Starting phenix.real_space_refine on Sun Mar 17 06:10:57 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xsr_33432/03_2024/7xsr_33432.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xsr_33432/03_2024/7xsr_33432.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.97 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xsr_33432/03_2024/7xsr_33432.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xsr_33432/03_2024/7xsr_33432.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xsr_33432/03_2024/7xsr_33432.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xsr_33432/03_2024/7xsr_33432.pdb" } resolution = 2.97 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= 0.003 sd= 0.044 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 4 6.06 5 P 49 5.49 5 S 57 5.16 5 C 10558 2.51 5 N 2934 2.21 5 O 3305 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B GLU 11": "OE1" <-> "OE2" Residue "B GLU 73": "OE1" <-> "OE2" Residue "B GLU 125": "OE1" <-> "OE2" Residue "B ASP 150": "OD1" <-> "OD2" Residue "B ASP 159": "OD1" <-> "OD2" Residue "B GLU 163": "OE1" <-> "OE2" Residue "B ASP 184": "OD1" <-> "OD2" Residue "B ASP 198": "OD1" <-> "OD2" Residue "B GLU 200": "OE1" <-> "OE2" Residue "B ASP 268": "OD1" <-> "OD2" Residue "B ASP 271": "OD1" <-> "OD2" Residue "B GLU 272": "OE1" <-> "OE2" Residue "B ASP 288": "OD1" <-> "OD2" Residue "B ASP 298": "OD1" <-> "OD2" Residue "B ASP 314": "OD1" <-> "OD2" Residue "B GLU 315": "OE1" <-> "OE2" Residue "B GLU 360": "OE1" <-> "OE2" Residue "B GLU 373": "OE1" <-> "OE2" Residue "B PHE 381": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 389": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 397": "OE1" <-> "OE2" Residue "B ASP 400": "OD1" <-> "OD2" Residue "B GLU 443": "OE1" <-> "OE2" Residue "B GLU 447": "OE1" <-> "OE2" Residue "B ASP 448": "OD1" <-> "OD2" Residue "B PHE 458": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 465": "OE1" <-> "OE2" Residue "B ASP 520": "OD1" <-> "OD2" Residue "B ASP 547": "OD1" <-> "OD2" Residue "B GLU 553": "OE1" <-> "OE2" Residue "B GLU 581": "OE1" <-> "OE2" Residue "B ASP 583": "OD1" <-> "OD2" Residue "B ASP 613": "OD1" <-> "OD2" Residue "B TYR 621": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 624": "OE1" <-> "OE2" Residue "B GLU 636": "OE1" <-> "OE2" Residue "B GLU 663": "OE1" <-> "OE2" Residue "B ASP 698": "OD1" <-> "OD2" Residue "B ASP 709": "OD1" <-> "OD2" Residue "B ASP 741": "OD1" <-> "OD2" Residue "B GLU 745": "OE1" <-> "OE2" Residue "B GLU 748": "OE1" <-> "OE2" Residue "B GLU 761": "OE1" <-> "OE2" Residue "B GLU 763": "OE1" <-> "OE2" Residue "B GLU 773": "OE1" <-> "OE2" Residue "B GLU 781": "OE1" <-> "OE2" Residue "B ASP 788": "OD1" <-> "OD2" Residue "B ASP 801": "OD1" <-> "OD2" Residue "B ASP 806": "OD1" <-> "OD2" Residue "B ASP 833": "OD1" <-> "OD2" Residue "B ASP 847": "OD1" <-> "OD2" Residue "B ASP 869": "OD1" <-> "OD2" Residue "B ASP 875": "OD1" <-> "OD2" Residue "B ASP 902": "OD1" <-> "OD2" Residue "B TYR 921": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 926": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 934": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 938": "OD1" <-> "OD2" Residue "B GLU 948": "OE1" <-> "OE2" Residue "B GLU 959": "OE1" <-> "OE2" Residue "B ASP 971": "OD1" <-> "OD2" Residue "B PHE 990": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 1011": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 1024": "OE1" <-> "OE2" Residue "B ASP 1025": "OD1" <-> "OD2" Residue "B ASP 1411": "OD1" <-> "OD2" Residue "B ASP 1471": "OD1" <-> "OD2" Residue "B GLU 1496": "OE1" <-> "OE2" Residue "B GLU 1499": "OE1" <-> "OE2" Residue "B GLU 1504": "OE1" <-> "OE2" Residue "B ASP 1521": "OD1" <-> "OD2" Residue "B ASP 1565": "OD1" <-> "OD2" Residue "B PHE 1570": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 1577": "OD1" <-> "OD2" Residue "B GLU 1589": "OE1" <-> "OE2" Residue "B GLU 1600": "OE1" <-> "OE2" Residue "B ASP 1670": "OD1" <-> "OD2" Residue "C GLU 17": "OE1" <-> "OE2" Residue "C GLU 25": "OE1" <-> "OE2" Residue "C ASP 29": "OD1" <-> "OD2" Residue "C GLU 30": "OE1" <-> "OE2" Residue "C PHE 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 40": "OD1" <-> "OD2" Residue "C ASP 61": "OD1" <-> "OD2" Residue "C ASP 62": "OD1" <-> "OD2" Residue "C PHE 68": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 95": "OE1" <-> "OE2" Residue "C GLU 102": "OE1" <-> "OE2" Residue "C ASP 105": "OD1" <-> "OD2" Residue "C PHE 111": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 117": "OD1" <-> "OD2" Residue "C GLU 131": "OE1" <-> "OE2" Residue "C ASP 136": "OD1" <-> "OD2" Residue "C GLU 138": "OE1" <-> "OE2" Residue "C GLU 151": "OE1" <-> "OE2" Residue "C ASP 166": "OD1" <-> "OD2" Residue "C GLU 181": "OE1" <-> "OE2" Residue "C TYR 225": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 246": "OD1" <-> "OD2" Residue "C GLU 266": "OE1" <-> "OE2" Residue "C GLU 268": "OE1" <-> "OE2" Residue "C ASP 286": "OD1" <-> "OD2" Residue "C PHE 289": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 294": "OE1" <-> "OE2" Residue "C ASP 298": "OD1" <-> "OD2" Residue "C GLU 300": "OE1" <-> "OE2" Residue "C ASP 302": "OD1" <-> "OD2" Residue "C ASP 318": "OD1" <-> "OD2" Residue "C ASP 330": "OD1" <-> "OD2" Residue "C GLU 332": "OE1" <-> "OE2" Residue "C ASP 338": "OD1" <-> "OD2" Residue "C ASP 339": "OD1" <-> "OD2" Residue "C GLU 344": "OE1" <-> "OE2" Residue "C ASP 350": "OD1" <-> "OD2" Residue "C ASP 358": "OD1" <-> "OD2" Residue "C GLU 411": "OE1" <-> "OE2" Residue "C PHE 431": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 435": "OE1" <-> "OE2" Residue "C GLU 456": "OE1" <-> "OE2" Residue "C GLU 467": "OE1" <-> "OE2" Residue "C GLU 529": "OE1" <-> "OE2" Residue "C ASP 543": "OD1" <-> "OD2" Residue "C PHE 547": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 548": "OE1" <-> "OE2" Residue "C ASP 568": "OD1" <-> "OD2" Residue "C ASP 569": "OD1" <-> "OD2" Residue "C GLU 609": "OE1" <-> "OE2" Residue "C GLU 641": "OE1" <-> "OE2" Residue "C GLU 674": "OE1" <-> "OE2" Residue "C GLU 678": "OE1" <-> "OE2" Residue "C GLU 681": "OE1" <-> "OE2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 16907 Number of models: 1 Model: "" Number of chains: 5 Chain: "B" Number of atoms: 10378 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1287, 10378 Classifications: {'peptide': 1287} Link IDs: {'PTRANS': 60, 'TRANS': 1226} Chain breaks: 3 Chain: "C" Number of atoms: 5482 Number of conformers: 1 Conformer: "" Number of residues, atoms: 676, 5482 Classifications: {'peptide': 676} Link IDs: {'PTRANS': 20, 'TRANS': 655} Chain breaks: 1 Chain: "A" Number of atoms: 331 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 331 Classifications: {'RNA': 15} Modifications used: {'rna2p_pur': 1, 'rna2p_pyr': 1, 'rna3p_pur': 11, 'rna3p_pyr': 2} Link IDs: {'rna2p': 1, 'rna3p': 13} Chain: "D" Number of atoms: 712 Number of conformers: 1 Conformer: "" Number of residues, atoms: 34, 712 Classifications: {'RNA': 34} Modifications used: {'rna2p_pur': 11, 'rna2p_pyr': 8, 'rna3p_pur': 2, 'rna3p_pyr': 13} Link IDs: {'rna2p': 19, 'rna3p': 14} Chain: "B" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Unusual residues: {' ZN': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 676 SG CYS B 88 90.553 35.311 38.173 1.00 33.30 S ATOM 947 SG CYS B 121 94.678 33.022 37.660 1.00 41.85 S ATOM 993 SG CYS B 127 94.923 36.292 40.080 1.00 31.93 S ATOM 1017 SG CYS B 130 92.866 33.583 41.273 1.00 29.20 S ATOM 3755 SG CYS B 491 64.651 52.396 51.436 1.00 34.19 S ATOM 3837 SG CYS B 503 66.139 54.198 48.666 1.00 31.01 S ATOM 3859 SG CYS B 506 69.366 52.378 51.448 1.00 29.73 S ATOM 5830 SG CYS B 750 41.081 64.124 69.071 1.00 47.55 S ATOM 5843 SG CYS B 752 42.051 68.235 68.440 1.00 40.60 S ATOM 5865 SG CYS B 755 44.819 66.200 69.641 1.00 34.26 S ATOM 7868 SG CYS B1018 35.862 82.640 102.441 1.00 31.62 S ATOM 8039 SG CYS B1406 35.145 79.400 100.591 1.00 35.05 S ATOM 8090 SG CYS B1414 33.705 83.417 98.992 1.00 31.82 S ATOM 8107 SG CYS B1417 37.109 82.215 98.694 1.00 28.08 S Time building chain proxies: 8.97, per 1000 atoms: 0.53 Number of scatterers: 16907 At special positions: 0 Unit cell: (118.845, 136.8, 143.64, 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 4 29.99 S 57 16.00 P 49 15.00 O 3305 8.00 N 2934 7.00 C 10558 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: 6.06 Conformation dependent library (CDL) restraints added in 2.6 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN B1801 " pdb="ZN ZN B1801 " - pdb=" SG CYS B 127 " pdb="ZN ZN B1801 " - pdb=" SG CYS B 130 " pdb="ZN ZN B1801 " - pdb=" SG CYS B 121 " pdb="ZN ZN B1801 " - pdb=" SG CYS B 88 " pdb=" ZN B1802 " pdb="ZN ZN B1802 " - pdb=" SG CYS B 506 " pdb="ZN ZN B1802 " - pdb=" SG CYS B 503 " pdb="ZN ZN B1802 " - pdb=" SG CYS B 491 " pdb=" ZN B1803 " pdb="ZN ZN B1803 " - pdb=" ND1 HIS B 747 " pdb="ZN ZN B1803 " - pdb=" SG CYS B 752 " pdb="ZN ZN B1803 " - pdb=" SG CYS B 750 " pdb="ZN ZN B1803 " - pdb=" SG CYS B 755 " pdb=" ZN B1804 " pdb="ZN ZN B1804 " - pdb=" SG CYS B1406 " pdb="ZN ZN B1804 " - pdb=" SG CYS B1414 " pdb="ZN ZN B1804 " - pdb=" SG CYS B1018 " pdb="ZN ZN B1804 " - pdb=" SG CYS B1417 " Number of angles added : 15 3902 Ramachandran restraints generated. 1951 Oldfield, 0 Emsley, 1951 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3636 Finding SS restraints... Secondary structure from input PDB file: 68 helices and 20 sheets defined 39.3% alpha, 17.3% beta 5 base pairs and 13 stacking pairs defined. Time for finding SS restraints: 5.07 Creating SS restraints... Processing helix chain 'B' and resid 27 through 32 Processing helix chain 'B' and resid 33 through 38 Processing helix chain 'B' and resid 59 through 78 removed outlier: 3.786A pdb=" N VAL B 63 " --> pdb=" O THR B 59 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ASN B 78 " --> pdb=" O LEU B 74 " (cutoff:3.500A) Processing helix chain 'B' and resid 127 through 134 Processing helix chain 'B' and resid 216 through 224 Processing helix chain 'B' and resid 267 through 287 removed outlier: 3.871A pdb=" N ASN B 287 " --> pdb=" O ALA B 283 " (cutoff:3.500A) Processing helix chain 'B' and resid 288 through 290 No H-bonds generated for 'chain 'B' and resid 288 through 290' Processing helix chain 'B' and resid 291 through 303 removed outlier: 4.331A pdb=" N ILE B 295 " --> pdb=" O GLU B 291 " (cutoff:3.500A) Processing helix chain 'B' and resid 308 through 313 Processing helix chain 'B' and resid 338 through 350 Processing helix chain 'B' and resid 351 through 353 No H-bonds generated for 'chain 'B' and resid 351 through 353' Processing helix chain 'B' and resid 354 through 375 removed outlier: 3.508A pdb=" N PHE B 358 " --> pdb=" O GLY B 354 " (cutoff:3.500A) Processing helix chain 'B' and resid 471 through 488 removed outlier: 3.614A pdb=" N LEU B 475 " --> pdb=" O PRO B 471 " (cutoff:3.500A) Processing helix chain 'B' and resid 503 through 510 Processing helix chain 'B' and resid 569 through 580 Processing helix chain 'B' and resid 595 through 598 Processing helix chain 'B' and resid 617 through 625 Processing helix chain 'B' and resid 626 through 628 No H-bonds generated for 'chain 'B' and resid 626 through 628' Processing helix chain 'B' and resid 630 through 637 removed outlier: 3.792A pdb=" N LEU B 634 " --> pdb=" O LYS B 630 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N LEU B 635 " --> pdb=" O GLU B 631 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N GLU B 636 " --> pdb=" O LYS B 632 " (cutoff:3.500A) Processing helix chain 'B' and resid 654 through 658 removed outlier: 3.724A pdb=" N LEU B 658 " --> pdb=" O ARG B 655 " (cutoff:3.500A) Processing helix chain 'B' and resid 688 through 693 Processing helix chain 'B' and resid 723 through 740 removed outlier: 3.770A pdb=" N HIS B 727 " --> pdb=" O LYS B 723 " (cutoff:3.500A) Processing helix chain 'B' and resid 