Starting phenix.real_space_refine on Wed Aug 7 23:20:47 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8u4j_41884/08_2024/8u4j_41884_trim.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8u4j_41884/08_2024/8u4j_41884.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8u4j_41884/08_2024/8u4j_41884.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8u4j_41884/08_2024/8u4j_41884.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8u4j_41884/08_2024/8u4j_41884_trim.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8u4j_41884/08_2024/8u4j_41884_trim.cif" } resolution = 3.7 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= 0.030 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 128 5.16 5 C 6691 2.51 5 N 1805 2.21 5 O 2226 1.98 5 H 9582 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 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 47": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 50": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 72": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 78": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 81": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 95": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 103": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 106": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 114": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 124": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 168": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 188": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 196": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 210": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 220": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 232": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 306": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 393": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 396": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 426": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 484": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 488": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 491": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 524": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 525": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 528": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 530": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 544": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 612": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C ARG 68": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C ARG 81": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C ARG 83": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C ARG 103": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C ARG 106": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D ARG 68": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D ARG 81": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D ARG 83": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D ARG 103": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D ARG 106": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/chem_data/mon_lib" Total number of atoms: 20432 Number of models: 1 Model: "" Number of chains: 20 Chain: "A" Number of atoms: 9092 Number of conformers: 1 Conformer: "" Number of residues, atoms: 601, 9092 Classifications: {'peptide': 601} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 27, 'TRANS': 573} Chain breaks: 2 Chain: "B" Number of atoms: 9088 Number of conformers: 1 Conformer: "" Number of residues, atoms: 600, 9088 Classifications: {'peptide': 600} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 27, 'TRANS': 572} Chain breaks: 2 Chain: "C" Number of atoms: 762 Number of conformers: 1 Conformer: "" Number of residues, atoms: 48, 762 Classifications: {'peptide': 48} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 2, 'TRANS': 45} Chain: "D" Number of atoms: 762 Number of conformers: 1 Conformer: "" Number of residues, atoms: 48, 762 Classifications: {'peptide': 48} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 2, 'TRANS': 45} Chain: "E" 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: "F" 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: "G" 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: "H" 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: "I" 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: "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: 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: "L" 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: "M" 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: "N" 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: "O" 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: "P" 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: "Q" 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: "R" 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: "A" 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 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: 10.50, per 1000 atoms: 0.51 Number of scatterers: 20432 At special positions: 0 Unit cell: (86.005, 142.785, 138.61, 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 128 16.00 O 2226 8.00 N 1805 7.00 C 6691 6.00 H 9582 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=56, symmetry=0 Simple disulfide: pdb=" SG CYS A 29 " - pdb=" SG CYS A 56 " distance=2.15 Simple disulfide: pdb=" SG CYS A 156 " - pdb=" SG CYS A 186 " distance=2.01 Simple disulfide: pdb=" SG CYS A 189 " - pdb=" SG CYS A 197 " distance=2.07 Simple disulfide: pdb=" SG CYS A 193 " - pdb=" SG CYS A 205 " distance=2.04 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=2.03 Simple disulfide: pdb=" SG CYS A 230 " - pdb=" SG CYS A 238 " distance=2.01 Simple disulfide: pdb=" SG CYS A 234 " - pdb=" SG CYS A 246 " distance=2.02 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=2.01 Simple disulfide: pdb=" SG CYS A 293 " - pdb=" SG CYS A 304 " distance=2.05 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=2.24 Simple disulfide: pdb=" SG CYS A 334 " - pdb=" SG CYS A 359 " distance=2.03 Simple disulfide: pdb=" SG CYS A 467 " - pdb=" SG CYS A 496 " distance=2.16 Simple disulfide: pdb=" SG CYS A 503 " - pdb=" SG CYS A 512 " distance=2.02 Simple disulfide: pdb=" SG CYS A 507 " - pdb=" SG CYS A 520 " distance=2.06 Simple disulfide: pdb=" SG CYS A 523 " - pdb=" SG CYS A 532 " distance=2.04 