Starting phenix.real_space_refine on Tue May 14 00:35:49 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8rbo_19033/05_2024/8rbo_19033.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8rbo_19033/05_2024/8rbo_19033.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.02 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8rbo_19033/05_2024/8rbo_19033.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8rbo_19033/05_2024/8rbo_19033.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8rbo_19033/05_2024/8rbo_19033.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8rbo_19033/05_2024/8rbo_19033.pdb" } resolution = 3.02 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= 0.001 sd= 0.022 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians Zn 5 6.06 5 Mg 1 5.21 5 S 112 5.16 5 C 16774 2.51 5 N 4583 2.21 5 O 4893 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 52": "OD1" <-> "OD2" Residue "A GLU 99": "OE1" <-> "OE2" Residue "A GLU 169": "OE1" <-> "OE2" Residue "A GLU 483": "OE1" <-> "OE2" Residue "A GLU 563": "OE1" <-> "OE2" Residue "A ASP 594": "OD1" <-> "OD2" Residue "A ASP 855": "OD1" <-> "OD2" Residue "B TYR 101": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 155": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 156": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 182": "OE1" <-> "OE2" Residue "B GLU 285": "OE1" <-> "OE2" Residue "B ASP 980": "OD1" <-> "OD2" Residue "B GLU 1049": "OE1" <-> "OE2" Residue "C TYR 26": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 245": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 275": "OE1" <-> "OE2" Residue "D GLU 127": "OE1" <-> "OE2" Residue "E TYR 2": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 24": "OE1" <-> "OE2" Residue "E GLU 32": "OE1" <-> "OE2" Residue "E GLU 69": "OE1" <-> "OE2" Residue "E ASP 73": "OD1" <-> "OD2" Residue "E ASP 115": "OD1" <-> "OD2" Residue "F TYR 11": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 51": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 24": "OE1" <-> "OE2" Residue "H GLU 25": "OE1" <-> "OE2" Residue "H ASP 59": "OD1" <-> "OD2" Residue "H GLU 62": "OE1" <-> "OE2" Residue "H TYR 73": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ASP 29": "OD1" <-> "OD2" Residue "K GLU 38": "OE1" <-> "OE2" Residue "K PHE 44": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K GLU 45": "OE1" <-> "OE2" Residue "N GLU 32": "OE1" <-> "OE2" Residue "N GLU 54": "OE1" <-> "OE2" Residue "P ASP 24": "OD1" <-> "OD2" Residue "P TYR 29": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.09s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5322/modules/chem_data/mon_lib" Total number of atoms: 26368 Number of models: 1 Model: "" Number of chains: 15 Chain: "A" Number of atoms: 7197 Number of conformers: 1 Conformer: "" Number of residues, atoms: 901, 7197 Classifications: {'peptide': 901} Link IDs: {'PCIS': 1, 'PTRANS': 51, 'TRANS': 848} Chain: "B" Number of atoms: 8803 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1098, 8803 Classifications: {'peptide': 1098} Link IDs: {'PTRANS': 61, 'TRANS': 1036} Chain breaks: 1 Chain: "C" Number of atoms: 3057 Number of conformers: 1 Conformer: "" Number of residues, atoms: 390, 3057 Classifications: {'peptide': 390} Link IDs: {'PTRANS': 16, 'TRANS': 373} Chain: "D" Number of atoms: 2086 Number of conformers: 1 Conformer: "" Number of residues, atoms: 258, 2086 Classifications: {'peptide': 258} Link IDs: {'PTRANS': 15, 'TRANS': 242} Chain: "E" Number of atoms: 1528 Number of conformers: 1 Conformer: "" Number of residues, atoms: 189, 1528 Classifications: {'peptide': 189} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 8, 'TRANS': 180} Chain: "F" Number of atoms: 946 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 946 Classifications: {'peptide': 116} Link IDs: {'PTRANS': 4, 'TRANS': 111} Chain: "H" Number of atoms: 600 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 600 Classifications: {'peptide': 75} Link IDs: {'PTRANS': 5, 'TRANS': 69} Chain: "K" Number of atoms: 432 Number of conformers: 1 Conformer: "" Number of residues, atoms: 56, 432 Classifications: {'peptide': 56} Link IDs: {'PTRANS': 6, 'TRANS': 49} Chain: "L" Number of atoms: 777 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 777 Classifications: {'peptide': 94} Link IDs: {'PTRANS': 4, 'TRANS': 89} Chain: "N" Number of atoms: 543 Number of conformers: 1 Conformer: "" Number of residues, atoms: 65, 543 Classifications: {'peptide': 65} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 62} Chain: "P" Number of atoms: 393 Number of conformers: 1 Conformer: "" Number of residues, atoms: 48, 393 Classifications: {'peptide': 48} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 43} Chain: "A" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' MG': 1, ' ZN': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "N" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "P" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 434 SG CYS A 57 95.712 90.655 55.603 1.00 0.73 S ATOM 456 SG CYS A 60 93.380 92.863 57.552 1.00 30.00 S ATOM 499 SG CYS A 67 92.745 89.071 57.394 1.00 0.77 S ATOM 736 SG CYS A 97 61.285 86.157 20.467 1.00 0.80 S ATOM 762 SG CYS A 100 61.364 89.892 20.165 1.00 0.73 S ATOM 1138 SG CYS A 144 58.017 88.094 19.818 1.00 0.72 S ATOM 1161 SG CYS A 147 60.602 87.732 17.091 1.00 0.78 S ATOM 15532 SG CYS B1059 79.702 101.951 50.261 1.00 0.85 S ATOM 15555 SG CYS B1062 78.844 100.778 46.785 1.00 30.00 S ATOM 15685 SG CYS B1077 82.339 100.209 48.605 1.00 0.84 S ATOM 15705 SG CYS B1080 80.976 103.304 46.494 1.00 0.68 S ATOM 25480 SG CYS N 7 74.542 47.527 113.120 1.00 0.59 S ATOM 25504 SG CYS N 10 74.130 48.598 116.785 1.00 0.59 S ATOM 25784 SG CYS N 44 71.065 47.459 114.609 1.00 0.60 S ATOM 25790 SG CYS N 45 73.576 45.187 116.170 1.00 0.60 S ATOM 26026 SG CYS P 8 107.456 40.766 84.122 1.00 86.83 S ATOM 26052 SG CYS P 11 108.976 37.965 85.953 1.00 84.70 S ATOM 26181 SG CYS P 27 110.951 39.773 83.090 1.00 79.74 S ATOM 26206 SG CYS P 30 108.039 37.481 82.285 1.00 30.00 S Time building chain proxies: 13.42, per 1000 atoms: 0.51 Number of scatterers: 26368 At special positions: 0 Unit cell: (133.584, 168.432, 154.88, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Zn 5 29.99 S 112 16.00 Mg 1 11.99 O 4893 8.00 N 4583 7.00 C 16774 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: 10.45 Conformation dependent library (CDL) restraints added in 5.1 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A1000 " pdb="ZN ZN A1000 " - pdb=" NE2 HIS A 70 " pdb="ZN ZN A1000 " - pdb=" SG CYS A 57 " pdb="ZN ZN A1000 " - pdb=" SG CYS A 60 " pdb="ZN ZN A1000 " - pdb=" SG CYS A 67 " pdb=" ZN A1001 " pdb="ZN ZN A1001 " - pdb=" SG CYS A 97 " pdb="ZN ZN A1001 " - pdb=" SG CYS A 100 " pdb="ZN ZN A1001 " - pdb=" SG CYS A 147 " pdb="ZN ZN A1001 " - pdb=" SG CYS A 144 " pdb=" ZN B1201 " pdb="ZN ZN B1201 " - pdb=" SG CYS B1062 " pdb="ZN ZN B1201 " - pdb=" SG CYS B1077 " pdb="ZN ZN B1201 " - pdb=" SG CYS B1059 " pdb="ZN ZN B1201 " - pdb=" SG CYS B1080 " pdb=" ZN N 101 " pdb="ZN ZN N 101 " - pdb=" SG CYS N 45 " pdb="ZN ZN N 101 " - pdb=" SG CYS N 10 " pdb="ZN ZN N 101 " - pdb=" SG CYS N 44 " pdb="ZN ZN N 101 " - pdb=" SG CYS N 7 " pdb=" ZN P 101 " pdb="ZN ZN P 101 " - pdb=" SG CYS P 8 " pdb="ZN ZN P 101 " - pdb=" SG CYS P 11 " pdb="ZN ZN P 101 " - pdb=" SG CYS P 30 " pdb="ZN ZN P 101 " - pdb=" SG CYS P 27 " Number of angles added : 27 6532 Ramachandran restraints generated. 3266 Oldfield, 0 Emsley, 3266 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6108 Finding SS restraints... Secondary structure from input PDB file: 127 helices and 41 sheets defined 43.0% alpha, 19.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.53 Creating SS restraints... Processing helix chain 'A' and resid 14 through 22 Processing helix chain 'A' and resid 85 through 96 Processing helix chain 'A' and resid 106 through 119 Processing helix chain 'A' and resid 123 through 141 removed outlier: 3.558A pdb=" N PHE A 127 " --> pdb=" O ARG A 123 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N ARG A 141 " --> pdb=" O LYS A 137 " (cutoff:3.500A) Processing helix chain 'A' and resid 168 through 172 Processing helix chain 'A' and resid 179 through 189 removed outlier: 3.517A pdb=" N LYS A 189 " --> pdb=" O ASP A 185 " (cutoff:3.500A) Processing helix chain 'A' and resid 194 through 199 Processing helix chain 'A' and resid 206 through 209 Processing helix chain 'A' and resid 236 through 259 Processing helix chain 'A' and resid 261 through 281 removed outlier: 3.631A pdb=" N ILE A 265 " --> pdb=" O PRO A 261 " (cutoff:3.500A) Processing helix chain 'A' and resid 300 through 306 Processing helix chain 'A' and resid 344 through 350 removed outlier: 3.503A pdb=" N GLU A 349 " --> pdb=" O GLU A 345 " (cutoff:3.500A) Processing helix chain 'A' and resid 360 through 371 removed outlier: 3.606A pdb=" N GLY A 371 " --> pdb=" O MET A 367 " (cutoff:3.500A) Processing helix chain 'A' and resid 395 through 403 Processing helix chain 'A' and resid 428 through 430 No H-bonds generated for 'chain 'A' and resid 428 through 430' Processing helix chain 'A' and resid 451 through 456 removed outlier: 3.814A pdb=" N TYR A 455 " --> pdb=" O VAL A 451 " (cutoff:3.500A) Processing helix chain 'A' and resid 471 through 482 Processing helix chain 'A' and resid 483 through 488 removed outlier: 3.955A pdb=" N ILE A 488 " --> pdb=" O GLN A 485 " (cutoff:3.500A) Processing helix chain 'A' and resid 502 through 513 Processing helix chain 'A' and resid 519 through 531 Processing helix chain 'A' and resid 545 through 547 No H-bonds generated for 'chain 'A' and resid 545 through 547' Processing helix chain 'A' and resid 553 through 559 Processing helix chain 'A' and resid 576 through 590 removed outlier: 3.804A pdb=" N CYS A 580 " --> pdb=" O GLU A 576 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N LYS A 590 " --> pdb=" O LEU A 586 " (cutoff:3.500A) Processing helix chain 'A' and resid 594 through 601 Processing helix chain 'A' and resid 620 through 625 removed outlier: 4.134A pdb=" N TYR A 624 " --> pdb=" O ASP A 620 " (cutoff:3.500A) Processing helix chain 'A' and resid 629 through 639 Processing helix chain 'A' and resid 640 through 663 removed outlier: 3.890A pdb=" N LYS A 653 " --> pdb=" O ASP A 649 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N GLY A 663 " --> pdb=" O ILE A 659 " (cutoff:3.500A) Processing helix chain 'A' and resid 667 through 672 removed outlier: 3.871A pdb=" N GLU A 671 " --> pdb=" O ILE A 668 " (cutoff:3.500A) Processing helix chain 'A' and resid 674 through 701 Processing helix chain 'A' and resid 711 through 738 Processing helix chain 'A' and resid 743 through 751 Processing helix chain 'A' and resid 756 through 765 removed outlier: 3.634A pdb=" N ILE A 760 " --> pdb=" O LYS A 756 " (cutoff:3.500A) Processing helix chain 'A' and resid 796 through 799 Processing helix chain 'A' and resid 811 through 847 removed outlier: 3.901A pdb=" N GLU A 824 " --> pdb=" O MET A 820 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N GLY A 825 " --> pdb=" O GLY A 821 " (cutoff:3.500A) removed outlier: 4.156A pdb=" N ALA A 834 " --> pdb=" O ALA A 830 " (cutoff:3.500A) Processing helix chain 'A' and resid 869 through 873 Processing helix chain 'A' and resid 887 through 901 Processing helix chain 'B' and resid 10 through 25 removed outlier: 3.794A pdb=" N SER B 20 " --> pdb=" O ILE B 16 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N TYR B 21 " --> pdb=" O VAL B 17 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N TRP B 22 " --> pdb=" O MET B 18 " (cutoff:3.500A) Processing helix chain 'B' and resid 28 through 51 removed outlier: 3.901A pdb=" N SER B 34 " --> pdb=" O GLN B 30 " (cutoff:3.500A) removed outlier: 5.125A pdb=" N LEU