752 through 759 Processing helix chain 'B' and resid 831 through 848 Processing helix chain 'B' and resid 855 through 859 Processing helix chain 'B' and resid 873 through 883 Processing helix chain 'B' and resid 999 through 1015 removed outlier: 3.802A pdb=" N LEU B1003 " --> pdb=" O PRO B 999 " (cutoff:3.500A) Processing helix chain 'B' and resid 1400 through 1404 removed outlier: 3.720A pdb=" N HIS B1404 " --> pdb=" O LYS B1401 " (cutoff:3.500A) Processing helix chain 'B' and resid 1414 through 1420 Processing helix chain 'B' and resid 1463 through 1468 removed outlier: 4.212A pdb=" N SER B1467 " --> pdb=" O ARG B1463 " (cutoff:3.500A) Processing helix chain 'B' and resid 1486 through 1493 removed outlier: 3.942A pdb=" N ILE B1490 " --> pdb=" O GLY B1486 " (cutoff:3.500A) Processing helix chain 'B' and resid 1494 through 1499 Processing helix chain 'B' and resid 1528 through 1540 Processing helix chain 'B' and resid 1583 through 1603 removed outlier: 3.505A pdb=" N ILE B1587 " --> pdb=" O PRO B1583 " (cutoff:3.500A) Processing helix chain 'B' and resid 1615 through 1618 removed outlier: 3.659A pdb=" N VAL B1618 " --> pdb=" O GLN B1615 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 1615 through 1618' Processing helix chain 'B' and resid 1619 through 1629 Processing helix chain 'B' and resid 1673 through 1683 removed outlier: 3.570A pdb=" N THR B1683 " --> pdb=" O LYS B1679 " (cutoff:3.500A) Processing helix chain 'C' and resid 16 through 33 Processing helix chain 'C' and resid 37 through 59 Processing helix chain 'C' and resid 64 through 81 removed outlier: 3.757A pdb=" N PHE C 68 " --> pdb=" O THR C 64 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N THR C 81 " --> pdb=" O LEU C 77 " (cutoff:3.500A) Processing helix chain 'C' and resid 90 through 109 removed outlier: 3.811A pdb=" N LYS C 94 " --> pdb=" O PRO C 90 " (cutoff:3.500A) Processing helix chain 'C' and resid 114 through 136 Processing helix chain 'C' and resid 141 through 156 Processing helix chain 'C' and resid 163 through 177 removed outlier: 4.107A pdb=" N ILE C 167 " --> pdb=" O TYR C 163 " (cutoff:3.500A) Processing helix chain 'C' and resid 183 through 190 Processing helix chain 'C' and resid 194 through 205 Processing helix chain 'C' and resid 209 through 223 Processing helix chain 'C' and resid 230 through 246 removed outlier: 4.258A pdb=" N ASP C 234 " --> pdb=" O HIS C 230 " (cutoff:3.500A) Processing helix chain 'C' and resid 250 through 267 removed outlier: 3.982A pdb=" N ILE C 256 " --> pdb=" O ARG C 252 " (cutoff:3.500A) Processing helix chain 'C' and resid 280 through 298 Processing helix chain 'C' and resid 302 through 322 removed outlier: 3.845A pdb=" N LYS C 306 " --> pdb=" O ASP C 302 " (cutoff:3.500A) Processing helix chain 'C' and resid 328 through 334 Processing helix chain 'C' and resid 340 through 362 removed outlier: 3.975A pdb=" N TYR C 360 " --> pdb=" O TYR C 356 " (cutoff:3.500A) removed outlier: 4.153A pdb=" N ILE C 362 " --> pdb=" O ASP C 358 " (cutoff:3.500A) Processing helix chain 'C' and resid 433 through 451 removed outlier: 3.517A pdb=" N PHE C 437 " --> pdb=" O TYR C 433 " (cutoff:3.500A) Processing helix chain 'C' and resid 454 through 469 Processing helix chain 'C' and resid 470 through 473 Processing helix chain 'C' and resid 490 through 494 Processing helix chain 'C' and resid 509 through 513 removed outlier: 3.688A pdb=" N GLU C 512 " --> pdb=" O LEU C 509 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N ASN C 513 " --> pdb=" O PHE C 510 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 509 through 513' Processing helix chain 'C' and resid 521 through 525 Processing helix chain 'C' and resid 547 through 552 Processing helix chain 'C' and resid 566 through 571 Processing helix chain 'C' and resid 592 through 596 removed outlier: 3.710A pdb=" N SER C 596 " --> pdb=" O PRO C 593 " (cutoff:3.500A) Processing helix chain 'C' and resid 606 through 613 Processing helix chain 'C' and resid 627 through 631 Processing helix chain 'C' and resid 644 through 653 removed outlier: 3.851A pdb=" N ALA C 648 " --> pdb=" O SER C 644 " (cutoff:3.500A) Processing helix chain 'C' and resid 665 through 679 removed outlier: 3.849A pdb=" N THR C 669 " --> pdb=" O ARG C 665 " (cutoff:3.500A) Processing helix chain 'C' and resid 683 through 691 removed outlier: 4.032A pdb=" N TRP C 687 " --> pdb=" O LYS C 683 " (cutoff:3.500A) Processing helix chain 'C' and resid 699 through 707 removed outlier: 3.718A pdb=" N PHE C 703 " --> pdb=" O HIS C 699 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N ILE C 707 " --> pdb=" O PHE C 703 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 151 through 153 removed outlier: 3.748A pdb=" N LEU B 158 " --> pdb=" O SER B 56 " (cutoff:3.500A) removed outlier: 7.338A pdb=" N SER B 56 " --> pdb=" O LEU B 158 " (cutoff:3.500A) removed outlier: 6.623A pdb=" N ARG B 19 " --> pdb=" O ALA B 42 " (cutoff:3.500A) removed outlier: 7.674A pdb=" N TRP B 44 " --> pdb=" O ARG B 19 " (cutoff:3.500A) removed outlier: 6.538A pdb=" N VAL B 21 " --> pdb=" O TRP B 44 " (cutoff:3.500A) removed outlier: 8.431A pdb=" N TRP B 46 " --> pdb=" O VAL B 21 " (cutoff:3.500A) removed outlier: 4.057A pdb=" N TRP B 195 " --> pdb=" O LEU B 20 " (cutoff:3.500A) removed outlier: 10.062A pdb=" N GLU B 22 " --> pdb=" O ARG B 193 " (cutoff:3.500A) removed outlier: 13.887A pdb=" N ARG B 193 " --> pdb=" O GLU B 22 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N ASP B 190 " --> pdb=" O ARG B 180 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N PHE B 192 " --> pdb=" O LEU B 178 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 167 through 168 removed outlier: 3.922A pdb=" N LEU B 167 " --> pdb=" O GLY B 54 " (cutoff:3.500A) removed outlier: 7.338A pdb=" N SER B 56 " --> pdb=" O LEU B 158 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N LEU B 158 " --> pdb=" O SER B 56 " (cutoff:3.500A) removed outlier: 4.253A pdb=" N THR B 9 " --> pdb=" O ILE B 240 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 81 through 82 removed outlier: 3.627A pdb=" N VAL B 85 " --> pdb=" O TRP B 82 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 110 through 111 removed outlier: 6.355A pdb=" N THR B 110 " --> pdb=" O VAL B 405 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'B' and resid 512 through 513 removed outlier: 6.753A pdb=" N GLU B 415 " --> pdb=" O GLU B 611 " (cutoff:3.500A) removed outlier: 4.650A pdb=" N GLU B 611 " --> pdb=" O GLU B 415 " (cutoff:3.500A) removed outlier: 6.617A pdb=" N ILE B 417 " --> pdb=" O ILE B 609 " (cutoff:3.500A) removed outlier: 4.433A pdb=" N ILE B 609 " --> pdb=" O ILE B 417 " (cutoff:3.500A) removed outlier: 6.689A pdb=" N VAL B 419 " --> pdb=" O ILE B 607 " (cutoff:3.500A) removed outlier: 4.216A pdb=" N ILE B 607 " --> pdb=" O VAL B 419 " (cutoff:3.500A) removed outlier: 4.457A pdb=" N GLY B 600 " --> pdb=" O LEU B 591 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 512 through 513 removed outlier: 6.753A pdb=" N GLU B 415 " --> pdb=" O GLU B 611 " (cutoff:3.500A) removed outlier: 4.650A pdb=" N GLU B 611 " --> pdb=" O GLU B 415 " (cutoff:3.500A) removed outlier: 6.617A pdb=" N ILE B 417 " --> pdb=" O ILE B 609 " (cutoff:3.500A) removed outlier: 4.433A pdb=" N ILE B 609 " --> pdb=" O ILE B 417 " (cutoff:3.500A) removed outlier: 6.689A pdb=" N VAL B 419 " --> pdb=" O ILE B 607 " (cutoff:3.500A) removed outlier: 4.216A pdb=" N ILE B 607 " --> pdb=" O VAL B 419 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 431 through 432 removed outlier: 3.693A pdb=" N VAL B 432 " --> pdb=" O ASN B 459 " (cutoff:3.500A) removed outlier: 4.444A pdb=" N ASN B 459 " --> pdb=" O VAL B 432 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'B' and resid 469 through 470 Processing sheet with id=AA9, first strand: chain 'B' and resid 526 through 530 Processing sheet with id=AB1, first strand: chain 'B' and resid 533 through 534 removed outlier: 3.726A pdb=" N THR B 539 " --> pdb=" O ASN B 534 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 703 through 704 removed outlier: 3.542A pdb=" N ARG B 719 " --> pdb=" O LYS B 704 " (cutoff:3.500A) removed outlier: 6.059A pdb=" N PHE B 720 " --> pdb=" O LEU B 774 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 703 through 704 removed outlier: 3.542A pdb=" N ARG B 719 " --> pdb=" O LYS B 704 " (cutoff:3.500A) removed outlier: 6.059A pdb=" N PHE B 720 " --> pdb=" O LEU B 774 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 699 through 700 removed outlier: 6.942A pdb=" N ALA B 699 " --> pdb=" O TYR B 808 " (cutoff:3.500A) removed outlier: 6.522A pdb=" N ALA B 803 " --> pdb=" O ALA B 791 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 924 through 927 Processing sheet with id=AB6, first strand: chain 'B' and resid 991 through 992 removed outlier: 6.975A pdb=" N LEU B 996 " --> pdb=" O TYR B1436 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N TYR B1436 " --> pdb=" O LEU B 996 " (cutoff:3.500A) removed outlier: 6.911A pdb=" N VAL B1517 " --> pdb=" O GLU B1437 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 991 through 992 removed outlier: 6.975A pdb=" N LEU B 996 " --> pdb=" O TYR B1436 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N TYR B1436 " --> pdb=" O LEU B 996 " (cutoff:3.500A) removed outlier: 6.911A pdb=" N VAL B1517 " --> pdb=" O GLU B1437 " (cutoff:3.500A) removed outlier: 5.609A pdb=" N LEU B 950 " --> pdb=" O ASN B1526 " (cutoff:3.500A) removed outlier: 6.414A pdb=" N LYS B 957 " --> pdb=" O ILE B1564 " (cutoff:3.500A) removed outlier: 5.256A pdb=" N ILE B1564 " --> pdb=" O LYS B 957 " (cutoff:3.500A) removed outlier: 7.201A pdb=" N GLU B 959 " --> pdb=" O ILE B1562 " (cutoff:3.500A) removed outlier: 5.543A pdb=" N ILE B1562 " --> pdb=" O GLU B 959 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 985 through 986 removed outlier: 6.469A pdb=" N LYS B 985 " --> pdb=" O THR B1508 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 425 through 431 removed outlier: 3.588A pdb=" N PHE C 405 " --> pdb=" O VAL C 487 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 562 through 563 removed outlier: 7.961A pdb=" N LYS C 562 " --> pdb=" O TYR C 536 " (cutoff:3.500A) removed outlier: 6.159A pdb=" N LEU C 538 " --> pdb=" O LYS C 562 " (cutoff:3.500A) removed outlier: 4.716A pdb=" N THR C 660 " --> pdb=" O LEU C 624 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 586 through 587 666 hydrogen bonds defined for protein. 