REVERT: F 82 CYS cc_start: 0.8591 (m) cc_final: 0.8255 (t) REVERT: 3 547 LYS cc_start: 0.7448 (mptt) cc_final: 0.7179 (tmtt) REVERT: 4 650 MET cc_start: 0.8656 (mtp) cc_final: 0.8379 (mtt) REVERT: 4 699 MET cc_start: 0.6007 (mmm) cc_final: 0.5562 (mmm) REVERT: 5 589 MET cc_start: 0.7831 (ttp) cc_final: 0.7604 (ttp) REVERT: 6 450 MET cc_start: 0.8235 (OUTLIER) cc_final: 0.7882 (mtm) REVERT: 6 527 MET cc_start: 0.7681 (mmm) cc_final: 0.7200 (ttp) REVERT: 7 450 MET cc_start: 0.6914 (mmp) cc_final: 0.6380 (mmt) REVERT: 7 565 MET cc_start: 0.5944 (tmm) cc_final: 0.5743 (tmm) outliers start: 57 outliers final: 38 residues processed: 320 average time/residue: 0.4049 time to fit residues: 211.8121 Evaluate side-chains 297 residues out of total 3358 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 258 time to evaluate : 3.687 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 25 GLU Chi-restraints excluded: chain F residue 36 VAL Chi-restraints excluded: chain F residue 125 LEU Chi-restraints excluded: chain F residue 128 THR Chi-restraints excluded: chain F residue 162 VAL Chi-restraints excluded: chain 2 residue 260 ASP Chi-restraints excluded: chain 2 residue 316 THR Chi-restraints excluded: chain 2 residue 406 CYS Chi-restraints excluded: chain 2 residue 421 ASN Chi-restraints excluded: chain 2 residue 592 MET Chi-restraints excluded: chain 2 residue 653 ILE Chi-restraints excluded: chain 2 residue 720 LEU Chi-restraints excluded: chain 2 residue 764 VAL Chi-restraints excluded: chain 2 residue 780 ILE Chi-restraints excluded: chain 3 residue 28 ASP Chi-restraints excluded: chain 3 residue 237 VAL Chi-restraints excluded: chain 3 residue 322 LEU Chi-restraints excluded: chain 3 residue 379 THR Chi-restraints excluded: chain 4 residue 239 MET Chi-restraints excluded: chain 4 residue 488 THR Chi-restraints excluded: chain 5 residue 99 LEU Chi-restraints excluded: chain 5 residue 124 ILE Chi-restraints excluded: chain 5 residue 255 ASP Chi-restraints excluded: chain 5 residue 296 VAL Chi-restraints excluded: chain 5 residue 448 ASP Chi-restraints excluded: chain 5 residue 574 LEU Chi-restraints excluded: chain 6 residue 193 LEU Chi-restraints excluded: chain 6 residue 293 SER Chi-restraints excluded: chain 6 residue 299 LEU Chi-restraints excluded: chain 6 residue 450 MET Chi-restraints excluded: chain 6 residue 594 ILE Chi-restraints excluded: chain 6 residue 618 VAL Chi-restraints excluded: chain 6 residue 651 LEU Chi-restraints excluded: chain 6 residue 782 HIS Chi-restraints excluded: chain 7 residue 21 TYR Chi-restraints excluded: chain 7 residue 223 GLN Chi-restraints excluded: chain 7 residue 385 VAL Chi-restraints excluded: chain 7 residue 540 VAL Chi-restraints excluded: chain 7 residue 640 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 388 random chunks: chunk 290 optimal weight: 1.9990 chunk 358 optimal weight: 4.9990 chunk 86 optimal weight: 2.9990 chunk 222 optimal weight: 0.2980 chunk 280 optimal weight: 1.9990 chunk 58 optimal weight: 0.0570 chunk 258 optimal weight: 3.9990 chunk 242 optimal weight: 0.6980 chunk 315 optimal weight: 0.8980 chunk 151 optimal weight: 0.0010 chunk 23 optimal weight: 0.9990 overall best weight: 0.3904 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 2 683 HIS 2 687 HIS 3 461 GLN ** 6 187 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4259 r_free = 0.4259 target = 0.148285 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3821 r_free = 0.3821 target = 0.115766 restraints weight = 64948.201| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3844 r_free = 0.3844 target = 0.118510 restraints weight = 39130.784| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3854 r_free = 0.3854 target = 0.119480 restraints weight = 26694.708| |-----------------------------------------------------------------------------| r_work (final): 0.3866 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7217 moved from start: 0.2823 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.048 33157 Z= 0.099 Angle : 0.507 8.209 45157 Z= 0.261 Chirality : 0.040 0.145 5144 Planarity : 0.003 0.059 5476 Dihedral : 16.191 173.332 5274 Min Nonbonded Distance : 1.985 Molprobity Statistics. All-atom Clashscore : 4.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 1.82 % Allowed : 11.38 % Favored : 86.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.25 (0.14), residues: 3768 helix: 2.06 (0.13), residues: 1615 sheet: 0.34 (0.20), residues: 704 loop : -0.27 (0.16), residues: 1449 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP 6 614 HIS 0.006 0.001 HIS 7 536 PHE 0.045 0.001 PHE 7 77 TYR 0.022 0.001 TYR 6 575 ARG 0.006 0.000 ARG 4 319 Details of bonding type rmsd hydrogen bonds : bond 0.02999 ( 1422) hydrogen bonds : angle 3.80396 ( 3997) metal coordination : bond 0.00549 ( 19) metal coordination : angle 3.79732 ( 24) covalent geometry : bond 0.00214 (33138) covalent geometry : angle 0.49991 (45133) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7536 Ramachandran restraints generated. 3768 Oldfield, 0 Emsley, 3768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7536 Ramachandran restraints generated. 