Starting phenix.real_space_refine on Mon Mar 18 13:34:11 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6sl1_10234/03_2024/6sl1_10234_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6sl1_10234/03_2024/6sl1_10234.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6sl1_10234/03_2024/6sl1_10234.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6sl1_10234/03_2024/6sl1_10234.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6sl1_10234/03_2024/6sl1_10234_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6sl1_10234/03_2024/6sl1_10234_updated.pdb" } resolution = 3.6 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.001 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 P 3 5.49 5 Mg 1 5.21 5 S 96 5.16 5 C 13371 2.51 5 N 3670 2.21 5 O 3900 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 14": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 56": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 92": "OE1" <-> "OE2" Residue "A TYR 140": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 145": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 171": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 276": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 317": "NH1" <-> "NH2" Residue "A ASP 318": "OD1" <-> "OD2" Residue "A TYR 330": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 343": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 349": "OE1" <-> "OE2" Residue "A TYR 358": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 361": "NH1" <-> "NH2" Residue "A ARG 366": "NH1" <-> "NH2" Residue "A TYR 415": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 470": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 544": "NH1" <-> "NH2" Residue "A PHE 618": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 663": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 680": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 683": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 721": "NH1" <-> "NH2" Residue "A PHE 728": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 811": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 843": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 854": "NH1" <-> "NH2" Residue "A ARG 891": "NH1" <-> "NH2" Residue "A PHE 903": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 947": "NH1" <-> "NH2" Residue "A PHE 949": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 970": "OE1" <-> "OE2" Residue "A GLU 985": "OE1" <-> "OE2" Residue "A ASP 996": "OD1" <-> "OD2" Residue "A PHE 998": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 1004": "OD1" <-> "OD2" Residue "A GLU 1051": "OE1" <-> "OE2" Residue "A TYR 1079": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1088": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1119": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1122": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 1137": "NH1" <-> "NH2" Residue "A PHE 1143": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 1184": "OE1" <-> "OE2" Residue "A GLU 1209": "OE1" <-> "OE2" Residue "A TYR 1265": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1279": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 1287": "NH1" <-> "NH2" Residue "A PHE 1314": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1330": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1332": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1376": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 1461": "NH1" <-> "NH2" Residue "A ARG 1468": "NH1" <-> "NH2" Residue "A PHE 1511": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1518": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 1529": "OD1" <-> "OD2" Residue "A PHE 1536": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1641": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 1694": "OE1" <-> "OE2" Residue "A TYR 1733": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 1769": "NH1" <-> "NH2" Residue "A PHE 1830": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 1857": "OE1" <-> "OE2" Residue "A ASP 1862": "OD1" <-> "OD2" Residue "A ARG 1863": "NH1" <-> "NH2" Residue "A ARG 1880": "NH1" <-> "NH2" Residue "A TYR 1931": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 1945": "NH1" <-> "NH2" Residue "A TYR 1948": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 1959": "NH1" <-> "NH2" Residue "A TYR 1963": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 2019": "NH1" <-> "NH2" Residue "A ARG 2056": "NH1" <-> "NH2" Residue "A ARG 2068": "NH1" <-> "NH2" Residue "A ARG 2081": "NH1" <-> "NH2" Residue "A ARG 2100": "NH1" <-> "NH2" Residue "A GLU 2113": "OE1" <-> "OE2" Residue "A ARG 2115": "NH1" <-> "NH2" Residue "A ARG 2123": "NH1" <-> "NH2" Residue "A ARG 2134": "NH1" <-> "NH2" Residue "A ARG 2158": "NH1" <-> "NH2" Residue "A ARG 2163": "NH1" <-> "NH2" Residue "A ARG 2173": "NH1" <-> "NH2" Residue "A PHE 2174": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 2176": "NH1" <-> "NH2" Residue "A ARG 2178": "NH1" <-> "NH2" Residue "A ASP 2216": "OD1" <-> "OD2" Residue "A GLU 2219": "OE1" <-> "OE2" Residue "A ARG 2225": "NH1" <-> "NH2" Residue "A ARG 2245": "NH1" <-> "NH2" Residue "A TYR 2254": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 2260": "NH1" <-> "NH2" Residue "A ARG 2286": "NH1" <-> "NH2" Residue "A ARG 2314": "NH1" <-> "NH2" Residue "A ARG 2364": "NH1" <-> "NH2" Residue "A ARG 2365": "NH1" <-> "NH2" Residue "A ARG 2370": "NH1" <-> "NH2" Residue "A ASP 2394": "OD1" <-> "OD2" Residue "A ARG 2397": "NH1" <-> "NH2" Residue "A ARG 2425": "NH1" <-> "NH2" Residue "A PHE 2445": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 2455": "NH1" <-> "NH2" Residue "A ARG 2473": "NH1" <-> "NH2" Residue "A ARG 2515": "NH1" <-> "NH2" Residue "A PHE 2579": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 2603": "NH1" <-> "NH2" Residue "A ARG 2617": "NH1" <-> "NH2" Residue "A ARG 2637": "NH1" <-> "NH2" Residue "A ARG 2640": "NH1" <-> "NH2" Residue "A ARG 2642": "NH1" <-> "NH2" Residue "A ARG 2647": "NH1" <-> "NH2" Residue "A TYR 2649": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 2662": "OE1" <-> "OE2" Residue "A GLU 2672": "OE1" <-> "OE2" Residue "A ARG 2680": "NH1" <-> "NH2" Residue "A GLU 2694": "OE1" <-> "OE2" Residue "A ARG 2706": "NH1" <-> "NH2" Residue "A TYR 2710": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 2711": "NH1" <-> "NH2" Residue "A ARG 2712": "NH1" <-> "NH2" Residue "A ARG 2716": "NH1" <-> "NH2" Residue "A ARG 2722": "NH1" <-> "NH2" Residue "A TYR 2723": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 2724": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 2728": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 2739": "NH1" <-> "NH2" Residue "A ARG 2744": "NH1" <-> "NH2" Residue "A ARG 2761": "NH1" <-> "NH2" Residue "A ARG 2788": "NH1" <-> "NH2" Residue "A PHE 2798": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 2799": "NH1" <-> "NH2" Residue "A ARG 2818": "NH1" <-> "NH2" Residue "A ARG 2819": "NH1" <-> "NH2" Residue "A ARG 2829": "NH1" <-> "NH2" Residue "A ARG 2843": "NH1" <-> "NH2" Residue "A ARG 2901": "NH1" <-> "NH2" Residue "A TYR 2943": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 21041 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 21041 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2654, 21041 Unusual residues: {' MG': 1, 'AGS': 1} Inner-chain residues flagged as termini: ['pdbres="ALA A2944 "'] Classifications: {'peptide': 2652, 'undetermined': 2} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 112, 'TRANS': 2538, None: 2} Not linked: pdbres="ALA A2944 " pdbres="AGS A3001 " Not linked: pdbres="AGS A3001 " pdbres=" MG A3002 " Chain breaks: 19 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 3 Time building chain proxies: 11.60, per 1000 atoms: 0.55 Number of scatterers: 21041 At special positions: 0 Unit cell: (114.372, 140.847, 210.741, 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) S 96 16.00 P 3 15.00 Mg 1 11.99 O 3900 8.00 N 3670 7.00 C 13371 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS A1408 " - pdb=" SG CYS A1447 " distance=2.04 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: 9.39 Conformation dependent library (CDL) restraints added in 4.0 seconds 5224 Ramachandran restraints generated. 2612 Oldfield, 0 Emsley, 2612 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5090 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 148 helices and 3 sheets defined 61.8% alpha, 1.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 9.21 Creating SS restraints... Processing helix chain 'A' and resid 15 through 21 removed outlier: 4.033A pdb=" N LEU A 21 " --> pdb=" O ILE A 17 " (cutoff:3.500A) Processing helix chain 'A' and resid 30 through 39 removed outlier: 3.574A pdb=" N ILE A 37 " --> pdb=" O VAL A 33 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ALA A 38 " --> pdb=" O GLU A 34 " (cutoff:3.500A) Processing helix chain 'A' and resid 56 through 73 removed outlier: 3.629A pdb=" N ARG A 65 " --> pdb=" O GLU A 61 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N ALA A 73 " --> pdb=" O ILE A 69 " (cutoff:3.500A) Processing helix chain 'A' and resid 88 through 90 No H-bonds generated for 'chain 'A' and resid 88 through 90' Processing helix chain 'A' and resid 94 through 98 Processing helix chain 'A' and resid 111 through 124 removed outlier: 3.998A pdb=" N ALA A 116 " --> pdb=" O LYS A 112 " (cutoff:3.500A) Processing helix chain 'A' and resid 137 through 146 removed outlier: 4.020A pdb=" N LYS A 142 " --> pdb=" O ALA A 138 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N VAL A 143 " --> pdb=" O GLY A 139 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N LEU A 144 " --> pdb=" O TYR A 140 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N TYR A 145 " --> pdb=" O VAL A 141 " (cutoff:3.500A) Processing helix chain 'A' and resid 163 through 178 removed outlier: 3.891A pdb=" N VAL A 167 " --> pdb=" O GLU A 163 " (cutoff:3.500A) removed outlier: 4.227A pdb=" N CYS A 168 " --> pdb=" O GLY A 164 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N VAL A 169 " --> pdb=" O TRP A 165 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N VAL A 175 " --> pdb=" O PHE A 171 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N LEU A 176 " --> pdb=" O CYS A 172 " (cutoff:3.500A) Processing helix chain 'A' and resid 218 through 232 removed outlier: 4.555A pdb=" N ASP A 223 " --> pdb=" O HIS A 219 " (cutoff:3.500A) removed outlier: 4.131A pdb=" N SER A 226 " --> pdb=" O VAL A 222 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N CYS A 227 " --> pdb=" O ASP A 223 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N MET A 230 " --> pdb=" O SER A 226 " (cutoff:3.500A) Processing helix chain 'A' and resid 240 through 242 No H-bonds generated for 'chain 'A' and resid 240 through 242' Processing helix chain 'A' and resid 246 through 248 No H-bonds generated for 'chain 'A' and resid 246 through 248' Processing helix chain 'A' and resid 250 through 253 No H-bonds generated for 'chain 'A' and resid 250 through 253' Processing helix chain 'A' and resid 271 through 274 No H-bonds generated for 'chain 'A' and resid 271 through 274' Processing helix chain 'A' and resid 276 through 278 No H-bonds generated for 'chain 'A' and resid 276 through 278' Processing helix chain 'A' and resid 284 through 298 removed outlier: 4.030A pdb=" N THR A 289 " --> pdb=" O ALA A 285 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N LYS A 292 " --> pdb=" O LYS A 288 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N GLN A 293 " --> pdb=" O THR A 289 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N VAL A 294 " --> pdb=" O LEU A 290 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N VAL A 295 " --> pdb=" O VAL A 291 " (cutoff:3.500A) Proline residue: A 296 - end of helix Processing helix chain 'A' and resid 313 through 315 No H-bonds generated for 'chain 'A' and resid 313 through 315' Processing helix chain 'A' and resid 319 through 327 removed outlier: 3.923A pdb=" N THR A 327 " --> pdb=" O THR A 323 " (cutoff:3.500A) Processing helix chain 'A' and resid 330 through 333 No H-bonds generated for 'chain 'A' and resid 330 through 333' Processing helix chain 'A' and resid 347 through 356 removed outlier: 4.058A pdb=" N TRP A 355 " --> pdb=" O LEU A 351 " (cutoff:3.500A) Processing helix chain 'A' and resid 359 through 361 No H-bonds generated for 'chain 'A' and resid 359 through 361' Processing helix chain 'A' and resid 369 through 371 No H-bonds generated for 'chain 'A' and resid 369 through 371' Processing helix chain 'A' and resid 400 through 411 Processing helix chain 'A' and resid 450 through 452 No H-bonds generated for 'chain 'A' and resid 450 through 452' Processing helix chain 'A' and resid 458 through 460 No H-bonds generated for 'chain 'A' and resid 458 through 460' Processing helix chain 'A' and resid 462 through 473 removed outlier: 4.062A pdb=" N ILE A 468 " --> pdb=" O ALA A 464 " (cutoff:3.500A) Proline residue: A 469 - end of helix Processing helix chain 'A' and resid 482 through 491 removed outlier: 3.997A pdb=" N ASP A 488 " --> pdb=" O GLU A 484 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N LYS A 491 " --> pdb=" O GLU A 487 " (cutoff:3.500A) Processing helix chain 'A' and resid 500 through 512 removed outlier: 4.572A pdb=" N MET A 505 " --> pdb=" O ALA A 501 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N CYS A 508 " --> pdb=" O ALA A 504 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N LEU A 511 " --> pdb=" O ALA A 507 " (cutoff:3.500A) Processing helix chain 'A' and resid 520 through 522 No H-bonds generated for 'chain 'A' and resid 520 through 522' Processing helix chain 'A' and resid 525 through 534 removed outlier: 4.160A pdb=" N TRP A 530 " --> pdb=" O TRP A 526 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N GLN A 531 " --> pdb=" O LYS A 527 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N LEU A 532 " --> pdb=" O GLN A 528 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N ALA A 533 " --> pdb=" O LEU A 529 " (cutoff:3.500A) Processing helix chain 'A' and resid 544 through 556 removed outlier: 3.759A pdb=" N LEU A 549 " --> pdb=" O ALA A 545 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N LEU A 550 " --> pdb=" O SER A 546 " (cutoff:3.500A) Processing helix chain 'A' and resid 566 through 574 removed outlier: 4.142A pdb=" N ILE A 571 " --> pdb=" O ASP A 567 " (cutoff:3.500A) Processing helix chain 'A' and resid 585 through 597 removed outlier: 4.430A pdb=" N LEU A 592 " --> pdb=" O LEU A 588 