Simple disulfide: pdb=" SG CYS A 536 " - pdb=" SG CYS A 552 " distance=2.03 Simple disulfide: pdb=" SG CYS A 555 " - pdb=" SG CYS A 569 " distance=2.04 Simple disulfide: pdb=" SG CYS A 559 " - pdb=" SG CYS A 577 " distance=2.04 Simple disulfide: pdb=" SG CYS A 580 " - pdb=" SG CYS A 589 " distance=2.12 Simple disulfide: pdb=" SG CYS A 593 " - pdb=" SG CYS A 614 " distance=2.06 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 625 " distance=2.04 Simple disulfide: pdb=" SG CYS A 621 " - pdb=" SG CYS A 633 " distance=2.03 Simple disulfide: pdb=" SG CYS B 29 " - pdb=" SG CYS B 56 " distance=2.05 Simple disulfide: pdb=" SG CYS B 156 " - pdb=" SG CYS B 186 " distance=2.03 Simple disulfide: pdb=" SG CYS B 189 " - pdb=" SG CYS B 197 " distance=2.01 Simple disulfide: pdb=" SG CYS B 193 " - pdb=" SG CYS B 205 " distance=2.03 Simple disulfide: pdb=" SG CYS B 213 " - pdb=" SG CYS B 221 " distance=2.07 Simple disulfide: pdb=" SG CYS B 217 " - pdb=" SG CYS B 229 " distance=2.02 Simple disulfide: pdb=" SG CYS B 230 " - pdb=" SG CYS B 238 " distance=2.02 Simple disulfide: pdb=" SG CYS B 234 " - pdb=" SG CYS B 246 " distance=2.05 Simple disulfide: pdb=" SG CYS B 249 " - pdb=" SG CYS B 258 " distance=2.04 Simple disulfide: pdb=" SG CYS B 262 " - pdb=" SG CYS B 289 " distance=2.05 Simple disulfide: pdb=" SG CYS B 293 " - pdb=" SG CYS B 304 " distance=2.02 Simple disulfide: pdb=" SG CYS B 308 " - pdb=" SG CYS B 323 " distance=2.02 Simple disulfide: pdb=" SG CYS B 326 " - pdb=" SG CYS B 330 " distance=2.03 Simple disulfide: pdb=" SG CYS B 334 " - pdb=" SG CYS B 359 " distance=2.04 Simple disulfide: pdb=" SG CYS B 467 " - pdb=" SG CYS B 496 " distance=2.18 Simple disulfide: pdb=" SG CYS B 503 " - pdb=" SG CYS B 512 " distance=2.04 Simple disulfide: pdb=" SG CYS B 507 " - pdb=" SG CYS B 520 " distance=2.06 Simple disulfide: pdb=" SG CYS B 523 " - pdb=" SG CYS B 532 " distance=2.02 Simple disulfide: pdb=" SG CYS B 536 " - pdb=" SG CYS B 552 " distance=2.01 Simple disulfide: pdb=" SG CYS B 555 " - pdb=" SG CYS B 569 " distance=2.03 Simple disulfide: pdb=" SG CYS B 559 " - pdb=" SG CYS B 577 " distance=2.00 Simple disulfide: pdb=" SG CYS B 580 " - pdb=" SG CYS B 589 " distance=2.04 Simple disulfide: pdb=" SG CYS B 593 " - pdb=" SG CYS B 614 " distance=2.08 Simple disulfide: pdb=" SG CYS B 617 " - pdb=" SG CYS B 625 " distance=2.02 Simple disulfide: pdb=" SG CYS B 621 " - pdb=" SG CYS B 633 " distance=2.12 Simple disulfide: pdb=" SG CYS C 69 " - pdb=" SG CYS C 82 " distance=2.07 Simple disulfide: pdb=" SG CYS C 77 " - pdb=" SG CYS C 93 " distance=2.01 Simple disulfide: pdb=" SG CYS C 95 " - pdb=" SG CYS C 104 " distance=2.03 Simple disulfide: pdb=" SG CYS D 69 " - pdb=" SG CYS D 82 " distance=2.04 Simple disulfide: pdb=" SG CYS D 77 " - pdb=" SG CYS D 93 " distance=2.02 Simple disulfide: pdb=" SG CYS D 95 " - pdb=" SG CYS D 104 " distance=2.02 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 F 3 " - " MAN F 4 " " BMA H 3 " - " MAN H 4 " " BMA I 3 " - " MAN I 4 " " BMA K 3 " - " MAN K 4 " " BMA L 3 " - " MAN L 4 " " BMA M 3 " - " MAN M 4 " " BMA N 3 " - " MAN N 4 " " BMA R 3 " - " MAN R 4 " ALPHA1-6 " BMA F 3 " - " MAN F 5 " " BMA H 3 " - " MAN H 5 " " BMA I 3 " - " MAN I 5 " " BMA K 3 " - " MAN K 5 " " BMA L 3 " - " MAN L 5 " " BMA M 3 " - " MAN M 5 " " BMA N 3 " - " MAN N 5 " " BMA R 3 " - " MAN R 5 " BETA1-4 " 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 M 2 " - " BMA M 3 " " NAG N 1 " - " NAG N 2 " " NAG N 2 " - " BMA N 3 " " NAG O 1 " - " NAG O 2 " " NAG P 1 " - " NAG P 2 " " NAG P 2 " - " BMA P 3 " " NAG Q 1 " - " NAG Q 2 " " NAG Q 2 " - " BMA Q 3 " " NAG R 1 " - " NAG R 2 " " NAG R 2 " - " BMA R 3 " NAG-ASN " NAG A 701 " - " ASN A 495 " " NAG B 701 " - " ASN B 495 " " NAG E 1 " - " ASN A 548 " " NAG F 1 " - " ASN A 576 " " NAG G 1 " - " ASN A 473 " " NAG H 1 " - " ASN A 253 " " NAG I 1 " - " ASN A 358 " " NAG J 1 " - " ASN A 410 " " NAG K 1 " - " ASN A 138 " " NAG L 1 " - " ASN B 138 " " NAG M 1 " - " ASN B 253 " " NAG N 1 " - " ASN B 358 " " NAG O 1 " - " ASN B 410 " " NAG P 1 " - " ASN B 473 " " NAG Q 1 " - " ASN B 548 " " NAG R 1 " - " ASN B 576 " Time building additional restraints: 17.32 Conformation dependent library (CDL) restraints added in 2.3 seconds 2562 Ramachandran restraints generated. 1281 Oldfield, 0 Emsley, 1281 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2388 Finding SS restraints... Secondary structure from input PDB file: 32 helices and 32 sheets defined 15.7% alpha, 16.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.96 Creating SS restraints... Processing helix chain 'A' and resid 41 through 54 Processing helix chain 'A' and resid 74 through 80 removed outlier: 3.928A 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 157 through 161 Processing helix chain 'A' and resid 162 through 167 removed outlier: 4.403A pdb=" N ILE A 166 " --> pdb=" O HIS A 162 " (cutoff:3.500A) Processing helix chain 'A' and resid 225 through 229 Processing helix chain 'A' and resid 339 through 343 Processing helix chain 'A' and resid 352 through 357 removed outlier: 3.942A pdb=" N ILE A 357 " --> pdb=" O ASP A 354 " (cutoff:3.500A) Processing helix chain 'A' and resid 369 through 374 Processing helix chain 'A' and resid 385 through 395 removed outlier: 4.242A pdb=" N THR A 394 " --> pdb=" O VAL A 391 " (cutoff:3.500A) Processing helix chain 'A' and resid 414 through 418 Processing helix chain 'A' and resid 467 through 472 removed outlier: 3.598A pdb=" N HIS A 470 " --> pdb=" O CYS A 467 " (cutoff:3.500A) Processing helix chain 'A' and resid 473 through 477 Processing helix chain 'A' and resid 492 through 499 Processing helix chain 'A' and resid 629 through 633 Processing helix chain 'B' and resid 41 through 54 Processing helix chain 'B' and resid 74 through 80 removed outlier: 3.623A pdb=" N SER B 79 " --> pdb=" O PHE B 76 " (cutoff:3.500A) Processing helix chain 'B' and resid 110 through 113 Processing helix chain 'B' and resid 157 through 161 Processing helix chain 'B' and resid 162 through 166 removed outlier: 3.622A pdb=" N ASP B 165 " --> pdb=" O HIS B 162 " (cutoff:3.500A) Processing helix chain 'B' and resid 225 through 229 Processing helix chain 'B' and resid 339 through 343 Processing helix chain 'B' and resid 352 through 357 Processing helix chain 'B' and resid 369 through 375 Processing helix chain 'B' and resid 376 through 380 Processing helix chain 'B' and resid 385 through 395 removed outlier: 4.229A pdb=" N THR B 394 " --> pdb=" O VAL B 391 " (cutoff:3.500A) Processing helix chain 'B' and resid 414 through 418 Processing helix chain 'B' and resid 473 through 478 Processing helix chain 'B' and resid 492 through 499 Processing helix chain 'B' and resid 629 through 631 No H-bonds generated for 'chain 'B' and resid 629 through 631' Processing helix chain 'C' and resid 70 through 74 Processing helix chain 'D' and resid 70 through 74 Processing sheet with id=AA1, first strand: chain 'A' and resid 28 through 29 Processing sheet with id=AA2, first strand: chain 'A' and resid 63 through 66 removed outlier: 6.359A pdb=" N LEU A 63 " --> pdb=" O LEU A 88 " (cutoff:3.500A) removed outlier: 7.696A pdb=" N ALA A 90 " --> pdb=" O LEU A 63 " (cutoff:3.500A) removed outlier: 6.464A pdb=" N ILE A 65 " --> pdb=" O ALA A 90 " (cutoff:3.500A) removed outlier: 5.460A pdb=" N GLY A 146 " --> pdb=" O TYR A 115 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N VAL A 149 " --> pdb=" O LEU A 177 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 234 through 238 removed outlier: 7.784A pdb=" N GLY A 237 " --> pdb=" O CYS A 246 " (cutoff:3.500A) removed outlier: 5.586A pdb=" N CYS A 246 " --> pdb=" O GLY A 237 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 252 through 254 Processing sheet with id=AA5, first strand: chain 'A' and resid 266 through 268 Processing sheet with id=AA6, first strand: chain 'A' and resid 283 through 285 Processing sheet with id=AA7, first strand: chain 'A' and resid 298 through 300 Processing sheet with id=AA8, first strand: chain 'A' and resid 312 through 317 Processing sheet with id=AA9, first strand: chain 'A' and resid 333 through 335 removed outlier: 6.688A pdb=" N CYS A 334 " --> pdb=" O ASN A 363 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 366 through 368 removed outlier: 5.511A pdb=" N ASN A 457 " --> pdb=" O LEU A 432 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N LEU A 434 " --> pdb=" O ASN A 457 " (cutoff:3.500A) removed outlier: 6.647A pdb=" N ILE A 458 " --> pdb=" O VAL A 486 " (cutoff:3.500A) removed outlier: 8.352A pdb=" N ARG A 488 " --> pdb=" O ILE A 458 " (cutoff:3.500A) removed outlier: 6.712A pdb=" N ILE A 460 " --> pdb=" O ARG A 488 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 526 through 528 removed outlier: 3.758A pdb=" N ILE A 531 " --> pdb=" O ARG A 528 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 545 through 548 Processing sheet with id=AB4, first strand: chain 'A' and resid 583 through 585 Processing sheet with id=AB5, first strand: chain 'A' and resid 605 through 608 removed outlier: 4.120A pdb=" N PHE A 605 " --> pdb=" O CYS A 617 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 28 through 29 Processing sheet with id=AB7, first strand: chain 'B' and resid 38 through 39 removed outlier: 7.340A pdb=" N SER B 38 " --> pdb=" O CYS D 95 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 63 through 66 removed outlier: 6.507A pdb=" N LEU B 63 " --> pdb=" O LEU B 88 " (cutoff:3.500A) removed outlier: 7.872A pdb=" N ALA B 90 " --> pdb=" O LEU B 63 " (cutoff:3.500A) removed outlier: 6.492A pdb=" N ILE B 65 " --> pdb=" O ALA B 90 " (cutoff:3.500A) removed outlier: 5.500A pdb=" N GLY B 146 " --> pdb=" O TYR B 115 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N LEU B 117 " --> pdb=" O GLY B 146 " (cutoff:3.500A) removed outlier: 5.956A pdb=" N VAL B 147 " --> pdb=" O LEU B 177 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 252 through 254 Processing sheet with id=AC1, first strand: chain 'B' and resid 266 through 269 removed outlier: 3.773A pdb=" N GLN B 274 " --> pdb=" O ASN B 269 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 283 through 285 Processing sheet with id=AC3, first strand: chain 'B' and resid 298 through 300 Processing sheet with id=AC4, first strand: chain 'B' and resid 312 through 317 Processing sheet with id=AC5, first strand: chain 'B' and resid 333 through 335 removed outlier: 6.521A pdb=" N CYS B 334 " --> pdb=" O ASN B 363 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 366 through 368 removed outlier: 4.684A pdb=" N LEU B 432 " --> pdb=" O ASN B 457 " (cutoff:3.500A) removed outlier: 7.886A pdb=" N TYR B 459 " --> pdb=" O LEU B 432 " (cutoff:3.500A) removed outlier: 6.722A pdb=" N LEU B 434 " --> pdb=" O TYR B 459 " (cutoff:3.500A) removed outlier: 8.032A pdb=" N THR B 461 " --> pdb=" O LEU B 434 " (cutoff:3.500A) removed outlier: 6.538A pdb=" N ILE B 436 " --> pdb=" O THR B 461 " (cutoff:3.500A) removed outlier: 6.564A pdb=" N ILE B 458 " --> pdb=" O VAL B 486 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 527 through 528 Processing sheet with id=AC8, first strand: chain 'B' and resid 545 through 548 Processing sheet with id=AC9, first strand: chain 'B' and resid 583 through 584 Processing sheet with id=AD1, first strand: chain 'B' and resid 606 through 608 Processing sheet with id=AD2, first strand: chain 'B' and resid 624 through 625 Processing sheet with id=AD3, first strand: chain 'C' and resid 66 through 67 Processing sheet with id=AD4, first strand: chain 'C' and resid 99 through 100 Processing sheet with id=AD5, first strand: chain 'D' and resid 99 through 100 227 hydrogen bonds defined for protein. 414 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: 7.36 Time building geometry restraints manager: 18.28 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: 9582 1.13 - 1.31: 1806 1.31 - 1.48: 4444 1.48 - 1.65: 4673 1.65 - 1.82: 144 Bond restraints: 20649 Sorted by residual: bond pdb=" ND2 ASN B 174 " pdb="HD22 ASN B 174 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.68e+01 bond pdb=" CZ PHE A 273 " pdb=" HZ PHE A 273 " ideal model delta sigma weight residual 0.930 1.081 -0.151 2.00e-02 2.50e+03 5.68e+01 bond pdb=" N HIS A 204 " pdb=" H HIS A 204 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.68e+01 bond pdb=" N GLU A 54 " pdb=" H GLU A 54 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.68e+01 bond pdb=" N LEU A 434 " pdb=" H LEU A 434 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.68e+01 ... (remaining 20644 not shown) Histogram of bond angle deviations from ideal: 97.15 - 104.62: 247 104.62 - 112.09: 22169 112.09 - 119.56: 6727 119.56 - 127.03: 7585 127.03 - 134.50: 94 Bond angle restraints: 36822 Sorted by residual: angle pdb=" CA ASN A 138 " pdb=" CB ASN A 138 " pdb=" CG ASN A 138 " ideal model delta sigma weight residual 112.60 119.89 -7.29 1.00e+00 1.00e+00 5.31e+01 angle pdb=" N ILE A 357 " pdb=" CA ILE A 357 " pdb=" C ILE A 357 " ideal model delta