3768 Oldfield, 0 Emsley, 3768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 356 residues out of total 3358 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 295 time to evaluate : 3.811 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 6 ILE cc_start: 0.6766 (OUTLIER) cc_final: 0.6147 (pt) REVERT: F 35 CYS cc_start: 0.7869 (m) cc_final: 0.7252 (t) REVERT: F 50 MET cc_start: 0.6705 (mtt) cc_final: 0.6466 (mtp) REVERT: F 59 MET cc_start: 0.7320 (mmm) cc_final: 0.6991 (mmm) REVERT: F 82 CYS cc_start: 0.8591 (m) cc_final: 0.8333 (t) REVERT: 2 683 HIS cc_start: 0.8502 (OUTLIER) cc_final: 0.7960 (t70) REVERT: 3 47 LEU cc_start: 0.7850 (tp) cc_final: 0.7595 (mt) REVERT: 3 70 PHE cc_start: 0.7091 (OUTLIER) cc_final: 0.6812 (m-80) REVERT: 3 547 LYS cc_start: 0.7450 (mptt) cc_final: 0.7195 (tmtt) REVERT: 4 650 MET cc_start: 0.8638 (mtp) cc_final: 0.8334 (mtt) REVERT: 4 699 MET cc_start: 0.5916 (mmm) cc_final: 0.5486 (mmt) REVERT: 5 145 MET cc_start: 0.8156 (tpp) cc_final: 0.7877 (tpp) REVERT: 6 450 MET cc_start: 0.8145 (OUTLIER) cc_final: 0.7822 (mtt) REVERT: 6 477 MET cc_start: 0.7924 (mtp) cc_final: 0.7708 (mtp) REVERT: 6 527 MET cc_start: 0.7607 (mmm) cc_final: 0.7102 (ttp) REVERT: 7 108 MET cc_start: 0.5734 (ppp) cc_final: 0.4783 (ppp) REVERT: 7 531 LEU cc_start: 0.8172 (mt) cc_final: 0.7963 (mt) outliers start: 61 outliers final: 36 residues processed: 331 average time/residue: 0.4010 time to fit residues: 220.6258 Evaluate side-chains 301 residues out of total 3358 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 261 time to evaluate : 3.384 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 6 ILE Chi-restraints excluded: chain F residue 25 GLU Chi-restraints excluded: chain F residue 128 THR Chi-restraints excluded: chain F residue 162 VAL Chi-restraints excluded: chain F residue 172 PHE Chi-restraints excluded: chain 2 residue 260 ASP Chi-restraints excluded: chain 2 residue 316 THR Chi-restraints excluded: chain 2 residue 421 ASN Chi-restraints excluded: chain 2 residue 683 HIS Chi-restraints excluded: chain 2 residue 720 LEU Chi-restraints excluded: chain 2 residue 764 VAL Chi-restraints excluded: chain 3 residue 70 PHE Chi-restraints excluded: chain 3 residue 237 VAL Chi-restraints excluded: chain 3 residue 322 LEU Chi-restraints excluded: chain 3 residue 379 THR Chi-restraints excluded: chain 3 residue 456 TYR Chi-restraints excluded: chain 3 residue 486 LEU Chi-restraints excluded: chain 5 residue 99 LEU Chi-restraints excluded: chain 5 residue 127 MET Chi-restraints excluded: chain 5 residue 353 ILE Chi-restraints excluded: chain 5 residue 448 ASP Chi-restraints excluded: chain 5 residue 574 LEU Chi-restraints excluded: chain 6 residue 193 LEU Chi-restraints excluded: chain 6 residue 293 SER Chi-restraints excluded: chain 6 residue 299 LEU Chi-restraints excluded: chain 6 residue 331 VAL Chi-restraints excluded: chain 6 residue 450 MET Chi-restraints excluded: chain 6 residue 594 ILE Chi-restraints excluded: chain 6 residue 651 LEU Chi-restraints excluded: chain 6 residue 782 HIS Chi-restraints excluded: chain 7 residue 16 PHE Chi-restraints excluded: chain 7 residue 21 TYR Chi-restraints excluded: chain 7 residue 52 LEU Chi-restraints excluded: chain 7 residue 102 TYR Chi-restraints excluded: chain 7 residue 197 SER Chi-restraints excluded: chain 7 residue 223 GLN Chi-restraints excluded: chain 7 residue 257 VAL Chi-restraints excluded: chain 7 residue 293 LEU Chi-restraints excluded: chain 7 residue 385 VAL Chi-restraints excluded: chain 7 residue 640 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 388 random chunks: chunk 253 optimal weight: 6.9990 chunk 293 optimal weight: 0.6980 chunk 39 optimal weight: 0.7980 chunk 114 optimal weight: 4.9990 chunk 25 optimal weight: 8.9990 chunk 238 optimal weight: 0.9990 chunk 184 optimal weight: 0.7980 chunk 268 optimal weight: 0.8980 chunk 150 optimal weight: 9.9990 chunk 51 optimal weight: 1.9990 chunk 380 optimal weight: 20.0000 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 129 GLN ** F 178 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 2 683 HIS 3 353 GLN ** 6 187 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4247 r_free = 0.4247 target = 0.147126 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3811 r_free = 0.3811 target = 0.114944 restraints weight = 64700.353| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3827 r_free = 0.3827 target = 0.117122 restraints weight = 39426.185| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3831 r_free = 0.3831 target = 0.117603 restraints weight = 27892.273| |-----------------------------------------------------------------------------| r_work (final): 0.3842 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7266 moved from start: 0.3022 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 33157 Z= 0.110 Angle : 0.511 9.634 45157 Z= 0.262 Chirality : 0.040 0.165 5144 Planarity : 0.004 0.062 5476 Dihedral : 16.120 173.761 5274 Min Nonbonded Distance : 1.918 Molprobity Statistics. All-atom Clashscore : 5.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 1.82 % Allowed : 12.10 % Favored : 86.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.29 (0.14), residues: 3768 helix: 2.10 (0.13), residues: 1602 sheet: 0.33 (0.19), residues: 718 loop : -0.24 (0.16), residues: 1448 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP 2 569 HIS 0.026 0.001 HIS 2 683 PHE 0.032 0.001 PHE 7 77 TYR 0.019 0.001 TYR F 121 ARG 0.007 0.000 ARG 2 812 Details of bonding type rmsd hydrogen bonds : bond 0.03083 ( 1422) hydrogen bonds : angle 3.77489 ( 3997) metal coordination : bond 0.00560 ( 19) metal coordination : angle 3.23440 ( 24) covalent geometry : bond 0.00248 (33138) covalent geometry : angle 0.50566 (45133) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7536 Ramachandran restraints generated. 3768 Oldfield, 0 Emsley, 3768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7536 Ramachandran restraints generated. 