Starting phenix.real_space_refine on Fri Sep 19 01:09:00 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7jgs_22330/09_2025/7jgs_22330.cif Found real_map, /net/cci-nas-00/data/ceres_data/7jgs_22330/09_2025/7jgs_22330.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7jgs_22330/09_2025/7jgs_22330.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7jgs_22330/09_2025/7jgs_22330.map" model { file = "/net/cci-nas-00/data/ceres_data/7jgs_22330/09_2025/7jgs_22330.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7jgs_22330/09_2025/7jgs_22330.cif" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.003 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 82 5.49 5 Mg 4 5.21 5 S 111 5.16 5 C 13591 2.51 5 N 3810 2.21 5 O 4145 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 78 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 21743 Number of models: 1 Model: "" Number of chains: 13 Chain: "B" Number of atoms: 2290 Number of conformers: 1 Conformer: "" Number of residues, atoms: 285, 2290 Classifications: {'peptide': 285} Link IDs: {'PTRANS': 11, 'TRANS': 273} Chain breaks: 4 Chain: "C" Number of atoms: 4934 Number of conformers: 1 Conformer: "" Number of residues, atoms: 614, 4934 Classifications: {'peptide': 614} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 23, 'TRANS': 590} Chain breaks: 6 Chain: "D" Number of atoms: 3549 Number of conformers: 1 Conformer: "" Number of residues, atoms: 441, 3549 Classifications: {'peptide': 441} Link IDs: {'PTRANS': 11, 'TRANS': 429} Chain breaks: 2 Chain: "E" Number of atoms: 3161 Number of conformers: 1 Conformer: "" Number of residues, atoms: 398, 3161 Classifications: {'peptide': 398} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 11, 'TRANS': 386} Chain breaks: 4 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "F" Number of atoms: 143 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 143 Classifications: {'peptide': 17} Link IDs: {'TRANS': 16} Chain: "A" Number of atoms: 3129 Number of conformers: 1 Conformer: "" Number of residues, atoms: 401, 3129 Classifications: {'peptide': 401} Link IDs: {'CIS': 1, 'PTRANS': 16, 'TRANS': 383} Chain: "G" Number of atoms: 2974 Number of conformers: 1 Conformer: "" Number of residues, atoms: 372, 2974 Classifications: {'peptide': 372} Link IDs: {'PTRANS': 13, 'TRANS': 358} Chain breaks: 2 Chain: "H" Number of atoms: 700 Number of conformers: 1 Conformer: "" Number of residues, atoms: 35, 700 Classifications: {'DNA': 35} Link IDs: {'rna3p': 34} Chain: "I" Number of atoms: 735 Number of conformers: 1 Conformer: "" Number of residues, atoms: 35, 735 Classifications: {'DNA': 35} Link IDs: {'rna3p': 34} Chain: "D" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "A" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "G" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 4.74, per 1000 atoms: 0.22 Number of scatterers: 21743 At special positions: 0 Unit cell: (123.981, 162.129, 119.646, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 111 16.00 P 82 15.00 Mg 4 11.99 O 4145 8.00 N 3810 7.00 C 13591 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: 2.06 Conformation dependent library (CDL) restraints added in 1.0 seconds Enol-peptide restraints added in 715.3 nanoseconds 4956 Ramachandran restraints generated. 2478 Oldfield, 0 Emsley, 2478 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4840 Finding SS restraints... Secondary structure from input PDB file: 138 helices and 14 sheets defined 64.8% alpha, 7.0% beta 35 base pairs and 68 stacking pairs defined. Time for finding SS restraints: 2.99 Creating SS restraints... Processing helix chain 'B' and resid 280 through 285 Processing helix chain 'B' and resid 324 through 338 Processing helix chain 'B' and resid 339 through 349 removed outlier: 3.610A pdb=" N GLU B 349 " --> pdb=" O CYS B 345 " (cutoff:3.500A) Processing helix chain 'B' and resid 361 through 372 Processing helix chain 'B' and resid 389 through 401 Processing helix chain 'B' and resid 410 through 423 Processing helix chain 'B' and resid 444 through 456 removed outlier: 3.653A pdb=" N GLN B 448 " --> pdb=" O ASN B 444 " (cutoff:3.500A) Processing helix chain 'B' and resid 470 through 474 Processing helix chain 'B' and resid 476 through 483 Processing helix chain 'B' and resid 516 through 524 Processing helix chain 'B' and resid 527 through 544 Processing helix chain 'B' and resid 554 through 565 Processing helix chain 'B' and resid 570 through 584 removed outlier: 3.845A pdb=" N LEU B 574 " --> pdb=" O SER B 570 " (cutoff:3.500A) Processing helix chain 'B' and resid 604 through 615 Processing helix chain 'C' and resid 41 through 46 removed outlier: 3.615A pdb=" N VAL C 45 " --> pdb=" O GLY C 41 " (cutoff:3.500A) Processing helix chain 'C' and resid 47 through 89 removed outlier: 3.510A pdb=" N GLU C 51 " --> pdb=" O GLN C 47 " (cutoff:3.500A) removed outlier: 5.049A pdb=" N ARG C 74 " --> pdb=" O ARG C 70 " (cutoff:3.500A) removed outlier: 5.293A pdb=" N THR C 75 " --> pdb=" O SER C 71 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N ARG C 89 " --> pdb=" O GLY C 85 " (cutoff:3.500A) Processing helix chain 'C' and resid 106 through 109 Processing helix chain 'C' and resid 110 through 124 removed outlier: 3.574A pdb=" N GLN C 124 " --> pdb=" O ARG C 120 " (cutoff:3.500A) Processing helix chain 'C' and resid 133 through 137 removed outlier: 3.555A pdb=" N CYS C 137 " --> pdb=" O SER C 134 " (cutoff:3.500A) Processing helix chain 'C' and resid 139 through 159 removed outlier: 3.608A pdb=" N GLU C 159 " --> pdb=" O ASN C 155 " (cutoff:3.500A) Processing helix chain 'C' and resid 179 through 183 Processing helix chain 'C' and resid 184 through 196 Processing helix chain 'C' and resid 216 through 230 Processing helix chain 'C' and resid 245 through 253 removed outlier: 4.090A pdb=" N VAL C 249 " --> pdb=" O ALA C 245 " (cutoff:3.500A) Processing helix chain 'C' and resid 254 through 259 removed outlier: 3.608A pdb=" N SER C 259 " --> pdb=" O TYR C 255 " (cutoff:3.500A) Processing helix chain 'C' and resid 270 through 282 Processing helix chain 'C' and resid 293 through 307 Processing helix chain 'C' and resid 310 through 327 Processing helix chain 'C' and resid 328 through 335 removed outlier: 5.844A pdb=" N ALA C 331 " --> pdb=" O GLY C 328 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N CYS C 335 " --> pdb=" O PHE C 332 " (cutoff:3.500A) Processing helix chain 'C' and resid 337 through 348 Processing helix chain 'C' and resid 349 through 358 removed outlier: 3.989A pdb=" N MET C 353 " --> pdb=" O THR C 349 " (cutoff:3.500A) Processing helix chain 'C' and resid 361 through 368 removed outlier: 3.950A pdb=" N TYR C 365 " --> pdb=" O SER C 361 " (cutoff:3.500A) Processing helix chain 'C' and resid 371 through 380 removed outlier: 3.962A pdb=" N ILE C 375 " --> pdb=" O ASP C 371 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N ILE C 376 " --> pdb=" O CYS C 372 " (cutoff:3.500A) Processing helix chain 'C' and resid 383 through 415 Proline residue: C 390 - end of helix Processing helix chain 'C' and resid 425 through 436 removed outlier: 3.710A pdb=" N LEU C 429 " --> pdb=" O LEU C 425 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ARG C 436 " --> pdb=" O ASN C 432 " (cutoff:3.500A) Processing helix chain 'C' and resid 441 through 453 removed outlier: 3.524A pdb=" N LYS C 445 " --> pdb=" O THR C 441 " (cutoff:3.500A) Processing helix chain 'C' and resid 455 through 477 Processing helix chain 'C' and resid 484 through 508 Proline residue: C 493 - end of helix Processing helix chain 'C' and resid 563 through 581 removed outlier: 3.664A pdb=" N LYS C 567 " --> pdb=" O ARG C 563 " (cutoff:3.500A) removed outlier: 5.839A pdb=" N GLN C 578 " --> pdb=" O THR C 574 " (cutoff:3.500A) removed outlier: 5.459A pdb=" N ASP C 579 " --> pdb=" O GLN C 575 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N LEU C 581 " --> pdb=" O VAL C 577 " (cutoff:3.500A) Processing helix chain 'C' and resid 599 through 607 Processing helix chain 'C' and resid 609 through 620 Processing helix chain 'C' and resid 621 through 626 Processing helix chain 'C' and resid 643 through 654 removed outlier: 3.588A pdb=" N VAL C 647 " --> pdb=" O PRO C 643 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N VAL C 648 " --> pdb=" O ASP C 644 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N GLU C 654 " --> pdb=" O LYS C 650 " (cutoff:3.500A) Processing helix chain 'C' and resid 661 through 672 Processing helix chain 'C' and resid 688 through 703 removed outlier: 3.510A pdb=" N LEU C 703 " --> pdb=" O GLU C 699 " (cutoff:3.500A) Processing helix chain 'D' and resid 3 through 21 removed outlier: 3.936A pdb=" N LEU D 8 " --> pdb=" O ALA D 4 " (cutoff:3.500A) Processing helix chain 'D' and resid 29 through 47 removed outlier: 3.537A pdb=" N ARG D 33 " --> pdb=" O TYR D 29 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N SER D 34 " --> pdb=" O ALA D 30 " (cutoff:3.500A) Processing helix chain 'D' and resid 61 through 74 Processing helix chain 'D' and resid 75 through 77 No H-bonds generated for 'chain 'D' and resid 75 through 77' Processing helix chain 'D' and resid 95 through 107 Processing helix chain 'D' and resid 120 through 135 removed outlier: 3.640A pdb=" N GLY D 135 " --> pdb=" O CYS D 131 " (cutoff:3.500A) Processing helix chain 'D' and resid 148 through 153 removed outlier: 3.847A pdb=" N PHE D 152 " --> pdb=" O GLU D 148 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N CYS D 153 " --> pdb=" O PHE D 149 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 148 through 153' Processing helix chain 'D' and resid 155 through 157 No H-bonds generated for 'chain 'D' and resid 155 through 157' Processing helix chain 'D' and resid 158 through 169 removed outlier: 3.780A pdb=" N SER D 168 " --> pdb=" O LEU D 164 " (cutoff:3.500A) Processing helix chain 'D' and resid 185 through 189 removed outlier: 3.668A pdb=" N GLU D 188 " --> pdb=" O ASP D 185 " (cutoff:3.500A) Processing helix chain 'D' and resid 191 through 198 Processing helix chain 'D' and resid 211 through 222 Processing helix chain 'D' and resid 227 through 244 removed outlier: 3.949A pdb=" N ILE D 244 " --> pdb=" O ASN D 240 " (cutoff:3.500A) Processing helix chain 'D' and resid 250 through 254 removed outlier: 4.213A pdb=" N ARG D 253 " --> pdb=" O TYR D 250 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N ASN D 254 " --> pdb=" O PHE D 251 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 250 through 254' Processing helix chain 'D' and resid 264 through 280 Processing helix chain 'D' and resid 281 through 295 removed outlier: 3.658A pdb=" N ARG D 285 " --> pdb=" O THR D 281 " (cutoff:3.500A) Processing helix chain 'D' and resid 297 through 310 removed outlier: 3.645A pdb=" N LEU D 301 " --> pdb=" O SER D 297 " (cutoff:3.500A) Processing helix chain 'D' and resid 320 through 333 removed outlier: 3.570A pdb=" N GLY D 333 " --> pdb=" O SER D 329 " (cutoff:3.500A) Processing helix chain 'D' and resid 335 through 341 Processing helix chain 'D' and resid 344 through 361 Processing helix chain 'D' and resid 367 through 380 removed outlier: 3.787A pdb=" N PHE D 378 " --> pdb=" O ARG D 374 " (cutoff:3.500A) Processing helix chain 'D' and resid 389 through 403 removed outlier: 3.580A pdb=" N VAL D 393 " --> pdb=" O GLU D 389 " (cutoff:3.500A) Processing helix chain 'D' and resid 432 through 443 removed outlier: 3.612A pdb=" N ILE D 436 " --> pdb=" O THR D 432 " (cutoff:3.500A) Processing helix chain 'D' and resid 447 through 456 removed outlier: 3.830A pdb=" N GLN D 455 " --> pdb=" O ALA D 451 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N SER D 456 " --> pdb=" O GLN D 452 " (cutoff:3.500A) Processing helix chain 'E' and resid 2 through 12 Proline residue: E 10 - end of helix Processing helix chain 'E' and resid 15 through 27 Processing helix chain 'E' and resid 47 through 62 removed outlier: 3.555A pdb=" N THR E 51 " --> pdb=" O LYS E 47 " (cutoff:3.500A) Processing helix chain 'E' and resid 76 through 89 removed outlier: 3.818A pdb=" N MET E 80 " --> pdb=" O THR E 76 " (cutoff:3.500A) Processing helix chain 'E' and resid 92 through 96 removed outlier: 3.673A pdb=" N ALA E 95 " --> pdb=" O GLN E 92 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N LEU E 96 " --> pdb=" O GLY E 93 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 92 through 96' Processing helix chain 'E' and resid 100 through 110 removed outlier: 3.743A pdb=" N ARG E 110 " --> pdb=" O GLU E 106 " (cutoff:3.500A) Processing helix chain 'E' and resid 127 through 134 removed outlier: 3.918A pdb=" N ARG E 132 " --> pdb=" O GLU E 129 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N MET E 134 " --> pdb=" O LEU E 131 " (cutoff:3.500A) Processing helix chain 'E' and resid 138 through 143 Processing helix chain 'E' and resid 144 through 150 Processing helix chain 'E' and resid 162 through 166 Processing helix chain 'E' and resid 184 through 194 Processing helix chain 'E' and resid 195 through 206 removed outlier: 3.590A pdb=" N GLU E 205 " --> pdb=" O ASN E 201 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N GLN E 206 " --> pdb=" O GLN E 202 " (cutoff:3.500A) Processing helix chain 'E' and resid 212 through 220 removed outlier: 3.807A pdb=" N GLU E 219 " --> pdb=" O GLU E 215 " (cutoff:3.500A) removed outlier: 4.112A pdb=" N ALA E 220 " --> pdb=" O ILE E 216 " (cutoff:3.500A) Processing helix chain 'E' and resid 222 through 238 removed outlier: 3.977A pdb=" N VAL E 236 " --> pdb=" O LEU E 232 " (cutoff:3.500A) Processing helix chain 'E' and resid 243 through 259 removed outlier: 4.000A pdb=" N LYS E 253 " --> pdb=" O LEU E 249 " (cutoff:3.500A) Processing helix chain 'E' and resid 259 through 265 Processing helix chain 'E' and resid 275 through 288 Proline residue: E 282 - end of helix removed outlier: 3.987A pdb=" N THR E 288 " --> pdb=" O ARG E 284 " (cutoff:3.500A) Processing helix chain 'E' and resid 322 through 338 Processing helix chain 'E' and resid 342 through 348 removed outlier: 3.958A pdb=" N VAL E 348 " --> pdb=" O LYS E 344 " (cutoff:3.500A) Processing helix chain 'E' and resid 381 through 394 removed outlier: 4.433A pdb=" N GLU E 394 " --> pdb=" O TYR E 390 " (cutoff:3.500A) Processing helix chain 'E' and resid 400 through 413 removed outlier: 4.171A pdb=" N LEU E 404 " --> pdb=" O THR E 400 " (cutoff:3.500A) Processing helix chain 'E' and resid 437 through 449 removed outlier: 3.594A pdb=" N VAL E 441 " --> pdb=" O GLY E 437 " (cutoff:3.500A) Processing helix chain 'F' and resid 224 through 238 Processing helix chain 'A' and resid 520 through 529 Processing helix chain 'A' and resid 545 through 549 removed outlier: 3.571A pdb=" N SER A 548 " --> pdb=" O LYS A 545 " (cutoff:3.500A) Processing helix chain 'A' and resid 550 through 559 Processing helix chain 'A' and resid 571 through 589 Processing helix chain 'A' and resid 603 through 621 removed outlier: 3.616A pdb=" N THR A 607 " --> pdb=" O GLY A 603 " (cutoff:3.500A) Processing helix chain 'A' and resid 635 through 637 No H-bonds generated for 'chain 'A' and resid 635 through 637' Processing helix chain 'A' and resid 639 through 641 No H-bonds generated for 'chain 'A' and resid 639 through 641' Processing helix chain 'A' and resid 642 through 650 removed outlier: 3.504A pdb=" N GLN A 650 " --> pdb=" O GLN A 646 " (cutoff:3.500A) Processing helix chain 'A' and resid 657 through 670 Processing helix chain 'A' and resid 685 through 690 removed outlier: 3.980A pdb=" N LEU A 689 " --> pdb=" O GLU A 685 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N CYS A 690 " --> pdb=" O LEU A 686 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 685 through 690' Processing helix chain 'A' and resid 695 through 703 Processing helix chain 'A' and resid 704 through 706 No H-bonds generated for 'chain 'A' and resid 704 through 706' Processing helix chain 'A' and resid 721 through 726 removed outlier: 3.541A pdb=" N LEU A 726 " --> pdb=" O LEU A 722 " (cutoff:3.500A) Processing helix chain 'A' and resid 728 through 736 removed outlier: 3.576A pdb=" N GLY A 736 " --> pdb=" O THR A 732 " (cutoff:3.500A) Processing helix chain 'A' and resid 746 through 759 removed outlier: 3.781A pdb=" N VAL A 754 " --> pdb=" O LEU A 750 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N GLY A 759 " --> pdb=" O THR A 755 " (cutoff:3.500A) Processing helix chain 'A' and resid 765 through 777 removed outlier: 3.590A pdb=" N VAL A 769 " --> pdb=" O LYS A 765 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N GLN A 770 " --> pdb=" O GLY A 766 " (cutoff:3.500A) Processing helix chain 'A' and resid 782 through 800 removed outlier: 3.867A pdb=" N ALA A 786 " --> pdb=" O ASP A 782 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N ARG A 791 " --> pdb=" O LEU A 787 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N THR A 799 " --> pdb=" O GLU A 795 " (cutoff:3.500A) Processing helix chain 'A' and resid 806 through 818 removed outlier: 3.514A pdb=" N VAL A 810 " --> pdb=" O THR A 806 " (cutoff:3.500A) Processing helix chain 'A' and resid 822 through 828 Processing helix chain 'A' and resid 830 through 848 removed outlier: 3.531A pdb=" N ALA A 841 " --> pdb=" O LEU A 837 " (cutoff:3.500A) Processing helix chain 'A' and resid 854 through 869 Processing helix chain 'A' and resid 874 through 888 removed outlier: 3.527A pdb=" N GLU A 888 " --> pdb=" O LYS A 884 " (cutoff:3.500A) Processing helix chain 'A' and resid 909 through 918 removed outlier: 3.580A pdb=" N ILE A 913 " --> pdb=" O SER A 909 " (cutoff:3.500A) Processing helix chain 'G' and resid 250 through 260 removed outlier: 4.145A pdb=" N ASN G 260 " --> pdb=" O ARG G 256 " (cutoff:3.500A) Processing helix chain 'G' and resid 271 through 287 removed outlier: 3.507A pdb=" N SER G 287 " --> pdb=" O ASN G 283 " (cutoff:3.500A) Processing helix chain 'G' and resid 302 through 310 Processing helix chain 'G' and resid 313 through 319 Processing helix chain 'G' and resid 332 through 334 No H-bonds generated for 'chain 'G' and resid 332 through 334' Processing helix chain 'G' and resid 335 through 345 Processing helix chain 'G' and resid 352 through 366 removed outlier: 3.530A pdb=" N HIS G 356 " --> pdb=" O THR G 352 " (cutoff:3.500A) Processing helix chain 'G' and resid 378 through 382 removed outlier: 3.537A pdb=" N CYS G 382 " --> pdb=" O ASP G 379 " (cutoff:3.500A) Processing helix chain 'G' and resid 386 through 393 Processing helix chain 'G' and resid 394 through 398 Processing helix chain 'G' and resid 413 through 418 Processing helix chain 'G' and resid 419 through 425 removed outlier: 3.527A pdb=" N ARG G 425 " --> pdb=" O LEU G 422 " (cutoff:3.500A) Processing helix chain 'G' and resid 439 through 453 removed outlier: 3.503A pdb=" N ILE G 443 " --> pdb=" O SER G 439 " (cutoff:3.500A) Processing helix chain 'G' and resid 456 through 460 removed outlier: 3.584A pdb=" N VAL G 459 " --> pdb=" O VAL G 456 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N PHE G 460 " --> pdb=" O LEU G 457 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 456 through 460' Processing helix chain 'G' and resid 461 through 476 removed outlier: 3.566A pdb=" N LEU G 465 " --> pdb=" O PRO G 461 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N ALA G 470 " --> pdb=" O GLN G 466 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N ALA G 474 " --> pdb=" O ALA G 470 " (cutoff:3.500A) Processing helix chain 'G' and resid 478 through 498 removed outlier: 3.806A pdb=" N ALA G 482 " --> pdb=" O ASP G 478 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N VAL G 490 " --> pdb=" O GLY G 486 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N GLN G 495 " --> pdb=" O GLU G 491 " (cutoff:3.500A) Processing helix chain 'G' and resid 530 through 542 removed outlier: 3.519A pdb=" N VAL G 534 " --> pdb=" O GLN G 530 " (cutoff:3.500A) Processing helix chain 'G' and resid 557 through 574 Processing helix chain 