Starting phenix.real_space_refine on Fri May 23 16:29:18 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9arj_43784/05_2025/9arj_43784.cif Found real_map, /net/cci-nas-00/data/ceres_data/9arj_43784/05_2025/9arj_43784.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9arj_43784/05_2025/9arj_43784.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9arj_43784/05_2025/9arj_43784.map" model { file = "/net/cci-nas-00/data/ceres_data/9arj_43784/05_2025/9arj_43784.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9arj_43784/05_2025/9arj_43784.cif" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.009 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: 4 Type Number sf(0) Gaussians S 54 5.16 5 C 15503 2.51 5 N 3960 2.21 5 O 4671 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 9 residue(s): 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 24188 Number of models: 1 Model: "" Number of chains: 3 Chain: "C" Number of atoms: 4550 Number of conformers: 1 Conformer: "" Number of residues, atoms: 578, 4550 Classifications: {'peptide': 578} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 22, 'TRANS': 555} Unresolved non-hydrogen bonds: 29 Unresolved non-hydrogen angles: 30 Unresolved non-hydrogen dihedrals: 28 Planarities with less than four sites: {'ASN:plan1': 1} Unresolved non-hydrogen planarities: 3 Chain: "A" Number of atoms: 9965 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1241, 9965 Classifications: {'peptide': 1241} Incomplete info: {'truncation_to_alanine': 23} Link IDs: {'PTRANS': 34, 'TRANS': 1206} Chain breaks: 2 Unresolved non-hydrogen bonds: 89 Unresolved non-hydrogen angles: 99 Unresolved non-hydrogen dihedrals: 79 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 2, 'ARG:plan': 2, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 35 Chain: "B" Number of atoms: 9673 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1163, 9673 Classifications: {'peptide': 1163} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 32, 'TRANS': 1129} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Time building chain proxies: 15.41, per 1000 atoms: 0.64 Number of scatterers: 24188 At special positions: 0 Unit cell: (111.896, 125.292, 241.128, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 54 16.00 O 4671 8.00 N 3960 7.00 C 15503 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS A 412 " - pdb=" SG CYS A 426 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 5.81 Conformation dependent library (CDL) restraints added in 3.2 seconds 5944 Ramachandran restraints generated. 2972 Oldfield, 0 Emsley, 2972 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5722 Finding SS restraints... Secondary structure from input PDB file: 80 helices and 40 sheets defined 34.9% alpha, 22.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.30 Creating SS restraints... Processing helix chain 'C' and resid 181 through 192 removed outlier: 3.516A pdb=" N ASN C 192 " --> pdb=" O ILE C 188 " (cutoff:3.500A) Processing helix chain 'C' and resid 314 through 330 removed outlier: 3.886A pdb=" N SER C 318 " --> pdb=" O GLY C 314 " (cutoff:3.500A) Processing helix chain 'C' and resid 349 through 356 removed outlier: 4.131A pdb=" N TRP C 354 " --> pdb=" O GLU C 351 " (cutoff:3.500A) Processing helix chain 'C' and resid 407 through 414 removed outlier: 3.508A pdb=" N GLU C 411 " --> pdb=" O ASN C 407 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N LYS C 414 " --> pdb=" O LEU C 410 " (cutoff:3.500A) Processing helix chain 'C' and resid 422 through 438 removed outlier: 4.967A pdb=" N VAL C 432 " --> pdb=" O LYS C 428 " (cutoff:3.500A) removed outlier: 4.875A pdb=" N THR C 433 " --> pdb=" O HIS C 429 " (cutoff:3.500A) Processing helix chain 'C' and resid 467 through 471 removed outlier: 3.852A pdb=" N ASN C 470 " --> pdb=" O GLN C 467 " (cutoff:3.500A) Processing helix chain 'C' and resid 544 through 551 Processing helix chain 'C' and resid 551 through 567 Processing helix chain 'C' and resid 576 through 587 removed outlier: 3.751A pdb=" N TYR C 580 " --> pdb=" O SER C 576 " (cutoff:3.500A) Processing helix chain 'C' and resid 601 through 610 removed outlier: 3.680A pdb=" N GLU C 608 " --> pdb=" O ASN C 604 " (cutoff:3.500A) Processing helix chain 'C' and resid 613 through 633 Processing helix chain 'C' and resid 642 through 650 removed outlier: 3.757A pdb=" N LEU C 646 " --> pdb=" O SER C 642 " (cutoff:3.500A) Processing helix chain 'C' and resid 655 through 674 Processing helix chain 'C' and resid 682 through 697 Processing helix chain 'C' and resid 705 through 713 Processing helix chain 'A' and resid 51 through 56 Processing helix chain 'A' and resid 76 through 97 removed outlier: 3.757A pdb=" N ASN A 97 " --> pdb=" O ARG A 93 " (cutoff:3.500A) Processing helix chain 'A' and resid 97 through 109 Processing helix chain 'A' and resid 205 through 222 Processing helix chain 'A' and resid 224 through 229 removed outlier: 4.391A pdb=" N THR A 228 " --> pdb=" O ALA A 224 " (cutoff:3.500A) Processing helix chain 'A' and resid 249 through 256 Processing helix chain 'A' and resid 258 through 262 Processing helix chain 'A' and resid 264 through 287 Processing helix chain 'A' and resid 296 through 307 removed outlier: 3.954A pdb=" N LYS A 300 " --> pdb=" O LEU A 296 " (cutoff:3.500A) removed outlier: 4.074A pdb=" N ASP A 301 " --> pdb=" O ASN A 297 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N TYR A 307 " --> pdb=" O PHE A 303 " (cutoff:3.500A) Processing helix chain 'A' and resid 320 through 334 removed outlier: 3.686A pdb=" N PHE A 334 " --> pdb=" O LYS A 330 " (cutoff:3.500A) Processing helix chain 'A' and resid 335 through 343 Processing helix chain 'A' and resid 377 through 388 removed outlier: 3.806A pdb=" N VAL A 382 " --> pdb=" O ASN A 379 " (cutoff:3.500A) removed outlier: 5.434A pdb=" N ASN A 383 " --> pdb=" O LEU A 380 " (cutoff:3.500A) removed outlier: 5.813A pdb=" N GLY A 386 " --> pdb=" O ASN A 383 " (cutoff:3.500A) Processing helix chain 'A' and resid 392 through 394 No H-bonds generated for 'chain 'A' and resid 392 through 394' Processing helix chain 'A' and resid 432 through 434 No H-bonds generated for 'chain 'A' and resid 432 through 434' Processing helix chain 'A' and resid 467 through 474 removed outlier: 3.505A pdb=" N VAL A 471 " --> pdb=" O ASP A 467 " (cutoff:3.500A) Processing helix chain 'A' and resid 518 through 527 removed outlier: 3.572A pdb=" N TYR A 522 " --> pdb=" O ASN A 518 " (cutoff:3.500A) Processing helix chain 'A' and resid 540 through 547 Processing helix chain 'A' and resid 556 through 565 Processing helix chain 'A' and resid 568 through 570 No H-bonds generated for 'chain 'A' and resid 568 through 570' Processing helix chain 'A' and resid 571 through 588 Processing helix chain 'A' and resid 603 through 605 No H-bonds generated for 'chain 'A' and resid 603 through 605' Processing helix chain 'A' and resid 606 through 611 Processing helix chain 'A' and resid 614 through 620 Processing helix chain 'A' and resid 620 through 629 Processing helix chain 'A' and resid 630 through 633 removed outlier: 3.597A pdb=" N LEU A 633 " --> pdb=" O ALA A 630 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 630 through 633' Processing helix chain 'A' and resid 661 through 726 removed outlier: 4.504A pdb=" N ASN A 694 " --> pdb=" O MET A 690 " (cutoff:3.500A) removed outlier: 5.446A pdb=" N THR A 695 " --> pdb=" O THR A 691 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N GLN A 696 " --> pdb=" O LYS A 692 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N TYR A 726 " --> pdb=" O LYS A 722 " (cutoff:3.500A) Processing helix chain 'A' and resid 743 through 781 removed outlier: 3.665A pdb=" N ASN A 757 " --> pdb=" O ILE A 753 " (cutoff:3.500A) Processing helix chain 'A' and resid 781 through 801 Processing helix chain 'A' and resid 808 through 821 removed outlier: 3.826A pdb=" N ASN A 821 " --> pdb=" O ASP A 817 " (cutoff:3.500A) Processing helix chain 'A' and resid 835 through 850 removed outlier: 5.039A pdb=" N ILE A 847 " --> pdb=" O PHE A 843 " (cutoff:3.500A) removed outlier: 4.733A pdb=" N LYS A 848 " --> pdb=" O PHE A 844 " (cutoff:3.500A) Processing helix chain 'A' and resid 1055 through 1066 Processing helix chain 'A' and resid 1223 through 1228 removed outlier: 3.685A pdb=" N THR A1227 " --> pdb=" O THR A1223 " (cutoff:3.500A) removed outlier: 4.369A pdb=" N HIS A1228 " --> pdb=" O TRP A1224 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1223 through 1228' Processing helix chain 'B' and resid 71 through 92 removed outlier: 3.932A pdb=" N ASN B 92 " --> pdb=" O ARG B 88 " (cutoff:3.500A) Processing helix chain 'B' and resid 92 through 105 Processing helix chain 'B' and resid 154 through 160 Processing helix chain 'B' and resid 184 through 202 removed outlier: 3.573A pdb=" N TYR B 198 " --> pdb=" O ILE B 194 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N TYR B 199 " --> pdb=" O LYS B 195 " (cutoff:3.500A) Processing helix chain 'B' and resid 229 through 236 removed outlier: 4.009A pdb=" N GLY B 236 " --> pdb=" O PHE B 232 " (cutoff:3.500A) Processing helix chain 'B' and resid 236 through 244 removed outlier: 3.709A pdb=" N TYR B 240 " --> pdb=" O GLY B 236 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N LYS B 241 " --> pdb=" O GLY B 237 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N LEU B 242 " --> pdb=" O ILE B 238 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N LEU B 243 " --> pdb=" O ASP B 239 " (cutoff:3.500A) Processing helix chain 'B' and resid 253 through 273 removed outlier: 3.815A pdb=" N SER B 259 " --> pdb=" O PHE B 255 " (cutoff:3.500A) Processing helix chain 'B' and resid 280 through 291 Processing helix chain 'B' and resid 294 through 301 removed outlier: 3.680A pdb=" N ILE B 298 " --> pdb=" O ASN B 294 " (cutoff:3.500A) Processing helix chain 'B' and resid 302 through 311 Processing helix chain 'B' and resid 321 through 326 removed outlier: 3.808A pdb=" N TYR B 325 " --> pdb=" O ALA B 321 " (cutoff:3.500A) Processing helix chain 'B' and resid 346 through 351 removed outlier: 4.049A pdb=" N LYS B 350 " --> pdb=" O ASN B 346 " (cutoff:3.500A) Processing helix chain 'B' and resid 356 through 361 removed outlier: 4.087A pdb=" N LYS B 360 " --> pdb=" O LYS B 357 " (cutoff:3.500A) Processing helix chain 'B' and resid 397 through 400 Processing helix chain 'B' and resid 422 through 428 removed outlier: 3.744A pdb=" N ILE B 426 " --> pdb=" O ASN B 422 " (cutoff:3.500A) Processing helix chain 'B' and resid 465 through 473 Processing helix chain 'B' and resid 485 through 492 Processing helix chain 'B' and resid 501 through 511 Processing helix chain 'B' and resid 519 through 539 Processing helix chain 'B' and resid 556 through 562 Processing helix chain 'B' and resid 569 through 578 Processing helix chain 'B' and resid 579 through 583 removed outlier: 3.692A pdb=" N ILE B 583 " --> pdb=" O ILE B 580 " (cutoff:3.500A) Processing helix chain 'B' and resid 600 through 604 removed outlier: 4.084A pdb=" N MET B 603 " --> pdb=" O PRO B 600 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N LEU B 604 " --> pdb=" O SER B 601 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 600 through 604' Processing helix chain 'B' and resid 607 through 641 Processing helix chain 'B' and resid 641 through 677 removed outlier: 3.602A pdb=" N TYR B 645 " --> pdb=" O TYR B 641 " (cutoff:3.500A) Processing helix chain 'B' and resid 681 through 725 removed outlier: 3.794A pdb=" N LEU B 687 " --> pdb=" O THR B 683 " (cutoff:3.500A) Processing helix chain 'B' and resid 725 through 752 removed outlier: 3.695A pdb=" N GLN B 736 " --> pdb=" O SER B 732 " (cutoff:3.500A) Processing helix chain 'B' and resid 756 through 768 Processing helix chain 'B' and resid 778 through 784 Processing helix chain 'B' and resid 788 through 798 Processing helix chain 'B' and resid 857 through 861 Processing helix chain 'B' and resid 990 through 1003 removed outlier: 3.677A pdb=" N ASN B1003 " --> pdb=" O PHE B 999 " (cutoff:3.500A) Processing helix chain 'B' and resid 1103 through 1107 Processing sheet with id=AA1, first strand: chain 'C' and resid 359 through 365 Processing sheet with id=AA2, first strand: chain 'C' and resid 198 through 204 Processing sheet with id=AA3, first strand: chain 'C' and resid 219 through 220 removed outlier: 6.261A pdb=" N GLN C 258 " --> pdb=" O LEU C 299 " (cutoff:3.500A) removed outlier: 5.365A pdb=" N LEU C 299 " --> pdb=" O GLN C 258 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 261 through 267 Processing sheet with id=AA5, first strand: chain 'C' and resid 368 through 370 Processing sheet with id=AA6, first strand: chain 'C' and resid 446 through 449 Processing sheet with id=AA7, first strand: chain 'C' and resid 483 through 487 removed outlier: 7.954A pdb=" N GLN C 490 " --> pdb=" O LEU C 518 " (cutoff:3.500A) removed outlier: 7.636A pdb=" N LEU C 518 " --> pdb=" O GLN C 490 " (cutoff:3.500A) removed outlier: 5.346A pdb=" N VAL C 492 " --> pdb=" O TYR C 516 " (cutoff:3.500A) removed outlier: 7.081A pdb=" N TYR C 516 " --> pdb=" O VAL C 492 " (cutoff:3.500A) removed outlier: 4.970A pdb=" N GLU C 494 " --> pdb=" O GLN C 514 " (cutoff:3.500A) removed outlier: 7.361A pdb=" N GLN C 514 " --> pdb=" O GLU C 494 " (cutoff:3.500A) removed outlier: 5.175A pdb=" N VAL C 496 " --> pdb=" O TYR C 512 " (cutoff:3.500A) removed outlier: 5.626A pdb=" N TYR C 512 " --> pdb=" O VAL C 496 " (cutoff:3.500A) removed outlier: 4.147A pdb=" N GLN C 502 " --> pdb=" O VAL C 506 " (cutoff:3.500A) removed outlier: 7.953A pdb=" N VAL C 506 " --> pdb=" O GLN C 502 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 483 through 487 removed outlier: 7.954A pdb=" N GLN C 490 " --> pdb=" O LEU C 518 " (cutoff:3.500A) removed outlier: 7.636A pdb=" N LEU C 518 " --> pdb=" O GLN C 490 " (cutoff:3.500A) removed outlier: 5.346A pdb=" N VAL C 492 " --> pdb=" O TYR C 516 " (cutoff:3.500A) removed