sigma weight residual 110.62 117.31 -6.69 1.14e+00 7.69e-01 3.45e+01 angle pdb=" C ARG A 525 " pdb=" CA ARG A 525 " pdb=" CB ARG A 525 " ideal model delta sigma weight residual 117.23 109.27 7.96 1.36e+00 5.41e-01 3.42e+01 angle pdb=" N PHE A 120 " pdb=" CA PHE A 120 " pdb=" C PHE A 120 " ideal model delta sigma weight residual 108.79 117.16 -8.37 1.53e+00 4.27e-01 3.00e+01 angle pdb=" N ILE B 357 " pdb=" CA ILE B 357 " pdb=" C ILE B 357 " ideal model delta sigma weight residual 110.62 116.08 -5.46 1.02e+00 9.61e-01 2.86e+01 ... (remaining 36817 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.98: 9939 21.98 - 43.97: 439 43.97 - 65.95: 269 65.95 - 87.94: 81 87.94 - 109.92: 51 Dihedral angle restraints: 10779 sinusoidal: 6383 harmonic: 4396 Sorted by residual: dihedral pdb=" CB CYS B 621 " pdb=" SG CYS B 621 " pdb=" SG CYS B 633 " pdb=" CB CYS B 633 " ideal model delta sinusoidal sigma weight residual -86.00 -167.30 81.30 1 1.00e+01 1.00e-02 8.15e+01 dihedral pdb=" CB CYS A 593 " pdb=" SG CYS A 593 " pdb=" SG CYS A 614 " pdb=" CB CYS A 614 " ideal model delta sinusoidal sigma weight residual 93.00 162.52 -69.52 1 1.00e+01 1.00e-02 6.24e+01 dihedral pdb=" CB CYS D 77 " pdb=" SG CYS D 77 " pdb=" SG CYS D 93 " pdb=" CB CYS D 93 " ideal model delta sinusoidal sigma weight residual 93.00 158.06 -65.06 1 1.00e+01 1.00e-02 5.55e+01 ... (remaining 10776 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.122: 1557 0.122 - 0.244: 207 0.244 - 0.366: 27 0.366 - 0.488: 7 0.488 - 0.610: 1 Chirality restraints: 1799 Sorted by residual: chirality pdb=" C1 BMA P 3 " pdb=" O4 NAG P 2 " pdb=" C2 BMA P 3 " pdb=" O5 BMA P 3 " both_signs ideal model delta sigma weight residual False -2.40 -2.19 -0.21 2.00e-02 2.50e+03 1.13e+02 chirality pdb=" C1 MAN M 4 " pdb=" O3 BMA M 3 " pdb=" C2 MAN M 4 " pdb=" O5 MAN M 4 " both_signs ideal model delta sigma weight residual False 2.40 2.19 0.21 2.00e-02 2.50e+03 1.12e+02 chirality pdb=" C1 BMA H 3 " pdb=" O4 NAG H 2 " pdb=" C2 BMA H 3 " pdb=" O5 BMA H 3 " both_signs ideal model delta sigma weight residual False -2.40 -2.59 0.19 2.00e-02 2.50e+03 8.98e+01 ... (remaining 1796 not shown) Planarity restraints: 3125 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG M 1 " 0.345 2.00e-02 2.50e+03 2.98e-01 1.11e+03 pdb=" C7 NAG M 1 " -0.084 2.00e-02 2.50e+03 pdb=" C8 NAG M 1 " 0.124 2.00e-02 2.50e+03 pdb=" N2 NAG M 1 " -0.530 2.00e-02 2.50e+03 pdb=" O7 NAG M 1 " 0.145 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG M 2 " -0.321 2.00e-02 2.50e+03 2.77e-01 9.57e+02 pdb=" C7 NAG M 2 " 0.075 2.00e-02 2.50e+03 pdb=" C8 NAG M 2 " -0.026 2.00e-02 2.50e+03 pdb=" N2 NAG M 2 " 0.480 2.00e-02 2.50e+03 pdb=" O7 NAG M 2 " -0.208 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 138 " 0.210 2.00e-02 2.50e+03 1.52e-01 3.48e+02 pdb=" CG ASN A 138 " -0.072 2.00e-02 2.50e+03 pdb=" OD1 ASN A 138 " -0.108 2.00e-02 2.50e+03 pdb=" ND2 ASN A 138 " -0.039 2.00e-02 2.50e+03 pdb="HD21 ASN A 138 " -0.191 2.00e-02 2.50e+03 pdb=" C1 NAG K 1 " 0.201 2.00e-02 2.50e+03 ... (remaining 3122 not shown) Histogram of nonbonded interaction distances: 1.42 - 2.06: 752 2.06 - 2.69: 25825 2.69 - 3.33: 56785 3.33 - 3.96: 74117 3.96 - 4.60: 107747 Nonbonded interactions: 265226 Sorted by model distance: nonbonded pdb=" H GLY A 364 " pdb=" HG1 THR A 399 " model vdw 1.419 2.100 nonbonded pdb=" OE2 GLU B 317 " pdb=" HZ1 LYS B 324 " model vdw 1.431 2.450 nonbonded pdb=" O TYR C 76 " pdb=" HE ARG C 103 " model vdw 1.493 2.450 nonbonded pdb=" H GLY A 364 " pdb=" OG1 THR A 399 " model vdw 1.540 2.450 nonbonded pdb=" HB3 ASN B 251 " pdb=" H PHE B 252 " model vdw 1.575 2.270 ... (remaining 265221 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 26 through 595 or resid 604 through 634 or resid 701)) selection = (chain 'B' and (resid 26 through 137 or (resid 138 and (name N or name CA or nam \ e C or name O or name CB or name CG or name OD1 or name ND2 or name H or name HB \ 2 or name HB3 or name HD21)) or resid 139 through 634 or resid 701)) } ncs_group { reference = chain 'C' selection = chain 'D' } ncs_group { reference = chain 'E' selection = chain 'G' selection = chain 'P' selection = chain 'Q' } ncs_group { reference = chain 'F' selection = chain 'H' selection = chain 'I' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'R' } ncs_group { reference = chain 'J' selection = chain 'O' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.470 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: 0.320 Extract box with map and model: 0.860 Check model and map are aligned: 0.150 Set scattering table: 0.210 Process input model: 68.350 Find NCS groups from input model: 0.900 Set up NCS constraints: 0.100 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 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: 78.070 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7910 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 : 0.014 0.087 11067 Z= 0.863 Angle : 1.540 9.972 14980 Z= 1.008 Chirality : 0.087 0.610 1799 Planarity : 0.014 0.298 1878 Dihedral : 16.947 109.924 4966 Min Nonbonded Distance : 2.219 Molprobity Statistics. All-atom Clashscore : 0.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Rotamer: Outliers : 0.17 % Allowed : 0.61 % Favored : 99.22 % Cbeta Deviations : 0.25 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.45 (0.22), residues: 1281 helix: -2.74 (0.43), residues: 88 sheet: -1.36 (0.37), residues: 154 loop : 0.17 (0.19), residues: 1039 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.065 0.005 TRP B 198 HIS 0.008 0.001 HIS B 570 PHE 0.056 0.004 PHE B 154 TYR 0.102 0.006 TYR A 157 ARG 0.006 0.000 ARG A 106 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2562 Ramachandran restraints generated. 1281 Oldfield, 0 Emsley, 1281 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2562 Ramachandran restraints generated. 