Starting phenix.real_space_refine on Sun Dec 10 16:03:05 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5nd1_3619/12_2023/5nd1_3619.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5nd1_3619/12_2023/5nd1_3619.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5nd1_3619/12_2023/5nd1_3619.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5nd1_3619/12_2023/5nd1_3619.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5nd1_3619/12_2023/5nd1_3619.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5nd1_3619/12_2023/5nd1_3619.pdb" } resolution = 3.7 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 ------------------------------------------------------------------------------- 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= 0.001 sd= 0.090 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 103 5.16 5 C 9278 2.51 5 N 2702 2.21 5 O 2880 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 8": "NH1" <-> "NH2" Residue "A GLU 12": "OE1" <-> "OE2" Residue "A GLU 13": "OE1" <-> "OE2" Residue "A GLU 69": "OE1" <-> "OE2" Residue "A ARG 72": "NH1" <-> "NH2" Residue "A GLU 76": "OE1" <-> "OE2" Residue "A ARG 103": "NH1" <-> "NH2" Residue "A ARG 118": "NH1" <-> "NH2" Residue "A ARG 120": "NH1" <-> "NH2" Residue "A GLU 163": "OE1" <-> "OE2" Residue "A ARG 176": "NH1" <-> "NH2" Residue "A ARG 189": "NH1" <-> "NH2" Residue "A ARG 214": "NH1" <-> "NH2" Residue "A GLU 217": "OE1" <-> "OE2" Residue "A GLU 220": "OE1" <-> "OE2" Residue "A ARG 272": "NH1" <-> "NH2" Residue "A GLU 294": "OE1" <-> "OE2" Residue "A GLU 328": "OE1" <-> "OE2" Residue "A ARG 336": "NH1" <-> "NH2" Residue "A GLU 361": "OE1" <-> "OE2" Residue "A GLU 382": "OE1" <-> "OE2" Residue "A ARG 425": "NH1" <-> "NH2" Residue "A ARG 452": "NH1" <-> "NH2" Residue "A GLU 517": "OE1" <-> "OE2" Residue "A GLU 543": "OE1" <-> "OE2" Residue "A GLU 570": "OE1" <-> "OE2" Residue "A ARG 607": "NH1" <-> "NH2" Residue "A ARG 638": "NH1" <-> "NH2" Residue "A GLU 661": "OE1" <-> "OE2" Residue "A GLU 706": "OE1" <-> "OE2" Residue "A GLU 750": "OE1" <-> "OE2" Residue "A ARG 756": "NH1" <-> "NH2" Residue "A ARG 767": "NH1" <-> "NH2" Residue "A ARG 780": "NH1" <-> "NH2" Residue "A ARG 802": "NH1" <-> "NH2" Residue "A GLU 878": "OE1" <-> "OE2" Residue "A GLU 915": "OE1" <-> "OE2" Residue "A ARG 932": "NH1" <-> "NH2" Residue "A GLU 969": "OE1" <-> "OE2" Residue "A GLU 972": "OE1" <-> "OE2" Residue "B GLU 10": "OE1" <-> "OE2" Residue "B GLU 36": "OE1" <-> "OE2" Residue "B GLU 65": "OE1" <-> "OE2" Residue "B GLU 81": "OE1" <-> "OE2" Residue "B GLU 97": "OE1" <-> "OE2" Residue "B GLU 147": "OE1" <-> "OE2" Residue "B GLU 366": "OE1" <-> "OE2" Residue "B GLU 409": "OE1" <-> "OE2" Residue "B GLU 432": "OE1" <-> "OE2" Residue "B GLU 455": "OE1" <-> "OE2" Residue "B PHE 479": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 516": "NH1" <-> "NH2" Residue "B GLU 650": "OE1" <-> "OE2" Residue "B GLU 700": "OE1" <-> "OE2" Residue "B GLU 708": "OE1" <-> "OE2" Residue "B GLU 852": "OE1" <-> "OE2" Residue "B GLU 910": "OE1" <-> "OE2" Residue "B GLU 917": "OE1" <-> "OE2" Residue "B GLU 964": "OE1" <-> "OE2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/chem_data/mon_lib" Total number of atoms: 14963 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 7371 Number of conformers: 1 Conformer: "" Number of residues, atoms: 972, 7371 Classifications: {'peptide': 972} Link IDs: {'CIS': 1, 'PCIS': 2, 'PTRANS': 34, 'TRANS': 934} Chain: "B" Number of atoms: 7592 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1005, 7592 Classifications: {'peptide': 1005} Link IDs: {'PCIS': 1, 'PTRANS': 29, 'TRANS': 974} Unresolved chain links: 1 Unresolved chain link angles: 3 Unresolved chain link dihedrals: 4 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 8.16, per 1000 atoms: 0.55 Number of scatterers: 14963 At special positions: 0 Unit cell: (140.7, 116.58, 107.2, 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 103 16.00 O 2880 8.00 N 2702 7.00 C 9278 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 5.81 Conformation dependent library (CDL) restraints added in 2.8 seconds 3942 Ramachandran restraints generated. 1971 Oldfield, 0 Emsley, 1971 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3624 Finding SS restraints... Secondary structure from input PDB file: 67 helices and 17 sheets defined 35.5% alpha, 8.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.75 Creating SS restraints... Processing helix chain 'A' and resid 3 through 7 Processing helix chain 'A' and resid 10 through 28 removed outlier: 3.957A pdb=" N LYS A 27 " --> pdb=" O ARG A 23 " (cutoff:3.500A) removed outlier: 4.413A pdb=" N ASP A 28 " --> pdb=" O SER A 24 " (cutoff:3.500A) Processing helix chain 'A' and resid 42 through 46 removed outlier: 3.590A pdb=" N ASP A 45 " --> pdb=" O GLY A 42 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N LEU A 46 " --> pdb=" O GLY A 43 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 42 through 46' Processing helix chain 'A' and resid 52 through 58 removed outlier: 3.522A pdb=" N ALA A 57 " --> pdb=" O ASP A 53 " (cutoff:3.500A) Processing helix chain 'A' and resid 129 through 136 Processing helix chain 'A' and resid 144 through 152 removed outlier: 4.079A pdb=" N ARG A 150 " --> pdb=" O SER A 146 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N ASN A 151 " --> pdb=" O ALA A 147 " (cutoff:3.500A) Processing helix chain 'A' and resid 153 through 175 removed outlier: 3.806A pdb=" N MET A 157 " --> pdb=" O THR A 153 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N SER A 161 " --> pdb=" O MET A 157 " (cutoff:3.500A) removed outlier: 4.121A pdb=" N ARG A 162 " --> pdb=" O ASN A 158 " (cutoff:3.500A) Processing helix chain 'A' and resid 188 through 203 removed outlier: 3.506A pdb=" N MET A 201 " --> pdb=" O SER A 197 " (cutoff:3.500A) Processing helix chain 'A' and resid 249 through 254 removed outlier: 4.059A pdb=" N LEU A 253 " --> pdb=" O PRO A 249 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ASP A 254 " --> pdb=" O ALA A 250 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 249 through 254' Processing helix chain 'A' and resid 260 through 273 removed outlier: 3.552A pdb=" N VAL A 265 " --> pdb=" O GLY A 261 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N GLU A 268 " --> pdb=" O ARG A 264 " (cutoff:3.500A) removed outlier: 4.126A pdb=" N ALA A 269 " --> pdb=" O VAL A 265 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N LEU A 273 " --> pdb=" O ALA A 269 " (cutoff:3.500A) Processing helix chain 'A' and resid 319 through 327 removed outlier: 4.089A pdb=" N SER A 326 " --> pdb=" O ALA A 322 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N GLY A 327 " --> pdb=" O GLY A 323 " (cutoff:3.500A) Processing