Starting phenix.real_space_refine on Mon Feb 19 22:19:40 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xw6_33492/02_2024/7xw6_33492_neut_trim_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xw6_33492/02_2024/7xw6_33492.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.78 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xw6_33492/02_2024/7xw6_33492.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xw6_33492/02_2024/7xw6_33492.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xw6_33492/02_2024/7xw6_33492_neut_trim_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xw6_33492/02_2024/7xw6_33492_neut_trim_updated.pdb" } resolution = 2.78 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= 0.002 sd= 0.029 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: 5 Type Number sf(0) Gaussians S 75 5.16 5 C 8370 2.51 5 N 2099 2.21 5 O 2337 1.98 5 H 12117 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 13": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 20": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 38": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 42": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 61": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 228": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 231": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 232": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 255": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 270": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 273": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A PHE 302": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A ARG 307": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 323": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 326": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 332": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 337": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 346": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 363": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 364": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 370": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 375": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 379": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A GLU 382": "OE1" <-> "OE2" Residue "B ARG 8": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 19": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 22": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 42": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 46": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 48": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 49": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 52": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 68": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 96": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 129": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 134": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 137": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 150": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 197": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 214": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 219": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 251": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 256": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B GLU 260": "OE1" <-> "OE2" Residue "B ARG 283": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 304": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 314": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "G ARG 13": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "G ARG 27": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "G ARG 62": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "L ARG 16": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "L ARG 18": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "L ARG 61": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "L ARG 66": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "L ARG 76": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "L ARG 103": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "N ARG 19": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "N ARG 38": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "N ARG 67": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "N ARG 72": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "N ARG 98": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "N ARG 105": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "N ARG 118": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "R ARG 38": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "R ARG 46": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "R ARG 65": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "R ARG 80": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "R ARG 109": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "R ARG 112": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "R PHE 153": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "R ARG 255": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "R ARG 274": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "R ARG 418": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "R ARG 450": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "R ARG 519": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "R ARG 528": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "R ARG 531": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "R ARG 534": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "R ARG 536": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "R ARG 609": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "R ARG 625": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "R ARG 687": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "Y GLU 16": "OE1" <-> "OE2" Residue "Y ARG 23": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "Y ARG 28": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "Y ARG 38": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "Y ARG 50": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "Y ARG 94": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 24998 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 3879 Number of conformers: 1 Conformer: "" Number of residues, atoms: 233, 3879 Classifications: {'peptide': 233} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 226} Chain breaks: 1 Chain: "B" Number of atoms: 5107 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 5107 Classifications: {'peptide': 338} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 332} Chain: "G" Number of atoms: 885 Number of conformers: 1 Conformer: "" Number of residues, atoms: 57, 885 Classifications: {'peptide': 57} Link IDs: {'PTRANS': 4, 'TRANS': 52} Chain: "L" Number of atoms: 1648 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 1648 Classifications: {'peptide': 112} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 6, 'TRANS': 105} Chain: "N" Number of atoms: 1911 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 1911 Classifications: {'peptide': 128} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 5, 'TRANS': 122} Chain: "R" Number of atoms: 9053 Number of conformers: 1 Conformer: "" Number of residues, atoms: 562, 9053 Classifications: {'peptide': 562} Link IDs: {'PCIS': 2, 'PTRANS': 24, 'TRANS': 535} Chain breaks: 2 Chain: "Y" Number of atoms: 1854 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 1854 Classifications: {'peptide': 120} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 5, 'TRANS': 114} Chain: "R" Number of atoms: 661 Number of conformers: 1 Conformer: "" Number of residues, atoms: 27, 661 Unusual residues: {'CLR': 17, 'HOI': 1, 'NAG': 4, 'PLM': 5} Classifications: {'undetermined': 27} Link IDs: {None: 26} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Time building chain proxies: 11.49, per 1000 atoms: 0.46 Number of scatterers: 24998 At special positions: 0 Unit cell: (83.224, 103, 191.992, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 75 16.00 O 2337 8.00 N 2099 7.00 C 8370 6.00 H 12117 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=8, symmetry=0 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.05 Simple disulfide: pdb=" SG CYS N 22 " - pdb=" SG CYS N 96 " distance=2.03 Simple disulfide: pdb=" SG CYS N 99 " - pdb=" SG CYS N 107 " distance=2.04 Simple disulfide: pdb=" SG CYS R 29 " - pdb=" SG CYS R 41 " distance=2.05 Simple disulfide: pdb=" SG CYS R 283 " - pdb=" SG CYS R 398 " distance=2.03 Simple disulfide: pdb=" SG CYS R 284 " - pdb=" SG CYS R 408 " distance=2.01 Simple disulfide: pdb=" SG CYS R 494 " - pdb=" SG CYS R 569 " distance=2.01 Simple disulfide: pdb=" SG CYS Y 22 " - pdb=" SG CYS Y 92 " 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 Links applied NAG-ASN " NAG R 801 " - " ASN R 198 " " NAG R 802 " - " ASN R 177 " " NAG R 803 " - " ASN R 99 " " NAG R 804 " - " ASN R 77 " Time building additional restraints: 21.49 Conformation dependent library (CDL) restraints added in 3.2 seconds 3060 Ramachandran restraints generated. 