1281 Oldfield, 0 Emsley, 1281 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 1148 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 181 time to evaluate : 1.735 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 260 THR cc_start: 0.8907 (p) cc_final: 0.8668 (m) REVERT: B 251 ASN cc_start: 0.8169 (m-40) cc_final: 0.7465 (m-40) REVERT: B 331 PRO cc_start: 0.7434 (Cg_exo) cc_final: 0.6954 (Cg_endo) REVERT: D 68 ARG cc_start: 0.8468 (ttt180) cc_final: 0.7890 (tpm170) outliers start: 2 outliers final: 2 residues processed: 183 average time/residue: 0.7239 time to fit residues: 167.5503 Evaluate side-chains 97 residues out of total 1148 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 95 time to evaluate : 1.709 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 201 THR Chi-restraints excluded: chain B residue 410 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 108 optimal weight: 0.9990 chunk 97 optimal weight: 0.8980 chunk 53 optimal weight: 5.9990 chunk 33 optimal weight: 0.8980 chunk 65 optimal weight: 0.6980 chunk 51 optimal weight: 5.9990 chunk 100 optimal weight: 0.7980 chunk 38 optimal weight: 0.9990 chunk 61 optimal weight: 0.8980 chunk 74 optimal weight: 0.9990 chunk 116 optimal weight: 20.0000 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 631 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8006 moved from start: 0.2692 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 11067 Z= 0.227 Angle : 0.712 7.823 14980 Z= 0.367 Chirality : 0.049 0.319 1799 Planarity : 0.005 0.061 1878 Dihedral : 15.333 88.676 2575 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 2.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 0.44 % Allowed : 4.53 % Favored : 95.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.72 (0.23), residues: 1281 helix: -2.14 (0.49), residues: 94 sheet: -1.35 (0.35), residues: 172 loop : -0.10 (0.20), residues: 1015 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 513 HIS 0.009 0.001 HIS B 505 PHE 0.014 0.001 PHE B 154 TYR 0.013 0.001 TYR B 53 ARG 0.006 0.001 ARG B 114 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2562 Ramachandran restraints generated. 1281 Oldfield, 0 Emsley, 1281 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2562 Ramachandran restraints generated. 1281 Oldfield, 0 Emsley, 1281 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 1148 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 96 time to evaluate : 1.758 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 318 ASN cc_start: 0.8282 (p0) cc_final: 0.7806 (p0) REVERT: C 110 PHE cc_start: 0.8089 (m-80) cc_final: 0.7571 (m-10) REVERT: D 68 ARG cc_start: 0.8641 (ttt180) cc_final: 0.8009 (tpm170) outliers start: 5 outliers final: 4 residues processed: 99 average time/residue: 0.7470 time to fit residues: 94.8257 Evaluate side-chains 83 residues out of total 1148 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 79 time to evaluate : 1.556 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 171 TRP Chi-restraints excluded: chain B residue 410 ASN Chi-restraints excluded: chain C residue 66 PHE Chi-restraints excluded: chain C residue 96 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 64 optimal weight: 1.9990 chunk 36 optimal weight: 1.9990 chunk 96 optimal weight: 0.6980 chunk 79 optimal weight: 0.0870 chunk 32 optimal weight: 0.9990 chunk 116 optimal weight: 4.9990 chunk 125 optimal weight: 0.7980 chunk 103 optimal weight: 1.9990 chunk 115 optimal weight: 9.9990 chunk 39 optimal weight: 2.9990 chunk 93 optimal weight: 0.5980 overall best weight: 0.6360 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8036 moved from start: 0.3256 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 11067 Z= 0.163 Angle : 0.602 6.992 14980 Z= 0.304 Chirality : 0.048 0.225 1799 Planarity : 0.004 0.054 1878 Dihedral : 12.039 73.383 2574 Min Nonbonded Distance : 2.361 Molprobity Statistics. All-atom Clashscore : 2.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer: Outliers : 0.70 % Allowed : 5.40 % Favored : 93.90 % 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: -0.88 (0.23), residues: 1281 helix: -2.08 (0.48), residues: 94 sheet: -1.47 (0.35), residues: 161 loop : -0.26 (0.19), residues: 1026 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 474 HIS 0.004 0.001 HIS A 470 PHE 0.010 0.001 PHE B 154 TYR 0.009 0.001 TYR A 148 ARG 0.006 0.000 ARG A 95 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2562 Ramachandran restraints generated. 1281 Oldfield, 0 Emsley, 1281 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2562 Ramachandran restraints generated. 1281 Oldfield, 0 Emsley, 1281 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 1148 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 86 time to evaluate : 1.447 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 318 ASN cc_start: 0.8241 (p0) cc_final: 0.7779 (p0) REVERT: C 110 PHE cc_start: 0.7983 (m-80) cc_final: 0.7540 (m-10) outliers start: 8 outliers final: 6 residues processed: 91 average time/residue: 0.6452 time to fit residues: 77.2637 Evaluate side-chains 75 residues out of total 1148 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 69 time to evaluate : 1.554 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 322 MET Chi-restraints excluded: chain B residue 171 TRP Chi-restraints excluded: chain B residue 365 ASN Chi-restraints excluded: chain B residue 410 ASN Chi-restraints excluded: chain C residue 66 PHE Chi-restraints excluded: chain C residue 100 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 115 optimal weight: 9.9990 chunk 87 optimal weight: 3.9990 chunk 60 optimal weight: 2.9990 chunk 12 optimal weight: 0.8980 chunk 55 optimal weight: 5.9990 chunk 78 optimal weight: 3.9990 chunk 116 optimal weight: 9.9990 chunk 123 optimal weight: 2.9990 chunk 61 optimal weight: 1.9990 chunk 110 optimal weight: 0.8980 chunk 33 optimal weight: 3.9990 overall best weight: 1.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8166 moved from start: 0.3777 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.059 11067 Z= 0.314 Angle : 0.642 8.329 14980 Z= 0.326 Chirality : 0.049 0.236 1799 Planarity : 0.004 0.054 1878 Dihedral : 9.888 63.371 2574 Min Nonbonded Distance : 2.373 Molprobity Statistics. All-atom Clashscore : 3.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.59 % Favored : 96.41 % Rotamer: Outliers : 1.22 % Allowed : 6.36 % Favored : 92.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.10 (0.23), residues: 1281 helix: -2.05 (0.50), residues: 90 sheet: -1.50 (0.37), residues: 153 loop : -0.48 (0.19), residues: 1038 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP B 198 HIS 0.006 0.001 HIS B 374 PHE 0.013 0.002 PHE B 252 TYR 0.012 0.002 TYR B 53 ARG 0.006 0.001 ARG A 106 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2562 Ramachandran restraints generated. 1281 Oldfield, 0 Emsley, 1281 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2562 Ramachandran restraints generated. 