helix chain 'A' and resid 346 through 350 removed outlier: 4.063A pdb=" N TYR A 350 " --> pdb=" O LEU A 346 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 346 through 350' Processing helix chain 'A' and resid 377 through 385 Processing helix chain 'A' and resid 398 through 411 removed outlier: 3.563A pdb=" N ALA A 410 " --> pdb=" O VAL A 406 " (cutoff:3.500A) Processing helix chain 'A' and resid 432 through 437 Processing helix chain 'A' and resid 440 through 447 removed outlier: 3.555A pdb=" N MET A 444 " --> pdb=" O THR A 440 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N TYR A 447 " --> pdb=" O LEU A 443 " (cutoff:3.500A) Processing helix chain 'A' and resid 450 through 466 removed outlier: 3.747A pdb=" N PHE A 456 " --> pdb=" O ARG A 452 " (cutoff:3.500A) Processing helix chain 'A' and resid 492 through 498 removed outlier: 4.183A pdb=" N PHE A 497 " --> pdb=" O GLN A 493 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N TRP A 498 " --> pdb=" O GLY A 494 " (cutoff:3.500A) Processing helix chain 'A' and resid 515 through 540 removed outlier: 3.833A pdb=" N GLY A 526 " --> pdb=" O THR A 522 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N ALA A 527 " --> pdb=" O TYR A 523 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N ALA A 532 " --> pdb=" O MET A 528 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N HIS A 533 " --> pdb=" O ALA A 529 " (cutoff:3.500A) Processing helix chain 'A' and resid 554 through 564 removed outlier: 3.573A pdb=" N THR A 560 " --> pdb=" O HIS A 556 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N ASP A 561 " --> pdb=" O THR A 557 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N LEU A 562 " --> pdb=" O VAL A 558 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N PHE A 563 " --> pdb=" O ALA A 559 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N ARG A 564 " --> pdb=" O THR A 560 " (cutoff:3.500A) Processing helix chain 'A' and resid 589 through 592 Processing helix chain 'A' and resid 593 through 598 Processing helix chain 'A' and resid 599 through 603 removed outlier: 4.057A pdb=" N GLU A 603 " --> pdb=" O SER A 600 " (cutoff:3.500A) Processing helix chain 'A' and resid 606 through 615 removed outlier: 3.739A pdb=" N ASN A 612 " --> pdb=" O LEU A 608 " (cutoff:3.500A) Processing helix chain 'A' and resid 643 through 648 removed outlier: 3.603A pdb=" N ILE A 647 " --> pdb=" O ALA A 643 " (cutoff:3.500A) Processing helix chain 'A' and resid 703 through 707 Processing helix chain 'A' and resid 738 through 748 removed outlier: 4.059A pdb=" N MET A 742 " --> pdb=" O CYS A 738 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N ALA A 743 " --> pdb=" O ALA A 739 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N ILE A 747 " --> pdb=" O ALA A 743 " (cutoff:3.500A) Processing helix chain 'A' and resid 757 through 761 Processing helix chain 'A' and resid 766 through 782 removed outlier: 3.661A pdb=" N ASN A 770 " --> pdb=" O ALA A 766 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N ILE A 771 " --> pdb=" O ARG A 767 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N VAL A 772 " --> pdb=" O THR A 768 " (cutoff:3.500A) removed outlier: 4.166A pdb=" N ASN A 781 " --> pdb=" O LEU A 777 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N GLY A 782 " --> pdb=" O GLY A 778 " (cutoff:3.500A) Processing helix chain 'A' and resid 807 through 812 removed outlier: 3.541A pdb=" N MET A 812 " --> pdb=" O ALA A 808 " (cutoff:3.500A) Processing helix chain 'A' and resid 837 through 847 removed outlier: 3.832A pdb=" N HIS A 841 " --> pdb=" O SER A 837 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N LEU A 846 " --> pdb=" O ARG A 842 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N ALA A 847 " --> pdb=" O ARG A 843 " (cutoff:3.500A) Processing helix chain 'A' and resid 892 through 896 Processing helix chain 'A' and resid 898 through 904 removed outlier: 4.052A pdb=" N MET A 902 " --> pdb=" O THR A 898 " (cutoff:3.500A) Processing helix chain 'A' and resid 939 through 943 removed outlier: 4.283A pdb=" N LEU A 942 " --> pdb=" O ASN A 939 " (cutoff:3.500A) Processing helix chain 'A' and resid 963 through 971 removed outlier: 3.621A pdb=" N GLN A 967 " --> pdb=" O ASP A 963 " (cutoff:3.500A) Processing helix chain 'B' and resid 5 through 10 Processing helix chain 'B' and resid 22 through 26 Processing helix chain 'B' and resid 67 through 78 removed outlier: 3.652A pdb=" N LEU B 77 " --> pdb=" O LYS B 73 " (cutoff:3.500A) Processing helix chain 'B' and resid 95 through 108 removed outlier: 3.848A pdb=" N ASN B 100 " --> pdb=" O GLN B 96 " (cutoff:3.500A) removed outlier: 4.557A pdb=" N ILE B 101 " --> pdb=" O GLU B 97 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N CYS B 104 " --> pdb=" O ASN B 100 " (cutoff:3.500A) removed outlier: 4.446A pdb=" N ALA B 108 " --> pdb=" O CYS B 104 " (cutoff:3.500A) Processing helix chain 'B' and resid 174 through 187 Processing helix chain 'B' and resid 204 through 212 removed outlier: 3.788A pdb=" N ARG B 211 " --> pdb=" O THR B 207 " (cutoff:3.500A) Processing helix chain 'B' and resid 219 through 237 removed outlier: 3.830A pdb=" N THR B 225 " --> pdb=" O HIS B 221 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N THR B 226 " --> pdb=" O ALA B 222 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N VAL B 227 " --> pdb=" O ALA B 223 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N MET B 236 " --> pdb=" O VAL B 232 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N HIS B 237 " --> pdb=" O GLY B 233 " (cutoff:3.500A) Processing helix chain 'B' and resid 246 through 253 Processing helix chain 'B' and resid 272 through 284 Processing helix chain 'B' and resid 296 through 298 No H-bonds generated for 'chain 'B' and resid 296 through 298' Processing helix chain 'B' and resid 304 through 309 removed outlier: 3.557A pdb=" N GLN B 308 " --> pdb=" O THR B 304 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N THR B 309 " --> pdb=" O LEU B 305 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 304 through 309' Processing helix chain 'B' and resid 335 through 346 removed outlier: 3.663A pdb=" N ALA B 339 " --> pdb=" O ASP B 335 " (cutoff:3.500A) removed outlier: 4.109A pdb=" N THR B 346 " --> pdb=" O ALA B 342 " (cutoff:3.500A) Processing helix chain 'B' and resid 357 through 367 removed outlier: 3.612A pdb=" N THR B 361 " --> pdb=" O HIS B 357 " (cutoff:3.500A) removed outlier: 4.175A pdb=" N MET B 364 " --> pdb=" O LEU B 360 " (cutoff:3.500A) removed outlier: 4.622A pdb=" N SER B 365 " --> pdb=" O THR B 361 " (cutoff:3.500A) Processing helix chain 'B' and resid 389 through 404 removed outlier: 3.521A pdb=" N LEU B 396 " --> pdb=" O GLU B 392 