outlier: 7.081A pdb=" N TYR C 516 " --> pdb=" O VAL C 492 " (cutoff:3.500A) removed outlier: 4.970A pdb=" N GLU C 494 " --> pdb=" O GLN C 514 " (cutoff:3.500A) removed outlier: 7.361A pdb=" N GLN C 514 " --> pdb=" O GLU C 494 " (cutoff:3.500A) removed outlier: 5.175A pdb=" N VAL C 496 " --> pdb=" O TYR C 512 " (cutoff:3.500A) removed outlier: 5.626A pdb=" N TYR C 512 " --> pdb=" O VAL C 496 " (cutoff:3.500A) removed outlier: 4.147A pdb=" N GLN C 502 " --> pdb=" O VAL C 506 " (cutoff:3.500A) removed outlier: 7.953A pdb=" N VAL C 506 " --> pdb=" O GLN C 502 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 141 through 144 removed outlier: 4.056A pdb=" N GLU A 133 " --> pdb=" O LYS A 22 " (cutoff:3.500A) removed outlier: 7.029A pdb=" N ILE A 39 " --> pdb=" O ILE A 35 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N VAL A 184 " --> pdb=" O ILE A 149 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 60 through 61 Processing sheet with id=AB2, first strand: chain 'A' and resid 67 through 68 Processing sheet with id=AB3, first strand: chain 'A' and resid 201 through 203 removed outlier: 3.917A pdb=" N LYS A 356 " --> pdb=" O ARG A 193 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 232 through 233 Processing sheet with id=AB5, first strand: chain 'A' and resid 309 through 311 Processing sheet with id=AB6, first strand: chain 'A' and resid 422 through 430 removed outlier: 3.928A pdb=" N GLU A 510 " --> pdb=" O ILE A 408 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 536 through 538 Processing sheet with id=AB8, first strand: chain 'A' and resid 591 through 592 Processing sheet with id=AB9, first strand: chain 'A' and resid 862 through 864 removed outlier: 6.266A pdb=" N ILE A1049 " --> pdb=" O VAL A 852 " (cutoff:3.500A) removed outlier: 4.489A pdb=" N ASN A 854 " --> pdb=" O PHE A1047 " (cutoff:3.500A) removed outlier: 7.141A pdb=" N PHE A1047 " --> pdb=" O ASN A 854 " (cutoff:3.500A) removed outlier: 8.870A pdb=" N ARG A 856 " --> pdb=" O ARG A1045 " (cutoff:3.500A) removed outlier: 10.376A pdb=" N ARG A1045 " --> pdb=" O ARG A 856 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'A' and resid 862 through 864 removed outlier: 6.266A pdb=" N ILE A1049 " --> pdb=" O VAL A 852 " (cutoff:3.500A) removed outlier: 4.489A pdb=" N ASN A 854 " --> pdb=" O PHE A1047 " (cutoff:3.500A) removed outlier: 7.141A pdb=" N PHE A1047 " --> pdb=" O ASN A 854 " (cutoff:3.500A) removed outlier: 8.870A pdb=" N ARG A 856 " --> pdb=" O ARG A1045 " (cutoff:3.500A) removed outlier: 10.376A pdb=" N ARG A1045 " --> pdb=" O ARG A 856 " (cutoff:3.500A) removed outlier: 5.545A pdb=" N ILE A1044 " --> pdb=" O ARG A 922 " (cutoff:3.500A) removed outlier: 7.008A pdb=" N ARG A 922 " --> pdb=" O ILE A1044 " (cutoff:3.500A) removed outlier: 5.491A pdb=" N TYR A1046 " --> pdb=" O TRP A 920 " (cutoff:3.500A) removed outlier: 4.498A pdb=" N TRP A 920 " --> pdb=" O TYR A1046 " (cutoff:3.500A) removed outlier: 6.289A pdb=" N ILE A1007 " --> pdb=" O LEU A1011 " (cutoff:3.500A) removed outlier: 5.416A pdb=" N LEU A1011 " --> pdb=" O ILE A1007 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'A' and resid 871 through 875 removed outlier: 7.280A pdb=" N ASN A1028 " --> pdb=" O MET A 943 " (cutoff:3.500A) removed outlier: 5.485A pdb=" N MET A 943 " --> pdb=" O ASN A1028 " (cutoff:3.500A) removed outlier: 6.792A pdb=" N VAL A 952 " --> pdb=" O ILE A 939 " (cutoff:3.500A) removed outlier: 5.125A pdb=" N ASN A 941 " --> pdb=" O TRP A 950 " (cutoff:3.500A) removed outlier: 7.170A pdb=" N TRP A 950 " --> pdb=" O ASN A 941 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'A' and resid 1147 through 1153 removed outlier: 15.019A pdb=" N VAL A1148 " --> pdb=" O ALA A1164 " (cutoff:3.500A) removed outlier: 10.962A pdb=" N ALA A1164 " --> pdb=" O VAL A1148 " (cutoff:3.500A) removed outlier: 5.761A pdb=" N ILE A1150 " --> pdb=" O LEU A1162 " (cutoff:3.500A) removed outlier: 6.300A pdb=" N VAL A1219 " --> pdb=" O ILE A1175 " (cutoff:3.500A) removed outlier: 6.024A pdb=" N ASN A1208 " --> pdb=" O ASN A1203 " (cutoff:3.500A) removed outlier: 6.750A pdb=" N ASN A1203 " --> pdb=" O ASN A1208 " (cutoff:3.500A) removed outlier: 5.376A pdb=" N MET A1199 " --> pdb=" O LEU A1212 " (cutoff:3.500A) removed outlier: 10.798A pdb=" N PHE A1214 " --> pdb=" O CYS A1197 " (cutoff:3.500A) removed outlier: 15.430A pdb=" N CYS A1197 " --> pdb=" O PHE A1214 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 1196 through 1203 current: chain 'A' and resid 1126 through 1131 removed outlier: 3.528A pdb=" N ASN A1196 " --> pdb=" O VAL A1193 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N ASN A1196 " --> pdb=" O VAL A1193 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'A' and resid 1099 through 1101 Processing sheet with id=AC5, first strand: chain 'B' and resid 131 through 132 removed outlier: 4.580A pdb=" N SER B 124 " --> pdb=" O ARG B 22 " (cutoff:3.500A) removed outlier: 5.472A pdb=" N GLN B 34 " --> pdb=" O ILE B 41 " (cutoff:3.500A) removed outlier: 6.631A pdb=" N ILE B 41 " --> pdb=" O GLN B 34 " (cutoff:3.500A) removed outlier: 6.978A pdb=" N TRP B 40 " --> pdb=" O ILE B 138 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 111 through 113 Processing sheet with id=AC7, first strand: chain 'B' and resid 181 through 182 Processing sheet with id=AC8, first strand: chain 'B' and resid 210 through 215 removed outlier: 6.184A pdb=" N LEU B 227 " --> pdb=" O PRO B 212 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 339 through 340 Processing sheet with id=AD1, first strand: chain 'B' and resid 379 through 385 removed outlier: 6.635A pdb=" N LEU B 372 " --> pdb=" O LEU B 380 " (cutoff:3.500A) removed outlier: 4.354A pdb=" N LYS B 382 " --> pdb=" O VAL B 370 " (cutoff:3.500A) removed outlier: 6.519A pdb=" N VAL B 370 " --> pdb=" O LYS B 382 " (cutoff:3.500A) removed outlier: 4.675A pdb=" N ASN B 384 " --> pdb=" O LEU B 368 " (cutoff:3.500A) removed outlier: 6.840A pdb=" N LEU B 368 " --> pdb=" O ASN B 384 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 402 through 403 Processing sheet with id=AD3, first strand: chain 'B' and resid 482 through 483 Processing sheet with id=AD4, first strand: chain 'B' and resid 542 through 546 Processing sheet with id=AD5, first strand: chain 'B' and resid 814 through 818 removed outlier: 6.126A pdb=" N VAL B 984 " --> pdb=" O GLU B 802 " (cutoff:3.500A) removed outlier: 4.282A pdb=" N SER B 804 " --> pdb=" O LEU B 982 " (cutoff:3.500A) removed outlier: 7.090A pdb=" N LEU B 982 " --> pdb=" O SER B 804 " (cutoff:3.500A) removed outlier: 9.008A pdb=" N TYR B 806 " --> pdb=" O GLU B 980 " (cutoff:3.500A) removed outlier: 10.025A pdb=" N GLU B 980 " --> pdb=" O TYR B 806 " (cutoff:3.500A) removed outlier: 14.118A pdb=" N PHE B 808 " --> pdb=" O TYR B 978 " (cutoff:3.500A) removed outlier: 15.864A pdb=" N TYR B 978 " --> pdb=" O PHE B 808 " (cutoff:3.500A) removed outlier: 6.020A pdb=" N GLY B 981 " --> pdb=" O ASN B 841 " (cutoff:3.500A) removed outlier: 10.406A pdb=" N ASN B 841 " --> pdb=" O GLY B 981 " (cutoff:3.500A) removed outlier: 4.153A pdb=" N GLY B 833 " --> pdb=" O HIS B 844 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'B' and resid 814 through 818 removed outlier: 6.126A pdb=" N VAL B 984 " --> pdb=" O GLU B 802 " (cutoff:3.500A) removed outlier: 4.282A pdb=" N SER B 804 " --> pdb=" O LEU B 982 " (cutoff:3.500A) removed outlier: 7.090A pdb=" N LEU B 982 " --> pdb=" O SER B 804 " (cutoff:3.500A) removed outlier: 9.008A pdb=" N TYR B 806 " --> pdb=" O GLU B 980 " (cutoff:3.500A) removed outlier: 10.025A pdb=" N GLU B 980 " --> pdb=" O TYR B 806 " (cutoff:3.500A) removed outlier: 14.118A pdb=" N PHE B 808 " --> pdb=" O TYR B 978 " (cutoff:3.500A) removed outlier: 15.864A pdb=" N TYR B 978 " --> pdb=" O PHE B 808 " (cutoff:3.500A) removed outlier: 4.410A pdb=" N LEU B 982 " --> pdb=" O TYR B 870 " (cutoff:3.500A) removed outlier: 6.841A pdb=" N TYR B 870 " --> pdb=" O LEU B 982 " (cutoff:3.500A) removed outlier: 4.540A pdb=" N VAL B 984 " --> pdb=" O SER B 868 " (cutoff:3.500A) removed outlier: 6.586A pdb=" N SER B 868 " --> pdb=" O VAL B 984 " (cutoff:3.500A) removed outlier: 6.835A pdb=" N ILE B 946 " --> pdb=" O LEU B 950 " (cutoff:3.500A) removed outlier: 5.560A pdb=" N LEU B 950 " --> pdb=" O ILE B 946 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'B' and resid 825 through 827 Processing sheet with id=AD8, first strand: chain 'B' and resid 883 through 890 removed outlier: 6.699A pdb=" N ILE B 897 " --> pdb=" O LEU B 885 " (cutoff:3.500A) removed outlier: 4.775A pdb=" N GLY B 887 " --> pdb=" O TRP B 895 " (cutoff:3.500A) removed outlier: 6.731A pdb=" N TRP B 895 " --> pdb=" O GLY B 887 " (cutoff:3.500A) removed outlier: 4.337A pdb=" N LYS B 889 " --> pdb=" O CYS B 893 " (cutoff:3.500A) removed outlier: 5.851A pdb=" N CYS B 893 " --> pdb=" O LYS B 889 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'B' and resid 1022 through 1025 Processing sheet with id=AE1, first strand: chain 'B' and resid 1034 through 1038 Processing sheet with id=AE2, first strand: chain 'B' and resid 1059 through 1062 removed outlier: 15.713A pdb=" N VAL B1077 " --> pdb=" O ILE B1091 " (cutoff:3.500A) removed outlier: 10.809A pdb=" N ILE B1091 " --> pdb=" O VAL B1077 " (cutoff:3.500A) removed outlier: 5.992A pdb=" N PHE B1079 " --> pdb=" O LEU B1089 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N LEU B1089 " --> pdb=" O PHE B1079 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'B' and resid 1059 through 1062 removed outlier: 3.693A pdb=" N ASP B1075 " --> pdb=" O ILE B1112 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'B' and resid 1132 through 1137 removed outlier: 4.428A pdb=" N TRP B1142 " --> pdb=" O SER B1134 " (cutoff:3.500A) removed outlier: 5.337A pdb=" N LYS B1136 " --> pdb=" O TYR B1140 " (cutoff:3.500A) removed outlier: 5.715A pdb=" N TYR B1140 " --> pdb=" O LYS B1136 " (cutoff:3.500A) 1098 hydrogen bonds defined for protein. 3027 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 10.94 Time building geometry restraints manager: 6.83 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: 4934 1.33 - 1.45: 5859 1.45 - 1.57: 13806 1.57 - 1.69: 0 1.69 - 1.81: 90 Bond restraints: 24689 Sorted by residual: bond pdb=" CA LEU A 331 " pdb=" C LEU A 331 " ideal model delta sigma weight residual 1.523 1.488 0.035 1.30e-02 5.92e+03 7.43e+00 bond pdb=" C LYS A 329 " pdb=" O LYS A 329 " ideal model delta sigma weight residual 1.237 1.206 0.030 1.17e-02 7.31e+03 6.69e+00 bond pdb=" C ILE A 327 " pdb=" O ILE A 327 " ideal model delta sigma weight residual 1.237 1.209 0.028 1.17e-02 7.31e+03 5.61e+00 bond pdb=" C LEU A 331 " pdb=" O LEU A 331 " ideal model delta sigma weight residual 1.237 1.210 0.027 1.17e-02 7.31e+03 5.33e+00 bond pdb=" CA SER A 333 " pdb=" C SER A 333 " ideal model delta sigma weight residual 1.523 1.495 0.028 1.37e-02 5.33e+03 4.26e+00 ... (remaining 24684 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.43: 33297 2.43 - 4.87: 181 4.87 - 7.30: 11 7.30 - 9.73: 2 9.73 - 12.17: 2 Bond angle restraints: 33493 Sorted by residual: angle pdb=" N ASN B 406 " pdb=" CA ASN B 406 " pdb=" C ASN B 406 " ideal model delta sigma weight residual 111.36 121.10 -9.74 1.09e+00 8.42e-01 7.99e+01 angle pdb=" N TYR B 409 " pdb=" CA TYR B 409 " pdb=" C TYR B 409 " ideal model delta sigma weight residual 110.80 122.97 -12.17 2.13e+00 2.20e-01 3.26e+01 angle pdb=" N LEU B 407 " pdb=" CA LEU B 407 " pdb=" C LEU B 407 " ideal model delta sigma weight residual 108.41 116.49 -8.08 1.63e+00 3.76e-01 2.46e+01 angle pdb=" N ASN B 408 " pdb=" CA ASN B 408 " pdb=" C ASN B 408 " ideal model delta sigma weight residual 114.39 107.41 6.98 1.45e+00 4.76e-01 2.31e+01 angle pdb=" N GLY B1084 " pdb=" CA GLY B1084 " pdb=" C GLY B1084 " ideal model delta sigma weight residual 115.42 109.41 6.01 1.27e+00 6.20e-01 2.24e+01 ... (remaining 33488 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.75: 13860 17.75 - 35.50: 775 35.50 - 53.25: 165 53.25 - 71.00: 21 71.00 - 88.75: 8 Dihedral angle restraints: 14829 sinusoidal: 5962 harmonic: 8867 Sorted by residual: dihedral pdb=" CA ARG A1101 " pdb=" C ARG A1101 " pdb=" N LYS A1102 " pdb=" CA LYS A1102 " ideal model delta harmonic sigma weight residual -180.00 -162.56 -17.44 0 5.00e+00 4.00e-02 1.22e+01 dihedral pdb=" CA ARG A1143 " pdb=" C ARG A1143 " pdb=" N LYS A1144 " pdb=" CA LYS A1144 " ideal model delta harmonic sigma weight residual 180.00 -163.02 -16.98 0 5.00e+00 4.00e-02 1.15e+01 dihedral pdb=" CA GLN A 568 " pdb=" C GLN A 568 " pdb=" N ALA A 569 " pdb=" CA ALA A 569 " ideal model delta harmonic sigma weight residual 180.00 164.19 15.81 0 5.00e+00 4.00e-02 1.00e+01 ... (remaining 14826 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.081: 3413 0.081 - 0.163: 319 0.163 - 0.244: 4 0.244 - 0.326: 0 0.326 - 0.407: 3 Chirality restraints: 3739 Sorted by residual: chirality pdb=" CA ASN B 406 " pdb=" N ASN B 406 " pdb=" C ASN B 406 " pdb=" CB ASN B 406 " both_signs ideal model delta sigma weight residual False 2.51 2.10 0.41 2.00e-01 2.50e+01 4.15e+00 chirality pdb=" CA TYR B 409 " pdb=" N TYR B 409 " pdb=" C TYR B 409 " pdb=" CB TYR B 409 " both_signs ideal model delta sigma weight residual False 2.51 2.11 0.40 2.00e-01 2.50e+01 4.08e+00 chirality pdb=" CA TYR A 332 " pdb=" N TYR A 332 " pdb=" C TYR A 332 " pdb=" CB TYR A 332 " both_signs ideal model delta sigma weight residual False 2.51 2.14 0.37 2.00e-01 2.50e+01 3.36e+00 ... (remaining 3736 not shown) Planarity restraints: 4328 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA CYS A 942 " -0.010 2.00e-02 2.50e+03 1.99e-02 3.95e+00 pdb=" C CYS A 942 " 0.034 2.00e-02 2.50e+03 pdb=" O CYS A 942 " -0.013 2.00e-02 2.50e+03 pdb=" N MET A 943 " -0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLU A 154 " 0.031 5.00e-02 4.00e+02 4.65e-02 3.46e+00 pdb=" N PRO A 155 " -0.080 5.00e-02 4.00e+02 pdb=" CA PRO A 155 " 0.024 5.00e-02 4.00e+02 pdb=" CD PRO A 155 " 0.026 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA LYS A 329 " -0.009 2.00e-02 2.50e+03 1.79e-02 3.19e+00 pdb=" C LYS A 329 " 0.031 2.00e-02 2.50e+03 pdb=" O LYS A 329 " -0.012 2.00e-02 2.50e+03 pdb=" N LYS A 330 " -0.010 2.00e-02 2.50e+03 ... (remaining 4325 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 2400 2.75 - 3.28: 25231 3.28 - 3.82: 40758 3.82 - 4.36: 49317 4.36 - 4.90: 84516 Nonbonded interactions: 202222 Sorted by model distance: nonbonded pdb=" O ALA A 587 " pdb=" OH TYR A 605 " model vdw 2.207 3.040 nonbonded pdb=" OG SER C 636 " pdb=" OD1 ASN C 638 " model vdw 2.208 3.040 nonbonded pdb=" N ASN B1120 " pdb=" OD1 ASN B1120 " model vdw 2.217 3.120 nonbonded pdb=" OG SER C 534 " pdb=" OD2 ASP C 536 " model vdw 2.233 3.040 nonbonded pdb=" O PRO A1067 " pdb=" NZ LYS A1073 " model vdw 2.236 3.120 ... (remaining 202217 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: 11.100 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.960 Check model and map are aligned: 0.210 Set scattering table: 0.230 Process input model: 58.490 Find NCS groups from input model: 0.440 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.810 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 74.350 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7914 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 24690 Z= 0.144 Angle : 0.484 12.168 33495 Z= 0.270 Chirality : 0.045 0.407 3739 Planarity : 0.003 0.047 4328 Dihedral : 11.643 88.752 9104 Min Nonbonded Distance : 2.207 Molprobity Statistics. All-atom Clashscore : 8.67 Ramachandran Plot: Outliers : 0.10 % Allowed : 5.08 % Favored : 94.82 % Rotamer: Outliers : 3.19 % Allowed : 10.93 % Favored : 85.