Starting phenix.real_space_refine on Thu Feb 15 22:59:17 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8cau_16534/02_2024/8cau_16534_trim_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8cau_16534/02_2024/8cau_16534.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8cau_16534/02_2024/8cau_16534.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8cau_16534/02_2024/8cau_16534.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8cau_16534/02_2024/8cau_16534_trim_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8cau_16534/02_2024/8cau_16534_trim_updated.pdb" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.001 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 60 5.16 5 C 8695 2.51 5 N 2240 2.21 5 O 2550 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 161": "OE1" <-> "OE2" Residue "B GLU 161": "OE1" <-> "OE2" Residue "H GLU 90": "OE1" <-> "OE2" Residue "I TYR 61": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 69": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I GLU 90": "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: 13545 Number of models: 1 Model: "" Number of chains: 20 Chain: "A" Number of atoms: 1721 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 206, 1714 Classifications: {'peptide': 206} Link IDs: {'PTRANS': 13, 'TRANS': 192} Conformer: "B" Number of residues, atoms: 206, 1714 Classifications: {'peptide': 206} Link IDs: {'PTRANS': 13, 'TRANS': 192} bond proxies already assigned to first conformer: 1760 Chain: "B" Number of atoms: 1721 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 206, 1714 Classifications: {'peptide': 206} Link IDs: {'PTRANS': 13, 'TRANS': 192} Conformer: "B" Number of residues, atoms: 206, 1714 Classifications: {'peptide': 206} Link IDs: {'PTRANS': 13, 'TRANS': 192} bond proxies already assigned to first conformer: 1760 Chain: "C" Number of atoms: 1721 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 206, 1714 Classifications: {'peptide': 206} Link IDs: {'PTRANS': 13, 'TRANS': 192} Conformer: "B" Number of residues, atoms: 206, 1714 Classifications: {'peptide': 206} Link IDs: {'PTRANS': 13, 'TRANS': 192} bond proxies already assigned to first conformer: 1760 Chain: "D" Number of atoms: 1721 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 206, 1714 Classifications: {'peptide': 206} Link IDs: {'PTRANS': 13, 'TRANS': 192} Conformer: "B" Number of residues, atoms: 206, 1714 Classifications: {'peptide': 206} Link IDs: {'PTRANS': 13, 'TRANS': 192} bond proxies already assigned to first conformer: 1760 Chain: "E" Number of atoms: 1721 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 206, 1714 Classifications: {'peptide': 206} Link IDs: {'PTRANS': 13, 'TRANS': 192} Conformer: "B" Number of residues, atoms: 206, 1714 Classifications: {'peptide': 206} Link IDs: {'PTRANS': 13, 'TRANS': 192} bond proxies already assigned to first conformer: 1760 Chain: "F" Number of atoms: 920 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 920 Classifications: {'peptide': 121} Link IDs: {'PTRANS': 2, 'TRANS': 118} Chain: "G" Number of atoms: 920 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 920 Classifications: {'peptide': 121} Link IDs: {'PTRANS': 2, 'TRANS': 118} Chain: "H" Number of atoms: 920 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 920 Classifications: {'peptide': 121} Link IDs: {'PTRANS': 2, 'TRANS': 118} Chain: "I" Number of atoms: 920 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 920 Classifications: {'peptide': 121} Link IDs: {'PTRANS': 2, 'TRANS': 118} Chain: "J" Number of atoms: 920 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 920 Classifications: {'peptide': 121} Link IDs: {'PTRANS': 2, 'TRANS': 118} Chain: "P" 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: "Q" 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: "R" 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: "S" 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: "T" 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: 40 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 40 Unusual residues: {'NAG': 2, 'NCT': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "B" Number of atoms: 40 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 40 Unusual residues: {'NAG': 2, 'NCT': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "C" Number of atoms: 40 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 40 Unusual residues: {'NAG': 2, 'NCT': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "D" Number of atoms: 40 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 40 Unusual residues: {'NAG': 2, 'NCT': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "E" Number of atoms: 40 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 40 Unusual residues: {'NAG': 2, 'NCT': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Time building chain proxies: 11.47, per 1000 atoms: 0.85 Number of scatterers: 13545 At special positions: 0 Unit cell: (92.02, 92.88, 118.68, 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 60 16.00 O 2550 8.00 N 2240 7.00 C 8695 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=5, symmetry=0 Simple disulfide: pdb=" SG CYS A 127 " - pdb=" SG CYS A 141 " distance=2.03 Simple disulfide: pdb=" SG CYS B 127 " - pdb=" SG CYS B 141 " distance=2.03 Simple disulfide: pdb=" SG CYS C 127 " - pdb=" SG CYS C 141 " distance=2.03 Simple disulfide: pdb=" SG CYS D 127 " - pdb=" SG CYS D 141 " distance=2.03 Simple disulfide: pdb=" SG CYS E 127 " - pdb=" SG CYS E 141 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG P 1 " - " NAG P 2 " " NAG Q 1 " - " NAG Q 2 " " NAG R 1 " - " NAG R 2 " " NAG S 1 " - " NAG S 2 " " NAG T 1 " - " NAG T 2 " NAG-ASN " NAG A 501 " - " ASN A 23 " " NAG A 502 " - " ASN A 67 " " NAG B 501 " - " ASN B 23 " " NAG B 502 " - " ASN B 67 " " NAG C 501 " - " ASN C 23 " " NAG C 502 " - " ASN C 67 " " NAG D 501 " - " ASN D 23 " " NAG D 502 " - " ASN D 67 " " NAG E 501 " - " ASN E 23 " " NAG E 502 " - " ASN E 67 " " NAG P 1 " - " ASN A 110 " " NAG Q 1 " - " ASN B 110 " " NAG R 1 " - " ASN C 110 " " NAG S 1 " - " ASN D 110 " " NAG T 1 " - " ASN E 110 " Time building additional restraints: 5.18 Conformation dependent library (CDL) restraints added in 3.8 seconds 3240 Ramachandran restraints generated. 1620 Oldfield, 0 Emsley, 1620 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3030 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 11 helices and 34 sheets defined 3.5% alpha, 33.