Starting phenix.real_space_refine on Mon Mar 18 04:41:45 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6yhs_10809/03_2024/6yhs_10809.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6yhs_10809/03_2024/6yhs_10809.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6yhs_10809/03_2024/6yhs_10809.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6yhs_10809/03_2024/6yhs_10809.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6yhs_10809/03_2024/6yhs_10809.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6yhs_10809/03_2024/6yhs_10809.pdb" } resolution = 2.7 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.006 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: 7 Type Number sf(0) Gaussians Zn 1 6.06 5 P 2800 5.49 5 Mg 160 5.21 5 S 68 5.16 5 C 41336 2.51 5 N 15545 2.21 5 O 23604 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 69": "NH1" <-> "NH2" Residue "A ASP 72": "OD1" <-> "OD2" Residue "A ARG 80": "NH1" <-> "NH2" Residue "A TYR 83": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 98": "OD1" <-> "OD2" Residue "A GLU 100": "OE1" <-> "OE2" Residue "A ASP 114": "OD1" <-> "OD2" Residue "A ARG 125": "NH1" <-> "NH2" Residue "A GLU 145": "OE1" <-> "OE2" Residue "A ARG 156": "NH1" <-> "NH2" Residue "A ARG 214": "NH1" <-> "NH2" Residue "A ARG 217": "NH1" <-> "NH2" Residue "A ARG 221": "NH1" <-> "NH2" Residue "A ARG 258": "NH1" <-> "NH2" Residue "A ARG 269": "NH1" <-> "NH2" Residue "A ARG 271": "NH1" <-> "NH2" Residue "B ASP 18": "OD1" <-> "OD2" Residue "B ARG 34": "NH1" <-> "NH2" Residue "B GLU 42": "OE1" <-> "OE2" Residue "B GLU 58": "OE1" <-> "OE2" Residue "B GLU 87": "OE1" <-> "OE2" Residue "B GLU 94": "OE1" <-> "OE2" Residue "B ARG 131": "NH1" <-> "NH2" Residue "B ASP 134": "OD1" <-> "OD2" Residue "B ARG 157": "NH1" <-> "NH2" Residue "B GLU 171": "OE1" <-> "OE2" Residue "B GLU 186": "OE1" <-> "OE2" Residue "B ARG 187": "NH1" <-> "NH2" Residue "C GLU 15": "OE1" <-> "OE2" Residue "C ARG 20": "NH1" <-> "NH2" Residue "C ARG 39": "NH1" <-> "NH2" Residue "C ASP 50": "OD1" <-> "OD2" Residue "C ARG 66": "NH1" <-> "NH2" Residue "C ARG 73": "NH1" <-> "NH2" Residue "C ASP 90": "OD1" <-> "OD2" Residue "C TYR 100": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 101": "NH1" <-> "NH2" Residue "C ARG 113": "NH1" <-> "NH2" Residue "C ASP 115": "OD1" <-> "OD2" Residue "C ARG 116": "NH1" <-> "NH2" Residue "C PHE 123": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 132": "OE1" <-> "OE2" Residue "C ARG 144": "NH1" <-> "NH2" Residue "C ARG 161": "NH1" <-> "NH2" Residue "C ASP 167": "OD1" <-> "OD2" Residue "C GLU 198": "OE1" <-> "OE2" Residue "E ARG 3": "NH1" <-> "NH2" Residue "E ARG 22": "NH1" <-> "NH2" Residue "E PHE 35": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 42": "OE1" <-> "OE2" Residue "E GLU 57": "OE1" <-> "OE2" Residue "E ASP 60": "OD1" <-> "OD2" Residue "E PHE 83": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 85": "NH1" <-> "NH2" Residue "E ASP 114": "OD1" <-> "OD2" Residue "E GLU 130": "OE1" <-> "OE2" Residue "E ARG 152": "NH1" <-> "NH2" Residue "E ARG 171": "NH1" <-> "NH2" Residue "E GLU 173": "OE1" <-> "OE2" Residue "F ASP 19": "OD1" <-> "OD2" Residue "F GLU 79": "OE1" <-> "OE2" Residue "F GLU 86": "OE1" <-> "OE2" Residue "F GLU 90": "OE1" <-> "OE2" Residue "F GLU 99": "OE1" <-> "OE2" Residue "F GLU 102": "OE1" <-> "OE2" Residue "F GLU 129": "OE1" <-> "OE2" Residue "G GLU 5": "OE1" <-> "OE2" Residue "G ASP 9": "OD1" <-> "OD2" Residue "G ASP 37": "OD1" <-> "OD2" Residue "G GLU 45": "OE1" <-> "OE2" Residue "G ARG 49": "NH1" <-> "NH2" Residue "G ASP 80": "OD1" <-> "OD2" Residue "H GLU 12": "OE1" <-> "OE2" Residue "H ARG 43": "NH1" <-> "NH2" Residue "H GLU 53": "OE1" <-> "OE2" Residue "H GLU 83": "OE1" <-> "OE2" Residue "H GLU 95": "OE1" <-> "OE2" Residue "H ARG 111": "NH1" <-> "NH2" Residue "H GLU 138": "OE1" <-> "OE2" Residue "I ARG 56": "NH1" <-> "NH2" Residue "I PHE 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I GLU 80": "OE1" <-> "OE2" Residue "I GLU 111": "OE1" <-> "OE2" Residue "I GLU 116": "OE1" <-> "OE2" Residue "J ARG 2": "NH1" <-> "NH2" Residue "J ARG 46": "NH1" <-> "NH2" Residue "J ARG 63": "NH1" <-> "NH2" Residue "J ASP 117": "OD1" <-> "OD2" Residue "K TYR 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ARG 60": "NH1" <-> "NH2" Residue "K GLU 68": "OE1" <-> "OE2" Residue "L ASP 27": "OD1" <-> "OD2" Residue "L ARG 75": "NH1" <-> "NH2" Residue "L PHE 77": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ARG 91": "NH1" <-> "NH2" Residue "M ARG 3": "NH1" <-> "NH2" Residue "M ARG 13": "NH1" <-> "NH2" Residue "M ARG 30": "NH1" <-> "NH2" Residue "M TYR 76": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M ASP 102": "OD1" <-> "OD2" Residue "M PHE 106": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N TYR 2": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N ARG 13": "NH1" <-> "NH2" Residue "N GLU 16": "OE1" <-> "OE2" Residue "N GLU 28": "OE1" <-> "OE2" Residue "N PHE 35": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N ARG 79": "NH1" <-> "NH2" Residue "O ARG 9": "NH1" <-> "NH2" Residue "O ASP 23": "OD1" <-> "OD2" Residue "O GLU 60": "OE1" <-> "OE2" Residue "O ASP 66": "OD1" <-> "OD2" Residue "O ASP 68": "OD1" <-> "OD2" Residue "O ASP 69": "OD1" <-> "OD2" Residue "O ARG 96": "NH1" <-> "NH2" Residue "O ARG 100": "NH1" <-> "NH2" Residue "P GLU 4": "OE1" <-> "OE2" Residue "P ARG 5": "NH1" <-> "NH2" Residue "P GLU 53": "OE1" <-> "OE2" Residue "P ARG 68": "NH1" <-> "NH2" Residue "P PHE 69": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P ARG 71": "NH1" <-> "NH2" Residue "P ARG 75": "NH1" <-> "NH2" Residue "Q ASP 30": "OD1" <-> "OD2" Residue "Q ARG 92": "NH1" <-> "NH2" Residue "Q GLU 99": "OE1" <-> "OE2" Residue "R ARG 11": "NH1" <-> "NH2" Residue "R GLU 13": "OE1" <-> "OE2" Residue "R ARG 23": "NH1" <-> "NH2" Residue "R GLU 27": "OE1" <-> "OE2" Residue "R GLU 40": "OE1" <-> "OE2" Residue "R GLU 47": "OE1" <-> "OE2" Residue "R ARG 49": "NH1" <-> "NH2" Residue "R GLU 50": "OE1" <-> "OE2" Residue "R PHE 61": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R GLU 62": "OE1" <-> "OE2" Residue "R ASP 71": "OD1" <-> "OD2" Residue "S TYR 79": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T PHE 29": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T ARG 48": "NH1" <-> "NH2" Residue "T ARG 57": "NH1" <-> "NH2" Residue "T ASP 60": "OD1" <-> "OD2" Residue "U GLU 8": "OE1" <-> "OE2" Residue "U GLU 13": "OE1" <-> "OE2" Residue "U GLU 20": "OE1" <-> "OE2" Residue "U GLU 59": "OE1" <-> "OE2" Residue "V GLU 36": "OE1" <-> "OE2" Residue "V TYR 52": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V GLU 57": "OE1" <-> "OE2" Residue "X PHE 54": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y ASP 3": "OD1" <-> "OD2" Residue "Y TYR 17": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y GLU 28": "OE1" <-> "OE2" Residue "Y GLU 31": "OE1" <-> "OE2" Residue "Z GLU 9": "OE1" <-> "OE2" Residue "a ARG 29": "NH1" <-> "NH2" Residue "b ARG 36": "NH1" <-> "NH2" Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 83514 Number of models: 1 Model: "" Number of chains: 34 Chain: "1" Number of atoms: 57324 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2672, 57324 Classifications: {'RNA': 2672} Modifications used: {'rna2p_pur': 258, 'rna2p_pyr': 148, 'rna3p_pur': 1278, 'rna3p_pyr': 988} Link IDs: {'rna2p': 406, 'rna3p': 2265} Chain breaks: 5 Chain: "5" Number of atoms: 2450 Number of conformers: 1 Conformer: "" Number of residues, atoms: 115, 2450 Classifications: {'RNA': 115} Modifications used: {'rna2p_pur': 8, 'rna2p_pyr': 5, 'rna3p_pur': 52, 'rna3p_pyr': 50} Link IDs: {'rna2p': 13, 'rna3p': 101} Chain: "6" Number of atoms: 112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 112 Classifications: {'RNA': 5} Modifications used: {'rna2p_pur': 1, 'rna3p_pur': 3, 'rna3p_pyr': 1} Link IDs: {'rna2p': 1, 'rna3p': 3} Chain: "8" Number of atoms: 169 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 169 Classifications: {'RNA': 8} Modifications used: {'rna2p_pur': 1, 'rna2p_pyr': 2, 'rna3p_pur': 3, 'rna3p_pyr': 2} Link IDs: {'rna2p': 2, 'rna3p': 5} Chain: "A" Number of atoms: 2109 Number of conformers: 1 Conformer: "" Number of residues, atoms: 272, 2109 Classifications: {'peptide': 272} Link IDs: {'PTRANS': 16, 'TRANS': 255} Chain: "B" Number of atoms: 1571 Number of conformers: 1 Conformer: "" Number of residues, atoms: 211, 1571 Classifications: {'peptide': 211} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 205} Chain: "C" Number of atoms: 1485 Number of conformers: 1 Conformer: "" Number of residues, atoms: 199, 1485 Classifications: {'peptide': 199} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 6, 'TRANS': 192} Unresolved non-hydrogen bonds: 22 Unresolved non-hydrogen angles: 28 Unresolved non-hydrogen dihedrals: 16 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLU:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 7 Chain: "D" Number of atoms: 865 Number of conformers: 1 Conformer: "" Number of residues, atoms: 176, 865 Classifications: {'peptide': 176} Incomplete info: {'truncation_to_alanine': 145} Link IDs: {'PTRANS': 6, 'TRANS': 169} Unresolved chain link angles: 6 Unresolved non-hydrogen bonds: 542 Unresolved non-hydrogen angles: 679 Unresolved non-hydrogen dihedrals: 447 Unresolved non-hydrogen chiralities: 49 Planarities with less than four sites: {'GLN:plan1': 5, 'TYR:plan': 3, 'ASN:plan1': 4, 'TRP:plan': 1, 'ASP:plan': 15, 'PHE:plan': 10, 'GLU:plan': 8, 'ARG:plan': 16} Unresolved non-hydrogen planarities: 279 Chain: "E" Number of atoms: 1327 Number of conformers: 1 Conformer: "" Number of residues, atoms: 175, 1327 Classifications: {'peptide': 175} Link IDs: {'PTRANS': 8, 'TRANS': 166} Chain: "F" Number of atoms: 1122 Number of conformers: 1 Conformer: "" Number of residues, atoms: 142, 1122 Classifications: {'peptide': 142} Link IDs: {'PTRANS': 8, 'TRANS': 133} Chain: "G" Number of atoms: 945 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 945 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 5, 'TRANS': 116} Chain: "H" Number of atoms: 1071 Number of conformers: 1 Conformer: "" Number of residues, atoms: 144, 1071 Classifications: {'peptide': 144} Link IDs: {'PTRANS': 3, 'TRANS': 140} Chain: "I" Number of atoms: 1086 Number of conformers: 1 Conformer: "" Number of residues, atoms: 137, 1086 Classifications: {'peptide': 137} Link IDs: {'PTRANS': 6, 'TRANS': 130} Chain: "J" Number of atoms: 950 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 119, 942 Classifications: {'peptide': 119} Link IDs: {'PTRANS': 4, 'TRANS': 114} Conformer: "B" Number of residues, atoms: 119, 942 Classifications: {'peptide': 119} Link IDs: {'PTRANS': 4, 'TRANS': 114} bond proxies already assigned to first conformer: 946 Chain: "K" Number of atoms: 864 Number of conformers: 1 Conformer: "" Number of residues, atoms: 115, 864 Classifications: {'peptide': 115} Link IDs: {'PTRANS': 1, 'TRANS': 113} Chain: "L" Number of atoms: 919 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 919 Classifications: {'peptide': 117} Link IDs: {'PTRANS': 5, 'TRANS': 111} Chain: "M" Number of atoms: 934 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 934 Classifications: {'peptide': 117} Link IDs: {'TRANS': 116} Chain: "N" Number of atoms: 806 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 806 Classifications: {'peptide': 103} Link IDs: {'PCIS': 1, 'TRANS': 101} Chain: "O" Number of atoms: 825 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 825 Classifications: {'peptide': 109} Link IDs: {'PTRANS': 1, 'TRANS': 107} Chain: "P" Number of atoms: 717 Number of conformers: 1 Conformer: "" Number of residues, atoms: 92, 717 Classifications: {'peptide': 92} Link IDs: {'PTRANS': 1, 'TRANS': 90} Chain: "Q" Number of atoms: 761 Number of conformers: 1 Conformer: "" Number of residues, atoms: 102, 761 Classifications: {'peptide': 102} Link IDs: {'PTRANS': 1, 'TRANS': 100} Chain: "R" Number of atoms: 753 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 753 Classifications: {'peptide': 96} Link IDs: {'PTRANS': 4, 'TRANS': 91} Chain: "S" Number of atoms: 577 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 577 Classifications: {'peptide': 76} Link IDs: {'PTRANS': 1, 'TRANS': 74} Chain: "T" Number of atoms: 631 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 631 Classifications: {'peptide': 77} Link IDs: {'PTRANS': 2, 'TRANS': 74} Chain: "U" Number of atoms: 490 Number of conformers: 1 Conformer: "" Number of residues, atoms: 61, 490 Classifications: {'peptide': 61} Link IDs: {'TRANS': 60} Chain: "V" Number of atoms: 453 Number of conformers: 1 Conformer: "" Number of residues, atoms: 57, 453 Classifications: {'peptide': 57} Link IDs: {'PTRANS': 1, 'TRANS': 55} Chain: "X" Number of atoms: 447 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 447 Classifications: {'peptide': 54} Link IDs: {'TRANS': 53} Chain: "Y" Number of atoms: 426 Number of conformers: 1 Conformer: "" Number of residues, atoms: 51, 426 Classifications: {'peptide': 51} Link IDs: {'PTRANS': 2, 'TRANS': 48} Chain: "Z" Number of atoms: 362 Number of conformers: 1 Conformer: "" Number of residues, atoms: 44, 362 Classifications: {'peptide': 44} Link IDs: {'PTRANS': 1, 'TRANS': 42} Chain: "a" Number of atoms: 508 Number of conformers: 1 Conformer: "" Number of residues, atoms: 63, 508 Classifications: {'peptide': 63} Link IDs: {'PTRANS': 1, 'TRANS': 61} Chain: "b" Number of atoms: 294 Number of conformers: 1 Conformer: "" Number of residues, atoms: 38, 294 Classifications: {'peptide': 38} Link IDs: {'PTRANS': 1, 'TRANS': 36} Chain: "1" Number of atoms: 157 Number of conformers: 1 Conformer: "" Number of residues, atoms: 157, 157 Unusual residues: {' MG': 157} Classifications: {'undetermined': 157} Link IDs: {None: 156} Chain: "5" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' MG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "b" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 83142 SG CYS b 11 112.936 51.846 184.643 1.00 24.03 S ATOM 83158 SG CYS b 14 114.363 54.777 182.653 1.00 25.61 S ATOM 83263 SG CYS b 27 116.654 50.952 183.339 1.00 23.72 S Time building chain proxies: 32.77, per 1000 atoms: 0.39 Number of scatterers: 83514 At special positions: 0 Unit cell: (207.58, 192.6, 224.7, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 1 29.99 S 68 16.00 P 2800 15.00 Mg 160 11.99 O 23604 8.00 N 15545 7.00 C 41336 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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 Time building additional restraints: 32.29 Conformation dependent library (CDL) restraints added in 3.7 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN b 101 " pdb="ZN ZN b 101 " - pdb=" SG CYS b 11 " pdb="ZN ZN b 101 " - pdb=" SG CYS b 14 " pdb="ZN ZN b 101 " - pdb=" ND1 HIS b 33 " pdb="ZN ZN b 101 " - pdb=" SG CYS b 27 " Number of angles added : 3 6032 Ramachandran restraints generated. 