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.38 (0.16), residues: 2972 helix: 1.63 (0.17), residues: 951 sheet: 0.21 (0.22), residues: 563 loop : -0.63 (0.16), residues: 1458 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 920 HIS 0.002 0.001 HIS B 762 PHE 0.014 0.001 PHE B1024 TYR 0.016 0.001 TYR B 870 ARG 0.002 0.000 ARG B 937 Details of bonding type rmsd hydrogen bonds : bond 0.12077 ( 1069) hydrogen bonds : angle 5.97883 ( 3027) SS BOND : bond 0.00257 ( 1) SS BOND : angle 0.63510 ( 2) covalent geometry : bond 0.00305 (24689) covalent geometry : angle 0.48407 (33493) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5944 Ramachandran restraints generated. 2972 Oldfield, 0 Emsley, 2972 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5944 Ramachandran restraints generated. 2972 Oldfield, 0 Emsley, 2972 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 362 residues out of total 2760 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 275 time to evaluate : 2.542 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 378 GLU cc_start: 0.6744 (OUTLIER) cc_final: 0.6494 (tm-30) REVERT: C 698 ASN cc_start: 0.1708 (p0) cc_final: 0.1495 (p0) REVERT: A 16 ARG cc_start: 0.7066 (mtm-85) cc_final: 0.6540 (mtm-85) REVERT: A 123 GLN cc_start: 0.8179 (pt0) cc_final: 0.7542 (tp40) REVERT: A 291 VAL cc_start: 0.6129 (OUTLIER) cc_final: 0.5620 (m) REVERT: A 628 LEU cc_start: 0.9192 (mt) cc_final: 0.8846 (mt) REVERT: A 808 GLN cc_start: 0.7979 (mt0) cc_final: 0.7752 (mt0) REVERT: A 812 ASN cc_start: 0.8133 (m110) cc_final: 0.7830 (m110) REVERT: A 1040 ARG cc_start: 0.8613 (OUTLIER) cc_final: 0.8292 (ptp-170) REVERT: A 1126 LYS cc_start: 0.7598 (OUTLIER) cc_final: 0.7348 (mtmm) REVERT: B 115 GLU cc_start: 0.8366 (OUTLIER) cc_final: 0.8116 (mp0) REVERT: B 278 TYR cc_start: 0.8754 (m-80) cc_final: 0.8441 (m-80) REVERT: B 337 LYS cc_start: 0.8914 (ttmm) cc_final: 0.8632 (tttm) REVERT: B 488 LYS cc_start: 0.8979 (mtpt) cc_final: 0.8720 (mtpp) REVERT: B 512 LYS cc_start: 0.8309 (tmmt) cc_final: 0.8007 (ptmm) REVERT: B 619 TYR cc_start: 0.7854 (t80) cc_final: 0.7585 (t80) REVERT: B 792 LEU cc_start: 0.8389 (OUTLIER) cc_final: 0.8011 (tt) REVERT: B 1103 ASN cc_start: 0.7830 (p0) cc_final: 0.7478 (p0) REVERT: B 1151 ILE cc_start: 0.7986 (mm) cc_final: 0.7492 (tp) REVERT: B 1154 LYS cc_start: 0.8881 (ttpt) cc_final: 0.8613 (ttmm) outliers start: 87 outliers final: 43 residues processed: 350 average time/residue: 0.3286 time to fit residues: 183.9843 Evaluate side-chains 242 residues out of total 2760 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 193 time to evaluate : 2.596 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 179 VAL Chi-restraints excluded: chain C residue 242 ILE Chi-restraints excluded: chain C residue 295 ASN Chi-restraints excluded: chain C residue 305 THR Chi-restraints excluded: chain C residue 319 LEU Chi-restraints excluded: chain C residue 343 LEU Chi-restraints excluded: chain C residue 378 GLU Chi-restraints excluded: chain C residue 382 LEU Chi-restraints excluded: chain C residue 506 VAL Chi-restraints excluded: chain C residue 683 LEU Chi-restraints excluded: chain C residue 716 ILE Chi-restraints excluded: chain A residue 150 ILE Chi-restraints excluded: chain A residue 258 THR Chi-restraints excluded: chain A residue 260 LEU Chi-restraints excluded: chain A residue 291 VAL Chi-restraints excluded: chain A residue 319 VAL Chi-restraints excluded: chain A residue 405 VAL Chi-restraints excluded: chain A residue 416 VAL Chi-restraints excluded: chain A residue 425 ILE Chi-restraints excluded: chain A residue 467 ASP Chi-restraints excluded: chain A residue 488 LEU Chi-restraints excluded: chain A residue 495 ASP Chi-restraints excluded: chain A residue 519 VAL Chi-restraints excluded: chain A residue 528 VAL Chi-restraints excluded: chain A residue 535 VAL Chi-restraints excluded: chain A residue 641 LEU Chi-restraints excluded: chain A residue 728 LEU Chi-restraints excluded: chain A residue 782 LEU Chi-restraints excluded: chain A residue 906 ILE Chi-restraints excluded: chain A residue 911 LYS Chi-restraints excluded: chain A residue 914 ASN Chi-restraints excluded: chain A residue 1040 ARG Chi-restraints excluded: chain A residue 1126 LYS Chi-restraints excluded: chain A residue 1127 VAL Chi-restraints excluded: chain A residue 1129 ILE Chi-restraints excluded: chain A residue 1236 ASN Chi-restraints excluded: chain B residue 93 VAL Chi-restraints excluded: chain B residue 115 GLU Chi-restraints excluded: chain B residue 133 THR Chi-restraints excluded: chain B residue 137 VAL Chi-restraints excluded: chain B residue 293 ILE Chi-restraints excluded: chain B residue 332 VAL Chi-restraints excluded: chain B residue 782 MET Chi-restraints excluded: chain B residue 792 LEU Chi-restraints excluded: chain B residue 869 ILE Chi-restraints excluded: chain B residue 1009 ASN Chi-restraints excluded: chain B residue 1109 ILE Chi-restraints excluded: chain B residue 1120 ASN Chi-restraints excluded: chain B residue 1141 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 250 optimal weight: 1.9990 chunk 225 optimal weight: 0.0060 chunk 124 optimal weight: 1.9990 chunk 76 optimal weight: 2.9990 chunk 151 optimal weight: 3.9990 chunk 120 optimal weight: 3.9990 chunk 232 optimal weight: 0.7980 chunk 90 optimal weight: 0.6980 chunk 141 optimal weight: 3.9990 chunk 173 optimal weight: 6.9990 chunk 269 optimal weight: 3.9990 overall best weight: 1.1000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 185 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 402 ASN C 509 HIS C 637 GLN ** C 732 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 147 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 290 GLN A 376 ASN A 518 ASN A 757 ASN A 988 ASN A1151 ASN A1182 ASN ** B 17 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 311 GLN B 408 ASN B 443 ASN B 614 ASN ** B 948 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1047 ASN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3875 r_free = 0.3875 target = 0.139274 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3359 r_free = 0.3359 target = 0.103965 restraints weight = 44629.260| |-----------------------------------------------------------------------------| r_work (start): 0.3339 rms_B_bonded: 3.06 r_work: 0.3063 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work (final): 0.3063 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8411 moved from start: 0.0827 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 24690 Z= 0.171 Angle : 0.536 10.134 33495 Z= 0.285 Chirality : 0.046 0.228 3739 Planarity : 0.003 0.043 4328 Dihedral : 6.240 59.572 3296 Min Nonbonded Distance : 2.337 Molprobity Statistics. All-atom Clashscore : 7.42 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.05 % Favored : 94.89 % Rotamer: Outliers : 3.48 % Allowed : 13.60 % Favored : 82.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.34 (0.16), residues: 2972 helix: 1.65 (0.17), residues: 949 sheet: 0.17 (0.22), residues: 559 loop : -0.68 (0.16), residues: 1464 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 500 HIS 0.008 0.001 HIS B 762 PHE 0.024 0.001 PHE A 475 TYR 0.021 0.001 TYR A 738 ARG 0.005 0.000 ARG B 672 Details of bonding type rmsd hydrogen bonds : bond 0.03796 ( 1069) hydrogen bonds : angle 4.78993 ( 3027) SS BOND : bond 0.00041 ( 1) SS BOND : angle 0.25088 ( 2) covalent geometry : bond 0.00392 (24689) covalent geometry : angle 0.53587 (33493) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5944 Ramachandran restraints generated. 2972 Oldfield, 0 Emsley, 2972 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5944 Ramachandran restraints generated. 2972 Oldfield, 0 Emsley, 2972 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 305 residues out of total 2760 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 210 time to evaluate : 2.543 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 369 MET cc_start: 0.5960 (ppp) cc_final: 0.5576 (ppp) REVERT: C 698 ASN cc_start: 0.1694 (p0) cc_final: 0.1478 (p0) REVERT: A 16 ARG cc_start: 0.7478 (mtm-85) cc_final: 0.6994 (mtm-85) REVERT: A 123 GLN cc_start: 0.8102 (pt0) cc_final: 0.7900 (tp40) REVERT: A 291 VAL cc_start: 0.5709 (OUTLIER) cc_final: 0.5452 (m) REVERT: A 303 PHE cc_start: 0.7435 (m-80) cc_final: 0.7123 (m-80) REVERT: A 628 LEU cc_start: 0.9342 (mt) cc_final: 0.9015 (mt) REVERT: A 808 GLN cc_start: 0.8250 (mt0) cc_final: 0.8017 (mt0) REVERT: A 812 ASN cc_start: 0.8820 (m110) cc_final: 0.8608 (m110) REVERT: A 1040 ARG cc_start: 0.8699 (OUTLIER) cc_final: 0.8323 (ptp-110) REVERT: A 1126 LYS cc_start: 0.7972 (OUTLIER) cc_final: 0.7689 (ttmm) REVERT: B 488 LYS cc_start: 0.8991 (mtpt) cc_final: 0.8767 (mtpp) REVERT: B 787 ASN cc_start: 0.8183 (p0) cc_final: 0.7918 (p0) REVERT: B 792 LEU cc_start: 0.8889 (OUTLIER) cc_final: 0.8576 (tt) REVERT: B 1103 ASN cc_start: 0.8216 (p0) cc_final: 0.7993 (p0) REVERT: B 1151 ILE cc_start: 0.7911 (mm) cc_final: 0.7626 (tp) outliers start: 95 outliers final: 54 residues processed: 292 average time/residue: 0.3363 time to fit residues: 159.4484 Evaluate side-chains 250 residues out of total 2760 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 192 time to evaluate : 2.645 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 242 ILE Chi-restraints excluded: chain C residue 282 PHE Chi-restraints excluded: chain C residue 305 THR Chi-restraints excluded: chain C residue 319 LEU Chi-restraints excluded: chain C residue 382 LEU Chi-restraints excluded: chain C residue 506 VAL Chi-restraints excluded: chain C residue 651 ASN Chi-restraints excluded: chain C residue 656 ILE Chi-restraints excluded: chain C residue 683 LEU Chi-restraints excluded: chain C residue 716 ILE Chi-restraints excluded: chain A residue 53 GLN Chi-restraints excluded: chain A residue 150 ILE Chi-restraints excluded: chain A residue 209 THR Chi-restraints excluded: chain A residue 258 THR Chi-restraints excluded: chain A residue 260 LEU Chi-restraints excluded: chain A residue 291 VAL Chi-restraints excluded: chain A residue 319 VAL Chi-restraints excluded: chain A residue 405 VAL Chi-restraints excluded: chain A residue 416 VAL Chi-restraints excluded: chain A residue 425 ILE Chi-restraints excluded: chain A residue 488 LEU Chi-restraints excluded: chain A residue 495 ASP Chi-restraints excluded: chain A residue 519 VAL Chi-restraints excluded: chain A residue 528 VAL Chi-restraints excluded: chain A residue 535 VAL Chi-restraints excluded: chain A residue 641 LEU Chi-restraints excluded: chain A residue 779 ILE Chi-restraints excluded: chain A residue 782 LEU Chi-restraints excluded: chain A residue 906 ILE Chi-restraints excluded: chain A residue 911 LYS Chi-restraints excluded: chain A residue 914 ASN Chi-restraints excluded: chain A residue 938 THR Chi-restraints excluded: chain A residue 988 ASN Chi-restraints excluded: chain A residue 1040 ARG Chi-restraints excluded: chain A residue 1126 LYS Chi-restraints excluded: chain A residue 1127 VAL Chi-restraints excluded: chain A residue 1129 ILE Chi-restraints excluded: chain A residue 1166 THR Chi-restraints excluded: chain A residue 1236 ASN Chi-restraints excluded: chain B residue 93 VAL Chi-restraints excluded: chain B residue 137 VAL Chi-restraints excluded: chain B residue 293 ILE Chi-restraints excluded: chain B residue 332 VAL Chi-restraints excluded: chain B residue 518 ASP Chi-restraints excluded: chain B residue 648 LEU Chi-restraints excluded: chain B residue 687 LEU Chi-restraints excluded: chain B residue 712 LYS Chi-restraints excluded: chain B residue 721 VAL Chi-restraints excluded: chain B residue 782 MET Chi-restraints excluded: chain B residue 792 LEU Chi-restraints excluded: chain B residue 830 LYS Chi-restraints excluded: chain B residue 869 ILE Chi-restraints excluded: chain B residue 992 ASN Chi-restraints excluded: chain B residue 1046 ILE Chi-restraints excluded: chain B residue 1085 THR Chi-restraints excluded: chain B residue 1109 ILE Chi-restraints excluded: chain B residue 1120 ASN Chi-restraints excluded: chain B residue 1141 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 125 optimal weight: 0.9990 chunk 102 optimal weight: 6.9990 chunk 281 optimal weight: 2.9990 chunk 92 optimal weight: 0.8980 chunk 94 optimal weight: 0.8980 chunk 27 optimal weight: 0.7980 chunk 25 optimal weight: 0.5980 chunk 289 optimal weight: 0.7980 chunk 155 optimal weight: 0.9980 chunk 277 optimal weight: 3.9990 chunk 104 optimal weight: 5.