Starting phenix.real_space_refine on Fri Feb 16 17:56:30 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6swy_10333/02_2024/6swy_10333.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6swy_10333/02_2024/6swy_10333.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6swy_10333/02_2024/6swy_10333.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6swy_10333/02_2024/6swy_10333.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6swy_10333/02_2024/6swy_10333.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6swy_10333/02_2024/6swy_10333.pdb" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.005 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: 4 Type Number sf(0) Gaussians S 71 5.16 5 C 10334 2.51 5 N 2682 2.21 5 O 2970 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "5 ASP 26": "OD1" <-> "OD2" Residue "5 PHE 28": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "5 TYR 76": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "5 PHE 93": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "5 PHE 130": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "5 GLU 147": "OE1" <-> "OE2" Residue "5 GLU 177": "OE1" <-> "OE2" Residue "5 ARG 179": "NH1" <-> "NH2" Residue "5 GLU 183": "OE1" <-> "OE2" Residue "5 PHE 190": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "5 PHE 235": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "5 ARG 279": "NH1" <-> "NH2" Residue "5 PHE 309": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "5 ARG 325": "NH1" <-> "NH2" Residue "5 ASP 341": "OD1" <-> "OD2" Residue "5 ASP 348": "OD1" <-> "OD2" Residue "5 GLU 362": "OE1" <-> "OE2" Residue "5 GLU 440": "OE1" <-> "OE2" Residue "5 GLU 458": "OE1" <-> "OE2" Residue "5 GLU 520": "OE1" <-> "OE2" Residue "5 TYR 522": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "5 PHE 528": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "5 PHE 546": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "5 PHE 550": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "5 PHE 556": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "5 ARG 589": "NH1" <-> "NH2" Residue "5 GLU 693": "OE1" <-> "OE2" Residue "5 ASP 706": "OD1" <-> "OD2" Residue "5 TYR 718": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "5 GLU 736": "OE1" <-> "OE2" Residue "5 TYR 889": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "5 ARG 893": "NH1" <-> "NH2" Residue "5 ASP 915": "OD1" <-> "OD2" Residue "8 PHE 34": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "8 GLU 38": "OE1" <-> "OE2" Residue "8 TYR 46": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "8 TYR 53": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "8 GLU 86": "OE1" <-> "OE2" Residue "8 ARG 108": "NH1" <-> "NH2" Residue "8 ASP 121": "OD1" <-> "OD2" Residue "8 TYR 129": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "8 GLU 160": "OE1" <-> "OE2" Residue "8 GLU 204": "OE1" <-> "OE2" Residue "8 TYR 229": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "8 TYR 278": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "8 ARG 283": "NH1" <-> "NH2" Residue "8 GLU 292": "OE1" <-> "OE2" Residue "8 PHE 304": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "8 PHE 328": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "8 TYR 331": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "8 ASP 350": "OD1" <-> "OD2" Residue "8 GLU 355": "OE1" <-> "OE2" Residue "8 ARG 374": "NH1" <-> "NH2" Residue "8 PHE 387": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "8 GLU 391": "OE1" <-> "OE2" Residue "8 TYR 395": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "8 TYR 419": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "8 ARG 452": "NH1" <-> "NH2" Residue "8 GLU 454": "OE1" <-> "OE2" Residue "1 GLU 11": "OE1" <-> "OE2" Residue "1 PHE 12": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "1 TYR 34": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "1 ARG 38": "NH1" <-> "NH2" Residue "1 TYR 103": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "1 PHE 104": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "1 ASP 316": "OD1" <-> "OD2" Residue "1 ASP 352": "OD1" <-> "OD2" Residue "1 ASP 384": "OD1" <-> "OD2" Residue "1 PHE 385": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "1 GLU 415": "OE1" <-> "OE2" Residue "1 TYR 503": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "1 PHE 533": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "1 ARG 535": "NH1" <-> "NH2" Residue "1 PHE 551": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "1 PHE 571": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "1 TYR 574": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "1 PHE 593": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "1 TYR 600": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "1 ARG 694": "NH1" <-> "NH2" Residue "1 ASP 706": "OD1" <-> "OD2" Residue "1 TYR 721": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "1 GLU 725": "OE1" <-> "OE2" Residue "1 ASP 737": "OD1" <-> "OD2" Residue "1 ASP 741": "OD1" <-> "OD2" Residue "1 ARG 768": "NH1" <-> "NH2" Residue "1 GLU 916": "OE1" <-> "OE2" Residue "1 ARG 944": "NH1" <-> "NH2" Residue "4 ARG 91": "NH1" <-> "NH2" Residue "4 GLU 97": "OE1" <-> "OE2" Residue "4 GLU 105": "OE1" <-> "OE2" Residue "4 ARG 124": "NH1" <-> "NH2" Residue "4 ARG 126": "NH1" <-> "NH2" Residue "4 ASP 150": "OD1" <-> "OD2" Residue "4 GLU 178": "OE1" <-> "OE2" Residue "4 ASP 202": "OD1" <-> "OD2" Residue "4 GLU 203": "OE1" <-> "OE2" Residue "4 PHE 223": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "4 ARG 227": "NH1" <-> "NH2" Residue "4 PHE 230": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "4 TYR 282": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "4 PHE 287": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "4 ASP 321": "OD1" <-> "OD2" Residue "4 PHE 330": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "4 TYR 331": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "4 TYR 332": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "4 ASP 335": "OD1" <-> "OD2" Residue "4 PHE 339": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "4 ASP 356": "OD1" <-> "OD2" Residue "4 PHE 359": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "4 GLU 360": "OE1" <-> "OE2" Residue "9 ARG 230": "NH1" <-> "NH2" Residue "9 TYR 234": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "9 GLU 236": "OE1" <-> "OE2" Residue "9 PHE 253": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "9 PHE 262": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "9 PHE 274": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "9 ASP 306": "OD1" <-> "OD2" Residue "9 PHE 309": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "9 ARG 319": "NH1" <-> "NH2" Residue "9 PHE 344": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "9 ARG 346": "NH1" <-> "NH2" Time to flip residues: 0.11s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 16057 Number of models: 1 Model: "" Number of chains: 5 Chain: "5" Number of atoms: 6417 Number of conformers: 1 Conformer: "" Number of residues, atoms: 789, 6417 Classifications: {'peptide': 789} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 23, 'TRANS': 765} Chain breaks: 3 Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 13 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'GLU:plan': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 10 Chain: "8" Number of atoms: 2682 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 325, 2676 Classifications: {'peptide': 325} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 10, 'TRANS': 314} Chain breaks: 7 Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 11 Planarities with less than four sites: {'GLN:plan1': 2} Unresolved non-hydrogen planarities: 8 Conformer: "B" Number of residues, atoms: 325, 2676 Classifications: {'peptide': 325} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 10, 'TRANS': 314} Chain breaks: 7 Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 11 Planarities with less than four sites: {'GLN:plan1': 2} Unresolved non-hydrogen