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N ASN A 593 " --> pdb=" O GLY A 589 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N LEU A 594 " --> pdb=" O LEU A 590 " (cutoff:3.500A) Processing helix chain 'A' and resid 607 through 620 removed outlier: 3.685A pdb=" N ASN A 611 " --> pdb=" O GLN A 607 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N HIS A 612 " --> pdb=" O ALA A 608 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N ILE A 613 " --> pdb=" O THR A 609 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N ARG A 615 " --> pdb=" O ASN A 611 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N TRP A 616 " --> pdb=" O HIS A 612 " (cutoff:3.500A) Processing helix chain 'A' and resid 628 through 631 No H-bonds generated for 'chain 'A' and resid 628 through 631' Processing helix chain 'A' and resid 638 through 647 removed outlier: 3.648A pdb=" N VAL A 642 " --> pdb=" O PRO A 638 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N LEU A 644 " --> pdb=" O ASP A 640 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N LEU A 645 " --> pdb=" O LEU A 641 " (cutoff:3.500A) removed outlier: 4.279A pdb=" N ALA A 647 " --> pdb=" O ASN A 643 " (cutoff:3.500A) Processing helix chain 'A' and resid 666 through 677 removed outlier: 4.213A pdb=" N TRP A 671 " --> pdb=" O ILE A 667 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N GLU A 673 " --> pdb=" O LEU A 669 " (cutoff:3.500A) removed outlier: 4.246A pdb=" N GLN A 674 " --> pdb=" O HIS A 670 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N GLU A 676 " --> pdb=" O LYS A 672 " (cutoff:3.500A) removed outlier: 5.260A pdb=" N MET A 677 " --> pdb=" O GLU A 673 " (cutoff:3.500A) Processing helix chain 'A' and resid 718 through 738 removed outlier: 4.500A pdb=" N LEU A 723 " --> pdb=" O ALA A 719 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N TYR A 729 " --> pdb=" O LEU A 725 " (cutoff:3.500A) Proline residue: A 730 - end of helix removed outlier: 4.441A pdb=" N LEU A 738 " --> pdb=" O GLU A 734 " (cutoff:3.500A) Processing helix chain 'A' and resid 756 through 768 removed outlier: 4.053A pdb=" N SER A 760 " --> pdb=" O GLU A 756 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N MET A 761 " --> pdb=" O ARG A 757 " (cutoff:3.500A) removed outlier: 4.078A pdb=" N CYS A 765 " --> pdb=" O MET A 761 " (cutoff:3.500A) removed outlier: 4.634A pdb=" N LEU A 766 " --> pdb=" O VAL A 762 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N THR A 767 " --> pdb=" O LEU A 763 " (cutoff:3.500A) Processing helix chain 'A' and resid 773 through 775 No H-bonds generated for 'chain 'A' and resid 773 through 775' Processing helix chain 'A' and resid 784 through 792 removed outlier: 4.208A pdb=" N ALA A 789 " --> pdb=" O ASP A 785 " (cutoff:3.500A) removed outlier: 4.079A pdb=" N PHE A 791 " --> pdb=" O GLU A 787 " (cutoff:3.500A) removed outlier: 4.546A pdb=" N SER A 792 " --> pdb=" O SER A 788 " (cutoff:3.500A) Processing helix chain 'A' and resid 794 through 800 Processing helix chain 'A' and resid 810 through 821 removed outlier: 3.914A pdb=" N ILE A 814 " --> pdb=" O LEU A 810 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N LEU A 815 " --> pdb=" O PHE A 811 " (cutoff:3.500A) Proline residue: A 820 - end of helix Processing helix chain 'A' and resid 827 through 834 removed outlier: 4.188A pdb=" N ALA A 832 " --> pdb=" O PRO A 828 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N LEU A 833 " --> pdb=" O GLU A 829 " (cutoff:3.500A) Processing helix chain 'A' and resid 838 through 856 removed outlier: 4.071A pdb=" N GLU A 849 " --> pdb=" O GLY A 845 " (cutoff:3.500A) removed outlier: 4.435A pdb=" N GLU A 853 " --> pdb=" O GLU A 849 " (cutoff:3.500A) removed outlier: 5.162A pdb=" N ARG A 854 " --> pdb=" O ALA A 850 " (cutoff:3.500A) removed outlier: 4.313A pdb=" N SER A 855 " --> pdb=" O LEU A 851 " (cutoff:3.500A) Processing helix chain 'A' and resid 894 through 898 removed outlier: 4.331A pdb=" N SER A 897 " --> pdb=" O ILE A 894 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N TYR A 898 " --> pdb=" O LEU A 895 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 894 through 898' Processing helix chain 'A' and resid 900 through 918 removed outlier: 3.567A pdb=" N TYR A 904 " --> pdb=" O PRO A 900 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N THR A 907 " --> pdb=" O PHE A 903 " (cutoff:3.500A) removed outlier: 4.804A pdb=" N SER A 908 " --> pdb=" O TYR A 904 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N LEU A 909 " --> pdb=" O LEU A 905 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N HIS A 912 " --> pdb=" O SER A 908 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N ILE A 917 " --> pdb=" O PHE A 913 " (cutoff:3.500A) Processing helix chain 'A' and resid 921 through 923 No H-bonds generated for 'chain 'A' and resid 921 through 923' Processing helix chain 'A' and resid 929 through 937 removed outlier: 3.640A pdb=" N ALA A 936 " --> pdb=" O ILE A 932 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N GLY A 937 " --> pdb=" O ASN A 933 " (cutoff:3.500A) Processing helix chain 'A' and resid 941 through 946 removed outlier: 3.818A pdb=" N CYS A 946 " --> pdb=" O GLN A 942 " (cutoff:3.500A) Processing helix chain 'A' and resid 950 through 953 No H-bonds generated for 'chain 'A' and resid 950 through 953' Processing helix chain 'A' and resid 962 through 976 removed outlier: 4.286A pdb=" N THR A 966 " --> pdb=" O LEU A 962 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N GLY A 973 " --> pdb=" O LEU A 969 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N VAL A 976 " --> pdb=" O ALA A 972 " (cutoff:3.500A) Processing helix chain 'A' and resid 985 through 998 removed outlier: 3.732A pdb=" N ASP A 996 " --> pdb=" O ILE A 992 " (cutoff:3.500A) removed outlier: 4.107A pdb=" N SER A 997 " --> pdb=" O ASP A 993 " (cutoff:3.500A) Processing helix chain 'A' and resid 1012 through 1022 removed outlier: 4.220A pdb=" N TYR A1019 " --> pdb=" O ASP A1015 " (cutoff:3.500A) Processing helix chain 'A' and resid 1032 through 1046 removed outlier: 3.645A pdb=" N ARG A1037 " --> pdb=" O ALA A1033 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N LEU A1041 " --> pdb=" O ARG A1037 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N LEU A1042 " --> pdb=" O LEU A1038 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N HIS A1044 " --> pdb=" O SER A1040 " (cutoff:3.500A) Processing helix chain 'A' and resid 1053 through 1056 No H-bonds generated for 'chain 'A' and resid 1053 through 1056' Processing helix chain 'A' and resid 1063 through 1070 Processing helix chain 'A' and resid 1074 through 1089 removed outlier: 3.647A pdb=" N TYR A1079 " --> pdb=" O LYS A1075 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N LEU A1082 " --> pdb=" O HIS A1078 " (cutoff:3.500A) Proline residue: A1085 - end of helix removed outlier: 3.717A pdb=" N PHE A1088 " --> pdb=" O ILE A1084 " (cutoff:3.500A) removed outlier: 4.599A pdb=" N GLY A1089 " --> pdb=" O PRO A1085 " (cutoff:3.500A) Processing helix chain 'A' and resid 1093 through 1106 removed outlier: 5.033A pdb=" N ASP A1097 " --> pdb=" O LYS A1094 " (cutoff:3.500A) removed outlier: 4.317A pdb=" N PHE A1100 " --> pdb=" O ASP A1097 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N VAL A1103 " --> pdb=" O PHE A1100 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N LEU A1104 " --> pdb=" O VAL A1101 " (cutoff:3.500A) Processing helix chain 'A' and resid 1114 through 1128 removed outlier: 4.632A pdb=" N PHE A1119 " --> pdb=" O GLU A1115 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N PHE A1122 " --> pdb=" O ALA A1118 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N ALA A1125 " --> pdb=" O LEU A1121 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N GLU A1126 " --> pdb=" O PHE A1122 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N LEU A1127 " --> pdb=" O VAL A1123 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ALA A1128 " --> pdb=" O LEU A1124 " (cutoff:3.500A) Processing helix chain 'A' and resid 1132 through 1145 removed outlier: 5.613A pdb=" N ARG A1136 " --> pdb=" O THR A1133 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N ARG A1137 " --> pdb=" O LEU A1134 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N SER A1138 " --> pdb=" O LEU A1135 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N HIS A1141 " --> pdb=" O SER A1138 " (cutoff:3.500A) Processing helix chain 'A' and resid 1159 through 1177 removed outlier: 3.664A pdb=" N ALA A1163 " --> pdb=" O VAL A1159 " (cutoff:3.500A) removed outlier: 4.556A pdb=" N LEU A1164 " --> pdb=" O THR A1160 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N TYR A1165 " --> pdb=" O HIS A1161 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ALA A1166 " --> pdb=" O SER A1162 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N ALA A1167 " --> pdb=" O ALA A1163 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N SER A1168 " --> pdb=" O LEU A1164 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N ILE A1170 " --> pdb=" O ALA A1166 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N ALA A1174 " --> pdb=" O ILE A1170 " (cutoff:3.500A) Processing helix chain 'A' and resid 1182 through 1187 Processing helix chain 'A' and resid 1190 through 1197 removed outlier: 3.518A pdb=" N THR A1196 " --> pdb=" O GLN A1192 " (cutoff:3.500A) Processing helix chain 'A' and resid 1210 through 1212 No H-bonds generated for 'chain 'A' and resid 1210 through 1212' Processing helix chain 'A' and resid 1216 through 1233 removed outlier: 6.193A pdb=" N THR A1225 " --> pdb=" O ARG A1221 " (cutoff:3.500A) removed outlier: 6.595A pdb=" N GLU A1226 " --> pdb=" O GLU A1222 " (cutoff:3.500A) Processing helix chain 'A' and resid 1237 through 1247 Processing helix chain 'A' and resid 1251 through 1257 Processing helix chain 'A' and resid 1259 through 1270 removed outlier: 3.732A pdb=" N ASP A1270 " --> pdb=" O SER A1266 " (cutoff:3.500A) Processing helix chain 'A' and resid 1284 through 1289 Processing helix chain 'A' and resid 1291 through 1301 removed outlier: 4.111A pdb=" N LEU A1296 " --> pdb=" O LYS A1292 " (cutoff:3.500A) Processing helix chain 'A' and resid 1303 through 1312 Processing helix chain 'A' and resid 1321 through 1325 removed outlier: 3.698A pdb=" N ARG A1325 " --> pdb=" O GLU A1321 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1321 through 1325' Processing helix chain 'A' and resid 1332 through 1343 Processing helix chain 'A' and resid 1363 through 1374 removed outlier: 3.999A pdb=" N VAL A1368 " --> pdb=" O PRO A1364 " (cutoff:3.500A) Processing helix chain 'A' and resid 1384 through 1397 Processing helix chain 'A' and resid 1400 through 1402 No H-bonds generated for 'chain 'A' and resid 1400 through 1402' Processing helix chain 'A' and resid 1404 through 1421 removed outlier: 3.600A pdb=" N CYS A1408 " --> pdb=" O PRO A1404 " (cutoff:3.500A) Processing helix chain 'A' and resid 1429 through 1442 removed outlier: 4.465A pdb=" N VAL A1440 " --> pdb=" O HIS A1436 " (cutoff:3.500A) removed outlier: 4.130A pdb=" N PHE A1441 " --> pdb=" O SER A1437 " (cutoff:3.500A) Processing helix chain 'A' and resid 1449 through 1461 Processing helix chain 'A' and resid 1470 through 1489 Processing helix chain 'A' and resid 1498 through 1521 Processing helix chain 'A' and resid 1530 through 1543 Processing helix chain 'A' and resid 1557 through 1569 Processing helix chain 'A' and resid 1578 through 1584 removed outlier: 3.740A pdb=" N VAL A1583 " --> pdb=" O PRO A1579 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N ALA A1584 " --> pdb=" O ALA A1580 " (cutoff:3.500A) Processing helix chain 'A' and resid 1606 through 1611 removed outlier: 3.915A pdb=" N LYS A1611 " --> pdb=" O GLU A1607 " (cutoff:3.500A) Processing helix chain 'A' and resid 1615 through 1619 Processing helix chain 'A' and resid 1627 through 1644 removed outlier: 3.581A pdb=" N ALA A1642 " --> pdb=" O GLY A1638 " (cutoff:3.500A) Processing helix chain 'A' and resid 1657 through 1663 Processing helix chain 'A' and resid 1670 through 1679 Processing helix chain 'A' and resid 1689 through 1707 Processing helix chain 'A' and resid 1710 through 1719 Processing helix chain 'A' and resid 1722 through 1726 Processing helix chain 'A' and resid 1762 through 1773 removed outlier: 3.876A pdb=" N SER A1773 " --> pdb=" O ARG A1769 " (cutoff:3.500A) Processing helix chain 'A' and resid 1778 through 1781 No H-bonds generated for 'chain 'A' and resid 1778 through 1781' Processing helix chain 'A' and resid 1783 through 1789 Processing helix chain 'A' and resid 1793 through 1810 Proline residue: A1799 - end of helix removed outlier: 3.702A pdb=" N LEU A1810 " --> pdb=" O LEU A1806 " (cutoff:3.500A) Processing helix chain 'A' and resid 1815 through 1827 removed outlier: 4.107A pdb=" N GLN A1825 " --> pdb=" O SER A1821 " (cutoff:3.500A) removed outlier: 4.468A pdb=" N GLU A1826 " --> pdb=" O GLU A1822 " (cutoff:3.500A) Processing helix chain 'A' and resid 1836 through 1851 removed outlier: 3.805A pdb=" N LEU A1841 " --> pdb=" O GLU A1837 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N THR A1851 " --> pdb=" O LEU A1847 " (cutoff:3.500A) Processing helix chain 'A' and resid 1860 through 1862 No H-bonds generated for 'chain 'A' and resid 1860 through 1862' Processing helix chain 'A' and resid 1871 through 1880 Processing helix chain 'A' and resid 1884 through 1898 Processing helix chain 'A' and resid 1916 through 1923 removed outlier: 3.738A pdb=" N ASN A1923 " --> pdb=" O GLU A1919 " (cutoff:3.500A) Processing helix chain 'A' and resid 1929 through 1932 Processing helix chain 'A' and resid 1939 through 1948 Processing helix chain 'A' and resid 1953 through 1968 removed outlier: 3.790A pdb=" N PHE A1958 " --> pdb=" O LYS A1954 " (cutoff:3.500A) Processing helix chain 'A' and resid 1972 through 1988 removed outlier: 3.739A pdb=" N ARG A1975 " --> pdb=" O LEU A1972 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N LEU A1988 " --> pdb=" O LEU A1985 " (cutoff:3.500A) Processing helix chain 'A' and resid 1991 through 1999 Processing helix chain 'A' and resid 2011 through 2021 Processing helix chain 'A' and resid 2035 through 2047 Processing helix chain 'A' and resid 2052 through 2072 removed outlier: 4.068A pdb=" N SER A2057 " --> pdb=" O ASP A2053 " (cutoff:3.500A) Processing helix chain 'A' and resid 2079 through 2098 removed outlier: 3.644A pdb=" N ASN A2098 " --> pdb=" O ASP A2094 " (cutoff:3.500A) Processing helix chain 'A' and resid 2102 through 2121 removed outlier: 3.507A pdb=" N LYS A2117 " --> pdb=" O GLU A2113 " (cutoff:3.500A) removed outlier: 4.085A pdb=" N TRP A2118 " --> pdb=" O LYS A2114 " (cutoff:3.500A) removed outlier: 4.892A pdb=" N SER A2121 " --> pdb=" O LYS A2117 " (cutoff:3.500A) Processing helix chain 'A' and resid 2124 through 2143 removed outlier: 3.597A pdb=" N ILE A2130 " --> pdb=" O ASP A2126 " (cutoff:3.500A) Processing helix chain 'A' and resid 2154 through 2174 Processing helix chain 'A' and resid 2178 through 2197 removed outlier: 3.803A pdb=" N LEU A2191 " --> pdb=" O ALA A2187 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N ILE A2192 " --> pdb=" O LEU A2188 " (cutoff:3.500A) Proline residue: A2193 - end of helix removed outlier: 3.592A pdb=" N SER A2197 " --> pdb=" O PRO A2193 " (cutoff:3.500A) Processing helix chain 'A' and resid 2203 through 2217 Processing helix chain 'A' and resid 2220 through 2232 Processing helix chain 'A' and resid 2245 through 2258 Processing helix chain 'A' and resid 2267 through 2270 No H-bonds generated for 'chain 'A' and resid 2267 through 2270' Processing helix chain 'A' and resid 2272 through 2278 Processing helix chain 'A' and resid 2286 through 2303 Processing helix chain 'A' and resid 2306 through 2328 Processing helix chain 'A' and resid 2348 through 2385 Processing helix chain 'A' and resid 2394 through 2404 Processing helix chain 'A' and resid 2409 through 2421 removed outlier: 5.207A pdb=" N ASN A2420 " --> pdb=" O LYS A2416 " (cutoff:3.500A) removed outlier: 6.240A pdb=" N LYS A2421 " --> pdb=" O LYS A2417 " (cutoff:3.500A) Processing helix chain 'A' and resid 2424 through 2426 No H-bonds generated for 'chain 'A' and resid 2424 through 2426' Processing helix chain 'A' and resid 2428 through 2434 removed outlier: 3.960A pdb=" N MET A2431 " --> pdb=" O ALA A2428 " (cutoff:3.500A) removed outlier: 5.125A pdb=" N ASN A2432 " --> pdb=" O LEU A2429 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N GLN A2433 " --> pdb=" O LEU A2430 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N LEU A2434 " --> pdb=" O MET A2431 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 2428 through 2434' Processing helix chain 'A' and resid 2444 through 2459 removed outlier: 3.735A pdb=" N ASP A2451 " --> pdb=" O LYS A2447 " (cutoff:3.500A) Processing helix chain 'A' and resid 2461 through 2473 removed outlier: 5.657A pdb=" N TYR A2466 " --> pdb=" O TYR A2462 " (cutoff:3.500A) removed outlier: 5.471A pdb=" N HIS A2467 " --> pdb=" O HIS A2463 " (cutoff:3.500A) Processing helix chain 'A' and resid 2483 through 2499 removed outlier: 3.927A pdb=" N LYS A2499 " --> pdb=" O LYS A2495 " (cutoff:3.500A) Processing helix chain 'A' and resid 2507 through 2522 Processing helix chain 'A' and resid 2541 through 2552 Processing helix chain 'A' and resid 2616 through 2635 removed outlier: 4.024A pdb=" N LYS A2634 " --> pdb=" O SER A2630 " (cutoff:3.500A) removed outlier: 4.594A pdb=" N LEU A2635 " --> pdb=" O GLU A2631 " (cutoff:3.500A) Processing helix chain 'A' and resid 2637 through 2641 Processing helix chain 'A' and resid 2670 through 2681 Proline residue: A2676 - end of helix removed outlier: 3.966A pdb=" N GLU A2679 " --> pdb=" O MET A2675 " (cutoff:3.500A) Processing helix chain 'A' and resid 2688 through 2699 removed outlier: 3.824A pdb=" N ALA A2698 " --> pdb=" O GLU A2694 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N GLN A2699 " --> pdb=" O ILE A2695 " (cutoff:3.500A) Processing helix chain 'A' and resid 2703 through 2716 removed outlier: 3.954A pdb=" N ARG A2716 " --> pdb=" O ARG A2712 " (cutoff:3.500A) Processing helix chain 'A' and resid 2721 through 2727 removed outlier: 3.614A pdb=" N PHE A2725 " --> pdb=" O ARG A2722 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N GLU A2727 " --> pdb=" O PHE A2724 " (cutoff:3.500A) Processing helix chain 'A' and resid 2732 through 2755 removed outlier: 4.024A pdb=" N GLN A2737 " --> pdb=" O ASP A2733 " (cutoff:3.500A) Processing helix chain 'A' and resid 2763 through 2765 No H-bonds generated for 'chain 'A' and resid 2763 through 2765' Processing helix chain 'A' and resid 2786 through 2788 No H-bonds generated for 'chain 'A' and resid 2786 through 2788' Processing helix chain 'A' and resid 2802 through 2806 Processing helix chain 'A' and resid 2816 through 2828 Processing helix chain 'A' and resid 2832 through 2843 Processing helix chain 'A' and resid 2854 through 2860 Processing helix chain 'A' and resid 2898 through 2909 Processing helix chain 'A' and resid 2916 through 2927 Processing helix chain 'A' and resid 2930 through 2933 No H-bonds generated for 'chain 'A' and resid 2930 through 2933' Processing sheet with id= A, first strand: chain 'A' and resid 2534 through 2536 Processing sheet with id= B, first strand: chain 'A' and resid 2658 through 2662 removed outlier: 3.602A pdb=" N LYS A2593 " --> pdb=" O VAL A2609 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 2667 through 2669 893 hydrogen bonds defined for protein. 2592 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 9.17 Time building geometry restraints manager: 9.93 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.36: 7281 1.36 - 1.51: 6789 1.51 - 1.65: 7234 1.65 - 1.80: 126 1.80 - 1.95: 24 Bond restraints: 21454 Sorted by residual: bond pdb=" N PRO A1378 " pdb=" CD PRO A1378 " ideal model delta sigma weight residual 1.473 1.528 -0.055 1.40e-02 5.10e+03 1.54e+01 bond pdb=" CG LEU A2084 " pdb=" CD2 LEU A2084 " ideal model delta sigma weight residual 1.521 1.412 0.109 3.30e-02 9.18e+02 1.08e+01 bond pdb=" CG LEU A2608 " pdb=" CD1 LEU A2608 " ideal model delta sigma weight residual 1.521 1.415 0.106 3.30e-02 9.18e+02 1.03e+01 bond pdb=" CB VAL A2067 " pdb=" CG2 VAL A2067 " ideal model delta sigma weight residual 1.521 1.416 0.105 3.30e-02 9.18e+02 1.02e+01 bond pdb=" CA SER A 897 " pdb=" C SER A 897 " ideal model delta sigma weight residual 1.523 1.479 0.044 1.80e-02 3.09e+03 6.05e+00 ... (remaining 21449 not shown) Histogram of bond angle deviations from ideal: 95.53 - 103.32: 258 103.32 - 111.10: 8768 111.10 - 118.88: 8779 118.88 - 126.66: 10948 126.66 - 134.44: 319 Bond angle restraints: 29072 Sorted by residual: angle pdb=" CA PRO A1378 " pdb=" N PRO A1378 " pdb=" CD PRO A1378 " ideal model delta sigma weight residual 112.00 99.07 12.93 1.40e+00 5.10e-01 8.53e+01 angle pdb=" N VAL A2482 " pdb=" CA VAL A2482 " pdb=" C VAL A2482 " ideal model delta sigma weight residual 109.34 119.20 -9.86 2.08e+00 2.31e-01 2.25e+01 angle pdb=" C VAL A2482 " pdb=" CA VAL A2482 " pdb=" CB VAL A2482 " ideal model delta sigma weight residual 111.29 105.49 5.80 1.64e+00 3.72e-01 1.25e+01 angle pdb=" CA LEU A1652 " pdb=" CB LEU A1652 " pdb=" CG LEU A1652 " ideal model delta sigma weight residual 116.30 127.71 -11.41 3.50e+00 8.16e-02 1.06e+01 angle pdb=" CB LEU A2608 " pdb=" CG LEU A2608 " pdb=" CD1 LEU A2608 " ideal model delta sigma weight residual 110.70 101.66 9.04 3.00e+00 1.11e-01 9.07e+00 ... (remaining 29067 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 30.39: 12608 30.39 - 60.79: 449 60.79 - 91.18: 30 91.18 - 121.57: 0 121.57 - 151.96: 1 Dihedral angle restraints: 13088 sinusoidal: 5289 harmonic: 7799 Sorted by residual: dihedral pdb=" CA GLU A2481 " pdb=" C GLU A2481 " pdb=" N VAL A2482 " pdb=" CA VAL A2482 " ideal model delta harmonic sigma weight residual -180.00 -123.75 -56.25 0 5.00e+00 4.00e-02 1.27e+02 dihedral pdb=" CA MET A 677 " pdb=" C MET A 677 " pdb=" N GLU A 678 " pdb=" CA GLU A 678 " ideal model delta harmonic sigma weight residual 180.00 146.14 33.86 0 5.00e+00 4.00e-02 4.59e+01 dihedral pdb=" CA MET A 259 " pdb=" C MET A 259 " pdb=" N LYS A 260 " pdb=" CA LYS A 260 " ideal model delta harmonic sigma weight residual -180.00 -148.85 -31.15 0 5.00e+00 4.00e-02 3.88e+01 ... (remaining 13085 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.037: 1828 0.037 - 0.074: 1108 0.074 - 0.110: 307 0.110 - 0.147: 84 0.147 - 0.184: 6 Chirality restraints: 3333 Sorted by residual: chirality pdb=" CB ILE A2852 " pdb=" CA ILE A2852 " pdb=" CG1 ILE A2852 " pdb=" CG2 ILE A2852 " both_signs ideal model delta sigma weight residual False 2.64 2.46 0.18 2.00e-01 2.50e+01 8.45e-01 chirality pdb=" CA PRO A2732 " pdb=" N PRO A2732 " pdb=" C PRO A2732 " pdb=" CB PRO A2732 " both_signs ideal model delta sigma weight residual False 2.72 2.55 0.17 2.00e-01 2.50e+01 6.84e-01 chirality pdb=" CA ARG A1863 " pdb=" N ARG A1863 " pdb=" C ARG A1863 " pdb=" CB ARG A1863 " both_signs ideal model delta sigma weight residual False 2.51 2.36 0.15 2.00e-01 2.50e+01 5.90e-01 ... (remaining 3330 not shown) Planarity restraints: 3710 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLU A1377 " 0.131 5.00e-02 4.00e+02 1.84e-01 5.42e+01 pdb=" N PRO A1378 " -0.318 5.00e-02 4.00e+02 pdb=" CA PRO A1378 " 0.103 5.00e-02 4.00e+02 pdb=" CD PRO A1378 " 0.084 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA GLU A2481 " 0.019 2.00e-02 2.50e+03 3.82e-02 1.46e+01 pdb=" C GLU A2481 " -0.066 2.00e-02 2.50e+03 pdb=" O GLU A2481 " 0.025 2.00e-02 2.50e+03 pdb=" N VAL A2482 " 0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL A1443 " 0.011 2.00e-02 2.50e+03 2.31e-02 5.32e+00 pdb=" C VAL A1443 " -0.040 2.00e-02 2.50e+03 pdb=" O VAL A1443 " 0.015 2.00e-02 2.50e+03 pdb=" N ASP A1444 " 0.013 2.00e-02 2.50e+03 ... (remaining 3707 not shown) Histogram of nonbonded interaction distances: 2.02 - 2.59: 265 2.59 - 3.17: 18921 3.17 - 3.75: 31128 3.75 - 4.32: 45143 4.32 - 4.90: 73898 Nonbonded interactions: 169355 Sorted by model distance: nonbonded pdb=" O2A AGS A3001 " pdb="MG MG A3002 " model vdw 2.016 2.170 nonbonded pdb=" NH1 ARG A2647 " pdb=" OE2 GLU A2774 " model vdw 2.064 2.520 nonbonded pdb=" O ASN A 569 " pdb=" OG1 THR A 573 " model vdw 2.065 2.440 nonbonded pdb=" OD1 ASP A2012 " pdb=" OG SER A2034 " model vdw 2.097 2.440 nonbonded pdb=" O ALA A 764 " pdb=" OG1 THR A 767 " model vdw 2.101 2.440 ... (remaining 169350 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 6.920 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: 0.000 Extract box with map and model: 10.140 Check model and map are aligned: 0.310 Set scattering table: 0.230 Process input model: 61.940 Find NCS groups from input model: 0.710 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.630 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 82.960 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7818 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 : 0.011 0.109 21454 Z= 0.680 Angle : 0.825 12.933 29072 Z= 0.436 Chirality : 0.048 0.184 3333 Planarity : 0.006 0.184 3710 Dihedral : 14.944 151.964 7995 Min Nonbonded Distance : 2.016 Molprobity Statistics. All-atom Clashscore : 13.54 Ramachandran Plot: Outliers : 0.15 % Allowed : 8.42 % Favored : 91.42 % Rotamer: Outliers : 6.72 % Allowed : 9.17 % Favored : 84.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.16 % 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: -4.42 (0.13), residues: 2612 helix: -2.51 (0.10), residues: 1720 sheet: -1.78 (0.85), residues: 31 loop : -3.58 (0.17), residues: 861 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.003 TRP A2940 HIS 0.008 0.001 HIS A 474 PHE 0.023 0.002 PHE A2724 TYR 0.022 0.002 TYR A2742 ARG 0.006 0.001 ARG A2799 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5224 Ramachandran restraints generated. 2612 Oldfield, 0 Emsley, 2612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5224 Ramachandran restraints generated. 2612 Oldfield, 0 Emsley, 2612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 609 residues out of total 2292 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 154 poor density : 455 time to evaluate : 2.391 Fit side-chains TARDY: cannot create tardy model for: "THR A 27 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 56 TYR cc_start: 0.6829 (OUTLIER) cc_final: 0.5077 (m-80) REVERT: A 136 LEU cc_start: 0.5293 (OUTLIER) cc_final: 0.5074 (pt) REVERT: A 269 PHE cc_start: 0.8020 (OUTLIER) cc_final: 0.7005 (t80) REVERT: A 272 PHE cc_start: 0.7664 (t80) cc_final: 0.7406 (t80) REVERT: A 274 ILE cc_start: 0.8125 (mt) cc_final: 0.7920 (mp) REVERT: A 327 THR cc_start: 0.8180 (OUTLIER) cc_final: 0.7971 (m) REVERT: A 330 TYR cc_start: 0.8547 (m-80) cc_final: 0.7742 (m-80) REVERT: A 358 TYR cc_start: 0.6400 (OUTLIER) cc_final: 0.6105 (t80) REVERT: A 366 ARG cc_start: 0.6604 (mtm180) cc_final: 0.5962 (mtp-110) REVERT: A 450 HIS cc_start: 0.7624 (OUTLIER) cc_final: 0.7164 (t70) REVERT: A 601 MET cc_start: 0.7339 (mtp) cc_final: 0.6906 (mtt) REVERT: A 671 TRP cc_start: 0.7972 (t60) cc_final: 0.7723 (t60) REVERT: A 892 ARG cc_start: 0.6880 (OUTLIER) cc_final: 0.6460 (mtt-85) REVERT: A 947 ARG cc_start: 0.7824 (OUTLIER) cc_final: 0.7416 (ptm160) REVERT: A 980 GLU cc_start: 0.8182 (OUTLIER) cc_final: 0.7926 (mp0) REVERT: A 1051 GLU cc_start: 0.6847 (OUTLIER) cc_final: 0.5496 (pp20) REVERT: A 1075 LYS cc_start: 0.7887 (mttt) cc_final: 0.7336 (mptt) REVERT: A 1185 LEU cc_start: 0.9191 (OUTLIER) cc_final: 0.8945 (mp) REVERT: A 1204 GLN cc_start: 0.8421 (OUTLIER) cc_final: 0.7533 (mp10) REVERT: A 1314 PHE cc_start: 0.8952 (OUTLIER) cc_final: 0.8330 (p90) REVERT: A 1316 GLN cc_start: 0.8255 (OUTLIER) cc_final: 0.8030 (pm20) REVERT: A 1558 GLU cc_start: 0.7515 (mp0) cc_final: 0.7300 (mt-10) REVERT: A 1709 ASP cc_start: 0.6866 (m-30) cc_final: 0.6641 (m-30) REVERT: A 1968 ARG cc_start: 0.7573 (ttm-80) cc_final: 0.6364 (tpm170) outliers start: 154 outliers final: 80 residues processed: 586 average time/residue: 0.3744 time to fit residues: 326.2013 Evaluate side-chains 344 residues out of total 2292 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 94 poor density : 250 time to evaluate : 2.409 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 THR Chi-restraints excluded: chain A residue 31 ASP Chi-restraints excluded: chain A residue 36 LEU Chi-restraints excluded: chain A residue 56 TYR Chi-restraints excluded: chain A residue 106 VAL Chi-restraints excluded: chain A residue 136 LEU Chi-restraints excluded: chain A residue 140 TYR Chi-restraints excluded: chain A residue 167 VAL Chi-restraints excluded: chain A residue 222 VAL Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 261 ILE Chi-restraints excluded: chain A residue 269 PHE Chi-restraints excluded: chain A residue 314 ASN Chi-restraints excluded: chain A residue 316 ILE Chi-restraints excluded: chain A residue 325 TYR Chi-restraints excluded: chain A residue 327 THR Chi-restraints excluded: chain A residue 358 TYR Chi-restraints excluded: chain A residue 360 ARG Chi-restraints excluded: chain A residue 362 GLU Chi-restraints excluded: chain A residue 377 MET Chi-restraints excluded: chain