Starting phenix.real_space_refine on Tue Dec 12 11:00:51 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6sl1_10234/12_2023/6sl1_10234_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6sl1_10234/12_2023/6sl1_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_10234/12_2023/6sl1_10234.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6sl1_10234/12_2023/6sl1_10234.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6sl1_10234/12_2023/6sl1_10234_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6sl1_10234/12_2023/6sl1_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-1.21rc1-5172/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: 11.15, per 1000 atoms: 0.53 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: 8.44 Conformation dependent library (CDL) restraints added in 3.9 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: 8.96 Time building geometry restraints manager: 9.07 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: 2.810 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 9.950 Check model and map are aligned: 0.310 Set scattering table: 0.190 Process input model: 59.350 Find NCS groups from input model: 0.820 Set up NCS constraints: 0.100 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:2.800 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 76.340 ------------------------------------------------------------------------------- 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 : 2.321 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 outliers start: 154 outliers final: 80 residues processed: 586 average time/residue: 0.3771 time to fit residues: 328.2892 Evaluate side-chains 331 residues out of total 2292 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 80 poor density : 251 time to evaluate : 2.381 Switching outliers to nearest non-outliers TARDY: cannot create tardy model for: "THR A 27 " (corrupted residue). Skipping it. outliers start: 80 outliers final: 1 residues processed: 80 average time/residue: 0.2195 time to fit residues: 35.0971 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.8980 chunk 111 optimal weight: 3.9990 chunk 68 optimal weight: 0.8980 chunk 135 optimal weight: 0.9980 chunk 107 optimal weight: 0.6980 chunk 207 optimal weight: 0.9990 chunk 80 optimal weight: 0.7980 chunk 126 optimal weight: 3.9990 chunk 154 optimal weight: 0.9980 chunk 240 optimal weight: 0.3980 overall best weight: 0.7380 ------------------------------------------------------------------------------- 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 383 HIS A 418 HIS A 450 HIS A 454 HIS A 557 ASN 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: 45 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7830 moved from start: 0.2413 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 21454 Z= 0.220 Angle : 0.649 11.296 29072 Z= 0.323 Chirality : 0.041 0.226 3333 Planarity : 0.005 0.077 3710 Dihedral : 6.455 156.138 2895 Min Nonbonded Distance : 2.110 Molprobity Statistics. All-atom Clashscore : 10.25 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.79 % Favored : 95.18 % Rotamer: Outliers : 2.66 % Allowed : 15.89 % Favored : 81.45 % 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: -2.49 (0.15), residues: 2612 helix: -1.03 (0.12), residues: 1761 sheet: -1.01 (0.91), residues: 31 loop : -2.87 (0.19), residues: 820 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 302 HIS 0.010 0.001 HIS A 418 PHE 0.030 0.002 PHE A2112 TYR 0.022 0.002 TYR A 140 ARG 0.005 0.000 ARG A 682 *********************** 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 348 residues out of total 2292 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 287 time to evaluate : 2.503 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 outliers start: 61 outliers final: 25 residues processed: 334 average time/residue: 0.3722 time to fit residues: 188.9541 Evaluate side-chains 245 residues out of total 2292 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 220 time to evaluate : 2.391 Switching outliers to nearest non-outliers TARDY: cannot create tardy model for: "THR A 27 " (corrupted residue). Skipping it. outliers start: 25 outliers final: 1 residues processed: 25 average time/residue: 0.2135 time to fit residues: 13.0844 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 5.9990 chunk 200 optimal weight: 1.9990 chunk 163 optimal weight: 0.9990 chunk 66 optimal weight: 5.9990 chunk 241 optimal weight: 0.5980 chunk 260 optimal weight: 0.8980 chunk 214 optimal weight: 0.0980 chunk 239 optimal weight: 0.9990 chunk 82 optimal weight: 0.9980 chunk 193 optimal weight: 3.9990 overall best weight: 0.