Starting phenix.real_space_refine on Wed Feb 21 20:11:11 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8f38_28833/02_2024/8f38_28833_neut.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8f38_28833/02_2024/8f38_28833.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.64 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8f38_28833/02_2024/8f38_28833.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8f38_28833/02_2024/8f38_28833.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8f38_28833/02_2024/8f38_28833_neut.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8f38_28833/02_2024/8f38_28833_neut.pdb" } resolution = 2.64 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= -0.001 sd= 0.079 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 14871 atoms to isotropic. Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 81 5.16 5 C 10644 2.51 5 N 2829 2.21 5 O 3398 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "D GLU 10": "OE1" <-> "OE2" Residue "D GLU 46": "OE1" <-> "OE2" Residue "E GLU 46": "OE1" <-> "OE2" Residue "F GLU 10": "OE1" <-> "OE2" Residue "F GLU 46": "OE1" <-> "OE2" Residue "A GLU 103": "OE1" <-> "OE2" Residue "A GLU 354": "OE1" <-> "OE2" Residue "A TYR 367": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 400": "OE1" <-> "OE2" Residue "A GLU 490": "OE1" <-> "OE2" Residue "B GLU 103": "OE1" <-> "OE2" Residue "B GLU 354": "OE1" <-> "OE2" Residue "B TYR 367": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 400": "OE1" <-> "OE2" Residue "B GLU 490": "OE1" <-> "OE2" Residue "C GLU 103": "OE1" <-> "OE2" Residue "C GLU 354": "OE1" <-> "OE2" Residue "C TYR 367": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 400": "OE1" <-> "OE2" Residue "C GLU 490": "OE1" <-> "OE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 16952 Number of models: 1 Model: "" Number of chains: 21 Chain: "G" Number of atoms: 783 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 783 Classifications: {'peptide': 109} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 8, 'TRANS': 100} Unresolved non-hydrogen bonds: 25 Unresolved non-hydrogen angles: 28 Unresolved non-hydrogen dihedrals: 22 Planarities with less than four sites: {'ASN:plan1': 1, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 13 Chain: "D" Number of atoms: 901 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 118, 899 Classifications: {'peptide': 118} Link IDs: {'PTRANS': 6, 'TRANS': 111} Conformer: "B" Number of residues, atoms: 118, 899 Classifications: {'peptide': 118} Link IDs: {'PTRANS': 6, 'TRANS': 111} bond proxies already assigned to first conformer: 917 Chain: "E" Number of atoms: 901 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 118, 899 Classifications: {'peptide': 118} Link IDs: {'PTRANS': 6, 'TRANS': 111} Conformer: "B" Number of residues, atoms: 118, 899 Classifications: {'peptide': 118} Link IDs: {'PTRANS': 6, 'TRANS': 111} bond proxies already assigned to first conformer: 917 Chain: "F" Number of atoms: 901 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 118, 899 Classifications: {'peptide': 118} Link IDs: {'PTRANS': 6, 'TRANS': 111} Conformer: "B" Number of residues, atoms: 118, 899 Classifications: {'peptide': 118} Link IDs: {'PTRANS': 6, 'TRANS': 111} bond proxies already assigned to first conformer: 917 Chain: "A" Number of atoms: 3799 Number of conformers: 1 Conformer: "" Number of residues, atoms: 480, 3799 Classifications: {'peptide': 480} Link IDs: {'PTRANS': 21, 'TRANS': 458} Chain breaks: 1 Chain: "B" Number of atoms: 3799 Number of conformers: 1 Conformer: "" Number of residues, atoms: 480, 3799 Classifications: {'peptide': 480} Link IDs: {'PTRANS': 21, 'TRANS': 458} Chain breaks: 1 Chain: "C" Number of atoms: 3799 Number of conformers: 1 Conformer: "" Number of residues, atoms: 480, 3799 Classifications: {'peptide': 480} Link IDs: {'PTRANS': 21, 'TRANS': 458} Chain breaks: 1 Chain: "H" Number of atoms: 783 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 783 Classifications: {'peptide': 109} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 8, 'TRANS': 100} Unresolved non-hydrogen bonds: 25 Unresolved non-hydrogen angles: 28 Unresolved non-hydrogen dihedrals: 22 Planarities with less than four sites: {'ASN:plan1': 1, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 13 Chain: "I" Number of atoms: 783 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 783 Classifications: {'peptide': 109} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 8, 'TRANS': 100} Unresolved non-hydrogen bonds: 25 Unresolved non-hydrogen angles: 28 Unresolved non-hydrogen dihedrals: 22 Planarities with less than four sites: {'ASN:plan1': 1, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 13 Chain: "K" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "L" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "N" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "O" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 84 Unusual residues: {'NAG': 6} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "B" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 84 Unusual residues: {'NAG': 6} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "C" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 84 Unusual residues: {'NAG': 6} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "A" Number of atoms: 35 Number of conformers: 1 Conformer: "" Number of residues, atoms: 35, 35 Classifications: {'water': 35} Link IDs: {None: 34} Chain: "B" Number of atoms: 7 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 7 Classifications: {'water': 7} Link IDs: {None: 6} Chain: "C" Number of atoms: 8 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 8 Classifications: {'water': 8} Link IDs: {None: 7} Time building chain proxies: 11.02, per 1000 atoms: 0.65 Number of scatterers: 16952 At special positions: 0 Unit cell: (135, 127.575, 143.1, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 81 16.00 O 3398 8.00 N 2829 7.00 C 10644 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=18, symmetry=0 Simple disulfide: pdb=" SG CYS D 22 " - pdb=" SG CYS D 96 " distance=2.04 Simple disulfide: pdb=" SG CYS E 22 " - pdb=" SG CYS E 96 " distance=2.04 Simple disulfide: pdb=" SG CYS F 22 " - pdb=" SG CYS F 96 " distance=2.04 Simple disulfide: pdb=" SG CYS A 21 " - pdb=" SG CYS A 480 " distance=2.03 Simple disulfide: pdb=" SG CYS A 72 " - pdb=" SG CYS A 84 " distance=2.03 Simple disulfide: pdb=" SG CYS A 107 " - pdb=" SG CYS A 152 " distance=2.03 Simple disulfide: pdb=" SG CYS A 295 " - pdb=" SG CYS A 319 " distance=2.03 Simple disulfide: pdb=" SG CYS A 487 " - pdb=" SG CYS A 491 " distance=2.03 Simple disulfide: pdb=" SG CYS B 21 " - pdb=" SG CYS B 480 " distance=2.03 Simple disulfide: pdb=" SG CYS B 72 " - pdb=" SG CYS B 84 " distance=2.03 Simple disulfide: pdb=" SG CYS B 107 " - pdb=" SG CYS B 152 " distance=2.03 Simple disulfide: pdb=" SG CYS B 295 " - pdb=" SG CYS B 319 " distance=2.03 Simple disulfide: pdb=" SG CYS B 487 " - pdb=" SG CYS B 491 " distance=2.03 Simple disulfide: pdb=" SG CYS C 21 " - pdb=" SG CYS C 480 " distance=2.03 Simple disulfide: pdb=" SG CYS C 72 " - pdb=" SG CYS C 84 " distance=2.03 Simple disulfide: pdb=" SG CYS C 107 " - pdb=" SG CYS C 152 " distance=2.03 Simple disulfide: pdb=" SG CYS C 295 " - pdb=" SG CYS C 319 " distance=2.03 Simple disulfide: pdb=" SG CYS C 487 " - pdb=" SG CYS C 491 " 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 Atom "HETATM16567 O5 NAG M 1 .*. O " rejected from bonding due to valence issues. Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG K 2 " - " BMA K 3 " " NAG L 1 " - " NAG L 2 " " NAG L 2 " - " BMA L 3 " " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " NAG N 2 " - " BMA N 3 " " NAG O 1 " - " NAG O 2 " NAG-ASN " NAG A 601 " - " ASN A 28 " " NAG A 602 " - " ASN A 142 " " NAG A 603 " - " ASN A 303 " " NAG A 604 " - " ASN A 497 " " NAG A 605 " - " ASN A 71 " " NAG A 606 " - " ASN A 176 " " NAG B 601 " - " ASN B 28 " " NAG B 602 " - " ASN B 142 " " NAG B 603 " - " ASN B 303 " " NAG B 604 " - " ASN B 497 " " NAG B 605 " - " ASN B 71 " " NAG B 606 " - " ASN B 176 " " NAG C 601 " - " ASN C 142 " " NAG C 602 " - " ASN C 303 " " NAG C 603 " - " ASN C 497 " " NAG C 604 " - " ASN C 71 " " NAG C 605 " - " ASN C 176 " " NAG C 606 " - " ASN C 28 " " NAG J 1 " - " ASN A 40 " " NAG K 1 " - " ASN A 104 " " NAG L 1 " - " ASN B 104 " " NAG M 1 " - " ASN B 40 " " NAG N 1 " - " ASN C 104 " " NAG O 1 " - " ASN C 40 " Time building additional restraints: 6.74 Conformation dependent library (CDL) restraints added in 3.7 seconds 4200 Ramachandran restraints generated. 2100 Oldfield, 0 Emsley, 2100 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3864 Finding SS restraints... Secondary structure from input PDB file: 27 helices and 54 sheets defined 18.4% alpha, 33.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.38 Creating SS restraints... Processing helix chain 'D' and resid 87 through 91 removed outlier: 3.754A pdb=" N THR D 91 " --> pdb=" O SER D 88 " (cutoff:3.500A) Processing helix chain 'E' and resid 87 through 91 removed outlier: 3.735A pdb=" N THR E 91 " --> pdb=" O SER E 88 " (cutoff:3.500A) Processing helix chain 'F' and resid 87 through 91 removed outlier: 3.744A pdb=" N THR F 91 " --> pdb=" O SER F 88 " (cutoff:3.500A) Processing helix chain 'A' and resid 73 through 80 Processing helix chain 'A' and resid 84 through 88 Processing helix chain 'A' and resid 114 through 123 Processing helix chain 'A' and resid 200 through 209 Processing helix chain 'A' and resid 380 through 402 removed outlier: 3.676A pdb=" N THR A 384 " --> pdb=" O ASP A 380 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N ASN A 386 " --> pdb=" O LYS A 382 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N MET A 402 " --> pdb=" O VAL A 398 " (cutoff:3.500A) Processing helix chain 'A' and resid 417 through 470 removed outlier: 3.954A pdb=" N GLU A 448 " --> pdb=" O LEU A 444 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N ARG A 449 " --> pdb=" O LEU A 445 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N LEU A 451 " --> pdb=" O ASN A 447 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N GLN A 468 " --> pdb=" O LYS A 464 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N LEU A 469 " --> pdb=" O VAL A 465 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N LYS A 470 " --> pdb=" O LYS A 466 " (cutoff:3.500A) Processing helix chain 'A' and resid 488 through 496 Processing helix chain 'A' and resid 501 through 506 removed outlier: 3.847A pdb=" N TYR A 505 " --> pdb=" O ASP A 501 " (cutoff:3.500A) Processing helix chain 'B' and resid 73 through 80 Processing helix chain 'B' and resid 84 through 88 Processing helix chain 'B' and resid 114 through 123 Processing helix chain 'B' and resid 200 through 209 Processing helix chain 'B' and resid 380 through 402 removed outlier: 3.675A pdb=" N THR B 384 " --> pdb=" O ASP B 380 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N ASN B 386 " --> pdb=" O LYS B 382 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N MET B 402 " --> pdb=" O VAL B 398 " (cutoff:3.500A) Processing helix chain 'B' and resid 417 through 470 removed outlier: 3.954A pdb=" N GLU B 448 " --> pdb=" O LEU B 444 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N ARG B 449 " --> pdb=" O LEU B 445 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N LEU B 451 " --> pdb=" O ASN B 447 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N GLN B 468 " --> pdb=" O LYS B 464 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N LEU B 469 " --> pdb=" O VAL B 465 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N LYS B 470 " --> pdb=" O LYS B 466 " (cutoff:3.500A) Processing helix chain 'B' and resid 488 through 496 Processing helix chain 'B' and resid 501 through 506 removed outlier: 3.847A pdb=" N TYR B 505 " --> pdb=" O ASP B 501 " (cutoff:3.500A) Processing helix chain 'C' and resid 73 through 80 Processing helix chain 'C' and resid 84 through 88 Processing helix chain 'C' and resid 114 through 