3768 Oldfield, 0 Emsley, 3768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 337 residues out of total 3358 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 276 time to evaluate : 4.130 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: F 35 CYS cc_start: 0.7972 (m) cc_final: 0.7323 (t) REVERT: F 50 MET cc_start: 0.6733 (mtt) cc_final: 0.6312 (mtp) REVERT: F 59 MET cc_start: 0.7320 (mmm) cc_final: 0.6973 (mmm) REVERT: F 121 TYR cc_start: 0.6708 (t80) cc_final: 0.6331 (t80) REVERT: 3 70 PHE cc_start: 0.7105 (OUTLIER) cc_final: 0.6854 (m-80) REVERT: 3 547 LYS cc_start: 0.7499 (mptt) cc_final: 0.7235 (tmtt) REVERT: 4 699 MET cc_start: 0.5942 (mmm) cc_final: 0.5491 (mmt) REVERT: 5 145 MET cc_start: 0.8206 (tpp) cc_final: 0.7953 (tpp) REVERT: 6 220 ILE cc_start: 0.8842 (OUTLIER) cc_final: 0.8606 (pt) REVERT: 6 450 MET cc_start: 0.8141 (OUTLIER) cc_final: 0.7830 (mtt) REVERT: 6 527 MET cc_start: 0.7631 (mmm) cc_final: 0.7149 (ttp) REVERT: 7 108 MET cc_start: 0.6179 (ppp) cc_final: 0.5340 (ppp) REVERT: 7 223 GLN cc_start: 0.6378 (OUTLIER) cc_final: 0.5833 (tt0) REVERT: 7 269 ASP cc_start: 0.7375 (t0) cc_final: 0.7086 (t0) REVERT: 7 531 LEU cc_start: 0.8204 (mt) cc_final: 0.7992 (mt) outliers start: 61 outliers final: 45 residues processed: 316 average time/residue: 0.3952 time to fit residues: 208.3871 Evaluate side-chains 309 residues out of total 3358 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 260 time to evaluate : 3.362 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 25 GLU Chi-restraints excluded: chain F residue 36 VAL Chi-restraints excluded: chain F residue 128 THR Chi-restraints excluded: chain F residue 162 VAL Chi-restraints excluded: chain F residue 172 PHE Chi-restraints excluded: chain 2 residue 260 ASP Chi-restraints excluded: chain 2 residue 316 THR Chi-restraints excluded: chain 2 residue 406 CYS Chi-restraints excluded: chain 2 residue 419 HIS Chi-restraints excluded: chain 2 residue 653 ILE Chi-restraints excluded: chain 2 residue 720 LEU Chi-restraints excluded: chain 2 residue 764 VAL Chi-restraints excluded: chain 3 residue 70 PHE Chi-restraints excluded: chain 3 residue 237 VAL Chi-restraints excluded: chain 3 residue 322 LEU Chi-restraints excluded: chain 3 residue 379 THR Chi-restraints excluded: chain 3 residue 456 TYR Chi-restraints excluded: chain 3 residue 486 LEU Chi-restraints excluded: chain 4 residue 207 PHE Chi-restraints excluded: chain 4 residue 239 MET Chi-restraints excluded: chain 4 residue 286 SER Chi-restraints excluded: chain 4 residue 488 THR Chi-restraints excluded: chain 5 residue 99 LEU Chi-restraints excluded: chain 5 residue 124 ILE Chi-restraints excluded: chain 5 residue 296 VAL Chi-restraints excluded: chain 5 residue 353 ILE Chi-restraints excluded: chain 5 residue 448 ASP Chi-restraints excluded: chain 5 residue 574 LEU Chi-restraints excluded: chain 6 residue 193 LEU Chi-restraints excluded: chain 6 residue 220 ILE Chi-restraints excluded: chain 6 residue 293 SER Chi-restraints excluded: chain 6 residue 299 LEU Chi-restraints excluded: chain 6 residue 331 VAL Chi-restraints excluded: chain 6 residue 450 MET Chi-restraints excluded: chain 6 residue 520 ILE Chi-restraints excluded: chain 6 residue 594 ILE Chi-restraints excluded: chain 6 residue 618 VAL Chi-restraints excluded: chain 6 residue 651 LEU Chi-restraints excluded: chain 6 residue 782 HIS Chi-restraints excluded: chain 7 residue 16 PHE Chi-restraints excluded: chain 7 residue 21 TYR Chi-restraints excluded: chain 7 residue 52 LEU Chi-restraints excluded: chain 7 residue 197 SER Chi-restraints excluded: chain 7 residue 223 GLN Chi-restraints excluded: chain 7 residue 242 ASP Chi-restraints excluded: chain 7 residue 257 VAL Chi-restraints excluded: chain 7 residue 293 LEU Chi-restraints excluded: chain 7 residue 385 VAL Chi-restraints excluded: chain 7 residue 640 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 388 random chunks: chunk 10 optimal weight: 0.7980 chunk 287 optimal weight: 1.9990 chunk 144 optimal weight: 1.9990 chunk 137 optimal weight: 2.9990 chunk 312 optimal weight: 7.9990 chunk 369 optimal weight: 1.9990 chunk 89 optimal weight: 10.0000 chunk 43 optimal weight: 0.7980 chunk 333 optimal weight: 1.9990 chunk 217 optimal weight: 2.9990 chunk 161 optimal weight: 5.9990 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 129 GLN 4 350 GLN ** 6 187 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4213 r_free = 0.4213 target = 0.144289 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3740 r_free = 0.3740 target = 0.110977 restraints weight = 65010.028| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3795 r_free = 0.3795 target = 0.114791 restraints weight = 39499.260| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3800 r_free = 0.3800 target = 0.115393 restraints weight = 26236.890| |-----------------------------------------------------------------------------| r_work (final): 0.3806 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7323 moved from start: 0.3275 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 33157 Z= 0.148 Angle : 0.546 8.703 45157 Z= 0.281 Chirality : 0.041 0.146 5144 Planarity : 0.004 0.057 5476 Dihedral : 16.133 175.479 5274 Min Nonbonded Distance : 1.853 Molprobity Statistics. All-atom Clashscore : 5.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.42 % Favored : 96.58 % Rotamer: Outliers : 2.03 % Allowed : 13.26 % Favored : 84.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.12 (0.14), residues: 3768 helix: 2.00 (0.13), residues: 1608 sheet: 0.17 (0.20), residues: 707 loop : -0.34 (0.16), residues: 1453 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP 6 751 HIS 0.006 0.001 HIS 7 543 PHE 0.026 0.002 PHE 7 77 TYR 0.030 0.001 TYR F 121 ARG 0.008 0.000 ARG 7 302 Details of bonding type rmsd hydrogen bonds : bond 0.03523 ( 1422) hydrogen bonds : angle 3.89739 ( 3997) metal coordination : bond 0.00629 ( 19) metal coordination : angle 2.98263 ( 24) covalent geometry : bond 0.00348 (33138) covalent geometry : angle 0.54175 (45133) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7536 Ramachandran restraints generated. 3768 Oldfield, 0 Emsley, 3768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7536 Ramachandran restraints generated. 