Starting phenix.real_space_refine on Tue Aug 6 17:17:34 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6rd8_4809/08_2024/6rd8_4809.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6rd8_4809/08_2024/6rd8_4809.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.08 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6rd8_4809/08_2024/6rd8_4809.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6rd8_4809/08_2024/6rd8_4809.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6rd8_4809/08_2024/6rd8_4809.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6rd8_4809/08_2024/6rd8_4809.cif" } resolution = 3.08 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: 5 Type Number sf(0) Gaussians Zn 1 6.06 5 S 58 5.16 5 C 11231 2.51 5 N 2862 2.21 5 O 3160 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "0 PHE 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "1 ARG 28": "NH1" <-> "NH2" Residue "1 ASP 30": "OD1" <-> "OD2" Residue "1 PHE 31": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "1 GLU 34": "OE1" <-> "OE2" Residue "1 ASP 69": "OD1" <-> "OD2" Residue "1 ARG 118": "NH1" <-> "NH2" Residue "1 ARG 150": "NH1" <-> "NH2" Residue "1 ARG 182": "NH1" <-> "NH2" Residue "1 ASP 199": "OD1" <-> "OD2" Residue "1 PHE 200": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "1 GLU 229": "OE1" <-> "OE2" Residue "1 PHE 237": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "1 GLU 255": "OE1" <-> "OE2" Residue "1 ARG 259": "NH1" <-> "NH2" Residue "1 GLU 281": "OE1" <-> "OE2" Residue "1 PHE 321": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "1 GLU 339": "OE1" <-> "OE2" Residue "1 GLU 341": "OE1" <-> "OE2" Residue "1 GLU 352": "OE1" <-> "OE2" Residue "1 ARG 359": "NH1" <-> "NH2" Residue "1 GLU 385": "OE1" <-> "OE2" Residue "1 ARG 387": "NH1" <-> "NH2" Residue "1 GLU 409": "OE1" <-> "OE2" Residue "1 GLU 415": "OE1" <-> "OE2" Residue "1 TYR 420": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "1 ASP 422": "OD1" <-> "OD2" Residue "1 ASP 425": "OD1" <-> "OD2" Residue "1 ARG 434": "NH1" <-> "NH2" Residue "1 ASP 442": "OD1" <-> "OD2" Residue "1 GLU 452": "OE1" <-> "OE2" Residue "1 GLU 457": "OE1" <-> "OE2" Residue "1 ASP 486": "OD1" <-> "OD2" Residue "1 GLU 496": "OE1" <-> "OE2" Residue "1 GLU 513": "OE1" <-> "OE2" Residue "1 GLU 577": "OE1" <-> "OE2" Residue "1 GLU 581": "OE1" <-> "OE2" Residue "1 ARG 597": "NH1" <-> "NH2" Residue "1 ARG 609": "NH1" <-> "NH2" Residue "3 PHE 85": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "3 GLU 92": "OE1" <-> "OE2" Residue "3 ASP 119": "OD1" <-> "OD2" Residue "3 ASP 156": "OD1" <-> "OD2" Residue "3 GLU 162": "OE1" <-> "OE2" Residue "3 PHE 172": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "3 PHE 184": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "3 ASP 196": "OD1" <-> "OD2" Residue "3 ARG 213": "NH1" <-> "NH2" Residue "3 TYR 226": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "3 ARG 233": "NH1" <-> "NH2" Residue "3 ARG 242": "NH1" <-> "NH2" Residue "3 ARG 257": "NH1" <-> "NH2" Residue "3 PHE 273": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "3 TYR 292": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "3 GLU 299": "OE1" <-> "OE2" Residue "3 GLU 308": "OE1" <-> "OE2" Residue "5 GLU 6": "OE1" <-> "OE2" Residue "5 ARG 36": "NH1" <-> "NH2" Residue "5 TYR 51": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "5 ASP 104": "OD1" <-> "OD2" Residue "5 ARG 112": "NH1" <-> "NH2" Residue "5 PHE 123": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "6 PHE 80": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "6 ARG 89": "NH1" <-> "NH2" Residue "6 PHE 146": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "8 ARG 13": "NH1" <-> "NH2" Residue "8 ARG 65": "NH1" <-> "NH2" Residue "8 ASP 66": "OD1" <-> "OD2" Residue "8 TYR 84": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "9 PHE 6": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "9 PHE 15": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "9 TYR 16": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "9 ASP 17": "OD1" <-> "OD2" Residue "9 ARG 28": "NH1" <-> "NH2" Residue "9 ARG 40": "NH1" <-> "NH2" Residue "9 PHE 57": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "9 PHE 59": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "9 PHE 63": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "9 ASP 82": "OD1" <-> "OD2" Residue "9 GLU 88": "OE1" <-> "OE2" Residue "C GLU 111": "OE1" <-> "OE2" Residue "D ARG 91": "NH1" <-> "NH2" Residue "D GLU 111": "OE1" <-> "OE2" Residue "E GLU 111": "OE1" <-> "OE2" Residue "F ARG 91": "NH1" <-> "NH2" Residue "F GLU 111": "OE1" <-> "OE2" Residue "G ARG 91": "NH1" <-> "NH2" Residue "H ARG 91": "NH1" <-> "NH2" Residue "M ARG 115": "NH1" <-> "NH2" Residue "M GLU 124": "OE1" <-> "OE2" Residue "M ARG 133": "NH1" <-> "NH2" Residue "M GLU 172": "OE1" <-> "OE2" Residue "M PHE 180": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M PHE 204": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M ARG 232": "NH1" <-> "NH2" Residue "M PHE 263": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M GLU 288": "OE1" <-> "OE2" Residue "M PHE 299": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M GLU 309": "OE1" <-> "OE2" Residue "M ASP 313": "OD1" <-> "OD2" Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/chem_data/mon_lib" Total number of atoms: 17312 Number of models: 1 Model: "" Number of chains: 26 Chain: "0" Number of atoms: 605 Number of conformers: 1 Conformer: "" Number of residues, atoms: 81, 605 Classifications: {'peptide': 81} Link IDs: {'PTRANS': 8, 'TRANS': 72} Chain: "1" Number of atoms: 4661 Number of conformers: 1 Conformer: "" Number of residues, atoms: 595, 4661 Classifications: {'peptide': 595} Link IDs: {'PTRANS': 31, 'TRANS': 563} Chain: "3" Number of atoms: 1874 Number of conformers: 1 Conformer: "" Number of residues, atoms: 245, 1874 Classifications: {'peptide': 245} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 5, 'TRANS': 239} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 7 Chain: "5" Number of atoms: 986 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 986 Classifications: {'peptide': 123} Link IDs: {'PTRANS': 7, 'TRANS': 115} Chain: "6" Number of atoms: 926 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 926 Classifications: {'peptide': 124} Link IDs: {'PTRANS': 4, 'TRANS': 119} Chain: "8" Number of atoms: 692 Number of conformers: 1 Conformer: "" Number of residues, atoms: 88, 692 Classifications: {'peptide': 88} Link IDs: {'PTRANS': 7, 'TRANS': 80} Chain: "9" Number of atoms: 768 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 768 Classifications: {'peptide': 96} Link IDs: {'PTRANS': 5, 'TRANS': 90} Chain: "A" Number of atoms: 515 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 515 Classifications: {'peptide': 74} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 72} Chain: "B" Number of atoms: 514 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 514 Classifications: {'peptide': 74} Link IDs: {'PTRANS': 