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.80 Creating SS restraints... Processing helix chain 'A' and resid 2 through 9 removed outlier: 3.504A pdb=" N TYR A 7 " --> pdb=" O GLN A 3 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N LYS A 8 " --> pdb=" O ARG A 4 " (cutoff:3.500A) Processing helix chain 'B' and resid 2 through 9 removed outlier: 3.550A pdb=" N TYR B 7 " --> pdb=" O GLN B 3 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N LYS B 8 " --> pdb=" O ARG B 4 " (cutoff:3.500A) Processing helix chain 'C' and resid 2 through 9 Processing helix chain 'D' and resid 2 through 9 removed outlier: 3.512A pdb=" N TYR D 7 " --> pdb=" O GLN D 3 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N LYS D 8 " --> pdb=" O ARG D 4 " (cutoff:3.500A) Processing helix chain 'E' and resid 2 through 9 Processing helix chain 'F' and resid 30 through 32 No H-bonds generated for 'chain 'F' and resid 30 through 32' Processing helix chain 'G' and resid 30 through 32 No H-bonds generated for 'chain 'G' and resid 30 through 32' Processing helix chain 'H' and resid 30 through 32 No H-bonds generated for 'chain 'H' and resid 30 through 32' Processing helix chain 'I' and resid 30 through 32 No H-bonds generated for 'chain 'I' and resid 30 through 32' Processing helix chain 'J' and resid 30 through 32 No H-bonds generated for 'chain 'J' and resid 30 through 32' Processing helix chain 'J' and resid 63 through 65 No H-bonds generated for 'chain 'J' and resid 63 through 65' Processing sheet with id= A, first strand: chain 'A' and resid 155 through 159 removed outlier: 6.644A pdb=" N LEU A 28 " --> pdb=" O ASP A 156 " (cutoff:3.500A) removed outlier: 7.360A pdb=" N GLN A 158 " --> pdb=" O LEU A 28 " (cutoff:3.500A) removed outlier: 6.434A pdb=" N VAL A 30 " --> pdb=" O GLN A 158 " (cutoff:3.500A) removed outlier: 6.613A pdb=" N ASN A 52 " --> pdb=" O LEU A 37 " (cutoff:3.500A) removed outlier: 5.181A pdb=" N ILE A 39 " --> pdb=" O THR A 50 " (cutoff:3.500A) removed outlier: 7.060A pdb=" N THR A 50 " --> pdb=" O ILE A 39 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 41 through 43 removed outlier: 3.994A pdb=" N VAL A 48 " --> pdb=" O ASP A 43 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 57 through 60 Processing sheet with id= D, first strand: chain 'A' and resid 76 through 79 Processing sheet with id= E, first strand: chain 'A' and resid 89 through 91 removed outlier: 4.605A pdb=" N SER A 147 " --> pdb=" O PRO A 195 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N GLY A 177 " --> pdb=" O THR A 202 " (cutoff:3.500A) removed outlier: 5.834A pdb=" N ARG A 204 " --> pdb=" O LEU A 175 " (cutoff:3.500A) removed outlier: 5.484A pdb=" N LEU A 175 " --> pdb=" O ARG A 204 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 155 through 159 removed outlier: 6.658A pdb=" N LEU B 28 " --> pdb=" O ASP B 156 " (cutoff:3.500A) removed outlier: 7.394A pdb=" N GLN B 158 " --> pdb=" O LEU B 28 " (cutoff:3.500A) removed outlier: 6.383A pdb=" N VAL B 30 " --> pdb=" O GLN B 158 " (cutoff:3.500A) removed outlier: 6.601A pdb=" N ASN B 52 " --> pdb=" O LEU B 37 " (cutoff:3.500A) removed outlier: 5.179A pdb=" N ILE B 39 " --> pdb=" O THR B 50 " (cutoff:3.500A) removed outlier: 7.029A pdb=" N THR B 50 " --> pdb=" O ILE B 39 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N LEU B 49 " --> pdb=" O SER B 125 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'B' and resid 41 through 43 removed outlier: 4.007A pdb=" N VAL B 48 " --> pdb=" O ASP B 43 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'B' and resid 76 through 79 Processing sheet with id= I, first strand: chain 'B' and resid 89 through 91 removed outlier: 4.586A pdb=" N SER B 147 " --> pdb=" O PRO B 195 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N GLY B 177 " --> pdb=" O THR B 202 " (cutoff:3.500A) removed outlier: 5.848A pdb=" N ARG B 204 " --> pdb=" O LEU B 175 " (cutoff:3.500A) removed outlier: 5.457A pdb=" N LEU B 175 " --> pdb=" O ARG B 204 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'C' and resid 155 through 159 removed outlier: 6.723A pdb=" N LEU C 28 " --> pdb=" O ASP C 156 " (cutoff:3.500A) removed outlier: 7.427A pdb=" N GLN C 158 " --> pdb=" O LEU C 28 " (cutoff:3.500A) removed outlier: 6.411A pdb=" N VAL C 30 " --> pdb=" O GLN C 158 " (cutoff:3.500A) removed outlier: 6.642A pdb=" N ASN C 52 " --> pdb=" O LEU C 37 " (cutoff:3.500A) removed outlier: 5.136A pdb=" N ILE C 39 " --> pdb=" O THR C 50 " (cutoff:3.500A) removed outlier: 6.995A pdb=" N THR C 50 " --> pdb=" O ILE C 39 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N LEU C 49 " --> pdb=" O SER C 125 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'C' and resid 41 through 43 removed outlier: 3.985A pdb=" N VAL C 48 " --> pdb=" O ASP C 43 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'C' and resid 57 through 60 removed outlier: 3.543A pdb=" N TRP C 59 " --> pdb=" O CYS C 115 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'C' and resid 76 through 79 Processing sheet with id= N, first strand: chain 'C' and resid 89 through 91 removed outlier: 4.581A pdb=" N SER C 147 " --> pdb=" O PRO C 195 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N GLY C 177 " --> pdb=" O THR C 202 " (cutoff:3.500A) removed outlier: 5.850A pdb=" N ARG C 204 " --> pdb=" O LEU C 175 " (cutoff:3.500A) removed outlier: 5.469A pdb=" N LEU C 175 " --> pdb=" O ARG C 204 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'D' and resid 155 through 159 removed outlier: 6.679A pdb=" N LEU D 28 " --> pdb=" O ASP D 156 " (cutoff:3.500A) removed outlier: 7.421A pdb=" N GLN D 158 " --> pdb=" O LEU D 28 " (cutoff:3.500A) removed outlier: 6.405A pdb=" N VAL D 30 " --> pdb=" O GLN D 158 " (cutoff:3.500A) removed outlier: 6.630A pdb=" N ASN D 52 " --> pdb=" O LEU D 37 " (cutoff:3.500A) removed outlier: 5.185A pdb=" N ILE D 39 " --> pdb=" O THR D 50 " (cutoff:3.500A) removed outlier: 7.069A pdb=" N THR D 50 " --> pdb=" O ILE D 39 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'D' and resid 41 through 43 removed outlier: 3.959A pdb=" N VAL D 48 " --> pdb=" O ASP D 43 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'D' and resid 57 through 60 Processing sheet with id= R, first strand: chain 'D' and resid 76 through 79 Processing sheet with id= S, first strand: chain 'D' and resid 89 through 91 removed outlier: 4.586A pdb=" N SER D 147 " --> pdb=" O PRO D 195 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N GLY D 177 " --> pdb=" O THR D 202 " (cutoff:3.500A) removed outlier: 5.863A pdb=" N ARG D 204 " --> pdb=" O LEU D 175 " (cutoff:3.500A) removed outlier: 5.470A pdb=" N LEU D 175 " --> pdb=" O ARG D 204 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'E' and resid 155 through 159 removed outlier: 6.675A pdb=" N LEU E 28 " --> pdb=" O ASP E 156 " (cutoff:3.500A) removed outlier: 7.410A pdb=" N GLN E 158 " --> pdb=" O LEU E 28 " (cutoff:3.500A) removed outlier: 6.384A pdb=" N VAL E 30 " --> pdb=" O GLN E 158 " (cutoff:3.500A) removed outlier: 6.634A pdb=" N ASN E 52 " --> pdb=" O LEU E 37 " (cutoff:3.500A) removed outlier: 5.205A pdb=" N ILE E 39 " --> pdb=" O THR E 50 " (cutoff:3.500A) removed outlier: 7.085A pdb=" N THR E 50 " --> pdb=" O ILE E 39 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'E' and resid 41 through 43 removed outlier: 3.920A pdb=" N VAL E 48 " --> pdb=" O ASP E 43 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'E' and resid 57 through 60 Processing sheet with id= W, first strand: chain 'E' and resid 76 through 79 Processing sheet with id= X, first strand: chain 'E' and resid 89 through 91 removed outlier: 4.563A pdb=" N SER E 147 " --> pdb=" O PRO E 195 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N GLY E 177 " --> pdb=" O THR E 202 " (cutoff:3.500A) removed outlier: 5.904A pdb=" N ARG E 204 " --> pdb=" O LEU E 175 " (cutoff:3.500A) removed outlier: 5.464A pdb=" N LEU E 175 " --> pdb=" O ARG E 204 " (cutoff:3.500A) Processing sheet with id= Y, first strand: chain 'F' and resid 4 through 8 removed outlier: 3.605A pdb=" N LEU F 21 " --> pdb=" O LEU F 82 " (cutoff:3.500A) Processing sheet with id= Z, first strand: chain 'F' and resid 94 through 98 removed outlier: 3.659A pdb=" N ALA F 50 " --> pdb=" O TRP F 37 " (cutoff:3.500A) removed outlier: 5.390A pdb=" N ARG F 39 " --> pdb=" O PHE F 48 " (cutoff:3.500A) removed outlier: 5.433A pdb=" N PHE F 48 " --> pdb=" O ARG F 39 " (cutoff:3.500A) Processing sheet with id= AA, first strand: chain 'G' and resid 4 through 8 removed outlier: 3.610A pdb=" N LEU G 21 " --> pdb=" O LEU G 82 " (cutoff:3.500A) Processing sheet with id= AB, first strand: chain 'G' and resid 94 through 98 removed outlier: 3.647A pdb=" N ALA G 50 " --> pdb=" O TRP G 37 " (cutoff:3.500A) removed outlier: 5.397A pdb=" N ARG G 39 " --> pdb=" O PHE G 48 " (cutoff:3.500A) removed outlier: 5.446A pdb=" N PHE G 48 " --> pdb=" O ARG G 39 " (cutoff:3.500A) Processing sheet with id= AC, first strand: chain 'H' and resid 4 through 8 removed outlier: 3.623A pdb=" N LEU H 21 " --> pdb=" O LEU H 82 " (cutoff:3.500A) Processing sheet with id= AD, first strand: chain 'H' and resid 94 through 98 removed outlier: 3.649A pdb=" N ALA H 50 " --> pdb=" O TRP H 37 " (cutoff:3.500A) removed outlier: 5.431A pdb=" N ARG H 39 " --> pdb=" O PHE H 48 " (cutoff:3.500A) removed outlier: 5.466A pdb=" N PHE H 48 " --> pdb=" O ARG H 39 " (cutoff:3.500A) Processing sheet with id= AE, first strand: chain 'I' and resid 4 through 8 removed outlier: 3.612A pdb=" N LEU I 21 " --> pdb=" O LEU I 82 " (cutoff:3.500A) Processing sheet with id= AF, first strand: chain 'I' and resid 94 through 98 removed outlier: 3.655A pdb=" N ALA I 50 " --> pdb=" O TRP I 37 " (cutoff:3.500A) removed outlier: 5.424A pdb=" N ARG I 39 " --> pdb=" O PHE I 48 " (cutoff:3.500A) removed outlier: 5.448A pdb=" N PHE I 48 " --> pdb=" O ARG I 39 " (cutoff:3.500A) Processing sheet with id= AG, first strand: chain 'J' and resid 4 through 8 removed outlier: 3.622A pdb=" N LEU J 21 " --> pdb=" O LEU J 82 " (cutoff:3.500A) Processing sheet with id= AH, first strand: chain 'J' and resid 94 through 98 removed outlier: 3.539A pdb=" N TRP J 37 " --> pdb=" O ALA J 50 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N ALA J 50 " --> pdb=" O TRP J 37 " (cutoff:3.500A) removed outlier: 5.424A pdb=" N ARG J 39 " --> pdb=" O PHE J 48 " (cutoff:3.500A) removed outlier: 5.432A pdb=" N PHE J 48 " --> pdb=" O ARG J 39 " (cutoff:3.500A) 326 hydrogen bonds defined for protein. 837 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: 3.69 Time building geometry restraints manager: 5.64 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 4245 1.34 - 1.46: 3300 1.46 - 1.57: 6310 1.57 - 1.69: 0 1.69 - 1.81: 90 Bond restraints: 13945 Sorted by residual: bond pdb=" C1 NAG R 2 " pdb=" O5 NAG R 2 " ideal model delta sigma weight residual 1.406 1.447 -0.041 2.00e-02 2.50e+03 4.20e+00 bond pdb=" C1 NAG T 2 " pdb=" O5 NAG T 2 " ideal model delta sigma weight residual 1.406 1.446 -0.040 2.00e-02 2.50e+03 4.00e+00 bond pdb=" C1 NAG P 2 " pdb=" O5 NAG P 2 " ideal model delta sigma weight residual 1.406 1.446 -0.040 2.00e-02 2.50e+03 3.98e+00 bond pdb=" C1 NAG Q 2 " pdb=" O5 NAG Q 2 " ideal model delta sigma weight residual 1.406 1.446 -0.040 2.00e-02 2.50e+03 3.92e+00 bond pdb=" C1 NAG S 2 " pdb=" O5 NAG S 2 " ideal model delta sigma weight residual 1.406 1.445 -0.039 2.00e-02 2.50e+03 3.83e+00 ... (remaining 13940 not shown) Histogram of bond angle deviations from ideal: 100.50 - 107.21: 514 107.21 - 113.93: 7588 113.93 - 120.64: 5082 120.64 - 127.35: 5585 127.35 - 134.06: 191 Bond angle restraints: 18960 Sorted by residual: angle pdb=" N GLY C 166 " pdb=" CA GLY C 166 " pdb=" C GLY C 166 " ideal model delta sigma weight residual 115.80 110.89 4.91 1.74e+00 3.30e-01 7.98e+00 angle pdb=" CA GLY C 166 " pdb=" C GLY C 166 " pdb=" N TYR C 167 " ideal model delta sigma weight residual 118.95 115.96 2.99 1.06e+00 8.90e-01 7.96e+00 angle pdb=" N GLY B 166 " pdb=" CA GLY B 166 " pdb=" C GLY B 166 " ideal model delta sigma weight residual 115.80 110.91 4.89 1.74e+00 3.30e-01 7.88e+00 angle pdb=" CA GLY B 166 " pdb=" C GLY B 166 " pdb=" N TYR B 167 " ideal model delta sigma weight residual 118.95 116.00 2.95 1.06e+00 8.90e-01 7.74e+00 angle pdb=" CA GLY B 166 " pdb=" C GLY B 166 " pdb=" O GLY B 166 " ideal model delta sigma weight residual 119.04 121.02 -1.98 9.10e-01 1.21e+00 4.72e+00 ... (remaining 18955 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.94: 7315 17.94 - 35.88: 794 35.88 - 53.82: 193 53.82 - 71.76: 56 71.76 - 89.70: 12 Dihedral angle restraints: 8370 sinusoidal: 3605 harmonic: 4765 Sorted by residual: dihedral pdb=" CA LYS E 45 " pdb=" C LYS E 45 " pdb=" N ASN E 46 " pdb=" CA ASN E 46 " ideal model delta harmonic sigma weight residual 180.00 163.52 16.48 0 5.00e+00 4.00e-02 1.09e+01 dihedral pdb=" CB CYS C 127 " pdb=" SG CYS C 127 " pdb=" SG CYS C 141 " pdb=" CB CYS C 141 " ideal model delta sinusoidal sigma weight residual -86.00 -112.75 26.75 1 1.00e+01 1.00e-02 1.03e+01 dihedral pdb=" CB CYS B 127 " pdb=" SG CYS B 127 " pdb=" SG CYS B 141 " pdb=" CB CYS B 141 " ideal model delta sinusoidal sigma weight residual -86.00 -112.41 26.41 1 1.00e+01 1.00e-02 1.00e+01 ... (remaining 8367 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.040: 1437 0.040 - 0.079: 379 0.079 - 0.119: 183 0.119 - 0.158: 16 0.158 - 0.198: 5 Chirality restraints: 2020 Sorted by residual: chirality pdb=" C1 NAG S 2 " pdb=" O4 NAG S 1 " pdb=" C2 NAG S 2 " pdb=" O5 NAG S 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.38 -0.02 2.00e-02 2.50e+03 1.25e+00 chirality pdb=" C1 NAG T 1 " pdb=" ND2 ASN E 110 " pdb=" C2 NAG T 1 " pdb=" O5 NAG T 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.20 -0.20 2.00e-01 2.50e+01 9.76e-01 chirality pdb=" C1 NAG Q 1 " pdb=" ND2 ASN B 110 " pdb=" C2 NAG Q 1 " pdb=" O5 NAG Q 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.21 -0.19 2.00e-01 2.50e+01 9.17e-01 ... (remaining 2017 not shown) Planarity restraints: 2415 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PHE B 79 " -0.041 5.00e-02 4.00e+02 6.24e-02 6.24e+00 pdb=" N PRO B 80 " 0.108 5.00e-02 4.00e+02 pdb=" CA PRO B 80 " -0.033 5.00e-02 4.00e+02 pdb=" CD PRO B 80 " -0.034 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE A 79 " -0.039 5.00e-02 4.00e+02 5.99e-02 5.74e+00 pdb=" N PRO A 80 " 0.104 5.00e-02 4.00e+02 pdb=" CA PRO A 80 " -0.032 5.00e-02 4.00e+02 pdb=" CD PRO A 80 " -0.033 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE C 79 " 0.038 5.00e-02 4.00e+02 5.88e-02 5.52e+00 pdb=" N PRO C 80 " -0.102 5.00e-02 4.00e+02 pdb=" CA PRO C 80 " 0.031 5.00e-02 4.00e+02 pdb=" CD PRO C 80 " 0.032 5.00e-02 4.00e+02 ... (remaining 2412 not shown) Histogram of nonbonded interaction distances: 2.03 - 2.61: 177 2.61 - 3.18: 11209 3.18 - 3.75: 17673 3.75 - 4.33: 26327 4.33 - 4.90: 45705 Nonbonded interactions: 101091 Sorted by model distance: nonbonded pdb=" N GLU F 90 " pdb=" OE1 GLU F 90 " model vdw 2.033 2.520 nonbonded pdb=" OG SER D 183 " pdb=" OD1 ASP D 196 " model vdw 2.046 2.440 nonbonded pdb=" OG SER B 183 " pdb=" OD1 ASP B 196 " model vdw 2.062 2.440 nonbonded pdb=" OG SER A 183 " pdb=" OD1 ASP A 196 " model vdw 2.063 2.440 nonbonded pdb=" OG SER C 183 " pdb=" OD1 ASP C 196 " model vdw 2.076 2.440 ... (remaining 101086 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 1 through 113 or resid 115 through 206 or resid 501 throug \ h 503)) selection = (chain 'B' and (resid 1 through 113 or resid 115 through 206 or resid 501 throug \ h 503)) selection = (chain 'C' and (resid 1 through 113 or resid 115 through 206 or resid 501 throug \ h 503)) selection = (chain 'D' and (resid 1 through 113 or resid 115 through 206 or resid 501 throug \ h 503)) selection = (chain 'E' and (resid 1 through 113 or resid 115 through 206 or resid 501 throug \ h 503)) } ncs_group { reference = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' } ncs_group { reference = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'T' } 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=0.45 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.130 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 6.130 Check model and map are aligned: 0.210 Set scattering table: 0.130 Process input model: 43.750 Find NCS groups from input model: 0.950 Set up NCS constraints: 0.170 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.890 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 55.370 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8755 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 0.041 13945 Z= 0.191 Angle : 0.517 4.914 18960 Z= 0.267 Chirality : 0.043 0.198 2020 Planarity : 0.005 0.062 2400 Dihedral : 16.187 89.698 5325 Min Nonbonded Distance : 2.033 Molprobity Statistics. All-atom Clashscore : 21.