1530 Oldfield, 0 Emsley, 1530 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2916 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 35 helices and 17 sheets defined 27.4% alpha, 23.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.62 Creating SS restraints... Processing helix chain 'A' and resid 14 through 39 removed outlier: 3.581A pdb=" N VAL A 36 " --> pdb=" O LYS A 32 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N ALA A 39 " --> pdb=" O GLN A 35 " (cutoff:3.500A) Processing helix chain 'A' and resid 53 through 63 removed outlier: 4.457A pdb=" N ILE A 62 " --> pdb=" O LYS A 58 " (cutoff:3.500A) removed outlier: 4.951A pdb=" N LEU A 63 " --> pdb=" O GLN A 59 " (cutoff:3.500A) Processing helix chain 'A' and resid 234 through 238 Processing helix chain 'A' and resid 255 through 268 Processing helix chain 'A' and resid 284 through 292 Processing helix chain 'A' and resid 297 through 300 Processing helix chain 'A' and resid 303 through 306 Processing helix chain 'A' and resid 322 through 341 Processing helix chain 'A' and resid 359 through 380 removed outlier: 4.085A pdb=" N ALA A 362 " --> pdb=" O THR A 359 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N CYS A 369 " --> pdb=" O PHE A 366 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N ARG A 370 " --> pdb=" O ASN A 367 " (cutoff:3.500A) Processing helix chain 'B' and resid 5 through 25 removed outlier: 4.446A pdb=" N GLU B 10 " --> pdb=" O GLN B 6 " (cutoff:3.500A) removed outlier: 4.493A pdb=" N GLN B 13 " --> pdb=" O GLN B 9 " (cutoff:3.500A) Processing helix chain 'B' and resid 30 through 36 removed outlier: 5.901A pdb=" N ASN B 36 " --> pdb=" O GLN B 32 " (cutoff:3.500A) Processing helix chain 'G' and resid 7 through 23 Processing helix chain 'G' and resid 30 through 43 Processing helix chain 'G' and resid 45 through 47 No H-bonds generated for 'chain 'G' and resid 45 through 47' Processing helix chain 'L' and resid 80 through 82 No H-bonds generated for 'chain 'L' and resid 80 through 82' Processing helix chain 'N' and resid 29 through 31 No H-bonds generated for 'chain 'N' and resid 29 through 31' Processing helix chain 'N' and resid 62 through 64 No H-bonds generated for 'chain 'N' and resid 62 through 64' Processing helix chain 'N' and resid 88 through 90 No H-bonds generated for 'chain 'N' and resid 88 through 90' Processing helix chain 'R' and resid 266 through 269 Processing helix chain 'R' and resid 280 through 289 removed outlier: 3.839A pdb=" N CYS R 283 " --> pdb=" O PRO R 280 " (cutoff:3.500A) removed outlier: 4.655A pdb=" N ASN R 288 " --> pdb=" O ALA R 285 " (cutoff:3.500A) Processing helix chain 'R' and resid 415 through 427 removed outlier: 4.554A pdb=" N TRP R 422 " --> pdb=" O ARG R 418 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N PHE R 423 " --> pdb=" O ILE R 419 " (cutoff:3.500A) Processing helix chain 'R' and resid 432 through 441 Processing helix chain 'R' and resid 448 through 477 Processing helix chain 'R' and resid 481 through 483 No H-bonds generated for 'chain 'R' and resid 481 through 483' Processing helix chain 'R' and resid 485 through 490 Processing helix chain 'R' and resid 492 through 524 Processing helix chain 'R' and resid 529 through 531 No H-bonds generated for 'chain 'R' and resid 529 through 531' Processing helix chain 'R' and resid 535 through 558 Proline residue: R 556 - end of helix Processing helix chain 'R' and resid 577 through 608 Processing helix chain 'R' and resid 618 through 648 removed outlier: 3.593A pdb=" N ALA R 623 " --> pdb=" O ASP R 619 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N LEU R 629 " --> pdb=" O ARG R 625 " (cutoff:3.500A) Proline residue: R 639 - end of helix Processing helix chain 'R' and resid 658 through 665 removed outlier: 3.821A pdb=" N LEU R 665 " --> pdb=" O LEU R 662 " (cutoff:3.500A) Processing helix chain 'R' and resid 669 through 678 Proline residue: R 675 - end of helix Processing helix chain 'R' and resid 683 through 695 removed outlier: 3.836A pdb=" N LYS R 695 " --> pdb=" O ILE R 691 " (cutoff:3.500A) Processing helix chain 'Y' and resid 29 through 31 No H-bonds generated for 'chain 'Y' and resid 29 through 31' Processing helix chain 'Y' and resid 84 through 86 No H-bonds generated for 'chain 'Y' and resid 84 through 86' Processing sheet with id= A, first strand: chain 'A' and resid 349 through 353 removed outlier: 7.144A pdb=" N VAL A 277 " --> pdb=" O TYR A 350 " (cutoff:3.500A) removed outlier: 7.829A pdb=" N HIS A 352 " --> pdb=" O VAL A 277 " (cutoff:3.500A) removed outlier: 6.252A pdb=" N LEU A 279 " --> pdb=" O HIS A 352 " (cutoff:3.500A) removed outlier: 6.154A pdb=" N ILE A 244 " --> pdb=" O ILE A 278 " (cutoff:3.500A) removed outlier: 7.159A pdb=" N PHE A 280 " --> pdb=" O ILE A 244 " (cutoff:3.500A) removed outlier: 6.491A pdb=" N PHE A 246 " --> pdb=" O PHE A 280 " (cutoff:3.500A) removed outlier: 6.574A pdb=" N ASN A 282 " --> pdb=" O PHE A 246 " (cutoff:3.500A) removed outlier: 6.182A pdb=" N VAL A 248 " --> pdb=" O ASN A 282 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N ALA A 243 " --> pdb=" O ARG A 42 " (cutoff:3.500A) removed outlier: 7.117A pdb=" N ASN A 218 " --> pdb=" O HIS A 41 " (cutoff:3.500A) removed outlier: 8.079A pdb=" N LEU A 43 " --> pdb=" O ASN A 218 " (cutoff:3.500A) removed outlier: 6.547A pdb=" N HIS A 220 " --> pdb=" O LEU A 43 " (cutoff:3.500A) removed outlier: 7.572A pdb=" N LEU A 45 " --> pdb=" O HIS A 220 " (cutoff:3.500A) removed outlier: 6.790A pdb=" N PHE A 222 " --> pdb=" O LEU A 45 " (cutoff:3.500A) removed outlier: 8.715A pdb=" N GLY A 47 " --> pdb=" O PHE A 222 " (cutoff:3.500A) removed outlier: 8.180A pdb=" N VAL A 224 " --> pdb=" O GLY A 47 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'B' and resid 58 through 63 removed outlier: 6.958A pdb=" N ALA B 73 " --> pdb=" O TYR B 59 " (cutoff:3.500A) removed outlier: 4.545A pdb=" N MET B 61 " --> pdb=" O VAL B 71 " (cutoff:3.500A) removed outlier: 6.808A pdb=" N VAL B 71 " --> pdb=" O MET B 61 " (cutoff:3.500A) removed outlier: 4.842A pdb=" N TRP B 63 " --> pdb=" O LEU B 69 " (cutoff:3.500A) removed outlier: 7.284A pdb=" N LEU B 69 " --> pdb=" O TRP B 63 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 6.518A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 5.833A pdb=" N LYS B 89 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'B' and resid 100 through 105 removed outlier: 6.805A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.429A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.559A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 5.080A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 7.268A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 6.364A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 6.577A pdb=" N VAL B 135 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 146 through 151 removed outlier: 6.504A pdb=" N SER B 160 " --> pdb=" O SER B 147 " (cutoff:3.500A) removed outlier: 4.459A pdb=" N CYS B 149 " --> pdb=" O VAL B 158 " (cutoff:3.500A) removed outlier: 6.770A pdb=" N VAL B 158 " --> pdb=" O CYS B 149 " (cutoff:3.500A) removed outlier: 4.851A pdb=" N PHE B 151 " --> pdb=" O GLN B 156 " (cutoff:3.500A) removed outlier: 7.486A pdb=" N GLN B 156 " --> pdb=" O PHE B 151 " (cutoff:3.500A) removed outlier: 6.555A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 6.058A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 187 through 192 removed outlier: 6.789A pdb=" N GLY B 202 " --> pdb=" O MET B 188 " (cutoff:3.500A) removed