123 Processing helix chain 'C' and resid 200 through 209 Processing helix chain 'C' and resid 380 through 402 removed outlier: 3.675A pdb=" N THR C 384 " --> pdb=" O ASP C 380 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N ASN C 386 " --> pdb=" O LYS C 382 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N MET C 402 " --> pdb=" O VAL C 398 " (cutoff:3.500A) Processing helix chain 'C' and resid 417 through 470 removed outlier: 3.954A pdb=" N GLU C 448 " --> pdb=" O LEU C 444 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N ARG C 449 " --> pdb=" O LEU C 445 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N LEU C 451 " --> pdb=" O ASN C 447 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N GLN C 468 " --> pdb=" O LYS C 464 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N LEU C 469 " --> pdb=" O VAL C 465 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N LYS C 470 " --> pdb=" O LYS C 466 " (cutoff:3.500A) Processing helix chain 'C' and resid 488 through 496 Processing helix chain 'C' and resid 501 through 506 removed outlier: 3.847A pdb=" N TYR C 505 " --> pdb=" O ASP C 501 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'G' and resid 9 through 12 removed outlier: 6.438A pdb=" N TRP G 36 " --> pdb=" O LEU G 48 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'G' and resid 9 through 12 Processing sheet with id=AA3, first strand: chain 'G' and resid 17 through 20 Processing sheet with id=AA4, first strand: chain 'D' and resid 4 through 6 Processing sheet with id=AA5, first strand: chain 'D' and resid 10 through 11 removed outlier: 6.627A pdb=" N ILE D 34 " --> pdb=" O GLY D 50 " (cutoff:3.500A) removed outlier: 4.508A pdb=" N GLY D 50 " --> pdb=" O ILE D 34 " (cutoff:3.500A) removed outlier: 6.838A pdb=" N TRP D 36 " --> pdb=" O MET D 48 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'D' and resid 10 through 11 removed outlier: 3.825A pdb=" N VAL D 110 " --> pdb=" O LYS D 98 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'E' and resid 4 through 6 Processing sheet with id=AA8, first strand: chain 'E' and resid 10 through 11 removed outlier: 6.620A pdb=" N ILE E 34 " --> pdb=" O GLY E 50 " (cutoff:3.500A) removed outlier: 4.495A pdb=" N GLY E 50 " --> pdb=" O ILE E 34 " (cutoff:3.500A) removed outlier: 6.825A pdb=" N TRP E 36 " --> pdb=" O MET E 48 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'E' and resid 10 through 11 removed outlier: 3.820A pdb=" N VAL E 110 " --> pdb=" O LYS E 98 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'F' and resid 4 through 6 Processing sheet with id=AB2, first strand: chain 'F' and resid 10 through 11 removed outlier: 6.613A pdb=" N ILE F 34 " --> pdb=" O GLY F 50 " (cutoff:3.500A) removed outlier: 4.496A pdb=" N GLY F 50 " --> pdb=" O ILE F 34 " (cutoff:3.500A) removed outlier: 6.821A pdb=" N TRP F 36 " --> pdb=" O MET F 48 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'F' and resid 10 through 11 removed outlier: 3.816A pdb=" N VAL F 110 " --> pdb=" O LYS F 98 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 374 through 379 Processing sheet with id=AB5, first strand: chain 'A' and resid 32 through 33 Processing sheet with id=AB6, first strand: chain 'A' and resid 46 through 48 Processing sheet with id=AB7, first strand: chain 'A' and resid 50 through 51 Processing sheet with id=AB8, first strand: chain 'A' and resid 58 through 61 removed outlier: 6.436A pdb=" N LEU A 58 " --> pdb=" O ASP A 289 " (cutoff:3.500A) removed outlier: 5.596A pdb=" N CYS A 291 " --> pdb=" O LEU A 58 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'A' and resid 67 through 68 removed outlier: 6.539A pdb=" N LEU A 67 " --> pdb=" O VAL A 97 " (cutoff:3.500A) removed outlier: 6.280A pdb=" N ILE A 96 " --> pdb=" O ILE A 282 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB9 Processing sheet with id=AC1, first strand: chain 'A' and resid 125 through 132 removed outlier: 3.605A pdb=" N SER A 127 " --> pdb=" O SER A 274 " (cutoff:3.500A) removed outlier: 6.675A pdb=" N TYR A 269 " --> pdb=" O LEU A 192 " (cutoff:3.500A) removed outlier: 5.381A pdb=" N LEU A 192 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N PHE A 271 " --> pdb=" O LEU A 190 " (cutoff:3.500A) removed outlier: 8.017A pdb=" N LEU A 192 " --> pdb=" O PRO A 267 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'A' and resid 125 through 132 removed outlier: 3.605A pdb=" N SER A 127 " --> pdb=" O SER A 274 " (cutoff:3.500A) removed outlier: 6.675A pdb=" N TYR A 269 " --> pdb=" O LEU A 192 " (cutoff:3.500A) removed outlier: 5.381A pdb=" N LEU A 192 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N PHE A 271 " --> pdb=" O LEU A 190 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'A' and resid 143 through 144 Processing sheet with id=AC4, first strand: chain 'A' and resid 149 through 154 removed outlier: 4.721A pdb=" N CYS A 152 " --> pdb=" O SER A 159 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'A' and resid 177 through 182 Processing sheet with id=AC6, first strand: chain 'A' and resid 301 through 302 removed outlier: 3.895A pdb=" N CYS A 295 " --> pdb=" O ILE A 302 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 374 through 379 Processing sheet with id=AC8, first strand: chain 'B' and resid 32 through 33 Processing sheet with id=AC9, first strand: chain 'B' and resid 46 through 48 Processing sheet with id=AD1, first strand: chain 'B' and resid 50 through 51 Processing sheet with id=AD2, first strand: chain 'B' and resid 58 through 61 removed outlier: 6.436A pdb=" N LEU B 58 " --> pdb=" O ASP B 289 " (cutoff:3.500A) removed outlier: 5.597A pdb=" N CYS B 291 " --> pdb=" O LEU B 58 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 67 through 68 removed outlier: 6.539A pdb=" N LEU B 67 " --> pdb=" O VAL B 97 " (cutoff:3.500A) removed outlier: 6.280A pdb=" N ILE B 96 " --> pdb=" O ILE B 282 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD3 Processing sheet with id=AD4, first strand: chain 'B' and resid 125 through 132 removed outlier: 3.605A pdb=" N SER B 127 " --> pdb=" O SER B 274 " (cutoff:3.500A) removed outlier: 6.674A pdb=" N TYR B 269 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 5.381A pdb=" N LEU B 192 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N PHE B 271 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 8.018A pdb=" N LEU B 192 " --> pdb=" O PRO B 267 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'B' and resid 125 through 132 removed outlier: 3.605A pdb=" N SER B 127 " --> pdb=" O SER B 274 " (cutoff:3.500A) removed outlier: 6.674A pdb=" N TYR B 269 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 5.381A pdb=" N LEU B 192 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N PHE B 271 " --> pdb=" O LEU B 190 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'B' and resid 143 through 144 Processing sheet with id=AD7, first strand: chain 'B' and resid 149 through 154 removed outlier: 4.721A pdb=" N CYS B 152 " --> pdb=" O SER B 159 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'B' and resid 177 through 182 Processing sheet with id=AD9, first strand: chain 'B' and resid 301 through 302 removed outlier: 3.895A pdb=" N CYS B 295 " --> pdb=" O ILE B 302 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 374 through 379 Processing sheet with id=AE2, first strand: chain 'C' and resid 32 through 33 Processing sheet with id=AE3, first strand: chain 'C' and resid 46 through 48 Processing sheet with id=AE4, first strand: chain 'C' and resid 50 through 51 Processing sheet with id=AE5, first strand: chain 'C' and resid 58 through 61 removed outlier: 6.435A pdb=" N LEU C 58 " --> pdb=" O ASP C 289 " (cutoff:3.500A) removed outlier: 5.596A pdb=" N CYS C 291 " --> pdb=" O LEU C 58 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 67 through 68 removed outlier: 6.539A pdb=" N LEU C 67 " --> pdb=" O VAL C 97 " (cutoff:3.500A) removed outlier: 6.279A pdb=" N ILE C 96 " --> pdb=" O ILE C 282 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE6 Processing sheet with id=AE7, first strand: chain 'C' and resid 125 through 132 removed outlier: 3.605A pdb=" N SER C 127 " --> pdb=" O SER C 274 " (cutoff:3.500A) removed outlier: 6.675A pdb=" N TYR C 269 " --> pdb=" O LEU C 192 " (cutoff:3.500A) removed outlier: 5.381A pdb=" N LEU C 192 " --> pdb=" O TYR C 269 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N PHE C 271 " --> pdb=" O LEU C 190 " (cutoff:3.500A) removed outlier: 8.018A pdb=" N LEU C 192 " --> pdb=" O PRO C 267 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'C' and resid 125 through 132 removed outlier: 3.605A pdb=" N SER C 127 " --> pdb=" O SER C 274 " (cutoff:3.500A) removed outlier: 6.675A pdb=" N TYR C 269 " --> pdb=" O LEU C 192 " (cutoff:3.500A) removed outlier: 5.381A pdb=" N LEU C 192 " --> pdb=" O TYR C 269 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N PHE C 271 " --> pdb=" O LEU C 190 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'C' and resid 143 through 144 Processing sheet with id=AF1, first strand: chain 'C' and resid 149 through 154 removed outlier: 4.720A pdb=" N CYS C 152 " --> pdb=" O SER C 159 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'C' and resid 177 through 182 Processing sheet with id=AF3, first strand: chain 'C' and resid 301 through 302 removed outlier: 3.895A pdb=" N CYS C 295 " --> pdb=" O ILE C 302 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'H' and resid 9 through 12 removed outlier: 6.438A pdb=" N TRP H 36 " --> pdb=" O LEU H 48 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'H' and resid 9 through 12 Processing sheet with id=AF6, first strand: chain 'H' and resid 17 through 20 Processing sheet with id=AF7, first strand: chain 'I' and resid 9 through 12 removed outlier: 6.438A pdb=" N TRP I 36 " --> pdb=" O LEU I 48 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'I' and resid 9 through 12 Processing sheet with id=AF9, first strand: chain 'I' and resid 17 through 20 684 hydrogen bonds defined for protein. 1809 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: 6.92 Time building geometry restraints manager: 7.31 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 3209 1.33 - 1.45: 4698 1.45 - 1.58: 9286 1.58 - 1.70: 0 1.70 - 1.83: 114 Bond restraints: 17307 Sorted by residual: bond pdb=" C CYS C 291 " pdb=" O CYS C 291 " ideal model delta sigma weight residual 1.233 1.201 0.032 1.28e-02 6.10e+03 6.38e+00 bond pdb=" C CYS A 291 " pdb=" O CYS A 291 " ideal model delta sigma weight residual 1.233 1.201 0.032 1.28e-02 6.10e+03 6.26e+00 bond pdb=" C CYS B 291 " pdb=" O CYS B 291 " ideal model delta sigma weight residual 1.233 1.201 0.032 1.28e-02 6.10e+03 6.22e+00 bond pdb=" N CYS H 22 " pdb=" CA CYS H 22 " ideal model delta sigma weight residual 1.457 1.485 -0.028 1.29e-02 6.01e+03 4.67e+00 bond pdb=" N SER H 23 " pdb=" CA SER H 23 " ideal model delta sigma weight residual 1.460 1.486 -0.026 1.20e-02 6.94e+03 4.64e+00 ... (remaining 17302 not shown) Histogram of bond angle deviations from ideal: 100.60 - 107.28: 664 107.28 - 113.97: 9659 113.97 - 120.66: 6375 120.66 - 127.35: 6615 127.35 - 134.03: 201 Bond angle restraints: 23514 Sorted by residual: angle pdb=" C GLU C 290 " pdb=" N CYS C 291 " pdb=" CA CYS C 291 " ideal model delta sigma weight residual 122.02 116.04 5.98 1.89e+00 2.80e-01 1.00e+01 angle pdb=" C GLU A 290 " pdb=" N CYS A 291 " pdb=" CA CYS A 291 " ideal model delta sigma weight residual 122.02 116.05 5.97 1.89e+00 2.80e-01 9.96e+00 angle pdb=" C GLU B 290 " pdb=" N CYS B 291 " pdb=" CA CYS B 291 " ideal model delta sigma weight residual 122.02 116.06 5.96 1.89e+00 2.80e-01 9.93e+00 angle pdb=" O GLU C 290 " pdb=" C GLU C 290 " pdb=" N CYS C 291 " ideal model delta sigma weight residual 122.19 118.21 3.98 1.29e+00 6.01e-01 9.54e+00 angle pdb=" O GLU A 290 " pdb=" C GLU A 290 " pdb=" N CYS A 291 " ideal model delta sigma weight residual 122.19 118.21 3.98 1.29e+00 6.01e-01 9.53e+00 ... (remaining 23509 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.58: 