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.36 % Favored : 91.64 % Rotamer: Outliers : 0.14 % Allowed : 20.07 % Favored : 79.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.17 (0.19), residues: 1620 helix: -3.56 (0.62), residues: 45 sheet: -1.10 (0.20), residues: 660 loop : -2.92 (0.17), residues: 915 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP D 133 HIS 0.002 0.001 HIS D 140 PHE 0.006 0.001 PHE I 69 TYR 0.011 0.001 TYR A 117 ARG 0.005 0.000 ARG C 4 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3240 Ramachandran restraints generated. 1620 Oldfield, 0 Emsley, 1620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3240 Ramachandran restraints generated. 1620 Oldfield, 0 Emsley, 1620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 300 residues out of total 1410 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 298 time to evaluate : 1.684 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 60 TYR cc_start: 0.8597 (m-80) cc_final: 0.8329 (m-10) REVERT: F 74 ASP cc_start: 0.7938 (t0) cc_final: 0.7689 (t0) REVERT: F 91 ASP cc_start: 0.9111 (m-30) cc_final: 0.8721 (m-30) REVERT: G 7 GLU cc_start: 0.8264 (mp0) cc_final: 0.7929 (mp0) REVERT: G 74 ASP cc_start: 0.7984 (t0) cc_final: 0.7737 (t0) REVERT: H 74 ASP cc_start: 0.8049 (t0) cc_final: 0.7731 (t0) REVERT: H 91 ASP cc_start: 0.9003 (m-30) cc_final: 0.8601 (m-30) REVERT: I 74 ASP cc_start: 0.7846 (t0) cc_final: 0.7617 (t0) REVERT: J 74 ASP cc_start: 0.8032 (t0) cc_final: 0.7749 (t0) outliers start: 2 outliers final: 1 residues processed: 298 average time/residue: 0.3296 time to fit residues: 131.1019 Evaluate side-chains 269 residues out of total 1410 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 268 time to evaluate : 1.528 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 181 LYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 135 optimal weight: 8.9990 chunk 121 optimal weight: 0.9980 chunk 67 optimal weight: 3.9990 chunk 41 optimal weight: 0.9990 chunk 81 optimal weight: 0.9980 chunk 64 optimal weight: 3.9990 chunk 125 optimal weight: 20.0000 chunk 48 optimal weight: 2.9990 chunk 76 optimal weight: 2.9990 chunk 93 optimal weight: 10.0000 chunk 145 optimal weight: 9.9990 overall best weight: 1.7986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 75 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8793 moved from start: 0.1285 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 13945 Z= 0.248 Angle : 0.679 9.380 18960 Z= 0.334 Chirality : 0.049 0.213 2020 Planarity : 0.005 0.057 2400 Dihedral : 10.821 72.176 2299 Min Nonbonded Distance : 2.185 Molprobity Statistics. All-atom Clashscore : 9.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.41 % Favored : 90.59 % Rotamer: Outliers : 1.41 % Allowed : 19.44 % Favored : 79.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.97 (0.19), residues: 1620 helix: -2.50 (0.72), residues: 45 sheet: -0.79 (0.20), residues: 690 loop : -3.07 (0.17), residues: 885 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRP A 133 HIS 0.002 0.001 HIS A 140 PHE 0.020 0.001 PHE D 134 TYR 0.025 0.001 TYR G 60 ARG 0.005 0.000 ARG A 78 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3240 Ramachandran restraints generated. 1620 Oldfield, 0 Emsley, 1620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3240 Ramachandran restraints generated. 1620 Oldfield, 0 Emsley, 1620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 302 residues out of total 1410 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 282 time to evaluate : 1.585 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 205 ARG cc_start: 0.8833 (ttm110) cc_final: 0.8446 (ttm110) REVERT: F 2 GLN cc_start: 0.8149 (mp10) cc_final: 0.7763 (pm20) REVERT: F 66 LYS cc_start: 0.9089 (tppt) cc_final: 0.8809 (tppp) REVERT: F 74 ASP cc_start: 0.8076 (t0) cc_final: 0.7852 (t0) REVERT: G 44 LYS cc_start: 0.9012 (mppt) cc_final: 0.8481 (mppt) REVERT: G 61 TYR cc_start: 0.8842 (m-80) cc_final: 0.8568 (m-80) REVERT: G 74 ASP cc_start: 0.8062 (t0) cc_final: 0.7784 (t0) REVERT: G 88 LYS cc_start: 0.9271 (mmtm) cc_final: 0.8948 (mppt) REVERT: H 74 ASP cc_start: 0.8226 (t0) cc_final: 0.7898 (t0) REVERT: I 74 ASP cc_start: 0.7986 (t0) cc_final: 0.7755 (t0) REVERT: J 66 LYS cc_start: 0.9030 (tppt) cc_final: 0.8699 (tppt) REVERT: J 74 ASP cc_start: 0.8125 (t0) cc_final: 0.7822 (t0) outliers start: 20 outliers final: 9 residues processed: 295 average time/residue: 0.3314 time to fit residues: 131.9869 Evaluate side-chains 272 residues out of total 1410 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 263 time to evaluate : 1.523 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 149 SER Chi-restraints excluded: chain B residue 60 THR Chi-restraints excluded: chain B residue 191 LYS Chi-restraints excluded: chain C residue 57 MET Chi-restraints excluded: chain C residue 136 PHE Chi-restraints excluded: chain D residue 60 THR Chi-restraints excluded: chain D residue 203 MET Chi-restraints excluded: chain E residue 136 PHE Chi-restraints excluded: chain E residue 149 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 80 optimal weight: 3.9990 chunk 45 optimal weight: 0.8980 chunk 120 optimal weight: 9.9990 chunk 98 optimal weight: 0.9980 chunk 40 optimal weight: 4.9990 chunk 145 optimal weight: 8.9990 chunk 157 optimal weight: 10.0000 chunk 129 optimal weight: 6.9990 chunk 144 optimal weight: 7.9990 chunk 49 optimal weight: 0.0570 chunk 116 optimal weight: 2.9990 overall best weight: 1.7902 ------------------------------------------------------------------------------- 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: 0.8809 moved from start: 0.1691 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 13945 Z= 0.230 Angle : 0.658 9.413 18960 Z= 0.322 Chirality : 0.047 0.238 2020 Planarity : 0.005 0.050 2400 Dihedral : 9.958 63.756 2295 Min Nonbonded Distance : 2.219 Molprobity Statistics. All-atom Clashscore : 8.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.80 % Favored : 92.20 % Rotamer: Outliers : 1.41 % Allowed : 19.93 % Favored : 78.66 % 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: -2.69 (0.19), residues: 1620 helix: -1.78 (0.81), residues: 45 sheet: -0.59 (0.20), residues: 690 loop : -2.91 (0.17), residues: 885 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.001 TRP A 133 HIS 0.003 0.001 HIS A 140 PHE 0.009 0.001 PHE I 69 TYR 0.019 0.001 TYR G 60 ARG 0.005 0.000 ARG A 78 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3240 Ramachandran restraints generated. 1620 Oldfield, 0 Emsley, 1620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3240 Ramachandran restraints generated. 