B 43 " --> pdb=" O ILE B 39 " (cutoff:3.500A) removed outlier: 5.583A pdb=" N GLN B 44 " --> pdb=" O GLU B 40 " (cutoff:3.500A) Processing helix chain 'B' and resid 85 through 93 Processing helix chain 'B' and resid 138 through 146 Processing helix chain 'B' and resid 225 through 232 Processing helix chain 'B' and resid 236 through 245 removed outlier: 3.537A pdb=" N ILE B 240 " --> pdb=" O ARG B 236 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N GLY B 245 " --> pdb=" O VAL B 241 " (cutoff:3.500A) Processing helix chain 'B' and resid 247 through 261 Processing helix chain 'B' and resid 266 through 279 Processing helix chain 'B' and resid 283 through 299 removed outlier: 3.861A pdb=" N LEU B 288 " --> pdb=" O ARG B 284 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N LEU B 299 " --> pdb=" O ILE B 295 " (cutoff:3.500A) Processing helix chain 'B' and resid 300 through 304 Processing helix chain 'B' and resid 306 through 308 No H-bonds generated for 'chain 'B' and resid 306 through 308' Processing helix chain 'B' and resid 309 through 329 Processing helix chain 'B' and resid 347 through 378 removed outlier: 3.582A pdb=" N GLN B 362 " --> pdb=" O VAL B 358 " (cutoff:3.500A) Processing helix chain 'B' and resid 379 through 386 removed outlier: 4.351A pdb=" N ASN B 386 " --> pdb=" O TYR B 382 " (cutoff:3.500A) Processing helix chain 'B' and resid 386 through 394 Processing helix chain 'B' and resid 397 through 411 removed outlier: 3.512A pdb=" N ARG B 403 " --> pdb=" O VAL B 399 " (cutoff:3.500A) Processing helix chain 'B' and resid 428 through 436 Processing helix chain 'B' and resid 449 through 454 removed outlier: 3.734A pdb=" N ASP B 454 " --> pdb=" O PHE B 450 " (cutoff:3.500A) Processing helix chain 'B' and resid 456 through 460 removed outlier: 3.580A pdb=" N TRP B 460 " --> pdb=" O GLY B 457 " (cutoff:3.500A) Processing helix chain 'B' and resid 491 through 503 removed outlier: 3.637A pdb=" N ILE B 495 " --> pdb=" O PRO B 491 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N GLY B 503 " --> pdb=" O LEU B 499 " (cutoff:3.500A) Processing helix chain 'B' and resid 531 through 546 Processing helix chain 'B' and resid 587 through 596 Processing helix chain 'B' and resid 600 through 607 Processing helix chain 'B' and resid 616 through 621 Processing helix chain 'B' and resid 626 through 630 removed outlier: 3.680A pdb=" N VAL B 630 " --> pdb=" O PRO B 627 " (cutoff:3.500A) Processing helix chain 'B' and resid 640 through 645 removed outlier: 3.989A pdb=" N LEU B 645 " --> pdb=" O ALA B 642 " (cutoff:3.500A) Processing helix chain 'B' and resid 647 through 652 removed outlier: 3.615A pdb=" N VAL B 652 " --> pdb=" O ALA B 649 " (cutoff:3.500A) Processing helix chain 'B' and resid 654 through 658 removed outlier: 3.667A pdb=" N ASN B 658 " --> pdb=" O PRO B 655 " (cutoff:3.500A) Processing helix chain 'B' and resid 659 through 670 Processing helix chain 'B' and resid 702 through 708 removed outlier: 4.222A pdb=" N LYS B 706 " --> pdb=" O SER B 702 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N ALA B 707 " --> pdb=" O ARG B 703 " (cutoff:3.500A) Processing helix chain 'B' and resid 709 through 713 Processing helix chain 'B' and resid 739 through 744 Processing helix chain 'B' and resid 891 through 895 Processing helix chain 'B' and resid 909 through 913 removed outlier: 3.543A pdb=" N ILE B 913 " --> pdb=" O PRO B 910 " (cutoff:3.500A) Processing helix chain 'B' and resid 918 through 935 removed outlier: 3.963A pdb=" N LEU B 922 " --> pdb=" O THR B 918 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N LYS B 929 " --> pdb=" O ALA B 925 " (cutoff:3.500A) Processing helix chain 'B' and resid 947 through 958 Processing helix chain 'B' and resid 994 through 998 Processing helix chain 'B' and resid 1027 through 1038 Processing helix chain 'B' and resid 1039 through 1048 Processing helix chain 'B' and resid 1093 through 1105 removed outlier: 3.584A pdb=" N MET B1105 " --> pdb=" O GLU B1101 " (cutoff:3.500A) Processing helix chain 'C' and resid 2 through 14 Processing helix chain 'C' and resid 18 through 36 Processing helix chain 'C' and resid 39 through 57 Processing helix chain 'C' and resid 64 through 75 Processing helix chain 'C' and resid 76 through 79 Processing helix chain 'C' and resid 98 through 108 Processing helix chain 'C' and resid 128 through 140 Processing helix chain 'C' and resid 144 through 147 No H-bonds generated for 'chain 'C' and resid 144 through 147' Processing helix chain 'C' and resid 165 through 173 removed outlier: 4.405A pdb=" N LEU C 169 " --> pdb=" O ASP C 165 " (cutoff:3.500A) Processing helix chain 'C' and resid 175 through 187 Processing helix chain 'C' and resid 203 through 208 removed outlier: 3.833A pdb=" N LYS C 208 " --> pdb=" O LYS C 205 " (cutoff:3.500A) Processing helix chain 'C' and resid 212 through 222 removed outlier: 3.687A pdb=" N HIS C 222 " --> pdb=" O LYS C 218 " (cutoff:3.500A) Processing helix chain 'C' and resid 250 through 255 removed outlier: 3.865A pdb=" N LEU C 255 " --> pdb=" O PHE C 251 " (cutoff:3.500A) Processing helix chain 'C' and resid 269 through 277 Processing helix chain 'C' and resid 278 through 298 removed outlier: 3.596A pdb=" N ASN C 284 " --> pdb=" O GLU C 280 " (cutoff:3.500A) Processing helix chain 'C' and resid 302 through 314 removed outlier: 4.158A pdb=" N ILE C 306 " --> pdb=" O ASP C 302 " (cutoff:3.500A) Processing helix chain 'C' and resid 327 through 331 Processing helix chain 'C' and resid 333 through 341 removed outlier: 3.535A pdb=" N PHE C 340 " --> pdb=" O ALA C 336 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N GLU C 341 " --> pdb=" O ARG C 337 " (cutoff:3.500A) Processing helix chain 'C' and resid 342 through 354 Processing helix chain 'C' and resid 361 through 369 removed outlier: 3.665A pdb=" N ASN C 365 " --> pdb=" O GLY C 361 " (cutoff:3.500A) Processing helix chain 'C' and resid 374 through 379 removed outlier: 3.536A pdb=" N VAL C 379 " --> pdb=" O THR C 376 " (cutoff:3.500A) Processing helix chain 'D' and resid 24 through 38 Processing helix chain 'D' and resid 57 through 68 removed outlier: 3.616A pdb=" N HIS D 63 " --> pdb=" O GLU D 59 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N ILE D 68 " --> pdb=" O ARG D 64 " (cutoff:3.500A) Processing helix chain 'D' and resid 104 through 106 No H-bonds generated for 'chain 'D' and resid 104 through 106' Processing helix chain 'D' and resid 145 through 149 Processing helix chain 'D' and resid 169 through 181 removed outlier: 3.717A pdb=" N LEU D 173 " --> pdb=" O GLU D 169 " (cutoff:3.500A) Processing helix chain 'D' and resid 203 through 209 removed outlier: 4.024A pdb=" N GLU D 207 " --> pdb=" O ASP D 204 " (cutoff:3.500A) Processing helix chain 'D' and resid 233 through 258 Processing helix chain 'E' and resid 14 through 18 Processing helix chain 'E' and resid 21 through 34 Processing helix chain 'E' and resid 111 through 114 Processing helix chain 'E' and resid 172 through 189 Processing helix chain 'F' and resid 13 through 16 Processing helix chain 'F' and resid 17 through 31 Processing helix chain 'F' and resid 41 through 51 removed outlier: 3.533A pdb=" N HIS F 47 " --> pdb=" O LEU F 43 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N PHE F 51 " --> pdb=" O HIS F 47 " (cutoff:3.500A) Processing helix chain 'F' and resid 55 through 70 removed outlier: 3.598A pdb=" N PHE F 70 " --> pdb=" O LEU F 66 " (cutoff:3.500A) Processing helix chain 'F' and resid 74 through 85 Processing helix chain 'F' and resid 88 through 99 Processing helix chain 'F' and resid 104 through 116 removed outlier: 3.714A pdb=" N MET F 108 " --> pdb=" O THR F 104 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N ASP F 116 " --> pdb=" O LEU F 112 " (cutoff:3.500A) Processing helix chain 'H' and resid 8 through 12 Processing helix chain 'H' and resid 22 through 33 removed outlier: 3.557A pdb=" N TYR H 33 " --> pdb=" O LEU H 29 " (cutoff:3.500A) Processing helix chain 'H' and resid 36 through 40 removed outlier: 3.704A pdb=" N LEU H 40 " --> pdb=" O LEU H 37 " (cutoff:3.500A) Processing helix chain 'H' and resid 47 through 54 Processing helix chain 'K' and resid 5 through 23 Processing helix chain 'K' and resid 35 through 47 Processing helix chain 'L' and resid 21 through 33 removed outlier: 4.018A pdb=" N LEU L 27 " --> pdb=" O THR L 23 " (cutoff:3.500A) Processing helix chain 'L' and resid 66 through 94 removed outlier: 3.542A pdb=" N GLU L 72 " --> pdb=" O GLU L 68 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N LYS L 94 " --> pdb=" O GLU L 90 " (cutoff:3.500A) Processing helix chain 'N' and resid 14 through 16 No H-bonds generated for 'chain 'N' and resid 14 through 16' Processing helix chain 'N' and resid 17 through 28 Processing helix chain 'N' and resid 30 through 38 Processing helix chain 'N' and resid 42 through 51 removed outlier: 3.815A pdb=" N MET N 48 " --> pdb=" O CYS N 44 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N LEU N 49 " --> pdb=" O CYS N 45 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 1107 through 1114 removed outlier: 5.952A pdb=" N SER B1114 " --> pdb=" O ILE A 5 " (cutoff:3.500A) removed outlier: 5.111A pdb=" N ILE A 5 " --> pdb=" O SER B1114 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 72 through 81 removed outlier: 6.713A pdb=" N THR A 213 " --> pdb=" O LEU A 76 " (cutoff:3.500A) removed outlier: 10.466A pdb=" N ARG A 78 " --> pdb=" O VAL A 211 " (cutoff:3.500A) removed outlier: 10.447A pdb=" N VAL A 211 " --> pdb=" O ARG A 78 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 156 through 157 Processing sheet with id=AA4, first strand: chain 'A' and resid 319 through 321 removed outlier: 3.968A pdb=" N LEU B1024 " --> pdb=" O VAL A 321 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 1000 through 1002 removed outlier: 5.935A pdb=" N VAL A 340 " --> pdb=" O ARG A 438 " (cutoff:3.500A) removed outlier: 6.821A pdb=" N MET A 440 " --> pdb=" O VAL A 340 " (cutoff:3.500A) removed outlier: 5.813A pdb=" N VAL A 342 " --> pdb=" O MET A 440 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 351 through 355 removed outlier: 3.899A pdb=" N TYR A 380 " --> pdb=" O GLU A 410 " (cutoff:3.500A) removed outlier: 6.308A pdb=" N HIS A 412 " --> pdb=" O ALA A 378 " (cutoff:3.500A) removed outlier: 7.108A pdb=" N ALA A 378 " --> pdb=" O HIS A 412 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 517 through 518 Processing sheet with id=AA8, first strand: chain 'A' and resid 566 through 570 removed outlier: 6.808A pdb=" N TYR A 608 " --> pdb=" O LEU A 615 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 768 through 769 Processing sheet with id=AB1, first strand: chain 'A' and resid 771 through 772 Processing sheet with id=AB2, first strand: chain 'A' and resid 851 through 852 removed outlier: 4.416A pdb=" N LYS A 851 " --> pdb=" O ARG A 859 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N ARG A 859 " --> pdb=" O LYS A 851 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 52 through 53 removed outlier: 6.441A pdb=" N GLU B 103 " --> pdb=" O GLY B 65 " (cutoff:3.500A) removed outlier: 4.496A pdb=" N ILE B 67 " --> pdb=" O TYR B 101 " (cutoff:3.500A) removed outlier: 6.704A pdb=" N TYR B 101 " --> pdb=" O ILE B 67 " (cutoff:3.500A) removed outlier: 4.742A pdb=" N VAL B 69 " --> pdb=" O PRO B 99 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 52 through 53 removed outlier: 6.441A pdb=" N GLU B 103 " --> pdb=" O GLY B 65 " (cutoff:3.500A) removed outlier: 4.496A pdb=" N ILE B 67 " --> pdb=" O TYR B 101 " (cutoff:3.500A) removed outlier: 6.704A pdb=" N TYR B 101 " --> pdb=" O ILE B 67 " (cutoff:3.500A) removed outlier: 4.742A pdb=" N VAL B 69 " --> pdb=" O PRO B 99 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N GLY B 121 " --> pdb=" O