Starting phenix.real_space_refine on Thu Feb 15 16:36:55 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7dd5_30644/02_2024/7dd5_30644_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7dd5_30644/02_2024/7dd5_30644.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7dd5_30644/02_2024/7dd5_30644_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7dd5_30644/02_2024/7dd5_30644_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7dd5_30644/02_2024/7dd5_30644_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7dd5_30644/02_2024/7dd5_30644.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7dd5_30644/02_2024/7dd5_30644.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7dd5_30644/02_2024/7dd5_30644_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7dd5_30644/02_2024/7dd5_30644_updated.pdb" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.002 sd= 0.082 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: 6 Type Number sf(0) Gaussians Ca 6 9.91 5 S 70 5.16 5 Cl 4 4.86 5 C 8303 2.51 5 N 2049 2.21 5 O 2378 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 38": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 50": "OD1" <-> "OD2" Residue "A GLU 59": "OE1" <-> "OE2" Residue "A GLU 79": "OE1" <-> "OE2" Residue "A GLU 109": "OE1" <-> "OE2" Residue "A TYR 161": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 216": "OD1" <-> "OD2" Residue "A ASP 217": "OD1" <-> "OD2" Residue "A ARG 220": "NH1" <-> "NH2" Residue "A PHE 239": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 241": "OE1" <-> "OE2" Residue "A ASP 248": "OD1" <-> "OD2" Residue "A GLU 250": "OE1" <-> "OE2" Residue "A GLU 251": "OE1" <-> "OE2" Residue "A GLU 282": "OE1" <-> "OE2" Residue "A ARG 286": "NH1" <-> "NH2" Residue "A GLU 297": "OE1" <-> "OE2" Residue "A PHE 320": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 331": "NH1" <-> "NH2" Residue "A PHE 347": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 353": "OE1" <-> "OE2" Residue "A GLU 404": "OE1" <-> "OE2" Residue "A ASP 409": "OD1" <-> "OD2" Residue "A PHE 410": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 434": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 474": "OE1" <-> "OE2" Residue "A ASP 477": "OD1" <-> "OD2" Residue "A ASP 483": "OD1" <-> "OD2" Residue "A GLU 506": "OE1" <-> "OE2" Residue "A ARG 550": "NH1" <-> "NH2" Residue "A TYR 572": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 588": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 592": "OE1" <-> "OE2" Residue "A PHE 604": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 611": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 633": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 724": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 732": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 787": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 789": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 800": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 802": "OE1" <-> "OE2" Residue "A TYR 824": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 48": "OD1" <-> "OD2" Residue "B PHE 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 199": "OD1" <-> "OD2" Residue "B GLU 202": "OE1" <-> "OE2" Residue "B ASP 217": "OD1" <-> "OD2" Residue "B ARG 220": "NH1" <-> "NH2" Residue "B GLU 224": "OE1" <-> "OE2" Residue "B ARG 227": "NH1" <-> "NH2" Residue "B GLU 229": "OE1" <-> "OE2" Residue "B PHE 239": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 241": "OE1" <-> "OE2" Residue "B ASP 248": "OD1" <-> "OD2" Residue "B GLU 250": "OE1" <-> "OE2" Residue "B GLU 282": "OE1" <-> "OE2" Residue "B ARG 285": "NH1" <-> "NH2" Residue "B ARG 286": "NH1" <-> "NH2" Residue "B PHE 320": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 331": "NH1" <-> "NH2" Residue "B GLU 332": "OE1" <-> "OE2" Residue "B GLU 354": "OE1" <-> "OE2" Residue "B ASP 409": "OD1" <-> "OD2" Residue "B PHE 410": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 424": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 434": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 443": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 468": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 477": "OD1" <-> "OD2" Residue "B ASP 483": "OD1" <-> "OD2" Residue "B GLU 498": "OE1" <-> "OE2" Residue "B GLU 518": "OE1" <-> "OE2" Residue "B ARG 543": "NH1" <-> "NH2" Residue "B ARG 550": "NH1" <-> "NH2" Residue "B TYR 572": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 586": "OE1" <-> "OE2" Residue "B TYR 588": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 604": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 611": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 624": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 633": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 636": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 648": "OE1" <-> "OE2" Residue "B PHE 687": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 724": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 754": "OE1" <-> "OE2" Residue "B PHE 787": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 789": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 800": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 808": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 836": "OE1" <-> "OE2" Residue "B PHE 845": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 852": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 857": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 861": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 12810 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 6247 Number of conformers: 1 Conformer: "" Number of residues, atoms: 798, 6247 Classifications: {'peptide': 798} Incomplete info: {'truncation_to_alanine': 28} Link IDs: {'PTRANS': 34, 'TRANS': 763} Chain breaks: 3 Unresolved non-hydrogen bonds: 129 Unresolved non-hydrogen angles: 167 Unresolved non-hydrogen dihedrals: 117 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'TYR:plan': 2, 'ASN:plan1': 2, 'TRP:plan': 2, 'HIS:plan': 2, 'PHE:plan': 1, 'GLU:plan': 2, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 82 Chain: "B" Number of atoms: 6269 Number of conformers: 1 Conformer: "" Number of residues, atoms: 799, 6269 Classifications: {'peptide': 799} Incomplete info: {'truncation_to_alanine': 26} Link IDs: {'PTRANS': 33, 'TRANS': 765} Chain breaks: 3 Unresolved non-hydrogen bonds: 111 Unresolved non-hydrogen angles: 142 Unresolved non-hydrogen dihedrals: 98 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'GLN:plan1': 1, 'ASN:plan1': 2, 'TRP:plan': 2, 'HIS:plan': 1, 'PHE:plan': 1, 'GLU:plan': 2, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 67 Chain: "C" 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: "D" 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: "E" 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: "F" 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: 91 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 91 Unusual residues: {' CA': 4, ' CL': 1, 'NAG': 3, 'YP1': 1} Inner-chain residues flagged as termini: ['pdbres="TRP A1108 "'] Classifications: {'peptide': 1, 'undetermined': 9} Modifications used: {'COO': 1} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "B" Number of atoms: 89 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 89 Unusual residues: {' CA': 2, ' CL': 1, 'NAG': 3, 'YP1': 1} Inner-chain residues flagged as termini: ['pdbres="TRP B1107 "'] Classifications: {'peptide': 1, 'undetermined': 7} Modifications used: {'COO': 1} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Time building chain proxies: 7.29, per 1000 atoms: 0.57 Number of scatterers: 12810 At special positions: 0 Unit cell: (100.386, 93.288, 181.506, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Ca 6 19.99 Cl 4 17.00 S 70 16.00 O 2378 8.00 N 2049 7.00 C 8303 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=17, symmetry=0 Simple disulfide: pdb=" SG CYS A 60 " - pdb=" SG CYS A 101 " distance=2.03 Simple disulfide: pdb=" SG CYS A 236 " - pdb=" SG CYS A 560 " distance=2.03 Simple disulfide: pdb=" SG CYS A 358 " - pdb=" SG CYS A 394 " distance=2.03 Simple disulfide: pdb=" SG CYS A 436 " - pdb=" SG CYS A 448 " distance=2.19 Simple disulfide: pdb=" SG CYS A 541 " - pdb=" SG CYS A 561 " distance=2.03 Simple disulfide: pdb=" SG CYS A 545 " - pdb=" SG CYS A 564 " distance=2.03 Simple disulfide: pdb=" SG CYS A 567 " - pdb=" SG CYS A 581 " distance=1.82 Simple disulfide: pdb=" SG CYS A 584 " - pdb=" SG CYS A 597 " distance=2.03 Simple disulfide: pdb=" SG CYS A 676 " - pdb=" SG CYS A 764 " distance=2.03 Simple disulfide: pdb=" SG CYS B 60 " - pdb=" SG CYS B 101 " distance=2.03 Simple disulfide: pdb=" SG CYS B 236 " - pdb=" SG CYS B 560 " distance=2.03 Simple disulfide: pdb=" SG CYS B 358 " - pdb=" SG CYS B 394 " distance=2.03 Simple disulfide: pdb=" SG CYS B 436 " - pdb=" SG CYS B 448 " distance=2.03 Simple disulfide: pdb=" SG CYS B 541 " - pdb=" SG CYS B 561 " distance=2.04 Simple disulfide: pdb=" SG CYS B 567 " - pdb=" SG CYS B 581 " distance=2.03 Simple disulfide: pdb=" SG CYS B 584 " - pdb=" SG CYS B 597 " distance=2.03 Simple disulfide: pdb=" SG CYS B 676 " - pdb=" SG CYS B 764 " distance=2.03 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=1, symmetry=0 Links applied BETA1-4 " NAG C 1 " - " NAG C 2 " " NAG D 1 " - " NAG D 2 " " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " NAG-ASN " NAG A1105 " - " ASN A 287 " " NAG A1106 " - " ASN A 399 " " NAG A1107 " - " ASN A 467 " " NAG B1104 " - " ASN B 287 " " NAG B1105 " - " ASN B 399 " " NAG B1106 " - " ASN B 467 " " NAG C 1 " - " ASN A 487 " " NAG D 1 " - " ASN A 540 " " NAG E 1 " - " ASN B 487 " " NAG F 1 " - " ASN B 540 " Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 5.42 Conformation dependent library (CDL) restraints added in 2.3 seconds 3162 Ramachandran restraints generated. 