1, 'TRANS': 72} Chain: "C" Number of atoms: 514 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 514 Classifications: {'peptide': 74} Link IDs: {'PTRANS': 1, 'TRANS': 72} Chain: "D" Number of atoms: 514 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 514 Classifications: {'peptide': 74} Link IDs: {'PTRANS': 1, 'TRANS': 72} Chain: "E" Number of atoms: 514 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 514 Classifications: {'peptide': 74} Link IDs: {'PTRANS': 1, 'TRANS': 72} Chain: "F" Number of atoms: 514 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 514 Classifications: {'peptide': 74} Link IDs: {'PTRANS': 1, 'TRANS': 72} Chain: "G" Number of atoms: 514 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 514 Classifications: {'peptide': 74} Link IDs: {'PTRANS': 1, 'TRANS': 72} Chain: "H" Number of atoms: 514 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 514 Classifications: {'peptide': 74} Link IDs: {'PTRANS': 1, 'TRANS': 72} Chain: "I" Number of atoms: 514 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 514 Classifications: {'peptide': 74} Link IDs: {'PTRANS': 1, 'TRANS': 72} Chain: "J" Number of atoms: 514 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 514 Classifications: {'peptide': 74} Link IDs: {'PTRANS': 1, 'TRANS': 72} Chain: "M" Number of atoms: 1640 Number of conformers: 1 Conformer: "" Number of residues, atoms: 217, 1640 Classifications: {'peptide': 217} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 12, 'TRANS': 204} Chain breaks: 1 Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 13 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PHE:plan': 1} Unresolved non-hydrogen planarities: 6 Chain: "M" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "0" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "1" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "3" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "5" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "6" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "M" Number of atoms: 9 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 9 Classifications: {'water': 9} Link IDs: {None: 8} Time building chain proxies: 10.47, per 1000 atoms: 0.60 Number of scatterers: 17312 At special positions: 0 Unit cell: (131.625, 117.936, 220.077, 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) Zn 1 29.99 S 58 16.00 O 3160 8.00 N 2862 7.00 C 11231 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS 9 69 " - pdb=" SG CYS 9 79 " distance=2.21 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 6.78 Conformation dependent library (CDL) restraints added in 3.3 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN M 600 " pdb="ZN ZN M 600 " - pdb=" NE2 HIS M 248 " pdb="ZN ZN M 600 " - pdb=" NE2 HIS M 252 " 4542 Ramachandran restraints generated. 2271 Oldfield, 0 Emsley, 2271 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4248 Finding SS restraints... Secondary structure from input PDB file: 107 helices and 2 sheets defined 79.1% alpha, 0.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.46 Creating SS restraints... Processing helix chain '0' and resid 3 through 10 removed outlier: 3.901A pdb=" N ALA 0 10 " --> pdb=" O TYR 0 6 " (cutoff:3.500A) Processing helix chain '0' and resid 17 through 31 Processing helix chain '0' and resid 43 through 50 Processing helix chain '0' and resid 51 through 56 Processing helix chain '0' and resid 57 through 61 removed outlier: 3.518A pdb=" N GLN 0 60 " --> pdb=" O SER 0 57 " (cutoff:3.500A) Processing helix chain '1' and resid 45 through 74 Processing helix chain '1' and resid 106 through 143 removed outlier: 4.229A pdb=" N LYS 1 143 " --> pdb=" O ALA 1 139 " (cutoff:3.500A) Processing helix chain '1' and resid 163 through 177 Processing helix chain '1' and resid 190 through 205 Processing helix chain '1' and resid 209 through 223 Processing helix chain '1' and resid 241 through 271 removed outlier: 3.573A pdb=" N ARG 1 267 " --> pdb=" O LEU 1 263 " (cutoff:3.500A) Processing helix chain '1' and resid 272 through 277 removed outlier: 3.694A pdb=" N ALA 1 275 " --> pdb=" O PRO 1 272 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N ILE 1 276 " --> pdb=" O GLU 1 273 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N VAL 1 277 " --> pdb=" O LEU 1 274 " (cutoff:3.500A) No H-bonds generated for 'chain '1' and resid 272 through 277' Processing helix chain '1' and resid 278 through 282 Processing helix chain '1' and resid 289 through 293 Processing helix chain '1' and resid 297 through 306 Processing helix chain '1' and resid 310 through 317 Processing helix chain '1' and resid 318 through 322 removed outlier: 3.616A pdb=" N PHE 1 321 " --> pdb=" O SER 1 318 " (cutoff:3.500A) Processing helix chain '1' and resid 323 through 327 removed outlier: 3.784A pdb=" N LYS 1 327 " --> pdb=" O PHE 1 324 " (cutoff:3.500A) Processing helix chain '1' and resid 338 through 351 Processing helix chain '1' and resid 353 through 363 Processing helix chain '1' and resid 364 through 367 removed outlier: 3.505A pdb=" N GLU 1 367 " --> pdb=" O PRO 1 364 " (cutoff:3.500A) No H-bonds generated for 'chain '1' and resid 364 through 367' Processing helix chain '1' and resid 375 through 388 Processing helix chain '1' and resid 392 through 421 removed outlier: 3.659A pdb=" N LYS 1 396 " --> pdb=" O ARG 1 392 " (cutoff:3.500A) removed outlier: 4.640A pdb=" N VAL 1 418 " --> pdb=" O GLU 1 414 " (cutoff:3.500A) removed outlier: 4.724A pdb=" N ILE 1 419 " --> pdb=" O GLU 1 415 " (cutoff:3.500A) Processing helix chain '1' and resid 425 through 432 removed outlier: 3.871A pdb=" N PHE 1 429 " --> pdb=" O ASP 1 425 " (cutoff:3.500A) Processing helix chain '1' and resid 435 through 446 removed outlier: 3.716A pdb=" N ASN 1 446 " --> pdb=" O ASP 1 442 " (cutoff:3.500A) Processing helix chain '1' and resid 446 through 461 removed outlier: 3.820A pdb=" N ALA 1 459 " --> pdb=" O ALA 1 455 " (cutoff:3.500A) Processing helix chain '1' and resid 463 through 479 removed outlier: 3.935A pdb=" N ASP 1 479 " --> pdb=" O GLU 1 475 " (cutoff:3.500A) Processing helix chain '1' and resid 480 through 483 removed outlier: 3.603A pdb=" N ILE 1 483 " --> pdb=" O PRO 1 480 " (cutoff:3.500A) No H-bonds generated for 'chain '1' and resid 480 through 483' Processing helix chain '1' and resid 485 through 490 Processing helix chain '1' and resid 490 through 515 removed outlier: 4.214A pdb=" N ASP 1 504 " --> pdb=" O LEU 1 500 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N ILE 1 505 " --> pdb=" O GLU 1 501 " (cutoff:3.500A) Processing helix chain '1' and resid 518 through 540 removed outlier: 3.647A pdb=" N LEU 1 522 " --> pdb=" O GLU 1 518 " (cutoff:3.500A) removed outlier: 5.951A pdb=" N GLY 1 537 " --> pdb=" O GLN 1 533 " (cutoff:3.500A) removed outlier: 6.000A pdb=" N ILE 1 538 " --> pdb=" O LYS 1 534 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N LEU 1 540 " --> pdb=" O PHE 1 536 " (cutoff:3.500A) Processing helix