1890 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 12 hydrogen bonds 24 hydrogen bond angles 0 basepair planarities 5 basepair parallelities 13 stacking parallelities Total time for adding SS restraints: 6.65 Time building geometry restraints manager: 6.61 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 3255 1.33 - 1.45: 4542 1.45 - 1.57: 9445 1.57 - 1.69: 62 1.69 - 1.81: 80 Bond restraints: 17384 Sorted by residual: bond pdb=" O3' G A 27 " pdb=" P C A 28 " ideal model delta sigma weight residual 1.607 1.475 0.132 1.50e-02 4.44e+03 7.70e+01 bond pdb=" O3' C D 9 " pdb=" P U D 10 " ideal model delta sigma weight residual 1.607 1.481 0.126 1.50e-02 4.44e+03 7.03e+01 bond pdb=" O3' U D 8 " pdb=" P C D 9 " ideal model delta sigma weight residual 1.607 1.488 0.119 1.50e-02 4.44e+03 6.31e+01 bond pdb=" O3' U D -2 " pdb=" P A D -1 " ideal model delta sigma weight residual 1.607 1.491 0.116 1.50e-02 4.44e+03 6.03e+01 bond pdb=" O3' G D -9 " pdb=" P U D -8 " ideal model delta sigma weight residual 1.607 1.493 0.114 1.50e-02 4.44e+03 5.77e+01 ... (remaining 17379 not shown) Histogram of bond angle deviations from ideal: 91.70 - 100.38: 19 100.38 - 109.06: 1772 109.06 - 117.74: 11305 117.74 - 126.43: 10136 126.43 - 135.11: 441 Bond angle restraints: 23673 Sorted by residual: angle pdb=" O3' C D 13 " pdb=" C3' C D 13 " pdb=" C2' C D 13 " ideal model delta sigma weight residual 113.70 132.27 -18.57 1.50e+00 4.44e-01 1.53e+02 angle pdb=" O2' C D 1 " pdb=" C2' C D 1 " pdb=" C1' C D 1 " ideal model delta sigma weight residual 108.40 91.70 16.70 1.50e+00 4.44e-01 1.24e+02 angle pdb=" O2' U D -2 " pdb=" C2' U D -2 " pdb=" C1' U D -2 " ideal model delta sigma weight residual 111.80 100.28 11.52 1.50e+00 4.44e-01 5.89e+01 angle pdb=" O4' A D -1 " pdb=" C1' A D -1 " pdb=" C2' A D -1 " ideal model delta sigma weight residual 105.80 99.29 6.51 1.00e+00 1.00e+00 4.23e+01 angle pdb=" O2' C D -7 " pdb=" C2' C D -7 " pdb=" C1' C D -7 " ideal model delta sigma weight residual 108.40 117.85 -9.45 1.50e+00 4.44e-01 3.97e+01 ... (remaining 23668 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.72: 10009 33.72 - 67.43: 471 67.43 - 101.15: 38 101.15 - 134.87: 2 134.87 - 168.58: 4 Dihedral angle restraints: 10524 sinusoidal: 4865 harmonic: 5659 Sorted by residual: dihedral pdb=" O4' U D -13 " pdb=" C1' U D -13 " pdb=" N1 U D -13 " pdb=" C2 U D -13 " ideal model delta sinusoidal sigma weight residual -160.00 5.71 -165.71 1 1.50e+01 4.44e-03 8.40e+01 dihedral pdb=" O4' C D -7 " pdb=" C1' C D -7 " pdb=" N1 C D -7 " pdb=" C2 C D -7 " ideal model delta sinusoidal sigma weight residual 200.00 50.53 149.47 1 1.50e+01 4.44e-03 7.94e+01 dihedral pdb=" O4' U D -8 " pdb=" C1' U D -8 " pdb=" N1 U D -8 " pdb=" C2 U D -8 " ideal model delta sinusoidal sigma weight residual -128.00 40.58 -168.58 1 1.70e+01 3.46e-03 6.58e+01 ... (remaining 10521 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.181: 2518 0.181 - 0.363: 40 0.363 - 0.544: 3 0.544 - 0.725: 1 0.725 - 0.907: 1 Chirality restraints: 2563 Sorted by residual: chirality pdb=" C3' C D 13 " pdb=" C4' C D 13 " pdb=" O3' C D 13 " pdb=" C2' C D 13 " both_signs ideal model delta sigma weight residual False -2.48 -1.57 -0.91 2.00e-01 2.50e+01 2.06e+01 chirality pdb=" C2' C D -7 " pdb=" C3' C D -7 " pdb=" O2' C D -7 " pdb=" C1' C D -7 " both_signs ideal model delta sigma weight residual False -2.75 -2.19 -0.56 2.00e-01 2.50e+01 7.91e+00 chirality pdb=" C2' C D 13 " pdb=" C3' C D 13 " pdb=" O2' C D 13 " pdb=" C1' C D 13 " both_signs ideal model delta sigma weight residual False -2.75 -2.32 -0.43 2.00e-01 2.50e+01 4.60e+00 ... (remaining 2560 not shown) Planarity restraints: 2873 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' A D -1 " 0.093 2.00e-02 2.50e+03 4.23e-02 4.93e+01 pdb=" N9 A D -1 " -0.089 2.00e-02 2.50e+03 pdb=" C8 A D -1 " 0.008 2.00e-02 2.50e+03 pdb=" N7 A D -1 " -0.002 2.00e-02 2.50e+03 pdb=" C5 A D -1 " -0.010 2.00e-02 2.50e+03 pdb=" C6 A D -1 " 0.029 2.00e-02 2.50e+03 pdb=" N6 A D -1 " 0.013 2.00e-02 2.50e+03 pdb=" N1 A D -1 " 0.020 2.00e-02 2.50e+03 pdb=" C2 A D -1 " -0.006 2.00e-02 2.50e+03 pdb=" N3 A D -1 " -0.021 2.00e-02 2.50e+03 pdb=" C4 A D -1 " -0.034 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' A A 34 " 0.077 2.00e-02 2.50e+03 3.25e-02 2.90e+01 pdb=" N9 A A 34 " -0.048 2.00e-02 2.50e+03 pdb=" C8 A A 34 " -0.008 2.00e-02 2.50e+03 pdb=" N7 A A 34 " -0.009 2.00e-02 2.50e+03 pdb=" C5 A A 34 " -0.000 2.00e-02 2.50e+03 pdb=" C6 A A 34 " 0.017 2.00e-02 2.50e+03 pdb=" N6 A A 34 " 0.014 2.00e-02 2.50e+03 pdb=" N1 A A 34 " 0.027 2.00e-02 2.50e+03 pdb=" C2 A A 34 " -0.008 2.00e-02 2.50e+03 pdb=" N3 A A 34 " -0.032 2.00e-02 2.50e+03 pdb=" C4 A A 34 " -0.030 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LYS B 442 " -0.020 2.00e-02 2.50e+03 3.93e-02 1.54e+01 pdb=" C LYS B 442 " 0.068 2.00e-02 2.50e+03 pdb=" O LYS B 442 " -0.026 2.00e-02 2.50e+03 pdb=" N GLU B 443 " -0.023 2.00e-02 2.50e+03 ... (remaining 2870 not shown) Histogram of nonbonded interaction distances: 2.27 - 2.79: 4099 2.79 - 3.32: 13688 3.32 - 3.85: 26543 3.85 - 4.37: 30891 4.37 - 4.90: 54969 Nonbonded interactions: 130190 Sorted by model distance: nonbonded pdb=" OG SER B 378 " pdb=" OD1 ASN B 453 " model vdw 2.268 2.440 nonbonded pdb=" O ASN B 179 " pdb=" O2' G D -3 " model vdw 2.282 2.440 nonbonded pdb=" OH TYR B1645 " pdb=" OP1 C D 14 " model vdw 2.328 2.440 nonbonded pdb=" O THR C 702 " pdb=" OG SER C 706 " model vdw 2.329 2.440 nonbonded pdb=" OH TYR B 191 " pdb=" OD1 ASP B 386 " model vdw 2.333 2.440 ... (remaining 130185 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: 1.050 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 5.340 Check model and map are aligned: 0.230 Set scattering table: 0.130 Process input model: 49.700 Find NCS groups from input model: 0.430 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:11.420 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 68.370 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7509 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 : 0.007 0.132 17384 Z= 0.464 Angle : 0.969 18.809 23673 Z= 0.568 Chirality : 0.066 0.907 2563 Planarity : 0.008 0.088 2873 Dihedral : 18.284 168.585 6888 Min Nonbonded Distance : 2.268 Molprobity Statistics. All-atom Clashscore : 3.17 Ramachandran Plot: Outliers : 0.10 % Allowed : 5.69 % Favored : 94.21 % Rotamer: Outliers : 3.94 % Allowed : 12.64 % Favored : 83.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.57 (0.15), residues: 1951 helix: -1.57 (0.15), residues: 692 sheet: 0.06 (0.31), residues: 267 loop : -2.35 (0.15), residues: 992 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP C 443 HIS 0.006 0.001 HIS B 924 PHE 0.025 0.002 PHE B 805 TYR 0.022 0.002 TYR C 75 ARG 0.013 0.001 ARG C 21 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3902 Ramachandran restraints generated. 1951 Oldfield, 0 Emsley, 1951 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3902 Ramachandran restraints generated. 1951 Oldfield, 0 Emsley, 1951 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 482 residues out of total 1725 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 414 time to evaluate : 1.853 Fit side-chains revert: symmetry clash REVERT: B 184 ASP cc_start: 0.7111 (m-30) cc_final: 0.6910 (m-30) REVERT: B 315 GLU cc_start: 0.7349 (tt0) cc_final: 0.7135 (mt-10) REVERT: B 318 ASP cc_start: 0.6903 (t0) cc_final: 0.6654 (t0) REVERT: B 351 LYS cc_start: 0.8446 (ttmm) cc_final: 0.8234 (tttt) REVERT: B 401 LEU cc_start: 0.8564 (OUTLIER) cc_final: 0.8340 (mp) REVERT: B 516 ASP cc_start: 0.6923 (OUTLIER) cc_final: 0.6715 (p0) REVERT: B 547 ASP cc_start: 0.7473 (p0) cc_final: 0.7230 (p0) REVERT: B 651 PHE cc_start: 0.8405 (m-80) cc_final: 0.8188 (m-80) REVERT: B 698 ASP cc_start: 0.7080 (m-30) cc_final: 0.6834 (m-30) REVERT: B 807 THR cc_start: 0.8431 (p) cc_final: 0.8181 (m) REVERT: B 918 LYS cc_start: 0.5955 (mptt) cc_final: 0.5167 (mppt) REVERT: B 1400 ASP cc_start: 0.7527 (m-30) cc_final: 0.7319 (m-30) REVERT: B 1436 TYR cc_start: 0.8182 (t80) cc_final: 0.7922 (t80) REVERT: B 1565 ASP cc_start: 0.7212 (t0) cc_final: 0.6915 (m-30) REVERT: B 1660 ASP cc_start: 0.6454 (m-30) cc_final: 0.6123 (m-30) REVERT: B 1665 LYS cc_start: 0.7888 (mtpt) cc_final: 0.7685 (mtpt) REVERT: B 1666 LEU cc_start: 0.8495 (OUTLIER) cc_final: 0.7980 (mp) REVERT: C 167 ILE cc_start: 0.8093 (mt) cc_final: 0.7789 (mt) REVERT: C 267 LYS cc_start: 0.7937 (tttm) cc_final: 0.7646 (tttt) REVERT: C 352 CYS cc_start: 0.6977 (m) cc_final: 0.6451 (m) REVERT: C 483 ASP cc_start: 0.7792 (OUTLIER) cc_final: 0.7125 (m-30) REVERT: C 613 SER cc_start: 0.7965 (m) cc_final: 0.7742 (m) outliers start: 68 outliers final: 15 residues processed: 466 average time/residue: 1.3337 time to fit residues: 688.6862 Evaluate side-chains 365 residues out of total 1725 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 346 time to evaluate : 1.685 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 85 VAL Chi-restraints excluded: chain B residue 160 HIS Chi-restraints excluded: chain B residue 201 THR Chi-restraints excluded: chain B residue 310 VAL Chi-restraints excluded: chain B residue 401 LEU Chi-restraints excluded: chain B residue 473 SER Chi-restraints excluded: chain B residue 516 ASP Chi-restraints excluded: chain B residue 724 SER Chi-restraints excluded: chain B residue 831 SER Chi-restraints excluded: chain B residue 969 THR Chi-restraints excluded: chain B residue 1424 ASP Chi-restraints excluded: chain B residue 1454 LEU Chi-restraints excluded: chain B residue 1458 VAL Chi-restraints excluded: chain B residue 1666 LEU Chi-restraints excluded: chain C residue 71 ILE Chi-restraints excluded: chain C residue 129 SER Chi-restraints excluded: chain C residue 475 ASP Chi-restraints excluded: chain C residue 483 ASP Chi-restraints excluded: chain C residue 680 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 199 random chunks: chunk 168 optimal weight: 1.9990 chunk 150 optimal weight: 2.9990 chunk 83 optimal weight: 0.1980 chunk 51 optimal weight: 1.9990 chunk 101 optimal weight: 0.6980 chunk 80 optimal weight: 0.5980 chunk 155 optimal weight: 0.9990 chunk 60 optimal weight: 2.9990 chunk 94 optimal weight: 3.9990 chunk 116 optimal weight: 2.9990 chunk 180 optimal weight: 7.9990 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 286 GLN B 434 GLN ** B 453 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 708 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 881 ASN B 900 ASN B 908 HIS ** B 917 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 919 ASN B1404 HIS B1596 GLN B1604 ASN C 147 ASN C 183 HIS C 513 ASN C 552 ASN C 572 ASN C 592 ASN C 602 ASN C 642 HIS Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7545 moved from start: 0.1916 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 17384 Z= 0.209 Angle : 0.582 11.359 23673 Z= 0.305 Chirality : 0.042 0.220 2563 Planarity : 0.005 0.070 2873 Dihedral : 15.183 176.063 2912 Min Nonbonded Distance : 2.169 Molprobity Statistics. All-atom Clashscore : 5.64 Ramachandran Plot: Outliers : 0.10 % Allowed : 5.54 % Favored : 94.36 % Rotamer: Outliers : 4.58 % Allowed : 21.04 % Favored : 74.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.92 (0.17), residues: 1951 helix: 0.68 (0.19), residues: 696 sheet: 0.37 (0.31), residues: 256 loop : -1.89 (0.16), residues: 999 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 278 HIS 0.009 0.001 HIS B 908 PHE 0.018 0.002 PHE B 546 TYR 0.014 0.001 TYR C 607 ARG 0.006 0.000 ARG C 260 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3902 Ramachandran restraints generated. 1951 Oldfield, 0 Emsley, 1951 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3902 Ramachandran restraints generated. 