planarities: 8 bond proxies already assigned to first conformer: 2721 Chain: "1" Number of atoms: 4038 Number of conformers: 1 Conformer: "" Number of residues, atoms: 542, 4038 Classifications: {'peptide': 542} Incomplete info: {'truncation_to_alanine': 120} Link IDs: {'PTRANS': 14, 'TRANS': 527} Chain breaks: 12 Unresolved non-hydrogen bonds: 257 Unresolved non-hydrogen angles: 377 Unresolved non-hydrogen dihedrals: 142 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'ASN:plan1': 1, 'TYR:plan': 1, 'UNK:plan-1': 106, 'ASP:plan': 2, 'PHE:plan': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 132 Chain: "4" Number of atoms: 1783 Number of conformers: 1 Conformer: "" Number of residues, atoms: 217, 1783 Classifications: {'peptide': 217} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 10, 'TRANS': 206} Chain breaks: 4 Unresolved non-hydrogen bonds: 29 Unresolved non-hydrogen angles: 36 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 14 Chain: "9" Number of atoms: 1137 Number of conformers: 1 Conformer: "" Number of residues, atoms: 157, 1137 Classifications: {'peptide': 157} Incomplete info: {'truncation_to_alanine': 56} Link IDs: {'PTRANS': 2, 'TRANS': 154} Chain breaks: 4 Unresolved non-hydrogen bonds: 134 Unresolved non-hydrogen angles: 193 Unresolved non-hydrogen dihedrals: 85 Planarities with less than four sites: {'PHE:plan': 2, 'TYR:plan': 2, 'UNK:plan-1': 48, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 77 Time building chain proxies: 11.16, per 1000 atoms: 0.70 Number of scatterers: 16057 At special positions: 0 Unit cell: (122.08, 164.59, 128.62, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 71 16.00 O 2970 8.00 N 2682 7.00 C 10334 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 8.11 Conformation dependent library (CDL) restraints added in 3.2 seconds 3642 Ramachandran restraints generated. 1821 Oldfield, 0 Emsley, 1821 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3940 Finding SS restraints... Secondary structure from input PDB file: 96 helices and 7 sheets defined 66.2% alpha, 6.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.65 Creating SS restraints... Processing helix chain '5' and resid 6 through 18 Processing helix chain '5' and resid 20 through 27 Processing helix chain '5' and resid 28 through 33 Proline residue: 5 31 - end of helix No H-bonds generated for 'chain '5' and resid 28 through 33' Processing helix chain '5' and resid 34 through 40 removed outlier: 3.891A pdb=" N CYS 5 38 " --> pdb=" O GLN 5 34 " (cutoff:3.500A) Processing helix chain '5' and resid 47 through 62 Processing helix chain '5' and resid 65 through 73 removed outlier: 4.167A pdb=" N ILE 5 71 " --> pdb=" O GLN 5 67 " (cutoff:3.500A) Processing helix chain '5' and resid 74 through 86 Processing helix chain '5' and resid 97 through 115 Processing helix chain '5' and resid 122 through 137 removed outlier: 3.554A pdb=" N LEU 5 126 " --> pdb=" O ASP 5 122 " (cutoff:3.500A) Processing helix chain '5' and resid 144 through 160 Processing helix chain '5' and resid 182 through 205 removed outlier: 4.212A pdb=" N GLN 5 188 " --> pdb=" O THR 5 184 " (cutoff:3.500A) Processing helix chain '5' and resid 206 through 211 removed outlier: 5.337A pdb=" N ASP 5 209 " --> pdb=" O LYS 5 206 " (cutoff:3.500A) Processing helix chain '5' and resid 254 through 272 Processing helix chain '5' and resid 273 through 275 No H-bonds generated for 'chain '5' and resid 273 through 275' Processing helix chain '5' and resid 285 through 295 removed outlier: 3.961A pdb=" N MET 5 289 " --> pdb=" O ALA 5 285 " (cutoff:3.500A) Processing helix chain '5' and resid 299 through 317 Proline residue: 5 313 - end of helix Processing helix chain '5' and resid 319 through 322 removed outlier: 3.629A pdb=" N GLU 5 322 " --> pdb=" O LYS 5 319 " (cutoff:3.500A) No H-bonds generated for 'chain '5' and resid 319 through 322' Processing helix chain '5' and resid 323 through 337 removed outlier: 3.691A pdb=" N LEU 5 327 " --> pdb=" O ASP 5 323 " (cutoff:3.500A) Proline residue: 5 332 - end of helix Processing helix chain '5' and resid 348 through 364 removed outlier: 3.531A pdb=" N THR 5 364 " --> pdb=" O TYR 5 360 " (cutoff:3.500A) Processing helix chain '5' and resid 368 through 377 removed outlier: 3.557A pdb=" N THR 5 377 " --> pdb=" O THR 5 373 " (cutoff:3.500A) Processing helix chain '5' and resid 378 through 392 removed outlier: 3.652A pdb=" N CYS 5 382 " --> pdb=" O ASN 5 378 " (cutoff:3.500A) Processing helix chain '5' and resid 397 through 416 Processing helix chain '5' and resid 418 through 427 Processing helix chain '5' and resid 430 through 461 removed outlier: 3.930A pdb=" N HIS 5 434 " --> pdb=" O LEU 5 430 " (cutoff:3.500A) removed outlier: 5.347A pdb=" N ASP 5 454 " --> pdb=" O ILE 5 450 " (cutoff:3.500A) removed outlier: 5.997A pdb=" N GLU 5 455 " --> pdb=" O SER 5 451 " (cutoff:3.500A) Processing helix chain '5' and resid 473 through 488 Processing helix chain '5' and resid 490 through 496 Processing helix chain '5' and resid 500 through 521 removed outlier: 3.874A pdb=" N ALA 5 504 " --> pdb=" O ARG 5 500 " (cutoff:3.500A) Processing helix chain '5' and resid 522 through 525 removed outlier: 3.571A pdb=" N GLY 5 525 " --> pdb=" O TYR 5 522 " (cutoff:3.500A) No H-bonds generated for 'chain '5' and resid 522 through 525' Processing helix chain '5' and resid 529 through 547 removed outlier: 4.451A pdb=" N ASN 5 545 " --> pdb=" O GLY 5 541 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N PHE 5 546 " --> pdb=" O SER 5 542 " (cutoff:3.500A) Processing helix chain '5' and resid 553 through 560 Processing helix chain '5' and resid 561 through 571 removed outlier: 4.047A pdb=" N ILE 5 565 " --> pdb=" O GLY 5 561 " (cutoff:3.500A) Processing helix chain '5' and resid 585 through 593 Processing helix chain '5' and resid 598 through 612 Processing helix chain '5' and resid 616 through 627 Processing helix chain '5' and resid 628 through 634 Processing helix chain '5' and resid 640 through 656 Processing helix chain '5' and resid 658 through 668 removed outlier: 3.752A pdb=" N VAL 5 662 " --> pdb=" O SER 5 658 " (cutoff:3.500A) Processing helix chain '5' and resid 690 through 702 Processing helix chain '5' and resid 706 through 725 Processing helix chain '5' and resid 727 through 737 removed outlier: 3.838A pdb=" N GLN 5 737 " --> pdb=" O LEU 5 733 " (cutoff:3.500A) Processing helix chain '5' and resid 738 through 749 Processing helix chain '5' and resid 761 through 777 Processing helix chain '5' and resid 874 through 886 removed outlier: 3.666A pdb=" N GLU 5 878 " --> pdb=" O ARG 5 874 " (cutoff:3.500A) Processing helix chain '5' and resid 887 through 895 removed outlier: 3.614A pdb=" N LEU 5 891 " --> pdb=" O GLY 5 887 " (cutoff:3.500A) Processing helix chain '5' and resid 896 through 898 No H-bonds generated for 'chain '5' and resid 896 through 898' Processing helix chain '5' and resid 900 through 918 Processing helix chain '8' and resid 35 through 53 removed outlier: 3.986A pdb=" N TYR 8 46 " --> pdb=" O GLN 8 42 " (cutoff:3.500A) removed outlier: 5.065A pdb=" N ALA 8 48 " --> pdb=" O ALA 8 44 " (cutoff:3.500A) removed outlier: 6.307A pdb=" N MET 8 49 " --> pdb=" O LYS 8 45 " (cutoff:3.500A) removed outlier: 4.322A pdb=" N GLY 8 50 " --> pdb=" O TYR 8 46 " (cutoff:3.500A) removed outlier: 4.184A pdb=" N GLU 8 51 " --> pdb=" O SER 8 47 " (cutoff:3.500A) Processing helix chain '8' and resid 88 through 100 Processing helix chain '8' and resid 102 through 114 Processing helix chain '8' and resid 118 through 130 Processing helix chain '8' and resid 130 through 143 Processing helix chain '8' and resid 145 through 157 Processing helix chain '8' and resid 193 through 211 Processing helix chain '8' and resid 220 through 234 Processing helix chain '8' and resid 234 through 240 removed outlier: 3.993A pdb=" N SER 8 240 " --> pdb=" O ILE 8 236 " (cutoff:3.500A) Processing helix chain '8' and resid 242 through 257 Processing helix chain '8' and resid 273 through 