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N LEU B 397 " --> pdb=" O LEU B 393 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N ARG B 402 " --> pdb=" O GLY B 398 " (cutoff:3.500A) Processing helix chain 'B' and resid 405 through 408 Processing helix chain 'B' and resid 410 through 422 removed outlier: 3.814A pdb=" N LEU B 416 " --> pdb=" O ILE B 412 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N ALA B 417 " --> pdb=" O ARG B 413 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N GLN B 418 " --> pdb=" O ASN B 414 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N LEU B 422 " --> pdb=" O GLN B 418 " (cutoff:3.500A) Processing helix chain 'B' and resid 451 through 458 Processing helix chain 'B' and resid 470 through 505 removed outlier: 4.111A pdb=" N LEU B 474 " --> pdb=" O ASP B 470 " (cutoff:3.500A) removed outlier: 4.279A pdb=" N THR B 488 " --> pdb=" O ALA B 484 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N VAL B 489 " --> pdb=" O GLN B 485 " (cutoff:3.500A) Processing helix chain 'B' and resid 513 through 527 removed outlier: 3.624A pdb=" N ASP B 520 " --> pdb=" O ARG B 516 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N LEU B 521 " --> pdb=" O LEU B 517 " (cutoff:3.500A) Processing helix chain 'B' and resid 537 through 544 removed outlier: 3.532A pdb=" N GLN B 541 " --> pdb=" O VAL B 537 " (cutoff:3.500A) Processing helix chain 'B' and resid 553 through 562 removed outlier: 3.782A pdb=" N LEU B 557 " --> pdb=" O PRO B 553 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N ALA B 558 " --> pdb=" O VAL B 554 " (cutoff:3.500A) Processing helix chain 'B' and resid 608 through 618 removed outlier: 3.745A pdb=" N TYR B 612 " --> pdb=" O SER B 608 " (cutoff:3.500A) Processing helix chain 'B' and resid 667 through 681 removed outlier: 3.656A pdb=" N HIS B 677 " --> pdb=" O TRP B 673 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N LYS B 680 " --> pdb=" O TRP B 676 " (cutoff:3.500A) Processing helix chain 'B' and resid 691 through 704 removed outlier: 3.767A pdb=" N VAL B 695 " --> pdb=" O GLY B 691 " (cutoff:3.500A) Processing helix chain 'B' and resid 706 through 716 Processing helix chain 'B' and resid 762 through 767 Processing helix chain 'B' and resid 770 through 785 Processing helix chain 'B' and resid 787 through 794 removed outlier: 3.520A pdb=" N SER B 792 " --> pdb=" O LEU B 788 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N VAL B 793 " --> pdb=" O MET B 789 " (cutoff:3.500A) Processing helix chain 'B' and resid 817 through 831 removed outlier: 3.793A pdb=" N VAL B 831 " --> pdb=" O CYS B 827 " (cutoff:3.500A) Processing helix chain 'B' and resid 859 through 873 removed outlier: 4.084A pdb=" N VAL B 863 " --> pdb=" O PRO B 859 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N HIS B 872 " --> pdb=" O THR B 868 " (cutoff:3.500A) Processing helix chain 'B' and resid 923 through 929 removed outlier: 3.916A pdb=" N ASP B 928 " --> pdb=" O GLU B 924 " (cutoff:3.500A) removed outlier: 4.253A pdb=" N THR B 929 " --> pdb=" O ALA B 925 " (cutoff:3.500A) Processing helix chain 'B' and resid 957 through 962 removed outlier: 3.925A pdb=" N THR B 961 " --> pdb=" O SER B 957 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 100 through 103 removed outlier: 3.581A pdb=" N GLY A 100 " --> pdb=" O GLU A 79 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N GLU A 79 " --> pdb=" O GLY A 100 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 94 through 97 removed outlier: 3.843A pdb=" N VAL A 83 " --> pdb=" O TYR A 96 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N THR A 82 " --> pdb=" O ASP A 853 " (cutoff:3.500A) removed outlier: 4.071A pdb=" N ASP A 853 " --> pdb=" O THR A 82 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N HIS A 851 " --> pdb=" O THR A 84 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 216 through 217 removed outlier: 4.170A pdb=" N ARG A 206 " --> pdb=" O THR A 231 " (cutoff:3.500A) removed outlier: 4.175A pdb=" N VAL A 340 " --> pdb=" O LEU A 234 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N THR A 331 " --> pdb=" O THR A 343 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N VAL A 283 " --> pdb=" O TYR A 330 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N CYS A 280 " --> pdb=" O ARG A 303 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N ARG A 303 " --> pdb=" O CYS A 280 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 243 through 245 removed outlier: 3.633A pdb=" N ARG A 728 " --> pdb=" O SER A 629 " (cutoff:3.500A) removed outlier: 4.481A pdb=" N ALA A 725 " --> pdb=" O PHE A 691 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N PHE A 691 " --> pdb=" O ALA A 725 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 367 through 370 removed outlier: 6.407A pdb=" N ILE A 367 " --> pdb=" O PHE A 418 " (cutoff:3.500A) removed outlier: 7.611A pdb=" N ALA A 420 " --> pdb=" O ILE A 367 " (cutoff:3.500A) removed outlier: 6.301A pdb=" N TYR A 369 " --> pdb=" O ALA A 420 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'A' and resid 547 through 549 removed outlier: 3.971A pdb=" N VAL A 549 " --> pdb=" O HIS A 679 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N HIS A 679 " --> pdb=" O VAL A 549 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 652 through 657 removed outlier: 3.565A pdb=" N TRP A 657 " --> pdb=" O ARG A 802 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 669 through 670 removed outlier: 3.971A pdb=" N GLY A 686 " --> pdb=" O ILE A 669 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 928 through 929 removed outlier: 3.693A pdb=" N GLN A 929 " --> pdb=" O VAL B 599 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'A' and resid 952 through 953 removed outlier: 3.605A pdb=" N THR A 953 " --> pdb=" O ALA B 293 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N ALA B 293 " --> pdb=" O THR A 953 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 35 through 36 removed outlier: 3.743A pdb=" N LYS B 979 " --> pdb=" O GLY B 35 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 137 through 140 Processing sheet with id=AB4, first strand: chain 'B' and resid 137 through 140 Processing sheet with id=AB5, first strand: chain 'B' and resid 160 through 163 removed outlier: 6.568A pdb=" N THR B 160 " --> pdb=" O MET B 441 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 263 through 264 Processing sheet with id=AB7, first strand: chain 'B' and resid 641 through 644 removed outlier: 3.655A pdb=" N ILE B 813 " --> pdb=" O GLY B 641 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 886 through 889 removed outlier: 4.174A pdb=" N GLU B 910 " --> pdb=" O ASN B 878 " (cutoff:3.500A) removed outlier: 6.055A pdb=" N VAL B 880 " --> pdb=" O VAL B 908 " (cutoff:3.500A) removed outlier: 5.240A pdb=" N VAL B 908 " --> pdb=" O VAL B 880 " (cutoff:3.500A) 437 hydrogen bonds defined for protein. 