Starting phenix.real_space_refine on Sat Jun 21 03:08:50 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9arj_43784/06_2025/9arj_43784.cif Found real_map, /net/cci-nas-00/data/ceres_data/9arj_43784/06_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_43784/06_2025/9arj_43784.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9arj_43784/06_2025/9arj_43784.map" model { file = "/net/cci-nas-00/data/ceres_data/9arj_43784/06_2025/9arj_43784.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9arj_43784/06_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): 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/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: 15.28, per 1000 atoms: 0.63 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: 6.14 Conformation dependent library (CDL) restraints added in 3.1 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: 3.75 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: 11.47 Time building geometry restraints manager: 7.34 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: 8.770 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 1.080 Check model and map are aligned: 0.170 Set scattering table: 0.240 Process input model: 60.290 Find NCS groups from input model: 0.380 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.880 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 73.910 ------------------------------------------------------------------------------- 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 : 2.737 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: 0.3382 time to fit residues: 189.5639 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 : 2.611 ------------------------------------------------------------------------------- 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 = 0.103967 restraints weight = 44629.351| |-----------------------------------------------------------------------------| 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 4.78994 ( 3027) SS BOND : bond 0.00041 ( 1) SS BOND : angle 0.25094 ( 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 : 2.814 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 369 MET cc_start: 0.5959 (ppp) cc_final: 0.5576 (ppp) REVERT: C 698 ASN cc_start: 0.1692 (p0) cc_final: 0.1476 (p0) REVERT: A 16 ARG cc_start: 0.7478 (mtm-85) cc_final: 0.6994 (mtm-85) REVERT: A 123 GLN cc_start: 0.8107 (pt0) cc_final: 0.7896 (tp40) REVERT: A 291 VAL cc_start: 0.5713 (OUTLIER) cc_final: 0.5456 (m) REVERT: A 303 PHE cc_start: 0.7433 (m-80) cc_final: 0.7119 (m-80) REVERT: A 628 LEU cc_start: 0.9343 (mt) cc_final: 0.9016 (mt) REVERT: A 808 GLN cc_start: 0.8250 (mt0) cc_final: 0.8017 (mt0) REVERT: A 812 ASN cc_start: 0.8821 (m110) cc_final: 0.8607 (m110) REVERT: A 1040 ARG cc_start: 0.8699 (OUTLIER) cc_final: 0.8324 (ptp-110) REVERT: A 1126 LYS cc_start: 0.7973 (OUTLIER) cc_final: 0.7690 (ttmm) REVERT: B 488 LYS cc_start: 0.8992 (mtpt) cc_final: 0.8768 (mtpp) REVERT: B 787 ASN cc_start: 0.8184 (p0) cc_final: 0.7919 (p0) REVERT: B 792 LEU cc_start: 0.8890 (OUTLIER) cc_final: 0.8578 (tt) REVERT: B 1103 ASN cc_start: 0.8217 (p0) cc_final: 0.7992 (p0) REVERT: B 1151 ILE cc_start: 0.7912 (mm) cc_final: 0.7627 (tp) outliers start: 95 outliers final: 54 residues processed: 292 average time/residue: 0.3502 time to fit residues: 165.2898 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 : 2.836 ------------------------------------------------------------------------------- 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: 0.9980 chunk 102 optimal weight: 6.9990 chunk 281 optimal weight: 0.0470 chunk 92 optimal weight: 0.6980 chunk 94 optimal weight: 0.9980 chunk 27 optimal weight: 0.5980 chunk 25 optimal weight: 1.9990 chunk 289 optimal weight: 1.9990 chunk 155 optimal weight: 0.9990 chunk 277 optimal weight: 4.9990 chunk 104 optimal weight: 4.9990 overall best weight: 0.6678 ------------------------------------------------------------------------------- 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** A1207 ASN ** A1236 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 17 ASN ** 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: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3889 r_free = 0.3889 target = 0.140279 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.104458 restraints weight = 44275.064| |-----------------------------------------------------------------------------| r_work (start): 0.3335 rms_B_bonded: 2.99 r_work: 0.3059 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work (final): 0.3059 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8393 moved from start: 0.1045 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= 0.124 Angle : 0.500 9.271 33495 Z= 0.265 Chirality : 0.044 0.205 3739 Planarity : 0.003 0.044 4328 Dihedral : 5.846 59.784 3278 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 7.15 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.81 % Favored : 95.09 % Rotamer: Outliers : 3.67 % Allowed : 14.08 % Favored : 82.25 % 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: 0.43 (0.16), residues: 2972 helix: 1.73 (0.17), residues: 950 sheet: 0.21 (0.22), residues: 561 loop : -0.63 (0.16), residues: 1461 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 0.022 0.001 PHE B 774 TYR 0.020 0.001 TYR A 738 ARG 0.003 0.000 ARG B 672 Details of bonding type rmsd hydrogen bonds : bond 0.03373 ( 1069) hydrogen