1581 Oldfield, 0 Emsley, 1581 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3012 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 51 helices and 14 sheets defined 43.7% alpha, 9.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.39 Creating SS restraints... Processing helix chain 'A' and resid 65 through 83 Processing helix chain 'A' and resid 104 through 116 Processing helix chain 'A' and resid 148 through 160 removed outlier: 3.775A pdb=" N LEU A 156 " --> pdb=" O ALA A 152 " (cutoff:3.500A) removed outlier: 4.076A pdb=" N LEU A 159 " --> pdb=" O ASN A 155 " (cutoff:3.500A) removed outlier: 4.204A pdb=" N PHE A 160 " --> pdb=" O LEU A 156 " (cutoff:3.500A) Processing helix chain 'A' and resid 172 through 175 removed outlier: 3.512A pdb=" N SER A 175 " --> pdb=" O ARG A 172 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 172 through 175' Processing helix chain 'A' and resid 191 through 203 Processing helix chain 'A' and resid 219 through 232 Processing helix chain 'A' and resid 249 through 260 Processing helix chain 'A' and resid 273 through 286 Proline residue: A 278 - end of helix Processing helix chain 'A' and resid 308 through 314 removed outlier: 4.022A pdb=" N VAL A 313 " --> pdb=" O GLU A 309 " (cutoff:3.500A) Processing helix chain 'A' and resid 331 through 336 removed outlier: 4.061A pdb=" N LYS A 336 " --> pdb=" O GLU A 332 " (cutoff:3.500A) Processing helix chain 'A' and resid 348 through 356 Processing helix chain 'A' and resid 400 through 402 No H-bonds generated for 'chain 'A' and resid 400 through 402' Processing helix chain 'A' and resid 415 through 434 Processing helix chain 'A' and resid 444 through 446 No H-bonds generated for 'chain 'A' and resid 444 through 446' Processing helix chain 'A' and resid 456 through 464 Processing helix chain 'A' and resid 524 through 526 No H-bonds generated for 'chain 'A' and resid 524 through 526' Processing helix chain 'A' and resid 529 through 531 No H-bonds generated for 'chain 'A' and resid 529 through 531' Processing helix chain 'A' and resid 610 through 636 Processing helix chain 'A' and resid 640 through 643 No H-bonds generated for 'chain 'A' and resid 640 through 643' Processing helix chain 'A' and resid 647 through 667 removed outlier: 4.112A pdb=" N SER A 664 " --> pdb=" O CYS A 660 " (cutoff:3.500A) removed outlier: 4.992A pdb=" N LEU A 665 " --> pdb=" O PHE A 661 " (cutoff:3.500A) removed outlier: 4.536A pdb=" N PHE A 666 " --> pdb=" O SER A 662 " (cutoff:3.500A) removed outlier: 4.559A pdb=" N PHE A 667 " --> pdb=" O SER A 663 " (cutoff:3.500A) Processing helix chain 'A' and resid 673 through 696 Proline residue: A 681 - end of helix Processing helix chain 'A' and resid 701 through 705 Processing helix chain 'A' and resid 712 through 716 Processing helix chain 'A' and resid 720 through 744 removed outlier: 5.296A pdb=" N THR A 731 " --> pdb=" O PHE A 728 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N THR A 744 " --> pdb=" O TRP A 741 " (cutoff:3.500A) Processing helix chain 'A' and resid 769 through 792 Processing helix chain 'A' and resid 802 through 826 Proline residue: A 822 - end of helix Processing helix chain 'A' and resid 829 through 860 removed outlier: 3.880A pdb=" N SER A 833 " --> pdb=" O GLY A 829 " (cutoff:3.500A) removed outlier: 5.271A pdb=" N ASN A 854 " --> pdb=" O CYS A 850 " (cutoff:3.500A) removed outlier: 4.956A pdb=" N LYS A 855 " --> pdb=" O ILE A 851 " (cutoff:3.500A) Processing helix chain 'B' and resid 65 through 83 Processing helix chain 'B' and resid 104 through 114 Processing helix chain 'B' and resid 116 through 121 removed outlier: 4.195A pdb=" N ASP B 121 " --> pdb=" O GLN B 117 " (cutoff:3.500A) Processing helix chain 'B' and resid 147 through 157 removed outlier: 3.994A pdb=" N LEU B 156 " --> pdb=" O ALA B 152 " (cutoff:3.500A) Processing helix chain 'B' and resid 172 through 175 removed outlier: 3.554A pdb=" N SER B 175 " --> pdb=" O ARG B 172 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 172 through 175' Processing helix chain 'B' and resid 191 through 203 Processing helix chain 'B' and resid 219 through 232 Processing helix chain 'B' and resid 249 through 260 Processing helix chain 'B' and resid 273 through 286 Proline residue: B 278 - end of helix Processing helix chain 'B' and resid 297 through 300 No H-bonds generated for 'chain 'B' and resid 297 through 300' Processing helix chain 'B' and resid 310 through 312 No H-bonds generated for 'chain 'B' and resid 310 through 312' Processing helix chain 'B' and resid 330 through 336 removed outlier: 3.678A pdb=" N LYS B 336 " --> pdb=" O GLU B 332 " (cutoff:3.500A) Processing helix chain 'B' and resid 348 through 355 Processing helix chain 'B' and resid 416 through 434 Processing helix chain 'B' and resid 456 through 464 Processing helix chain 'B' and resid 610 through 635 Processing helix chain 'B' and resid 647 through 667 removed outlier: 3.865A pdb=" N SER B 664 " --> pdb=" O CYS B 660 " (cutoff:3.500A) removed outlier: 4.694A pdb=" N LEU B 665 " --> pdb=" O PHE B 661 " (cutoff:3.500A) removed outlier: 4.447A pdb=" N PHE B 666 " --> pdb=" O SER B 662 " (cutoff:3.500A) removed outlier: 4.837A pdb=" N PHE B 667 " --> pdb=" O SER B 663 " (cutoff:3.500A) Processing helix chain 'B' and resid 673 through 696 Proline residue: B 681 - end of helix Processing helix chain 'B' and resid 701 through 705 Processing helix chain 'B' and resid 712 through 715 No H-bonds generated for 'chain 'B' and resid 712 through 715' Processing helix chain 'B' and resid 720 through 743 removed outlier: 5.651A pdb=" N THR B 731 " --> pdb=" O PHE B 728 " (cutoff:3.500A) Processing helix chain 'B' and resid 769 through 793 removed outlier: 3.561A pdb=" N SER B 793 " --> pdb=" O PHE B 789 " (cutoff:3.500A) Processing helix chain 'B' and resid 802 through 826 Proline residue: B 822 - end of helix Processing helix chain 'B' and resid 829 through 861 removed outlier: 3.778A pdb=" N SER B 833 " --> pdb=" O GLY B 829 " (cutoff:3.500A) removed outlier: 5.018A pdb=" N ASN B 854 " --> pdb=" O CYS B 850 " (cutoff:3.500A) removed outlier: 5.136A pdb=" N LYS B 855 " --> pdb=" O ILE B 851 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 26 through 28 removed outlier: 6.056A pdb=" N ILE A 32 " --> pdb=" O GLY A 94 " (cutoff:3.500A) removed outlier: 7.486A pdb=" N ARG A 96 " --> pdb=" O ILE A 32 " (cutoff:3.500A) removed outlier: 6.751A pdb=" N LEU A 34 " --> pdb=" O ARG A 96 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 140 through 142 Processing sheet with id= C, first strand: chain 'A' and resid 240 through 243 removed outlier: 9.377A pdb=" N GLU A 241 " --> pdb=" O VAL A 209 " (cutoff:3.500A) removed outlier: 6.668A pdb=" N THR A 211 " --> pdb=" O GLU A 241 " (cutoff:3.500A) removed outlier: 7.996A pdb=" N ILE A 243 " --> pdb=" O THR A 211 " (cutoff:3.500A) removed outlier: 6.419A pdb=" N ALA A 213 " --> pdb=" O ILE A 243 " (cutoff:3.500A) removed outlier: 6.457A pdb=" N VAL A 266 " --> pdb=" O GLY A 210 " (cutoff:3.500A) removed outlier: 7.889A pdb=" N ILE A 212 " --> pdb=" O VAL A 266 " (cutoff:3.500A) removed outlier: 6.199A pdb=" N VAL A 268 " --> pdb=" O ILE A 212 " (cutoff:3.500A) removed outlier: 7.994A pdb=" N ALA A 214 " --> pdb=" O VAL A 268 " (cutoff:3.500A) removed outlier: 7.793A pdb=" N PHE A 270 " --> pdb=" O ALA A 214 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N ILE A 292 " --> pdb=" O ILE A 267 " (cutoff:3.500A) removed outlier: 7.201A pdb=" N VAL A 269 " --> pdb=" O ILE A 292 " (cutoff:3.500A) removed outlier: 6.015A pdb=" N LEU A 294 " --> pdb=" O VAL A 269 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N PHE A 320 " --> pdb=" O ALA A 295 " (cutoff:3.500A) removed outlier: 5.184A pdb=" N THR A 317 " --> pdb=" O TRP A 493 " (cutoff:3.500A) removed outlier: 6.004A pdb=" N ASN A 492 " --> pdb=" O GLU A 506 " (cutoff:3.500A) removed outlier: 5.571A pdb=" N GLU A 506 " --> pdb=" O ASN A 492 " (cutoff:3.500A) removed outlier: 6.631A pdb=" N HIS A 494 " --> pdb=" O PHE A 504 " (cutoff:3.500A) removed outlier: 4.876A pdb=" N PHE A 504 " --> pdb=" O HIS A 494 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 467 through 470 Processing sheet with id= E, first strand: chain 'A' and resid 549 through 553 Processing sheet with id= F, first strand: chain 'A' and resid 588 through 590 Processing sheet with id= G, first strand: chain 'A' and resid 601 through 603 removed outlier: 4.176A pdb=" N ILE A 762 " --> pdb=" O GLU A 603 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'B' and resid 26 through 28 removed outlier: 5.977A pdb=" N ILE B 32 " --> pdb=" O GLY B 94 " (cutoff:3.500A) removed outlier: 7.540A pdb=" N ARG B 96 " --> pdb=" O ILE B 32 " (cutoff:3.500A) removed outlier: 6.696A pdb=" N LEU B 34 " --> pdb=" O ARG B 96 " (cutoff:3.500A) removed outlier: 7.583A pdb=" N PHE B 98 " --> pdb=" O LEU B 34 " (cutoff:3.500A) removed outlier: 6.225A pdb=" N GLY B 36 " --> pdb=" O PHE B 98 " (cutoff:3.500A) removed outlier: 7.554A pdb=" N GLY B 35 " --> pdb=" O ILE B 139 " (cutoff:3.500A) removed outlier: 4.289A pdb=" N VAL B 141 " --> pdb=" O GLY B 35 " (cutoff:3.500A) removed outlier: 7.214A pdb=" N LEU B 37 " --> pdb=" O VAL B 141 " (cutoff:3.500A) removed outlier: 5.042A pdb=" N GLY B 143 " --> pdb=" O LEU B 37 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'B' and resid 164 through 166 Processing sheet with id= J, first strand: chain 'B' and resid 240 through 243 removed outlier: 9.598A pdb=" N