1620 Oldfield, 0 Emsley, 1620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 294 residues out of total 1410 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 274 time to evaluate : 1.586 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 205 ARG cc_start: 0.8820 (ttm110) cc_final: 0.8489 (ttm110) REVERT: D 138 VAL cc_start: 0.9276 (OUTLIER) cc_final: 0.8994 (t) REVERT: F 2 GLN cc_start: 0.8234 (mp10) cc_final: 0.7971 (mp10) REVERT: F 66 LYS cc_start: 0.9093 (tppt) cc_final: 0.8854 (tppt) REVERT: F 74 ASP cc_start: 0.8177 (t0) cc_final: 0.7964 (t0) REVERT: G 61 TYR cc_start: 0.8873 (m-80) cc_final: 0.8661 (m-80) REVERT: G 74 ASP cc_start: 0.8098 (t0) cc_final: 0.7821 (t0) REVERT: G 88 LYS cc_start: 0.9183 (mmtm) cc_final: 0.8884 (mppt) REVERT: H 74 ASP cc_start: 0.8257 (t0) cc_final: 0.7946 (t0) REVERT: I 74 ASP cc_start: 0.8048 (t0) cc_final: 0.7825 (t0) REVERT: J 66 LYS cc_start: 0.9004 (tppt) cc_final: 0.8733 (tppt) REVERT: J 74 ASP cc_start: 0.8174 (t0) cc_final: 0.7882 (t0) outliers start: 20 outliers final: 13 residues processed: 287 average time/residue: 0.3319 time to fit residues: 127.8950 Evaluate side-chains 279 residues out of total 1410 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 265 time to evaluate : 1.437 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 149 SER Chi-restraints excluded: chain B residue 60 THR Chi-restraints excluded: chain B residue 191 LYS Chi-restraints excluded: chain C residue 57 MET Chi-restraints excluded: chain D residue 138 VAL Chi-restraints excluded: chain D residue 203 MET Chi-restraints excluded: chain E residue 149 SER Chi-restraints excluded: chain F residue 104 VAL Chi-restraints excluded: chain G residue 104 VAL Chi-restraints excluded: chain H residue 104 VAL Chi-restraints excluded: chain I residue 80 VAL Chi-restraints excluded: chain I residue 104 VAL Chi-restraints excluded: chain J residue 77 LYS Chi-restraints excluded: chain J residue 104 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 143 optimal weight: 4.9990 chunk 109 optimal weight: 9.9990 chunk 75 optimal weight: 6.9990 chunk 16 optimal weight: 0.8980 chunk 69 optimal weight: 0.0470 chunk 97 optimal weight: 0.7980 chunk 146 optimal weight: 10.0000 chunk 154 optimal weight: 0.5980 chunk 76 optimal weight: 0.5980 chunk 138 optimal weight: 0.9990 chunk 41 optimal weight: 0.0570 overall best weight: 0.4196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 170 ASN D 170 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8762 moved from start: 0.2051 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 13945 Z= 0.145 Angle : 0.635 9.486 18960 Z= 0.307 Chirality : 0.047 0.243 2020 Planarity : 0.005 0.054 2400 Dihedral : 8.597 56.688 2295 Min Nonbonded Distance : 2.224 Molprobity Statistics. All-atom Clashscore : 6.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.81 % Favored : 93.19 % Rotamer: Outliers : 1.97 % Allowed : 19.93 % Favored : 78.10 % 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: -2.42 (0.19), residues: 1620 helix: -1.46 (0.83), residues: 45 sheet: -0.46 (0.20), residues: 675 loop : -2.66 (0.17), residues: 900 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.001 TRP A 133 HIS 0.003 0.001 HIS E 140 PHE 0.025 0.001 PHE A 134 TYR 0.014 0.001 TYR G 60 ARG 0.003 0.000 ARG G 46 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3240 Ramachandran restraints generated. 1620 Oldfield, 0 Emsley, 1620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3240 Ramachandran restraints generated. 1620 Oldfield, 0 Emsley, 1620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 314 residues out of total 1410 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 286 time to evaluate : 1.640 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 205 ARG cc_start: 0.8766 (ttm110) cc_final: 0.8492 (ttm110) REVERT: D 138 VAL cc_start: 0.9300 (OUTLIER) cc_final: 0.9019 (t) REVERT: F 2 GLN cc_start: 0.8336 (mp10) cc_final: 0.8010 (mp10) REVERT: F 66 LYS cc_start: 0.8930 (tppt) cc_final: 0.8691 (tppt) REVERT: G 74 ASP cc_start: 0.8137 (t0) cc_final: 0.7896 (t0) REVERT: H 74 ASP cc_start: 0.8257 (t0) cc_final: 0.8014 (t0) REVERT: I 74 ASP cc_start: 0.8071 (t0) cc_final: 0.7868 (t0) REVERT: J 74 ASP cc_start: 0.8147 (t0) cc_final: 0.7872 (t0) outliers start: 28 outliers final: 12 residues processed: 307 average time/residue: 0.3150 time to fit residues: 131.1865 Evaluate side-chains 279 residues out of total 1410 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 266 time to evaluate : 1.580 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 60 THR Chi-restraints excluded: chain C residue 57 MET Chi-restraints excluded: chain D residue 34 LEU Chi-restraints excluded: chain D residue 60 THR Chi-restraints excluded: chain D residue 138 VAL Chi-restraints excluded: chain D residue 203 MET Chi-restraints excluded: chain E residue 137 ASP Chi-restraints excluded: chain F residue 12 LEU Chi-restraints excluded: chain F residue 104 VAL Chi-restraints excluded: chain G residue 104 VAL Chi-restraints excluded: chain H residue 104 VAL Chi-restraints excluded: chain I residue 104 VAL Chi-restraints excluded: chain J residue 104 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 128 optimal weight: 8.9990 chunk 87 optimal weight: 0.9980 chunk 2 optimal weight: 0.0670 chunk 115 optimal weight: 7.9990 chunk 63 optimal weight: 4.9990 chunk 131 optimal weight: 4.9990 chunk 106 optimal weight: 5.9990 chunk 0 optimal weight: 6.9990 chunk 78 optimal weight: 0.8980 chunk 138 optimal weight: 4.9990 chunk 39 optimal weight: 0.3980 overall best weight: 1.4720 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 170 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8791 moved from start: 0.2239 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 13945 Z= 0.203 Angle : 0.637 9.533 18960 Z= 0.307 Chirality : 0.046 0.243 2020 Planarity : 0.004 0.045 2400 Dihedral : 8.147 56.814 2295 Min Nonbonded Distance : 2.169 Molprobity Statistics. All-atom Clashscore : 8.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.43 % Favored : 92.57 % Rotamer: Outliers : 1.83 % Allowed : 20.07 % Favored : 78.10 % 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: -2.27 (0.20), residues: 1620 helix: -1.14 (0.84), residues: 45 sheet: -0.41 (0.20), residues: 680 loop : -2.53 (0.18), residues: 895 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.001 TRP C 133 HIS 0.003 0.001 HIS E 140 PHE 0.022 0.001 PHE D 134 TYR 0.016 0.001 TYR H 60 ARG 0.004 0.000 ARG G 68 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3240 Ramachandran restraints generated. 1620 Oldfield, 0 Emsley, 1620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3240 Ramachandran restraints generated. 