bonds : angle 4.55528 ( 3027) SS BOND : bond 0.00044 ( 1) SS BOND : angle 0.22619 ( 2) covalent geometry : bond 0.00277 (24689) covalent geometry : angle 0.49955 (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 313 residues out of total 2760 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 100 poor density : 213 time to evaluate : 2.763 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 369 MET cc_start: 0.6599 (ppp) cc_final: 0.6320 (ppp) REVERT: C 698 ASN cc_start: 0.1579 (p0) cc_final: 0.1360 (p0) REVERT: C 741 LEU cc_start: 0.6935 (OUTLIER) cc_final: 0.6649 (tp) REVERT: A 8 ASN cc_start: 0.7642 (OUTLIER) cc_final: 0.7216 (m-40) REVERT: A 16 ARG cc_start: 0.7459 (mtm-85) cc_final: 0.6990 (mtm-85) REVERT: A 123 GLN cc_start: 0.8123 (pt0) cc_final: 0.7832 (tp40) REVERT: A 253 LEU cc_start: 0.8760 (OUTLIER) cc_final: 0.8399 (mp) REVERT: A 291 VAL cc_start: 0.5767 (OUTLIER) cc_final: 0.5184 (m) REVERT: A 303 PHE cc_start: 0.7451 (m-80) cc_final: 0.7111 (m-80) REVERT: A 808 GLN cc_start: 0.8195 (mt0) cc_final: 0.7952 (mt0) REVERT: A 812 ASN cc_start: 0.8792 (m110) cc_final: 0.8563 (m110) REVERT: A 1040 ARG cc_start: 0.8666 (OUTLIER) cc_final: 0.8332 (ptp-110) REVERT: A 1126 LYS cc_start: 0.7941 (OUTLIER) cc_final: 0.7633 (ttmm) REVERT: B 24 ARG cc_start: 0.8657 (OUTLIER) cc_final: 0.6542 (mpt-90) REVERT: B 787 ASN cc_start: 0.8247 (p0) cc_final: 0.7979 (p0) REVERT: B 792 LEU cc_start: 0.8893 (OUTLIER) cc_final: 0.8640 (tt) REVERT: B 1103 ASN cc_start: 0.8229 (p0) cc_final: 0.8003 (p0) REVERT: B 1135 ILE cc_start: 0.8712 (OUTLIER) cc_final: 0.8453 (pt) REVERT: B 1151 ILE cc_start: 0.7915 (mm) cc_final: 0.7607 (tp) outliers start: 100 outliers final: 56 residues processed: 294 average time/residue: 0.3580 time to fit residues: 171.0198 Evaluate side-chains 252 residues out of total 2760 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 187 time to evaluate : 2.594 ------------------------------------------------------------------------------- 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 150 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 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 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 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 1000 SER Chi-restraints excluded: chain B residue 1026 TYR Chi-restraints excluded: chain B residue 1109 ILE Chi-restraints excluded: chain B residue 1120 ASN Chi-restraints excluded: chain B residue 1135 ILE 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: 0.9980 chunk 184 optimal weight: 2.9990 chunk 85 optimal weight: 4.9990 chunk 86 optimal weight: 0.8980 chunk 145 optimal weight: 0.9980 chunk 11 optimal weight: 7.9990 chunk 244 optimal weight: 1.9990 chunk 256 optimal weight: 9.9990 chunk 238 optimal weight: 1.9990 chunk 125 optimal weight: 0.5980 overall best weight: 1.0982 ------------------------------------------------------------------------------- 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 A1207 ASN ** A1236 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: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3873 r_free = 0.3873 target = 0.139085 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3350 r_free = 0.3350 target = 0.103401 restraints weight = 44739.417| |-----------------------------------------------------------------------------| r_work (start): 0.3317 rms_B_bonded: 2.95 r_work: 0.3049 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work: 0.2918 rms_B_bonded: 4.88 restraints_weight: 0.2500 r_work (final): 0.2918 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8514 moved from start: 0.1184 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= 0.167 Angle : 0.519 8.269 33495 Z= 0.275 Chirality : 0.045 0.220 3739 Planarity : 0.003 0.043 4328 Dihedral : 5.879 59.792 3273 Min Nonbonded Distance : 2.370 Molprobity Statistics. All-atom Clashscore : 7.88 Ramachandran Plot: Outliers : 0.10 % Allowed : 5.22 % Favored : 94.68 % Rotamer: Outliers : 4.14 % Allowed : 14.37 % Favored : 81.48 % 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: 0.30 (0.16), residues: 2972 helix: 1.60 (0.17), residues: 957 sheet: 0.12 (0.22), residues: 551 loop : -0.69 (0.16), residues: 1464 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 689 HIS 0.007 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 0.03454 ( 1069) hydrogen bonds : angle 4.54427 ( 3027) SS BOND : bond 0.00003 ( 1) SS BOND : angle 0.12609 ( 2) covalent geometry : bond 0.00384 (24689) covalent geometry : angle 0.51905 (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 309 residues out of total 2760 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 113 poor density : 196 time to evaluate : 2.964 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 220 MET cc_start: 0.6734 (tpp) cc_final: 0.6438 (tpp) REVERT: C 231 PHE cc_start: 0.8095 (OUTLIER) cc_final: 0.7659 (m-10) REVERT: C 698 ASN cc_start: 0.1522 (p0) cc_final: 0.0686 (t0) REVERT: C 741 LEU cc_start: 0.6930 (OUTLIER) cc_final: 0.6636 (tp) REVERT: A 8 ASN cc_start: 0.7711 (OUTLIER) cc_final: 0.7295 (m-40) REVERT: A 16 ARG cc_start: 0.7501 (mtm-85) cc_final: 0.6982 (mtm-85) REVERT: A 123 GLN cc_start: 0.8281 (pt0) cc_final: 0.7850 (tp40) REVERT: A 253 LEU cc_start: 0.8921 (OUTLIER) cc_final: 0.8570 (mp) REVERT: A 291 VAL cc_start: 0.5696 (OUTLIER) cc_final: 0.5386 (m) REVERT: A 303 PHE cc_start: 0.7627 (m-80) cc_final: 