'G' and resid 581 through 595 removed outlier: 3.613A pdb=" N VAL G 587 " --> pdb=" O ARG G 583 " (cutoff:3.500A) Processing helix chain 'G' and resid 601 through 614 removed outlier: 3.817A pdb=" N GLY G 607 " --> pdb=" O ALA G 603 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N THR G 614 " --> pdb=" O ASP G 610 " (cutoff:3.500A) Processing helix chain 'G' and resid 625 through 628 Processing helix chain 'G' and resid 636 through 645 removed outlier: 3.667A pdb=" N SER G 645 " --> pdb=" O HIS G 641 " (cutoff:3.500A) Processing helix chain 'G' and resid 646 through 655 removed outlier: 3.728A pdb=" N SER G 652 " --> pdb=" O GLN G 648 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N SER G 655 " --> pdb=" O ALA G 651 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 485 through 488 removed outlier: 6.196A pdb=" N ASN B 352 " --> pdb=" O SER B 486 " (cutoff:3.500A) removed outlier: 7.163A pdb=" N TRP B 488 " --> pdb=" O ASN B 352 " (cutoff:3.500A) removed outlier: 6.157A pdb=" N LEU B 354 " --> pdb=" O TRP B 488 " (cutoff:3.500A) removed outlier: 6.684A pdb=" N THR B 377 " --> pdb=" O PHE B 431 " (cutoff:3.500A) removed outlier: 7.785A pdb=" N ILE B 433 " --> pdb=" O THR B 377 " (cutoff:3.500A) removed outlier: 6.619A pdb=" N LEU B 379 " --> pdb=" O ILE B 433 " (cutoff:3.500A) removed outlier: 7.396A pdb=" N HIS B 435 " --> pdb=" O LEU B 379 " (cutoff:3.500A) removed outlier: 6.646A pdb=" N VAL B 381 " --> pdb=" O HIS B 435 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 588 through 590 Processing sheet with id=AA3, first strand: chain 'C' and resid 98 through 99 removed outlier: 6.188A pdb=" N MET C 128 " --> pdb=" O VAL C 206 " (cutoff:3.500A) removed outlier: 7.738A pdb=" N ILE C 208 " --> pdb=" O MET C 128 " (cutoff:3.500A) removed outlier: 6.586A pdb=" N CYS C 130 " --> pdb=" O ILE C 208 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 101 through 102 Processing sheet with id=AA5, first strand: chain 'C' and resid 291 through 292 removed outlier: 7.814A pdb=" N HIS C 291 " --> pdb=" O PHE C 596 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'C' and resid 658 through 659 removed outlier: 3.616A pdb=" N HIS C 715 " --> pdb=" O SER C 709 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 83 through 89 removed outlier: 6.692A pdb=" N VAL D 142 " --> pdb=" O CYS D 176 " (cutoff:3.500A) removed outlier: 7.721A pdb=" N LEU D 178 " --> pdb=" O VAL D 142 " (cutoff:3.500A) removed outlier: 6.662A pdb=" N PHE D 144 " --> pdb=" O LEU D 178 " (cutoff:3.500A) removed outlier: 7.664A pdb=" N VAL D 180 " --> pdb=" O PHE D 144 " (cutoff:3.500A) removed outlier: 6.388A pdb=" N LEU D 146 " --> pdb=" O VAL D 180 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N ASN D 50 " --> pdb=" O ILE D 175 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 406 through 408 Processing sheet with id=AA9, first strand: chain 'E' and resid 64 through 70 removed outlier: 6.672A pdb=" N PHE E 121 " --> pdb=" O CYS E 154 " (cutoff:3.500A) removed outlier: 7.722A pdb=" N ILE E 156 " --> pdb=" O PHE E 121 " (cutoff:3.500A) removed outlier: 6.134A pdb=" N ILE E 123 " --> pdb=" O ILE E 156 " (cutoff:3.500A) removed outlier: 7.514A pdb=" N LEU E 158 " --> pdb=" O ILE E 123 " (cutoff:3.500A) removed outlier: 6.622A pdb=" N VAL E 125 " --> pdb=" O LEU E 158 " (cutoff:3.500A) removed outlier: 6.727A pdb=" N ILE E 37 " --> pdb=" O LEU E 157 " (cutoff:3.500A) removed outlier: 8.222A pdb=" N SER E 159 " --> pdb=" O ILE E 37 " (cutoff:3.500A) removed outlier: 6.725A pdb=" N LEU E 39 " --> pdb=" O SER E 159 " (cutoff:3.500A) removed outlier: 7.235A pdb=" N ALA E 36 " --> pdb=" O VAL E 176 " (cutoff:3.500A) removed outlier: 8.109A pdb=" N LEU E 178 " --> pdb=" O ALA E 36 " (cutoff:3.500A) removed outlier: 6.276A pdb=" N TYR E 38 " --> pdb=" O LEU E 178 " (cutoff:3.500A) removed outlier: 7.412A pdb=" N LEU E 180 " --> pdb=" O TYR E 38 " (cutoff:3.500A) removed outlier: 6.573A pdb=" N PHE E 40 " --> pdb=" O LEU E 180 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'E' and resid 416 through 420 removed outlier: 7.032A pdb=" N ARG E 431 " --> pdb=" O VAL E 419 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 627 through 633 removed outlier: 6.489A pdb=" N GLY A 592 " --> pdb=" O VAL A 713 " (cutoff:3.500A) removed outlier: 8.193A pdb=" N THR A 715 " --> pdb=" O GLY A 592 " (cutoff:3.500A) removed outlier: 6.584A pdb=" N MET A 594 " --> pdb=" O THR A 715 " (cutoff:3.500A) removed outlier: 8.009A pdb=" N ALA A 717 " --> pdb=" O MET A 594 " (cutoff:3.500A) removed outlier: 6.389A pdb=" N VAL A 596 " --> pdb=" O ALA A 717 " (cutoff:3.500A) removed outlier: 8.818A pdb=" N LEU A 740 " --> pdb=" O CYS A 593 " (cutoff:3.500A) removed outlier: 6.503A pdb=" N TYR A 595 " --> pdb=" O LEU A 740 " (cutoff:3.500A) removed outlier: 7.908A pdb=" N PHE A 742 " --> pdb=" O TYR A 595 " (cutoff:3.500A) removed outlier: 6.765A pdb=" N SER A 597 " --> pdb=" O PHE A 742 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 852 through 853 Processing sheet with id=AB4, first strand: chain 'G' and resid 320 through 326 removed outlier: 6.795A pdb=" N LEU G 293 " --> pdb=" O GLY G 407 " (cutoff:3.500A) removed outlier: 8.170A pdb=" N ALA G 409 " --> pdb=" O LEU G 293 " (cutoff:3.500A) removed outlier: 6.457A pdb=" N VAL G 295 " --> pdb=" O ALA G 409 " (cutoff:3.500A) removed outlier: 6.474A pdb=" N TYR G 294 " --> pdb=" O MET G 433 " (cutoff:3.500A) removed outlier: 7.508A pdb=" N PHE G 435 " --> pdb=" O TYR G 294 " (cutoff:3.500A) removed outlier: 6.656A pdb=" N SER G 296 " --> pdb=" O PHE G 435 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'G' and resid 579 through 580 removed outlier: 4.453A pdb=" N ILE G 579 " --> pdb=" O VAL G 631 " (cutoff:3.500A) 1069 hydrogen bonds defined for protein. 3126 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 70 hydrogen bonds 140 hydrogen bond angles 0 basepair planarities 35 basepair parallelities 68 stacking parallelities Total time for adding SS restraints: 4.78 Time building geometry restraints manager: 2.76 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 5797 1.33 - 1.46: 4953 1.46 - 1.58: 11194 1.58 - 1.70: 157 1.70 - 1.83: 163 Bond restraints: 22264 Sorted by residual: bond pdb=" C4 ATP D 901 " pdb=" C5 ATP D 901 " ideal model delta sigma weight residual 1.388 1.468 -0.080 1.00e-02 1.00e+04 6.34e+01 bond pdb=" C4 ATP E 901 " pdb=" C5 ATP E 901 " ideal model delta sigma weight residual 1.388 1.466 -0.078 1.00e-02 1.00e+04 6.07e+01 bond pdb=" C4 ATP A1001 " pdb=" C5 ATP A1001 " ideal model delta sigma weight residual 1.388 1.466 -0.078 1.00e-02 1.00e+04 6.02e+01 bond pdb=" C4 ATP G 901 " pdb=" C5 ATP G 901 " ideal model delta sigma weight residual 1.388 1.465 -0.077 1.00e-02 1.00e+04 5.93e+01 bond pdb=" C5 ATP E 901 " pdb=" C6 ATP E 901 " ideal model delta sigma weight residual 1.409 1.475 -0.066 1.00e-02 1.00e+04 4.39e+01 ... (remaining 22259 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.86: 30182 3.86 - 7.72: 184 7.72 - 11.58: 27 11.58 - 15.44: 3 15.44 - 19.30: 4 Bond angle restraints: 30400 Sorted by residual: angle pdb=" PB ATP D 901 " pdb=" O3B ATP D 901 " pdb=" PG ATP D 901 " ideal model delta sigma weight residual 139.87 120.57 19.30 1.00e+00 1.00e+00 3.72e+02 angle pdb=" PB ATP G 901 " pdb=" O3B ATP G 901 " pdb=" PG ATP G 901 " ideal model delta sigma weight residual 139.87 121.67 18.20 1.00e+00 1.00e+00 3.31e+02 angle pdb=" PA ATP A1001 " pdb=" O3A ATP A1001 " pdb=" PB ATP A1001 " ideal model delta sigma weight residual 136.83 119.26 17.57 1.00e+00 1.00e+00 3.09e+02 angle pdb=" PB ATP E 901 " pdb=" O3B ATP E 901 " pdb=" PG ATP E 901 " ideal model delta sigma weight residual 139.87 124.37 15.50 1.00e+00 1.00e+00 2.40e+02 angle pdb=" PA ATP E 901 " pdb=" O3A ATP E 901 " pdb=" PB ATP E 901 " ideal model delta sigma weight residual 136.83 121.59 15.24 1.00e+00 1.00e+00 2.32e+02 ... (remaining 30395 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.97: 11482 17.97 - 35.94: 1379 35.94 - 53.91: 527 53.91 - 71.89: 102 71.89 - 89.86: 36 Dihedral angle restraints: 13526 sinusoidal: 6113 harmonic: 7413 Sorted by residual: dihedral pdb=" CA LEU G 259 " pdb=" C LEU G 259 " pdb=" N ASN G 260 " pdb=" CA ASN G 260 " ideal model delta harmonic sigma weight residual 180.00 149.83 30.17 0 5.00e+00 4.00e-02 3.64e+01 dihedral pdb=" CA MET E 134 " pdb=" C MET E 134 " pdb=" N ASP E 135 " pdb=" CA ASP E 135 " ideal model delta harmonic sigma weight residual -180.00 -150.35 -29.65 0 5.00e+00 4.00e-02 3.52e+01 dihedral pdb=" CA MET C 128 " pdb=" C MET C 128 " pdb=" N VAL C 129 " pdb=" CA VAL C 129 " ideal model delta harmonic sigma weight residual -180.00 -156.62 -23.38 0 5.00e+00 4.00e-02 2.19e+01 ... (remaining 13523 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.042: 2320 0.042 - 0.084: 876 0.084 - 0.127: 233 0.127 - 0.169: 63 0.169 - 0.211: 16 Chirality restraints: 3508 Sorted by residual: chirality pdb=" CB ILE C 590 " pdb=" CA ILE C 590 " pdb=" CG1 ILE C 590 " pdb=" CG2 ILE C 590 " both_signs ideal model delta sigma weight residual False 2.64 2.43 0.21 2.00e-01 2.50e+01 1.11e+00 chirality pdb=" CB VAL E 221 " pdb=" CA VAL E 221 " pdb=" CG1 VAL E 221 " pdb=" CG2 VAL E 221 " both_signs ideal model delta sigma weight residual False -2.63 -2.42 -0.20 2.00e-01 2.50e+01 1.04e+00 chirality pdb=" CB ILE C 5 " pdb=" CA ILE C 5 " pdb=" CG1 ILE C 5 " pdb=" CG2 ILE C 5 " both_signs ideal model delta sigma weight residual False 2.64 2.44 0.20 2.00e-01 2.50e+01 1.04e+00 ... (remaining 3505 not shown) Planarity restraints: 3607 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PHE A 872 " 0.059 5.00e-02 4.00e+02 8.90e-02 1.27e+01 pdb=" N PRO A 873 " -0.154 5.00e-02 4.00e+02 pdb=" CA PRO A 873 " 0.047 5.00e-02 4.00e+02 pdb=" CD PRO A 873 " 0.048 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA C 587 " -0.057 5.00e-02 4.00e+02 8.56e-02 1.17e+01 pdb=" N PRO C 588 " 0.148 5.00e-02 4.00e+02 pdb=" CA PRO C 588 " -0.045 5.00e-02 4.00e+02 pdb=" CD PRO