Starting phenix.real_space_refine on Sun Feb 18 06:05:32 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6rbe_4793/02_2024/6rbe_4793.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6rbe_4793/02_2024/6rbe_4793.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6rbe_4793/02_2024/6rbe_4793.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6rbe_4793/02_2024/6rbe_4793.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6rbe_4793/02_2024/6rbe_4793.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6rbe_4793/02_2024/6rbe_4793.pdb" } resolution = 3.8 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= 0.003 sd= 0.020 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 1750 5.49 5 S 76 5.16 5 C 39072 2.51 5 N 13190 2.21 5 O 18633 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 41": "NH1" <-> "NH2" Residue "B ARG 144": "NH1" <-> "NH2" Residue "B ARG 152": "NH1" <-> "NH2" Residue "B ARG 213": "NH1" <-> "NH2" Residue "C ARG 91": "NH1" <-> "NH2" Residue "C ARG 141": "NH1" <-> "NH2" Residue "E ARG 11": "NH1" <-> "NH2" Residue "E ARG 49": "NH1" <-> "NH2" Residue "E ARG 59": "NH1" <-> "NH2" Residue "E ARG 108": "NH1" <-> "NH2" Residue "E ARG 148": "NH1" <-> "NH2" Residue "E ARG 200": "NH1" <-> "NH2" Residue "E PHE 226": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 252": "NH1" <-> "NH2" Residue "G ARG 23": "NH1" <-> "NH2" Residue "G ARG 92": "NH1" <-> "NH2" Residue "G ARG 98": "NH1" <-> "NH2" Residue "G ARG 137": "NH1" <-> "NH2" Residue "G ARG 191": "NH1" <-> "NH2" Residue "H ARG 39": "NH1" <-> "NH2" Residue "H PHE 92": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ARG 104": "NH1" <-> "NH2" Residue "I ARG 8": "NH1" <-> "NH2" Residue "I ARG 22": "NH1" <-> "NH2" Residue "I PHE 27": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ARG 47": "NH1" <-> "NH2" Residue "I ARG 59": "NH1" <-> "NH2" Residue "I ARG 110": "NH1" <-> "NH2" Residue "I TYR 117": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ARG 164": "NH1" <-> "NH2" Residue "I ARG 178": "NH1" <-> "NH2" Residue "I ARG 194": "NH1" <-> "NH2" Residue "J ARG 3": "NH1" <-> "NH2" Residue "J ARG 17": "NH1" <-> "NH2" Residue "J ARG 53": "NH1" <-> "NH2" Residue "J ARG 54": "NH1" <-> "NH2" Residue "J ARG 62": "NH1" <-> "NH2" Residue "J ARG 78": "NH1" <-> "NH2" Residue "J ARG 168": "NH1" <-> "NH2" Residue "J ARG 171": "NH1" <-> "NH2" Residue "L ARG 30": "NH1" <-> "NH2" Residue "L ARG 33": "NH1" <-> "NH2" Residue "L ARG 116": "NH1" <-> "NH2" Residue "N ARG 104": "NH1" <-> "NH2" Residue "N ARG 106": "NH1" <-> "NH2" Residue "R ARG 3": "NH1" <-> "NH2" Residue "R ARG 33": "NH1" <-> "NH2" Residue "R ARG 67": "NH1" <-> "NH2" Residue "R PHE 71": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R ARG 80": "NH1" <-> "NH2" Residue "V ARG 60": "NH1" <-> "NH2" Residue "V ARG 71": "NH1" <-> "NH2" Residue "W PHE 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W TYR 130": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X ARG 16": "NH1" <-> "NH2" Residue "X ARG 19": "NH1" <-> "NH2" Residue "X ARG 144": "NH1" <-> "NH2" Residue "Y ARG 20": "NH1" <-> "NH2" Residue "Y ARG 32": "NH1" <-> "NH2" Residue "Y ARG 131": "NH1" <-> "NH2" Residue "b TYR 31": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d TYR 14": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "e ARG 54": "NH1" <-> "NH2" Residue "D ARG 9": "NH1" <-> "NH2" Residue "D ARG 65": "NH1" <-> "NH2" Residue "D ARG 90": "NH1" <-> "NH2" Residue "D ARG 124": "NH1" <-> "NH2" Residue "D ARG 143": "NH1" <-> "NH2" Residue "D ARG 146": "NH1" <-> "NH2" Residue "F ARG 65": "NH1" <-> "NH2" Residue "F ARG 76": "NH1" <-> "NH2" Residue "F ARG 148": "NH1" <-> "NH2" Residue "F ARG 219": "NH1" <-> "NH2" Residue "P ARG 47": "NH1" <-> "NH2" Residue "P ARG 77": "NH1" <-> "NH2" Residue "P TYR 123": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P ARG 127": "NH1" <-> "NH2" Residue "Q ARG 114": "NH1" <-> "NH2" Residue "Q ARG 143": "NH1" <-> "NH2" Residue "S ARG 88": "NH1" <-> "NH2" Residue "S ARG 115": "NH1" <-> "NH2" Residue "S ARG 120": "NH1" <-> "NH2" Residue "S ARG 144": "NH1" <-> "NH2" Residue "S ARG 145": "NH1" <-> "NH2" Residue "T PHE 54": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U ARG 57": "NH1" <-> "NH2" Residue "U ARG 89": "NH1" <-> "NH2" Residue "U TYR 90": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z ARG 49": "NH1" <-> "NH2" Residue "Z ARG 103": "NH1" <-> "NH2" Residue "c ARG 65": "NH1" <-> "NH2" Residue "f TYR 106": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "f ARG 119": "NH1" <-> "NH2" Residue "g TYR 232": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "g PHE 245": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "g TYR 305": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.09s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 72721 Number of models: 1 Model: "" Number of chains: 33 Chain: "2" Number of atoms: 37285 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1750, 37285 Classifications: {'RNA': 1750} Modifications used: {'rna2p_pur': 149, 'rna2p_pyr': 159, 'rna3p_pur': 770, 'rna3p_pyr': 672} Link IDs: {'rna2p': 307, 'rna3p': 1442} Chain breaks: 6 Chain: "A" Number of atoms: 1577 Number of conformers: 1 Conformer: "" Number of residues, atoms: 206, 1577 Classifications: {'peptide': 206} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PCIS': 1, 'PTRANS': 15, 'TRANS': 189} Unresolved non-hydrogen bonds: 36 Unresolved non-hydrogen angles: 46 Unresolved non-hydrogen dihedrals: 29 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 1, 'ARG:plan': 2, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 27 Chain: "B" Number of atoms: 918 Number of conformers: 1 Conformer: "" Number of residues, atoms: 113, 918 Classifications: {'peptide': 113} Link IDs: {'PTRANS': 2, 'TRANS': 110} Chain: "C" Number of atoms: 1635 Number of conformers: 1 Conformer: "" Number of residues, atoms: 217, 1635 Classifications: {'peptide': 217} Link IDs: {'PTRANS': 13, 'TRANS': 203} Chain: "E" Number of atoms: 2068 Number of conformers: 1 Conformer: "" Number of residues, atoms: 260, 2068 Classifications: {'peptide': 260} Link IDs: {'PTRANS': 12, 'TRANS': 247} Chain: "G" Number of atoms: 1799 Number of conformers: 1 Conformer: "" Number of residues, atoms: 226, 1799 Classifications: {'peptide': 226} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 9, 'TRANS': 216} Unresolved non-hydrogen bonds: 21 Unresolved non-hydrogen angles: 25 Unresolved non-hydrogen dihedrals: 17 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 2, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 13 Chain: "H" Number of atoms: 1481 Number of conformers: 1 Conformer: "" Number of residues, atoms: 184, 1481 Classifications: {'peptide': 184} Link IDs: {'CIS': 1, 'PTRANS': 10, 'TRANS': 172} Chain: "I" Number of atoms: 1489 Number of conformers: 1 Conformer: "" Number of residues, atoms: 188, 1489 Classifications: {'peptide': 188} Link IDs: {'PTRANS': 4, 'TRANS': 183} Chain breaks: 1 Chain: "J" Number of atoms: 1494 Number of conformers: 1 Conformer: "" Number of residues, atoms: 185, 1494 Classifications: {'peptide': 185} Link IDs: {'PTRANS': 8, 'TRANS': 176} Chain: "L" Number of atoms: 1213 Number of conformers: 1 Conformer: "" Number of residues, atoms: 155, 1213 Classifications: {'peptide': 155} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 8, 'TRANS': 146} Unresolved non-hydrogen bonds: 33 Unresolved non-hydrogen angles: 39 Unresolved non-hydrogen dihedrals: 31 Planarities with less than four sites: {'GLN:plan1': 1, 'PHE:plan': 2, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 19 Chain: "N" Number of atoms: 1192 Number of conformers: 1 Conformer: "" Number of residues, atoms: 150, 1192 Classifications: {'peptide': 150} Link IDs: {'PTRANS': 7, 'TRANS': 142} Chain: "O" Number of atoms: 141 Number of conformers: 1 Conformer: "" Number of residues, atoms: 18, 141 Classifications: {'peptide': 18} Link IDs: {'PTRANS': 1, 'TRANS': 16} Chain: "R" Number of atoms: 926 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 926 Classifications: {'peptide': 120} Incomplete info: {'truncation_to_alanine': 15} Link IDs: {'CIS': 1, 'PTRANS': 4, 'TRANS': 114} Chain breaks: 1 Unresolved non-hydrogen bonds: 39 Unresolved non-hydrogen angles: 50 Unresolved non-hydrogen dihedrals: 28 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'ARG:plan': 1, 'ASN:plan1': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 14 Chain: "V" Number of atoms: 684 Number of conformers: 1 Conformer: "" Number of residues, atoms: 87, 684 Classifications: {'peptide': 87} Link IDs: {'PTRANS': 2, 'TRANS': 84} Chain: "W" Number of atoms: 1021 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 1021 Classifications: {'peptide': 129} Link IDs: {'PCIS': 2, 'PTRANS': 1, 'TRANS': 125} Chain: "X" Number of atoms: 1121 Number of conformers: 1 Conformer: "" Number of residues, atoms: 144, 1121 Classifications: {'peptide': 144} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 137} Chain: "Y" Number of atoms: 1073 Number of conformers: 1 Conformer: "" Number of residues, atoms: 134, 1073 Classifications: {'peptide': 134} Link IDs: {'PTRANS': 3, 'TRANS': 130} Chain: "b" Number of atoms: 610 Number of conformers: 1 Conformer: "" Number of residues, atoms: 81, 610 Classifications: {'peptide': 81} Link IDs: {'PTRANS': 4, 'TRANS': 76} Chain: "d" Number of atoms: 442 Number of conformers: 1 Conformer: "" Number of residues, atoms: 53, 442 Classifications: {'peptide': 53} Link IDs: {'PTRANS': 1, 'TRANS': 51} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Chain: "e" Number of atoms: 475 Number of conformers: 1 Conformer: "" Number of residues, atoms: 60, 475 Classifications: {'peptide': 60} Link IDs: {'PTRANS': 5, 'TRANS': 54} Chain: "D" Number of atoms: 1734 Number of conformers: 1 Conformer: "" Number of residues, atoms: 223, 1734 Classifications: {'peptide': 223} Link IDs: {'PTRANS': 9, 'TRANS': 213} Chain: "F" Number of atoms: 1609 Number of conformers: 1 Conformer: "" Number of residues, atoms: 206, 1609 Classifications: {'peptide': 206} Link IDs: {'CIS': 1, 'PTRANS': 8, 'TRANS': 196} Chain: "K" Number of atoms: 772 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 772 Classifications: {'peptide': 96} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PTRANS': 3, 'TRANS': 92} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 48 Unresolved non-hydrogen angles: 63 Unresolved non-hydrogen dihedrals: 39 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 1, 'ASN:plan1': 1, 'HIS:plan': 1, 'GLU:plan': 2, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 32 Chain: "M" Number of atoms: 890 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 890 Classifications: {'peptide': 124} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PTRANS': 2, 'TRANS': 121} Unresolved non-hydrogen bonds: 44 Unresolved non-hydrogen angles: 54 Unresolved non-hydrogen dihedrals: 34 