9451 21.58 - 43.15: 912 43.15 - 64.73: 229 64.73 - 86.30: 70 86.30 - 107.88: 30 Dihedral angle restraints: 10692 sinusoidal: 4605 harmonic: 6087 Sorted by residual: dihedral pdb=" CB CYS B 487 " pdb=" SG CYS B 487 " pdb=" SG CYS B 491 " pdb=" CB CYS B 491 " ideal model delta sinusoidal sigma weight residual -86.00 -33.91 -52.09 1 1.00e+01 1.00e-02 3.70e+01 dihedral pdb=" CB CYS A 487 " pdb=" SG CYS A 487 " pdb=" SG CYS A 491 " pdb=" CB CYS A 491 " ideal model delta sinusoidal sigma weight residual -86.00 -33.95 -52.05 1 1.00e+01 1.00e-02 3.70e+01 dihedral pdb=" CB CYS C 487 " pdb=" SG CYS C 487 " pdb=" SG CYS C 491 " pdb=" CB CYS C 491 " ideal model delta sinusoidal sigma weight residual -86.00 -33.97 -52.03 1 1.00e+01 1.00e-02 3.69e+01 ... (remaining 10689 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.106: 2559 0.106 - 0.211: 68 0.211 - 0.317: 8 0.317 - 0.423: 3 0.423 - 0.528: 2 Chirality restraints: 2640 Sorted by residual: chirality pdb=" C1 NAG B 606 " pdb=" ND2 ASN B 176 " pdb=" C2 NAG B 606 " pdb=" O5 NAG B 606 " both_signs ideal model delta sigma weight residual False -2.40 -1.87 -0.53 2.00e-01 2.50e+01 6.98e+00 chirality pdb=" C1 NAG O 1 " pdb=" ND2 ASN C 40 " pdb=" C2 NAG O 1 " pdb=" O5 NAG O 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.90 0.50 2.00e-01 2.50e+01 6.13e+00 chirality pdb=" C1 NAG C 601 " pdb=" ND2 ASN C 142 " pdb=" C2 NAG C 601 " pdb=" O5 NAG C 601 " both_signs ideal model delta sigma weight residual False -2.40 -2.04 -0.36 2.00e-01 2.50e+01 3.16e+00 ... (remaining 2637 not shown) Planarity restraints: 3027 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN B 176 " -0.160 2.00e-02 2.50e+03 1.57e-01 3.09e+02 pdb=" CG ASN B 176 " 0.066 2.00e-02 2.50e+03 pdb=" OD1 ASN B 176 " 0.072 2.00e-02 2.50e+03 pdb=" ND2 ASN B 176 " 0.221 2.00e-02 2.50e+03 pdb=" C1 NAG B 606 " -0.199 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN B 40 " 0.156 2.00e-02 2.50e+03 1.45e-01 2.61e+02 pdb=" CG ASN B 40 " -0.078 2.00e-02 2.50e+03 pdb=" OD1 ASN B 40 " -0.093 2.00e-02 2.50e+03 pdb=" ND2 ASN B 40 " -0.174 2.00e-02 2.50e+03 pdb=" C1 NAG M 1 " 0.188 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN C 40 " -0.095 2.00e-02 2.50e+03 8.45e-02 8.93e+01 pdb=" CG ASN C 40 " 0.054 2.00e-02 2.50e+03 pdb=" OD1 ASN C 40 " 0.043 2.00e-02 2.50e+03 pdb=" ND2 ASN C 40 " 0.104 2.00e-02 2.50e+03 pdb=" C1 NAG O 1 " -0.106 2.00e-02 2.50e+03 ... (remaining 3024 not shown) Histogram of nonbonded interaction distances: 2.15 - 2.70: 499 2.70 - 3.25: 14295 3.25 - 3.80: 24846 3.80 - 4.35: 34185 4.35 - 4.90: 59293 Nonbonded interactions: 133118 Sorted by model distance: nonbonded pdb=" OD1 ASN C 176 " pdb=" C1 NAG C 605 " model vdw 2.148 2.776 nonbonded pdb=" OD1 ASN B 40 " pdb=" C1 NAG M 1 " model vdw 2.225 2.776 nonbonded pdb=" O GLY C 355 " pdb=" O HOH C 701 " model vdw 2.240 2.440 nonbonded pdb=" ND2 ASN B 176 " pdb=" N2 NAG B 606 " model vdw 2.257 2.560 nonbonded pdb=" O GLY A 355 " pdb=" O HOH A 701 " model vdw 2.262 2.440 ... (remaining 133113 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' selection = chain 'B' selection = chain 'C' } ncs_group { reference = (chain 'D' and (resid 2 through 29 or resid 31 through 119)) selection = (chain 'E' and (resid 2 through 29 or resid 31 through 119)) selection = (chain 'F' and (resid 2 through 29 or resid 31 through 119)) } ncs_group { reference = chain 'G' selection = chain 'H' selection = chain 'I' } ncs_group { reference = chain 'J' selection = chain 'M' selection = chain 'O' } ncs_group { reference = chain 'K' selection = chain 'L' selection = chain 'N' } 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: 12.520 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.200 Construct map_model_manager: 0.010 Extract box with map and model: 36.420 Check model and map are aligned: 0.260 Set scattering table: 0.140 Process input model: 50.960 Find NCS groups from input model: 0.990 Set up NCS constraints: 0.150 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:11.740 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 113.390 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8239 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 : 0.003 0.040 17307 Z= 0.226 Angle : 0.603 6.185 23514 Z= 0.317 Chirality : 0.049 0.528 2640 Planarity : 0.005 0.078 3003 Dihedral : 19.167 107.878 6774 Min Nonbonded Distance : 2.148 Molprobity Statistics. All-atom Clashscore : 3.68 Ramachandran Plot: Outliers : 0.29 % Allowed : 2.29 % Favored : 97.42 % Rotamer: Outliers : 4.08 % Allowed : 24.85 % Favored : 71.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.19 (0.18), residues: 2100 helix: 2.55 (0.29), residues: 318 sheet: 0.73 (0.21), residues: 615 loop : -0.94 (0.16), residues: 1167 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 435 HIS 0.005 0.001 HIS A 369 PHE 0.013 0.001 PHE A 453 TYR 0.012 0.001 TYR I 99 ARG 0.003 0.000 ARG C 162 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4200 Ramachandran restraints generated. 2100 Oldfield, 0 Emsley, 2100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4200 Ramachandran restraints generated. 2100 Oldfield, 0 Emsley, 2100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 269 residues out of total 1806 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 202 time to evaluate : 1.803 Fit side-chains REVERT: G 5 THR cc_start: 0.6825 (OUTLIER) cc_final: 0.6409 (p) REVERT: D 74 ASP cc_start: 0.8252 (m-30) cc_final: 0.8017 (m-30) REVERT: A 162 ARG cc_start: 0.8278 (mpt180) cc_final: 0.8053 (mpt90) REVERT: A 400 GLU cc_start: 0.7969 (tt0) cc_final: 0.7665 (tt0) REVERT: A 459 LYS cc_start: 0.8181 (tttm) cc_final: 0.7730 (tttt) REVERT: B 162 ARG cc_start: 0.8310 (mpt180) cc_final: 0.8067 (mpt90) REVERT: B 400 GLU cc_start: 0.8070 (tt0) cc_final: 0.7808 (tt0) REVERT: B 403 ASN cc_start: 0.7258 (m-40) cc_final: 0.6965 (m-40) REVERT: B 420 MET cc_start: 0.7958 (ttm) cc_final: 0.7585 (mmm) REVERT: B 459 LYS cc_start: 0.8071 (tttm) cc_final: 0.7630 (tttt) REVERT: C 64 ILE cc_start: 0.8550 (mt) cc_final: 0.8173 (mt) REVERT: C 162 ARG cc_start: 0.8297 (mpt180) cc_final: 0.8059 (mpt90) REVERT: C 370 GLN cc_start: 0.7780 (OUTLIER) cc_final: 0.7339 (tp-100) REVERT: C 381 GLN cc_start: 0.7715 (tm-30) cc_final: 0.7361 (tm-30) REVERT: C 400 GLU cc_start: 0.8047 (tt0) cc_final: 0.7755 (tt0) REVERT: C 459 LYS cc_start: 0.8143 (tttm) cc_final: 0.7714 (tttt) REVERT: H 5 THR cc_start: 0.6892 (OUTLIER) cc_final: 0.6610 (p) REVERT: I 5 THR cc_start: 0.6572 (OUTLIER) cc_final: 0.6115 (p) outliers start: 67 outliers final: 46 residues processed: 262 average time/residue: 1.2364 time to fit residues: 363.2066 Evaluate side-chains 225 residues out of total 1806 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 175 time to evaluate : 1.883 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 5 THR Chi-restraints excluded: chain G residue 25 SER Chi-restraints excluded: chain G residue 49 ILE Chi-restraints excluded: chain G residue 52 ASN Chi-restraints excluded: chain G residue 101 VAL Chi-restraints excluded: chain D residue 116 THR Chi-restraints excluded: chain E residue 118 THR Chi-restraints excluded: chain F residue 118 THR Chi-restraints excluded: chain A residue 29 SER Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 78 ILE Chi-restraints excluded: chain A residue 128 PHE Chi-restraints excluded: chain A residue 187 LYS Chi-restraints excluded: chain A residue 291 CYS Chi-restraints excluded: chain A residue 305 SER Chi-restraints excluded: chain A residue 334 LEU Chi-restraints excluded: chain A residue 383 SER Chi-restraints excluded: chain A residue 409 VAL Chi-restraints excluded: chain A residue 491 CYS Chi-restraints excluded: chain A residue 494 SER Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 128 PHE Chi-restraints excluded: chain B residue 291 CYS Chi-restraints excluded: chain B residue 305 SER Chi-restraints excluded: chain B residue 353 ILE Chi-restraints excluded: chain B residue 383 SER Chi-restraints excluded: chain B residue 409 VAL Chi-restraints excluded: chain B residue 491 CYS Chi-restraints excluded: chain B residue 494 SER Chi-restraints excluded: chain C residue 29 SER Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 128 PHE Chi-restraints excluded: chain C residue 187 LYS Chi-restraints excluded: chain C residue 291 CYS Chi-restraints excluded: chain C residue 305 SER Chi-restraints excluded: chain C residue 334 LEU Chi-restraints excluded: chain C residue 353 ILE Chi-restraints excluded: chain C residue 370 GLN Chi-restraints excluded: chain C residue 383 SER Chi-restraints excluded: chain C residue 409 VAL Chi-restraints excluded: chain C residue 491 CYS Chi-restraints excluded: chain C residue 494 SER Chi-restraints excluded: chain H residue 5 THR Chi-restraints excluded: chain H residue 25 SER Chi-restraints excluded: chain H residue 49 ILE Chi-restraints excluded: chain H residue 101 VAL Chi-restraints excluded: chain I residue 5 THR Chi-restraints excluded: chain I residue 25 SER Chi-restraints excluded: chain I residue 49 ILE Chi-restraints excluded: chain I residue 52 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 174 optimal weight: 2.9990 chunk 156 optimal weight: 5.9990 chunk 87 optimal weight: 7.9990 chunk 53 optimal weight: 0.0030 chunk 105 optimal weight: 0.5980 chunk 83 optimal weight: 4.9990 chunk 162 optimal weight: 3.9990 chunk 62 optimal weight: 6.9990 chunk 98 optimal weight: 5.9990 chunk 120 optimal weight: 2.9990 chunk 187 optimal weight: 10.0000 overall best weight: 2.1196 ------------------------------------------------------------------------------- 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: 0.8293 moved from start: 0.0865 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 17307 Z= 0.280 Angle : 0.645 8.498 23514 Z= 0.333 Chirality : 0.048 0.379 2640 Planarity : 0.005 0.060 3003 Dihedral : 11.281 68.561 3050 Min Nonbonded Distance : 2.187 Molprobity Statistics. All-atom Clashscore : 3.77 Ramachandran Plot: Outliers : 0.14 % Allowed : 2.53 % Favored : 97.33 % Rotamer: Outliers : 4.86 % Allowed : 23.06 % Favored : 72.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.26 (0.18), residues: 2100 helix: 2.43 (0.28), residues: 330 sheet: 0.90 (0.21), residues: 612 loop : -0.95 (0.16), residues: 1158 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 435 HIS 0.005 0.001 HIS A 25 PHE 0.019 0.002 PHE B 128 TYR 0.013 0.002 TYR I 99 ARG 0.004 0.000 ARG E 30 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4200 Ramachandran restraints generated. 2100 Oldfield, 0 Emsley, 2100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4200 Ramachandran restraints generated. 