outlier: 4.446A pdb=" N LEU B 190 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 6.749A pdb=" N VAL B 200 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 5.105A pdb=" N LEU B 192 " --> pdb=" O LEU B 198 " (cutoff:3.500A) removed outlier: 7.555A pdb=" N LEU B 198 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 4.273A pdb=" N SER B 207 " --> pdb=" O ALA B 203 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) removed outlier: 6.783A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.411A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.717A pdb=" N GLY B 244 " --> pdb=" O ASN B 230 " (cutoff:3.500A) removed outlier: 4.516A pdb=" N ILE B 232 " --> pdb=" O ALA B 242 " (cutoff:3.500A) removed outlier: 6.796A pdb=" N ALA B 242 " --> pdb=" O ILE B 232 " (cutoff:3.500A) removed outlier: 4.981A pdb=" N PHE B 234 " --> pdb=" O ALA B 240 " (cutoff:3.500A) removed outlier: 7.286A pdb=" N ALA B 240 " --> pdb=" O PHE B 234 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N MET B 262 " --> pdb=" O LEU B 252 " (cutoff:3.500A) removed outlier: 6.487A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 6.242A pdb=" N GLU B 260 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'B' and resid 273 through 278 removed outlier: 6.593A pdb=" N GLY B 288 " --> pdb=" O THR B 274 " (cutoff:3.500A) removed outlier: 4.413A pdb=" N VAL B 276 " --> pdb=" O LEU B 286 " (cutoff:3.500A) removed outlier: 6.774A pdb=" N LEU B 286 " --> pdb=" O VAL B 276 " (cutoff:3.500A) removed outlier: 4.491A pdb=" N PHE B 278 " --> pdb=" O LEU B 284 " (cutoff:3.500A) removed outlier: 7.029A pdb=" N LEU B 284 " --> pdb=" O PHE B 278 " (cutoff:3.500A) removed outlier: 4.914A pdb=" N ASN B 293 " --> pdb=" O TYR B 289 " (cutoff:3.500A) removed outlier: 6.463A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.437A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'B' and resid 46 through 51 removed outlier: 6.735A pdb=" N ILE B 338 " --> pdb=" O ARG B 48 " (cutoff:3.500A) removed outlier: 4.515A pdb=" N THR B 50 " --> pdb=" O LEU B 336 " (cutoff:3.500A) removed outlier: 6.374A pdb=" N LEU B 336 " --> pdb=" O THR B 50 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'L' and resid 9 through 14 removed outlier: 6.209A pdb=" N ARG L 103 " --> pdb=" O VAL L 11 " (cutoff:3.500A) removed outlier: 8.331A pdb=" N GLY L 13 " --> pdb=" O ARG L 103 " (cutoff:3.500A) removed outlier: 6.784A pdb=" N THR L 105 " --> pdb=" O GLY L 13 " (cutoff:3.500A) No H-bonds generated for sheet with id= I Processing sheet with id= J, first strand: chain 'L' and resid 19 through 24 Processing sheet with id= K, first strand: chain 'L' and resid 95B through 98 removed outlier: 6.026A pdb=" N GLN L 37 " --> pdb=" O LEU L 46 " (cutoff:3.500A) removed outlier: 5.444A pdb=" N LEU L 46 " --> pdb=" O GLN L 37 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'N' and resid 3 through 8 Processing sheet with id= M, first strand: chain 'N' and resid 10 through 12 removed outlier: 3.604A pdb=" N SER N 49 " --> pdb=" O TRP N 36 " (cutoff:3.500A) removed outlier: 5.957A pdb=" N ARG N 38 " --> pdb=" O TRP N 47 " (cutoff:3.500A) removed outlier: 5.381A pdb=" N TRP N 47 " --> pdb=" O ARG N 38 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'R' and resid 29 through 33 removed outlier: 7.366A pdb=" N VAL R 39 " --> pdb=" O GLN R 55 " (cutoff:3.500A) removed outlier: 4.201A pdb=" N LEU R 57 " --> pdb=" O VAL R 39 " (cutoff:3.500A) removed outlier: 7.199A pdb=" N CYS R 41 " --> pdb=" O LEU R 57 " (cutoff:3.500A) removed outlier: 4.595A pdb=" N LEU R 59 " --> pdb=" O CYS R 41 " (cutoff:3.500A) removed outlier: 6.975A pdb=" N ARG R 80 " --> pdb=" O LEU R 57 " (cutoff:3.500A) removed outlier: 8.173A pdb=" N LEU R 59 " --> pdb=" O ARG R 80 " (cutoff:3.500A) removed outlier: 6.516A pdb=" N TYR R 82 " --> pdb=" O LEU R 59 " (cutoff:3.500A) removed outlier: 6.732A pdb=" N HIS R 105 " --> pdb=" O ILE R 81 " (cutoff:3.500A) removed outlier: 8.211A pdb=" N VAL R 83 " --> pdb=" O HIS R 105 " (cutoff:3.500A) removed outlier: 6.704A pdb=" N GLU R 107 " --> pdb=" O VAL R 83 " (cutoff:3.500A) removed outlier: 7.179A pdb=" N ILE R 85 " --> pdb=" O GLU R 107 " (cutoff:3.500A) removed outlier: 7.524A pdb=" N ARG R 109 " --> pdb=" O ILE R 85 " (cutoff:3.500A) removed outlier: 6.236A pdb=" N PHE R 130 " --> pdb=" O ILE R 106 " (cutoff:3.500A) removed outlier: 8.094A pdb=" N ILE R 108 " --> pdb=" O PHE R 130 " (cutoff:3.500A) removed outlier: 6.085A pdb=" N GLY R 132 " --> pdb=" O ILE R 108 " (cutoff:3.500A) removed outlier: 9.059A pdb=" N LEU R 131 " --> pdb=" O PHE R 153 " (cutoff:3.500A) removed outlier: 7.236A pdb=" N ILE R 155 " --> pdb=" O LEU R 131 " (cutoff:3.500A) removed outlier: 8.285A pdb=" N ILE R 133 " --> pdb=" O ILE R 155 " (cutoff:3.500A) removed outlier: 6.857A pdb=" N GLU R 157 " --> pdb=" O ILE R 133 " (cutoff:3.500A) removed outlier: 6.840A pdb=" N THR R 179 " --> pdb=" O PHE R 154 " (cutoff:3.500A) removed outlier: 7.890A pdb=" N LEU R 156 " --> pdb=" O THR R 179 " (cutoff:3.500A) removed outlier: 6.462A pdb=" N THR R 181 " --> pdb=" O LEU R 156 " (cutoff:3.500A) removed outlier: 7.803A pdb=" N ILE R 158 " --> pdb=" O THR R 181 " (cutoff:3.500A) removed outlier: 6.281A pdb=" N LYS R 183 " --> pdb=" O ILE R 158 " (cutoff:3.500A) removed outlier: 6.424A pdb=" N LYS R 201 " --> pdb=" O LEU R 180 " (cutoff:3.500A) removed outlier: 8.168A pdb=" N LEU R 182 " --> pdb=" O LYS R 201 " (cutoff:3.500A) removed outlier: 8.447A pdb=" N ASP R 203 " --> pdb=" O LEU R 182 " (cutoff:3.500A) removed outlier: 6.741A pdb=" N LEU R 230 " --> pdb=" O VAL R 205 " (cutoff:3.500A) removed outlier: 6.711A pdb=" N GLU R 251 " --> pdb=" O LEU R 231 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N ARG R 274 " --> pdb=" O LEU R 252 " (cutoff:3.500A) removed outlier: 6.535A pdb=" N VAL R 397 " --> pdb=" O ALA R 275 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'Y' and resid 3 through 6 removed outlier: 3.776A pdb=" N GLN Y 3 " --> pdb=" O SER Y 25 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'Y' and resid 10 through 13 removed outlier: 4.263A pdb=" N SER Y 112 " --> pdb=" O LYS Y 12 " (cutoff:3.500A) removed outlier: 6.038A pdb=" N ARG Y 38 " --> pdb=" O TRP Y 47 " (cutoff:3.500A) removed outlier: 5.564A pdb=" N TRP Y 47 " --> pdb=" O ARG Y 38 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'Y' and resid 93 through 95 removed outlier: 4.432A pdb=" N ASN Y 102 " --> pdb=" O ARG Y 94 " (cutoff:3.500A) 457 hydrogen bonds defined for protein. 1164 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: 9.65 Time building geometry restraints manager: 21.81 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.82 - 1.02: 2777 1.02 - 1.22: 9416 1.22 - 1.42: 5377 1.42 - 1.62: 7638 1.62 - 1.82: 103 Bond restraints: 25311 Sorted by residual: bond pdb=" CD1 PHE R 269 " pdb=" HD1 PHE R 269 " ideal model delta sigma weight residual 0.930 1.081 -0.151 2.00e-02 2.50e+03 5.72e+01 bond pdb=" CE3 TRP R 546 " pdb=" HE3 TRP R 546 " ideal model delta sigma weight residual 0.930 1.081 -0.151 2.00e-02 2.50e+03 5.71e+01 bond pdb=" N ASN A 367 " pdb=" H ASN A 367 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.71e+01 bond pdb=" CD2 HIS B 91 " pdb=" HD2 HIS B 91 " ideal model delta sigma weight residual 0.930 1.081 -0.151 2.00e-02 2.50e+03 5.71e+01 bond pdb=" NH1 ARG A 332 " pdb="HH11 ARG A 332 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.71e+01 ... (remaining 25306 not shown) Histogram of bond angle deviations from ideal: 77.91 - 89.32: 3 89.32 - 100.73: 56 100.73 - 112.14: 27258 112.14 - 123.56: 16538 123.56 - 134.97: 1518 Bond angle restraints: 45373 Sorted by residual: angle pdb=" N TYR R 225 " pdb=" CA TYR R 225 " pdb=" HA TYR R 225 " ideal model delta sigma weight residual 110.00 77.91 32.09 3.00e+00 1.11e-01 1.14e+02 angle pdb=" N TYR R 225 " pdb=" CA TYR R 225 " pdb=" C TYR R 225 " ideal model delta sigma weight residual 111.71 123.68 -11.97 1.15e+00 7.56e-01 1.08e+02 angle pdb=" C TYR R 225 " pdb=" CA TYR R 225 " pdb=" HA TYR R 225 " ideal model delta sigma weight residual 109.00 82.37 26.63 3.00e+00 1.11e-01 7.88e+01 angle pdb=" CB TYR R 225 " pdb=" CA TYR R 225 " pdb=" HA TYR R 225 " ideal model delta sigma weight residual 109.00 83.93 25.07 3.00e+00 1.11e-01 6.98e+01 angle pdb=" CA PHE N 68 " pdb=" CB PHE N 68 " pdb=" CG PHE N 68 " ideal model delta sigma weight