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLU:plan': 2, 'ARG:plan': 2, 'ASN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 24 Chain: "P" Number of atoms: 977 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 977 Classifications: {'peptide': 124} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 8, 'TRANS': 115} Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 13 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "Q" Number of atoms: 1105 Number of conformers: 1 Conformer: "" Number of residues, atoms: 141, 1105 Classifications: {'peptide': 141} Link IDs: {'PTRANS': 6, 'TRANS': 134} Chain: "S" Number of atoms: 1192 Number of conformers: 1 Conformer: "" Number of residues, atoms: 145, 1192 Classifications: {'peptide': 145} Link IDs: {'PTRANS': 2, 'TRANS': 142} Chain: "T" Number of atoms: 1112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 143, 1112 Classifications: {'peptide': 143} Link IDs: {'PTRANS': 5, 'TRANS': 137} Chain: "U" Number of atoms: 792 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 792 Classifications: {'peptide': 98} Link IDs: {'PTRANS': 4, 'TRANS': 93} Chain breaks: 3 Chain: "Z" Number of atoms: 563 Number of conformers: 1 Conformer: "" Number of residues, atoms: 70, 563 Classifications: {'peptide': 70} Link IDs: {'PTRANS': 2, 'TRANS': 67} Chain: "c" Number of atoms: 497 Number of conformers: 1 Conformer: "" Number of residues, atoms: 63, 497 Classifications: {'peptide': 63} Link IDs: {'PTRANS': 2, 'TRANS': 60} Chain: "f" Number of atoms: 397 Number of conformers: 1 Conformer: "" Number of residues, atoms: 51, 397 Classifications: {'peptide': 51} Link IDs: {'CIS': 1, 'PTRANS': 1, 'TRANS': 48} Chain: "g" Number of atoms: 2437 Number of conformers: 1 Conformer: "" Number of residues, atoms: 318, 2437 Classifications: {'peptide': 318} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 309} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Time building chain proxies: 27.46, per 1000 atoms: 0.38 Number of scatterers: 72721 At special positions: 0 Unit cell: (214.467, 276.353, 178.189, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 76 16.00 P 1750 15.00 O 18633 8.00 N 13190 7.00 C 39072 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: 27.49 Conformation dependent library (CDL) restraints added in 5.1 seconds 8876 Ramachandran restraints generated. 4438 Oldfield, 0 Emsley, 4438 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8398 Finding SS restraints... Secondary structure from input PDB file: 141 helices and 0 sheets defined 34.1% alpha, 0.0% beta 492 base pairs and 907 stacking pairs defined. Time for finding SS restraints: 21.29 Creating SS restraints... Processing helix chain 'A' and resid 10 through 20 Processing helix chain 'A' and resid 49 through 65 Processing helix chain 'A' and resid 69 through 71 No H-bonds generated for 'chain 'A' and resid 69 through 71' Processing helix chain 'A' and resid 79 through 81 No H-bonds generated for 'chain 'A' and resid 79 through 81' Processing helix chain 'A' and resid 82 through 93 Processing helix chain 'A' and resid 129 through 138 Processing helix chain 'A' and resid 168 through 184 Processing helix chain 'B' and resid 108 through 114 Processing helix chain 'B' and resid 159 through 176 removed outlier: 3.547A pdb=" N VAL B 176 " --> pdb=" O LEU B 172 " (cutoff:3.500A) Processing helix chain 'B' and resid 180 through 189 Processing helix chain 'B' and resid 191 through 202 Processing helix chain 'C' and resid 40 through 47 Processing helix chain 'C' and resid 52 through 59 removed outlier: 3.938A pdb=" N ILE C 56 " --> pdb=" O THR C 52 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N