3016 Oldfield, 0 Emsley, 3016 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5582 Finding SS restraints... Secondary structure from input PDB file: 90 helices and 47 sheets defined 28.8% alpha, 21.8% beta 901 base pairs and 1533 stacking pairs defined. Time for finding SS restraints: 29.72 Creating SS restraints... Processing helix chain 'A' and resid 30 through 32 No H-bonds generated for 'chain 'A' and resid 30 through 32' Processing helix chain 'A' and resid 133 through 135 No H-bonds generated for 'chain 'A' and resid 133 through 135' Processing helix chain 'A' and resid 199 through 203 Processing helix chain 'A' and resid 207 through 213 removed outlier: 3.873A pdb=" N ALA A 211 " --> pdb=" O LYS A 207 " (cutoff:3.500A) Processing helix chain 'A' and resid 221 through 225 Processing helix chain 'B' and resid 57 through 61 removed outlier: 3.701A pdb=" N VAL B 61 " --> pdb=" O GLU B 58 " (cutoff:3.500A) Processing helix chain 'B' and resid 62 through 72 removed outlier: 3.959A pdb=" N ALA B 72 " --> pdb=" O HIS B 68 " (cutoff:3.500A) Processing helix chain 'B' and resid 100 through 104 Processing helix chain 'B' and resid 123 through 128 Processing helix chain 'C' and resid 14 through 19 Processing helix chain 'C' and resid 23 through 37 Processing helix chain 'C' and resid 96 through 114 removed outlier: 3.516A pdb=" N CYS C 106 " --> pdb=" O GLY C 102 " (cutoff:3.500A) Processing helix chain 'C' and resid 129 through 137 removed outlier: 3.777A pdb=" N ALA C 135 " --> pdb=" O LYS C 131 " (cutoff:3.500A) Processing helix chain 'C' and resid 138 through 141 Processing helix chain 'C' and resid 153 through 160 Processing helix chain 'C' and resid 175 through 182 removed outlier: 3.534A pdb=" N LEU C 179 " --> pdb=" O ASP C 175 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N ILE C 180 " --> pdb=" O PRO C 176 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N PHE C 182 " --> pdb=" O SER C 178 " (cutoff:3.500A) Processing helix chain 'C' and resid 189 through 200 removed outlier: 3.753A pdb=" N VAL C 197 " --> pdb=" O LYS C 193 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N GLU C 198 " --> pdb=" O LYS C 194 " (cutoff:3.500A) Processing helix chain 'D' and resid 5 through 10 Processing helix chain 'D' and resid 11 through 20 removed outlier: 4.375A pdb=" N GLN D 17 " --> pdb=" O LYS D 13 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N GLU D 18 " --> pdb=" O ALA D 14 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N LEU D 20 " --> pdb=" O LEU D 16 " (cutoff:3.500A) Processing helix chain 'D' and resid 40 through 45 removed outlier: 3.880A pdb=" N ALA D 44 " --> pdb=" O GLY D 41 " (cutoff:3.500A) Processing helix chain 'D' and resid 47 through 54 removed outlier: 3.552A pdb=" N ASP D 51 " --> pdb=" O LYS D 47 " (cutoff:3.500A) Processing helix chain 'D' and resid 56 through 61 removed outlier: 3.880A pdb=" N ILE D 60 " --> pdb=" O ASP D 56 " (cutoff:3.500A) Processing helix chain 'D' and resid 96 through 100 Processing helix chain 'D' and resid 107 through 111 removed outlier: 3.821A pdb=" N ARG D 110 " --> pdb=" O ALA D 107 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N ILE D 111 " --> pdb=" O ILE D 108 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 107 through 111' Processing helix chain 'D' and resid 134 through 138 Processing helix chain 'D' and resid 162 through 172 removed outlier: 3.664A pdb=" N GLY D 166 " --> pdb=" O THR D 162 " (cutoff:3.500A) Processing helix chain 'E' and resid 58 through 81 removed outlier: 3.647A pdb=" N MET E 63 " --> pdb=" O LYS E 59 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N THR E 67 " --> pdb=" O MET E 63 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N ALA E 70 " --> pdb=" O GLY E 66 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N LEU E 72 " --> pdb=" O ALA E 68 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N SER E 80 " --> pdb=" O VAL E 76 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N GLU E 81 " --> pdb=" O LYS E 77 " (cutoff:3.500A) Processing helix chain 'E' and resid 137 through 150 Processing helix chain 'F' and resid 24 through 38 removed outlier: 4.255A pdb=" N GLU F 31 " --> pdb=" O ARG F 27 " (cutoff:3.500A) Processing helix chain 'F' and resid 58 through 62 removed outlier: 3.918A pdb=" N VAL F 62 " --> pdb=" O ALA F 59 " (cutoff:3.500A) Processing helix chain 'F' and resid 67 through 72 Processing helix chain 'F' and resid 88 through 94 removed outlier: 3.643A pdb=" N LEU F 92 " --> pdb=" O ASN F 88 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N ALA F 94 " --> pdb=" O GLU F 90 " (cutoff:3.500A) Processing helix chain 'F' and resid 96 through 107 removed outlier: 3.982A pdb=" N ILE F 100 " --> pdb=" O LYS F 96 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N PHE F 101 " --> pdb=" O PRO F 97 " (cutoff:3.500A) Processing helix chain 'F' and resid 112 through 119 Processing helix chain 'F' and resid 132 through 136 removed outlier: 3.654A pdb=" N GLN F 136 " --> pdb=" O ALA F 133 " (cutoff:3.500A) Processing helix chain 'G' and resid 105 through 107 No H-bonds generated for 'chain 'G' and resid 105 through 107' Processing helix chain 'G' and resid 111 through 118 removed outlier: 3.607A pdb=" N ILE G 115 " --> pdb=" O PHE G 111 " (cutoff:3.500A) Processing helix chain 'H' and resid 58 through 63 removed outlier: 3.634A pdb=" N LEU H 63 " --> pdb=" O ILE H 59 " (cutoff:3.500A) Processing helix chain 'H' and resid 71 through 74 Processing helix chain 'H' and resid 82 through 87 Processing helix chain 'H' and resid 93 through 100 Processing helix chain 'H' and resid 130 through 140 removed outlier: 3.575A pdb=" N LYS H 134 " --> pdb=" O THR H 130 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N ALA H 135 " --> pdb=" O LYS H 131 " (cutoff:3.500A) Processing helix chain 'I' and resid 44 through 58 Processing helix chain 'I' and resid 110 through 122 Processing helix chain 'I' and resid 123 through 125 No H-bonds generated for 'chain 'I' and resid 123 through 125' Processing helix chain 'J' and resid 13 through 32 Processing helix chain 'J' and resid 38 through 55 removed outlier: 3.652A pdb=" N GLU J 43 " --> pdb=" O PRO J 39 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N ARG J 45 " --> pdb=" O ALA J 41 " (cutoff:3.500A) removed outlier: 4.589A pdb=" N ARG J 46 " --> pdb=" O LYS J 42 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N VAL J 47 " --> pdb=" O GLU J 43 " (cutoff:3.500A) Proline residue: J 50 - end of helix Processing helix chain 'J' and resid 59 through 71 Processing helix chain 'J' and resid 72 through 82 Processing helix chain 'J' and resid 82 through 87 Processing helix chain 'K' and resid 4 through 12 removed outlier: 3.737A pdb=" N ARG K 10 " --> pdb=" O GLN K 6 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N ARG K 11 " --> pdb=" O SER K 7 " (cutoff:3.500A) Processing helix chain 'K' and resid 12 through 23 Processing helix chain 'K' and resid 66 through 82 removed outlier: 3.843A pdb=" N LYS K 72 " --> pdb=" O GLU K 68 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N VAL K 73 " --> pdb=" O ALA K 69 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N LYS K 82 " --> pdb=" O ALA K 78 " (cutoff:3.500A) Processing helix chain 'K' and resid 100 through 112 Processing helix chain 'L' and resid 5 through 14 removed outlier: 3.895A pdb=" N SER L 14 " --> pdb=" O ALA L 10 " (cutoff:3.500A) Processing helix chain 'L' and resid 56 through 59 Processing helix chain 'L' and resid 100 through 106 removed outlier: 3.557A pdb=" N LEU L 103 " --> pdb=" O LEU L 100 " (cutoff:3.500A) Processing helix chain 'L' and resid 107 through 112 removed outlier: 3.659A pdb=" N ALA L 110 " --> pdb=" O SER L 107 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N ARG L 112 " --> pdb=" O LYS L 109 " (cutoff:3.500A) Processing helix chain 'M' and resid 7 through 20 removed outlier: 3.538A pdb=" N ARG M 20 " --> pdb=" O LYS M 16 " (cutoff:3.500A) Processing helix chain 'M' and resid 25 through 30 Processing helix chain 'M' and resid 31 through 72 removed outlier: 3.764A pdb=" N GLN M 37 " --> pdb=" O ARG M 33 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N ARG M 51 " --> pdb=" O TYR M 47 " (cutoff:3.500A) removed outlier: 4.409A pdb=" N LYS M 54 " --> pdb=" O ARG M 50 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N ARG M 55 " --> pdb=" O ARG M 51 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N GLN M 71 " --> pdb=" O ALA M 67 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N ASN M 72 " --> pdb=" O GLY M 68 " (cutoff:3.500A) Processing helix chain 'M' and resid 75 through 86 Processing helix chain 'M' and resid 91 through 102 Processing helix chain 'M' and resid 102 through 118 Processing helix chain 'O' and resid 14 through 26 removed outlier: 3.975A pdb=" N LEU O 20 " --> pdb=" O GLN O 16 " (cutoff:3.500A) removed outlier: 4.204A pdb=" N VAL O 21 " --> pdb=" O LYS O 17 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N LEU O 24 " --> pdb=" O LEU O 20 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N ILE O 25 " --> pdb=" O VAL O 21 " (cutoff:3.500A) Processing helix chain 'O' and resid 29 through 39 Processing helix chain 'O' and resid 43 through 62 removed outlier: 4.017A pdb=" N LEU O 47 " --> pdb=" O LYS O 43 " (cutoff:3.500A) Processing helix chain 'O' and resid 90 through 92 No H-bonds generated for 'chain 'O' and resid 90 through 92' Processing helix chain 'P' and resid 2 through 9 removed outlier: 4.043A pdb=" N ILE P 6 " --> pdb=" O ASN P 2 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N TYR P 7 " --> pdb=" O ASN P 3 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N GLN P 8 " --> pdb=" O GLU P 4 " (cutoff:3.500A) Processing helix chain 'P' and resid 16 through 27 Processing helix chain 'P' and resid 38 through 51 Processing helix chain 'R' and resid 18 through 26 Processing helix chain 'R' and resid 48 through 55 Processing helix chain 'R' and resid 56 through 62 removed outlier: 6.526A pdb=" N ALA R 59 " --> pdb=" O GLU R 56 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N PHE R 61 " --> pdb=" O ASN R 58 " (cutoff:3.500A) Processing helix chain 'T' and resid 41 through 44 Processing helix chain 'T' and resid 53 through 63 Processing helix chain 'T' and resid 63 through 74 Processing helix chain 'U' and resid 12 through 34 removed outlier: 4.210A pdb=" N ALA U 16 " --> pdb=" O GLU U 12 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N LEU U 17 " --> pdb=" O GLU U 13 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N THR U 34 " --> pdb=" O MET U 30 " (cutoff:3.500A) Processing helix chain 'U' and resid 41 through 61 removed outlier: 3.862A pdb=" N VAL U 45 " --> pdb=" O HIS U 41 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N GLN U 61 " --> pdb=" O LEU U 57 " (cutoff:3.500A) Processing helix chain 'V' and resid 16 through 25 Processing helix chain 'V' and resid 40 through 50 removed outlier: 3.792A pdb=" N MET V 46 " --> pdb=" O SER V 42 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N VAL V 50 " --> pdb=" O MET V 46 " (cutoff:3.500A) Processing helix chain 'X' and resid 9 through 17 removed outlier: 3.534A pdb=" N ARG X 16 " --> pdb=" O ARG X 12 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N ARG X 17 " --> pdb=" O ARG X 13 " (cutoff:3.500A) Processing helix chain 'X' and resid 18 through 20 No H-bonds generated for 'chain 'X' and resid 18 through 20' Processing helix chain 'Z' and resid 8 through 17 Processing helix chain 'Z' and resid 17 through 23 Processing helix chain 'Z' and resid 24 through 38 Processing helix chain 'a' and resid 7 through 12 Processing helix chain 'a' and resid 36 through 43 Processing helix chain 'a' and resid 53 through 61 Processing helix chain 'b' and resid 30 through 33 Processing sheet with id=AA1, first strand: chain 'A' and resid 3 through 5 Processing sheet with id=AA2, first strand: chain 'A' and resid 34 through 37 removed outlier: 3.802A pdb=" N LYS A 37 " --> pdb=" O GLN A 60 " (cutoff:3.500A) removed outlier: 4.806A pdb=" N GLN A 60 " --> pdb=" O LYS A 37 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 101 through 105 removed outlier: 6.544A pdb=" N ILE A 91 " --> pdb=" O ILE A 81 " (cutoff:3.500A) removed outlier: 4.533A pdb=" N ILE A 81 " --> pdb=" O ILE A 91 " (cutoff:3.500A) removed outlier: 6.751A pdb=" N LEU A 93 " --> pdb=" O GLU A 79 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N VAL A 116 " --> pdb=" O ALA A 76 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 129 through 131 removed outlier: 5.994A pdb=" N LEU A 164 " --> pdb=" O ARG A 175 " (cutoff:3.500A) removed outlier: 6.887A pdb=" N ARG A 175 " --> pdb=" O LEU A 164 " (cutoff:3.500A) removed outlier: 6.704A pdb=" N MET A 181 " --> pdb=" O ILE A 268 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 144 through 145 removed outlier: 6.315A pdb=" N VAL A 144 " --> pdb=" O GLN A 153 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 5 through 16 removed outlier: 5.599A pdb=" N LYS B 9 " --> pdb=" O GLU B 29 " (cutoff:3.500A) removed outlier: 6.318A pdb=" N GLU B 29 " --> pdb=" O LYS B 9 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N GLY B 11 " --> pdb=" O VAL B 27 " (cutoff:3.500A) removed outlier: 6.548A pdb=" N VAL B 189 " --> pdb=" O VAL B 183 " (cutoff:3.500A) removed outlier: 4.622A pdb=" N VAL B 183 " --> pdb=" O VAL B 189 " (cutoff:3.500A) removed outlier: 6.675A pdb=" N VAL B 191 " --> pdb=" O VAL B 181 " (cutoff:3.500A) removed outlier: 4.742A pdb=" N GLU B 179 " --> pdb=" O LYS B 193 " (cutoff:3.500A) removed outlier: 5.287A pdb=" N THR B 174 " --> pdb=" O GLY B 114 " (cutoff:3.500A) removed outlier: 7.235A pdb=" N GLY B 114 " --> pdb=" O THR B 174 " (cutoff:3.500A) removed outlier: 5.467A pdb=" N GLN B 176 " --> pdb=" O VAL B 112 " (cutoff:3.500A) removed outlier: 6.828A pdb=" N VAL B 112 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 4.602A pdb=" N GLN B 115 " --> pdb=" O ASP B 203 " (cutoff:3.500A) removed outlier: 7.065A pdb=" N ASP B 203 " --> pdb=" O GLN B 115 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 79 through 84 removed outlier: 3.751A pdb=" N LEU B 79 " --> pdb=" O THR B 53 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N THR B 53 " --> pdb=" O LEU B 79 " (cutoff:3.500A) removed outlier: 6.444A pdb=" N ALA B 48 " --> pdb=" O ILE B 38 " (cutoff:3.500A) removed outlier: 4.675A pdb=" N ILE B 38 " --> pdb=" O ALA B 48 " (cutoff:3.500A) removed outlier: 6.699A pdb=" N GLN B 50 " --> pdb=" O THR B 36 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 118 through 122 removed outlier: 3.606A pdb=" N GLY B 120 " --> pdb=" O LEU B 168 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 3 through 4 removed outlier: 3.789A pdb=" N LEU C 3 " --> pdb=" O VAL C 11 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N VAL C 11 " --> pdb=" O LEU C 3 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'C' and resid 117 through 120 removed outlier: 6.355A pdb=" N LEU C 146 " --> pdb=" O VAL C 186 " (cutoff:3.500A) removed outlier: 7.547A pdb=" N SER C 188 " --> pdb=" O LEU C 146 " (cutoff:3.500A) removed outlier: 7.432A pdb=" N VAL C 148 " --> pdb=" O SER C 188 " (cutoff:3.500A) removed outlier: 6.310A pdb=" N ALA C 145 " --> pdb=" O ASP C 167 " (cutoff:3.500A) removed outlier: 7.752A pdb=" N VAL C 169 " --> pdb=" O ALA C 145 " (cutoff:3.500A) removed outlier: 6.255A pdb=" N ILE C 147 " --> pdb=" O VAL C 169 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 31 through 35 removed outlier: 3.793A pdb=" N LYS D 33 " --> pdb=" O THR D 157 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'E' and resid 9 through 10 removed outlier: 3.604A pdb=" N VAL E 9 " --> pdb=" O LEU E 50 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'E' and resid 16 through 18 removed outlier: 3.521A pdb=" N THR E 18 " --> pdb=" O GLU E 25 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'E' and resid 41 through 43 Processing sheet with id=AB6, first strand: chain 'E' and resid 122 through 124 Processing sheet with id=AB7, first strand: chain 'E' and resid 95 through 99 Processing sheet with id=AB8, first strand: chain 'F' and resid 122 through 124 Processing sheet with id=AB9, first strand: chain 'F' and resid 74 through 77 Processing sheet with id=AC1, first strand: chain 'G' and resid 7 through 10 removed outlier: 6.521A pdb=" N ARG G 17 " --> pdb=" O VAL G 10 " (cutoff:3.500A) removed outlier: 6.535A pdb=" N GLU G 45 " --> pdb=" O ARG G 17 " (cutoff:3.500A) removed outlier: 6.865A pdb=" N VAL G 19 " --> pdb=" O VAL G 43 " (cutoff:3.500A) removed outlier: 6.909A pdb=" N VAL G 43 " --> pdb=" O VAL G 19 " (cutoff:3.500A) removed outlier: 6.776A pdb=" N CYS G 21 " --> pdb=" O VAL G 41 " (cutoff:3.500A) removed outlier: 6.575A pdb=" N VAL G 41 " --> pdb=" O CYS G 21 " (cutoff:3.500A) removed outlier: 6.890A pdb=" N LYS G 23 " --> pdb=" O ILE G 39 " (cutoff:3.500A) removed outlier: 5.135A pdb=" N ILE G 39 " --> pdb=" O LYS G 23 " (cutoff:3.500A) removed outlier: 6.383A pdb=" N ALA G 83 " --> pdb=" O VAL G 63 " (cutoff:3.500A) removed outlier: 7.933A pdb=" N ALA G 84 " --> pdb=" O MET G 7 " (cutoff:3.500A) removed outlier: 6.341A pdb=" N ASP G 9 " --> pdb=" O ALA G 84 " (cutoff:3.500A) removed outlier: 7.550A pdb=" N ILE G 86 " --> pdb=" O ASP G 9 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'G' and resid 69 through 70 removed outlier: 4.027A pdb=" N VAL G 76 " --> pdb=" O VAL L 76 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N ALA L 52 " --> pdb=" O THR L 63 " (cutoff:3.500A) removed outlier: 6.669A pdb=" N ARG L 65 " --> pdb=" O VAL L 50 " (cutoff:3.500A) removed outlier: 5.630A pdb=" N VAL L 50 " --> pdb=" O ARG L 65 " (cutoff:3.500A) removed outlier: 8.821A pdb=" N ILE L 67 " --> pdb=" O GLY L 48 " (cutoff:3.500A) removed outlier: 8.682A pdb=" N GLY L 48 " --> pdb=" O ILE L 67 " (cutoff:3.500A) removed outlier: 7.262A pdb=" N THR L 28 " --> pdb=" O VAL L 89 " (cutoff:3.500A) removed outlier: 4.817A pdb=" N VAL L 89 " --> pdb=" O THR L 28 " (cutoff:3.500A) removed outlier: 6.638A pdb=" N VAL L 30 " --> pdb=" O ILE L 87 " (cutoff:3.500A) removed outlier: 4.409A pdb=" N ILE L 87 " --> pdb=" O VAL L 30 " (cutoff:3.500A) removed outlier: 6.573A pdb=" N GLN L 32 " --> pdb=" O ALA L 85 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'G' and resid 101 through 103 removed outlier: 6.655A pdb=" N VAL G 102 " --> pdb=" O LEU G 122 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC3 Processing sheet with id=AC4, first strand: chain 'H' and resid 76 through 80 Processing sheet with