0.7245 (m-80) REVERT: A 808 GLN cc_start: 0.8273 (mt0) cc_final: 0.8006 (mt0) REVERT: A 812 ASN cc_start: 0.8819 (m110) cc_final: 0.8580 (m110) REVERT: A 1040 ARG cc_start: 0.8776 (OUTLIER) cc_final: 0.8422 (ptp-170) REVERT: A 1126 LYS cc_start: 0.8142 (OUTLIER) cc_final: 0.7900 (mtmm) REVERT: B 24 ARG cc_start: 0.8657 (OUTLIER) cc_final: 0.6499 (mpt-90) REVERT: B 787 ASN cc_start: 0.8476 (p0) cc_final: 0.8249 (p0) REVERT: B 792 LEU cc_start: 0.8980 (OUTLIER) cc_final: 0.8727 (tt) REVERT: B 810 GLU cc_start: 0.7239 (OUTLIER) cc_final: 0.6472 (tp30) REVERT: B 1151 ILE cc_start: 0.8074 (mm) cc_final: 0.7785 (tp) outliers start: 113 outliers final: 70 residues processed: 292 average time/residue: 0.3444 time to fit residues: 165.1823 Evaluate side-chains 264 residues out of total 2760 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 184 time to evaluate : 2.856 ------------------------------------------------------------------------------- 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 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 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 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 249 optimal weight: 0.4980 chunk 109 optimal weight: 0.8980 chunk 99 optimal weight: 0.0970 chunk 0 optimal weight: 10.0000 chunk 265 optimal weight: 5.9990 chunk 184 optimal weight: 2.9990 chunk 193 optimal weight: 3.9990 chunk 47 optimal weight: 4.9990 chunk 242 optimal weight: 2.9990 chunk 181 optimal weight: 0.9980 chunk 134 optimal weight: 3.9990 overall best weight: 1.0980 ------------------------------------------------------------------------------- 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 ** 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 = 0.3873 r_free = 0.3873 target = 0.139016 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.104253 restraints weight = 44757.989| |-----------------------------------------------------------------------------| r_work (start): 0.3330 rms_B_bonded: 2.90 r_work: 0.3049 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work: 0.2920 rms_B_bonded: 4.86 restraints_weight: 0.2500 r_work (final): 0.2920 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8516 moved from start: 0.1276 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= 0.165 Angle : 0.522 9.994 33495 Z= 0.276 Chirality : 0.045 0.202 3739 Planarity : 0.003 0.044 4328 Dihedral : 5.879 59.202 3273 Min Nonbonded Distance : 2.358 Molprobity Statistics. All-atom Clashscore : 8.05 Ramachandran Plot: Outliers : 0.10 % Allowed : 5.05 % Favored : 94.85 % Rotamer: Outliers : 3.92 % Allowed : 15.40 % Favored : 80.67 % 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: 0.27 (0.15), residues: 2972 helix: 1.59 (0.17), residues: 957 sheet: 0.10 (0.22), residues: 548 loop : -0.73 (0.16), residues: 1467 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 689 HIS 0.006 0.001 HIS B 762 PHE 0.021 0.001 PHE B 733 TYR 0.023 0.001 TYR A 738 ARG 0.003 0.000 ARG B1019 Details of bonding type rmsd hydrogen bonds : bond 0.03428 ( 1069) hydrogen bonds : angle 4.52733 ( 3027) SS BOND : bond 0.00025 ( 1) SS BOND : angle 0.16855 ( 2) covalent geometry : bond 0.00382 (24689) covalent geometry : angle 0.52198 (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 304 residues out of total 2760 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 107 poor density : 197 time to evaluate : 3.231 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 184 MET cc_start: 0.8887 (tmm) cc_final: 0.8672 (tmm) REVERT: C 220 MET cc_start: 0.6974 (tpp) cc_final: 0.6630 (tpp) REVERT: C 231 PHE cc_start: 0.8066 (OUTLIER) cc_final: 0.7649 (m-10) REVERT: C 698 ASN cc_start: 0.1466 (p0) cc_final: 0.0646 (t0) REVERT: C 741 LEU cc_start: 0.6982 (OUTLIER) cc_final: 0.6708 (tp) REVERT: A 8 ASN cc_start: 0.7686 (OUTLIER) cc_final: 0.7279 (m-40) REVERT: A 16 ARG cc_start: 0.7502 (mtm-85) cc_final: 0.7001 (mtm-85) REVERT: A 123 GLN cc_start: 0.8283 (pt0) cc_final: 0.7847 (tp40) REVERT: A 253 LEU cc_start: 0.8884 (OUTLIER) cc_final: 0.8537 (mp) REVERT: A 291 VAL cc_start: 0.5772 (OUTLIER) cc_final: 0.5200 (m) REVERT: A 303 PHE cc_start: 0.7660 (m-80) cc_final: 0.7321 (m-80) REVERT: A 808 GLN cc_start: 0.8286 (mt0) cc_final: 0.8004 (mt0) REVERT: A 812 ASN cc_start: 0.8817 (m110) cc_final: 0.8567 (m110) REVERT: A 1040 ARG cc_start: 0.8772 (OUTLIER) cc_final: 0.8434 (ptp-110) REVERT: A 1126 LYS cc_start: 0.8139 (OUTLIER) cc_final: 0.7894 (mtmm) REVERT: A 1190 MET cc_start: 0.8285 (mmm) cc_final: 0.7981 (mmm) REVERT: B 24 ARG cc_start: 0.8655 (OUTLIER) cc_final: 0.6475 (mpt-90) REVERT: B 25 LYS cc_start: 0.8966 (OUTLIER) cc_final: 0.8455 (ptmt) REVERT: B 787 ASN cc_start: 0.8517 (p0) cc_final: 0.8254 (p0) REVERT: B 792 LEU cc_start: 0.8964 (OUTLIER) cc_final: 0.8728 (tt) REVERT: B 810 GLU cc_start: 0.7211 (OUTLIER) cc_final: 0.6465 (tp30) REVERT: B 1151 ILE cc_start: 0.8068 (mm) cc_final: 0.7781 (tp) outliers start: 107 outliers final: 73 residues processed: 288 average time/residue: 0.4073 time to fit residues: 191.9007 Evaluate side-chains 268 residues out of total 2760 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 184 time to evaluate : 2.695 ------------------------------------------------------------------------------- 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 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 59 THR 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 