HIS C 59 " --> pdb=" O GLU C 55 " (cutoff:3.500A) Processing helix chain 'C' and resid 65 through 73 removed outlier: 4.344A pdb=" N ILE C 69 " --> pdb=" O GLU C 65 " (cutoff:3.500A) Processing helix chain 'C' and resid 120 through 135 Processing helix chain 'C' and resid 181 through 191 Processing helix chain 'C' and resid 206 through 220 Processing helix chain 'C' and resid 221 through 223 No H-bonds generated for 'chain 'C' and resid 221 through 223' Processing helix chain 'C' and resid 226 through 230 Processing helix chain 'C' and resid 238 through 243 removed outlier: 3.544A pdb=" N ILE C 242 " --> pdb=" O SER C 238 " (cutoff:3.500A) Processing helix chain 'E' and resid 15 through 19 Processing helix chain 'E' and resid 43 through 50 removed outlier: 3.536A pdb=" N PHE E 47 " --> pdb=" O PRO E 43 " (cutoff:3.500A) Processing helix chain 'E' and resid 58 through 66 removed outlier: 3.697A pdb=" N LYS E 62 " --> pdb=" O GLY E 58 " (cutoff:3.500A) Processing helix chain 'E' and resid 117 through 121 removed outlier: 3.607A pdb=" N TYR E 121 " --> pdb=" O GLU E 118 " (cutoff:3.500A) Processing helix chain 'E' and resid 133 through 135 No H-bonds generated for 'chain 'E' and resid 133 through 135' Processing helix chain 'E' and resid 247 through 256 Processing helix chain 'G' and resid 20 through 25 removed outlier: 3.704A pdb=" N ILE G 24 " --> pdb=" O ASP G 20 " (cutoff:3.500A) Processing helix chain 'G' and resid 26 through 28 No H-bonds generated for 'chain 'G' and resid 26 through 28' Processing helix chain 'G' and resid 59 through 61 No H-bonds generated for 'chain 'G' and resid 59 through 61' Processing helix chain 'G' and resid 137 through 146 Processing helix chain 'G' and resid 152 through 157 removed outlier: 3.613A pdb=" N ASP G 155 " --> pdb=" O ASP G 152 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N VAL G 157 " --> pdb=" O ARG G 154 " (cutoff:3.500A) Processing helix chain 'G' and resid 180 through 226 removed outlier: 3.643A pdb=" N LEU G 184 " --> pdb=" O THR G 180 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N ILE G 226 " --> pdb=" O GLU G 222 " (cutoff:3.500A) Processing helix chain 'H' and resid 14 through 29 removed outlier: 3.523A pdb=" N LEU H 18 " --> pdb=" O THR H 14 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N GLN H 19 " --> pdb=" O GLU H 15 " (cutoff:3.500A) Processing helix chain 'H' and resid 30 through 35 Processing helix chain 'H' and resid 66 through 85 removed outlier: 4.945A pdb=" N THR H 75 " --> pdb=" O HIS H 71 " (cutoff:3.500A) removed outlier: 6.502A pdb=" N LYS H 76 " --> pdb=" O LYS H 72 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N LEU H 77 " --> pdb=" O VAL H 73 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N PHE H 85 " --> pdb=" O LEU H 81 " (cutoff:3.500A) Processing helix chain 'H' and resid 117 through 130 removed outlier: 3.818A pdb=" N VAL H 130 " --> pdb=" O LEU H 126 " (cutoff:3.500A) Processing helix chain 'H' and resid 159 through 164 removed outlier: 4.007A pdb=" N TYR H 164 " --> pdb=" O GLN H 160 " (cutoff:3.500A) Processing helix chain 'H' and resid 165 through 178 removed outlier: 3.811A pdb=" N PHE H 169 " --> pdb=" O LYS H 165 " (cutoff:3.500A) Processing helix chain 'I' and resid 87 through 93 removed outlier: 3.735A pdb=" N VAL I 91 " --> pdb=" O ASN I 87 " (cutoff:3.500A) Processing helix chain 'I' and resid 106 through 117 removed outlier: 3.709A pdb=" N ARG I 110 " --> pdb=" O ALA I 106 " (cutoff:3.500A) Processing helix chain 'I' and resid 136 through 146 Processing helix chain 'I' and resid 153 through 163 Processing helix chain 'I' and resid 