id=AC5, first strand: chain 'H' and resid 91 through 92 Processing sheet with id=AC6, first strand: chain 'I' and resid 63 through 66 removed outlier: 6.693A pdb=" N ILE I 34 " --> pdb=" O LEU I 103 " (cutoff:3.500A) removed outlier: 4.611A pdb=" N GLU I 105 " --> pdb=" O ILE I 32 " (cutoff:3.500A) removed outlier: 6.941A pdb=" N ILE I 32 " --> pdb=" O GLU I 105 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'I' and resid 40 through 43 removed outlier: 6.947A pdb=" N ILE I 74 " --> pdb=" O GLU I 91 " (cutoff:3.500A) removed outlier: 4.568A pdb=" N TRP I 93 " --> pdb=" O LYS I 72 " (cutoff:3.500A) removed outlier: 6.302A pdb=" N LYS I 72 " --> pdb=" O TRP I 93 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'J' and resid 33 through 37 removed outlier: 5.050A pdb=" N MET J 110 " --> pdb=" O ALA J 100 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'K' and resid 48 through 53 removed outlier: 6.760A pdb=" N VAL K 40 " --> pdb=" O LEU K 49 " (cutoff:3.500A) removed outlier: 4.561A pdb=" N GLN K 51 " --> pdb=" O ALA K 38 " (cutoff:3.500A) removed outlier: 6.899A pdb=" N ALA K 38 " --> pdb=" O GLN K 51 " (cutoff:3.500A) removed outlier: 4.657A pdb=" N SER K 53 " --> pdb=" O ILE K 36 " (cutoff:3.500A) removed outlier: 7.066A pdb=" N ILE K 36 " --> pdb=" O SER K 53 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N VAL K 29 " --> pdb=" O ASP K 92 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'N' and resid 10 through 14 removed outlier: 6.556A pdb=" N VAL N 4 " --> pdb=" O LEU N 39 " (cutoff:3.500A) removed outlier: 6.912A pdb=" N LEU N 39 " --> pdb=" O GLY N 50 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'N' and resid 19 through 23 removed outlier: 3.655A pdb=" N GLY N 65 " --> pdb=" O GLU N 95 " (cutoff:3.500A) removed outlier: 6.993A pdb=" N LYS N 97 " --> pdb=" O VAL N 63 " (cutoff:3.500A) removed outlier: 5.815A pdb=" N VAL N 63 " --> pdb=" O LYS N 97 " (cutoff:3.500A) removed outlier: 6.170A pdb=" N THR N 99 " --> pdb=" O ALA N 61 " (cutoff:3.500A) removed outlier: 7.170A pdb=" N ALA N 61 " --> pdb=" O THR N 99 " (cutoff:3.500A) removed outlier: 6.953A pdb=" N ILE N 101 " --> pdb=" O VAL N 59 " (cutoff:3.500A) removed outlier: 6.988A pdb=" N VAL N 59 " --> pdb=" O ILE N 101 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'N' and resid 72 through 78 removed outlier: 4.193A pdb=" N TYR N 83 " --> pdb=" O ARG N 78 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'O' and resid 3 through 11 removed outlier: 5.523A pdb=" N CYS O 102 " --> pdb=" O GLY O 10 " (cutoff:3.500A) removed outlier: 6.724A pdb=" N GLY O 109 " --> pdb=" O VAL O 72 " (cutoff:3.500A) removed outlier: 5.069A pdb=" N VAL O 72 " --> pdb=" O GLY O 109 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'O' and resid 83 through 88 Processing sheet with id=AD6, first strand: chain 'P' and resid 10 through 13 removed outlier: 3.582A pdb=" N GLY P 12 " --> pdb=" O LYS P 32 " (cutoff:3.500A) removed outlier: 4.204A pdb=" N LYS P 80 " --> pdb=" O VAL P 33 " (cutoff:3.500A) removed outlier: 6.626A pdb=" N VAL P 79 " --> pdb=" O ILE P 61 " (cutoff:3.500A) removed outlier: 4.501A pdb=" N ILE P 61 " --> pdb=" O VAL P 79 " (cutoff:3.500A) removed outlier: 6.691A pdb=" N LYS P 81 " --> pdb=" O THR P 59 " (cutoff:3.500A) removed outlier: 4.556A pdb=" N THR P 59 " --> pdb=" O LYS P 81 " (cutoff:3.500A) removed outlier: 6.640A pdb=" N TYR P 83 " --> pdb=" O VAL P 57 " (cutoff:3.500A) removed outlier: 4.318A pdb=" N VAL P 57 " --> pdb=" O TYR P 83 " (cutoff:3.500A) removed outlier: 6.583A pdb=" N THR P 85 " --> pdb=" O VAL P 55 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'P' and resid 66 through 68 Processing sheet with id=AD8, first strand: chain 'Q' and resid 63 through 64 removed outlier: 6.929A pdb=" N ARG Q 31 " --> pdb=" O VAL Q 27 " (cutoff:3.500A) removed outlier: 4.730A pdb=" N VAL Q 27 " --> pdb=" O ARG Q 31 " (cutoff:3.500A) removed outlier: 6.609A pdb=" N LYS Q 33 " --> pdb=" O LEU Q 25 " (cutoff:3.500A) removed outlier: 6.380A pdb=" N GLN Q 9 " --> pdb=" O LEU Q 71 " (cutoff:3.500A) removed outlier: 4.116A pdb=" N ILE Q 70 " --> pdb=" O ASP Q 79 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ASP Q 79 " --> pdb=" O ILE Q 70 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'Q' and resid 39 through 44 Processing sheet with id=AE1, first strand: chain 'Q' and resid 81 through 86 Processing sheet with id=AE2, first strand: chain 'R' and resid 5 through 7 removed outlier: 6.243A pdb=" N VAL R 76 " --> pdb=" O ARG R 97 " (cutoff:3.500A) removed outlier: 6.655A pdb=" N ARG R 97 " --> pdb=" O VAL R 76 " (cutoff:3.500A) removed outlier: 6.858A pdb=" N ILE R 78 " --> pdb=" O PHE R 95 " (cutoff:3.500A) removed outlier: 6.565A pdb=" N PHE R 95 " --> pdb=" O ILE R 78 " (cutoff:3.500A) removed outlier: 6.495A pdb=" N ALA R 80 " --> pdb=" O ALA R 93 " (cutoff:3.500A) removed outlier: 4.619A pdb=" N ALA R 93 " --> pdb=" O ALA R 80 " (cutoff:3.500A) removed outlier: 6.562A pdb=" N GLN R 82 " --> pdb=" O MET R 91 " (cutoff:3.500A) removed outlier: 8.613A pdb=" N LEU R 29 " --> pdb=" O MET R 91 " (cutoff:3.500A) removed outlier: 9.526A pdb=" N ALA R 93 " --> pdb=" O LEU R 29 " (cutoff:3.500A) removed outlier: 8.583A pdb=" N PHE R 95 " --> pdb=" O PRO R 31 " (cutoff:3.500A) removed outlier: 6.558A pdb=" N ILE R 33 " --> pdb=" O PHE R 95 " (cutoff:3.500A) removed outlier: 7.535A pdb=" N ARG R 97 " --> pdb=" O ILE R 33 " (cutoff:3.500A) removed outlier: 7.506A pdb=" N TYR R 35 " --> pdb=" O ARG R 97 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'S' and resid 22 through 23 removed outlier: 6.804A pdb=" N LEU S 59 " --> pdb=" O ILE S 37 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'S' and resid 30 through 31 Processing sheet with id=AE5, first strand: chain 'T' and resid 13 through 18 Processing sheet with id=AE6, first strand: chain 'T' and resid 33 through 40 Processing sheet with id=AE7, first strand: chain 'V' and resid 34 through 38 Processing sheet with id=AE8, first strand: chain 'X' and resid 27 through 29 Processing sheet with id=AE9, first strand: chain 'Y' and resid 16 through 22 Processing sheet with id=AF1, first strand: chain 'a' and resid 15 through 16 Processing sheet with id=AF2, first strand: chain 'b' and resid 2 through 4 removed outlier: 5.962A pdb=" N LYS b 2 " --> pdb=" O ARG b 36 " (cutoff:3.500A) removed outlier: 5.200A pdb=" N ILE b 23 " --> pdb=" O GLN b 37 " (cutoff:3.500A) 821 hydrogen bonds defined for protein. 2226 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 2258 hydrogen bonds 3482 hydrogen bond angles 0 basepair planarities 901 basepair parallelities 1533 stacking parallelities Total time for adding SS restraints: 163.98 Time building geometry restraints manager: 35.15 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 9376 1.32 - 1.44: 39563 1.44 - 1.57: 36190 1.57 - 1.69: 5591 1.69 - 1.81: 120 Bond restraints: 90840 Sorted by residual: bond pdb=" CA ARG X 17 " pdb=" C ARG X 17 " ideal model delta sigma weight residual 1.523 1.474 0.049 1.80e-02 3.09e+03 7.51e+00 bond pdb=" C GLU I 76 " pdb=" N LYS I 77 " ideal model delta sigma weight residual 1.331 1.285 0.046 2.07e-02 2.33e+03 5.01e+00 bond pdb=" O3' U 1 567 " pdb=" P G 1 568 " ideal model delta sigma weight residual 1.607 1.581 0.026 1.50e-02 4.44e+03 2.89e+00 bond pdb=" P G 12434 " pdb=" OP1 G 12434 " ideal model delta sigma weight residual 1.485 1.451 0.034 2.00e-02 2.50e+03 2.84e+00 bond pdb=" P G 11981 " pdb=" OP2 G 11981 " ideal model delta sigma weight residual 1.485 1.452 0.033 2.00e-02 2.50e+03 2.73e+00 ... (remaining 90835 not shown) Histogram of bond angle deviations from ideal: 98.92 - 106.20: 16473 106.20 - 113.47: 54292 113.47 - 120.74: 36307 120.74 - 128.02: 24733 128.02 - 135.29: 4732 Bond angle restraints: 136537 Sorted by residual: angle pdb=" C LYS H 38 " pdb=" N GLY H 39 " pdb=" CA GLY H 39 " ideal model delta sigma weight residual 122.43 116.38 6.05 8.90e-01 1.26e+00 4.62e+01 angle pdb=" O3' A 11746 " pdb=" C3' A 11746 " pdb=" C2' A 11746 " ideal model delta sigma weight residual 109.50 117.13 -7.63 1.50e+00 4.44e-01 2.58e+01 angle pdb=" O4' G 1 504 " pdb=" C1' G 1 504 " pdb=" N9 G 1 504 " ideal model delta sigma weight residual 108.20 115.09 -6.89 1.50e+00 4.44e-01 2.11e+01 angle pdb=" O3' U 1 567 " pdb=" C3' U 1 567 " pdb=" C2' U 1 567 " ideal model delta sigma weight residual 113.70 120.33 -6.63 1.50e+00 4.44e-01 1.95e+01 angle pdb=" C3' A 11746 " pdb=" O3' A 11746 " pdb=" P A 11747 " ideal model delta sigma weight residual 120.20 126.69 -6.49 1.50e+00 4.44e-01 1.87e+01 ... (remaining 136532 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.67: 50889 35.67 - 71.34: 6343 71.34 - 107.01: 712 107.01 - 142.68: 11 142.68 - 178.35: 20 Dihedral angle restraints: 57975 sinusoidal: 49293 harmonic: 8682 Sorted by residual: dihedral pdb=" CA HIS a 30 " pdb=" C HIS a 30 " pdb=" N ILE a 31 " pdb=" CA ILE a 31 " ideal model delta harmonic sigma weight residual -180.00 -131.20 -48.80 0 5.00e+00 4.00e-02 9.53e+01 dihedral pdb=" O4' U 1 138 " pdb=" C1' U 1 138 " pdb=" N1 U 1 138 " pdb=" C2 U 1 138 " ideal model delta sinusoidal sigma weight residual 200.00 29.82 170.18 1 1.50e+01 4.44e-03 8.47e+01 dihedral pdb=" O4' C 11130 " pdb=" C1' C 11130 " pdb=" N1 C 11130 " pdb=" C2 C 11130 " ideal model delta sinusoidal sigma weight residual -160.00 10.04 -170.04 1 1.50e+01 4.44e-03 8.47e+01 ... (remaining 57972 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.080: 16057 0.080 - 0.161: 1423 0.161 - 0.241: 104 0.241 - 0.321: 14 0.321 - 0.402: 2 Chirality restraints: 17600 Sorted by residual: chirality pdb=" C3' U 1 567 " pdb=" C4' U 1 567 " pdb=" O3' U 1 567 " pdb=" C2' U 1 567 " both_signs ideal model delta sigma weight residual False -2.48 -2.08 -0.40 2.00e-01 2.50e+01 4.03e+00 chirality pdb=" C3' A 11746 " pdb=" C4' A 11746 " pdb=" O3' A 11746 " pdb=" C2' A 11746 " both_signs ideal model delta sigma weight residual False -2.74 -2.35 -0.39 2.00e-01 2.50e+01 3.87e+00 chirality pdb=" C3' C 11171 " pdb=" C4' C 11171 " pdb=" O3' C 11171 " pdb=" C2' C 11171 " both_signs ideal model delta sigma weight residual False -2.48 -2.16 -0.32 2.00e-01 2.50e+01 2.52e+00 ... (remaining 17597 not shown) Planarity restraints: 6899 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' G 1 504 " -0.067 2.00e-02 2.50e+03 2.73e-02 2.24e+01 pdb=" N9 G 1 504 " 0.059 2.00e-02 2.50e+03 pdb=" C8 G 1 504 " 0.007 2.00e-02 2.50e+03 pdb=" N7 G 1 504 " 0.001 2.00e-02 2.50e+03 pdb=" C5 G 1 504 " 0.004 2.00e-02 2.50e+03 pdb=" C6 G 1 504 " -0.016 2.00e-02 2.50e+03 pdb=" O6 G 1 504 " -0.016 2.00e-02 2.50e+03 pdb=" N1 G 1 504 " -0.007 2.00e-02 2.50e+03 pdb=" C2 G 1 504 " 0.005 2.00e-02 2.50e+03 pdb=" N2 G 1 504 " 0.002 2.00e-02 2.50e+03 pdb=" N3 G 1 504 " 0.015 2.00e-02 2.50e+03 pdb=" C4 G 1 504 " 0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' U 12696 " -0.050 2.00e-02 2.50e+03 2.65e-02 1.58e+01 pdb=" N1 U 12696 " 0.058 2.00e-02 2.50e+03 pdb=" C2 U 12696 " 0.005 2.00e-02 2.50e+03 pdb=" O2 U 12696 " 0.005 2.00e-02 2.50e+03 pdb=" N3 U 12696 " -0.007 2.00e-02 2.50e+03 pdb=" C4 U 12696 " -0.012 2.00e-02 2.50e+03 pdb=" O4 U 12696 " -0.010 2.00e-02 2.50e+03 pdb=" C5 U 12696 " 0.002 2.00e-02 2.50e+03 pdb=" C6 U 12696 " 0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' A 1 970 " 0.053 2.00e-02 2.50e+03 2.37e-02 1.55e+01 pdb=" N9 A 1 970 " -0.054 2.00e-02 2.50e+03 pdb=" C8 A 1 970 " -0.003 2.00e-02 2.50e+03 pdb=" N7 A 1 970 " -0.000 2.00e-02 2.50e+03 pdb=" C5 A 1 970 " 0.001 2.00e-02 2.50e+03 pdb=" C6 A 1 970 " 0.007 2.00e-02 2.50e+03 pdb=" N6 A 1 970 " 0.015 2.00e-02 2.50e+03 pdb=" N1 A 1 970 " 0.003 2.00e-02 2.50e+03 pdb=" C2 A 1 970 " -0.004 2.00e-02 2.50e+03 pdb=" N3 A 1 970 " -0.007 2.00e-02 2.50e+03 pdb=" C4 A 1 970 " -0.011 2.00e-02 2.50e+03 ... (remaining 6896 not shown) Histogram of nonbonded interaction distances: 1.89 - 2.49: 339 2.49 - 3.09: 50222 3.09 - 3.70: 148377 3.70 - 4.30: 241427 4.30 - 4.90: 313211 Nonbonded interactions: 753576 Sorted by model distance: nonbonded pdb=" OP1 A 12578 " pdb="MG MG 13015 " model vdw 1.890 2.170 nonbonded pdb=" O2 U 1 536 " pdb=" O6 G 1 539 " model vdw 1.892 2.432 nonbonded pdb=" OP1 A 11769 " pdb="MG MG 13078 " model vdw 1.910 2.170 nonbonded pdb=" OP2 G 12811 " pdb="MG MG 13157 " model vdw 1.932 2.170 nonbonded pdb=" O4 U 11662 " pdb="MG MG 13117 " model vdw 1.956 2.170 ... (remaining 753571 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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: 3.090 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: 0.070 Extract box with map and model: 16.450 Check model and map are aligned: 0.890 Set scattering table: 0.590 Process input model: 332.490 Find NCS groups from input model: 1.500 Set up NCS constraints: 0.240 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: 0.030 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: 367.090 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8586 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 : 0.007 0.056 90840 Z= 0.439 Angle : 0.787 9.618 136537 Z= 0.416 Chirality : 0.047 0.402 17600 Planarity : 0.006 0.062 6899 Dihedral : 23.304 178.353 52393 Min Nonbonded Distance : 1.890 Molprobity Statistics. All-atom Clashscore : 3.54 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.51 % Favored : 94.46 % Rotamer: Outliers : 7.08 % Allowed : 17.75 % Favored : 75.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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: -2.86 (0.13), residues: 3016 helix: -1.90 (0.16), residues: 728 sheet: -1.19 (0.19), residues: 642 loop : -2.22 (0.12), residues: 1646 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A 248 HIS 0.011 0.002 HIS K 99 PHE 0.019 0.002 PHE M 57 TYR 0.021 0.003 TYR F 125 ARG 0.012 0.001 ARG M 51 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6032 Ramachandran restraints generated. 3016 Oldfield, 0 Emsley, 3016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6032 Ramachandran restraints generated. 3016 Oldfield, 0 Emsley, 3016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 685 residues out of total 2484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 165 poor density : 520 time to evaluate : 3.322 Fit side-chains REVERT: B 188 SER cc_start: 0.8990 (t) cc_final: 0.8660 (t) REVERT: C 110 GLU cc_start: 0.7643 (tp30) cc_final: 0.7439 (tp30) REVERT: E 49 LYS cc_start: 0.6663 (OUTLIER) cc_final: 0.5791 (mmtm) REVERT: E 98 VAL cc_start: 0.7454 (p) cc_final: 0.7232 (t) REVERT: E 139 GLN cc_start: 0.8635 (tm-30) cc_final: 0.8427 (tm130) REVERT: E 160 LYS cc_start: 0.7492 (OUTLIER) cc_final: 0.6826 (mtmt) REVERT: F 96 LYS cc_start: 0.8658 (tttt) cc_final: 0.8403 (tttp) REVERT: H 16 ARG cc_start: 0.8146 (mtp85) cc_final: 0.7848 (mtp85) REVERT: H 19 ARG cc_start: 0.8305 (ttm-80) cc_final: 0.8045 (ttt180) REVERT: H 134 LYS cc_start: 0.8410 (tttt) cc_final: 0.8050 (ttmt) REVERT: I 82 ARG cc_start: 0.9068 (OUTLIER) cc_final: 0.8455 (mmt-90) REVERT: I 85 ASN cc_start: 0.8595 (t0) cc_final: 0.8177 (m-40) REVERT: L 44 GLN cc_start: 0.8754 (tt0) cc_final: 0.8486 (tt0) REVERT: L 109 LYS cc_start: 0.6446 (OUTLIER) cc_final: 0.6221 (mttp) REVERT: L 115 GLU cc_start: 0.8158 (OUTLIER) cc_final: 0.7944 (tt0) REVERT: M 80 ILE cc_start: 0.9019 (mm) cc_final: 0.8679 (mm) REVERT: N 37 ASP cc_start: 0.7368 (OUTLIER) cc_final: 0.6935 (p0) REVERT: N 43 ASN cc_start: 0.7885 (t0) cc_final: 0.7480 (t0) REVERT: P 44 LYS cc_start: 0.8205 (OUTLIER) cc_final: 0.7977 (mmmm) REVERT: Q 79 ASP cc_start: 0.6744 (OUTLIER) cc_final: 0.6326 (t0) REVERT: Q 95 LYS cc_start: 0.7287 (ttmt) cc_final: 0.6696 (tttp) REVERT: R 7 ASN cc_start: 0.8343 (m-40) cc_final: 0.8042 (m-40) REVERT: S 10 THR cc_start: 0.7431 (OUTLIER) cc_final: 0.7143 (m) REVERT: T 24 LYS cc_start: 0.9110 (OUTLIER) cc_final: 0.8665 (mmtp) REVERT: T 27 ARG cc_start: 0.9046 (OUTLIER) cc_final: 0.8284 (ttt180) REVERT: Z 41 SER cc_start: 0.8956 (p) cc_final: 0.8641 (t) outliers start: 165 outliers final: 97 residues processed: 647 average time/residue: 1.7249 time to fit residues: 1476.3324 Evaluate side-chains 588 residues out of total 2484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 108 poor density : 480 time to evaluate : 3.348 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 SER Chi-restraints excluded: chain A residue 20 VAL Chi-restraints excluded: chain A residue 86 SER Chi-restraints excluded: chain A residue 88 THR Chi-restraints excluded: chain A residue 118 SER Chi-restraints excluded: chain A residue 139 SER Chi-restraints excluded: chain A residue 170 SER Chi-restraints excluded: chain A residue 186 VAL Chi-restraints excluded: chain A residue 228 ILE Chi-restraints excluded: chain B residue 13 THR Chi-restraints excluded: chain B residue 18 ASP