1951 Oldfield, 0 Emsley, 1951 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 444 residues out of total 1725 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 79 poor density : 365 time to evaluate : 1.776 Fit side-chains REVERT: B 202 TYR cc_start: 0.8634 (m-80) cc_final: 0.8426 (m-80) REVERT: B 315 GLU cc_start: 0.7465 (tt0) cc_final: 0.7229 (mt-10) REVERT: B 318 ASP cc_start: 0.6951 (t0) cc_final: 0.6733 (t0) REVERT: B 348 GLN cc_start: 0.7753 (OUTLIER) cc_final: 0.7123 (mp10) REVERT: B 351 LYS cc_start: 0.8468 (ttmm) cc_final: 0.8248 (tttt) REVERT: B 547 ASP cc_start: 0.7483 (p0) cc_final: 0.7274 (p0) REVERT: B 651 PHE cc_start: 0.8408 (m-80) cc_final: 0.8182 (m-80) REVERT: B 807 THR cc_start: 0.8491 (p) cc_final: 0.8221 (m) REVERT: B 918 LYS cc_start: 0.5864 (mptt) cc_final: 0.4728 (mppt) REVERT: B 1436 TYR cc_start: 0.8146 (t80) cc_final: 0.7920 (t80) REVERT: B 1491 ARG cc_start: 0.8085 (OUTLIER) cc_final: 0.6911 (ttt180) REVERT: B 1565 ASP cc_start: 0.7237 (t0) cc_final: 0.6941 (m-30) REVERT: B 1660 ASP cc_start: 0.6565 (m-30) cc_final: 0.6184 (m-30) REVERT: B 1665 LYS cc_start: 0.7978 (mtpt) cc_final: 0.7696 (mtpt) REVERT: B 1671 ASN cc_start: 0.6732 (p0) cc_final: 0.6498 (p0) REVERT: C 102 GLU cc_start: 0.6808 (tt0) cc_final: 0.6522 (tt0) REVERT: C 155 LYS cc_start: 0.6509 (tmmt) cc_final: 0.6222 (tmtt) REVERT: C 217 ASP cc_start: 0.6978 (t0) cc_final: 0.6769 (t0) REVERT: C 265 GLN cc_start: 0.7962 (tm-30) cc_final: 0.7749 (tp-100) REVERT: C 393 LEU cc_start: 0.8755 (mm) cc_final: 0.8451 (mt) REVERT: C 483 ASP cc_start: 0.7748 (m-30) cc_final: 0.7132 (m-30) outliers start: 79 outliers final: 29 residues processed: 410 average time/residue: 1.3766 time to fit residues: 624.4601 Evaluate side-chains 377 residues out of total 1725 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 346 time to evaluate : 1.947 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 25 ASP Chi-restraints excluded: chain B residue 56 SER Chi-restraints excluded: chain B residue 79 ASN Chi-restraints excluded: chain B residue 160 HIS Chi-restraints excluded: chain B residue 311 ILE Chi-restraints excluded: chain B residue 314 ASP Chi-restraints excluded: chain B residue 348 GLN Chi-restraints excluded: chain B residue 399 SER Chi-restraints excluded: chain B residue 426 THR Chi-restraints excluded: chain B residue 475 LEU Chi-restraints excluded: chain B residue 518 VAL Chi-restraints excluded: chain B residue 586 ASN Chi-restraints excluded: chain B residue 596 SER Chi-restraints excluded: chain B residue 711 ASN Chi-restraints excluded: chain B residue 714 ILE Chi-restraints excluded: chain B residue 763 GLU Chi-restraints excluded: chain B residue 788 ASP Chi-restraints excluded: chain B residue 931 SER Chi-restraints excluded: chain B residue 1458 VAL Chi-restraints excluded: chain B residue 1459 LEU Chi-restraints excluded: chain B residue 1491 ARG Chi-restraints excluded: chain B residue 1506 ASN Chi-restraints excluded: chain C residue 46 ASN Chi-restraints excluded: chain C residue 71 ILE Chi-restraints excluded: chain C residue 78 VAL Chi-restraints excluded: chain C residue 145 LEU Chi-restraints excluded: chain C residue 279 SER Chi-restraints excluded: chain C residue 413 MET Chi-restraints excluded: chain C residue 490 ASP Chi-restraints excluded: chain C residue 652 ILE Chi-restraints excluded: chain C residue 683 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 199 random chunks: chunk 100 optimal weight: 2.9990 chunk 56 optimal weight: 3.9990 chunk 150 optimal weight: 2.9990 chunk 123 optimal weight: 6.9990 chunk 49 optimal weight: 0.7980 chunk 181 optimal weight: 4.9990 chunk 195 optimal weight: 3.9990 chunk 161 optimal weight: 4.9990 chunk 179 optimal weight: 0.9990 chunk 61 optimal weight: 0.4980 chunk 145 optimal weight: 6.9990 overall best weight: 1.6586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 79 ASN B 112 GLN B 498 GLN B 673 GLN ** B 708 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 871 ASN B 908 HIS ** B 917 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 919 ASN B 924 HIS B1573 ASN B1584 GLN ** C 357 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 514 HIS C 642 HIS Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7605 moved from start: 0.2578 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 17384 Z= 0.330 Angle : 0.644 11.278 23673 Z= 0.334 Chirality : 0.045 0.209 2563 Planarity : 0.006 0.072 2873 Dihedral : 15.033 171.778 2888 Min Nonbonded Distance : 2.154 Molprobity Statistics. All-atom Clashscore : 5.55 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.95 % Favored : 94.00 % Rotamer: Outliers : 5.91 % Allowed : 22.03 % Favored : 72.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 (0.18), residues: 1951 helix: 1.17 (0.19), residues: 702 sheet: 0.51 (0.31), residues: 262 loop : -1.76 (0.17), residues: 987 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP C 278 HIS 0.011 0.002 HIS B 908 PHE 0.021 0.002 PHE B 546 TYR 0.019 0.002 TYR B 149 ARG 0.006 0.001 ARG C 260 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3902 Ramachandran restraints generated. 1951 Oldfield, 0 Emsley, 1951 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3902 Ramachandran restraints generated. 1951 Oldfield, 0 Emsley, 1951 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 468 residues out of total 1725 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 102 poor density : 366 time to evaluate : 1.979 Fit side-chains REVERT: B 55 LYS cc_start: 0.8192 (OUTLIER) cc_final: 0.7776 (ptpt) REVERT: B 56 SER cc_start: 0.8517 (OUTLIER) cc_final: 0.8242 (t) REVERT: B 91 SER cc_start: 0.8288 (p) cc_final: 0.7965 (t) REVERT: B 131 ILE cc_start: 0.8375 (pt) cc_final: 0.8152 (pt) REVERT: B 202 TYR cc_start: 0.8662 (m-80) cc_final: 0.8369 (m-80) REVERT: B 313 LYS cc_start: 0.8410 (mtpt) cc_final: 0.8174 (mtpp) REVERT: B 315 GLU cc_start: 0.7586 (tt0) cc_final: 0.7290 (mt-10) REVERT: B 318 ASP cc_start: 0.6984 (t0) cc_final: 0.6783 (t0) REVERT: B 348 GLN cc_start: 0.7816 (OUTLIER) cc_final: 0.6909 (mp10) REVERT: B 666 LYS cc_start: 0.8325 (OUTLIER) cc_final: 0.8036 (tttm) REVERT: B 836 LEU cc_start: 0.8101 (OUTLIER) cc_final: 0.7834 (mt) REVERT: B 918 LYS cc_start: 0.6167 (mptt) cc_final: 0.5084 (mppt) REVERT: B 1430 LYS cc_start: 0.8285 (mtmm) cc_final: 0.8063 (mttt) REVERT: B 1436 TYR cc_start: 0.8307 (t80) cc_final: 0.8024 (t80) REVERT: B 1444 ILE cc_start: 0.8241 (mm) cc_final: 0.7980 (mp) REVERT: B 1491 ARG cc_start: 0.8237 (OUTLIER) cc_final: 0.7170 (ttt180) REVERT: B 1666 LEU cc_start: 0.8675 (OUTLIER) cc_final: 0.8390 (mp) REVERT: C 102 GLU cc_start: 0.6771 (tt0) cc_final: 0.6476 (tt0) REVERT: C 151 GLU cc_start: 0.6912 (OUTLIER) cc_final: 0.6598 (mp0) REVERT: C 217 ASP cc_start: 0.7045 (t0) cc_final: 0.6831 (t0) REVERT: C 318 ASP cc_start: 0.7455 (t70) cc_final: 0.7254 (t0) REVERT: C 393 LEU cc_start: 0.8765 (mm) cc_final: 0.8554 (mt) REVERT: C 483 ASP cc_start: 0.7825 (OUTLIER) cc_final: 0.7196 (m-30) outliers start: 102 outliers final: 52 residues processed: 420 average time/residue: 1.3180 time to fit residues: 613.4248 Evaluate side-chains 413 residues out of total 1725 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 352 time to evaluate : 1.843 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 25 ASP Chi-restraints excluded: chain B residue 27 ASP Chi-restraints excluded: chain B residue 55 LYS Chi-restraints excluded: chain B residue 56 SER Chi-restraints excluded: chain B residue 74 LEU Chi-restraints excluded: chain B residue 79 ASN Chi-restraints excluded: chain B residue 190 ASP Chi-restraints excluded: chain B residue 201 THR Chi-restraints excluded: chain B residue 314 ASP Chi-restraints excluded: chain B residue 348 GLN Chi-restraints excluded: chain B residue 399 SER Chi-restraints excluded: chain B residue 413 THR Chi-restraints excluded: chain B residue 426 THR Chi-restraints excluded: chain B residue 475 LEU Chi-restraints excluded: chain B residue 518 VAL Chi-restraints excluded: chain B residue 580 GLU Chi-restraints excluded: chain B residue 586 ASN Chi-restraints excluded: chain B residue 605 LYS Chi-restraints excluded: chain B residue 612 TRP Chi-restraints excluded: chain B residue 666 LYS Chi-restraints excluded: chain B residue 711 ASN Chi-restraints excluded: chain B residue 714 ILE Chi-restraints excluded: chain B residue 763 GLU Chi-restraints excluded: chain B residue 778 ASN Chi-restraints excluded: chain B residue 788 ASP Chi-restraints excluded: chain B residue 836 LEU Chi-restraints excluded: chain B residue 858 VAL Chi-restraints excluded: chain B residue 866 ILE Chi-restraints excluded: chain B residue 929 SER Chi-restraints excluded: chain B residue 931 SER Chi-restraints excluded: chain B residue 969 THR Chi-restraints excluded: chain B residue 975 LEU Chi-restraints excluded: chain B residue 986 ASN Chi-restraints excluded: chain B residue 1411 ASP Chi-restraints excluded: chain B residue 1445 THR Chi-restraints excluded: chain B residue 1454 LEU Chi-restraints excluded: chain B residue 1458 VAL Chi-restraints excluded: chain B residue 1474 GLU Chi-restraints excluded: chain B residue 1491 ARG Chi-restraints excluded: chain B residue 1506 ASN Chi-restraints excluded: chain B residue 1573 ASN Chi-restraints excluded: chain B residue 1643 VAL Chi-restraints excluded: chain B residue 1666 LEU Chi-restraints excluded: chain B residue 1672 LEU Chi-restraints excluded: chain C residue 42 LYS Chi-restraints excluded: chain C residue 46 ASN Chi-restraints excluded: chain C residue 145 LEU Chi-restraints excluded: chain C residue 151 GLU Chi-restraints excluded: chain C residue 195 ASP Chi-restraints excluded: chain C residue 246 ASP Chi-restraints excluded: chain C residue 258 THR Chi-restraints excluded: chain C residue 279 SER Chi-restraints excluded: chain C residue 287 MET Chi-restraints excluded: chain C residue 413 MET Chi-restraints excluded: chain C residue 475 ASP Chi-restraints excluded: chain C residue 483 ASP Chi-restraints excluded: chain C residue 517 CYS Chi-restraints excluded: chain C residue 563 ASP Chi-restraints excluded: chain C residue 652 ILE Chi-restraints excluded: chain C residue 698 ASP Chi-restraints excluded: chain C residue 699 HIS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 199 random chunks: chunk 178 optimal weight: 5.9990 chunk 136 optimal weight: 3.9990 chunk 93 optimal weight: 0.6980 chunk 20 optimal weight: 0.9990 chunk 86 optimal weight: 0.9990 chunk 121 optimal weight: 2.9990 chunk 181 optimal weight: 5.9990 chunk 192 optimal weight: 3.9990 chunk 94 optimal weight: 0.9980 chunk 172 optimal weight: 1.9990 chunk 51 optimal weight: 3.9990 overall best weight: 1.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 348 GLN B 498 GLN ** B 708 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 908 HIS ** B 917 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 919 ASN B1596 GLN ** C 357 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 448 ASN C 541 ASN C 642 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7586 moved from start: 0.2758 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 17384 Z= 0.241 Angle : 0.581 10.869 23673 Z= 0.304 Chirality : 0.043 0.196 2563 Planarity : 0.005 0.067 2873 Dihedral : 14.957 172.692 2884 Min Nonbonded Distance : 2.171 Molprobity Statistics. All-atom Clashscore : 5.64 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.48 % Favored : 94.46 % Rotamer: Outliers : 5.22 % Allowed : 24.29 % Favored : 70.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 (0.18), residues: 1951 helix: 1.48 (0.20), residues: 702 sheet: 0.57 (0.31), residues: 261 loop : -1.69 (0.17), residues: 988 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B1530 HIS 0.013 0.001 HIS B 908 PHE 0.015 0.001 PHE B 546 TYR 0.016 0.001 TYR C 607 ARG 0.005 0.000 ARG B1644 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3902 Ramachandran restraints generated. 1951 Oldfield, 0 Emsley, 1951 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3902 Ramachandran restraints generated. 