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 687 LEU Chi-restraints excluded: chain B residue 703 SER 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 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 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 59 optimal weight: 0.6980 chunk 53 optimal weight: 0.0570 chunk 80 optimal weight: 1.9990 chunk 2 optimal weight: 5.9990 chunk 28 optimal weight: 0.9980 chunk 137 optimal weight: 0.8980 chunk 291 optimal weight: 0.5980 chunk 170 optimal weight: 1.9990 chunk 123 optimal weight: 0.6980 chunk 145 optimal weight: 0.9990 chunk 225 optimal weight: 1.9990 overall best weight: 0.5898 ------------------------------------------------------------------------------- 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 ** 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 = 0.3891 r_free = 0.3891 target = 0.140347 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.104438 restraints weight = 44296.840| |-----------------------------------------------------------------------------| r_work (start): 0.3335 rms_B_bonded: 2.94 r_work: 0.3074 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work: 0.2941 rms_B_bonded: 4.95 restraints_weight: 0.2500 r_work (final): 0.2941 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8490 moved from start: 0.1352 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= 0.115 Angle : 0.493 9.782 33495 Z= 0.260 Chirality : 0.044 0.205 3739 Planarity : 0.003 0.044 4328 Dihedral : 5.710 59.520 3271 Min Nonbonded Distance : 2.335 Molprobity Statistics. All-atom Clashscore : 7.53 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.01 % Favored : 94.92 % Rotamer: Outliers : 3.70 % Allowed : 15.95 % 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: 0.37 (0.16), residues: 2972 helix: 1.72 (0.17), residues: 957 sheet: 0.11 (0.22), residues: 557 loop : -0.67 (0.16), residues: 1458 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 689 HIS 0.006 0.001 HIS C 429 PHE 0.022 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 0.03169 ( 1069) hydrogen bonds : angle 4.40780 ( 3027) SS BOND : bond 0.00042 ( 1) SS BOND : angle 0.14307 ( 2) covalent geometry : bond 0.00258 (24689) covalent geometry : angle 0.49346 (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 296 residues out of total 2760 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 101 poor density : 195 time to evaluate : 3.263 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 220 MET cc_start: 0.7038 (tpp) cc_final: 0.6709 (tpp) REVERT: C 230 ARG cc_start: 0.7822 (ttm170) cc_final: 0.7469 (ttm170) REVERT: C 231 PHE cc_start: 0.8035 (OUTLIER) cc_final: 0.7683 (m-10) REVERT: C 378 GLU cc_start: 0.6441 (OUTLIER) cc_final: 0.5820 (tp30) REVERT: C 698 ASN cc_start: 0.1504 (p0) cc_final: 0.0629 (t0) REVERT: C 741 LEU cc_start: 0.6934 (OUTLIER) cc_final: 0.6645 (tp) REVERT: A 8 ASN cc_start: 0.7679 (OUTLIER) cc_final: 0.7260 (m-40) REVERT: A 16 ARG cc_start: 0.7484 (mtm-85) cc_final: 0.6988 (mtm-85) REVERT: A 123 GLN cc_start: 0.8275 (pt0) cc_final: 0.7853 (tp40) REVERT: A 253 LEU cc_start: 0.8822 (OUTLIER) cc_final: 0.8536 (mp) REVERT: A 291 VAL cc_start: 0.5635 (OUTLIER) cc_final: 0.5075 (m) REVERT: A 303 PHE cc_start: 0.7592 (m-80) cc_final: 0.7256 (m-80) REVERT: A 808 GLN cc_start: 0.8288 (mt0) cc_final: 0.7827 (mt0) REVERT: A 812 ASN cc_start: 0.8780 (m110) cc_final: 0.8512 (m110) REVERT: A 1040 ARG cc_start: 0.8779 (OUTLIER) cc_final: 0.8437 (ptp-110) REVERT: A 1126 LYS cc_start: 0.8131 (OUTLIER) cc_final: 0.7868 (mtmm) REVERT: B 24 ARG cc_start: 0.8609 (OUTLIER) cc_final: 0.6387 (mpt-90) REVERT: B 25 LYS cc_start: 0.8937 (OUTLIER) cc_final: 0.8416 (ptmt) REVERT: B 787 ASN cc_start: 0.8501 (p0) cc_final: 0.8220 (p0) REVERT: B 792 LEU cc_start: 0.8960 (OUTLIER) cc_final: 0.8698 (tt) REVERT: B 810 GLU cc_start: 0.7054 (OUTLIER) cc_final: 0.6300 (tp30) REVERT: B 1151 ILE cc_start: 0.8029 (mm) cc_final: 0.7731 (tp) outliers start: 101 outliers final: 66 residues processed: 279 average time/residue: 0.3824 time to fit residues: 173.9695 Evaluate side-chains 257 residues out of total 2760 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 179 time to evaluate : 3.490 ------------------------------------------------------------------------------- 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 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 321 ILE 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 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 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 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 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 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 Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 95 optimal weight: 0.6980 chunk 167 optimal weight: 0.0870 chunk 265 optimal weight: 5.9990 chunk 267 optimal weight: 2.9990 chunk 218 optimal weight: 2.9990 chunk 171 optimal weight: 0.0040 chunk 39 optimal weight: 30.0000 chunk 249 optimal weight: 0.9980 chunk 186 optimal weight: 0.0070 chunk 112 optimal weight: 0.1980 chunk 282 optimal weight: 2.9990 overall best weight: 0.1988 ------------------------------------------------------------------------------- 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 A1207 ASN ** A1236 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 948 