LEU B 100 " (cutoff:3.500A) removed outlier: 6.783A pdb=" N LEU B 102 " --> pdb=" O ARG B 119 " (cutoff:3.500A) removed outlier: 5.175A pdb=" N ARG B 119 " --> pdb=" O LEU B 102 " (cutoff:3.500A) removed outlier: 6.850A pdb=" N MET B 104 " --> pdb=" O GLU B 117 " (cutoff:3.500A) removed outlier: 5.642A pdb=" N GLU B 117 " --> pdb=" O MET B 104 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 73 through 75 Processing sheet with id=AB6, first strand: chain 'B' and resid 156 through 158 Processing sheet with id=AB7, first strand: chain 'B' and resid 343 through 346 removed outlier: 6.313A pdb=" N SER B 167 " --> pdb=" O THR B 440 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 177 through 181 Processing sheet with id=AB9, first strand: chain 'B' and resid 485 through 486 Processing sheet with id=AC1, first strand: chain 'B' and resid 583 through 584 Processing sheet with id=AC2, first strand: chain 'B' and resid 505 through 506 removed outlier: 5.644A pdb=" N LEU B 525 " --> pdb=" O LEU B 521 " (cutoff:3.500A) removed outlier: 6.080A pdb=" N LEU B 521 " --> pdb=" O LEU B 525 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N GLY B 527 " --> pdb=" O VAL B 519 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 688 through 692 removed outlier: 3.553A pdb=" N SER B 749 " --> pdb=" O ARG B 868 " (cutoff:3.500A) removed outlier: 6.783A pdb=" N LEU B 859 " --> pdb=" O ILE B 850 " (cutoff:3.500A) removed outlier: 4.617A pdb=" N ILE B 850 " --> pdb=" O LEU B 859 " (cutoff:3.500A) removed outlier: 6.714A pdb=" N LYS B 861 " --> pdb=" O VAL B 848 " (cutoff:3.500A) removed outlier: 4.498A pdb=" N VAL B 848 " --> pdb=" O LYS B 861 " (cutoff:3.500A) removed outlier: 6.877A pdb=" N THR B 863 " --> pdb=" O ASP B 846 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 688 through 692 removed outlier: 3.553A pdb=" N SER B 749 " --> pdb=" O ARG B 868 " (cutoff:3.500A) removed outlier: 6.783A pdb=" N LEU B 859 " --> pdb=" O ILE B 850 " (cutoff:3.500A) removed outlier: 4.617A pdb=" N ILE B 850 " --> pdb=" O LEU B 859 " (cutoff:3.500A) removed outlier: 6.714A pdb=" N LYS B 861 " --> pdb=" O VAL B 848 " (cutoff:3.500A) removed outlier: 4.498A pdb=" N VAL B 848 " --> pdb=" O LYS B 861 " (cutoff:3.500A) removed outlier: 6.877A pdb=" N THR B 863 " --> pdb=" O ASP B 846 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 700 through 701 Processing sheet with id=AC6, first strand: chain 'B' and resid 965 through 966 removed outlier: 7.148A pdb=" N ILE B 735 " --> pdb=" O GLY B 887 " (cutoff:3.500A) removed outlier: 6.352A pdb=" N ILE B 889 " --> pdb=" O ILE B 735 " (cutoff:3.500A) removed outlier: 6.884A pdb=" N ILE B 737 " --> pdb=" O ILE B 889 " (cutoff:3.500A) removed outlier: 8.553A pdb=" N LEU B 906 " --> pdb=" O ASN B 718 " (cutoff:3.500A) removed outlier: 6.083A pdb=" N VAL B 720 " --> pdb=" O LEU B 906 " (cutoff:3.500A) removed outlier: 7.682A pdb=" N VAL B 908 " --> pdb=" O VAL B 720 " (cutoff:3.500A) removed outlier: 6.511A pdb=" N ALA B 722 " --> pdb=" O VAL B 908 " (cutoff:3.500A) removed outlier: 4.707A pdb=" N PHE B 982 " --> pdb=" O VAL B 723 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 769 through 770 removed outlier: 3.520A pdb=" N LYS B 769 " --> pdb=" O THR B 811 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 806 through 808 removed outlier: 6.809A pdb=" N VAL B 835 " --> pdb=" O LEU B 807 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 897 through 898 Processing sheet with id=AD1, first strand: chain 'B' and resid 1053 through 1059 Processing sheet with id=AD2, first strand: chain 'B' and resid 1067 through 1069 Processing sheet with id=AD3, first strand: chain 'C' and resid 233 through 238 removed outlier: 3.600A pdb=" N THR C 246 " --> pdb=" O MET C 117 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'C' and resid 142 through 143 removed outlier: 3.844A pdb=" N THR C 142 " --> pdb=" O LEU C 224 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'C' and resid 148 through 154 removed outlier: 3.876A pdb=" N VAL C 162 " --> pdb=" O LEU C 199 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N LEU C 199 " --> pdb=" O VAL C 162 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'E' and resid 37 through 39 removed outlier: 3.747A pdb=" N THR E 37 " --> pdb=" O ILE E 45 " (cutoff:3.500A) removed outlier: 9.823A pdb=" N SER E 47 " --> pdb=" O TRP E 77 " (cutoff:3.500A) removed outlier: 8.718A pdb=" N TRP E 77 " --> pdb=" O SER E 47 " (cutoff:3.500A) removed outlier: 7.466A pdb=" N LEU E 49 " --> pdb=" O LEU E 75 " (cutoff:3.500A) removed outlier: 8.697A pdb=" N LEU E 75 " --> pdb=" O LEU E 49 " (cutoff:3.500A) removed outlier: 6.147A pdb=" N VAL E 51 " --> pdb=" O ASP E 73 " (cutoff:3.500A) removed outlier: 7.293A pdb=" N ASP E 73 " --> pdb=" O VAL E 51 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N ASP E 53 " --> pdb=" O VAL E 71 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N VAL E 71 " --> pdb=" O ASP E 53 " (cutoff:3.500A) removed outlier: 5.345A pdb=" N GLU E 69 " --> pdb=" O LYS E 55 " (cutoff:3.500A) removed outlier: 4.314A pdb=" N GLY E 57 " --> pdb=" O TYR E 67 " (cutoff:3.500A) removed outlier: 5.719A pdb=" N TYR E 67 " --> pdb=" O GLY E 57 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N GLY F 8 " --> pdb=" O THR E 6 " (cutoff:3.500A) removed outlier: 6.790A pdb=" N LYS E 8 " --> pdb=" O LYS F 6 " (cutoff:3.500A) removed outlier: 6.104A pdb=" N LYS F 6 " --> pdb=" O LYS E 8 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'E' and resid 37 through 39 removed outlier: 3.747A pdb=" N THR E 37 " --> pdb=" O ILE E 45 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N GLY E 57 " --> pdb=" O MET C 383 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N MET C 383 " --> pdb=" O GLY E 57 " (cutoff:3.500A) removed outlier: 5.097A pdb=" N LEU C 381 " --> pdb=" O ILE E 59 " (cutoff:3.500A) removed outlier: 4.670A pdb=" N LYS C 380 " --> pdb=" O ILE K 54 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'D' and resid 5 through 11 removed outlier: 7.009A pdb=" N LYS D 17 " --> pdb=" O LEU D 9 " (cutoff:3.500A) removed outlier: 5.043A pdb=" N LYS D 11 " --> pdb=" O SER D 15 " (cutoff:3.500A) removed outlier: 6.861A pdb=" N SER D 15 " --> pdb=" O LYS D 11 " (cutoff:3.500A) removed outlier: 5.088A pdb=" N TYR D 158 " --> pdb=" O VAL D 218 " (cutoff:3.500A) removed outlier: 9.055A pdb=" N ASN D 220 " --> pdb=" O LYS D 156 " (cutoff:3.500A) removed outlier: 11.043A pdb=" N LYS D 156 " --> pdb=" O ASN D 220 " (cutoff:3.500A) removed outlier: 9.789A pdb=" N TYR D 222 " --> pdb=" O TYR D 154 " (cutoff:3.500A) removed outlier: 10.691A pdb=" N TYR D 154 " --> pdb=" O TYR D 222 " (cutoff:3.500A) removed outlier: 10.270A pdb=" N PHE D 224 " --> pdb=" O PHE D 152 " (cutoff:3.500A) removed outlier: 11.453A pdb=" N PHE D 152 " --> pdb=" O PHE D 224 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'D' and resid 107 through 108 removed outlier: 6.522A pdb=" N ARG D 130 " --> pdb=" O GLU D 51 " (cutoff:3.500A) removed outlier: 6.118A pdb=" N GLU D 51 " --> pdb=" O ARG D 130 " (cutoff:3.500A) removed outlier: 7.669A pdb=" N VAL D 132 " --> pdb=" O PHE D 49 " (cutoff:3.500A) removed outlier: 5.019A pdb=" N PHE D 49 " --> pdb=" O VAL D 132 " (cutoff:3.500A) removed outlier: 6.453A pdb=" N ASN D 134 " --> pdb=" O VAL D 47 " (cutoff:3.500A) removed outlier: 4.830A pdb=" N VAL D 47 " --> pdb=" O ASN D 134 " (cutoff:3.500A) removed outlier: 6.760A pdb=" N TYR D 136 " --> pdb=" O ASP D 45 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N ALA D 43 " --> pdb=" O LYS D 138 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'D' and resid 99 through 102 removed outlier: 6.690A pdb=" N GLY D 99 " --> pdb=" O LYS D 124 " (cutoff:3.500A) removed outlier: 4.857A pdb=" N LYS D 124 " --> pdb=" O GLY D 99 " (cutoff:3.500A) removed outlier: 6.818A pdb=" N VAL D 101 " --> pdb=" O ILE D 122 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'E' and resid 85 through 93 removed outlier: 5.007A pdb=" N VAL E 92 " --> pdb=" O GLY E 96 " (cutoff:3.500A) removed outlier: 6.838A pdb=" N GLY E 96 " --> pdb=" O VAL E 92 " (cutoff:3.500A) removed outlier: 4.115A pdb=" N ILE E 161 " --> pdb=" O ASP E 105 " (cutoff:3.500A) removed outlier: 4.266A pdb=" N HIS E 109 " --> pdb=" O LEU E 163 " (cutoff:3.500A) removed outlier: 6.856A pdb=" N GLY E 162 " --> pdb=" O ILE E 147 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'H' and resid 17 through 20 removed outlier: 3.715A pdb=" N GLU H 17 " --> pdb=" O LYS H 64 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N TYR H 73 " --> pdb=" O ARG H 65 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'L' and resid 2 through 9 removed outlier: 6.787A pdb=" N GLU L 14 " --> pdb=" O ILE L 6 " (cutoff:3.500A) removed outlier: 4.796A pdb=" N LYS L 8 " --> pdb=" O LEU L 12 " (cutoff:3.500A) removed outlier: 7.125A pdb=" N LEU L 12 " --> pdb=" O LYS L 8 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'P' and resid 5 through 7 1217 hydrogen bonds defined for protein. 3357 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: 11.21 Time building geometry restraints manager: 11.28 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 8806 1.34 - 1.46: 5438 1.46 - 1.58: 12422 1.58 - 1.70: 0 1.70 - 1.82: 198 Bond restraints: 26864 Sorted by residual: bond pdb=" CA ILE A 165 " pdb=" CB ILE A 165 " ideal model delta sigma weight residual 1.527 1.546 -0.019 1.31e-02 5.83e+03 2.15e+00 bond pdb=" CG1 ILE F 95 " pdb=" CD1 ILE F 95 " ideal model delta sigma weight residual 1.513 1.466 0.047 3.90e-02 6.57e+02 1.42e+00 bond pdb=" N HIS C 86 " pdb=" CA HIS C 86 " ideal model delta sigma weight residual 1.457 1.472 -0.015 1.29e-02 6.01e+03 1.32e+00 bond pdb=" CA ASP A 52 " pdb=" CB ASP A 52 " ideal model delta sigma weight residual 1.525 1.541 -0.016 1.52e-02 4.33e+03 1.11e+00 bond pdb=" CG1 ILE K 41 " pdb=" CD1 ILE K 41 " ideal model delta sigma weight residual 1.513 1.472 0.041 3.90e-02 6.57e+02 1.09e+00 ... (remaining 26859 not shown) Histogram of bond angle deviations from ideal: 98.67 - 105.74: 665 105.74 - 112.81: 14276 112.81 - 119.88: 9180 119.88 - 126.95: 11856 126.95 - 134.01: 289 Bond angle restraints: 36266 Sorted by residual: angle pdb=" N GLY D 151 " pdb=" CA GLY D 151 " pdb=" C GLY D 151 " ideal model delta sigma weight residual 111.56 115.46 -3.90 1.01e+00 9.80e-01 1.49e+01 angle pdb=" CB MET F 108 " pdb=" CG MET F 108 " pdb=" SD MET F 108 " ideal model delta sigma weight residual 112.70 122.69 -9.99 3.00e+00 1.11e-01 1.11e+01 angle pdb=" CA ARG F 50 " pdb=" CB ARG F 50 " pdb=" CG ARG F 50 " ideal model delta sigma weight residual 114.10 120.63 -6.53 2.00e+00 2.50e-01 1.06e+01 angle pdb=" CA MET B 483 " pdb=" CB MET B 483 " pdb=" CG MET B 483 " ideal model delta sigma weight residual 114.10 120.38 -6.28 2.00e+00 2.50e-01 9.87e+00 angle pdb=" CA MET E 1 " pdb=" CB MET E 1 " pdb=" CG MET E 1 " ideal model delta sigma weight residual 114.10 120.34 -6.24 2.00e+00 2.50e-01 9.75e+00 ... (remaining 36261 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.00: 14154 18.00 - 35.99: 1824 35.99 - 53.99: 441 53.99 - 71.99: 88 71.99 - 89.99: 48 Dihedral angle restraints: 16555 sinusoidal: 7046 harmonic: 9509 Sorted by residual: dihedral pdb=" CA GLN A 848 " pdb=" C GLN A 848 " pdb=" N ASP A 849 " pdb=" CA ASP A 849 " ideal model delta harmonic sigma weight residual -180.00 -161.22 -18.78 0 5.00e+00 4.00e-02 1.41e+01 dihedral pdb=" CA PRO E 94 " pdb=" C PRO E 94 " pdb=" N PHE E 95 " pdb=" CA PHE E 95 " ideal model delta harmonic sigma weight residual 180.00 161.47 18.53 0 5.00e+00 4.00e-02 1.37e+01 dihedral pdb=" CA ASP E 21 " pdb=" CB ASP E 21 " pdb=" CG ASP E 21 " pdb=" OD1 ASP E 21 " ideal model delta sinusoidal sigma weight residual -30.00 -89.24 59.24 1 2.00e+01 2.50e-03 1.17e+01 ... (remaining 16552 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.032: 2564 0.032 - 0.065: 920 0.065 - 0.097: 321 0.097 - 0.130: 205 0.130 - 0.162: 11 Chirality restraints: 4021 Sorted by residual: chirality pdb=" CA PRO E 94 " pdb=" N PRO E 94 " pdb=" C PRO E 94 " pdb=" CB PRO E 94 " both_signs ideal model delta sigma weight residual False 2.72 2.56 0.16 2.00e-01 2.50e+01 6.57e-01 chirality pdb=" CA MET E 93 " pdb=" N MET E 93 " pdb=" C MET E 93 " pdb=" CB MET E 93 " both_signs ideal model delta sigma weight residual False 2.51 2.66 -0.15 2.00e-01 2.50e+01 5.79e-01 chirality pdb=" CA GLN F 110 " pdb=" N GLN F 110 " pdb=" C GLN F 110 " pdb=" CB GLN F 110 " both_signs ideal model delta sigma weight residual False 2.51 2.36 0.15 2.00e-01 2.50e+01 5.37e-01 ... (remaining 4018 not shown) Planarity restraints: 4702 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C MET E 93 " 0.046 5.00e-02 4.00e+02 6.90e-02 7.62e+00 pdb=" N PRO E 94 " -0.119 5.00e-02 4.00e+02 pdb=" CA PRO E 94 " 0.036 5.00e-02 4.00e+02 pdb=" CD PRO E 94 " 0.038 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP H 47 " -0.036 5.00e-02 4.00e+02 5.43e-02 4.72e+00 pdb=" N PRO H 48 " 0.094 5.00e-02 4.00e+02 pdb=" CA PRO H 48 " -0.028 5.00e-02 4.00e+02 pdb=" CD PRO H 48 " -0.030 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA A 260 " -0.035 5.00e-02 4.00e+02 5.39e-02 4.64e+00 pdb=" N PRO A 261 " 0.093 5.00e-02 4.00e+02 pdb=" CA PRO A 261 " -0.028 5.00e-02 4.00e+02 pdb=" CD PRO A 261 " -0.030 5.00e-02 4.00e+02 ... (remaining 4699 not shown) Histogram of nonbonded interaction distances: 2.08 - 2.64: 332 2.64 - 3.21: 24759 3.21 - 3.77: 41013 3.77 - 4.34: 56219 4.34 - 4.90: 93541 Nonbonded interactions: 215864 Sorted by model distance: nonbonded pdb=" OD1 ASP A 462 " pdb="MG MG A1002 " model vdw 2.081 2.170 nonbonded pdb=" O TYR A 279 " pdb=" OG1 THR A 300 " model vdw 2.168 2.440 nonbonded pdb=" OG SER A 14 " pdb=" OE1 GLN A 16 " model vdw 2.183 2.440 nonbonded pdb=" O ALA C 91 " pdb=" NH1 ARG C 236 " model vdw 2.216 2.520 nonbonded pdb=" OH TYR A 113 " pdb=" OE1 GLU A 133 " model vdw 2.224 2.440 ... (remaining 215859 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.600 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 7.230 Check model and map are aligned: 0.200 Set scattering table: 0.260 Process input model: 76.310 Find NCS groups from input model: 0.740 Set up NCS constraints: 0.110 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:3.050 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 89.530 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4315 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 0.047 26864 Z= 0.219 Angle : 0.558 9.988 36266 Z= 0.294 Chirality : 0.043 0.162 4021 Planarity : 0.004 0.069 4702 Dihedral : 17.235 89.986 10447 Min Nonbonded Distance : 2.081 Molprobity Statistics. All-atom Clashscore : 9.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 0.07 % Allowed : 24.73 % Favored : 75.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.56 % 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: 0.49 (0.15), residues: 3266 helix: 1.49 (0.15), residues: 1246 sheet: -0.64 (0.23), residues: 496 loop : -0.23 (0.17), residues: 1524 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 163 HIS 0.007 0.001 HIS B 911 PHE 0.034 0.001 PHE E 95 TYR 0.016 0.001 TYR F 38 ARG 0.010 0.000 ARG F 50 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6532 Ramachandran restraints generated. 3266 Oldfield, 0 Emsley, 3266 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6532 Ramachandran restraints generated. 3266 Oldfield, 0 Emsley, 3266 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 761 residues out of total 2855 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 759 time to evaluate : 3.192 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: F 70 PHE cc_start: 0.4648 (p90) cc_final: 0.4274 (p90) outliers start: 2 outliers final: 1 residues processed: 761 average time/residue: 0.4500 time to fit residues: 513.4532 Evaluate side-chains 426 residues out of total 2855 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 425 time to evaluate : 3.511 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 786 TYR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 323 random chunks: chunk 272 optimal weight: 10.0000 chunk 244 optimal weight: 6.9990 chunk 135 optimal weight: 0.6980 chunk 83 optimal weight: 4.9990 chunk 165 optimal weight: 7.9990 chunk 130 optimal weight: 0.4980 chunk 253 optimal weight: 4.9990 chunk 97 optimal weight: 9.9990 chunk 153 optimal weight: 2.9990 chunk 188 optimal weight: 8.9990 chunk 293 optimal weight: 0.9980 overall best weight: 2.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 249 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 315 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 402 GLN A 424 GLN A 818 HIS ** A 867 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 36 ASN B 459 HIS ** B 636 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 680 ASN B 690 HIS B 921 GLN B1000 HIS ** C 253 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 297 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 365 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 105 GLN ** H 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 52 HIS Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5015 moved from start: 0.3657 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.086 26864 Z= 0.314 Angle : 0.720 13.670 36266 Z= 0.371 Chirality : 0.048 0.259 4021 Planarity : 0.006 0.075 4702 Dihedral : 4.393 40.302 3645 Min Nonbonded Distance : 2.071 Molprobity Statistics. All-atom Clashscore : 15.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer: Outliers : 4.48 % Allowed : 25.99 % Favored : 69.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.56 % 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 (0.15), residues: 3266 helix: 1.23 (0.15), residues: 1264 sheet: -0.67 (0.24), residues: 439 loop : -0.25 (0.16), residues: 1563 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.003 TRP B1057 HIS 0.010 0.002 HIS A 818 PHE 0.035 0.003 PHE B 273 TYR 0.033 0.002 TYR E 134 ARG 0.027 0.001 ARG B 331 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6532 Ramachandran restraints generated. 3266 Oldfield, 0 Emsley, 3266 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6532 Ramachandran restraints generated. 3266 Oldfield, 0 Emsley, 3266 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 589 residues out of total 2855 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 128 poor density : 461 time to evaluate : 3.166 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: C 116 MET cc_start: 0.5263 (tmm) cc_final: 0.5021 (tmm) REVERT: C 168 ARG cc_start: 0.3123 (OUTLIER) cc_final: 0.2662 (tpp-160) REVERT: E 92 VAL cc_start: 0.3834 (OUTLIER) cc_final: 0.2635 (m) REVERT: E 170 LEU cc_start: 0.5581 (OUTLIER) cc_final: 0.4938 (mt) REVERT: F 21 LEU cc_start: 0.7077 (OUTLIER) cc_final: 0.6852 (mm) REVERT: F 42 ARG cc_start: 0.4504 (ptt-90) cc_final: 0.3333 (ptt-90) REVERT: F 45 LEU cc_start: 0.7430 (tp) cc_final: 0.6671 (mt) REVERT: F 51 PHE cc_start: 0.0155 (OUTLIER) cc_final: -0.0856 (p90) REVERT: L 58 ARG cc_start: 0.8014 (OUTLIER) cc_final: 0.7541 (ttp-170) REVERT: N 60 MET cc_start: 0.3659 (ppp) cc_final: 0.3445 (ppp) outliers start: 128 outliers final: 51 residues processed: 556 average time/residue: 0.3991 time to fit residues: 352.2587 Evaluate side-chains 421 residues out of total 2855 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 364 time to evaluate : 3.188 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 ILE Chi-restraints excluded: chain A residue 106 THR Chi-restraints excluded: chain A residue 107 ASP Chi-restraints excluded: chain A residue 129 GLU Chi-restraints excluded: chain A residue 221 THR Chi-restraints excluded: chain A residue 226 ILE Chi-restraints excluded: chain A residue 409 VAL Chi-restraints excluded: chain A residue 437 VAL Chi-restraints excluded: chain A residue 447 LEU Chi-restraints excluded: chain A residue 465 ASN Chi-restraints excluded: chain A residue 574 CYS Chi-restraints excluded: chain A residue 616 SER Chi-restraints excluded: chain A residue 619 ILE Chi-restraints excluded: chain A residue 666 THR Chi-restraints excluded: chain A residue 772 ILE Chi-restraints excluded: chain A residue 777 LEU Chi-restraints excluded: chain A residue 828 ASP Chi-restraints excluded: chain A residue 889 ASP Chi-restraints excluded: chain B residue 69 VAL Chi-restraints excluded: chain B residue 123 LEU Chi-restraints excluded: chain B residue 199 ARG Chi-restraints excluded: chain B residue 320 MET Chi-restraints excluded: chain B residue 422 GLN Chi-restraints excluded: chain B residue 560 VAL Chi-restraints excluded: chain B residue 697 ILE Chi-restraints excluded: chain B residue 705 MET Chi-restraints excluded: chain B residue 786 TYR Chi-restraints excluded: chain B residue 864 VAL Chi-restraints excluded: chain B residue 900 SER Chi-restraints excluded: chain B residue 944 ILE Chi-restraints excluded: chain B residue 1052 ASP Chi-restraints excluded: chain B residue 1099 LEU Chi-restraints excluded: chain C residue 95 VAL Chi-restraints excluded: chain C residue 117 MET Chi-restraints excluded: chain C residue 168 ARG Chi-restraints excluded: chain C residue 356 VAL Chi-restraints excluded: chain C residue 362 VAL Chi-restraints excluded: chain C residue 366 VAL Chi-restraints excluded: chain D residue 58 ASP Chi-restraints excluded: chain D residue 120 ILE Chi-restraints excluded: chain D residue 217 ILE Chi-restraints excluded: chain E residue 76 VAL Chi-restraints excluded: chain E residue 92 VAL Chi-restraints excluded: chain E residue 108 VAL Chi-restraints excluded: chain E residue 170 LEU Chi-restraints excluded: chain F residue 21 LEU Chi-restraints excluded: chain F residue 51 PHE Chi-restraints excluded: chain F residue 110 GLN Chi-restraints excluded: chain K residue 3 LYS Chi-restraints excluded: chain K residue 51 ILE Chi-restraints excluded: chain L residue 41 THR Chi-restraints excluded: chain L residue 45 ILE Chi-restraints excluded: chain L residue 58 ARG Chi-restraints excluded: chain N residue 20 GLU Chi-restraints excluded: chain N residue 57 ASP Chi-restraints excluded: chain P residue 42 VAL Chi-restraints excluded: chain P residue 46 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 323 random chunks: chunk 163 optimal weight: 5.9990 chunk 91 optimal weight: 0.8980 chunk 244 optimal weight: 7.9990 chunk 199 optimal weight: 3.9990 chunk 80 optimal weight: 7.9990 chunk 293 optimal weight: 9.9990 chunk 317 optimal weight: 0.4980 chunk 261 optimal weight: 3.9990 chunk 291 optimal weight: 9.9990 chunk 100 optimal weight: 6.9990 chunk 235 optimal weight: 5.9990 overall best weight: 3.0786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 249 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 730 ASN A 762 GLN ** A 788 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 818 HIS B 388 HIS ** B 485 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 592 GLN C 157 ASN ** C 253 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 365 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5745 moved from start: 0.6772 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.199 26864 Z= 0.407 Angle : 0.782 17.587 36266 Z= 0.407 Chirality : 0.051 0.330 4021 Planarity : 0.006 0.099 4702 Dihedral : 4.982 42.057 3645 Min Nonbonded Distance : 1.934 Molprobity Statistics. All-atom Clashscore : 17.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.09 % Favored : 96.91 % Rotamer: Outliers : 5.60 % Allowed : 24.94 % Favored : 69.