1951 Oldfield, 0 Emsley, 1951 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 438 residues out of total 1725 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 90 poor density : 348 time to evaluate : 2.053 Fit side-chains REVERT: B 7 ASN cc_start: 0.7251 (OUTLIER) cc_final: 0.6979 (m110) REVERT: B 56 SER cc_start: 0.8518 (OUTLIER) cc_final: 0.8271 (t) REVERT: B 91 SER cc_start: 0.8258 (p) cc_final: 0.7954 (t) REVERT: B 202 TYR cc_start: 0.8620 (m-80) cc_final: 0.8306 (m-80) REVERT: B 313 LYS cc_start: 0.8376 (mtpt) cc_final: 0.8143 (mtpp) REVERT: B 318 ASP cc_start: 0.6936 (t0) cc_final: 0.6726 (t0) REVERT: B 666 LYS cc_start: 0.8295 (OUTLIER) cc_final: 0.8000 (tttm) REVERT: B 687 THR cc_start: 0.7714 (m) cc_final: 0.7390 (p) REVERT: B 836 LEU cc_start: 0.8087 (OUTLIER) cc_final: 0.7796 (mt) REVERT: B 918 LYS cc_start: 0.6094 (mptt) cc_final: 0.4994 (mppt) REVERT: B 1430 LYS cc_start: 0.8266 (mtmm) cc_final: 0.8044 (mttt) REVERT: B 1436 TYR cc_start: 0.8268 (t80) cc_final: 0.8002 (t80) REVERT: B 1444 ILE cc_start: 0.8227 (mm) cc_final: 0.7965 (mp) REVERT: B 1491 ARG cc_start: 0.8195 (OUTLIER) cc_final: 0.7040 (ttt180) REVERT: B 1666 LEU cc_start: 0.8679 (OUTLIER) cc_final: 0.8420 (mp) REVERT: B 1671 ASN cc_start: 0.7476 (OUTLIER) cc_final: 0.7263 (p0) REVERT: C 102 GLU cc_start: 0.6747 (tt0) cc_final: 0.6467 (mt-10) REVERT: C 151 GLU cc_start: 0.6936 (OUTLIER) cc_final: 0.6657 (mp0) REVERT: C 197 GLN cc_start: 0.8636 (OUTLIER) cc_final: 0.7322 (mt0) REVERT: C 209 ASP cc_start: 0.7638 (OUTLIER) cc_final: 0.7318 (m-30) REVERT: C 217 ASP cc_start: 0.6989 (t0) cc_final: 0.6785 (t0) REVERT: C 483 ASP cc_start: 0.7803 (m-30) cc_final: 0.7157 (m-30) outliers start: 90 outliers final: 54 residues processed: 395 average time/residue: 1.4103 time to fit residues: 615.1141 Evaluate side-chains 399 residues out of total 1725 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 335 time to evaluate : 1.893 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 7 ASN Chi-restraints excluded: chain B residue 25 ASP Chi-restraints excluded: chain B residue 56 SER Chi-restraints excluded: chain B residue 74 LEU Chi-restraints excluded: chain B residue 79 ASN Chi-restraints excluded: chain B residue 190 ASP Chi-restraints excluded: chain B residue 201 THR Chi-restraints excluded: chain B residue 314 ASP Chi-restraints excluded: chain B residue 349 SER Chi-restraints excluded: chain B residue 413 THR Chi-restraints excluded: chain B residue 426 THR Chi-restraints excluded: chain B residue 444 LYS Chi-restraints excluded: chain B residue 475 LEU Chi-restraints excluded: chain B residue 518 VAL Chi-restraints excluded: chain B residue 553 GLU Chi-restraints excluded: chain B residue 586 ASN Chi-restraints excluded: chain B residue 596 SER Chi-restraints excluded: chain B residue 605 LYS Chi-restraints excluded: chain B residue 666 LYS Chi-restraints excluded: chain B residue 711 ASN Chi-restraints excluded: chain B residue 763 GLU Chi-restraints excluded: chain B residue 778 ASN Chi-restraints excluded: chain B residue 788 ASP Chi-restraints excluded: chain B residue 826 ILE Chi-restraints excluded: chain B residue 830 PHE Chi-restraints excluded: chain B residue 836 LEU Chi-restraints excluded: chain B residue 858 VAL Chi-restraints excluded: chain B residue 866 ILE Chi-restraints excluded: chain B residue 969 THR Chi-restraints excluded: chain B residue 975 LEU Chi-restraints excluded: chain B residue 1454 LEU Chi-restraints excluded: chain B residue 1458 VAL Chi-restraints excluded: chain B residue 1468 ILE Chi-restraints excluded: chain B residue 1474 GLU Chi-restraints excluded: chain B residue 1491 ARG Chi-restraints excluded: chain B residue 1497 ILE Chi-restraints excluded: chain B residue 1506 ASN Chi-restraints excluded: chain B residue 1643 VAL Chi-restraints excluded: chain B residue 1647 VAL Chi-restraints excluded: chain B residue 1656 ILE Chi-restraints excluded: chain B residue 1666 LEU Chi-restraints excluded: chain B residue 1671 ASN Chi-restraints excluded: chain B residue 1679 LYS Chi-restraints excluded: chain C residue 42 LYS Chi-restraints excluded: chain C residue 46 ASN Chi-restraints excluded: chain C residue 145 LEU Chi-restraints excluded: chain C residue 151 GLU Chi-restraints excluded: chain C residue 179 ASP Chi-restraints excluded: chain C residue 195 ASP Chi-restraints excluded: chain C residue 197 GLN Chi-restraints excluded: chain C residue 209 ASP Chi-restraints excluded: chain C residue 246 ASP Chi-restraints excluded: chain C residue 258 THR Chi-restraints excluded: chain C residue 267 LYS Chi-restraints excluded: chain C residue 279 SER Chi-restraints excluded: chain C residue 287 MET Chi-restraints excluded: chain C residue 334 MET Chi-restraints excluded: chain C residue 391 LEU Chi-restraints excluded: chain C residue 475 ASP Chi-restraints excluded: chain C residue 490 ASP Chi-restraints excluded: chain C residue 517 CYS Chi-restraints excluded: chain C residue 555 ILE Chi-restraints excluded: chain C residue 563 ASP Chi-restraints excluded: chain C residue 698 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 199 random chunks: chunk 160 optimal weight: 8.9990 chunk 109 optimal weight: 0.0980 chunk 2 optimal weight: 2.9990 chunk 143 optimal weight: 4.9990 chunk 79 optimal weight: 0.6980 chunk 164 optimal weight: 0.9990 chunk 132 optimal weight: 5.9990 chunk 0 optimal weight: 4.9990 chunk 98 optimal weight: 2.9990 chunk 172 optimal weight: 0.8980 chunk 48 optimal weight: 0.9990 overall best weight: 0.7384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 79 ASN ** B 116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 348 GLN B 498 GLN B 615 ASN B 908 HIS ** B 917 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 919 ASN B1596 GLN C 295 GLN ** C 357 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 541 ASN C 642 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7563 moved from start: 0.2884 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 17384 Z= 0.184 Angle : 0.544 12.489 23673 Z= 0.283 Chirality : 0.041 0.192 2563 Planarity : 0.005 0.066 2873 Dihedral : 14.856 173.531 2884 Min Nonbonded Distance : 2.185 Molprobity Statistics. All-atom Clashscore : 5.97 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.54 % Favored : 94.41 % Rotamer: Outliers : 5.45 % Allowed : 24.75 % Favored : 69.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.05 (0.18), residues: 1951 helix: 1.72 (0.20), residues: 702 sheet: 0.53 (0.31), residues: 265 loop : -1.59 (0.17), residues: 984 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 443 HIS 0.013 0.001 HIS B 908 PHE 0.013 0.001 PHE B 824 TYR 0.014 0.001 TYR C 607 ARG 0.005 0.000 ARG B1644 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3902 Ramachandran restraints generated. 1951 Oldfield, 0 Emsley, 1951 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3902 Ramachandran restraints generated. 1951 Oldfield, 0 Emsley, 1951 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 437 residues out of total 1725 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 94 poor density : 343 time to evaluate : 1.968 Fit side-chains REVERT: B 7 ASN cc_start: 0.7242 (OUTLIER) cc_final: 0.7006 (m110) REVERT: B 55 LYS cc_start: 0.8158 (OUTLIER) cc_final: 0.7800 (ptpt) REVERT: B 56 SER cc_start: 0.8532 (OUTLIER) cc_final: 0.8276 (t) REVERT: B 91 SER cc_start: 0.8235 (p) cc_final: 0.7954 (t) REVERT: B 174 SER cc_start: 0.8356 (m) cc_final: 0.8136 (t) REVERT: B 202 TYR cc_start: 0.8608 (m-80) cc_final: 0.8301 (m-80) REVERT: B 315 GLU cc_start: 0.7580 (tt0) cc_final: 0.7368 (mt-10) REVERT: B 318 ASP cc_start: 0.6942 (t0) cc_final: 0.6717 (t0) REVERT: B 452 ILE cc_start: 0.7995 (OUTLIER) cc_final: 0.7372 (pp) REVERT: B 666 LYS cc_start: 0.8269 (OUTLIER) cc_final: 0.7961 (tttm) REVERT: B 788 ASP cc_start: 0.7633 (OUTLIER) cc_final: 0.7423 (p0) REVERT: B 918 LYS cc_start: 0.6079 (mptt) cc_final: 0.4963 (mppt) REVERT: B 1430 LYS cc_start: 0.8255 (mtmm) cc_final: 0.8038 (mttt) REVERT: B 1444 ILE cc_start: 0.8188 (mm) cc_final: 0.7956 (mp) REVERT: B 1458 VAL cc_start: 0.8228 (OUTLIER) cc_final: 0.8014 (t) REVERT: B 1491 ARG cc_start: 0.8203 (OUTLIER) cc_final: 0.7997 (ttp-170) REVERT: B 1668 ASP cc_start: 0.5037 (OUTLIER) cc_final: 0.4741 (t70) REVERT: C 102 GLU cc_start: 0.6710 (tt0) cc_final: 0.6446 (mt-10) REVERT: C 151 GLU cc_start: 0.6909 (OUTLIER) cc_final: 0.6653 (mp0) REVERT: C 209 ASP cc_start: 0.7622 (OUTLIER) cc_final: 0.7214 (m-30) REVERT: C 224 LYS cc_start: 0.8104 (OUTLIER) cc_final: 0.7735 (tmmm) REVERT: C 234 ASP cc_start: 0.6945 (t70) cc_final: 0.6543 (t0) REVERT: C 424 ASN cc_start: 0.8146 (t0) cc_final: 0.7801 (t0) REVERT: C 483 ASP cc_start: 0.7782 (OUTLIER) cc_final: 0.7135 (m-30) outliers start: 94 outliers final: 46 residues processed: 400 average time/residue: 1.3692 time to fit residues: 605.4717 Evaluate side-chains 395 residues out of total 1725 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 336 time to evaluate : 1.964 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 7 ASN Chi-restraints excluded: chain B residue 25 ASP Chi-restraints excluded: chain B residue 55 LYS Chi-restraints excluded: chain B residue 56 SER Chi-restraints excluded: chain B residue 74 LEU Chi-restraints excluded: chain B residue 85 VAL Chi-restraints excluded: chain B residue 190 ASP Chi-restraints excluded: chain B residue 201 THR Chi-restraints excluded: chain B residue 314 ASP Chi-restraints excluded: chain B residue 349 SER Chi-restraints excluded: chain B residue 413 THR Chi-restraints excluded: chain B residue 426 THR Chi-restraints excluded: chain B residue 452 ILE Chi-restraints excluded: chain B residue 475 LEU Chi-restraints excluded: chain B residue 518 VAL Chi-restraints excluded: chain B residue 553 GLU Chi-restraints excluded: chain B residue 581 GLU Chi-restraints excluded: chain B residue 586 ASN Chi-restraints excluded: chain B residue 666 LYS Chi-restraints excluded: chain B residue 711 ASN Chi-restraints excluded: chain B residue 763 GLU Chi-restraints excluded: chain B residue 788 ASP Chi-restraints excluded: chain B residue 826 ILE Chi-restraints excluded: chain B residue 858 VAL Chi-restraints excluded: chain B residue 866 ILE Chi-restraints excluded: chain B residue 969 THR Chi-restraints excluded: chain B residue 975 LEU Chi-restraints excluded: chain B residue 1454 LEU Chi-restraints excluded: chain B residue 1458 VAL Chi-restraints excluded: chain B residue 1471 ASP Chi-restraints excluded: chain B residue 1474 GLU Chi-restraints excluded: chain B residue 1491 ARG Chi-restraints excluded: chain B residue 1497 ILE Chi-restraints excluded: chain B residue 1506 ASN Chi-restraints excluded: chain B residue 1599 ILE Chi-restraints excluded: chain B residue 1643 VAL Chi-restraints excluded: chain B residue 1647 VAL Chi-restraints excluded: chain B residue 1656 ILE Chi-restraints excluded: chain B residue 1668 ASP Chi-restraints excluded: chain B residue 1672 LEU Chi-restraints excluded: chain B residue 1679 LYS Chi-restraints excluded: chain C residue 46 ASN Chi-restraints excluded: chain C residue 145 LEU Chi-restraints excluded: chain C residue 151 GLU Chi-restraints excluded: chain C residue 195 ASP Chi-restraints excluded: chain C residue 209 ASP Chi-restraints excluded: chain C residue 224 LYS Chi-restraints excluded: chain C residue 246 ASP Chi-restraints excluded: chain C residue 258 THR Chi-restraints excluded: chain C residue 279 SER Chi-restraints excluded: chain C residue 334 MET Chi-restraints excluded: chain C residue 475 ASP Chi-restraints excluded: chain C residue 483 ASP Chi-restraints excluded: chain C residue 490 ASP Chi-restraints excluded: chain C residue 517 CYS Chi-restraints excluded: chain C residue 563 ASP Chi-restraints excluded: chain C residue 652 ILE Chi-restraints excluded: chain C residue 683 LYS Chi-restraints excluded: chain C residue 699 HIS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 199 random chunks: chunk 64 optimal weight: 3.9990 chunk 173 optimal weight: 0.6980 chunk 38 optimal weight: 0.8980 chunk 112 optimal weight: 4.9990 chunk 47 optimal weight: 5.9990 chunk 192 optimal weight: 2.9990 chunk 159 optimal weight: 4.9990 chunk 89 optimal weight: 4.9990 chunk 16 optimal weight: 0.9990 chunk 63 optimal weight: 0.8980 chunk 101 optimal weight: 0.8980 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 79 ASN ** B 116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 348 GLN B 615 ASN B 908 HIS ** B 917 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 919 ASN B1573 ASN B1596 GLN C 295 GLN ** C 357 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 541 ASN C 642 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7566 moved from start: 0.2987 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 17384 Z= 0.202 Angle : 0.560 12.475 23673 Z= 0.289 Chirality : 0.041 0.153 2563 Planarity : 0.005 0.066 2873 Dihedral : 14.821 173.469 2884 Min Nonbonded Distance : 2.173 Molprobity Statistics. All-atom Clashscore : 6.03 Ramachandran Plot: Outliers : 0.10 % Allowed : 5.38 % Favored : 94.52 % Rotamer: Outliers : 5.22 % Allowed : 25.16 % Favored : 69.