3768 Oldfield, 0 Emsley, 3768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 341 residues out of total 3358 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 273 time to evaluate : 3.344 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 26 GLU cc_start: 0.7703 (OUTLIER) cc_final: 0.7389 (tp30) REVERT: F 59 MET cc_start: 0.7359 (mmm) cc_final: 0.6785 (mmm) REVERT: 2 746 MET cc_start: 0.8344 (tpp) cc_final: 0.7275 (mmm) REVERT: 3 547 LYS cc_start: 0.7511 (mptt) cc_final: 0.7231 (tmtt) REVERT: 3 568 MET cc_start: 0.7795 (OUTLIER) cc_final: 0.7303 (ttp) REVERT: 4 699 MET cc_start: 0.5990 (mmm) cc_final: 0.5530 (mmt) REVERT: 5 145 MET cc_start: 0.8209 (tpp) cc_final: 0.7994 (tpt) REVERT: 6 450 MET cc_start: 0.8264 (OUTLIER) cc_final: 0.7947 (mtt) REVERT: 6 527 MET cc_start: 0.7468 (mmm) cc_final: 0.7191 (ttp) REVERT: 7 108 MET cc_start: 0.6332 (ppp) cc_final: 0.5485 (ppp) REVERT: 7 223 GLN cc_start: 0.6648 (OUTLIER) cc_final: 0.6040 (tt0) REVERT: 7 269 ASP cc_start: 0.7372 (t0) cc_final: 0.7104 (t0) outliers start: 68 outliers final: 50 residues processed: 318 average time/residue: 0.3898 time to fit residues: 207.8607 Evaluate side-chains 306 residues out of total 3358 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 252 time to evaluate : 3.990 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 25 GLU Chi-restraints excluded: chain F residue 26 GLU Chi-restraints excluded: chain F residue 36 VAL Chi-restraints excluded: chain F residue 68 LEU Chi-restraints excluded: chain F residue 128 THR Chi-restraints excluded: chain F residue 162 VAL Chi-restraints excluded: chain F residue 172 PHE Chi-restraints excluded: chain F residue 179 LEU Chi-restraints excluded: chain 2 residue 260 ASP Chi-restraints excluded: chain 2 residue 406 CYS Chi-restraints excluded: chain 2 residue 419 HIS Chi-restraints excluded: chain 2 residue 534 LYS Chi-restraints excluded: chain 2 residue 653 ILE Chi-restraints excluded: chain 2 residue 720 LEU Chi-restraints excluded: chain 2 residue 764 VAL Chi-restraints excluded: chain 2 residue 780 ILE Chi-restraints excluded: chain 3 residue 237 VAL Chi-restraints excluded: chain 3 residue 322 LEU Chi-restraints excluded: chain 3 residue 379 THR Chi-restraints excluded: chain 3 residue 486 LEU Chi-restraints excluded: chain 3 residue 568 MET Chi-restraints excluded: chain 4 residue 195 GLN Chi-restraints excluded: chain 4 residue 207 PHE Chi-restraints excluded: chain 4 residue 239 MET Chi-restraints excluded: chain 4 residue 488 THR Chi-restraints excluded: chain 5 residue 99 LEU Chi-restraints excluded: chain 5 residue 124 ILE Chi-restraints excluded: chain 5 residue 296 VAL Chi-restraints excluded: chain 5 residue 353 ILE Chi-restraints excluded: chain 5 residue 448 ASP Chi-restraints excluded: chain 5 residue 458 ILE Chi-restraints excluded: chain 5 residue 574 LEU Chi-restraints excluded: chain 5 residue 619 ILE Chi-restraints excluded: chain 6 residue 193 LEU Chi-restraints excluded: chain 6 residue 220 ILE Chi-restraints excluded: chain 6 residue 247 THR Chi-restraints excluded: chain 6 residue 293 SER Chi-restraints excluded: chain 6 residue 299 LEU Chi-restraints excluded: chain 6 residue 331 VAL Chi-restraints excluded: chain 6 residue 450 MET Chi-restraints excluded: chain 6 residue 520 ILE Chi-restraints excluded: chain 6 residue 618 VAL Chi-restraints excluded: chain 6 residue 782 HIS Chi-restraints excluded: chain 7 residue 16 PHE Chi-restraints excluded: chain 7 residue 21 TYR Chi-restraints excluded: chain 7 residue 52 LEU Chi-restraints excluded: chain 7 residue 55 VAL Chi-restraints excluded: chain 7 residue 197 SER Chi-restraints excluded: chain 7 residue 223 GLN Chi-restraints excluded: chain 7 residue 242 ASP Chi-restraints excluded: chain 7 residue 257 VAL Chi-restraints excluded: chain 7 residue 293 LEU Chi-restraints excluded: chain 7 residue 385 VAL Chi-restraints excluded: chain 7 residue 640 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 388 random chunks: chunk 322 optimal weight: 8.9990 chunk 20 optimal weight: 2.9990 chunk 360 optimal weight: 0.0170 chunk 348 optimal weight: 5.9990 chunk 287 optimal weight: 0.9990 chunk 361 optimal weight: 1.9990 chunk 19 optimal weight: 1.9990 chunk 289 optimal weight: 0.8980 chunk 357 optimal weight: 0.7980 chunk 42 optimal weight: 0.9980 chunk 239 optimal weight: 0.4980 overall best weight: 0.6418 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 6 187 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 542 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4235 r_free = 0.4235 target = 0.145980 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3787 r_free = 0.3787 target = 0.113586 restraints weight = 64666.789| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3816 r_free = 0.3816 target = 0.116425 restraints weight = 38879.825| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3827 r_free = 0.3827 target = 0.117366 restraints weight = 26983.323| |-----------------------------------------------------------------------------| r_work (final): 0.3840 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7277 moved from start: 0.3396 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 33157 Z= 0.101 Angle : 0.512 13.864 45157 Z= 0.261 Chirality : 0.040 0.148 5144 Planarity : 0.003 0.056 5476 Dihedral : 15.999 175.571 5274 Min Nonbonded Distance : 1.944 Molprobity Statistics. All-atom Clashscore : 5.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.47 % Favored : 97.53 % Rotamer: Outliers : 1.73 % Allowed : 13.95 % Favored : 84.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.24 (0.14), residues: 3768 helix: 2.08 (0.13), residues: 1612 sheet: 0.21 (0.20), residues: 722 loop : -0.25 (0.17), residues: 1434 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP 6 751 HIS 0.005 0.001 HIS 7 536 PHE 0.022 0.001 PHE 7 77 TYR 0.031 0.001 TYR 2 821 ARG 0.010 0.000 ARG 2 812 Details of bonding type rmsd hydrogen bonds : bond 0.02957 ( 1422) hydrogen bonds : angle 3.73576 ( 3997) metal coordination : bond 0.00461 ( 19) metal coordination : angle 2.59461 ( 24) covalent geometry : bond 0.00226 (33138) covalent geometry : angle 0.50868 (45133) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7536 Ramachandran restraints generated. 3768 Oldfield, 0 Emsley, 3768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7536 Ramachandran restraints generated. 