2100 Oldfield, 0 Emsley, 2100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 262 residues out of total 1806 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 81 poor density : 181 time to evaluate : 1.711 Fit side-chains REVERT: G 19 THR cc_start: 0.6098 (OUTLIER) cc_final: 0.5852 (t) REVERT: D 74 ASP cc_start: 0.8276 (m-30) cc_final: 0.8039 (m-30) REVERT: D 87 ARG cc_start: 0.7208 (mpt-90) cc_final: 0.6898 (mpt-90) REVERT: A 162 ARG cc_start: 0.8383 (mpt180) cc_final: 0.8067 (mpt90) REVERT: A 381 GLN cc_start: 0.7487 (OUTLIER) cc_final: 0.7230 (tm-30) REVERT: A 400 GLU cc_start: 0.8134 (tm-30) cc_final: 0.7848 (tt0) REVERT: A 403 ASN cc_start: 0.7324 (m-40) cc_final: 0.7042 (m-40) REVERT: A 459 LYS cc_start: 0.8334 (tttm) cc_final: 0.7897 (tttt) REVERT: B 162 ARG cc_start: 0.8414 (mpt180) cc_final: 0.8026 (mpt90) REVERT: B 400 GLU cc_start: 0.8189 (tm-30) cc_final: 0.7928 (tt0) REVERT: B 403 ASN cc_start: 0.7292 (m-40) cc_final: 0.6988 (m-40) REVERT: B 459 LYS cc_start: 0.8250 (tttm) cc_final: 0.7815 (tttt) REVERT: C 64 ILE cc_start: 0.8531 (OUTLIER) cc_final: 0.8117 (mt) REVERT: C 162 ARG cc_start: 0.8380 (mpt180) cc_final: 0.8148 (mpt90) REVERT: C 299 GLN cc_start: 0.8624 (mm-40) cc_final: 0.8376 (mm-40) REVERT: C 400 GLU cc_start: 0.8179 (tm-30) cc_final: 0.7902 (tt0) REVERT: C 459 LYS cc_start: 0.8261 (tttm) cc_final: 0.7832 (tttt) REVERT: H 19 THR cc_start: 0.6085 (OUTLIER) cc_final: 0.5838 (t) REVERT: I 19 THR cc_start: 0.5895 (OUTLIER) cc_final: 0.5670 (t) outliers start: 81 outliers final: 37 residues processed: 239 average time/residue: 1.3192 time to fit residues: 350.6724 Evaluate side-chains 210 residues out of total 1806 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 168 time to evaluate : 1.862 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 19 THR Chi-restraints excluded: chain G residue 49 ILE Chi-restraints excluded: chain G residue 52 ASN Chi-restraints excluded: chain G residue 101 VAL Chi-restraints excluded: chain D residue 11 VAL Chi-restraints excluded: chain D residue 46 GLU Chi-restraints excluded: chain D residue 107 THR Chi-restraints excluded: chain E residue 107 THR Chi-restraints excluded: chain F residue 69 THR Chi-restraints excluded: chain A residue 99 THR Chi-restraints excluded: chain A residue 128 PHE Chi-restraints excluded: chain A residue 330 MET Chi-restraints excluded: chain A residue 334 LEU Chi-restraints excluded: chain A residue 381 GLN Chi-restraints excluded: chain A residue 409 VAL Chi-restraints excluded: chain A residue 420 MET Chi-restraints excluded: chain A residue 476 ILE Chi-restraints excluded: chain A residue 491 CYS Chi-restraints excluded: chain B residue 123 SER Chi-restraints excluded: chain B residue 128 PHE Chi-restraints excluded: chain B residue 330 MET Chi-restraints excluded: chain B residue 362 ASP Chi-restraints excluded: chain B residue 409 VAL Chi-restraints excluded: chain B residue 476 ILE Chi-restraints excluded: chain B residue 491 CYS Chi-restraints excluded: chain C residue 64 ILE Chi-restraints excluded: chain C residue 78 ILE Chi-restraints excluded: chain C residue 99 THR Chi-restraints excluded: chain C residue 128 PHE Chi-restraints excluded: chain C residue 330 MET Chi-restraints excluded: chain C residue 334 LEU Chi-restraints excluded: chain C residue 353 ILE Chi-restraints excluded: chain C residue 362 ASP Chi-restraints excluded: chain C residue 409 VAL Chi-restraints excluded: chain C residue 476 ILE Chi-restraints excluded: chain C residue 491 CYS Chi-restraints excluded: chain H residue 19 THR Chi-restraints excluded: chain H residue 49 ILE Chi-restraints excluded: chain H residue 101 VAL Chi-restraints excluded: chain I residue 19 THR Chi-restraints excluded: chain I residue 49 ILE Chi-restraints excluded: chain I residue 52 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 104 optimal weight: 2.9990 chunk 58 optimal weight: 7.9990 chunk 156 optimal weight: 5.9990 chunk 128 optimal weight: 4.9990 chunk 51 optimal weight: 3.9990 chunk 188 optimal weight: 0.0670 chunk 203 optimal weight: 5.9990 chunk 167 optimal weight: 5.9990 chunk 186 optimal weight: 0.8980 chunk 64 optimal weight: 2.9990 chunk 151 optimal weight: 0.7980 overall best weight: 1.5522 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 39 GLN D 39 GLN E 39 GLN F 39 GLN C 403 ASN H 6 GLN H 38 GLN H 39 GLN ** I 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 39 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8278 moved from start: 0.1044 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 17307 Z= 0.218 Angle : 0.584 9.169 23514 Z= 0.303 Chirality : 0.046 0.380 2640 Planarity : 0.005 0.054 3003 Dihedral : 7.889 53.651 3009 Min Nonbonded Distance : 2.217 Molprobity Statistics. All-atom Clashscore : 3.56 Ramachandran Plot: Outliers : 0.14 % Allowed : 2.43 % Favored : 97.42 % Rotamer: Outliers : 5.14 % Allowed : 23.12 % Favored : 71.75 % 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: 0.40 (0.18), residues: 2100 helix: 2.36 (0.28), residues: 348 sheet: 1.10 (0.21), residues: 606 loop : -0.92 (0.17), residues: 1146 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 435 HIS 0.005 0.001 HIS A 25 PHE 0.019 0.002 PHE C 128 TYR 0.011 0.001 TYR I 99 ARG 0.003 0.000 ARG E 30 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4200 Ramachandran restraints generated. 2100 Oldfield, 0 Emsley, 2100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4200 Ramachandran restraints generated. 2100 Oldfield, 0 Emsley, 2100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 258 residues out of total 1806 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 86 poor density : 172 time to evaluate : 2.037 Fit side-chains REVERT: G 19 THR cc_start: 0.6085 (OUTLIER) cc_final: 0.5852 (t) REVERT: G 52 ASN cc_start: 0.6467 (OUTLIER) cc_final: 0.6170 (t160) REVERT: D 74 ASP cc_start: 0.8308 (m-30) cc_final: 0.8073 (m-30) REVERT: A 162 ARG cc_start: 0.8397 (mpt180) cc_final: 0.8057 (mpt90) REVERT: A 232 LYS cc_start: 0.8030 (OUTLIER) cc_final: 0.7275 (tptm) REVERT: A 400 GLU cc_start: 0.8039 (OUTLIER) cc_final: 0.7761 (tt0) REVERT: A 403 ASN cc_start: 0.7320 (m-40) cc_final: 0.7089 (m-40) REVERT: A 459 LYS cc_start: 0.8295 (tttm) cc_final: 0.7854 (tttt) REVERT: B 90 LYS cc_start: 0.8276 (OUTLIER) cc_final: 0.7842 (tttm) REVERT: B 162 ARG cc_start: 0.8399 (mpt180) cc_final: 0.8060 (mpt90) REVERT: B 232 LYS cc_start: 0.8081 (OUTLIER) cc_final: 0.7320 (tptm) REVERT: B 400 GLU cc_start: 0.8115 (OUTLIER) cc_final: 0.7840 (tt0) REVERT: B 403 ASN cc_start: 0.7308 (m-40) cc_final: 0.7014 (m-40) REVERT: B 420 MET cc_start: 0.8279 (OUTLIER) cc_final: 0.7841 (mmm) REVERT: B 459 LYS cc_start: 0.8237 (tttm) cc_final: 0.7797 (tttt) REVERT: C 22 ILE cc_start: 0.8942 (OUTLIER) cc_final: 0.8580 (mm) REVERT: C 64 ILE cc_start: 0.8517 (OUTLIER) cc_final: 0.8073 (mt) REVERT: C 90 LYS cc_start: 0.8234 (OUTLIER) cc_final: 0.8032 (tttm) REVERT: C 162 ARG cc_start: 0.8351 (mpt180) cc_final: 0.8109 (mpt90) REVERT: C 232 LYS cc_start: 0.8019 (OUTLIER) cc_final: 0.7233 (tptm) REVERT: C 299 GLN cc_start: 0.8598 (mm-40) cc_final: 0.8350 (mm-40) REVERT: C 400 GLU cc_start: 0.8087 (OUTLIER) cc_final: 0.7800 (tt0) REVERT: C 459 LYS cc_start: 0.8243 (tttm) cc_final: 0.7806 (tttt) REVERT: H 19 THR cc_start: 0.6032 (OUTLIER) cc_final: 0.5799 (t) outliers start: 86 outliers final: 49 residues processed: 232 average time/residue: 1.3206 time to fit residues: 341.2280 Evaluate side-chains 229 residues out of total 1806 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 166 time to evaluate : 1.739 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 19 THR Chi-restraints excluded: chain G residue 49 ILE Chi-restraints excluded: chain G residue 52 ASN Chi-restraints excluded: chain G residue 101 VAL Chi-restraints excluded: chain G residue 110 VAL Chi-restraints excluded: chain D residue 46 GLU Chi-restraints excluded: chain D residue 69 THR Chi-restraints excluded: chain D residue 107 THR Chi-restraints excluded: chain E residue 69 THR Chi-restraints excluded: chain E residue 107 THR Chi-restraints excluded: chain A residue 19 THR Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 99 THR Chi-restraints excluded: chain A residue 128 PHE Chi-restraints excluded: chain A residue 168 THR Chi-restraints excluded: chain A residue 232 LYS Chi-restraints excluded: chain A residue 330 MET Chi-restraints excluded: chain A residue 334 LEU Chi-restraints excluded: chain A residue 400 GLU Chi-restraints excluded: chain A residue 409 VAL Chi-restraints excluded: chain A residue 476 ILE Chi-restraints excluded: chain A residue 491 CYS Chi-restraints excluded: chain B residue 19 THR Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 90 LYS Chi-restraints excluded: chain B residue 123 SER Chi-restraints excluded: chain B residue 128 PHE Chi-restraints excluded: chain B residue 168 THR Chi-restraints excluded: chain B residue 207 LEU Chi-restraints excluded: chain B residue 232 LYS Chi-restraints excluded: chain B residue 238 ASP Chi-restraints excluded: chain B residue 330 MET Chi-restraints excluded: chain B residue 362 ASP Chi-restraints excluded: chain B residue 400 GLU Chi-restraints excluded: chain B residue 409 VAL Chi-restraints excluded: chain B residue 420 MET Chi-restraints excluded: chain B residue 476 ILE Chi-restraints excluded: chain B residue 491 CYS Chi-restraints excluded: chain C residue 19 THR Chi-restraints excluded: chain C residue 22 ILE Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 64 ILE Chi-restraints excluded: chain C residue 90 LYS Chi-restraints excluded: chain C residue 99 THR Chi-restraints excluded: chain C residue 128 PHE Chi-restraints excluded: chain C residue 168 THR Chi-restraints excluded: chain C residue 232 LYS Chi-restraints excluded: chain C residue 294 LYS Chi-restraints excluded: chain C residue 330 MET Chi-restraints excluded: chain C residue 334 LEU Chi-restraints excluded: chain C residue 362 ASP Chi-restraints excluded: chain C residue 400 GLU Chi-restraints excluded: chain C residue 409 VAL Chi-restraints excluded: chain C residue 476 ILE Chi-restraints excluded: chain C residue 491 CYS Chi-restraints excluded: chain H residue 19 THR Chi-restraints excluded: chain H residue 32 ASP Chi-restraints excluded: chain H residue 49 ILE Chi-restraints excluded: chain H residue 52 ASN Chi-restraints excluded: chain H residue 101 VAL Chi-restraints excluded: chain I residue 49 ILE Chi-restraints excluded: chain I residue 52 ASN Chi-restraints excluded: chain I residue 91 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 186 optimal weight: 3.9990 chunk 141 optimal weight: 3.9990 chunk 97 optimal weight: 2.9990 chunk 20 optimal weight: 0.4980 chunk 89 optimal weight: 3.9990 chunk 126 optimal weight: 0.7980 chunk 188 optimal weight: 6.9990 chunk 200 optimal weight: 9.9990 chunk 98 optimal weight: 0.0020 chunk 179 optimal weight: 2.9990 chunk 53 optimal weight: 6.9990 overall best weight: 1.4592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 6 GLN C 403 ASN H 6 GLN I 38 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8277 moved from start: 0.1151 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 17307 Z= 0.209 Angle : 0.569 8.892 23514 Z= 0.298 Chirality : 0.046 0.384 2640 Planarity : 0.005 0.053 3003 Dihedral : 7.135 54.184 3007 Min Nonbonded Distance : 2.210 Molprobity Statistics. All-atom Clashscore : 3.68 Ramachandran Plot: Outliers : 0.14 % Allowed : 2.34 % Favored : 97.52 % Rotamer: Outliers : 5.53 % Allowed : 22.61 % Favored : 71.86 % 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: 0.48 (0.18), residues: 2100 helix: 2.42 (0.28), residues: 348 sheet: 1.21 (0.21), residues: 606 loop : -0.90 (0.17), residues: 1146 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 435 HIS 0.005 0.001 HIS A 25 PHE 0.018 0.002 PHE C 128 TYR 0.011 0.001 TYR I 99 ARG 0.003 0.000 ARG E 30 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4200 Ramachandran restraints generated. 2100 Oldfield, 0 Emsley, 2100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4200 Ramachandran restraints generated. 