Starting phenix.real_space_refine on Mon Jul 22 19:31:01 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8u4l_41886/07_2024/8u4l_41886_trim.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8u4l_41886/07_2024/8u4l_41886.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.31 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8u4l_41886/07_2024/8u4l_41886.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8u4l_41886/07_2024/8u4l_41886.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8u4l_41886/07_2024/8u4l_41886_trim.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8u4l_41886/07_2024/8u4l_41886_trim.cif" } resolution = 3.31 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= 0.028 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians S 118 5.16 5 C 6179 2.51 5 N 1708 2.21 5 O 1984 1.98 5 H 9080 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 47": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 50": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 72": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 78": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 81": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 95": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 103": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 106": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 114": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 124": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 168": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 188": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 196": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 210": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 220": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 232": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A PHE 279": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A ARG 306": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 393": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 396": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 426": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 484": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 488": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 491": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 524": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 525": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 528": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 530": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 544": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 612": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 34": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 47": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 92": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 98": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 100": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 103": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 138": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 143": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 157": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 188": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 190": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 203": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 217": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 226": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 288": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 330": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 340": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 351": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 354": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 432": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 434": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 456": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 459": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 487": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 499": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 517": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 536": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 545": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 552": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 558": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 599": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C ARG 207": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C ARG 220": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/chem_data/mon_lib" Total number of atoms: 19069 Number of models: 1 Model: "" Number of chains: 15 Chain: "A" Number of atoms: 9061 Number of conformers: 1 Conformer: "" Number of residues, atoms: 598, 9061 Classifications: {'peptide': 598} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 27, 'TRANS': 570} Chain breaks: 3 Chain: "B" Number of atoms: 8787 Number of conformers: 1 Conformer: "" Number of residues, atoms: 582, 8787 Classifications: {'peptide': 582} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 38, 'TRANS': 543} Chain breaks: 2 Chain: "C" Number of atoms: 767 Number of conformers: 1 Conformer: "" Number of residues, atoms: 50, 767 Classifications: {'peptide': 50} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 2, 'TRANS': 47} Chain breaks: 1 Chain: "D" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "E" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "F" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "G" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "H" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "I" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "K" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "L" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "B" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 9.63, per 1000 atoms: 0.51 Number of scatterers: 19069 At special positions: 0 Unit cell: (80.995, 146.96, 136.94, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 118 16.00 O 1984 8.00 N 1708 7.00 C 6179 6.00 H 9080 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=51, symmetry=0 Simple disulfide: pdb=" SG CYS A 29 " - pdb=" SG CYS A 56 " distance=2.08 Simple disulfide: pdb=" SG CYS A 156 " - pdb=" SG CYS A 186 " distance=2.03 Simple disulfide: pdb=" SG CYS A 189 " - pdb=" SG CYS A 197 " distance=2.08 Simple disulfide: pdb=" SG CYS A 193 " - pdb=" SG CYS A 205 " distance=2.08 