A residue 383 HIS Chi-restraints excluded: chain A residue 450 HIS Chi-restraints excluded: chain A residue 485 THR Chi-restraints excluded: chain A residue 494 THR Chi-restraints excluded: chain A residue 500 VAL Chi-restraints excluded: chain A residue 502 SER Chi-restraints excluded: chain A residue 522 LEU Chi-restraints excluded: chain A residue 523 SER Chi-restraints excluded: chain A residue 532 LEU Chi-restraints excluded: chain A residue 542 ILE Chi-restraints excluded: chain A residue 564 LEU Chi-restraints excluded: chain A residue 582 ILE Chi-restraints excluded: chain A residue 602 PHE Chi-restraints excluded: chain A residue 613 ILE Chi-restraints excluded: chain A residue 632 HIS Chi-restraints excluded: chain A residue 649 TYR Chi-restraints excluded: chain A residue 651 ILE Chi-restraints excluded: chain A residue 660 LEU Chi-restraints excluded: chain A residue 667 ILE Chi-restraints excluded: chain A residue 683 TYR Chi-restraints excluded: chain A residue 756 GLU Chi-restraints excluded: chain A residue 766 LEU Chi-restraints excluded: chain A residue 767 THR Chi-restraints excluded: chain A residue 774 ASP Chi-restraints excluded: chain A residue 777 ASN Chi-restraints excluded: chain A residue 781 SER Chi-restraints excluded: chain A residue 811 PHE Chi-restraints excluded: chain A residue 831 ILE Chi-restraints excluded: chain A residue 833 LEU Chi-restraints excluded: chain A residue 841 LEU Chi-restraints excluded: chain A residue 854 ARG Chi-restraints excluded: chain A residue 892 ARG Chi-restraints excluded: chain A residue 894 ILE Chi-restraints excluded: chain A residue 915 ASP Chi-restraints excluded: chain A residue 931 ILE Chi-restraints excluded: chain A residue 947 ARG Chi-restraints excluded: chain A residue 956 SER Chi-restraints excluded: chain A residue 968 ILE Chi-restraints excluded: chain A residue 980 GLU Chi-restraints excluded: chain A residue 986 VAL Chi-restraints excluded: chain A residue 997 SER Chi-restraints excluded: chain A residue 1012 MET Chi-restraints excluded: chain A residue 1051 GLU Chi-restraints excluded: chain A residue 1063 SER Chi-restraints excluded: chain A residue 1076 LEU Chi-restraints excluded: chain A residue 1080 ILE Chi-restraints excluded: chain A residue 1127 LEU Chi-restraints excluded: chain A residue 1160 THR Chi-restraints excluded: chain A residue 1161 HIS Chi-restraints excluded: chain A residue 1164 LEU Chi-restraints excluded: chain A residue 1185 LEU Chi-restraints excluded: chain A residue 1202 SER Chi-restraints excluded: chain A residue 1204 GLN Chi-restraints excluded: chain A residue 1218 ASP Chi-restraints excluded: chain A residue 1219 LEU Chi-restraints excluded: chain A residue 1230 ILE Chi-restraints excluded: chain A residue 1258 SER Chi-restraints excluded: chain A residue 1262 ILE Chi-restraints excluded: chain A residue 1271 ILE Chi-restraints excluded: chain A residue 1314 PHE Chi-restraints excluded: chain A residue 1316 GLN Chi-restraints excluded: chain A residue 1372 SER Chi-restraints excluded: chain A residue 1397 THR Chi-restraints excluded: chain A residue 1410 VAL Chi-restraints excluded: chain A residue 1414 ILE Chi-restraints excluded: chain A residue 1450 ASP Chi-restraints excluded: chain A residue 1527 PHE Chi-restraints excluded: chain A residue 2126 ASP Chi-restraints excluded: chain A residue 2410 VAL Chi-restraints excluded: chain A residue 2547 LEU Chi-restraints excluded: chain A residue 2600 THR Chi-restraints excluded: chain A residue 2613 ASN Chi-restraints excluded: chain A residue 2649 TYR Chi-restraints excluded: chain A residue 2792 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 265 random chunks: chunk 223 optimal weight: 0.9980 chunk 200 optimal weight: 0.9990 chunk 111 optimal weight: 2.9990 chunk 68 optimal weight: 4.9990 chunk 135 optimal weight: 0.9980 chunk 107 optimal weight: 7.9990 chunk 207 optimal weight: 0.9990 chunk 80 optimal weight: 0.8980 chunk 126 optimal weight: 3.9990 chunk 154 optimal weight: 0.9980 chunk 240 optimal weight: 0.5980 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 248 HIS A 252 GLN A 293 GLN A 418 HIS A 454 HIS A 607 GLN A 643 ASN A 824 HIS A 933 ASN A1027 ASN A1062 GLN A1106 HIS A1192 GLN A1298 ASN A1345 HIS A1354 GLN A1512 HIS A1542 ASN A1551 ASN A1574 GLN A1577 ASN ** A1656 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1665 GLN A1844 ASN A2179 GLN A2239 GLN A2255 GLN A2294 GLN A2304 GLN A2354 GLN A2356 GLN A2360 GLN A2380 ASN A2446 GLN A2518 HIS A2572 HIS A2624 GLN A2641 GLN A2678 HIS A2754 HIS A2770 HIS A2861 GLN A2925 ASN Total number of N/Q/H flips: 42 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7854 moved from start: 0.2363 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 21454 Z= 0.227 Angle : 0.647 11.010 29072 Z= 0.321 Chirality : 0.041 0.257 3333 Planarity : 0.005 0.073 3710 Dihedral : 9.633 156.535 3073 Min Nonbonded Distance : 2.112 Molprobity Statistics. All-atom Clashscore : 9.92 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.59 % Favored : 95.37 % Rotamer: Outliers : 5.28 % Allowed : 14.84 % Favored : 79.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % 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: -2.47 (0.15), residues: 2612 helix: -1.00 (0.12), residues: 1750 sheet: -0.96 (0.91), residues: 31 loop : -2.87 (0.19), residues: 831 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A1730 HIS 0.007 0.001 HIS A2518 PHE 0.032 0.001 PHE A2112 TYR 0.017 0.001 TYR A 325 ARG 0.005 0.000 ARG A 328 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5224 Ramachandran restraints generated. 2612 Oldfield, 0 Emsley, 2612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5224 Ramachandran restraints generated. 2612 Oldfield, 0 Emsley, 2612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 408 residues out of total 2292 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 121 poor density : 287 time to evaluate : 2.569 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 248 HIS cc_start: 0.5963 (OUTLIER) cc_final: 0.5517 (t-90) REVERT: A 269 PHE cc_start: 0.7957 (OUTLIER) cc_final: 0.6967 (t80) REVERT: A 330 TYR cc_start: 0.8389 (m-80) cc_final: 0.7596 (m-80) REVERT: A 366 ARG cc_start: 0.6612 (mtm180) cc_final: 0.5973 (mtp-110) REVERT: A 368 GLN cc_start: 0.6963 (OUTLIER) cc_final: 0.6194 (mm110) REVERT: A 450 HIS cc_start: 0.7149 (OUTLIER) cc_final: 0.6748 (t70) REVERT: A 523 SER cc_start: 0.5911 (OUTLIER) cc_final: 0.5356 (p) REVERT: A 641 LEU cc_start: 0.8465 (tt) cc_final: 0.8103 (mp) REVERT: A 892 ARG cc_start: 0.6515 (OUTLIER) cc_final: 0.6112 (mtt-85) REVERT: A 947 ARG cc_start: 0.7696 (OUTLIER) cc_final: 0.7436 (ptm160) REVERT: A 961 PRO cc_start: 0.6974 (Cg_exo) cc_final: 0.6760 (Cg_endo) REVERT: A 1051 GLU cc_start: 0.6921 (OUTLIER) cc_final: 0.5484 (pp20) REVERT: A 1442 VAL cc_start: 0.8452 (t) cc_final: 0.8222 (t) REVERT: A 1558 GLU cc_start: 0.7527 (mp0) cc_final: 0.7258 (mt-10) REVERT: A 1871 MET cc_start: 0.8844 (mmt) cc_final: 0.8504 (mmt) REVERT: A 1968 ARG cc_start: 0.7556 (ttm-80) cc_final: 0.6441 (tpm170) REVERT: A 2147 LEU cc_start: 0.8147 (OUTLIER) cc_final: 0.7893 (mp) REVERT: A 2637 ARG cc_start: 0.8383 (OUTLIER) cc_final: 0.8034 (ttt90) outliers start: 121 outliers final: 66 residues processed: 386 average time/residue: 0.3410 time to fit residues: 201.6300 Evaluate side-chains 307 residues out of total 2292 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 76 poor density : 231 time to evaluate : 2.415 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 ASP Chi-restraints excluded: chain A residue 140 TYR Chi-restraints excluded: chain A residue 167 VAL Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 248 HIS Chi-restraints excluded: chain A residue 261 ILE Chi-restraints excluded: chain A residue 269 PHE Chi-restraints excluded: chain A residue 314 ASN Chi-restraints excluded: chain A residue 325 TYR Chi-restraints excluded: chain A residue 327 THR Chi-restraints excluded: chain A residue 360 ARG Chi-restraints excluded: chain A residue 368 GLN Chi-restraints excluded: chain A residue 383 HIS Chi-restraints excluded: chain A residue 450 HIS Chi-restraints excluded: chain A residue 494 THR Chi-restraints excluded: chain A residue 523 SER Chi-restraints excluded: chain A residue 532 LEU Chi-restraints excluded: chain A residue 542 ILE Chi-restraints excluded: chain A residue 573 THR Chi-restraints excluded: chain A residue 602 PHE Chi-restraints excluded: chain A residue 626 LEU Chi-restraints excluded: chain A residue 632 HIS Chi-restraints excluded: chain A residue 649 TYR Chi-restraints excluded: chain A residue 667 ILE Chi-restraints excluded: chain A residue 728 PHE Chi-restraints excluded: chain A residue 756 GLU Chi-restraints excluded: chain A residue 774 ASP Chi-restraints excluded: chain A residue 777 ASN Chi-restraints excluded: chain A residue 781 SER Chi-restraints excluded: chain A residue 811 PHE Chi-restraints excluded: chain A residue 831 ILE Chi-restraints excluded: chain A residue 833 LEU Chi-restraints excluded: chain A residue 892 ARG Chi-restraints excluded: chain A residue 896 LEU Chi-restraints excluded: chain A residue 914 LEU Chi-restraints excluded: chain A residue 915 ASP Chi-restraints excluded: chain A residue 931 ILE Chi-restraints excluded: chain A residue 947 ARG Chi-restraints excluded: chain A residue 960 VAL Chi-restraints excluded: chain A residue 986 VAL Chi-restraints excluded: chain A residue 997 SER Chi-restraints excluded: chain A residue 1012 MET Chi-restraints excluded: chain A residue 1051 GLU Chi-restraints excluded: chain A residue 1076 LEU Chi-restraints excluded: chain A residue 1127 LEU Chi-restraints excluded: chain A residue 1139 ILE Chi-restraints excluded: chain A residue 1160 THR Chi-restraints excluded: chain A residue 1161 HIS Chi-restraints excluded: chain A residue 1164 LEU Chi-restraints excluded: chain A residue 1202 SER Chi-restraints excluded: chain A residue 1218 ASP Chi-restraints excluded: chain A residue 1397 THR Chi-restraints excluded: chain A residue 1450 ASP Chi-restraints excluded: chain A residue 1527 PHE Chi-restraints excluded: chain A residue 1654 GLU Chi-restraints excluded: chain A residue 1686 ASP Chi-restraints excluded: chain A residue 2045 SER Chi-restraints excluded: chain A residue 2057 SER Chi-restraints excluded: chain A residue 2074 SER Chi-restraints excluded: chain A residue 2126 ASP Chi-restraints excluded: chain A residue 2147 LEU Chi-restraints excluded: chain A residue 2230 ILE Chi-restraints excluded: chain A residue 2282 LYS Chi-restraints excluded: chain A residue 2392 ASP Chi-restraints excluded: chain A residue 2540 SER Chi-restraints excluded: chain A residue 2565 SER Chi-restraints excluded: chain A residue 2600 THR Chi-restraints excluded: chain A residue 2613 ASN Chi-restraints excluded: chain A residue 2637 ARG Chi-restraints excluded: chain A residue 2649 TYR Chi-restraints excluded: chain A residue 2705 THR Chi-restraints excluded: chain A residue 2709 VAL Chi-restraints excluded: chain A residue 2752 LEU Chi-restraints excluded: chain A residue 2801 THR Chi-restraints excluded: chain A residue 2853 SER Chi-restraints excluded: chain A residue 2917 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 265 random chunks: chunk 133 optimal weight: 8.9990 chunk 74 optimal weight: 0.0170 chunk 200 optimal weight: 1.9990 chunk 163 optimal weight: 1.9990 chunk 66 optimal weight: 3.9990 chunk 241 optimal weight: 0.6980 chunk 260 optimal weight: 0.8980 chunk 214 optimal weight: 0.1980 chunk 239 optimal weight: 0.6980 chunk 82 optimal weight: 1.9990 chunk 193 optimal weight: 0.0170 overall best weight: 0.3256 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 293 GLN A 383 HIS A 418 HIS ** A1656 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7822 moved from start: 0.2970 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 21454 Z= 0.159 Angle : 0.567 10.188 29072 Z= 0.279 Chirality : 0.039 0.391 3333 Planarity : 0.004 0.056 3710 Dihedral : 8.111 157.796 2990 Min Nonbonded Distance : 2.118 Molprobity Statistics. All-atom Clashscore : 9.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.36 % Favored : 95.64 % Rotamer: Outliers : 3.75 % Allowed : 17.24 % Favored : 79.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.50 (0.16), residues: 2612 helix: -0.23 (0.13), residues: 1768 sheet: -0.91 (0.87), residues: 38 loop : -2.59 (0.20), residues: 806 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A1730 HIS 0.021 0.001 HIS A 248 PHE 0.017 0.001 PHE A2112 TYR 0.012 0.001 TYR A1079 ARG 0.007 0.000 ARG A1287 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5224 Ramachandran restraints generated. 2612 Oldfield, 0 Emsley, 2612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5224 Ramachandran restraints generated. 