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 185 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 402 ASN ** C 732 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 147 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 489 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 518 ASN A 956 HIS ** A 988 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1236 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 17 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 948 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1106 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3884 r_free = 0.3884 target = 0.139896 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3359 r_free = 0.3359 target = 0.103833 restraints weight = 44278.435| |-----------------------------------------------------------------------------| r_work (start): 0.3324 rms_B_bonded: 2.96 r_work: 0.3051 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work (final): 0.3051 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8403 moved from start: 0.1032 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 24690 Z= 0.136 Angle : 0.505 9.293 33495 Z= 0.268 Chirality : 0.045 0.209 3739 Planarity : 0.003 0.043 4328 Dihedral : 5.888 59.540 3278 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 7.36 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.95 % Favored : 94.95 % Rotamer: Outliers : 3.85 % Allowed : 13.82 % Favored : 82.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.40 (0.16), residues: 2972 helix: 1.70 (0.17), residues: 950 sheet: 0.24 (0.22), residues: 548 loop : -0.67 (0.16), residues: 1474 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 500 HIS 0.007 0.001 HIS B 762 PHE 0.021 0.001 PHE B 774 TYR 0.022 0.001 TYR A 738 ARG 0.003 0.000 ARG B 672 Details of bonding type rmsd hydrogen bonds : bond 0.03437 ( 1069) hydrogen bonds : angle 4.58480 ( 3027) SS BOND : bond 0.00043 ( 1) SS BOND : angle 0.18944 ( 2) covalent geometry : bond 0.00308 (24689) covalent geometry : angle 0.50506 (33493) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5944 Ramachandran restraints generated. 2972 Oldfield, 0 Emsley, 2972 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5944 Ramachandran restraints generated. 2972 Oldfield, 0 Emsley, 2972 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 316 residues out of total 2760 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 105 poor density : 211 time to evaluate : 2.995 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 369 MET cc_start: 0.6584 (ppp) cc_final: 0.6286 (ppp) REVERT: C 698 ASN cc_start: 0.1620 (p0) cc_final: 0.1393 (p0) REVERT: C 741 LEU cc_start: 0.6983 (OUTLIER) cc_final: 0.6711 (tp) REVERT: A 8 ASN cc_start: 0.7643 (OUTLIER) cc_final: 0.7213 (m-40) REVERT: A 16 ARG cc_start: 0.7441 (mtm-85) cc_final: 0.6964 (mtm-85) REVERT: A 123 GLN cc_start: 0.8140 (pt0) cc_final: 0.7825 (tp40) REVERT: A 253 LEU cc_start: 0.8767 (OUTLIER) cc_final: 0.8400 (mp) REVERT: A 291 VAL cc_start: 0.5771 (OUTLIER) cc_final: 0.5188 (m) REVERT: A 303 PHE cc_start: 0.7478 (m-80) cc_final: 0.7147 (m-80) REVERT: A 808 GLN cc_start: 0.8211 (mt0) cc_final: 0.7979 (mt0) REVERT: A 812 ASN cc_start: 0.8801 (m110) cc_final: 0.8574 (m110) REVERT: A 1040 ARG cc_start: 0.8675 (OUTLIER) cc_final: 0.8342 (ptp-110) REVERT: A 1126 LYS cc_start: 0.7951 (OUTLIER) cc_final: 0.7644 (ttmm) REVERT: B 24 ARG cc_start: 0.8673 (OUTLIER) cc_final: 0.6569 (mpt-90) REVERT: B 787 ASN cc_start: 0.8289 (p0) cc_final: 0.8024 (p0) REVERT: B 792 LEU cc_start: 0.8892 (OUTLIER) cc_final: 0.8632 (tt) REVERT: B 1103 ASN cc_start: 0.8238 (p0) cc_final: 0.8007 (p0) REVERT: B 1151 ILE cc_start: 0.7904 (mm) cc_final: 0.7596 (tp) outliers start: 105 outliers final: 61 residues processed: 295 average time/residue: 0.3341 time to fit residues: 160.2746 Evaluate side-chains 256 residues out of total 2760 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 187 time to evaluate : 2.675 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 242 ILE Chi-restraints excluded: chain C residue 305 THR Chi-restraints excluded: chain C residue 319 LEU Chi-restraints excluded: chain C residue 343 LEU Chi-restraints excluded: chain C residue 382 LEU Chi-restraints excluded: chain C residue 429 HIS Chi-restraints excluded: chain C residue 491 VAL Chi-restraints excluded: chain C residue 506 VAL Chi-restraints excluded: chain C residue 618 LEU Chi-restraints excluded: chain C residue 651 ASN Chi-restraints excluded: chain C residue 656 ILE Chi-restraints excluded: chain C residue 683 LEU Chi-restraints excluded: chain C residue 716 ILE Chi-restraints excluded: chain C residue 741 LEU Chi-restraints excluded: chain A residue 8 ASN Chi-restraints excluded: chain A residue 53 GLN Chi-restraints excluded: chain A residue 66 SER Chi-restraints excluded: chain A residue 150 ILE Chi-restraints excluded: chain A residue 209 THR Chi-restraints excluded: chain A residue 253 LEU Chi-restraints excluded: chain A residue 258 THR Chi-restraints excluded: chain A residue 260 LEU Chi-restraints excluded: chain A residue 291 VAL Chi-restraints excluded: chain A residue 319 VAL Chi-restraints excluded: chain A residue 405 VAL Chi-restraints excluded: chain A residue 416 VAL Chi-restraints excluded: chain A residue 425 ILE Chi-restraints excluded: chain A residue 467 ASP Chi-restraints excluded: chain A residue 488 LEU Chi-restraints excluded: chain A residue 495 ASP Chi-restraints excluded: chain A residue 519 VAL Chi-restraints excluded: chain A residue 528 VAL Chi-restraints excluded: chain A residue 535 VAL Chi-restraints excluded: chain A residue 606 ILE Chi-restraints excluded: chain A residue 641 LEU Chi-restraints excluded: chain A residue 779 ILE Chi-restraints excluded: chain A residue 782 LEU Chi-restraints excluded: chain A residue 834 LYS Chi-restraints excluded: chain A residue 906 ILE Chi-restraints excluded: chain A residue 911 LYS Chi-restraints excluded: chain A residue 914 ASN Chi-restraints excluded: chain A residue 938 THR Chi-restraints excluded: chain A residue 1040 ARG Chi-restraints excluded: chain A residue 1126 LYS Chi-restraints excluded: chain A residue 1129 ILE Chi-restraints excluded: chain A residue 1166 THR Chi-restraints excluded: chain B residue 3 ILE Chi-restraints excluded: chain B residue 24 ARG Chi-restraints excluded: chain B residue 93 VAL Chi-restraints excluded: chain B residue 133 THR Chi-restraints excluded: chain B residue 137 VAL Chi-restraints excluded: chain B residue 293 ILE Chi-restraints excluded: chain B residue 332 VAL Chi-restraints excluded: chain B residue 487 LEU Chi-restraints excluded: chain B residue 518 ASP Chi-restraints excluded: chain B residue 687 LEU Chi-restraints excluded: chain B residue 721 VAL Chi-restraints excluded: chain B residue 782 MET Chi-restraints excluded: chain B residue 792 LEU Chi-restraints excluded: chain B residue 810 GLU Chi-restraints excluded: chain B residue 816 ILE Chi-restraints excluded: chain B residue 830 LYS Chi-restraints excluded: chain B residue 869 ILE Chi-restraints excluded: chain B residue 907 ASN Chi-restraints excluded: chain B residue 992 ASN Chi-restraints excluded: chain B residue 1000 SER Chi-restraints excluded: chain B residue 1109 ILE Chi-restraints excluded: chain B residue 1120 ASN Chi-restraints excluded: chain B residue 1141 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 132 optimal weight: 2.9990 chunk 128 optimal weight: 3.9990 chunk 184 optimal weight: 2.9990 chunk 85 optimal weight: 1.9990 chunk 86 optimal weight: 0.9990 chunk 145 optimal weight: 0.7980 chunk 11 optimal weight: 6.9990 chunk 244 optimal weight: 1.9990 chunk 256 optimal weight: 8.9990 chunk 238 optimal weight: 1.9990 chunk 125 optimal weight: 0.5980 overall best weight: 1.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 185 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 402 ASN ** C 732 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 518 ASN A 988 ASN ** A1236 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 17 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 948 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1025 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3866 r_free = 0.3866 target = 0.138632 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.103834 restraints weight = 44733.349| |-----------------------------------------------------------------------------| r_work (start): 0.3332 rms_B_bonded: 2.92 r_work: 0.3049 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.2919 rms_B_bonded: 4.84 restraints_weight: 0.2500 r_work (final): 0.2919 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8521 moved from start: 0.1191 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 24690 Z= 0.186 Angle : 0.529 8.262 33495 Z= 0.281 Chirality : 0.046 0.201 3739 Planarity : 0.003 0.043 4328 Dihedral : 5.990 59.692 3275 Min Nonbonded Distance : 2.356 Molprobity Statistics. All-atom Clashscore : 8.11 Ramachandran Plot: Outliers : 0.10 % Allowed : 5.28 % Favored : 94.62 % Rotamer: Outliers : 4.14 % Allowed : 14.52 % Favored : 81.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.28 (0.15), residues: 2972 helix: 1.58 (0.17), residues: 951 sheet: 0.11 (0.22), residues: 538 loop : -0.69 (0.16), residues: 1483 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 689 HIS 0.006 0.001 HIS B 762 PHE 0.021 0.001 PHE B 774 TYR 0.021 0.001 TYR A 738 ARG 0.005 0.000 ARG B 672 Details of bonding type rmsd hydrogen bonds : bond 0.03551 ( 1069) hydrogen bonds : angle 4.59684 ( 3027) SS BOND : bond 0.00003 ( 1) SS BOND : angle 0.14464 ( 2) covalent geometry : bond 0.00430 (24689) covalent geometry : angle 0.52947 (33493) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5944 Ramachandran restraints generated. 2972 Oldfield, 0 Emsley, 2972 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5944 Ramachandran restraints generated. 2972 Oldfield, 0 Emsley, 2972 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 305 residues out of total 2760 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 113 poor density : 192 time to evaluate : 2.588 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 220 MET cc_start: 0.6792 (tpp) cc_final: 0.6482 (tpp) REVERT: C 231 PHE cc_start: 0.8088 (OUTLIER) cc_final: 0.7655 (m-10) REVERT: C 369 MET cc_start: 0.6693 (ppp) cc_final: 0.6406 (ppp) REVERT: C 698 ASN cc_start: 0.1500 (p0) cc_final: 0.0671 (t0) REVERT: C 741 LEU cc_start: 0.6913 (OUTLIER) cc_final: 0.6604 (tp) REVERT: A 8 ASN cc_start: 0.7677 (OUTLIER) cc_final: 0.7273 (m-40) REVERT: A 16 ARG cc_start: 0.7519 (mtm-85) cc_final: 0.7000 (mtm-85) REVERT: A 123 GLN cc_start: 0.8295 (pt0) cc_final: 0.7860 (tp40) REVERT: A 253 LEU cc_start: 0.8955 (OUTLIER) cc_final: 0.8572 (mp) REVERT: A 291 VAL cc_start: 0.5691 (OUTLIER) cc_final: 0.5333 (m) REVERT: A 303 PHE cc_start: 0.7694 (m-80) cc_final: 0.7354 (m-80) REVERT: A 808 GLN cc_start: 0.8264 (mt0) cc_final: 0.7991 (mt0) REVERT: A 812 ASN cc_start: 0.8812 (m110) cc_final: 0.8564 (m110) REVERT: A 1040 ARG cc_start: 0.8791 (OUTLIER) cc_final: 0.8448 (ptp-110) REVERT: A 1126 LYS cc_start: 0.8153 (OUTLIER) cc_final: 0.7905 (mtmm) REVERT: B 24 ARG cc_start: 0.8672 (OUTLIER) cc_final: 0.6514 (mpt-90) REVERT: B 787 ASN cc_start: 0.8497 (p0) cc_final: 0.8263 (p0) REVERT: B 792 LEU cc_start: 0.8978 (OUTLIER) cc_final: 0.8725 (tt) REVERT: B 810 GLU cc_start: 0.7220 (OUTLIER) cc_final: 0.6467 (tp30) REVERT: B 1151 ILE cc_start: 0.8070 (mm) cc_final: 0.7788 (tp) outliers start: 113 outliers final: 70 residues processed: 289 average time/residue: 0.3197 time to fit residues: 150.6854 Evaluate side-chains 261 residues out of total 2760 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 181 time to evaluate : 2.544 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 231 PHE Chi-restraints excluded: chain C residue 242 ILE Chi-restraints excluded: chain C residue 282 PHE Chi-restraints excluded: chain C residue 304 ILE Chi-restraints excluded: chain C residue 305 THR Chi-restraints excluded: chain C residue 319 LEU Chi-restraints excluded: chain C residue 343 LEU Chi-restraints excluded: chain C residue 382 LEU Chi-restraints excluded: chain C residue 491 VAL Chi-restraints excluded: chain C residue 506 VAL Chi-restraints excluded: chain C residue 618 LEU Chi-restraints excluded: chain C residue 651 ASN Chi-restraints excluded: chain C residue 656 ILE Chi-restraints excluded: chain C residue 683 LEU Chi-restraints excluded: chain C residue 716 ILE Chi-restraints excluded: chain C residue 741 LEU Chi-restraints excluded: chain A residue 8 ASN Chi-restraints excluded: chain A residue 53 GLN Chi-restraints excluded: chain A residue 66 SER Chi-restraints excluded: chain A residue 150 ILE Chi-restraints excluded: chain A residue 209 THR Chi-restraints excluded: chain A residue 253 LEU Chi-restraints excluded: chain A residue 258 THR Chi-restraints excluded: chain A residue 260 LEU Chi-restraints excluded: chain A residue 291 VAL Chi-restraints excluded: chain A residue 319 VAL Chi-restraints excluded: chain A residue 405 VAL Chi-restraints excluded: chain A residue 416 VAL Chi-restraints excluded: chain A residue 425 ILE Chi-restraints excluded: chain A residue 467 ASP Chi-restraints excluded: chain A residue 488 LEU Chi-restraints excluded: chain A residue 495 ASP Chi-restraints excluded: chain A residue 509 ILE Chi-restraints excluded: chain A residue 519 VAL Chi-restraints excluded: chain A residue 528 VAL Chi-restraints excluded: chain A residue 535 VAL Chi-restraints excluded: chain A residue 606 ILE Chi-restraints excluded: chain A residue 641 LEU Chi-restraints