172 through 177 Processing helix chain 'I' and resid 186 through 198 Processing helix chain 'J' and resid 20 through 35 Processing helix chain 'J' and resid 39 through 61 removed outlier: 3.936A pdb=" N ILE J 45 " --> pdb=" O GLU J 41 " (cutoff:3.500A) Processing helix chain 'J' and resid 66 through 83 removed outlier: 3.719A pdb=" N VAL J 83 " --> pdb=" O ARG J 79 " (cutoff:3.500A) Processing helix chain 'J' and resid 100 through 106 removed outlier: 3.735A pdb=" N PHE J 104 " --> pdb=" O LYS J 100 " (cutoff:3.500A) Processing helix chain 'J' and resid 108 through 116 removed outlier: 3.699A pdb=" N TYR J 114 " --> pdb=" O GLN J 110 " (cutoff:3.500A) Processing helix chain 'J' and resid 121 through 131 Processing helix chain 'J' and resid 170 through 184 removed outlier: 3.941A pdb=" N ARG J 174 " --> pdb=" O GLY J 170 " (cutoff:3.500A) Processing helix chain 'L' and resid 45 through 51 removed outlier: 3.790A pdb=" N ILE L 49 " --> pdb=" O PRO L 45 " (cutoff:3.500A) Processing helix chain 'N' and resid 29 through 44 removed outlier: 4.085A pdb=" N VAL N 33 " --> pdb=" O SER N 29 " (cutoff:3.500A) Processing helix chain 'N' and resid 46 through 57 Processing helix chain 'N' and resid 62 through 67 removed outlier: 3.995A pdb=" N ILE N 66 " --> pdb=" O GLN N 62 " (cutoff:3.500A) Processing helix chain 'N' and resid 70 through 78 Processing helix chain 'N' and resid 85 through 105 Processing helix chain 'N' and resid 108 through 132 removed outlier: 3.573A pdb=" N LYS N 112 " --> pdb=" O ASP N 108 " (cutoff:3.500A) Processing helix chain 'N' and resid 142 through 150 removed outlier: 4.523A pdb=" N ALA N 148 " --> pdb=" O ALA N 144 " (cutoff:3.500A) Processing helix chain 'R' and resid 6 through 21 Processing helix chain 'R' and resid 27 through 39 removed outlier: 3.781A pdb=" N ARG R 33 " --> pdb=" O GLN R 29 " (cutoff:3.500A) Processing helix chain 'R' and resid 43 through 62 Processing helix chain 'R' and resid 72 through 79 Processing helix chain 'R' and resid 103 through 114 Processing helix chain 'V' and resid 56 through 63 Processing helix chain 'V' and resid 64 through 75 removed outlier: 3.523A pdb=" N SER V 68 " --> pdb=" O GLU V 64 " (cutoff:3.500A) Processing helix chain 'W' and resid 6 through 20 Processing helix chain 'W' and resid 31 through 45 removed outlier: 3.559A pdb=" N HIS W 44 " --> pdb=" O VAL W 40 " (cutoff:3.500A) Processing helix chain 'W' and resid 82 through 84 No H-bonds generated for 'chain 'W' and resid 82 through 84' Processing helix chain 'W' and resid 85 through 93 Processing helix chain 'W' and resid 113 through 119 Processing helix chain 'X' and resid 11 through 24 removed outlier: 3.645A pdb=" N LEU X 15 " --> pdb=" O SER X 11 " (cutoff:3.500A) Processing helix chain 'X' and resid 27 through 35 Processing helix chain 'X' and resid 35 through 40 Processing helix chain 'X' and resid 131 through 138 removed outlier: 3.930A pdb=" N GLU X 138 " --> pdb=" O ALA X 134 " (cutoff:3.500A) Processing helix chain 'Y' and resid 16 through 18 No H-bonds generated for 'chain 'Y' and resid 16 through 18' Processing helix chain 'Y' and resid 37 through 46 removed outlier: 3.985A pdb=" N GLU Y 46 " --> pdb=" O GLU Y 42 " (cutoff:3.500A) Processing helix chain 'Y' and resid 51 through 53 No H-bonds generated for 'chain 'Y' and resid 51 through 53' Processing helix chain 'Y' and resid 78 through 86 Processing helix chain 'Y' and resid 87 through 95 removed outlier: 3.525A pdb=" N LEU Y 91 " --> pdb=" O PRO Y 87 " (cutoff:3.500A) Processing helix chain 'Y' and resid 104 through 116 Processing helix chain 'Y' and resid 122 through 133 removed outlier: 