C 588 " -0.046 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLU E 9 " -0.050 5.00e-02 4.00e+02 7.48e-02 8.96e+00 pdb=" N PRO E 10 " 0.129 5.00e-02 4.00e+02 pdb=" CA PRO E 10 " -0.037 5.00e-02 4.00e+02 pdb=" CD PRO E 10 " -0.042 5.00e-02 4.00e+02 ... (remaining 3604 not shown) Histogram of nonbonded interaction distances: 1.39 - 2.09: 7 2.09 - 2.80: 5303 2.80 - 3.50: 27585 3.50 - 4.20: 52196 4.20 - 4.90: 91105 Nonbonded interactions: 176196 Sorted by model distance: nonbonded pdb=" NH1 ARG C 711 " pdb=" C4' DA I 44 " model vdw 1.392 3.550 nonbonded pdb=" NH1 ARG C 711 " pdb=" O3' DA I 44 " model vdw 1.479 3.120 nonbonded pdb=" NH1 ARG C 711 " pdb=" C3' DA I 44 " model vdw 1.628 3.550 nonbonded pdb=" OG SER C 709 " pdb=" O HIS C 715 " model vdw 2.031 3.040 nonbonded pdb=" OG1 THR E 48 " pdb="MG MG E 902 " model vdw 2.068 2.170 ... (remaining 176191 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.720 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: 0.010 Extract box with map and model: 0.290 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 23.280 Find NCS groups from input model: 0.170 Set up NCS constraints: 0.060 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:1.630 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.240 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8527 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 : 0.006 0.080 22264 Z= 0.308 Angle : 0.938 19.298 30400 Z= 0.583 Chirality : 0.049 0.211 3508 Planarity : 0.007 0.089 3607 Dihedral : 18.330 89.857 8686 Min Nonbonded Distance : 1.392 Molprobity Statistics. All-atom Clashscore : 4.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer: Outliers : 0.18 % Allowed : 6.18 % Favored : 93.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.04 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.49 (0.13), residues: 2478 helix: -2.42 (0.09), residues: 1450 sheet: -2.18 (0.28), residues: 228 loop : -1.65 (0.18), residues: 800 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG G 322 TYR 0.021 0.002 TYR E 323 PHE 0.019 0.002 PHE G 447 TRP 0.020 0.002 TRP C 664 HIS 0.009 0.001 HIS C 652 Details of bonding type rmsd covalent geometry : bond 0.00555 (22264) covalent geometry : angle 0.93754 (30400) hydrogen bonds : bond 0.15436 ( 1139) hydrogen bonds : angle 6.55005 ( 3266) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4956 Ramachandran restraints generated. 2478 Oldfield, 0 Emsley, 2478 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4956 Ramachandran restraints generated. 2478 Oldfield, 0 Emsley, 2478 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 310 residues out of total 2219 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 306 time to evaluate : 0.651 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 540 TYR cc_start: 0.7672 (t80) cc_final: 0.7307 (t80) REVERT: B 562 CYS cc_start: 0.8065 (m) cc_final: 0.7778 (m) REVERT: B 583 ASP cc_start: 0.8326 (t70) cc_final: 0.7845 (m-30) REVERT: B 584 HIS cc_start: 0.8122 (m90) cc_final: 0.7880 (m170) REVERT: C 398 LEU cc_start: 0.8588 (tp) cc_final: 0.8335 (tt) REVERT: C 435 ASN cc_start: 0.9079 (m-40) cc_final: 0.8838 (t0) REVERT: C 450 MET cc_start: 0.8680 (mtp) cc_final: 0.7817 (mtp) REVERT: C 451 LEU cc_start: 0.9276 (mt) cc_final: 0.8724 (pp) REVERT: C 457 ASP cc_start: 0.8536 (p0) cc_final: 0.8297 (p0) REVERT: C 699 GLU cc_start: 0.8014 (tt0) cc_final: 0.7445 (mt-10) REVERT: D 185 ASP cc_start: 0.8212 (p0) cc_final: 0.8007 (p0) REVERT: D 347 GLU cc_start: 0.9057 (mp0) cc_final: 0.8578 (mp0) REVERT: D 389 GLU cc_start: 0.8348 (mm-30) cc_final: 0.8001 (mt-10) REVERT: D 426 MET cc_start: 0.8648 (mmm) cc_final: 0.8292 (mmm) REVERT: E 414 ASN cc_start: 0.8993 (t0) cc_final: 0.8635 (p0) REVERT: E 417 SER cc_start: 0.9075 (t) cc_final: 0.8689 (p) REVERT: F 224 ASP cc_start: 0.8881 (t70) cc_final: 0.8235 (p0) REVERT: F 226 GLU cc_start: 0.9235 (mm-30) cc_final: 0.8875 (mp0) REVERT: F 231 ARG cc_start: 0.9049 (ttp80) cc_final: 0.8734 (ttp80) REVERT: F 232 MET cc_start: 0.9345 (tpt) cc_final: 0.9067 (tpp) REVERT: A 618 MET cc_start: 0.8498 (mtp) cc_final: 0.8135 (mtt) REVERT: G 345 GLN cc_start: 0.8993 (mp10) cc_final: 0.8744 (mp10) REVERT: G 570 MET cc_start: 0.7777 (mtp) cc_final: 0.7518 (mtp) outliers start: 4 outliers final: 1 residues processed: 310 average time/residue: 0.1946 time to fit residues: 86.8486 Evaluate side-chains 168 residues out of total 2219 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 167 time to evaluate : 0.781 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 474 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 197 optimal weight: 6.9990 chunk 215 optimal weight: 1.9990 chunk 20 optimal weight: 9.9990 chunk 132 optimal weight: 3.9990 chunk 248 optimal weight: 6.9990 chunk 207 optimal weight: 0.9980 chunk 155 optimal weight: 0.8980 chunk 244 optimal weight: 9.9990 chunk 183 optimal weight: 0.9980 chunk 111 optimal weight: 9.9990 chunk 71 optimal weight: 7.9990 overall best weight: 1.7784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 285 HIS B 325 HIS B 366 GLN B 429 HIS B 544 ASN B 609 GLN B 615 GLN C 46 GLN C 133 GLN C 194 ASN C 370 ASN C 449 GLN ** C 580 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 619 ASN C 666 GLN D 202 GLN ** D 386 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 68 HIS ** A 553 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 828 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 838 GLN G 356 HIS G 410 ASN G 530 GLN G 573 ASN G 585 HIS Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3615 r_free = 0.3615 target = 0.088068 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3134 r_free = 0.3134 target = 0.063310 restraints weight = 57280.371| |-----------------------------------------------------------------------------| r_work (start): 0.3070 rms_B_bonded: 3.20 r_work: 0.2938 rms_B_bonded: 3.81 restraints_weight: 0.5000 r_work (final): 0.2938 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8764 moved from start: 0.1783 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 22264 Z= 0.152 Angle : 0.571 9.778 30400 Z= 0.309 Chirality : 0.039 0.132 3508 Planarity : 0.005 0.063 3607 Dihedral : 17.518 86.570 3716 Min Nonbonded Distance : 1.924 Molprobity Statistics. All-atom Clashscore : 6.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.18 % Favored : 97.82 % Rotamer: Outliers : 1.08 % Allowed : 9.69 % Favored : 89.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.04 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.89 (0.16), residues: 2478 helix: -0.09 (0.12), residues: 1467 sheet: -1.75 (0.30), residues: 247 loop : -0.85 (0.21), residues: 764 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 70 TYR 0.018 0.001 TYR C 255 PHE 0.020 0.001 PHE C 459 TRP 0.018 0.001 TRP C 664 HIS 0.004 0.001 HIS D 138 Details of bonding type rmsd covalent geometry : bond 0.00341 (22264) covalent geometry : angle 0.57060 (30400) hydrogen bonds : bond 0.03967 ( 1139) hydrogen bonds : angle 4.28454 ( 3266) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4956 Ramachandran restraints generated. 2478 Oldfield, 0 Emsley, 2478 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4956 Ramachandran restraints generated. 2478 Oldfield, 0 Emsley, 2478 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 2219 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 182 time to evaluate : 0.578 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: B 391 LYS cc_start: 0.9073 (tptt) cc_final: 0.8839 (tptt) REVERT: B 421 GLU cc_start: 0.8036 (mm-30) cc_final: 0.7619 (mm-30) REVERT: B 540 TYR cc_start: 0.7651 (t80) cc_final: 0.7333 (t80) REVERT: B 564 GLU cc_start: 0.9014 (mm-30) cc_final: 0.8791 (mm-30) REVERT: B 583 ASP cc_start: 0.8291 (t70) cc_final: 0.7796 (m-30) REVERT: B 584 HIS cc_start: 0.8037 (m90) cc_final: 0.7607 (m-70) REVERT: C 398 LEU cc_start: 0.8526 (tp) cc_final: 0.8205 (tt) REVERT: C 435 ASN cc_start: 0.9139 (m-40) cc_final: 0.8836 (t0) REVERT: C 457 ASP cc_start: 0.8693 (p0) cc_final: 0.8479 (p0) REVERT: C 699 GLU cc_start: 0.8217 (tt0) cc_final: 0.7340 (mt-10) REVERT: D 185 ASP cc_start: 0.8488 (p0) cc_final: 0.8061 (p0) REVERT: D 347 GLU cc_start: 0.9258 (mp0) cc_final: 0.9026 (mp0) REVERT: D 389 GLU cc_start: 0.8922 (mm-30) cc_final: 0.8580 (mt-10) REVERT: D 426 MET cc_start: 0.9047 (mmm) cc_final: 0.8678 (mmm) REVERT: E 254 CYS cc_start: 0.8646 (m) cc_final: 0.8078 (t) REVERT: E 412 HIS cc_start: 0.8629 (OUTLIER) cc_final: 0.8424 (m-70) REVERT: E 417 SER cc_start: 0.8926 (t) cc_final: 0.8402 (p) REVERT: E 455 TYR cc_start: 0.8980 (m-80) cc_final: 0.8638 (m-80) REVERT: F 227 ILE cc_start: 0.8475 (OUTLIER) cc_final: 0.8020 (pt) REVERT: F 232 MET cc_start: 0.9346 (tpt) cc_final: 0.9135 (mmm) REVERT: G 345 GLN cc_start: 0.9201 (mp10) cc_final: 0.8891 (mp10) REVERT: G 385 ARG cc_start: 0.8453 (mmp80) cc_final: 0.8243 (mmp80) outliers start: 24 outliers final: 12 residues processed: 198 average time/residue: 0.1383 time to fit residues: 43.1308 Evaluate side-chains 171 residues out of total 2219 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 157 time to evaluate : 0.706 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 277 VAL Chi-restraints excluded: chain B residue 388 LEU Chi-restraints excluded: chain B residue 406 ILE Chi-restraints excluded: chain B residue 474 LEU Chi-restraints excluded: chain C residue 98 THR Chi-restraints excluded: chain C residue 242 VAL Chi-restraints excluded: chain C residue 410 LEU Chi-restraints excluded: chain C residue 417 LEU Chi-restraints excluded: chain D residue 100 LEU Chi-restraints excluded: chain E residue 75 TYR Chi-restraints excluded: chain E residue 412 HIS Chi-restraints excluded: chain F residue 227 ILE Chi-restraints excluded: chain A residue 804 CYS Chi-restraints excluded: chain G residue 464 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 148 optimal weight: 2.9990 chunk 88 optimal weight: 9.9990 chunk 141 optimal weight: 0.7980 chunk 92 optimal weight: 0.8980 chunk 160 optimal weight: 0.9990 chunk 177 optimal weight: 0.5980 chunk 252 optimal weight: 10.0000 chunk 55 optimal weight: 2.9990 chunk 110 optimal weight: 0.9990 chunk 156 optimal weight: 2.9990 chunk 158 optimal weight: 3.9990 overall best weight: 0.