278 Processing helix chain '8' and resid 280 through 308 removed outlier: 3.649A pdb=" N SER 8 284 " --> pdb=" O ILE 8 280 " (cutoff:3.500A) Proline residue: 8 300 - end of helix Processing helix chain '8' and resid 352 through 356 Processing helix chain '8' and resid 394 through 401 removed outlier: 4.376A pdb=" N GLU 8 401 " --> pdb=" O ASN 8 397 " (cutoff:3.500A) Processing helix chain '8' and resid 417 through 423 Processing helix chain '8' and resid 427 through 446 removed outlier: 3.626A pdb=" N GLN 8 431 " --> pdb=" O PRO 8 427 " (cutoff:3.500A) Processing helix chain '1' and resid 6 through 17 Processing helix chain '1' and resid 18 through 23 Processing helix chain '1' and resid 26 through 37 Processing helix chain '1' and resid 38 through 41 Processing helix chain '1' and resid 70 through 81 Processing helix chain '1' and resid 107 through 116 removed outlier: 3.555A pdb=" N PHE 1 111 " --> pdb=" O ASP 1 107 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N THR 1 112 " --> pdb=" O VAL 1 108 " (cutoff:3.500A) Processing helix chain '1' and resid 317 through 321 Processing helix chain '1' and resid 497 through 504 Processing helix chain '1' and resid 596 through 613 removed outlier: 3.548A pdb=" N TYR 1 600 " --> pdb=" O ASP 1 596 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N LYS 1 603 " --> pdb=" O GLY 1 599 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N TRP 1 604 " --> pdb=" O TYR 1 600 " (cutoff:3.500A) Processing helix chain '1' and resid 708 through 725 removed outlier: 3.733A pdb=" N ASN 1 712 " --> pdb=" O GLY 1 708 " (cutoff:3.500A) Processing helix chain '1' and resid 727 through 742 Processing helix chain '1' and resid 752 through 781 Processing helix chain '1' and resid 914 through 932 removed outlier: 3.518A pdb=" N THR 1 922 " --> pdb=" O VAL 1 918 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N ARG 1 923 " --> pdb=" O ILE 1 919 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N SER 1 927 " --> pdb=" O ARG 1 923 " (cutoff:3.500A) Processing helix chain '1' and resid 944 through 949 removed outlier: 3.524A pdb=" N LYS 1 947 " --> pdb=" O ARG 1 944 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N ILE 1 949 " --> pdb=" O TYR 1 946 " (cutoff:3.500A) Processing helix chain '1' and resid 950 through 955 Processing helix chain '1' and resid 3786 through 3799 Processing helix chain '1' and resid 3810 through 3827 removed outlier: 4.358A pdb=" N UNK 13814 " --> pdb=" O UNK 13810 " (cutoff:3.500A) removed outlier: 4.600A pdb=" N UNK 13816 " --> pdb=" O UNK 13812 " (cutoff:3.500A) Processing helix chain '1' and resid 3837 through 3849 removed outlier: 4.260A pdb=" N UNK 13843 " --> pdb=" O UNK 13839 " (cutoff:3.500A) Processing helix chain '1' and resid 3856 through 3880 removed outlier: 3.711A pdb=" N UNK 13865 " --> pdb=" O UNK 13861 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N UNK 13874 " --> pdb=" O UNK 13870 " (cutoff:3.500A) removed outlier: 4.173A pdb=" N UNK 13877 " --> pdb=" O UNK 13873 " (cutoff:3.500A) removed outlier: 4.505A pdb=" N UNK 13878 " --> pdb=" O UNK 13874 " (cutoff:3.500A) Processing helix chain '1' and resid 3891 through 3908 Processing helix chain '4' and resid 92 through 97 Processing helix chain '4' and resid 205 through 209 removed outlier: 4.307A pdb=" N GLU 4 208 " --> pdb=" O VAL 4 205 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N PHE 4 209 " --> pdb=" O LEU 4 206 " (cutoff:3.500A) No H-bonds generated for 'chain '4' and resid 205 through 209' Processing helix chain '4' and resid 212 through 221 Processing helix chain '4' and resid 223 through 230 removed outlier: 3.722A pdb=" N PHE 4 230 " --> pdb=" O PHE 4 226 " (cutoff:3.500A) Processing helix chain '4' and resid 271 through 277 removed outlier: 4.320A pdb=" N LYS 4 277 " --> pdb=" O PHE 4 273 " (cutoff:3.500A) Processing helix chain '9' and resid 224 through 240 removed outlier: 3.768A pdb=" N VAL 9 240 " --> pdb=" O GLU 9 236 " (cutoff:3.500A) Processing helix chain '9' and resid 243 through 254 Processing helix chain '9' and resid 261 through 279 removed outlier: 3.662A pdb=" N LEU 9 265 " --> pdb=" O ASN 9 261 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N ILE 9 273 " --> pdb=" O SER 9 269 " (cutoff:3.500A) removed outlier: 5.958A pdb=" N LYS 9 276 " --> pdb=" O LEU 9 272 " (cutoff:3.500A) removed outlier: 5.036A pdb=" N TYR 9 277 " --> pdb=" O ILE 9 273 " (cutoff:3.500A) Processing helix chain '9' and resid 304 through 314 Processing helix chain '9' and resid 345 through 350 Processing helix chain '9' and resid 352 through 371 removed outlier: 3.765A pdb=" N TRP 9 356 " --> pdb=" O ASP 9 352 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N TYR 9 371 " --> pdb=" O PHE 9 367 " (cutoff:3.500A) Processing helix chain '9' and resid 3188 through 3199 Processing helix chain '9' and resid 3205 through 3215 Processing helix chain '9' and resid 3292 through 3298 removed outlier: 3.927A pdb=" N UNK 93296 " --> pdb=" O UNK 93292 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain '5' and resid 214 through 218 Processing sheet with id=AA2, first strand: chain '8' and resid 32 through 33 removed outlier: 7.040A pdb=" N LYS 8 32 " --> pdb=" O GLY 8 449 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain '1' and resid 337 through 339 Processing sheet with id=AA4, first strand: chain '1' and resid 386 through 389 Processing sheet with id=AA5, first strand: chain '1' and resid 557 through 564 removed outlier: 5.553A pdb=" N HIS 1 558 " --> pdb=" O LYS 1 554 " (cutoff:3.500A) removed outlier: 6.749A pdb=" N LYS 1 554 " --> pdb=" O HIS 1 558 " (cutoff:3.500A) removed outlier: 4.784A pdb=" N GLY 1 560 " --> pdb=" O PHE 1 552 " (cutoff:3.500A) removed outlier: 4.098A pdb=" N PHE 1 552 " --> pdb=" O GLY 1 560 " (cutoff:3.500A) removed outlier: 6.706A pdb=" N ILE 1 550 " --> pdb=" O ALA 1 562 " (cutoff:3.500A) removed outlier: 6.004A pdb=" N SER 1 582 " --> pdb=" O LEU 1 409 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain '1' and resid 687 through 688 Processing sheet with id=AA7, first strand: chain '4' and resid 128 through 135 removed outlier: 3.887A pdb=" N GLN 4 141 " --> pdb=" O ARG 4 170 " (cutoff:3.500A) removed outlier: 6.917A pdb=" N SER 4 164 " --> pdb=" O LYS 4 147 " (cutoff:3.500A) removed outlier: 7.983A pdb=" N SER 4 180 " --> pdb=" O LEU 4 297 " (cutoff:3.500A) removed outlier: 4.833A pdb=" N LEU 4 297 " --> pdb=" O SER 4 180 " (cutoff:3.500A) removed outlier: 6.836A pdb=" N TYR 4 182 " --> pdb=" O LYS 4 295 " (cutoff:3.500A) 879 hydrogen bonds defined for protein. 2591 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: 4.70 Time building geometry restraints manager: 8.65 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 5150 1.34 - 1.46: 2703 1.46 - 1.58: 8400 1.58 - 1.69: 0 1.69 - 1.81: 108 Bond restraints: 16361 Sorted by residual: bond pdb=" C ASP 4 150 " pdb=" N LEU 4 151 " ideal model delta sigma weight residual 1.331 1.287 0.044 2.07e-02 2.33e+03 4.49e+00 bond pdb=" CG1 ILE 1 612 " pdb=" CD1 ILE 1 612 " ideal model delta sigma weight residual 1.513 1.453 0.060 3.90e-02 6.57e+02 2.37e+00 bond pdb=" C LYS 9 239 " pdb=" N VAL 9 240 " ideal model delta sigma weight residual 1.334 1.316 0.018 1.24e-02 6.50e+03 2.13e+00 bond pdb=" CG1 ILE 8 146 " pdb=" CD1 ILE 8 146 " ideal model delta sigma weight residual 1.513 1.470 0.043 3.90e-02 6.57e+02 1.19e+00 bond pdb=" CG PRO 8 424 " pdb=" CD PRO 8 424 " ideal model delta sigma weight residual 1.503 1.471 0.032 3.40e-02 8.65e+02 8.99e-01 ... (remaining 16356 not shown) Histogram of bond angle deviations from ideal: 99.65 - 106.54: 319 106.54 - 113.42: 8969 113.42 - 120.31: 6229 120.31 - 127.20: 6475 127.20 - 134.09: 138 Bond angle restraints: 22130 Sorted by residual: angle pdb=" C GLY 1 534 " pdb=" N ARG 1 535 " pdb=" CA ARG 1 535 " ideal model delta sigma weight residual 121.54 130.20 -8.66 1.91e+00 2.74e-01 2.06e+01 angle pdb=" C LYS 4 191 " pdb=" N GLU 4 192 " pdb=" CA GLU 4 192 " ideal model delta sigma