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.05 (0.18), residues: 1951 helix: 1.84 (0.20), residues: 696 sheet: 0.58 (0.31), residues: 265 loop : -1.55 (0.17), residues: 990 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 443 HIS 0.016 0.001 HIS B 908 PHE 0.013 0.001 PHE B 546 TYR 0.015 0.001 TYR C 607 ARG 0.006 0.000 ARG B1644 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3902 Ramachandran restraints generated. 1951 Oldfield, 0 Emsley, 1951 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3902 Ramachandran restraints generated. 1951 Oldfield, 0 Emsley, 1951 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 430 residues out of total 1725 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 90 poor density : 340 time to evaluate : 1.880 Fit side-chains REVERT: B 7 ASN cc_start: 0.7253 (OUTLIER) cc_final: 0.7000 (m110) REVERT: B 55 LYS cc_start: 0.8164 (OUTLIER) cc_final: 0.7816 (ptpt) REVERT: B 56 SER cc_start: 0.8533 (OUTLIER) cc_final: 0.8274 (t) REVERT: B 91 SER cc_start: 0.8213 (p) cc_final: 0.7955 (t) REVERT: B 123 LYS cc_start: 0.7871 (tttm) cc_final: 0.7642 (ttpt) REVERT: B 174 SER cc_start: 0.8362 (m) cc_final: 0.8140 (t) REVERT: B 202 TYR cc_start: 0.8613 (m-80) cc_final: 0.8340 (m-80) REVERT: B 315 GLU cc_start: 0.7596 (tt0) cc_final: 0.7375 (mt-10) REVERT: B 318 ASP cc_start: 0.6934 (t0) cc_final: 0.6731 (t0) REVERT: B 452 ILE cc_start: 0.7994 (OUTLIER) cc_final: 0.7525 (mt) REVERT: B 666 LYS cc_start: 0.8266 (OUTLIER) cc_final: 0.7950 (tttm) REVERT: B 788 ASP cc_start: 0.7631 (OUTLIER) cc_final: 0.7428 (p0) REVERT: B 801 ASP cc_start: 0.6726 (OUTLIER) cc_final: 0.6513 (t70) REVERT: B 918 LYS cc_start: 0.6032 (mptt) cc_final: 0.4928 (mppt) REVERT: B 1430 LYS cc_start: 0.8254 (mtmm) cc_final: 0.8033 (mttt) REVERT: B 1444 ILE cc_start: 0.8216 (mm) cc_final: 0.7973 (mp) REVERT: B 1491 ARG cc_start: 0.8175 (OUTLIER) cc_final: 0.7048 (ttt180) REVERT: B 1666 LEU cc_start: 0.8630 (OUTLIER) cc_final: 0.8298 (mp) REVERT: B 1668 ASP cc_start: 0.5079 (OUTLIER) cc_final: 0.4762 (t70) REVERT: C 102 GLU cc_start: 0.6721 (tt0) cc_final: 0.6453 (mt-10) REVERT: C 151 GLU cc_start: 0.6904 (OUTLIER) cc_final: 0.6636 (mp0) REVERT: C 197 GLN cc_start: 0.8621 (OUTLIER) cc_final: 0.7524 (mt0) REVERT: C 224 LYS cc_start: 0.8108 (OUTLIER) cc_final: 0.7721 (tmmm) REVERT: C 472 LEU cc_start: 0.7860 (OUTLIER) cc_final: 0.7653 (pp) REVERT: C 483 ASP cc_start: 0.7788 (OUTLIER) cc_final: 0.7109 (m-30) outliers start: 90 outliers final: 54 residues processed: 385 average time/residue: 1.4179 time to fit residues: 604.5167 Evaluate side-chains 402 residues out of total 1725 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 333 time to evaluate : 1.854 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 7 ASN Chi-restraints excluded: chain B residue 25 ASP Chi-restraints excluded: chain B residue 55 LYS Chi-restraints excluded: chain B residue 56 SER Chi-restraints excluded: chain B residue 74 LEU Chi-restraints excluded: chain B residue 85 VAL Chi-restraints excluded: chain B residue 190 ASP Chi-restraints excluded: chain B residue 201 THR Chi-restraints excluded: chain B residue 314 ASP Chi-restraints excluded: chain B residue 349 SER Chi-restraints excluded: chain B residue 413 THR Chi-restraints excluded: chain B residue 426 THR Chi-restraints excluded: chain B residue 452 ILE Chi-restraints excluded: chain B residue 475 LEU Chi-restraints excluded: chain B residue 518 VAL Chi-restraints excluded: chain B residue 553 GLU Chi-restraints excluded: chain B residue 581 GLU Chi-restraints excluded: chain B residue 586 ASN Chi-restraints excluded: chain B residue 605 LYS Chi-restraints excluded: chain B residue 666 LYS Chi-restraints excluded: chain B residue 711 ASN Chi-restraints excluded: chain B residue 763 GLU Chi-restraints excluded: chain B residue 788 ASP Chi-restraints excluded: chain B residue 801 ASP Chi-restraints excluded: chain B residue 826 ILE Chi-restraints excluded: chain B residue 858 VAL Chi-restraints excluded: chain B residue 866 ILE Chi-restraints excluded: chain B residue 969 THR Chi-restraints excluded: chain B residue 975 LEU Chi-restraints excluded: chain B residue 986 ASN Chi-restraints excluded: chain B residue 1468 ILE Chi-restraints excluded: chain B residue 1474 GLU Chi-restraints excluded: chain B residue 1491 ARG Chi-restraints excluded: chain B residue 1497 ILE Chi-restraints excluded: chain B residue 1506 ASN Chi-restraints excluded: chain B residue 1514 LYS Chi-restraints excluded: chain B residue 1573 ASN Chi-restraints excluded: chain B residue 1643 VAL Chi-restraints excluded: chain B residue 1647 VAL Chi-restraints excluded: chain B residue 1656 ILE Chi-restraints excluded: chain B residue 1666 LEU Chi-restraints excluded: chain B residue 1668 ASP Chi-restraints excluded: chain B residue 1672 LEU Chi-restraints excluded: chain B residue 1679 LYS Chi-restraints excluded: chain C residue 46 ASN Chi-restraints excluded: chain C residue 145 LEU Chi-restraints excluded: chain C residue 148 LEU Chi-restraints excluded: chain C residue 151 GLU Chi-restraints excluded: chain C residue 173 LEU Chi-restraints excluded: chain C residue 195 ASP Chi-restraints excluded: chain C residue 197 GLN Chi-restraints excluded: chain C residue 224 LYS Chi-restraints excluded: chain C residue 246 ASP Chi-restraints excluded: chain C residue 258 THR Chi-restraints excluded: chain C residue 279 SER Chi-restraints excluded: chain C residue 287 MET Chi-restraints excluded: chain C residue 334 MET Chi-restraints excluded: chain C residue 350 ASP Chi-restraints excluded: chain C residue 391 LEU Chi-restraints excluded: chain C residue 396 VAL Chi-restraints excluded: chain C residue 472 LEU Chi-restraints excluded: chain C residue 475 ASP Chi-restraints excluded: chain C residue 483 ASP Chi-restraints excluded: chain C residue 490 ASP Chi-restraints excluded: chain C residue 517 CYS Chi-restraints excluded: chain C residue 563 ASP Chi-restraints excluded: chain C residue 683 LYS Chi-restraints excluded: chain C residue 685 ASN Chi-restraints excluded: chain C residue 699 HIS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 199 random chunks: chunk 185 optimal weight: 0.6980 chunk 21 optimal weight: 3.9990 chunk 109 optimal weight: 0.0870 chunk 140 optimal weight: 4.9990 chunk 108 optimal weight: 1.9990 chunk 162 optimal weight: 4.9990 chunk 107 optimal weight: 0.8980 chunk 191 optimal weight: 2.9990 chunk 120 optimal weight: 0.0970 chunk 116 optimal weight: 0.8980 chunk 88 optimal weight: 0.8980 overall best weight: 0.5356 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 79 ASN ** B 116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 498 GLN B 615 ASN ** B 908 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 917 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 919 ASN B1596 GLN ** C 357 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 415 ASN C 541 ASN C 642 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7539 moved from start: 0.3092 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 17384 Z= 0.154 Angle : 0.531 12.711 23673 Z= 0.274 Chirality : 0.040 0.158 2563 Planarity : 0.004 0.064 2873 Dihedral : 14.735 174.398 2883 Min Nonbonded Distance : 2.186 Molprobity Statistics. All-atom Clashscore : 5.70 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.13 % Favored : 94.82 % Rotamer: Outliers : 5.16 % Allowed : 25.28 % Favored : 69.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.19 (0.18), residues: 1951 helix: 1.95 (0.20), residues: 701 sheet: 0.65 (0.31), residues: 265 loop : -1.47 (0.17), residues: 985 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 443 HIS 0.014 0.001 HIS B 908 PHE 0.014 0.001 PHE C 254 TYR 0.013 0.001 TYR C 607 ARG 0.007 0.000 ARG C 260 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3902 Ramachandran restraints generated. 1951 Oldfield, 0 Emsley, 1951 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3902 Ramachandran restraints generated. 1951 Oldfield, 0 Emsley, 1951 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 428 residues out of total 1725 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 89 poor density : 339 time to evaluate : 1.988 Fit side-chains REVERT: B 7 ASN cc_start: 0.7226 (OUTLIER) cc_final: 0.6989 (m110) REVERT: B 15 PHE cc_start: 0.8631 (m-80) cc_final: 0.8257 (m-80) REVERT: B 55 LYS cc_start: 0.8139 (OUTLIER) cc_final: 0.7798 (ptpt) REVERT: B 56 SER cc_start: 0.8536 (OUTLIER) cc_final: 0.8278 (t) REVERT: B 91 SER cc_start: 0.8201 (p) cc_final: 0.7935 (t) REVERT: B 123 LYS cc_start: 0.7849 (tttm) cc_final: 0.7615 (ttpt) REVERT: B 132 LEU cc_start: 0.8724 (OUTLIER) cc_final: 0.8520 (mt) REVERT: B 174 SER cc_start: 0.8334 (m) cc_final: 0.8112 (t) REVERT: B 202 TYR cc_start: 0.8594 (m-80) cc_final: 0.8307 (m-80) REVERT: B 315 GLU cc_start: 0.7609 (tt0) cc_final: 0.7347 (mt-10) REVERT: B 452 ILE cc_start: 0.7948 (OUTLIER) cc_final: 0.7329 (pp) REVERT: B 666 LYS cc_start: 0.8236 (OUTLIER) cc_final: 0.7894 (tttm) REVERT: B 705 ARG cc_start: 0.7514 (OUTLIER) cc_final: 0.7287 (ttp-170) REVERT: B 801 ASP cc_start: 0.6702 (OUTLIER) cc_final: 0.6468 (t70) REVERT: B 918 LYS cc_start: 0.5980 (mptt) cc_final: 0.5290 (mppt) REVERT: B 1430 LYS cc_start: 0.8242 (mtmm) cc_final: 0.8020 (mttt) REVERT: B 1444 ILE cc_start: 0.8184 (mm) cc_final: 0.7979 (mp) REVERT: B 1668 ASP cc_start: 0.5159 (OUTLIER) cc_final: 0.4875 (t70) REVERT: C 102 GLU cc_start: 0.6696 (tt0) cc_final: 0.6443 (mt-10) REVERT: C 151 GLU cc_start: 0.6905 (OUTLIER) cc_final: 0.6599 (mp0) REVERT: C 224 LYS cc_start: 0.8051 (OUTLIER) cc_final: 0.7702 (tmmm) REVERT: C 234 ASP cc_start: 0.6915 (t70) cc_final: 0.6530 (t0) REVERT: C 318 ASP cc_start: 0.7388 (t0) cc_final: 0.7161 (t70) REVERT: C 483 ASP cc_start: 0.7768 (OUTLIER) cc_final: 0.7062 (m-30) outliers start: 89 outliers final: 51 residues processed: 385 average time/residue: 1.3804 time to fit residues: 586.6580 Evaluate side-chains 401 residues out of total 1725 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 338 time to evaluate : 1.743 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 7 ASN Chi-restraints excluded: chain B residue 25 ASP Chi-restraints excluded: chain B residue 55 LYS Chi-restraints excluded: chain B residue 56 SER Chi-restraints excluded: chain B residue 74 LEU Chi-restraints excluded: chain B residue 85 VAL Chi-restraints excluded: chain B residue 132 LEU Chi-restraints excluded: chain B residue 190 ASP Chi-restraints excluded: chain B residue 201 THR Chi-restraints excluded: chain B residue 314 ASP Chi-restraints excluded: chain B residue 349 SER Chi-restraints excluded: chain B residue 426 THR Chi-restraints excluded: chain B residue 444 LYS Chi-restraints excluded: chain B residue 452 ILE Chi-restraints excluded: chain B residue 464 LYS Chi-restraints excluded: chain B residue 553 GLU Chi-restraints excluded: chain B residue 581 GLU Chi-restraints excluded: chain B residue 596 SER Chi-restraints excluded: chain B residue 605 LYS Chi-restraints excluded: chain B residue 666 LYS Chi-restraints excluded: chain B residue 705 ARG Chi-restraints excluded: chain B residue 711 ASN Chi-restraints excluded: chain B residue 763 GLU Chi-restraints excluded: chain B residue 778 ASN Chi-restraints excluded: chain B residue 801 ASP Chi-restraints excluded: chain B residue 826 ILE Chi-restraints excluded: chain B residue 858 VAL Chi-restraints excluded: chain B residue 866 ILE Chi-restraints excluded: chain B residue 969 THR Chi-restraints excluded: chain B residue 975 LEU Chi-restraints excluded: chain B residue 986 ASN Chi-restraints excluded: chain B residue 1474 GLU Chi-restraints excluded: chain B residue 1497 ILE Chi-restraints excluded: chain B residue 1506 ASN Chi-restraints excluded: chain B residue 1509 THR Chi-restraints excluded: chain B residue 