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1016 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3912 r_free = 0.3912 target = 0.141927 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3406 r_free = 0.3406 target = 0.106662 restraints weight = 44515.926| |-----------------------------------------------------------------------------| r_work (start): 0.3373 rms_B_bonded: 2.70 r_work: 0.3118 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.2988 rms_B_bonded: 4.83 restraints_weight: 0.2500 r_work (final): 0.2988 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8439 moved from start: 0.1514 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 24690 Z= 0.095 Angle : 0.494 11.682 33495 Z= 0.259 Chirality : 0.044 0.212 3739 Planarity : 0.003 0.046 4328 Dihedral : 5.471 58.133 3264 Min Nonbonded Distance : 2.317 Molprobity Statistics. All-atom Clashscore : 7.09 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.64 % Favored : 95.29 % Rotamer: Outliers : 3.41 % Allowed : 16.43 % 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: 0.46 (0.16), residues: 2972 helix: 1.83 (0.18), residues: 959 sheet: 0.14 (0.22), residues: 551 loop : -0.65 (0.16), residues: 1462 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A1224 HIS 0.005 0.001 HIS B 762 PHE 0.021 0.001 PHE B 774 TYR 0.024 0.001 TYR A1226 ARG 0.007 0.000 ARG B1019 Details of bonding type rmsd hydrogen bonds : bond 0.02929 ( 1069) hydrogen bonds : angle 4.27377 ( 3027) SS BOND : bond 0.00048 ( 1) SS BOND : angle 0.14485 ( 2) covalent geometry : bond 0.00199 (24689) covalent geometry : angle 0.49408 (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 290 residues out of total 2760 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 197 time to evaluate : 3.766 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: 0.6988 (tpp) cc_final: 0.6630 (tpp) REVERT: C 230 ARG cc_start: 0.7735 (ttm170) cc_final: 0.7444 (ttm170) REVERT: C 231 PHE cc_start: 0.8011 (OUTLIER) cc_final: 0.7676 (m-10) REVERT: C 378 GLU cc_start: 0.6471 (OUTLIER) cc_final: 0.5869 (tp30) REVERT: C 698 ASN cc_start: 0.1460 (p0) cc_final: 0.0585 (t0) REVERT: C 741 LEU cc_start: 0.6902 (OUTLIER) cc_final: 0.6597 (tp) REVERT: A 8 ASN cc_start: 0.7661 (OUTLIER) cc_final: 0.7261 (m-40) REVERT: A 16 ARG cc_start: 0.7462 (mtm-85) cc_final: 0.6992 (mtm-85) REVERT: A 123 GLN cc_start: 0.8185 (pt0) cc_final: 0.7848 (tp40) REVERT: A 291 VAL cc_start: 0.5537 (OUTLIER) cc_final: 0.4933 (m) REVERT: A 303 PHE cc_start: 0.7521 (m-10) cc_final: 0.7184 (m-80) REVERT: A 808 GLN cc_start: 0.8312 (mt0) cc_final: 0.8007 (mm-40) REVERT: A 812 ASN cc_start: 0.8744 (m110) cc_final: 0.8479 (m110) REVERT: A 1040 ARG cc_start: 0.8732 (OUTLIER) cc_final: 0.8388 (ptp-170) REVERT: B 24 ARG cc_start: 0.8565 (OUTLIER) cc_final: 0.6407 (mpt-90) REVERT: B 25 LYS cc_start: 0.8911 (OUTLIER) cc_final: 0.8462 (ptmt) REVERT: B 675 MET cc_start: 0.8501 (ttm) cc_final: 0.8277 (ttm) REVERT: B 787 ASN cc_start: 0.8486 (p0) cc_final: 0.8220 (p0) REVERT: B 792 LEU cc_start: 0.8927 (OUTLIER) cc_final: 0.8671 (tt) REVERT: B 810 GLU cc_start: 0.6927 (OUTLIER) cc_final: 0.6111 (tp30) REVERT: B 1151 ILE cc_start: 0.8012 (mm) cc_final: 0.7738 (tp) outliers start: 93 outliers final: 58 residues processed: 275 average time/residue: 0.3665 time to fit residues: 165.3803 Evaluate side-chains 248 residues out of total 2760 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 180 time to evaluate : 2.731 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 231 PHE 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 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 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 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 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 528 VAL Chi-restraints excluded: chain A residue 641 LEU Chi-restraints excluded: chain A residue 782 LEU 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 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 518 ASP Chi-restraints excluded: chain B residue 648 LEU Chi-restraints excluded: chain B residue 687 LEU 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 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 1135 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 116 optimal weight: 0.5980 chunk 128 optimal weight: 0.0070 chunk 54 optimal weight: 0.0980 chunk 184 optimal weight: 0.0570 chunk 238 optimal weight: 2.9990 chunk 17 optimal weight: 20.0000 chunk 288 optimal weight: 3.9990 chunk 126 optimal weight: 2.9990 chunk 50 optimal weight: 20.0000 chunk 1 optimal weight: 5.9990 chunk 225 optimal weight: 0.2980 overall best weight: 0.2116 ------------------------------------------------------------------------------- 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 489 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1096 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1236 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 443 ASN ** B 948 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 = 0.3921 r_free = 0.3921 target = 0.142666 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.107302 restraints weight = 44442.810| |-----------------------------------------------------------------------------| r_work (start): 0.3383 rms_B_bonded: 2.70 r_work: 0.3133 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.3002 rms_B_bonded: 4.90 restraints_weight: 0.2500 