weight residual 121.54 127.90 -6.36 1.91e+00 2.74e-01 1.11e+01 angle pdb=" N ALA 5 30 " pdb=" CA ALA 5 30 " pdb=" C ALA 5 30 " ideal model delta sigma weight residual 109.81 116.25 -6.44 2.21e+00 2.05e-01 8.50e+00 angle pdb=" N GLU 8 103 " pdb=" CA GLU 8 103 " pdb=" C GLU 8 103 " ideal model delta sigma weight residual 111.14 114.14 -3.00 1.08e+00 8.57e-01 7.72e+00 angle pdb=" C ASN 4 189 " pdb=" N HIS 4 190 " pdb=" CA HIS 4 190 " ideal model delta sigma weight residual 121.54 126.41 -4.87 1.91e+00 2.74e-01 6.50e+00 ... (remaining 22125 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.84: 8950 17.84 - 35.68: 745 35.68 - 53.53: 113 53.53 - 71.37: 26 71.37 - 89.21: 18 Dihedral angle restraints: 9852 sinusoidal: 3828 harmonic: 6024 Sorted by residual: dihedral pdb=" CA VAL 4 108 " pdb=" C VAL 4 108 " pdb=" N ILE 4 109 " pdb=" CA ILE 4 109 " ideal model delta harmonic sigma weight residual 180.00 -153.40 -26.60 0 5.00e+00 4.00e-02 2.83e+01 dihedral pdb=" CA TYR 5 271 " pdb=" C TYR 5 271 " pdb=" N HIS 5 272 " pdb=" CA HIS 5 272 " ideal model delta harmonic sigma weight residual -180.00 -157.03 -22.97 0 5.00e+00 4.00e-02 2.11e+01 dihedral pdb=" CA LEU 5 29 " pdb=" C LEU 5 29 " pdb=" N ALA 5 30 " pdb=" CA ALA 5 30 " ideal model delta harmonic sigma weight residual -180.00 -159.38 -20.62 0 5.00e+00 4.00e-02 1.70e+01 ... (remaining 9849 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.031: 1527 0.031 - 0.062: 659 0.062 - 0.092: 225 0.092 - 0.123: 103 0.123 - 0.154: 14 Chirality restraints: 2528 Sorted by residual: chirality pdb=" CA ILE 5 627 " pdb=" N ILE 5 627 " pdb=" C ILE 5 627 " pdb=" CB ILE 5 627 " both_signs ideal model delta sigma weight residual False 2.43 2.59 -0.15 2.00e-01 2.50e+01 5.93e-01 chirality pdb=" CA ILE 4 327 " pdb=" N ILE 4 327 " pdb=" C ILE 4 327 " pdb=" CB ILE 4 327 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.64e-01 chirality pdb=" CA ILE 4 169 " pdb=" N ILE 4 169 " pdb=" C ILE 4 169 " pdb=" CB ILE 4 169 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.14 2.00e-01 2.50e+01 5.14e-01 ... (remaining 2525 not shown) Planarity restraints: 2804 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP 5 606 " 0.033 2.00e-02 2.50e+03 3.20e-02 2.55e+01 pdb=" CG TRP 5 606 " -0.084 2.00e-02 2.50e+03 pdb=" CD1 TRP 5 606 " 0.045 2.00e-02 2.50e+03 pdb=" CD2 TRP 5 606 " -0.003 2.00e-02 2.50e+03 pdb=" NE1 TRP 5 606 " -0.004 2.00e-02 2.50e+03 pdb=" CE2 TRP 5 606 " -0.004 2.00e-02 2.50e+03 pdb=" CE3 TRP 5 606 " 0.004 2.00e-02 2.50e+03 pdb=" CZ2 TRP 5 606 " 0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP 5 606 " 0.008 2.00e-02 2.50e+03 pdb=" CH2 TRP 5 606 " 0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ARG 4 124 " 0.041 5.00e-02 4.00e+02 6.14e-02 6.04e+00 pdb=" N PRO 4 125 " -0.106 5.00e-02 4.00e+02 pdb=" CA PRO 4 125 " 0.032 5.00e-02 4.00e+02 pdb=" CD PRO 4 125 " 0.034 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL 1 572 " 0.033 5.00e-02 4.00e+02 4.99e-02 3.98e+00 pdb=" N PRO 1 573 " -0.086 5.00e-02 4.00e+02 pdb=" CA PRO 1 573 " 0.026 5.00e-02 4.00e+02 pdb=" CD PRO 1 573 " 0.028 5.00e-02 4.00e+02 ... (remaining 2801 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 1487 2.74 - 3.28: 15566 3.28 - 3.82: 25009 3.82 - 4.36: 30120 4.36 - 4.90: 53526 Nonbonded interactions: 125708 Sorted by model distance: nonbonded pdb=" O ASN 8 276 " pdb=" OG SER 8 279 " model vdw 2.202 2.440 nonbonded pdb=" OH TYR 5 515 " pdb=" OD2 ASP 5 572 " model vdw 2.224 2.440 nonbonded pdb=" ND2 ASN 5 109 " pdb=" OE1 GLU 5 153 " model vdw 2.227 2.520 nonbonded pdb=" NH2 ARG 8 207 " pdb=" O TYR 8 278 " model vdw 2.244 2.520 nonbonded pdb=" O ARG 1 10 " pdb=" ND2 ASN 1 14 " model vdw 2.246 2.520 ... (remaining 125703 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=0.50 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: 0.880 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 5.260 Check model and map are aligned: 0.270 Set scattering table: 0.170 Process input model: 48.340 Find NCS groups from input model: 0.470 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: 0.010 Load rotamer database and sin/cos tables:2.800 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 58.280 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8334 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 : 0.004 0.060 16361 Z= 0.274 Angle : 0.622 8.662 22130 Z= 0.346 Chirality : 0.042 0.154 2528 Planarity : 0.004 0.061 2804 Dihedral : 13.996 89.211 5912 Min Nonbonded Distance : 2.202 Molprobity Statistics. All-atom Clashscore : 6.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.99 % Favored : 94.01 % Rotamer: Outliers : 0.06 % Allowed : 0.47 % Favored : 99.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.07 (0.20), residues: 1821 helix: 1.20 (0.16), residues: 1029 sheet: 0.34 (0.47), residues: 132 loop : -1.93 (0.22), residues: 660 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.084 0.002 TRP 5 606 HIS 0.006 0.001 HIS 5 272 PHE 0.015 0.002 PHE 1 515 TYR 0.014 0.002 TYR 5 84 ARG 0.009 0.001 ARG 8 117 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3642 Ramachandran restraints generated. 1821 Oldfield, 0 Emsley, 1821 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3642 Ramachandran restraints generated. 1821 Oldfield, 0 Emsley, 1821 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 1739 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 188 time to evaluate : 1.994 Fit side-chains REVERT: 5 473 ASP cc_start: 0.7357 (t0) cc_final: 0.7067 (t70) REVERT: 1 502 LYS cc_start: 0.8831 (tttm) cc_final: 0.8631 (tttm) REVERT: 4 284 ASN cc_start: 0.8217 (t0) cc_final: 0.7873 (t0) outliers start: 0 outliers final: 0 residues processed: 188 average time/residue: 0.3191 time to fit residues: 86.6690 Evaluate side-chains 160 residues out of total 1739 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 160 time to evaluate : 1.786 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 156 optimal weight: 20.0000 chunk 140 optimal weight: 0.0970 chunk 77 optimal weight: 2.9990 chunk 47 optimal weight: 0.8980 chunk 94 optimal weight: 4.9990 chunk 74 optimal weight: 4.9990 chunk 145 optimal weight: 0.9990 chunk 56 optimal weight: 7.9990 chunk 88 optimal weight: 4.9990 chunk 107 optimal weight: 1.9990 chunk 168 optimal weight: 5.9990 overall best weight: 1.3984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 5 368 ASN 5 434 HIS 5 598 HIS 1 525 GLN ** 1 581 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 1 712 ASN ** 4 162 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 9 251 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8343 moved from start: 0.0520 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 16361 Z= 0.262 Angle : 0.552 8.907 22130 Z= 0.287 Chirality : 0.041 0.143 2528 Planarity : 0.004 0.060 2804 Dihedral : 4.513 26.020 2153 Min Nonbonded Distance : 2.205 Molprobity Statistics. All-atom Clashscore : 5.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.99 % Favored : 94.01 % Rotamer: Outliers : 1.06 % Allowed : 5.81 % Favored : 93.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.45 (0.20), residues: 1821 helix: 1.51 (0.16), residues: 1035 sheet: 0.54 (0.47), residues: 131 loop : -1.81 (0.23), residues: 655 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.002 TRP 5 606 HIS 0.004 0.001 HIS 5 474 PHE 0.025 0.001 PHE 1 515 TYR 0.015 0.001 TYR 1 103 ARG 0.006 0.000 ARG 8 117 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3642 Ramachandran restraints generated. 1821 Oldfield, 0 Emsley, 1821 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3642 Ramachandran restraints generated. 