1620 Oldfield, 0 Emsley, 1620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 291 residues out of total 1410 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 265 time to evaluate : 1.693 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 134 PHE cc_start: 0.8389 (t80) cc_final: 0.8172 (t80) REVERT: C 205 ARG cc_start: 0.8774 (ttm110) cc_final: 0.8497 (ttm110) REVERT: D 138 VAL cc_start: 0.9378 (OUTLIER) cc_final: 0.9111 (t) REVERT: F 2 GLN cc_start: 0.8359 (mp10) cc_final: 0.8028 (mp10) REVERT: F 66 LYS cc_start: 0.8947 (tppt) cc_final: 0.8699 (tppt) REVERT: G 74 ASP cc_start: 0.8248 (t0) cc_final: 0.8013 (t0) REVERT: H 74 ASP cc_start: 0.8297 (t0) cc_final: 0.8044 (t0) REVERT: I 74 ASP cc_start: 0.8183 (t0) cc_final: 0.7933 (t0) REVERT: J 74 ASP cc_start: 0.8227 (t0) cc_final: 0.7928 (t0) outliers start: 26 outliers final: 19 residues processed: 285 average time/residue: 0.3430 time to fit residues: 132.0905 Evaluate side-chains 281 residues out of total 1410 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 261 time to evaluate : 1.627 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 137 ASP Chi-restraints excluded: chain B residue 60 THR Chi-restraints excluded: chain B residue 137 ASP Chi-restraints excluded: chain B residue 191 LYS Chi-restraints excluded: chain C residue 57 MET Chi-restraints excluded: chain C residue 137 ASP Chi-restraints excluded: chain C residue 191 LYS Chi-restraints excluded: chain D residue 34 LEU Chi-restraints excluded: chain D residue 60 THR Chi-restraints excluded: chain D residue 137 ASP Chi-restraints excluded: chain D residue 138 VAL Chi-restraints excluded: chain E residue 137 ASP Chi-restraints excluded: chain F residue 3 VAL Chi-restraints excluded: chain F residue 12 LEU Chi-restraints excluded: chain F residue 104 VAL Chi-restraints excluded: chain G residue 104 VAL Chi-restraints excluded: chain I residue 80 VAL Chi-restraints excluded: chain I residue 104 VAL Chi-restraints excluded: chain J residue 77 LYS Chi-restraints excluded: chain J residue 104 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 52 optimal weight: 6.9990 chunk 139 optimal weight: 9.9990 chunk 30 optimal weight: 6.9990 chunk 90 optimal weight: 3.9990 chunk 38 optimal weight: 0.6980 chunk 154 optimal weight: 0.5980 chunk 128 optimal weight: 6.9990 chunk 71 optimal weight: 0.9990 chunk 12 optimal weight: 8.9990 chunk 51 optimal weight: 2.9990 chunk 81 optimal weight: 5.9990 overall best weight: 1.8586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 13 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8812 moved from start: 0.2430 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 13945 Z= 0.230 Angle : 0.647 10.480 18960 Z= 0.311 Chirality : 0.046 0.242 2020 Planarity : 0.004 0.045 2400 Dihedral : 7.897 58.127 2295 Min Nonbonded Distance : 2.241 Molprobity Statistics. All-atom Clashscore : 8.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.74 % Favored : 92.26 % Rotamer: Outliers : 2.32 % Allowed : 20.21 % Favored : 77.46 % 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: -2.14 (0.20), residues: 1620 helix: -0.75 (0.85), residues: 45 sheet: -0.32 (0.20), residues: 680 loop : -2.46 (0.18), residues: 895 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.001 TRP A 133 HIS 0.002 0.001 HIS E 140 PHE 0.024 0.001 PHE A 134 TYR 0.011 0.001 TYR H 60 ARG 0.004 0.000 ARG H 46 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3240 Ramachandran restraints generated. 1620 Oldfield, 0 Emsley, 1620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3240 Ramachandran restraints generated. 1620 Oldfield, 0 Emsley, 1620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 296 residues out of total 1410 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 263 time to evaluate : 1.467 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 134 PHE cc_start: 0.8400 (t80) cc_final: 0.8174 (t80) REVERT: C 138 VAL cc_start: 0.9399 (OUTLIER) cc_final: 0.9189 (t) REVERT: C 205 ARG cc_start: 0.8767 (ttm110) cc_final: 0.8497 (ttm110) REVERT: D 138 VAL cc_start: 0.9425 (OUTLIER) cc_final: 0.9175 (t) REVERT: E 138 VAL cc_start: 0.9324 (OUTLIER) cc_final: 0.9050 (t) REVERT: F 66 LYS cc_start: 0.9030 (tppt) cc_final: 0.8798 (tppt) REVERT: G 74 ASP cc_start: 0.8281 (t0) cc_final: 0.8055 (t0) REVERT: H 74 ASP cc_start: 0.8353 (t0) cc_final: 0.8101 (t0) REVERT: I 74 ASP cc_start: 0.8284 (t0) cc_final: 0.8054 (t0) REVERT: J 74 ASP cc_start: 0.8290 (t0) cc_final: 0.8000 (t0) outliers start: 33 outliers final: 25 residues processed: 287 average time/residue: 0.3249 time to fit residues: 125.8621 Evaluate side-chains 286 residues out of total 1410 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 258 time to evaluate : 1.577 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 137 ASP Chi-restraints excluded: chain A residue 149 SER Chi-restraints excluded: chain B residue 60 THR Chi-restraints excluded: chain B residue 137 ASP Chi-restraints excluded: chain B residue 191 LYS Chi-restraints excluded: chain C residue 57 MET Chi-restraints excluded: chain C residue 137 ASP Chi-restraints excluded: chain C residue 138 VAL Chi-restraints excluded: chain C residue 191 LYS Chi-restraints excluded: chain D residue 34 LEU Chi-restraints excluded: chain D residue 60 THR Chi-restraints excluded: chain D residue 137 ASP Chi-restraints excluded: chain D residue 138 VAL Chi-restraints excluded: chain E residue 137 ASP Chi-restraints excluded: chain E residue 138 VAL Chi-restraints excluded: chain E residue 149 SER Chi-restraints excluded: chain F residue 3 VAL Chi-restraints excluded: chain F residue 104 VAL Chi-restraints excluded: chain G residue 104 VAL Chi-restraints excluded: chain G residue 109 ASP Chi-restraints excluded: chain H residue 12 LEU Chi-restraints excluded: chain H residue 104 VAL Chi-restraints excluded: chain H residue 109 ASP Chi-restraints excluded: chain I residue 80 VAL Chi-restraints excluded: chain I residue 84 MET Chi-restraints excluded: chain I residue 104 VAL Chi-restraints excluded: chain J residue 77 LYS Chi-restraints excluded: chain J residue 104 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 149 optimal weight: 20.0000 chunk 17 optimal weight: 5.9990 chunk 88 optimal weight: 1.9990 chunk 113 optimal weight: 20.0000 chunk 87 optimal weight: 0.5980 chunk 130 optimal weight: 1.9990 chunk 86 optimal weight: 4.9990 chunk 154 optimal weight: 7.9990 chunk 96 optimal weight: 0.9990 chunk 94 optimal weight: 6.9990 chunk 71 optimal weight: 1.9990 overall best weight: 1.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 13 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8807 moved from start: 0.2524 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 13945 Z= 0.202 Angle : 0.640 10.638 18960 Z= 0.307 Chirality : 0.046 0.241 2020 Planarity : 0.004 0.046 2400 Dihedral : 7.696 57.790 2295 Min Nonbonded Distance : 2.258 Molprobity Statistics. All-atom Clashscore : 8.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.18 % Favored : 92.82 % Rotamer: Outliers : 1.90 % Allowed : 20.85 % Favored : 77.25 % 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: -2.05 (0.20), residues: 1620 helix: -0.40 (0.85), residues: 45 sheet: -0.26 (0.20), residues: 690 loop : -2.44 (0.18), residues: 885 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.001 TRP A 133 HIS 0.003 0.001 HIS E 140 PHE 0.025 0.001 PHE D 134 TYR 0.012 0.001 TYR J 112 ARG 0.003 0.000 ARG A 78 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3240 Ramachandran restraints generated. 1620 Oldfield, 0 Emsley, 1620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3240 Ramachandran restraints generated. 