2612 Oldfield, 0 Emsley, 2612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 339 residues out of total 2292 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 86 poor density : 253 time to evaluate : 2.541 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 60 PHE cc_start: 0.5923 (OUTLIER) cc_final: 0.5116 (m-80) REVERT: A 137 LEU cc_start: 0.7898 (tp) cc_final: 0.7678 (tp) REVERT: A 269 PHE cc_start: 0.7925 (OUTLIER) cc_final: 0.6892 (t80) REVERT: A 327 THR cc_start: 0.8382 (OUTLIER) cc_final: 0.7966 (p) REVERT: A 330 TYR cc_start: 0.8285 (m-80) cc_final: 0.7506 (m-80) REVERT: A 360 ARG cc_start: 0.5332 (OUTLIER) cc_final: 0.4849 (mtt180) REVERT: A 366 ARG cc_start: 0.6451 (mtm180) cc_final: 0.6081 (mtp-110) REVERT: A 641 LEU cc_start: 0.8471 (tt) cc_final: 0.8235 (mp) REVERT: A 811 PHE cc_start: 0.5276 (OUTLIER) cc_final: 0.4952 (t80) REVERT: A 947 ARG cc_start: 0.7717 (OUTLIER) cc_final: 0.7433 (ptm160) REVERT: A 961 PRO cc_start: 0.7125 (Cg_exo) cc_final: 0.6872 (Cg_endo) REVERT: A 1051 GLU cc_start: 0.6986 (OUTLIER) cc_final: 0.5649 (pp20) REVERT: A 1249 LEU cc_start: 0.8744 (OUTLIER) cc_final: 0.8247 (pp) REVERT: A 1442 VAL cc_start: 0.8538 (t) cc_final: 0.8325 (t) REVERT: A 1968 ARG cc_start: 0.7525 (ttm-80) cc_final: 0.6416 (tpm170) REVERT: A 2593 LYS cc_start: 0.8009 (OUTLIER) cc_final: 0.6284 (ptpp) REVERT: A 2637 ARG cc_start: 0.8390 (OUTLIER) cc_final: 0.8048 (ttt90) REVERT: A 2836 GLN cc_start: 0.8001 (tm-30) cc_final: 0.7626 (tm-30) outliers start: 86 outliers final: 49 residues processed: 326 average time/residue: 0.3328 time to fit residues: 168.4126 Evaluate side-chains 275 residues out of total 2292 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 216 time to evaluate : 2.399 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 ASP Chi-restraints excluded: chain A residue 60 PHE Chi-restraints excluded: chain A residue 140 TYR Chi-restraints excluded: chain A residue 167 VAL Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 261 ILE Chi-restraints excluded: chain A residue 269 PHE Chi-restraints excluded: chain A residue 325 TYR Chi-restraints excluded: chain A residue 327 THR Chi-restraints excluded: chain A residue 360 ARG Chi-restraints excluded: chain A residue 383 HIS Chi-restraints excluded: chain A residue 522 LEU Chi-restraints excluded: chain A residue 602 PHE Chi-restraints excluded: chain A residue 632 HIS Chi-restraints excluded: chain A residue 649 TYR Chi-restraints excluded: chain A residue 654 LEU Chi-restraints excluded: chain A residue 667 ILE Chi-restraints excluded: chain A residue 728 PHE Chi-restraints excluded: chain A residue 756 GLU Chi-restraints excluded: chain A residue 774 ASP Chi-restraints excluded: chain A residue 777 ASN Chi-restraints excluded: chain A residue 811 PHE Chi-restraints excluded: chain A residue 831 ILE Chi-restraints excluded: chain A residue 833 LEU Chi-restraints excluded: chain A residue 896 LEU Chi-restraints excluded: chain A residue 914 LEU Chi-restraints excluded: chain A residue 915 ASP Chi-restraints excluded: chain A residue 931 ILE Chi-restraints excluded: chain A residue 947 ARG Chi-restraints excluded: chain A residue 980 GLU Chi-restraints excluded: chain A residue 986 VAL Chi-restraints excluded: chain A residue 1012 MET Chi-restraints excluded: chain A residue 1051 GLU Chi-restraints excluded: chain A residue 1076 LEU Chi-restraints excluded: chain A residue 1127 LEU Chi-restraints excluded: chain A residue 1133 THR Chi-restraints excluded: chain A residue 1139 ILE Chi-restraints excluded: chain A residue 1160 THR Chi-restraints excluded: chain A residue 1161 HIS Chi-restraints excluded: chain A residue 1202 SER Chi-restraints excluded: chain A residue 1218 ASP Chi-restraints excluded: chain A residue 1221 ARG Chi-restraints excluded: chain A residue 1249 LEU Chi-restraints excluded: chain A residue 1398 ILE Chi-restraints excluded: chain A residue 1450 ASP Chi-restraints excluded: chain A residue 1527 PHE Chi-restraints excluded: chain A residue 1654 GLU Chi-restraints excluded: chain A residue 1717 GLN Chi-restraints excluded: chain A residue 1758 GLU Chi-restraints excluded: chain A residue 2045 SER Chi-restraints excluded: chain A residue 2057 SER Chi-restraints excluded: chain A residue 2126 ASP Chi-restraints excluded: chain A residue 2392 ASP Chi-restraints excluded: chain A residue 2540 SER Chi-restraints excluded: chain A residue 2593 LYS Chi-restraints excluded: chain A residue 2613 ASN Chi-restraints excluded: chain A residue 2637 ARG Chi-restraints excluded: chain A residue 2733 ASP Chi-restraints excluded: chain A residue 2853 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 265 random chunks: chunk 238 optimal weight: 2.9990 chunk 181 optimal weight: 2.9990 chunk 125 optimal weight: 1.9990 chunk 26 optimal weight: 6.9990 chunk 115 optimal weight: 0.9990 chunk 161 optimal weight: 0.9980 chunk 241 optimal weight: 0.6980 chunk 256 optimal weight: 1.9990 chunk 126 optimal weight: 0.1980 chunk 229 optimal weight: 2.9990 chunk 69 optimal weight: 4.9990 overall best weight: 0.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 248 HIS A 293 GLN A 418 HIS A 450 HIS A 557 ASN A 600 ASN A1551 ASN ** A1656 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A2129 GLN A2290 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7889 moved from start: 0.3289 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 21454 Z= 0.222 Angle : 0.570 9.783 29072 Z= 0.279 Chirality : 0.040 0.388 3333 Planarity : 0.004 0.049 3710 Dihedral : 7.695 157.995 2968 Min Nonbonded Distance : 2.078 Molprobity Statistics. All-atom Clashscore : 8.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.79 % Favored : 95.21 % Rotamer: Outliers : 4.76 % Allowed : 17.63 % Favored : 77.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.11 (0.17), residues: 2612 helix: 0.06 (0.13), residues: 1772 sheet: -0.73 (0.87), residues: 38 loop : -2.45 (0.20), residues: 802 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP A1730 HIS 0.008 0.001 HIS A 612 PHE 0.022 0.001 PHE A2112 TYR 0.017 0.001 TYR A2649 ARG 0.005 0.000 ARG A2603 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5224 Ramachandran restraints generated. 2612 Oldfield, 0 Emsley, 2612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5224 Ramachandran restraints generated. 2612 Oldfield, 0 Emsley, 2612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 351 residues out of total 2292 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 109 poor density : 242 time to evaluate : 2.416 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 60 PHE cc_start: 0.5851 (OUTLIER) cc_final: 0.5047 (m-80) REVERT: A 248 HIS cc_start: 0.5797 (OUTLIER) cc_final: 0.5341 (t-90) REVERT: A 269 PHE cc_start: 0.8059 (OUTLIER) cc_final: 0.7104 (t80) REVERT: A 293 GLN cc_start: 0.6529 (pt0) cc_final: 0.6123 (tp-100) REVERT: A 327 THR cc_start: 0.8566 (OUTLIER) cc_final: 0.8106 (p) REVERT: A 330 TYR cc_start: 0.8260 (m-80) cc_final: 0.7467 (m-80) REVERT: A 360 ARG cc_start: 0.5105 (OUTLIER) cc_final: 0.4769 (mtt180) REVERT: A 366 ARG cc_start: 0.6461 (mtm180) cc_final: 0.6128 (mtp-110) REVERT: A 408 LEU cc_start: 0.8335 (tp) cc_final: 0.8124 (tp) REVERT: A 734 GLU cc_start: 0.7096 (OUTLIER) cc_final: 0.6558 (tt0) REVERT: A 811 PHE cc_start: 0.5250 (OUTLIER) cc_final: 0.4990 (t80) REVERT: A 919 LEU cc_start: 0.8462 (mm) cc_final: 0.8117 (mt) REVERT: A 961 PRO cc_start: 0.7049 (Cg_exo) cc_final: 0.6791 (Cg_endo) REVERT: A 1051 GLU cc_start: 0.7063 (OUTLIER) cc_final: 0.5693 (pp20) REVERT: A 1249 LEU cc_start: 0.8748 (OUTLIER) cc_final: 0.8274 (pp) REVERT: A 1270 ASP cc_start: 0.7884 (m-30) cc_final: 0.7201 (p0) REVERT: A 1442 VAL cc_start: 0.8559 (t) cc_final: 0.8351 (t) REVERT: A 1610 ILE cc_start: 0.8166 (tt) cc_final: 0.7624 (mt) REVERT: A 1628 GLU cc_start: 0.6842 (mp0) cc_final: 0.6542 (mp0) REVERT: A 1659 GLU cc_start: 0.7566 (OUTLIER) cc_final: 0.7058 (mp0) REVERT: A 1968 ARG cc_start: 0.7578 (ttm-80) cc_final: 0.6521 (tpm170) REVERT: A 2147 LEU cc_start: 0.8082 (OUTLIER) cc_final: 0.7855 (mp) REVERT: A 2550 MET cc_start: 0.8395 (mmm) cc_final: 0.8101 (mmm) REVERT: A 2593 LYS cc_start: 0.8170 (OUTLIER) cc_final: 0.6474 (ptpp) REVERT: A 2637 ARG cc_start: 0.8428 (OUTLIER) cc_final: 0.8112 (ttt90) REVERT: A 2836 GLN cc_start: 0.8185 (tm-30) cc_final: 0.7741 (tm-30) outliers start: 109 outliers final: 67 residues processed: 333 average time/residue: 0.3208 time to fit residues: 167.9816 Evaluate side-chains 298 residues out of total 2292 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 80 poor density : 218 time to evaluate : 2.606 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 ASP Chi-restraints excluded: chain A residue 60 PHE Chi-restraints excluded: chain A residue 140 TYR Chi-restraints excluded: chain A residue 167 VAL Chi-restraints excluded: chain A residue 176 LEU Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 248 HIS Chi-restraints excluded: chain A residue 261 ILE Chi-restraints excluded: chain A residue 269 PHE Chi-restraints excluded: chain A residue 271 THR Chi-restraints excluded: chain A residue 314 ASN Chi-restraints excluded: chain A residue 325 TYR Chi-restraints excluded: chain A residue 327 THR Chi-restraints excluded: chain A residue 360 ARG Chi-restraints excluded: chain A residue 377 MET Chi-restraints excluded: chain A residue 383 HIS Chi-restraints excluded: chain A residue 494 THR Chi-restraints excluded: chain A residue 522 LEU Chi-restraints excluded: chain A residue 526 TRP Chi-restraints excluded: chain A residue 542 ILE Chi-restraints excluded: chain A residue 595 LEU Chi-restraints excluded: chain A residue 602 PHE Chi-restraints excluded: chain A residue 632 HIS Chi-restraints excluded: chain A residue 649 TYR Chi-restraints excluded: chain A residue 667 ILE Chi-restraints excluded: chain A residue 728 PHE Chi-restraints excluded: chain A residue 734 GLU Chi-restraints excluded: chain A residue 756 GLU Chi-restraints excluded: chain A residue 774 ASP Chi-restraints excluded: chain A residue 777 ASN Chi-restraints excluded: chain A residue 811 PHE Chi-restraints excluded: chain A residue 831 ILE Chi-restraints excluded: chain A residue 896 LEU Chi-restraints excluded: chain A residue 914 LEU Chi-restraints excluded: chain A residue 915 ASP Chi-restraints excluded: chain A residue 931 ILE Chi-restraints excluded: chain A residue 959 ILE Chi-restraints excluded: chain A residue 960 VAL Chi-restraints excluded: chain A residue 980 GLU Chi-restraints excluded: chain A residue 986 VAL Chi-restraints excluded: chain A residue 1051 GLU Chi-restraints excluded: chain A residue 1127 LEU Chi-restraints excluded: chain A residue 1133 THR Chi-restraints excluded: chain A residue 1160 THR Chi-restraints excluded: chain A residue 1161 HIS Chi-restraints excluded: chain A residue 1202 SER Chi-restraints excluded: chain A residue 1218 ASP Chi-restraints excluded: chain A residue 1249 LEU Chi-restraints excluded: chain A residue 1398 ILE Chi-restraints excluded: chain A residue 1450 ASP Chi-restraints excluded: chain A residue 1527 PHE Chi-restraints excluded: chain A residue 1608 ASP Chi-restraints excluded: chain A residue 1654 GLU Chi-restraints excluded: chain A residue 1659 GLU Chi-restraints excluded: chain A residue 1686 ASP Chi-restraints excluded: chain A residue 1717 GLN Chi-restraints excluded: chain A residue 1757 LEU Chi-restraints excluded: chain A residue 1758 GLU Chi-restraints excluded: chain A residue 2057 SER Chi-restraints excluded: chain A residue 2147 LEU Chi-restraints excluded: chain A residue 2208 MET Chi-restraints excluded: chain A residue 2230 ILE Chi-restraints excluded: chain A residue 2392 ASP Chi-restraints excluded: chain A residue 2539 ASN Chi-restraints excluded: chain A residue 2540 SER Chi-restraints excluded: chain A residue 2565 SER Chi-restraints excluded: chain A residue 2593 LYS Chi-restraints excluded: chain A residue 2613 ASN Chi-restraints excluded: chain A residue 2630 SER Chi-restraints excluded: chain A residue 2637 ARG Chi-restraints excluded: chain A residue 2651 VAL Chi-restraints excluded: chain A residue 2666 ASN Chi-restraints excluded: chain A residue 2705 THR Chi-restraints excluded: chain A residue 2713 VAL Chi-restraints excluded: chain A residue 2733 ASP Chi-restraints excluded: chain A residue 2752 LEU Chi-restraints excluded: chain A residue 2774 GLU Chi-restraints excluded: chain A residue 2801 THR Chi-restraints excluded: chain A residue 2853 SER Chi-restraints excluded: chain A residue 2917 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 265 random chunks: chunk 213 optimal weight: 0.4980 chunk 145 optimal weight: 1.9990 chunk 3 optimal weight: 6.9990 chunk 190 optimal weight: 4.9990 chunk 105 optimal weight: 0.9980 chunk 218 optimal weight: 1.9990 chunk 177 optimal weight: 0.6980 chunk 0 optimal weight: 10.0000 chunk 130 optimal weight: 0.9990 chunk 229 optimal weight: 0.0040 chunk 64 optimal weight: 0.0170 overall best weight: 0.4430 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 248 HIS A 418 HIS A1551 ASN ** A1656 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1870 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7856 moved from start: 0.3557 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.064 21454 Z= 0.151 Angle : 0.535 9.681 29072 Z= 0.261 Chirality : 0.039 0.348 3333 Planarity : 0.004 0.046 3710 Dihedral : 7.376 159.934 2955 Min Nonbonded Distance : 2.119 Molprobity Statistics. All-atom Clashscore : 8.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.98 % Favored : 96.02 % Rotamer: Outliers : 3.49 % Allowed : 19.55 % Favored : 76.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.88 % 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: -0.66 (0.17), residues: 2612 helix: 0.40 (0.13), residues: 1775 sheet: -0.48 (0.88), residues: 38 loop : -2.29 (0.20), residues: 799 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 616 HIS 0.018 0.001 HIS A 248 PHE 0.012 0.001 PHE A2112 TYR 0.010 0.001 TYR A2649 ARG 0.004 0.000 ARG A2603 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5224 Ramachandran restraints generated. 2612 Oldfield, 0 Emsley, 2612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5224 Ramachandran restraints generated. 