3768 Oldfield, 0 Emsley, 3768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 327 residues out of total 3358 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 269 time to evaluate : 3.516 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 26 GLU cc_start: 0.7663 (OUTLIER) cc_final: 0.7362 (tp30) REVERT: F 59 MET cc_start: 0.7305 (mmm) cc_final: 0.6933 (mmm) REVERT: 2 793 MET cc_start: 0.7402 (tpt) cc_final: 0.7164 (tpp) REVERT: 3 47 LEU cc_start: 0.7877 (tp) cc_final: 0.7660 (mt) REVERT: 3 547 LYS cc_start: 0.7612 (mptt) cc_final: 0.7310 (tmtt) REVERT: 3 552 LEU cc_start: 0.8818 (OUTLIER) cc_final: 0.8400 (tp) REVERT: 4 699 MET cc_start: 0.5919 (mmm) cc_final: 0.5471 (mmt) REVERT: 6 450 MET cc_start: 0.8150 (OUTLIER) cc_final: 0.7854 (mtt) REVERT: 6 527 MET cc_start: 0.7509 (mmm) cc_final: 0.7246 (ttp) REVERT: 7 223 GLN cc_start: 0.6431 (OUTLIER) cc_final: 0.6048 (tt0) REVERT: 7 269 ASP cc_start: 0.7336 (t0) cc_final: 0.7066 (t0) outliers start: 58 outliers final: 43 residues processed: 305 average time/residue: 0.3934 time to fit residues: 200.6527 Evaluate side-chains 308 residues out of total 3358 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 261 time to evaluate : 3.509 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 25 GLU Chi-restraints excluded: chain F residue 26 GLU Chi-restraints excluded: chain F residue 36 VAL Chi-restraints excluded: chain F residue 162 VAL Chi-restraints excluded: chain F residue 172 PHE Chi-restraints excluded: chain F residue 179 LEU Chi-restraints excluded: chain 2 residue 260 ASP Chi-restraints excluded: chain 2 residue 406 CYS Chi-restraints excluded: chain 2 residue 419 HIS Chi-restraints excluded: chain 2 residue 720 LEU Chi-restraints excluded: chain 2 residue 764 VAL Chi-restraints excluded: chain 3 residue 237 VAL Chi-restraints excluded: chain 3 residue 379 THR Chi-restraints excluded: chain 3 residue 456 TYR Chi-restraints excluded: chain 3 residue 486 LEU Chi-restraints excluded: chain 3 residue 552 LEU Chi-restraints excluded: chain 4 residue 195 GLN Chi-restraints excluded: chain 4 residue 207 PHE Chi-restraints excluded: chain 4 residue 239 MET Chi-restraints excluded: chain 5 residue 99 LEU Chi-restraints excluded: chain 5 residue 296 VAL Chi-restraints excluded: chain 5 residue 353 ILE Chi-restraints excluded: chain 5 residue 400 ILE Chi-restraints excluded: chain 5 residue 448 ASP Chi-restraints excluded: chain 5 residue 574 LEU Chi-restraints excluded: chain 6 residue 193 LEU Chi-restraints excluded: chain 6 residue 220 ILE Chi-restraints excluded: chain 6 residue 235 SER Chi-restraints excluded: chain 6 residue 293 SER Chi-restraints excluded: chain 6 residue 299 LEU Chi-restraints excluded: chain 6 residue 331 VAL Chi-restraints excluded: chain 6 residue 346 LEU Chi-restraints excluded: chain 6 residue 450 MET Chi-restraints excluded: chain 6 residue 625 ILE Chi-restraints excluded: chain 6 residue 631 MET Chi-restraints excluded: chain 6 residue 782 HIS Chi-restraints excluded: chain 7 residue 16 PHE Chi-restraints excluded: chain 7 residue 21 TYR Chi-restraints excluded: chain 7 residue 197 SER Chi-restraints excluded: chain 7 residue 223 GLN Chi-restraints excluded: chain 7 residue 242 ASP Chi-restraints excluded: chain 7 residue 257 VAL Chi-restraints excluded: chain 7 residue 293 LEU Chi-restraints excluded: chain 7 residue 298 LEU Chi-restraints excluded: chain 7 residue 385 VAL Chi-restraints excluded: chain 7 residue 625 VAL Chi-restraints excluded: chain 7 residue 640 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 388 random chunks: chunk 59 optimal weight: 0.0270 chunk 258 optimal weight: 0.9980 chunk 339 optimal weight: 1.9990 chunk 200 optimal weight: 3.9990 chunk 249 optimal weight: 2.9990 chunk 245 optimal weight: 8.9990 chunk 138 optimal weight: 4.9990 chunk 175 optimal weight: 0.9980 chunk 45 optimal weight: 5.9990 chunk 20 optimal weight: 0.0270 chunk 268 optimal weight: 0.7980 overall best weight: 0.5696 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 178 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 187 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 6 597 GLN ** 7 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4239 r_free = 0.4239 target = 0.146287 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3790 r_free = 0.3790 target = 0.113724 restraints weight = 65009.948| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3820 r_free = 0.3820 target = 0.116817 restraints weight = 38808.379| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3830 r_free = 0.3830 target = 0.117569 restraints weight = 27140.303| |-----------------------------------------------------------------------------| r_work (final): 0.3843 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7274 moved from start: 0.3516 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 33157 Z= 0.099 Angle : 0.511 9.881 45157 Z= 0.260 Chirality : 0.039 0.177 5144 Planarity : 0.003 0.055 5476 Dihedral : 15.877 176.561 5274 Min Nonbonded Distance : 1.956 Molprobity Statistics. All-atom Clashscore : 5.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer: Outliers : 1.76 % Allowed : 13.83 % Favored : 84.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.30 (0.14), residues: 3768 helix: 2.11 (0.13), residues: 1612 sheet: 0.25 (0.20), residues: 722 loop : -0.21 (0.17), residues: 1434 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP 6 751 HIS 0.005 0.001 HIS 7 536 PHE 0.043 0.001 PHE 6 649 TYR 0.024 0.001 TYR 2 821 ARG 0.009 0.000 ARG 2 812 Details of bonding type rmsd hydrogen bonds : bond 0.02883 ( 1422) hydrogen bonds : angle 3.70315 ( 3997) metal coordination : bond 0.00396 ( 19) metal coordination : angle 2.40190 ( 24) covalent geometry : bond 0.00220 (33138) covalent geometry : angle 0.50855 (45133) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7536 Ramachandran restraints generated. 3768 Oldfield, 0 Emsley, 3768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7536 Ramachandran restraints generated. 