1599 ILE Chi-restraints excluded: chain B residue 1643 VAL Chi-restraints excluded: chain B residue 1647 VAL Chi-restraints excluded: chain B residue 1656 ILE Chi-restraints excluded: chain B residue 1668 ASP Chi-restraints excluded: chain B residue 1672 LEU Chi-restraints excluded: chain B residue 1679 LYS Chi-restraints excluded: chain C residue 46 ASN Chi-restraints excluded: chain C residue 145 LEU Chi-restraints excluded: chain C residue 148 LEU Chi-restraints excluded: chain C residue 151 GLU Chi-restraints excluded: chain C residue 195 ASP Chi-restraints excluded: chain C residue 224 LYS Chi-restraints excluded: chain C residue 246 ASP Chi-restraints excluded: chain C residue 279 SER Chi-restraints excluded: chain C residue 287 MET Chi-restraints excluded: chain C residue 334 MET Chi-restraints excluded: chain C residue 350 ASP Chi-restraints excluded: chain C residue 391 LEU Chi-restraints excluded: chain C residue 396 VAL Chi-restraints excluded: chain C residue 475 ASP Chi-restraints excluded: chain C residue 483 ASP Chi-restraints excluded: chain C residue 517 CYS Chi-restraints excluded: chain C residue 652 ILE Chi-restraints excluded: chain C residue 663 LYS Chi-restraints excluded: chain C residue 683 LYS Chi-restraints excluded: chain C residue 685 ASN Chi-restraints excluded: chain C residue 699 HIS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 199 random chunks: chunk 118 optimal weight: 1.9990 chunk 76 optimal weight: 0.8980 chunk 114 optimal weight: 2.9990 chunk 57 optimal weight: 2.9990 chunk 37 optimal weight: 0.0570 chunk 121 optimal weight: 0.9980 chunk 130 optimal weight: 0.5980 chunk 94 optimal weight: 0.3980 chunk 17 optimal weight: 1.9990 chunk 150 optimal weight: 3.9990 chunk 174 optimal weight: 3.9990 overall best weight: 0.5898 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 79 ASN B 348 GLN B 434 GLN B 498 GLN B 534 ASN ** B 908 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 917 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 919 ASN B1596 GLN C 357 GLN C 541 ASN C 642 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7539 moved from start: 0.3178 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 17384 Z= 0.164 Angle : 0.543 12.540 23673 Z= 0.279 Chirality : 0.040 0.155 2563 Planarity : 0.004 0.063 2873 Dihedral : 14.704 174.232 2883 Min Nonbonded Distance : 2.193 Molprobity Statistics. All-atom Clashscore : 6.09 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.38 % Favored : 94.57 % Rotamer: Outliers : 4.81 % Allowed : 25.86 % Favored : 69.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.24 (0.18), residues: 1951 helix: 1.99 (0.20), residues: 703 sheet: 0.64 (0.31), residues: 265 loop : -1.43 (0.17), residues: 983 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 443 HIS 0.017 0.001 HIS B 908 PHE 0.013 0.001 PHE B 824 TYR 0.013 0.001 TYR C 607 ARG 0.008 0.000 ARG C 120 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3902 Ramachandran restraints generated. 1951 Oldfield, 0 Emsley, 1951 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3902 Ramachandran restraints generated. 1951 Oldfield, 0 Emsley, 1951 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 423 residues out of total 1725 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 83 poor density : 340 time to evaluate : 1.748 Fit side-chains REVERT: B 7 ASN cc_start: 0.7230 (OUTLIER) cc_final: 0.7004 (m110) REVERT: B 15 PHE cc_start: 0.8645 (m-80) cc_final: 0.8258 (m-80) REVERT: B 55 LYS cc_start: 0.8131 (OUTLIER) cc_final: 0.7789 (ptpt) REVERT: B 56 SER cc_start: 0.8540 (OUTLIER) cc_final: 0.8282 (t) REVERT: B 91 SER cc_start: 0.8207 (p) cc_final: 0.7949 (t) REVERT: B 123 LYS cc_start: 0.7837 (tttm) cc_final: 0.7606 (ttpt) REVERT: B 132 LEU cc_start: 0.8730 (OUTLIER) cc_final: 0.8521 (mt) REVERT: B 174 SER cc_start: 0.8349 (m) cc_final: 0.8121 (t) REVERT: B 202 TYR cc_start: 0.8613 (m-80) cc_final: 0.8321 (m-80) REVERT: B 315 GLU cc_start: 0.7556 (tt0) cc_final: 0.7282 (mt-10) REVERT: B 452 ILE cc_start: 0.7860 (OUTLIER) cc_final: 0.7461 (mt) REVERT: B 503 CYS cc_start: 0.5456 (OUTLIER) cc_final: 0.5215 (p) REVERT: B 666 LYS cc_start: 0.8230 (OUTLIER) cc_final: 0.7893 (tttm) REVERT: B 705 ARG cc_start: 0.7522 (OUTLIER) cc_final: 0.7311 (ttp-170) REVERT: B 801 ASP cc_start: 0.6698 (OUTLIER) cc_final: 0.6480 (t70) REVERT: B 918 LYS cc_start: 0.5996 (mptt) cc_final: 0.5306 (mppt) REVERT: B 1430 LYS cc_start: 0.8238 (mtmm) cc_final: 0.8021 (mttt) REVERT: B 1444 ILE cc_start: 0.8199 (mm) cc_final: 0.7947 (mp) REVERT: B 1668 ASP cc_start: 0.5199 (OUTLIER) cc_final: 0.4866 (t70) REVERT: C 102 GLU cc_start: 0.6696 (tt0) cc_final: 0.6435 (mt-10) REVERT: C 151 GLU cc_start: 0.6903 (OUTLIER) cc_final: 0.6581 (mp0) REVERT: C 224 LYS cc_start: 0.8080 (OUTLIER) cc_final: 0.7697 (tmmm) REVERT: C 483 ASP cc_start: 0.7767 (OUTLIER) cc_final: 0.7059 (m-30) outliers start: 83 outliers final: 50 residues processed: 380 average time/residue: 1.3815 time to fit residues: 580.1414 Evaluate side-chains 396 residues out of total 1725 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 333 time to evaluate : 1.839 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 7 ASN Chi-restraints excluded: chain B residue 25 ASP Chi-restraints excluded: chain B residue 27 ASP Chi-restraints excluded: chain B residue 55 LYS Chi-restraints excluded: chain B residue 56 SER Chi-restraints excluded: chain B residue 74 LEU Chi-restraints excluded: chain B residue 85 VAL Chi-restraints excluded: chain B residue 132 LEU Chi-restraints excluded: chain B residue 190 ASP Chi-restraints excluded: chain B residue 201 THR Chi-restraints excluded: chain B residue 314 ASP Chi-restraints excluded: chain B residue 349 SER Chi-restraints excluded: chain B residue 419 VAL Chi-restraints excluded: chain B residue 426 THR Chi-restraints excluded: chain B residue 444 LYS Chi-restraints excluded: chain B residue 452 ILE Chi-restraints excluded: chain B residue 503 CYS Chi-restraints excluded: chain B residue 553 GLU Chi-restraints excluded: chain B residue 596 SER Chi-restraints excluded: chain B residue 605 LYS Chi-restraints excluded: chain B residue 666 LYS Chi-restraints excluded: chain B residue 705 ARG Chi-restraints excluded: chain B residue 711 ASN Chi-restraints excluded: chain B residue 763 GLU Chi-restraints excluded: chain B residue 801 ASP Chi-restraints excluded: chain B residue 826 ILE Chi-restraints excluded: chain B residue 858 VAL Chi-restraints excluded: chain B residue 866 ILE Chi-restraints excluded: chain B residue 969 THR Chi-restraints excluded: chain B residue 975 LEU Chi-restraints excluded: chain B residue 986 ASN Chi-restraints excluded: chain B residue 1454 LEU Chi-restraints excluded: chain B residue 1474 GLU Chi-restraints excluded: chain B residue 1497 ILE Chi-restraints excluded: chain B residue 1506 ASN Chi-restraints excluded: chain B residue 1514 LYS Chi-restraints excluded: chain B residue 1643 VAL Chi-restraints excluded: chain B residue 1647 VAL Chi-restraints excluded: chain B residue 1656 ILE Chi-restraints excluded: chain B residue 1668 ASP Chi-restraints excluded: chain B residue 1672 LEU Chi-restraints excluded: chain B residue 1679 LYS Chi-restraints excluded: chain C residue 46 ASN Chi-restraints excluded: chain C residue 145 LEU Chi-restraints excluded: chain C residue 151 GLU Chi-restraints excluded: chain C residue 173 LEU Chi-restraints excluded: chain C residue 195 ASP Chi-restraints excluded: chain C residue 224 LYS Chi-restraints excluded: chain C residue 246 ASP Chi-restraints excluded: chain C residue 258 THR Chi-restraints excluded: chain C residue 279 SER Chi-restraints excluded: chain C residue 334 MET Chi-restraints excluded: chain C residue 350 ASP Chi-restraints excluded: chain C residue 391 LEU Chi-restraints excluded: chain C residue 396 VAL Chi-restraints excluded: chain C residue 475 ASP Chi-restraints excluded: chain C residue 483 ASP Chi-restraints excluded: chain C residue 517 CYS Chi-restraints excluded: chain C residue 628 GLU Chi-restraints excluded: chain C residue 663 LYS Chi-restraints excluded: chain C residue 683 LYS Chi-restraints excluded: chain C residue 685 ASN Chi-restraints excluded: chain C residue 699 HIS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 199 random chunks: chunk 183 optimal weight: 3.9990 chunk 167 optimal weight: 1.9990 chunk 178 optimal weight: 5.9990 chunk 107 optimal weight: 3.9990 chunk 77 optimal weight: 3.9990 chunk 140 optimal weight: 3.9990 chunk 54 optimal weight: 0.4980 chunk 161 optimal weight: 3.9990 chunk 169 optimal weight: 2.9990 chunk 117 optimal weight: 0.3980 chunk 189 optimal weight: 4.9990 overall best weight: 1.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 79 ASN B 348 GLN ** B 908 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 917 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 919 ASN B1573 ASN B1596 GLN B1671 ASN C 197 GLN C 541 ASN C 642 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7614 moved from start: 0.3269 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.044 17384 Z= 0.386 Angle : 0.673 12.746 23673 Z= 0.346 Chirality : 0.046 0.211 2563 Planarity : 0.005 0.066 2873 Dihedral : 14.962 173.140 2883 Min Nonbonded Distance : 2.130 Molprobity Statistics. All-atom Clashscore : 6.82 Ramachandran Plot: Outliers : 0.05 % Allowed : 6.15 % Favored : 93.80 % Rotamer: Outliers : 5.16 % Allowed : 25.45 % Favored : 69.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.08 (0.18), residues: 1951 helix: 1.67 (0.19), residues: 698 sheet: 0.58 (0.31), residues: 265 loop : -1.60 (0.17), residues: 988 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP C 165 HIS 0.022 0.002 HIS B 908 PHE 0.020 0.002 PHE B 153 TYR 0.019 0.002 TYR B 149 ARG 0.010 0.001 ARG C 120 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3902 Ramachandran restraints generated. 1951 Oldfield, 0 Emsley, 1951 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3902 Ramachandran restraints generated. 1951 Oldfield, 0 Emsley, 1951 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 429 residues out of total 1725 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 89 poor density : 340 time to evaluate : 2.003 Fit side-chains REVERT: B 7 ASN cc_start: 0.7298 (OUTLIER) cc_final: 0.7027 (m110) REVERT: B 55 LYS cc_start: 0.8227 (OUTLIER) cc_final: 0.7865 (ptpt) REVERT: B 56 SER cc_start: 0.8540 (OUTLIER) cc_final: 0.8268 (t) REVERT: B 91 SER cc_start: 0.8197 (p) cc_final: 0.7974 (t) REVERT: B 131 ILE cc_start: 0.8426 (pt) cc_final: 0.8185 (pt) REVERT: B 202 TYR cc_start: 0.8636 (m-80) cc_final: 0.8407 (m-80) REVERT: B 315 GLU cc_start: 0.7628 (tt0) cc_final: 0.7350 (mt-10) REVERT: B 452 ILE cc_start: 0.8047 (OUTLIER) cc_final: 0.7658 (mt) REVERT: B 503 CYS cc_start: 0.5919 (OUTLIER) cc_final: 0.5670 (p) REVERT: B 666 LYS cc_start: 0.8307 (OUTLIER) cc_final: 0.8005 (tttm) REVERT: B 687 THR cc_start: 0.7681 (m) cc_final: 0.7402 (p) REVERT: B 705 ARG cc_start: 0.7627 (OUTLIER) cc_final: 0.7378 (ttp-170) REVERT: B 836 LEU cc_start: 0.8145 (OUTLIER) cc_final: 0.7829 (mt) REVERT: B 918 LYS cc_start: 0.6156 (mptt) cc_final: 0.4974 (mtmm) REVERT: B 1430 LYS cc_start: 0.8280 (mtmm) cc_final: 0.8062 (mttt) REVERT: B 1444 ILE cc_start: 0.8314 (mm) cc_final: 0.8095 (mm) REVERT: B 1491 ARG cc_start: 0.8318 (ttp-170) cc_final: 0.8018 (ttp-170) REVERT: B 1668 ASP cc_start: 0.5440 (OUTLIER) cc_final: 0.5091 (t70) REVERT: C 102 GLU cc_start: 0.6736 (tt0) cc_final: 0.6461 (mt-10) REVERT: C 151 GLU cc_start: 0.6916 (OUTLIER) cc_final: 0.6633 (mp0) REVERT: C 224 LYS cc_start: 0.8081 (OUTLIER) cc_final: 0.7681 (tmmm) REVERT: C 234 ASP cc_start: 0.6946 (t70) cc_final: 0.6576 (t0) REVERT: C 483 ASP cc_start: 0.7861 (OUTLIER) cc_final: 0.7168 (m-30) outliers start: 89 outliers final: 57 residues processed: 387 average time/residue: 1.4063 