residual 113.80 120.02 -6.22 1.00e+00 1.00e+00 3.87e+01 ... (remaining 45368 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.94: 12277 23.94 - 47.87: 441 47.87 - 71.81: 184 71.81 - 95.75: 22 95.75 - 119.68: 2 Dihedral angle restraints: 12926 sinusoidal: 7555 harmonic: 5371 Sorted by residual: dihedral pdb=" N TYR R 225 " pdb=" C TYR R 225 " pdb=" CA TYR R 225 " pdb=" CB TYR R 225 " ideal model delta harmonic sigma weight residual 122.80 149.88 -27.08 0 2.50e+00 1.60e-01 1.17e+02 dihedral pdb=" C TYR R 225 " pdb=" N TYR R 225 " pdb=" CA TYR R 225 " pdb=" CB TYR R 225 " ideal model delta harmonic sigma weight residual -122.60 -149.16 26.56 0 2.50e+00 1.60e-01 1.13e+02 dihedral pdb=" C LEU A 256 " pdb=" N LEU A 256 " pdb=" CA LEU A 256 " pdb=" CB LEU A 256 " ideal model delta harmonic sigma weight residual -122.60 -138.08 15.48 0 2.50e+00 1.60e-01 3.83e+01 ... (remaining 12923 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.235: 2008 0.235 - 0.470: 60 0.470 - 0.704: 3 0.704 - 0.939: 0 0.939 - 1.174: 1 Chirality restraints: 2072 Sorted by residual: chirality pdb=" CA TYR R 225 " pdb=" N TYR R 225 " pdb=" C TYR R 225 " pdb=" CB TYR R 225 " both_signs ideal model delta sigma weight residual False 2.51 1.34 1.17 2.00e-01 2.50e+01 3.45e+01 chirality pdb=" CA LEU A 256 " pdb=" N LEU A 256 " pdb=" C LEU A 256 " pdb=" CB LEU A 256 " both_signs ideal model delta sigma weight residual False 2.51 1.96 0.55 2.00e-01 2.50e+01 7.44e+00 chirality pdb=" CA LEU R 207 " pdb=" N LEU R 207 " pdb=" C LEU R 207 " pdb=" CB LEU R 207 " both_signs ideal model delta sigma weight residual False 2.51 2.01 0.50 2.00e-01 2.50e+01 6.15e+00 ... (remaining 2069 not shown) Planarity restraints: 3656 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C10 HOI R 827 " 0.096 2.00e-02 2.50e+03 1.71e-01 6.61e+02 pdb=" C11 HOI R 827 " 0.010 2.00e-02 2.50e+03 pdb=" C12 HOI R 827 " 0.114 2.00e-02 2.50e+03 pdb=" C13 HOI R 827 " 0.201 2.00e-02 2.50e+03 pdb=" C14 HOI R 827 " 0.062 2.00e-02 2.50e+03 pdb=" C15 HOI R 827 " 0.054 2.00e-02 2.50e+03 pdb=" C16 HOI R 827 " -0.296 2.00e-02 2.50e+03 pdb=" C9 HOI R 827 " 0.079 2.00e-02 2.50e+03 pdb=" O5 HOI R 827 " -0.318 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN R 99 " -0.213 2.00e-02 2.50e+03 1.59e-01 3.81e+02 pdb=" CG ASN R 99 " 0.069 2.00e-02 2.50e+03 pdb=" OD1 ASN R 99 " 0.107 2.00e-02 2.50e+03 pdb=" ND2 ASN R 99 " 0.122 2.00e-02 2.50e+03 pdb="HD21 ASN R 99 " 0.148 2.00e-02 2.50e+03 pdb=" C1 NAG R 803 " -0.232 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN R 77 " -0.190 2.00e-02 2.50e+03 1.56e-01 3.67e+02 pdb=" CG ASN R 77 " 0.038 2.00e-02 2.50e+03 pdb=" OD1 ASN R 77 " 0.153 2.00e-02 2.50e+03 pdb=" ND2 ASN R 77 " -0.035 2.00e-02 2.50e+03 pdb="HD21 ASN R 77 " 0.222 2.00e-02 2.50e+03 pdb=" C1 NAG R 804 " -0.188 2.00e-02 2.50e+03 ... (remaining 3653 not shown) Histogram of nonbonded interaction distances: 1.58 - 2.18: 1674 2.18 - 2.79: 42777 2.79 - 3.39: 69407 3.39 - 4.00: 94230 4.00 - 4.60: 136732 Nonbonded interactions: 344820 Sorted by model distance: nonbonded pdb=" HG SER B 108 " pdb=" OD1 ASP B 154 " model vdw 1.577 1.850 nonbonded pdb=" OD1 ASP R 143 " pdb=" HG1 THR R 145 " model vdw 1.589 1.850 nonbonded pdb=" OD1 ASP Y 72 " pdb=" HG SER Y 74 " model vdw 1.601 1.850 nonbonded pdb=" HG SER B 74 " pdb=" OD1 ASP B 76 " model vdw 1.603 1.850 nonbonded pdb=" OD1 ASP A 249 " pdb=" HG SER A 251 " model vdw 1.610 1.850 ... (remaining 344815 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.350 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: 0.370 Extract box with map and model: 6.860 Check model and map are aligned: 0.380 Set scattering table: 0.240 Process input model: 86.540 Find NCS groups from input model: 0.540 Set up NCS constraints: 0.070 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:11.560 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 107.910 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7277 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 : 0.013 0.075 13194 Z= 0.860 Angle : 1.790 11.972 17967 Z= 1.176 Chirality : 0.108 1.174 2072 Planarity : 0.015 0.171 2169 Dihedral : 12.297 119.682 5817 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 0.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.51 % Favored : 95.49 % Rotamer: Outliers : 0.07 % Allowed : 0.59 % Favored : 99.33 % Cbeta Deviations : 0.75 % Peptide Plane: Cis-proline : 3.51 % 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: -0.16 (0.21), residues: 1530 helix: -0.07 (0.24), residues: 385 sheet: 0.67 (0.28), residues: 323 loop : -0.37 (0.22), residues: 822 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.119 0.022 TRP R 488 HIS 0.013 0.004 HIS R 282 PHE 0.064 0.014 PHE A 222 TYR 0.111 0.018 TYR Y 56 ARG 0.011 0.001 ARG B 48 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3060 Ramachandran restraints generated. 1530 Oldfield, 0 Emsley, 1530 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3060 Ramachandran restraints generated. 1530 Oldfield, 0 Emsley, 1530 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 378 residues out of total 1349 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 377 time to evaluate : 2.077 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 60 MET cc_start: 0.7339 (mmm) cc_final: 0.7052 (mtp) REVERT: A 334 GLU cc_start: 0.7714 (mm-30) cc_final: 0.7125 (mm-30) REVERT: B 155 ASN cc_start: 0.7666 (t0) cc_final: 0.7086 (t0) REVERT: B 218 CYS cc_start: 0.7690 (p) cc_final: 0.7428 (p) REVERT: G 17 GLU cc_start: 0.7831 (tp30) cc_final: 0.7608 (tp30) REVERT: G 24 ASN cc_start: 0.7492 (m-40) cc_final: 0.6946 (m-40) REVERT: R 134 PHE cc_start: 0.8013 (m-80) cc_final: 0.7798 (m-80) REVERT: R 239 THR cc_start: 0.8355 (p) cc_final: 0.8144 (m) REVERT: R 465 MET cc_start: 0.7774 (tpt) cc_final: 0.7499 (tpt) REVERT: R 642 PHE cc_start: 0.8138 (t80) cc_final: 0.7916 (t80) REVERT: R 658 ASN cc_start: 0.8600 (m-40) cc_final: 0.8353 (m-40) outliers start: 1 outliers final: 0 residues processed: 378 average time/residue: 2.2456 time to fit residues: 939.0920 Evaluate side-chains 325 residues out of total 1349 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 325 time to evaluate : 1.970 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 128 optimal weight: 0.8980 chunk 115 optimal weight: 1.9990 chunk 63 optimal weight: 9.9990 chunk 39 optimal weight: 0.8980 chunk 77 optimal weight: 0.8980 chunk 61 optimal weight: 5.9990 chunk 119 optimal weight: 0.9990 chunk 46 optimal weight: 0.6980 chunk 72 optimal weight: 1.9990 chunk 88 optimal weight: 6.9990 chunk 138 optimal weight: 0.8980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 59 GLN B 88 ASN B 125 ASN B 268 ASN B 340 ASN N 120 GLN R 32 HIS Y 66 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7355 moved from start: 0.2759 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.106 13194 Z= 0.258 Angle : 0.648 8.992 17967 Z= 0.343 Chirality : 0.044 0.380 2072 Planarity : 0.005 0.054 2169 Dihedral : 7.273 78.179 2974 Min Nonbonded Distance : 2.168 Molprobity Statistics. All-atom Clashscore : 3.27 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.16 % Favored : 97.78 % Rotamer: Outliers : 1.85 % Allowed : 9.34 % Favored : 88.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.51 % 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 (0.21), residues: 1530 helix: 0.86 (0.26), residues: 396 sheet: 0.22 (0.26), residues: 362 loop : -0.28 (0.22), residues: 772 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP B 82 HIS 0.007 0.002 HIS R 105 PHE 0.016 0.002 PHE B 235 TYR 0.016 0.002 TYR R 667 ARG 0.006 0.001 ARG R 625 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3060 Ramachandran restraints generated. 1530 Oldfield, 0 Emsley, 1530 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3060 Ramachandran restraints generated. 