Chi-restraints excluded: chain B residue 40 THR Chi-restraints excluded: chain B residue 43 THR Chi-restraints excluded: chain B residue 51 VAL Chi-restraints excluded: chain B residue 53 THR Chi-restraints excluded: chain B residue 59 SER Chi-restraints excluded: chain B residue 101 VAL Chi-restraints excluded: chain B residue 113 THR Chi-restraints excluded: chain B residue 141 VAL Chi-restraints excluded: chain B residue 153 GLN Chi-restraints excluded: chain B residue 185 THR Chi-restraints excluded: chain B residue 189 VAL Chi-restraints excluded: chain B residue 191 VAL Chi-restraints excluded: chain C residue 149 THR Chi-restraints excluded: chain E residue 20 ASN Chi-restraints excluded: chain E residue 24 VAL Chi-restraints excluded: chain E residue 27 LYS Chi-restraints excluded: chain E residue 40 LEU Chi-restraints excluded: chain E residue 49 LYS Chi-restraints excluded: chain E residue 67 THR Chi-restraints excluded: chain E residue 129 THR Chi-restraints excluded: chain E residue 133 LEU Chi-restraints excluded: chain E residue 160 LYS Chi-restraints excluded: chain E residue 175 LYS Chi-restraints excluded: chain F residue 4 LEU Chi-restraints excluded: chain F residue 62 VAL Chi-restraints excluded: chain G residue 45 GLU Chi-restraints excluded: chain G residue 47 ILE Chi-restraints excluded: chain G residue 73 ASP Chi-restraints excluded: chain G residue 75 SER Chi-restraints excluded: chain G residue 76 VAL Chi-restraints excluded: chain G residue 102 VAL Chi-restraints excluded: chain G residue 108 THR Chi-restraints excluded: chain H residue 29 VAL Chi-restraints excluded: chain H residue 117 GLU Chi-restraints excluded: chain H residue 123 THR Chi-restraints excluded: chain I residue 58 ILE Chi-restraints excluded: chain I residue 79 LEU Chi-restraints excluded: chain I residue 80 GLU Chi-restraints excluded: chain I residue 82 ARG Chi-restraints excluded: chain I residue 132 VAL Chi-restraints excluded: chain I residue 136 VAL Chi-restraints excluded: chain J residue 6 SER Chi-restraints excluded: chain K residue 27 LEU Chi-restraints excluded: chain K residue 44 ASP Chi-restraints excluded: chain K residue 61 SER Chi-restraints excluded: chain L residue 68 SER Chi-restraints excluded: chain L residue 73 VAL Chi-restraints excluded: chain L residue 109 LYS Chi-restraints excluded: chain L residue 115 GLU Chi-restraints excluded: chain N residue 32 THR Chi-restraints excluded: chain N residue 33 ILE Chi-restraints excluded: chain N residue 34 THR Chi-restraints excluded: chain N residue 37 ASP Chi-restraints excluded: chain N residue 99 THR Chi-restraints excluded: chain O residue 5 THR Chi-restraints excluded: chain O residue 29 SER Chi-restraints excluded: chain O residue 54 SER Chi-restraints excluded: chain O residue 74 THR Chi-restraints excluded: chain O residue 98 THR Chi-restraints excluded: chain O residue 108 VAL Chi-restraints excluded: chain O residue 110 VAL Chi-restraints excluded: chain P residue 44 LYS Chi-restraints excluded: chain P residue 52 VAL Chi-restraints excluded: chain P residue 55 VAL Chi-restraints excluded: chain P residue 66 THR Chi-restraints excluded: chain P residue 78 ASP Chi-restraints excluded: chain P residue 86 LEU Chi-restraints excluded: chain P residue 92 VAL Chi-restraints excluded: chain Q residue 28 SER Chi-restraints excluded: chain Q residue 40 VAL Chi-restraints excluded: chain Q residue 57 VAL Chi-restraints excluded: chain Q residue 58 THR Chi-restraints excluded: chain Q residue 60 GLU Chi-restraints excluded: chain Q residue 62 SER Chi-restraints excluded: chain Q residue 66 SER Chi-restraints excluded: chain Q residue 74 THR Chi-restraints excluded: chain Q residue 79 ASP Chi-restraints excluded: chain Q residue 100 SER Chi-restraints excluded: chain R residue 30 VAL Chi-restraints excluded: chain R residue 44 VAL Chi-restraints excluded: chain S residue 9 SER Chi-restraints excluded: chain S residue 10 THR Chi-restraints excluded: chain T residue 19 SER Chi-restraints excluded: chain T residue 22 ASN Chi-restraints excluded: chain T residue 24 LYS Chi-restraints excluded: chain T residue 27 ARG Chi-restraints excluded: chain U residue 11 VAL Chi-restraints excluded: chain U residue 17 LEU Chi-restraints excluded: chain U residue 34 THR Chi-restraints excluded: chain U residue 37 LEU Chi-restraints excluded: chain U residue 47 ARG Chi-restraints excluded: chain V residue 57 GLU Chi-restraints excluded: chain X residue 53 LEU Chi-restraints excluded: chain a residue 30 HIS Chi-restraints excluded: chain a residue 31 ILE Chi-restraints excluded: chain a residue 64 ILE Chi-restraints excluded: chain b residue 6 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 572 random chunks: chunk 483 optimal weight: 0.9990 chunk 433 optimal weight: 0.8980 chunk 240 optimal weight: 6.9990 chunk 148 optimal weight: 5.9990 chunk 292 optimal weight: 8.9990 chunk 231 optimal weight: 5.9990 chunk 448 optimal weight: 9.9990 chunk 173 optimal weight: 20.0000 chunk 272 optimal weight: 10.0000 chunk 333 optimal weight: 2.9990 chunk 519 optimal weight: 1.9990 overall best weight: 2.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 134 ASN A 142 HIS E 19 GLN E 45 GLN E 106 ASN F 136 GLN G 88 ASN L 5 HIS L 15 GLN O 63 ASN P 90 GLN Q 43 HIS S 17 ASN T 6 GLN T 23 ASN X 37 HIS a 30 HIS b 35 GLN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8542 moved from start: 0.0663 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 90840 Z= 0.237 Angle : 0.610 9.239 136537 Z= 0.323 Chirality : 0.039 0.310 17600 Planarity : 0.005 0.060 6899 Dihedral : 23.024 178.943 46990 Min Nonbonded Distance : 1.892 Molprobity Statistics. All-atom Clashscore : 3.82 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.38 % Favored : 95.59 % Rotamer: Outliers : 5.40 % Allowed : 21.83 % Favored : 72.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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 (0.14), residues: 3016 helix: -0.49 (0.18), residues: 748 sheet: -0.66 (0.19), residues: 659 loop : -1.78 (0.13), residues: 1609 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP A 248 HIS 0.006 0.001 HIS K 99 PHE 0.014 0.002 PHE M 57 TYR 0.014 0.002 TYR F 125 ARG 0.007 0.000 ARG G 51 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6032 Ramachandran restraints generated. 3016 Oldfield, 0 Emsley, 3016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6032 Ramachandran restraints generated. 3016 Oldfield, 0 Emsley, 3016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 627 residues out of total 2484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 126 poor density : 501 time to evaluate : 3.421 Fit side-chains revert: symmetry clash REVERT: A 17 GLU cc_start: 0.7806 (OUTLIER) cc_final: 0.7354 (mt-10) REVERT: A 84 ASP cc_start: 0.8817 (t0) cc_final: 0.8471 (t70) REVERT: A 130 LEU cc_start: 0.8727 (OUTLIER) cc_final: 0.8401 (mp) REVERT: B 42 GLU cc_start: 0.6567 (OUTLIER) cc_final: 0.6321 (mt-10) REVERT: B 188 SER cc_start: 0.8920 (t) cc_final: 0.8617 (t) REVERT: C 131 LYS cc_start: 0.7315 (OUTLIER) cc_final: 0.7096 (ttmm) REVERT: E 37 LEU cc_start: 0.7594 (OUTLIER) cc_final: 0.7252 (mp) REVERT: E 153 SER cc_start: 0.8436 (OUTLIER) cc_final: 0.8063 (m) REVERT: F 73 LYS cc_start: 0.8594 (OUTLIER) cc_final: 0.8172 (mmtt) REVERT: F 96 LYS cc_start: 0.8475 (tttt) cc_final: 0.8225 (tttp) REVERT: G 54 LYS cc_start: 0.8697 (tttm) cc_final: 0.8397 (tttm) REVERT: H 16 ARG cc_start: 0.8048 (mtp85) cc_final: 0.7766 (mtp85) REVERT: H 96 THR cc_start: 0.9097 (m) cc_final: 0.8864 (m) REVERT: H 134 LYS cc_start: 0.8197 (tttt) cc_final: 0.7994 (ttmm) REVERT: I 14 LYS cc_start: 0.9093 (OUTLIER) cc_final: 0.8744 (ttmt) REVERT: I 82 ARG cc_start: 0.9043 (OUTLIER) cc_final: 0.8397 (mmt-90) REVERT: I 85 ASN cc_start: 0.8472 (t0) cc_final: 0.8111 (m-40) REVERT: J 114 GLU cc_start: 0.8012 (OUTLIER) cc_final: 0.7412 (pt0) REVERT: L 44 GLN cc_start: 0.8710 (tt0) cc_final: 0.8496 (tt0) REVERT: L 115 GLU cc_start: 0.8204 (OUTLIER) cc_final: 0.7890 (tt0) REVERT: M 74 LEU cc_start: 0.8655 (OUTLIER) cc_final: 0.8337 (mt) REVERT: M 80 ILE cc_start: 0.8929 (mm) cc_final: 0.8640 (mm) REVERT: N 37 ASP cc_start: 0.7064 (p0) cc_final: 0.6786 (p0) REVERT: N 73 ARG cc_start: 0.8499 (mtp-110) cc_final: 0.8281 (mtt-85) REVERT: P 17 GLU cc_start: 0.7935 (OUTLIER) cc_final: 0.7538 (tm-30) REVERT: R 7 ASN cc_start: 0.8292 (m-40) cc_final: 0.8059 (m-40) REVERT: S 11 LYS cc_start: 0.7814 (OUTLIER) cc_final: 0.7409 (mptt) REVERT: S 84 THR cc_start: 0.8527 (p) cc_final: 0.8294 (p) REVERT: T 27 ARG cc_start: 0.8917 (OUTLIER) cc_final: 0.8258 (tmt170) REVERT: Z 41 SER cc_start: 0.8941 (p) cc_final: 0.8645 (t) REVERT: a 31 ILE cc_start: 0.7529 (OUTLIER) cc_final: 0.7023 (pt) REVERT: b 36 ARG cc_start: 0.8976 (OUTLIER) cc_final: 0.8477 (ttp-170) outliers start: 126 outliers final: 60 residues processed: 585 average time/residue: 1.7466 time to fit residues: 1351.1335 Evaluate side-chains 550 residues out of total 2484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 77 poor density : 473 time to evaluate : 3.311 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 GLU Chi-restraints excluded: chain A residue 20 VAL Chi-restraints excluded: chain A residue 86 SER Chi-restraints excluded: chain A residue 88 THR Chi-restraints excluded: chain A residue 130 LEU Chi-restraints excluded: chain A residue 228 ILE Chi-restraints excluded: chain B residue 13 THR Chi-restraints excluded: chain B residue 42 GLU Chi-restraints excluded: chain B residue 43 THR Chi-restraints excluded: chain B residue 51 VAL Chi-restraints excluded: chain B residue 113 THR Chi-restraints excluded: chain B residue 153 GLN Chi-restraints excluded: chain B residue 191 VAL Chi-restraints excluded: chain C residue 131 LYS Chi-restraints excluded: chain E residue 20 ASN Chi-restraints excluded: chain E residue 25 GLU Chi-restraints excluded: chain E residue 32 THR Chi-restraints excluded: chain E residue 37 LEU Chi-restraints excluded: chain E residue 58 SER Chi-restraints excluded: chain E residue 129 THR Chi-restraints excluded: chain E residue 153 SER Chi-restraints excluded: chain F residue 5 SER Chi-restraints excluded: chain F residue 21 THR Chi-restraints excluded: chain F residue 60 GLU Chi-restraints excluded: chain F residue 73 LYS Chi-restraints excluded: chain G residue 34 SER Chi-restraints excluded: chain G residue 45 GLU Chi-restraints excluded: chain G residue 80 ASP Chi-restraints excluded: chain G residue 102 VAL Chi-restraints excluded: chain G residue 108 THR Chi-restraints excluded: chain G residue 116 SER Chi-restraints excluded: chain H residue 29 VAL Chi-restraints excluded: chain H residue 85 SER Chi-restraints excluded: chain H residue 117 GLU Chi-restraints excluded: chain H residue 123 THR Chi-restraints excluded: chain I residue 14 LYS Chi-restraints excluded: chain I residue 79 LEU Chi-restraints excluded: chain I residue 82 ARG Chi-restraints excluded: chain I residue 132 VAL Chi-restraints excluded: chain I residue 136 VAL Chi-restraints excluded: chain J residue 6 SER Chi-restraints excluded: chain J residue 114 GLU Chi-restraints excluded: chain L residue 36 LYS Chi-restraints excluded: chain L residue 86 LYS Chi-restraints excluded: chain L residue 115 GLU Chi-restraints excluded: chain M residue 74 LEU Chi-restraints excluded: chain M residue 104 VAL Chi-restraints excluded: chain N residue 32 THR Chi-restraints excluded: chain N residue 34 THR Chi-restraints excluded: chain O residue 2 MET Chi-restraints excluded: chain O residue 5 THR Chi-restraints excluded: chain O residue 101 THR Chi-restraints excluded: chain O residue 108 VAL Chi-restraints excluded: chain P residue 17 GLU Chi-restraints excluded: chain P residue 77 SER Chi-restraints excluded: chain P residue 78 ASP Chi-restraints excluded: chain Q residue 40 VAL Chi-restraints excluded: chain Q residue 60 GLU Chi-restraints excluded: chain Q residue 66 SER Chi-restraints excluded: chain R residue 27 GLU Chi-restraints excluded: chain R residue 44 VAL Chi-restraints excluded: chain S residue 9 SER Chi-restraints excluded: chain S residue 11 LYS Chi-restraints excluded: chain T residue 22 ASN Chi-restraints excluded: chain T residue 27 ARG Chi-restraints excluded: chain T residue 62 LEU Chi-restraints excluded: chain U residue 32 LYS Chi-restraints excluded: chain U residue 34 THR Chi-restraints excluded: chain U residue 37 LEU Chi-restraints excluded: chain V residue 4 ILE Chi-restraints excluded: chain X residue 35 GLU Chi-restraints excluded: chain X residue 44 LYS Chi-restraints excluded: chain Y residue 25 THR Chi-restraints excluded: chain Y residue 51 LYS Chi-restraints excluded: chain a residue 31 ILE Chi-restraints excluded: chain a residue 47 VAL Chi-restraints excluded: chain b residue 36 ARG Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 572 random chunks: chunk 288 optimal weight: 2.9990 chunk 161 optimal weight: 10.0000 chunk 432 optimal weight: 9.9990 chunk 353 optimal weight: 30.0000 chunk 143 optimal weight: 10.0000 chunk 520 optimal weight: 5.9990 chunk 562 optimal weight: 0.9990 chunk 463 optimal weight: 10.0000 chunk 516 optimal weight: 6.9990 chunk 177 optimal weight: 20.0000 chunk 417 optimal weight: 8.9990 overall best weight: 5.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 106 ASN E 139 GLN F 95 HIS J 62 ASN L 15 GLN N 43 ASN S 17 ASN X 6 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8588 moved from start: 0.0488 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.075 90840 Z= 0.453 Angle : 0.792 9.621 136537 Z= 0.404 Chirality : 0.048 0.414 17600 Planarity : 0.006 0.065 6899 Dihedral : 23.149 179.244 46876 Min Nonbonded Distance : 1.843 Molprobity Statistics. All-atom Clashscore : 3.67 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.21 % Favored : 94.76 % Rotamer: Outliers : 7.50 % Allowed : 20.88 % Favored : 71.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: -1.59 (0.14), residues: 3016 helix: -0.36 (0.18), residues: 754 sheet: -0.47 (0.20), residues: 645 loop : -1.65 (0.14), residues: 1617 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.003 TRP E 62 HIS 0.014 0.002 HIS F 95 PHE 0.019 0.003 PHE M 57 TYR 0.022 0.003 TYR F 125 ARG 0.007 0.001 ARG G 51 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6032 Ramachandran restraints generated. 3016 Oldfield, 0 Emsley, 3016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6032 Ramachandran restraints generated. 