excluded: chain A residue 779 ILE Chi-restraints excluded: chain A residue 782 LEU Chi-restraints excluded: chain A residue 831 THR Chi-restraints excluded: chain A residue 834 LYS Chi-restraints excluded: chain A residue 906 ILE Chi-restraints excluded: chain A residue 911 LYS Chi-restraints excluded: chain A residue 914 ASN Chi-restraints excluded: chain A residue 938 THR Chi-restraints excluded: chain A residue 988 ASN Chi-restraints excluded: chain A residue 1040 ARG Chi-restraints excluded: chain A residue 1126 LYS Chi-restraints excluded: chain A residue 1129 ILE Chi-restraints excluded: chain A residue 1166 THR Chi-restraints excluded: chain B residue 3 ILE Chi-restraints excluded: chain B residue 24 ARG Chi-restraints excluded: chain B residue 93 VAL Chi-restraints excluded: chain B residue 100 SER Chi-restraints excluded: chain B residue 133 THR Chi-restraints excluded: chain B residue 137 VAL Chi-restraints excluded: chain B residue 196 SER Chi-restraints excluded: chain B residue 293 ILE Chi-restraints excluded: chain B residue 332 VAL Chi-restraints excluded: chain B residue 487 LEU Chi-restraints excluded: chain B residue 518 ASP Chi-restraints excluded: chain B residue 648 LEU Chi-restraints excluded: chain B residue 687 LEU Chi-restraints excluded: chain B residue 712 LYS Chi-restraints excluded: chain B residue 721 VAL Chi-restraints excluded: chain B residue 782 MET Chi-restraints excluded: chain B residue 792 LEU Chi-restraints excluded: chain B residue 810 GLU Chi-restraints excluded: chain B residue 816 ILE Chi-restraints excluded: chain B residue 830 LYS Chi-restraints excluded: chain B residue 869 ILE Chi-restraints excluded: chain B residue 907 ASN Chi-restraints excluded: chain B residue 992 ASN Chi-restraints excluded: chain B residue 1000 SER Chi-restraints excluded: chain B residue 1026 TYR Chi-restraints excluded: chain B residue 1085 THR Chi-restraints excluded: chain B residue 1109 ILE Chi-restraints excluded: chain B residue 1120 ASN Chi-restraints excluded: chain B residue 1141 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 249 optimal weight: 0.9990 chunk 109 optimal weight: 0.8980 chunk 99 optimal weight: 0.8980 chunk 0 optimal weight: 9.9990 chunk 265 optimal weight: 4.9990 chunk 184 optimal weight: 0.6980 chunk 193 optimal weight: 2.9990 chunk 47 optimal weight: 30.0000 chunk 242 optimal weight: 3.9990 chunk 181 optimal weight: 3.9990 chunk 134 optimal weight: 0.8980 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 185 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 402 ASN ** C 732 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 988 ASN ** A1096 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1236 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 17 ASN ** B 948 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1016 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1025 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3876 r_free = 0.3876 target = 0.139371 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3360 r_free = 0.3360 target = 0.103824 restraints weight = 44806.123| |-----------------------------------------------------------------------------| r_work (start): 0.3331 rms_B_bonded: 3.00 r_work: 0.3049 rms_B_bonded: 3.30 restraints_weight: 0.5000 r_work (final): 0.3049 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8413 moved from start: 0.1268 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 24690 Z= 0.144 Angle : 0.511 9.949 33495 Z= 0.270 Chirality : 0.045 0.206 3739 Planarity : 0.003 0.044 4328 Dihedral : 5.905 58.163 3275 Min Nonbonded Distance : 2.335 Molprobity Statistics. All-atom Clashscore : 7.90 Ramachandran Plot: Outliers : 0.10 % Allowed : 5.08 % Favored : 94.82 % Rotamer: Outliers : 3.67 % Allowed : 15.58 % Favored : 80.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.28 (0.16), residues: 2972 helix: 1.61 (0.17), residues: 957 sheet: 0.09 (0.22), residues: 548 loop : -0.72 (0.16), residues: 1467 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 689 HIS 0.006 0.001 HIS B 762 PHE 0.021 0.001 PHE B 774 TYR 0.023 0.001 TYR A 738 ARG 0.004 0.000 ARG B1019 Details of bonding type rmsd hydrogen bonds : bond 0.03359 ( 1069) hydrogen bonds : angle 4.51916 ( 3027) SS BOND : bond 0.00031 ( 1) SS BOND : angle 0.15474 ( 2) covalent geometry : bond 0.00328 (24689) covalent geometry : angle 0.51100 (33493) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5944 Ramachandran restraints generated. 2972 Oldfield, 0 Emsley, 2972 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5944 Ramachandran restraints generated. 2972 Oldfield, 0 Emsley, 2972 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 301 residues out of total 2760 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 100 poor density : 201 time to evaluate : 2.588 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 184 MET cc_start: 0.8765 (tmm) cc_final: 0.8546 (tmm) REVERT: C 220 MET cc_start: 0.6993 (tpp) cc_final: 0.6669 (tpp) REVERT: C 231 PHE cc_start: 0.8066 (OUTLIER) cc_final: 0.7652 (m-10) REVERT: C 369 MET cc_start: 0.6825 (ppp) cc_final: 0.6521 (ppp) REVERT: C 378 GLU cc_start: 0.6721 (OUTLIER) cc_final: 0.6235 (tp30) REVERT: C 698 ASN cc_start: 0.1332 (p0) cc_final: 0.0540 (t0) REVERT: C 741 LEU cc_start: 0.6947 (OUTLIER) cc_final: 0.6671 (tp) REVERT: A 8 ASN cc_start: 0.7638 (OUTLIER) cc_final: 0.7217 (m-40) REVERT: A 16 ARG cc_start: 0.7431 (mtm-85) cc_final: 0.6951 (mtm-85) REVERT: A 123 GLN cc_start: 0.8147 (pt0) cc_final: 0.7908 (tp40) REVERT: A 253 LEU cc_start: 0.8811 (OUTLIER) cc_final: 0.8428 (mp) REVERT: A 291 VAL cc_start: 0.5540 (OUTLIER) cc_final: 0.5248 (m) REVERT: A 303 PHE cc_start: 0.7591 (m-80) cc_final: 0.7318 (m-80) REVERT: A 812 ASN cc_start: 0.8808 (m110) cc_final: 0.8576 (m110) REVERT: A 1040 ARG cc_start: 0.8661 (OUTLIER) cc_final: 0.8330 (ptp-110) REVERT: A 1126 LYS cc_start: 0.7971 (OUTLIER) cc_final: 0.7723 (mtmm) REVERT: B 24 ARG cc_start: 0.8640 (OUTLIER) cc_final: 0.6362 (mpt-90) REVERT: B 25 LYS cc_start: 0.8910 (OUTLIER) cc_final: 0.8396 (ptmt) REVERT: B 787 ASN cc_start: 0.8413 (p0) cc_final: 0.8120 (p0) REVERT: B 792 LEU cc_start: 0.8882 (OUTLIER) cc_final: 0.8646 (tt) REVERT: B 810 GLU cc_start: 0.6981 (OUTLIER) cc_final: 0.6231 (tp30) REVERT: B 1151 ILE cc_start: 0.7910 (mm) cc_final: 0.7640 (tp) outliers start: 100 outliers final: 74 residues processed: 286 average time/residue: 0.3287 time to fit residues: 151.7416 Evaluate side-chains 274 residues out of total 2760 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 188 time to evaluate : 2.545 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 231 PHE Chi-restraints excluded: chain C residue 242 ILE Chi-restraints excluded: chain C residue 282 PHE Chi-restraints excluded: chain C residue 304 ILE Chi-restraints excluded: chain C residue 305 THR Chi-restraints excluded: chain C residue 319 LEU Chi-restraints excluded: chain C residue 343 LEU Chi-restraints excluded: chain C residue 378 GLU Chi-restraints excluded: chain C residue 382 LEU Chi-restraints excluded: chain C residue 456 THR Chi-restraints excluded: chain C residue 491 VAL Chi-restraints excluded: chain C residue 506 VAL Chi-restraints excluded: chain C residue 618 LEU Chi-restraints excluded: chain C residue 651 ASN Chi-restraints excluded: chain C residue 656 ILE Chi-restraints excluded: chain C residue 683 LEU Chi-restraints excluded: chain C residue 716 ILE Chi-restraints excluded: chain C residue 741 LEU Chi-restraints excluded: chain A residue 8 ASN Chi-restraints excluded: chain A residue 53 GLN Chi-restraints excluded: chain A residue 66 SER Chi-restraints excluded: chain A residue 150 ILE Chi-restraints excluded: chain A residue 209 THR Chi-restraints excluded: chain A residue 244 ILE Chi-restraints excluded: chain A residue 253 LEU Chi-restraints excluded: chain A residue 258 THR Chi-restraints excluded: chain A residue 260 LEU Chi-restraints excluded: chain A residue 291 VAL Chi-restraints excluded: chain A residue 319 VAL Chi-restraints excluded: chain A residue 405 VAL Chi-restraints excluded: chain A residue 416 VAL Chi-restraints excluded: chain A residue 425 ILE Chi-restraints excluded: chain A residue 467 ASP Chi-restraints excluded: chain A residue 488 LEU Chi-restraints excluded: chain A residue 495 ASP Chi-restraints excluded: chain A residue 509 ILE Chi-restraints excluded: chain A residue 519 VAL Chi-restraints excluded: chain A residue 528 VAL Chi-restraints excluded: chain A residue 535 VAL Chi-restraints excluded: chain A residue 606 ILE Chi-restraints excluded: chain A residue 641 LEU Chi-restraints excluded: chain A residue 779 ILE Chi-restraints excluded: chain A residue 782 LEU Chi-restraints excluded: chain A residue 831 THR Chi-restraints excluded: chain A residue 834 LYS Chi-restraints excluded: chain A residue 906 ILE Chi-restraints excluded: chain A residue 911 LYS Chi-restraints excluded: chain A residue 914 ASN Chi-restraints excluded: chain A residue 938 THR Chi-restraints excluded: chain A residue 1040 ARG Chi-restraints excluded: chain A residue 1126 LYS Chi-restraints excluded: chain A residue 1129 ILE Chi-restraints excluded: chain A residue 1166 THR Chi-restraints excluded: chain A residue 1236 ASN Chi-restraints excluded: chain B residue 3 ILE Chi-restraints excluded: chain B residue 24 ARG Chi-restraints excluded: chain B residue 25 LYS Chi-restraints excluded: chain B residue 93 VAL Chi-restraints excluded: chain B residue 100 SER Chi-restraints excluded: chain B residue 133 THR Chi-restraints excluded: chain B residue 137 VAL Chi-restraints excluded: chain B residue 293 ILE Chi-restraints excluded: chain B residue 332 VAL Chi-restraints excluded: chain B residue 487 LEU Chi-restraints excluded: chain B residue 518 ASP Chi-restraints excluded: chain B residue 648 LEU Chi-restraints excluded: chain B residue 687 LEU Chi-restraints excluded: chain B residue 721 VAL Chi-restraints excluded: chain B residue 782 MET Chi-restraints excluded: chain B residue 785 LEU Chi-restraints excluded: chain B residue 792 LEU Chi-restraints excluded: chain B residue 810 GLU Chi-restraints excluded: chain B residue 811 GLN Chi-restraints excluded: chain B residue 816 ILE Chi-restraints excluded: chain B residue 830 LYS Chi-restraints excluded: chain B residue 869 ILE Chi-restraints excluded: chain B residue 892 ASN Chi-restraints excluded: chain B residue 907 ASN Chi-restraints excluded: chain B residue 992 ASN Chi-restraints excluded: chain B residue 1000 SER Chi-restraints excluded: chain B residue 1026 TYR Chi-restraints excluded: chain B residue 1082 LEU Chi-restraints excluded: chain B residue 1085 THR Chi-restraints excluded: chain B residue 1109 ILE Chi-restraints excluded: chain B residue 1120 ASN Chi-restraints excluded: chain B residue 1141 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 59 optimal weight: 1.9990 chunk 53 optimal weight: 6.9990 chunk 80 optimal weight: 1.9990 chunk 2 optimal weight: 3.9990 chunk 28 optimal weight: 0.4980 chunk 137 optimal weight: 0.9990 chunk 291 optimal weight: 4.9990 chunk 170 optimal weight: 0.6980 chunk 123 optimal weight: 0.6980 chunk 145 optimal weight: 0.5980 chunk 225 optimal weight: 1.9990 overall best weight: 0.6982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 185 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 402 ASN ** C 732 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1096 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1207 ASN ** A1236 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 948 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1016 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1025 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 = 0.3886 r_free = 0.3886 target = 0.140036 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3363 r_free = 0.3363 target = 0.104007 restraints weight = 44306.854| |-----------------------------------------------------------------------------| r_work (start): 0.3327 rms_B_bonded: 2.69 r_work: 0.3075 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.2946 rms_B_bonded: 4.82 restraints_weight: 0.2500 r_work (final): 0.2946 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8489 moved from start: 0.1356 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 24690 Z= 0.125 Angle : 0.496 10.822 33495 Z= 0.262 Chirality : 0.044 0.204 3739 Planarity : 0.003 0.044 4328 Dihedral : 5.771 58.489 3275 Min Nonbonded Distance : 2.333 Molprobity Statistics. All-atom Clashscore : 7.48 Ramachandran Plot: Outliers : 0.10 % Allowed : 5.15 % Favored : 94.75 % Rotamer: Outliers : 3.67 % Allowed : 15.99 % Favored : 80.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.34 (0.16), residues: 2972 helix: 1.69 (0.17), residues: 957 sheet: 0.10 (0.22), residues: 548 loop : -0.70 (0.16), residues: 1467 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 689 HIS 0.006 0.001 HIS B 762 PHE 0.024 0.001 PHE B 774 TYR 0.020 0.001 TYR A 738 ARG 0.006 0.000 ARG B 672 Details of bonding type rmsd hydrogen bonds : bond 0.03210 ( 1069) hydrogen bonds : angle 4.42004 ( 3027) SS BOND : bond 0.00022 ( 1) SS BOND : angle 0.09689 ( 2) covalent geometry : bond 0.00282 (24689) covalent geometry : angle 0.49626 (33493) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5944 Ramachandran restraints generated. 2972 Oldfield, 0 Emsley, 2972 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5944 Ramachandran restraints generated. 