1821 Oldfield, 0 Emsley, 1821 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 1739 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 166 time to evaluate : 2.071 Fit side-chains REVERT: 5 473 ASP cc_start: 0.7441 (t0) cc_final: 0.7139 (t70) REVERT: 5 584 ASN cc_start: 0.8523 (OUTLIER) cc_final: 0.8235 (m110) REVERT: 8 227 ILE cc_start: 0.8967 (mt) cc_final: 0.8609 (mp) REVERT: 4 191 LYS cc_start: 0.7858 (pttt) cc_final: 0.7408 (ptpp) REVERT: 4 284 ASN cc_start: 0.8175 (t0) cc_final: 0.7736 (t0) REVERT: 9 234 TYR cc_start: 0.7205 (t80) cc_final: 0.6845 (t80) REVERT: 9 310 GLN cc_start: 0.8237 (tm-30) cc_final: 0.8007 (tm-30) outliers start: 17 outliers final: 10 residues processed: 175 average time/residue: 0.3149 time to fit residues: 80.6530 Evaluate side-chains 169 residues out of total 1739 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 158 time to evaluate : 2.338 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 5 residue 584 ASN Chi-restraints excluded: chain 5 residue 743 ILE Chi-restraints excluded: chain 8 residue 52 LEU Chi-restraints excluded: chain 8 residue 289 LEU Chi-restraints excluded: chain 1 residue 507 LEU Chi-restraints excluded: chain 1 residue 612 ILE Chi-restraints excluded: chain 1 residue 723 ILE Chi-restraints excluded: chain 4 residue 155 ASP Chi-restraints excluded: chain 4 residue 274 SER Chi-restraints excluded: chain 4 residue 280 ASP Chi-restraints excluded: chain 4 residue 290 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 93 optimal weight: 3.9990 chunk 52 optimal weight: 0.5980 chunk 139 optimal weight: 0.0370 chunk 114 optimal weight: 3.9990 chunk 46 optimal weight: 0.6980 chunk 168 optimal weight: 0.9990 chunk 181 optimal weight: 0.3980 chunk 149 optimal weight: 4.9990 chunk 166 optimal weight: 8.9990 chunk 57 optimal weight: 2.9990 chunk 135 optimal weight: 0.7980 overall best weight: 0.5058 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 5 128 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 188 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 5 272 HIS ** 5 368 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 8 398 GLN ** 8 446 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 1 525 GLN 1 581 ASN 1 712 ASN ** 4 162 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 9 251 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8273 moved from start: 0.0957 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 16361 Z= 0.135 Angle : 0.467 9.504 22130 Z= 0.244 Chirality : 0.037 0.142 2528 Planarity : 0.003 0.051 2804 Dihedral : 4.020 21.093 2153 Min Nonbonded Distance : 2.224 Molprobity Statistics. All-atom Clashscore : 5.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.40 % Favored : 95.60 % Rotamer: Outliers : 1.12 % Allowed : 7.39 % Favored : 91.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.00 (0.20), residues: 1821 helix: 1.97 (0.17), residues: 1037 sheet: 0.73 (0.46), residues: 132 loop : -1.59 (0.23), residues: 652 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP 5 606 HIS 0.002 0.001 HIS 5 474 PHE 0.022 0.001 PHE 1 515 TYR 0.011 0.001 TYR 5 360 ARG 0.005 0.000 ARG 8 117 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3642 Ramachandran restraints generated. 1821 Oldfield, 0 Emsley, 1821 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3642 Ramachandran restraints generated. 1821 Oldfield, 0 Emsley, 1821 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 1739 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 187 time to evaluate : 1.846 Fit side-chains REVERT: 8 227 ILE cc_start: 0.8951 (mt) cc_final: 0.8588 (mp) REVERT: 1 691 LYS cc_start: 0.7562 (tmmt) cc_final: 0.7347 (tmmt) REVERT: 4 284 ASN cc_start: 0.8237 (t0) cc_final: 0.7808 (t0) outliers start: 17 outliers final: 12 residues processed: 195 average time/residue: 0.2892 time to fit residues: 83.4856 Evaluate side-chains 178 residues out of total 1739 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 166 time to evaluate : 1.838 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 5 residue 67 GLN Chi-restraints excluded: chain 5 residue 216 ILE Chi-restraints excluded: chain 5 residue 584 ASN Chi-restraints excluded: chain 1 residue 13 ILE Chi-restraints excluded: chain 1 residue 26 VAL Chi-restraints excluded: chain 1 residue 409 LEU Chi-restraints excluded: chain 1 residue 507 LEU Chi-restraints excluded: chain 1 residue 516 ASP Chi-restraints excluded: chain 1 residue 612 ILE Chi-restraints excluded: chain 1 residue 723 ILE Chi-restraints excluded: chain 4 residue 274 SER Chi-restraints excluded: chain 4 residue 290 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 166 optimal weight: 3.9990 chunk 126 optimal weight: 4.9990 chunk 87 optimal weight: 0.8980 chunk 18 optimal weight: 0.9980 chunk 80 optimal weight: 0.9990 chunk 113 optimal weight: 5.9990 chunk 168 optimal weight: 6.9990 chunk 178 optimal weight: 4.9990 chunk 88 optimal weight: 1.9990 chunk 160 optimal weight: 20.0000 chunk 48 optimal weight: 3.9990 overall best weight: 1.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 5 368 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 5 447 GLN 8 398 GLN 1 525 GLN ** 4 162 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8355 moved from start: 0.0875 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 16361 Z= 0.315 Angle : 0.553 9.211 22130 Z= 0.288 Chirality : 0.041 0.151 2528 Planarity : 0.004 0.053 2804 Dihedral : 4.360 23.506 2153 Min Nonbonded Distance : 2.190 Molprobity Statistics. All-atom Clashscore : 5.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.99 % Favored : 94.01 % Rotamer: Outliers : 1.47 % Allowed : 9.27 % Favored : 89.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.82 (0.20), residues: 1821 helix: 1.83 (0.16), residues: 1036 sheet: 0.50 (0.45), residues: 140 loop : -1.67 (0.23), residues: 645 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP 5 606 HIS 0.004 0.001 HIS 4 162 PHE 0.021 0.002 PHE 1 515 TYR 0.013 0.002 TYR 5 333 ARG 0.004 0.000 ARG 8 117 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3642 Ramachandran restraints generated. 1821 Oldfield, 0 Emsley, 1821 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3642 Ramachandran restraints generated. 1821 Oldfield, 0 Emsley, 1821 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 1739 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 161 time to evaluate : 2.146 Fit side-chains REVERT: 8 227 ILE cc_start: 0.8975 (mt) cc_final: 0.8629 (mp) REVERT: 1 503 TYR cc_start: 0.8356 (m-80) cc_final: 0.8148 (m-80) REVERT: 4 284 ASN cc_start: 0.8162 (t0) cc_final: 0.7689 (t0) REVERT: 9 350 LEU cc_start: 0.8522 (OUTLIER) cc_final: 0.8274 (mp) outliers start: 23 outliers final: 14 residues processed: 177 average time/residue: 0.2972 time to fit residues: 78.3473 Evaluate side-chains 171 residues out of total 1739 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 156 time to evaluate : 1.932 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 5 residue 514 THR Chi-restraints excluded: chain 5 residue 534 MET Chi-restraints excluded: chain 5 residue 584 ASN Chi-restraints excluded: chain 8 residue 52 LEU Chi-restraints excluded: chain 1 residue 13 ILE Chi-restraints excluded: chain 1 residue 26 VAL Chi-restraints excluded: chain 1 residue 339 LEU Chi-restraints excluded: chain 1 residue 507 LEU Chi-restraints excluded: chain 1 residue 516 ASP Chi-restraints excluded: chain 1 residue 612 ILE Chi-restraints excluded: chain 1 residue 723 ILE Chi-restraints excluded: chain 4 residue 163 LEU Chi-restraints excluded: chain 4 residue 274 SER Chi-restraints excluded: chain 4 residue 290 MET Chi-restraints excluded: chain 9 residue 350 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 148 optimal weight: 3.9990 chunk 101 optimal weight: 1.9990 chunk 2 optimal weight: 1.9990 chunk 133 optimal weight: 0.4980 chunk 73 optimal weight: 0.9980 chunk 152 optimal weight: 0.6980 chunk 123 optimal weight: 0.1980 chunk 0 optimal weight: 4.9990 chunk 91 optimal weight: 1.9990 chunk 160 optimal weight: 20.0000 chunk 45 optimal weight: 0.0570 overall best weight: 0.4898 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 5 128 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 188 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 368 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 8 398 GLN ** 8 446 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 1 525 GLN 4 162 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8277 moved from start: 0.1176 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 16361 Z= 0.132 Angle : 0.465 10.622 22130 Z= 0.242 Chirality : 0.037 0.140 2528 Planarity : 0.003 0.047 2804 Dihedral : 3.948 20.262 2153 Min Nonbonded Distance : 2.255 Molprobity Statistics. All-atom Clashscore : 5.