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 113 GLN ** C 580 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 386 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 137 ASN E 150 ASN A 553 GLN A 622 ASN ** A 828 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3633 r_free = 0.3633 target = 0.089390 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3145 r_free = 0.3145 target = 0.064037 restraints weight = 57221.753| |-----------------------------------------------------------------------------| r_work (start): 0.3128 rms_B_bonded: 3.27 r_work: 0.3002 rms_B_bonded: 3.83 restraints_weight: 0.5000 r_work (final): 0.3002 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8758 moved from start: 0.2219 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 22264 Z= 0.109 Angle : 0.513 7.937 30400 Z= 0.273 Chirality : 0.037 0.128 3508 Planarity : 0.004 0.054 3607 Dihedral : 17.445 80.202 3716 Min Nonbonded Distance : 1.957 Molprobity Statistics. All-atom Clashscore : 5.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer: Outliers : 1.35 % Allowed : 10.73 % Favored : 87.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.04 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.46 (0.17), residues: 2478 helix: 1.05 (0.14), residues: 1467 sheet: -1.17 (0.32), residues: 238 loop : -0.49 (0.22), residues: 773 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 419 TYR 0.016 0.001 TYR C 384 PHE 0.017 0.001 PHE C 459 TRP 0.015 0.001 TRP C 191 HIS 0.004 0.001 HIS E 278 Details of bonding type rmsd covalent geometry : bond 0.00235 (22264) covalent geometry : angle 0.51271 (30400) hydrogen bonds : bond 0.03244 ( 1139) hydrogen bonds : angle 3.88447 ( 3266) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4956 Ramachandran restraints generated. 2478 Oldfield, 0 Emsley, 2478 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4956 Ramachandran restraints generated. 2478 Oldfield, 0 Emsley, 2478 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 205 residues out of total 2219 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 175 time to evaluate : 0.893 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: B 333 MET cc_start: 0.9312 (tpp) cc_final: 0.9091 (mmm) REVERT: B 391 LYS cc_start: 0.9149 (tptt) cc_final: 0.8902 (tptt) REVERT: B 421 GLU cc_start: 0.8098 (mm-30) cc_final: 0.7654 (mm-30) REVERT: B 519 MET cc_start: 0.8088 (tmm) cc_final: 0.7819 (tmm) REVERT: B 540 TYR cc_start: 0.7511 (t80) cc_final: 0.7277 (t80) REVERT: B 562 CYS cc_start: 0.7555 (m) cc_final: 0.7341 (m) REVERT: B 584 HIS cc_start: 0.7953 (m90) cc_final: 0.7326 (m-70) REVERT: C 384 TYR cc_start: 0.8414 (t80) cc_final: 0.8193 (t80) REVERT: C 435 ASN cc_start: 0.9105 (m-40) cc_final: 0.8815 (t0) REVERT: C 457 ASP cc_start: 0.8467 (p0) cc_final: 0.8265 (p0) REVERT: C 699 GLU cc_start: 0.8197 (tt0) cc_final: 0.7418 (mt-10) REVERT: D 185 ASP cc_start: 0.8452 (p0) cc_final: 0.8125 (p0) REVERT: D 426 MET cc_start: 0.9023 (mmm) cc_final: 0.8747 (mmm) REVERT: E 254 CYS cc_start: 0.8582 (m) cc_final: 0.8162 (t) REVERT: E 412 HIS cc_start: 0.8545 (OUTLIER) cc_final: 0.8337 (m-70) REVERT: E 417 SER cc_start: 0.8990 (t) cc_final: 0.8498 (p) REVERT: E 455 TYR cc_start: 0.8997 (m-80) cc_final: 0.8714 (m-80) REVERT: A 775 LYS cc_start: 0.9207 (mttt) cc_final: 0.8947 (mptt) REVERT: G 345 GLN cc_start: 0.9141 (mp10) cc_final: 0.8880 (mp10) outliers start: 30 outliers final: 18 residues processed: 194 average time/residue: 0.1496 time to fit residues: 45.6732 Evaluate side-chains 179 residues out of total 2219 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 160 time to evaluate : 0.770 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 277 VAL Chi-restraints excluded: chain B residue 388 LEU Chi-restraints excluded: chain B residue 406 ILE Chi-restraints excluded: chain C residue 98 THR Chi-restraints excluded: chain C residue 242 VAL Chi-restraints excluded: chain C residue 410 LEU Chi-restraints excluded: chain C residue 429 LEU Chi-restraints excluded: chain C residue 565 LEU Chi-restraints excluded: chain C residue 652 HIS Chi-restraints excluded: chain D residue 100 LEU Chi-restraints excluded: chain E residue 75 TYR Chi-restraints excluded: chain E residue 217 CYS Chi-restraints excluded: chain E residue 412 HIS Chi-restraints excluded: chain A residue 738 THR Chi-restraints excluded: chain G residue 403 ILE Chi-restraints excluded: chain G residue 413 ASP Chi-restraints excluded: chain G residue 456 VAL Chi-restraints excluded: chain G residue 464 THR Chi-restraints excluded: chain G residue 571 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 219 optimal weight: 5.9990 chunk 77 optimal weight: 3.9990 chunk 238 optimal weight: 7.9990 chunk 46 optimal weight: 5.9990 chunk 80 optimal weight: 2.9990 chunk 50 optimal weight: 2.9990 chunk 237 optimal weight: 0.9980 chunk 11 optimal weight: 2.9990 chunk 69 optimal weight: 4.9990 chunk 252 optimal weight: 10.0000 chunk 183 optimal weight: 7.9990 overall best weight: 2.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 580 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 82 ASN ** D 386 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 622 ASN ** A 828 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3581 r_free = 0.3581 target = 0.086056 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3082 r_free = 0.3082 target = 0.060910 restraints weight = 57628.071| |-----------------------------------------------------------------------------| r_work (start): 0.3029 rms_B_bonded: 3.19 r_work: 0.2895 rms_B_bonded: 3.79 restraints_weight: 0.5000 r_work (final): 0.2895 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8816 moved from start: 0.2464 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 22264 Z= 0.193 Angle : 0.562 12.138 30400 Z= 0.294 Chirality : 0.039 0.150 3508 Planarity : 0.004 0.051 3607 Dihedral : 17.323 78.085 3714 Min Nonbonded Distance : 1.861 Molprobity Statistics. All-atom Clashscore : 6.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer: Outliers : 1.44 % Allowed : 11.77 % Favored : 86.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.04 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.05 (0.17), residues: 2478 helix: 1.57 (0.14), residues: 1472 sheet: -1.08 (0.33), residues: 247 loop : -0.28 (0.23), residues: 759 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG F 231 TYR 0.026 0.001 TYR C 72 PHE 0.013 0.001 PHE C 459 TRP 0.017 0.001 TRP C 664 HIS 0.006 0.001 HIS C 230 Details of bonding type rmsd covalent geometry : bond 0.00442 (22264) covalent geometry : angle 0.56208 (30400) hydrogen bonds : bond 0.03676 ( 1139) hydrogen bonds : angle 3.84783 ( 3266) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4956 Ramachandran restraints generated. 2478 Oldfield, 0 Emsley, 2478 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4956 Ramachandran restraints generated. 2478 Oldfield, 0 Emsley, 2478 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 2219 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 156 time to evaluate : 0.883 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 391 LYS cc_start: 0.9132 (tptt) cc_final: 0.8830 (tptt) REVERT: B 421 GLU cc_start: 0.8320 (mm-30) cc_final: 0.7880 (mm-30) REVERT: B 540 TYR cc_start: 0.7489 (t80) cc_final: 0.7115 (t80) REVERT: B 584 HIS cc_start: 0.8018 (m90) cc_final: 0.7347 (m-70) REVERT: C 457 ASP cc_start: 0.8425 (p0) cc_final: 0.8170 (p0) REVERT: D 253 ARG cc_start: 0.8862 (tpm170) cc_final: 0.8570 (tpt-90) REVERT: D 426 MET cc_start: 0.8942 (mmm) cc_final: 0.8506 (mmm) REVERT: D 440 MET cc_start: 0.8873 (mmm) cc_final: 0.8582 (mmm) REVERT: E 254 CYS cc_start: 0.8603 (m) cc_final: 0.8114 (t) REVERT: E 417 SER cc_start: 0.8969 (t) cc_final: 0.8433 (p) REVERT: G 345 GLN cc_start: 0.9164 (mp10) cc_final: 0.8828 (mp10) REVERT: G 385 ARG cc_start: 0.8501 (mtp85) cc_final: 0.8257 (mtp85) outliers start: 32 outliers final: 18 residues processed: 181 average time/residue: 0.1577 time to fit residues: 44.2260 Evaluate side-chains 161 residues out of total 2219 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 143 time to evaluate : 0.835 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 277 VAL Chi-restraints excluded: chain B residue 388 LEU Chi-restraints excluded: chain B residue 503 GLU Chi-restraints excluded: chain C residue 98 THR Chi-restraints excluded: chain C residue 242 VAL Chi-restraints excluded: chain C residue 410 LEU Chi-restraints excluded: chain C residue 429 LEU Chi-restraints excluded: chain C residue 565 LEU Chi-restraints excluded: chain C residue 652 HIS Chi-restraints excluded: chain D residue 100 LEU Chi-restraints excluded: chain D residue 227 THR Chi-restraints excluded: chain E residue 75 TYR Chi-restraints excluded: chain E residue 203 LEU Chi-restraints excluded: chain A residue 679 THR Chi-restraints excluded: chain A residue 804 CYS Chi-restraints excluded: chain A residue 810 VAL Chi-restraints excluded: chain G residue 413 ASP Chi-restraints excluded: chain G residue 464 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 80 optimal weight: 6.9990 chunk 166 optimal weight: 5.9990 chunk 160 optimal weight: 5.9990 chunk 51 optimal weight: 5.9990 chunk 222 optimal weight: 0.9990 chunk 32 optimal weight: 1.9990 chunk 254 optimal weight: 10.0000 chunk 243 optimal weight: 7.9990 chunk 101 optimal weight: 5.9990 chunk 100 optimal weight: 6.9990 chunk 136 optimal weight: 0.