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.56 % 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: -0.07 (0.15), residues: 3266 helix: 0.90 (0.14), residues: 1259 sheet: -0.90 (0.23), residues: 473 loop : -0.46 (0.16), residues: 1534 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.051 0.003 TRP B1057 HIS 0.019 0.002 HIS D 145 PHE 0.031 0.003 PHE B 273 TYR 0.029 0.003 TYR B 315 ARG 0.021 0.001 ARG E 157 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6532 Ramachandran restraints generated. 3266 Oldfield, 0 Emsley, 3266 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6532 Ramachandran restraints generated. 3266 Oldfield, 0 Emsley, 3266 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 570 residues out of total 2855 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 160 poor density : 410 time to evaluate : 3.410 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 566 ASN cc_start: 0.3688 (OUTLIER) cc_final: 0.3374 (p0) REVERT: C 294 MET cc_start: 0.8668 (mmp) cc_final: 0.8389 (mmt) REVERT: E 9 ASP cc_start: 0.5224 (t0) cc_final: 0.4279 (t0) REVERT: F 51 PHE cc_start: 0.0868 (OUTLIER) cc_final: -0.0304 (p90) outliers start: 160 outliers final: 67 residues processed: 534 average time/residue: 0.4027 time to fit residues: 336.0521 Evaluate side-chains 388 residues out of total 2855 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 319 time to evaluate : 3.148 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 ILE Chi-restraints excluded: chain A residue 39 ILE Chi-restraints excluded: chain A residue 103 ILE Chi-restraints excluded: chain A residue 106 THR Chi-restraints excluded: chain A residue 107 ASP Chi-restraints excluded: chain A residue 129 GLU Chi-restraints excluded: chain A residue 185 ASP Chi-restraints excluded: chain A residue 220 VAL Chi-restraints excluded: chain A residue 221 THR Chi-restraints excluded: chain A residue 226 ILE Chi-restraints excluded: chain A residue 305 LEU Chi-restraints excluded: chain A residue 420 LEU Chi-restraints excluded: chain A residue 428 HIS Chi-restraints excluded: chain A residue 437 VAL Chi-restraints excluded: chain A residue 447 LEU Chi-restraints excluded: chain A residue 451 VAL Chi-restraints excluded: chain A residue 484 VAL Chi-restraints excluded: chain A residue 574 CYS Chi-restraints excluded: chain A residue 619 ILE Chi-restraints excluded: chain A residue 772 ILE Chi-restraints excluded: chain A residue 865 ILE Chi-restraints excluded: chain A residue 889 ASP Chi-restraints excluded: chain B residue 49 GLU Chi-restraints excluded: chain B residue 88 ASP Chi-restraints excluded: chain B residue 123 LEU Chi-restraints excluded: chain B residue 161 SER Chi-restraints excluded: chain B residue 199 ARG Chi-restraints excluded: chain B residue 342 ASN Chi-restraints excluded: chain B residue 470 GLU Chi-restraints excluded: chain B residue 566 ASN Chi-restraints excluded: chain B residue 697 ILE Chi-restraints excluded: chain B residue 721 VAL Chi-restraints excluded: chain B residue 806 VAL Chi-restraints excluded: chain B residue 851 THR Chi-restraints excluded: chain B residue 864 VAL Chi-restraints excluded: chain B residue 900 SER Chi-restraints excluded: chain B residue 1052 ASP Chi-restraints excluded: chain B residue 1053 LYS Chi-restraints excluded: chain C residue 36 TYR Chi-restraints excluded: chain C residue 95 VAL Chi-restraints excluded: chain C residue 151 THR Chi-restraints excluded: chain C residue 235 VAL Chi-restraints excluded: chain C residue 356 VAL Chi-restraints excluded: chain C residue 362 VAL Chi-restraints excluded: chain C residue 379 VAL Chi-restraints excluded: chain D residue 58 ASP Chi-restraints excluded: chain D residue 86 ASP Chi-restraints excluded: chain D residue 217 ILE Chi-restraints excluded: chain D residue 253 ILE Chi-restraints excluded: chain E residue 6 THR Chi-restraints excluded: chain E residue 76 VAL Chi-restraints excluded: chain E residue 84 VAL Chi-restraints excluded: chain E residue 108 VAL Chi-restraints excluded: chain E residue 110 ILE Chi-restraints excluded: chain E residue 147 ILE Chi-restraints excluded: chain E residue 159 ASN Chi-restraints excluded: chain E residue 163 LEU Chi-restraints excluded: chain F residue 38 TYR Chi-restraints excluded: chain F residue 51 PHE Chi-restraints excluded: chain F residue 110 GLN Chi-restraints excluded: chain H residue 75 TYR Chi-restraints excluded: chain K residue 51 ILE Chi-restraints excluded: chain K residue 54 ILE Chi-restraints excluded: chain L residue 8 LYS Chi-restraints excluded: chain L residue 41 THR Chi-restraints excluded: chain L residue 61 THR Chi-restraints excluded: chain N residue 57 ASP Chi-restraints excluded: chain P residue 35 LEU Chi-restraints excluded: chain P residue 46 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 323 random chunks: chunk 290 optimal weight: 20.0000 chunk 220 optimal weight: 20.0000 chunk 152 optimal weight: 0.8980 chunk 32 optimal weight: 6.9990 chunk 140 optimal weight: 7.9990 chunk 197 optimal weight: 2.9990 chunk 294 optimal weight: 4.9990 chunk 312 optimal weight: 2.9990 chunk 154 optimal weight: 0.0070 chunk 279 optimal weight: 8.9990 chunk 84 optimal weight: 5.9990 overall best weight: 2.3804 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 292 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 315 ASN A 611 ASN A 693 ASN B 297 ASN B 485 GLN ** C 365 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5932 moved from start: 0.8159 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.076 26864 Z= 0.286 Angle : 0.686 14.063 36266 Z= 0.349 Chirality : 0.047 0.199 4021 Planarity : 0.005 0.053 4702 Dihedral : 4.480 34.375 3643 Min Nonbonded Distance : 2.084 Molprobity Statistics. All-atom Clashscore : 15.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer: Outliers : 4.48 % Allowed : 25.81 % Favored : 69.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.56 % 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: 0.10 (0.15), residues: 3266 helix: 1.05 (0.15), residues: 1274 sheet: -0.72 (0.24), residues: 442 loop : -0.44 (0.16), residues: 1550 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP A 209 HIS 0.014 0.001 HIS A 292 PHE 0.023 0.002 PHE B 356 TYR 0.028 0.002 TYR B 564 ARG 0.015 0.001 ARG C 337 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6532 Ramachandran restraints generated. 3266 Oldfield, 0 Emsley, 3266 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6532 Ramachandran restraints generated. 3266 Oldfield, 0 Emsley, 3266 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 466 residues out of total 2855 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 128 poor density : 338 time to evaluate : 3.326 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: A 71 PHE cc_start: 0.4324 (OUTLIER) cc_final: 0.3848 (t80) REVERT: C 294 MET cc_start: 0.8709 (mmp) cc_final: 0.8497 (mmt) REVERT: C 312 MET cc_start: 0.8323 (tpp) cc_final: 0.8118 (tpt) REVERT: F 51 PHE cc_start: 0.0819 (OUTLIER) cc_final: -0.0582 (p90) REVERT: N 48 MET cc_start: 0.5824 (OUTLIER) cc_final: 0.5552 (mtt) outliers start: 128 outliers final: 67 residues processed: 442 average time/residue: 0.4265 time to fit residues: 296.3979 Evaluate side-chains 362 residues out of total 2855 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 292 time to evaluate : 3.872 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 ILE Chi-restraints excluded: chain A residue 31 THR Chi-restraints excluded: chain A residue 43 VAL Chi-restraints excluded: chain A residue 71 PHE Chi-restraints excluded: chain A residue 107 ASP Chi-restraints excluded: chain A residue 129 GLU Chi-restraints excluded: chain A residue 185 ASP Chi-restraints excluded: chain A residue 226 ILE Chi-restraints excluded: chain A residue 237 ASP Chi-restraints excluded: chain A residue 268 LEU Chi-restraints excluded: chain A residue 272 LEU Chi-restraints excluded: chain A residue 399 LEU Chi-restraints excluded: chain A residue 426 SER Chi-restraints excluded: chain A residue 447 LEU Chi-restraints excluded: chain A residue 451 VAL Chi-restraints excluded: chain A residue 574 CYS Chi-restraints excluded: chain A residue 616 SER Chi-restraints excluded: chain A residue 619 ILE Chi-restraints excluded: chain A residue 690 GLU Chi-restraints excluded: chain A residue 885 THR Chi-restraints excluded: chain B residue 123 LEU Chi-restraints excluded: chain B residue 199 ARG Chi-restraints excluded: chain B residue 204 VAL Chi-restraints excluded: chain B residue 273 PHE Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 309 ASP Chi-restraints excluded: chain B residue 327 LEU Chi-restraints excluded: chain B residue 356 PHE Chi-restraints excluded: chain B residue 422 GLN Chi-restraints excluded: chain B residue 450 PHE Chi-restraints excluded: chain B residue 470 GLU Chi-restraints excluded: chain B residue 559 ASP Chi-restraints excluded: chain B residue 560 VAL Chi-restraints excluded: chain B residue 697 ILE Chi-restraints excluded: chain B residue 851 THR Chi-restraints excluded: chain B residue 863 THR Chi-restraints excluded: chain B residue 1053 LYS Chi-restraints excluded: chain C residue 65 VAL Chi-restraints excluded: chain C residue 96 THR Chi-restraints excluded: chain C residue 175 THR Chi-restraints excluded: chain C residue 176 MET Chi-restraints excluded: chain C residue 303 ILE Chi-restraints excluded: chain C residue 344 VAL Chi-restraints excluded: chain C residue 356 VAL Chi-restraints excluded: chain C residue 379 VAL Chi-restraints excluded: chain D residue 58 ASP Chi-restraints excluded: chain D residue 105 ASP Chi-restraints excluded: chain D residue 194 THR Chi-restraints excluded: chain D residue 217 ILE Chi-restraints excluded: chain D residue 253 ILE Chi-restraints excluded: chain E residue 108 VAL Chi-restraints excluded: chain E residue 110 ILE Chi-restraints excluded: chain E residue 147 ILE Chi-restraints excluded: chain F residue 23 LYS Chi-restraints excluded: chain F residue 38 TYR Chi-restraints excluded: chain F residue 51 PHE Chi-restraints excluded: chain F residue 54 LEU Chi-restraints excluded: chain F residue 110 GLN Chi-restraints excluded: chain H residue 26 LYS Chi-restraints excluded: chain H residue 51 LYS Chi-restraints excluded: chain H residue 75 TYR Chi-restraints excluded: chain H residue 80 VAL Chi-restraints excluded: chain K residue 27 LEU Chi-restraints excluded: chain K residue 35 THR Chi-restraints excluded: chain K residue 51 ILE Chi-restraints excluded: chain L residue 41 THR Chi-restraints excluded: chain L residue 61 THR Chi-restraints excluded: chain N residue 48 MET Chi-restraints excluded: chain N residue 57 ASP Chi-restraints excluded: chain P residue 42 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 323 random chunks: chunk 260 optimal weight: 0.6980 chunk 177 optimal weight: 0.9990 chunk 4 optimal weight: 10.0000 chunk 232 optimal weight: 4.9990 chunk 128 optimal weight: 0.9990 chunk 266 optimal weight: 10.0000 chunk 215 optimal weight: 0.0570 chunk 0 optimal weight: 10.0000 chunk 159 optimal weight: 0.9990 chunk 280 optimal weight: 20.0000 chunk 78 optimal weight: 8.9990 overall best weight: 0.7504 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 297 ASN C 365 ASN ** F 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5916 moved from start: 0.8459 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 26864 Z= 0.167 Angle : 0.594 10.734 36266 Z= 0.301 Chirality : 0.045 0.273 4021 Planarity : 0.004 0.053 4702 Dihedral : 4.254 34.641 3643 Min Nonbonded Distance : 2.089 Molprobity Statistics. All-atom Clashscore : 13.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Rotamer: Outliers : 3.54 % Allowed : 27.18 % Favored : 69.