4.019A pdb=" N ARG Y 131 " --> pdb=" O LYS Y 127 " (cutoff:3.500A) Processing helix chain 'b' and resid 11 through 18 removed outlier: 3.842A pdb=" N LYS b 18 " --> pdb=" O SER b 14 " (cutoff:3.500A) Processing helix chain 'd' and resid 15 through 19 removed outlier: 4.403A pdb=" N ARG d 19 " --> pdb=" O LYS d 16 " (cutoff:3.500A) Processing helix chain 'd' and resid 32 through 36 removed outlier: 4.184A pdb=" N LEU d 36 " --> pdb=" O LYS d 33 " (cutoff:3.500A) Processing helix chain 'd' and resid 39 through 47 Processing helix chain 'e' and resid 12 through 17 removed outlier: 3.621A pdb=" N SER e 16 " --> pdb=" O GLY e 12 " (cutoff:3.500A) Processing helix chain 'e' and resid 32 through 45 removed outlier: 3.530A pdb=" N LYS e 36 " --> pdb=" O GLY e 32 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N ARG e 43 " --> pdb=" O LEU e 39 " (cutoff:3.500A) Processing helix chain 'D' and resid 6 through 29 Processing helix chain 'D' and resid 30 through 32 No H-bonds generated for 'chain 'D' and resid 30 through 32' Processing helix chain 'D' and resid 55 through 60 removed outlier: 3.749A pdb=" N GLY D 60 " --> pdb=" O GLN D 56 " (cutoff:3.500A) Processing helix chain 'D' and resid 65 through 78 Processing helix chain 'D' and resid 93 through 96 Processing helix chain 'D' and resid 97 through 111 Processing helix chain 'D' and resid 116 through 129 Processing helix chain 'D' and resid 160 through 167 removed outlier: 3.643A pdb=" N ASN D 165 " --> pdb=" O GLY D 161 " (cutoff:3.500A) Processing helix chain 'D' and resid 191 through 195 Processing helix chain 'F' and resid 30 through 40 removed outlier: 3.551A pdb=" N GLU F 39 " --> pdb=" O GLN F 35 " (cutoff:3.500A) Processing helix chain 'F' and resid 88 through 98 Processing helix chain 'F' and resid 106 through 124 Processing helix chain 'F' and resid 129 through 140 Processing helix chain 'F' and resid 163 through 184 Processing helix chain 'F' and resid 189 through 203 removed outlier: 3.934A pdb=" N LYS F 203 " --> pdb=" O ILE F 199 " (cutoff:3.500A) Processing helix chain 'F' and resid 208 through 224 removed outlier: 3.787A pdb=" N LYS F 212 " --> pdb=" O SER F 208 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N ASN F 224 " --> pdb=" O VAL F 220 " (cutoff:3.500A) Processing helix chain 'K' and resid 4 through 19 Processing helix chain 'K' and resid 38 through 51 Processing helix chain 'K' and resid 69 through 80 Processing helix chain 'M' and resid 26 through 38 removed outlier: 3.958A pdb=" N VAL M 31 " --> pdb=" O ALA M 27 " (cutoff:3.500A) Processing helix chain 'M' and resid 44 through 53 Processing helix chain 'M' and resid 69 through 81 Processing helix chain 'M' and resid 93 through 101 Processing helix chain 'M' and resid 131 through 142 Processing helix chain 'P' and resid 22 through 27 removed outlier: 4.328A pdb=" N GLU P 27 " --> pdb=" O GLU P 23 " (cutoff:3.500A) Processing helix chain 'P' and resid 30 through 37 Processing helix chain 'P' and resid 38 through 47 removed outlier: 3.528A pdb=" N ARG P 47 " --> pdb=" O ARG P 43 " (cutoff:3.500A) Processing helix chain 'P' and resid 53 through 66 removed outlier: 3.845A pdb=" N LYS P 58 " --> pdb=" O ALA P 54 " (cutoff:3.500A) Processing helix chain 'P' and resid 86 through 90 removed outlier: 3.630A pdb=" N ILE P 90 " --> pdb=" O PRO P 87 " (cutoff:3.500A) Processing helix chain 'P' and resid 108 through 112 removed outlier: 4.107A pdb=" N LEU P 112 " --> pdb=" O PRO P 109 " (cutoff:3.500A) Processing helix chain 'P' and resid 115 through 120 removed outlier: 3.745A pdb=" N SER P 120 " --> pdb=" O GLY P 117 " (cutoff:3.500A) Processing helix