1530 Oldfield, 0 Emsley, 1530 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 364 residues out of total 1349 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 339 time to evaluate : 1.898 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 59 GLN cc_start: 0.7755 (mm-40) cc_final: 0.7498 (mp10) REVERT: A 60 MET cc_start: 0.7291 (mmm) cc_final: 0.7070 (mtp) REVERT: B 99 TRP cc_start: 0.8064 (m-90) cc_final: 0.7406 (m-90) REVERT: B 155 ASN cc_start: 0.7534 (t0) cc_final: 0.7021 (t0) REVERT: B 163 ASP cc_start: 0.6533 (t0) cc_final: 0.6155 (t0) REVERT: B 191 SER cc_start: 0.8707 (p) cc_final: 0.8454 (t) REVERT: B 336 LEU cc_start: 0.8455 (OUTLIER) cc_final: 0.8249 (tp) REVERT: G 24 ASN cc_start: 0.7607 (m-40) cc_final: 0.7112 (m-40) REVERT: L 35 TRP cc_start: 0.7682 (m100) cc_final: 0.7089 (m100) REVERT: N 21 SER cc_start: 0.8107 (t) cc_final: 0.7867 (p) REVERT: N 113 THR cc_start: 0.8712 (t) cc_final: 0.8478 (p) REVERT: R 30 GLU cc_start: 0.6100 (tm-30) cc_final: 0.5895 (tm-30) REVERT: R 123 LYS cc_start: 0.8123 (pttt) cc_final: 0.7628 (pttt) REVERT: R 134 PHE cc_start: 0.7819 (m-80) cc_final: 0.7447 (m-80) REVERT: R 239 THR cc_start: 0.8505 (p) cc_final: 0.8305 (m) REVERT: R 463 MET cc_start: 0.7780 (tpp) cc_final: 0.7552 (tpp) REVERT: R 465 MET cc_start: 0.7835 (tpt) cc_final: 0.7547 (tpt) REVERT: R 608 VAL cc_start: 0.8106 (OUTLIER) cc_final: 0.7881 (t) REVERT: Y 59 TYR cc_start: 0.7952 (m-80) cc_final: 0.7729 (m-80) REVERT: Y 91 TYR cc_start: 0.6778 (m-80) cc_final: 0.6505 (m-80) outliers start: 25 outliers final: 13 residues processed: 346 average time/residue: 2.3468 time to fit residues: 893.9828 Evaluate side-chains 334 residues out of total 1349 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 319 time to evaluate : 1.811 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 307 VAL Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain B residue 340 ASN Chi-restraints excluded: chain L residue 9 SER Chi-restraints excluded: chain L residue 58 VAL Chi-restraints excluded: chain R residue 99 ASN Chi-restraints excluded: chain R residue 426 LEU Chi-restraints excluded: chain R residue 427 LEU Chi-restraints excluded: chain R residue 439 LEU Chi-restraints excluded: chain R residue 470 ILE Chi-restraints excluded: chain R residue 478 HIS Chi-restraints excluded: chain R residue 608 VAL Chi-restraints excluded: chain R residue 655 THR Chi-restraints excluded: chain Y residue 66 HIS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 76 optimal weight: 4.9990 chunk 42 optimal weight: 0.8980 chunk 114 optimal weight: 2.9990 chunk 93 optimal weight: 5.9990 chunk 38 optimal weight: 0.5980 chunk 138 optimal weight: 0.9980 chunk 149 optimal weight: 4.9990 chunk 123 optimal weight: 1.9990 chunk 137 optimal weight: 0.9990 chunk 47 optimal weight: 0.8980 chunk 110 optimal weight: 1.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 176 GLN ** B 237 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 18 GLN N 120 GLN R 186 ASN Y 66 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7373 moved from start: 0.3316 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.071 13194 Z= 0.233 Angle : 0.571 6.535 17967 Z= 0.302 Chirality : 0.042 0.359 2072 Planarity : 0.004 0.047 2169 Dihedral : 6.535 64.628 2974 Min Nonbonded Distance : 2.077 Molprobity Statistics. All-atom Clashscore : 4.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer: Outliers : 1.63 % Allowed : 13.42 % Favored : 84.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.51 % 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: 0.31 (0.21), residues: 1530 helix: 1.14 (0.27), residues: 396 sheet: 0.10 (0.26), residues: 374 loop : -0.14 (0.23), residues: 760 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP B 82 HIS 0.029 0.002 HIS Y 66 PHE 0.019 0.001 PHE A 222 TYR 0.014 0.001 TYR L 49 ARG 0.009 0.000 ARG A 270 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3060 Ramachandran restraints generated. 1530 Oldfield, 0 Emsley, 1530 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3060 Ramachandran restraints generated. 1530 Oldfield, 0 Emsley, 1530 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 347 residues out of total 1349 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 325 time to evaluate : 2.004 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 59 GLN cc_start: 0.7791 (mm-40) cc_final: 0.7574 (mp10) REVERT: A 334 GLU cc_start: 0.7662 (mm-30) cc_final: 0.7460 (mm-30) REVERT: B 163 ASP cc_start: 0.6557 (t0) cc_final: 0.6276 (t0) REVERT: B 191 SER cc_start: 0.8654 (p) cc_final: 0.8453 (t) REVERT: G 24 ASN cc_start: 0.7655 (m-40) cc_final: 0.7183 (m-40) REVERT: L 35 TRP cc_start: 0.7728 (m100) cc_final: 0.7253 (m100) REVERT: L 87 TYR cc_start: 0.6262 (m-80) cc_final: 0.5837 (m-80) REVERT: N 7 SER cc_start: 0.7431 (p) cc_final: 0.7208 (p) REVERT: N 21 SER cc_start: 0.8082 (t) cc_final: 0.7847 (p) REVERT: N 113 THR cc_start: 0.8630 (t) cc_final: 0.8428 (p) REVERT: R 30 GLU cc_start: 0.6040 (tm-30) cc_final: 0.5789 (tm-30) REVERT: R 123 LYS cc_start: 0.8172 (pttt) cc_final: 0.7629 (pttt) REVERT: R 134 PHE cc_start: 0.7919 (m-80) cc_final: 0.7629 (m-80) REVERT: R 239 THR cc_start: 0.8516 (p) cc_final: 0.8309 (m) REVERT: R 427 LEU cc_start: 0.8570 (OUTLIER) cc_final: 0.8369 (tt) REVERT: R 465 MET cc_start: 0.7851 (tpt) cc_final: 0.7544 (tpt) REVERT: R 608 VAL cc_start: 0.8234 (OUTLIER) cc_final: 0.8032 (t) outliers start: 22 outliers final: 16 residues processed: 334 average time/residue: 2.4742 time to fit residues: 909.8746 Evaluate side-chains 331 residues out of total 1349 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 313 time to evaluate : 2.109 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 122 SER Chi-restraints excluded: chain B residue 251 ARG Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 307 VAL Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain L residue 65 SER Chi-restraints excluded: chain N residue 31 ASN Chi-restraints excluded: chain N residue 59 SER Chi-restraints excluded: chain R residue 99 ASN Chi-restraints excluded: chain R residue 427 LEU Chi-restraints excluded: chain R residue 439 LEU Chi-restraints excluded: chain R residue 470 ILE Chi-restraints excluded: chain R residue 478 HIS Chi-restraints excluded: chain R residue 608 VAL Chi-restraints excluded: chain Y residue 3 GLN Chi-restraints excluded: chain Y residue 66 HIS Chi-restraints excluded: chain Y residue 70 SER Chi-restraints excluded: chain Y residue 100 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 136 optimal weight: 1.9990 chunk 103 optimal weight: 3.9990 chunk 71 optimal weight: 5.9990 chunk 15 optimal weight: 0.9990 chunk 65 optimal weight: 3.9990 chunk 92 optimal weight: 2.9990 chunk 138 optimal weight: 2.9990 chunk 146 optimal weight: 3.9990 chunk 72 optimal weight: 3.9990 chunk 131 optimal weight: 1.9990 chunk 39 optimal weight: 1.9990 overall best weight: 1.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 35 GLN B 36 ASN L 37 GLN N 3 GLN ** R 95 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7436 moved from start: 0.3718 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.066 13194 Z= 0.464 Angle : 0.632 7.557 17967 Z= 0.335 Chirality : 0.045 0.362 2072 Planarity : 0.005 0.059 2169 Dihedral : 6.534 58.317 2974 Min Nonbonded Distance : 1.888 Molprobity Statistics. All-atom Clashscore : 6.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.66 % Favored : 96.34 % Rotamer: Outliers : 2.08 % Allowed : 14.08 % Favored : 83.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.51 % 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 (0.21), residues: 1530 helix: 0.90 (0.26), residues: 397 sheet: -0.05 (0.26), residues: 391 loop : -0.25 (0.23), residues: 742 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.003 TRP A 234 HIS 0.011 0.002 HIS R 105 PHE 0.021 0.002 PHE B 235 TYR 0.019 0.002 TYR R 582 ARG 0.008 0.001 ARG A 270 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3060 Ramachandran restraints generated. 1530 Oldfield, 0 Emsley, 1530 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3060 Ramachandran restraints generated. 