3016 Oldfield, 0 Emsley, 3016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 646 residues out of total 2484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 175 poor density : 471 time to evaluate : 3.490 Fit side-chains revert: symmetry clash REVERT: A 5 LYS cc_start: 0.8327 (ttpp) cc_final: 0.8123 (tptt) REVERT: A 17 GLU cc_start: 0.7867 (OUTLIER) cc_final: 0.7536 (mt-10) REVERT: B 42 GLU cc_start: 0.6631 (OUTLIER) cc_final: 0.6399 (mt-10) REVERT: B 94 GLU cc_start: 0.7014 (OUTLIER) cc_final: 0.6436 (mt-10) REVERT: B 188 SER cc_start: 0.8919 (t) cc_final: 0.8574 (t) REVERT: C 131 LYS cc_start: 0.7373 (OUTLIER) cc_final: 0.7157 (ttmm) REVERT: E 37 LEU cc_start: 0.7787 (OUTLIER) cc_final: 0.7446 (mp) REVERT: E 153 SER cc_start: 0.8450 (OUTLIER) cc_final: 0.8097 (m) REVERT: F 73 LYS cc_start: 0.8602 (OUTLIER) cc_final: 0.8232 (mmtt) REVERT: F 96 LYS cc_start: 0.8633 (tttt) cc_final: 0.8381 (tttp) REVERT: G 54 LYS cc_start: 0.8736 (tttm) cc_final: 0.8410 (tttp) REVERT: H 16 ARG cc_start: 0.8156 (mtp85) cc_final: 0.7846 (mtp85) REVERT: H 19 ARG cc_start: 0.8239 (OUTLIER) cc_final: 0.7777 (ttt180) REVERT: H 96 THR cc_start: 0.9114 (m) cc_final: 0.8903 (m) REVERT: H 134 LYS cc_start: 0.8204 (tttt) cc_final: 0.7980 (ttmm) REVERT: I 14 LYS cc_start: 0.9121 (OUTLIER) cc_final: 0.8815 (ttmt) REVERT: I 82 ARG cc_start: 0.9083 (OUTLIER) cc_final: 0.8514 (mmt-90) REVERT: I 85 ASN cc_start: 0.8562 (t0) cc_final: 0.8163 (m-40) REVERT: L 44 GLN cc_start: 0.8740 (tt0) cc_final: 0.8480 (tt0) REVERT: L 115 GLU cc_start: 0.8198 (OUTLIER) cc_final: 0.7963 (tt0) REVERT: M 74 LEU cc_start: 0.8658 (OUTLIER) cc_final: 0.8308 (mt) REVERT: M 80 ILE cc_start: 0.8926 (mm) cc_final: 0.8623 (mm) REVERT: N 1 MET cc_start: 0.6688 (OUTLIER) cc_final: 0.6300 (ttp) REVERT: N 37 ASP cc_start: 0.7150 (OUTLIER) cc_final: 0.6826 (p0) REVERT: P 17 GLU cc_start: 0.7953 (OUTLIER) cc_final: 0.7575 (tm-30) REVERT: Q 21 GLN cc_start: 0.8325 (OUTLIER) cc_final: 0.7692 (pt0) REVERT: R 7 ASN cc_start: 0.8370 (m-40) cc_final: 0.8090 (m-40) REVERT: R 62 GLU cc_start: 0.7631 (OUTLIER) cc_final: 0.7264 (mt-10) REVERT: S 10 THR cc_start: 0.7433 (OUTLIER) cc_final: 0.7215 (m) REVERT: S 11 LYS cc_start: 0.7809 (OUTLIER) cc_final: 0.7386 (mptt) REVERT: S 84 THR cc_start: 0.8607 (p) cc_final: 0.8338 (p) REVERT: T 27 ARG cc_start: 0.8983 (OUTLIER) cc_final: 0.8264 (ttt180) REVERT: Z 41 SER cc_start: 0.8966 (p) cc_final: 0.8658 (t) REVERT: a 31 ILE cc_start: 0.7893 (OUTLIER) cc_final: 0.7115 (pt) REVERT: b 36 ARG cc_start: 0.9000 (OUTLIER) cc_final: 0.8502 (ttp-170) outliers start: 175 outliers final: 93 residues processed: 592 average time/residue: 1.7798 time to fit residues: 1412.1047 Evaluate side-chains 582 residues out of total 2484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 115 poor density : 467 time to evaluate : 3.363 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 GLU Chi-restraints excluded: chain A residue 20 VAL Chi-restraints excluded: chain A residue 86 SER Chi-restraints excluded: chain A residue 88 THR Chi-restraints excluded: chain A residue 139 SER Chi-restraints excluded: chain A residue 174 ILE Chi-restraints excluded: chain A residue 178 SER Chi-restraints excluded: chain A residue 228 ILE Chi-restraints excluded: chain B residue 13 THR Chi-restraints excluded: chain B residue 18 ASP Chi-restraints excluded: chain B residue 40 THR Chi-restraints excluded: chain B residue 42 GLU Chi-restraints excluded: chain B residue 43 THR Chi-restraints excluded: chain B residue 51 VAL Chi-restraints excluded: chain B residue 59 SER Chi-restraints excluded: chain B residue 94 GLU Chi-restraints excluded: chain B residue 113 THR Chi-restraints excluded: chain B residue 141 VAL Chi-restraints excluded: chain B residue 153 GLN Chi-restraints excluded: chain B residue 185 THR Chi-restraints excluded: chain B residue 191 VAL Chi-restraints excluded: chain B residue 200 THR Chi-restraints excluded: chain C residue 131 LYS Chi-restraints excluded: chain C residue 199 LEU Chi-restraints excluded: chain E residue 18 THR Chi-restraints excluded: chain E residue 29 SER Chi-restraints excluded: chain E residue 32 THR Chi-restraints excluded: chain E residue 34 SER Chi-restraints excluded: chain E residue 37 LEU Chi-restraints excluded: chain E residue 105 LEU Chi-restraints excluded: chain E residue 129 THR Chi-restraints excluded: chain E residue 153 SER Chi-restraints excluded: chain E residue 168 VAL Chi-restraints excluded: chain E residue 170 LEU Chi-restraints excluded: chain F residue 4 LEU Chi-restraints excluded: chain F residue 5 SER Chi-restraints excluded: chain F residue 62 VAL Chi-restraints excluded: chain F residue 73 LYS Chi-restraints excluded: chain F residue 106 LYS Chi-restraints excluded: chain G residue 45 GLU Chi-restraints excluded: chain G residue 73 ASP Chi-restraints excluded: chain G residue 76 VAL Chi-restraints excluded: chain G residue 80 ASP Chi-restraints excluded: chain G residue 102 VAL Chi-restraints excluded: chain G residue 108 THR Chi-restraints excluded: chain G residue 116 SER Chi-restraints excluded: chain H residue 19 ARG Chi-restraints excluded: chain H residue 29 VAL Chi-restraints excluded: chain H residue 85 SER Chi-restraints excluded: chain H residue 117 GLU Chi-restraints excluded: chain H residue 119 THR Chi-restraints excluded: chain H residue 123 THR Chi-restraints excluded: chain I residue 14 LYS Chi-restraints excluded: chain I residue 58 ILE Chi-restraints excluded: chain I residue 79 LEU Chi-restraints excluded: chain I residue 80 GLU Chi-restraints excluded: chain I residue 82 ARG Chi-restraints excluded: chain I residue 132 VAL Chi-restraints excluded: chain I residue 133 THR Chi-restraints excluded: chain I residue 136 VAL Chi-restraints excluded: chain J residue 6 SER Chi-restraints excluded: chain K residue 9 LEU Chi-restraints excluded: chain K residue 27 LEU Chi-restraints excluded: chain K residue 58 SER Chi-restraints excluded: chain K residue 99 HIS Chi-restraints excluded: chain L residue 18 THR Chi-restraints excluded: chain L residue 36 LYS Chi-restraints excluded: chain L residue 86 LYS Chi-restraints excluded: chain L residue 88 GLU Chi-restraints excluded: chain L residue 115 GLU Chi-restraints excluded: chain M residue 74 LEU Chi-restraints excluded: chain M residue 104 VAL Chi-restraints excluded: chain N residue 1 MET Chi-restraints excluded: chain N residue 2 TYR Chi-restraints excluded: chain N residue 32 THR Chi-restraints excluded: chain N residue 33 ILE Chi-restraints excluded: chain N residue 34 THR Chi-restraints excluded: chain N residue 37 ASP Chi-restraints excluded: chain N residue 49 ILE Chi-restraints excluded: chain N residue 87 GLN Chi-restraints excluded: chain N residue 99 THR Chi-restraints excluded: chain O residue 2 MET Chi-restraints excluded: chain O residue 5 THR Chi-restraints excluded: chain O residue 24 LEU Chi-restraints excluded: chain O residue 101 THR Chi-restraints excluded: chain O residue 108 VAL Chi-restraints excluded: chain O residue 110 VAL Chi-restraints excluded: chain P residue 17 GLU Chi-restraints excluded: chain P residue 77 SER Chi-restraints excluded: chain P residue 92 VAL Chi-restraints excluded: chain Q residue 21 GLN Chi-restraints excluded: chain Q residue 40 VAL Chi-restraints excluded: chain Q residue 60 GLU Chi-restraints excluded: chain Q residue 66 SER Chi-restraints excluded: chain R residue 27 GLU Chi-restraints excluded: chain R residue 44 VAL Chi-restraints excluded: chain R residue 62 GLU Chi-restraints excluded: chain S residue 9 SER Chi-restraints excluded: chain S residue 10 THR Chi-restraints excluded: chain S residue 11 LYS Chi-restraints excluded: chain T residue 22 ASN Chi-restraints excluded: chain T residue 27 ARG Chi-restraints excluded: chain T residue 62 LEU Chi-restraints excluded: chain U residue 11 VAL Chi-restraints excluded: chain U residue 17 LEU Chi-restraints excluded: chain U residue 32 LYS Chi-restraints excluded: chain U residue 34 THR Chi-restraints excluded: chain U residue 37 LEU Chi-restraints excluded: chain V residue 4 ILE Chi-restraints excluded: chain X residue 44 LYS Chi-restraints excluded: chain Y residue 25 THR Chi-restraints excluded: chain a residue 31 ILE Chi-restraints excluded: chain a residue 47 VAL Chi-restraints excluded: chain b residue 6 SER Chi-restraints excluded: chain b residue 36 ARG Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 572 random chunks: chunk 514 optimal weight: 6.9990 chunk 391 optimal weight: 3.9990 chunk 270 optimal weight: 20.0000 chunk 57 optimal weight: 3.9990 chunk 248 optimal weight: 4.9990 chunk 349 optimal weight: 3.9990 chunk 522 optimal weight: 0.7980 chunk 552 optimal weight: 4.9990 chunk 272 optimal weight: 10.0000 chunk 494 optimal weight: 10.0000 chunk 149 optimal weight: 2.9990 overall best weight: 3.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 106 ASN E 139 GLN F 95 HIS F 136 GLN L 15 GLN M 72 ASN N 43 ASN S 17 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8564 moved from start: 0.0545 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 90840 Z= 0.286 Angle : 0.668 9.511 136537 Z= 0.352 Chirality : 0.041 0.356 17600 Planarity : 0.005 0.062 6899 Dihedral : 23.114 179.167 46872 Min Nonbonded Distance : 1.874 Molprobity Statistics. All-atom Clashscore : 3.87 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.84 % Favored : 95.12 % Rotamer: Outliers : 6.13 % Allowed : 22.08 % Favored : 71.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.33 (0.14), residues: 3016 helix: 0.01 (0.19), residues: 745 sheet: -0.38 (0.20), residues: 651 loop : -1.55 (0.14), residues: 1620 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP E 62 HIS 0.015 0.001 HIS F 95 PHE 0.016 0.002 PHE X 54 TYR 0.017 0.002 TYR F 125 ARG 0.007 0.001 ARG X 51 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6032 Ramachandran restraints generated. 3016 Oldfield, 0 Emsley, 3016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6032 Ramachandran restraints generated. 3016 Oldfield, 0 Emsley, 3016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 614 residues out of total 2484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 143 poor density : 471 time to evaluate : 3.402 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 17 GLU cc_start: 0.7839 (OUTLIER) cc_final: 0.7359 (mt-10) REVERT: B 42 GLU cc_start: 0.6568 (OUTLIER) cc_final: 0.6333 (mt-10) REVERT: B 188 SER cc_start: 0.8968 (t) cc_final: 0.8647 (t) REVERT: C 131 LYS cc_start: 0.7339 (OUTLIER) cc_final: 0.7123 (ttmm) REVERT: E 37 LEU cc_start: 0.7762 (OUTLIER) cc_final: 0.7428 (mp) REVERT: E 153 SER cc_start: 0.8448 (OUTLIER) cc_final: 0.8089 (m) REVERT: F 73 LYS cc_start: 0.8596 (OUTLIER) cc_final: 0.8195 (mmtt) REVERT: G 54 LYS cc_start: 0.8726 (tttm) cc_final: 0.8417 (tttm) REVERT: H 16 ARG cc_start: 0.8137 (mtp85) cc_final: 0.7833 (mtp85) REVERT: H 96 THR cc_start: 0.9138 (m) cc_final: 0.8914 (m) REVERT: I 14 LYS cc_start: 0.9105 (OUTLIER) cc_final: 0.8792 (ttmt) REVERT: I 39 ARG cc_start: 0.8953 (OUTLIER) cc_final: 0.7823 (ptp90) REVERT: I 82 ARG cc_start: 0.9062 (OUTLIER) cc_final: 0.8470 (mmt-90) REVERT: I 85 ASN cc_start: 0.8514 (t0) cc_final: 0.8149 (m-40) REVERT: L 44 GLN cc_start: 0.8720 (tt0) cc_final: 0.8473 (tt0) REVERT: L 115 GLU cc_start: 0.8200 (OUTLIER) cc_final: 0.7780 (tt0) REVERT: M 6 ARG cc_start: 0.8234 (OUTLIER) cc_final: 0.7819 (mtp180) REVERT: M 74 LEU cc_start: 0.8630 (OUTLIER) cc_final: 0.8293 (mt) REVERT: M 79 MET cc_start: 0.8770 (OUTLIER) cc_final: 0.7918 (ttt) REVERT: M 80 ILE cc_start: 0.8906 (mm) cc_final: 0.8627 (mm) REVERT: N 1 MET cc_start: 0.6599 (OUTLIER) cc_final: 0.6215 (ttp) REVERT: N 37 ASP cc_start: 0.7194 (OUTLIER) cc_final: 0.6829 (p0) REVERT: P 17 GLU cc_start: 0.7936 (OUTLIER) cc_final: 0.7548 (tm-30) REVERT: Q 21 GLN cc_start: 0.8290 (OUTLIER) cc_final: 0.7661 (pt0) REVERT: R 7 ASN cc_start: 0.8358 (m-40) cc_final: 0.8085 (m-40) REVERT: R 26 ARG cc_start: 0.8149 (OUTLIER) cc_final: 0.7782 (mtm110) REVERT: R 62 GLU cc_start: 0.7627 (OUTLIER) cc_final: 0.7247 (mt-10) REVERT: S 11 LYS cc_start: 0.7819 (OUTLIER) cc_final: 0.7363 (mptt) REVERT: S 84 THR cc_start: 0.8592 (p) cc_final: 0.8378 (p) REVERT: T 27 ARG cc_start: 0.8934 (OUTLIER) cc_final: 0.8259 (ttt180) REVERT: Z 41 SER cc_start: 0.8955 (p) cc_final: 0.8676 (t) REVERT: a 31 ILE cc_start: 0.7740 (OUTLIER) cc_final: 0.6986 (pt) REVERT: b 36 ARG cc_start: 0.8981 (OUTLIER) cc_final: 0.8474 (ttp-170) outliers start: 143 outliers final: 94 residues processed: 566 average time/residue: 1.7053 time to fit residues: 1284.3473 Evaluate side-chains 583 residues out of total 2484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 117 poor density : 466 time to evaluate : 3.355 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 GLU Chi-restraints excluded: chain A residue 20 VAL Chi-restraints excluded: chain A residue 86 SER Chi-restraints excluded: chain A residue 88 THR Chi-restraints excluded: chain A residue 139 SER Chi-restraints excluded: chain A residue 228 ILE Chi-restraints excluded: chain B residue 13 THR Chi-restraints excluded: chain B residue 18 ASP Chi-restraints excluded: chain B residue 40 THR Chi-restraints excluded: chain B residue 42 GLU Chi-restraints excluded: chain B residue 43 THR Chi-restraints excluded: chain B residue 51 VAL Chi-restraints excluded: chain B residue 59 SER Chi-restraints excluded: chain B residue 113 THR Chi-restraints excluded: chain B residue 153 GLN Chi-restraints excluded: chain B residue 185 THR Chi-restraints excluded: chain B residue 191 VAL Chi-restraints excluded: chain B residue 200 THR Chi-restraints excluded: chain C residue 131 LYS Chi-restraints excluded: chain C residue 199 LEU Chi-restraints excluded: chain E residue 18 THR Chi-restraints excluded: chain E residue 20 ASN Chi-restraints excluded: chain E residue 25 GLU Chi-restraints excluded: chain E residue 32 THR Chi-restraints excluded: chain E residue 34 SER Chi-restraints excluded: chain E residue 37 LEU Chi-restraints excluded: chain E residue 40 LEU Chi-restraints excluded: chain E residue 58 SER Chi-restraints excluded: chain E residue 129 THR Chi-restraints excluded: chain E residue 153 SER Chi-restraints excluded: chain E residue 167 GLU Chi-restraints excluded: chain E residue 168 VAL Chi-restraints excluded: chain E residue 170 LEU Chi-restraints excluded: chain F residue 4 LEU Chi-restraints excluded: chain F residue 5 SER Chi-restraints excluded: chain F residue 60 GLU Chi-restraints excluded: chain F residue 73 LYS Chi-restraints excluded: chain G residue 34 SER Chi-restraints excluded: chain G residue 45 GLU Chi-restraints excluded: chain G residue 73 ASP Chi-restraints excluded: chain G residue 76 VAL Chi-restraints excluded: chain G residue 80 ASP Chi-restraints excluded: chain G residue 102 VAL Chi-restraints excluded: chain G residue 108 THR Chi-restraints excluded: chain G residue 116 SER Chi-restraints excluded: chain H residue 29 VAL Chi-restraints excluded: chain H residue 85 SER Chi-restraints excluded: chain H residue 117 GLU Chi-restraints excluded: chain H residue 123 THR Chi-restraints excluded: chain I residue 14 LYS Chi-restraints excluded: chain I residue 39 ARG Chi-restraints excluded: chain I residue 58 ILE Chi-restraints excluded: chain I residue 79 LEU Chi-restraints excluded: chain I residue 80 GLU Chi-restraints excluded: chain I residue 82 ARG Chi-restraints excluded: chain I residue 132 VAL Chi-restraints excluded: chain I residue 133 THR Chi-restraints excluded: chain I residue 136 VAL Chi-restraints excluded: chain J residue 6 SER Chi-restraints excluded: chain K residue 9 LEU Chi-restraints excluded: chain K residue 27 LEU Chi-restraints excluded: chain K residue 58 SER Chi-restraints excluded: chain K residue 99 HIS Chi-restraints excluded: chain L residue 18 THR Chi-restraints excluded: chain L residue 86 LYS Chi-restraints excluded: chain L residue 88 GLU Chi-restraints excluded: chain L residue 115 GLU Chi-restraints excluded: chain M residue 6 ARG Chi-restraints excluded: chain M residue 74 LEU Chi-restraints excluded: chain M residue 79 MET Chi-restraints excluded: chain M residue 104 VAL Chi-restraints excluded: chain M residue 112 LYS Chi-restraints excluded: chain N residue 1 MET Chi-restraints excluded: chain N residue 2 TYR Chi-restraints excluded: chain N residue 32 THR Chi-restraints excluded: chain N residue 33 ILE Chi-restraints excluded: chain N residue 37 ASP Chi-restraints excluded: chain N residue 49 ILE Chi-restraints excluded: chain N residue 87 GLN Chi-restraints excluded: chain N residue 99 THR Chi-restraints excluded: chain O residue 2 MET Chi-restraints excluded: chain O residue 5 THR Chi-restraints excluded: chain O residue 24 LEU Chi-restraints excluded: chain O residue 108 VAL Chi-restraints excluded: chain O residue 110 VAL Chi-restraints excluded: chain P residue 17 GLU Chi-restraints excluded: chain P residue 77 SER Chi-restraints excluded: chain P residue 87 LYS Chi-restraints excluded: chain P residue 92 VAL Chi-restraints excluded: chain Q residue 21 GLN Chi-restraints excluded: chain Q residue 40 VAL Chi-restraints excluded: chain Q residue 57 VAL Chi-restraints excluded: chain Q residue 60 GLU Chi-restraints excluded: chain Q residue 62 SER Chi-restraints excluded: chain Q residue 66 SER Chi-restraints excluded: chain R residue 26 ARG Chi-restraints excluded: chain R residue 27 GLU Chi-restraints excluded: chain R residue 44 VAL Chi-restraints excluded: chain R residue 62 GLU Chi-restraints excluded: chain S residue 9 SER Chi-restraints excluded: chain S residue 11 LYS Chi-restraints excluded: chain T residue 22 ASN Chi-restraints excluded: chain T residue 27 ARG Chi-restraints excluded: chain T residue 62 LEU Chi-restraints excluded: chain U residue 11 VAL Chi-restraints excluded: chain U residue 17 LEU Chi-restraints excluded: chain U residue 32 LYS Chi-restraints excluded: chain U residue 34 THR Chi-restraints excluded: chain U residue 37 LEU Chi-restraints excluded: chain V residue 4 ILE Chi-restraints excluded: chain X residue 44 LYS Chi-restraints excluded: chain Y residue 25 THR Chi-restraints excluded: chain Y residue 51 LYS Chi-restraints excluded: chain a residue 31 ILE Chi-restraints excluded: chain a residue 47 VAL Chi-restraints excluded: chain b residue 6 SER Chi-restraints excluded: chain b residue 36 ARG Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 572 random chunks: chunk 460 optimal weight: 0.9980 chunk 313 optimal weight: 9.9990 chunk 8 optimal weight: 10.0000 chunk 411 optimal weight: 4.9990 chunk 228 optimal weight: 6.9990 chunk 471 optimal weight: 4.9990 chunk 382 optimal weight: 0.9990 chunk 0 optimal weight: 10.0000 chunk 282 optimal weight: 0.0970 chunk 496 optimal weight: 0.9980 chunk 139 optimal weight: 10.0000 overall best weight: 1.6182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 106 ASN E 139 GLN F 95 HIS F 136 GLN H 6 ASN I 110 ASN L 15 GLN N 43 ASN S 17 ASN T 35 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8498 moved from start: 0.1077 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 90840 Z= 0.160 Angle : 0.537 9.136 136537 Z= 0.287 Chirality : 0.035 0.263 17600 Planarity : 0.004 0.056 6899 Dihedral : 22.853 179.729 46871 Min Nonbonded Distance : 1.938 Molprobity Statistics. All-atom Clashscore : 4.24 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.88 % Favored : 96.09 % Rotamer: Outliers : 5.02 % Allowed : 24.31 % Favored : 70.