GLU B 241 " --> pdb=" O VAL B 209 " (cutoff:3.500A) removed outlier: 6.832A pdb=" N THR B 211 " --> pdb=" O GLU B 241 " (cutoff:3.500A) removed outlier: 8.253A pdb=" N ILE B 243 " --> pdb=" O THR B 211 " (cutoff:3.500A) removed outlier: 6.457A pdb=" N ALA B 213 " --> pdb=" O ILE B 243 " (cutoff:3.500A) removed outlier: 6.443A pdb=" N VAL B 266 " --> pdb=" O GLY B 210 " (cutoff:3.500A) removed outlier: 7.827A pdb=" N ILE B 212 " --> pdb=" O VAL B 266 " (cutoff:3.500A) removed outlier: 6.198A pdb=" N VAL B 268 " --> pdb=" O ILE B 212 " (cutoff:3.500A) removed outlier: 8.009A pdb=" N ALA B 214 " --> pdb=" O VAL B 268 " (cutoff:3.500A) removed outlier: 7.369A pdb=" N PHE B 270 " --> pdb=" O ALA B 214 " (cutoff:3.500A) removed outlier: 6.412A pdb=" N ILE B 292 " --> pdb=" O ILE B 267 " (cutoff:3.500A) removed outlier: 7.302A pdb=" N VAL B 269 " --> pdb=" O ILE B 292 " (cutoff:3.500A) removed outlier: 6.387A pdb=" N LEU B 294 " --> pdb=" O VAL B 269 " (cutoff:3.500A) No H-bonds generated for sheet with id= J Processing sheet with id= K, first strand: chain 'B' and resid 318 through 322 removed outlier: 6.231A pdb=" N ASN B 492 " --> pdb=" O GLU B 506 " (cutoff:3.500A) removed outlier: 5.204A pdb=" N GLU B 506 " --> pdb=" O ASN B 492 " (cutoff:3.500A) removed outlier: 6.765A pdb=" N HIS B 494 " --> pdb=" O PHE B 504 " (cutoff:3.500A) removed outlier: 5.034A pdb=" N PHE B 504 " --> pdb=" O HIS B 494 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'B' and resid 467 through 469 Processing sheet with id= M, first strand: chain 'B' and resid 549 through 552 Processing sheet with id= N, first strand: chain 'B' and resid 748 through 752 523 hydrogen bonds defined for protein. 1422 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 4.32 Time building geometry restraints manager: 5.80 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.13 - 1.27: 2068 1.27 - 1.41: 3464 1.41 - 1.55: 7505 1.55 - 1.69: 0 1.69 - 1.83: 88 Bond restraints: 13125 Sorted by residual: bond pdb=" C7 NAG A1107 " pdb=" N2 NAG A1107 " ideal model delta sigma weight residual 1.346 1.454 -0.108 2.00e-02 2.50e+03 2.93e+01 bond pdb=" C7 NAG B1104 " pdb=" N2 NAG B1104 " ideal model delta sigma weight residual 1.346 1.453 -0.107 2.00e-02 2.50e+03 2.84e+01 bond pdb=" C7 NAG B1106 " pdb=" N2 NAG B1106 " ideal model delta sigma weight residual 1.346 1.452 -0.106 2.00e-02 2.50e+03 2.81e+01 bond pdb=" C7 NAG C 1 " pdb=" N2 NAG C 1 " ideal model delta sigma weight residual 1.346 1.452 -0.106 2.00e-02 2.50e+03 2.80e+01 bond pdb=" C7 NAG B1105 " pdb=" N2 NAG B1105 " ideal model delta sigma weight residual 1.346 1.452 -0.106 2.00e-02 2.50e+03 2.80e+01 ... (remaining 13120 not shown) Histogram of bond angle deviations from ideal: 98.67 - 114.92: 8159 114.92 - 131.16: 9622 131.16 - 147.41: 47 147.41 - 163.66: 0 163.66 - 179.91: 2 Bond angle restraints: 17830 Sorted by residual: angle pdb=" N LYS B 697 " pdb=" CA LYS B 697 " pdb=" C LYS B 697 " ideal model delta sigma weight residual 113.20 108.35 4.85 1.36e+00 5.41e-01 1.27e+01 angle pdb=" CA ARG A 700 " pdb=" C ARG A 700 " pdb=" O ARG A 700 " ideal model delta sigma weight residual 122.13 118.28 3.85 1.13e+00 7.83e-01 1.16e+01 angle pdb=" C ALA A 144 " pdb=" N THR A 145 " pdb=" CA THR A 145 " ideal model delta sigma weight residual 121.54 128.03 -6.49 1.91e+00 2.74e-01 1.16e+01 angle pdb=" C3 NAG C 1 " pdb=" C4 NAG C 1 " pdb=" C5 NAG C 1 " ideal model delta sigma weight residual 109.38 119.39 -10.01 3.00e+00 1.11e-01 1.11e+01 angle pdb=" N VAL A 507 " pdb=" CA VAL A 507 " pdb=" C VAL A 507 " ideal model delta sigma weight residual 113.71 110.56 3.15 9.50e-01 1.11e+00 1.10e+01 ... (remaining 17825 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.79: 7226 23.79 - 47.58: 547 47.58 - 71.37: 77 71.37 - 95.16: 27 95.16 - 118.96: 11 Dihedral angle restraints: 7888 sinusoidal: 3238 harmonic: 4650 Sorted by residual: dihedral pdb=" CB CYS A 436 " pdb=" SG CYS A 436 " pdb=" SG CYS A 448 " pdb=" CB CYS A 448 " ideal model delta sinusoidal sigma weight residual 93.00 -178.79 -88.21 1 1.00e+01 1.00e-02 9.30e+01 dihedral pdb=" CB CYS A 545 " pdb=" SG CYS A 545 " pdb=" SG CYS A 564 " pdb=" CB CYS A 564 " ideal model delta sinusoidal sigma weight residual -86.00 -157.76 71.76 1 1.00e+01 1.00e-02 6.59e+01 dihedral pdb=" CB CYS B 541 " pdb=" SG CYS B 541 " pdb=" SG CYS B 561 " pdb=" CB CYS B 561 " ideal model delta sinusoidal sigma weight residual -86.00 -52.00 -34.00 1 1.00e+01 1.00e-02 1.64e+01 ... (remaining 7885 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.111: 1956 0.111 - 0.221: 65 0.221 - 0.332: 1 0.332 - 0.442: 0 0.442 - 0.553: 1 Chirality restraints: 2023 Sorted by residual: chirality pdb=" C1 NAG C 1 " pdb=" ND2 ASN A 487 " pdb=" C2 NAG C 1 " pdb=" O5 NAG C 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.85 -0.55 2.00e-01 2.50e+01 7.65e+00 chirality pdb=" C1 NAG A1107 " pdb=" ND2 ASN A 467 " pdb=" C2 NAG A1107 " pdb=" O5 NAG A1107 " both_signs ideal model delta sigma weight residual False -2.40 -2.15 -0.25 2.00e-01 2.50e+01 1.55e+00 chirality pdb=" C2 NAG C 1 " pdb=" C1 NAG C 1 " pdb=" C3 NAG C 1 " pdb=" N2 NAG C 1 " both_signs ideal model delta sigma weight residual False -2.49 -2.69 0.20 2.00e-01 2.50e+01 9.98e-01 ... (remaining 2020 not shown) Planarity restraints: 2258 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA VAL B 727 " 0.010 2.00e-02 2.50e+03 1.99e-02 3.95e+00 pdb=" C VAL B 727 " -0.034 2.00e-02 2.50e+03 pdb=" O VAL B 727 " 0.013 2.00e-02 2.50e+03 pdb=" N PHE B 728 " 0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLU A 670 " -0.026 5.00e-02 4.00e+02 3.86e-02 2.38e+00 pdb=" N PRO A 671 " 0.067 5.00e-02 4.00e+02 pdb=" CA PRO A 671 " -0.020 5.00e-02 4.00e+02 pdb=" CD PRO A 671 " -0.021 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR B 405 " -0.025 5.00e-02 4.00e+02 3.74e-02 2.23e+00 pdb=" N PRO B 406 " 0.065 5.00e-02 4.00e+02 pdb=" CA PRO B 406 " -0.019 5.00e-02 4.00e+02 pdb=" CD PRO B 406 " -0.021 5.00e-02 4.00e+02 ... (remaining 2255 not shown) Histogram of nonbonded interaction distances: 1.99 - 2.57: 183 2.57 - 3.15: 11304 3.15 - 3.73: 19686 3.73 - 4.32: 27146 4.32 - 4.90: 43520 Nonbonded interactions: 101839 Sorted by model distance: nonbonded pdb=" OE1 GLU A 836 " pdb=" O2 YP1 A1109 " model vdw 1.985 2.440 nonbonded pdb=" OE2 GLU B 836 " pdb=" O2 YP1 B1108 " model vdw 2.080 2.440 nonbonded pdb=" CD2 TYR A 824 " pdb=" CG1 VAL A 832 " model vdw 2.138 3.760 nonbonded pdb=" N GLU B 498 " pdb=" OE1 GLU B 498 " model vdw 2.146 2.520 nonbonded pdb=" OG1 THR A 395 " pdb=" OD1 ASP A 397 " model vdw 2.188 2.440 ... (remaining 101834 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 'A' and (resid 22 through 119 or resid 136 through 600 or (resid 601 and \ (name N or name CA or name C or name O or name CB )) or resid 602 through 867 or \ resid 1101 through 1103 or resid 1105 through 1106 or resid 1108 through 1109)) \ selection = (chain 'B' and (resid 22 through 119 or resid 136 through 358 or (resid 359 and \ (name N or name CA or name C or name O or name CB )) or resid 392 through 867 or \ resid 1101 through 1103 or resid 1105 through 1108)) } ncs_group { reference = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.50 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.130 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 5.150 Check model and map are aligned: 0.200 Set scattering table: 0.110 Process input model: 38.430 Find NCS groups from input model: 0.790 Set up NCS constraints: 0.080 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:2.950 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 48.850 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7186 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.108 13125 Z= 0.534 Angle : 0.735 10.015 17830 Z= 0.409 Chirality : 0.048 0.553 2023 Planarity : 0.004 0.039 2248 Dihedral : 17.456 118.955 4825 Min Nonbonded Distance : 1.985 Molprobity Statistics. All-atom Clashscore : 17.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.87 % Favored : 95.13 % Rotamer: Outliers : 0.15 % Allowed : 20.28 % Favored : 79.57 % 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: -3.16 (0.18), residues: 1581 helix: -1.13 (0.17), residues: 706 sheet: -2.81 (0.34), residues: 180 loop : -2.90 (0.19), residues: 695 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 299 HIS 0.004 0.001 HIS A 753 PHE 0.012 0.001 PHE A 667 TYR 0.011 0.001 TYR B 857 ARG 0.003 0.000 ARG B 265 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3162 Ramachandran restraints generated. 1581 Oldfield, 0 Emsley, 1581 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3162 Ramachandran restraints generated. 