1620 Oldfield, 0 Emsley, 1620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 290 residues out of total 1410 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 263 time to evaluate : 1.696 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 138 VAL cc_start: 0.9401 (OUTLIER) cc_final: 0.9187 (t) REVERT: C 205 ARG cc_start: 0.8761 (ttm110) cc_final: 0.8504 (ttm110) REVERT: D 138 VAL cc_start: 0.9454 (OUTLIER) cc_final: 0.9218 (t) REVERT: E 138 VAL cc_start: 0.9378 (OUTLIER) cc_final: 0.9118 (t) REVERT: G 74 ASP cc_start: 0.8355 (t0) cc_final: 0.8105 (t0) REVERT: H 74 ASP cc_start: 0.8380 (t0) cc_final: 0.8141 (t0) REVERT: I 74 ASP cc_start: 0.8307 (t0) cc_final: 0.8066 (t0) REVERT: J 74 ASP cc_start: 0.8282 (t0) cc_final: 0.7995 (t0) outliers start: 27 outliers final: 21 residues processed: 282 average time/residue: 0.3272 time to fit residues: 124.1305 Evaluate side-chains 285 residues out of total 1410 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 261 time to evaluate : 1.662 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 137 ASP Chi-restraints excluded: chain B residue 44 GLU Chi-restraints excluded: chain B residue 60 THR Chi-restraints excluded: chain B residue 137 ASP Chi-restraints excluded: chain B residue 191 LYS Chi-restraints excluded: chain C residue 57 MET Chi-restraints excluded: chain C residue 137 ASP Chi-restraints excluded: chain C residue 138 VAL Chi-restraints excluded: chain C residue 191 LYS Chi-restraints excluded: chain D residue 34 LEU Chi-restraints excluded: chain D residue 60 THR Chi-restraints excluded: chain D residue 137 ASP Chi-restraints excluded: chain D residue 138 VAL Chi-restraints excluded: chain E residue 137 ASP Chi-restraints excluded: chain E residue 138 VAL Chi-restraints excluded: chain F residue 3 VAL Chi-restraints excluded: chain F residue 12 LEU Chi-restraints excluded: chain F residue 104 VAL Chi-restraints excluded: chain G residue 104 VAL Chi-restraints excluded: chain H residue 12 LEU Chi-restraints excluded: chain H residue 104 VAL Chi-restraints excluded: chain I residue 104 VAL Chi-restraints excluded: chain J residue 77 LYS Chi-restraints excluded: chain J residue 104 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 95 optimal weight: 6.9990 chunk 61 optimal weight: 3.9990 chunk 92 optimal weight: 2.9990 chunk 46 optimal weight: 6.9990 chunk 30 optimal weight: 5.9990 chunk 29 optimal weight: 1.9990 chunk 98 optimal weight: 4.9990 chunk 105 optimal weight: 9.9990 chunk 76 optimal weight: 2.9990 chunk 14 optimal weight: 5.9990 chunk 121 optimal weight: 10.0000 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 4 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8867 moved from start: 0.2668 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.039 13945 Z= 0.380 Angle : 0.695 9.552 18960 Z= 0.337 Chirality : 0.047 0.242 2020 Planarity : 0.004 0.043 2400 Dihedral : 8.046 59.870 2295 Min Nonbonded Distance : 2.227 Molprobity Statistics. All-atom Clashscore : 9.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.04 % Favored : 90.96 % Rotamer: Outliers : 2.18 % Allowed : 20.92 % Favored : 76.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.04 (0.20), residues: 1620 helix: -0.47 (0.82), residues: 45 sheet: -0.22 (0.20), residues: 685 loop : -2.44 (0.18), residues: 890 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.001 TRP E 133 HIS 0.002 0.001 HIS I 32 PHE 0.026 0.002 PHE E 134 TYR 0.019 0.001 TYR E 71 ARG 0.004 0.000 ARG A 78 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3240 Ramachandran restraints generated. 1620 Oldfield, 0 Emsley, 1620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3240 Ramachandran restraints generated. 1620 Oldfield, 0 Emsley, 1620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 287 residues out of total 1410 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 256 time to evaluate : 1.963 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 181 LYS cc_start: 0.8818 (OUTLIER) cc_final: 0.8589 (ttmm) REVERT: C 138 VAL cc_start: 0.9476 (OUTLIER) cc_final: 0.9271 (t) REVERT: D 138 VAL cc_start: 0.9505 (OUTLIER) cc_final: 0.9295 (t) REVERT: E 138 VAL cc_start: 0.9455 (OUTLIER) cc_final: 0.9214 (t) REVERT: F 66 LYS cc_start: 0.9246 (tppt) cc_final: 0.8936 (tppt) REVERT: G 74 ASP cc_start: 0.8367 (t0) cc_final: 0.8104 (t0) REVERT: H 74 ASP cc_start: 0.8441 (t0) cc_final: 0.8186 (t0) REVERT: I 74 ASP cc_start: 0.8387 (t0) cc_final: 0.8152 (t0) REVERT: J 74 ASP cc_start: 0.8365 (t0) cc_final: 0.8110 (t0) outliers start: 31 outliers final: 23 residues processed: 277 average time/residue: 0.3403 time to fit residues: 126.7386 Evaluate side-chains 279 residues out of total 1410 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 252 time to evaluate : 2.012 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 137 ASP Chi-restraints excluded: chain A residue 149 SER Chi-restraints excluded: chain B residue 60 THR Chi-restraints excluded: chain B residue 137 ASP Chi-restraints excluded: chain B residue 181 LYS Chi-restraints excluded: chain B residue 191 LYS Chi-restraints excluded: chain C residue 57 MET Chi-restraints excluded: chain C residue 137 ASP Chi-restraints excluded: chain C residue 138 VAL Chi-restraints excluded: chain D residue 34 LEU Chi-restraints excluded: chain D residue 60 THR Chi-restraints excluded: chain D residue 137 ASP Chi-restraints excluded: chain D residue 138 VAL Chi-restraints excluded: chain E residue 44 GLU Chi-restraints excluded: chain E residue 137 ASP Chi-restraints excluded: chain E residue 138 VAL Chi-restraints excluded: chain E residue 149 SER Chi-restraints excluded: chain F residue 3 VAL Chi-restraints excluded: chain F residue 12 LEU Chi-restraints excluded: chain F residue 104 VAL Chi-restraints excluded: chain G residue 104 VAL Chi-restraints excluded: chain H residue 12 LEU Chi-restraints excluded: chain H residue 104 VAL Chi-restraints excluded: chain H residue 109 ASP Chi-restraints excluded: chain I residue 104 VAL Chi-restraints excluded: chain J residue 77 LYS Chi-restraints excluded: chain J residue 104 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 140 optimal weight: 0.0170 chunk 147 optimal weight: 0.8980 chunk 134 optimal weight: 7.9990 chunk 143 optimal weight: 6.9990 chunk 86 optimal weight: 1.9990 chunk 62 optimal weight: 0.3980 chunk 112 optimal weight: 5.9990 chunk 44 optimal weight: 2.9990 chunk 129 optimal weight: 8.9990 chunk 135 optimal weight: 4.9990 chunk 94 optimal weight: 3.9990 overall best weight: 1.2622 ------------------------------------------------------------------------------- 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: 0.8815 moved from start: 0.2766 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 13945 Z= 0.190 Angle : 0.655 12.697 18960 Z= 0.314 Chirality : 0.046 0.237 2020 Planarity : 0.004 0.046 2400 Dihedral : 7.590 58.633 2295 Min Nonbonded Distance : 2.254 Molprobity Statistics. All-atom Clashscore : 8.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.56 % Favored : 93.44 % Rotamer: Outliers : 1.76 % Allowed : 21.13 % Favored : 77.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.92 (0.20), residues: 1620 helix: 0.08 (0.88), residues: 45 sheet: -0.07 (0.19), residues: 705 loop : -2.51 (0.18), residues: 870 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.001 TRP A 133 HIS 0.003 0.001 HIS D 140 PHE 0.010 0.001 PHE H 69 TYR 0.010 0.001 TYR G 60 ARG 0.006 0.000 ARG H 46 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3240 Ramachandran restraints generated. 1620 Oldfield, 0 Emsley, 1620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3240 Ramachandran restraints generated. 