Simple disulfide: pdb=" SG CYS A 213 " - pdb=" SG CYS A 221 " distance=2.03 Simple disulfide: pdb=" SG CYS A 217 " - pdb=" SG CYS A 229 " distance=2.02 Simple disulfide: pdb=" SG CYS A 230 " - pdb=" SG CYS A 238 " distance=1.84 Simple disulfide: pdb=" SG CYS A 234 " - pdb=" SG CYS A 246 " distance=1.99 Simple disulfide: pdb=" SG CYS A 249 " - pdb=" SG CYS A 258 " distance=2.04 Simple disulfide: pdb=" SG CYS A 262 " - pdb=" SG CYS A 289 " distance=2.02 Simple disulfide: pdb=" SG CYS A 293 " - pdb=" SG CYS A 304 " distance=2.02 Simple disulfide: pdb=" SG CYS A 308 " - pdb=" SG CYS A 323 " distance=2.02 Simple disulfide: pdb=" SG CYS A 326 " - pdb=" SG CYS A 330 " distance=2.03 Simple disulfide: pdb=" SG CYS A 334 " - pdb=" SG CYS A 359 " distance=2.06 Simple disulfide: pdb=" SG CYS A 467 " - pdb=" SG CYS A 496 " distance=2.03 Simple disulfide: pdb=" SG CYS A 503 " - pdb=" SG CYS A 512 " distance=2.08 Simple disulfide: pdb=" SG CYS A 507 " - pdb=" SG CYS A 520 " distance=2.04 Simple disulfide: pdb=" SG CYS A 523 " - pdb=" SG CYS A 532 " distance=2.02 Simple disulfide: pdb=" SG CYS A 536 " - pdb=" SG CYS A 552 " distance=2.02 Simple disulfide: pdb=" SG CYS A 555 " - pdb=" SG CYS A 569 " distance=2.03 Simple disulfide: pdb=" SG CYS A 559 " - pdb=" SG CYS A 577 " distance=2.03 Simple disulfide: pdb=" SG CYS A 580 " - pdb=" SG CYS A 589 " distance=2.07 Simple disulfide: pdb=" SG CYS A 593 " - pdb=" SG CYS A 614 " distance=2.12 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 625 " distance=2.01 Simple disulfide: pdb=" SG CYS A 621 " - pdb=" SG CYS A 633 " distance=2.13 Simple disulfide: pdb=" SG CYS B 26 " - pdb=" SG CYS B 53 " distance=2.07 Simple disulfide: pdb=" SG CYS B 162 " - pdb=" SG CYS B 192 " distance=2.06 Simple disulfide: pdb=" SG CYS B 195 " - pdb=" SG CYS B 204 " distance=2.01 Simple disulfide: pdb=" SG CYS B 199 " - pdb=" SG CYS B 212 " distance=2.08 Simple disulfide: pdb=" SG CYS B 220 " - pdb=" SG CYS B 227 " distance=2.02 Simple disulfide: pdb=" SG CYS B 224 " - pdb=" SG CYS B 235 " distance=2.02 Simple disulfide: pdb=" SG CYS B 236 " - pdb=" SG CYS B 244 " distance=2.02 Simple disulfide: pdb=" SG CYS B 240 " - pdb=" SG CYS B 252 " distance=2.04 Simple disulfide: pdb=" SG CYS B 255 " - pdb=" SG CYS B 264 " distance=2.15 Simple disulfide: pdb=" SG CYS B 268 " - pdb=" SG CYS B 295 " distance=2.15 Simple disulfide: pdb=" SG CYS B 299 " - pdb=" SG CYS B 311 " distance=1.98 Simple disulfide: pdb=" SG CYS B 315 " - pdb=" SG CYS B 331 " distance=2.11 Simple disulfide: pdb=" SG CYS B 334 " - pdb=" SG CYS B 338 " distance=2.14 Simple disulfide: pdb=" SG CYS B 342 " - pdb=" SG CYS B 367 " distance=2.02 Simple disulfide: pdb=" SG CYS B 475 " - pdb=" SG CYS B 504 " distance=2.03 Simple disulfide: pdb=" SG CYS B 511 " - pdb=" SG CYS B 520 " distance=2.03 Simple disulfide: pdb=" SG CYS B 515 " - pdb=" SG CYS B 528 " distance=2.03 Simple disulfide: pdb=" SG CYS B 531 " - pdb=" SG CYS B 540 " distance=2.03 Simple disulfide: pdb=" SG CYS B 544 " - pdb=" SG CYS B 560 " distance=2.02 Simple disulfide: pdb=" SG CYS B 563 " - pdb=" SG CYS B 576 " distance=2.35 Simple disulfide: pdb=" SG CYS B 567 " - pdb=" SG CYS B 584 " distance=2.11 Simple disulfide: pdb=" SG CYS B 587 " - pdb=" SG CYS B 596 " distance=2.03 Simple disulfide: pdb=" SG CYS B 600 " - pdb=" SG CYS B 623 " distance=2.03 Simple disulfide: pdb=" SG CYS C 182 " - pdb=" SG CYS C 196 " distance=2.05 Simple disulfide: pdb=" SG CYS C 190 " - pdb=" SG CYS C 210 " distance=2.02 Simple disulfide: pdb=" SG CYS C 212 " - pdb=" SG CYS C 221 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied ALPHA1-3 " BMA D 3 " - " MAN D 4 " " BMA E 3 " - " MAN E 4 " ALPHA1-6 " BMA E 3 " - " MAN E 5 " " BMA G 3 " - " MAN G 4 " BETA1-4 " NAG D 1 " - " NAG D 2 " " NAG D 2 " - " BMA D 3 " " NAG E 1 " - " NAG E 2 " " NAG E 2 " - " BMA E 3 " " NAG F 1 " - " NAG F 2 " " NAG F 2 " - " BMA F 3 " " NAG G 1 " - " NAG G 2 " " NAG G 2 " - " BMA G 3 " " NAG H 1 " - " NAG H 2 " " NAG H 2 " - " BMA H 3 " " NAG I 1 " - " NAG I 2 " " NAG I 2 " - " BMA I 3 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG K 2 " - " BMA K 3 " " NAG L 1 " - " NAG L 2 " " NAG L 2 " - " BMA L 3 " " NAG M 1 " - " NAG M 2 " NAG-ASN " NAG A 701 " - " ASN A 410 " " NAG A 702 " - " ASN A 495 " " NAG B 701 " - " ASN B 68 " " NAG D 1 " - " ASN A 138 " " NAG E 1 " - " ASN A 358 " " NAG F 1 " - " ASN A 473 " " NAG G 1 " - " ASN A 576 " " NAG H 1 " - " ASN A 548 " " NAG I 1 " - " ASN A 253 " " NAG J 1 " - " ASN B 187 " " NAG K 1 " - " ASN B 259 " " NAG L 1 " - " ASN B 530 " " NAG M 1 " - " ASN B 571 " Time building additional restraints: 17.23 Conformation dependent library (CDL) restraints added in 2.2 seconds 2424 Ramachandran restraints generated. 1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2270 Finding SS restraints... Secondary structure from input PDB file: 35 helices and 30 sheets defined 16.7% alpha, 15.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.57 Creating SS restraints... Processing helix chain 'A' and resid 41 through 54 Processing helix chain 'A' and resid 74 through 80 removed outlier: 3.931A pdb=" N SER A 79 " --> pdb=" O PHE A 76 " (cutoff:3.500A) Processing helix chain 'A' and resid 110 through 113 Processing helix chain 'A' and resid 162 through 167 removed outlier: 4.070A pdb=" N ILE A 166 " --> pdb=" O HIS A 162 " (cutoff:3.500A) Processing helix chain 'A' and resid 201 through 205 removed outlier: 3.811A pdb=" N CYS A 205 " --> pdb=" O GLU A 202 " (cutoff:3.500A) Processing helix chain 'A' and resid 225 through 229 removed outlier: 3.928A pdb=" N CYS A 229 " --> pdb=" O VAL A 226 " (cutoff:3.500A) Processing helix chain 'A' and resid 339 through 343 Processing helix chain 'A' and resid 352 through 357 Processing helix chain 'A' and resid 369 through 374 Processing helix chain 'A' and resid 385 through 395 removed outlier: 3.781A pdb=" N THR A 394 " --> pdb=" O VAL A 391 " (cutoff:3.500A) Processing helix chain 'A' and resid 468 through 472 Processing helix chain 'A' and resid 473 through 477 Processing helix chain 'A' and resid 492 through 500 Processing helix chain 'A' and resid 573 through 577 removed outlier: 3.853A pdb=" N CYS A 577 " --> pdb=" O PRO A 574 " (cutoff:3.500A) Processing helix chain 'A' and resid 629 through 633 removed outlier: 4.317A pdb=" N CYS A 633 " --> pdb=" O SER A 630 " (cutoff:3.500A) Processing helix chain 'B' and resid 38 through 40 No H-bonds generated for 'chain 'B' and resid 38 through 40' Processing helix