time to fit residues: 602.2322 Evaluate side-chains 402 residues out of total 1725 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 333 time to evaluate : 1.819 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 7 ASN Chi-restraints excluded: chain B residue 25 ASP Chi-restraints excluded: chain B residue 27 ASP Chi-restraints excluded: chain B residue 55 LYS Chi-restraints excluded: chain B residue 56 SER Chi-restraints excluded: chain B residue 74 LEU Chi-restraints excluded: chain B residue 79 ASN Chi-restraints excluded: chain B residue 85 VAL Chi-restraints excluded: chain B residue 201 THR Chi-restraints excluded: chain B residue 314 ASP Chi-restraints excluded: chain B residue 419 VAL Chi-restraints excluded: chain B residue 452 ILE Chi-restraints excluded: chain B residue 503 CYS Chi-restraints excluded: chain B residue 553 GLU Chi-restraints excluded: chain B residue 581 GLU Chi-restraints excluded: chain B residue 596 SER Chi-restraints excluded: chain B residue 605 LYS Chi-restraints excluded: chain B residue 666 LYS Chi-restraints excluded: chain B residue 705 ARG Chi-restraints excluded: chain B residue 711 ASN Chi-restraints excluded: chain B residue 763 GLU Chi-restraints excluded: chain B residue 778 ASN Chi-restraints excluded: chain B residue 826 ILE Chi-restraints excluded: chain B residue 830 PHE Chi-restraints excluded: chain B residue 836 LEU Chi-restraints excluded: chain B residue 858 VAL Chi-restraints excluded: chain B residue 866 ILE Chi-restraints excluded: chain B residue 929 SER Chi-restraints excluded: chain B residue 969 THR Chi-restraints excluded: chain B residue 975 LEU Chi-restraints excluded: chain B residue 986 ASN Chi-restraints excluded: chain B residue 1411 ASP Chi-restraints excluded: chain B residue 1454 LEU Chi-restraints excluded: chain B residue 1467 SER Chi-restraints excluded: chain B residue 1506 ASN Chi-restraints excluded: chain B residue 1514 LYS Chi-restraints excluded: chain B residue 1593 LYS Chi-restraints excluded: chain B residue 1599 ILE Chi-restraints excluded: chain B residue 1643 VAL Chi-restraints excluded: chain B residue 1647 VAL Chi-restraints excluded: chain B residue 1656 ILE Chi-restraints excluded: chain B residue 1666 LEU Chi-restraints excluded: chain B residue 1668 ASP Chi-restraints excluded: chain B residue 1671 ASN Chi-restraints excluded: chain B residue 1672 LEU Chi-restraints excluded: chain C residue 46 ASN Chi-restraints excluded: chain C residue 145 LEU Chi-restraints excluded: chain C residue 151 GLU Chi-restraints excluded: chain C residue 173 LEU Chi-restraints excluded: chain C residue 197 GLN Chi-restraints excluded: chain C residue 224 LYS Chi-restraints excluded: chain C residue 246 ASP Chi-restraints excluded: chain C residue 258 THR Chi-restraints excluded: chain C residue 279 SER Chi-restraints excluded: chain C residue 287 MET Chi-restraints excluded: chain C residue 303 VAL Chi-restraints excluded: chain C residue 334 MET Chi-restraints excluded: chain C residue 350 ASP Chi-restraints excluded: chain C residue 391 LEU Chi-restraints excluded: chain C residue 396 VAL Chi-restraints excluded: chain C residue 483 ASP Chi-restraints excluded: chain C residue 517 CYS Chi-restraints excluded: chain C residue 519 LEU Chi-restraints excluded: chain C residue 563 ASP Chi-restraints excluded: chain C residue 628 GLU Chi-restraints excluded: chain C residue 652 ILE Chi-restraints excluded: chain C residue 663 LYS Chi-restraints excluded: chain C residue 683 LYS Chi-restraints excluded: chain C residue 685 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 199 random chunks: chunk 115 optimal weight: 0.9980 chunk 89 optimal weight: 3.9990 chunk 131 optimal weight: 3.9990 chunk 198 optimal weight: 3.9990 chunk 182 optimal weight: 0.3980 chunk 157 optimal weight: 0.6980 chunk 16 optimal weight: 0.6980 chunk 121 optimal weight: 0.9980 chunk 96 optimal weight: 0.9980 chunk 125 optimal weight: 1.9990 chunk 168 optimal weight: 0.6980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 79 ASN B 348 GLN B 498 GLN ** B 908 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 917 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 919 ASN B1544 ASN B1596 GLN C 541 ASN C 642 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7565 moved from start: 0.3288 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 17384 Z= 0.183 Angle : 0.587 14.252 23673 Z= 0.302 Chirality : 0.041 0.185 2563 Planarity : 0.005 0.065 2873 Dihedral : 14.857 173.998 2883 Min Nonbonded Distance : 2.163 Molprobity Statistics. All-atom Clashscore : 6.39 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.38 % Favored : 94.57 % Rotamer: Outliers : 3.83 % Allowed : 27.07 % Favored : 69.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 (0.18), residues: 1951 helix: 1.86 (0.20), residues: 700 sheet: 0.57 (0.31), residues: 265 loop : -1.51 (0.17), residues: 986 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 443 HIS 0.010 0.001 HIS B 328 PHE 0.013 0.001 PHE B 824 TYR 0.015 0.001 TYR C 607 ARG 0.009 0.000 ARG C 120 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3902 Ramachandran restraints generated. 1951 Oldfield, 0 Emsley, 1951 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3902 Ramachandran restraints generated. 1951 Oldfield, 0 Emsley, 1951 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 400 residues out of total 1725 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 334 time to evaluate : 1.999 Fit side-chains REVERT: B 7 ASN cc_start: 0.7268 (OUTLIER) cc_final: 0.7000 (m110) REVERT: B 55 LYS cc_start: 0.8172 (OUTLIER) cc_final: 0.7825 (ptpt) REVERT: B 56 SER cc_start: 0.8539 (OUTLIER) cc_final: 0.8281 (t) REVERT: B 91 SER cc_start: 0.8167 (p) cc_final: 0.7938 (t) REVERT: B 131 ILE cc_start: 0.8354 (pt) cc_final: 0.8130 (pt) REVERT: B 202 TYR cc_start: 0.8561 (m-80) cc_final: 0.8302 (m-80) REVERT: B 315 GLU cc_start: 0.7610 (tt0) cc_final: 0.7335 (mt-10) REVERT: B 452 ILE cc_start: 0.7962 (OUTLIER) cc_final: 0.7608 (mt) REVERT: B 666 LYS cc_start: 0.8243 (OUTLIER) cc_final: 0.7954 (tttm) REVERT: B 705 ARG cc_start: 0.7581 (OUTLIER) cc_final: 0.7315 (ttp-170) REVERT: B 918 LYS cc_start: 0.6119 (mptt) cc_final: 0.5065 (mppt) REVERT: B 1430 LYS cc_start: 0.8246 (mtmm) cc_final: 0.8033 (mttt) REVERT: B 1444 ILE cc_start: 0.8234 (mm) cc_final: 0.8012 (mp) REVERT: B 1491 ARG cc_start: 0.8265 (ttp-170) cc_final: 0.7960 (ttp-170) REVERT: B 1668 ASP cc_start: 0.5302 (OUTLIER) cc_final: 0.4998 (t70) REVERT: C 102 GLU cc_start: 0.6716 (tt0) cc_final: 0.6451 (mt-10) REVERT: C 151 GLU cc_start: 0.6859 (OUTLIER) cc_final: 0.6527 (mp0) REVERT: C 224 LYS cc_start: 0.8067 (OUTLIER) cc_final: 0.7676 (tmmm) REVERT: C 234 ASP cc_start: 0.6897 (t70) cc_final: 0.6530 (t0) REVERT: C 483 ASP cc_start: 0.7786 (OUTLIER) cc_final: 0.7093 (m-30) outliers start: 66 outliers final: 42 residues processed: 370 average time/residue: 1.3941 time to fit residues: 569.7976 Evaluate side-chains 383 residues out of total 1725 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 331 time to evaluate : 1.670 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 7 ASN Chi-restraints excluded: chain B residue 25 ASP Chi-restraints excluded: chain B residue 27 ASP Chi-restraints excluded: chain B residue 55 LYS Chi-restraints excluded: chain B residue 56 SER Chi-restraints excluded: chain B residue 74 LEU Chi-restraints excluded: chain B residue 201 THR Chi-restraints excluded: chain B residue 314 ASP Chi-restraints excluded: chain B residue 399 SER Chi-restraints excluded: chain B residue 419 VAL Chi-restraints excluded: chain B residue 452 ILE Chi-restraints excluded: chain B residue 553 GLU Chi-restraints excluded: chain B residue 596 SER Chi-restraints excluded: chain B residue 644 ASP Chi-restraints excluded: chain B residue 666 LYS Chi-restraints excluded: chain B residue 705 ARG Chi-restraints excluded: chain B residue 711 ASN Chi-restraints excluded: chain B residue 763 GLU Chi-restraints excluded: chain B residue 778 ASN Chi-restraints excluded: chain B residue 826 ILE Chi-restraints excluded: chain B residue 830 PHE Chi-restraints excluded: chain B residue 858 VAL Chi-restraints excluded: chain B residue 866 ILE Chi-restraints excluded: chain B residue 969 THR Chi-restraints excluded: chain B residue 975 LEU Chi-restraints excluded: chain B residue 986 ASN Chi-restraints excluded: chain B residue 1454 LEU Chi-restraints excluded: chain B residue 1474 GLU Chi-restraints excluded: chain B residue 1497 ILE Chi-restraints excluded: chain B residue 1514 LYS Chi-restraints excluded: chain B residue 1544 ASN Chi-restraints excluded: chain B residue 1573 ASN Chi-restraints excluded: chain B residue 1643 VAL Chi-restraints excluded: chain B residue 1647 VAL Chi-restraints excluded: chain B residue 1666 LEU Chi-restraints excluded: chain B residue 1668 ASP Chi-restraints excluded: chain B residue 1672 LEU Chi-restraints excluded: chain C residue 46 ASN Chi-restraints excluded: chain C residue 145 LEU Chi-restraints excluded: chain C residue 151 GLU Chi-restraints excluded: chain C residue 173 LEU Chi-restraints excluded: chain C residue 224 LYS Chi-restraints excluded: chain C residue 246 ASP Chi-restraints excluded: chain C residue 258 THR Chi-restraints excluded: chain C residue 279 SER Chi-restraints excluded: chain C residue 334 MET Chi-restraints excluded: chain C residue 350 ASP Chi-restraints excluded: chain C residue 391 LEU Chi-restraints excluded: chain C residue 396 VAL Chi-restraints excluded: chain C residue 483 ASP Chi-restraints excluded: chain C residue 663 LYS Chi-restraints excluded: chain C residue 685 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 199 random chunks: chunk 48 optimal weight: 1.9990 chunk 145 optimal weight: 4.9990 chunk 23 optimal weight: 2.9990 chunk 43 optimal weight: 3.9990 chunk 158 optimal weight: 0.6980 chunk 66 optimal weight: 0.8980 chunk 162 optimal weight: 3.9990 chunk 20 optimal weight: 3.9990 chunk 29 optimal weight: 6.9990 chunk 138 optimal weight: 0.6980 chunk 9 optimal weight: 0.3980 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 79 ASN B 348 GLN B 498 GLN ** B 908 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 917 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 919 ASN ** B1544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1596 GLN C 197 GLN C 541 ASN C 642 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3572 r_free = 0.3572 target = 0.124826 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3264 r_free = 0.3264 target = 0.103643 restraints weight = 23403.460| |-----------------------------------------------------------------------------| r_work (start): 0.3262 rms_B_bonded: 1.93 r_work: 0.3146 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.2993 rms_B_bonded: 4.21 restraints_weight: 0.2500 r_work (final): 0.2993 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7915 moved from start: 0.3305 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.140 17384 Z= 0.256 Angle : 0.777 59.189 23673 Z= 0.453 Chirality : 0.042 0.287 2563 Planarity : 0.005 0.064 2873 Dihedral : 14.873 173.979 2883 Min Nonbonded Distance : 2.057 Molprobity Statistics. All-atom Clashscore : 7.33 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.38 % Favored : 94.57 % Rotamer: Outliers : 3.42 % Allowed : 27.65 % Favored : 68.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.11 (0.18), residues: 1951 helix: 1.87 (0.20), residues: 700 sheet: 0.59 (0.31), residues: 265 loop : -1.50 (0.17), residues: 986 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 443 HIS 0.009 0.001 HIS B 328 PHE 0.013 0.001 PHE B 824 TYR 0.015 0.001 TYR C 607 ARG 0.007 0.000 ARG C 120 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8632.79 seconds wall clock time: 151 minutes 49.21 seconds (9109.21 seconds total)