1227 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: 5.06 Time building geometry restraints manager: 6.27 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.16 - 1.29: 2523 1.29 - 1.42: 3935 1.42 - 1.55: 8554 1.55 - 1.68: 59 1.68 - 1.82: 179 Bond restraints: 15250 Sorted by residual: bond pdb=" C ALA A 235 " pdb=" N CYS A 236 " ideal model delta sigma weight residual 1.330 1.605 -0.275 1.26e-02 6.30e+03 4.78e+02 bond pdb=" C ALA B 196 " pdb=" N PRO B 197 " ideal model delta sigma weight residual 1.333 1.407 -0.075 1.17e-02 7.31e+03 4.06e+01 bond pdb=" C MET B 364 " pdb=" O MET B 364 " ideal model delta sigma weight residual 1.236 1.165 0.072 1.15e-02 7.56e+03 3.92e+01 bond pdb=" CA THR A 440 " pdb=" C THR A 440 " ideal model delta sigma weight residual 1.519 1.438 0.081 1.32e-02 5.74e+03 3.77e+01 bond pdb=" C ILE A 685 " pdb=" O ILE A 685 " ideal model delta sigma weight residual 1.236 1.173 0.063 1.02e-02 9.61e+03 3.77e+01 ... (remaining 15245 not shown) Histogram of bond angle deviations from ideal: 89.43 - 99.88: 65 99.88 - 110.33: 4338 110.33 - 120.78: 11153 120.78 - 131.22: 5078 131.22 - 141.67: 69 Bond angle restraints: 20703 Sorted by residual: angle pdb=" N VAL A 621 " pdb=" CA VAL A 621 " pdb=" C VAL A 621 " ideal model delta sigma weight residual 113.10 128.65 -15.55 9.70e-01 1.06e+00 2.57e+02 angle pdb=" N GLY A 476 " pdb=" CA GLY A 476 " pdb=" C GLY A 476 " ideal model delta sigma weight residual 112.73 131.77 -19.04 1.20e+00 6.94e-01 2.52e+02 angle pdb=" N LYS A 433 " pdb=" CA LYS A 433 " pdb=" C LYS A 433 " ideal model delta sigma weight residual 111.82 93.45 18.37 1.16e+00 7.43e-01 2.51e+02 angle pdb=" C ILE A 747 " pdb=" CA ILE A 747 " pdb=" CB ILE A 747 " ideal model delta sigma weight residual 111.06 99.30 11.76 8.80e-01 1.29e+00 1.78e+02 angle pdb=" N TYR A 229 " pdb=" CA TYR A 229 " pdb=" C TYR A 229 " ideal model delta sigma weight residual 110.20 89.43 20.77 1.58e+00 4.01e-01 1.73e+02 ... (remaining 20698 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.54: 7263 17.54 - 35.07: 1064 35.07 - 52.61: 546 52.61 - 70.15: 206 70.15 - 87.68: 17 Dihedral angle restraints: 9096 sinusoidal: 3444 harmonic: 5652 Sorted by residual: dihedral pdb=" C LEU A 623 " pdb=" N LEU A 623 " pdb=" CA LEU A 623 " pdb=" CB LEU A 623 " ideal model delta harmonic sigma weight residual -122.60 -148.83 26.23 0 2.50e+00 1.60e-01 1.10e+02 dihedral pdb=" CA THR A 953 " pdb=" C THR A 953 " pdb=" N ALA A 954 " pdb=" CA ALA A 954 " ideal model delta harmonic sigma weight residual -180.00 -128.94 -51.06 0 5.00e+00 4.00e-02 1.04e+02 dihedral pdb=" C CYS B 679 " pdb=" N CYS B 679 " pdb=" CA CYS B 679 " pdb=" CB CYS B 679 " ideal model delta harmonic sigma weight residual -122.60 -147.43 24.83 0 2.50e+00 1.60e-01 9.87e+01 ... (remaining 9093 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.239: 2121 0.239 - 0.478: 203 0.478 - 0.717: 25 0.717 - 0.956: 3 0.956 - 1.195: 4 Chirality restraints: 2356 Sorted by residual: chirality pdb=" CA LEU A 623 " pdb=" N LEU A 623 " pdb=" C LEU A 623 " pdb=" CB LEU A 623 " both_signs ideal model delta sigma weight residual False 2.51 1.32 1.19 2.00e-01 2.50e+01 3.57e+01 chirality pdb=" CA MET A 307 " pdb=" N MET A 307 " pdb=" C MET A 307 " pdb=" CB MET A 307 " both_signs ideal model delta sigma weight residual False 2.51 1.40 1.11 2.00e-01 2.50e+01 3.07e+01 chirality pdb=" CA LEU A 671 " pdb=" N LEU A 671 " pdb=" C LEU A 671 " pdb=" CB LEU A 671 " both_signs ideal model delta sigma weight residual False 2.51 1.51 1.01 2.00e-01 2.50e+01 2.53e+01 ... (remaining 2353 not shown) Planarity restraints: 2702 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C HIS B 752 " 0.114 5.00e-02 4.00e+02 1.76e-01 4.97e+01 pdb=" N PRO B 753 " -0.305 5.00e-02 4.00e+02 pdb=" CA PRO B 753 " 0.101 5.00e-02 4.00e+02 pdb=" CD PRO B 753 " 0.091 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR B 264 " 0.105 5.00e-02 4.00e+02 1.63e-01 4.27e+01 pdb=" N PRO B 265 " -0.283 5.00e-02 4.00e+02 pdb=" CA PRO B 265 " 0.091 5.00e-02 4.00e+02 pdb=" CD PRO B 265 " 0.087 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR B 381 " -0.098 5.00e-02 4.00e+02 1.52e-01 3.68e+01 pdb=" N PRO B 382 " 0.262 5.00e-02 4.00e+02 pdb=" CA PRO B 382 " -0.092 5.00e-02 4.00e+02 pdb=" CD PRO B 382 " -0.072 5.00e-02 4.00e+02 ... (remaining 2699 not shown) Histogram of nonbonded interaction distances: 0.20 - 1.14: 23 1.14 - 2.08: 185 2.08 - 3.02: 10958 3.02 - 3.96: 37571 3.96 - 4.90: 71458 Warning: very small nonbonded interaction distances. Nonbonded interactions: 120195 Sorted by model distance: nonbonded pdb=" NZ LYS A 918 " pdb=" ND2 ASN A 922 " model vdw 0.204 3.200 nonbonded pdb=" O GLY B 377 " pdb=" OG SER B 464 " model vdw 0.248 2.440 nonbonded pdb=" NH2 ARG A 324 " pdb=" OE1 GLN A 413 " model vdw 0.412 2.520 nonbonded pdb=" O GLY B 44 " pdb=" CD1 ILE B 53 " model vdw 0.485 3.460 nonbonded pdb=" CD1 LEU A 55 " pdb=" CE MET A 528 " model vdw 0.485 3.880 ... (remaining 120190 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.690 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: 14.180 Check model and map are aligned: 0.200 Set scattering table: 0.120 Process input model: 41.380 Find NCS groups from input model: 0.560 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.900 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 62.120 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7891 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 : 0.017 0.275 15250 Z= 1.140 Angle : 2.274 20.773 20703 Z= 1.540 Chirality : 0.152 1.195 2356 Planarity : 0.015 0.176 2702 Dihedral : 22.442 87.682 5472 Min Nonbonded Distance : 0.204 Molprobity Statistics. All-atom Clashscore : 100.40 Ramachandran Plot: Outliers : 2.49 % Allowed : 7.81 % Favored : 89.70 % Rotamer: Outliers : 32.66 % Allowed : 17.03 % Favored : 50.32 % Cbeta Deviations : 2.98 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.05 % Twisted Proline : 3.03 % Twisted General : 0.68 % 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: -2.95 (0.16), residues: 1971 helix: -1.04 (0.20), residues: 566 sheet: -1.12 (0.31), residues: 229 loop : -2.75 (0.15), residues: 1176 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.052 0.003 TRP A 690 HIS 0.014 0.002 HIS A 202 PHE 0.033 0.002 PHE A 191 TYR 0.084 0.003 TYR B 295 ARG 0.009 0.001 ARG A 607 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3942 Ramachandran restraints generated. 1971 Oldfield, 0 Emsley, 1971 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3942 Ramachandran restraints generated. 