chain 'B' and resid 41 through 51 Processing helix chain 'B' and resid 71 through 77 removed outlier: 4.345A pdb=" N ASP B 76 " --> pdb=" O PHE B 73 " (cutoff:3.500A) Processing helix chain 'B' and resid 107 through 110 Processing helix chain 'B' and resid 168 through 172 Processing helix chain 'B' and resid 208 through 212 removed outlier: 4.138A pdb=" N CYS B 212 " --> pdb=" O SER B 209 " (cutoff:3.500A) Processing helix chain 'B' and resid 231 through 235 Processing helix chain 'B' and resid 347 through 351 Processing helix chain 'B' and resid 360 through 365 Processing helix chain 'B' and resid 384 through 388 removed outlier: 3.590A pdb=" N ASN B 388 " --> pdb=" O PRO B 385 " (cutoff:3.500A) Processing helix chain 'B' and resid 393 through 398 removed outlier: 3.811A pdb=" N GLN B 398 " --> pdb=" O PRO B 394 " (cutoff:3.500A) Processing helix chain 'B' and resid 399 through 401 No H-bonds generated for 'chain 'B' and resid 399 through 401' Processing helix chain 'B' and resid 422 through 426 Processing helix chain 'B' and resid 436 through 439 Processing helix chain 'B' and resid 475 through 479 removed outlier: 3.712A pdb=" N HIS B 478 " --> pdb=" O CYS B 475 " (cutoff:3.500A) Processing helix chain 'B' and resid 481 through 486 removed outlier: 3.873A pdb=" N LEU B 485 " --> pdb=" O PRO B 481 " (cutoff:3.500A) Processing helix chain 'B' and resid 500 through 507 removed outlier: 3.666A pdb=" N GLU B 507 " --> pdb=" O GLU B 503 " (cutoff:3.500A) Processing helix chain 'B' and resid 515 through 519 removed outlier: 3.785A pdb=" N GLY B 518 " --> pdb=" O CYS B 515 " (cutoff:3.500A) Processing helix chain 'B' and resid 580 through 584 Processing helix chain 'C' and resid 186 through 190 removed outlier: 3.925A pdb=" N CYS C 190 " --> pdb=" O LYS C 187 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 28 through 30 removed outlier: 6.553A pdb=" N CYS A 29 " --> pdb=" O MET A 60 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 38 through 39 removed outlier: 7.077A pdb=" N SER A 38 " --> pdb=" O CYS C 212 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 63 through 66 removed outlier: 5.666A pdb=" N GLY A 146 " --> pdb=" O TYR A 115 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 234 through 238 removed outlier: 5.623A pdb=" N ALA A 235 " --> pdb=" O CYS A 249 " (cutoff:3.500A) removed outlier: 4.776A pdb=" N CYS A 249 " --> pdb=" O ALA A 235 " (cutoff:3.500A) removed outlier: 7.177A pdb=" N GLY A 237 " --> pdb=" O PHE A 247 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 252 through 254 Processing sheet with id=AA6, first strand: chain 'A' and resid 266 through 268 Processing sheet with id=AA7, first strand: chain 'A' and resid 283 through 285 Processing sheet with id=AA8, first strand: chain 'A' and resid 298 through 299 Processing sheet with id=AA9, first strand: chain 'A' and resid 312 through 317 Processing sheet with id=AB1, first strand: chain 'A' and resid 334 through 335 removed outlier: 6.425A pdb=" N CYS A 334 " --> pdb=" O ASN A 363 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 366 through 368 removed outlier: 7.632A pdb=" N TYR A 459 " --> pdb=" O SER A 433 " (cutoff:3.500A) removed outlier: 4.446A pdb=" N LEU A 435 " --> pdb=" O TYR A 459 " (cutoff:3.500A) removed outlier: 7.833A pdb=" N THR A 461 " --> pdb=" O LEU A 435 " (cutoff:3.500A) removed outlier: 4.585A pdb=" N LEU A 437 " --> pdb=" O THR A 461 " (cutoff:3.500A) removed outlier: 6.578A pdb=" N ILE A 458 " --> pdb=" O VAL A 486 " (cutoff:3.500A) removed outlier: 8.290A pdb=" N ARG A 488 " --> pdb=" O ILE A 458 " (cutoff:3.500A) removed outlier: 6.655A pdb=" N ILE A 460 " --> pdb=" O ARG A 488 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 526 through 528 Processing sheet with id=AB4, first strand: chain 'A' and resid 545 through 546 Processing sheet with id=AB5, first strand: chain 'A' and resid 583 through 585 removed outlier: 3.690A pdb=" N PHE A 583 " --> pdb=" O VAL A 590 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 606 through 607 Processing sheet with id=AB7, first strand: chain 'B' and resid 25 through 27 removed outlier: 6.669A pdb=" N CYS B 26 " --> pdb=" O GLN B 57 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 60 through 63 removed outlier: 5.348A pdb=" N GLY B 152 " --> pdb=" O TYR B 112 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 240 through 244 removed outlier: 7.514A pdb=" N GLY B 243 " --> pdb=" O CYS B 252 " (cutoff:3.500A) removed outlier: 5.196A pdb=" N CYS B 252 " --> pdb=" O GLY B 243 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 258 through 260 Processing sheet with id=AC2, first strand: chain 'B' and resid 272 through 275 removed outlier: 3.752A pdb=" N GLU B 280 " --> pdb=" O ASN B 275 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 289 through 291 Processing sheet with id=AC4, first strand: chain 'B' and resid 304 through 306 removed outlier: 3.623A pdb=" N SER B 310 " --> pdb=" O THR B 306 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 319 through 322 Processing sheet with id=AC6, first strand: chain 'B' and resid 369 through 370 Processing sheet with id=AC7, first strand: chain 'B' and resid 374 through 376 removed outlier: 4.597A pdb=" N TYR B 441 " --> pdb=" O LEU B 465 " (cutoff:3.500A) removed outlier: 7.393A pdb=" N LEU B 467 " --> pdb=" O TYR B 441 " (cutoff:3.500A) removed outlier: 6.632A pdb=" N LEU B 443 " --> pdb=" O LEU B 467 " (cutoff:3.500A) removed outlier: 8.044A pdb=" N HIS B 469 " --> pdb=" O LEU B 443 " (cutoff:3.500A) removed outlier: 6.571A pdb=" N LEU B 445 " --> pdb=" O HIS B 469 " (cutoff:3.500A) removed outlier: 6.390A pdb=" N ALA B 466 " --> pdb=" O LEU B 494 " (cutoff:3.500A) removed outlier: 8.352A pdb=" N THR B 496 " --> pdb=" O ALA B 466 " (cutoff:3.500A) removed outlier: 6.781A pdb=" N ILE B 468 " --> pdb=" O THR B 496 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 534 through 536 Processing sheet with id=AC9, first strand: chain 'B' and resid 553 through 555 Processing sheet with id=AD1, first strand: chain 'B' and resid 591 through 592 Processing sheet with id=AD2, first strand: chain 'B' and resid 615 through 617 Processing sheet with id=AD3, first strand: chain 'C' and resid 216 through 217 194 hydrogen bonds defined for protein. 