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.07 % Favored : 95.93 % Rotamer: Outliers : 1.58 % Allowed : 9.86 % Favored : 88.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.21 (0.20), residues: 1821 helix: 2.13 (0.17), residues: 1036 sheet: 0.76 (0.47), residues: 133 loop : -1.47 (0.23), residues: 652 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP 5 606 HIS 0.002 0.000 HIS 5 474 PHE 0.020 0.001 PHE 1 515 TYR 0.009 0.001 TYR 1 103 ARG 0.005 0.000 ARG 5 893 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3642 Ramachandran restraints generated. 1821 Oldfield, 0 Emsley, 1821 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3642 Ramachandran restraints generated. 1821 Oldfield, 0 Emsley, 1821 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 1739 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 164 time to evaluate : 1.993 Fit side-chains REVERT: 5 773 ASN cc_start: 0.8644 (t0) cc_final: 0.8192 (t0) REVERT: 8 227 ILE cc_start: 0.8972 (mt) cc_final: 0.8615 (mp) REVERT: 4 284 ASN cc_start: 0.8193 (t0) cc_final: 0.7730 (t0) REVERT: 9 310 GLN cc_start: 0.8187 (tm-30) cc_final: 0.7960 (tm-30) outliers start: 25 outliers final: 18 residues processed: 179 average time/residue: 0.2998 time to fit residues: 81.3616 Evaluate side-chains 176 residues out of total 1739 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 158 time to evaluate : 2.062 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 5 residue 216 ILE Chi-restraints excluded: chain 5 residue 514 THR Chi-restraints excluded: chain 5 residue 584 ASN Chi-restraints excluded: chain 8 residue 289 LEU Chi-restraints excluded: chain 8 residue 324 ILE Chi-restraints excluded: chain 1 residue 26 VAL Chi-restraints excluded: chain 1 residue 339 LEU Chi-restraints excluded: chain 1 residue 400 THR Chi-restraints excluded: chain 1 residue 409 LEU Chi-restraints excluded: chain 1 residue 507 LEU Chi-restraints excluded: chain 1 residue 516 ASP Chi-restraints excluded: chain 1 residue 564 THR Chi-restraints excluded: chain 1 residue 612 ILE Chi-restraints excluded: chain 1 residue 723 ILE Chi-restraints excluded: chain 4 residue 155 ASP Chi-restraints excluded: chain 4 residue 163 LEU Chi-restraints excluded: chain 4 residue 274 SER Chi-restraints excluded: chain 4 residue 290 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 60 optimal weight: 1.9990 chunk 161 optimal weight: 20.0000 chunk 35 optimal weight: 0.9990 chunk 104 optimal weight: 2.9990 chunk 44 optimal weight: 2.9990 chunk 178 optimal weight: 4.9990 chunk 148 optimal weight: 5.9990 chunk 82 optimal weight: 0.9990 chunk 14 optimal weight: 0.8980 chunk 59 optimal weight: 0.0020 chunk 93 optimal weight: 0.8980 overall best weight: 0.7592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 5 128 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 188 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 368 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 8 398 GLN ** 8 446 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 1 525 GLN 1 957 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8295 moved from start: 0.1193 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 16361 Z= 0.166 Angle : 0.478 10.502 22130 Z= 0.248 Chirality : 0.038 0.141 2528 Planarity : 0.003 0.048 2804 Dihedral : 3.935 20.453 2153 Min Nonbonded Distance : 2.256 Molprobity Statistics. All-atom Clashscore : 5.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.95 % Favored : 95.05 % Rotamer: Outliers : 1.76 % Allowed : 10.21 % Favored : 88.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.29 (0.20), residues: 1821 helix: 2.18 (0.17), residues: 1038 sheet: 0.82 (0.47), residues: 133 loop : -1.42 (0.24), residues: 650 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP 5 606 HIS 0.003 0.001 HIS 5 474 PHE 0.021 0.001 PHE 1 515 TYR 0.010 0.001 TYR 1 103 ARG 0.005 0.000 ARG 5 893 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3642 Ramachandran restraints generated. 1821 Oldfield, 0 Emsley, 1821 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3642 Ramachandran restraints generated. 1821 Oldfield, 0 Emsley, 1821 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 1739 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 166 time to evaluate : 1.931 Fit side-chains REVERT: 8 227 ILE cc_start: 0.8949 (mt) cc_final: 0.8572 (mp) REVERT: 1 536 ASP cc_start: 0.7148 (t0) cc_final: 0.6678 (t0) REVERT: 4 284 ASN cc_start: 0.8236 (t0) cc_final: 0.7772 (t0) outliers start: 28 outliers final: 23 residues processed: 183 average time/residue: 0.2780 time to fit residues: 77.0680 Evaluate side-chains 184 residues out of total 1739 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 161 time to evaluate : 1.890 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 5 residue 84 TYR Chi-restraints excluded: chain 5 residue 184 THR Chi-restraints excluded: chain 5 residue 514 THR Chi-restraints excluded: chain 5 residue 584 ASN Chi-restraints excluded: chain 5 residue 597 VAL Chi-restraints excluded: chain 8 residue 52 LEU Chi-restraints excluded: chain 8 residue 289 LEU Chi-restraints excluded: chain 1 residue 13 ILE Chi-restraints excluded: chain 1 residue 26 VAL Chi-restraints excluded: chain 1 residue 339 LEU Chi-restraints excluded: chain 1 residue 383 VAL Chi-restraints excluded: chain 1 residue 400 THR Chi-restraints excluded: chain 1 residue 409 LEU Chi-restraints excluded: chain 1 residue 507 LEU Chi-restraints excluded: chain 1 residue 515 PHE Chi-restraints excluded: chain 1 residue 516 ASP Chi-restraints excluded: chain 1 residue 564 THR Chi-restraints excluded: chain 1 residue 612 ILE Chi-restraints excluded: chain 1 residue 723 ILE Chi-restraints excluded: chain 4 residue 155 ASP Chi-restraints excluded: chain 4 residue 163 LEU Chi-restraints excluded: chain 4 residue 274 SER Chi-restraints excluded: chain 4 residue 290 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 172 optimal weight: 1.9990 chunk 20 optimal weight: 0.2980 chunk 101 optimal weight: 4.9990 chunk 130 optimal weight: 2.9990 chunk 150 optimal weight: 0.9990 chunk 99 optimal weight: 3.9990 chunk 178 optimal weight: 5.9990 chunk 111 optimal weight: 0.9980 chunk 108 optimal weight: 0.9980 chunk 82 optimal weight: 0.7980 chunk 110 optimal weight: 0.9980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 5 128 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 188 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 368 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 8 398 GLN ** 8 446 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 1 525 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8296 moved from start: 0.1250 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 16361 Z= 0.172 Angle : 0.482 11.365 22130 Z= 0.250 Chirality : 0.038 0.140 2528 Planarity : 0.003 0.047 2804 Dihedral : 3.920 20.024 2153 Min Nonbonded Distance : 2.252 Molprobity Statistics. All-atom Clashscore : 5.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.95 % Favored : 95.05 % Rotamer: Outliers : 1.88 % Allowed : 10.56 % Favored : 87.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.34 (0.20), residues: 1821 helix: 2.21 (0.17), residues: 1037 sheet: 0.80 (0.47), residues: 133 loop : -1.38 (0.24), residues: 651 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP 5 606 HIS 0.003 0.001 HIS 5 474 PHE 0.022 0.001 PHE 1 515 TYR 0.014 0.001 TYR 9 234 ARG 0.006 0.000 ARG 5 893 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3642 Ramachandran restraints generated. 1821 Oldfield, 0 Emsley, 1821 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3642 Ramachandran restraints generated. 