chain '1' and resid 541 through 549 Processing helix chain '1' and resid 549 through 562 removed outlier: 3.594A pdb=" N GLU 1 559 " --> pdb=" O LYS 1 555 " (cutoff:3.500A) Processing helix chain '1' and resid 566 through 574 Processing helix chain '1' and resid 576 through 588 Processing helix chain '1' and resid 589 through 591 No H-bonds generated for 'chain '1' and resid 589 through 591' Processing helix chain '1' and resid 592 through 606 Processing helix chain '3' and resid 78 through 87 removed outlier: 3.638A pdb=" N ASN 3 87 " --> pdb=" O SER 3 83 " (cutoff:3.500A) Processing helix chain '3' and resid 91 through 99 Processing helix chain '3' and resid 102 through 114 Processing helix chain '3' and resid 117 through 129 removed outlier: 3.516A pdb=" N PHE 3 121 " --> pdb=" O SER 3 117 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N GLU 3 126 " --> pdb=" O VAL 3 122 " (cutoff:3.500A) Processing helix chain '3' and resid 136 through 151 Processing helix chain '3' and resid 154 through 168 Processing helix chain '3' and resid 173 through 187 Processing helix chain '3' and resid 191 through 204 Processing helix chain '3' and resid 215 through 229 removed outlier: 3.514A pdb=" N LEU 3 219 " --> pdb=" O GLY 3 215 " (cutoff:3.500A) Processing helix chain '3' and resid 233 through 241 Processing helix chain '3' and resid 245 through 251 Processing helix chain '3' and resid 253 through 272 Processing helix chain '3' and resid 275 through 277 No H-bonds generated for 'chain '3' and resid 275 through 277' Processing helix chain '3' and resid 278 through 287 Processing helix chain '3' and resid 293 through 312 Processing helix chain '5' and resid 7 through 29 Processing helix chain '5' and resid 29 through 59 removed outlier: 4.150A pdb=" N THR 5 33 " --> pdb=" O GLN 5 29 " (cutoff:3.500A) removed outlier: 5.730A pdb=" N LYS 5 49 " --> pdb=" O ALA 5 45 " (cutoff:3.500A) removed outlier: 5.445A pdb=" N ARG 5 50 " --> pdb=" O ALA 5 46 " (cutoff:3.500A) Processing helix chain '5' and resid 63 through 68 Processing helix chain '5' and resid 72 through 81 removed outlier: 3.541A pdb=" N PHE 5 81 " --> pdb=" O LEU 5 77 " (cutoff:3.500A) Processing helix chain '5' and resid 87 through 107 removed outlier: 4.324A pdb=" N HIS 5 91 " --> pdb=" O ALA 5 87 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N LEU 5 92 " --> pdb=" O PRO 5 88 " (cutoff:3.500A) Processing helix chain '5' and resid 114 through 119 Processing helix chain '6' and resid 30 through 42 Processing helix chain '6' and resid 46 through 58 removed outlier: 5.092A pdb=" N LYS 6 52 " --> pdb=" O LEU 6 48 " (cutoff:3.500A) removed outlier: 4.908A pdb=" N THR 6 53 " --> pdb=" O SER 6 49 " (cutoff:3.500A) Processing helix chain '6' and resid 72 through 96 Processing helix chain '6' and resid 98 through 120 removed outlier: 3.618A pdb=" N VAL 6 107 " --> pdb=" O LEU 6 103 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N TRP 6 112 " --> pdb=" O LEU 6 108 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N SER 6 117 " --> pdb=" O LEU 6 113 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N SER 6 118 " --> pdb=" O ILE 6 114 " (cutoff:3.500A) Processing helix chain '6' and resid 121 through 133 removed outlier: 3.721A pdb=" N ALA 6 133 " --> pdb=" O PHE 6 129 " (cutoff:3.500A) Processing helix chain '6' and resid 133 through 138 removed outlier: 3.874A pdb=" N SER 6 138 " --> pdb=" O PRO 6 134 " (cutoff:3.500A) Processing helix chain '8' and resid 5 through 9 removed outlier: 3.901A pdb=" N LYS 8 9 " --> pdb=" O VAL 8 6 " (cutoff:3.500A) Processing helix chain '8' and resid 26 through 31 Processing helix chain '8' and resid 31 through 39 removed outlier: 3.582A pdb=" N TYR 8 35 " --> pdb=" O SER 8 31 " (cutoff:3.500A) Processing helix chain '8' and resid 39 through 79 removed outlier: 3.656A pdb=" N TRP 8 45 " --> pdb=" O ILE 8 41 " (cutoff:3.500A) removed outlier: 6.880A pdb=" N TYR 8 46 " --> pdb=" O PRO 8 42 " (cutoff:3.500A) removed outlier: 5.792A pdb=" N LEU 8 47 " --> pdb=" O ARG 8 43 " (cutoff:3.500A) Processing helix chain '9' and resid 2 through 17 removed outlier: 4.050A pdb=" N PHE 9 6 " --> pdb=" O ALA 9 2 " (cutoff:3.500A) Processing helix chain '9' and resid 32 through 56 removed outlier: 3.512A pdb=" N ASN 9 56 " --> pdb=" O LEU 9 52 " (cutoff:3.500A) Processing helix chain '9' and resid 82 through 95 Processing helix chain 'A' and resid 55 through 68 Processing helix chain 'A' and resid 69 through 92 removed outlier: 4.042A pdb=" N GLY A 73 " --> pdb=" O ILE A 69 " (cutoff:3.500A) Processing helix chain 'A' and resid 95 through 126 removed outlier: 3.887A pdb=" N GLY A 101 " --> pdb=" O LYS A 97 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N ILE A 113 " --> pdb=" O LEU A 109 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N ALA A 114 " --> pdb=" O THR A 110 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N VAL A 120 " --> pdb=" O PHE A 116 " (cutoff:3.500A) Processing helix chain 'B' and resid 55 through 67 Processing helix chain 'B' and resid 69 through 92 removed outlier: 4.165A pdb=" N GLY B 73 " --> pdb=" O ILE B 69 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N VAL B 74 " --> pdb=" O ALA B 70 " (cutoff:3.500A) Processing helix chain 'B' and resid 95 through 125 removed outlier: 3.601A pdb=" N ILE B 113 " --> pdb=" O LEU B 109 " (cutoff:3.500A) Processing helix chain 'C' and resid 55 through 69 Processing helix chain 'C' and resid 70 through 92 removed outlier: 3.917A pdb=" N VAL C 74 " --> pdb=" O ALA C 70 " (cutoff:3.500A) Processing helix chain 'C' and resid 95 through 126 removed outlier: 3.773A pdb=" N ILE C 113 " --> pdb=" O LEU C 109 " (cutoff:3.500A) Processing helix chain 'D' and resid 55 through 68 Processing helix chain 'D' and resid 70 through 92 removed outlier: 3.864A pdb=" N VAL D 74 " --> pdb=" O ALA D 70 " (cutoff:3.500A) Processing helix chain 'D' and resid 95 through 126 removed outlier: 3.573A pdb=" N ILE D 113 " --> pdb=" O LEU D 109 " (cutoff:3.500A) Processing helix chain 'E' and resid 55 through 68 removed outlier: 3.900A pdb=" N MET E 61 " --> pdb=" O ALA E 57 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N VAL E 62 " --> pdb=" O ALA E 58 " (cutoff:3.500A) Processing helix chain 'E' and resid 70 through 92 removed outlier: 3.739A pdb=" N VAL E 74 " --> pdb=" O ALA E 70 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N ILE E 86 " --> pdb=" O PHE E 82 " (cutoff:3.500A) Processing helix chain 'E' and resid 95 through 126 removed outlier: 3.673A pdb=" N ILE E 113 " --> pdb=" O LEU E 109 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N PHE E 126 " --> pdb=" O PHE E 122 " (cutoff:3.500A) Processing helix chain 'F' and resid 55 through 69 removed outlier: 4.137A pdb=" N MET F 61 " --> pdb=" O ALA F 57 " (cutoff:3.500A) Processing helix chain 'F' and resid 70 through 92 removed outlier: 3.938A pdb=" N VAL F 74 " --> pdb=" O ALA F 70 " (cutoff:3.500A) Processing helix chain 'F' and resid 95 through 126 