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 122 HIS ** C 580 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 386 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 622 ASN ** A 828 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3548 r_free = 0.3548 target = 0.084690 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3073 r_free = 0.3073 target = 0.060049 restraints weight = 57113.100| |-----------------------------------------------------------------------------| r_work (start): 0.3023 rms_B_bonded: 3.07 r_work: 0.2889 rms_B_bonded: 3.70 restraints_weight: 0.5000 r_work (final): 0.2889 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8838 moved from start: 0.2664 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 22264 Z= 0.208 Angle : 0.577 11.866 30400 Z= 0.299 Chirality : 0.039 0.149 3508 Planarity : 0.004 0.051 3607 Dihedral : 17.285 80.412 3714 Min Nonbonded Distance : 1.861 Molprobity Statistics. All-atom Clashscore : 6.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 1.58 % Allowed : 12.67 % Favored : 85.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.04 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.32 (0.18), residues: 2478 helix: 1.76 (0.14), residues: 1475 sheet: -0.96 (0.34), residues: 245 loop : -0.13 (0.24), residues: 758 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG C 419 TYR 0.015 0.001 TYR C 72 PHE 0.019 0.001 PHE B 611 TRP 0.017 0.001 TRP C 664 HIS 0.006 0.001 HIS C 230 Details of bonding type rmsd covalent geometry : bond 0.00475 (22264) covalent geometry : angle 0.57732 (30400) hydrogen bonds : bond 0.03658 ( 1139) hydrogen bonds : angle 3.85311 ( 3266) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4956 Ramachandran restraints generated. 2478 Oldfield, 0 Emsley, 2478 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4956 Ramachandran restraints generated. 2478 Oldfield, 0 Emsley, 2478 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 2219 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 149 time to evaluate : 0.860 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 333 MET cc_start: 0.9331 (tpp) cc_final: 0.9094 (mmm) REVERT: B 391 LYS cc_start: 0.9068 (tptt) cc_final: 0.8385 (tptt) REVERT: B 395 ASP cc_start: 0.8772 (m-30) cc_final: 0.7724 (m-30) REVERT: B 421 GLU cc_start: 0.8389 (mm-30) cc_final: 0.7990 (mm-30) REVERT: B 540 TYR cc_start: 0.7726 (t80) cc_final: 0.7331 (t80) REVERT: B 584 HIS cc_start: 0.8067 (m90) cc_final: 0.7385 (m-70) REVERT: C 323 MET cc_start: 0.9134 (ttp) cc_final: 0.8933 (ttp) REVERT: C 457 ASP cc_start: 0.8526 (p0) cc_final: 0.8263 (p0) REVERT: D 426 MET cc_start: 0.8951 (mmm) cc_final: 0.8443 (mmm) REVERT: E 254 CYS cc_start: 0.8598 (m) cc_final: 0.8138 (t) REVERT: E 417 SER cc_start: 0.8983 (t) cc_final: 0.8453 (p) REVERT: G 345 GLN cc_start: 0.9149 (mp10) cc_final: 0.8821 (mp10) outliers start: 35 outliers final: 24 residues processed: 177 average time/residue: 0.1415 time to fit residues: 40.5416 Evaluate side-chains 167 residues out of total 2219 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 143 time to evaluate : 0.590 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 277 VAL Chi-restraints excluded: chain B residue 388 LEU Chi-restraints excluded: chain B residue 393 MET Chi-restraints excluded: chain C residue 5 ILE Chi-restraints excluded: chain C residue 98 THR Chi-restraints excluded: chain C residue 242 VAL Chi-restraints excluded: chain C residue 410 LEU Chi-restraints excluded: chain C residue 429 LEU Chi-restraints excluded: chain C residue 441 THR Chi-restraints excluded: chain C residue 565 LEU Chi-restraints excluded: chain C residue 652 HIS Chi-restraints excluded: chain C residue 658 MET Chi-restraints excluded: chain D residue 100 LEU Chi-restraints excluded: chain D residue 227 THR Chi-restraints excluded: chain E residue 135 ASP Chi-restraints excluded: chain E residue 203 LEU Chi-restraints excluded: chain E residue 217 CYS Chi-restraints excluded: chain E residue 329 LEU Chi-restraints excluded: chain E residue 419 VAL Chi-restraints excluded: chain A residue 679 THR Chi-restraints excluded: chain A residue 804 CYS Chi-restraints excluded: chain A residue 810 VAL Chi-restraints excluded: chain G residue 413 ASP Chi-restraints excluded: chain G residue 464 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 194 optimal weight: 0.8980 chunk 21 optimal weight: 0.9990 chunk 58 optimal weight: 6.9990 chunk 234 optimal weight: 2.9990 chunk 110 optimal weight: 0.7980 chunk 193 optimal weight: 2.9990 chunk 242 optimal weight: 0.4980 chunk 145 optimal weight: 0.8980 chunk 180 optimal weight: 2.9990 chunk 178 optimal weight: 4.9990 chunk 62 optimal weight: 5.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 348 ASN B 610 GLN ** C 580 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 386 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 622 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3613 r_free = 0.3613 target = 0.087467 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3138 r_free = 0.3138 target = 0.063095 restraints weight = 56939.918| |-----------------------------------------------------------------------------| r_work (start): 0.3103 rms_B_bonded: 3.13 r_work: 0.2977 rms_B_bonded: 3.73 restraints_weight: 0.5000 r_work (final): 0.2977 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8787 moved from start: 0.2819 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 22264 Z= 0.107 Angle : 0.517 12.605 30400 Z= 0.269 Chirality : 0.037 0.132 3508 Planarity : 0.003 0.048 3607 Dihedral : 17.104 82.590 3714 Min Nonbonded Distance : 1.974 Molprobity Statistics. All-atom Clashscore : 5.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer: Outliers : 1.22 % Allowed : 13.84 % Favored : 84.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.04 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.59 (0.18), residues: 2478 helix: 1.94 (0.14), residues: 1481 sheet: -0.53 (0.34), residues: 225 loop : -0.10 (0.23), residues: 772 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG D 253 TYR 0.017 0.001 TYR G 588 PHE 0.013 0.001 PHE B 611 TRP 0.015 0.001 TRP C 191 HIS 0.005 0.000 HIS G 284 Details of bonding type rmsd covalent geometry : bond 0.00232 (22264) covalent geometry : angle 0.51686 (30400) hydrogen bonds : bond 0.02976 ( 1139) hydrogen bonds : angle 3.63454 ( 3266) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4956 Ramachandran restraints generated. 2478 Oldfield, 0 Emsley, 2478 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4956 Ramachandran restraints generated. 2478 Oldfield, 0 Emsley, 2478 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 2219 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 163 time to evaluate : 0.669 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 333 MET cc_start: 0.9354 (tpp) cc_final: 0.9120 (mmm) REVERT: B 421 GLU cc_start: 0.8306 (mm-30) cc_final: 0.7917 (mm-30) REVERT: B 503 GLU cc_start: 0.8059 (OUTLIER) cc_final: 0.7828 (pm20) REVERT: B 540 TYR cc_start: 0.7704 (t80) cc_final: 0.7350 (t80) REVERT: B 584 HIS cc_start: 0.8041 (m90) cc_final: 0.7348 (m-70) REVERT: C 185 MET cc_start: 0.8667 (mmm) cc_final: 0.8459 (mmm) REVERT: C 446 GLU cc_start: 0.8701 (mm-30) cc_final: 0.8378 (tp30) REVERT: C 457 ASP cc_start: 0.8507 (p0) cc_final: 0.8269 (p0) REVERT: C 699 GLU cc_start: 0.7897 (mm-30) cc_final: 0.7591 (mm-30) REVERT: D 253 ARG cc_start: 0.8677 (tpt90) cc_final: 0.7947 (tpt-90) REVERT: D 426 MET cc_start: 0.8921 (mmm) cc_final: 0.8468 (mmm) REVERT: E 254 CYS cc_start: 0.8471 (m) cc_final: 0.8114 (t) REVERT: E 417 SER cc_start: 0.8949 (t) cc_final: 0.8490 (p) outliers start: 27 outliers final: 17 residues processed: 181 average time/residue: 0.1456 time to fit residues: 42.3001 Evaluate side-chains 166 residues out of total 2219 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 148 time to evaluate : 0.669 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 277 VAL Chi-restraints excluded: chain B residue 388 LEU Chi-restraints excluded: chain B residue 503 GLU Chi-restraints excluded: chain C residue 98 THR Chi-restraints excluded: chain C residue 242 VAL Chi-restraints excluded: chain C residue 410 LEU Chi-restraints excluded: chain C residue 429 LEU Chi-restraints excluded: chain C residue 652 HIS Chi-restraints excluded: chain C residue 658 MET Chi-restraints excluded: chain D residue 100 LEU Chi-restraints excluded: chain D residue 227 THR Chi-restraints excluded: chain D residue 351 ILE Chi-restraints excluded: chain E residue 75 TYR Chi-restraints excluded: chain E residue 203 LEU Chi-restraints excluded: chain A residue 679 THR Chi-restraints excluded: chain A residue 738 THR Chi-restraints excluded: chain A residue 810 VAL Chi-restraints excluded: chain G residue 464 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 87 optimal weight: 8.9990 chunk 22 optimal weight: 9.9990 chunk 132 optimal weight: 4.9990 chunk 249 optimal weight: 5.9990 chunk 203 optimal weight: 0.5980 chunk 88 optimal weight: 5.9990 chunk 69 optimal weight: 10.0000 chunk 75 optimal weight: 4.9990 chunk 244 optimal weight: 0.9990 chunk 139 optimal weight: 0.8980 chunk 8 optimal weight: 7.9990 overall best weight: 2.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 580 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 386 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 622 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3559 r_free = 0.3559 target = 0.085032 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3091 r_free = 0.3091 target = 0.060633 restraints weight = 57215.522| |-----------------------------------------------------------------------------| r_work (start): 0.3041 rms_B_bonded: 3.08 r_work: 0.2910 rms_B_bonded: 3.69 restraints_weight: 0.5000 r_work (final): 0.2910 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8822 moved from start: 0.2897 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 22264 Z= 0.174 Angle : 0.567 12.773 30400 Z= 0.290 Chirality : 0.039 0.167 3508 Planarity : 0.003 0.047 3607 Dihedral : 17.078 82.840 3714 Min Nonbonded Distance : 1.869 Molprobity Statistics. All-atom Clashscore : 6.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer: Outliers : 1.35 % Allowed : 13.93 % Favored : 84.