2972 Oldfield, 0 Emsley, 2972 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 295 residues out of total 2760 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 100 poor density : 195 time to evaluate : 2.593 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: C 220 MET cc_start: 0.7000 (tpp) cc_final: 0.6655 (tpp) REVERT: C 230 ARG cc_start: 0.7797 (ttm170) cc_final: 0.7464 (ttm170) REVERT: C 231 PHE cc_start: 0.8053 (OUTLIER) cc_final: 0.7707 (m-10) REVERT: C 303 ARG cc_start: 0.6827 (ptm160) cc_final: 0.6618 (ptm160) REVERT: C 369 MET cc_start: 0.6839 (ppp) cc_final: 0.6523 (ppp) REVERT: C 378 GLU cc_start: 0.6495 (OUTLIER) cc_final: 0.5394 (tp30) REVERT: C 698 ASN cc_start: 0.1445 (p0) cc_final: 0.0581 (t0) REVERT: C 741 LEU cc_start: 0.6931 (OUTLIER) cc_final: 0.6638 (tp) REVERT: A 8 ASN cc_start: 0.7660 (OUTLIER) cc_final: 0.7258 (m-40) REVERT: A 16 ARG cc_start: 0.7485 (mtm-85) cc_final: 0.6994 (mtm-85) REVERT: A 123 GLN cc_start: 0.8249 (pt0) cc_final: 0.7854 (tp40) REVERT: A 253 LEU cc_start: 0.8827 (OUTLIER) cc_final: 0.8553 (mp) REVERT: A 291 VAL cc_start: 0.5616 (OUTLIER) cc_final: 0.5057 (m) REVERT: A 303 PHE cc_start: 0.7630 (m-80) cc_final: 0.7310 (m-80) REVERT: A 449 ASN cc_start: 0.8611 (t0) cc_final: 0.8363 (t0) REVERT: A 808 GLN cc_start: 0.8625 (mt0) cc_final: 0.8083 (mt0) REVERT: A 812 ASN cc_start: 0.8788 (m110) cc_final: 0.8499 (m110) REVERT: A 1040 ARG cc_start: 0.8752 (OUTLIER) cc_final: 0.8412 (ptp-110) REVERT: B 24 ARG cc_start: 0.8629 (OUTLIER) cc_final: 0.6433 (mpt-90) REVERT: B 25 LYS cc_start: 0.8940 (OUTLIER) cc_final: 0.8431 (ptmt) REVERT: B 787 ASN cc_start: 0.8527 (p0) cc_final: 0.8237 (p0) REVERT: B 792 LEU cc_start: 0.8939 (OUTLIER) cc_final: 0.8680 (tt) REVERT: B 810 GLU cc_start: 0.7061 (OUTLIER) cc_final: 0.6298 (tp30) REVERT: B 1151 ILE cc_start: 0.8012 (mm) cc_final: 0.7717 (tp) outliers start: 100 outliers final: 63 residues processed: 281 average time/residue: 0.3272 time to fit residues: 149.9537 Evaluate side-chains 259 residues out of total 2760 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 185 time to evaluate : 2.800 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 231 PHE Chi-restraints excluded: chain C residue 242 ILE Chi-restraints excluded: chain C residue 282 PHE Chi-restraints excluded: chain C residue 304 ILE Chi-restraints excluded: chain C residue 305 THR Chi-restraints excluded: chain C residue 319 LEU Chi-restraints excluded: chain C residue 320 GLU Chi-restraints excluded: chain C residue 343 LEU Chi-restraints excluded: chain C residue 378 GLU Chi-restraints excluded: chain C residue 382 LEU Chi-restraints excluded: chain C residue 429 HIS Chi-restraints excluded: chain C residue 456 THR Chi-restraints excluded: chain C residue 491 VAL Chi-restraints excluded: chain C residue 506 VAL Chi-restraints excluded: chain C residue 618 LEU Chi-restraints excluded: chain C residue 651 ASN Chi-restraints excluded: chain C residue 656 ILE Chi-restraints excluded: chain C residue 683 LEU Chi-restraints excluded: chain C residue 716 ILE Chi-restraints excluded: chain C residue 741 LEU Chi-restraints excluded: chain A residue 8 ASN Chi-restraints excluded: chain A residue 53 GLN Chi-restraints excluded: chain A residue 66 SER Chi-restraints excluded: chain A residue 150 ILE Chi-restraints excluded: chain A residue 183 ILE Chi-restraints excluded: chain A residue 253 LEU Chi-restraints excluded: chain A residue 258 THR Chi-restraints excluded: chain A residue 260 LEU Chi-restraints excluded: chain A residue 291 VAL Chi-restraints excluded: chain A residue 319 VAL Chi-restraints excluded: chain A residue 331 LEU Chi-restraints excluded: chain A residue 405 VAL Chi-restraints excluded: chain A residue 416 VAL Chi-restraints excluded: chain A residue 425 ILE Chi-restraints excluded: chain A residue 488 LEU Chi-restraints excluded: chain A residue 509 ILE Chi-restraints excluded: chain A residue 528 VAL Chi-restraints excluded: chain A residue 535 VAL Chi-restraints excluded: chain A residue 606 ILE Chi-restraints excluded: chain A residue 641 LEU Chi-restraints excluded: chain A residue 779 ILE Chi-restraints excluded: chain A residue 782 LEU Chi-restraints excluded: chain A residue 831 THR Chi-restraints excluded: chain A residue 906 ILE Chi-restraints excluded: chain A residue 911 LYS Chi-restraints excluded: chain A residue 938 THR Chi-restraints excluded: chain A residue 1040 ARG Chi-restraints excluded: chain A residue 1166 THR Chi-restraints excluded: chain A residue 1236 ASN Chi-restraints excluded: chain B residue 24 ARG Chi-restraints excluded: chain B residue 25 LYS Chi-restraints excluded: chain B residue 93 VAL Chi-restraints excluded: chain B residue 100 SER Chi-restraints excluded: chain B residue 133 THR Chi-restraints excluded: chain B residue 137 VAL Chi-restraints excluded: chain B residue 293 ILE Chi-restraints excluded: chain B residue 332 VAL Chi-restraints excluded: chain B residue 487 LEU Chi-restraints excluded: chain B residue 648 LEU Chi-restraints excluded: chain B residue 687 LEU Chi-restraints excluded: chain B residue 721 VAL Chi-restraints excluded: chain B residue 782 MET Chi-restraints excluded: chain B residue 792 LEU Chi-restraints excluded: chain B residue 810 GLU Chi-restraints excluded: chain B residue 811 GLN Chi-restraints excluded: chain B residue 816 ILE Chi-restraints excluded: chain B residue 830 LYS Chi-restraints excluded: chain B residue 869 ILE Chi-restraints excluded: chain B residue 907 ASN Chi-restraints excluded: chain B residue 1000 SER Chi-restraints excluded: chain B residue 1026 TYR Chi-restraints excluded: chain B residue 1082 LEU Chi-restraints excluded: chain B residue 1085 THR Chi-restraints excluded: chain B residue 1109 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 95 optimal weight: 0.0270 chunk 167 optimal weight: 2.9990 chunk 265 optimal weight: 4.9990 chunk 267 optimal weight: 2.9990 chunk 218 optimal weight: 1.9990 chunk 171 optimal weight: 4.9990 chunk 39 optimal weight: 30.0000 chunk 249 optimal weight: 0.9990 chunk 186 optimal weight: 0.0770 chunk 112 optimal weight: 0.5980 chunk 282 optimal weight: 2.9990 overall best weight: 0.7400 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 185 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 402 ASN ** C 732 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1096 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1236 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 948 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1016 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1025 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3885 r_free = 0.3885 target = 0.139900 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3363 r_free = 0.3363 target = 0.104170 restraints weight = 44520.599| |-----------------------------------------------------------------------------| r_work (start): 0.3333 rms_B_bonded: 2.76 r_work: 0.3077 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.2947 rms_B_bonded: 4.79 restraints_weight: 0.2500 r_work (final): 0.2947 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8491 moved from start: 0.1419 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 24690 Z= 0.128 Angle : 0.504 11.397 33495 Z= 0.265 Chirality : 0.045 0.208 3739 Planarity : 0.003 0.043 4328 Dihedral : 5.569 59.379 3260 Min Nonbonded Distance : 2.304 Molprobity Statistics. All-atom Clashscore : 7.53 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.11 % Favored : 94.82 % Rotamer: Outliers : 3.81 % Allowed : 16.02 % Favored : 80.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.33 (0.16), residues: 2972 helix: 1.70 (0.17), residues: 958 sheet: 0.04 (0.22), residues: 545 loop : -0.69 (0.16), residues: 1469 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 689 HIS 0.005 0.001 HIS B 762 PHE 0.021 0.001 PHE B 774 TYR 0.022 0.001 TYR A1226 ARG 0.005 0.000 ARG B1019 Details of bonding type rmsd hydrogen bonds : bond 0.03187 ( 1069) hydrogen bonds : angle 4.38344 ( 3027) SS BOND : bond 0.00057 ( 1) SS BOND : angle 0.19105 ( 2) covalent geometry : bond 0.00292 (24689) covalent geometry : angle 0.50394 (33493) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5944 Ramachandran restraints generated. 2972 Oldfield, 0 Emsley, 2972 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5944 Ramachandran restraints generated. 2972 Oldfield, 0 Emsley, 2972 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 299 residues out of total 2760 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 104 poor density : 195 time to evaluate : 2.871 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: C 220 MET cc_start: 0.7102 (tpp) cc_final: 0.6761 (tpp) REVERT: C 230 ARG cc_start: 0.7748 (ttm170) cc_final: 0.7473 (ttm170) REVERT: C 231 PHE cc_start: 0.8056 (OUTLIER) cc_final: 0.7715 (m-10) REVERT: C 369 MET cc_start: 0.6932 (ppp) cc_final: 0.6670 (ppp) REVERT: C 378 GLU cc_start: 0.6410 (OUTLIER) cc_final: 0.5283 (tp30) REVERT: C 698 ASN cc_start: 0.1527 (p0) cc_final: 0.0648 (t0) REVERT: C 741 LEU cc_start: 0.6967 (OUTLIER) cc_final: 0.6680 (tp) REVERT: A 8 ASN cc_start: 0.7686 (OUTLIER) cc_final: 0.7284 (m-40) REVERT: A 16 ARG cc_start: 0.7496 (mtm-85) cc_final: 0.7017 (mtm-85) REVERT: A 123 GLN cc_start: 0.8248 (pt0) cc_final: 0.7865 (tp40) REVERT: A 253 LEU cc_start: 0.8836 (OUTLIER) cc_final: 0.8599 (mp) REVERT: A 291 VAL cc_start: 0.5406 (OUTLIER) cc_final: 0.4648 (m) REVERT: A 303 PHE cc_start: 0.7637 (m-10) cc_final: 0.7309 (m-80) REVERT: A 449 ASN cc_start: 0.8593 (t0) cc_final: 0.8336 (t0) REVERT: A 516 GLU cc_start: 0.8160 (OUTLIER) cc_final: 0.7725 (pp20) REVERT: A 808 GLN cc_start: 0.8623 (mt0) cc_final: 0.8225 (mm-40) REVERT: A 812 ASN cc_start: 0.8804 (m110) cc_final: 0.8527 (m110) REVERT: A 1040 ARG cc_start: 0.8728 (OUTLIER) cc_final: 0.8394 (ptp-110) REVERT: B 24 ARG cc_start: 0.8626 (OUTLIER) cc_final: 0.6454 (mpt-90) REVERT: B 25 LYS cc_start: 0.8918 (OUTLIER) cc_final: 0.8404 (ptmt) REVERT: B 787 ASN cc_start: 0.8573 (p0) cc_final: 0.8310 (p0) REVERT: B 792 LEU cc_start: 0.8913 (OUTLIER) cc_final: 0.8665 (tt) REVERT: B 810 GLU cc_start: 0.7037 (OUTLIER) cc_final: 0.6285 (tp30) REVERT: B 1151 ILE cc_start: 0.8007 (mm) cc_final: 0.7727 (tp) outliers start: 104 outliers final: 75 residues processed: 286 average time/residue: 0.3431 time to fit residues: 161.2366 Evaluate side-chains 271 residues out of total 2760 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 184 time to evaluate : 2.582 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 231 PHE Chi-restraints excluded: chain C residue 242 ILE Chi-restraints excluded: chain C residue 304 ILE Chi-restraints excluded: chain C residue 305 THR Chi-restraints excluded: chain C residue 319 LEU Chi-restraints excluded: chain C residue 320 GLU Chi-restraints excluded: chain C residue 343 LEU Chi-restraints excluded: chain C residue 378 GLU Chi-restraints excluded: chain C residue 382 LEU Chi-restraints excluded: chain C residue 456 THR Chi-restraints excluded: chain C residue 491 VAL Chi-restraints excluded: chain C residue 506 VAL Chi-restraints excluded: chain C residue 618 LEU Chi-restraints excluded: chain C residue 634 LEU Chi-restraints excluded: chain C residue 651 ASN Chi-restraints excluded: chain C residue 656 ILE Chi-restraints excluded: chain C residue 683 LEU Chi-restraints excluded: chain C residue 716 ILE Chi-restraints excluded: chain C residue 741 LEU Chi-restraints excluded: chain A residue 8 ASN Chi-restraints excluded: chain A residue 53 GLN Chi-restraints excluded: chain A residue 59 THR Chi-restraints excluded: chain A residue 66 SER Chi-restraints excluded: chain A residue 150 ILE Chi-restraints excluded: chain A residue 183 ILE Chi-restraints excluded: chain A residue 209 THR Chi-restraints excluded: chain A residue 253 LEU Chi-restraints excluded: chain A residue 258 THR Chi-restraints excluded: chain A residue 260 LEU Chi-restraints excluded: chain A residue 291 VAL Chi-restraints excluded: chain A residue 319 VAL Chi-restraints excluded: chain A residue 331 LEU Chi-restraints excluded: chain A residue 405 VAL Chi-restraints excluded: chain A residue 416 VAL Chi-restraints excluded: chain A residue 425 ILE Chi-restraints excluded: chain A residue 467 ASP Chi-restraints excluded: chain A residue 488 LEU Chi-restraints excluded: chain A residue 509 ILE Chi-restraints excluded: chain A residue 516 GLU Chi-restraints excluded: chain A residue 519 VAL Chi-restraints excluded: chain A residue 528 VAL Chi-restraints excluded: chain A residue 535 VAL Chi-restraints excluded: chain A residue 606 ILE Chi-restraints excluded: chain A residue 641 LEU Chi-restraints excluded: chain A residue 708 LEU Chi-restraints excluded: chain A residue 779 ILE Chi-restraints excluded: chain A residue 782 LEU Chi-restraints excluded: chain A residue 831 THR Chi-restraints excluded: chain A residue 834 LYS Chi-restraints excluded: chain A residue 906 ILE Chi-restraints excluded: chain A residue 911 LYS Chi-restraints excluded: chain A residue 914 ASN Chi-restraints excluded: chain A residue 938 THR Chi-restraints excluded: chain A residue 953 SER Chi-restraints excluded: chain A residue 1040 ARG Chi-restraints excluded: chain A residue 1115 ILE Chi-restraints excluded: chain A residue 1166 THR Chi-restraints excluded: chain A residue 1236 ASN Chi-restraints excluded: chain B residue 3 ILE Chi-restraints excluded: chain B residue 24 ARG Chi-restraints excluded: chain B residue 25 LYS Chi-restraints excluded: chain B residue 93 VAL Chi-restraints excluded: chain B residue 100 SER Chi-restraints excluded: chain B residue 133 THR Chi-restraints excluded: chain B residue 137 VAL Chi-restraints excluded: chain B residue 293 ILE Chi-restraints excluded: chain B residue 332 VAL Chi-restraints excluded: chain B residue 487 LEU Chi-restraints excluded: chain B residue 518 ASP Chi-restraints excluded: chain B residue 648 LEU Chi-restraints excluded: chain B residue 687 LEU Chi-restraints excluded: chain B residue 703 SER Chi-restraints excluded: chain B residue 721 VAL Chi-restraints excluded: chain B residue 782 MET Chi-restraints excluded: chain B residue 785 LEU Chi-restraints excluded: chain B residue 792 LEU Chi-restraints excluded: chain B residue 810 GLU Chi-restraints excluded: chain B residue 811 GLN Chi-restraints excluded: chain B residue 816 ILE