1971 Oldfield, 0 Emsley, 1971 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 814 residues out of total 1574 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 514 poor density : 300 time to evaluate : 1.613 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 514 outliers final: 277 residues processed: 713 average time/residue: 0.3234 time to fit residues: 319.8127 Evaluate side-chains 541 residues out of total 1574 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 277 poor density : 264 time to evaluate : 1.646 Switching outliers to nearest non-outliers revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 277 outliers final: 24 residues processed: 277 average time/residue: 0.2175 time to fit residues: 96.1948 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 197 random chunks: chunk 166 optimal weight: 7.9990 chunk 149 optimal weight: 1.9990 chunk 82 optimal weight: 2.9990 chunk 51 optimal weight: 5.9990 chunk 100 optimal weight: 0.9990 chunk 79 optimal weight: 8.9990 chunk 154 optimal weight: 1.9990 chunk 59 optimal weight: 6.9990 chunk 93 optimal weight: 0.0060 chunk 114 optimal weight: 1.9990 chunk 178 optimal weight: 0.9990 overall best weight: 1.2004 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 17 ASN A 20 HIS A 40 GLN ** A 70 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 203 ASN A 221 ASN A 299 HIS A 341 HIS A 387 ASN A 393 HIS A 407 HIS A 414 ASN ** A 435 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 455 HIS A 496 GLN ** A 556 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 592 GLN A 612 ASN A 667 GLN A 714 ASN A 757 HIS ** A 800 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 922 ASN B 19 ASN B 26 GLN B 100 ASN B 184 GLN B 204 GLN B 220 HIS ** B 221 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 253 HIS B 383 HIS ** B 414 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 431 HIS B 467 GLN B 482 GLN ** B 523 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 538 GLN B 555 ASN B 636 ASN B 705 ASN B 744 ASN B 769 ASN ** B 794 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 805 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 842 ASN B 854 ASN B 881 ASN ** B 885 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 902 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 982 ASN Total number of N/Q/H flips: 40 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7770 moved from start: 0.3919 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.077 15250 Z= 0.312 Angle : 0.936 13.245 20703 Z= 0.492 Chirality : 0.052 0.328 2356 Planarity : 0.007 0.098 2702 Dihedral : 7.783 35.726 2148 Min Nonbonded Distance : 2.027 Molprobity Statistics. All-atom Clashscore : 20.99 Ramachandran Plot: Outliers : 0.81 % Allowed : 7.76 % Favored : 91.43 % Rotamer: Outliers : 7.50 % Allowed : 26.30 % Favored : 66.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.05 % Twisted Proline : 1.52 % Twisted General : 0.21 % 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: -2.71 (0.16), residues: 1971 helix: -0.66 (0.20), residues: 612 sheet: -1.02 (0.29), residues: 258 loop : -2.79 (0.15), residues: 1101 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.003 TRP A 309 HIS 0.023 0.003 HIS A 208 PHE 0.030 0.003 PHE B 399 TYR 0.043 0.003 TYR B 754 ARG 0.012 0.001 ARG A 324 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3942 Ramachandran restraints generated. 1971 Oldfield, 0 Emsley, 1971 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3942 Ramachandran restraints generated. 1971 Oldfield, 0 Emsley, 1971 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 478 residues out of total 1574 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 118 poor density : 360 time to evaluate : 1.614 Fit side-chains outliers start: 118 outliers final: 49 residues processed: 443 average time/residue: 0.2909 time to fit residues: 187.2010 Evaluate side-chains 309 residues out of total 1574 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 260 time to evaluate : 1.509 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 49 outliers final: 1 residues processed: 49 average time/residue: 0.1688 time to fit residues: 17.0186 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 197 random chunks: chunk 99 optimal weight: 0.0170 chunk 55 optimal weight: 3.9990 chunk 148 optimal weight: 10.0000 chunk 121 optimal weight: 7.9990 chunk 49 optimal weight: 5.9990 chunk 179 optimal weight: 10.0000 chunk 193 optimal weight: 7.9990 chunk 159 optimal weight: 0.6980 chunk 177 optimal weight: 10.0000 chunk 61 optimal weight: 4.9990 chunk 143 optimal weight: 20.0000 overall best weight: 3.1424 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 393 HIS A 612 ASN ** A 649 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 800 HIS A 811 ASN A 900 HIS B 100 ASN B 110 GLN ** B 221 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 414 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 478 HIS ** B 523 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 677 HIS B 794 GLN B 805 HIS ** B 818 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 885 ASN B 902 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7866 moved from start: 0.4714 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.058 15250 Z= 0.309 Angle : 0.800 9.938 20703 Z= 0.417 Chirality : 0.048 0.286 2356 Planarity : 0.005 0.065 2702 Dihedral : 6.837 30.666 2148 Min Nonbonded Distance : 2.043 Molprobity Statistics. All-atom Clashscore : 16.77 Ramachandran Plot: Outliers : 0.76 % Allowed : 8.27 % Favored : 90.97 % Rotamer: Outliers : 6.67 % Allowed : 26.87 % Favored : 66.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.05 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: -2.54 (0.17), residues: 1971 helix: -0.53 (0.20), residues: 617 sheet: -0.86 (0.29), residues: 265 loop : -2.71 (0.16), residues: 1089 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A 333 HIS 0.013 0.002 HIS B 523 PHE 0.014 0.002 PHE B 399 TYR 0.019 0.002 TYR B 327 ARG 0.007 0.001 ARG A 452 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3942 Ramachandran restraints generated. 1971 Oldfield, 0 Emsley, 1971 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3942 Ramachandran restraints generated. 1971 Oldfield, 0 Emsley, 1971 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 388 residues out of total 1574 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 105 poor density : 283 time to evaluate : 1.453 Fit side-chains outliers start: 105 outliers final: 51 residues processed: 359 average time/residue: 0.2768 time to fit residues: 147.9846 Evaluate side-chains 305 residues out of total 1574 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 254 time to evaluate : 1.769 Switching outliers to nearest non-outliers outliers start: 51 outliers final: 0 residues processed: 51 average time/residue: 0.1555 time to fit residues: 17.0485 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 197 random chunks: chunk 177 optimal weight: 0.3980 chunk 134 optimal weight: 6.9990 chunk 93 optimal weight: 9.9990 chunk 19 optimal weight: 0.9980 chunk 85 optimal weight: 20.0000 chunk 120 optimal weight: 0.9990 chunk 179 optimal weight: 2.9990 chunk 190 optimal weight: 8.9990 chunk 170 optimal weight: 6.9990 chunk 51 optimal weight: 1.9990 chunk 158 optimal weight: 1.9990 overall best weight: 1.