363 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: 7.66 Time building geometry restraints manager: 18.11 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.96 - 1.13: 9079 1.13 - 1.30: 1704 1.30 - 1.48: 3989 1.48 - 1.65: 4373 1.65 - 1.82: 133 Bond restraints: 19278 Sorted by residual: bond pdb=" N MET B 282 " pdb=" H MET B 282 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.68e+01 bond pdb=" NE2 GLN A 206 " pdb="HE21 GLN A 206 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.68e+01 bond pdb=" ND2 ASN A 352 " pdb="HD22 ASN A 352 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.68e+01 bond pdb=" N ASN A 358 " pdb=" H ASN A 358 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.67e+01 bond pdb=" N CYS A 625 " pdb=" H CYS A 625 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.67e+01 ... (remaining 19273 not shown) Histogram of bond angle deviations from ideal: 99.57 - 106.61: 499 106.61 - 113.66: 21575 113.66 - 120.70: 8612 120.70 - 127.74: 3791 127.74 - 134.79: 77 Bond angle restraints: 34554 Sorted by residual: angle pdb=" N GLU A 141 " pdb=" CA GLU A 141 " pdb=" C GLU A 141 " ideal model delta sigma weight residual 108.99 118.71 -9.72 1.57e+00 4.06e-01 3.83e+01 angle pdb=" C GLU B 348 " pdb=" CA GLU B 348 " pdb=" CB GLU B 348 " ideal model delta sigma weight residual 116.54 109.47 7.07 1.15e+00 7.56e-01 3.78e+01 angle pdb=" C ASP A 328 " pdb=" CA ASP A 328 " pdb=" CB ASP A 328 " ideal model delta sigma weight residual 116.54 109.93 6.61 1.15e+00 7.56e-01 3.31e+01 angle pdb=" C LYS A 35 " pdb=" CA LYS A 35 " pdb=" CB LYS A 35 " ideal model delta sigma weight residual 116.63 110.14 6.49 1.16e+00 7.43e-01 3.13e+01 angle pdb=" C LYS B 32 " pdb=" CA LYS B 32 " pdb=" CB LYS B 32 " ideal model delta sigma weight residual 116.54 110.22 6.32 1.15e+00 7.56e-01 3.02e+01 ... (remaining 34549 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.25: 9033 21.25 - 42.49: 420 42.49 - 63.74: 234 63.74 - 84.98: 68 84.98 - 106.23: 36 Dihedral angle restraints: 9791 sinusoidal: 5677 harmonic: 4114 Sorted by residual: dihedral pdb=" CB CYS A 217 " pdb=" SG CYS A 217 " pdb=" SG CYS A 229 " pdb=" CB CYS A 229 " ideal model delta sinusoidal sigma weight residual -86.00 -176.48 90.48 1 1.00e+01 1.00e-02 9.68e+01 dihedral pdb=" CB CYS A 293 " pdb=" SG CYS A 293 " pdb=" SG CYS A 304 " pdb=" CB CYS A 304 " ideal model delta sinusoidal sigma weight residual 93.00 177.18 -84.18 1 1.00e+01 1.00e-02 8.63e+01 dihedral pdb=" CB CYS B 315 " pdb=" SG CYS B 315 " pdb=" SG CYS B 331 " pdb=" CB CYS B 331 " ideal model delta sinusoidal sigma weight residual 93.00 176.91 -83.91 1 1.00e+01 1.00e-02 8.58e+01 ... (remaining 9788 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.095: 1310 0.095 - 0.189: 252 0.189 - 0.284: 40 0.284 - 0.379: 15 0.379 - 0.474: 3 Chirality restraints: 1620 Sorted by residual: chirality pdb=" C1 NAG E 2 " pdb=" O4 NAG E 1 " pdb=" C2 NAG E 2 " pdb=" O5 NAG E 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.01 -0.39 2.00e-02 2.50e+03 3.75e+02 chirality pdb=" C1 NAG G 2 " pdb=" O4 NAG G 1 " pdb=" C2 NAG G 2 " pdb=" O5 NAG G 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.09 -0.31 2.00e-02 2.50e+03 2.39e+02 chirality pdb=" C1 MAN D 4 " pdb=" O3 BMA D 3 " pdb=" C2 MAN D 4 " pdb=" O5 MAN D 4 " both_signs ideal model delta sigma weight residual False 2.40 2.10 0.30 2.00e-02 2.50e+03 2.22e+02 ... (remaining 1617 not shown) Planarity restraints: 2940 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG E 1 " -0.319 2.00e-02 2.50e+03 2.70e-01 9.13e+02 pdb=" C7 NAG E 1 " 0.085 2.00e-02 2.50e+03 pdb=" C8 NAG E 1 " -0.184 2.00e-02 2.50e+03 pdb=" N2 NAG E 1 " 0.469 2.00e-02 2.50e+03 pdb=" O7 NAG E 1 " -0.051 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 410 " 0.250 2.00e-02 2.50e+03 1.99e-01 5.97e+02 pdb=" CG ASN A 410 " -0.021 2.00e-02 2.50e+03 pdb=" OD1 ASN A 410 " -0.198 2.00e-02 2.50e+03 pdb=" ND2 ASN A 410 " -0.034 2.00e-02 2.50e+03 pdb="HD21 ASN A 410 " -0.258 2.00e-02 2.50e+03 pdb=" C1 NAG A 701 " 0.262 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG E 2 " -0.189 2.00e-02 2.50e+03 1.58e-01 3.13e+02 pdb=" C7 NAG E 2 " 0.042 2.00e-02 2.50e+03 pdb=" C8 NAG E 2 " -0.132 2.00e-02 2.50e+03 pdb=" N2 NAG E 2 " 0.265 2.00e-02 2.50e+03 pdb=" O7 NAG E 2 " 0.015 2.00e-02 2.50e+03 ... (remaining 2937 not shown) Histogram of nonbonded interaction distances: 1.45 - 2.08: 746 2.08 - 2.71: 25626 2.71 - 3.34: 52693 3.34 - 3.97: 68678 3.97 - 4.60: 99884 Nonbonded interactions: 247627 Sorted by model distance: nonbonded pdb=" OE2 GLU A 317 " pdb=" HZ1 LYS A 324 " model vdw 1.452 1.850 nonbonded pdb=" HB3 LYS B 32 " pdb=" H LEU B 33 " model vdw 1.504 2.270 nonbonded pdb=" HG SER B 358 " pdb=" O ALA B 390 " model vdw 1.531 1.850 nonbonded pdb=" OE1 GLU A 202 " pdb=" H GLU A 202 " model vdw 1.601 1.850 nonbonded pdb=" OG1 THR A 209 " pdb="HH11 ARG A 220 " model vdw 1.610 1.850 ... (remaining 247622 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'D' selection = chain 'G' } ncs_group { reference = chain 'F' selection = chain 'H' selection = chain 'I' selection = chain 'K' selection = chain 'L' } ncs_group { reference = chain 'J' selection = chain 'M' } 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: 5.120 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: 0.270 Extract box with map and model: 0.830 Check model and map are aligned: 0.130 Set scattering table: 0.190 Process input model: 64.570 Find NCS groups from input model: 0.670 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.720 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 74.590 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8164 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.013 0.085 10198 Z= 0.825 Angle : 1.524 9.721 13829 Z= 1.019 Chirality : 0.085 0.474 1620 Planarity : 0.013 0.270 1772 Dihedral : 15.706 106.231 4294 Min Nonbonded Distance : 2.364 Molprobity Statistics. All-atom Clashscore : 1.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.98 % Favored : 98.02 % Rotamer: Outliers : 0.09 % Allowed : 0.93 % Favored : 98.98 % Cbeta Deviations : 0.18 % 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: -0.38 (0.22), residues: 1212 helix: -2.96 (0.45), residues: 80 sheet: -0.96 (0.39), residues: 139 loop : 0.16 (0.19), residues: 993 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.101 0.007 TRP B 205 HIS 0.007 0.001 HIS B 519 PHE 0.050 0.003 PHE A 252 TYR 0.083 0.007 TYR B 303 ARG 0.006 0.001 ARG A 106 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2424 Ramachandran restraints generated. 1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2424 Ramachandran restraints generated. 