r_work (final): 0.3002 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8424 moved from start: 0.1642 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 24690 Z= 0.093 Angle : 0.497 17.043 33495 Z= 0.258 Chirality : 0.044 0.251 3739 Planarity : 0.003 0.045 4328 Dihedral : 5.099 55.949 3252 Min Nonbonded Distance : 2.298 Molprobity Statistics. All-atom Clashscore : 6.88 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.71 % Favored : 95.26 % Rotamer: Outliers : 2.93 % Allowed : 17.24 % Favored : 79.83 % 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: 0.51 (0.16), residues: 2972 helix: 1.90 (0.18), residues: 960 sheet: 0.16 (0.22), residues: 544 loop : -0.63 (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 0.020 0.001 PHE B 774 TYR 0.018 0.001 TYR A 738 ARG 0.006 0.000 ARG B1019 Details of bonding type rmsd hydrogen bonds : bond 0.02888 ( 1069) hydrogen bonds : angle 4.19107 ( 3027) SS BOND : bond 0.00042 ( 1) SS BOND : angle 0.33018 ( 2) covalent geometry : bond 0.00195 (24689) covalent geometry : angle 0.49746 (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 290 residues out of total 2760 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 210 time to evaluate : 2.573 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 220 MET cc_start: 0.7044 (tpp) cc_final: 0.6734 (tpp) REVERT: C 230 ARG cc_start: 0.7660 (ttm170) cc_final: 0.7455 (ttm170) REVERT: C 231 PHE cc_start: 0.7997 (OUTLIER) cc_final: 0.7651 (m-10) REVERT: C 698 ASN cc_start: 0.1433 (p0) cc_final: 0.0566 (t0) REVERT: C 741 LEU cc_start: 0.6865 (OUTLIER) cc_final: 0.6543 (tp) REVERT: A 8 ASN cc_start: 0.7682 (OUTLIER) cc_final: 0.7327 (m-40) REVERT: A 16 ARG cc_start: 0.7469 (mtm-85) cc_final: 0.6993 (mtm-85) REVERT: A 123 GLN cc_start: 0.8096 (pt0) cc_final: 0.7785 (tp40) REVERT: A 291 VAL cc_start: 0.5332 (OUTLIER) cc_final: 0.4633 (m) REVERT: A 303 PHE cc_start: 0.7491 (m-10) cc_final: 0.7150 (m-80) REVERT: A 516 GLU cc_start: 0.8108 (OUTLIER) cc_final: 0.7665 (pp20) REVERT: A 628 LEU cc_start: 0.9343 (mt) cc_final: 0.9028 (mt) REVERT: A 808 GLN cc_start: 0.8368 (mt0) cc_final: 0.8053 (mm-40) REVERT: A 812 ASN cc_start: 0.8729 (m110) cc_final: 0.8481 (m110) REVERT: A 1040 ARG cc_start: 0.8724 (OUTLIER) cc_final: 0.8398 (ptp-110) REVERT: A 1116 LEU cc_start: 0.9011 (tp) cc_final: 0.8671 (tt) REVERT: B 24 ARG cc_start: 0.8543 (OUTLIER) cc_final: 0.6418 (mpt-90) REVERT: B 25 LYS cc_start: 0.8873 (OUTLIER) cc_final: 0.8483 (ptmt) REVERT: B 675 MET cc_start: 0.8505 (ttm) cc_final: 0.8284 (ttm) REVERT: B 787 ASN cc_start: 0.8518 (p0) cc_final: 0.8246 (p0) REVERT: B 792 LEU cc_start: 0.8902 (OUTLIER) cc_final: 0.8662 (tt) REVERT: B 810 GLU cc_start: 0.6935 (OUTLIER) cc_final: 0.6042 (tp30) REVERT: B 1151 ILE cc_start: 0.8032 (mm) cc_final: 0.7745 (tp) outliers start: 80 outliers final: 57 residues processed: 274 average time/residue: 0.3384 time to fit residues: 151.0484 Evaluate side-chains 262 residues out of total 2760 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 195 time to evaluate : 3.070 ------------------------------------------------------------------------------- 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 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 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 258 THR Chi-restraints excluded: chain A residue 260 LEU Chi-restraints excluded: chain A residue 291 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 516 GLU 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 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 3 ILE Chi-restraints excluded: chain B residue 24 ARG Chi-restraints excluded: chain B residue 25 LYS 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 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 792 LEU Chi-restraints excluded: chain B residue 810 GLU Chi-restraints excluded: chain B residue 811 GLN Chi-restraints excluded: chain B residue 869 ILE Chi-restraints excluded: chain B residue 907 ASN 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 1135 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 40 optimal weight: 0.5980 chunk 12 optimal weight: 0.6980 chunk 109 optimal weight: 3.9990 chunk 294 optimal weight: 0.0670 chunk 218 optimal weight: 0.7980 chunk 66 optimal weight: 4.9990 chunk 169 optimal weight: 5.9990 chunk 242 optimal weight: 2.9990 chunk 108 optimal weight: 1.9990 chunk 226 optimal weight: 2.9990 chunk 189 optimal weight: 1.9990 overall best weight: 0.8320 ------------------------------------------------------------------------------- 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 ** A1236 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 948 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 = 0.3892 r_free = 0.3892 target = 0.140381 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.104872 restraints weight = 44662.925| |-----------------------------------------------------------------------------| r_work (start): 0.3346 rms_B_bonded: 2.77 r_work: 0.3086 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.2957 rms_B_bonded: 4.82 restraints_weight: 0.2500 r_work (final): 0.2957 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8475 moved from start: 0.1578 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= 0.137 Angle : 0.523 11.837 33495 Z= 0.272 Chirality : 0.046 0.569 3739 Planarity : 0.003 0.044 4328 Dihedral : 5.204 56.560 3250 Min Nonbonded