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 38 ASN ** A 282 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 387 ASN A 393 HIS A 612 ASN ** A 649 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 722 HIS B 100 ASN B 110 GLN B 169 GLN ** B 221 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 414 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 490 ASN ** B 500 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 523 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7807 moved from start: 0.5186 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 15250 Z= 0.204 Angle : 0.716 9.629 20703 Z= 0.369 Chirality : 0.044 0.280 2356 Planarity : 0.004 0.046 2702 Dihedral : 6.162 28.197 2148 Min Nonbonded Distance : 2.101 Molprobity Statistics. All-atom Clashscore : 15.12 Ramachandran Plot: Outliers : 0.66 % Allowed : 8.02 % Favored : 91.32 % Rotamer: Outliers : 3.62 % Allowed : 28.84 % Favored : 67.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.05 % 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: -2.16 (0.17), residues: 1971 helix: -0.15 (0.21), residues: 606 sheet: -0.78 (0.29), residues: 278 loop : -2.47 (0.17), residues: 1087 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 309 HIS 0.012 0.002 HIS B 735 PHE 0.014 0.002 PHE A 724 TYR 0.015 0.001 TYR B 754 ARG 0.008 0.000 ARG A 833 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3942 Ramachandran restraints generated. 1971 Oldfield, 0 Emsley, 1971 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3942 Ramachandran restraints generated. 1971 Oldfield, 0 Emsley, 1971 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 359 residues out of total 1574 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 302 time to evaluate : 1.496 Fit side-chains outliers start: 57 outliers final: 20 residues processed: 341 average time/residue: 0.2785 time to fit residues: 141.5856 Evaluate side-chains 278 residues out of total 1574 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 258 time to evaluate : 1.669 Switching outliers to nearest non-outliers outliers start: 20 outliers final: 0 residues processed: 20 average time/residue: 0.1820 time to fit residues: 8.6828 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 197 random chunks: chunk 108 optimal weight: 10.0000 chunk 2 optimal weight: 0.0870 chunk 141 optimal weight: 6.9990 chunk 78 optimal weight: 5.9990 chunk 162 optimal weight: 10.0000 chunk 131 optimal weight: 4.9990 chunk 0 optimal weight: 10.0000 chunk 97 optimal weight: 30.0000 chunk 170 optimal weight: 20.0000 chunk 48 optimal weight: 1.9990 chunk 64 optimal weight: 1.9990 overall best weight: 3.0166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 282 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 393 HIS A 415 GLN A 612 ASN B 100 ASN B 110 GLN ** B 221 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 237 HIS ** B 414 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 478 HIS B 606 HIS ** B 818 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7876 moved from start: 0.5340 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 15250 Z= 0.271 Angle : 0.723 10.102 20703 Z= 0.370 Chirality : 0.044 0.305 2356 Planarity : 0.004 0.039 2702 Dihedral : 5.954 27.137 2148 Min Nonbonded Distance : 2.086 Molprobity Statistics. All-atom Clashscore : 15.22 Ramachandran Plot: Outliers : 0.61 % Allowed : 8.47 % Favored : 90.92 % Rotamer: Outliers : 3.49 % Allowed : 30.43 % Favored : 66.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.05 % 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: -2.16 (0.18), residues: 1971 helix: -0.21 (0.20), residues: 621 sheet: -0.82 (0.29), residues: 287 loop : -2.46 (0.17), residues: 1063 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.045 0.002 TRP A 309 HIS 0.012 0.002 HIS B 523 PHE 0.015 0.002 PHE A 431 TYR 0.017 0.002 TYR B 499 ARG 0.007 0.000 ARG A 174 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3942 Ramachandran restraints generated. 1971 Oldfield, 0 Emsley, 1971 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3942 Ramachandran restraints generated. 1971 Oldfield, 0 Emsley, 1971 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 329 residues out of total 1574 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 274 time to evaluate : 1.659 Fit side-chains revert: symmetry clash outliers start: 55 outliers final: 32 residues processed: 312 average time/residue: 0.2798 time to fit residues: 130.5854 Evaluate side-chains 292 residues out of total 1574 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 260 time to evaluate : 1.603 Switching outliers to nearest non-outliers outliers start: 32 outliers final: 0 residues processed: 32 average time/residue: 0.1560 time to fit residues: 12.2492 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 197 random chunks: chunk 171 optimal weight: 0.9990 chunk 37 optimal weight: 4.9990 chunk 111 optimal weight: 5.9990 chunk 47 optimal weight: 2.9990 chunk 190 optimal weight: 8.9990 chunk 158 optimal weight: 8.9990 chunk 88 optimal weight: 8.9990 chunk 15 optimal weight: 10.0000 chunk 63 optimal weight: 9.9990 chunk 100 optimal weight: 9.9990 chunk 183 optimal weight: 0.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 20 HIS ** A 282 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 612 ASN B 110 GLN ** B 221 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 414 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 705 ASN ** B 818 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7902 moved from start: 0.5491 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 15250 Z= 0.271 Angle : 0.708 10.524 20703 Z= 0.365 Chirality : 0.044 0.318 2356 Planarity : 0.004 0.035 2702 Dihedral : 5.853 26.753 2148 Min Nonbonded Distance : 2.085 Molprobity Statistics. All-atom Clashscore : 14.98 Ramachandran Plot: Outliers : 0.56 % Allowed : 8.52 % Favored : 90.92 % Rotamer: Outliers : 2.48 % Allowed : 31.00 % Favored : 66.