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: -0.89 (0.15), residues: 3016 helix: 0.57 (0.19), residues: 748 sheet: -0.21 (0.20), residues: 644 loop : -1.32 (0.14), residues: 1624 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP E 62 HIS 0.013 0.001 HIS F 95 PHE 0.011 0.001 PHE M 57 TYR 0.011 0.001 TYR F 125 ARG 0.006 0.000 ARG X 51 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6032 Ramachandran restraints generated. 3016 Oldfield, 0 Emsley, 3016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6032 Ramachandran restraints generated. 3016 Oldfield, 0 Emsley, 3016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 599 residues out of total 2484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 117 poor density : 482 time to evaluate : 3.342 Fit side-chains revert: symmetry clash REVERT: A 17 GLU cc_start: 0.7779 (OUTLIER) cc_final: 0.7328 (mt-10) REVERT: A 84 ASP cc_start: 0.8770 (t0) cc_final: 0.8368 (t70) REVERT: A 203 ARG cc_start: 0.8451 (OUTLIER) cc_final: 0.8040 (ttm-80) REVERT: B 44 ASP cc_start: 0.8060 (m-30) cc_final: 0.7804 (m-30) REVERT: B 94 GLU cc_start: 0.6997 (OUTLIER) cc_final: 0.6404 (mt-10) REVERT: B 188 SER cc_start: 0.8874 (t) cc_final: 0.8578 (t) REVERT: C 131 LYS cc_start: 0.7249 (OUTLIER) cc_final: 0.7045 (ttmm) REVERT: E 153 SER cc_start: 0.8467 (OUTLIER) cc_final: 0.8040 (m) REVERT: F 73 LYS cc_start: 0.8528 (OUTLIER) cc_final: 0.8180 (mmtt) REVERT: G 54 LYS cc_start: 0.8683 (tttm) cc_final: 0.8349 (tttm) REVERT: H 16 ARG cc_start: 0.8084 (mtp85) cc_final: 0.7777 (mtp85) REVERT: I 39 ARG cc_start: 0.8957 (OUTLIER) cc_final: 0.7876 (ptp90) REVERT: I 85 ASN cc_start: 0.8433 (t0) cc_final: 0.8164 (m-40) REVERT: K 88 LYS cc_start: 0.7290 (tttt) cc_final: 0.7057 (tttp) REVERT: L 44 GLN cc_start: 0.8723 (tt0) cc_final: 0.8514 (tt0) REVERT: M 74 LEU cc_start: 0.8610 (OUTLIER) cc_final: 0.8297 (mt) REVERT: N 37 ASP cc_start: 0.7101 (OUTLIER) cc_final: 0.6827 (p0) REVERT: P 17 GLU cc_start: 0.7918 (OUTLIER) cc_final: 0.7505 (tm-30) REVERT: Q 21 GLN cc_start: 0.8244 (OUTLIER) cc_final: 0.7673 (pt0) REVERT: R 7 ASN cc_start: 0.8332 (m-40) cc_final: 0.8097 (m-40) REVERT: S 84 THR cc_start: 0.8491 (p) cc_final: 0.8274 (p) REVERT: T 27 ARG cc_start: 0.8855 (OUTLIER) cc_final: 0.8058 (tmt90) REVERT: Z 41 SER cc_start: 0.8928 (p) cc_final: 0.8686 (t) REVERT: b 36 ARG cc_start: 0.9000 (OUTLIER) cc_final: 0.8469 (ttp-170) outliers start: 117 outliers final: 66 residues processed: 564 average time/residue: 1.7583 time to fit residues: 1307.6977 Evaluate side-chains 554 residues out of total 2484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 79 poor density : 475 time to evaluate : 3.327 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 GLU Chi-restraints excluded: chain A residue 20 VAL Chi-restraints excluded: chain A residue 86 SER Chi-restraints excluded: chain A residue 139 SER Chi-restraints excluded: chain A residue 203 ARG Chi-restraints excluded: chain A residue 228 ILE Chi-restraints excluded: chain B residue 13 THR Chi-restraints excluded: chain B residue 51 VAL Chi-restraints excluded: chain B residue 59 SER Chi-restraints excluded: chain B residue 94 GLU Chi-restraints excluded: chain B residue 113 THR Chi-restraints excluded: chain B residue 153 GLN Chi-restraints excluded: chain C residue 131 LYS Chi-restraints excluded: chain E residue 18 THR Chi-restraints excluded: chain E residue 20 ASN Chi-restraints excluded: chain E residue 25 GLU Chi-restraints excluded: chain E residue 29 SER Chi-restraints excluded: chain E residue 32 THR Chi-restraints excluded: chain E residue 34 SER Chi-restraints excluded: chain E residue 52 LEU Chi-restraints excluded: chain E residue 129 THR Chi-restraints excluded: chain E residue 153 SER Chi-restraints excluded: chain E residue 168 VAL Chi-restraints excluded: chain F residue 4 LEU Chi-restraints excluded: chain F residue 5 SER Chi-restraints excluded: chain F residue 60 GLU Chi-restraints excluded: chain F residue 62 VAL Chi-restraints excluded: chain F residue 73 LYS Chi-restraints excluded: chain F residue 106 LYS Chi-restraints excluded: chain G residue 34 SER Chi-restraints excluded: chain G residue 45 GLU Chi-restraints excluded: chain G residue 73 ASP Chi-restraints excluded: chain G residue 80 ASP Chi-restraints excluded: chain G residue 102 VAL Chi-restraints excluded: chain H residue 29 VAL Chi-restraints excluded: chain H residue 117 GLU Chi-restraints excluded: chain H residue 123 THR Chi-restraints excluded: chain I residue 39 ARG Chi-restraints excluded: chain I residue 124 LYS Chi-restraints excluded: chain I residue 132 VAL Chi-restraints excluded: chain I residue 136 VAL Chi-restraints excluded: chain J residue 6 SER Chi-restraints excluded: chain K residue 99 HIS Chi-restraints excluded: chain L residue 36 LYS Chi-restraints excluded: chain L residue 86 LYS Chi-restraints excluded: chain L residue 115 GLU Chi-restraints excluded: chain M residue 74 LEU Chi-restraints excluded: chain M residue 104 VAL Chi-restraints excluded: chain N residue 32 THR Chi-restraints excluded: chain N residue 34 THR Chi-restraints excluded: chain N residue 36 ASP Chi-restraints excluded: chain N residue 37 ASP Chi-restraints excluded: chain O residue 2 MET Chi-restraints excluded: chain O residue 101 THR Chi-restraints excluded: chain O residue 110 VAL Chi-restraints excluded: chain P residue 17 GLU Chi-restraints excluded: chain P residue 68 ARG Chi-restraints excluded: chain P residue 92 VAL Chi-restraints excluded: chain Q residue 21 GLN Chi-restraints excluded: chain Q residue 62 SER Chi-restraints excluded: chain Q residue 66 SER Chi-restraints excluded: chain Q residue 70 ILE Chi-restraints excluded: chain R residue 27 GLU Chi-restraints excluded: chain R residue 44 VAL Chi-restraints excluded: chain T residue 22 ASN Chi-restraints excluded: chain T residue 27 ARG Chi-restraints excluded: chain T residue 62 LEU Chi-restraints excluded: chain U residue 11 VAL Chi-restraints excluded: chain U residue 34 THR Chi-restraints excluded: chain U residue 37 LEU Chi-restraints excluded: chain V residue 4 ILE Chi-restraints excluded: chain V residue 6 VAL Chi-restraints excluded: chain X residue 44 LYS Chi-restraints excluded: chain Y residue 51 LYS Chi-restraints excluded: chain a residue 31 ILE Chi-restraints excluded: chain a residue 46 CYS Chi-restraints excluded: chain a residue 47 VAL Chi-restraints excluded: chain b residue 6 SER Chi-restraints excluded: chain b residue 36 ARG Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 572 random chunks: chunk 186 optimal weight: 6.9990 chunk 497 optimal weight: 6.9990 chunk 109 optimal weight: 6.9990 chunk 324 optimal weight: 1.9990 chunk 136 optimal weight: 10.0000 chunk 553 optimal weight: 10.0000 chunk 459 optimal weight: 0.9990 chunk 256 optimal weight: 20.0000 chunk 46 optimal weight: 7.9990 chunk 183 optimal weight: 7.9990 chunk 290 optimal weight: 7.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 106 ASN E 139 GLN F 95 HIS F 136 GLN L 15 GLN M 72 ASN O 62 ASN S 17 ASN U 44 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8581 moved from start: 0.0628 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.075 90840 Z= 0.419 Angle : 0.762 9.589 136537 Z= 0.390 Chirality : 0.046 0.400 17600 Planarity : 0.006 0.063 6899 Dihedral : 23.046 179.778 46854 Min Nonbonded Distance : 1.861 Molprobity Statistics. All-atom Clashscore : 3.62 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.07 % Favored : 94.89 % Rotamer: Outliers : 6.13 % Allowed : 23.63 % Favored : 70.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: -1.06 (0.14), residues: 3016 helix: 0.21 (0.19), residues: 749 sheet: -0.12 (0.20), residues: 652 loop : -1.41 (0.14), residues: 1615 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.003 TRP E 62 HIS 0.014 0.002 HIS F 95 PHE 0.020 0.002 PHE M 57 TYR 0.022 0.003 TYR F 125 ARG 0.007 0.001 ARG X 51 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6032 Ramachandran restraints generated. 3016 Oldfield, 0 Emsley, 3016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6032 Ramachandran restraints generated. 3016 Oldfield, 0 Emsley, 3016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 617 residues out of total 2484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 143 poor density : 474 time to evaluate : 3.409 Fit side-chains revert: symmetry clash REVERT: A 5 LYS cc_start: 0.8320 (ttpp) cc_final: 0.8106 (tptt) REVERT: A 17 GLU cc_start: 0.7865 (OUTLIER) cc_final: 0.7526 (mt-10) REVERT: A 130 LEU cc_start: 0.8800 (OUTLIER) cc_final: 0.8478 (mp) REVERT: A 203 ARG cc_start: 0.8525 (OUTLIER) cc_final: 0.8092 (ttm-80) REVERT: B 94 GLU cc_start: 0.6994 (OUTLIER) cc_final: 0.6400 (mt-10) REVERT: B 188 SER cc_start: 0.8918 (t) cc_final: 0.8572 (t) REVERT: C 131 LYS cc_start: 0.7371 (OUTLIER) cc_final: 0.7158 (ttmm) REVERT: F 73 LYS cc_start: 0.8570 (OUTLIER) cc_final: 0.8221 (mmtt) REVERT: G 54 LYS cc_start: 0.8710 (tttm) cc_final: 0.8407 (tttm) REVERT: H 15 LYS cc_start: 0.9093 (mptm) cc_final: 0.8749 (mptm) REVERT: H 16 ARG cc_start: 0.8130 (mtp85) cc_final: 0.7783 (mtp85) REVERT: I 14 LYS cc_start: 0.9131 (OUTLIER) cc_final: 0.8805 (ttmt) REVERT: I 39 ARG cc_start: 0.8953 (OUTLIER) cc_final: 0.7799 (ptp90) REVERT: I 85 ASN cc_start: 0.8505 (t0) cc_final: 0.8146 (m-40) REVERT: L 44 GLN cc_start: 0.8747 (tt0) cc_final: 0.8484 (tt0) REVERT: L 115 GLU cc_start: 0.8197 (OUTLIER) cc_final: 0.7949 (tt0) REVERT: M 51 ARG cc_start: 0.9233 (OUTLIER) cc_final: 0.8871 (mpt90) REVERT: M 74 LEU cc_start: 0.8639 (OUTLIER) cc_final: 0.8284 (mt) REVERT: M 80 ILE cc_start: 0.8905 (mm) cc_final: 0.8599 (mm) REVERT: N 37 ASP cc_start: 0.7138 (OUTLIER) cc_final: 0.6831 (p0) REVERT: P 17 GLU cc_start: 0.7929 (OUTLIER) cc_final: 0.7556 (tm-30) REVERT: Q 21 GLN cc_start: 0.8311 (OUTLIER) cc_final: 0.7695 (pt0) REVERT: Q 95 LYS cc_start: 0.7467 (ttpt) cc_final: 0.6908 (tptt) REVERT: R 7 ASN cc_start: 0.8329 (m-40) cc_final: 0.8093 (m-40) REVERT: R 26 ARG cc_start: 0.8200 (OUTLIER) cc_final: 0.7859 (mtm110) REVERT: R 62 GLU cc_start: 0.7634 (OUTLIER) cc_final: 0.7261 (mt-10) REVERT: S 11 LYS cc_start: 0.7890 (OUTLIER) cc_final: 0.7433 (mptt) REVERT: S 84 THR cc_start: 0.8598 (p) cc_final: 0.8346 (p) REVERT: T 27 ARG cc_start: 0.8971 (OUTLIER) cc_final: 0.8272 (ttt180) REVERT: Z 41 SER cc_start: 0.8959 (p) cc_final: 0.8684 (t) REVERT: b 36 ARG cc_start: 0.9033 (OUTLIER) cc_final: 0.8503 (ttp-170) outliers start: 143 outliers final: 91 residues processed: 575 average time/residue: 1.7438 time to fit residues: 1327.4024 Evaluate side-chains 579 residues out of total 2484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 110 poor density : 469 time to evaluate : 3.327 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 GLU Chi-restraints excluded: chain A residue 20 VAL Chi-restraints excluded: chain A residue 86 SER Chi-restraints excluded: chain A residue 130 LEU Chi-restraints excluded: chain A residue 134 ASN Chi-restraints excluded: chain A residue 139 SER Chi-restraints excluded: chain A residue 178 SER Chi-restraints excluded: chain A residue 203 ARG Chi-restraints excluded: chain A residue 228 ILE Chi-restraints excluded: chain B residue 13 THR Chi-restraints excluded: chain B residue 18 ASP Chi-restraints excluded: chain B residue 51 VAL Chi-restraints excluded: chain B residue 59 SER Chi-restraints excluded: chain B residue 94 GLU Chi-restraints excluded: chain B residue 113 THR Chi-restraints excluded: chain B residue 141 VAL Chi-restraints excluded: chain B residue 153 GLN Chi-restraints excluded: chain B residue 182 SER Chi-restraints excluded: chain B residue 185 THR Chi-restraints excluded: chain B residue 191 VAL Chi-restraints excluded: chain C residue 89 GLN Chi-restraints excluded: chain C residue 131 LYS Chi-restraints excluded: chain E residue 18 THR Chi-restraints excluded: chain E residue 25 GLU Chi-restraints excluded: chain E residue 29 SER Chi-restraints excluded: chain E residue 32 THR Chi-restraints excluded: chain E residue 34 SER Chi-restraints excluded: chain E residue 37 LEU Chi-restraints excluded: chain E residue 52 LEU Chi-restraints excluded: chain E residue 58 SER Chi-restraints excluded: chain E residue 105 LEU Chi-restraints excluded: chain E residue 129 THR Chi-restraints excluded: chain E residue 153 SER Chi-restraints excluded: chain E residue 168 VAL Chi-restraints excluded: chain E residue 170 LEU Chi-restraints excluded: chain F residue 4 LEU Chi-restraints excluded: chain F residue 5 SER Chi-restraints excluded: chain F residue 62 VAL Chi-restraints excluded: chain F residue 73 LYS Chi-restraints excluded: chain F residue 106 LYS Chi-restraints excluded: chain G residue 45 GLU Chi-restraints excluded: chain G residue 73 ASP Chi-restraints excluded: chain G residue 75 SER Chi-restraints excluded: chain G residue 80 ASP Chi-restraints excluded: chain G residue 102 VAL Chi-restraints excluded: chain G residue 116 SER Chi-restraints excluded: chain H residue 29 VAL Chi-restraints excluded: chain H residue 85 SER Chi-restraints excluded: chain H residue 117 GLU Chi-restraints excluded: chain H residue 123 THR Chi-restraints excluded: chain I residue 14 LYS Chi-restraints excluded: chain I residue 39 ARG Chi-restraints excluded: chain I residue 80 GLU Chi-restraints excluded: chain I residue 124 LYS Chi-restraints excluded: chain I residue 132 VAL Chi-restraints excluded: chain I residue 136 VAL Chi-restraints excluded: chain J residue 6 SER Chi-restraints excluded: chain K residue 9 LEU Chi-restraints excluded: chain K residue 27 LEU Chi-restraints excluded: chain K residue 58 SER Chi-restraints excluded: chain K residue 99 HIS Chi-restraints excluded: chain L residue 18 THR Chi-restraints excluded: chain L residue 86 LYS Chi-restraints excluded: chain L residue 88 GLU Chi-restraints excluded: chain L residue 115 GLU Chi-restraints excluded: chain M residue 51 ARG Chi-restraints excluded: chain M residue 74 LEU Chi-restraints excluded: chain M residue 104 VAL Chi-restraints excluded: chain N residue 32 THR Chi-restraints excluded: chain N residue 34 THR Chi-restraints excluded: chain N residue 37 ASP Chi-restraints excluded: chain N residue 49 ILE Chi-restraints excluded: chain N residue 99 THR Chi-restraints excluded: chain O residue 2 MET Chi-restraints excluded: chain O residue 5 THR Chi-restraints excluded: chain O residue 24 LEU Chi-restraints excluded: chain O residue 110 VAL Chi-restraints excluded: chain P residue 17 GLU Chi-restraints excluded: chain P residue 67 LYS Chi-restraints excluded: chain P residue 68 ARG Chi-restraints excluded: chain P residue 77 SER Chi-restraints excluded: chain P residue 92 VAL Chi-restraints excluded: chain Q residue 21 GLN Chi-restraints excluded: chain Q residue 40 VAL Chi-restraints excluded: chain Q residue 57 VAL Chi-restraints excluded: chain Q residue 60 GLU Chi-restraints excluded: chain Q residue 62 SER Chi-restraints excluded: chain R residue 26 ARG Chi-restraints excluded: chain R residue 27 GLU Chi-restraints excluded: chain R residue 30 VAL Chi-restraints excluded: chain R residue 44 VAL Chi-restraints excluded: chain R residue 62 GLU Chi-restraints excluded: chain S residue 10 THR Chi-restraints excluded: chain S residue 11 LYS Chi-restraints excluded: chain T residue 22 ASN Chi-restraints excluded: chain T residue 27 ARG Chi-restraints excluded: chain T residue 62 LEU Chi-restraints excluded: chain U residue 11 VAL Chi-restraints excluded: chain U residue 17 LEU Chi-restraints excluded: chain U residue 34 THR Chi-restraints excluded: chain U residue 37 LEU Chi-restraints excluded: chain V residue 4 ILE Chi-restraints excluded: chain V residue 6 VAL Chi-restraints excluded: chain X residue 44 LYS Chi-restraints excluded: chain Y residue 25 THR Chi-restraints excluded: chain Y residue 39 ILE Chi-restraints excluded: chain a residue 31 ILE Chi-restraints excluded: chain a residue 47 VAL Chi-restraints excluded: chain b residue 6 SER Chi-restraints excluded: chain b residue 36 ARG Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 572 random chunks: chunk 533 optimal weight: 2.9990 chunk 62 optimal weight: 6.9990 chunk 315 optimal weight: 0.0980 chunk 404 optimal weight: 4.9990 chunk 313 optimal weight: 2.9990 chunk 465 optimal weight: 0.9990 chunk 309 optimal weight: 7.9990 chunk 551 optimal weight: 6.9990 chunk 345 optimal weight: 0.0970 chunk 336 optimal weight: 0.9980 chunk 254 optimal weight: 5.9990 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 134 ASN B 143 HIS ** C 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 106 ASN E 139 GLN F 95 HIS F 136 GLN H 6 ASN L 15 GLN N 43 ASN O 62 ASN S 17 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8462 moved from start: 0.1326 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 90840 Z= 0.123 Angle : 0.507 8.851 136537 Z= 0.271 Chirality : 0.033 0.237 17600 Planarity : 0.004 0.056 6899 Dihedral : 22.771 179.949 46853 Min Nonbonded Distance : 1.953 Molprobity Statistics. All-atom Clashscore : 4.37 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.58 % Favored : 96.38 % Rotamer: Outliers : 3.99 % Allowed : 26.20 % Favored : 69.