1530 Oldfield, 0 Emsley, 1530 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 353 residues out of total 1349 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 325 time to evaluate : 2.141 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 59 GLN cc_start: 0.7882 (mm-40) cc_final: 0.7674 (mp10) REVERT: A 256 LEU cc_start: 0.7239 (OUTLIER) cc_final: 0.6979 (tp) REVERT: A 324 VAL cc_start: 0.8014 (p) cc_final: 0.7648 (m) REVERT: B 163 ASP cc_start: 0.6699 (t0) cc_final: 0.6490 (t0) REVERT: G 24 ASN cc_start: 0.7704 (m-40) cc_final: 0.7283 (m-40) REVERT: L 35 TRP cc_start: 0.7809 (m100) cc_final: 0.7323 (m100) REVERT: N 7 SER cc_start: 0.7425 (p) cc_final: 0.7170 (p) REVERT: N 21 SER cc_start: 0.8116 (t) cc_final: 0.7857 (p) REVERT: N 113 THR cc_start: 0.8539 (t) cc_final: 0.8321 (m) REVERT: R 30 GLU cc_start: 0.6053 (tm-30) cc_final: 0.5823 (tm-30) REVERT: R 438 ILE cc_start: 0.8439 (mm) cc_final: 0.8209 (mt) REVERT: R 463 MET cc_start: 0.7614 (tpp) cc_final: 0.7381 (tpp) REVERT: R 465 MET cc_start: 0.7883 (tpt) cc_final: 0.7599 (tpt) outliers start: 28 outliers final: 18 residues processed: 334 average time/residue: 2.3459 time to fit residues: 864.1273 Evaluate side-chains 331 residues out of total 1349 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 312 time to evaluate : 2.192 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 222 PHE Chi-restraints excluded: chain A residue 256 LEU Chi-restraints excluded: chain A residue 355 CYS Chi-restraints excluded: chain A residue 369 CYS Chi-restraints excluded: chain B residue 122 SER Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain L residue 58 VAL Chi-restraints excluded: chain L residue 65 SER Chi-restraints excluded: chain N residue 59 SER Chi-restraints excluded: chain R residue 81 ILE Chi-restraints excluded: chain R residue 99 ASN Chi-restraints excluded: chain R residue 181 THR Chi-restraints excluded: chain R residue 439 LEU Chi-restraints excluded: chain R residue 470 ILE Chi-restraints excluded: chain R residue 478 HIS Chi-restraints excluded: chain Y residue 3 GLN Chi-restraints excluded: chain Y residue 70 SER Chi-restraints excluded: chain Y residue 100 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 122 optimal weight: 0.9990 chunk 83 optimal weight: 0.7980 chunk 2 optimal weight: 1.9990 chunk 109 optimal weight: 0.4980 chunk 60 optimal weight: 0.4980 chunk 125 optimal weight: 0.6980 chunk 101 optimal weight: 0.9980 chunk 0 optimal weight: 3.9990 chunk 75 optimal weight: 1.9990 chunk 131 optimal weight: 0.7980 chunk 37 optimal weight: 1.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 155 ASN ** B 237 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 18 GLN ** L 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 3 GLN Y 66 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7386 moved from start: 0.3936 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 13194 Z= 0.188 Angle : 0.528 5.845 17967 Z= 0.276 Chirality : 0.040 0.354 2072 Planarity : 0.004 0.048 2169 Dihedral : 6.130 56.269 2974 Min Nonbonded Distance : 1.937 Molprobity Statistics. All-atom Clashscore : 5.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 1.63 % Allowed : 15.49 % Favored : 82.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.51 % Cis-general : 0.00 % Twisted Proline : 1.75 % 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: 0.30 (0.22), residues: 1530 helix: 1.27 (0.27), residues: 393 sheet: 0.10 (0.26), residues: 377 loop : -0.23 (0.23), residues: 760 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP B 82 HIS 0.006 0.001 HIS R 105 PHE 0.010 0.001 PHE N 108 TYR 0.011 0.001 TYR R 582 ARG 0.006 0.000 ARG L 76 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3060 Ramachandran restraints generated. 1530 Oldfield, 0 Emsley, 1530 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3060 Ramachandran restraints generated. 1530 Oldfield, 0 Emsley, 1530 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 339 residues out of total 1349 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 317 time to evaluate : 1.621 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 256 LEU cc_start: 0.6983 (OUTLIER) cc_final: 0.6687 (tt) REVERT: B 155 ASN cc_start: 0.7794 (t0) cc_final: 0.7435 (t0) REVERT: B 163 ASP cc_start: 0.6634 (t0) cc_final: 0.6407 (t0) REVERT: G 24 ASN cc_start: 0.7713 (m-40) cc_final: 0.7308 (m-40) REVERT: L 35 TRP cc_start: 0.7644 (m100) cc_final: 0.7196 (m100) REVERT: N 21 SER cc_start: 0.8060 (t) cc_final: 0.7787 (p) REVERT: N 113 THR cc_start: 0.8515 (t) cc_final: 0.8275 (m) REVERT: R 30 GLU cc_start: 0.6028 (tm-30) cc_final: 0.5775 (tm-30) REVERT: R 123 LYS cc_start: 0.8257 (pttt) cc_final: 0.7775 (pttt) REVERT: R 438 ILE cc_start: 0.8481 (mm) cc_final: 0.8267 (mm) REVERT: R 463 MET cc_start: 0.7640 (tpp) cc_final: 0.7059 (tpp) REVERT: R 465 MET cc_start: 0.7865 (tpt) cc_final: 0.7598 (tpt) outliers start: 22 outliers final: 14 residues processed: 326 average time/residue: 2.4166 time to fit residues: 864.4322 Evaluate side-chains 322 residues out of total 1349 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 307 time to evaluate : 1.994 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 256 LEU Chi-restraints excluded: chain B residue 67 SER Chi-restraints excluded: chain B residue 218 CYS Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 316 SER Chi-restraints excluded: chain L residue 65 SER Chi-restraints excluded: chain L residue 96 GLN Chi-restraints excluded: chain R residue 99 ASN Chi-restraints excluded: chain R residue 209 LYS Chi-restraints excluded: chain R residue 272 LEU Chi-restraints excluded: chain R residue 470 ILE Chi-restraints excluded: chain R residue 478 HIS Chi-restraints excluded: chain R residue 680 ILE Chi-restraints excluded: chain Y residue 66 HIS Chi-restraints excluded: chain Y residue 70 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 49 optimal weight: 1.9990 chunk 132 optimal weight: 3.9990 chunk 29 optimal weight: 1.9990 chunk 86 optimal weight: 7.9990 chunk 36 optimal weight: 1.9990 chunk 147 optimal weight: 4.9990 chunk 122 optimal weight: 0.9990 chunk 68 optimal weight: 9.9990 chunk 12 optimal weight: 2.9990 chunk 48 optimal weight: 0.9980 chunk 77 optimal weight: 2.9990 overall best weight: 1.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 75 GLN ** B 237 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 239 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 66 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7429 moved from start: 0.4136 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.050 13194 Z= 0.373 Angle : 0.571 6.430 17967 Z= 0.301 Chirality : 0.043 0.361 2072 Planarity : 0.004 0.049 2169 Dihedral : 6.184 55.554 2974 Min Nonbonded Distance : 1.899 Molprobity Statistics. All-atom Clashscore : 6.39 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.59 % Favored : 96.34 % Rotamer: Outliers : 1.85 % Allowed : 16.60 % Favored : 81.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.51 % 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: 0.16 (0.21), residues: 1530 helix: 1.03 (0.27), residues: 394 sheet: 0.10 (0.26), residues: 377 loop : -0.30 (0.23), residues: 759 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A 234 HIS 0.008 0.002 HIS R 105 PHE 0.018 0.002 PHE N 108 TYR 0.018 0.002 TYR R 582 ARG 0.007 0.000 ARG L 76 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3060 Ramachandran restraints generated. 1530 Oldfield, 0 Emsley, 1530 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3060 Ramachandran restraints generated. 1530 Oldfield, 0 Emsley, 1530 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 334 residues out of total 1349 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 309 time to evaluate : 2.232 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 60 MET cc_start: 0.7449 (mmm) cc_final: 0.7225 (mtp) REVERT: B 155 ASN cc_start: 0.7852 (t0) cc_final: 0.7499 (t0) REVERT: G 24 ASN cc_start: 0.7755 (m-40) cc_final: 0.7365 (m-40) REVERT: L 35 TRP cc_start: 0.7779 (m100) cc_final: 0.7340 (m100) REVERT: N 21 SER cc_start: 0.8058 (t) cc_final: 0.7750 (p) REVERT: R 30 GLU cc_start: 0.6031 (tm-30) cc_final: 0.5763 (tm-30) REVERT: R 438 ILE cc_start: 0.8398 (mm) cc_final: 0.8154 (mt) REVERT: R 463 MET cc_start: 0.7621 (tpp) cc_final: 0.6954 (tpp) REVERT: R 465 MET cc_start: 0.7894 (tpt) cc_final: 0.7608 (tpt) REVERT: Y 100 SER cc_start: 0.7794 (OUTLIER) cc_final: 0.7585 (t) outliers start: 25 outliers final: 17 residues processed: 321 average time/residue: 2.5316 time to fit residues: 896.2571 Evaluate side-chains 322 residues out of total 1349 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 304 time to evaluate : 2.031 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 222 PHE Chi-restraints excluded: chain B residue 67 SER Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain L residue 65 SER Chi-restraints excluded: chain N residue 96 CYS Chi-restraints excluded: chain N residue 111 THR Chi-restraints excluded: chain R residue 99 ASN Chi-restraints excluded: chain R residue 115 THR Chi-restraints excluded: chain R residue 181 THR Chi-restraints excluded: chain R residue 207 LEU Chi-restraints excluded: chain R residue 209 LYS Chi-restraints excluded: chain R residue 470 ILE Chi-restraints excluded: chain R residue 478 HIS Chi-restraints excluded: chain Y residue 66 HIS Chi-restraints excluded: chain Y residue 70 SER Chi-restraints excluded: chain Y residue 100 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 141 optimal weight: 9.9990 chunk 16 optimal weight: 0.3980 chunk 83 optimal weight: 1.9990 chunk 107 optimal weight: 0.7980 chunk 123 optimal weight: 0.9980 chunk 82 optimal weight: 0.7980 chunk 146 optimal weight: 0.8980 chunk 91 optimal weight: 1.9990 chunk 89 optimal weight: 0.9990 chunk 67 optimal weight: 2.9990 chunk 90 optimal weight: 1.