2100 Oldfield, 0 Emsley, 2100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 269 residues out of total 1806 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 93 poor density : 176 time to evaluate : 1.813 Fit side-chains REVERT: G 19 THR cc_start: 0.6107 (OUTLIER) cc_final: 0.5870 (t) REVERT: G 52 ASN cc_start: 0.6325 (OUTLIER) cc_final: 0.6018 (t160) REVERT: D 74 ASP cc_start: 0.8321 (m-30) cc_final: 0.8094 (m-30) REVERT: A 162 ARG cc_start: 0.8379 (mpt180) cc_final: 0.8043 (mpt90) REVERT: A 232 LYS cc_start: 0.7991 (OUTLIER) cc_final: 0.7239 (tptm) REVERT: A 400 GLU cc_start: 0.8051 (OUTLIER) cc_final: 0.7766 (tt0) REVERT: A 403 ASN cc_start: 0.7328 (m-40) cc_final: 0.7102 (m-40) REVERT: A 459 LYS cc_start: 0.8276 (tttm) cc_final: 0.7835 (tttt) REVERT: A 486 LYS cc_start: 0.6697 (mmpt) cc_final: 0.6322 (pptt) REVERT: B 90 LYS cc_start: 0.8276 (OUTLIER) cc_final: 0.7880 (tttm) REVERT: B 162 ARG cc_start: 0.8399 (mpt180) cc_final: 0.8066 (mpt90) REVERT: B 232 LYS cc_start: 0.8079 (OUTLIER) cc_final: 0.7316 (tptm) REVERT: B 400 GLU cc_start: 0.8132 (OUTLIER) cc_final: 0.7855 (tt0) REVERT: B 403 ASN cc_start: 0.7299 (m-40) cc_final: 0.7029 (m-40) REVERT: B 420 MET cc_start: 0.8279 (OUTLIER) cc_final: 0.7834 (mmm) REVERT: B 459 LYS cc_start: 0.8224 (tttm) cc_final: 0.7787 (tttt) REVERT: B 486 LYS cc_start: 0.6827 (mmpt) cc_final: 0.6414 (pptt) REVERT: C 22 ILE cc_start: 0.8939 (OUTLIER) cc_final: 0.8580 (mm) REVERT: C 64 ILE cc_start: 0.8503 (mt) cc_final: 0.8044 (mt) REVERT: C 162 ARG cc_start: 0.8335 (mpt180) cc_final: 0.8092 (mpt90) REVERT: C 232 LYS cc_start: 0.8011 (OUTLIER) cc_final: 0.7218 (tptm) REVERT: C 299 GLN cc_start: 0.8589 (mm-40) cc_final: 0.8345 (mm-40) REVERT: C 370 GLN cc_start: 0.7861 (OUTLIER) cc_final: 0.6934 (tp-100) REVERT: C 400 GLU cc_start: 0.8093 (OUTLIER) cc_final: 0.7798 (tt0) REVERT: C 459 LYS cc_start: 0.8236 (tttm) cc_final: 0.7800 (tttt) REVERT: C 486 LYS cc_start: 0.6771 (mmpt) cc_final: 0.6359 (pptt) REVERT: H 19 THR cc_start: 0.6003 (OUTLIER) cc_final: 0.5778 (t) outliers start: 93 outliers final: 55 residues processed: 244 average time/residue: 1.3078 time to fit residues: 354.4146 Evaluate side-chains 236 residues out of total 1806 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 168 time to evaluate : 1.947 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 19 THR Chi-restraints excluded: chain G residue 32 ASP Chi-restraints excluded: chain G residue 49 ILE Chi-restraints excluded: chain G residue 52 ASN Chi-restraints excluded: chain G residue 101 VAL Chi-restraints excluded: chain G residue 110 VAL Chi-restraints excluded: chain D residue 46 GLU Chi-restraints excluded: chain D residue 107 THR Chi-restraints excluded: chain E residue 107 THR Chi-restraints excluded: chain F residue 107 THR Chi-restraints excluded: chain A residue 19 THR Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 99 THR Chi-restraints excluded: chain A residue 128 PHE Chi-restraints excluded: chain A residue 201 ILE Chi-restraints excluded: chain A residue 232 LYS Chi-restraints excluded: chain A residue 238 ASP Chi-restraints excluded: chain A residue 291 CYS Chi-restraints excluded: chain A residue 330 MET Chi-restraints excluded: chain A residue 334 LEU Chi-restraints excluded: chain A residue 400 GLU Chi-restraints excluded: chain A residue 409 VAL Chi-restraints excluded: chain A residue 420 MET Chi-restraints excluded: chain A residue 476 ILE Chi-restraints excluded: chain A residue 491 CYS Chi-restraints excluded: chain B residue 19 THR Chi-restraints excluded: chain B residue 90 LYS Chi-restraints excluded: chain B residue 123 SER Chi-restraints excluded: chain B residue 128 PHE Chi-restraints excluded: chain B residue 168 THR Chi-restraints excluded: chain B residue 232 LYS Chi-restraints excluded: chain B residue 238 ASP Chi-restraints excluded: chain B residue 274 SER Chi-restraints excluded: chain B residue 291 CYS Chi-restraints excluded: chain B residue 330 MET Chi-restraints excluded: chain B residue 362 ASP Chi-restraints excluded: chain B residue 400 GLU Chi-restraints excluded: chain B residue 420 MET Chi-restraints excluded: chain B residue 476 ILE Chi-restraints excluded: chain B residue 491 CYS Chi-restraints excluded: chain C residue 19 THR Chi-restraints excluded: chain C residue 22 ILE Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 99 THR Chi-restraints excluded: chain C residue 128 PHE Chi-restraints excluded: chain C residue 168 THR Chi-restraints excluded: chain C residue 187 LYS Chi-restraints excluded: chain C residue 232 LYS Chi-restraints excluded: chain C residue 274 SER Chi-restraints excluded: chain C residue 330 MET Chi-restraints excluded: chain C residue 334 LEU Chi-restraints excluded: chain C residue 362 ASP Chi-restraints excluded: chain C residue 370 GLN Chi-restraints excluded: chain C residue 372 GLU Chi-restraints excluded: chain C residue 400 GLU Chi-restraints excluded: chain C residue 409 VAL Chi-restraints excluded: chain C residue 476 ILE Chi-restraints excluded: chain C residue 491 CYS Chi-restraints excluded: chain H residue 19 THR Chi-restraints excluded: chain H residue 49 ILE Chi-restraints excluded: chain H residue 52 ASN Chi-restraints excluded: chain H residue 101 VAL Chi-restraints excluded: chain H residue 110 VAL Chi-restraints excluded: chain I residue 19 THR Chi-restraints excluded: chain I residue 49 ILE Chi-restraints excluded: chain I residue 52 ASN Chi-restraints excluded: chain I residue 91 THR Chi-restraints excluded: chain I residue 110 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 166 optimal weight: 9.9990 chunk 113 optimal weight: 1.9990 chunk 2 optimal weight: 20.0000 chunk 148 optimal weight: 0.5980 chunk 82 optimal weight: 3.9990 chunk 170 optimal weight: 0.4980 chunk 138 optimal weight: 0.8980 chunk 0 optimal weight: 9.9990 chunk 102 optimal weight: 0.9980 chunk 179 optimal weight: 4.9990 chunk 50 optimal weight: 0.4980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 6 GLN G 38 GLN C 403 ASN H 6 GLN I 6 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8236 moved from start: 0.1145 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 17307 Z= 0.139 Angle : 0.496 8.601 23514 Z= 0.260 Chirality : 0.043 0.332 2640 Planarity : 0.004 0.052 3003 Dihedral : 6.581 54.622 3006 Min Nonbonded Distance : 2.240 Molprobity Statistics. All-atom Clashscore : 3.65 Ramachandran Plot: Outliers : 0.14 % Allowed : 2.34 % Favored : 97.52 % Rotamer: Outliers : 4.69 % Allowed : 23.79 % Favored : 71.52 % 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: 0.67 (0.18), residues: 2100 helix: 2.65 (0.28), residues: 342 sheet: 1.39 (0.21), residues: 600 loop : -0.81 (0.17), residues: 1158 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 435 HIS 0.004 0.001 HIS A 369 PHE 0.016 0.001 PHE B 128 TYR 0.010 0.001 TYR G 33 ARG 0.002 0.000 ARG F 87 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4200 Ramachandran restraints generated. 2100 Oldfield, 0 Emsley, 2100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4200 Ramachandran restraints generated. 2100 Oldfield, 0 Emsley, 2100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 258 residues out of total 1806 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 78 poor density : 180 time to evaluate : 2.004 Fit side-chains revert: symmetry clash REVERT: G 52 ASN cc_start: 0.6127 (OUTLIER) cc_final: 0.5860 (t160) REVERT: D 74 ASP cc_start: 0.8293 (m-30) cc_final: 0.8049 (m-30) REVERT: A 162 ARG cc_start: 0.8366 (mpt180) cc_final: 0.8054 (mpt90) REVERT: A 232 LYS cc_start: 0.7937 (OUTLIER) cc_final: 0.7232 (tptm) REVERT: A 400 GLU cc_start: 0.7929 (OUTLIER) cc_final: 0.7640 (tt0) REVERT: A 403 ASN cc_start: 0.7306 (m-40) cc_final: 0.7092 (m-40) REVERT: A 459 LYS cc_start: 0.8196 (tttm) cc_final: 0.7746 (tttt) REVERT: A 486 LYS cc_start: 0.6737 (mmpt) cc_final: 0.6367 (pptt) REVERT: B 39 LYS cc_start: 0.8900 (OUTLIER) cc_final: 0.8317 (mmtt) REVERT: B 90 LYS cc_start: 0.8251 (OUTLIER) cc_final: 0.7855 (tttm) REVERT: B 162 ARG cc_start: 0.8388 (mpt180) cc_final: 0.8071 (mpt90) REVERT: B 232 LYS cc_start: 0.8032 (OUTLIER) cc_final: 0.7312 (tptm) REVERT: B 400 GLU cc_start: 0.7991 (OUTLIER) cc_final: 0.7715 (tt0) REVERT: B 403 ASN cc_start: 0.7279 (m-40) cc_final: 0.7015 (m-40) REVERT: B 420 MET cc_start: 0.8093 (OUTLIER) cc_final: 0.7686 (mmm) REVERT: B 459 LYS cc_start: 0.8118 (tttm) cc_final: 0.7677 (tttt) REVERT: B 486 LYS cc_start: 0.6746 (mmpt) cc_final: 0.6383 (pptt) REVERT: C 64 ILE cc_start: 0.8465 (mt) cc_final: 0.8006 (mt) REVERT: C 90 LYS cc_start: 0.8210 (OUTLIER) cc_final: 0.7993 (tttm) REVERT: C 162 ARG cc_start: 0.8325 (mpt180) cc_final: 0.8108 (mpt90) REVERT: C 232 LYS cc_start: 0.7934 (OUTLIER) cc_final: 0.7166 (tptm) REVERT: C 259 GLU cc_start: 0.8102 (OUTLIER) cc_final: 0.7849 (mt-10) REVERT: C 299 GLN cc_start: 0.8557 (mm-40) cc_final: 0.8313 (mm-40) REVERT: C 370 GLN cc_start: 0.7778 (OUTLIER) cc_final: 0.7254 (tp-100) REVERT: C 400 GLU cc_start: 0.7971 (OUTLIER) cc_final: 0.7681 (tt0) REVERT: C 420 MET cc_start: 0.8071 (OUTLIER) cc_final: 0.7694 (mmm) REVERT: C 459 LYS cc_start: 0.8157 (tttm) cc_final: 0.7721 (tttt) REVERT: C 486 LYS cc_start: 0.6793 (mmpt) cc_final: 0.6381 (pptt) outliers start: 78 outliers final: 43 residues processed: 237 average time/residue: 1.3789 time to fit residues: 361.4345 Evaluate side-chains 232 residues out of total 1806 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 175 time to evaluate : 2.000 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 49 ILE Chi-restraints excluded: chain G residue 52 ASN Chi-restraints excluded: chain G residue 101 VAL Chi-restraints excluded: chain D residue 46 GLU Chi-restraints excluded: chain D residue 107 THR Chi-restraints excluded: chain E residue 46 GLU Chi-restraints excluded: chain E residue 107 THR Chi-restraints excluded: chain F residue 107 THR Chi-restraints excluded: chain A residue 19 THR Chi-restraints excluded: chain A residue 99 THR Chi-restraints excluded: chain A residue 168 THR Chi-restraints excluded: chain A residue 201 ILE Chi-restraints excluded: chain A residue 232 LYS Chi-restraints excluded: chain A residue 330 MET Chi-restraints excluded: chain A residue 334 LEU Chi-restraints excluded: chain A residue 400 GLU Chi-restraints excluded: chain A residue 409 VAL Chi-restraints excluded: chain A residue 476 ILE Chi-restraints excluded: chain A residue 491 CYS Chi-restraints excluded: chain B residue 19 THR Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 39 LYS Chi-restraints excluded: chain B residue 90 LYS Chi-restraints excluded: chain B residue 98 GLU Chi-restraints excluded: chain B residue 123 SER Chi-restraints excluded: chain B residue 168 THR Chi-restraints excluded: chain B residue 232 LYS Chi-restraints excluded: chain B residue 238 ASP Chi-restraints excluded: chain B residue 291 CYS Chi-restraints excluded: chain B residue 334 LEU Chi-restraints excluded: chain B residue 362 ASP Chi-restraints excluded: chain B residue 400 GLU Chi-restraints excluded: chain B residue 420 MET Chi-restraints excluded: chain B residue 476 ILE Chi-restraints excluded: chain B residue 487 CYS Chi-restraints excluded: chain B residue 491 CYS Chi-restraints excluded: chain C residue 90 LYS Chi-restraints excluded: chain C residue 99 THR Chi-restraints excluded: chain C residue 168 THR Chi-restraints excluded: chain C residue 232 LYS Chi-restraints excluded: chain C residue 259 GLU Chi-restraints excluded: chain C residue 291 CYS Chi-restraints excluded: chain C residue 294 LYS Chi-restraints excluded: chain C residue 330 MET Chi-restraints excluded: chain C residue 334 LEU Chi-restraints excluded: chain C residue 370 GLN Chi-restraints excluded: chain C residue 400 GLU Chi-restraints excluded: chain C residue 409 VAL Chi-restraints excluded: chain C residue 420 MET Chi-restraints excluded: chain C residue 476 ILE Chi-restraints excluded: chain C residue 491 CYS Chi-restraints excluded: chain H residue 32 ASP Chi-restraints excluded: chain H residue 49 ILE Chi-restraints excluded: chain H residue 101 VAL Chi-restraints excluded: chain I residue 19 THR Chi-restraints excluded: chain I residue 49 ILE Chi-restraints excluded: chain I residue 91 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 67 optimal weight: 0.9990 chunk 180 optimal weight: 2.9990 chunk 39 optimal weight: 3.9990 chunk 117 optimal weight: 0.0570 chunk 49 optimal weight: 2.9990 chunk 200 optimal weight: 0.6980 chunk 166 optimal weight: 10.0000 chunk 92 optimal weight: 0.9990 chunk 16 optimal weight: 4.9990 chunk 66 optimal weight: 2.9990 chunk 105 optimal weight: 7.9990 overall best weight: 1.1504 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 6 GLN C 403 ASN ** I 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8256 moved from start: 0.1205 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 17307 Z= 0.178 Angle : 0.529 8.872 23514 Z= 0.277 Chirality : 0.044 0.345 2640 Planarity : 0.004 0.051 3003 Dihedral : 6.223 54.478 2998 Min Nonbonded Distance : 2.227 Molprobity Statistics. All-atom Clashscore : 3.65 Ramachandran Plot: Outliers : 0.14 % Allowed : 2.24 % Favored : 97.62 % Rotamer: Outliers : 5.03 % Allowed : 23.62 % Favored : 71.