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: -0.64 (0.15), residues: 3016 helix: 0.83 (0.19), residues: 754 sheet: -0.11 (0.20), residues: 649 loop : -1.18 (0.14), residues: 1613 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP E 62 HIS 0.012 0.001 HIS F 95 PHE 0.008 0.001 PHE X 54 TYR 0.008 0.001 TYR E 164 ARG 0.007 0.000 ARG X 51 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6032 Ramachandran restraints generated. 3016 Oldfield, 0 Emsley, 3016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6032 Ramachandran restraints generated. 3016 Oldfield, 0 Emsley, 3016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 581 residues out of total 2484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 93 poor density : 488 time to evaluate : 3.440 Fit side-chains REVERT: A 84 ASP cc_start: 0.8771 (t0) cc_final: 0.8339 (t70) REVERT: B 44 ASP cc_start: 0.8104 (m-30) cc_final: 0.7798 (m-30) REVERT: B 94 GLU cc_start: 0.7014 (OUTLIER) cc_final: 0.6410 (mt-10) REVERT: B 188 SER cc_start: 0.8857 (t) cc_final: 0.8562 (t) REVERT: C 131 LYS cc_start: 0.7127 (OUTLIER) cc_final: 0.6905 (ttmm) REVERT: E 42 GLU cc_start: 0.6302 (mm-30) cc_final: 0.6089 (tp30) REVERT: E 50 LEU cc_start: 0.7564 (mm) cc_final: 0.7288 (mt) REVERT: E 63 MET cc_start: 0.7815 (ttp) cc_final: 0.7369 (ttp) REVERT: G 54 LYS cc_start: 0.8588 (tttm) cc_final: 0.8274 (tttt) REVERT: H 16 ARG cc_start: 0.8081 (mtp85) cc_final: 0.7705 (ttt90) REVERT: I 85 ASN cc_start: 0.8396 (t0) cc_final: 0.8142 (m-40) REVERT: K 88 LYS cc_start: 0.7272 (tttt) cc_final: 0.7049 (tttp) REVERT: L 44 GLN cc_start: 0.8720 (tt0) cc_final: 0.8508 (tt0) REVERT: N 37 ASP cc_start: 0.7066 (OUTLIER) cc_final: 0.6814 (p0) REVERT: P 17 GLU cc_start: 0.7877 (OUTLIER) cc_final: 0.7436 (tm-30) REVERT: R 7 ASN cc_start: 0.8338 (m-40) cc_final: 0.8114 (m-40) REVERT: R 26 ARG cc_start: 0.8132 (OUTLIER) cc_final: 0.7823 (mtm180) REVERT: S 84 THR cc_start: 0.8468 (p) cc_final: 0.8254 (p) REVERT: Y 26 MET cc_start: 0.7870 (ttt) cc_final: 0.7664 (ttt) REVERT: Z 41 SER cc_start: 0.8911 (p) cc_final: 0.8689 (t) REVERT: b 36 ARG cc_start: 0.8997 (OUTLIER) cc_final: 0.8445 (ttp-170) outliers start: 93 outliers final: 54 residues processed: 547 average time/residue: 1.8012 time to fit residues: 1305.3214 Evaluate side-chains 539 residues out of total 2484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 479 time to evaluate : 3.348 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 VAL Chi-restraints excluded: chain A residue 134 ASN Chi-restraints excluded: chain A residue 139 SER Chi-restraints excluded: chain B residue 13 THR Chi-restraints excluded: chain B residue 51 VAL Chi-restraints excluded: chain B residue 59 SER Chi-restraints excluded: chain B residue 94 GLU Chi-restraints excluded: chain B residue 113 THR Chi-restraints excluded: chain B residue 153 GLN Chi-restraints excluded: chain C residue 89 GLN Chi-restraints excluded: chain C residue 131 LYS Chi-restraints excluded: chain E residue 18 THR Chi-restraints excluded: chain E residue 34 SER Chi-restraints excluded: chain E residue 153 SER Chi-restraints excluded: chain E residue 168 VAL Chi-restraints excluded: chain F residue 4 LEU Chi-restraints excluded: chain F residue 5 SER Chi-restraints excluded: chain F residue 62 VAL Chi-restraints excluded: chain G residue 45 GLU Chi-restraints excluded: chain G residue 73 ASP Chi-restraints excluded: chain G residue 80 ASP Chi-restraints excluded: chain G residue 102 VAL Chi-restraints excluded: chain G residue 116 SER Chi-restraints excluded: chain H residue 29 VAL Chi-restraints excluded: chain H residue 117 GLU Chi-restraints excluded: chain H residue 123 THR Chi-restraints excluded: chain H residue 129 LEU Chi-restraints excluded: chain I residue 132 VAL Chi-restraints excluded: chain I residue 136 VAL Chi-restraints excluded: chain J residue 6 SER Chi-restraints excluded: chain K residue 99 HIS Chi-restraints excluded: chain L residue 86 LYS Chi-restraints excluded: chain L residue 115 GLU Chi-restraints excluded: chain M residue 117 LEU Chi-restraints excluded: chain N residue 36 ASP Chi-restraints excluded: chain N residue 37 ASP Chi-restraints excluded: chain O residue 2 MET Chi-restraints excluded: chain O residue 5 THR Chi-restraints excluded: chain O residue 24 LEU Chi-restraints excluded: chain O residue 98 THR Chi-restraints excluded: chain O residue 101 THR Chi-restraints excluded: chain O residue 110 VAL Chi-restraints excluded: chain P residue 17 GLU Chi-restraints excluded: chain P residue 92 VAL Chi-restraints excluded: chain Q residue 40 VAL Chi-restraints excluded: chain Q residue 62 SER Chi-restraints excluded: chain R residue 26 ARG Chi-restraints excluded: chain R residue 44 VAL Chi-restraints excluded: chain S residue 10 THR Chi-restraints excluded: chain T residue 22 ASN Chi-restraints excluded: chain T residue 62 LEU Chi-restraints excluded: chain U residue 11 VAL Chi-restraints excluded: chain U residue 34 THR Chi-restraints excluded: chain U residue 37 LEU Chi-restraints excluded: chain X residue 44 LYS Chi-restraints excluded: chain Y residue 51 LYS Chi-restraints excluded: chain a residue 31 ILE Chi-restraints excluded: chain a residue 47 VAL Chi-restraints excluded: chain b residue 6 SER Chi-restraints excluded: chain b residue 36 ARG Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 572 random chunks: chunk 341 optimal weight: 9.9990 chunk 220 optimal weight: 7.9990 chunk 329 optimal weight: 6.9990 chunk 166 optimal weight: 7.9990 chunk 108 optimal weight: 7.9990 chunk 106 optimal weight: 6.9990 chunk 350 optimal weight: 0.9990 chunk 375 optimal weight: 5.9990 chunk 272 optimal weight: 10.0000 chunk 51 optimal weight: 7.9990 chunk 433 optimal weight: 2.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 106 ASN E 139 GLN F 95 HIS H 6 ASN ** K 99 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 15 GLN O 62 ASN S 17 ASN a 42 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8579 moved from start: 0.0718 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.076 90840 Z= 0.418 Angle : 0.756 9.628 136537 Z= 0.386 Chirality : 0.046 0.396 17600 Planarity : 0.006 0.062 6899 Dihedral : 22.993 179.977 46844 Min Nonbonded Distance : 1.857 Molprobity Statistics. All-atom Clashscore : 3.54 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.94 % Favored : 95.02 % Rotamer: Outliers : 4.89 % Allowed : 25.30 % Favored : 69.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: -0.93 (0.14), residues: 3016 helix: 0.33 (0.19), residues: 757 sheet: -0.09 (0.20), residues: 665 loop : -1.32 (0.14), residues: 1594 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.003 TRP E 62 HIS 0.014 0.001 HIS F 95 PHE 0.019 0.002 PHE M 57 TYR 0.024 0.003 TYR F 125 ARG 0.008 0.001 ARG X 51 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6032 Ramachandran restraints generated. 3016 Oldfield, 0 Emsley, 3016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6032 Ramachandran restraints generated. 3016 Oldfield, 0 Emsley, 3016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 582 residues out of total 2484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 114 poor density : 468 time to evaluate : 3.425 Fit side-chains revert: symmetry clash REVERT: A 17 GLU cc_start: 0.7847 (OUTLIER) cc_final: 0.7375 (mt-10) REVERT: A 130 LEU cc_start: 0.8809 (OUTLIER) cc_final: 0.8487 (mp) REVERT: A 203 ARG cc_start: 0.8521 (OUTLIER) cc_final: 0.8088 (ttm-80) REVERT: B 94 GLU cc_start: 0.6951 (OUTLIER) cc_final: 0.6379 (mt-10) REVERT: B 188 SER cc_start: 0.8916 (t) cc_final: 0.8570 (t) REVERT: C 131 LYS cc_start: 0.7227 (OUTLIER) cc_final: 0.7025 (ttmm) REVERT: E 50 LEU cc_start: 0.7644 (mm) cc_final: 0.7316 (mt) REVERT: E 63 MET cc_start: 0.7809 (ttp) cc_final: 0.7415 (ttp) REVERT: F 60 GLU cc_start: 0.8296 (OUTLIER) cc_final: 0.7945 (pp20) REVERT: F 73 LYS cc_start: 0.8525 (OUTLIER) cc_final: 0.8169 (mmtt) REVERT: G 54 LYS cc_start: 0.8691 (tttm) cc_final: 0.8380 (tttm) REVERT: H 16 ARG cc_start: 0.8148 (mtp85) cc_final: 0.7800 (mtp85) REVERT: I 14 LYS cc_start: 0.9104 (OUTLIER) cc_final: 0.8760 (ttmt) REVERT: I 39 ARG cc_start: 0.8995 (OUTLIER) cc_final: 0.7892 (ptp90) REVERT: I 85 ASN cc_start: 0.8497 (t0) cc_final: 0.8148 (m-40) REVERT: L 44 GLN cc_start: 0.8746 (tt0) cc_final: 0.8478 (tt0) REVERT: M 80 ILE cc_start: 0.8903 (mm) cc_final: 0.8585 (mm) REVERT: N 37 ASP cc_start: 0.7290 (OUTLIER) cc_final: 0.6951 (p0) REVERT: P 17 GLU cc_start: 0.7927 (OUTLIER) cc_final: 0.7552 (tm-30) REVERT: Q 21 GLN cc_start: 0.8304 (OUTLIER) cc_final: 0.7691 (pt0) REVERT: Q 95 LYS cc_start: 0.7477 (ttpt) cc_final: 0.6914 (tptt) REVERT: R 7 ASN cc_start: 0.8384 (m-40) cc_final: 0.8105 (m-40) REVERT: R 26 ARG cc_start: 0.8198 (OUTLIER) cc_final: 0.7845 (mtm180) REVERT: R 62 GLU cc_start: 0.7675 (OUTLIER) cc_final: 0.7243 (mt-10) REVERT: S 84 THR cc_start: 0.8603 (p) cc_final: 0.8367 (p) REVERT: Z 41 SER cc_start: 0.8936 (OUTLIER) cc_final: 0.8666 (t) REVERT: b 36 ARG cc_start: 0.9029 (OUTLIER) cc_final: 0.8509 (ttp-170) outliers start: 114 outliers final: 74 residues processed: 546 average time/residue: 1.8011 time to fit residues: 1304.7007 Evaluate side-chains 557 residues out of total 2484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 90 poor density : 467 time to evaluate : 3.329 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 GLU Chi-restraints excluded: chain A residue 20 VAL Chi-restraints excluded: chain A residue 130 LEU Chi-restraints excluded: chain A residue 139 SER Chi-restraints excluded: chain A residue 203 ARG Chi-restraints excluded: chain A residue 228 ILE Chi-restraints excluded: chain B residue 13 THR Chi-restraints excluded: chain B residue 51 VAL Chi-restraints excluded: chain B residue 59 SER Chi-restraints excluded: chain B residue 94 GLU Chi-restraints excluded: chain B residue 113 THR Chi-restraints excluded: chain B residue 141 VAL Chi-restraints excluded: chain B residue 153 GLN Chi-restraints excluded: chain B residue 182 SER Chi-restraints excluded: chain B residue 185 THR Chi-restraints excluded: chain C residue 131 LYS Chi-restraints excluded: chain E residue 18 THR Chi-restraints excluded: chain E residue 22 ARG Chi-restraints excluded: chain E residue 29 SER Chi-restraints excluded: chain E residue 32 THR Chi-restraints excluded: chain E residue 34 SER Chi-restraints excluded: chain E residue 37 LEU Chi-restraints excluded: chain E residue 58 SER Chi-restraints excluded: chain E residue 132 ILE Chi-restraints excluded: chain E residue 153 SER Chi-restraints excluded: chain E residue 168 VAL Chi-restraints excluded: chain E residue 170 LEU Chi-restraints excluded: chain F residue 4 LEU Chi-restraints excluded: chain F residue 5 SER Chi-restraints excluded: chain F residue 60 GLU Chi-restraints excluded: chain F residue 62 VAL Chi-restraints excluded: chain F residue 73 LYS Chi-restraints excluded: chain G residue 45 GLU Chi-restraints excluded: chain G residue 73 ASP Chi-restraints excluded: chain G residue 75 SER Chi-restraints excluded: chain G residue 80 ASP Chi-restraints excluded: chain G residue 102 VAL Chi-restraints excluded: chain G residue 116 SER Chi-restraints excluded: chain H residue 29 VAL Chi-restraints excluded: chain H residue 85 SER Chi-restraints excluded: chain H residue 117 GLU Chi-restraints excluded: chain H residue 123 THR Chi-restraints excluded: chain I residue 14 LYS Chi-restraints excluded: chain I residue 39 ARG Chi-restraints excluded: chain I residue 124 LYS Chi-restraints excluded: chain I residue 132 VAL Chi-restraints excluded: chain I residue 136 VAL Chi-restraints excluded: chain J residue 6 SER Chi-restraints excluded: chain K residue 9 LEU Chi-restraints excluded: chain K residue 27 LEU Chi-restraints excluded: chain K residue 99 HIS Chi-restraints excluded: chain L residue 36 LYS Chi-restraints excluded: chain L residue 86 LYS Chi-restraints excluded: chain L residue 115 GLU Chi-restraints excluded: chain M residue 104 VAL Chi-restraints excluded: chain N residue 37 ASP Chi-restraints excluded: chain N residue 99 THR Chi-restraints excluded: chain O residue 2 MET Chi-restraints excluded: chain O residue 5 THR Chi-restraints excluded: chain O residue 24 LEU Chi-restraints excluded: chain O residue 98 THR Chi-restraints excluded: chain O residue 110 VAL Chi-restraints excluded: chain P residue 17 GLU Chi-restraints excluded: chain P residue 52 VAL Chi-restraints excluded: chain P residue 68 ARG Chi-restraints excluded: chain P residue 92 VAL Chi-restraints excluded: chain Q residue 21 GLN Chi-restraints excluded: chain Q residue 25 LEU Chi-restraints excluded: chain Q residue 40 VAL Chi-restraints excluded: chain Q residue 62 SER Chi-restraints excluded: chain R residue 26 ARG Chi-restraints excluded: chain R residue 44 VAL Chi-restraints excluded: chain R residue 62 GLU Chi-restraints excluded: chain S residue 10 THR Chi-restraints excluded: chain T residue 22 ASN Chi-restraints excluded: chain T residue 62 LEU Chi-restraints excluded: chain U residue 11 VAL Chi-restraints excluded: chain U residue 34 THR Chi-restraints excluded: chain U residue 37 LEU Chi-restraints excluded: chain V residue 4 ILE Chi-restraints excluded: chain X residue 44 LYS Chi-restraints excluded: chain Y residue 25 THR Chi-restraints excluded: chain Y residue 33 LYS Chi-restraints excluded: chain Y residue 51 LYS Chi-restraints excluded: chain Z residue 13 LYS Chi-restraints excluded: chain Z residue 41 SER Chi-restraints excluded: chain a residue 31 ILE Chi-restraints excluded: chain a residue 47 VAL Chi-restraints excluded: chain b residue 6 SER Chi-restraints excluded: chain b residue 36 ARG Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 572 random chunks: chunk 501 optimal weight: 4.9990 chunk 528 optimal weight: 2.9990 chunk 481 optimal weight: 6.9990 chunk 513 optimal weight: 0.0010 chunk 309 optimal weight: 6.9990 chunk 223 optimal weight: 7.9990 chunk 403 optimal weight: 10.0000 chunk 157 optimal weight: 6.9990 chunk 464 optimal weight: 3.9990 chunk 485 optimal weight: 6.9990 chunk 511 optimal weight: 7.9990 overall best weight: 3.7994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 106 ASN E 139 GLN F 95 HIS F 136 GLN H 6 ASN L 15 GLN N 43 ASN O 62 ASN S 17 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8570 moved from start: 0.0722 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.065 90840 Z= 0.336 Angle : 0.695 9.648 136537 Z= 0.362 Chirality : 0.043 0.370 17600 Planarity : 0.005 0.062 6899 Dihedral : 22.982 179.853 46844 Min Nonbonded Distance : 1.861 Molprobity Statistics. All-atom Clashscore : 3.62 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.78 % Favored : 95.19 % Rotamer: Outliers : 4.72 % Allowed : 25.43 % Favored : 69.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: -0.93 (0.14), residues: 3016 helix: 0.32 (0.19), residues: 756 sheet: -0.04 (0.20), residues: 656 loop : -1.34 (0.14), residues: 1604 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP E 62 HIS 0.015 0.001 HIS F 95 PHE 0.017 0.002 PHE X 54 TYR 0.021 0.002 TYR F 125 ARG 0.009 0.001 ARG X 51 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6032 Ramachandran restraints generated. 3016 Oldfield, 0 Emsley, 3016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6032 Ramachandran restraints generated. 