1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 1076 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 156 time to evaluate : 1.559 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 165 ASP cc_start: 0.7880 (t70) cc_final: 0.7579 (t0) REVERT: C 188 THR cc_start: 0.8279 (p) cc_final: 0.8069 (t) outliers start: 1 outliers final: 1 residues processed: 157 average time/residue: 0.5938 time to fit residues: 121.8188 Evaluate side-chains 74 residues out of total 1076 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 73 time to evaluate : 1.566 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 280 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 103 optimal weight: 0.9990 chunk 92 optimal weight: 0.6980 chunk 51 optimal weight: 5.9990 chunk 31 optimal weight: 0.7980 chunk 62 optimal weight: 0.8980 chunk 49 optimal weight: 5.9990 chunk 95 optimal weight: 0.7980 chunk 37 optimal weight: 0.8980 chunk 58 optimal weight: 10.0000 chunk 71 optimal weight: 1.9990 chunk 110 optimal weight: 5.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 346 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 239 GLN B 302 ASN B 329 GLN B 470 HIS ** C 222 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8265 moved from start: 0.2663 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.072 10198 Z= 0.259 Angle : 0.706 9.862 13829 Z= 0.367 Chirality : 0.051 0.463 1620 Planarity : 0.005 0.043 1772 Dihedral : 13.811 77.156 2035 Min Nonbonded Distance : 2.159 Molprobity Statistics. All-atom Clashscore : 3.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.98 % Favored : 98.02 % Rotamer: Outliers : 0.93 % Allowed : 5.39 % Favored : 93.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: -0.70 (0.23), residues: 1212 helix: -2.53 (0.48), residues: 92 sheet: -0.81 (0.36), residues: 166 loop : -0.14 (0.19), residues: 954 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP B 205 HIS 0.008 0.001 HIS A 505 PHE 0.013 0.001 PHE A 447 TYR 0.011 0.001 TYR B 303 ARG 0.003 0.000 ARG A 525 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2424 Ramachandran restraints generated. 1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2424 Ramachandran restraints generated. 1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 1076 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 76 time to evaluate : 1.490 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 165 ASP cc_start: 0.8247 (t70) cc_final: 0.7982 (t0) outliers start: 10 outliers final: 8 residues processed: 85 average time/residue: 0.5302 time to fit residues: 61.5069 Evaluate side-chains 71 residues out of total 1076 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 63 time to evaluate : 1.542 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 384 ILE Chi-restraints excluded: chain A residue 570 HIS Chi-restraints excluded: chain B residue 38 SER Chi-restraints excluded: chain B residue 59 ASN Chi-restraints excluded: chain B residue 158 ASN Chi-restraints excluded: chain B residue 255 CYS Chi-restraints excluded: chain B residue 302 ASN Chi-restraints excluded: chain B residue 373 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 61 optimal weight: 0.0870 chunk 34 optimal weight: 1.9990 chunk 92 optimal weight: 1.9990 chunk 75 optimal weight: 0.4980 chunk 30 optimal weight: 2.9990 chunk 110 optimal weight: 10.0000 chunk 119 optimal weight: 2.9990 chunk 98 optimal weight: 1.9990 chunk 37 optimal weight: 0.9990 chunk 89 optimal weight: 0.6980 chunk 109 optimal weight: 4.9990 overall best weight: 0.8562 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 204 HIS ** A 346 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 222 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8292 moved from start: 0.3097 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.096 10198 Z= 0.221 Angle : 0.645 8.643 13829 Z= 0.333 Chirality : 0.050 0.384 1620 Planarity : 0.004 0.037 1772 Dihedral : 10.384 63.143 2033 Min Nonbonded Distance : 2.162 Molprobity Statistics. All-atom Clashscore : 3.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.31 % Favored : 97.69 % Rotamer: Outliers : 0.93 % Allowed : 6.13 % Favored : 92.94 % 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: -0.75 (0.23), residues: 1212 helix: -2.21 (0.52), residues: 89 sheet: -0.78 (0.36), residues: 171 loop : -0.24 (0.19), residues: 952 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 205 HIS 0.006 0.001 HIS A 70 PHE 0.014 0.001 PHE A 583 TYR 0.009 0.001 TYR B 274 ARG 0.002 0.000 ARG B 487 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2424 Ramachandran restraints generated. 1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2424 Ramachandran restraints generated. 1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 78 residues out of total 1076 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 68 time to evaluate : 1.604 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 165 ASP cc_start: 0.8470 (t70) cc_final: 0.8225 (t0) REVERT: B 184 ILE cc_start: 0.8200 (mm) cc_final: 0.7731 (pt) REVERT: B 193 HIS cc_start: 0.8020 (t70) cc_final: 0.7716 (t70) outliers start: 10 outliers final: 7 residues processed: 77 average time/residue: 0.5160 time to fit residues: 55.1095 Evaluate side-chains 69 residues out of total 1076 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 62 time to evaluate : 1.494 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 384 ILE Chi-restraints excluded: chain A residue 413 ASP Chi-restraints excluded: chain A residue 570 HIS Chi-restraints excluded: chain B residue 38 SER Chi-restraints excluded: chain B residue 59 ASN Chi-restraints excluded: chain B residue 373 SER Chi-restraints excluded: chain B residue 377 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 83 optimal weight: 0.5980 chunk 57 optimal weight: 4.9990 chunk 12 optimal weight: 1.9990 chunk 52 optimal weight: 0.9990 chunk 74 optimal weight: 0.3980 chunk 111 optimal weight: 8.9990 chunk 117 optimal weight: 0.8980 chunk 58 optimal weight: 8.9990 chunk 105 optimal weight: 3.9990 chunk 31 optimal weight: 1.9990 chunk 98 optimal weight: 0.9980 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 346 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 249 HIS ** C 222 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8308 moved from start: 0.3420 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.169 10198 Z= 0.237 Angle : 0.584 8.086 13829 Z= 0.299 Chirality : 0.047 0.346 1620 Planarity : 0.004 0.033 1772 Dihedral : 7.727 48.454 2033 Min Nonbonded Distance : 2.166 Molprobity Statistics. All-atom Clashscore : 3.