1281 Oldfield, 0 Emsley, 1281 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 1148 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 74 time to evaluate : 1.750 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 110 PHE cc_start: 0.8111 (m-80) cc_final: 0.7715 (m-10) outliers start: 14 outliers final: 12 residues processed: 81 average time/residue: 0.6324 time to fit residues: 68.5971 Evaluate side-chains 78 residues out of total 1148 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 66 time to evaluate : 1.591 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 150 ASP Chi-restraints excluded: chain A residue 322 MET Chi-restraints excluded: chain A residue 365 ASN Chi-restraints excluded: chain B residue 134 LEU Chi-restraints excluded: chain B residue 171 TRP Chi-restraints excluded: chain B residue 365 ASN Chi-restraints excluded: chain B residue 410 ASN Chi-restraints excluded: chain B residue 576 ASN Chi-restraints excluded: chain C residue 66 PHE Chi-restraints excluded: chain C residue 96 ASP Chi-restraints excluded: chain C residue 100 ILE Chi-restraints excluded: chain D residue 88 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 103 optimal weight: 1.9990 chunk 70 optimal weight: 2.9990 chunk 1 optimal weight: 1.9990 chunk 92 optimal weight: 1.9990 chunk 51 optimal weight: 8.9990 chunk 105 optimal weight: 0.9980 chunk 85 optimal weight: 4.9990 chunk 0 optimal weight: 2.9990 chunk 63 optimal weight: 0.9990 chunk 111 optimal weight: 8.9990 chunk 31 optimal weight: 2.9990 overall best weight: 1.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8175 moved from start: 0.4082 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.076 11067 Z= 0.245 Angle : 0.596 6.708 14980 Z= 0.304 Chirality : 0.047 0.241 1799 Planarity : 0.004 0.061 1878 Dihedral : 8.715 57.459 2574 Min Nonbonded Distance : 2.316 Molprobity Statistics. All-atom Clashscore : 3.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.59 % Favored : 96.41 % Rotamer: Outliers : 1.31 % Allowed : 7.06 % 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: -1.18 (0.23), residues: 1281 helix: -2.01 (0.51), residues: 90 sheet: -1.56 (0.37), residues: 157 loop : -0.55 (0.20), residues: 1034 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 198 HIS 0.004 0.001 HIS C 75 PHE 0.012 0.001 PHE B 447 TYR 0.009 0.001 TYR A 148 ARG 0.007 0.001 ARG B 232 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2562 Ramachandran restraints generated. 1281 Oldfield, 0 Emsley, 1281 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2562 Ramachandran restraints generated. 1281 Oldfield, 0 Emsley, 1281 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 1148 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 67 time to evaluate : 1.664 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 60 MET cc_start: 0.8530 (mmp) cc_final: 0.8310 (mmt) REVERT: C 110 PHE cc_start: 0.8123 (m-80) cc_final: 0.7568 (m-80) outliers start: 15 outliers final: 14 residues processed: 77 average time/residue: 0.5192 time to fit residues: 56.6876 Evaluate side-chains 76 residues out of total 1148 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 62 time to evaluate : 1.578 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 ASP Chi-restraints excluded: chain A residue 150 ASP Chi-restraints excluded: chain A residue 322 MET Chi-restraints excluded: chain A residue 365 ASN Chi-restraints excluded: chain A residue 384 ILE Chi-restraints excluded: chain B residue 134 LEU Chi-restraints excluded: chain B residue 171 TRP Chi-restraints excluded: chain B residue 365 ASN Chi-restraints excluded: chain B residue 410 ASN Chi-restraints excluded: chain B residue 576 ASN Chi-restraints excluded: chain C residue 66 PHE Chi-restraints excluded: chain C residue 69 CYS Chi-restraints excluded: chain C residue 100 ILE Chi-restraints excluded: chain D residue 88 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 41 optimal weight: 1.9990 chunk 111 optimal weight: 5.9990 chunk 24 optimal weight: 1.9990 chunk 72 optimal weight: 2.9990 chunk 30 optimal weight: 0.0670 chunk 123 optimal weight: 0.9980 chunk 102 optimal weight: 0.9980 chunk 57 optimal weight: 9.9990 chunk 10 optimal weight: 3.9990 chunk 40 optimal weight: 0.9990 chunk 65 optimal weight: 1.9990 overall best weight: 1.0122 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 26 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8166 moved from start: 0.4288 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 11067 Z= 0.183 Angle : 0.553 6.331 14980 Z= 0.279 Chirality : 0.046 0.224 1799 Planarity : 0.004 0.063 1878 Dihedral : 7.646 58.453 2574 Min Nonbonded Distance : 2.298 Molprobity Statistics. All-atom Clashscore : 3.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.75 % Favored : 96.25 % Rotamer: Outliers : 1.22 % Allowed : 7.14 % 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: -1.12 (0.23), residues: 1281 helix: -1.93 (0.51), residues: 90 sheet: -1.47 (0.38), residues: 162 loop : -0.51 (0.20), residues: 1029 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 474 HIS 0.004 0.001 HIS A 204 PHE 0.022 0.001 PHE A 129 TYR 0.009 0.001 TYR B 53 ARG 0.009 0.000 ARG A 124 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2562 Ramachandran restraints generated. 1281 Oldfield, 0 Emsley, 1281 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2562 Ramachandran restraints generated. 1281 Oldfield, 0 Emsley, 1281 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 1148 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 63 time to evaluate : 1.593 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 outliers start: 14 outliers final: 13 residues processed: 72 average time/residue: 0.5220 time to fit residues: 53.5395 Evaluate side-chains 76 residues out of total 1148 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 63 time to evaluate : 1.585 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 150 ASP Chi-restraints excluded: chain A residue 250 MET Chi-restraints excluded: chain A residue 322 MET Chi-restraints excluded: chain A residue 365 ASN Chi-restraints excluded: chain A residue 384 ILE Chi-restraints excluded: chain B residue 134 LEU Chi-restraints excluded: chain B residue 238 CYS Chi-restraints excluded: chain B residue 365 ASN Chi-restraints excluded: chain B residue 410 ASN Chi-restraints excluded: chain B residue 576 ASN Chi-restraints excluded: chain C residue 66 PHE Chi-restraints excluded: chain C residue 100 ILE Chi-restraints excluded: chain D residue 88 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 119 optimal weight: 1.9990 chunk 13 optimal weight: 2.9990 chunk 70 optimal weight: 2.9990 chunk 90 optimal weight: 3.9990 chunk 104 optimal weight: 2.9990 chunk 69 optimal weight: 1.9990 chunk 123 optimal weight: 1.9990 chunk 77 optimal weight: 1.9990 chunk 75 optimal weight: 4.9990 chunk 56 optimal weight: 10.0000 chunk 76 optimal weight: 2.9990 overall best weight: 2.