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 293 GLN A 418 HIS ** A1656 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2294 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7850 moved from start: 0.3064 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 21454 Z= 0.198 Angle : 0.593 10.415 29072 Z= 0.291 Chirality : 0.040 0.392 3333 Planarity : 0.004 0.056 3710 Dihedral : 6.073 157.312 2895 Min Nonbonded Distance : 2.111 Molprobity Statistics. All-atom Clashscore : 9.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.56 % Favored : 95.44 % Rotamer: Outliers : 2.27 % Allowed : 17.33 % Favored : 80.40 % 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: -1.56 (0.16), residues: 2612 helix: -0.29 (0.12), residues: 1772 sheet: -0.92 (0.88), residues: 38 loop : -2.62 (0.20), residues: 802 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A1730 HIS 0.006 0.001 HIS A 632 PHE 0.021 0.001 PHE A2112 TYR 0.009 0.001 TYR A 683 ARG 0.009 0.000 ARG A 596 *********************** 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 304 residues out of total 2292 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 252 time to evaluate : 2.459 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 outliers start: 52 outliers final: 21 residues processed: 293 average time/residue: 0.3651 time to fit residues: 165.9609 Evaluate side-chains 231 residues out of total 2292 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 210 time to evaluate : 2.378 Switching outliers to nearest non-outliers TARDY: cannot create tardy model for: "THR A 27 " (corrupted residue). Skipping it. outliers start: 21 outliers final: 1 residues processed: 21 average time/residue: 0.2373 time to fit residues: 12.0450 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 265 random chunks: chunk 238 optimal weight: 0.9990 chunk 181 optimal weight: 1.9990 chunk 125 optimal weight: 0.8980 chunk 26 optimal weight: 0.6980 chunk 115 optimal weight: 0.8980 chunk 161 optimal weight: 0.9990 chunk 241 optimal weight: 0.6980 chunk 256 optimal weight: 0.9990 chunk 126 optimal weight: 2.9990 chunk 229 optimal weight: 2.9990 chunk 69 optimal weight: 0.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 120 HIS A1656 GLN A1870 ASN A2129 GLN ** A2294 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7870 moved from start: 0.3411 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 21454 Z= 0.202 Angle : 0.581 12.257 29072 Z= 0.281 Chirality : 0.040 0.293 3333 Planarity : 0.004 0.049 3710 Dihedral : 5.939 158.603 2895 Min Nonbonded Distance : 2.090 Molprobity Statistics. All-atom Clashscore : 8.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.79 % Favored : 95.21 % Rotamer: Outliers : 1.53 % Allowed : 18.99 % Favored : 79.48 % 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: -1.06 (0.17), residues: 2612 helix: 0.07 (0.13), residues: 1769 sheet: -0.67 (0.89), residues: 38 loop : -2.37 (0.21), residues: 805 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP A1730 HIS 0.006 0.001 HIS A 632 PHE 0.020 0.001 PHE A2112 TYR 0.014 0.001 TYR A1079 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 279 residues out of total 2292 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 244 time to evaluate : 2.731 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 outliers start: 35 outliers final: 13 residues processed: 269 average time/residue: 0.3262 time to fit residues: 139.5495 Evaluate side-chains 227 residues out of total 2292 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 214 time to evaluate : 2.347 Switching outliers to nearest non-outliers TARDY: cannot create tardy model for: "THR A 27 " (corrupted residue). Skipping it. outliers start: 13 outliers final: 1 residues processed: 13 average time/residue: 0.2001 time to fit residues: 8.1809 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 265 random chunks: chunk 213 optimal weight: 0.7980 chunk 145 optimal weight: 2.9990 chunk 3 optimal weight: 0.9990 chunk 190 optimal weight: 2.9990 chunk 105 optimal weight: 0.2980 chunk 218 optimal weight: 2.9990 chunk 177 optimal weight: 0.9980 chunk 0 optimal weight: 0.9990 chunk 130 optimal weight: 0.6980 chunk 229 optimal weight: 0.9990 chunk 64 optimal weight: 8.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 383 HIS A1870 ASN ** A2294 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7874 moved from start: 0.3687 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 21454 Z= 0.189 Angle : 0.565 10.728 29072 Z= 0.274 Chirality : 0.039 0.384 3333 Planarity : 0.004 0.048 3710 Dihedral : 5.831 159.944 2895 Min Nonbonded Distance : 2.087 Molprobity Statistics. All-atom Clashscore : 8.