1620 Oldfield, 0 Emsley, 1620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 278 residues out of total 1410 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 253 time to evaluate : 1.605 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 133 TRP cc_start: 0.8166 (m-90) cc_final: 0.7932 (m-90) REVERT: C 205 ARG cc_start: 0.8777 (ttm110) cc_final: 0.8520 (ttm110) REVERT: D 138 VAL cc_start: 0.9468 (OUTLIER) cc_final: 0.9253 (t) REVERT: E 138 VAL cc_start: 0.9447 (OUTLIER) cc_final: 0.9217 (t) REVERT: F 66 LYS cc_start: 0.9120 (tppt) cc_final: 0.8862 (tppt) REVERT: G 7 GLU cc_start: 0.8440 (mp0) cc_final: 0.8187 (mp0) REVERT: G 74 ASP cc_start: 0.8367 (t0) cc_final: 0.8124 (t0) REVERT: H 74 ASP cc_start: 0.8372 (t0) cc_final: 0.8122 (t0) REVERT: I 74 ASP cc_start: 0.8341 (t0) cc_final: 0.8101 (t0) REVERT: J 74 ASP cc_start: 0.8296 (t0) cc_final: 0.8011 (t0) outliers start: 25 outliers final: 19 residues processed: 271 average time/residue: 0.3358 time to fit residues: 121.9360 Evaluate side-chains 269 residues out of total 1410 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 248 time to evaluate : 1.643 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 137 ASP Chi-restraints excluded: chain B residue 60 THR Chi-restraints excluded: chain B residue 137 ASP Chi-restraints excluded: chain C residue 57 MET Chi-restraints excluded: chain C residue 137 ASP Chi-restraints excluded: chain D residue 34 LEU Chi-restraints excluded: chain D residue 60 THR Chi-restraints excluded: chain D residue 137 ASP Chi-restraints excluded: chain D residue 138 VAL Chi-restraints excluded: chain E residue 44 GLU Chi-restraints excluded: chain E residue 137 ASP Chi-restraints excluded: chain E residue 138 VAL Chi-restraints excluded: chain F residue 3 VAL Chi-restraints excluded: chain F residue 12 LEU Chi-restraints excluded: chain F residue 104 VAL Chi-restraints excluded: chain G residue 104 VAL Chi-restraints excluded: chain H residue 104 VAL Chi-restraints excluded: chain I residue 80 VAL Chi-restraints excluded: chain I residue 104 VAL Chi-restraints excluded: chain J residue 77 LYS Chi-restraints excluded: chain J residue 104 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 151 optimal weight: 6.9990 chunk 92 optimal weight: 0.9990 chunk 72 optimal weight: 5.9990 chunk 105 optimal weight: 1.9990 chunk 159 optimal weight: 3.9990 chunk 146 optimal weight: 9.9990 chunk 126 optimal weight: 4.9990 chunk 13 optimal weight: 10.0000 chunk 98 optimal weight: 5.9990 chunk 77 optimal weight: 0.7980 chunk 100 optimal weight: 0.0970 overall best weight: 1.5784 ------------------------------------------------------------------------------- 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: 0.8822 moved from start: 0.2856 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 13945 Z= 0.214 Angle : 0.658 13.382 18960 Z= 0.315 Chirality : 0.046 0.243 2020 Planarity : 0.004 0.046 2400 Dihedral : 7.508 57.551 2295 Min Nonbonded Distance : 2.233 Molprobity Statistics. All-atom Clashscore : 8.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.68 % Favored : 92.32 % Rotamer: Outliers : 1.62 % Allowed : 21.48 % Favored : 76.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.82 (0.20), residues: 1620 helix: 0.25 (0.90), residues: 45 sheet: -0.01 (0.19), residues: 725 loop : -2.49 (0.19), residues: 850 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.001 TRP E 133 HIS 0.004 0.001 HIS C 140 PHE 0.025 0.001 PHE C 134 TYR 0.013 0.001 TYR A 71 ARG 0.006 0.000 ARG J 46 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3240 Ramachandran restraints generated. 1620 Oldfield, 0 Emsley, 1620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3240 Ramachandran restraints generated. 1620 Oldfield, 0 Emsley, 1620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 267 residues out of total 1410 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 244 time to evaluate : 1.630 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 133 TRP cc_start: 0.8163 (m-90) cc_final: 0.7930 (m-90) REVERT: C 205 ARG cc_start: 0.8804 (ttm110) cc_final: 0.8528 (ttm110) REVERT: D 138 VAL cc_start: 0.9474 (OUTLIER) cc_final: 0.9260 (t) REVERT: E 138 VAL cc_start: 0.9449 (OUTLIER) cc_final: 0.9222 (t) REVERT: F 66 LYS cc_start: 0.9075 (tppt) cc_final: 0.8822 (tppt) REVERT: G 7 GLU cc_start: 0.8422 (mp0) cc_final: 0.8133 (mp0) REVERT: G 74 ASP cc_start: 0.8396 (t0) cc_final: 0.8147 (t0) REVERT: H 74 ASP cc_start: 0.8420 (t0) cc_final: 0.8168 (t0) REVERT: I 69 PHE cc_start: 0.7447 (m-80) cc_final: 0.6931 (m-80) REVERT: I 74 ASP cc_start: 0.8366 (t0) cc_final: 0.8138 (t0) REVERT: J 74 ASP cc_start: 0.8319 (t0) cc_final: 0.8067 (t0) outliers start: 23 outliers final: 20 residues processed: 261 average time/residue: 0.3400 time to fit residues: 118.0850 Evaluate side-chains 265 residues out of total 1410 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 243 time to evaluate : 1.405 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 137 ASP Chi-restraints excluded: chain B residue 60 THR Chi-restraints excluded: chain B residue 137 ASP Chi-restraints excluded: chain C residue 57 MET Chi-restraints excluded: chain C residue 137 ASP Chi-restraints excluded: chain D residue 34 LEU Chi-restraints excluded: chain D residue 57 MET Chi-restraints excluded: chain D residue 60 THR Chi-restraints excluded: chain D residue 137 ASP Chi-restraints excluded: chain D residue 138 VAL Chi-restraints excluded: chain E residue 44 GLU Chi-restraints excluded: chain E residue 137 ASP Chi-restraints excluded: chain E residue 138 VAL Chi-restraints excluded: chain F residue 3 VAL Chi-restraints excluded: chain F residue 12 LEU Chi-restraints excluded: chain F residue 104 VAL Chi-restraints excluded: chain G residue 104 VAL Chi-restraints excluded: chain H residue 104 VAL Chi-restraints excluded: chain I residue 80 VAL Chi-restraints excluded: chain I residue 104 VAL Chi-restraints excluded: chain J residue 77 LYS Chi-restraints excluded: chain J residue 104 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 135 optimal weight: 6.9990 chunk 38 optimal weight: 5.9990 chunk 117 optimal weight: 3.9990 chunk 18 optimal weight: 4.9990 chunk 35 optimal weight: 0.9980 chunk 127 optimal weight: 6.9990 chunk 53 optimal weight: 0.0370 chunk 130 optimal weight: 2.9990 chunk 16 optimal weight: 4.9990 chunk 23 optimal weight: 1.9990 chunk 111 optimal weight: 3.9990 overall best weight: 2.0064 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3017 r_free = 0.3017 target = 0.065193 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2556 r_free = 0.2556 target = 0.046098 restraints weight = 74391.045| |-----------------------------------------------------------------------------| r_work (start): 0.2518 rms_B_bonded: 5.25 r_work: 0.2330 rms_B_bonded: 5.05 restraints_weight: 2.0000 r_work (final): 0.2330 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2340 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2340 r_free = 0.2340 target_work(ls_wunit_k1) = 0.039 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2340 r_free = 0.2340 target_work(ls_wunit_k1) = 0.039 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2340 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9030 moved from start: 0.2888 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 13945 Z= 0.249 Angle : 0.664 12.689 18960 Z= 0.319 Chirality : 0.046 0.243 2020 Planarity : 0.004 0.046 2400 Dihedral : 7.526 58.429 2295 Min Nonbonded Distance : 2.235 Molprobity Statistics. All-atom Clashscore : 8.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.43 % Favored : 92.57 % Rotamer: Outliers : 1.69 % Allowed : 21.34 % Favored : 76.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.80 (0.20), residues: 1620 helix: 0.22 (0.89), residues: 45 sheet: 0.06 (0.19), residues: 700 loop : -2.46 (0.18), residues: 875 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.001 TRP A 133 HIS 0.002 0.001 HIS C 140 PHE 0.016 0.001 PHE F 69 TYR 0.010 0.001 TYR G 60 ARG 0.006 0.000 ARG J 46 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3327.76 seconds wall clock time: 60 minutes 51.27 seconds (3651.27 seconds total)