1821 Oldfield, 0 Emsley, 1821 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 1739 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 167 time to evaluate : 1.933 Fit side-chains REVERT: 5 773 ASN cc_start: 0.8642 (t0) cc_final: 0.8192 (t0) REVERT: 8 227 ILE cc_start: 0.8950 (mt) cc_final: 0.8572 (mp) REVERT: 1 536 ASP cc_start: 0.7108 (OUTLIER) cc_final: 0.6624 (t0) REVERT: 1 590 ASN cc_start: 0.8125 (p0) cc_final: 0.7914 (p0) REVERT: 4 284 ASN cc_start: 0.8224 (t0) cc_final: 0.7780 (t0) outliers start: 30 outliers final: 26 residues processed: 185 average time/residue: 0.2751 time to fit residues: 77.0294 Evaluate side-chains 189 residues out of total 1739 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 162 time to evaluate : 1.812 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 5 residue 84 TYR Chi-restraints excluded: chain 5 residue 184 THR Chi-restraints excluded: chain 5 residue 243 THR Chi-restraints excluded: chain 5 residue 514 THR Chi-restraints excluded: chain 5 residue 584 ASN Chi-restraints excluded: chain 5 residue 597 VAL Chi-restraints excluded: chain 8 residue 35 THR Chi-restraints excluded: chain 8 residue 52 LEU Chi-restraints excluded: chain 8 residue 289 LEU Chi-restraints excluded: chain 1 residue 13 ILE Chi-restraints excluded: chain 1 residue 26 VAL Chi-restraints excluded: chain 1 residue 339 LEU Chi-restraints excluded: chain 1 residue 383 VAL Chi-restraints excluded: chain 1 residue 400 THR Chi-restraints excluded: chain 1 residue 409 LEU Chi-restraints excluded: chain 1 residue 507 LEU Chi-restraints excluded: chain 1 residue 515 PHE Chi-restraints excluded: chain 1 residue 516 ASP Chi-restraints excluded: chain 1 residue 536 ASP Chi-restraints excluded: chain 1 residue 564 THR Chi-restraints excluded: chain 1 residue 612 ILE Chi-restraints excluded: chain 1 residue 723 ILE Chi-restraints excluded: chain 4 residue 109 ILE Chi-restraints excluded: chain 4 residue 155 ASP Chi-restraints excluded: chain 4 residue 163 LEU Chi-restraints excluded: chain 4 residue 274 SER Chi-restraints excluded: chain 4 residue 290 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 71 optimal weight: 0.2980 chunk 106 optimal weight: 2.9990 chunk 53 optimal weight: 0.6980 chunk 35 optimal weight: 0.9980 chunk 34 optimal weight: 0.3980 chunk 113 optimal weight: 4.9990 chunk 121 optimal weight: 0.1980 chunk 88 optimal weight: 3.9990 chunk 16 optimal weight: 9.9990 chunk 140 optimal weight: 4.9990 chunk 162 optimal weight: 20.0000 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 5 128 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 188 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 368 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 8 446 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 1 525 GLN 1 561 ASN 1 957 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8270 moved from start: 0.1420 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 16361 Z= 0.135 Angle : 0.463 12.071 22130 Z= 0.239 Chirality : 0.037 0.139 2528 Planarity : 0.003 0.046 2804 Dihedral : 3.775 19.766 2153 Min Nonbonded Distance : 2.251 Molprobity Statistics. All-atom Clashscore : 5.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.78 % Favored : 95.22 % Rotamer: Outliers : 1.94 % Allowed : 10.56 % Favored : 87.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.46 (0.21), residues: 1821 helix: 2.30 (0.17), residues: 1039 sheet: 0.85 (0.47), residues: 133 loop : -1.32 (0.24), residues: 649 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP 4 220 HIS 0.002 0.001 HIS 5 474 PHE 0.020 0.001 PHE 1 515 TYR 0.012 0.001 TYR 9 234 ARG 0.005 0.000 ARG 5 893 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3642 Ramachandran restraints generated. 1821 Oldfield, 0 Emsley, 1821 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3642 Ramachandran restraints generated. 1821 Oldfield, 0 Emsley, 1821 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 202 residues out of total 1739 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 171 time to evaluate : 1.912 Fit side-chains REVERT: 5 773 ASN cc_start: 0.8624 (t0) cc_final: 0.8185 (t0) REVERT: 8 227 ILE cc_start: 0.8916 (mt) cc_final: 0.8537 (mp) REVERT: 4 284 ASN cc_start: 0.8225 (t0) cc_final: 0.7790 (t0) outliers start: 31 outliers final: 28 residues processed: 191 average time/residue: 0.2975 time to fit residues: 85.2396 Evaluate side-chains 192 residues out of total 1739 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 164 time to evaluate : 1.907 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 5 residue 84 TYR Chi-restraints excluded: chain 5 residue 184 THR Chi-restraints excluded: chain 5 residue 243 THR Chi-restraints excluded: chain 5 residue 380 ILE Chi-restraints excluded: chain 5 residue 514 THR Chi-restraints excluded: chain 5 residue 584 ASN Chi-restraints excluded: chain 5 residue 597 VAL Chi-restraints excluded: chain 8 residue 35 THR Chi-restraints excluded: chain 8 residue 289 LEU Chi-restraints excluded: chain 8 residue 324 ILE Chi-restraints excluded: chain 1 residue 13 ILE Chi-restraints excluded: chain 1 residue 26 VAL Chi-restraints excluded: chain 1 residue 339 LEU Chi-restraints excluded: chain 1 residue 383 VAL Chi-restraints excluded: chain 1 residue 400 THR Chi-restraints excluded: chain 1 residue 409 LEU Chi-restraints excluded: chain 1 residue 507 LEU Chi-restraints excluded: chain 1 residue 515 PHE Chi-restraints excluded: chain 1 residue 516 ASP Chi-restraints excluded: chain 1 residue 564 THR Chi-restraints excluded: chain 1 residue 612 ILE Chi-restraints excluded: chain 1 residue 687 PHE Chi-restraints excluded: chain 1 residue 709 SER Chi-restraints excluded: chain 4 residue 109 ILE Chi-restraints excluded: chain 4 residue 155 ASP Chi-restraints excluded: chain 4 residue 163 LEU Chi-restraints excluded: chain 4 residue 274 SER Chi-restraints excluded: chain 4 residue 290 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 170 optimal weight: 1.9990 chunk 155 optimal weight: 10.0000 chunk 166 optimal weight: 2.9990 chunk 100 optimal weight: 0.6980 chunk 72 optimal weight: 5.9990 chunk 130 optimal weight: 1.9990 chunk 50 optimal weight: 0.8980 chunk 150 optimal weight: 0.9990 chunk 157 optimal weight: 20.0000 chunk 165 optimal weight: 2.9990 chunk 109 optimal weight: 2.9990 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 5 128 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 188 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 368 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 8 398 GLN ** 8 446 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 1 525 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8329 moved from start: 0.1237 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 16361 Z= 0.245 Angle : 0.525 12.287 22130 Z= 0.271 Chirality : 0.039 0.169 2528 Planarity : 0.003 0.048 2804 Dihedral : 4.070 20.192 2153 Min Nonbonded Distance : 2.204 Molprobity Statistics. All-atom Clashscore : 5.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.44 % Favored : 94.56 % Rotamer: Outliers : 2.05 % Allowed : 10.56 % Favored : 87.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.25 (0.20), residues: 1821 helix: 2.14 (0.16), residues: 1037 sheet: 0.66 (0.45), residues: 141 loop : -1.40 (0.24), residues: 643 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP 5 606 HIS 0.004 0.001 HIS 5 474 PHE 0.023 0.001 PHE 1 515 TYR 0.013 0.001 TYR 9 234 ARG 0.005 0.000 ARG 5 893 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3642 Ramachandran restraints generated. 1821 Oldfield, 0 Emsley, 1821 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3642 Ramachandran restraints generated. 