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.44 % Favored : 95.56 % Rotamer: Outliers : 1.27 % Allowed : 19.77 % Favored : 78.96 % 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: -0.69 (0.17), residues: 2612 helix: 0.33 (0.13), residues: 1769 sheet: -0.59 (0.87), residues: 38 loop : -2.17 (0.21), residues: 805 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A 355 HIS 0.004 0.001 HIS A1269 PHE 0.017 0.001 PHE A2112 TYR 0.015 0.001 TYR A1079 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 266 residues out of total 2292 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 237 time to evaluate : 2.394 Fit side-chains TARDY: cannot create tardy model for: "THR A 27 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash outliers start: 29 outliers final: 16 residues processed: 258 average time/residue: 0.3301 time to fit residues: 135.4550 Evaluate side-chains 219 residues out of total 2292 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 203 time to evaluate : 2.271 Switching outliers to nearest non-outliers TARDY: cannot create tardy model for: "THR A 27 " (corrupted residue). Skipping it. revert: symmetry clash outliers start: 16 outliers final: 2 residues processed: 16 average time/residue: 0.2077 time to fit residues: 9.1963 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 1.9990 chunk 50 optimal weight: 6.9990 chunk 150 optimal weight: 0.8980 chunk 63 optimal weight: 0.7980 chunk 256 optimal weight: 0.5980 chunk 212 optimal weight: 1.9990 chunk 118 optimal weight: 0.9990 chunk 21 optimal weight: 0.0020 chunk 84 optimal weight: 0.8980 chunk 134 optimal weight: 0.7980 overall best weight: 0.6188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 120 HIS A 383 HIS ** A 632 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1717 GLN A1870 ASN ** A2294 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7864 moved from start: 0.3927 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= 0.168 Angle : 0.556 11.572 29072 Z= 0.267 Chirality : 0.039 0.343 3333 Planarity : 0.004 0.046 3710 Dihedral : 5.713 161.151 2895 Min Nonbonded Distance : 2.095 Molprobity Statistics. All-atom Clashscore : 8.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.21 % Favored : 95.79 % Rotamer: Outliers : 0.96 % Allowed : 20.65 % Favored : 78.39 % 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: -0.38 (0.17), residues: 2612 helix: 0.54 (0.13), residues: 1766 sheet: -0.50 (0.86), residues: 38 loop : -1.95 (0.21), residues: 808 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 616 HIS 0.007 0.001 HIS A 632 PHE 0.013 0.001 PHE A2112 TYR 0.015 0.001 TYR A1079 ARG 0.006 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 246 residues out of total 2292 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 224 time to evaluate : 2.472 Fit side-chains TARDY: cannot create tardy model for: "THR A 27 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash outliers start: 22 outliers final: 11 residues processed: 242 average time/residue: 0.3238 time to fit residues: 125.8945 Evaluate side-chains 214 residues out of total 2292 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 203 time to evaluate : 2.554 Switching outliers to nearest non-outliers TARDY: cannot create tardy model for: "THR A 27 " (corrupted residue). Skipping it. revert: symmetry clash outliers start: 11 outliers final: 2 residues processed: 11 average time/residue: 0.2080 time to fit residues: 7.6385 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 265 random chunks: chunk 247 optimal weight: 0.6980 chunk 28 optimal weight: 0.9980 chunk 146 optimal weight: 2.9990 chunk 187 optimal weight: 0.5980 chunk 145 optimal weight: 1.9990 chunk 215 optimal weight: 1.9990 chunk 143 optimal weight: 0.9990 chunk 255 optimal weight: 0.5980 chunk 159 optimal weight: 0.8980 chunk 155 optimal weight: 2.9990 chunk 117 optimal weight: 4.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 293 GLN A 394 HIS ** A 632 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1717 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2294 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7878 moved from start: 0.4030 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.074 21454 Z= 0.183 Angle : 0.543 10.568 29072 Z= 0.263 Chirality : 0.039 0.345 3333 Planarity : 0.004 0.045 3710 Dihedral : 5.667 161.767 2895 Min Nonbonded Distance : 2.080 Molprobity Statistics. All-atom Clashscore : 8.