2612 Oldfield, 0 Emsley, 2612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 313 residues out of total 2292 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 80 poor density : 233 time to evaluate : 2.443 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 137 LEU cc_start: 0.7958 (tp) cc_final: 0.7668 (tp) REVERT: A 140 TYR cc_start: 0.7133 (OUTLIER) cc_final: 0.6757 (m-10) REVERT: A 269 PHE cc_start: 0.7984 (OUTLIER) cc_final: 0.7043 (t80) REVERT: A 293 GLN cc_start: 0.6388 (pt0) cc_final: 0.6097 (tp-100) REVERT: A 327 THR cc_start: 0.8572 (OUTLIER) cc_final: 0.8107 (p) REVERT: A 330 TYR cc_start: 0.8231 (m-80) cc_final: 0.7415 (m-80) REVERT: A 366 ARG cc_start: 0.6444 (mtm180) cc_final: 0.6042 (mtp-110) REVERT: A 399 GLU cc_start: 0.6688 (pm20) cc_final: 0.6420 (pm20) REVERT: A 734 GLU cc_start: 0.7046 (OUTLIER) cc_final: 0.6448 (tt0) REVERT: A 811 PHE cc_start: 0.5093 (OUTLIER) cc_final: 0.4868 (t80) REVERT: A 919 LEU cc_start: 0.8460 (mm) cc_final: 0.8111 (mt) REVERT: A 961 PRO cc_start: 0.7088 (Cg_exo) cc_final: 0.6811 (Cg_endo) REVERT: A 1051 GLU cc_start: 0.7105 (OUTLIER) cc_final: 0.5781 (pp20) REVERT: A 1249 LEU cc_start: 0.8726 (OUTLIER) cc_final: 0.8255 (pp) REVERT: A 1270 ASP cc_start: 0.7786 (m-30) cc_final: 0.7103 (p0) REVERT: A 1442 VAL cc_start: 0.8492 (t) cc_final: 0.8284 (t) REVERT: A 1610 ILE cc_start: 0.8190 (tt) cc_final: 0.7703 (mt) REVERT: A 1628 GLU cc_start: 0.6929 (mp0) cc_final: 0.6634 (mp0) REVERT: A 1659 GLU cc_start: 0.7518 (OUTLIER) cc_final: 0.7031 (mp0) REVERT: A 1968 ARG cc_start: 0.7585 (ttm-80) cc_final: 0.6524 (tpm170) REVERT: A 2140 MET cc_start: 0.7785 (tpt) cc_final: 0.7533 (tpt) REVERT: A 2147 LEU cc_start: 0.8044 (OUTLIER) cc_final: 0.7821 (mp) REVERT: A 2593 LYS cc_start: 0.8151 (OUTLIER) cc_final: 0.7738 (ptpp) REVERT: A 2836 GLN cc_start: 0.8115 (tm-30) cc_final: 0.7549 (tm-30) outliers start: 80 outliers final: 52 residues processed: 300 average time/residue: 0.3388 time to fit residues: 160.7537 Evaluate side-chains 269 residues out of total 2292 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 207 time to evaluate : 2.461 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 ASP Chi-restraints excluded: chain A residue 140 TYR Chi-restraints excluded: chain A residue 167 VAL Chi-restraints excluded: chain A residue 261 ILE Chi-restraints excluded: chain A residue 269 PHE Chi-restraints excluded: chain A residue 271 THR Chi-restraints excluded: chain A residue 325 TYR Chi-restraints excluded: chain A residue 327 THR Chi-restraints excluded: chain A residue 383 HIS Chi-restraints excluded: chain A residue 522 LEU Chi-restraints excluded: chain A residue 526 TRP Chi-restraints excluded: chain A residue 542 ILE Chi-restraints excluded: chain A residue 602 PHE Chi-restraints excluded: chain A residue 632 HIS Chi-restraints excluded: chain A residue 649 TYR Chi-restraints excluded: chain A residue 728 PHE Chi-restraints excluded: chain A residue 734 GLU Chi-restraints excluded: chain A residue 756 GLU Chi-restraints excluded: chain A residue 774 ASP Chi-restraints excluded: chain A residue 777 ASN Chi-restraints excluded: chain A residue 811 PHE Chi-restraints excluded: chain A residue 831 ILE Chi-restraints excluded: chain A residue 896 LEU Chi-restraints excluded: chain A residue 897 SER Chi-restraints excluded: chain A residue 914 LEU Chi-restraints excluded: chain A residue 915 ASP Chi-restraints excluded: chain A residue 931 ILE Chi-restraints excluded: chain A residue 950 MET Chi-restraints excluded: chain A residue 980 GLU Chi-restraints excluded: chain A residue 986 VAL Chi-restraints excluded: chain A residue 1016 LEU Chi-restraints excluded: chain A residue 1051 GLU Chi-restraints excluded: chain A residue 1127 LEU Chi-restraints excluded: chain A residue 1133 THR Chi-restraints excluded: chain A residue 1160 THR Chi-restraints excluded: chain A residue 1161 HIS Chi-restraints excluded: chain A residue 1249 LEU Chi-restraints excluded: chain A residue 1398 ILE Chi-restraints excluded: chain A residue 1450 ASP Chi-restraints excluded: chain A residue 1527 PHE Chi-restraints excluded: chain A residue 1571 ARG Chi-restraints excluded: chain A residue 1594 ILE Chi-restraints excluded: chain A residue 1652 LEU Chi-restraints excluded: chain A residue 1654 GLU Chi-restraints excluded: chain A residue 1659 GLU Chi-restraints excluded: chain A residue 1686 ASP Chi-restraints excluded: chain A residue 1717 GLN Chi-restraints excluded: chain A residue 1758 GLU Chi-restraints excluded: chain A residue 2057 SER Chi-restraints excluded: chain A residue 2147 LEU Chi-restraints excluded: chain A residue 2208 MET Chi-restraints excluded: chain A residue 2392 ASP Chi-restraints excluded: chain A residue 2540 SER Chi-restraints excluded: chain A residue 2547 LEU Chi-restraints excluded: chain A residue 2565 SER Chi-restraints excluded: chain A residue 2593 LYS Chi-restraints excluded: chain A residue 2613 ASN Chi-restraints excluded: chain A residue 2666 ASN Chi-restraints excluded: chain A residue 2733 ASP Chi-restraints excluded: chain A residue 2751 MET Chi-restraints excluded: chain A residue 2752 LEU Chi-restraints excluded: chain A residue 2853 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 265 random chunks: chunk 86 optimal weight: 10.0000 chunk 230 optimal weight: 0.7980 chunk 50 optimal weight: 0.8980 chunk 150 optimal weight: 0.4980 chunk 63 optimal weight: 6.9990 chunk 256 optimal weight: 2.9990 chunk 212 optimal weight: 1.9990 chunk 118 optimal weight: 1.9990 chunk 21 optimal weight: 2.9990 chunk 84 optimal weight: 0.9990 chunk 134 optimal weight: 2.9990 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 248 HIS A 394 HIS A1161 HIS ** A1656 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7904 moved from start: 0.3735 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 21454 Z= 0.221 Angle : 0.559 11.938 29072 Z= 0.272 Chirality : 0.040 0.322 3333 Planarity : 0.004 0.046 3710 Dihedral : 7.212 160.244 2945 Min Nonbonded Distance : 2.059 Molprobity Statistics. All-atom Clashscore : 8.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.71 % Favored : 95.29 % Rotamer: Outliers : 4.19 % Allowed : 19.55 % Favored : 76.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.88 % 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: -0.57 (0.17), residues: 2612 helix: 0.44 (0.13), residues: 1783 sheet: -0.50 (0.87), residues: 38 loop : -2.20 (0.21), residues: 791 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 616 HIS 0.004 0.001 HIS A 248 PHE 0.016 0.001 PHE A2112 TYR 0.014 0.001 TYR A2649 ARG 0.005 0.000 ARG A2603 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5224 Ramachandran restraints generated. 2612 Oldfield, 0 Emsley, 2612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5224 Ramachandran restraints generated. 2612 Oldfield, 0 Emsley, 2612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 322 residues out of total 2292 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 96 poor density : 226 time to evaluate : 2.469 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 60 PHE cc_start: 0.5906 (OUTLIER) cc_final: 0.5188 (m-80) REVERT: A 137 LEU cc_start: 0.8057 (tp) cc_final: 0.7817 (tp) REVERT: A 140 TYR cc_start: 0.7131 (OUTLIER) cc_final: 0.6755 (m-10) REVERT: A 269 PHE cc_start: 0.7991 (OUTLIER) cc_final: 0.7070 (t80) REVERT: A 293 GLN cc_start: 0.6443 (pt0) cc_final: 0.5927 (tp-100) REVERT: A 327 THR cc_start: 0.8382 (OUTLIER) cc_final: 0.7958 (p) REVERT: A 330 TYR cc_start: 0.8247 (m-80) cc_final: 0.7468 (m-80) REVERT: A 358 TYR cc_start: 0.6498 (OUTLIER) cc_final: 0.4660 (t80) REVERT: A 366 ARG cc_start: 0.6477 (mtm180) cc_final: 0.5975 (mtp-110) REVERT: A 399 GLU cc_start: 0.6607 (pm20) cc_final: 0.6087 (pm20) REVERT: A 734 GLU cc_start: 0.7095 (OUTLIER) cc_final: 0.6353 (tt0) REVERT: A 919 LEU cc_start: 0.8522 (mm) cc_final: 0.8218 (mt) REVERT: A 1051 GLU cc_start: 0.7089 (OUTLIER) cc_final: 0.5751 (pp20) REVERT: A 1249 LEU cc_start: 0.8749 (OUTLIER) cc_final: 0.8290 (pp) REVERT: A 1270 ASP cc_start: 0.7750 (m-30) cc_final: 0.7124 (p0) REVERT: A 1610 ILE cc_start: 0.8268 (tt) cc_final: 0.7959 (mt) REVERT: A 1659 GLU cc_start: 0.7613 (OUTLIER) cc_final: 0.7073 (mp0) REVERT: A 1730 TRP cc_start: 0.7606 (OUTLIER) cc_final: 0.6446 (m-10) REVERT: A 1968 ARG cc_start: 0.7619 (ttm-80) cc_final: 0.6552 (tpm170) REVERT: A 2140 MET cc_start: 0.7810 (tpt) cc_final: 0.7512 (tpt) REVERT: A 2147 LEU cc_start: 0.8079 (OUTLIER) cc_final: 0.7863 (mp) REVERT: A 2583 MET cc_start: 0.6869 (ptp) cc_final: 0.6596 (ptp) REVERT: A 2593 LYS cc_start: 0.8210 (OUTLIER) cc_final: 0.7778 (ptpp) REVERT: A 2637 ARG cc_start: 0.8413 (OUTLIER) cc_final: 0.8096 (ttt90) REVERT: A 2836 GLN cc_start: 0.8195 (tm-30) cc_final: 0.7886 (tm-30) outliers start: 96 outliers final: 67 residues processed: 308 average time/residue: 0.3248 time to fit residues: 157.4032 Evaluate side-chains 288 residues out of total 2292 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 80 poor density : 208 time to evaluate : 2.606 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 ASP Chi-restraints excluded: chain A residue 60 PHE Chi-restraints excluded: chain A residue 140 TYR Chi-restraints excluded: chain A residue 167 VAL Chi-restraints excluded: chain A residue 176 LEU Chi-restraints excluded: chain A residue 261 ILE Chi-restraints excluded: chain A residue 269 PHE Chi-restraints excluded: chain A residue 325 TYR Chi-restraints excluded: chain A residue 327 THR Chi-restraints excluded: chain A residue 358 TYR Chi-restraints excluded: chain A residue 377 MET Chi-restraints excluded: chain A residue 494 THR Chi-restraints excluded: chain A residue 522 LEU Chi-restraints excluded: chain A residue 526 TRP Chi-restraints excluded: chain A residue 542 ILE Chi-restraints excluded: chain A residue 602 PHE Chi-restraints excluded: chain A residue 632 HIS Chi-restraints excluded: chain A residue 649 TYR Chi-restraints excluded: chain A residue 728 PHE Chi-restraints excluded: chain A residue 734 GLU Chi-restraints excluded: chain A residue 756 GLU Chi-restraints excluded: chain A residue 774 ASP Chi-restraints excluded: chain A residue 777 ASN Chi-restraints excluded: chain A residue 831 ILE Chi-restraints excluded: chain A residue 833 LEU Chi-restraints excluded: chain A residue 894 ILE Chi-restraints excluded: chain A residue 896 LEU Chi-restraints excluded: chain A residue 897 SER Chi-restraints excluded: chain A residue 914 LEU Chi-restraints excluded: chain A residue 915 ASP Chi-restraints excluded: chain A residue 931 ILE Chi-restraints excluded: chain A residue 960 VAL Chi-restraints excluded: chain A residue 980 GLU Chi-restraints excluded: chain A residue 986 VAL Chi-restraints excluded: chain A residue 1016 LEU Chi-restraints excluded: chain A residue 1051 GLU Chi-restraints excluded: chain A residue 1127 LEU Chi-restraints excluded: chain A residue 1133 THR Chi-restraints excluded: chain A residue 1160 THR Chi-restraints excluded: chain A residue 1161 HIS Chi-restraints excluded: chain A residue 1221 ARG Chi-restraints excluded: chain A residue 1249 LEU Chi-restraints excluded: chain A residue 1398 ILE Chi-restraints excluded: chain A residue 1450 ASP Chi-restraints excluded: chain A residue 1527 PHE Chi-restraints excluded: chain A residue 1594 ILE Chi-restraints excluded: chain A residue 1606 ASP Chi-restraints excluded: chain A residue 1608 ASP Chi-restraints excluded: chain A residue 1652 LEU Chi-restraints excluded: chain A residue 1654 GLU Chi-restraints excluded: chain A residue 1659 GLU Chi-restraints excluded: chain A residue 1686 ASP Chi-restraints excluded: chain A residue 1717 GLN Chi-restraints excluded: chain A residue 1730 TRP Chi-restraints excluded: chain A residue 1757 LEU Chi-restraints excluded: chain A residue 1758 GLU Chi-restraints excluded: chain A residue 2057 SER Chi-restraints excluded: chain A residue 2119 MET Chi-restraints excluded: chain A residue 2147 LEU Chi-restraints excluded: chain A residue 2208 MET Chi-restraints excluded: chain A residue 2226 MET Chi-restraints excluded: chain A residue 2230 ILE Chi-restraints excluded: chain A residue 2392 ASP Chi-restraints excluded: chain A residue 2422 VAL Chi-restraints excluded: chain A residue 2443 THR Chi-restraints excluded: chain A residue 2514 SER Chi-restraints excluded: chain A residue 2540 SER Chi-restraints excluded: chain A residue 2565 SER Chi-restraints excluded: chain A residue 2593 LYS Chi-restraints excluded: chain A residue 2613 ASN Chi-restraints excluded: chain A residue 2637 ARG Chi-restraints excluded: chain A residue 2651 VAL Chi-restraints excluded: chain A residue 2666 ASN Chi-restraints excluded: chain A residue 2709 VAL Chi-restraints excluded: chain A residue 2713 VAL Chi-restraints excluded: chain A residue 2733 ASP Chi-restraints excluded: chain A residue 2751 MET Chi-restraints excluded: chain A residue 2752 LEU Chi-restraints excluded: chain A residue 2853 SER Chi-restraints excluded: chain A residue 2917 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 265 random chunks: chunk 247 optimal weight: 1.9990 chunk 28 optimal weight: 0.7980 chunk 146 optimal weight: 2.9990 chunk 187 optimal weight: 0.6980 chunk 145 optimal weight: 1.9990 chunk 215 optimal weight: 1.9990 chunk 143 optimal weight: 0.8980 chunk 255 optimal weight: 0.9990 chunk 159 optimal weight: 0.7980 chunk 155 optimal weight: 0.0670 chunk 117 optimal weight: 0.5980 overall best weight: 0.5918 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 248 HIS ** A1656 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7878 moved from start: 0.3912 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.085 21454 Z= 0.166 Angle : 0.532 11.500 29072 Z= 0.260 Chirality : 0.039 0.313 3333 Planarity : 0.004 0.045 3710 Dihedral : 6.971 161.756 2941 Min Nonbonded Distance : 2.092 Molprobity Statistics. All-atom Clashscore : 8.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.10 % Favored : 95.90 % Rotamer: Outliers : 3.84 % Allowed : 20.25 % Favored : 75.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.88 % 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: -0.32 (0.17), residues: 2612 helix: 0.61 (0.13), residues: 1783 sheet: -0.38 (0.86), residues: 38 loop : -2.07 (0.21), residues: 791 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A1617 HIS 0.006 0.001 HIS A 248 PHE 0.011 0.001 PHE A2112 TYR 0.010 0.001 TYR A2649 ARG 0.005 0.000 ARG A 892 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5224 Ramachandran restraints generated. 2612 Oldfield, 0 Emsley, 2612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5224 Ramachandran restraints generated. 