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.67 (0.18), residues: 2100 helix: 2.67 (0.28), residues: 342 sheet: 1.35 (0.21), residues: 606 loop : -0.80 (0.17), residues: 1152 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 435 HIS 0.004 0.001 HIS A 25 PHE 0.020 0.002 PHE B 128 TYR 0.010 0.001 TYR I 99 ARG 0.002 0.000 ARG E 30 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4200 Ramachandran restraints generated. 2100 Oldfield, 0 Emsley, 2100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4200 Ramachandran restraints generated. 2100 Oldfield, 0 Emsley, 2100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 259 residues out of total 1806 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 84 poor density : 175 time to evaluate : 2.117 Fit side-chains REVERT: G 19 THR cc_start: 0.6062 (OUTLIER) cc_final: 0.5840 (t) REVERT: D 74 ASP cc_start: 0.8292 (m-30) cc_final: 0.8045 (m-30) REVERT: A 68 GLN cc_start: 0.8868 (mt0) cc_final: 0.8375 (mt0) REVERT: A 162 ARG cc_start: 0.8382 (mpt180) cc_final: 0.8070 (mpt90) REVERT: A 232 LYS cc_start: 0.7962 (OUTLIER) cc_final: 0.7252 (tptm) REVERT: A 259 GLU cc_start: 0.8139 (OUTLIER) cc_final: 0.7937 (mt-10) REVERT: A 400 GLU cc_start: 0.8011 (OUTLIER) cc_final: 0.7738 (tt0) REVERT: A 403 ASN cc_start: 0.7315 (m-40) cc_final: 0.7089 (m-40) REVERT: A 459 LYS cc_start: 0.8216 (tttm) cc_final: 0.7776 (tttt) REVERT: A 486 LYS cc_start: 0.6764 (mmpt) cc_final: 0.6380 (pptt) REVERT: B 90 LYS cc_start: 0.8268 (OUTLIER) cc_final: 0.7892 (tttm) REVERT: B 162 ARG cc_start: 0.8400 (mpt180) cc_final: 0.8077 (mpt90) REVERT: B 232 LYS cc_start: 0.8058 (OUTLIER) cc_final: 0.7335 (tptm) REVERT: B 400 GLU cc_start: 0.8089 (OUTLIER) cc_final: 0.7811 (tt0) REVERT: B 403 ASN cc_start: 0.7301 (m-40) cc_final: 0.7033 (m-40) REVERT: B 420 MET cc_start: 0.8195 (OUTLIER) cc_final: 0.7767 (mmm) REVERT: B 459 LYS cc_start: 0.8156 (tttm) cc_final: 0.7727 (tttt) REVERT: B 486 LYS cc_start: 0.6783 (mmpt) cc_final: 0.6396 (pptt) REVERT: C 64 ILE cc_start: 0.8475 (mt) cc_final: 0.8016 (mt) REVERT: C 90 LYS cc_start: 0.8204 (OUTLIER) cc_final: 0.7986 (tttm) REVERT: C 162 ARG cc_start: 0.8332 (mpt180) cc_final: 0.8127 (mpt90) REVERT: C 232 LYS cc_start: 0.7956 (OUTLIER) cc_final: 0.7192 (tptm) REVERT: C 259 GLU cc_start: 0.8128 (OUTLIER) cc_final: 0.7874 (mt-10) REVERT: C 299 GLN cc_start: 0.8571 (mm-40) cc_final: 0.8328 (mm-40) REVERT: C 370 GLN cc_start: 0.7803 (OUTLIER) cc_final: 0.7040 (tp-100) REVERT: C 400 GLU cc_start: 0.8045 (OUTLIER) cc_final: 0.7751 (tt0) REVERT: C 459 LYS cc_start: 0.8169 (tttm) cc_final: 0.7737 (tttt) REVERT: C 486 LYS cc_start: 0.6775 (mmpt) cc_final: 0.6400 (pptt) outliers start: 84 outliers final: 55 residues processed: 236 average time/residue: 1.3448 time to fit residues: 351.6921 Evaluate side-chains 241 residues out of total 1806 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 173 time to evaluate : 1.735 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 19 THR Chi-restraints excluded: chain G residue 32 ASP Chi-restraints excluded: chain G residue 49 ILE Chi-restraints excluded: chain G residue 101 VAL Chi-restraints excluded: chain D residue 46 GLU Chi-restraints excluded: chain D residue 107 THR Chi-restraints excluded: chain E residue 46 GLU Chi-restraints excluded: chain E residue 107 THR Chi-restraints excluded: chain F residue 107 THR Chi-restraints excluded: chain A residue 19 THR Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 92 SER Chi-restraints excluded: chain A residue 99 THR Chi-restraints excluded: chain A residue 128 PHE Chi-restraints excluded: chain A residue 201 ILE Chi-restraints excluded: chain A residue 232 LYS Chi-restraints excluded: chain A residue 238 ASP Chi-restraints excluded: chain A residue 259 GLU Chi-restraints excluded: chain A residue 291 CYS Chi-restraints excluded: chain A residue 330 MET Chi-restraints excluded: chain A residue 334 LEU Chi-restraints excluded: chain A residue 400 GLU Chi-restraints excluded: chain A residue 409 VAL Chi-restraints excluded: chain A residue 420 MET Chi-restraints excluded: chain A residue 476 ILE Chi-restraints excluded: chain A residue 491 CYS Chi-restraints excluded: chain B residue 19 THR Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 90 LYS Chi-restraints excluded: chain B residue 99 THR Chi-restraints excluded: chain B residue 123 SER Chi-restraints excluded: chain B residue 128 PHE Chi-restraints excluded: chain B residue 168 THR Chi-restraints excluded: chain B residue 187 LYS Chi-restraints excluded: chain B residue 232 LYS Chi-restraints excluded: chain B residue 238 ASP Chi-restraints excluded: chain B residue 291 CYS Chi-restraints excluded: chain B residue 330 MET Chi-restraints excluded: chain B residue 334 LEU Chi-restraints excluded: chain B residue 400 GLU Chi-restraints excluded: chain B residue 420 MET Chi-restraints excluded: chain B residue 476 ILE Chi-restraints excluded: chain B residue 491 CYS Chi-restraints excluded: chain C residue 90 LYS Chi-restraints excluded: chain C residue 99 THR Chi-restraints excluded: chain C residue 128 PHE Chi-restraints excluded: chain C residue 168 THR Chi-restraints excluded: chain C residue 187 LYS Chi-restraints excluded: chain C residue 232 LYS Chi-restraints excluded: chain C residue 259 GLU Chi-restraints excluded: chain C residue 274 SER Chi-restraints excluded: chain C residue 291 CYS Chi-restraints excluded: chain C residue 294 LYS Chi-restraints excluded: chain C residue 330 MET Chi-restraints excluded: chain C residue 334 LEU Chi-restraints excluded: chain C residue 353 ILE Chi-restraints excluded: chain C residue 370 GLN Chi-restraints excluded: chain C residue 400 GLU Chi-restraints excluded: chain C residue 409 VAL Chi-restraints excluded: chain C residue 476 ILE Chi-restraints excluded: chain C residue 491 CYS Chi-restraints excluded: chain H residue 32 ASP Chi-restraints excluded: chain H residue 49 ILE Chi-restraints excluded: chain H residue 52 ASN Chi-restraints excluded: chain H residue 101 VAL Chi-restraints excluded: chain I residue 19 THR Chi-restraints excluded: chain I residue 49 ILE Chi-restraints excluded: chain I residue 91 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 193 optimal weight: 1.9990 chunk 22 optimal weight: 5.9990 chunk 114 optimal weight: 3.9990 chunk 146 optimal weight: 4.9990 chunk 113 optimal weight: 0.8980 chunk 168 optimal weight: 1.9990 chunk 111 optimal weight: 0.8980 chunk 199 optimal weight: 30.0000 chunk 124 optimal weight: 1.9990 chunk 121 optimal weight: 6.9990 chunk 92 optimal weight: 1.9990 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 403 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8279 moved from start: 0.1297 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 17307 Z= 0.222 Angle : 0.574 9.359 23514 Z= 0.301 Chirality : 0.046 0.381 2640 Planarity : 0.005 0.052 3003 Dihedral : 6.147 52.361 2996 Min Nonbonded Distance : 2.204 Molprobity Statistics. All-atom Clashscore : 3.68 Ramachandran Plot: Outliers : 0.14 % Allowed : 2.53 % Favored : 97.33 % Rotamer: Outliers : 4.91 % Allowed : 23.67 % Favored : 71.41 % 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: 0.63 (0.18), residues: 2100 helix: 2.64 (0.28), residues: 342 sheet: 1.38 (0.21), residues: 606 loop : -0.86 (0.16), residues: 1152 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 435 HIS 0.005 0.001 HIS A 25 PHE 0.024 0.002 PHE B 128 TYR 0.012 0.002 TYR I 99 ARG 0.003 0.000 ARG E 30 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4200 Ramachandran restraints generated. 2100 Oldfield, 0 Emsley, 2100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4200 Ramachandran restraints generated. 2100 Oldfield, 0 Emsley, 2100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 255 residues out of total 1806 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 82 poor density : 173 time to evaluate : 1.861 Fit side-chains REVERT: G 19 THR cc_start: 0.6080 (OUTLIER) cc_final: 0.5871 (t) REVERT: D 74 ASP cc_start: 0.8313 (m-30) cc_final: 0.8074 (m-30) REVERT: A 68 GLN cc_start: 0.8868 (mt0) cc_final: 0.8344 (mt0) REVERT: A 162 ARG cc_start: 0.8386 (mpt180) cc_final: 0.8059 (mpt90) REVERT: A 232 LYS cc_start: 0.7980 (OUTLIER) cc_final: 0.7238 (tptm) REVERT: A 381 GLN cc_start: 0.7563 (OUTLIER) cc_final: 0.7097 (mt0) REVERT: A 400 GLU cc_start: 0.8065 (OUTLIER) cc_final: 0.7790 (tt0) REVERT: A 403 ASN cc_start: 0.7319 (m-40) cc_final: 0.7087 (m-40) REVERT: A 459 LYS cc_start: 0.8298 (tttm) cc_final: 0.7864 (tttt) REVERT: A 486 LYS cc_start: 0.6768 (mmpt) cc_final: 0.6413 (pptt) REVERT: B 90 LYS cc_start: 0.8281 (OUTLIER) cc_final: 0.7870 (tttm) REVERT: B 162 ARG cc_start: 0.8406 (mpt180) cc_final: 0.8073 (mpt90) REVERT: B 232 LYS cc_start: 0.8087 (OUTLIER) cc_final: 0.7327 (tptm) REVERT: B 400 GLU cc_start: 0.8122 (OUTLIER) cc_final: 0.7850 (tt0) REVERT: B 403 ASN cc_start: 0.7326 (m-40) cc_final: 0.7054 (m-40) REVERT: B 420 MET cc_start: 0.8293 (OUTLIER) cc_final: 0.7837 (mmm) REVERT: B 459 LYS cc_start: 0.8228 (tttm) cc_final: 0.7794 (tttt) REVERT: B 486 LYS cc_start: 0.6810 (mmpt) cc_final: 0.6442 (pptt) REVERT: C 64 ILE cc_start: 0.8470 (mt) cc_final: 0.8012 (mt) REVERT: C 90 LYS cc_start: 0.8268 (OUTLIER) cc_final: 0.8061 (tttm) REVERT: C 162 ARG cc_start: 0.8346 (mpt180) cc_final: 0.8145 (mpt90) REVERT: C 232 LYS cc_start: 0.7972 (OUTLIER) cc_final: 0.7191 (tptm) REVERT: C 299 GLN cc_start: 0.8587 (mm-40) cc_final: 0.8350 (mm-40) REVERT: C 370 GLN cc_start: 0.7856 (OUTLIER) cc_final: 0.6895 (tp-100) REVERT: C 400 GLU cc_start: 0.8106 (OUTLIER) cc_final: 0.7812 (tt0) REVERT: C 403 ASN cc_start: 0.7339 (m-40) cc_final: 0.7077 (m-40) REVERT: C 459 LYS cc_start: 0.8225 (tttm) cc_final: 0.7795 (tttt) REVERT: C 486 LYS cc_start: 0.6782 (mmpt) cc_final: 0.6428 (pptt) REVERT: H 19 THR cc_start: 0.5992 (OUTLIER) cc_final: 0.5790 (t) outliers start: 82 outliers final: 54 residues processed: 233 average time/residue: 1.2747 time to fit residues: 331.4562 Evaluate side-chains 239 residues out of total 1806 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 172 time to evaluate : 1.883 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 19 THR Chi-restraints excluded: chain G residue 32 ASP Chi-restraints excluded: chain G residue 49 ILE Chi-restraints excluded: chain G residue 101 VAL Chi-restraints excluded: chain D residue 46 GLU Chi-restraints excluded: chain D residue 107 THR Chi-restraints excluded: chain E residue 107 THR Chi-restraints excluded: chain F residue 107 THR Chi-restraints excluded: chain A residue 19 THR Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 92 SER Chi-restraints excluded: chain A residue 99 THR Chi-restraints excluded: chain A residue 128 PHE Chi-restraints excluded: chain A residue 201 ILE Chi-restraints excluded: chain A residue 232 LYS Chi-restraints excluded: chain A residue 238 ASP Chi-restraints excluded: chain A residue 291 CYS Chi-restraints excluded: chain A residue 330 MET Chi-restraints excluded: chain A residue 334 LEU Chi-restraints excluded: chain A residue 381 GLN Chi-restraints excluded: chain A residue 400 GLU Chi-restraints excluded: chain A residue 409 VAL Chi-restraints excluded: chain A residue 420 MET Chi-restraints excluded: chain A residue 476 ILE Chi-restraints excluded: chain A residue 491 CYS Chi-restraints excluded: chain B residue 19 THR Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 90 LYS Chi-restraints excluded: chain B residue 123 SER Chi-restraints excluded: chain B residue 128 PHE Chi-restraints excluded: chain B residue 168 THR Chi-restraints excluded: chain B residue 187 LYS Chi-restraints excluded: chain B residue 232 LYS Chi-restraints excluded: chain B residue 238 ASP Chi-restraints excluded: chain B residue 274 SER Chi-restraints excluded: chain B residue 291 CYS Chi-restraints excluded: chain B residue 400 GLU Chi-restraints excluded: chain B residue 409 VAL Chi-restraints excluded: chain B residue 420 MET Chi-restraints excluded: chain B residue 476 ILE Chi-restraints excluded: chain B residue 491 CYS Chi-restraints excluded: chain C residue 19 