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.04 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.69 (0.18), residues: 2478 helix: 2.01 (0.14), residues: 1474 sheet: -0.45 (0.35), residues: 226 loop : -0.04 (0.24), residues: 778 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG F 231 TYR 0.039 0.001 TYR C 72 PHE 0.011 0.001 PHE B 611 TRP 0.028 0.002 TRP E 276 HIS 0.007 0.001 HIS C 230 Details of bonding type rmsd covalent geometry : bond 0.00398 (22264) covalent geometry : angle 0.56670 (30400) hydrogen bonds : bond 0.03448 ( 1139) hydrogen bonds : angle 3.75156 ( 3266) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4956 Ramachandran restraints generated. 2478 Oldfield, 0 Emsley, 2478 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4956 Ramachandran restraints generated. 2478 Oldfield, 0 Emsley, 2478 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 2219 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 145 time to evaluate : 0.868 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 333 MET cc_start: 0.9333 (tpp) cc_final: 0.9093 (mmm) REVERT: B 391 LYS cc_start: 0.9069 (tptt) cc_final: 0.8650 (tptt) REVERT: B 395 ASP cc_start: 0.8733 (m-30) cc_final: 0.8362 (m-30) REVERT: B 421 GLU cc_start: 0.8344 (mm-30) cc_final: 0.7948 (mm-30) REVERT: B 503 GLU cc_start: 0.8077 (OUTLIER) cc_final: 0.7822 (pm20) REVERT: B 540 TYR cc_start: 0.7645 (t80) cc_final: 0.7277 (t80) REVERT: B 584 HIS cc_start: 0.8117 (m90) cc_final: 0.7443 (m-70) REVERT: C 185 MET cc_start: 0.8883 (mmm) cc_final: 0.8582 (mmm) REVERT: C 457 ASP cc_start: 0.8494 (p0) cc_final: 0.8244 (p0) REVERT: D 426 MET cc_start: 0.8940 (mmm) cc_final: 0.8469 (mmm) REVERT: E 254 CYS cc_start: 0.8513 (m) cc_final: 0.8120 (t) REVERT: E 417 SER cc_start: 0.8974 (t) cc_final: 0.8483 (p) REVERT: G 385 ARG cc_start: 0.8753 (OUTLIER) cc_final: 0.8449 (mtp85) outliers start: 30 outliers final: 22 residues processed: 168 average time/residue: 0.1430 time to fit residues: 38.4184 Evaluate side-chains 166 residues out of total 2219 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 142 time to evaluate : 0.786 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 277 VAL Chi-restraints excluded: chain B residue 388 LEU Chi-restraints excluded: chain B residue 503 GLU Chi-restraints excluded: chain C residue 5 ILE Chi-restraints excluded: chain C residue 98 THR Chi-restraints excluded: chain C residue 242 VAL Chi-restraints excluded: chain C residue 410 LEU Chi-restraints excluded: chain C residue 429 LEU Chi-restraints excluded: chain C residue 441 THR Chi-restraints excluded: chain C residue 458 GLU Chi-restraints excluded: chain C residue 565 LEU Chi-restraints excluded: chain C residue 652 HIS Chi-restraints excluded: chain C residue 658 MET Chi-restraints excluded: chain D residue 100 LEU Chi-restraints excluded: chain D residue 227 THR Chi-restraints excluded: chain D residue 439 CYS Chi-restraints excluded: chain E residue 203 LEU Chi-restraints excluded: chain E residue 217 CYS Chi-restraints excluded: chain A residue 679 THR Chi-restraints excluded: chain A residue 804 CYS Chi-restraints excluded: chain A residue 810 VAL Chi-restraints excluded: chain G residue 385 ARG Chi-restraints excluded: chain G residue 403 ILE Chi-restraints excluded: chain G residue 464 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 157 optimal weight: 4.9990 chunk 167 optimal weight: 3.9990 chunk 92 optimal weight: 0.8980 chunk 236 optimal weight: 7.9990 chunk 212 optimal weight: 5.9990 chunk 141 optimal weight: 0.7980 chunk 59 optimal weight: 4.9990 chunk 187 optimal weight: 6.9990 chunk 9 optimal weight: 3.9990 chunk 222 optimal weight: 1.9990 chunk 40 optimal weight: 0.7980 overall best weight: 1.6984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 580 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 386 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 622 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3574 r_free = 0.3574 target = 0.085870 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3108 r_free = 0.3108 target = 0.061361 restraints weight = 56780.393| |-----------------------------------------------------------------------------| r_work (start): 0.3058 rms_B_bonded: 3.08 r_work: 0.2929 rms_B_bonded: 3.69 restraints_weight: 0.5000 r_work (final): 0.2929 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8803 moved from start: 0.2989 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 22264 Z= 0.133 Angle : 0.543 13.910 30400 Z= 0.278 Chirality : 0.038 0.154 3508 Planarity : 0.003 0.048 3607 Dihedral : 17.031 82.948 3714 Min Nonbonded Distance : 1.915 Molprobity Statistics. All-atom Clashscore : 6.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 1.49 % Allowed : 14.16 % Favored : 84.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.04 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.76 (0.18), residues: 2478 helix: 2.06 (0.14), residues: 1472 sheet: -0.38 (0.35), residues: 226 loop : 0.00 (0.24), residues: 780 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG F 231 TYR 0.027 0.001 TYR C 72 PHE 0.014 0.001 PHE E 196 TRP 0.021 0.001 TRP E 276 HIS 0.005 0.001 HIS C 230 Details of bonding type rmsd covalent geometry : bond 0.00300 (22264) covalent geometry : angle 0.54288 (30400) hydrogen bonds : bond 0.03150 ( 1139) hydrogen bonds : angle 3.67801 ( 3266) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4956 Ramachandran restraints generated. 2478 Oldfield, 0 Emsley, 2478 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4956 Ramachandran restraints generated. 2478 Oldfield, 0 Emsley, 2478 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 2219 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 147 time to evaluate : 0.855 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 333 MET cc_start: 0.9325 (tpp) cc_final: 0.9080 (mmm) REVERT: B 503 GLU cc_start: 0.8061 (OUTLIER) cc_final: 0.7821 (pm20) REVERT: B 540 TYR cc_start: 0.7581 (t80) cc_final: 0.7197 (t80) REVERT: B 584 HIS cc_start: 0.8091 (m90) cc_final: 0.7407 (m-70) REVERT: C 298 LYS cc_start: 0.9258 (tttt) cc_final: 0.8999 (tptp) REVERT: C 457 ASP cc_start: 0.8486 (p0) cc_final: 0.8233 (p0) REVERT: D 253 ARG cc_start: 0.8686 (tpt90) cc_final: 0.8456 (tpt90) REVERT: D 426 MET cc_start: 0.8932 (mmm) cc_final: 0.8467 (mmm) REVERT: E 254 CYS cc_start: 0.8471 (m) cc_final: 0.8084 (t) outliers start: 33 outliers final: 25 residues processed: 175 average time/residue: 0.1448 time to fit residues: 40.2272 Evaluate side-chains 166 residues out of total 2219 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 140 time to evaluate : 0.828 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 277 VAL Chi-restraints excluded: chain B residue 503 GLU Chi-restraints excluded: chain C residue 5 ILE Chi-restraints excluded: chain C residue 98 THR Chi-restraints excluded: chain C residue 242 VAL Chi-restraints excluded: chain C residue 410 LEU Chi-restraints excluded: chain C residue 429 LEU Chi-restraints excluded: chain C residue 441 THR Chi-restraints excluded: chain C residue 458 GLU Chi-restraints excluded: chain C residue 503 ASP Chi-restraints excluded: chain C residue 565 LEU Chi-restraints excluded: chain C residue 652 HIS Chi-restraints excluded: chain C residue 658 MET Chi-restraints excluded: chain D residue 100 LEU Chi-restraints excluded: chain D residue 227 THR Chi-restraints excluded: chain E residue 75 TYR Chi-restraints excluded: chain E residue 203 LEU Chi-restraints excluded: chain E residue 217 CYS Chi-restraints excluded: chain E residue 419 VAL Chi-restraints excluded: chain A residue 679 THR Chi-restraints excluded: chain A residue 738 THR Chi-restraints excluded: chain A residue 804 CYS Chi-restraints excluded: chain A residue 808 LEU Chi-restraints excluded: chain A residue 810 VAL Chi-restraints excluded: chain G residue 385 ARG Chi-restraints excluded: chain G residue 464 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 210 optimal weight: 0.8980 chunk 186 optimal weight: 7.9990 chunk 156 optimal weight: 6.9990 chunk 134 optimal weight: 5.9990 chunk 192 optimal weight: 0.6980 chunk 36 optimal weight: 8.9990 chunk 118 optimal weight: 0.8980 chunk 29 optimal weight: 7.9990 chunk 77 optimal weight: 4.9990 chunk 168 optimal weight: 1.9990 chunk 13 optimal weight: 0.6980 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 498 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 580 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 386 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 622 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3591 r_free = 0.3591 target = 0.086638 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3142 r_free = 0.3142 target = 0.062807 restraints weight = 56967.605| |-----------------------------------------------------------------------------| r_work (start): 0.3083 rms_B_bonded: 3.05 r_work: 0.2955 rms_B_bonded: 3.67 restraints_weight: 0.5000 r_work (final): 0.2955 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8781 moved from start: 0.3094 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 22264 Z= 0.111 Angle : 0.541 13.960 30400 Z= 0.276 Chirality : 0.037 0.147 3508 Planarity : 0.003 0.047 3607 Dihedral : 16.943 84.079 3714 Min Nonbonded Distance : 1.950 Molprobity Statistics. All-atom Clashscore : 6.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer: Outliers : 1.40 % Allowed : 14.43 % Favored : 84.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.04 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.83 (0.18), residues: 2478 helix: 2.10 (0.14), residues: 1474 sheet: -0.27 (0.35), residues: 224 loop : 0.02 (0.24), residues: 780 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG F 231 TYR 0.025 0.001 TYR C 72 PHE 0.010 0.001 PHE E 196 TRP 0.020 0.001 TRP E 276 HIS 0.005 0.001 HIS C 230 Details of bonding type rmsd covalent geometry : bond 0.00244 (22264) covalent geometry : angle 0.54079 (30400) hydrogen bonds : bond 0.03006 ( 1139) hydrogen bonds : angle 3.65803 ( 3266) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4956 Ramachandran restraints generated. 