removed outlier: 3.592A pdb=" N ILE F 113 " --> pdb=" O LEU F 109 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N VAL F 120 " --> pdb=" O PHE F 116 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N PHE F 122 " --> pdb=" O LEU F 118 " (cutoff:3.500A) Processing helix chain 'G' and resid 55 through 68 removed outlier: 3.598A pdb=" N MET G 61 " --> pdb=" O ALA G 57 " (cutoff:3.500A) Processing helix chain 'G' and resid 70 through 92 removed outlier: 4.142A pdb=" N VAL G 74 " --> pdb=" O ALA G 70 " (cutoff:3.500A) Processing helix chain 'G' and resid 95 through 126 removed outlier: 4.044A pdb=" N ILE G 113 " --> pdb=" O LEU G 109 " (cutoff:3.500A) Processing helix chain 'H' and resid 55 through 69 removed outlier: 3.864A pdb=" N MET H 61 " --> pdb=" O ALA H 57 " (cutoff:3.500A) Processing helix chain 'H' and resid 70 through 92 removed outlier: 4.119A pdb=" N VAL H 74 " --> pdb=" O ALA H 70 " (cutoff:3.500A) Processing helix chain 'H' and resid 95 through 127 removed outlier: 4.171A pdb=" N ILE H 113 " --> pdb=" O LEU H 109 " (cutoff:3.500A) Processing helix chain 'I' and resid 55 through 68 Processing helix chain 'I' and resid 70 through 92 removed outlier: 3.668A pdb=" N VAL I 74 " --> pdb=" O ALA I 70 " (cutoff:3.500A) Processing helix chain 'I' and resid 95 through 127 removed outlier: 4.536A pdb=" N ILE I 113 " --> pdb=" O LEU I 109 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N ALA I 114 " --> pdb=" O THR I 110 " (cutoff:3.500A) Processing helix chain 'J' and resid 55 through 68 Processing helix chain 'J' and resid 70 through 92 removed outlier: 4.068A pdb=" N VAL J 74 " --> pdb=" O ALA J 70 " (cutoff:3.500A) Processing helix chain 'J' and resid 95 through 126 removed outlier: 4.378A pdb=" N SER J 112 " --> pdb=" O ALA J 108 " (cutoff:3.500A) removed outlier: 4.910A pdb=" N ILE J 113 " --> pdb=" O LEU J 109 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N ALA J 114 " --> pdb=" O THR J 110 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N VAL J 120 " --> pdb=" O PHE J 116 " (cutoff:3.500A) Processing helix chain 'M' and resid 104 through 120 Processing helix chain 'M' and resid 134 through 145 Processing helix chain 'M' and resid 147 through 166 Processing helix chain 'M' and resid 177 through 200 removed outlier: 3.522A pdb=" N ALA M 181 " --> pdb=" O GLY M 177 " (cutoff:3.500A) Processing helix chain 'M' and resid 220 through 264 removed outlier: 3.891A pdb=" N LEU M 224 " --> pdb=" O ILE M 220 " (cutoff:3.500A) removed outlier: 4.216A pdb=" N ARG M 232 " --> pdb=" O SER M 228 " (cutoff:3.500A) removed outlier: 4.383A pdb=" N ALA M 233 " --> pdb=" O TYR M 229 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N VAL M 234 " --> pdb=" O THR M 230 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N GLY M 237 " --> pdb=" O ALA M 233 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N LEU M 240 " --> pdb=" O LEU M 236 " (cutoff:3.500A) Proline residue: M 262 - end of helix Processing helix chain 'M' and resid 270 through 309 removed outlier: 3.936A pdb=" N THR M 274 " --> pdb=" O MET M 270 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain '1' and resid 183 through 184 Processing sheet with id=AA2, first strand: chain '3' and resid 315 through 317 1317 hydrogen bonds defined for protein. 3915 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: 5.02 Time building geometry restraints manager: 7.27 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 4003 1.33 - 1.45: 3604 1.45 - 1.57: 9932 1.57 - 1.69: 0 1.69 - 1.81: 97 Bond restraints: 17636 Sorted by residual: bond pdb=" C VAL M 271 " pdb=" N PRO M 272 " ideal model delta sigma weight residual 1.336 1.386 -0.050 1.20e-02 6.94e+03 1.72e+01 bond pdb=" C VAL 1 107 " pdb=" N PRO 1 108 " ideal model delta sigma weight residual 1.336 1.382 -0.046 1.23e-02 6.61e+03 1.41e+01 bond pdb=" N LEU M 265 " pdb=" CA LEU M 265 " ideal model delta sigma weight residual 1.458 1.490 -0.032 1.00e-02 1.00e+04 1.05e+01 bond pdb=" N VAL 9 78 " pdb=" CA VAL 9 78 " ideal model delta sigma weight residual 1.454 1.492 -0.038 1.19e-02 7.06e+03 1.04e+01 bond pdb=" C ILE 8 41 " pdb=" N PRO 8 42 " ideal model delta sigma weight residual 1.336 1.375 -0.039 1.23e-02 6.61e+03 1.03e+01 ... (remaining 17631 not shown) Histogram of bond angle deviations from ideal: 98.92 - 106.16: 376 106.16 - 113.41: 10038 113.41 - 120.65: 7998 120.65 - 127.89: 5391 127.89 - 135.13: 130 Bond angle restraints: 23933 Sorted by residual: angle pdb=" N PRO 3 77 " pdb=" CA PRO 3 77 " pdb=" CB PRO 3 77 " ideal model delta sigma weight residual 103.00 110.50 -7.50 1.10e+00 8.26e-01 4.65e+01 angle pdb=" N GLY 1 231 " pdb=" CA GLY 1 231 " pdb=" C GLY 1 231 " ideal model delta sigma weight residual 115.80 107.66 8.14 1.74e+00 3.30e-01 2.19e+01 angle pdb=" C ASN 9 60 " pdb=" N PRO 9 61 " pdb=" CA PRO 9 61 " ideal model delta sigma weight residual 120.38 124.76 -4.38 1.03e+00 9.43e-01 1.81e+01 angle pdb=" N LYS 3 129 " pdb=" CA LYS 3 129 " pdb=" C LYS 3 129 " ideal model delta sigma weight residual 109.81 119.01 -9.20 2.21e+00 2.05e-01 1.73e+01 angle pdb=" N PRO 9 58 " pdb=" CA PRO 9 58 " pdb=" CB PRO 9 58 " ideal model delta sigma weight residual 103.25 98.92 4.33 1.05e+00 9.07e-01 1.70e+01 ... (remaining 23928 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 26.49: 9954 26.49 - 52.99: 429 52.99 - 79.48: 44 79.48 - 105.97: 7 105.97 - 132.46: 1 Dihedral angle restraints: 10435 sinusoidal: 3837 harmonic: 6598 Sorted by residual: dihedral pdb=" CA PHE 9 57 " pdb=" C PHE 9 57 " pdb=" N PRO 9 58 " pdb=" CA PRO 9 58 " ideal model delta harmonic sigma weight residual 180.00 47.54 132.46 0 5.00e+00 4.00e-02 7.02e+02 dihedral pdb=" CB CYS 9 69 " pdb=" SG CYS 9 69 " pdb=" SG CYS 9 79 " pdb=" CB CYS 9 79 " ideal model delta sinusoidal sigma weight residual 93.00 -179.66 -87.34 1 1.00e+01 1.00e-02 9.16e+01 dihedral pdb=" CA LEU 8 8 " pdb=" C LEU 8 8 " pdb=" N LYS 8 9 " pdb=" CA LYS 8 9 " ideal model delta harmonic sigma weight residual 180.00 -155.26 -24.74 0 5.00e+00 4.00e-02 2.45e+01 ... (remaining 10432 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.064: 2385 0.064 - 0.127: 381 0.127 - 0.191: 50 0.191 - 0.254: 11 0.254 - 0.318: 2 Chirality restraints: 2829 Sorted by residual: chirality pdb=" CB ILE H 95 " pdb=" CA ILE H 95 " pdb=" CG1 ILE H 95 " pdb=" CG2 ILE H 95 " both_signs ideal model delta sigma weight residual False 2.64 2.33 0.32 2.00e-01 2.50e+01 2.52e+00 chirality pdb=" CB ILE 3 101 " pdb=" CA ILE 3 101 " pdb=" CG1 ILE 3 101 " pdb=" CG2 ILE 3 101 " both_signs ideal model delta sigma weight residual False 2.64 2.36 0.28 2.00e-01 2.50e+01 1.98e+00 chirality pdb=" CA ALA 9 71 " pdb=" N ALA 9 71 " pdb=" C ALA 9 71 " pdb=" CB ALA 9 71 " both_signs ideal model delta sigma weight residual False 2.48 2.26 0.23 2.00e-01 2.50e+01 1.30e+00 ... (remaining 2826 not shown) Planarity restraints: 3017 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA PHE 9 59 " -0.019 2.00e-02 2.50e+03 4.04e-02 1.64e+01 pdb=" C PHE 9 