THR Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 90 LYS Chi-restraints excluded: chain C residue 99 THR Chi-restraints excluded: chain C residue 128 PHE Chi-restraints excluded: chain C residue 168 THR Chi-restraints excluded: chain C residue 187 LYS Chi-restraints excluded: chain C residue 232 LYS Chi-restraints excluded: chain C residue 274 SER Chi-restraints excluded: chain C residue 291 CYS Chi-restraints excluded: chain C residue 294 LYS Chi-restraints excluded: chain C residue 330 MET Chi-restraints excluded: chain C residue 334 LEU Chi-restraints excluded: chain C residue 353 ILE Chi-restraints excluded: chain C residue 370 GLN Chi-restraints excluded: chain C residue 400 GLU Chi-restraints excluded: chain C residue 409 VAL Chi-restraints excluded: chain C residue 476 ILE Chi-restraints excluded: chain C residue 491 CYS Chi-restraints excluded: chain H residue 19 THR Chi-restraints excluded: chain H residue 32 ASP Chi-restraints excluded: chain H residue 49 ILE Chi-restraints excluded: chain H residue 52 ASN Chi-restraints excluded: chain H residue 101 VAL Chi-restraints excluded: chain I residue 19 THR Chi-restraints excluded: chain I residue 49 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 123 optimal weight: 1.9990 chunk 79 optimal weight: 1.9990 chunk 119 optimal weight: 5.9990 chunk 60 optimal weight: 6.9990 chunk 39 optimal weight: 0.5980 chunk 38 optimal weight: 0.4980 chunk 126 optimal weight: 7.9990 chunk 135 optimal weight: 7.9990 chunk 98 optimal weight: 1.9990 chunk 18 optimal weight: 0.9990 chunk 156 optimal weight: 5.9990 overall best weight: 1.2186 ------------------------------------------------------------------------------- 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: 0.8264 moved from start: 0.1282 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 17307 Z= 0.185 Angle : 0.537 8.993 23514 Z= 0.282 Chirality : 0.045 0.365 2640 Planarity : 0.005 0.051 3003 Dihedral : 6.031 52.955 2996 Min Nonbonded Distance : 2.233 Molprobity Statistics. All-atom Clashscore : 3.53 Ramachandran Plot: Outliers : 0.14 % Allowed : 2.38 % Favored : 97.47 % Rotamer: Outliers : 4.63 % Allowed : 24.06 % Favored : 71.30 % 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: 0.67 (0.18), residues: 2100 helix: 2.73 (0.27), residues: 342 sheet: 1.37 (0.21), residues: 609 loop : -0.84 (0.17), residues: 1149 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 435 HIS 0.004 0.001 HIS A 25 PHE 0.020 0.002 PHE C 128 TYR 0.010 0.001 TYR I 99 ARG 0.002 0.000 ARG E 30 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4200 Ramachandran restraints generated. 2100 Oldfield, 0 Emsley, 2100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4200 Ramachandran restraints generated. 2100 Oldfield, 0 Emsley, 2100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 250 residues out of total 1806 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 77 poor density : 173 time to evaluate : 1.806 Fit side-chains REVERT: G 19 THR cc_start: 0.5979 (OUTLIER) cc_final: 0.5775 (t) REVERT: G 62 ARG cc_start: 0.4847 (OUTLIER) cc_final: 0.4070 (ptm160) REVERT: D 74 ASP cc_start: 0.8288 (m-30) cc_final: 0.8045 (m-30) REVERT: A 68 GLN cc_start: 0.8859 (mt0) cc_final: 0.8335 (mt0) REVERT: A 162 ARG cc_start: 0.8386 (mpt180) cc_final: 0.8074 (mpt90) REVERT: A 232 LYS cc_start: 0.7967 (OUTLIER) cc_final: 0.7253 (tptm) REVERT: A 259 GLU cc_start: 0.8192 (OUTLIER) cc_final: 0.7830 (mt-10) REVERT: A 400 GLU cc_start: 0.8013 (OUTLIER) cc_final: 0.7730 (tt0) REVERT: A 403 ASN cc_start: 0.7310 (m-40) cc_final: 0.7077 (m-40) REVERT: A 459 LYS cc_start: 0.8254 (tttm) cc_final: 0.7816 (tttt) REVERT: A 486 LYS cc_start: 0.6810 (mmpt) cc_final: 0.6459 (pptt) REVERT: B 39 LYS cc_start: 0.8910 (OUTLIER) cc_final: 0.8318 (mmtt) REVERT: B 90 LYS cc_start: 0.8273 (OUTLIER) cc_final: 0.7902 (tttm) REVERT: B 162 ARG cc_start: 0.8401 (mpt180) cc_final: 0.8077 (mpt90) REVERT: B 232 LYS cc_start: 0.8077 (OUTLIER) cc_final: 0.7322 (tptm) REVERT: B 400 GLU cc_start: 0.8088 (OUTLIER) cc_final: 0.7812 (tt0) REVERT: B 403 ASN cc_start: 0.7322 (m-40) cc_final: 0.7056 (m-40) REVERT: B 420 MET cc_start: 0.8227 (OUTLIER) cc_final: 0.7789 (mmm) REVERT: B 459 LYS cc_start: 0.8202 (tttm) cc_final: 0.7773 (tttt) REVERT: B 486 LYS cc_start: 0.6809 (mmpt) cc_final: 0.6422 (pptt) REVERT: C 64 ILE cc_start: 0.8458 (mt) cc_final: 0.8002 (mt) REVERT: C 90 LYS cc_start: 0.8200 (OUTLIER) cc_final: 0.7990 (tttm) REVERT: C 232 LYS cc_start: 0.7962 (OUTLIER) cc_final: 0.7200 (tptm) REVERT: C 299 GLN cc_start: 0.8578 (mm-40) cc_final: 0.8343 (mm-40) REVERT: C 370 GLN cc_start: 0.7810 (OUTLIER) cc_final: 0.6945 (tp-100) REVERT: C 400 GLU cc_start: 0.8055 (OUTLIER) cc_final: 0.7763 (tt0) REVERT: C 403 ASN cc_start: 0.7345 (m-40) cc_final: 0.7079 (m-40) REVERT: C 420 MET cc_start: 0.8179 (OUTLIER) cc_final: 0.7794 (mmm) REVERT: C 459 LYS cc_start: 0.8196 (tttm) cc_final: 0.7768 (tttt) REVERT: C 486 LYS cc_start: 0.6776 (mmpt) cc_final: 0.6445 (pptt) REVERT: H 62 ARG cc_start: 0.4836 (OUTLIER) cc_final: 0.4090 (ptm160) outliers start: 77 outliers final: 50 residues processed: 231 average time/residue: 1.3144 time to fit residues: 337.5244 Evaluate side-chains 235 residues out of total 1806 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 169 time to evaluate : 1.850 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 19 THR Chi-restraints excluded: chain G residue 32 ASP Chi-restraints excluded: chain G residue 49 ILE Chi-restraints excluded: chain G residue 62 ARG Chi-restraints excluded: chain G residue 101 VAL Chi-restraints excluded: chain D residue 46 GLU Chi-restraints excluded: chain D residue 107 THR Chi-restraints excluded: chain E residue 107 THR Chi-restraints excluded: chain F residue 107 THR Chi-restraints excluded: chain A residue 19 THR Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 92 SER Chi-restraints excluded: chain A residue 99 THR Chi-restraints excluded: chain A residue 201 ILE Chi-restraints excluded: chain A residue 232 LYS Chi-restraints excluded: chain A residue 238 ASP Chi-restraints excluded: chain A residue 259 GLU Chi-restraints excluded: chain A residue 291 CYS Chi-restraints excluded: chain A residue 330 MET Chi-restraints excluded: chain A residue 334 LEU Chi-restraints excluded: chain A residue 400 GLU Chi-restraints excluded: chain A residue 409 VAL Chi-restraints excluded: chain A residue 420 MET Chi-restraints excluded: chain A residue 476 ILE Chi-restraints excluded: chain A residue 491 CYS Chi-restraints excluded: chain B residue 19 THR Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 39 LYS Chi-restraints excluded: chain B residue 90 LYS Chi-restraints excluded: chain B residue 123 SER Chi-restraints excluded: chain B residue 168 THR Chi-restraints excluded: chain B residue 187 LYS Chi-restraints excluded: chain B residue 232 LYS Chi-restraints excluded: chain B residue 238 ASP Chi-restraints excluded: chain B residue 274 SER Chi-restraints excluded: chain B residue 291 CYS Chi-restraints excluded: chain B residue 400 GLU Chi-restraints excluded: chain B residue 409 VAL Chi-restraints excluded: chain B residue 420 MET Chi-restraints excluded: chain B residue 476 ILE Chi-restraints excluded: chain B residue 491 CYS Chi-restraints excluded: chain C residue 19 THR Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 90 LYS Chi-restraints excluded: chain C residue 99 THR Chi-restraints excluded: chain C residue 128 PHE Chi-restraints excluded: chain C residue 168 THR Chi-restraints excluded: chain C residue 187 LYS Chi-restraints excluded: chain C residue 232 LYS Chi-restraints excluded: chain C residue 291 CYS Chi-restraints excluded: chain C residue 294 LYS Chi-restraints excluded: chain C residue 330 MET Chi-restraints excluded: chain C residue 334 LEU Chi-restraints excluded: chain C residue 370 GLN Chi-restraints excluded: chain C residue 400 GLU Chi-restraints excluded: chain C residue 409 VAL Chi-restraints excluded: chain C residue 420 MET Chi-restraints excluded: chain C residue 476 ILE Chi-restraints excluded: chain C residue 491 CYS Chi-restraints excluded: chain H residue 32 ASP Chi-restraints excluded: chain H residue 49 ILE Chi-restraints excluded: chain H residue 52 ASN Chi-restraints excluded: chain H residue 62 ARG Chi-restraints excluded: chain H residue 101 VAL Chi-restraints excluded: chain I residue 19 THR Chi-restraints excluded: chain I residue 49 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 181 optimal weight: 3.9990 chunk 191 optimal weight: 2.9990 chunk 174 optimal weight: 5.9990 chunk 185 optimal weight: 2.9990 chunk 111 optimal weight: 3.9990 chunk 80 optimal weight: 0.8980 chunk 145 optimal weight: 0.7980 chunk 57 optimal weight: 5.9990 chunk 168 optimal weight: 0.0870 chunk 175 optimal weight: 0.7980 chunk 122 optimal weight: 0.6980 overall best weight: 0.6558 ------------------------------------------------------------------------------- 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: 0.8231 moved from start: 0.1300 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 17307 Z= 0.136 Angle : 0.491 8.585 23514 Z= 0.257 Chirality : 0.043 0.326 2640 Planarity : 0.004 0.051 3003 Dihedral : 5.812 52.869 2996 Min Nonbonded Distance : 2.235 Molprobity Statistics. All-atom Clashscore : 3.84 Ramachandran Plot: Outliers : 0.14 % Allowed : 2.34 % Favored : 97.52 % Rotamer: Outliers : 4.08 % Allowed : 24.46 % Favored : 71.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.79 (0.18), residues: 2100 helix: 2.84 (0.28), residues: 342 sheet: 1.48 (0.21), residues: 603 loop : -0.77 (0.17), residues: 1155 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 435 HIS 0.003 0.001 HIS A 369 PHE 0.015 0.001 PHE C 128 TYR 0.010 0.001 TYR H 33 ARG 0.001 0.000 ARG E 38 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4200 Ramachandran restraints generated. 2100 Oldfield, 0 Emsley, 2100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4200 Ramachandran restraints generated. 2100 Oldfield, 0 Emsley, 2100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 244 residues out of total 1806 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 177 time to evaluate : 1.941 Fit side-chains revert: symmetry clash REVERT: D 74 ASP cc_start: 0.8278 (m-30) cc_final: 0.8013 (m-30) REVERT: A 68 GLN cc_start: 0.8859 (mt0) cc_final: 0.8350 (mt0) REVERT: A 162 ARG cc_start: 0.8367 (mpt180) cc_final: 0.8078 (mpt90) REVERT: A 232 LYS cc_start: 0.7931 (OUTLIER) cc_final: 0.7227 (tptm) REVERT: A 259 GLU cc_start: 0.8139 (OUTLIER) cc_final: 0.7828 (mt-10) REVERT: A 400 GLU cc_start: 0.7925 (OUTLIER) cc_final: 0.7637 (tt0) REVERT: A 403 ASN cc_start: 0.7282 (m-40) cc_final: 0.7070 (m-40) REVERT: A 420 MET cc_start: 0.8094 (OUTLIER) cc_final: 0.7807 (mmm) REVERT: A 459 LYS cc_start: 0.8170 (tttm) cc_final: 0.7745 (tttt) REVERT: A 486 LYS cc_start: 0.6794 (mmpt) cc_final: 0.6445 (pptt) REVERT: B 90 LYS cc_start: 0.8247 (OUTLIER) cc_final: 0.7896 (tttm) REVERT: B 162 ARG cc_start: 0.8383 (mpt180) cc_final: 0.8081 (mpt90) REVERT: B 232 LYS cc_start: 0.8024 (OUTLIER) cc_final: 0.7299 (tptm) REVERT: B 400 GLU cc_start: 0.7983 (OUTLIER) cc_final: 0.7709 (tt0) REVERT: B 403 ASN cc_start: 0.7293 (m-40) cc_final: 0.7035 (m-40) REVERT: B 420 MET cc_start: 0.8080 (OUTLIER) cc_final: 0.7667 (mmm) REVERT: B 459 LYS cc_start: 0.8099 (tttm) cc_final: 0.7663 (tttt) REVERT: B 486 LYS cc_start: 0.6771 (mmpt) cc_final: 0.6431 (pptt) REVERT: C 64 ILE cc_start: 0.8448 (mt) cc_final: 0.7968 (mt) REVERT: C 90 LYS cc_start: 0.8204 (OUTLIER) cc_final: 0.7995 (tttm) REVERT: C 232 LYS cc_start: 0.7918 (OUTLIER) cc_final: 0.7147 (tptm) REVERT: C 370 GLN cc_start: 0.7776 (OUTLIER) cc_final: 0.7227 (tp-100) REVERT: C 400 GLU cc_start: 0.7964 (OUTLIER) cc_final: 0.7668 (tt0) REVERT: C 403 ASN cc_start: 0.7289 (m-40) cc_final: 0.7036 (m-40) REVERT: C 420 MET cc_start: 0.8072 (OUTLIER) cc_final: 0.7720 (mmm) REVERT: C 459 LYS cc_start: 0.8136 (tttm) cc_final: 0.7706 (tttt) REVERT: C 486 LYS cc_start: 0.6757 (mmpt) cc_final: 0.6449 (pptt) REVERT: H 62 ARG cc_start: 0.4814 (OUTLIER) cc_final: 0.4063 (ptm160) outliers start: 67 outliers final: 41 residues processed: 225 average time/residue: 1.3941 time to fit residues: 347.0324 Evaluate side-chains 228 residues out of total 1806 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 173 time to evaluate : 1.956 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 49 ILE Chi-restraints excluded: chain G residue 101 VAL Chi-restraints excluded: chain D residue 46 GLU Chi-restraints excluded: chain D residue 107 THR Chi-restraints excluded: chain E residue 107 THR Chi-restraints excluded: chain F residue 107 THR Chi-restraints excluded: chain A residue 19 THR Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 92 SER Chi-restraints excluded: chain A residue 99 THR Chi-restraints excluded: chain A residue 232 LYS Chi-restraints excluded: chain A residue 238 ASP Chi-restraints excluded: chain A residue 259 GLU Chi-restraints excluded: chain A residue 334 LEU Chi-restraints excluded: chain A residue 400 GLU Chi-restraints excluded: chain A residue 409 VAL Chi-restraints excluded: chain A residue 420 MET Chi-restraints excluded: chain A residue 476 ILE Chi-restraints excluded: chain A residue 491 CYS Chi-restraints excluded: chain B residue 19 THR Chi-restraints excluded: chain B residue 90 LYS Chi-restraints excluded: chain B residue 123 SER Chi-restraints excluded: chain B residue 168 THR Chi-restraints excluded: chain B residue 232 LYS Chi-restraints excluded: chain B residue 238 ASP Chi-restraints excluded: chain B residue 291 CYS Chi-restraints excluded: chain B residue 400 GLU Chi-restraints excluded: chain B residue 420 MET Chi-restraints excluded: chain B residue 476 ILE Chi-restraints excluded: chain B residue 491 CYS Chi-restraints excluded: chain C residue 19 THR Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 90 LYS Chi-restraints excluded: chain C residue 99 THR Chi-restraints excluded: chain C residue 168 THR Chi-restraints excluded: chain C residue 187 LYS Chi-restraints excluded: chain C residue 232 LYS Chi-restraints excluded: chain C residue 274 SER Chi-restraints excluded: chain C residue 291 CYS Chi-restraints excluded: chain C residue 294 LYS Chi-restraints excluded: chain C residue 330 MET Chi-restraints excluded: chain C residue 334 LEU Chi-restraints excluded: chain C residue 370 GLN Chi-restraints excluded: chain C residue 400 GLU Chi-restraints excluded: chain C residue 409 VAL Chi-restraints excluded: chain C residue 420 MET Chi-restraints excluded: chain C residue 476 ILE Chi-restraints excluded: chain C residue 491 CYS Chi-restraints excluded: chain H residue 32 ASP Chi-restraints excluded: chain H residue 49 ILE Chi-restraints excluded: chain H residue 52 ASN Chi-restraints excluded: chain H residue 62 ARG Chi-restraints excluded: chain H residue 101 VAL Chi-restraints excluded: chain I residue 19 THR Chi-restraints excluded: chain I residue 49 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 196 optimal weight: 10.0000 chunk 119 optimal weight: 5.9990 chunk 93 optimal weight: 6.9990 chunk 136 optimal weight: 6.9990 chunk 206 optimal weight: 5.9990 chunk 189 optimal weight: 7.9990 chunk 164 optimal weight: 2.9990 chunk 17 optimal weight: 2.9990 chunk 126 optimal weight: 8.9990 chunk 100 optimal weight: 5.9990 chunk 130 optimal weight: 3.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 48 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8336 moved from start: 0.1631 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.066 17307 Z= 0.532 Angle : 0.810 10.781 23514 Z= 0.426 Chirality : 0.057 0.489 2640 Planarity : 0.006 0.068 3003 Dihedral : 6.771 49.146 2996 Min Nonbonded Distance : 2.148 Molprobity Statistics. All-atom Clashscore : 4.62 Ramachandran Plot: Outliers : 0.14 % Allowed : 3.34 % Favored : 96.52 % Rotamer: Outliers : 4.91 % Allowed : 23.73 % Favored : 71.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.30 (0.17), residues: 2100 helix: 2.19 (0.27), residues: 342 sheet: 1.40 (0.21), residues: 591 loop : -1.13 (0.16), residues: 1167 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.003 TRP B 93 HIS 0.007 0.002 HIS A 25 PHE 0.044 0.003 PHE B 128 TYR 0.018 0.003 TYR C 214 ARG 0.008 0.001 ARG E 30 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4200 Ramachandran restraints generated. 2100 Oldfield, 0 Emsley, 2100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4200 Ramachandran restraints generated. 2100 Oldfield, 0 Emsley, 2100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 272 residues out of total 1806 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 82 poor density : 190 time to evaluate : 1.842 Fit side-chains REVERT: G 9 SER cc_start: 0.6729 (p) cc_final: 0.6472 (t) REVERT: G 19 THR cc_start: 0.6143 (OUTLIER) cc_final: 0.5939 (t) REVERT: G 62 ARG cc_start: 0.4866 (OUTLIER) cc_final: 0.4052 (ptm160) REVERT: D 74 ASP cc_start: 0.8351 (m-30) cc_final: 0.8123 (m-30) REVERT: A 68 GLN cc_start: 0.8897 (mt0) cc_final: 0.8385 (mt0) REVERT: A 162 ARG cc_start: 0.8415 (mpt180) cc_final: 0.8067 (mpt90) REVERT: A 232 LYS cc_start: 0.8078 (OUTLIER) cc_final: 0.7282 (tptm) REVERT: A 259 GLU cc_start: 0.8260 (OUTLIER) cc_final: 0.7907 (mt-10) REVERT: A 381 GLN cc_start: 0.7657 (OUTLIER) cc_final: 0.7162 (mt0) REVERT: A 400 GLU cc_start: 0.8293 (OUTLIER) cc_final: 0.8035 (tt0) REVERT: A 403 ASN cc_start: 0.7363 (m-40) cc_final: 0.7112 (m-40) REVERT: A 459 LYS cc_start: 0.8490 (tttm) cc_final: 0.8064 (tttt) REVERT: A 486 LYS cc_start: 0.6829 (mmpt) cc_final: 0.6480 (pptt) REVERT: B 39 LYS cc_start: 0.9039 (OUTLIER) cc_final: 0.8609 (mmtt) REVERT: B 90 LYS cc_start: 0.8318 (OUTLIER) cc_final: 0.7886 (tttm) REVERT: B 162 ARG cc_start: 0.8435 (mpt180) cc_final: 0.8159 (mpt90) REVERT: B 232 LYS cc_start: 0.8126 (OUTLIER) cc_final: 0.7316 (tptm) REVERT: B 381 GLN cc_start: 0.7560 (OUTLIER) cc_final: 0.7121 (mt0) REVERT: B 400 GLU cc_start: 0.8277 (OUTLIER) cc_final: 0.8019 (tt0) REVERT: B 403 ASN cc_start: 0.7387 (m-40) cc_final: 0.7086 (m-40) REVERT: B 459 LYS cc_start: 0.8384 (tttm) cc_final: 0.7972 (tttt) REVERT: B 486 LYS cc_start: 0.6911 (mmpt) cc_final: 0.6524 (pptt) REVERT: C 232 LYS cc_start: 0.8050 (OUTLIER) cc_final: 0.7274 (tptm) REVERT: C 370 GLN cc_start: 0.8016 (OUTLIER) cc_final: 0.7011 (tp-100) REVERT: C 400 GLU cc_start: 0.8265 (OUTLIER) cc_final: 0.7999 (tt0) REVERT: C 459 LYS cc_start: 0.8393 (tttm) cc_final: 0.7985 (tttt) REVERT: C 486 LYS cc_start: 0.6849 (mmpt) cc_final: 0.6515 (pptt) REVERT: H 33 TYR cc_start: 0.7321 (m-80) cc_final: 0.7110 (m-80) REVERT: H 62 ARG cc_start: 0.4912 (OUTLIER) cc_final: 0.4101 (ptm160) REVERT: I 9 SER cc_start: 0.6556 (p) cc_final: 0.6254 (t) outliers start: 82 outliers final: 46 residues processed: 252 average time/residue: 1.3075 time to fit residues: 367.3964 Evaluate side-chains 244 residues out of total 1806 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 183 time to evaluate : 1.903 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 19 THR Chi-restraints excluded: chain G residue 32 ASP Chi-restraints excluded: chain G residue 49 ILE Chi-restraints excluded: chain G residue 62 ARG Chi-restraints excluded: chain G residue 101 VAL Chi-restraints excluded: chain D residue 46 GLU Chi-restraints excluded: chain D residue 107 THR Chi-restraints excluded: chain E residue 107 THR Chi-restraints excluded: chain F residue 107 THR Chi-restraints excluded: chain A residue 19 THR Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 99 THR Chi-restraints excluded: chain A residue 128 PHE Chi-restraints excluded: chain A residue 232 LYS Chi-restraints excluded: chain A residue 259 GLU Chi-restraints excluded: chain A residue 334 LEU Chi-restraints excluded: chain A residue 381 GLN Chi-restraints excluded: chain A residue 400 GLU Chi-restraints excluded: chain A residue 409 VAL Chi-restraints excluded: chain A residue 420 MET Chi-restraints excluded: chain A residue 491 CYS Chi-restraints excluded: chain B residue 19 THR Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 39 LYS Chi-restraints excluded: chain B residue 90 LYS Chi-restraints excluded: chain B residue 99 THR Chi-restraints excluded: chain B residue 123 SER Chi-restraints excluded: chain B residue 128 PHE Chi-restraints excluded: chain B residue 168 THR Chi-restraints excluded: chain B residue 187 LYS Chi-restraints excluded: chain B residue 232 LYS Chi-restraints excluded: chain B residue 238 ASP Chi-restraints excluded: chain B residue 274 SER Chi-restraints excluded: chain B residue 291 CYS Chi-restraints excluded: chain B residue 381 GLN Chi-restraints excluded: chain B residue 400 GLU Chi-restraints excluded: chain B residue 409 VAL Chi-restraints excluded: chain B residue 491 CYS Chi-restraints excluded: chain C residue 19 THR Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 99 THR Chi-restraints excluded: chain C residue 128 PHE Chi-restraints excluded: chain C residue 187 LYS Chi-restraints excluded: chain C residue 232 LYS Chi-restraints excluded: chain C residue 274 SER Chi-restraints excluded: chain C residue 291 CYS Chi-restraints excluded: chain C residue 294 LYS Chi-restraints excluded: chain C residue 334 LEU Chi-restraints excluded: chain C residue 362 ASP Chi-restraints excluded: chain C residue 370 GLN Chi-restraints excluded: chain C residue 400 GLU Chi-restraints excluded: chain C residue 409 VAL Chi-restraints excluded: chain C residue 476 ILE Chi-restraints excluded: chain C residue 491 CYS Chi-restraints excluded: chain H residue 32 ASP Chi-restraints excluded: chain H residue 49 ILE Chi-restraints excluded: chain H residue 52 ASN Chi-restraints excluded: chain H residue 62 ARG Chi-restraints excluded: chain H residue 101 VAL Chi-restraints excluded: chain I residue 19 THR Chi-restraints excluded: chain I residue 49 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 174 optimal weight: 4.9990 chunk 50 optimal weight: 0.6980 chunk 151 optimal weight: 3.9990 chunk 24 optimal weight: 10.0000 chunk 45 optimal weight: 3.9990 chunk 164 optimal weight: 0.0270 chunk 68 optimal weight: 0.6980 chunk 168 optimal weight: 3.9990 chunk 20 optimal weight: 0.8980 chunk 30 optimal weight: 0.9980 chunk 144 optimal weight: 4.9990 overall best weight: 0.6638 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 403 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3835 r_free = 0.3835 target = 0.159155 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3458 r_free = 0.3458 target = 0.123679 restraints weight = 19045.757| |-----------------------------------------------------------------------------| r_work (start): 0.3446 rms_B_bonded: 2.23 r_work: 0.3260 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.3159 rms_B_bonded: 3.85 restraints_weight: 0.2500 r_work (final): 0.3159 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3107 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3107 r_free = 0.3107 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3107 r_free = 0.3107 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3107 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8690 moved from start: 0.1378 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 17307 Z= 0.147 Angle : 0.509 8.753 23514 Z= 0.268 Chirality : 0.044 0.353 2640 Planarity : 0.004 0.050 3003 Dihedral : 6.077 54.399 2996 Min Nonbonded Distance : 2.239 Molprobity Statistics. All-atom Clashscore : 4.29 Ramachandran Plot: Outliers : 0.14 % Allowed : 2.00 % Favored : 97.85 % Rotamer: Outliers : 3.02 % Allowed : 25.74 % Favored : 71.25 % 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: 0.61 (0.18), residues: 2100 helix: 2.62 (0.28), residues: 342 sheet: 1.35 (0.21), residues: 612 loop : -0.88 (0.16), residues: 1146 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP G 92 HIS 0.002 0.001 HIS E 99 PHE 0.017 0.001 PHE C 128 TYR 0.009 0.001 TYR I 99 ARG 0.003 0.000 ARG D 30 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6670.38 seconds wall clock time: 119 minutes 47.20 seconds (7187.20 seconds total)