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Rotamer: Outliers : 0.93 % Allowed : 6.60 % Favored : 92.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: -0.81 (0.23), residues: 1212 helix: -2.08 (0.52), residues: 89 sheet: -0.77 (0.37), residues: 172 loop : -0.31 (0.20), residues: 951 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 205 HIS 0.005 0.001 HIS A 231 PHE 0.011 0.001 PHE A 447 TYR 0.011 0.001 TYR B 303 ARG 0.002 0.000 ARG B 330 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2424 Ramachandran restraints generated. 1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2424 Ramachandran restraints generated. 1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 1076 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 62 time to evaluate : 1.608 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 165 ASP cc_start: 0.8611 (t70) cc_final: 0.8376 (t0) REVERT: A 583 PHE cc_start: 0.5780 (p90) cc_final: 0.5532 (p90) REVERT: B 181 LEU cc_start: 0.7656 (mt) cc_final: 0.7350 (tp) REVERT: B 193 HIS cc_start: 0.8020 (t70) cc_final: 0.7709 (t70) outliers start: 10 outliers final: 8 residues processed: 72 average time/residue: 0.5303 time to fit residues: 52.5579 Evaluate side-chains 67 residues out of total 1076 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 59 time to evaluate : 1.627 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 384 ILE Chi-restraints excluded: chain A residue 413 ASP Chi-restraints excluded: chain A residue 570 HIS Chi-restraints excluded: chain B residue 38 SER Chi-restraints excluded: chain B residue 59 ASN Chi-restraints excluded: chain B residue 255 CYS Chi-restraints excluded: chain B residue 373 SER Chi-restraints excluded: chain B residue 377 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 66 optimal weight: 0.9990 chunk 1 optimal weight: 2.9990 chunk 87 optimal weight: 4.9990 chunk 48 optimal weight: 0.9980 chunk 100 optimal weight: 1.9990 chunk 81 optimal weight: 0.9990 chunk 0 optimal weight: 2.9990 chunk 60 optimal weight: 2.9990 chunk 105 optimal weight: 0.8980 chunk 29 optimal weight: 0.9990 chunk 39 optimal weight: 0.9990 overall best weight: 0.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 346 GLN A 439 GLN B 320 GLN C 222 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8358 moved from start: 0.3833 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 10198 Z= 0.224 Angle : 0.559 7.618 13829 Z= 0.288 Chirality : 0.046 0.303 1620 Planarity : 0.004 0.035 1772 Dihedral : 6.204 50.593 2033 Min Nonbonded Distance : 2.073 Molprobity Statistics. All-atom Clashscore : 4.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer: Outliers : 1.30 % Allowed : 6.51 % Favored : 92.19 % 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: -0.78 (0.23), residues: 1212 helix: -1.94 (0.53), residues: 89 sheet: -0.62 (0.40), residues: 162 loop : -0.34 (0.20), residues: 961 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 205 HIS 0.004 0.001 HIS B 174 PHE 0.014 0.001 PHE A 447 TYR 0.008 0.001 TYR B 274 ARG 0.004 0.000 ARG A 72 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2424 Ramachandran restraints generated. 1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2424 Ramachandran restraints generated. 1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 75 residues out of total 1076 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 61 time to evaluate : 1.540 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 462 ASP cc_start: 0.8010 (t0) cc_final: 0.7713 (t0) REVERT: A 583 PHE cc_start: 0.5818 (p90) cc_final: 0.5599 (p90) REVERT: B 181 LEU cc_start: 0.7734 (mt) cc_final: 0.7368 (tp) REVERT: B 193 HIS cc_start: 0.7995 (t70) cc_final: 0.7670 (t70) outliers start: 14 outliers final: 11 residues processed: 73 average time/residue: 0.5314 time to fit residues: 53.4468 Evaluate side-chains 69 residues out of total 1076 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 58 time to evaluate : 1.623 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 238 CYS Chi-restraints excluded: chain A residue 258 CYS Chi-restraints excluded: chain A residue 384 ILE Chi-restraints excluded: chain A residue 413 ASP Chi-restraints excluded: chain A residue 423 ILE Chi-restraints excluded: chain B residue 38 SER Chi-restraints excluded: chain B residue 44 ASP Chi-restraints excluded: chain B residue 59 ASN Chi-restraints excluded: chain B residue 185 ASP Chi-restraints excluded: chain B residue 373 SER Chi-restraints excluded: chain B residue 377 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 106 optimal weight: 0.5980 chunk 23 optimal weight: 1.9990 chunk 69 optimal weight: 1.9990 chunk 29 optimal weight: 0.0980 chunk 118 optimal weight: 2.9990 chunk 97 optimal weight: 1.9990 chunk 54 optimal weight: 10.0000 chunk 9 optimal weight: 0.9990 chunk 39 optimal weight: 1.9990 chunk 61 optimal weight: 1.9990 chunk 113 optimal weight: 6.9990 overall best weight: 1.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 564 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8392 moved from start: 0.4140 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.093 10198 Z= 0.247 Angle : 0.555 7.318 13829 Z= 0.288 Chirality : 0.046 0.284 1620 Planarity : 0.004 0.038 1772 Dihedral : 5.854 55.234 2033 Min Nonbonded Distance : 2.020 Molprobity Statistics. All-atom Clashscore : 5.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.63 % Favored : 96.37 % Rotamer: Outliers : 1.30 % Allowed : 6.69 % Favored : 92.01 % 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: -0.76 (0.24), residues: 1212 helix: -1.97 (0.53), residues: 89 sheet: -0.65 (0.41), residues: 162 loop : -0.31 (0.20), residues: 961 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 205 HIS 0.005 0.001 HIS B 88 PHE 0.013 0.001 PHE A 447 TYR 0.010 0.001 TYR A 469 ARG 0.002 0.000 ARG B 330 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2424 Ramachandran restraints generated. 1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2424 Ramachandran restraints generated. 