59 " 0.070 2.00e-02 2.50e+03 pdb=" O PHE 9 59 " -0.027 2.00e-02 2.50e+03 pdb=" N ASN 9 60 " -0.024 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA B 108 " -0.015 2.00e-02 2.50e+03 3.10e-02 9.58e+00 pdb=" C ALA B 108 " 0.054 2.00e-02 2.50e+03 pdb=" O ALA B 108 " -0.020 2.00e-02 2.50e+03 pdb=" N LEU B 109 " -0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PHE C 107 " -0.015 2.00e-02 2.50e+03 3.05e-02 9.29e+00 pdb=" C PHE C 107 " 0.053 2.00e-02 2.50e+03 pdb=" O PHE C 107 " -0.020 2.00e-02 2.50e+03 pdb=" N ALA C 108 " -0.018 2.00e-02 2.50e+03 ... (remaining 3014 not shown) Histogram of nonbonded interaction distances: 1.79 - 2.41: 49 2.41 - 3.03: 9415 3.03 - 3.66: 27967 3.66 - 4.28: 40865 4.28 - 4.90: 67856 Nonbonded interactions: 146152 Sorted by model distance: nonbonded pdb=" O ASN 9 56 " pdb=" OD1 ASN 9 56 " model vdw 1.790 3.040 nonbonded pdb=" OE2 GLU A 111 " pdb=" OD1 ASN M 243 " model vdw 2.216 3.040 nonbonded pdb=" OH TYR 5 62 " pdb=" O PHE 6 146 " model vdw 2.241 3.040 nonbonded pdb=" O ALA C 64 " pdb=" OG1 THR C 68 " model vdw 2.266 3.040 nonbonded pdb=" O ILE 6 100 " pdb=" ND2 ASN 6 104 " model vdw 2.272 3.120 ... (remaining 146147 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 54 through 126 or (resid 127 and (name N or name CA or nam \ e C or name O or name CB )))) selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' } 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: 7.180 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: 0.020 Extract box with map and model: 0.650 Check model and map are aligned: 0.120 Set scattering table: 0.160 Process input model: 50.300 Find NCS groups from input model: 0.370 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:2.700 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 61.580 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8317 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 : 0.008 0.108 17636 Z= 0.539 Angle : 0.900 10.841 23933 Z= 0.535 Chirality : 0.050 0.318 2829 Planarity : 0.008 0.071 3017 Dihedral : 14.783 132.463 6184 Min Nonbonded Distance : 1.790 Molprobity Statistics. All-atom Clashscore : 6.40 Ramachandran Plot: Outliers : 0.13 % Allowed : 2.33 % Favored : 97.53 % Rotamer: Outliers : 0.45 % Allowed : 8.20 % Favored : 91.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.12 % 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: -2.59 (0.14), residues: 2271 helix: -1.46 (0.10), residues: 1701 sheet: None (None), residues: 0 loop : -1.93 (0.21), residues: 570 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP 3 109 HIS 0.008 0.002 HIS 9 41 PHE 0.026 0.002 PHE 9 63 TYR 0.015 0.002 TYR 5 51 ARG 0.007 0.001 ARG 1 434 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4542 Ramachandran restraints generated. 2271 Oldfield, 0 Emsley, 2271 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4542 Ramachandran restraints generated. 2271 Oldfield, 0 Emsley, 2271 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 391 residues out of total 1785 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 383 time to evaluate : 1.987 Fit side-chains REVERT: 0 40 LYS cc_start: 0.8920 (ttpt) cc_final: 0.7407 (mptt) REVERT: 0 41 GLU cc_start: 0.7218 (mt-10) cc_final: 0.6950 (pm20) REVERT: 1 34 GLU cc_start: 0.5822 (tp30) cc_final: 0.5082 (mm-30) REVERT: 1 150 ARG cc_start: 0.7728 (mmp-170) cc_final: 0.6729 (tpt170) REVERT: 1 194 LYS cc_start: 0.7777 (ttmt) cc_final: 0.7561 (tttp) REVERT: 1 441 PHE cc_start: 0.8693 (m-80) cc_final: 0.8380 (m-80) REVERT: 5 94 LYS cc_start: 0.8189 (mtpt) cc_final: 0.7338 (pttt) REVERT: 5 111 LYS cc_start: 0.6493 (tptt) cc_final: 0.5432 (mmtp) REVERT: 8 70 LYS cc_start: 0.8579 (ttpp) cc_final: 0.7225 (mptt) REVERT: A 81 MET cc_start: 0.8621 (ttp) cc_final: 0.8374 (ttp) REVERT: C 87 ASN cc_start: 0.8351 (t0) cc_final: 0.8080 (t0) REVERT: C 97 LYS cc_start: 0.8342 (tptt) cc_final: 0.7857 (tptt) REVERT: E 91 ARG cc_start: 0.8305 (ttm-80) cc_final: 0.7684 (mtt180) REVERT: F 86 ILE cc_start: 0.8997 (mt) cc_final: 0.8707 (mp) REVERT: H 86 ILE cc_start: 0.9192 (mt) cc_final: 0.8968 (mt) REVERT: I 61 MET cc_start: 0.7296 (mmt) cc_final: 0.6993 (mmm) REVERT: I 98 GLN cc_start: 0.7874 (tt0) cc_final: 0.7570 (tt0) REVERT: M 257 MET cc_start: 0.8234 (OUTLIER) cc_final: 0.7343 (mpt) REVERT: M 313 ASP cc_start: 0.7818 (t0) cc_final: 0.7584 (t0) REVERT: M 321 LYS cc_start: 0.8209 (ptmt) cc_final: 0.7958 (ptpt) outliers start: 8 outliers final: 6 residues processed: 388 average time/residue: 0.3115 time to fit residues: 176.3477 Evaluate side-chains 339 residues out of total 1785 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 332 time to evaluate : 1.900 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 6 residue 139 THR Chi-restraints excluded: chain M residue 240 LEU Chi-restraints excluded: chain M residue 242 VAL Chi-restraints excluded: chain M residue 254 LEU Chi-restraints excluded: chain M residue 257 MET Chi-restraints excluded: chain M residue 261 LEU Chi-restraints excluded: chain M residue 264 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 223 random chunks: chunk 188 optimal weight: 4.9990 chunk 169 optimal weight: 3.9990 chunk 93 optimal weight: 0.9990 chunk 57 optimal weight: 0.7980 chunk 114 optimal weight: 1.9990 chunk 90 optimal weight: 1.9990 chunk 174 optimal weight: 4.9990 chunk 67 optimal weight: 6.9990 chunk 106 optimal weight: 0.0870 chunk 130 optimal weight: 2.9990 chunk 202 optimal weight: 0.5980 overall best weight: 0.8962 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 0 48 ASN 1 166 ASN 1 257 HIS 1 285 GLN 1 313 GLN 1 316 ASN 1 482 ASN 3 179 GLN 3 206 ASN 5 29 GLN 5 79 ASN 6 40 ASN 8 26 HIS 9 35 GLN A 98 GLN B 94 ASN I 87 ASN M 163 ASN M 243 ASN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8301 moved from start: 0.1314 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 17636 Z= 0.216 Angle : 0.542 7.429 23933 Z= 0.285 Chirality : 0.037 0.171 2829 Planarity : 0.005 0.056 3017 Dihedral : 5.380 92.359 2424 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 7.23 Ramachandran Plot: Outliers : 0.04 % Allowed : 1.72 % Favored : 98.24 % Rotamer: Outliers : 2.19 % Allowed : 12.41 % Favored : 85.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.12 % 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: 0.18 (0.17), residues: 2271 helix: 0.57 (0.12), residues: 1715 sheet: None (None), residues: 0 loop : -1.02 (0.24), residues: 556 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP 3 109 HIS 0.006 0.001 HIS 8 44 PHE 0.017 0.002 PHE M 267 TYR 0.012 0.001 TYR 5 51 ARG 0.005 0.001 ARG H 91 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4542 Ramachandran restraints generated. 2271 Oldfield, 0 Emsley, 2271 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4542 Ramachandran restraints generated. 