3768 Oldfield, 0 Emsley, 3768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 334 residues out of total 3358 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 275 time to evaluate : 3.533 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: F 26 GLU cc_start: 0.7689 (OUTLIER) cc_final: 0.7384 (tp30) REVERT: F 59 MET cc_start: 0.7298 (mmm) cc_final: 0.6921 (mmm) REVERT: 3 47 LEU cc_start: 0.7892 (tp) cc_final: 0.7666 (mt) REVERT: 3 547 LYS cc_start: 0.7654 (mptt) cc_final: 0.7358 (tmtt) REVERT: 3 552 LEU cc_start: 0.8777 (OUTLIER) cc_final: 0.8404 (tp) REVERT: 4 699 MET cc_start: 0.5913 (mmm) cc_final: 0.5471 (mmt) REVERT: 6 450 MET cc_start: 0.8140 (OUTLIER) cc_final: 0.7837 (mtt) REVERT: 6 527 MET cc_start: 0.7498 (mmm) cc_final: 0.7255 (ttp) REVERT: 7 8 LEU cc_start: 0.8548 (mm) cc_final: 0.8205 (mp) REVERT: 7 108 MET cc_start: 0.5700 (ppp) cc_final: 0.4801 (ppp) REVERT: 7 223 GLN cc_start: 0.6425 (OUTLIER) cc_final: 0.6033 (tt0) REVERT: 7 269 ASP cc_start: 0.7342 (t0) cc_final: 0.7089 (t0) outliers start: 59 outliers final: 45 residues processed: 311 average time/residue: 0.4007 time to fit residues: 208.1263 Evaluate side-chains 305 residues out of total 3358 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 256 time to evaluate : 3.512 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 25 GLU Chi-restraints excluded: chain F residue 26 GLU Chi-restraints excluded: chain F residue 36 VAL Chi-restraints excluded: chain F residue 162 VAL Chi-restraints excluded: chain F residue 172 PHE Chi-restraints excluded: chain F residue 179 LEU Chi-restraints excluded: chain 2 residue 260 ASP Chi-restraints excluded: chain 2 residue 406 CYS Chi-restraints excluded: chain 2 residue 419 HIS Chi-restraints excluded: chain 2 residue 720 LEU Chi-restraints excluded: chain 2 residue 764 VAL Chi-restraints excluded: chain 3 residue 237 VAL Chi-restraints excluded: chain 3 residue 379 THR Chi-restraints excluded: chain 3 residue 456 TYR Chi-restraints excluded: chain 3 residue 486 LEU Chi-restraints excluded: chain 3 residue 552 LEU Chi-restraints excluded: chain 4 residue 195 GLN Chi-restraints excluded: chain 4 residue 207 PHE Chi-restraints excluded: chain 4 residue 239 MET Chi-restraints excluded: chain 5 residue 99 LEU Chi-restraints excluded: chain 5 residue 124 ILE Chi-restraints excluded: chain 5 residue 127 MET Chi-restraints excluded: chain 5 residue 196 LYS Chi-restraints excluded: chain 5 residue 296 VAL Chi-restraints excluded: chain 5 residue 353 ILE Chi-restraints excluded: chain 5 residue 458 ILE Chi-restraints excluded: chain 5 residue 574 LEU Chi-restraints excluded: chain 6 residue 193 LEU Chi-restraints excluded: chain 6 residue 220 ILE Chi-restraints excluded: chain 6 residue 235 SER Chi-restraints excluded: chain 6 residue 293 SER Chi-restraints excluded: chain 6 residue 299 LEU Chi-restraints excluded: chain 6 residue 331 VAL Chi-restraints excluded: chain 6 residue 346 LEU Chi-restraints excluded: chain 6 residue 450 MET Chi-restraints excluded: chain 6 residue 625 ILE Chi-restraints excluded: chain 6 residue 631 MET Chi-restraints excluded: chain 6 residue 782 HIS Chi-restraints excluded: chain 7 residue 16 PHE Chi-restraints excluded: chain 7 residue 21 TYR Chi-restraints excluded: chain 7 residue 55 VAL Chi-restraints excluded: chain 7 residue 197 SER Chi-restraints excluded: chain 7 residue 223 GLN Chi-restraints excluded: chain 7 residue 242 ASP Chi-restraints excluded: chain 7 residue 257 VAL Chi-restraints excluded: chain 7 residue 293 LEU Chi-restraints excluded: chain 7 residue 298 LEU Chi-restraints excluded: chain 7 residue 385 VAL Chi-restraints excluded: chain 7 residue 640 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 388 random chunks: chunk 276 optimal weight: 0.0040 chunk 194 optimal weight: 0.7980 chunk 86 optimal weight: 3.9990 chunk 253 optimal weight: 2.9990 chunk 10 optimal weight: 0.0370 chunk 108 optimal weight: 3.9990 chunk 171 optimal weight: 4.9990 chunk 318 optimal weight: 2.9990 chunk 159 optimal weight: 0.7980 chunk 0 optimal weight: 6.9990 chunk 133 optimal weight: 6.9990 overall best weight: 0.9272 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 2 838 GLN 3 553 HIS 4 593 GLN ** 6 187 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4225 r_free = 0.4225 target = 0.145087 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3786 r_free = 0.3786 target = 0.112942 restraints weight = 64994.878| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3806 r_free = 0.3806 target = 0.115627 restraints weight = 39341.669| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3816 r_free = 0.3816 target = 0.116412 restraints weight = 27598.694| |-----------------------------------------------------------------------------| r_work (final): 0.3828 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7291 moved from start: 0.3664 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 33157 Z= 0.112 Angle : 0.533 10.367 45157 Z= 0.269 Chirality : 0.040 0.146 5144 Planarity : 0.004 0.054 5476 Dihedral : 15.806 178.440 5274 Min Nonbonded Distance : 1.920 Molprobity Statistics. All-atom Clashscore : 5.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 1.70 % Allowed : 14.48 % Favored : 83.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.26 (0.14), residues: 3768 helix: 2.12 (0.13), residues: 1606 sheet: 0.21 (0.20), residues: 723 loop : -0.25 (0.17), residues: 1439 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.001 TRP 6 751 HIS 0.005 0.001 HIS 7 459 PHE 0.038 0.001 PHE 6 649 TYR 0.023 0.001 TYR 2 821 ARG 0.009 0.000 ARG 2 812 Details of bonding type rmsd hydrogen bonds : bond 0.03027 ( 1422) hydrogen bonds : angle 3.71953 ( 3997) metal coordination : bond 0.00612 ( 19) metal coordination : angle 3.28878 ( 24) covalent geometry : bond 0.00259 (33138) covalent geometry : angle 0.52750 (45133) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7536 Ramachandran restraints generated. 