1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 78 residues out of total 1076 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 64 time to evaluate : 1.555 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 462 ASP cc_start: 0.8028 (t0) cc_final: 0.7733 (t0) REVERT: B 193 HIS cc_start: 0.7957 (t70) cc_final: 0.7630 (t70) outliers start: 14 outliers final: 13 residues processed: 76 average time/residue: 0.5339 time to fit residues: 55.7705 Evaluate side-chains 68 residues out of total 1076 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 55 time to evaluate : 1.548 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 238 CYS Chi-restraints excluded: chain A residue 258 CYS Chi-restraints excluded: chain A residue 384 ILE Chi-restraints excluded: chain A residue 413 ASP Chi-restraints excluded: chain A residue 423 ILE Chi-restraints excluded: chain A residue 570 HIS Chi-restraints excluded: chain B residue 38 SER Chi-restraints excluded: chain B residue 59 ASN Chi-restraints excluded: chain B residue 185 ASP Chi-restraints excluded: chain B residue 249 HIS Chi-restraints excluded: chain B residue 373 SER Chi-restraints excluded: chain B residue 377 LEU Chi-restraints excluded: chain B residue 379 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 13 optimal weight: 0.9990 chunk 67 optimal weight: 1.9990 chunk 86 optimal weight: 0.7980 chunk 66 optimal weight: 0.4980 chunk 99 optimal weight: 1.9990 chunk 65 optimal weight: 0.5980 chunk 117 optimal weight: 0.2980 chunk 73 optimal weight: 2.9990 chunk 71 optimal weight: 0.9990 chunk 54 optimal weight: 8.9990 chunk 72 optimal weight: 0.4980 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 329 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8368 moved from start: 0.4269 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.053 10198 Z= 0.155 Angle : 0.518 7.346 13829 Z= 0.268 Chirality : 0.044 0.275 1620 Planarity : 0.004 0.038 1772 Dihedral : 5.608 56.733 2033 Min Nonbonded Distance : 2.014 Molprobity Statistics. All-atom Clashscore : 5.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.22 % Favored : 96.78 % Rotamer: Outliers : 0.93 % Allowed : 7.43 % Favored : 91.64 % 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: -0.65 (0.24), residues: 1212 helix: -2.02 (0.52), residues: 89 sheet: -0.63 (0.42), residues: 162 loop : -0.20 (0.20), residues: 961 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 205 HIS 0.004 0.001 HIS B 48 PHE 0.009 0.001 PHE A 447 TYR 0.015 0.001 TYR A 469 ARG 0.001 0.000 ARG A 124 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2424 Ramachandran restraints generated. 1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2424 Ramachandran restraints generated. 1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 66 residues out of total 1076 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 56 time to evaluate : 1.697 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 462 ASP cc_start: 0.8009 (t0) cc_final: 0.7723 (t0) REVERT: B 193 HIS cc_start: 0.7936 (t70) cc_final: 0.7616 (t70) outliers start: 10 outliers final: 10 residues processed: 64 average time/residue: 0.5545 time to fit residues: 49.1848 Evaluate side-chains 65 residues out of total 1076 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 55 time to evaluate : 1.414 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 238 CYS Chi-restraints excluded: chain A residue 258 CYS Chi-restraints excluded: chain A residue 384 ILE Chi-restraints excluded: chain A residue 413 ASP Chi-restraints excluded: chain A residue 423 ILE Chi-restraints excluded: chain B residue 59 ASN Chi-restraints excluded: chain B residue 185 ASP Chi-restraints excluded: chain B residue 373 SER Chi-restraints excluded: chain B residue 377 LEU Chi-restraints excluded: chain B residue 379 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 46 optimal weight: 2.9990 chunk 70 optimal weight: 0.5980 chunk 35 optimal weight: 0.5980 chunk 23 optimal weight: 0.1980 chunk 22 optimal weight: 0.8980 chunk 74 optimal weight: 3.9990 chunk 80 optimal weight: 1.9990 chunk 58 optimal weight: 10.0000 chunk 10 optimal weight: 1.9990 chunk 92 optimal weight: 1.9990 chunk 106 optimal weight: 4.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8389 moved from start: 0.4442 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 10198 Z= 0.201 Angle : 0.521 7.389 13829 Z= 0.270 Chirality : 0.044 0.267 1620 Planarity : 0.004 0.038 1772 Dihedral : 5.497 59.097 2033 Min Nonbonded Distance : 2.023 Molprobity Statistics. All-atom Clashscore : 5.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.80 % Favored : 96.20 % Rotamer: Outliers : 1.21 % Allowed : 7.43 % Favored : 91.36 % 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: -0.66 (0.24), residues: 1212 helix: -1.99 (0.52), residues: 89 sheet: -0.60 (0.42), residues: 162 loop : -0.23 (0.20), residues: 961 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 205 HIS 0.007 0.001 HIS B 478 PHE 0.010 0.001 PHE A 447 TYR 0.009 0.001 TYR B 303 ARG 0.002 0.000 ARG B 552 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2424 Ramachandran restraints generated. 1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2424 Ramachandran restraints generated. 1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 67 residues out of total 1076 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 54 time to evaluate : 1.633 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 462 ASP cc_start: 0.8019 (t0) cc_final: 0.7718 (t0) outliers start: 13 outliers final: 13 residues processed: 65 average time/residue: 0.5273 time to fit residues: 47.5277 Evaluate side-chains 66 residues out of total 1076 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 53 time to evaluate : 1.521 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 238 CYS Chi-restraints excluded: chain A residue 258 CYS Chi-restraints excluded: chain A residue 275 LEU Chi-restraints excluded: chain A residue 384 ILE Chi-restraints excluded: chain A residue 413 ASP Chi-restraints excluded: chain A residue 423 ILE Chi-restraints excluded: chain A residue 570 HIS Chi-restraints excluded: chain B residue 59 ASN Chi-restraints excluded: chain B residue 185 ASP Chi-restraints excluded: chain B residue 249 HIS Chi-restraints excluded: chain B residue 373 SER Chi-restraints excluded: chain B residue 377 LEU Chi-restraints excluded: chain B residue 379 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 112 optimal weight: 6.9990 chunk 102 optimal weight: 1.9990 chunk 109 optimal weight: 6.9990 chunk 65 optimal weight: 1.9990 chunk 47 optimal weight: 0.9990 chunk 86 optimal weight: 1.9990 chunk 33 optimal weight: 1.9990 chunk 99 optimal weight: 0.9990 chunk 103 optimal weight: 0.7980 chunk 71 optimal weight: 0.6980 chunk 115 optimal weight: 4.9990 overall best weight: 1.