1581 Oldfield, 0 Emsley, 1581 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 220 residues out of total 1400 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 218 time to evaluate : 1.495 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 229 GLU cc_start: 0.7383 (mm-30) cc_final: 0.6644 (mt-10) REVERT: A 251 GLU cc_start: 0.8330 (mt-10) cc_final: 0.7917 (mp0) REVERT: A 254 GLN cc_start: 0.8319 (mt0) cc_final: 0.8002 (tp40) REVERT: A 587 ASP cc_start: 0.9138 (m-30) cc_final: 0.8404 (m-30) REVERT: A 588 TYR cc_start: 0.9036 (m-80) cc_final: 0.8750 (m-80) REVERT: A 752 ASN cc_start: 0.8897 (t0) cc_final: 0.8558 (t0) REVERT: A 759 ILE cc_start: 0.7590 (mt) cc_final: 0.7142 (mt) REVERT: A 820 PHE cc_start: 0.7593 (t80) cc_final: 0.7350 (t80) REVERT: B 52 LYS cc_start: 0.9167 (mtmt) cc_final: 0.8859 (mtpp) REVERT: B 202 GLU cc_start: 0.7921 (tt0) cc_final: 0.7547 (tt0) REVERT: B 205 ARG cc_start: 0.7829 (mtt90) cc_final: 0.7286 (mmt180) REVERT: B 229 GLU cc_start: 0.7303 (mm-30) cc_final: 0.6992 (mm-30) REVERT: B 248 ASP cc_start: 0.8255 (m-30) cc_final: 0.8032 (m-30) REVERT: B 253 GLN cc_start: 0.8081 (mt0) cc_final: 0.7725 (tt0) REVERT: B 498 GLU cc_start: 0.8633 (pm20) cc_final: 0.8426 (pm20) REVERT: B 499 ASP cc_start: 0.8501 (t70) cc_final: 0.8208 (m-30) REVERT: B 753 HIS cc_start: 0.8720 (p-80) cc_final: 0.8298 (p-80) REVERT: B 762 ILE cc_start: 0.8629 (mt) cc_final: 0.8337 (tp) outliers start: 2 outliers final: 1 residues processed: 220 average time/residue: 0.2686 time to fit residues: 83.3975 Evaluate side-chains 128 residues out of total 1400 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 127 time to evaluate : 1.528 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 824 TYR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 133 optimal weight: 4.9990 chunk 119 optimal weight: 0.9980 chunk 66 optimal weight: 5.9990 chunk 40 optimal weight: 2.9990 chunk 80 optimal weight: 2.9990 chunk 63 optimal weight: 3.9990 chunk 123 optimal weight: 0.8980 chunk 47 optimal weight: 1.9990 chunk 75 optimal weight: 7.9990 chunk 92 optimal weight: 1.9990 chunk 143 optimal weight: 30.0000 overall best weight: 1.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 118 ASN A 193 GLN A 412 HIS A 593 ASN A 646 ASN ** A 753 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 117 GLN B 179 GLN B 193 GLN B 245 GLN B 260 GLN B 335 GLN B 465 HIS B 765 HIS Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7255 moved from start: 0.1702 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 13125 Z= 0.276 Angle : 0.664 10.938 17830 Z= 0.322 Chirality : 0.048 0.689 2023 Planarity : 0.004 0.042 2248 Dihedral : 11.662 109.409 2005 Min Nonbonded Distance : 2.216 Molprobity Statistics. All-atom Clashscore : 12.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.81 % Favored : 95.19 % Rotamer: Outliers : 4.90 % Allowed : 20.06 % Favored : 75.04 % 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: -1.93 (0.20), residues: 1581 helix: -0.12 (0.18), residues: 714 sheet: -2.39 (0.37), residues: 172 loop : -2.21 (0.22), residues: 695 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 208 HIS 0.005 0.001 HIS B 765 PHE 0.022 0.001 PHE A 661 TYR 0.015 0.001 TYR B 588 ARG 0.005 0.000 ARG A 312 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3162 Ramachandran restraints generated. 1581 Oldfield, 0 Emsley, 1581 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3162 Ramachandran restraints generated. 1581 Oldfield, 0 Emsley, 1581 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 199 residues out of total 1400 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 133 time to evaluate : 1.524 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 91 MET cc_start: 0.8726 (tpp) cc_final: 0.8173 (mmt) REVERT: A 191 GLU cc_start: 0.7832 (mm-30) cc_final: 0.7417 (mm-30) REVERT: A 229 GLU cc_start: 0.7181 (mm-30) cc_final: 0.6736 (mt-10) REVERT: A 516 LYS cc_start: 0.9074 (tptp) cc_final: 0.8793 (tppt) REVERT: A 588 TYR cc_start: 0.9133 (m-80) cc_final: 0.8862 (m-80) REVERT: A 752 ASN cc_start: 0.9154 (t0) cc_final: 0.8901 (t0) REVERT: A 810 MET cc_start: 0.8041 (mtm) cc_final: 0.7120 (ttp) REVERT: A 814 PHE cc_start: 0.8173 (m-80) cc_final: 0.7193 (m-80) REVERT: B 52 LYS cc_start: 0.9174 (mtmt) cc_final: 0.8887 (mtpp) REVERT: B 202 GLU cc_start: 0.8074 (tt0) cc_final: 0.7727 (tt0) REVERT: B 205 ARG cc_start: 0.7907 (mtt90) cc_final: 0.7495 (mmt180) REVERT: B 248 ASP cc_start: 0.8258 (m-30) cc_final: 0.8027 (m-30) REVERT: B 491 ILE cc_start: 0.8902 (OUTLIER) cc_final: 0.8525 (tp) REVERT: B 564 CYS cc_start: 0.8802 (OUTLIER) cc_final: 0.8421 (m) outliers start: 66 outliers final: 29 residues processed: 188 average time/residue: 0.2315 time to fit residues: 66.2408 Evaluate side-chains 146 residues out of total 1400 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 115 time to evaluate : 1.307 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 LYS Chi-restraints excluded: chain A residue 171 SER Chi-restraints excluded: chain A residue 200 ILE Chi-restraints excluded: chain A residue 296 SER Chi-restraints excluded: chain A residue 317 THR Chi-restraints excluded: chain A residue 606 SER Chi-restraints excluded: chain A residue 608 THR Chi-restraints excluded: chain A residue 611 PHE Chi-restraints excluded: chain A residue 639 THR Chi-restraints excluded: chain A residue 692 SER Chi-restraints excluded: chain A residue 694 ILE Chi-restraints excluded: chain A residue 782 LEU Chi-restraints excluded: chain A residue 838 ILE Chi-restraints excluded: chain B residue 142 VAL Chi-restraints excluded: chain B residue 270 PHE Chi-restraints excluded: chain B residue 289 THR Chi-restraints excluded: chain B residue 301 SER Chi-restraints excluded: chain B residue 313 VAL Chi-restraints excluded: chain B residue 317 THR Chi-restraints excluded: chain B residue 416 SER Chi-restraints excluded: chain B residue 491 ILE Chi-restraints excluded: chain B residue 564 CYS Chi-restraints excluded: chain B residue 641 ILE Chi-restraints excluded: chain B residue 691 ILE Chi-restraints excluded: chain B residue 696 VAL Chi-restraints excluded: chain B residue 725 LEU Chi-restraints excluded: chain B residue 755 LEU Chi-restraints excluded: chain B residue 765 HIS Chi-restraints excluded: chain B residue 795 LYS Chi-restraints excluded: chain B residue 814 PHE Chi-restraints excluded: chain B residue 820 PHE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 79 optimal weight: 7.9990 chunk 44 optimal weight: 5.9990 chunk 119 optimal weight: 5.9990 chunk 97 optimal weight: 4.9990 chunk 39 optimal weight: 0.7980 chunk 143 optimal weight: 0.5980 chunk 155 optimal weight: 9.9990 chunk 128 optimal weight: 0.5980 chunk 142 optimal weight: 20.0000 chunk 49 optimal weight: 4.9990 chunk 115 optimal weight: 0.7980 overall best weight: 1.5582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 492 ASN A 494 HIS ** A 753 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 24 GLN B 335 GLN B 765 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7262 moved from start: 0.2181 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 13125 Z= 0.240 Angle : 0.642 12.045 17830 Z= 0.307 Chirality : 0.047 0.694 2023 Planarity : 0.004 0.046 2248 Dihedral : 9.961 107.435 2003 Min Nonbonded Distance : 2.208 Molprobity Statistics. All-atom Clashscore : 10.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.17 % Favored : 95.83 % Rotamer: Outliers : 4.61 % Allowed : 20.06 % Favored : 75.33 % 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: -1.47 (0.21), residues: 1581 helix: 0.29 (0.19), residues: 719 sheet: -2.06 (0.36), residues: 187 loop : -2.03 (0.23), residues: 675 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 208 HIS 0.005 0.001 HIS B 462 PHE 0.022 0.001 PHE A 661 TYR 0.013 0.001 TYR B 420 ARG 0.005 0.000 ARG A 312 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3162 Ramachandran restraints generated. 1581 Oldfield, 0 Emsley, 1581 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3162 Ramachandran restraints generated. 1581 Oldfield, 0 Emsley, 1581 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 1400 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 122 time to evaluate : 1.479 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 23 ASN cc_start: 0.6978 (t0) cc_final: 0.6583 (t0) REVERT: A 91 MET cc_start: 0.8698 (tpp) cc_final: 0.8207 (mmm) REVERT: A 191 GLU cc_start: 0.7818 (mm-30) cc_final: 0.7300 (mm-30) REVERT: A 229 GLU cc_start: 0.7168 (mm-30) cc_final: 0.6732 (mt-10) REVERT: A 588 TYR cc_start: 0.9163 (m-80) cc_final: 0.8858 (m-80) REVERT: A 814 PHE cc_start: 0.8231 (m-80) cc_final: 0.7693 (m-80) REVERT: B 52 LYS cc_start: 0.9183 (mtmt) cc_final: 0.8908 (mtpp) REVERT: B 202 GLU cc_start: 0.8090 (tt0) cc_final: 0.7681 (tt0) REVERT: B 205 ARG cc_start: 0.7862 (mtt90) cc_final: 0.7277 (mmt180) REVERT: B 248 ASP cc_start: 0.8314 (m-30) cc_final: 0.8037 (m-30) REVERT: B 491 ILE cc_start: 0.8901 (OUTLIER) cc_final: 0.8588 (tp) REVERT: B 564 CYS cc_start: 0.8817 (OUTLIER) cc_final: 0.8441 (m) REVERT: B 607 TRP cc_start: 0.7750 (m100) cc_final: 0.7541 (m100) outliers start: 62 outliers final: 46 residues processed: 173 average time/residue: 0.2187 time to fit residues: 58.0293 Evaluate side-chains 160 residues out of total 1400 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 112 time to evaluate : 1.409 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 LYS Chi-restraints excluded: chain A residue 169 SER Chi-restraints excluded: chain A residue 171 SER Chi-restraints excluded: chain A residue 184 LEU Chi-restraints excluded: chain A residue 200 ILE Chi-restraints excluded: chain A residue 296 SER Chi-restraints excluded: chain A residue 301 SER Chi-restraints excluded: chain A residue 317 THR Chi-restraints excluded: chain A residue 403 VAL Chi-restraints excluded: chain A residue 425 SER Chi-restraints excluded: chain A residue 587 ASP Chi-restraints excluded: chain A residue 606 SER Chi-restraints excluded: chain A residue 608 THR Chi-restraints excluded: chain A residue 611 PHE Chi-restraints excluded: chain A residue 639 THR Chi-restraints excluded: chain A residue 694 ILE Chi-restraints excluded: chain A residue 782 LEU Chi-restraints excluded: chain A residue 838 ILE Chi-restraints excluded: chain B residue 87 LEU Chi-restraints excluded: chain B residue 142 VAL Chi-restraints excluded: chain B residue 171 SER Chi-restraints excluded: chain B residue 231 GLU Chi-restraints excluded: chain B residue 270 PHE Chi-restraints excluded: chain B residue 272 SER Chi-restraints excluded: chain B residue 289 THR Chi-restraints excluded: chain B residue 296 SER Chi-restraints excluded: chain B residue 301 SER Chi-restraints excluded: chain B residue 313 VAL Chi-restraints excluded: chain B residue 317 THR Chi-restraints excluded: chain B residue 352 TRP Chi-restraints excluded: chain B residue 416 SER Chi-restraints excluded: chain B residue 491 ILE Chi-restraints excluded: chain B residue 495 LEU Chi-restraints excluded: chain B residue 512 VAL Chi-restraints excluded: chain B residue 559 THR Chi-restraints excluded: chain B residue 564 CYS Chi-restraints excluded: chain B residue 590 SER Chi-restraints excluded: chain B residue 641 ILE Chi-restraints excluded: chain B residue 676 CYS Chi-restraints excluded: chain B residue 696 VAL Chi-restraints excluded: chain B residue 725 LEU Chi-restraints excluded: chain B residue 755 LEU Chi-restraints excluded: chain B residue 762 ILE Chi-restraints excluded: chain B residue 765 HIS Chi-restraints excluded: chain B residue 793 SER Chi-restraints excluded: chain B residue 795 LYS Chi-restraints excluded: chain B residue 814 PHE Chi-restraints excluded: chain B residue 860 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 142 optimal weight: 3.9990 chunk 108 optimal weight: 0.1980 chunk 74 optimal weight: 4.9990 chunk 15 optimal weight: 0.5980 chunk 68 optimal weight: 8.9990 chunk 96 optimal weight: 3.9990 chunk 144 optimal weight: 5.9990 chunk 152 optimal weight: 5.9990 chunk 75 optimal weight: 4.9990 chunk 136 optimal weight: 3.9990 chunk 41 optimal weight: 0.8980 overall best weight: 1.