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.44 % Favored : 95.56 % Rotamer: Outliers : 0.92 % Allowed : 20.91 % Favored : 78.18 % 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: -0.25 (0.17), residues: 2612 helix: 0.62 (0.13), residues: 1784 sheet: -0.48 (0.85), residues: 38 loop : -1.90 (0.21), residues: 790 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 616 HIS 0.004 0.001 HIS A2518 PHE 0.014 0.001 PHE A2112 TYR 0.015 0.001 TYR A1079 ARG 0.005 0.000 ARG A 328 *********************** 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 227 residues out of total 2292 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 206 time to evaluate : 2.686 Fit side-chains TARDY: cannot create tardy model for: "THR A 27 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash outliers start: 21 outliers final: 12 residues processed: 220 average time/residue: 0.3470 time to fit residues: 124.6662 Evaluate side-chains 215 residues out of total 2292 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 203 time to evaluate : 2.588 Switching outliers to nearest non-outliers TARDY: cannot create tardy model for: "THR A 27 " (corrupted residue). Skipping it. outliers start: 12 outliers final: 1 residues processed: 12 average time/residue: 0.2232 time to fit residues: 8.3642 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 265 random chunks: chunk 158 optimal weight: 0.4980 chunk 101 optimal weight: 0.9980 chunk 152 optimal weight: 0.0870 chunk 76 optimal weight: 7.9990 chunk 50 optimal weight: 5.9990 chunk 49 optimal weight: 0.8980 chunk 162 optimal weight: 0.5980 chunk 174 optimal weight: 0.7980 chunk 126 optimal weight: 0.0010 chunk 23 optimal weight: 0.6980 chunk 200 optimal weight: 0.7980 overall best weight: 0.3764 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 632 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1593 ASN A1870 ASN A2294 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7842 moved from start: 0.4247 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.080 21454 Z= 0.143 Angle : 0.532 11.323 29072 Z= 0.255 Chirality : 0.038 0.311 3333 Planarity : 0.003 0.041 3710 Dihedral : 5.533 163.301 2895 Min Nonbonded Distance : 2.114 Molprobity Statistics. All-atom Clashscore : 7.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.91 % Favored : 96.09 % Rotamer: Outliers : 0.70 % Allowed : 21.00 % Favored : 78.31 % 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: 0.07 (0.17), residues: 2612 helix: 0.84 (0.13), residues: 1779 sheet: -0.18 (0.87), residues: 38 loop : -1.72 (0.22), residues: 795 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP A 616 HIS 0.003 0.001 HIS A 20 PHE 0.015 0.001 PHE A1100 TYR 0.016 0.001 TYR A1079 ARG 0.005 0.000 ARG A2488 *********************** 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 230 residues out of total 2292 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 214 time to evaluate : 2.565 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 outliers start: 16 outliers final: 8 residues processed: 223 average time/residue: 0.3295 time to fit residues: 118.1077 Evaluate side-chains 208 residues out of total 2292 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 200 time to evaluate : 2.550 Switching outliers to nearest non-outliers TARDY: cannot create tardy model for: "THR A 27 " (corrupted residue). Skipping it. outliers start: 8 outliers final: 1 residues processed: 8 average time/residue: 0.2030 time to fit residues: 6.5549 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 265 random chunks: chunk 232 optimal weight: 1.9990 chunk 244 optimal weight: 0.9980 chunk 223 optimal weight: 0.9990 chunk 238 optimal weight: 1.9990 chunk 143 optimal weight: 0.0980 chunk 103 optimal weight: 0.7980 chunk 186 optimal weight: 0.7980 chunk 73 optimal weight: 0.3980 chunk 215 optimal weight: 0.9990 chunk 225 optimal weight: 0.6980 chunk 237 optimal weight: 0.8980 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 632 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1870 ASN A2294 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7858 moved from start: 0.4334 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.105 21454 Z= 0.168 Angle : 0.547 13.765 29072 Z= 0.262 Chirality : 0.039 0.390 3333 Planarity : 0.004 0.040 3710 Dihedral : 5.510 163.397 2895 Min Nonbonded Distance : 2.101 Molprobity Statistics. All-atom Clashscore : 8.