2271 Oldfield, 0 Emsley, 2271 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 402 residues out of total 1785 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 363 time to evaluate : 1.697 Fit side-chains REVERT: 0 40 LYS cc_start: 0.8887 (ttpt) cc_final: 0.7367 (mptt) REVERT: 0 41 GLU cc_start: 0.7129 (mt-10) cc_final: 0.6899 (pm20) REVERT: 1 34 GLU cc_start: 0.5431 (tp30) cc_final: 0.4835 (mm-30) REVERT: 1 150 ARG cc_start: 0.7914 (mmp-170) cc_final: 0.6731 (tpt170) REVERT: 1 604 ARG cc_start: 0.8124 (tpp-160) cc_final: 0.7907 (ttm170) REVERT: 3 271 PHE cc_start: 0.8770 (m-80) cc_final: 0.8344 (m-80) REVERT: 3 297 LEU cc_start: 0.9067 (OUTLIER) cc_final: 0.8566 (mt) REVERT: 5 94 LYS cc_start: 0.8156 (mtpt) cc_final: 0.7349 (pttt) REVERT: 8 67 SER cc_start: 0.8786 (m) cc_final: 0.8503 (m) REVERT: 8 70 LYS cc_start: 0.8580 (ttpp) cc_final: 0.7254 (mptt) REVERT: C 97 LYS cc_start: 0.8277 (tptt) cc_final: 0.7854 (tptt) REVERT: D 126 PHE cc_start: 0.8274 (m-80) cc_final: 0.8014 (m-80) REVERT: E 91 ARG cc_start: 0.8349 (ttm-80) cc_final: 0.7835 (mtt180) REVERT: I 61 MET cc_start: 0.7212 (mmt) cc_final: 0.6942 (mmm) outliers start: 39 outliers final: 21 residues processed: 387 average time/residue: 0.2967 time to fit residues: 173.4794 Evaluate side-chains 367 residues out of total 1785 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 345 time to evaluate : 2.101 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 188 VAL Chi-restraints excluded: chain 1 residue 234 VAL Chi-restraints excluded: chain 1 residue 240 VAL Chi-restraints excluded: chain 1 residue 463 SER Chi-restraints excluded: chain 1 residue 605 LYS Chi-restraints excluded: chain 3 residue 103 VAL Chi-restraints excluded: chain 3 residue 281 VAL Chi-restraints excluded: chain 3 residue 297 LEU Chi-restraints excluded: chain 6 residue 79 LEU Chi-restraints excluded: chain 6 residue 139 THR Chi-restraints excluded: chain 8 residue 52 THR Chi-restraints excluded: chain 8 residue 78 HIS Chi-restraints excluded: chain B residue 84 SER Chi-restraints excluded: chain C residue 105 LEU Chi-restraints excluded: chain D residue 74 VAL Chi-restraints excluded: chain E residue 95 ILE Chi-restraints excluded: chain E residue 105 LEU Chi-restraints excluded: chain H residue 74 VAL Chi-restraints excluded: chain H residue 84 SER Chi-restraints excluded: chain M residue 222 VAL Chi-restraints excluded: chain M residue 261 LEU Chi-restraints excluded: chain M residue 271 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 223 random chunks: chunk 112 optimal weight: 2.9990 chunk 62 optimal weight: 0.9980 chunk 168 optimal weight: 8.9990 chunk 137 optimal weight: 3.9990 chunk 55 optimal weight: 0.9990 chunk 202 optimal weight: 0.0040 chunk 219 optimal weight: 2.9990 chunk 180 optimal weight: 0.9990 chunk 201 optimal weight: 0.7980 chunk 69 optimal weight: 4.9990 chunk 162 optimal weight: 5.9990 overall best weight: 0.7596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 0 48 ASN 0 56 GLN 1 531 HIS 3 179 GLN 3 189 HIS 9 60 ASN C 98 GLN I 98 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8292 moved from start: 0.1693 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.066 17636 Z= 0.196 Angle : 0.509 8.388 23933 Z= 0.264 Chirality : 0.037 0.187 2829 Planarity : 0.004 0.060 3017 Dihedral : 4.753 79.720 2415 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 6.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.89 % Favored : 98.11 % Rotamer: Outliers : 2.70 % Allowed : 14.71 % Favored : 82.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.12 % 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: 1.17 (0.17), residues: 2271 helix: 1.28 (0.12), residues: 1732 sheet: None (None), residues: 0 loop : -0.73 (0.25), residues: 539 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP 3 109 HIS 0.004 0.001 HIS 8 44 PHE 0.019 0.001 PHE B 122 TYR 0.011 0.001 TYR 9 14 ARG 0.006 0.000 ARG H 91 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4542 Ramachandran restraints generated. 2271 Oldfield, 0 Emsley, 2271 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4542 Ramachandran restraints generated. 2271 Oldfield, 0 Emsley, 2271 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 398 residues out of total 1785 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 350 time to evaluate : 1.853 Fit side-chains REVERT: 0 40 LYS cc_start: 0.8904 (ttpt) cc_final: 0.7366 (mptt) REVERT: 0 41 GLU cc_start: 0.7128 (mt-10) cc_final: 0.6904 (pm20) REVERT: 1 34 GLU cc_start: 0.5540 (tp30) cc_final: 0.4870 (mm-30) REVERT: 1 150 ARG cc_start: 0.8230 (mmp-170) cc_final: 0.7057 (mmm160) REVERT: 1 456 LYS cc_start: 0.8458 (tmtt) cc_final: 0.7933 (mtmt) REVERT: 1 604 ARG cc_start: 0.8134 (tpp-160) cc_final: 0.7913 (ttm110) REVERT: 3 297 LEU cc_start: 0.9065 (OUTLIER) cc_final: 0.8564 (mt) REVERT: 5 94 LYS cc_start: 0.8222 (mtpt) cc_final: 0.7440 (pttt) REVERT: 8 67 SER cc_start: 0.8755 (m) cc_final: 0.8517 (m) REVERT: 9 50 ASN cc_start: 0.8982 (m-40) cc_final: 0.8737 (m110) REVERT: 9 66 ILE cc_start: 0.8743 (mm) cc_final: 0.8452 (mm) REVERT: 9 92 GLU cc_start: 0.7925 (OUTLIER) cc_final: 0.7185 (mp0) REVERT: B 60 LYS cc_start: 0.8158 (mttp) cc_final: 0.7952 (mttt) REVERT: B 87 ASN cc_start: 0.8205 (m-40) cc_final: 0.7796 (m-40) REVERT: C 97 LYS cc_start: 0.8279 (tptt) cc_final: 0.7853 (tptt) REVERT: C 122 PHE cc_start: 0.8257 (t80) cc_final: 0.8025 (t80) REVERT: D 118 LEU cc_start: 0.7737 (mt) cc_final: 0.7371 (mt) REVERT: D 126 PHE cc_start: 0.8305 (m-80) cc_final: 0.8043 (m-80) REVERT: I 61 MET cc_start: 0.7184 (mmt) cc_final: 0.6940 (mmm) REVERT: M 267 PHE cc_start: 0.6873 (m-10) cc_final: 0.6582 (m-10) REVERT: M 321 LYS cc_start: 0.8159 (ptmt) cc_final: 0.7851 (ptpt) outliers start: 48 outliers final: 29 residues processed: 373 average time/residue: 0.2960 time to fit residues: 165.7705 Evaluate side-chains 359 residues out of total 1785 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 328 time to evaluate : 1.789 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 19 SER Chi-restraints excluded: chain 1 residue 188 VAL Chi-restraints excluded: chain 1 residue 234 VAL Chi-restraints excluded: chain 1 residue 240 VAL Chi-restraints excluded: chain 1 residue 261 LEU Chi-restraints excluded: chain 1 residue 350 GLU Chi-restraints excluded: chain 1 residue 463 SER Chi-restraints excluded: chain 1 residue 512 LEU Chi-restraints excluded: chain 1 residue 519 GLU Chi-restraints excluded: chain 1 residue 605 LYS Chi-restraints excluded: chain 3 residue 103 VAL Chi-restraints excluded: chain 3 residue 297 LEU Chi-restraints excluded: chain 3 residue 314 GLU Chi-restraints excluded: chain 6 residue 79 LEU Chi-restraints excluded: chain 8 residue 78 HIS Chi-restraints excluded: chain 9 residue 92 GLU Chi-restraints excluded: chain B residue 84 SER Chi-restraints excluded: chain D residue 68 THR Chi-restraints excluded: chain D residue 74 VAL Chi-restraints excluded: chain E residue 84 SER Chi-restraints excluded: chain E residue 95 ILE Chi-restraints excluded: chain E residue 104 LEU Chi-restraints excluded: chain F residue 84 SER Chi-restraints excluded: chain F residue 95 ILE Chi-restraints excluded: chain H residue 69 ILE Chi-restraints excluded: chain H residue 74 VAL Chi-restraints excluded: chain H residue 84 SER Chi-restraints excluded: chain I residue 119 LEU Chi-restraints excluded: chain M residue 222 VAL Chi-restraints excluded: chain M residue 261 LEU Chi-restraints excluded: chain M residue 271 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 223 random chunks: chunk 200 optimal weight: 3.9990 chunk 152 optimal weight: 0.8980 chunk 105 optimal weight: 2.9990 chunk 22 optimal weight: 2.9990 chunk 96 optimal weight: 0.6980 chunk 136 optimal weight: 0.8980 chunk 203 optimal weight: 2.9990 chunk 215 optimal weight: 3.9990 chunk 106 optimal weight: 0.4980 chunk 192 optimal weight: 0.6980 chunk 58 optimal weight: 1.