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 752 ASN ** A 753 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 765 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7279 moved from start: 0.2466 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 13125 Z= 0.273 Angle : 0.620 10.045 17830 Z= 0.302 Chirality : 0.047 0.698 2023 Planarity : 0.004 0.051 2248 Dihedral : 9.134 105.727 2003 Min Nonbonded Distance : 2.216 Molprobity Statistics. All-atom Clashscore : 10.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.24 % Favored : 95.76 % Rotamer: Outliers : 5.13 % Allowed : 20.36 % Favored : 74.52 % 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: -1.20 (0.21), residues: 1581 helix: 0.54 (0.19), residues: 718 sheet: -1.90 (0.36), residues: 185 loop : -1.93 (0.23), residues: 678 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 208 HIS 0.005 0.001 HIS B 462 PHE 0.013 0.001 PHE A 661 TYR 0.014 0.001 TYR B 420 ARG 0.004 0.000 ARG A 312 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3162 Ramachandran restraints generated. 1581 Oldfield, 0 Emsley, 1581 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3162 Ramachandran restraints generated. 1581 Oldfield, 0 Emsley, 1581 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 1400 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 112 time to evaluate : 1.429 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 23 ASN cc_start: 0.7031 (t0) cc_final: 0.6653 (t0) REVERT: A 91 MET cc_start: 0.8697 (tpp) cc_final: 0.8345 (mmp) REVERT: A 191 GLU cc_start: 0.7842 (mm-30) cc_final: 0.7367 (mm-30) REVERT: A 588 TYR cc_start: 0.9138 (m-80) cc_final: 0.8790 (m-80) REVERT: A 750 TYR cc_start: 0.8218 (p90) cc_final: 0.7387 (p90) REVERT: A 769 LEU cc_start: 0.6910 (OUTLIER) cc_final: 0.6706 (pt) REVERT: A 810 MET cc_start: 0.7289 (mtt) cc_final: 0.7056 (mtt) REVERT: A 814 PHE cc_start: 0.8306 (m-80) cc_final: 0.7699 (m-80) REVERT: B 52 LYS cc_start: 0.9204 (mtmt) cc_final: 0.8933 (mtpp) REVERT: B 202 GLU cc_start: 0.8093 (tt0) cc_final: 0.7637 (tt0) REVERT: B 205 ARG cc_start: 0.7868 (mtt90) cc_final: 0.7322 (mmt180) REVERT: B 248 ASP cc_start: 0.8284 (m-30) cc_final: 0.8020 (m-30) REVERT: B 491 ILE cc_start: 0.8996 (OUTLIER) cc_final: 0.8716 (tp) REVERT: B 564 CYS cc_start: 0.8812 (OUTLIER) cc_final: 0.8435 (m) REVERT: B 607 TRP cc_start: 0.7767 (m100) cc_final: 0.7565 (m100) outliers start: 69 outliers final: 48 residues processed: 170 average time/residue: 0.2127 time to fit residues: 55.3940 Evaluate side-chains 162 residues out of total 1400 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 111 time to evaluate : 1.433 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 LYS Chi-restraints excluded: chain A residue 169 SER Chi-restraints excluded: chain A residue 171 SER Chi-restraints excluded: chain A residue 184 LEU Chi-restraints excluded: chain A residue 200 ILE Chi-restraints excluded: chain A residue 270 PHE Chi-restraints excluded: chain A residue 296 SER Chi-restraints excluded: chain A residue 301 SER Chi-restraints excluded: chain A residue 317 THR Chi-restraints excluded: chain A residue 403 VAL Chi-restraints excluded: chain A residue 425 SER Chi-restraints excluded: chain A residue 433 ILE Chi-restraints excluded: chain A residue 587 ASP Chi-restraints excluded: chain A residue 606 SER Chi-restraints excluded: chain A residue 608 THR Chi-restraints excluded: chain A residue 611 PHE Chi-restraints excluded: chain A residue 639 THR Chi-restraints excluded: chain A residue 694 ILE Chi-restraints excluded: chain A residue 696 VAL Chi-restraints excluded: chain A residue 769 LEU Chi-restraints excluded: chain A residue 782 LEU Chi-restraints excluded: chain A residue 841 LEU Chi-restraints excluded: chain B residue 87 LEU Chi-restraints excluded: chain B residue 105 SER Chi-restraints excluded: chain B residue 120 ILE Chi-restraints excluded: chain B residue 142 VAL Chi-restraints excluded: chain B residue 171 SER Chi-restraints excluded: chain B residue 231 GLU Chi-restraints excluded: chain B residue 270 PHE Chi-restraints excluded: chain B residue 272 SER Chi-restraints excluded: chain B residue 289 THR Chi-restraints excluded: chain B residue 296 SER Chi-restraints excluded: chain B residue 301 SER Chi-restraints excluded: chain B residue 313 VAL Chi-restraints excluded: chain B residue 317 THR Chi-restraints excluded: chain B residue 352 TRP Chi-restraints excluded: chain B residue 416 SER Chi-restraints excluded: chain B residue 491 ILE Chi-restraints excluded: chain B residue 495 LEU Chi-restraints excluded: chain B residue 512 VAL Chi-restraints excluded: chain B residue 564 CYS Chi-restraints excluded: chain B residue 590 SER Chi-restraints excluded: chain B residue 641 ILE Chi-restraints excluded: chain B residue 676 CYS Chi-restraints excluded: chain B residue 696 VAL Chi-restraints excluded: chain B residue 725 LEU Chi-restraints excluded: chain B residue 755 LEU Chi-restraints excluded: chain B residue 793 SER Chi-restraints excluded: chain B residue 795 LYS Chi-restraints excluded: chain B residue 814 PHE Chi-restraints excluded: chain B residue 860 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 127 optimal weight: 0.8980 chunk 86 optimal weight: 0.9990 chunk 2 optimal weight: 4.9990 chunk 113 optimal weight: 4.9990 chunk 63 optimal weight: 20.0000 chunk 130 optimal weight: 0.6980 chunk 105 optimal weight: 0.8980 chunk 0 optimal weight: 8.9990 chunk 77 optimal weight: 10.0000 chunk 137 optimal weight: 30.0000 chunk 38 optimal weight: 0.8980 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 753 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 646 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7254 moved from start: 0.2727 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 13125 Z= 0.168 Angle : 0.572 11.151 17830 Z= 0.280 Chirality : 0.046 0.680 2023 Planarity : 0.004 0.057 2248 Dihedral : 8.587 104.621 2003 Min Nonbonded Distance : 2.235 Molprobity Statistics. All-atom Clashscore : 8.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.42 % Favored : 96.58 % Rotamer: Outliers : 3.86 % Allowed : 21.99 % Favored : 74.15 % 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: -0.94 (0.21), residues: 1581 helix: 0.70 (0.20), residues: 705 sheet: -1.73 (0.36), residues: 195 loop : -1.69 (0.23), residues: 681 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 299 HIS 0.004 0.001 HIS B 462 PHE 0.012 0.001 PHE A 845 TYR 0.010 0.001 TYR B 420 ARG 0.007 0.000 ARG A 312 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3162 Ramachandran restraints generated. 1581 Oldfield, 0 Emsley, 1581 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3162 Ramachandran restraints generated. 1581 Oldfield, 0 Emsley, 1581 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 1400 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 120 time to evaluate : 1.271 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 23 ASN cc_start: 0.7017 (t0) cc_final: 0.6677 (t0) REVERT: A 91 MET cc_start: 0.8715 (tpp) cc_final: 0.8341 (mmp) REVERT: A 191 GLU cc_start: 0.7679 (mm-30) cc_final: 0.7017 (mm-30) REVERT: A 229 GLU cc_start: 0.7087 (mm-30) cc_final: 0.6679 (mt-10) REVERT: A 588 TYR cc_start: 0.9146 (m-80) cc_final: 0.8770 (m-80) REVERT: A 750 TYR cc_start: 0.8161 (p90) cc_final: 0.7481 (p90) REVERT: A 814 PHE cc_start: 0.8353 (m-80) cc_final: 0.7733 (m-80) REVERT: B 52 LYS cc_start: 0.9164 (mtmt) cc_final: 0.8942 (mtpp) REVERT: B 202 GLU cc_start: 0.8100 (tt0) cc_final: 0.7665 (tt0) REVERT: B 205 ARG cc_start: 0.7758 (mtt90) cc_final: 0.7240 (mmt180) REVERT: B 248 ASP cc_start: 0.8247 (m-30) cc_final: 0.7985 (m-30) REVERT: B 607 TRP cc_start: 0.7757 (m100) cc_final: 0.7547 (m100) REVERT: B 770 MET cc_start: 0.6524 (tpp) cc_final: 0.6294 (tpp) REVERT: B 810 MET cc_start: 0.7383 (ptt) cc_final: 0.7181 (ptm) outliers start: 52 outliers final: 38 residues processed: 158 average time/residue: 0.2162 time to fit residues: 51.9863 Evaluate side-chains 151 residues out of total 1400 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 113 time to evaluate : 1.396 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 LYS Chi-restraints excluded: chain A residue 184 LEU Chi-restraints excluded: chain A residue 200 ILE Chi-restraints excluded: chain A residue 270 PHE Chi-restraints excluded: chain A residue 301 SER Chi-restraints excluded: chain A residue 317 THR Chi-restraints excluded: chain A residue 559 THR Chi-restraints excluded: chain A residue 587 ASP Chi-restraints excluded: chain A residue 595 THR Chi-restraints excluded: chain A residue 608 THR Chi-restraints excluded: chain A residue 611 PHE Chi-restraints excluded: chain A residue 630 LEU Chi-restraints excluded: chain A residue 639 THR Chi-restraints excluded: chain A residue 694 ILE Chi-restraints excluded: chain A residue 696 VAL Chi-restraints excluded: chain A residue 782 LEU Chi-restraints excluded: chain A residue 838 ILE Chi-restraints excluded: chain A residue 841 LEU Chi-restraints excluded: chain B residue 87 LEU Chi-restraints excluded: chain B residue 105 SER Chi-restraints excluded: chain B residue 120 ILE Chi-restraints excluded: chain B residue 142 VAL Chi-restraints excluded: chain B residue 231 GLU Chi-restraints excluded: chain B residue 270 PHE Chi-restraints excluded: chain B residue 272 SER Chi-restraints excluded: chain B residue 296 SER Chi-restraints excluded: chain B residue 317 THR Chi-restraints excluded: chain B residue 352 TRP Chi-restraints excluded: chain B residue 359 TYR Chi-restraints excluded: chain B residue 416 SER Chi-restraints excluded: chain B residue 495 LEU Chi-restraints excluded: chain B residue 512 VAL Chi-restraints excluded: chain B residue 559 THR Chi-restraints excluded: chain B residue 676 CYS Chi-restraints excluded: chain B residue 725 LEU Chi-restraints excluded: chain B residue 755 LEU Chi-restraints excluded: chain B residue 820 PHE Chi-restraints excluded: chain B residue 860 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 51 optimal weight: 5.9990 chunk 137 optimal weight: 40.0000 chunk 30 optimal weight: 0.7980 chunk 89 optimal weight: 5.9990 chunk 37 optimal weight: 10.0000 chunk 152 optimal weight: 7.9990 chunk 126 optimal weight: 0.7980 chunk 70 optimal weight: 5.9990 chunk 12 optimal weight: 2.9990 chunk 50 optimal weight: 2.9990 chunk 80 optimal weight: 0.1980 overall best weight: 1.5584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 753 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7277 moved from start: 0.2972 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 13125 Z= 0.236 Angle : 0.569 9.275 17830 Z= 0.282 Chirality : 0.045 0.689 2023 Planarity : 0.004 0.059 2248 Dihedral : 8.278 102.194 2003 Min Nonbonded Distance : 2.035 Molprobity Statistics. All-atom Clashscore : 8.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.92 % Favored : 96.08 % Rotamer: Outliers : 3.86 % Allowed : 22.36 % Favored : 73.77 % 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: -0.85 (0.21), residues: 1581 helix: 0.69 (0.19), residues: 728 sheet: -1.59 (0.36), residues: 195 loop : -1.64 (0.23), residues: 658 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 817 HIS 0.004 0.001 HIS B 462 PHE 0.010 0.001 PHE B 443 TYR 0.013 0.001 TYR B 420 ARG 0.006 0.000 ARG A 312 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3162 Ramachandran restraints generated. 1581 Oldfield, 0 Emsley, 1581 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3162 Ramachandran restraints generated. 1581 Oldfield, 0 Emsley, 1581 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 1400 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 113 time to evaluate : 1.274 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 23 ASN cc_start: 0.7097 (t0) cc_final: 0.6760 (t0) REVERT: A 91 MET cc_start: 0.8746 (tpp) cc_final: 0.8373 (mmp) REVERT: A 191 GLU cc_start: 0.7754 (mm-30) cc_final: 0.7221 (mm-30) REVERT: A 588 TYR cc_start: 0.9148 (m-80) cc_final: 0.8737 (m-80) REVERT: A 750 TYR cc_start: 0.8189 (p90) cc_final: 0.7585 (p90) REVERT: A 810 MET cc_start: 0.6990 (mtt) cc_final: 0.6655 (mtt) REVERT: A 814 PHE cc_start: 0.8369 (m-80) cc_final: 0.7749 (m-80) REVERT: B 52 LYS cc_start: 0.9171 (mtmt) cc_final: 0.8942 (mtpp) REVERT: B 202 GLU cc_start: 0.8137 (tt0) cc_final: 0.7661 (tt0) REVERT: B 205 ARG cc_start: 0.7837 (mtt90) cc_final: 0.7340 (mmt180) REVERT: B 248 ASP cc_start: 0.8205 (m-30) cc_final: 0.7953 (m-30) REVERT: B 564 CYS cc_start: 0.9014 (OUTLIER) cc_final: 0.8632 (m) REVERT: B 770 MET cc_start: 0.6453 (tpp) cc_final: 0.6217 (tpp) REVERT: B 810 MET cc_start: 0.7501 (ptt) cc_final: 0.7252 (ptm) outliers start: 52 outliers final: 40 residues processed: 155 average time/residue: 0.2226 time to fit residues: 52.4220 Evaluate side-chains 149 residues out of total 1400 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 108 time to evaluate : 1.396 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 LYS Chi-restraints excluded: chain A residue 184 LEU Chi-restraints excluded: chain A residue 200 ILE Chi-restraints excluded: chain A residue 270 PHE Chi-restraints excluded: chain A residue 301 SER Chi-restraints excluded: chain A residue 403 VAL Chi-restraints excluded: chain A residue 424 TYR Chi-restraints excluded: chain A residue 425 SER Chi-restraints excluded: chain A residue 433 ILE Chi-restraints excluded: chain A residue 587 ASP Chi-restraints excluded: chain A residue 608 THR Chi-restraints excluded: chain A residue 611 PHE Chi-restraints excluded: chain A residue 639 THR Chi-restraints excluded: chain A residue 694 ILE Chi-restraints excluded: chain A residue 696 VAL Chi-restraints excluded: chain A residue 782 LEU Chi-restraints excluded: chain A residue 841 LEU Chi-restraints excluded: chain B residue 87 LEU Chi-restraints excluded: chain B residue 105 SER Chi-restraints excluded: chain B residue 120 ILE Chi-restraints excluded: chain B residue 142 VAL Chi-restraints excluded: chain B residue 231 GLU Chi-restraints excluded: chain B residue 270 PHE Chi-restraints excluded: chain B residue 272 SER Chi-restraints excluded: chain B residue 296 SER Chi-restraints excluded: chain B residue 317 THR Chi-restraints excluded: chain B residue 352 TRP Chi-restraints excluded: chain B residue 359 TYR Chi-restraints excluded: chain B residue 416 SER Chi-restraints excluded: chain B residue 462 HIS Chi-restraints excluded: chain B residue 495 LEU Chi-restraints excluded: chain B residue 512 VAL Chi-restraints excluded: chain B residue 559 THR Chi-restraints excluded: chain B residue 564 CYS Chi-restraints excluded: chain B residue 676 CYS Chi-restraints excluded: chain B residue 725 LEU Chi-restraints excluded: chain B residue 753 HIS Chi-restraints excluded: chain B residue 755 LEU Chi-restraints excluded: chain B residue 795 LYS Chi-restraints excluded: chain B residue 820 PHE Chi-restraints excluded: chain B residue 860 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 147 optimal weight: 9.9990 chunk 17 optimal weight: 0.7980 chunk 87 optimal weight: 1.9990 chunk 111 optimal weight: 3.9990 chunk 86 optimal weight: 2.9990 chunk 128 optimal weight: 0.6980 chunk 85 optimal weight: 0.9980 chunk 152 optimal weight: 8.9990 chunk 95 optimal weight: 0.8980 chunk 92 optimal weight: 2.9990 chunk 70 optimal weight: 5.9990 overall best weight: 1.0782 ------------------------------------------------------------------------------- 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: 0.7264 moved from start: 0.3128 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 13125 Z= 0.183 Angle : 0.567 11.939 17830 Z= 0.277 Chirality : 0.045 0.679 2023 Planarity : 0.004 0.059 2248 Dihedral : 8.047 100.965 2003 Min Nonbonded Distance : 2.113 Molprobity Statistics. All-atom Clashscore : 8.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.42 % Favored : 96.58 % Rotamer: Outliers : 3.86 % Allowed : 22.44 % Favored : 73.70 % 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 (0.21), residues: 1581 helix: 0.72 (0.20), residues: 724 sheet: -1.52 (0.37), residues: 193 loop : -1.53 (0.23), residues: 664 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 607 HIS 0.003 0.001 HIS B 462 PHE 0.015 0.001 PHE B 270 TYR 0.010 0.001 TYR B 420 ARG 0.006 0.000 ARG A 312 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3162 Ramachandran restraints generated. 1581 Oldfield, 0 Emsley, 1581 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3162 Ramachandran restraints generated. 