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.94 % Favored : 96.06 % Rotamer: Outliers : 0.48 % Allowed : 21.21 % Favored : 78.31 % 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: 0.21 (0.17), residues: 2612 helix: 0.94 (0.13), residues: 1779 sheet: -0.12 (0.87), residues: 38 loop : -1.64 (0.22), residues: 795 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP A 616 HIS 0.003 0.001 HIS A 120 PHE 0.013 0.001 PHE A1100 TYR 0.015 0.001 TYR A1079 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 224 residues out of total 2292 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 213 time to evaluate : 2.286 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 outliers start: 11 outliers final: 4 residues processed: 220 average time/residue: 0.3231 time to fit residues: 114.4168 Evaluate side-chains 211 residues out of total 2292 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 207 time to evaluate : 2.316 Switching outliers to nearest non-outliers TARDY: cannot create tardy model for: "THR A 27 " (corrupted residue). Skipping it. outliers start: 4 outliers final: 1 residues processed: 4 average time/residue: 0.2115 time to fit residues: 4.7057 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 265 random chunks: chunk 156 optimal weight: 1.9990 chunk 251 optimal weight: 2.9990 chunk 153 optimal weight: 5.9990 chunk 119 optimal weight: 0.3980 chunk 174 optimal weight: 1.9990 chunk 264 optimal weight: 0.9990 chunk 242 optimal weight: 0.6980 chunk 210 optimal weight: 0.6980 chunk 21 optimal weight: 0.9990 chunk 162 optimal weight: 0.9990 chunk 128 optimal weight: 0.0470 overall best weight: 0.5680 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 632 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A2294 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7855 moved from start: 0.4431 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.109 21454 Z= 0.177 Angle : 0.555 11.036 29072 Z= 0.267 Chirality : 0.039 0.309 3333 Planarity : 0.004 0.041 3710 Dihedral : 5.490 164.044 2895 Min Nonbonded Distance : 2.102 Molprobity Statistics. All-atom Clashscore : 8.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.71 % Favored : 96.29 % Rotamer: Outliers : 0.22 % Allowed : 21.69 % Favored : 78.09 % 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: 0.25 (0.17), residues: 2612 helix: 0.97 (0.13), residues: 1781 sheet: -0.09 (0.87), residues: 38 loop : -1.62 (0.22), residues: 793 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.053 0.001 TRP A 616 HIS 0.004 0.001 HIS A 612 PHE 0.013 0.001 PHE A1100 TYR 0.016 0.001 TYR A1079 ARG 0.007 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 220 residues out of total 2292 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 215 time to evaluate : 2.376 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 outliers start: 5 outliers final: 2 residues processed: 218 average time/residue: 0.3272 time to fit residues: 114.3409 Evaluate side-chains 208 residues out of total 2292 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 206 time to evaluate : 2.505 Switching outliers to nearest non-outliers TARDY: cannot create tardy model for: "THR A 27 " (corrupted residue). Skipping it. outliers start: 2 outliers final: 1 residues processed: 2 average time/residue: 0.2130 time to fit residues: 4.1004 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 265 random chunks: chunk 166 optimal weight: 1.9990 chunk 223 optimal weight: 0.7980 chunk 64 optimal weight: 2.9990 chunk 193 optimal weight: 0.7980 chunk 31 optimal weight: 5.9990 chunk 58 optimal weight: 0.9980 chunk 210 optimal weight: 0.6980 chunk 88 optimal weight: 0.7980 chunk 216 optimal weight: 0.3980 chunk 26 optimal weight: 4.9990 chunk 38 optimal weight: 0.9980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 632 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1035 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3870 r_free = 0.3870 target = 0.149303 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3549 r_free = 0.3549 target = 0.123837 restraints weight = 35269.754| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3526 r_free = 0.3526 target = 0.122887 restraints weight = 43220.353| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3544 r_free = 0.3544 target = 0.124436 restraints weight = 40039.508| |-----------------------------------------------------------------------------| r_work (final): 0.3544 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7839 moved from start: 0.4473 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.118 21454 Z= 0.189 Angle : 0.567 17.900 29072 Z= 0.271 Chirality : 0.039 0.305 3333 Planarity : 0.004 0.041 3710 Dihedral : 5.506 164.426 2895 Min Nonbonded Distance : 2.086 Molprobity Statistics. All-atom Clashscore : 8.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.98 % Favored : 96.02 % Rotamer: Outliers : 0.39 % Allowed : 21.91 % Favored : 77.70 % 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: 1.01 (0.13), residues: 1775 sheet: 0.25 (0.87), residues: 36 loop : -1.57 (0.22), residues: 801 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.046 0.001 TRP A 616 HIS 0.004 0.001 HIS A 612 PHE 0.012 0.001 PHE A1100 TYR 0.015 0.001 TYR A1079 ARG 0.006 0.000 ARG A2603 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4150.09 seconds wall clock time: 76 minutes 37.47 seconds (4597.47 seconds total)