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 36 ASN ** B 237 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7404 moved from start: 0.4283 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 13194 Z= 0.212 Angle : 0.531 6.249 17967 Z= 0.277 Chirality : 0.040 0.354 2072 Planarity : 0.004 0.044 2169 Dihedral : 6.004 54.976 2974 Min Nonbonded Distance : 1.889 Molprobity Statistics. All-atom Clashscore : 6.20 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.14 % Favored : 96.80 % Rotamer: Outliers : 1.63 % Allowed : 17.20 % Favored : 81.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.51 % 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: 0.31 (0.22), residues: 1530 helix: 1.27 (0.27), residues: 389 sheet: 0.11 (0.26), residues: 377 loop : -0.21 (0.23), residues: 764 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP B 82 HIS 0.006 0.001 HIS R 105 PHE 0.012 0.001 PHE N 108 TYR 0.012 0.001 TYR R 582 ARG 0.006 0.000 ARG L 76 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3060 Ramachandran restraints generated. 1530 Oldfield, 0 Emsley, 1530 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3060 Ramachandran restraints generated. 1530 Oldfield, 0 Emsley, 1530 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 333 residues out of total 1349 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 311 time to evaluate : 2.070 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 155 ASN cc_start: 0.7801 (t0) cc_final: 0.7436 (t0) REVERT: G 24 ASN cc_start: 0.7772 (m-40) cc_final: 0.7398 (m-40) REVERT: L 35 TRP cc_start: 0.7674 (m100) cc_final: 0.7228 (m100) REVERT: N 21 SER cc_start: 0.8047 (t) cc_final: 0.7741 (p) REVERT: R 30 GLU cc_start: 0.6021 (tm-30) cc_final: 0.5768 (tm-30) REVERT: R 129 LYS cc_start: 0.8013 (pttp) cc_final: 0.7632 (ptpp) REVERT: R 438 ILE cc_start: 0.8401 (mm) cc_final: 0.8131 (mt) REVERT: R 463 MET cc_start: 0.7608 (tpp) cc_final: 0.7017 (tpp) REVERT: R 465 MET cc_start: 0.7877 (tpt) cc_final: 0.7596 (tpt) REVERT: Y 100 SER cc_start: 0.7728 (OUTLIER) cc_final: 0.7522 (t) outliers start: 22 outliers final: 14 residues processed: 324 average time/residue: 2.4269 time to fit residues: 864.0835 Evaluate side-chains 321 residues out of total 1349 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 306 time to evaluate : 1.940 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 222 PHE Chi-restraints excluded: chain B residue 67 SER Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain L residue 65 SER Chi-restraints excluded: chain N residue 111 THR Chi-restraints excluded: chain R residue 99 ASN Chi-restraints excluded: chain R residue 115 THR Chi-restraints excluded: chain R residue 166 SER Chi-restraints excluded: chain R residue 209 LYS Chi-restraints excluded: chain R residue 470 ILE Chi-restraints excluded: chain R residue 478 HIS Chi-restraints excluded: chain Y residue 70 SER Chi-restraints excluded: chain Y residue 100 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 58 optimal weight: 1.9990 chunk 87 optimal weight: 7.9990 chunk 44 optimal weight: 0.3980 chunk 28 optimal weight: 2.9990 chunk 93 optimal weight: 0.9980 chunk 99 optimal weight: 0.6980 chunk 72 optimal weight: 4.9990 chunk 13 optimal weight: 1.9990 chunk 115 optimal weight: 0.5980 chunk 133 optimal weight: 2.9990 chunk 140 optimal weight: 5.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 187 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 66 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7409 moved from start: 0.4399 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 13194 Z= 0.244 Angle : 0.535 6.478 17967 Z= 0.279 Chirality : 0.040 0.357 2072 Planarity : 0.004 0.042 2169 Dihedral : 5.926 55.450 2974 Min Nonbonded Distance : 1.885 Molprobity Statistics. All-atom Clashscore : 6.74 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.27 % Favored : 96.67 % Rotamer: Outliers : 2.08 % Allowed : 17.87 % Favored : 80.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.51 % 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: 0.27 (0.22), residues: 1530 helix: 1.17 (0.27), residues: 395 sheet: 0.09 (0.26), residues: 383 loop : -0.21 (0.23), residues: 752 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP Y 36 HIS 0.007 0.001 HIS R 105 PHE 0.016 0.001 PHE R 434 TYR 0.014 0.001 TYR R 582 ARG 0.006 0.000 ARG L 76 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3060 Ramachandran restraints generated. 1530 Oldfield, 0 Emsley, 1530 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3060 Ramachandran restraints generated. 1530 Oldfield, 0 Emsley, 1530 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 342 residues out of total 1349 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 314 time to evaluate : 1.933 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 155 ASN cc_start: 0.7807 (t0) cc_final: 0.7424 (t0) REVERT: G 24 ASN cc_start: 0.7784 (m-40) cc_final: 0.7416 (m-40) REVERT: L 35 TRP cc_start: 0.7685 (m100) cc_final: 0.7229 (m100) REVERT: N 21 SER cc_start: 0.8050 (t) cc_final: 0.7735 (p) REVERT: R 30 GLU cc_start: 0.6017 (tm-30) cc_final: 0.5769 (tm-30) REVERT: R 122 LEU cc_start: 0.6630 (OUTLIER) cc_final: 0.6429 (pp) REVERT: R 123 LYS cc_start: 0.8264 (pttt) cc_final: 0.7856 (pttt) REVERT: R 173 GLN cc_start: 0.7356 (pt0) cc_final: 0.6988 (pt0) REVERT: R 438 ILE cc_start: 0.8385 (mm) cc_final: 0.8130 (mt) REVERT: R 463 MET cc_start: 0.7587 (tpp) cc_final: 0.6957 (tpp) REVERT: R 465 MET cc_start: 0.7880 (tpt) cc_final: 0.7586 (tpt) outliers start: 28 outliers final: 19 residues processed: 328 average time/residue: 2.3809 time to fit residues: 860.1563 Evaluate side-chains 330 residues out of total 1349 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 310 time to evaluate : 2.014 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 222 PHE Chi-restraints excluded: chain B residue 38 ASP Chi-restraints excluded: chain B residue 67 SER Chi-restraints excluded: chain B residue 82 TRP Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 316 SER Chi-restraints excluded: chain L residue 65 SER Chi-restraints excluded: chain N residue 96 CYS Chi-restraints excluded: chain N residue 111 THR Chi-restraints excluded: chain R residue 99 ASN Chi-restraints excluded: chain R residue 115 THR Chi-restraints excluded: chain R residue 122 LEU Chi-restraints excluded: chain R residue 166 SER Chi-restraints excluded: chain R residue 209 LYS Chi-restraints excluded: chain R residue 470 ILE Chi-restraints excluded: chain R residue 478 HIS Chi-restraints excluded: chain Y residue 66 HIS Chi-restraints excluded: chain Y residue 70 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 128 optimal weight: 0.8980 chunk 136 optimal weight: 2.9990 chunk 140 optimal weight: 5.9990 chunk 82 optimal weight: 0.9980 chunk 59 optimal weight: 1.9990 chunk 107 optimal weight: 1.9990 chunk 41 optimal weight: 3.9990 chunk 123 optimal weight: 0.9980 chunk 129 optimal weight: 0.5980 chunk 89 optimal weight: 0.9980 chunk 144 optimal weight: 6.9990 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 236 GLN ** L 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 187 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 66 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7406 moved from start: 0.4462 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 13194 Z= 0.232 Angle : 0.536 7.252 17967 Z= 0.278 Chirality : 0.040 0.358 2072 Planarity : 0.004 0.056 2169 Dihedral : 5.835 57.415 2974 Min Nonbonded Distance : 1.891 Molprobity Statistics. All-atom Clashscore : 6.89 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.14 % Favored : 96.80 % Rotamer: Outliers : 1.56 % Allowed : 18.61 % Favored : 79.