2612 Oldfield, 0 Emsley, 2612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 304 residues out of total 2292 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 88 poor density : 216 time to evaluate : 2.651 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 60 PHE cc_start: 0.5897 (OUTLIER) cc_final: 0.5260 (m-80) REVERT: A 140 TYR cc_start: 0.7085 (OUTLIER) cc_final: 0.6685 (m-10) REVERT: A 269 PHE cc_start: 0.8084 (OUTLIER) cc_final: 0.7252 (t80) REVERT: A 327 THR cc_start: 0.8431 (OUTLIER) cc_final: 0.8034 (p) REVERT: A 330 TYR cc_start: 0.8298 (m-80) cc_final: 0.7614 (m-80) REVERT: A 358 TYR cc_start: 0.6590 (OUTLIER) cc_final: 0.4846 (t80) REVERT: A 366 ARG cc_start: 0.6357 (mtm180) cc_final: 0.5914 (mtp-110) REVERT: A 399 GLU cc_start: 0.6583 (pm20) cc_final: 0.6062 (pm20) REVERT: A 734 GLU cc_start: 0.6894 (OUTLIER) cc_final: 0.6133 (tt0) REVERT: A 919 LEU cc_start: 0.8535 (mm) cc_final: 0.8231 (mt) REVERT: A 1051 GLU cc_start: 0.7202 (OUTLIER) cc_final: 0.5899 (pp20) REVERT: A 1249 LEU cc_start: 0.8779 (OUTLIER) cc_final: 0.8318 (pp) REVERT: A 1270 ASP cc_start: 0.7635 (m-30) cc_final: 0.7108 (p0) REVERT: A 1610 ILE cc_start: 0.8281 (tt) cc_final: 0.8044 (mt) REVERT: A 1659 GLU cc_start: 0.7598 (OUTLIER) cc_final: 0.7038 (mp0) REVERT: A 1730 TRP cc_start: 0.7635 (OUTLIER) cc_final: 0.6457 (m-10) REVERT: A 1968 ARG cc_start: 0.7719 (ttm-80) cc_final: 0.6601 (tpm170) REVERT: A 2140 MET cc_start: 0.7797 (tpt) cc_final: 0.7512 (tpt) REVERT: A 2147 LEU cc_start: 0.8071 (OUTLIER) cc_final: 0.7848 (mp) REVERT: A 2238 LYS cc_start: 0.6950 (pptt) cc_final: 0.6478 (pptt) REVERT: A 2522 MET cc_start: 0.5502 (mtp) cc_final: 0.5301 (mtp) REVERT: A 2583 MET cc_start: 0.6762 (ptp) cc_final: 0.6527 (ptp) REVERT: A 2593 LYS cc_start: 0.8355 (OUTLIER) cc_final: 0.7880 (ptpp) REVERT: A 2637 ARG cc_start: 0.8389 (OUTLIER) cc_final: 0.8037 (ttt90) REVERT: A 2836 GLN cc_start: 0.8199 (tm-30) cc_final: 0.7640 (tm-30) outliers start: 88 outliers final: 63 residues processed: 291 average time/residue: 0.3191 time to fit residues: 147.9026 Evaluate side-chains 281 residues out of total 2292 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 76 poor density : 205 time to evaluate : 2.273 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 PHE Chi-restraints excluded: chain A residue 140 TYR Chi-restraints excluded: chain A residue 167 VAL Chi-restraints excluded: chain A residue 261 ILE Chi-restraints excluded: chain A residue 269 PHE Chi-restraints excluded: chain A residue 314 ASN Chi-restraints excluded: chain A residue 325 TYR Chi-restraints excluded: chain A residue 327 THR Chi-restraints excluded: chain A residue 358 TYR Chi-restraints excluded: chain A residue 383 HIS Chi-restraints excluded: chain A residue 494 THR Chi-restraints excluded: chain A residue 522 LEU Chi-restraints excluded: chain A residue 526 TRP Chi-restraints excluded: chain A residue 542 ILE Chi-restraints excluded: chain A residue 602 PHE Chi-restraints excluded: chain A residue 632 HIS Chi-restraints excluded: chain A residue 649 TYR Chi-restraints excluded: chain A residue 654 LEU Chi-restraints excluded: chain A residue 728 PHE Chi-restraints excluded: chain A residue 734 GLU Chi-restraints excluded: chain A residue 756 GLU Chi-restraints excluded: chain A residue 774 ASP Chi-restraints excluded: chain A residue 777 ASN Chi-restraints excluded: chain A residue 831 ILE Chi-restraints excluded: chain A residue 833 LEU Chi-restraints excluded: chain A residue 894 ILE Chi-restraints excluded: chain A residue 896 LEU Chi-restraints excluded: chain A residue 897 SER Chi-restraints excluded: chain A residue 914 LEU Chi-restraints excluded: chain A residue 915 ASP Chi-restraints excluded: chain A residue 931 ILE Chi-restraints excluded: chain A residue 960 VAL Chi-restraints excluded: chain A residue 980 GLU Chi-restraints excluded: chain A residue 986 VAL Chi-restraints excluded: chain A residue 1016 LEU Chi-restraints excluded: chain A residue 1051 GLU Chi-restraints excluded: chain A residue 1076 LEU Chi-restraints excluded: chain A residue 1127 LEU Chi-restraints excluded: chain A residue 1133 THR Chi-restraints excluded: chain A residue 1160 THR Chi-restraints excluded: chain A residue 1161 HIS Chi-restraints excluded: chain A residue 1249 LEU Chi-restraints excluded: chain A residue 1398 ILE Chi-restraints excluded: chain A residue 1450 ASP Chi-restraints excluded: chain A residue 1527 PHE Chi-restraints excluded: chain A residue 1594 ILE Chi-restraints excluded: chain A residue 1606 ASP Chi-restraints excluded: chain A residue 1652 LEU Chi-restraints excluded: chain A residue 1654 GLU Chi-restraints excluded: chain A residue 1659 GLU Chi-restraints excluded: chain A residue 1686 ASP Chi-restraints excluded: chain A residue 1717 GLN Chi-restraints excluded: chain A residue 1730 TRP Chi-restraints excluded: chain A residue 1758 GLU Chi-restraints excluded: chain A residue 2057 SER Chi-restraints excluded: chain A residue 2147 LEU Chi-restraints excluded: chain A residue 2208 MET Chi-restraints excluded: chain A residue 2226 MET Chi-restraints excluded: chain A residue 2240 SER Chi-restraints excluded: chain A residue 2261 LEU Chi-restraints excluded: chain A residue 2392 ASP Chi-restraints excluded: chain A residue 2443 THR Chi-restraints excluded: chain A residue 2514 SER Chi-restraints excluded: chain A residue 2539 ASN Chi-restraints excluded: chain A residue 2540 SER Chi-restraints excluded: chain A residue 2565 SER Chi-restraints excluded: chain A residue 2593 LYS Chi-restraints excluded: chain A residue 2601 ASP Chi-restraints excluded: chain A residue 2637 ARG Chi-restraints excluded: chain A residue 2651 VAL Chi-restraints excluded: chain A residue 2666 ASN Chi-restraints excluded: chain A residue 2733 ASP Chi-restraints excluded: chain A residue 2751 MET Chi-restraints excluded: chain A residue 2752 LEU Chi-restraints excluded: chain A residue 2801 THR Chi-restraints excluded: chain A residue 2853 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 265 random chunks: chunk 158 optimal weight: 1.9990 chunk 101 optimal weight: 0.9980 chunk 152 optimal weight: 0.9990 chunk 76 optimal weight: 6.9990 chunk 50 optimal weight: 5.9990 chunk 49 optimal weight: 4.9990 chunk 162 optimal weight: 0.9980 chunk 174 optimal weight: 0.9980 chunk 126 optimal weight: 0.7980 chunk 23 optimal weight: 3.9990 chunk 200 optimal weight: 0.5980 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1593 ASN ** A1656 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7899 moved from start: 0.4028 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.085 21454 Z= 0.198 Angle : 0.545 9.286 29072 Z= 0.266 Chirality : 0.039 0.305 3333 Planarity : 0.004 0.045 3710 Dihedral : 6.940 162.242 2937 Min Nonbonded Distance : 2.064 Molprobity Statistics. All-atom Clashscore : 8.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.82 % Favored : 95.18 % Rotamer: Outliers : 3.93 % Allowed : 19.99 % Favored : 76.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.88 % 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 (0.17), residues: 2612 helix: 0.63 (0.13), residues: 1785 sheet: -0.35 (0.84), residues: 38 loop : -1.90 (0.22), residues: 789 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 616 HIS 0.006 0.001 HIS A 383 PHE 0.013 0.001 PHE A2112 TYR 0.012 0.001 TYR A2649 ARG 0.009 0.000 ARG A 892 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5224 Ramachandran restraints generated. 2612 Oldfield, 0 Emsley, 2612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5224 Ramachandran restraints generated. 2612 Oldfield, 0 Emsley, 2612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 293 residues out of total 2292 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 90 poor density : 203 time to evaluate : 2.860 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 60 PHE cc_start: 0.5775 (OUTLIER) cc_final: 0.5281 (m-80) REVERT: A 140 TYR cc_start: 0.7096 (OUTLIER) cc_final: 0.6632 (m-10) REVERT: A 269 PHE cc_start: 0.8124 (OUTLIER) cc_final: 0.7289 (t80) REVERT: A 327 THR cc_start: 0.8433 (OUTLIER) cc_final: 0.8010 (p) REVERT: A 330 TYR cc_start: 0.8294 (m-80) cc_final: 0.7578 (m-80) REVERT: A 358 TYR cc_start: 0.6672 (OUTLIER) cc_final: 0.5131 (t80) REVERT: A 399 GLU cc_start: 0.6634 (pm20) cc_final: 0.6133 (pm20) REVERT: A 734 GLU cc_start: 0.6803 (OUTLIER) cc_final: 0.6004 (tt0) REVERT: A 919 LEU cc_start: 0.8532 (mm) cc_final: 0.8231 (mt) REVERT: A 1051 GLU cc_start: 0.7161 (OUTLIER) cc_final: 0.5900 (pp20) REVERT: A 1249 LEU cc_start: 0.8722 (OUTLIER) cc_final: 0.8401 (pp) REVERT: A 1270 ASP cc_start: 0.7551 (m-30) cc_final: 0.7082 (p0) REVERT: A 1610 ILE cc_start: 0.8355 (tt) cc_final: 0.8135 (mt) REVERT: A 1659 GLU cc_start: 0.7654 (OUTLIER) cc_final: 0.7082 (mp0) REVERT: A 1730 TRP cc_start: 0.7670 (OUTLIER) cc_final: 0.6613 (m-10) REVERT: A 1939 LEU cc_start: 0.8502 (mt) cc_final: 0.8217 (mp) REVERT: A 1968 ARG cc_start: 0.7744 (ttm-80) cc_final: 0.6618 (tpm170) REVERT: A 2147 LEU cc_start: 0.8134 (OUTLIER) cc_final: 0.7902 (mp) REVERT: A 2238 LYS cc_start: 0.7028 (pptt) cc_final: 0.6493 (pptt) REVERT: A 2522 MET cc_start: 0.5627 (mtp) cc_final: 0.5410 (mtp) REVERT: A 2583 MET cc_start: 0.6886 (ptp) cc_final: 0.6675 (ptp) REVERT: A 2593 LYS cc_start: 0.8404 (OUTLIER) cc_final: 0.7917 (ptpp) REVERT: A 2637 ARG cc_start: 0.8383 (OUTLIER) cc_final: 0.8079 (ttt90) REVERT: A 2836 GLN cc_start: 0.8165 (tm-30) cc_final: 0.7624 (tm-30) outliers start: 90 outliers final: 68 residues processed: 279 average time/residue: 0.3266 time to fit residues: 148.1601 Evaluate side-chains 276 residues out of total 2292 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 81 poor density : 195 time to evaluate : 2.510 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 PHE Chi-restraints excluded: chain A residue 140 TYR Chi-restraints excluded: chain A residue 167 VAL Chi-restraints excluded: chain A residue 176 LEU Chi-restraints excluded: chain A residue 253 LEU Chi-restraints excluded: chain A residue 261 ILE Chi-restraints excluded: chain A residue 269 PHE Chi-restraints excluded: chain A residue 325 TYR Chi-restraints excluded: chain A residue 327 THR Chi-restraints excluded: chain A residue 358 TYR Chi-restraints excluded: chain A residue 377 MET Chi-restraints excluded: chain A residue 383 HIS Chi-restraints excluded: chain A residue 494 THR Chi-restraints excluded: chain A residue 522 LEU Chi-restraints excluded: chain A residue 526 TRP Chi-restraints excluded: chain A residue 542 ILE Chi-restraints excluded: chain A residue 602 PHE Chi-restraints excluded: chain A residue 632 HIS Chi-restraints excluded: chain A residue 641 LEU Chi-restraints excluded: chain A residue 649 TYR Chi-restraints excluded: chain A residue 651 ILE Chi-restraints excluded: chain A residue 654 LEU Chi-restraints excluded: chain A residue 728 PHE Chi-restraints excluded: chain A residue 734 GLU Chi-restraints excluded: chain A residue 756 GLU Chi-restraints excluded: chain A residue 766 LEU Chi-restraints excluded: chain A residue 777 ASN Chi-restraints excluded: chain A residue 786 LEU Chi-restraints excluded: chain A residue 831 ILE Chi-restraints excluded: chain A residue 833 LEU Chi-restraints excluded: chain A residue 894 ILE Chi-restraints excluded: chain A residue 896 LEU Chi-restraints excluded: chain A residue 897 SER Chi-restraints excluded: chain A residue 914 LEU Chi-restraints excluded: chain A residue 915 ASP Chi-restraints excluded: chain A residue 931 ILE Chi-restraints excluded: chain A residue 960 VAL Chi-restraints excluded: chain A residue 980 GLU Chi-restraints excluded: chain A residue 986 VAL Chi-restraints excluded: chain A residue 1016 LEU Chi-restraints excluded: chain A residue 1051 GLU Chi-restraints excluded: chain A residue 1076 LEU Chi-restraints excluded: chain A residue 1127 LEU Chi-restraints excluded: chain A residue 1133 THR Chi-restraints excluded: chain A residue 1160 THR Chi-restraints excluded: chain A residue 1161 HIS Chi-restraints excluded: chain A residue 1249 LEU Chi-restraints excluded: chain A residue 1398 ILE Chi-restraints excluded: chain A residue 1450 ASP Chi-restraints excluded: chain A residue 1527 PHE Chi-restraints excluded: chain A residue 1593 ASN Chi-restraints excluded: chain A residue 1594 ILE Chi-restraints excluded: chain A residue 1606 ASP Chi-restraints excluded: chain A residue 1608 ASP Chi-restraints excluded: chain A residue 1652 LEU Chi-restraints excluded: chain A residue 1654 GLU Chi-restraints excluded: chain A residue 1659 GLU Chi-restraints excluded: chain A residue 1686 ASP Chi-restraints excluded: chain A residue 1717 GLN Chi-restraints excluded: chain A residue 1730 TRP Chi-restraints excluded: chain A residue 1758 GLU Chi-restraints excluded: chain A residue 2057 SER Chi-restraints excluded: chain A residue 2147 LEU Chi-restraints excluded: chain A residue 2208 MET Chi-restraints excluded: chain A residue 2226 MET Chi-restraints excluded: chain A residue 2392 ASP Chi-restraints excluded: chain A residue 2422 VAL Chi-restraints excluded: chain A residue 2443 THR Chi-restraints excluded: chain A residue 2514 SER Chi-restraints excluded: chain A residue 2565 SER Chi-restraints excluded: chain A residue 2593 LYS Chi-restraints excluded: chain A residue 2601 ASP Chi-restraints excluded: chain A residue 2637 ARG Chi-restraints excluded: chain A residue 2651 VAL Chi-restraints excluded: chain A residue 2666 ASN Chi-restraints excluded: chain A residue 2713 VAL Chi-restraints excluded: chain A residue 2733 ASP Chi-restraints excluded: chain A residue 2751 MET Chi-restraints excluded: chain A residue 2752 LEU Chi-restraints excluded: chain A residue 2774 GLU Chi-restraints excluded: chain A residue 2801 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 265 random chunks: chunk 232 optimal weight: 2.9990 chunk 244 optimal weight: 0.3980 chunk 223 optimal weight: 3.9990 chunk 238 optimal weight: 1.9990 chunk 143 optimal weight: 0.7980 chunk 103 optimal weight: 6.9990 chunk 186 optimal weight: 0.8980 chunk 73 optimal weight: 0.6980 chunk 215 optimal weight: 0.9990 chunk 225 optimal weight: 0.7980 chunk 237 optimal weight: 0.5980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1656 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1717 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7886 moved from start: 0.4138 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.103 21454 Z= 0.177 Angle : 0.538 8.932 29072 Z= 0.262 Chirality : 0.039 0.307 3333 Planarity : 0.004 0.041 3710 Dihedral : 6.798 163.207 2935 Min Nonbonded Distance : 2.080 Molprobity Statistics. All-atom Clashscore : 8.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.21 % Favored : 95.79 % Rotamer: Outliers : 4.06 % Allowed : 19.73 % Favored : 76.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.88 % 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 (0.17), residues: 2612 helix: 0.74 (0.13), residues: 1786 sheet: 0.15 (0.85), residues: 36 loop : -1.86 (0.22), residues: 790 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 616 HIS 0.006 0.001 HIS A 383 PHE 0.013 0.001 PHE A1100 TYR 0.010 0.001 TYR A2649 ARG 0.004 0.000 ARG A2603 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5224 Ramachandran restraints generated. 2612 Oldfield, 0 Emsley, 2612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5224 Ramachandran restraints generated. 