Distance : 2.306 Molprobity Statistics. All-atom Clashscore : 7.26 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.91 % Favored : 95.05 % Rotamer: Outliers : 3.15 % Allowed : 17.24 % Favored : 79.61 % 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: 0.44 (0.16), residues: 2972 helix: 1.80 (0.17), residues: 962 sheet: 0.17 (0.22), residues: 543 loop : -0.67 (0.16), residues: 1467 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A1224 HIS 0.005 0.001 HIS B 762 PHE 0.020 0.001 PHE B 774 TYR 0.022 0.001 TYR A1226 ARG 0.006 0.000 ARG B1019 Details of bonding type rmsd hydrogen bonds : bond 0.03186 ( 1069) hydrogen bonds : angle 4.30796 ( 3027) SS BOND : bond 0.00041 ( 1) SS BOND : angle 0.32361 ( 2) covalent geometry : bond 0.00311 (24689) covalent geometry : angle 0.52337 (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 276 residues out of total 2760 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 190 time to evaluate : 3.680 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 220 MET cc_start: 0.7172 (tpp) cc_final: 0.6836 (tpp) REVERT: C 231 PHE cc_start: 0.7931 (OUTLIER) cc_final: 0.7636 (m-10) REVERT: C 698 ASN cc_start: 0.1531 (p0) cc_final: 0.0623 (t0) REVERT: C 741 LEU cc_start: 0.6932 (OUTLIER) cc_final: 0.6651 (tp) REVERT: A 8 ASN cc_start: 0.7721 (OUTLIER) cc_final: 0.7373 (m-40) REVERT: A 16 ARG cc_start: 0.7453 (mtm-85) cc_final: 0.6960 (mtm-85) REVERT: A 123 GLN cc_start: 0.8153 (pt0) cc_final: 0.7795 (tp40) REVERT: A 291 VAL cc_start: 0.5137 (OUTLIER) cc_final: 0.4510 (m) REVERT: A 303 PHE cc_start: 0.7525 (m-10) cc_final: 0.7173 (m-80) REVERT: A 516 GLU cc_start: 0.8136 (OUTLIER) cc_final: 0.7702 (pp20) REVERT: A 738 TYR cc_start: 0.7347 (OUTLIER) cc_final: 0.7081 (t80) REVERT: A 808 GLN cc_start: 0.8383 (mt0) cc_final: 0.8056 (mm-40) REVERT: A 812 ASN cc_start: 0.8740 (m110) cc_final: 0.8465 (m110) REVERT: B 24 ARG cc_start: 0.8528 (OUTLIER) cc_final: 0.6379 (mpt-90) REVERT: B 25 LYS cc_start: 0.8894 (OUTLIER) cc_final: 0.8437 (ptmt) REVERT: B 675 MET cc_start: 0.8565 (ttm) cc_final: 0.8328 (ttm) REVERT: B 787 ASN cc_start: 0.8633 (p0) cc_final: 0.8391 (p0) REVERT: B 810 GLU cc_start: 0.7032 (OUTLIER) cc_final: 0.6170 (tp30) REVERT: B 1151 ILE cc_start: 0.8028 (mm) cc_final: 0.7714 (tp) outliers start: 86 outliers final: 63 residues processed: 262 average time/residue: 0.4523 time to fit residues: 196.3081 Evaluate side-chains 257 residues out of total 2760 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 185 time to evaluate : 3.574 ------------------------------------------------------------------------------- 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 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 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 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 321 ILE 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 516 GLU Chi-restraints excluded: chain A residue 519 VAL Chi-restraints excluded: chain A residue 528 VAL Chi-restraints excluded: chain A residue 641 LEU Chi-restraints excluded: chain A residue 708 LEU Chi-restraints excluded: chain A residue 738 TYR 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 938 THR 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 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 487 LEU Chi-restraints excluded: chain B residue 618 ILE 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 869 ILE Chi-restraints excluded: chain B residue 907 ASN 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 1135 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 6 optimal weight: 0.9990 chunk 68 optimal weight: 0.0970 chunk 91 optimal weight: 0.6980 chunk 231 optimal weight: 2.9990 chunk 198 optimal weight: 0.9990 chunk 83 optimal weight: 0.9990 chunk 119 optimal weight: 0.5980 chunk 250 optimal weight: 1.9990 chunk 10 optimal weight: 0.9990 chunk 84 optimal weight: 0.7980 chunk 23 optimal weight: 8.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- 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 489 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1236 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 892 ASN ** B 948 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 = 0.3897 r_free = 0.3897 target = 0.140830 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3398 r_free = 0.3398 target = 0.105960 restraints weight = 44472.188| |-----------------------------------------------------------------------------| r_work (start): 0.3364 rms_B_bonded: 2.88 r_work: 0.3087 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work: 0.2955 rms_B_bonded: 4.98 restraints_weight: 0.2500 r_work (final): 0.2955 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8478 moved from start: 0.1606 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= 0.121 Angle : 0.521 11.484 33495 Z= 0.270 Chirality : 0.045 0.560 3739 Planarity : 0.003 0.053 4328 Dihedral : 5.040 55.223 3244 Min Nonbonded Distance : 2.264 Molprobity Statistics. All-atom Clashscore : 7.65 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.98 % Favored : 94.99 % Rotamer: Outliers : 2.93 % Allowed : 17.49 % 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: 0.43 (0.16), residues: 2972 helix: 1.80 (0.17), residues: 962 sheet: 0.18 (0.22), residues: 543 loop : -0.68 (0.16), residues: 1467 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 0.025 0.001 PHE B 774 TYR 0.019 