3016 Oldfield, 0 Emsley, 3016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 579 residues out of total 2484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 110 poor density : 469 time to evaluate : 3.440 Fit side-chains revert: symmetry clash REVERT: A 5 LYS cc_start: 0.8311 (ttpp) cc_final: 0.8032 (tptt) REVERT: A 17 GLU cc_start: 0.7852 (OUTLIER) cc_final: 0.7544 (mt-10) REVERT: B 94 GLU cc_start: 0.6941 (OUTLIER) cc_final: 0.6371 (mt-10) REVERT: B 188 SER cc_start: 0.8911 (t) cc_final: 0.8570 (t) REVERT: C 131 LYS cc_start: 0.7224 (OUTLIER) cc_final: 0.7018 (ttmm) REVERT: E 50 LEU cc_start: 0.7622 (mm) cc_final: 0.7323 (mt) REVERT: E 63 MET cc_start: 0.7742 (ttp) cc_final: 0.7414 (ttp) REVERT: E 153 SER cc_start: 0.8469 (OUTLIER) cc_final: 0.8066 (m) REVERT: F 60 GLU cc_start: 0.8286 (OUTLIER) cc_final: 0.7940 (pp20) REVERT: F 73 LYS cc_start: 0.8520 (OUTLIER) cc_final: 0.8164 (mmtt) REVERT: G 54 LYS cc_start: 0.8687 (tttm) cc_final: 0.8375 (tttm) REVERT: H 16 ARG cc_start: 0.8139 (mtp85) cc_final: 0.7791 (mtp85) REVERT: I 39 ARG cc_start: 0.8978 (OUTLIER) cc_final: 0.7862 (ptp90) REVERT: I 85 ASN cc_start: 0.8493 (t0) cc_final: 0.8148 (m-40) REVERT: L 44 GLN cc_start: 0.8743 (tt0) cc_final: 0.8472 (tt0) REVERT: M 51 ARG cc_start: 0.9214 (OUTLIER) cc_final: 0.8852 (mpt90) REVERT: M 80 ILE cc_start: 0.8892 (mm) cc_final: 0.8577 (mm) REVERT: N 37 ASP cc_start: 0.7281 (OUTLIER) cc_final: 0.6955 (p0) REVERT: P 17 GLU cc_start: 0.7922 (OUTLIER) cc_final: 0.7533 (tm-30) REVERT: Q 21 GLN cc_start: 0.8297 (OUTLIER) cc_final: 0.7689 (pt0) REVERT: Q 95 LYS cc_start: 0.7472 (ttpt) cc_final: 0.6916 (tptt) REVERT: R 7 ASN cc_start: 0.8380 (m-40) cc_final: 0.8094 (m-40) REVERT: R 26 ARG cc_start: 0.8192 (OUTLIER) cc_final: 0.7843 (mtm180) REVERT: R 62 GLU cc_start: 0.7668 (OUTLIER) cc_final: 0.7231 (mt-10) REVERT: S 84 THR cc_start: 0.8597 (p) cc_final: 0.8358 (p) REVERT: Z 41 SER cc_start: 0.8952 (OUTLIER) cc_final: 0.8686 (t) REVERT: b 36 ARG cc_start: 0.9022 (OUTLIER) cc_final: 0.8502 (ttp-170) outliers start: 110 outliers final: 81 residues processed: 544 average time/residue: 1.7770 time to fit residues: 1282.7088 Evaluate side-chains 563 residues out of total 2484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 96 poor density : 467 time to evaluate : 3.347 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 GLU Chi-restraints excluded: chain A residue 20 VAL Chi-restraints excluded: chain A residue 139 SER Chi-restraints excluded: chain A residue 178 SER Chi-restraints excluded: chain A residue 228 ILE Chi-restraints excluded: chain B residue 13 THR Chi-restraints excluded: chain B residue 18 ASP Chi-restraints excluded: chain B residue 51 VAL Chi-restraints excluded: chain B residue 59 SER Chi-restraints excluded: chain B residue 94 GLU Chi-restraints excluded: chain B residue 113 THR Chi-restraints excluded: chain B residue 141 VAL Chi-restraints excluded: chain B residue 153 GLN Chi-restraints excluded: chain B residue 182 SER Chi-restraints excluded: chain B residue 185 THR Chi-restraints excluded: chain B residue 200 THR Chi-restraints excluded: chain C residue 131 LYS Chi-restraints excluded: chain C residue 199 LEU Chi-restraints excluded: chain E residue 18 THR Chi-restraints excluded: chain E residue 29 SER Chi-restraints excluded: chain E residue 32 THR Chi-restraints excluded: chain E residue 34 SER Chi-restraints excluded: chain E residue 37 LEU Chi-restraints excluded: chain E residue 58 SER Chi-restraints excluded: chain E residue 132 ILE Chi-restraints excluded: chain E residue 153 SER Chi-restraints excluded: chain E residue 168 VAL Chi-restraints excluded: chain E residue 170 LEU Chi-restraints excluded: chain F residue 4 LEU Chi-restraints excluded: chain F residue 5 SER Chi-restraints excluded: chain F residue 60 GLU Chi-restraints excluded: chain F residue 62 VAL Chi-restraints excluded: chain F residue 73 LYS Chi-restraints excluded: chain G residue 45 GLU Chi-restraints excluded: chain G residue 73 ASP Chi-restraints excluded: chain G residue 75 SER Chi-restraints excluded: chain G residue 80 ASP Chi-restraints excluded: chain G residue 102 VAL Chi-restraints excluded: chain G residue 108 THR Chi-restraints excluded: chain G residue 116 SER Chi-restraints excluded: chain H residue 29 VAL Chi-restraints excluded: chain H residue 85 SER Chi-restraints excluded: chain H residue 117 GLU Chi-restraints excluded: chain H residue 123 THR Chi-restraints excluded: chain I residue 39 ARG Chi-restraints excluded: chain I residue 124 LYS Chi-restraints excluded: chain I residue 132 VAL Chi-restraints excluded: chain I residue 136 VAL Chi-restraints excluded: chain J residue 6 SER Chi-restraints excluded: chain K residue 9 LEU Chi-restraints excluded: chain K residue 27 LEU Chi-restraints excluded: chain K residue 99 HIS Chi-restraints excluded: chain L residue 36 LYS Chi-restraints excluded: chain L residue 86 LYS Chi-restraints excluded: chain L residue 115 GLU Chi-restraints excluded: chain M residue 51 ARG Chi-restraints excluded: chain M residue 104 VAL Chi-restraints excluded: chain N residue 37 ASP Chi-restraints excluded: chain N residue 49 ILE Chi-restraints excluded: chain O residue 5 THR Chi-restraints excluded: chain O residue 24 LEU Chi-restraints excluded: chain O residue 98 THR Chi-restraints excluded: chain O residue 110 VAL Chi-restraints excluded: chain P residue 17 GLU Chi-restraints excluded: chain P residue 52 VAL Chi-restraints excluded: chain P residue 68 ARG Chi-restraints excluded: chain P residue 77 SER Chi-restraints excluded: chain P residue 92 VAL Chi-restraints excluded: chain Q residue 21 GLN Chi-restraints excluded: chain Q residue 25 LEU Chi-restraints excluded: chain Q residue 28 SER Chi-restraints excluded: chain Q residue 40 VAL Chi-restraints excluded: chain Q residue 62 SER Chi-restraints excluded: chain R residue 26 ARG Chi-restraints excluded: chain R residue 30 VAL Chi-restraints excluded: chain R residue 44 VAL Chi-restraints excluded: chain R residue 62 GLU Chi-restraints excluded: chain S residue 10 THR Chi-restraints excluded: chain T residue 22 ASN Chi-restraints excluded: chain T residue 60 ASP Chi-restraints excluded: chain T residue 62 LEU Chi-restraints excluded: chain U residue 11 VAL Chi-restraints excluded: chain U residue 17 LEU Chi-restraints excluded: chain U residue 32 LYS Chi-restraints excluded: chain U residue 34 THR Chi-restraints excluded: chain U residue 37 LEU Chi-restraints excluded: chain V residue 4 ILE Chi-restraints excluded: chain X residue 44 LYS Chi-restraints excluded: chain Y residue 33 LYS Chi-restraints excluded: chain Y residue 51 LYS Chi-restraints excluded: chain Z residue 13 LYS Chi-restraints excluded: chain Z residue 41 SER Chi-restraints excluded: chain a residue 31 ILE Chi-restraints excluded: chain a residue 47 VAL Chi-restraints excluded: chain b residue 6 SER Chi-restraints excluded: chain b residue 36 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 572 random chunks: chunk 337 optimal weight: 0.3980 chunk 543 optimal weight: 5.9990 chunk 331 optimal weight: 0.7980 chunk 257 optimal weight: 10.0000 chunk 377 optimal weight: 1.9990 chunk 569 optimal weight: 3.9990 chunk 524 optimal weight: 2.9990 chunk 453 optimal weight: 4.9990 chunk 47 optimal weight: 10.0000 chunk 350 optimal weight: 7.9990 chunk 278 optimal weight: 6.9990 overall best weight: 2.0386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 134 ASN ** C 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 106 ASN E 139 GLN F 95 HIS F 136 GLN H 6 ASN L 15 GLN N 43 ASN O 62 ASN S 17 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8542 moved from start: 0.0814 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 90840 Z= 0.187 Angle : 0.601 9.460 136537 Z= 0.321 Chirality : 0.038 0.305 17600 Planarity : 0.005 0.060 6899 Dihedral : 22.958 179.856 46844 Min Nonbonded Distance : 1.892 Molprobity Statistics. All-atom Clashscore : 4.02 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.78 % Favored : 95.19 % Rotamer: Outliers : 3.90 % Allowed : 26.33 % Favored : 69.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.77 (0.15), residues: 3016 helix: 0.60 (0.19), residues: 749 sheet: -0.02 (0.20), residues: 655 loop : -1.28 (0.14), residues: 1612 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP E 62 HIS 0.015 0.001 HIS F 95 PHE 0.013 0.001 PHE M 57 TYR 0.015 0.002 TYR F 125 ARG 0.009 0.000 ARG X 51 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6032 Ramachandran restraints generated. 3016 Oldfield, 0 Emsley, 3016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6032 Ramachandran restraints generated. 3016 Oldfield, 0 Emsley, 3016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 557 residues out of total 2484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 91 poor density : 466 time to evaluate : 3.697 Fit side-chains revert: symmetry clash REVERT: A 17 GLU cc_start: 0.7848 (OUTLIER) cc_final: 0.7550 (mt-10) REVERT: B 94 GLU cc_start: 0.6917 (OUTLIER) cc_final: 0.6350 (mt-10) REVERT: B 188 SER cc_start: 0.8964 (t) cc_final: 0.8648 (t) REVERT: C 131 LYS cc_start: 0.7231 (OUTLIER) cc_final: 0.7031 (ttmm) REVERT: E 50 LEU cc_start: 0.7596 (mm) cc_final: 0.7303 (mt) REVERT: E 63 MET cc_start: 0.7735 (ttp) cc_final: 0.7403 (ttp) REVERT: E 153 SER cc_start: 0.8464 (OUTLIER) cc_final: 0.8068 (m) REVERT: F 60 GLU cc_start: 0.8279 (OUTLIER) cc_final: 0.7921 (pp20) REVERT: F 73 LYS cc_start: 0.8509 (OUTLIER) cc_final: 0.8162 (mmtt) REVERT: G 54 LYS cc_start: 0.8684 (tttm) cc_final: 0.8366 (tttm) REVERT: H 16 ARG cc_start: 0.8121 (mtp85) cc_final: 0.7773 (mtp85) REVERT: I 39 ARG cc_start: 0.8977 (OUTLIER) cc_final: 0.7881 (ptp90) REVERT: I 85 ASN cc_start: 0.8434 (t0) cc_final: 0.8092 (m-40) REVERT: L 44 GLN cc_start: 0.8720 (tt0) cc_final: 0.8457 (tt0) REVERT: M 80 ILE cc_start: 0.8872 (mm) cc_final: 0.8564 (mm) REVERT: N 37 ASP cc_start: 0.7127 (OUTLIER) cc_final: 0.6820 (p0) REVERT: P 17 GLU cc_start: 0.7901 (OUTLIER) cc_final: 0.7517 (tm-30) REVERT: Q 21 GLN cc_start: 0.8264 (OUTLIER) cc_final: 0.7659 (pt0) REVERT: Q 95 LYS cc_start: 0.7448 (ttpt) cc_final: 0.6896 (tptt) REVERT: R 7 ASN cc_start: 0.8387 (m-40) cc_final: 0.8098 (m-40) REVERT: R 26 ARG cc_start: 0.8179 (OUTLIER) cc_final: 0.7836 (mtm180) REVERT: R 62 GLU cc_start: 0.7654 (OUTLIER) cc_final: 0.7216 (mt-10) REVERT: S 84 THR cc_start: 0.8564 (p) cc_final: 0.8329 (p) REVERT: Z 41 SER cc_start: 0.8944 (OUTLIER) cc_final: 0.8700 (t) REVERT: b 36 ARG cc_start: 0.9007 (OUTLIER) cc_final: 0.8459 (ttp-170) outliers start: 91 outliers final: 70 residues processed: 534 average time/residue: 1.7494 time to fit residues: 1235.5552 Evaluate side-chains 549 residues out of total 2484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 84 poor density : 465 time to evaluate : 3.371 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 GLU Chi-restraints excluded: chain A residue 20 VAL Chi-restraints excluded: chain A residue 134 ASN Chi-restraints excluded: chain A residue 139 SER Chi-restraints excluded: chain A residue 178 SER Chi-restraints excluded: chain B residue 13 THR Chi-restraints excluded: chain B residue 18 ASP Chi-restraints excluded: chain B residue 51 VAL Chi-restraints excluded: chain B residue 59 SER Chi-restraints excluded: chain B residue 94 GLU Chi-restraints excluded: chain B residue 113 THR Chi-restraints excluded: chain B residue 153 GLN Chi-restraints excluded: chain B residue 182 SER Chi-restraints excluded: chain B residue 200 THR Chi-restraints excluded: chain C residue 131 LYS Chi-restraints excluded: chain E residue 18 THR Chi-restraints excluded: chain E residue 32 THR Chi-restraints excluded: chain E residue 34 SER Chi-restraints excluded: chain E residue 37 LEU Chi-restraints excluded: chain E residue 58 SER Chi-restraints excluded: chain E residue 153 SER Chi-restraints excluded: chain E residue 168 VAL Chi-restraints excluded: chain E residue 170 LEU Chi-restraints excluded: chain F residue 4 LEU Chi-restraints excluded: chain F residue 5 SER Chi-restraints excluded: chain F residue 60 GLU Chi-restraints excluded: chain F residue 62 VAL Chi-restraints excluded: chain F residue 73 LYS Chi-restraints excluded: chain G residue 45 GLU Chi-restraints excluded: chain G residue 73 ASP Chi-restraints excluded: chain G residue 80 ASP Chi-restraints excluded: chain G residue 102 VAL Chi-restraints excluded: chain G residue 116 SER Chi-restraints excluded: chain H residue 29 VAL Chi-restraints excluded: chain H residue 85 SER Chi-restraints excluded: chain H residue 117 GLU Chi-restraints excluded: chain H residue 123 THR Chi-restraints excluded: chain I residue 39 ARG Chi-restraints excluded: chain I residue 124 LYS Chi-restraints excluded: chain I residue 132 VAL Chi-restraints excluded: chain I residue 136 VAL Chi-restraints excluded: chain J residue 6 SER Chi-restraints excluded: chain K residue 9 LEU Chi-restraints excluded: chain K residue 99 HIS Chi-restraints excluded: chain L residue 18 THR Chi-restraints excluded: chain L residue 36 LYS Chi-restraints excluded: chain L residue 115 GLU Chi-restraints excluded: chain M residue 104 VAL Chi-restraints excluded: chain N residue 37 ASP Chi-restraints excluded: chain N residue 49 ILE Chi-restraints excluded: chain O residue 5 THR Chi-restraints excluded: chain O residue 24 LEU Chi-restraints excluded: chain O residue 98 THR Chi-restraints excluded: chain O residue 110 VAL Chi-restraints excluded: chain P residue 17 GLU Chi-restraints excluded: chain P residue 52 VAL Chi-restraints excluded: chain P residue 68 ARG Chi-restraints excluded: chain P residue 77 SER Chi-restraints excluded: chain P residue 92 VAL Chi-restraints excluded: chain Q residue 21 GLN Chi-restraints excluded: chain Q residue 25 LEU Chi-restraints excluded: chain Q residue 28 SER Chi-restraints excluded: chain Q residue 40 VAL Chi-restraints excluded: chain Q residue 62 SER Chi-restraints excluded: chain R residue 26 ARG Chi-restraints excluded: chain R residue 44 VAL Chi-restraints excluded: chain R residue 62 GLU Chi-restraints excluded: chain S residue 10 THR Chi-restraints excluded: chain T residue 22 ASN Chi-restraints excluded: chain T residue 62 LEU Chi-restraints excluded: chain U residue 11 VAL Chi-restraints excluded: chain U residue 32 LYS Chi-restraints excluded: chain U residue 34 THR Chi-restraints excluded: chain U residue 37 LEU Chi-restraints excluded: chain V residue 4 ILE Chi-restraints excluded: chain X residue 44 LYS Chi-restraints excluded: chain Y residue 33 LYS Chi-restraints excluded: chain Y residue 51 LYS Chi-restraints excluded: chain Z residue 41 SER Chi-restraints excluded: chain a residue 31 ILE Chi-restraints excluded: chain a residue 46 CYS Chi-restraints excluded: chain a residue 47 VAL Chi-restraints excluded: chain b residue 6 SER Chi-restraints excluded: chain b residue 36 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 572 random chunks: chunk 360 optimal weight: 30.0000 chunk 483 optimal weight: 3.9990 chunk 139 optimal weight: 10.0000 chunk 418 optimal weight: 1.9990 chunk 67 optimal weight: 5.9990 chunk 126 optimal weight: 6.9990 chunk 454 optimal weight: 0.0030 chunk 190 optimal weight: 6.9990 chunk 466 optimal weight: 0.5980 chunk 57 optimal weight: 6.9990 chunk 83 optimal weight: 10.0000 overall best weight: 2.5196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 106 ASN E 139 GLN F 95 HIS F 136 GLN H 6 ASN L 15 GLN N 43 ASN O 62 ASN S 17 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.136523 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.3192 r_free = 0.3192 target = 0.116371 restraints weight = 85817.090| |-----------------------------------------------------------------------------| r_work (start): 0.3195 rms_B_bonded: 0.54 r_work: 0.2856 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work: 0.2792 rms_B_bonded: 4.09 restraints_weight: 0.2500 r_work (final): 0.2792 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2765 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2765 r_free = 0.2765 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2765 r_free = 0.2765 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2765 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8775 moved from start: 0.0813 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.123 90840 Z= 0.214 Angle : 0.639 59.199 136537 Z= 0.349 Chirality : 0.039 0.536 17600 Planarity : 0.005 0.060 6899 Dihedral : 22.957 179.915 46844 Min Nonbonded Distance : 1.893 Molprobity Statistics. All-atom Clashscore : 4.05 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.71 % Favored : 95.22 % Rotamer: Outliers : 3.77 % Allowed : 26.54 % Favored : 69.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.77 (0.15), residues: 3016 helix: 0.60 (0.19), residues: 749 sheet: -0.01 (0.20), residues: 655 loop : -1.28 (0.14), residues: 1612 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP E 62 HIS 0.013 0.001 HIS F 95 PHE 0.013 0.001 PHE M 57 TYR 0.015 0.002 TYR F 125 ARG 0.008 0.000 ARG X 51 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 20003.06 seconds wall clock time: 351 minutes 23.91 seconds (21083.91 seconds total)