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 463 ASN ** B 62 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8242 moved from start: 0.4602 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.070 11067 Z= 0.342 Angle : 0.622 6.201 14980 Z= 0.319 Chirality : 0.047 0.216 1799 Planarity : 0.004 0.062 1878 Dihedral : 7.572 58.182 2574 Min Nonbonded Distance : 2.297 Molprobity Statistics. All-atom Clashscore : 4.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.93 % Favored : 94.07 % Rotamer: Outliers : 1.57 % Allowed : 6.88 % Favored : 91.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.49 (0.23), residues: 1281 helix: -2.08 (0.51), residues: 94 sheet: -1.59 (0.38), residues: 157 loop : -0.82 (0.19), residues: 1030 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP B 198 HIS 0.007 0.001 HIS B 374 PHE 0.016 0.002 PHE B 252 TYR 0.023 0.002 TYR B 459 ARG 0.005 0.001 ARG D 103 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2562 Ramachandran restraints generated. 1281 Oldfield, 0 Emsley, 1281 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2562 Ramachandran restraints generated. 1281 Oldfield, 0 Emsley, 1281 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 1148 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 64 time to evaluate : 1.712 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 18 outliers final: 16 residues processed: 75 average time/residue: 0.5468 time to fit residues: 57.0020 Evaluate side-chains 78 residues out of total 1148 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 62 time to evaluate : 1.656 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 ASP Chi-restraints excluded: chain A residue 150 ASP Chi-restraints excluded: chain A residue 250 MET Chi-restraints excluded: chain A residue 322 MET Chi-restraints excluded: chain A residue 365 ASN Chi-restraints excluded: chain A residue 384 ILE Chi-restraints excluded: chain B residue 62 ASN Chi-restraints excluded: chain B residue 134 LEU Chi-restraints excluded: chain B residue 171 TRP Chi-restraints excluded: chain B residue 238 CYS Chi-restraints excluded: chain B residue 365 ASN Chi-restraints excluded: chain B residue 410 ASN Chi-restraints excluded: chain B residue 576 ASN Chi-restraints excluded: chain C residue 66 PHE Chi-restraints excluded: chain C residue 96 ASP Chi-restraints excluded: chain D residue 88 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 49 optimal weight: 8.9990 chunk 73 optimal weight: 1.9990 chunk 37 optimal weight: 1.9990 chunk 24 optimal weight: 0.0770 chunk 23 optimal weight: 2.9990 chunk 78 optimal weight: 0.0370 chunk 84 optimal weight: 1.9990 chunk 60 optimal weight: 2.9990 chunk 11 optimal weight: 1.9990 chunk 96 optimal weight: 1.9990 chunk 112 optimal weight: 5.9990 overall best weight: 1.2222 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8213 moved from start: 0.4694 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 11067 Z= 0.208 Angle : 0.565 8.129 14980 Z= 0.287 Chirality : 0.045 0.196 1799 Planarity : 0.004 0.065 1878 Dihedral : 7.242 59.983 2574 Min Nonbonded Distance : 2.300 Molprobity Statistics. All-atom Clashscore : 4.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.84 % Favored : 95.16 % Rotamer: Outliers : 1.31 % Allowed : 7.32 % Favored : 91.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.38 (0.23), residues: 1281 helix: -1.96 (0.52), residues: 91 sheet: -1.52 (0.36), residues: 177 loop : -0.72 (0.20), residues: 1013 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 198 HIS 0.003 0.001 HIS A 204 PHE 0.013 0.001 PHE B 447 TYR 0.010 0.001 TYR B 459 ARG 0.010 0.001 ARG A 484 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2562 Ramachandran restraints generated. 1281 Oldfield, 0 Emsley, 1281 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2562 Ramachandran restraints generated. 1281 Oldfield, 0 Emsley, 1281 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 1148 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 66 time to evaluate : 1.584 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 60 MET cc_start: 0.8529 (mmp) cc_final: 0.8326 (mmt) outliers start: 15 outliers final: 15 residues processed: 76 average time/residue: 0.4993 time to fit residues: 53.8830 Evaluate side-chains 78 residues out of total 1148 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 63 time to evaluate : 1.600 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 CYS Chi-restraints excluded: chain A residue 150 ASP Chi-restraints excluded: chain A residue 250 MET Chi-restraints excluded: chain A residue 322 MET Chi-restraints excluded: chain A residue 365 ASN Chi-restraints excluded: chain A residue 384 ILE Chi-restraints excluded: chain B residue 134 LEU Chi-restraints excluded: chain B residue 238 CYS Chi-restraints excluded: chain B residue 365 ASN Chi-restraints excluded: chain B residue 410 ASN Chi-restraints excluded: chain B residue 576 ASN Chi-restraints excluded: chain C residue 66 PHE Chi-restraints excluded: chain C residue 69 CYS Chi-restraints excluded: chain C residue 100 ILE Chi-restraints excluded: chain D residue 88 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 118 optimal weight: 7.9990 chunk 107 optimal weight: 4.9990 chunk 114 optimal weight: 10.0000 chunk 69 optimal weight: 1.9990 chunk 50 optimal weight: 0.7980 chunk 90 optimal weight: 0.9990 chunk 35 optimal weight: 4.9990 chunk 103 optimal weight: 0.7980 chunk 108 optimal weight: 1.9990 chunk 75 optimal weight: 0.6980 chunk 121 optimal weight: 1.9990 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8206 moved from start: 0.4822 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 11067 Z= 0.187 Angle : 0.534 6.419 14980 Z= 0.272 Chirality : 0.044 0.194 1799 Planarity : 0.004 0.067 1878 Dihedral : 6.872 59.613 2574 Min Nonbonded Distance : 2.304 Molprobity Statistics. All-atom Clashscore : 4.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.76 % Favored : 95.24 % Rotamer: Outliers : 1.31 % Allowed : 7.32 % Favored : 91.