1581 Oldfield, 0 Emsley, 1581 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 1400 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 112 time to evaluate : 1.574 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 23 ASN cc_start: 0.7073 (t0) cc_final: 0.6758 (t0) REVERT: A 91 MET cc_start: 0.8739 (tpp) cc_final: 0.8198 (mmp) REVERT: A 191 GLU cc_start: 0.7686 (mm-30) cc_final: 0.6989 (mm-30) REVERT: A 229 GLU cc_start: 0.7164 (mm-30) cc_final: 0.6802 (mt-10) REVERT: A 588 TYR cc_start: 0.9154 (m-80) cc_final: 0.8750 (m-80) REVERT: A 750 TYR cc_start: 0.8211 (p90) cc_final: 0.7620 (p90) REVERT: A 810 MET cc_start: 0.6915 (mtt) cc_final: 0.6523 (tpp) REVERT: B 52 LYS cc_start: 0.9149 (mtmt) cc_final: 0.8925 (mtpp) REVERT: B 202 GLU cc_start: 0.8176 (tt0) cc_final: 0.7692 (tt0) REVERT: B 205 ARG cc_start: 0.7869 (mtt90) cc_final: 0.7374 (mmt180) REVERT: B 248 ASP cc_start: 0.8171 (m-30) cc_final: 0.7915 (m-30) REVERT: B 564 CYS cc_start: 0.8938 (OUTLIER) cc_final: 0.8573 (m) REVERT: B 770 MET cc_start: 0.6527 (tpp) cc_final: 0.6291 (tpp) REVERT: B 810 MET cc_start: 0.7408 (ptt) cc_final: 0.7028 (ptm) outliers start: 52 outliers final: 38 residues processed: 154 average time/residue: 0.2435 time to fit residues: 56.9860 Evaluate side-chains 147 residues out of total 1400 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 108 time to evaluate : 1.468 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 LYS Chi-restraints excluded: chain A residue 100 THR Chi-restraints excluded: chain A residue 184 LEU Chi-restraints excluded: chain A residue 200 ILE Chi-restraints excluded: chain A residue 270 PHE Chi-restraints excluded: chain A residue 301 SER Chi-restraints excluded: chain A residue 317 THR Chi-restraints excluded: chain A residue 403 VAL Chi-restraints excluded: chain A residue 416 SER Chi-restraints excluded: chain A residue 433 ILE Chi-restraints excluded: chain A residue 587 ASP Chi-restraints excluded: chain A residue 595 THR Chi-restraints excluded: chain A residue 606 SER Chi-restraints excluded: chain A residue 608 THR Chi-restraints excluded: chain A residue 611 PHE Chi-restraints excluded: chain A residue 630 LEU Chi-restraints excluded: chain A residue 639 THR Chi-restraints excluded: chain A residue 694 ILE Chi-restraints excluded: chain A residue 696 VAL Chi-restraints excluded: chain A residue 782 LEU Chi-restraints excluded: chain A residue 838 ILE Chi-restraints excluded: chain B residue 87 LEU Chi-restraints excluded: chain B residue 120 ILE Chi-restraints excluded: chain B residue 142 VAL Chi-restraints excluded: chain B residue 231 GLU Chi-restraints excluded: chain B residue 272 SER Chi-restraints excluded: chain B residue 296 SER Chi-restraints excluded: chain B residue 317 THR Chi-restraints excluded: chain B residue 352 TRP Chi-restraints excluded: chain B residue 359 TYR Chi-restraints excluded: chain B residue 416 SER Chi-restraints excluded: chain B residue 462 HIS Chi-restraints excluded: chain B residue 512 VAL Chi-restraints excluded: chain B residue 564 CYS Chi-restraints excluded: chain B residue 676 CYS Chi-restraints excluded: chain B residue 725 LEU Chi-restraints excluded: chain B residue 795 LYS Chi-restraints excluded: chain B residue 820 PHE Chi-restraints excluded: chain B residue 860 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 94 optimal weight: 3.9990 chunk 60 optimal weight: 5.9990 chunk 90 optimal weight: 0.7980 chunk 45 optimal weight: 4.9990 chunk 29 optimal weight: 3.9990 chunk 96 optimal weight: 4.9990 chunk 103 optimal weight: 2.9990 chunk 75 optimal weight: 5.9990 chunk 14 optimal weight: 3.9990 chunk 119 optimal weight: 5.9990 chunk 138 optimal weight: 2.9990 overall best weight: 2.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 594 HIS A 601 GLN B 638 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7316 moved from start: 0.3362 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.051 13125 Z= 0.398 Angle : 0.644 10.948 17830 Z= 0.324 Chirality : 0.048 0.726 2023 Planarity : 0.004 0.059 2248 Dihedral : 8.077 98.567 2003 Min Nonbonded Distance : 2.056 Molprobity Statistics. All-atom Clashscore : 10.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.00 % Favored : 95.00 % Rotamer: Outliers : 3.94 % Allowed : 22.36 % Favored : 73.70 % 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: -0.90 (0.21), residues: 1581 helix: 0.61 (0.19), residues: 731 sheet: -1.33 (0.38), residues: 186 loop : -1.73 (0.23), residues: 664 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A1108 HIS 0.006 0.001 HIS B 462 PHE 0.018 0.001 PHE A 791 TYR 0.018 0.001 TYR B 420 ARG 0.005 0.001 ARG A 62 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3162 Ramachandran restraints generated. 1581 Oldfield, 0 Emsley, 1581 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3162 Ramachandran restraints generated. 1581 Oldfield, 0 Emsley, 1581 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 1400 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 105 time to evaluate : 2.233 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 23 ASN cc_start: 0.7253 (t0) cc_final: 0.6941 (t0) REVERT: A 91 MET cc_start: 0.8795 (tpp) cc_final: 0.8223 (mmt) REVERT: A 191 GLU cc_start: 0.7909 (mm-30) cc_final: 0.7351 (mm-30) REVERT: A 229 GLU cc_start: 0.7403 (mm-30) cc_final: 0.7025 (mm-30) REVERT: A 588 TYR cc_start: 0.9149 (m-80) cc_final: 0.8758 (m-80) REVERT: A 687 PHE cc_start: 0.8159 (t80) cc_final: 0.7900 (t80) REVERT: A 750 TYR cc_start: 0.8241 (p90) cc_final: 0.7666 (p90) REVERT: B 52 LYS cc_start: 0.9235 (mtmt) cc_final: 0.9019 (mtpp) REVERT: B 202 GLU cc_start: 0.8201 (tt0) cc_final: 0.7918 (tt0) REVERT: B 248 ASP cc_start: 0.8158 (m-30) cc_final: 0.7869 (m-30) REVERT: B 564 CYS cc_start: 0.8730 (OUTLIER) cc_final: 0.8349 (m) REVERT: B 770 MET cc_start: 0.6593 (tpp) cc_final: 0.6363 (tpp) REVERT: B 810 MET cc_start: 0.7533 (ptt) cc_final: 0.7148 (ptm) outliers start: 53 outliers final: 47 residues processed: 147 average time/residue: 0.2382 time to fit residues: 52.7177 Evaluate side-chains 151 residues out of total 1400 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 103 time to evaluate : 1.323 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 LYS Chi-restraints excluded: chain A residue 100 THR Chi-restraints excluded: chain A residue 171 SER Chi-restraints excluded: chain A residue 184 LEU Chi-restraints excluded: chain A residue 200 ILE Chi-restraints excluded: chain A residue 270 PHE Chi-restraints excluded: chain A residue 296 SER Chi-restraints excluded: chain A residue 301 SER Chi-restraints excluded: chain A residue 317 THR Chi-restraints excluded: chain A residue 403 VAL Chi-restraints excluded: chain A residue 416 SER Chi-restraints excluded: chain A residue 425 SER Chi-restraints excluded: chain A residue 433 ILE Chi-restraints excluded: chain A residue 587 ASP Chi-restraints excluded: chain A residue 606 SER Chi-restraints excluded: chain A residue 608 THR Chi-restraints excluded: chain A residue 611 PHE Chi-restraints excluded: chain A residue 630 LEU Chi-restraints excluded: chain A residue 639 THR Chi-restraints excluded: chain A residue 694 ILE Chi-restraints excluded: chain A residue 696 VAL Chi-restraints excluded: chain A residue 782 LEU Chi-restraints excluded: chain A residue 827 THR Chi-restraints excluded: chain A residue 838 ILE Chi-restraints excluded: chain B residue 87 LEU Chi-restraints excluded: chain B residue 120 ILE Chi-restraints excluded: chain B residue 142 VAL Chi-restraints excluded: chain B residue 171 SER Chi-restraints excluded: chain B residue 231 GLU Chi-restraints excluded: chain B residue 272 SER Chi-restraints excluded: chain B residue 296 SER Chi-restraints excluded: chain B residue 301 SER Chi-restraints excluded: chain B residue 317 THR Chi-restraints excluded: chain B residue 352 TRP Chi-restraints excluded: chain B residue 359 TYR Chi-restraints excluded: chain B residue 416 SER Chi-restraints excluded: chain B residue 462 HIS Chi-restraints excluded: chain B residue 512 VAL Chi-restraints excluded: chain B residue 532 PHE Chi-restraints excluded: chain B residue 553 ILE Chi-restraints excluded: chain B residue 564 CYS Chi-restraints excluded: chain B residue 641 ILE Chi-restraints excluded: chain B residue 676 CYS Chi-restraints excluded: chain B residue 725 LEU Chi-restraints excluded: chain B residue 753 HIS Chi-restraints excluded: chain B residue 762 ILE Chi-restraints excluded: chain B residue 795 LYS Chi-restraints excluded: chain B residue 860 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 145 optimal weight: 0.1980 chunk 133 optimal weight: 6.9990 chunk 141 optimal weight: 8.9990 chunk 85 optimal weight: 0.9990 chunk 61 optimal weight: 6.9990 chunk 111 optimal weight: 0.0040 chunk 43 optimal weight: 3.9990 chunk 128 optimal weight: 3.9990 chunk 134 optimal weight: 7.9990 chunk 93 optimal weight: 2.9990 chunk 150 optimal weight: 5.9990 overall best weight: 1.6398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 799 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7290 moved from start: 0.3474 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 13125 Z= 0.240 Angle : 0.584 11.287 17830 Z= 0.290 Chirality : 0.046 0.706 2023 Planarity : 0.004 0.058 2248 Dihedral : 7.828 98.462 2003 Min Nonbonded Distance : 2.100 Molprobity Statistics. All-atom Clashscore : 9.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.17 % Favored : 95.83 % Rotamer: Outliers : 3.79 % Allowed : 22.73 % Favored : 73.48 % 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: -0.77 (0.21), residues: 1581 helix: 0.75 (0.19), residues: 726 sheet: -1.36 (0.39), residues: 182 loop : -1.67 (0.23), residues: 673 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 817 HIS 0.004 0.001 HIS B 462 PHE 0.035 0.001 PHE A 791 TYR 0.013 0.001 TYR B 420 ARG 0.006 0.000 ARG A 312 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3162 Ramachandran restraints generated. 1581 Oldfield, 0 Emsley, 1581 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3162 Ramachandran restraints generated. 