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.56 % 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 (0.15), residues: 3266 helix: 1.27 (0.15), residues: 1278 sheet: -0.70 (0.23), residues: 445 loop : -0.24 (0.17), residues: 1543 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A 209 HIS 0.006 0.001 HIS H 18 PHE 0.017 0.001 PHE C 251 TYR 0.028 0.001 TYR B 315 ARG 0.007 0.000 ARG B 236 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6532 Ramachandran restraints generated. 3266 Oldfield, 0 Emsley, 3266 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6532 Ramachandran restraints generated. 3266 Oldfield, 0 Emsley, 3266 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 426 residues out of total 2855 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 101 poor density : 325 time to evaluate : 3.440 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 51 PHE cc_start: 0.1418 (OUTLIER) cc_final: -0.0083 (p90) REVERT: N 48 MET cc_start: 0.5775 (OUTLIER) cc_final: 0.5498 (mtt) outliers start: 101 outliers final: 67 residues processed: 399 average time/residue: 0.4354 time to fit residues: 277.4599 Evaluate side-chains 359 residues out of total 2855 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 290 time to evaluate : 3.548 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 ILE Chi-restraints excluded: chain A residue 93 LEU Chi-restraints excluded: chain A residue 103 ILE Chi-restraints excluded: chain A residue 129 GLU Chi-restraints excluded: chain A residue 185 ASP Chi-restraints excluded: chain A residue 220 VAL Chi-restraints excluded: chain A residue 226 ILE Chi-restraints excluded: chain A residue 268 LEU Chi-restraints excluded: chain A residue 272 LEU Chi-restraints excluded: chain A residue 305 LEU Chi-restraints excluded: chain A residue 426 SER Chi-restraints excluded: chain A residue 428 HIS Chi-restraints excluded: chain A residue 451 VAL Chi-restraints excluded: chain A residue 473 GLU Chi-restraints excluded: chain A residue 574 CYS Chi-restraints excluded: chain A residue 619 ILE Chi-restraints excluded: chain A residue 772 ILE Chi-restraints excluded: chain A residue 865 ILE Chi-restraints excluded: chain A residue 889 ASP Chi-restraints excluded: chain B residue 69 VAL Chi-restraints excluded: chain B residue 129 SER Chi-restraints excluded: chain B residue 199 ARG Chi-restraints excluded: chain B residue 204 VAL Chi-restraints excluded: chain B residue 273 PHE Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 327 LEU Chi-restraints excluded: chain B residue 350 ASP Chi-restraints excluded: chain B residue 356 PHE Chi-restraints excluded: chain B residue 420 VAL Chi-restraints excluded: chain B residue 422 GLN Chi-restraints excluded: chain B residue 450 PHE Chi-restraints excluded: chain B residue 651 LEU Chi-restraints excluded: chain B residue 697 ILE Chi-restraints excluded: chain B residue 756 GLU Chi-restraints excluded: chain B residue 767 THR Chi-restraints excluded: chain B residue 851 THR Chi-restraints excluded: chain B residue 1053 LYS Chi-restraints excluded: chain B residue 1059 CYS Chi-restraints excluded: chain B residue 1080 CYS Chi-restraints excluded: chain C residue 79 GLN Chi-restraints excluded: chain C residue 96 THR Chi-restraints excluded: chain C residue 99 LEU Chi-restraints excluded: chain C residue 235 VAL Chi-restraints excluded: chain C residue 328 VAL Chi-restraints excluded: chain C residue 356 VAL Chi-restraints excluded: chain C residue 379 VAL Chi-restraints excluded: chain D residue 58 ASP Chi-restraints excluded: chain D residue 60 ILE Chi-restraints excluded: chain D residue 217 ILE Chi-restraints excluded: chain D residue 253 ILE Chi-restraints excluded: chain E residue 4 ILE Chi-restraints excluded: chain E residue 51 VAL Chi-restraints excluded: chain E residue 76 VAL Chi-restraints excluded: chain E residue 108 VAL Chi-restraints excluded: chain E residue 110 ILE Chi-restraints excluded: chain E residue 147 ILE Chi-restraints excluded: chain F residue 23 LYS Chi-restraints excluded: chain F residue 38 TYR Chi-restraints excluded: chain F residue 51 PHE Chi-restraints excluded: chain F residue 110 GLN Chi-restraints excluded: chain H residue 36 THR Chi-restraints excluded: chain H residue 51 LYS Chi-restraints excluded: chain H residue 75 TYR Chi-restraints excluded: chain K residue 51 ILE Chi-restraints excluded: chain L residue 41 THR Chi-restraints excluded: chain L residue 93 VAL Chi-restraints excluded: chain N residue 48 MET Chi-restraints excluded: chain N residue 57 ASP Chi-restraints excluded: chain P residue 46 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 323 random chunks: chunk 105 optimal weight: 1.9990 chunk 281 optimal weight: 9.9990 chunk 61 optimal weight: 10.0000 chunk 183 optimal weight: 5.9990 chunk 77 optimal weight: 7.9990 chunk 312 optimal weight: 2.9990 chunk 259 optimal weight: 9.9990 chunk 144 optimal weight: 0.0370 chunk 25 optimal weight: 6.9990 chunk 103 optimal weight: 7.9990 chunk 164 optimal weight: 0.9980 overall best weight: 2.4064 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 249 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 68 ASN K 19 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6163 moved from start: 0.9724 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.062 26864 Z= 0.302 Angle : 0.699 13.208 36266 Z= 0.352 Chirality : 0.047 0.299 4021 Planarity : 0.006 0.154 4702 Dihedral : 4.388 33.827 3643 Min Nonbonded Distance : 2.087 Molprobity Statistics. All-atom Clashscore : 16.11 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.21 % Favored : 96.75 % Rotamer: Outliers : 4.31 % Allowed : 27.50 % Favored : 68.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.56 % 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: 0.25 (0.15), residues: 3266 helix: 1.12 (0.15), residues: 1283 sheet: -0.66 (0.23), residues: 470 loop : -0.29 (0.17), residues: 1513 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP B1057 HIS 0.010 0.001 HIS D 145 PHE 0.019 0.002 PHE K 7 TYR 0.018 0.002 TYR E 34 ARG 0.009 0.001 ARG F 25 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6532 Ramachandran restraints generated. 3266 Oldfield, 0 Emsley, 3266 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6532 Ramachandran restraints generated. 3266 Oldfield, 0 Emsley, 3266 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 413 residues out of total 2855 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 123 poor density : 290 time to evaluate : 3.357 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 71 PHE cc_start: 0.4609 (OUTLIER) cc_final: 0.3907 (t80) REVERT: A 520 ARG cc_start: 0.6817 (OUTLIER) cc_final: 0.6267 (ttt-90) REVERT: B 611 GLU cc_start: 0.5419 (OUTLIER) cc_final: 0.5219 (mt-10) REVERT: C 379 VAL cc_start: 0.7733 (OUTLIER) cc_final: 0.7511 (m) REVERT: F 51 PHE cc_start: 0.1259 (OUTLIER) cc_final: -0.0352 (p90) REVERT: N 1 MET cc_start: 0.5836 (mmp) cc_final: 0.5485 (mmp) outliers start: 123 outliers final: 74 residues processed: 389 average time/residue: 0.3951 time to fit residues: 240.9801 Evaluate side-chains 338 residues out of total 2855 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 79 poor density : 259 time to evaluate : 3.047 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 ILE Chi-restraints excluded: chain A residue 31 THR Chi-restraints excluded: chain A residue 39 ILE Chi-restraints excluded: chain A residue 71 PHE Chi-restraints excluded: chain A residue 103 ILE Chi-restraints excluded: chain A residue 185 ASP Chi-restraints excluded: chain A residue 220 VAL Chi-restraints excluded: chain A residue 226 ILE Chi-restraints excluded: chain A residue 268 LEU Chi-restraints excluded: chain A residue 272 LEU Chi-restraints excluded: chain A residue 312 PHE Chi-restraints excluded: chain A residue 426 SER Chi-restraints excluded: chain A residue 428 HIS Chi-restraints excluded: chain A residue 473 GLU Chi-restraints excluded: chain A residue 520 ARG Chi-restraints excluded: chain A residue 574 CYS Chi-restraints excluded: chain A residue 616 SER Chi-restraints excluded: chain A residue 619 ILE Chi-restraints excluded: chain A residue 690 GLU Chi-restraints excluded: chain A residue 763 MET Chi-restraints excluded: chain A residue 772 ILE Chi-restraints excluded: chain A residue 865 ILE Chi-restraints excluded: chain A residue 885 THR Chi-restraints excluded: chain B residue 129 SER Chi-restraints excluded: chain B residue 199 ARG Chi-restraints excluded: chain B residue 204 VAL Chi-restraints excluded: chain B residue 226 VAL Chi-restraints excluded: chain B residue 240 ILE Chi-restraints excluded: chain B residue 273 PHE Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 327 LEU Chi-restraints excluded: chain B residue 350 ASP Chi-restraints excluded: chain B residue 360 PHE Chi-restraints excluded: chain B residue 410 THR Chi-restraints excluded: chain B residue 420 VAL Chi-restraints excluded: chain B residue 450 PHE Chi-restraints excluded: chain B residue 560 VAL Chi-restraints excluded: chain B residue 591 VAL Chi-restraints excluded: chain B residue 611 GLU Chi-restraints excluded: chain B residue 697 ILE Chi-restraints excluded: chain B residue 767 THR Chi-restraints excluded: chain B residue 851 THR Chi-restraints excluded: chain B residue 1052 ASP Chi-restraints excluded: chain B residue 1053 LYS Chi-restraints excluded: chain B residue 1080 CYS Chi-restraints excluded: chain C residue 79 GLN Chi-restraints excluded: chain C residue 95 VAL Chi-restraints excluded: chain C residue 96 THR Chi-restraints excluded: chain C residue 99 LEU Chi-restraints excluded: chain C residue 162 VAL Chi-restraints excluded: chain C residue 235 VAL Chi-restraints excluded: chain C residue 328 VAL Chi-restraints excluded: chain C residue 356 VAL Chi-restraints excluded: chain C residue 366 VAL Chi-restraints excluded: chain C residue 379 VAL Chi-restraints excluded: chain D residue 58 ASP Chi-restraints excluded: chain D residue 105 ASP Chi-restraints excluded: chain D residue 217 ILE Chi-restraints excluded: chain D residue 253 ILE Chi-restraints excluded: chain E residue 6 THR Chi-restraints excluded: chain E residue 46 LEU Chi-restraints excluded: chain E residue 84 VAL Chi-restraints excluded: chain E residue 110 ILE Chi-restraints excluded: chain E residue 147 ILE Chi-restraints excluded: chain F residue 23 LYS Chi-restraints excluded: chain F residue 38 TYR Chi-restraints excluded: chain F residue 51 PHE Chi-restraints excluded: chain F residue 54 LEU Chi-restraints excluded: chain F residue 110 GLN Chi-restraints excluded: chain H residue 51 LYS Chi-restraints excluded: chain H residue 75 TYR Chi-restraints excluded: chain K residue 27 LEU Chi-restraints excluded: chain K residue 35 THR Chi-restraints excluded: chain K residue 51 ILE Chi-restraints excluded: chain L residue 41 THR Chi-restraints excluded: chain N residue 57 ASP Chi-restraints excluded: chain P residue 3 GLU Chi-restraints excluded: chain P residue 42 VAL Chi-restraints excluded: chain P residue 46 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 323 random chunks: chunk 301 optimal weight: 2.9990 chunk 35 optimal weight: 2.9990 chunk 178 optimal weight: 0.2980 chunk 228 optimal weight: 2.9990 chunk 176 optimal weight: 6.9990 chunk 263 optimal weight: 10.0000 chunk 174 optimal weight: 9.9990 chunk 311 optimal weight: 7.9990 chunk 194 optimal weight: 1.9990 chunk 189 optimal weight: 10.0000 chunk 143 optimal weight: 0.7980 overall best weight: 1.8186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 249 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 867 GLN B 297 ASN ** F 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6169 moved from start: 1.0206 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.067 26864 Z= 0.221 Angle : 0.622 14.073 36266 Z= 0.313 Chirality : 0.045 0.211 4021 Planarity : 0.005 0.086 4702 Dihedral : 4.227 34.245 3643 Min Nonbonded Distance : 2.092 Molprobity Statistics. All-atom Clashscore : 14.