3768 Oldfield, 0 Emsley, 3768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7536 Ramachandran restraints generated. 3768 Oldfield, 0 Emsley, 3768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 323 residues out of total 3358 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 266 time to evaluate : 3.354 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: F 59 MET cc_start: 0.7310 (mmm) cc_final: 0.6923 (mmm) REVERT: F 122 GLU cc_start: 0.7506 (tm-30) cc_final: 0.7200 (tm-30) REVERT: 3 547 LYS cc_start: 0.7593 (mptt) cc_final: 0.7294 (tmtt) REVERT: 3 568 MET cc_start: 0.7726 (OUTLIER) cc_final: 0.7232 (ttp) REVERT: 4 699 MET cc_start: 0.5930 (mmm) cc_final: 0.5473 (mmt) REVERT: 5 145 MET cc_start: 0.8148 (tpp) cc_final: 0.7883 (tpt) REVERT: 6 450 MET cc_start: 0.8191 (OUTLIER) cc_final: 0.7887 (mtt) REVERT: 6 527 MET cc_start: 0.7644 (mmm) cc_final: 0.7316 (ttp) REVERT: 7 8 LEU cc_start: 0.8548 (mm) cc_final: 0.8198 (mp) REVERT: 7 108 MET cc_start: 0.5794 (ppp) cc_final: 0.4943 (ppp) REVERT: 7 223 GLN cc_start: 0.6572 (OUTLIER) cc_final: 0.6194 (tt0) REVERT: 7 269 ASP cc_start: 0.7399 (t0) cc_final: 0.7139 (t0) outliers start: 57 outliers final: 47 residues processed: 302 average time/residue: 0.3952 time to fit residues: 200.2184 Evaluate side-chains 309 residues out of total 3358 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 259 time to evaluate : 3.509 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 25 GLU Chi-restraints excluded: chain F residue 36 VAL Chi-restraints excluded: chain F residue 162 VAL Chi-restraints excluded: chain F residue 172 PHE Chi-restraints excluded: chain F residue 179 LEU Chi-restraints excluded: chain 2 residue 260 ASP Chi-restraints excluded: chain 2 residue 288 LEU Chi-restraints excluded: chain 2 residue 406 CYS Chi-restraints excluded: chain 2 residue 419 HIS Chi-restraints excluded: chain 2 residue 720 LEU Chi-restraints excluded: chain 2 residue 764 VAL Chi-restraints excluded: chain 2 residue 834 PHE Chi-restraints excluded: chain 3 residue 237 VAL Chi-restraints excluded: chain 3 residue 379 THR Chi-restraints excluded: chain 3 residue 456 TYR Chi-restraints excluded: chain 3 residue 486 LEU Chi-restraints excluded: chain 3 residue 568 MET Chi-restraints excluded: chain 4 residue 195 GLN Chi-restraints excluded: chain 4 residue 207 PHE Chi-restraints excluded: chain 4 residue 239 MET Chi-restraints excluded: chain 5 residue 99 LEU Chi-restraints excluded: chain 5 residue 124 ILE Chi-restraints excluded: chain 5 residue 196 LYS Chi-restraints excluded: chain 5 residue 296 VAL Chi-restraints excluded: chain 5 residue 353 ILE Chi-restraints excluded: chain 5 residue 458 ILE Chi-restraints excluded: chain 5 residue 574 LEU Chi-restraints excluded: chain 6 residue 193 LEU Chi-restraints excluded: chain 6 residue 220 ILE Chi-restraints excluded: chain 6 residue 234 GLU Chi-restraints excluded: chain 6 residue 293 SER Chi-restraints excluded: chain 6 residue 299 LEU Chi-restraints excluded: chain 6 residue 331 VAL Chi-restraints excluded: chain 6 residue 346 LEU Chi-restraints excluded: chain 6 residue 450 MET Chi-restraints excluded: chain 6 residue 618 VAL Chi-restraints excluded: chain 6 residue 625 ILE Chi-restraints excluded: chain 6 residue 631 MET Chi-restraints excluded: chain 6 residue 782 HIS Chi-restraints excluded: chain 7 residue 16 PHE Chi-restraints excluded: chain 7 residue 21 TYR Chi-restraints excluded: chain 7 residue 55 VAL Chi-restraints excluded: chain 7 residue 197 SER Chi-restraints excluded: chain 7 residue 223 GLN Chi-restraints excluded: chain 7 residue 242 ASP Chi-restraints excluded: chain 7 residue 257 VAL Chi-restraints excluded: chain 7 residue 293 LEU Chi-restraints excluded: chain 7 residue 298 LEU Chi-restraints excluded: chain 7 residue 385 VAL Chi-restraints excluded: chain 7 residue 640 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 388 random chunks: chunk 346 optimal weight: 3.9990 chunk 180 optimal weight: 0.0870 chunk 172 optimal weight: 2.9990 chunk 132 optimal weight: 8.9990 chunk 176 optimal weight: 2.9990 chunk 127 optimal weight: 6.9990 chunk 289 optimal weight: 0.6980 chunk 381 optimal weight: 10.0000 chunk 224 optimal weight: 0.9980 chunk 161 optimal weight: 0.0670 chunk 97 optimal weight: 0.3980 overall best weight: 0.4496 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 2 364 ASN ** 6 187 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4246 r_free = 0.4246 target = 0.146804 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3786 r_free = 0.3786 target = 0.114001 restraints weight = 65133.815| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3839 r_free = 0.3839 target = 0.117584 restraints weight = 40348.910| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3844 r_free = 0.3844 target = 0.118320 restraints weight = 26656.836| |-----------------------------------------------------------------------------| r_work (final): 0.3855 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7259 moved from start: 0.3800 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 33157 Z= 0.095 Angle : 0.523 11.717 45157 Z= 0.263 Chirality : 0.039 0.142 5144 Planarity : 0.003 0.051 5476 Dihedral : 15.668 179.656 5274 Min Nonbonded Distance : 1.998 Molprobity Statistics. All-atom Clashscore : 5.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer: Outliers : 1.43 % Allowed : 14.81 % Favored : 83.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.37 (0.14), residues: 3768 helix: 2.18 (0.13), residues: 1606 sheet: 0.35 (0.20), residues: 724 loop : -0.19 (0.17), residues: 1438 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.001 TRP 6 751 HIS 0.006 0.001 HIS 7 536 PHE 0.036 0.001 PHE 6 649 TYR 0.015 0.001 TYR F 121 ARG 0.010 0.000 ARG 2 812 Details of bonding type rmsd hydrogen bonds : bond 0.02751 ( 1422) hydrogen bonds : angle 3.62535 ( 3997) metal coordination : bond 0.00409 ( 19) metal coordination : angle 2.99471 ( 24) covalent geometry : bond 0.00211 (33138) covalent geometry : angle 0.51840 (45133) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7536 Ramachandran restraints generated. 