1581 Oldfield, 0 Emsley, 1581 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 1400 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 109 time to evaluate : 1.367 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 23 ASN cc_start: 0.7268 (t0) cc_final: 0.6994 (t0) REVERT: A 91 MET cc_start: 0.8784 (tpp) cc_final: 0.8200 (mmp) REVERT: A 191 GLU cc_start: 0.7774 (mm-30) cc_final: 0.7207 (mm-30) REVERT: A 229 GLU cc_start: 0.7274 (mm-30) cc_final: 0.6964 (mm-30) REVERT: A 588 TYR cc_start: 0.9179 (m-80) cc_final: 0.8778 (m-80) REVERT: A 687 PHE cc_start: 0.8136 (t80) cc_final: 0.7891 (t80) REVERT: A 750 TYR cc_start: 0.8321 (p90) cc_final: 0.7798 (p90) REVERT: B 202 GLU cc_start: 0.8171 (tt0) cc_final: 0.7877 (tt0) REVERT: B 248 ASP cc_start: 0.8151 (m-30) cc_final: 0.7876 (m-30) REVERT: B 564 CYS cc_start: 0.8757 (OUTLIER) cc_final: 0.8363 (m) REVERT: B 770 MET cc_start: 0.6615 (tpp) cc_final: 0.6397 (tpp) REVERT: B 810 MET cc_start: 0.7528 (ptt) cc_final: 0.7166 (ptm) outliers start: 51 outliers final: 47 residues processed: 149 average time/residue: 0.2270 time to fit residues: 51.0905 Evaluate side-chains 152 residues out of total 1400 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 104 time to evaluate : 1.432 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 LYS Chi-restraints excluded: chain A residue 100 THR Chi-restraints excluded: chain A residue 169 SER Chi-restraints excluded: chain A residue 184 LEU Chi-restraints excluded: chain A residue 200 ILE Chi-restraints excluded: chain A residue 263 THR Chi-restraints excluded: chain A residue 270 PHE Chi-restraints excluded: chain A residue 296 SER Chi-restraints excluded: chain A residue 301 SER Chi-restraints excluded: chain A residue 317 THR Chi-restraints excluded: chain A residue 403 VAL Chi-restraints excluded: chain A residue 416 SER Chi-restraints excluded: chain A residue 433 ILE Chi-restraints excluded: chain A residue 559 THR Chi-restraints excluded: chain A residue 587 ASP Chi-restraints excluded: chain A residue 606 SER Chi-restraints excluded: chain A residue 608 THR Chi-restraints excluded: chain A residue 611 PHE Chi-restraints excluded: chain A residue 630 LEU Chi-restraints excluded: chain A residue 639 THR Chi-restraints excluded: chain A residue 694 ILE Chi-restraints excluded: chain A residue 753 HIS Chi-restraints excluded: chain A residue 782 LEU Chi-restraints excluded: chain A residue 838 ILE Chi-restraints excluded: chain B residue 87 LEU Chi-restraints excluded: chain B residue 120 ILE Chi-restraints excluded: chain B residue 142 VAL Chi-restraints excluded: chain B residue 231 GLU Chi-restraints excluded: chain B residue 272 SER Chi-restraints excluded: chain B residue 289 THR Chi-restraints excluded: chain B residue 296 SER Chi-restraints excluded: chain B residue 301 SER Chi-restraints excluded: chain B residue 317 THR Chi-restraints excluded: chain B residue 352 TRP Chi-restraints excluded: chain B residue 359 TYR Chi-restraints excluded: chain B residue 416 SER Chi-restraints excluded: chain B residue 462 HIS Chi-restraints excluded: chain B residue 495 LEU Chi-restraints excluded: chain B residue 512 VAL Chi-restraints excluded: chain B residue 553 ILE Chi-restraints excluded: chain B residue 564 CYS Chi-restraints excluded: chain B residue 641 ILE Chi-restraints excluded: chain B residue 676 CYS Chi-restraints excluded: chain B residue 725 LEU Chi-restraints excluded: chain B residue 753 HIS Chi-restraints excluded: chain B residue 762 ILE Chi-restraints excluded: chain B residue 795 LYS Chi-restraints excluded: chain B residue 860 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 91 optimal weight: 0.7980 chunk 71 optimal weight: 1.9990 chunk 104 optimal weight: 0.9980 chunk 157 optimal weight: 8.9990 chunk 144 optimal weight: 7.9990 chunk 125 optimal weight: 1.9990 chunk 13 optimal weight: 0.7980 chunk 96 optimal weight: 3.9990 chunk 76 optimal weight: 2.9990 chunk 99 optimal weight: 3.9990 chunk 133 optimal weight: 2.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- 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: 0.7282 moved from start: 0.3591 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 13125 Z= 0.211 Angle : 0.582 11.211 17830 Z= 0.287 Chirality : 0.045 0.687 2023 Planarity : 0.004 0.059 2248 Dihedral : 7.622 96.940 2003 Min Nonbonded Distance : 2.099 Molprobity Statistics. All-atom Clashscore : 9.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.61 % Favored : 96.39 % Rotamer: Outliers : 3.57 % Allowed : 23.33 % Favored : 73.11 % 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: -0.69 (0.21), residues: 1581 helix: 0.82 (0.19), residues: 725 sheet: -1.32 (0.39), residues: 184 loop : -1.61 (0.23), residues: 672 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 817 HIS 0.003 0.001 HIS B 462 PHE 0.037 0.001 PHE A 791 TYR 0.012 0.001 TYR B 420 ARG 0.006 0.000 ARG A 312 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3162 Ramachandran restraints generated. 1581 Oldfield, 0 Emsley, 1581 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3162 Ramachandran restraints generated. 1581 Oldfield, 0 Emsley, 1581 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 1400 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 106 time to evaluate : 1.428 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 23 ASN cc_start: 0.7274 (t0) cc_final: 0.7015 (t0) REVERT: A 91 MET cc_start: 0.8792 (tpp) cc_final: 0.8200 (mmp) REVERT: A 191 GLU cc_start: 0.7738 (mm-30) cc_final: 0.7154 (mm-30) REVERT: A 229 GLU cc_start: 0.7237 (mm-30) cc_final: 0.6920 (mm-30) REVERT: A 588 TYR cc_start: 0.9135 (m-80) cc_final: 0.8715 (m-80) REVERT: A 687 PHE cc_start: 0.8144 (t80) cc_final: 0.7891 (t80) REVERT: A 814 PHE cc_start: 0.8451 (m-80) cc_final: 0.7801 (m-80) REVERT: B 202 GLU cc_start: 0.8158 (tt0) cc_final: 0.7896 (tt0) REVERT: B 205 ARG cc_start: 0.7981 (mtt-85) cc_final: 0.7705 (mtt-85) REVERT: B 248 ASP cc_start: 0.8243 (m-30) cc_final: 0.7920 (m-30) REVERT: B 564 CYS cc_start: 0.8709 (OUTLIER) cc_final: 0.8338 (m) REVERT: B 770 MET cc_start: 0.6670 (tpp) cc_final: 0.6464 (tpp) REVERT: B 810 MET cc_start: 0.7524 (ptt) cc_final: 0.7310 (ptm) outliers start: 48 outliers final: 42 residues processed: 143 average time/residue: 0.2295 time to fit residues: 49.5057 Evaluate side-chains 149 residues out of total 1400 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 106 time to evaluate : 1.421 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 LYS Chi-restraints excluded: chain A residue 100 THR Chi-restraints excluded: chain A residue 169 SER Chi-restraints excluded: chain A residue 184 LEU Chi-restraints excluded: chain A residue 200 ILE Chi-restraints excluded: chain A residue 270 PHE Chi-restraints excluded: chain A residue 296 SER Chi-restraints excluded: chain A residue 301 SER Chi-restraints excluded: chain A residue 317 THR Chi-restraints excluded: chain A residue 403 VAL Chi-restraints excluded: chain A residue 416 SER Chi-restraints excluded: chain A residue 433 ILE Chi-restraints excluded: chain A residue 587 ASP Chi-restraints excluded: chain A residue 606 SER Chi-restraints excluded: chain A residue 608 THR Chi-restraints excluded: chain A residue 611 PHE Chi-restraints excluded: chain A residue 630 LEU Chi-restraints excluded: chain A residue 639 THR Chi-restraints excluded: chain A residue 753 HIS Chi-restraints excluded: chain A residue 782 LEU Chi-restraints excluded: chain A residue 838 ILE Chi-restraints excluded: chain B residue 87 LEU Chi-restraints excluded: chain B residue 120 ILE Chi-restraints excluded: chain B residue 142 VAL Chi-restraints excluded: chain B residue 231 GLU Chi-restraints excluded: chain B residue 272 SER Chi-restraints excluded: chain B residue 289 THR Chi-restraints excluded: chain B residue 296 SER Chi-restraints excluded: chain B residue 301 SER Chi-restraints excluded: chain B residue 317 THR Chi-restraints excluded: chain B residue 352 TRP Chi-restraints excluded: chain B residue 359 TYR Chi-restraints excluded: chain B residue 416 SER Chi-restraints excluded: chain B residue 462 HIS Chi-restraints excluded: chain B residue 495 LEU Chi-restraints excluded: chain B residue 512 VAL Chi-restraints excluded: chain B residue 564 CYS Chi-restraints excluded: chain B residue 676 CYS Chi-restraints excluded: chain B residue 725 LEU Chi-restraints excluded: chain B residue 753 HIS Chi-restraints excluded: chain B residue 762 ILE Chi-restraints excluded: chain B residue 795 LYS Chi-restraints excluded: chain B residue 860 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 38 optimal weight: 5.9990 chunk 115 optimal weight: 6.9990 chunk 18 optimal weight: 0.7980 chunk 34 optimal weight: 3.9990 chunk 125 optimal weight: 1.9990 chunk 52 optimal weight: 8.9990 chunk 128 optimal weight: 3.9990 chunk 15 optimal weight: 0.9980 chunk 23 optimal weight: 0.7980 chunk 110 optimal weight: 4.9990 chunk 7 optimal weight: 0.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- 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 = 0.3977 r_free = 0.3977 target = 0.136636 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3300 r_free = 0.3300 target = 0.090597 restraints weight = 24188.227| |-----------------------------------------------------------------------------| r_work (start): 0.3259 rms_B_bonded: 3.27 r_work: 0.3092 rms_B_bonded: 3.69 restraints_weight: 0.5000 r_work (final): 0.3092 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3103 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3103 r_free = 0.3103 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3102 r_free = 0.3102 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.22 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3102 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7906 moved from start: 0.3701 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 13125 Z= 0.189 Angle : 0.565 11.144 17830 Z= 0.277 Chirality : 0.045 0.672 2023 Planarity : 0.004 0.057 2248 Dihedral : 7.416 94.650 2003 Min Nonbonded Distance : 2.112 Molprobity Statistics. All-atom Clashscore : 8.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.73 % Favored : 96.27 % Rotamer: Outliers : 3.27 % Allowed : 23.48 % Favored : 73.25 % 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: -0.59 (0.21), residues: 1581 helix: 0.89 (0.19), residues: 718 sheet: -1.30 (0.39), residues: 192 loop : -1.52 (0.23), residues: 671 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 817 HIS 0.003 0.001 HIS B 462 PHE 0.036 0.001 PHE A 791 TYR 0.010 0.001 TYR B 420 ARG 0.006 0.000 ARG A 312 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2867.07 seconds wall clock time: 52 minutes 41.89 seconds (3161.89 seconds total)