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 0 48 ASN 6 106 ASN ** I 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 94 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8288 moved from start: 0.1878 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 17636 Z= 0.184 Angle : 0.499 9.417 23933 Z= 0.257 Chirality : 0.036 0.142 2829 Planarity : 0.004 0.062 3017 Dihedral : 4.505 73.543 2414 Min Nonbonded Distance : 2.398 Molprobity Statistics. All-atom Clashscore : 6.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.89 % Favored : 98.11 % Rotamer: Outliers : 3.14 % Allowed : 15.50 % Favored : 81.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.12 % 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: 1.77 (0.17), residues: 2271 helix: 1.70 (0.12), residues: 1733 sheet: None (None), residues: 0 loop : -0.50 (0.26), residues: 538 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP 3 109 HIS 0.003 0.001 HIS 9 41 PHE 0.018 0.001 PHE D 122 TYR 0.013 0.001 TYR F 102 ARG 0.006 0.000 ARG H 91 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4542 Ramachandran restraints generated. 2271 Oldfield, 0 Emsley, 2271 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4542 Ramachandran restraints generated. 2271 Oldfield, 0 Emsley, 2271 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 401 residues out of total 1785 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 345 time to evaluate : 1.965 Fit side-chains REVERT: 0 1 MET cc_start: 0.6947 (OUTLIER) cc_final: 0.6735 (ttm) REVERT: 0 40 LYS cc_start: 0.8908 (ttpt) cc_final: 0.7363 (mptt) REVERT: 0 41 GLU cc_start: 0.7080 (mt-10) cc_final: 0.6852 (pm20) REVERT: 1 34 GLU cc_start: 0.5500 (tp30) cc_final: 0.4897 (mm-30) REVERT: 1 150 ARG cc_start: 0.8516 (mmp-170) cc_final: 0.7138 (mmm160) REVERT: 3 271 PHE cc_start: 0.8703 (m-80) cc_final: 0.8247 (m-80) REVERT: 3 297 LEU cc_start: 0.9052 (OUTLIER) cc_final: 0.8542 (mt) REVERT: 5 94 LYS cc_start: 0.8221 (mtpt) cc_final: 0.7385 (pttt) REVERT: 8 67 SER cc_start: 0.8770 (m) cc_final: 0.8504 (m) REVERT: 9 50 ASN cc_start: 0.8971 (m-40) cc_final: 0.8724 (m110) REVERT: 9 66 ILE cc_start: 0.8690 (mm) cc_final: 0.8336 (mm) REVERT: 9 92 GLU cc_start: 0.7784 (OUTLIER) cc_final: 0.7086 (mp0) REVERT: A 115 LEU cc_start: 0.8843 (mt) cc_final: 0.8619 (mt) REVERT: B 60 LYS cc_start: 0.8168 (mttp) cc_final: 0.7960 (mttt) REVERT: C 97 LYS cc_start: 0.8197 (tptt) cc_final: 0.7599 (tptt) REVERT: D 118 LEU cc_start: 0.7627 (mt) cc_final: 0.7252 (mt) REVERT: F 92 ASN cc_start: 0.8437 (p0) cc_final: 0.8129 (p0) REVERT: F 123 LEU cc_start: 0.8671 (mt) cc_final: 0.8403 (mp) REVERT: I 61 MET cc_start: 0.7180 (mmt) cc_final: 0.6948 (mmm) REVERT: J 115 LEU cc_start: 0.8962 (OUTLIER) cc_final: 0.8666 (mt) REVERT: M 264 SER cc_start: 0.8350 (OUTLIER) cc_final: 0.7742 (t) REVERT: M 267 PHE cc_start: 0.6861 (m-10) cc_final: 0.6527 (m-10) REVERT: M 321 LYS cc_start: 0.8174 (ptmt) cc_final: 0.7813 (pttt) outliers start: 56 outliers final: 35 residues processed: 374 average time/residue: 0.2827 time to fit residues: 159.6197 Evaluate side-chains 367 residues out of total 1785 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 327 time to evaluate : 1.907 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 1 MET Chi-restraints excluded: chain 0 residue 19 SER Chi-restraints excluded: chain 1 residue 102 LEU Chi-restraints excluded: chain 1 residue 234 VAL Chi-restraints excluded: chain 1 residue 240 VAL Chi-restraints excluded: chain 1 residue 261 LEU Chi-restraints excluded: chain 1 residue 350 GLU Chi-restraints excluded: chain 1 residue 393 LEU Chi-restraints excluded: chain 1 residue 463 SER Chi-restraints excluded: chain 1 residue 512 LEU Chi-restraints excluded: chain 1 residue 519 GLU Chi-restraints excluded: chain 1 residue 605 LYS Chi-restraints excluded: chain 3 residue 103 VAL Chi-restraints excluded: chain 3 residue 297 LEU Chi-restraints excluded: chain 3 residue 314 GLU Chi-restraints excluded: chain 6 residue 79 LEU Chi-restraints excluded: chain 6 residue 105 LEU Chi-restraints excluded: chain 6 residue 139 THR Chi-restraints excluded: chain 8 residue 78 HIS Chi-restraints excluded: chain 9 residue 19 SER Chi-restraints excluded: chain 9 residue 92 GLU Chi-restraints excluded: chain A residue 98 GLN Chi-restraints excluded: chain B residue 84 SER Chi-restraints excluded: chain D residue 68 THR Chi-restraints excluded: chain D residue 74 VAL Chi-restraints excluded: chain D residue 121 VAL Chi-restraints excluded: chain E residue 84 SER Chi-restraints excluded: chain E residue 95 ILE Chi-restraints excluded: chain F residue 84 SER Chi-restraints excluded: chain F residue 95 ILE Chi-restraints excluded: chain G residue 62 VAL Chi-restraints excluded: chain H residue 69 ILE Chi-restraints excluded: chain H residue 74 VAL Chi-restraints excluded: chain H residue 84 SER Chi-restraints excluded: chain I residue 119 LEU Chi-restraints excluded: chain J residue 115 LEU Chi-restraints excluded: chain M residue 222 VAL Chi-restraints excluded: chain M residue 261 LEU Chi-restraints excluded: chain M residue 264 SER Chi-restraints excluded: chain M residue 271 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 223 random chunks: chunk 179 optimal weight: 7.9990 chunk 122 optimal weight: 0.7980 chunk 3 optimal weight: 0.0270 chunk 160 optimal weight: 4.9990 chunk 88 optimal weight: 2.9990 chunk 183 optimal weight: 0.7980 chunk 148 optimal weight: 5.9990 chunk 0 optimal weight: 3.9990 chunk 110 optimal weight: 0.5980 chunk 193 optimal weight: 0.9990 chunk 54 optimal weight: 0.6980 overall best weight: 0.5838 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 0 48 ASN ** I 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8275 moved from start: 0.2041 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 17636 Z= 0.167 Angle : 0.493 8.260 23933 Z= 0.254 Chirality : 0.036 0.178 2829 Planarity : 0.004 0.058 3017 Dihedral : 4.335 67.108 2414 Min Nonbonded Distance : 2.360 Molprobity Statistics. All-atom Clashscore : 7.00 Ramachandran Plot: Outliers : 0.04 % Allowed : 1.98 % Favored : 97.97 % Rotamer: Outliers : 3.43 % Allowed : 15.55 % Favored : 81.