2478 Oldfield, 0 Emsley, 2478 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4956 Ramachandran restraints generated. 2478 Oldfield, 0 Emsley, 2478 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 2219 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 150 time to evaluate : 0.759 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 333 MET cc_start: 0.9320 (tpp) cc_final: 0.9074 (mmm) REVERT: B 503 GLU cc_start: 0.8004 (OUTLIER) cc_final: 0.7770 (pm20) REVERT: B 540 TYR cc_start: 0.7598 (t80) cc_final: 0.7243 (t80) REVERT: B 584 HIS cc_start: 0.8078 (m90) cc_final: 0.7404 (m-70) REVERT: C 298 LYS cc_start: 0.9240 (tttt) cc_final: 0.9005 (tptp) REVERT: C 457 ASP cc_start: 0.8425 (p0) cc_final: 0.8164 (p0) REVERT: D 253 ARG cc_start: 0.8731 (tpt90) cc_final: 0.8482 (tpt90) REVERT: D 426 MET cc_start: 0.8947 (mmm) cc_final: 0.8449 (mmm) REVERT: E 254 CYS cc_start: 0.8463 (m) cc_final: 0.8171 (t) REVERT: A 579 TYR cc_start: 0.8997 (t80) cc_final: 0.8680 (t80) REVERT: G 575 ARG cc_start: 0.7546 (tpt90) cc_final: 0.7260 (ttp80) outliers start: 31 outliers final: 24 residues processed: 173 average time/residue: 0.1371 time to fit residues: 37.4836 Evaluate side-chains 164 residues out of total 2219 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 139 time to evaluate : 0.792 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 277 VAL Chi-restraints excluded: chain B residue 388 LEU Chi-restraints excluded: chain B residue 503 GLU Chi-restraints excluded: chain C residue 5 ILE Chi-restraints excluded: chain C residue 98 THR Chi-restraints excluded: chain C residue 242 VAL Chi-restraints excluded: chain C residue 410 LEU Chi-restraints excluded: chain C residue 429 LEU Chi-restraints excluded: chain C residue 441 THR Chi-restraints excluded: chain C residue 458 GLU Chi-restraints excluded: chain C residue 503 ASP Chi-restraints excluded: chain C residue 652 HIS Chi-restraints excluded: chain C residue 658 MET Chi-restraints excluded: chain D residue 100 LEU Chi-restraints excluded: chain D residue 227 THR Chi-restraints excluded: chain D residue 439 CYS Chi-restraints excluded: chain E residue 75 TYR Chi-restraints excluded: chain E residue 203 LEU Chi-restraints excluded: chain E residue 217 CYS Chi-restraints excluded: chain A residue 679 THR Chi-restraints excluded: chain A residue 738 THR Chi-restraints excluded: chain A residue 808 LEU Chi-restraints excluded: chain A residue 810 VAL Chi-restraints excluded: chain G residue 385 ARG Chi-restraints excluded: chain G residue 464 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 190 optimal weight: 1.9990 chunk 169 optimal weight: 0.0570 chunk 69 optimal weight: 9.9990 chunk 224 optimal weight: 6.9990 chunk 87 optimal weight: 2.9990 chunk 202 optimal weight: 0.9990 chunk 182 optimal weight: 0.7980 chunk 41 optimal weight: 6.9990 chunk 60 optimal weight: 0.9990 chunk 254 optimal weight: 10.0000 chunk 170 optimal weight: 2.9990 overall best weight: 0.9704 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 498 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 580 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 386 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 622 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3623 r_free = 0.3623 target = 0.088264 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3155 r_free = 0.3155 target = 0.064043 restraints weight = 57350.493| |-----------------------------------------------------------------------------| r_work (start): 0.3114 rms_B_bonded: 3.15 r_work: 0.2989 rms_B_bonded: 3.74 restraints_weight: 0.5000 r_work (final): 0.2989 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8781 moved from start: 0.3213 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.054 22264 Z= 0.109 Angle : 0.543 14.377 30400 Z= 0.276 Chirality : 0.037 0.147 3508 Planarity : 0.003 0.047 3607 Dihedral : 16.863 85.367 3714 Min Nonbonded Distance : 1.943 Molprobity Statistics. All-atom Clashscore : 5.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Rotamer: Outliers : 1.44 % Allowed : 14.52 % Favored : 84.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.04 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.90 (0.18), residues: 2478 helix: 2.15 (0.14), residues: 1469 sheet: -0.23 (0.35), residues: 224 loop : 0.09 (0.24), residues: 785 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG F 231 TYR 0.023 0.001 TYR C 72 PHE 0.010 0.001 PHE B 611 TRP 0.019 0.001 TRP E 276 HIS 0.005 0.001 HIS C 230 Details of bonding type rmsd covalent geometry : bond 0.00243 (22264) covalent geometry : angle 0.54312 (30400) hydrogen bonds : bond 0.02975 ( 1139) hydrogen bonds : angle 3.63860 ( 3266) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4956 Ramachandran restraints generated. 2478 Oldfield, 0 Emsley, 2478 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4956 Ramachandran restraints generated. 2478 Oldfield, 0 Emsley, 2478 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 2219 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 152 time to evaluate : 0.810 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: B 333 MET cc_start: 0.9318 (tpp) cc_final: 0.9069 (mmm) REVERT: B 503 GLU cc_start: 0.7988 (OUTLIER) cc_final: 0.7775 (pm20) REVERT: B 540 TYR cc_start: 0.7814 (t80) cc_final: 0.7336 (t80) REVERT: B 584 HIS cc_start: 0.8074 (m90) cc_final: 0.7412 (m-70) REVERT: C 298 LYS cc_start: 0.9237 (tttt) cc_final: 0.9005 (tptp) REVERT: C 457 ASP cc_start: 0.8485 (p0) cc_final: 0.8245 (p0) REVERT: D 426 MET cc_start: 0.8963 (mmm) cc_final: 0.8497 (mmm) REVERT: E 1 MET cc_start: 0.8277 (tmm) cc_final: 0.8000 (tmm) REVERT: E 254 CYS cc_start: 0.8438 (m) cc_final: 0.8137 (t) REVERT: A 775 LYS cc_start: 0.9246 (mttt) cc_final: 0.8986 (mptt) REVERT: G 370 MET cc_start: 0.8978 (tpp) cc_final: 0.8752 (tpp) outliers start: 32 outliers final: 28 residues processed: 176 average time/residue: 0.1462 time to fit residues: 40.7923 Evaluate side-chains 172 residues out of total 2219 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 143 time to evaluate : 0.701 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 277 VAL Chi-restraints excluded: chain B residue 388 LEU Chi-restraints excluded: chain B residue 503 GLU Chi-restraints excluded: chain C residue 5 ILE Chi-restraints excluded: chain C residue 98 THR Chi-restraints excluded: chain C residue 242 VAL Chi-restraints excluded: chain C residue 410 LEU Chi-restraints excluded: chain C residue 429 LEU Chi-restraints excluded: chain C residue 441 THR Chi-restraints excluded: chain C residue 458 GLU Chi-restraints excluded: chain C residue 503 ASP Chi-restraints excluded: chain C residue 565 LEU Chi-restraints excluded: chain C residue 625 MET Chi-restraints excluded: chain C residue 652 HIS Chi-restraints excluded: chain C residue 658 MET Chi-restraints excluded: chain D residue 100 LEU Chi-restraints excluded: chain D residue 227 THR Chi-restraints excluded: chain D residue 439 CYS Chi-restraints excluded: chain E residue 75 TYR Chi-restraints excluded: chain E residue 203 LEU Chi-restraints excluded: chain E residue 217 CYS Chi-restraints excluded: chain E residue 329 LEU Chi-restraints excluded: chain E residue 419 VAL Chi-restraints excluded: chain A residue 679 THR Chi-restraints excluded: chain A residue 738 THR Chi-restraints excluded: chain A residue 808 LEU Chi-restraints excluded: chain A residue 810 VAL Chi-restraints excluded: chain G residue 385 ARG Chi-restraints excluded: chain G residue 464 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 157 optimal weight: 3.9990 chunk 83 optimal weight: 6.9990 chunk 125 optimal weight: 4.9990 chunk 22 optimal weight: 4.9990 chunk 19 optimal weight: 0.6980 chunk 8 optimal weight: 8.9990 chunk 218 optimal weight: 5.9990 chunk 31 optimal weight: 0.5980 chunk 207 optimal weight: 4.9990 chunk 243 optimal weight: 10.0000 chunk 14 optimal weight: 0.9980 overall best weight: 2.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 498 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 580 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 386 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 622 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3574 r_free = 0.3574 target = 0.085864 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3082 r_free = 0.3082 target = 0.060951 restraints weight = 57519.236| |-----------------------------------------------------------------------------| r_work (start): 0.3050 rms_B_bonded: 3.19 r_work: 0.2917 rms_B_bonded: 3.81 restraints_weight: 0.5000 r_work (final): 0.2917 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8821 moved from start: 0.3222 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 22264 Z= 0.160 Angle : 0.563 14.483 30400 Z= 0.288 Chirality : 0.038 0.174 3508 Planarity : 0.003 0.047 3607 Dihedral : 16.884 87.387 3714 Min Nonbonded Distance : 1.880 Molprobity Statistics. All-atom Clashscore : 6.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 1.31 % Allowed : 14.83 % Favored : 83.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.04 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.92 (0.18), residues: 2478 helix: 2.17 (0.14), residues: 1466 sheet: -0.24 (0.35), residues: 224 loop : 0.11 (0.24), residues: 788 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 675 TYR 0.022 0.001 TYR C 72 PHE 0.019 0.001 PHE B 611 TRP 0.017 0.001 TRP E 276 HIS 0.007 0.001 HIS C 230 Details of bonding type rmsd covalent geometry : bond 0.00369 (22264) covalent geometry : angle 0.56324 (30400) hydrogen bonds : bond 0.03289 ( 1139) hydrogen bonds : angle 3.69881 ( 3266) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4470.06 seconds wall clock time: 77 minutes 31.66 seconds (4651.66 seconds total)