Chi-restraints excluded: chain B residue 830 LYS Chi-restraints excluded: chain B residue 869 ILE Chi-restraints excluded: chain B residue 907 ASN Chi-restraints excluded: chain B residue 1000 SER Chi-restraints excluded: chain B residue 1026 TYR Chi-restraints excluded: chain B residue 1082 LEU Chi-restraints excluded: chain B residue 1085 THR Chi-restraints excluded: chain B residue 1109 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 116 optimal weight: 0.8980 chunk 128 optimal weight: 2.9990 chunk 54 optimal weight: 1.9990 chunk 184 optimal weight: 1.9990 chunk 238 optimal weight: 0.9990 chunk 17 optimal weight: 20.0000 chunk 288 optimal weight: 3.9990 chunk 126 optimal weight: 0.9980 chunk 50 optimal weight: 20.0000 chunk 1 optimal weight: 6.9990 chunk 225 optimal weight: 0.3980 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 185 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 402 ASN ** C 732 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1096 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1236 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 948 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1016 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1025 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3875 r_free = 0.3875 target = 0.139171 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3361 r_free = 0.3361 target = 0.103786 restraints weight = 44478.994| |-----------------------------------------------------------------------------| r_work (start): 0.3320 rms_B_bonded: 2.68 r_work: 0.3047 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work: 0.2916 rms_B_bonded: 4.97 restraints_weight: 0.2500 r_work (final): 0.2916 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8515 moved from start: 0.1451 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 24690 Z= 0.161 Angle : 0.521 9.309 33495 Z= 0.275 Chirality : 0.045 0.200 3739 Planarity : 0.003 0.043 4328 Dihedral : 5.643 58.784 3260 Min Nonbonded Distance : 2.306 Molprobity Statistics. All-atom Clashscore : 7.53 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.18 % Favored : 94.75 % Rotamer: Outliers : 3.70 % Allowed : 16.39 % Favored : 79.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.29 (0.16), residues: 2972 helix: 1.66 (0.17), residues: 952 sheet: 0.00 (0.22), residues: 534 loop : -0.69 (0.16), residues: 1486 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B1142 HIS 0.005 0.001 HIS B 762 PHE 0.020 0.001 PHE B 774 TYR 0.025 0.001 TYR A 738 ARG 0.007 0.000 ARG B 672 Details of bonding type rmsd hydrogen bonds : bond 0.03355 ( 1069) hydrogen bonds : angle 4.43132 ( 3027) SS BOND : bond 0.00054 ( 1) SS BOND : angle 0.23167 ( 2) covalent geometry : bond 0.00372 (24689) covalent geometry : angle 0.52105 (33493) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5944 Ramachandran restraints generated. 2972 Oldfield, 0 Emsley, 2972 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5944 Ramachandran restraints generated. 2972 Oldfield, 0 Emsley, 2972 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 289 residues out of total 2760 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 101 poor density : 188 time to evaluate : 2.910 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 220 MET cc_start: 0.7207 (tpp) cc_final: 0.6870 (tpp) REVERT: C 230 ARG cc_start: 0.7745 (ttm170) cc_final: 0.7516 (ttm170) REVERT: C 231 PHE cc_start: 0.8025 (OUTLIER) cc_final: 0.7726 (m-10) REVERT: C 698 ASN cc_start: 0.1425 (p0) cc_final: 0.0519 (t0) REVERT: C 741 LEU cc_start: 0.6925 (OUTLIER) cc_final: 0.6616 (tp) REVERT: A 8 ASN cc_start: 0.7729 (OUTLIER) cc_final: 0.7358 (m-40) REVERT: A 16 ARG cc_start: 0.7520 (mtm-85) cc_final: 0.7032 (mtm-85) REVERT: A 123 GLN cc_start: 0.8257 (pt0) cc_final: 0.7867 (tp40) REVERT: A 253 LEU cc_start: 0.8890 (OUTLIER) cc_final: 0.8588 (mp) REVERT: A 291 VAL cc_start: 0.5251 (OUTLIER) cc_final: 0.4412 (m) REVERT: A 449 ASN cc_start: 0.8579 (t0) cc_final: 0.8340 (t0) REVERT: A 516 GLU cc_start: 0.8169 (OUTLIER) cc_final: 0.7731 (pp20) REVERT: A 808 GLN cc_start: 0.8640 (mt0) cc_final: 0.8208 (mm-40) REVERT: A 812 ASN cc_start: 0.8822 (m110) cc_final: 0.8538 (m110) REVERT: A 1040 ARG cc_start: 0.8751 (OUTLIER) cc_final: 0.8418 (ptp-110) REVERT: B 24 ARG cc_start: 0.8636 (OUTLIER) cc_final: 0.6451 (mpt-90) REVERT: B 25 LYS cc_start: 0.8945 (OUTLIER) cc_final: 0.8407 (ptmt) REVERT: B 787 ASN cc_start: 0.8648 (p0) cc_final: 0.8407 (p0) REVERT: B 810 GLU cc_start: 0.7156 (OUTLIER) cc_final: 0.6369 (tp30) REVERT: B 1151 ILE cc_start: 0.8024 (mm) cc_final: 0.7735 (tp) outliers start: 101 outliers final: 75 residues processed: 276 average time/residue: 0.3338 time to fit residues: 151.7107 Evaluate side-chains 269 residues out of total 2760 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 184 time to evaluate : 2.556 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 231 PHE Chi-restraints excluded: chain C residue 242 ILE Chi-restraints excluded: chain C residue 304 ILE Chi-restraints excluded: chain C residue 305 THR Chi-restraints excluded: chain C residue 319 LEU Chi-restraints excluded: chain C residue 320 GLU Chi-restraints excluded: chain C residue 343 LEU Chi-restraints excluded: chain C residue 382 LEU Chi-restraints excluded: chain C residue 456 THR Chi-restraints excluded: chain C residue 491 VAL Chi-restraints excluded: chain C residue 506 VAL Chi-restraints excluded: chain C residue 617 LEU Chi-restraints excluded: chain C residue 618 LEU Chi-restraints excluded: chain C residue 634 LEU Chi-restraints excluded: chain C residue 651 ASN Chi-restraints excluded: chain C residue 656 ILE Chi-restraints excluded: chain C residue 683 LEU Chi-restraints excluded: chain C residue 716 ILE Chi-restraints excluded: chain C residue 741 LEU Chi-restraints excluded: chain A residue 8 ASN Chi-restraints excluded: chain A residue 53 GLN Chi-restraints excluded: chain A residue 59 THR Chi-restraints excluded: chain A residue 66 SER Chi-restraints excluded: chain A residue 150 ILE Chi-restraints excluded: chain A residue 183 ILE Chi-restraints excluded: chain A residue 209 THR Chi-restraints excluded: chain A residue 253 LEU Chi-restraints excluded: chain A residue 258 THR Chi-restraints excluded: chain A residue 260 LEU Chi-restraints excluded: chain A residue 291 VAL Chi-restraints excluded: chain A residue 296 LEU Chi-restraints excluded: chain A residue 319 VAL Chi-restraints excluded: chain A residue 331 LEU Chi-restraints excluded: chain A residue 405 VAL Chi-restraints excluded: chain A residue 416 VAL Chi-restraints excluded: chain A residue 425 ILE Chi-restraints excluded: chain A residue 467 ASP Chi-restraints excluded: chain A residue 488 LEU Chi-restraints excluded: chain A residue 509 ILE Chi-restraints excluded: chain A residue 516 GLU Chi-restraints excluded: chain A residue 519 VAL Chi-restraints excluded: chain A residue 528 VAL Chi-restraints excluded: chain A residue 535 VAL Chi-restraints excluded: chain A residue 606 ILE Chi-restraints excluded: chain A residue 641 LEU Chi-restraints excluded: chain A residue 708 LEU Chi-restraints excluded: chain A residue 779 ILE Chi-restraints excluded: chain A residue 782 LEU Chi-restraints excluded: chain A residue 831 THR Chi-restraints excluded: chain A residue 834 LYS Chi-restraints excluded: chain A residue 906 ILE Chi-restraints excluded: chain A residue 911 LYS Chi-restraints excluded: chain A residue 914 ASN Chi-restraints excluded: chain A residue 938 THR Chi-restraints excluded: chain A residue 953 SER Chi-restraints excluded: chain A residue 1040 ARG Chi-restraints excluded: chain A residue 1115 ILE Chi-restraints excluded: chain A residue 1166 THR Chi-restraints excluded: chain A residue 1236 ASN Chi-restraints excluded: chain B residue 3 ILE Chi-restraints excluded: chain B residue 24 ARG Chi-restraints excluded: chain B residue 25 LYS Chi-restraints excluded: chain B residue 93 VAL Chi-restraints excluded: chain B residue 133 THR Chi-restraints excluded: chain B residue 137 VAL Chi-restraints excluded: chain B residue 293 ILE Chi-restraints excluded: chain B residue 332 VAL Chi-restraints excluded: chain B residue 518 ASP Chi-restraints excluded: chain B residue 648 LEU Chi-restraints excluded: chain B residue 687 LEU Chi-restraints excluded: chain B residue 703 SER Chi-restraints excluded: chain B residue 721 VAL Chi-restraints excluded: chain B residue 782 MET Chi-restraints excluded: chain B residue 810 GLU Chi-restraints excluded: chain B residue 811 GLN Chi-restraints excluded: chain B residue 816 ILE Chi-restraints excluded: chain B residue 830 LYS Chi-restraints excluded: chain B residue 869 ILE Chi-restraints excluded: chain B residue 907 ASN Chi-restraints excluded: chain B residue 1000 SER Chi-restraints excluded: chain B residue 1026 TYR Chi-restraints excluded: chain B residue 1082 LEU Chi-restraints excluded: chain B residue 1085 THR Chi-restraints excluded: chain B residue 1109 ILE Chi-restraints excluded: chain B residue 1116 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 40 optimal weight: 0.7980 chunk 12 optimal weight: 0.0470 chunk 109 optimal weight: 2.9990 chunk 294 optimal weight: 0.6980 chunk 218 optimal weight: 2.9990 chunk 66 optimal weight: 4.9990 chunk 169 optimal weight: 4.9990 chunk 242 optimal weight: 0.6980 chunk 108 optimal weight: 1.9990 chunk 226 optimal weight: 0.8980 chunk 189 optimal weight: 0.9980 overall best weight: 0.6278 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 185 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 402 ASN ** C 732 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1096 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1236 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 948 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1016 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1025 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3888 r_free = 0.3888 target = 0.140220 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.104299 restraints weight = 44801.378| |-----------------------------------------------------------------------------| r_work (start): 0.3331 rms_B_bonded: 2.99 r_work: 0.3054 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work (final): 0.3054 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8397 moved from start: 0.1509 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 24690 Z= 0.120 Angle : 0.514 14.059 33495 Z= 0.269 Chirality : 0.045 0.204 3739 Planarity : 0.003 0.043 4328 Dihedral : 5.476 59.788 3258 Min Nonbonded Distance : 2.258 Molprobity Statistics. All-atom Clashscore : 7.48 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.08 % Favored : 94.89 % Rotamer: Outliers : 3.23 % Allowed : 16.91 % Favored : 79.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.34 (0.16), residues: 2972 helix: 1.71 (0.17), residues: 959 sheet: 0.07 (0.22), residues: 543 loop : -0.69 (0.16), residues: 1470 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A1224 HIS 0.005 0.001 HIS B 762 PHE 0.026 0.001 PHE A 303 TYR 0.023 0.001 TYR A1226 ARG 0.006 0.000 ARG B1019 Details of bonding type rmsd hydrogen bonds : bond 0.03165 ( 1069) hydrogen bonds : angle 4.37307 ( 3027) SS BOND : bond 0.00054 ( 1) SS BOND : angle 0.19191 ( 2) covalent geometry : bond 0.00270 (24689) covalent geometry : angle 0.51406 (33493) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5944 Ramachandran restraints generated. 2972 Oldfield, 0 Emsley, 2972 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5944 Ramachandran restraints generated. 2972 Oldfield, 0 Emsley, 2972 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 280 residues out of total 2760 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 192 time to evaluate : 2.554 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: C 168 LEU cc_start: 0.2096 (pp) cc_final: 0.1839 (pp) REVERT: C 220 MET cc_start: 0.7080 (tpp) cc_final: 0.6745 (tpp) REVERT: C 231 PHE cc_start: 0.8113 (OUTLIER) cc_final: 0.7762 (m-10) REVERT: C 698 ASN cc_start: 0.1564 (p0) cc_final: 0.0647 (t0) REVERT: C 741 LEU cc_start: 0.6912 (OUTLIER) cc_final: 0.6610 (tp) REVERT: A 8 ASN cc_start: 0.7723 (OUTLIER) cc_final: 0.7333 (m-40) REVERT: A 16 ARG cc_start: 0.7443 (mtm-85) cc_final: 0.6977 (mtm-85) REVERT: A 123 GLN cc_start: 0.8142 (pt0) cc_final: 0.7851 (tp40) REVERT: A 253 LEU cc_start: 0.8726 (OUTLIER) cc_final: 0.8495 (mp) REVERT: A 291 VAL cc_start: 0.5157 (OUTLIER) cc_final: 0.4397 (m) REVERT: A 303 PHE cc_start: 0.7455 (m-80) cc_final: 0.7042 (m-80) REVERT: A 449 ASN cc_start: 0.8503 (t0) cc_final: 0.8273 (t0) REVERT: A 516 GLU cc_start: 0.8056 (OUTLIER) cc_final: 0.7597 (pp20) REVERT: A 628 LEU cc_start: 0.9319 (mt) cc_final: 0.8996 (mt) REVERT: A 808 GLN cc_start: 0.8577 (mt0) cc_final: 0.8240 (mm-40) REVERT: A 812 ASN cc_start: 0.8784 (m110) cc_final: 0.8494 (m110) REVERT: A 1040 ARG cc_start: 0.8680 (OUTLIER) cc_final: 0.8367 (ptp-110) REVERT: B 24 ARG cc_start: 0.8577 (OUTLIER) cc_final: 0.6402 (mpt-90) REVERT: B 25 LYS cc_start: 0.8861 (OUTLIER) cc_final: 0.8362 (ptmt) REVERT: B 787 ASN cc_start: 0.8532 (p0) cc_final: 0.8273 (p0) REVERT: B 810 GLU cc_start: 0.6901 (OUTLIER) cc_final: 0.6144 (tp30) REVERT: B 1151 ILE cc_start: 0.7882 (mm) cc_final: 0.7585 (tp) outliers start: 88 outliers final: 67 residues processed: 267 average time/residue: 0.3378 time to fit residues: 146.6722 Evaluate side-chains 260 residues out of total 2760 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 183 time to evaluate : 2.672 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 231 PHE Chi-restraints excluded: chain C residue 242 ILE Chi-restraints excluded: chain C residue 304 ILE Chi-restraints excluded: chain C residue 305 THR Chi-restraints excluded: chain C residue 319 LEU Chi-restraints excluded: chain C residue 320 GLU Chi-restraints excluded: chain C residue 382 LEU Chi-restraints excluded: chain C