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.12 % 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: 2.08 (0.18), residues: 2271 helix: 1.92 (0.12), residues: 1735 sheet: None (None), residues: 0 loop : -0.35 (0.26), residues: 536 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP 3 109 HIS 0.003 0.000 HIS 9 41 PHE 0.012 0.001 PHE 1 529 TYR 0.012 0.001 TYR 9 14 ARG 0.006 0.000 ARG 0 34 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4542 Ramachandran restraints generated. 2271 Oldfield, 0 Emsley, 2271 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4542 Ramachandran restraints generated. 2271 Oldfield, 0 Emsley, 2271 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 401 residues out of total 1785 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 340 time to evaluate : 2.245 Fit side-chains REVERT: 0 1 MET cc_start: 0.6952 (OUTLIER) cc_final: 0.6727 (ttm) REVERT: 0 40 LYS cc_start: 0.8885 (ttpt) cc_final: 0.7351 (mptt) REVERT: 0 41 GLU cc_start: 0.7076 (mt-10) cc_final: 0.6849 (pm20) REVERT: 1 34 GLU cc_start: 0.5534 (tp30) cc_final: 0.4946 (mm-30) REVERT: 1 456 LYS cc_start: 0.8463 (tmtt) cc_final: 0.7882 (mtmt) REVERT: 3 297 LEU cc_start: 0.9022 (OUTLIER) cc_final: 0.8519 (mt) REVERT: 5 49 LYS cc_start: 0.8612 (mtpp) cc_final: 0.8411 (mtpt) REVERT: 5 94 LYS cc_start: 0.8203 (mtpt) cc_final: 0.7418 (pttt) REVERT: 8 67 SER cc_start: 0.8765 (m) cc_final: 0.8498 (m) REVERT: 9 50 ASN cc_start: 0.8951 (m-40) cc_final: 0.8711 (m110) REVERT: 9 66 ILE cc_start: 0.8609 (mm) cc_final: 0.8346 (mm) REVERT: 9 92 GLU cc_start: 0.7784 (OUTLIER) cc_final: 0.6995 (mp0) REVERT: A 115 LEU cc_start: 0.8843 (mt) cc_final: 0.8610 (mt) REVERT: B 60 LYS cc_start: 0.8141 (mttp) cc_final: 0.7920 (mttt) REVERT: C 97 LYS cc_start: 0.8167 (tptt) cc_final: 0.7520 (tptt) REVERT: D 126 PHE cc_start: 0.8152 (m-80) cc_final: 0.7676 (m-80) REVERT: F 92 ASN cc_start: 0.8431 (p0) cc_final: 0.8090 (p0) REVERT: F 123 LEU cc_start: 0.8624 (mt) cc_final: 0.8377 (mp) REVERT: I 61 MET cc_start: 0.7196 (mmt) cc_final: 0.6971 (mmm) REVERT: M 264 SER cc_start: 0.8206 (OUTLIER) cc_final: 0.7514 (t) REVERT: M 267 PHE cc_start: 0.6863 (m-10) cc_final: 0.6555 (m-10) REVERT: M 321 LYS cc_start: 0.8172 (ptmt) cc_final: 0.7803 (pttt) outliers start: 61 outliers final: 36 residues processed: 373 average time/residue: 0.3056 time to fit residues: 176.4170 Evaluate side-chains 370 residues out of total 1785 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 330 time to evaluate : 1.720 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 1 MET Chi-restraints excluded: chain 0 residue 48 ASN Chi-restraints excluded: chain 1 residue 102 LEU Chi-restraints excluded: chain 1 residue 234 VAL Chi-restraints excluded: chain 1 residue 240 VAL Chi-restraints excluded: chain 1 residue 261 LEU Chi-restraints excluded: chain 1 residue 350 GLU Chi-restraints excluded: chain 1 residue 435 THR Chi-restraints excluded: chain 1 residue 463 SER Chi-restraints excluded: chain 1 residue 512 LEU Chi-restraints excluded: chain 1 residue 519 GLU Chi-restraints excluded: chain 1 residue 605 LYS Chi-restraints excluded: chain 3 residue 103 VAL Chi-restraints excluded: chain 3 residue 281 VAL Chi-restraints excluded: chain 3 residue 297 LEU Chi-restraints excluded: chain 3 residue 314 GLU Chi-restraints excluded: chain 6 residue 79 LEU Chi-restraints excluded: chain 6 residue 105 LEU Chi-restraints excluded: chain 6 residue 139 THR Chi-restraints excluded: chain 8 residue 78 HIS Chi-restraints excluded: chain 9 residue 19 SER Chi-restraints excluded: chain 9 residue 92 GLU Chi-restraints excluded: chain A residue 98 GLN Chi-restraints excluded: chain B residue 84 SER Chi-restraints excluded: chain B residue 119 LEU Chi-restraints excluded: chain C residue 115 LEU Chi-restraints excluded: chain D residue 68 THR Chi-restraints excluded: chain D residue 74 VAL Chi-restraints excluded: chain E residue 95 ILE Chi-restraints excluded: chain E residue 115 LEU Chi-restraints excluded: chain F residue 84 SER Chi-restraints excluded: chain F residue 95 ILE Chi-restraints excluded: chain G residue 62 VAL Chi-restraints excluded: chain H residue 69 ILE Chi-restraints excluded: chain H residue 74 VAL Chi-restraints excluded: chain H residue 84 SER Chi-restraints excluded: chain I residue 119 LEU Chi-restraints excluded: chain M residue 222 VAL Chi-restraints excluded: chain M residue 264 SER Chi-restraints excluded: chain M residue 271 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/iotbx/cli_parser.py", line 946, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/programs/real_space_refine.py", line 200, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 766, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1479, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1381, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1262, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 57.5317 > 50: distance: 54 - 83: 3.440 distance: 58 - 88: 10.733 distance: 62 - 72: 3.937 distance: 63 - 99: 10.053 distance: 73 - 74: 6.658 distance: 73 - 76: 4.760 distance: 74 - 75: 3.296 distance: 74 - 83: 5.297 distance: 75 - 110: 6.621 distance: 77 - 78: 5.012 distance: 77 - 79: 6.052 distance: 78 - 80: 7.338 distance: 79 - 81: 3.115 distance: 80 - 82: 4.448 distance: 81 - 82: 4.629 distance: 83 - 84: 3.765 distance: 84 - 85: 8.472 distance: 84 - 87: 4.385 distance: 85 - 88: 4.830 distance: 86 - 114: 27.230 distance: 88 - 89: 9.872 distance: 89 - 90: 9.490 distance: 89 - 92: 5.777 distance: 90 - 91: 9.017 distance: 90 - 99: 7.814 distance: 93 - 94: 10.231 distance: 93 - 95: 15.039 distance: 94 - 96: 8.606 distance: 95 - 97: 9.659 distance: 96 - 98: 18.034 distance: 97 - 98: 11.117 distance: 99 - 100: 11.213 distance: 100 - 101: 5.586 distance: 100 - 103: 11.684 distance: 101 - 102: 4.217 distance: 101 - 110: 7.650 distance: 103 - 104: 8.531 distance: 104 - 105: 7.928 distance: 105 - 106: 6.437 distance: 106 - 107: 12.685 distance: 107 - 108: 8.830 distance: 107 - 109: 11.581 distance: 111 - 112: 8.174 distance: 112 - 113: 13.120 distance: 112 - 114: 13.624 distance: 114 - 115: 3.705 distance: 115 - 116: 8.572 distance: 115 - 118: 28.924 distance: 116 - 117: 18.688 distance: 116 - 122: 15.116 distance: 118 - 119: 29.770 distance: 119 - 120: 20.408 distance: 120 - 121: 26.693 distance: 122 - 123: 8.221 distance: 123 - 126: 24.157 distance: 124 - 125: 7.322 distance: 124 - 127: 16.357 distance: 125 - 146: 24.147 distance: 127 - 128: 12.849 distance: 127 - 133: 13.708 distance: 128 - 129: 16.506 distance: 128 - 131: 13.587 distance: 129 - 130: 26.761 distance: 129 - 134: 3.995 distance: 131 - 132: 10.633 distance: 132 - 133: 18.329 distance: 134 - 135: 14.839 distance: 135 - 136: 7.690 distance: 135 - 138: 31.456 distance: 136 - 137: 11.858 distance: 136 - 139: 5.727 distance: 139 - 140: 14.023 distance: 140 - 141: 13.450 distance: 140 - 143: 3.870 distance: 141 - 142: 17.240 distance: 141 - 146: 13.552 distance: 143 - 144: 9.191 distance: 143 - 145: 20.607