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % Rotamer: Outliers : 3.12 % Allowed : 28.34 % Favored : 68.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.56 % 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: 0.39 (0.15), residues: 3266 helix: 1.27 (0.15), residues: 1290 sheet: -0.63 (0.23), residues: 487 loop : -0.22 (0.17), residues: 1489 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 15 HIS 0.007 0.001 HIS H 18 PHE 0.013 0.001 PHE B 356 TYR 0.016 0.001 TYR B 293 ARG 0.019 0.001 ARG A 166 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6532 Ramachandran restraints generated. 3266 Oldfield, 0 Emsley, 3266 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6532 Ramachandran restraints generated. 3266 Oldfield, 0 Emsley, 3266 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 376 residues out of total 2855 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 89 poor density : 287 time to evaluate : 3.388 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: A 71 PHE cc_start: 0.4521 (OUTLIER) cc_final: 0.3976 (t80) REVERT: A 520 ARG cc_start: 0.6659 (OUTLIER) cc_final: 0.6168 (ttt-90) REVERT: F 51 PHE cc_start: 0.1196 (OUTLIER) cc_final: -0.0393 (p90) REVERT: N 1 MET cc_start: 0.5902 (mmp) cc_final: 0.5687 (mmp) outliers start: 89 outliers final: 63 residues processed: 361 average time/residue: 0.4186 time to fit residues: 238.7617 Evaluate side-chains 318 residues out of total 2855 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 252 time to evaluate : 3.392 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 ILE Chi-restraints excluded: chain A residue 39 ILE Chi-restraints excluded: chain A residue 57 CYS Chi-restraints excluded: chain A residue 71 PHE Chi-restraints excluded: chain A residue 103 ILE Chi-restraints excluded: chain A residue 129 GLU Chi-restraints excluded: chain A residue 163 TRP Chi-restraints excluded: chain A residue 185 ASP Chi-restraints excluded: chain A residue 220 VAL Chi-restraints excluded: chain A residue 226 ILE Chi-restraints excluded: chain A residue 268 LEU Chi-restraints excluded: chain A residue 272 LEU Chi-restraints excluded: chain A residue 305 LEU Chi-restraints excluded: chain A residue 315 ASN Chi-restraints excluded: chain A residue 426 SER Chi-restraints excluded: chain A residue 473 GLU Chi-restraints excluded: chain A residue 520 ARG Chi-restraints excluded: chain A residue 559 LEU Chi-restraints excluded: chain A residue 574 CYS Chi-restraints excluded: chain A residue 619 ILE Chi-restraints excluded: chain A residue 772 ILE Chi-restraints excluded: chain A residue 865 ILE Chi-restraints excluded: chain A residue 885 THR Chi-restraints excluded: chain B residue 129 SER Chi-restraints excluded: chain B residue 204 VAL Chi-restraints excluded: chain B residue 240 ILE Chi-restraints excluded: chain B residue 273 PHE Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 327 LEU Chi-restraints excluded: chain B residue 350 ASP Chi-restraints excluded: chain B residue 450 PHE Chi-restraints excluded: chain B residue 516 LEU Chi-restraints excluded: chain B residue 528 THR Chi-restraints excluded: chain B residue 548 ILE Chi-restraints excluded: chain B residue 560 VAL Chi-restraints excluded: chain B residue 697 ILE Chi-restraints excluded: chain B residue 767 THR Chi-restraints excluded: chain B residue 1053 LYS Chi-restraints excluded: chain B residue 1054 THR Chi-restraints excluded: chain C residue 79 GLN Chi-restraints excluded: chain C residue 96 THR Chi-restraints excluded: chain C residue 99 LEU Chi-restraints excluded: chain C residue 235 VAL Chi-restraints excluded: chain C residue 356 VAL Chi-restraints excluded: chain D residue 58 ASP Chi-restraints excluded: chain D residue 217 ILE Chi-restraints excluded: chain D residue 253 ILE Chi-restraints excluded: chain E residue 17 MET Chi-restraints excluded: chain E residue 46 LEU Chi-restraints excluded: chain E residue 84 VAL Chi-restraints excluded: chain E residue 110 ILE Chi-restraints excluded: chain E residue 147 ILE Chi-restraints excluded: chain F residue 23 LYS Chi-restraints excluded: chain F residue 38 TYR Chi-restraints excluded: chain F residue 51 PHE Chi-restraints excluded: chain F residue 54 LEU Chi-restraints excluded: chain F residue 110 GLN Chi-restraints excluded: chain H residue 51 LYS Chi-restraints excluded: chain H residue 75 TYR Chi-restraints excluded: chain K residue 35 THR Chi-restraints excluded: chain L residue 6 ILE Chi-restraints excluded: chain L residue 41 THR Chi-restraints excluded: chain L residue 61 THR Chi-restraints excluded: chain L residue 93 VAL Chi-restraints excluded: chain N residue 57 ASP Chi-restraints excluded: chain P residue 46 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 323 random chunks: chunk 192 optimal weight: 2.9990 chunk 124 optimal weight: 5.9990 chunk 185 optimal weight: 0.9990 chunk 93 optimal weight: 0.7980 chunk 61 optimal weight: 8.9990 chunk 60 optimal weight: 0.0770 chunk 197 optimal weight: 2.9990 chunk 212 optimal weight: 8.9990 chunk 153 optimal weight: 0.9980 chunk 29 optimal weight: 10.0000 chunk 244 optimal weight: 4.9990 overall best weight: 1.1742 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 249 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 315 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 297 ASN ** F 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 19 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6178 moved from start: 1.0505 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 26864 Z= 0.187 Angle : 0.616 12.801 36266 Z= 0.304 Chirality : 0.045 0.290 4021 Planarity : 0.004 0.054 4702 Dihedral : 4.114 33.653 3643 Min Nonbonded Distance : 2.091 Molprobity Statistics. All-atom Clashscore : 13.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.57 % Favored : 97.43 % Rotamer: Outliers : 3.01 % Allowed : 28.30 % Favored : 68.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.56 % 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: 0.50 (0.15), residues: 3266 helix: 1.34 (0.15), residues: 1290 sheet: -0.54 (0.24), residues: 454 loop : -0.17 (0.17), residues: 1522 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 15 HIS 0.008 0.001 HIS D 63 PHE 0.013 0.001 PHE B 356 TYR 0.025 0.001 TYR B 315 ARG 0.008 0.000 ARG E 166 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6532 Ramachandran restraints generated. 3266 Oldfield, 0 Emsley, 3266 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6532 Ramachandran restraints generated. 3266 Oldfield, 0 Emsley, 3266 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 362 residues out of total 2855 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 86 poor density : 276 time to evaluate : 3.203 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: A 71 PHE cc_start: 0.4418 (OUTLIER) cc_final: 0.3868 (t80) REVERT: A 520 ARG cc_start: 0.6638 (OUTLIER) cc_final: 0.6257 (ttt-90) REVERT: E 165 MET cc_start: 0.1726 (tpt) cc_final: 0.1343 (tpp) REVERT: F 51 PHE cc_start: 0.1114 (OUTLIER) cc_final: -0.0519 (p90) outliers start: 86 outliers final: 68 residues processed: 347 average time/residue: 0.4012 time to fit residues: 219.8983 Evaluate side-chains 324 residues out of total 2855 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 253 time to evaluate : 3.293 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 ILE Chi-restraints excluded: chain A residue 57 CYS Chi-restraints excluded: chain A residue 71 PHE Chi-restraints excluded: chain A residue 103 ILE Chi-restraints excluded: chain A residue 163 TRP Chi-restraints excluded: chain A residue 220 VAL Chi-restraints excluded: chain A residue 226 ILE Chi-restraints excluded: chain A residue 268 LEU Chi-restraints excluded: chain A residue 272 LEU Chi-restraints excluded: chain A residue 312 PHE Chi-restraints excluded: chain A residue 315 ASN Chi-restraints excluded: chain A residue 426 SER Chi-restraints excluded: chain A residue 473 GLU Chi-restraints excluded: chain A residue 520 ARG Chi-restraints excluded: chain A residue 559 LEU Chi-restraints excluded: chain A residue 574 CYS Chi-restraints excluded: chain A residue 619 ILE Chi-restraints excluded: chain A residue 865 ILE Chi-restraints excluded: chain A residue 885 THR Chi-restraints excluded: chain B residue 118 VAL Chi-restraints excluded: chain B residue 129 SER Chi-restraints excluded: chain B residue 204 VAL Chi-restraints excluded: chain B residue 240 ILE Chi-restraints excluded: chain B residue 273 PHE Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 327 LEU Chi-restraints excluded: chain B residue 360 PHE Chi-restraints excluded: chain B residue 420 VAL Chi-restraints excluded: chain B residue 422 GLN Chi-restraints excluded: chain B residue 450 PHE Chi-restraints excluded: chain B residue 516 LEU Chi-restraints excluded: chain B residue 528 THR Chi-restraints excluded: chain B residue 560 VAL Chi-restraints excluded: chain B residue 697 ILE Chi-restraints excluded: chain B residue 767 THR Chi-restraints excluded: chain B residue 851 THR Chi-restraints excluded: chain B residue 1053 LYS Chi-restraints excluded: chain B residue 1054 THR Chi-restraints excluded: chain B residue 1059 CYS Chi-restraints excluded: chain B residue 1080 CYS Chi-restraints excluded: chain C residue 95 VAL Chi-restraints excluded: chain C residue 96 THR Chi-restraints excluded: chain C residue 99 LEU Chi-restraints excluded: chain C residue 235 VAL Chi-restraints excluded: chain D residue 58 ASP Chi-restraints excluded: chain D residue 105 ASP Chi-restraints excluded: chain D residue 191 VAL Chi-restraints excluded: chain D residue 217 ILE Chi-restraints excluded: chain D residue 253 ILE Chi-restraints excluded: chain E residue 17 MET Chi-restraints excluded: chain E residue 46 LEU Chi-restraints excluded: chain E residue 84 VAL Chi-restraints excluded: chain E residue 110 ILE Chi-restraints excluded: chain E residue 147 ILE Chi-restraints excluded: chain E residue 170 LEU Chi-restraints excluded: chain F residue 23 LYS Chi-restraints excluded: chain F residue 38 TYR Chi-restraints excluded: chain F residue 39 TYR Chi-restraints excluded: chain F residue 51 PHE Chi-restraints excluded: chain F residue 54 LEU Chi-restraints excluded: chain F residue 88 ASP Chi-restraints excluded: chain F residue 110 GLN Chi-restraints excluded: chain H residue 51 LYS Chi-restraints excluded: chain H residue 75 TYR Chi-restraints excluded: chain K residue 35 THR Chi-restraints excluded: chain L residue 41 THR Chi-restraints excluded: chain L residue 61 THR Chi-restraints excluded: chain L residue 93 VAL Chi-restraints excluded: chain N residue 57 ASP Chi-restraints excluded: chain N residue 58 ASP Chi-restraints excluded: chain P residue 46 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 323 random chunks: chunk 283 optimal weight: 3.9990 chunk 298 optimal weight: 6.9990 chunk 272 optimal weight: 20.0000 chunk 290 optimal weight: 7.9990 chunk 174 optimal weight: 6.9990 chunk 126 optimal weight: 10.0000 chunk 227 optimal weight: 1.9990 chunk 89 optimal weight: 6.9990 chunk 262 optimal weight: 8.9990 chunk 274 optimal weight: 0.8980 chunk 289 optimal weight: 8.9990 overall best weight: 4.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 249 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 718 ASN ** F 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6391 moved from start: 1.1544 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.096 26864 Z= 0.427 Angle : 0.728 11.925 36266 Z= 0.372 Chirality : 0.048 0.256 4021 Planarity : 0.005 0.057 4702 Dihedral : 4.533 33.022 3643 Min Nonbonded Distance : 2.018 Molprobity Statistics. All-atom Clashscore : 17.