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.51 % 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: 0.29 (0.22), residues: 1530 helix: 1.21 (0.28), residues: 395 sheet: 0.14 (0.26), residues: 372 loop : -0.24 (0.23), residues: 763 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP Y 36 HIS 0.017 0.001 HIS Y 66 PHE 0.014 0.001 PHE N 108 TYR 0.013 0.001 TYR R 582 ARG 0.009 0.000 ARG R 625 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3060 Ramachandran restraints generated. 1530 Oldfield, 0 Emsley, 1530 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3060 Ramachandran restraints generated. 1530 Oldfield, 0 Emsley, 1530 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 333 residues out of total 1349 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 312 time to evaluate : 2.095 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 60 MET cc_start: 0.7443 (mtp) cc_final: 0.6993 (mtt) REVERT: B 155 ASN cc_start: 0.7787 (t0) cc_final: 0.7426 (t0) REVERT: G 24 ASN cc_start: 0.7790 (m-40) cc_final: 0.7430 (m-40) REVERT: L 35 TRP cc_start: 0.7675 (m100) cc_final: 0.7279 (m100) REVERT: N 21 SER cc_start: 0.8049 (t) cc_final: 0.7736 (p) REVERT: R 30 GLU cc_start: 0.6021 (tm-30) cc_final: 0.5740 (tm-30) REVERT: R 122 LEU cc_start: 0.6585 (OUTLIER) cc_final: 0.6384 (pp) REVERT: R 123 LYS cc_start: 0.8265 (pttt) cc_final: 0.7856 (pttt) REVERT: R 173 GLN cc_start: 0.7348 (pt0) cc_final: 0.7039 (pt0) REVERT: R 438 ILE cc_start: 0.8387 (mm) cc_final: 0.8126 (mt) REVERT: R 463 MET cc_start: 0.7583 (tpp) cc_final: 0.6940 (tpp) REVERT: R 465 MET cc_start: 0.7873 (tpt) cc_final: 0.7580 (tpt) outliers start: 21 outliers final: 18 residues processed: 323 average time/residue: 2.4244 time to fit residues: 866.8556 Evaluate side-chains 330 residues out of total 1349 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 311 time to evaluate : 1.974 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 222 PHE Chi-restraints excluded: chain B residue 67 SER Chi-restraints excluded: chain B residue 82 TRP Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 316 SER Chi-restraints excluded: chain L residue 65 SER Chi-restraints excluded: chain N residue 96 CYS Chi-restraints excluded: chain R residue 99 ASN Chi-restraints excluded: chain R residue 115 THR Chi-restraints excluded: chain R residue 122 LEU Chi-restraints excluded: chain R residue 166 SER Chi-restraints excluded: chain R residue 209 LYS Chi-restraints excluded: chain R residue 470 ILE Chi-restraints excluded: chain Y residue 66 HIS Chi-restraints excluded: chain Y residue 70 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 88 optimal weight: 0.8980 chunk 68 optimal weight: 8.9990 chunk 100 optimal weight: 3.9990 chunk 151 optimal weight: 5.9990 chunk 139 optimal weight: 3.9990 chunk 120 optimal weight: 0.9990 chunk 12 optimal weight: 1.9990 chunk 93 optimal weight: 1.9990 chunk 73 optimal weight: 0.7980 chunk 95 optimal weight: 1.9990 chunk 128 optimal weight: 0.6980 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 237 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 187 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 66 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7414 moved from start: 0.4514 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 13194 Z= 0.267 Angle : 0.546 7.458 17967 Z= 0.282 Chirality : 0.041 0.360 2072 Planarity : 0.004 0.053 2169 Dihedral : 5.808 57.775 2974 Min Nonbonded Distance : 1.884 Molprobity Statistics. All-atom Clashscore : 7.31 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.40 % Favored : 96.54 % Rotamer: Outliers : 1.56 % Allowed : 18.53 % Favored : 79.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.51 % 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 (0.22), residues: 1530 helix: 1.13 (0.27), residues: 400 sheet: 0.14 (0.26), residues: 374 loop : -0.28 (0.23), residues: 756 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP Y 36 HIS 0.015 0.001 HIS Y 66 PHE 0.016 0.001 PHE N 108 TYR 0.014 0.001 TYR R 582 ARG 0.009 0.000 ARG R 625 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3060 Ramachandran restraints generated. 1530 Oldfield, 0 Emsley, 1530 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3060 Ramachandran restraints generated. 1530 Oldfield, 0 Emsley, 1530 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 336 residues out of total 1349 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 315 time to evaluate : 2.260 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 60 MET cc_start: 0.7452 (mtp) cc_final: 0.6997 (mtt) REVERT: B 155 ASN cc_start: 0.7798 (t0) cc_final: 0.7432 (t0) REVERT: G 24 ASN cc_start: 0.7808 (m-40) cc_final: 0.7462 (m-40) REVERT: L 35 TRP cc_start: 0.7686 (m100) cc_final: 0.7253 (m100) REVERT: N 21 SER cc_start: 0.8049 (t) cc_final: 0.7717 (p) REVERT: N 80 TYR cc_start: 0.7180 (m-80) cc_final: 0.6658 (m-80) REVERT: R 30 GLU cc_start: 0.6027 (tm-30) cc_final: 0.5770 (tm-30) REVERT: R 123 LYS cc_start: 0.8272 (pttt) cc_final: 0.7867 (pttt) REVERT: R 173 GLN cc_start: 0.7342 (pt0) cc_final: 0.7036 (pt0) REVERT: R 438 ILE cc_start: 0.8393 (mm) cc_final: 0.8120 (mt) REVERT: R 465 MET cc_start: 0.7876 (tpt) cc_final: 0.7591 (tpt) outliers start: 21 outliers final: 19 residues processed: 327 average time/residue: 2.3514 time to fit residues: 847.7874 Evaluate side-chains 333 residues out of total 1349 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 314 time to evaluate : 1.877 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 222 PHE Chi-restraints excluded: chain B residue 67 SER Chi-restraints excluded: chain B residue 82 TRP Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 316 SER Chi-restraints excluded: chain L residue 65 SER Chi-restraints excluded: chain N residue 96 CYS Chi-restraints excluded: chain N residue 111 THR Chi-restraints excluded: chain R residue 99 ASN Chi-restraints excluded: chain R residue 115 THR Chi-restraints excluded: chain R residue 166 SER Chi-restraints excluded: chain R residue 209 LYS Chi-restraints excluded: chain R residue 470 ILE Chi-restraints excluded: chain Y residue 66 HIS Chi-restraints excluded: chain Y residue 70 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 36 optimal weight: 1.9990 chunk 111 optimal weight: 0.7980 chunk 17 optimal weight: 0.7980 chunk 33 optimal weight: 0.7980 chunk 120 optimal weight: 1.9990 chunk 50 optimal weight: 2.9990 chunk 124 optimal weight: 1.9990 chunk 15 optimal weight: 0.5980 chunk 22 optimal weight: 1.9990 chunk 106 optimal weight: 0.7980 chunk 6 optimal weight: 0.8980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 237 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 187 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 66 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4028 r_free = 0.4028 target = 0.154595 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3660 r_free = 0.3660 target = 0.125191 restraints weight = 49843.353| |-----------------------------------------------------------------------------| r_work (start): 0.3642 rms_B_bonded: 2.23 r_work: 0.3527 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.3366 rms_B_bonded: 4.35 restraints_weight: 0.2500 r_work (final): 0.3366 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7740 moved from start: 0.4563 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 13194 Z= 0.206 Angle : 0.525 7.648 17967 Z= 0.273 Chirality : 0.040 0.358 2072 Planarity : 0.004 0.051 2169 Dihedral : 5.702 56.799 2974 Min Nonbonded Distance : 1.904 Molprobity Statistics. All-atom Clashscore : 7.24 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.14 % Favored : 96.80 % Rotamer: Outliers : 1.48 % Allowed : 18.68 % Favored : 79.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.51 % 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: 0.31 (0.22), residues: 1530 helix: 1.20 (0.27), residues: 400 sheet: 0.18 (0.26), residues: 372 loop : -0.23 (0.23), residues: 758 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP Y 36 HIS 0.025 0.001 HIS Y 66 PHE 0.022 0.001 PHE R 434 TYR 0.017 0.001 TYR R 482 ARG 0.008 0.000 ARG R 625 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 13407.80 seconds wall clock time: 238 minutes 49.82 seconds (14329.82 seconds total)