residue 412 LEU Chi-restraints excluded: chain C residue 456 THR Chi-restraints excluded: chain C residue 491 VAL Chi-restraints excluded: chain C residue 506 VAL Chi-restraints excluded: chain C residue 617 LEU Chi-restraints excluded: chain C residue 618 LEU Chi-restraints excluded: chain C residue 634 LEU Chi-restraints excluded: chain C residue 651 ASN Chi-restraints excluded: chain C residue 656 ILE Chi-restraints excluded: chain C residue 683 LEU Chi-restraints excluded: chain C residue 716 ILE Chi-restraints excluded: chain C residue 741 LEU Chi-restraints excluded: chain A residue 8 ASN Chi-restraints excluded: chain A residue 53 GLN Chi-restraints excluded: chain A residue 150 ILE Chi-restraints excluded: chain A residue 183 ILE Chi-restraints excluded: chain A residue 253 LEU Chi-restraints excluded: chain A residue 258 THR Chi-restraints excluded: chain A residue 260 LEU Chi-restraints excluded: chain A residue 291 VAL Chi-restraints excluded: chain A residue 296 LEU Chi-restraints excluded: chain A residue 319 VAL Chi-restraints excluded: chain A residue 405 VAL Chi-restraints excluded: chain A residue 416 VAL Chi-restraints excluded: chain A residue 425 ILE Chi-restraints excluded: chain A residue 467 ASP Chi-restraints excluded: chain A residue 488 LEU Chi-restraints excluded: chain A residue 509 ILE Chi-restraints excluded: chain A residue 516 GLU Chi-restraints excluded: chain A residue 519 VAL Chi-restraints excluded: chain A residue 528 VAL Chi-restraints excluded: chain A residue 535 VAL Chi-restraints excluded: chain A residue 606 ILE Chi-restraints excluded: chain A residue 641 LEU Chi-restraints excluded: chain A residue 779 ILE Chi-restraints excluded: chain A residue 782 LEU Chi-restraints excluded: chain A residue 831 THR Chi-restraints excluded: chain A residue 834 LYS Chi-restraints excluded: chain A residue 911 LYS Chi-restraints excluded: chain A residue 938 THR Chi-restraints excluded: chain A residue 1040 ARG Chi-restraints excluded: chain A residue 1115 ILE Chi-restraints excluded: chain A residue 1166 THR Chi-restraints excluded: chain A residue 1236 ASN Chi-restraints excluded: chain B residue 24 ARG Chi-restraints excluded: chain B residue 25 LYS Chi-restraints excluded: chain B residue 93 VAL Chi-restraints excluded: chain B residue 133 THR Chi-restraints excluded: chain B residue 137 VAL Chi-restraints excluded: chain B residue 293 ILE Chi-restraints excluded: chain B residue 332 VAL Chi-restraints excluded: chain B residue 487 LEU Chi-restraints excluded: chain B residue 518 ASP Chi-restraints excluded: chain B residue 648 LEU Chi-restraints excluded: chain B residue 687 LEU Chi-restraints excluded: chain B residue 703 SER Chi-restraints excluded: chain B residue 721 VAL Chi-restraints excluded: chain B residue 782 MET Chi-restraints excluded: chain B residue 785 LEU Chi-restraints excluded: chain B residue 810 GLU Chi-restraints excluded: chain B residue 811 GLN Chi-restraints excluded: chain B residue 816 ILE Chi-restraints excluded: chain B residue 830 LYS Chi-restraints excluded: chain B residue 869 ILE Chi-restraints excluded: chain B residue 907 ASN Chi-restraints excluded: chain B residue 1000 SER Chi-restraints excluded: chain B residue 1026 TYR Chi-restraints excluded: chain B residue 1082 LEU Chi-restraints excluded: chain B residue 1109 ILE Chi-restraints excluded: chain B residue 1116 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 6 optimal weight: 0.8980 chunk 68 optimal weight: 0.0970 chunk 91 optimal weight: 3.9990 chunk 231 optimal weight: 2.9990 chunk 198 optimal weight: 0.8980 chunk 83 optimal weight: 3.9990 chunk 119 optimal weight: 2.9990 chunk 250 optimal weight: 1.9990 chunk 10 optimal weight: 0.2980 chunk 84 optimal weight: 0.5980 chunk 23 optimal weight: 0.8980 overall best weight: 0.5578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 185 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 402 ASN C 651 ASN ** C 732 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 757 ASN ** A1096 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1236 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 948 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1016 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3892 r_free = 0.3892 target = 0.140499 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.105255 restraints weight = 44582.295| |-----------------------------------------------------------------------------| r_work (start): 0.3350 rms_B_bonded: 2.94 r_work: 0.3076 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work (final): 0.3076 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8380 moved from start: 0.1566 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 24690 Z= 0.114 Angle : 0.512 11.917 33495 Z= 0.268 Chirality : 0.044 0.200 3739 Planarity : 0.003 0.047 4328 Dihedral : 5.331 59.551 3256 Min Nonbonded Distance : 2.256 Molprobity Statistics. All-atom Clashscore : 7.46 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.18 % Favored : 94.78 % Rotamer: Outliers : 3.04 % Allowed : 17.27 % Favored : 79.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.35 (0.16), residues: 2972 helix: 1.73 (0.17), residues: 962 sheet: 0.09 (0.22), residues: 542 loop : -0.71 (0.16), residues: 1468 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 928 HIS 0.005 0.001 HIS B 762 PHE 0.026 0.001 PHE A 303 TYR 0.022 0.001 TYR A 738 ARG 0.010 0.000 ARG B 672 Details of bonding type rmsd hydrogen bonds : bond 0.03094 ( 1069) hydrogen bonds : angle 4.33552 ( 3027) SS BOND : bond 0.00062 ( 1) SS BOND : angle 0.17646 ( 2) covalent geometry : bond 0.00256 (24689) covalent geometry : angle 0.51197 (33493) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5944 Ramachandran restraints generated. 2972 Oldfield, 0 Emsley, 2972 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5944 Ramachandran restraints generated. 2972 Oldfield, 0 Emsley, 2972 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 273 residues out of total 2760 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 190 time to evaluate : 2.762 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 168 LEU cc_start: 0.2185 (pp) cc_final: 0.1929 (pp) REVERT: C 220 MET cc_start: 0.7058 (tpp) cc_final: 0.6742 (tpp) REVERT: C 231 PHE cc_start: 0.8060 (OUTLIER) cc_final: 0.7716 (m-10) REVERT: C 698 ASN cc_start: 0.1640 (p0) cc_final: 0.0704 (t0) REVERT: C 741 LEU cc_start: 0.6949 (OUTLIER) cc_final: 0.6663 (tp) REVERT: A 8 ASN cc_start: 0.7725 (OUTLIER) cc_final: 0.7336 (m-40) REVERT: A 16 ARG cc_start: 0.7413 (mtm-85) cc_final: 0.6942 (mtm-85) REVERT: A 123 GLN cc_start: 0.8075 (pt0) cc_final: 0.7818 (tp40) REVERT: A 291 VAL cc_start: 0.5147 (OUTLIER) cc_final: 0.4347 (m) REVERT: A 303 PHE cc_start: 0.7465 (m-80) cc_final: 0.7111 (m-80) REVERT: A 516 GLU cc_start: 0.8042 (OUTLIER) cc_final: 0.7577 (pp20) REVERT: A 808 GLN cc_start: 0.8571 (mt0) cc_final: 0.8275 (mm-40) REVERT: A 812 ASN cc_start: 0.8763 (m110) cc_final: 0.8475 (m110) REVERT: A 1040 ARG cc_start: 0.8662 (OUTLIER) cc_final: 0.8358 (ptp-110) REVERT: B 24 ARG cc_start: 0.8556 (OUTLIER) cc_final: 0.6408 (mpt-90) REVERT: B 25 LYS cc_start: 0.8846 (OUTLIER) cc_final: 0.8372 (ptmt) REVERT: B 675 MET cc_start: 0.8376 (ttm) cc_final: 0.8161 (ttm) REVERT: B 787 ASN cc_start: 0.8519 (p0) cc_final: 0.8266 (p0) REVERT: B 810 GLU cc_start: 0.6881 (OUTLIER) cc_final: 0.6077 (tp30) REVERT: B 1151 ILE cc_start: 0.7864 (mm) cc_final: 0.7562 (tp) outliers start: 83 outliers final: 67 residues processed: 260 average time/residue: 0.3513 time to fit residues: 149.0197 Evaluate side-chains 257 residues out of total 2760 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 181 time to evaluate : 2.858 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 231 PHE Chi-restraints excluded: chain C residue 304 ILE Chi-restraints excluded: chain C residue 305 THR Chi-restraints excluded: chain C residue 319 LEU Chi-restraints excluded: chain C residue 320 GLU Chi-restraints excluded: chain C residue 343 LEU Chi-restraints excluded: chain C residue 382 LEU Chi-restraints excluded: chain C residue 412 LEU Chi-restraints excluded: chain C residue 456 THR Chi-restraints excluded: chain C residue 491 VAL Chi-restraints excluded: chain C residue 506 VAL Chi-restraints excluded: chain C residue 617 LEU Chi-restraints excluded: chain C residue 618 LEU Chi-restraints excluded: chain C residue 634 LEU Chi-restraints excluded: chain C residue 651 ASN Chi-restraints excluded: chain C residue 656 ILE Chi-restraints excluded: chain C residue 683 LEU Chi-restraints excluded: chain C residue 716 ILE Chi-restraints excluded: chain C residue 741 LEU Chi-restraints excluded: chain A residue 8 ASN Chi-restraints excluded: chain A residue 53 GLN Chi-restraints excluded: chain A residue 59 THR Chi-restraints excluded: chain A residue 150 ILE Chi-restraints excluded: chain A residue 183 ILE Chi-restraints excluded: chain A residue 209 THR Chi-restraints excluded: chain A residue 258 THR Chi-restraints excluded: chain A residue 260 LEU Chi-restraints excluded: chain A residue 291 VAL Chi-restraints excluded: chain A residue 296 LEU Chi-restraints excluded: chain A residue 319 VAL Chi-restraints excluded: chain A residue 405 VAL Chi-restraints excluded: chain A residue 416 VAL Chi-restraints excluded: chain A residue 425 ILE Chi-restraints excluded: chain A residue 467 ASP Chi-restraints excluded: chain A residue 488 LEU Chi-restraints excluded: chain A residue 509 ILE Chi-restraints excluded: chain A residue 516 GLU Chi-restraints excluded: chain A residue 519 VAL Chi-restraints excluded: chain A residue 528 VAL Chi-restraints excluded: chain A residue 606 ILE Chi-restraints excluded: chain A residue 641 LEU Chi-restraints excluded: chain A residue 782 LEU Chi-restraints excluded: chain A residue 831 THR Chi-restraints excluded: chain A residue 834 LYS Chi-restraints excluded: chain A residue 911 LYS Chi-restraints excluded: chain A residue 938 THR Chi-restraints excluded: chain A residue 953 SER Chi-restraints excluded: chain A residue 1040 ARG Chi-restraints excluded: chain A residue 1115 ILE Chi-restraints excluded: chain A residue 1166 THR Chi-restraints excluded: chain A residue 1236 ASN Chi-restraints excluded: chain B residue 24 ARG Chi-restraints excluded: chain B residue 25 LYS Chi-restraints excluded: chain B residue 93 VAL Chi-restraints excluded: chain B residue 133 THR Chi-restraints excluded: chain B residue 137 VAL Chi-restraints excluded: chain B residue 293 ILE Chi-restraints excluded: chain B residue 487 LEU Chi-restraints excluded: chain B residue 518 ASP Chi-restraints excluded: chain B residue 648 LEU Chi-restraints excluded: chain B residue 687 LEU Chi-restraints excluded: chain B residue 703 SER Chi-restraints excluded: chain B residue 721 VAL Chi-restraints excluded: chain B residue 782 MET Chi-restraints excluded: chain B residue 785 LEU Chi-restraints excluded: chain B residue 810 GLU Chi-restraints excluded: chain B residue 811 GLN Chi-restraints excluded: chain B residue 816 ILE Chi-restraints excluded: chain B residue 869 ILE Chi-restraints excluded: chain B residue 907 ASN Chi-restraints excluded: chain B residue 1000 SER Chi-restraints excluded: chain B residue 1026 TYR Chi-restraints excluded: chain B residue 1082 LEU Chi-restraints excluded: chain B residue 1109 ILE Chi-restraints excluded: chain B residue 1116 ILE Chi-restraints excluded: chain B residue 1120 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 92 optimal weight: 0.9990 chunk 44 optimal weight: 50.0000 chunk 109 optimal weight: 0.9980 chunk 108 optimal weight: 1.9990 chunk 116 optimal weight: 0.7980 chunk 103 optimal weight: 3.9990 chunk 132 optimal weight: 0.5980 chunk 18 optimal weight: 2.9990 chunk 127 optimal weight: 0.5980 chunk 63 optimal weight: 2.9990 chunk 229 optimal weight: 0.9980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 185 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 402 ASN ** C 732 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 390 ASN ** A1096 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1232 HIS ** A1236 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 948 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1016 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1025 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3886 r_free = 0.3886 target = 0.140040 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.104439 restraints weight = 44604.778| |-----------------------------------------------------------------------------| r_work (start): 0.3333 rms_B_bonded: 3.01 r_work: 0.3058 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work (final): 0.3058 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8396 moved from start: 0.1580 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 24690 Z= 0.135 Angle : 0.518 11.578 33495 Z= 0.271 Chirality : 0.045 0.198 3739 Planarity : 0.003 0.046 4328 Dihedral : 5.322 59.998 3252 Min Nonbonded Distance : 2.277 Molprobity Statistics. All-atom Clashscore : 7.61 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.25 % Favored : 94.72 % Rotamer: Outliers : 3.04 % Allowed : 17.38 % Favored : 79.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.33 (0.16), residues: 2972 helix: 1.70 (0.17), residues: 962 sheet: 0.03 (0.22), residues: 555 loop : -0.69 (0.16), residues: 1455 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A1224 HIS 0.005 0.001 HIS B 762 PHE 0.024 0.001 PHE A 303 TYR 0.023 0.001 TYR A 738 ARG 0.006 0.000 ARG B1019 Details of bonding type rmsd hydrogen bonds : bond 0.03176 ( 1069) hydrogen bonds : angle 4.36368 ( 3027) SS BOND : bond 0.00057 ( 1) SS BOND : angle 0.18262 ( 2) covalent geometry : bond 0.00309 (24689) covalent geometry : angle 0.51766 (33493) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 12142.15 seconds wall clock time: 212 minutes 41.67 seconds (12761.67 seconds total)