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.05 % 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: -2.13 (0.18), residues: 1971 helix: -0.16 (0.21), residues: 622 sheet: -0.74 (0.29), residues: 289 loop : -2.49 (0.17), residues: 1060 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP A 309 HIS 0.014 0.001 HIS B 735 PHE 0.015 0.002 PHE A 431 TYR 0.025 0.002 TYR B 327 ARG 0.010 0.000 ARG A 174 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3942 Ramachandran restraints generated. 1971 Oldfield, 0 Emsley, 1971 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3942 Ramachandran restraints generated. 1971 Oldfield, 0 Emsley, 1971 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 320 residues out of total 1574 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 281 time to evaluate : 1.615 Fit side-chains revert: symmetry clash outliers start: 39 outliers final: 24 residues processed: 304 average time/residue: 0.2771 time to fit residues: 125.5151 Evaluate side-chains 288 residues out of total 1574 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 264 time to evaluate : 1.680 Switching outliers to nearest non-outliers outliers start: 24 outliers final: 0 residues processed: 24 average time/residue: 0.1645 time to fit residues: 9.3713 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 197 random chunks: chunk 21 optimal weight: 9.9990 chunk 108 optimal weight: 9.9990 chunk 139 optimal weight: 0.8980 chunk 107 optimal weight: 0.9990 chunk 160 optimal weight: 5.9990 chunk 106 optimal weight: 5.9990 chunk 189 optimal weight: 0.0670 chunk 118 optimal weight: 7.9990 chunk 115 optimal weight: 0.7980 chunk 87 optimal weight: 8.9990 chunk 117 optimal weight: 6.9990 overall best weight: 1.7522 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 20 HIS ** A 282 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 414 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 612 ASN B 110 GLN ** B 414 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 818 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7858 moved from start: 0.5732 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 15250 Z= 0.204 Angle : 0.688 10.862 20703 Z= 0.349 Chirality : 0.043 0.334 2356 Planarity : 0.003 0.034 2702 Dihedral : 5.658 26.179 2148 Min Nonbonded Distance : 2.104 Molprobity Statistics. All-atom Clashscore : 15.09 Ramachandran Plot: Outliers : 0.56 % Allowed : 8.37 % Favored : 91.07 % Rotamer: Outliers : 2.03 % Allowed : 31.51 % Favored : 66.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.05 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.93 (0.18), residues: 1971 helix: 0.03 (0.21), residues: 613 sheet: -0.65 (0.30), residues: 289 loop : -2.35 (0.17), residues: 1069 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP A 309 HIS 0.012 0.001 HIS B 735 PHE 0.014 0.001 PHE A 431 TYR 0.017 0.001 TYR B 327 ARG 0.010 0.000 ARG A 174 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3942 Ramachandran restraints generated. 1971 Oldfield, 0 Emsley, 1971 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3942 Ramachandran restraints generated. 1971 Oldfield, 0 Emsley, 1971 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 322 residues out of total 1574 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 290 time to evaluate : 1.563 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 32 outliers final: 13 residues processed: 309 average time/residue: 0.2751 time to fit residues: 127.6406 Evaluate side-chains 289 residues out of total 1574 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 276 time to evaluate : 1.648 Switching outliers to nearest non-outliers outliers start: 13 outliers final: 0 residues processed: 13 average time/residue: 0.1429 time to fit residues: 5.7480 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 197 random chunks: chunk 75 optimal weight: 2.9990 chunk 113 optimal weight: 0.0570 chunk 57 optimal weight: 8.9990 chunk 37 optimal weight: 6.9990 chunk 36 optimal weight: 0.9990 chunk 120 optimal weight: 0.9990 chunk 129 optimal weight: 5.9990 chunk 93 optimal weight: 20.0000 chunk 17 optimal weight: 0.3980 chunk 149 optimal weight: 6.9990 chunk 172 optimal weight: 7.9990 overall best weight: 1.0904 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 62 ASN ** A 282 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 414 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 612 ASN B 110 GLN ** B 221 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 414 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 478 HIS ** B 818 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7821 moved from start: 0.5949 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 15250 Z= 0.186 Angle : 0.677 10.691 20703 Z= 0.342 Chirality : 0.042 0.301 2356 Planarity : 0.003 0.032 2702 Dihedral : 5.464 24.884 2148 Min Nonbonded Distance : 2.105 Molprobity Statistics. All-atom Clashscore : 14.28 Ramachandran Plot: Outliers : 0.51 % Allowed : 8.17 % Favored : 91.32 % Rotamer: Outliers : 1.40 % Allowed : 32.97 % Favored : 65.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.05 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.82 (0.18), residues: 1971 helix: 0.15 (0.21), residues: 619 sheet: -0.55 (0.30), residues: 279 loop : -2.32 (0.17), residues: 1073 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 347 HIS 0.009 0.001 HIS B 735 PHE 0.013 0.001 PHE A 431 TYR 0.015 0.001 TYR B 577 ARG 0.008 0.000 ARG A 174 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3942 Ramachandran restraints generated. 1971 Oldfield, 0 Emsley, 1971 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3942 Ramachandran restraints generated. 1971 Oldfield, 0 Emsley, 1971 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 313 residues out of total 1574 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 291 time to evaluate : 1.748 Fit side-chains revert: symmetry clash outliers start: 22 outliers final: 13 residues processed: 304 average time/residue: 0.2762 time to fit residues: 127.1485 Evaluate side-chains 285 residues out of total 1574 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 272 time to evaluate : 1.854 Switching outliers to nearest non-outliers outliers start: 13 outliers final: 0 residues processed: 13 average time/residue: 0.1527 time to fit residues: 6.0522 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 197 random chunks: chunk 181 optimal weight: 0.8980 chunk 165 optimal weight: 9.9990 chunk 176 optimal weight: 8.9990 chunk 106 optimal weight: 7.9990 chunk 77 optimal weight: 10.0000 chunk 138 optimal weight: 2.9990 chunk 54 optimal weight: 0.0470 chunk 159 optimal weight: 10.0000 chunk 167 optimal weight: 7.9990 chunk 116 optimal weight: 10.0000 chunk 187 optimal weight: 0.5980 overall best weight: 2.5082 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 20 HIS ** A 282 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 414 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 612 ASN A 770 ASN ** B 414 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 478 HIS ** B 818 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7861 moved from start: 0.5976 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 15250 Z= 0.235 Angle : 0.690 12.214 20703 Z= 0.349 Chirality : 0.043 0.284 2356 Planarity : 0.004 0.037 2702 Dihedral : 5.443 24.781 2148 Min Nonbonded Distance : 2.123 Molprobity Statistics. All-atom Clashscore : 15.12 Ramachandran Plot: Outliers : 0.46 % Allowed : 8.32 % Favored : 91.22 % Rotamer: Outliers : 1.14 % Allowed : 33.55 % Favored : 65.