3768 Oldfield, 0 Emsley, 3768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7536 Ramachandran restraints generated. 3768 Oldfield, 0 Emsley, 3768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 325 residues out of total 3358 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 277 time to evaluate : 3.621 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: F 59 MET cc_start: 0.7317 (mmm) cc_final: 0.6931 (mmm) REVERT: 2 838 GLN cc_start: 0.7756 (mm-40) cc_final: 0.7526 (tt0) REVERT: 3 547 LYS cc_start: 0.7592 (mptt) cc_final: 0.7257 (tmtt) REVERT: 4 699 MET cc_start: 0.5719 (mmm) cc_final: 0.5339 (mmt) REVERT: 5 145 MET cc_start: 0.8240 (tpp) cc_final: 0.7959 (mmm) REVERT: 6 235 SER cc_start: 0.7715 (m) cc_final: 0.7349 (m) REVERT: 6 450 MET cc_start: 0.8105 (OUTLIER) cc_final: 0.7811 (mtt) REVERT: 6 527 MET cc_start: 0.7516 (mmm) cc_final: 0.7265 (ttp) REVERT: 6 775 LYS cc_start: 0.8882 (mttt) cc_final: 0.8109 (tmtt) REVERT: 7 8 LEU cc_start: 0.8536 (mm) cc_final: 0.8159 (mp) REVERT: 7 108 MET cc_start: 0.5791 (ppp) cc_final: 0.4942 (ppp) REVERT: 7 223 GLN cc_start: 0.6352 (OUTLIER) cc_final: 0.5978 (tt0) REVERT: 7 269 ASP cc_start: 0.7340 (t0) cc_final: 0.7101 (t0) outliers start: 48 outliers final: 40 residues processed: 306 average time/residue: 0.4284 time to fit residues: 216.6121 Evaluate side-chains 303 residues out of total 3358 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 261 time to evaluate : 3.794 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 36 VAL Chi-restraints excluded: chain F residue 162 VAL Chi-restraints excluded: chain F residue 172 PHE Chi-restraints excluded: chain F residue 179 LEU Chi-restraints excluded: chain 2 residue 260 ASP Chi-restraints excluded: chain 2 residue 288 LEU Chi-restraints excluded: chain 2 residue 406 CYS Chi-restraints excluded: chain 2 residue 419 HIS Chi-restraints excluded: chain 2 residue 437 THR Chi-restraints excluded: chain 2 residue 720 LEU Chi-restraints excluded: chain 2 residue 764 VAL Chi-restraints excluded: chain 2 residue 834 PHE Chi-restraints excluded: chain 3 residue 237 VAL Chi-restraints excluded: chain 3 residue 456 TYR Chi-restraints excluded: chain 3 residue 486 LEU Chi-restraints excluded: chain 4 residue 195 GLN Chi-restraints excluded: chain 4 residue 207 PHE Chi-restraints excluded: chain 4 residue 317 MET Chi-restraints excluded: chain 4 residue 610 ARG Chi-restraints excluded: chain 5 residue 99 LEU Chi-restraints excluded: chain 5 residue 124 ILE Chi-restraints excluded: chain 5 residue 196 LYS Chi-restraints excluded: chain 5 residue 296 VAL Chi-restraints excluded: chain 5 residue 353 ILE Chi-restraints excluded: chain 5 residue 400 ILE Chi-restraints excluded: chain 5 residue 574 LEU Chi-restraints excluded: chain 6 residue 193 LEU Chi-restraints excluded: chain 6 residue 293 SER Chi-restraints excluded: chain 6 residue 299 LEU Chi-restraints excluded: chain 6 residue 331 VAL Chi-restraints excluded: chain 6 residue 346 LEU Chi-restraints excluded: chain 6 residue 450 MET Chi-restraints excluded: chain 6 residue 631 MET Chi-restraints excluded: chain 6 residue 782 HIS Chi-restraints excluded: chain 7 residue 16 PHE Chi-restraints excluded: chain 7 residue 21 TYR Chi-restraints excluded: chain 7 residue 55 VAL Chi-restraints excluded: chain 7 residue 197 SER Chi-restraints excluded: chain 7 residue 223 GLN Chi-restraints excluded: chain 7 residue 242 ASP Chi-restraints excluded: chain 7 residue 257 VAL Chi-restraints excluded: chain 7 residue 385 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 388 random chunks: chunk 56 optimal weight: 3.9990 chunk 298 optimal weight: 2.9990 chunk 7 optimal weight: 1.9990 chunk 152 optimal weight: 0.7980 chunk 35 optimal weight: 4.9990 chunk 275 optimal weight: 0.8980 chunk 131 optimal weight: 3.9990 chunk 280 optimal weight: 0.6980 chunk 261 optimal weight: 6.9990 chunk 179 optimal weight: 0.2980 chunk 238 optimal weight: 9.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 6 187 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4227 r_free = 0.4227 target = 0.145241 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3764 r_free = 0.3764 target = 0.112227 restraints weight = 65186.156| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3815 r_free = 0.3815 target = 0.116054 restraints weight = 38274.102| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3824 r_free = 0.3824 target = 0.116928 restraints weight = 25114.310| |-----------------------------------------------------------------------------| r_work (final): 0.3837 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7285 moved from start: 0.3883 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 33157 Z= 0.113 Angle : 0.539 11.388 45157 Z= 0.272 Chirality : 0.040 0.241 5144 Planarity : 0.004 0.073 5476 Dihedral : 15.640 178.642 5274 Min Nonbonded Distance : 1.928 Molprobity Statistics. All-atom Clashscore : 5.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 1.58 % Allowed : 14.93 % Favored : 83.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.33 (0.14), residues: 3768 helix: 2.13 (0.13), residues: 1605 sheet: 0.27 (0.20), residues: 721 loop : -0.17 (0.17), residues: 1442 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.001 TRP 6 751 HIS 0.005 0.001 HIS 7 536 PHE 0.036 0.001 PHE 6 649 TYR 0.026 0.001 TYR F 121 ARG 0.014 0.000 ARG 2 730 Details of bonding type rmsd hydrogen bonds : bond 0.02988 ( 1422) hydrogen bonds : angle 3.68014 ( 3997) metal coordination : bond 0.00475 ( 19) metal coordination : angle 2.87068 ( 24) covalent geometry : bond 0.00262 (33138) covalent geometry : angle 0.53494 (45133) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9437.95 seconds wall clock time: 166 minutes 21.40 seconds (9981.40 seconds total)