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.58 % Favored : 96.42 % Rotamer: Outliers : 2.77 % Allowed : 28.86 % Favored : 68.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.56 % 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: 0.18 (0.15), residues: 3266 helix: 1.05 (0.15), residues: 1289 sheet: -0.58 (0.25), residues: 422 loop : -0.38 (0.16), residues: 1555 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.043 0.002 TRP B1057 HIS 0.012 0.001 HIS H 18 PHE 0.015 0.002 PHE B 719 TYR 0.030 0.002 TYR A 37 ARG 0.009 0.001 ARG A 141 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6532 Ramachandran restraints generated. 3266 Oldfield, 0 Emsley, 3266 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6532 Ramachandran restraints generated. 3266 Oldfield, 0 Emsley, 3266 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 339 residues out of total 2855 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 79 poor density : 260 time to evaluate : 3.372 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: A 71 PHE cc_start: 0.4832 (OUTLIER) cc_final: 0.4190 (t80) REVERT: A 520 ARG cc_start: 0.6828 (OUTLIER) cc_final: 0.6269 (ttt-90) REVERT: C 171 ARG cc_start: 0.6272 (mmt180) cc_final: 0.5924 (mmt180) REVERT: E 165 MET cc_start: 0.2524 (tpt) cc_final: 0.2126 (tpp) REVERT: F 51 PHE cc_start: 0.1432 (OUTLIER) cc_final: -0.0332 (p90) outliers start: 79 outliers final: 60 residues processed: 329 average time/residue: 0.4232 time to fit residues: 219.2543 Evaluate side-chains 301 residues out of total 2855 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 238 time to evaluate : 3.378 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 ILE Chi-restraints excluded: chain A residue 39 ILE Chi-restraints excluded: chain A residue 57 CYS Chi-restraints excluded: chain A residue 71 PHE Chi-restraints excluded: chain A residue 103 ILE Chi-restraints excluded: chain A residue 163 TRP Chi-restraints excluded: chain A residue 220 VAL Chi-restraints excluded: chain A residue 226 ILE Chi-restraints excluded: chain A residue 268 LEU Chi-restraints excluded: chain A residue 272 LEU Chi-restraints excluded: chain A residue 301 LEU Chi-restraints excluded: chain A residue 312 PHE Chi-restraints excluded: chain A residue 315 ASN Chi-restraints excluded: chain A residue 473 GLU Chi-restraints excluded: chain A residue 520 ARG Chi-restraints excluded: chain A residue 559 LEU Chi-restraints excluded: chain A residue 574 CYS Chi-restraints excluded: chain A residue 619 ILE Chi-restraints excluded: chain A residue 865 ILE Chi-restraints excluded: chain A residue 885 THR Chi-restraints excluded: chain B residue 43 LEU Chi-restraints excluded: chain B residue 118 VAL Chi-restraints excluded: chain B residue 129 SER Chi-restraints excluded: chain B residue 176 THR Chi-restraints excluded: chain B residue 204 VAL Chi-restraints excluded: chain B residue 273 PHE Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 450 PHE Chi-restraints excluded: chain B residue 697 ILE Chi-restraints excluded: chain B residue 767 THR Chi-restraints excluded: chain B residue 851 THR Chi-restraints excluded: chain B residue 1053 LYS Chi-restraints excluded: chain B residue 1054 THR Chi-restraints excluded: chain B residue 1059 CYS Chi-restraints excluded: chain C residue 95 VAL Chi-restraints excluded: chain C residue 99 LEU Chi-restraints excluded: chain C residue 176 MET Chi-restraints excluded: chain C residue 235 VAL Chi-restraints excluded: chain D residue 58 ASP Chi-restraints excluded: chain D residue 191 VAL Chi-restraints excluded: chain D residue 217 ILE Chi-restraints excluded: chain D residue 253 ILE Chi-restraints excluded: chain E residue 46 LEU Chi-restraints excluded: chain E residue 84 VAL Chi-restraints excluded: chain E residue 110 ILE Chi-restraints excluded: chain E residue 136 LEU Chi-restraints excluded: chain E residue 147 ILE Chi-restraints excluded: chain E residue 170 LEU Chi-restraints excluded: chain F residue 38 TYR Chi-restraints excluded: chain F residue 51 PHE Chi-restraints excluded: chain F residue 54 LEU Chi-restraints excluded: chain F residue 88 ASP Chi-restraints excluded: chain F residue 110 GLN Chi-restraints excluded: chain H residue 51 LYS Chi-restraints excluded: chain H residue 75 TYR Chi-restraints excluded: chain K residue 35 THR Chi-restraints excluded: chain L residue 3 ILE Chi-restraints excluded: chain L residue 41 THR Chi-restraints excluded: chain L residue 61 THR Chi-restraints excluded: chain L residue 93 VAL Chi-restraints excluded: chain N residue 57 ASP Chi-restraints excluded: chain N residue 58 ASP Chi-restraints excluded: chain P residue 46 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 323 random chunks: chunk 190 optimal weight: 10.0000 chunk 306 optimal weight: 0.9980 chunk 187 optimal weight: 5.9990 chunk 145 optimal weight: 1.9990 chunk 213 optimal weight: 5.9990 chunk 321 optimal weight: 20.0000 chunk 296 optimal weight: 0.7980 chunk 256 optimal weight: 0.1980 chunk 26 optimal weight: 5.9990 chunk 197 optimal weight: 0.8980 chunk 157 optimal weight: 0.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 249 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 273 GLN ** A 315 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 68 ASN ** F 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6291 moved from start: 1.1639 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 26864 Z= 0.184 Angle : 0.655 13.284 36266 Z= 0.326 Chirality : 0.045 0.269 4021 Planarity : 0.004 0.057 4702 Dihedral : 4.321 34.178 3643 Min Nonbonded Distance : 2.060 Molprobity Statistics. All-atom Clashscore : 14.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer: Outliers : 2.17 % Allowed : 29.74 % Favored : 68.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.56 % 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: 0.36 (0.15), residues: 3266 helix: 1.19 (0.15), residues: 1291 sheet: -0.44 (0.25), residues: 429 loop : -0.28 (0.16), residues: 1546 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.001 TRP B1057 HIS 0.006 0.001 HIS H 18 PHE 0.014 0.001 PHE B 356 TYR 0.029 0.001 TYR B 382 ARG 0.015 0.000 ARG B 389 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6532 Ramachandran restraints generated. 3266 Oldfield, 0 Emsley, 3266 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6532 Ramachandran restraints generated. 3266 Oldfield, 0 Emsley, 3266 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 318 residues out of total 2855 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 256 time to evaluate : 3.393 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: A 446 ARG cc_start: 0.7310 (OUTLIER) cc_final: 0.6927 (mpt180) REVERT: A 520 ARG cc_start: 0.6580 (OUTLIER) cc_final: 0.6245 (ttt-90) REVERT: E 165 MET cc_start: 0.1992 (tpt) cc_final: 0.1642 (tpp) REVERT: F 51 PHE cc_start: 0.1220 (OUTLIER) cc_final: -0.0490 (p90) outliers start: 62 outliers final: 50 residues processed: 310 average time/residue: 0.4464 time to fit residues: 214.8507 Evaluate side-chains 290 residues out of total 2855 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 237 time to evaluate : 3.989 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 ILE Chi-restraints excluded: chain A residue 57 CYS Chi-restraints excluded: chain A residue 103 ILE Chi-restraints excluded: chain A residue 226 ILE Chi-restraints excluded: chain A residue 268 LEU Chi-restraints excluded: chain A residue 272 LEU Chi-restraints excluded: chain A residue 312 PHE Chi-restraints excluded: chain A residue 315 ASN Chi-restraints excluded: chain A residue 446 ARG Chi-restraints excluded: chain A residue 473 GLU Chi-restraints excluded: chain A residue 520 ARG Chi-restraints excluded: chain A residue 559 LEU Chi-restraints excluded: chain A residue 574 CYS Chi-restraints excluded: chain A residue 619 ILE Chi-restraints excluded: chain A residue 865 ILE Chi-restraints excluded: chain A residue 885 THR Chi-restraints excluded: chain B residue 43 LEU Chi-restraints excluded: chain B residue 129 SER Chi-restraints excluded: chain B residue 176 THR Chi-restraints excluded: chain B residue 204 VAL Chi-restraints excluded: chain B residue 273 PHE Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 450 PHE Chi-restraints excluded: chain B residue 697 ILE Chi-restraints excluded: chain B residue 767 THR Chi-restraints excluded: chain B residue 851 THR Chi-restraints excluded: chain B residue 1037 HIS Chi-restraints excluded: chain B residue 1053 LYS Chi-restraints excluded: chain B residue 1054 THR Chi-restraints excluded: chain B residue 1059 CYS Chi-restraints excluded: chain C residue 95 VAL Chi-restraints excluded: chain C residue 99 LEU Chi-restraints excluded: chain C residue 235 VAL Chi-restraints excluded: chain D residue 58 ASP Chi-restraints excluded: chain D residue 191 VAL Chi-restraints excluded: chain D residue 217 ILE Chi-restraints excluded: chain D residue 253 ILE Chi-restraints excluded: chain E residue 46 LEU Chi-restraints excluded: chain E residue 84 VAL Chi-restraints excluded: chain E residue 110 ILE Chi-restraints excluded: chain E residue 136 LEU Chi-restraints excluded: chain E residue 147 ILE Chi-restraints excluded: chain F residue 38 TYR Chi-restraints excluded: chain F residue 51 PHE Chi-restraints excluded: chain F residue 54 LEU Chi-restraints excluded: chain F residue 88 ASP Chi-restraints excluded: chain F residue 110 GLN Chi-restraints excluded: chain H residue 75 TYR Chi-restraints excluded: chain K residue 35 THR Chi-restraints excluded: chain L residue 41 THR Chi-restraints excluded: chain L residue 61 THR Chi-restraints excluded: chain N residue 57 ASP Chi-restraints excluded: chain P residue 46 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 323 random chunks: chunk 203 optimal weight: 8.9990 chunk 272 optimal weight: 0.6980 chunk 78 optimal weight: 8.9990 chunk 236 optimal weight: 2.9990 chunk 37 optimal weight: 6.9990 chunk 71 optimal weight: 9.9990 chunk 256 optimal weight: 10.0000 chunk 107 optimal weight: 4.9990 chunk 263 optimal weight: 10.0000 chunk 32 optimal weight: 4.9990 chunk 47 optimal weight: 6.9990 overall best weight: 4.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 249 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 346 HIS D 162 HIS ** F 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3677 r_free = 0.3677 target = 0.079642 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3139 r_free = 0.3139 target = 0.055159 restraints weight = 87937.986| |-----------------------------------------------------------------------------| r_work (start): 0.2953 rms_B_bonded: 4.18 r_work: 0.2792 rms_B_bonded: 4.62 restraints_weight: 0.5000 r_work (final): 0.2792 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8172 moved from start: 1.2337 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.084 26864 Z= 0.418 Angle : 0.747 12.415 36266 Z= 0.379 Chirality : 0.048 0.302 4021 Planarity : 0.005 0.059 4702 Dihedral : 4.628 34.025 3643 Min Nonbonded Distance : 2.025 Molprobity Statistics. All-atom Clashscore : 17.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.55 % Favored : 96.45 % Rotamer: Outliers : 2.07 % Allowed : 29.70 % Favored : 68.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.56 % 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: 0.09 (0.15), residues: 3266 helix: 0.93 (0.15), residues: 1280 sheet: -0.64 (0.24), residues: 469 loop : -0.36 (0.17), residues: 1517 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.050 0.002 TRP B1057 HIS 0.026 0.002 HIS B 302 PHE 0.031 0.002 PHE B 390 TYR 0.028 0.002 TYR B 382 ARG 0.019 0.001 ARG B 389 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6801.14 seconds wall clock time: 124 minutes 22.90 seconds (7462.90 seconds total)