1821 Oldfield, 0 Emsley, 1821 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 1739 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 159 time to evaluate : 2.006 Fit side-chains REVERT: 8 227 ILE cc_start: 0.8955 (mt) cc_final: 0.8589 (mp) REVERT: 1 536 ASP cc_start: 0.7201 (t0) cc_final: 0.6729 (t0) REVERT: 1 925 MET cc_start: 0.8473 (mtp) cc_final: 0.8226 (mtp) REVERT: 4 284 ASN cc_start: 0.8259 (t0) cc_final: 0.7811 (t0) outliers start: 33 outliers final: 27 residues processed: 182 average time/residue: 0.2799 time to fit residues: 77.4114 Evaluate side-chains 184 residues out of total 1739 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 157 time to evaluate : 2.030 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 5 residue 84 TYR Chi-restraints excluded: chain 5 residue 184 THR Chi-restraints excluded: chain 5 residue 274 MET Chi-restraints excluded: chain 5 residue 380 ILE Chi-restraints excluded: chain 5 residue 514 THR Chi-restraints excluded: chain 5 residue 584 ASN Chi-restraints excluded: chain 5 residue 597 VAL Chi-restraints excluded: chain 8 residue 35 THR Chi-restraints excluded: chain 8 residue 289 LEU Chi-restraints excluded: chain 8 residue 324 ILE Chi-restraints excluded: chain 1 residue 13 ILE Chi-restraints excluded: chain 1 residue 26 VAL Chi-restraints excluded: chain 1 residue 339 LEU Chi-restraints excluded: chain 1 residue 383 VAL Chi-restraints excluded: chain 1 residue 400 THR Chi-restraints excluded: chain 1 residue 409 LEU Chi-restraints excluded: chain 1 residue 507 LEU Chi-restraints excluded: chain 1 residue 515 PHE Chi-restraints excluded: chain 1 residue 516 ASP Chi-restraints excluded: chain 1 residue 612 ILE Chi-restraints excluded: chain 1 residue 687 PHE Chi-restraints excluded: chain 1 residue 709 SER Chi-restraints excluded: chain 4 residue 109 ILE Chi-restraints excluded: chain 4 residue 163 LEU Chi-restraints excluded: chain 4 residue 272 ILE Chi-restraints excluded: chain 4 residue 274 SER Chi-restraints excluded: chain 4 residue 290 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 175 optimal weight: 1.9990 chunk 107 optimal weight: 0.8980 chunk 83 optimal weight: 0.7980 chunk 122 optimal weight: 0.8980 chunk 184 optimal weight: 0.1980 chunk 169 optimal weight: 0.6980 chunk 146 optimal weight: 5.9990 chunk 15 optimal weight: 0.9980 chunk 113 optimal weight: 3.9990 chunk 89 optimal weight: 0.5980 chunk 116 optimal weight: 5.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 5 128 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 188 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 368 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 8 398 GLN ** 8 446 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 1 525 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8286 moved from start: 0.1394 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 16361 Z= 0.154 Angle : 0.482 12.708 22130 Z= 0.249 Chirality : 0.038 0.198 2528 Planarity : 0.003 0.046 2804 Dihedral : 3.879 19.898 2153 Min Nonbonded Distance : 2.246 Molprobity Statistics. All-atom Clashscore : 5.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.62 % Favored : 95.38 % Rotamer: Outliers : 1.82 % Allowed : 10.80 % Favored : 87.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.43 (0.21), residues: 1821 helix: 2.28 (0.17), residues: 1038 sheet: 0.84 (0.47), residues: 133 loop : -1.32 (0.24), residues: 650 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP 5 777 HIS 0.002 0.001 HIS 9 314 PHE 0.020 0.001 PHE 1 515 TYR 0.015 0.001 TYR 8 278 ARG 0.005 0.000 ARG 5 893 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3642 Ramachandran restraints generated. 1821 Oldfield, 0 Emsley, 1821 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3642 Ramachandran restraints generated. 1821 Oldfield, 0 Emsley, 1821 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 1739 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 163 time to evaluate : 2.015 Fit side-chains REVERT: 5 773 ASN cc_start: 0.8628 (t0) cc_final: 0.8193 (t0) REVERT: 8 227 ILE cc_start: 0.8935 (mt) cc_final: 0.8561 (mp) REVERT: 4 284 ASN cc_start: 0.8242 (t0) cc_final: 0.7831 (t0) outliers start: 29 outliers final: 28 residues processed: 182 average time/residue: 0.2866 time to fit residues: 79.5587 Evaluate side-chains 187 residues out of total 1739 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 159 time to evaluate : 1.909 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 5 residue 84 TYR Chi-restraints excluded: chain 5 residue 184 THR Chi-restraints excluded: chain 5 residue 274 MET Chi-restraints excluded: chain 5 residue 380 ILE Chi-restraints excluded: chain 5 residue 514 THR Chi-restraints excluded: chain 5 residue 584 ASN Chi-restraints excluded: chain 5 residue 597 VAL Chi-restraints excluded: chain 8 residue 35 THR Chi-restraints excluded: chain 8 residue 289 LEU Chi-restraints excluded: chain 8 residue 324 ILE Chi-restraints excluded: chain 1 residue 13 ILE Chi-restraints excluded: chain 1 residue 26 VAL Chi-restraints excluded: chain 1 residue 339 LEU Chi-restraints excluded: chain 1 residue 383 VAL Chi-restraints excluded: chain 1 residue 400 THR Chi-restraints excluded: chain 1 residue 409 LEU Chi-restraints excluded: chain 1 residue 507 LEU Chi-restraints excluded: chain 1 residue 515 PHE Chi-restraints excluded: chain 1 residue 516 ASP Chi-restraints excluded: chain 1 residue 612 ILE Chi-restraints excluded: chain 1 residue 687 PHE Chi-restraints excluded: chain 1 residue 709 SER Chi-restraints excluded: chain 4 residue 109 ILE Chi-restraints excluded: chain 4 residue 155 ASP Chi-restraints excluded: chain 4 residue 163 LEU Chi-restraints excluded: chain 4 residue 272 ILE Chi-restraints excluded: chain 4 residue 274 SER Chi-restraints excluded: chain 4 residue 290 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 156 optimal weight: 20.0000 chunk 44 optimal weight: 5.9990 chunk 135 optimal weight: 0.8980 chunk 21 optimal weight: 4.9990 chunk 40 optimal weight: 0.6980 chunk 146 optimal weight: 0.0370 chunk 61 optimal weight: 0.5980 chunk 150 optimal weight: 0.6980 chunk 18 optimal weight: 0.7980 chunk 27 optimal weight: 0.9980 chunk 129 optimal weight: 2.9990 overall best weight: 0.5658 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 5 128 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 188 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 368 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 8 446 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 1 525 GLN 1 957 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3585 r_free = 0.3585 target = 0.139809 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3208 r_free = 0.3208 target = 0.111725 restraints weight = 30985.309| |-----------------------------------------------------------------------------| r_work (start): 0.3075 rms_B_bonded: 3.36 r_work: 0.2791 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work (final): 0.2791 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2787 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2787 r_free = 0.2787 target_work(ls_wunit_k1) = 0.082 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2787 r_free = 0.2787 target_work(ls_wunit_k1) = 0.082 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2787 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8479 moved from start: 0.1476 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 16361 Z= 0.146 Angle : 0.475 12.323 22130 Z= 0.245 Chirality : 0.037 0.167 2528 Planarity : 0.003 0.045 2804 Dihedral : 3.793 19.465 2153 Min Nonbonded Distance : 2.247 Molprobity Statistics. All-atom Clashscore : 5.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.11 % Favored : 94.89 % Rotamer: Outliers : 1.82 % Allowed : 10.97 % Favored : 87.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.52 (0.21), residues: 1821 helix: 2.35 (0.17), residues: 1038 sheet: 0.85 (0.47), residues: 133 loop : -1.28 (0.24), residues: 650 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP 4 220 HIS 0.002 0.001 HIS 5 474 PHE 0.020 0.001 PHE 1 515 TYR 0.012 0.001 TYR 9 234 ARG 0.005 0.000 ARG 5 893 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3301.39 seconds wall clock time: 60 minutes 54.04 seconds (3654.04 seconds total)