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.31 (0.23), residues: 1281 helix: -1.64 (0.55), residues: 84 sheet: -1.61 (0.36), residues: 170 loop : -0.69 (0.20), residues: 1027 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 474 HIS 0.004 0.001 HIS A 204 PHE 0.012 0.001 PHE C 110 TYR 0.013 0.001 TYR B 459 ARG 0.009 0.001 ARG B 232 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2562 Ramachandran restraints generated. 1281 Oldfield, 0 Emsley, 1281 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2562 Ramachandran restraints generated. 1281 Oldfield, 0 Emsley, 1281 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 1148 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 64 time to evaluate : 1.581 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 60 MET cc_start: 0.8550 (mmp) cc_final: 0.8349 (mmt) REVERT: B 41 ASP cc_start: 0.7860 (t0) cc_final: 0.7091 (m-30) outliers start: 15 outliers final: 14 residues processed: 74 average time/residue: 0.4664 time to fit residues: 50.5771 Evaluate side-chains 73 residues out of total 1148 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 59 time to evaluate : 1.629 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 CYS Chi-restraints excluded: chain A residue 150 ASP Chi-restraints excluded: chain A residue 250 MET Chi-restraints excluded: chain A residue 322 MET Chi-restraints excluded: chain A residue 365 ASN Chi-restraints excluded: chain A residue 384 ILE Chi-restraints excluded: chain B residue 134 LEU Chi-restraints excluded: chain B residue 238 CYS Chi-restraints excluded: chain B residue 365 ASN Chi-restraints excluded: chain B residue 410 ASN Chi-restraints excluded: chain B residue 576 ASN Chi-restraints excluded: chain C residue 66 PHE Chi-restraints excluded: chain C residue 100 ILE Chi-restraints excluded: chain D residue 88 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 74 optimal weight: 0.7980 chunk 57 optimal weight: 5.9990 chunk 84 optimal weight: 0.0970 chunk 127 optimal weight: 1.9990 chunk 117 optimal weight: 2.9990 chunk 101 optimal weight: 1.9990 chunk 10 optimal weight: 3.9990 chunk 78 optimal weight: 1.9990 chunk 62 optimal weight: 1.9990 chunk 80 optimal weight: 1.9990 chunk 108 optimal weight: 0.8980 overall best weight: 1.1582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8208 moved from start: 0.4899 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 11067 Z= 0.195 Angle : 0.537 6.460 14980 Z= 0.275 Chirality : 0.044 0.195 1799 Planarity : 0.004 0.068 1878 Dihedral : 6.815 59.985 2574 Min Nonbonded Distance : 2.307 Molprobity Statistics. All-atom Clashscore : 4.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.61 % Favored : 95.39 % Rotamer: Outliers : 1.22 % Allowed : 7.23 % Favored : 91.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.30 (0.23), residues: 1281 helix: -1.62 (0.55), residues: 84 sheet: -1.56 (0.36), residues: 166 loop : -0.70 (0.20), residues: 1031 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 474 HIS 0.003 0.001 HIS A 204 PHE 0.011 0.001 PHE B 447 TYR 0.012 0.001 TYR B 459 ARG 0.006 0.000 ARG B 232 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2562 Ramachandran restraints generated. 1281 Oldfield, 0 Emsley, 1281 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2562 Ramachandran restraints generated. 1281 Oldfield, 0 Emsley, 1281 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 76 residues out of total 1148 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 62 time to evaluate : 1.683 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: A 60 MET cc_start: 0.8541 (mmp) cc_final: 0.8335 (mmt) REVERT: A 396 ARG cc_start: 0.8511 (mpt180) cc_final: 0.8304 (mmt-90) REVERT: B 41 ASP cc_start: 0.7905 (t0) cc_final: 0.7163 (m-30) outliers start: 14 outliers final: 14 residues processed: 72 average time/residue: 0.5050 time to fit residues: 51.7414 Evaluate side-chains 72 residues out of total 1148 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 58 time to evaluate : 1.685 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 CYS Chi-restraints excluded: chain A residue 150 ASP Chi-restraints excluded: chain A residue 250 MET Chi-restraints excluded: chain A residue 322 MET Chi-restraints excluded: chain A residue 365 ASN Chi-restraints excluded: chain A residue 384 ILE Chi-restraints excluded: chain B residue 134 LEU Chi-restraints excluded: chain B residue 238 CYS Chi-restraints excluded: chain B residue 365 ASN Chi-restraints excluded: chain B residue 410 ASN Chi-restraints excluded: chain B residue 576 ASN Chi-restraints excluded: chain C residue 66 PHE Chi-restraints excluded: chain C residue 100 ILE Chi-restraints excluded: chain D residue 88 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 31 optimal weight: 2.9990 chunk 93 optimal weight: 0.0570 chunk 14 optimal weight: 4.9990 chunk 28 optimal weight: 6.9990 chunk 101 optimal weight: 1.9990 chunk 42 optimal weight: 5.9990 chunk 104 optimal weight: 0.3980 chunk 12 optimal weight: 1.9990 chunk 18 optimal weight: 5.9990 chunk 89 optimal weight: 2.9990 chunk 5 optimal weight: 1.9990 overall best weight: 1.2904 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4243 r_free = 0.4243 target = 0.131095 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3598 r_free = 0.3598 target = 0.087426 restraints weight = 66245.679| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3668 r_free = 0.3668 target = 0.091558 restraints weight = 32974.706| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 53)----------------| | r_work = 0.3715 r_free = 0.3715 target = 0.094330 restraints weight = 21679.035| |-----------------------------------------------------------------------------| r_work (final): 0.3699 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7788 moved from start: 0.4988 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 11067 Z= 0.211 Angle : 0.540 6.480 14980 Z= 0.277 Chirality : 0.044 0.197 1799 Planarity : 0.004 0.067 1878 Dihedral : 6.791 59.753 2574 Min Nonbonded Distance : 2.308 Molprobity Statistics. All-atom Clashscore : 5.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.39 % Favored : 94.61 % Rotamer: Outliers : 1.31 % Allowed : 7.40 % Favored : 91.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.33 (0.23), residues: 1281 helix: -1.63 (0.55), residues: 84 sheet: -1.69 (0.36), residues: 170 loop : -0.70 (0.20), residues: 1027 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 198 HIS 0.004 0.001 HIS A 204 PHE 0.012 0.001 PHE B 447 TYR 0.012 0.001 TYR B 459 ARG 0.008 0.001 ARG C 83 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4181.00 seconds wall clock time: 73 minutes 43.31 seconds (4423.31 seconds total)