0.001 TYR A 738 ARG 0.010 0.000 ARG B 672 Details of bonding type rmsd hydrogen bonds : bond 0.03119 ( 1069) hydrogen bonds : angle 4.30976 ( 3027) SS BOND : bond 0.00040 ( 1) SS BOND : angle 0.24513 ( 2) covalent geometry : bond 0.00272 (24689) covalent geometry : angle 0.52077 (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: 80 poor density : 193 time to evaluate : 4.192 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 220 MET cc_start: 0.7074 (tpp) cc_final: 0.6744 (tpp) REVERT: C 231 PHE cc_start: 0.7912 (OUTLIER) cc_final: 0.7362 (m-10) REVERT: C 369 MET cc_start: 0.6109 (ppp) cc_final: 0.5568 (ppp) REVERT: C 698 ASN cc_start: 0.1604 (p0) cc_final: 0.0697 (t0) REVERT: C 741 LEU cc_start: 0.6912 (OUTLIER) cc_final: 0.6611 (tp) REVERT: A 8 ASN cc_start: 0.7732 (OUTLIER) cc_final: 0.7399 (m-40) REVERT: A 16 ARG cc_start: 0.7478 (mtm-85) cc_final: 0.6987 (mtm-85) REVERT: A 123 GLN cc_start: 0.8126 (pt0) cc_final: 0.7741 (tp40) REVERT: A 144 LEU cc_start: 0.8249 (tt) cc_final: 0.7982 (tp) REVERT: A 291 VAL cc_start: 0.4886 (OUTLIER) cc_final: 0.4068 (m) REVERT: A 303 PHE cc_start: 0.7549 (m-10) cc_final: 0.7205 (m-80) REVERT: A 516 GLU cc_start: 0.8197 (OUTLIER) cc_final: 0.7771 (pp20) REVERT: A 628 LEU cc_start: 0.9361 (mt) cc_final: 0.9056 (mt) REVERT: A 738 TYR cc_start: 0.7285 (OUTLIER) cc_final: 0.7056 (t80) REVERT: A 808 GLN cc_start: 0.8393 (mt0) cc_final: 0.8064 (mm-40) REVERT: A 812 ASN cc_start: 0.8758 (m110) cc_final: 0.8484 (m110) REVERT: A 1040 ARG cc_start: 0.8759 (OUTLIER) cc_final: 0.8157 (ptp-110) REVERT: B 24 ARG cc_start: 0.8554 (OUTLIER) cc_final: 0.6420 (mpt-90) REVERT: B 25 LYS cc_start: 0.8898 (OUTLIER) cc_final: 0.8453 (ptmt) REVERT: B 675 MET cc_start: 0.8545 (ttm) cc_final: 0.8327 (ttm) REVERT: B 787 ASN cc_start: 0.8620 (p0) cc_final: 0.8385 (p0) REVERT: B 810 GLU cc_start: 0.7039 (OUTLIER) cc_final: 0.6194 (tp30) REVERT: B 1151 ILE cc_start: 0.8046 (mm) cc_final: 0.7746 (tp) outliers start: 80 outliers final: 64 residues processed: 261 average time/residue: 0.6040 time to fit residues: 266.7584 Evaluate side-chains 261 residues out of total 2760 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 187 time to evaluate : 3.186 ------------------------------------------------------------------------------- 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 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 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 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 516 GLU Chi-restraints excluded: chain A residue 528 VAL Chi-restraints excluded: chain A residue 641 LEU Chi-restraints excluded: chain A residue 708 LEU Chi-restraints excluded: chain A residue 738 TYR 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 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 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 487 LEU Chi-restraints excluded: chain B residue 618 ILE 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 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 892 ASN 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 1135 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 92 optimal weight: 2.9990 chunk 44 optimal weight: 40.0000 chunk 109 optimal weight: 0.0670 chunk 108 optimal weight: 1.9990 chunk 116 optimal weight: 0.6980 chunk 103 optimal weight: 2.9990 chunk 132 optimal weight: 0.5980 chunk 18 optimal weight: 0.3980 chunk 127 optimal weight: 0.5980 chunk 63 optimal weight: 0.5980 chunk 229 optimal weight: 0.8980 overall best weight: 0.4518 ------------------------------------------------------------------------------- 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 489 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** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3899 r_free = 0.3899 target = 0.140929 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.105055 restraints weight = 44418.612| |-----------------------------------------------------------------------------| r_work (start): 0.3345 rms_B_bonded: 2.93 r_work: 0.3071 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work (final): 0.3071 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8382 moved from start: 0.1615 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.160 24690 Z= 0.175 Angle : 0.679 59.114 33495 Z= 0.381 Chirality : 0.046 0.643 3739 Planarity : 0.003 0.060 4328 Dihedral : 5.075 55.207 3242 Min Nonbonded Distance : 2.194 Molprobity Statistics. All-atom Clashscore : 8.11 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.95 % Favored : 94.99 % Rotamer: Outliers : 2.86 % Allowed : 17.46 % Favored : 79.68 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 1.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: 0.44 (0.16), residues: 2972 helix: 1.81 (0.17), residues: 962 sheet: 0.18 (0.22), residues: 543 loop : -0.69 (0.16), residues: 1467 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 928 HIS 0.004 0.001 HIS B 762 PHE 0.023 0.001 PHE B 774 TYR 0.019 0.001 TYR A 738 ARG 0.005 0.000 ARG B1019 Details of bonding type rmsd hydrogen bonds : bond 0.03111 ( 1069) hydrogen bonds : angle 4.30952 ( 3027) SS BOND : bond 0.00041 ( 1) SS BOND : angle 0.22866 ( 2) covalent geometry : bond 0.00336 (24689) covalent geometry : angle 0.67896 (33493) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 14783.03 seconds wall clock time: 263 minutes 34.60 seconds (15814.60 seconds total)