2612 Oldfield, 0 Emsley, 2612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 302 residues out of total 2292 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 93 poor density : 209 time to evaluate : 2.433 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 60 PHE cc_start: 0.5705 (OUTLIER) cc_final: 0.5250 (m-80) REVERT: A 140 TYR cc_start: 0.7080 (OUTLIER) cc_final: 0.6627 (m-10) REVERT: A 269 PHE cc_start: 0.8064 (OUTLIER) cc_final: 0.7264 (t80) REVERT: A 327 THR cc_start: 0.8434 (OUTLIER) cc_final: 0.8010 (p) REVERT: A 330 TYR cc_start: 0.8325 (m-80) cc_final: 0.7639 (m-80) REVERT: A 358 TYR cc_start: 0.6657 (OUTLIER) cc_final: 0.5177 (t80) REVERT: A 734 GLU cc_start: 0.6891 (OUTLIER) cc_final: 0.6137 (tt0) REVERT: A 919 LEU cc_start: 0.8510 (mm) cc_final: 0.8223 (mt) REVERT: A 1051 GLU cc_start: 0.7251 (OUTLIER) cc_final: 0.5985 (pp20) REVERT: A 1249 LEU cc_start: 0.8732 (OUTLIER) cc_final: 0.8408 (pp) REVERT: A 1270 ASP cc_start: 0.7458 (m-30) cc_final: 0.7051 (p0) REVERT: A 1659 GLU cc_start: 0.7634 (OUTLIER) cc_final: 0.7069 (mp0) REVERT: A 1717 GLN cc_start: 0.8194 (OUTLIER) cc_final: 0.6943 (mp-120) REVERT: A 1730 TRP cc_start: 0.7677 (OUTLIER) cc_final: 0.6491 (m-10) REVERT: A 1939 LEU cc_start: 0.8497 (mt) cc_final: 0.8199 (mp) REVERT: A 2147 LEU cc_start: 0.8153 (OUTLIER) cc_final: 0.7939 (mp) REVERT: A 2238 LYS cc_start: 0.6994 (pptt) cc_final: 0.6329 (pptt) REVERT: A 2593 LYS cc_start: 0.8360 (OUTLIER) cc_final: 0.7846 (ptpp) REVERT: A 2637 ARG cc_start: 0.8375 (OUTLIER) cc_final: 0.8062 (ttt90) REVERT: A 2836 GLN cc_start: 0.8242 (tm-30) cc_final: 0.7674 (tm-30) outliers start: 93 outliers final: 68 residues processed: 286 average time/residue: 0.3115 time to fit residues: 145.2032 Evaluate side-chains 281 residues out of total 2292 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 82 poor density : 199 time to evaluate : 2.505 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 PHE Chi-restraints excluded: chain A residue 120 HIS Chi-restraints excluded: chain A residue 140 TYR Chi-restraints excluded: chain A residue 167 VAL Chi-restraints excluded: chain A residue 176 LEU Chi-restraints excluded: chain A residue 253 LEU Chi-restraints excluded: chain A residue 261 ILE Chi-restraints excluded: chain A residue 269 PHE Chi-restraints excluded: chain A residue 325 TYR Chi-restraints excluded: chain A residue 327 THR Chi-restraints excluded: chain A residue 358 TYR Chi-restraints excluded: chain A residue 377 MET Chi-restraints excluded: chain A residue 383 HIS Chi-restraints excluded: chain A residue 494 THR Chi-restraints excluded: chain A residue 522 LEU Chi-restraints excluded: chain A residue 526 TRP Chi-restraints excluded: chain A residue 542 ILE Chi-restraints excluded: chain A residue 602 PHE Chi-restraints excluded: chain A residue 632 HIS Chi-restraints excluded: chain A residue 649 TYR Chi-restraints excluded: chain A residue 651 ILE Chi-restraints excluded: chain A residue 654 LEU Chi-restraints excluded: chain A residue 728 PHE Chi-restraints excluded: chain A residue 734 GLU Chi-restraints excluded: chain A residue 756 GLU Chi-restraints excluded: chain A residue 766 LEU Chi-restraints excluded: chain A residue 777 ASN Chi-restraints excluded: chain A residue 786 LEU Chi-restraints excluded: chain A residue 831 ILE Chi-restraints excluded: chain A residue 833 LEU Chi-restraints excluded: chain A residue 894 ILE Chi-restraints excluded: chain A residue 896 LEU Chi-restraints excluded: chain A residue 897 SER Chi-restraints excluded: chain A residue 914 LEU Chi-restraints excluded: chain A residue 915 ASP Chi-restraints excluded: chain A residue 931 ILE Chi-restraints excluded: chain A residue 960 VAL Chi-restraints excluded: chain A residue 980 GLU Chi-restraints excluded: chain A residue 986 VAL Chi-restraints excluded: chain A residue 1016 LEU Chi-restraints excluded: chain A residue 1051 GLU Chi-restraints excluded: chain A residue 1127 LEU Chi-restraints excluded: chain A residue 1133 THR Chi-restraints excluded: chain A residue 1160 THR Chi-restraints excluded: chain A residue 1161 HIS Chi-restraints excluded: chain A residue 1249 LEU Chi-restraints excluded: chain A residue 1258 SER Chi-restraints excluded: chain A residue 1398 ILE Chi-restraints excluded: chain A residue 1450 ASP Chi-restraints excluded: chain A residue 1527 PHE Chi-restraints excluded: chain A residue 1594 ILE Chi-restraints excluded: chain A residue 1606 ASP Chi-restraints excluded: chain A residue 1652 LEU Chi-restraints excluded: chain A residue 1654 GLU Chi-restraints excluded: chain A residue 1659 GLU Chi-restraints excluded: chain A residue 1686 ASP Chi-restraints excluded: chain A residue 1717 GLN Chi-restraints excluded: chain A residue 1730 TRP Chi-restraints excluded: chain A residue 1737 LEU Chi-restraints excluded: chain A residue 1758 GLU Chi-restraints excluded: chain A residue 2045 SER Chi-restraints excluded: chain A residue 2057 SER Chi-restraints excluded: chain A residue 2147 LEU Chi-restraints excluded: chain A residue 2208 MET Chi-restraints excluded: chain A residue 2226 MET Chi-restraints excluded: chain A residue 2240 SER Chi-restraints excluded: chain A residue 2261 LEU Chi-restraints excluded: chain A residue 2392 ASP Chi-restraints excluded: chain A residue 2422 VAL Chi-restraints excluded: chain A residue 2443 THR Chi-restraints excluded: chain A residue 2514 SER Chi-restraints excluded: chain A residue 2565 SER Chi-restraints excluded: chain A residue 2593 LYS Chi-restraints excluded: chain A residue 2601 ASP Chi-restraints excluded: chain A residue 2637 ARG Chi-restraints excluded: chain A residue 2651 VAL Chi-restraints excluded: chain A residue 2666 ASN Chi-restraints excluded: chain A residue 2733 ASP Chi-restraints excluded: chain A residue 2751 MET Chi-restraints excluded: chain A residue 2752 LEU Chi-restraints excluded: chain A residue 2774 GLU Chi-restraints excluded: chain A residue 2801 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 265 random chunks: chunk 156 optimal weight: 0.9990 chunk 251 optimal weight: 2.9990 chunk 153 optimal weight: 0.0980 chunk 119 optimal weight: 1.9990 chunk 174 optimal weight: 0.6980 chunk 264 optimal weight: 1.9990 chunk 242 optimal weight: 0.5980 chunk 210 optimal weight: 0.9980 chunk 21 optimal weight: 0.2980 chunk 162 optimal weight: 0.4980 chunk 128 optimal weight: 2.9990 overall best weight: 0.4380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1070 GLN A1269 HIS ** A1656 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1717 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7869 moved from start: 0.4260 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.115 21454 Z= 0.169 Angle : 0.544 12.305 29072 Z= 0.263 Chirality : 0.039 0.303 3333 Planarity : 0.004 0.041 3710 Dihedral : 6.729 163.868 2935 Min Nonbonded Distance : 2.098 Molprobity Statistics. All-atom Clashscore : 8.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.02 % Favored : 95.98 % Rotamer: Outliers : 3.80 % Allowed : 20.34 % Favored : 75.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.88 % 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: 0.04 (0.17), residues: 2612 helix: 0.84 (0.13), residues: 1791 sheet: 0.19 (0.85), residues: 36 loop : -1.85 (0.22), residues: 785 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.045 0.001 TRP A 616 HIS 0.005 0.001 HIS A 383 PHE 0.021 0.001 PHE A1100 TYR 0.016 0.001 TYR A1079 ARG 0.004 0.000 ARG A2603 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5224 Ramachandran restraints generated. 2612 Oldfield, 0 Emsley, 2612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5224 Ramachandran restraints generated. 2612 Oldfield, 0 Emsley, 2612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 288 residues out of total 2292 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 87 poor density : 201 time to evaluate : 2.328 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 60 PHE cc_start: 0.5791 (OUTLIER) cc_final: 0.5278 (m-80) REVERT: A 140 TYR cc_start: 0.7142 (OUTLIER) cc_final: 0.6625 (m-80) REVERT: A 269 PHE cc_start: 0.7986 (OUTLIER) cc_final: 0.7190 (t80) REVERT: A 327 THR cc_start: 0.8500 (OUTLIER) cc_final: 0.8062 (p) REVERT: A 330 TYR cc_start: 0.8314 (m-80) cc_final: 0.7515 (m-80) REVERT: A 358 TYR cc_start: 0.6582 (OUTLIER) cc_final: 0.5116 (t80) REVERT: A 734 GLU cc_start: 0.6886 (OUTLIER) cc_final: 0.6107 (tt0) REVERT: A 919 LEU cc_start: 0.8630 (mm) cc_final: 0.8337 (mt) REVERT: A 933 ASN cc_start: 0.7102 (p0) cc_final: 0.6830 (p0) REVERT: A 1051 GLU cc_start: 0.7256 (OUTLIER) cc_final: 0.6024 (pp20) REVERT: A 1249 LEU cc_start: 0.8734 (OUTLIER) cc_final: 0.8501 (pp) REVERT: A 1270 ASP cc_start: 0.7447 (m-30) cc_final: 0.7085 (p0) REVERT: A 1502 LYS cc_start: 0.7929 (ptpt) cc_final: 0.7580 (mmtp) REVERT: A 1659 GLU cc_start: 0.7614 (OUTLIER) cc_final: 0.7061 (mp0) REVERT: A 1717 GLN cc_start: 0.8325 (OUTLIER) cc_final: 0.7573 (mp-120) REVERT: A 1730 TRP cc_start: 0.7714 (OUTLIER) cc_final: 0.6606 (m-10) REVERT: A 1939 LEU cc_start: 0.8492 (mt) cc_final: 0.8193 (mp) REVERT: A 2140 MET cc_start: 0.7770 (tpt) cc_final: 0.7440 (tpt) REVERT: A 2147 LEU cc_start: 0.8093 (OUTLIER) cc_final: 0.7873 (mp) REVERT: A 2238 LYS cc_start: 0.6927 (pptt) cc_final: 0.6272 (pptt) REVERT: A 2593 LYS cc_start: 0.8317 (OUTLIER) cc_final: 0.7616 (mtmm) REVERT: A 2637 ARG cc_start: 0.8363 (OUTLIER) cc_final: 0.8080 (ttt90) REVERT: A 2836 GLN cc_start: 0.8245 (tm-30) cc_final: 0.7674 (tm-30) outliers start: 87 outliers final: 60 residues processed: 272 average time/residue: 0.3474 time to fit residues: 156.1754 Evaluate side-chains 267 residues out of total 2292 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 74 poor density : 193 time to evaluate : 2.348 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 PHE Chi-restraints excluded: chain A residue 63 LEU Chi-restraints excluded: chain A residue 140 TYR Chi-restraints excluded: chain A residue 167 VAL Chi-restraints excluded: chain A residue 253 LEU Chi-restraints excluded: chain A residue 261 ILE Chi-restraints excluded: chain A residue 269 PHE Chi-restraints excluded: chain A residue 325 TYR Chi-restraints excluded: chain A residue 327 THR Chi-restraints excluded: chain A residue 358 TYR Chi-restraints excluded: chain A residue 377 MET Chi-restraints excluded: chain A residue 383 HIS Chi-restraints excluded: chain A residue 494 THR Chi-restraints excluded: chain A residue 522 LEU Chi-restraints excluded: chain A residue 526 TRP Chi-restraints excluded: chain A residue 542 ILE Chi-restraints excluded: chain A residue 602 PHE Chi-restraints excluded: chain A residue 632 HIS Chi-restraints excluded: chain A residue 649 TYR Chi-restraints excluded: chain A residue 651 ILE Chi-restraints excluded: chain A residue 654 LEU Chi-restraints excluded: chain A residue 728 PHE Chi-restraints excluded: chain A residue 734 GLU Chi-restraints excluded: chain A residue 756 GLU Chi-restraints excluded: chain A residue 777 ASN Chi-restraints excluded: chain A residue 831 ILE Chi-restraints excluded: chain A residue 833 LEU Chi-restraints excluded: chain A residue 896 LEU Chi-restraints excluded: chain A residue 897 SER Chi-restraints excluded: chain A residue 914 LEU Chi-restraints excluded: chain A residue 915 ASP Chi-restraints excluded: chain A residue 931 ILE Chi-restraints excluded: chain A residue 960 VAL Chi-restraints excluded: chain A residue 986 VAL Chi-restraints excluded: chain A residue 1016 LEU Chi-restraints excluded: chain A residue 1051 GLU Chi-restraints excluded: chain A residue 1127 LEU Chi-restraints excluded: chain A residue 1160 THR Chi-restraints excluded: chain A residue 1161 HIS Chi-restraints excluded: chain A residue 1249 LEU Chi-restraints excluded: chain A residue 1258 SER Chi-restraints excluded: chain A residue 1398 ILE Chi-restraints excluded: chain A residue 1450 ASP Chi-restraints excluded: chain A residue 1527 PHE Chi-restraints excluded: chain A residue 1606 ASP Chi-restraints excluded: chain A residue 1608 ASP Chi-restraints excluded: chain A residue 1652 LEU Chi-restraints excluded: chain A residue 1659 GLU Chi-restraints excluded: chain A residue 1686 ASP Chi-restraints excluded: chain A residue 1717 GLN Chi-restraints excluded: chain A residue 1730 TRP Chi-restraints excluded: chain A residue 1758 GLU Chi-restraints excluded: chain A residue 2045 SER Chi-restraints excluded: chain A residue 2057 SER Chi-restraints excluded: chain A residue 2147 LEU Chi-restraints excluded: chain A residue 2208 MET Chi-restraints excluded: chain A residue 2226 MET Chi-restraints excluded: chain A residue 2240 SER Chi-restraints excluded: chain A residue 2261 LEU Chi-restraints excluded: chain A residue 2392 ASP Chi-restraints excluded: chain A residue 2422 VAL Chi-restraints excluded: chain A residue 2443 THR Chi-restraints excluded: chain A residue 2514 SER Chi-restraints excluded: chain A residue 2539 ASN Chi-restraints excluded: chain A residue 2565 SER Chi-restraints excluded: chain A residue 2593 LYS Chi-restraints excluded: chain A residue 2601 ASP Chi-restraints excluded: chain A residue 2637 ARG Chi-restraints excluded: chain A residue 2666 ASN Chi-restraints excluded: chain A residue 2733 ASP Chi-restraints excluded: chain A residue 2751 MET Chi-restraints excluded: chain A residue 2752 LEU Chi-restraints excluded: chain A residue 2774 GLU Chi-restraints excluded: chain A residue 2853 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 265 random chunks: chunk 166 optimal weight: 0.6980 chunk 223 optimal weight: 1.9990 chunk 64 optimal weight: 0.0970 chunk 193 optimal weight: 3.9990 chunk 31 optimal weight: 4.9990 chunk 58 optimal weight: 0.9990 chunk 210 optimal weight: 0.9980 chunk 88 optimal weight: 2.9990 chunk 216 optimal weight: 0.0030 chunk 26 optimal weight: 4.9990 chunk 38 optimal weight: 1.9990 overall best weight: 0.5590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 611 ASN ** A1656 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1717 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3866 r_free = 0.3866 target = 0.149010 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3546 r_free = 0.3546 target = 0.123594 restraints weight = 35210.632| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.122708 restraints weight = 43047.839| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3538 r_free = 0.3538 target = 0.123679 restraints weight = 39262.876| |-----------------------------------------------------------------------------| r_work (final): 0.3541 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7847 moved from start: 0.4317 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.115 21454 Z= 0.173 Angle : 0.546 10.431 29072 Z= 0.264 Chirality : 0.039 0.295 3333 Planarity : 0.004 0.041 3710 Dihedral : 6.685 164.189 2935 Min Nonbonded Distance : 2.094 Molprobity Statistics. All-atom Clashscore : 7.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.98 % Favored : 96.02 % Rotamer: Outliers : 3.54 % Allowed : 20.69 % Favored : 75.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.88 % 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: 0.14 (0.17), residues: 2612 helix: 0.90 (0.13), residues: 1788 sheet: 0.25 (0.86), residues: 36 loop : -1.76 (0.22), residues: 788 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.001 TRP A 616 HIS 0.005 0.001 HIS A 383 PHE 0.017 0.001 PHE A 949 TYR 0.017 0.001 TYR A1079 ARG 0.004 0.000 ARG A2603 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4399.78 seconds wall clock time: 80 minutes 37.84 seconds (4837.84 seconds total)