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8405 moved from start: 0.4554 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 10198 Z= 0.235 Angle : 0.530 7.371 13829 Z= 0.275 Chirality : 0.045 0.262 1620 Planarity : 0.004 0.037 1772 Dihedral : 5.486 59.896 2033 Min Nonbonded Distance : 2.026 Molprobity Statistics. All-atom Clashscore : 5.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.88 % Favored : 96.12 % Rotamer: Outliers : 1.30 % Allowed : 7.62 % Favored : 91.08 % 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: -0.70 (0.24), residues: 1212 helix: -2.02 (0.51), residues: 89 sheet: -0.59 (0.42), residues: 162 loop : -0.26 (0.20), residues: 961 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 205 HIS 0.003 0.001 HIS B 478 PHE 0.011 0.001 PHE A 447 TYR 0.009 0.001 TYR B 274 ARG 0.009 0.000 ARG A 95 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2424 Ramachandran restraints generated. 1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2424 Ramachandran restraints generated. 1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 67 residues out of total 1076 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 53 time to evaluate : 1.663 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 462 ASP cc_start: 0.8016 (t0) cc_final: 0.7709 (t0) outliers start: 14 outliers final: 13 residues processed: 65 average time/residue: 0.5231 time to fit residues: 47.8516 Evaluate side-chains 63 residues out of total 1076 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 50 time to evaluate : 1.545 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 238 CYS Chi-restraints excluded: chain A residue 258 CYS Chi-restraints excluded: chain A residue 275 LEU Chi-restraints excluded: chain A residue 384 ILE Chi-restraints excluded: chain A residue 413 ASP Chi-restraints excluded: chain A residue 423 ILE Chi-restraints excluded: chain A residue 570 HIS Chi-restraints excluded: chain B residue 59 ASN Chi-restraints excluded: chain B residue 185 ASP Chi-restraints excluded: chain B residue 249 HIS Chi-restraints excluded: chain B residue 373 SER Chi-restraints excluded: chain B residue 377 LEU Chi-restraints excluded: chain B residue 379 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 70 optimal weight: 0.0070 chunk 54 optimal weight: 7.9990 chunk 80 optimal weight: 1.9990 chunk 121 optimal weight: 1.9990 chunk 111 optimal weight: 6.9990 chunk 96 optimal weight: 0.9980 chunk 10 optimal weight: 1.9990 chunk 74 optimal weight: 0.4980 chunk 59 optimal weight: 0.0070 chunk 76 optimal weight: 3.9990 chunk 103 optimal weight: 0.9980 overall best weight: 0.5016 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8369 moved from start: 0.4648 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 10198 Z= 0.144 Angle : 0.497 7.224 13829 Z= 0.257 Chirality : 0.044 0.253 1620 Planarity : 0.004 0.035 1772 Dihedral : 5.271 58.730 2033 Min Nonbonded Distance : 2.001 Molprobity Statistics. All-atom Clashscore : 5.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.22 % Favored : 96.78 % Rotamer: Outliers : 1.21 % Allowed : 7.71 % Favored : 91.08 % 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: -0.60 (0.24), residues: 1212 helix: -2.05 (0.51), residues: 89 sheet: -0.57 (0.42), residues: 162 loop : -0.17 (0.21), residues: 961 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 205 HIS 0.004 0.001 HIS B 478 PHE 0.007 0.001 PHE B 577 TYR 0.007 0.001 TYR B 554 ARG 0.003 0.000 ARG A 95 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2424 Ramachandran restraints generated. 1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2424 Ramachandran restraints generated. 1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 65 residues out of total 1076 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 52 time to evaluate : 1.585 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 462 ASP cc_start: 0.8002 (t0) cc_final: 0.7711 (t0) outliers start: 13 outliers final: 13 residues processed: 62 average time/residue: 0.4535 time to fit residues: 41.1182 Evaluate side-chains 64 residues out of total 1076 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 51 time to evaluate : 1.731 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 238 CYS Chi-restraints excluded: chain A residue 258 CYS Chi-restraints excluded: chain A residue 275 LEU Chi-restraints excluded: chain A residue 384 ILE Chi-restraints excluded: chain A residue 423 ILE Chi-restraints excluded: chain A residue 570 HIS Chi-restraints excluded: chain B residue 59 ASN Chi-restraints excluded: chain B residue 185 ASP Chi-restraints excluded: chain B residue 249 HIS Chi-restraints excluded: chain B residue 373 SER Chi-restraints excluded: chain B residue 377 LEU Chi-restraints excluded: chain B residue 379 GLU Chi-restraints excluded: chain B residue 388 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 29 optimal weight: 0.7980 chunk 89 optimal weight: 0.6980 chunk 14 optimal weight: 0.0170 chunk 26 optimal weight: 0.6980 chunk 96 optimal weight: 1.9990 chunk 40 optimal weight: 0.9990 chunk 99 optimal weight: 0.7980 chunk 12 optimal weight: 1.9990 chunk 17 optimal weight: 0.9980 chunk 85 optimal weight: 0.8980 chunk 5 optimal weight: 1.9990 overall best weight: 0.6018 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4079 r_free = 0.4079 target = 0.135590 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.085498 restraints weight = 51587.610| |-----------------------------------------------------------------------------| r_work (start): 0.3396 rms_B_bonded: 4.06 r_work: 0.3232 rms_B_bonded: 3.75 restraints_weight: 0.5000 r_work (final): 0.3232 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8222 moved from start: 0.4735 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 10198 Z= 0.169 Angle : 0.496 7.262 13829 Z= 0.257 Chirality : 0.044 0.250 1620 Planarity : 0.004 0.037 1772 Dihedral : 5.176 56.893 2033 Min Nonbonded Distance : 2.030 Molprobity Statistics. All-atom Clashscore : 5.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.63 % Favored : 96.37 % Rotamer: Outliers : 1.21 % Allowed : 7.81 % Favored : 90.99 % 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: -0.57 (0.24), residues: 1212 helix: -1.99 (0.52), residues: 89 sheet: -0.52 (0.42), residues: 162 loop : -0.16 (0.21), residues: 961 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 205 HIS 0.003 0.001 HIS B 48 PHE 0.008 0.001 PHE A 447 TYR 0.008 0.001 TYR B 554 ARG 0.004 0.000 ARG A 95 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4313.79 seconds wall clock time: 75 minutes 41.84 seconds (4541.84 seconds total)