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.05 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.86 (0.18), residues: 1971 helix: 0.12 (0.21), residues: 618 sheet: -0.65 (0.30), residues: 289 loop : -2.33 (0.17), residues: 1064 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 309 HIS 0.018 0.001 HIS B 735 PHE 0.019 0.002 PHE B 178 TYR 0.031 0.002 TYR B 327 ARG 0.008 0.000 ARG A 174 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3942 Ramachandran restraints generated. 1971 Oldfield, 0 Emsley, 1971 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3942 Ramachandran restraints generated. 1971 Oldfield, 0 Emsley, 1971 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 301 residues out of total 1574 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 283 time to evaluate : 1.749 Fit side-chains revert: symmetry clash outliers start: 18 outliers final: 13 residues processed: 289 average time/residue: 0.2913 time to fit residues: 125.2170 Evaluate side-chains 285 residues out of total 1574 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 272 time to evaluate : 1.674 Switching outliers to nearest non-outliers outliers start: 13 outliers final: 0 residues processed: 13 average time/residue: 0.1872 time to fit residues: 6.1476 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 197 random chunks: chunk 114 optimal weight: 0.9980 chunk 88 optimal weight: 7.9990 chunk 130 optimal weight: 9.9990 chunk 196 optimal weight: 9.9990 chunk 180 optimal weight: 20.0000 chunk 156 optimal weight: 0.9980 chunk 16 optimal weight: 8.9990 chunk 120 optimal weight: 2.9990 chunk 95 optimal weight: 20.0000 chunk 124 optimal weight: 2.9990 chunk 166 optimal weight: 4.9990 overall best weight: 2.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 20 HIS ** A 282 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 414 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 302 HIS ** B 414 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 527 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 818 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7875 moved from start: 0.6047 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 15250 Z= 0.237 Angle : 0.700 11.706 20703 Z= 0.356 Chirality : 0.043 0.283 2356 Planarity : 0.004 0.037 2702 Dihedral : 5.459 24.750 2148 Min Nonbonded Distance : 2.105 Molprobity Statistics. All-atom Clashscore : 15.05 Ramachandran Plot: Outliers : 0.51 % Allowed : 8.57 % Favored : 90.92 % Rotamer: Outliers : 0.64 % Allowed : 33.55 % Favored : 65.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.05 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.85 (0.18), residues: 1971 helix: 0.08 (0.21), residues: 615 sheet: -0.68 (0.30), residues: 289 loop : -2.27 (0.17), residues: 1067 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP A 309 HIS 0.018 0.001 HIS B 735 PHE 0.014 0.001 PHE B 423 TYR 0.025 0.001 TYR B 327 ARG 0.008 0.000 ARG A 174 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3942 Ramachandran restraints generated. 1971 Oldfield, 0 Emsley, 1971 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3942 Ramachandran restraints generated. 1971 Oldfield, 0 Emsley, 1971 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 291 residues out of total 1574 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 281 time to evaluate : 1.738 Fit side-chains revert: symmetry clash outliers start: 10 outliers final: 7 residues processed: 287 average time/residue: 0.2923 time to fit residues: 125.9247 Evaluate side-chains 281 residues out of total 1574 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 274 time to evaluate : 1.621 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.1565 time to fit residues: 4.2774 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 197 random chunks: chunk 47 optimal weight: 3.9990 chunk 144 optimal weight: 8.9990 chunk 23 optimal weight: 0.2980 chunk 43 optimal weight: 10.0000 chunk 156 optimal weight: 5.9990 chunk 65 optimal weight: 5.9990 chunk 160 optimal weight: 10.0000 chunk 19 optimal weight: 1.9990 chunk 28 optimal weight: 5.9990 chunk 137 optimal weight: 7.9990 chunk 8 optimal weight: 10.0000 overall best weight: 3.6588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 282 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 414 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 613 GLN B 110 GLN ** B 237 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 414 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 818 HIS ** 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 = 0.3515 r_free = 0.3515 target = 0.142450 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.131868 restraints weight = 17298.824| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3422 r_free = 0.3422 target = 0.134130 restraints weight = 11289.996| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.135784 restraints weight = 7983.504| |-----------------------------------------------------------------------------| r_work (final): 0.3388 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7998 moved from start: 0.6036 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 15250 Z= 0.288 Angle : 0.728 11.757 20703 Z= 0.368 Chirality : 0.044 0.281 2356 Planarity : 0.004 0.045 2702 Dihedral : 5.568 24.913 2148 Min Nonbonded Distance : 2.091 Molprobity Statistics. All-atom Clashscore : 15.15 Ramachandran Plot: Outliers : 0.51 % Allowed : 9.28 % Favored : 90.21 % Rotamer: Outliers : 0.70 % Allowed : 33.74 % Favored : 65.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.05 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.95 (0.18), residues: 1971 helix: -0.07 (0.21), residues: 619 sheet: -0.72 (0.30), residues: 289 loop : -2.29 (0.17), residues: 1063 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP A 309 HIS 0.017 0.001 HIS B 735 PHE 0.015 0.002 PHE B 218 TYR 0.022 0.002 TYR A 850 ARG 0.007 0.000 ARG A 174 =============================================================================== Job complete usr+sys time: 3678.82 seconds wall clock time: 67 minutes 16.77 seconds (4036.77 seconds total)