chain 'Q' and resid 37 through 39 No H-bonds generated for 'chain 'Q' and resid 37 through 39' Processing helix chain 'Q' and resid 44 through 50 Processing helix chain 'Q' and resid 51 through 54 Processing helix chain 'Q' and resid 73 through 96 Processing helix chain 'Q' and resid 98 through 111 Processing helix chain 'S' and resid 27 through 32 Processing helix chain 'S' and resid 33 through 35 No H-bonds generated for 'chain 'S' and resid 33 through 35' Processing helix chain 'S' and resid 39 through 50 Processing helix chain 'S' and resid 62 through 74 removed outlier: 4.030A pdb=" N LEU S 66 " --> pdb=" O THR S 62 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N GLN S 74 " --> pdb=" O VAL S 70 " (cutoff:3.500A) Processing helix chain 'S' and resid 76 through 80 Processing helix chain 'S' and resid 104 through 120 removed outlier: 3.741A pdb=" N LYS S 117 " --> pdb=" O LEU S 113 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N LYS S 118 " --> pdb=" O GLU S 114 " (cutoff:3.500A) Processing helix chain 'S' and resid 121 through 129 removed outlier: 4.107A pdb=" N TRP S 129 " --> pdb=" O ILE S 125 " (cutoff:3.500A) Processing helix chain 'T' and resid 10 through 26 removed outlier: 3.740A pdb=" N PHE T 14 " --> pdb=" O ALA T 10 " (cutoff:3.500A) Processing helix chain 'T' and resid 53 through 67 Processing helix chain 'T' and resid 72 through 81 Processing helix chain 'T' and resid 97 through 111 removed outlier: 3.645A pdb=" N ASN T 101 " --> pdb=" O SER T 97 " (cutoff:3.500A) Processing helix chain 'T' and resid 125 through 142 Processing helix chain 'U' and resid 30 through 48 removed outlier: 4.082A pdb=" N HIS U 48 " --> pdb=" O ASN U 44 " (cutoff:3.500A) Processing helix chain 'U' and resid 96 through 106 Processing helix chain 'Z' and resid 44 through 52 removed outlier: 3.959A pdb=" N ASP Z 48 " --> pdb=" O GLN Z 44 " (cutoff:3.500A) Processing helix chain 'Z' and resid 61 through 67 Processing helix chain 'Z' and resid 75 through 85 930 hydrogen bonds defined for protein. 2736 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 1198 hydrogen bonds 1882 hydrogen bond angles 0 basepair planarities 492 basepair parallelities 907 stacking parallelities Total time for adding SS restraints: 45.29 Time building geometry restraints manager: 29.82 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: 8834 1.32 - 1.44: 30344 1.44 - 1.57: 34927 1.57 - 1.69: 3497 1.69 - 1.82: 121 Bond restraints: 77723 Sorted by residual: bond pdb=" C LEU C 225 " pdb=" N THR C 226 " ideal model delta sigma weight residual 1.331 1.195 0.136 2.07e-02 2.33e+03 4.29e+01 bond pdb=" C ALA H 12 " pdb=" N PRO H 13 " ideal model delta sigma weight residual 1.330 1.376 -0.046 1.25e-02 6.40e+03 1.38e+01 bond pdb=" CB TRP T 53 " pdb=" CG TRP T 53 " ideal model delta sigma weight residual 1.498 1.610 -0.112 3.10e-02 1.04e+03 1.31e+01 bond pdb=" C SER H 31 " pdb=" N PRO H 32 " ideal model delta sigma weight residual 1.335 1.381 -0.046 1.36e-02 5.41e+03 1.13e+01 bond pdb=" C LEU W 93 " pdb=" N LEU W 94 " ideal model delta sigma weight residual 1.332 1.284 0.048 1.46e-02 4.69e+03 1.06e+01 ... (remaining 77718 not shown) Histogram of bond angle deviations from ideal: 97.33 - 107.99: 17328 107.99 - 118.65: 55438 118.65 - 129.31: 39180 129.31 - 139.97: 1531 139.97 - 150.63: 1 Bond angle restraints: 113478 Sorted by residual: angle pdb=" C PRO Q 124 " pdb=" N GLU Q 125 " pdb=" CA GLU Q 125 " ideal model delta sigma weight residual 120.94 150.63 -29.69 1.90e+00 2.77e-01 2.44e+02 angle pdb=" C GLU Q 40 " pdb=" N PRO Q 41 " pdb=" CA PRO Q 41 " ideal model delta sigma weight residual 119.84 136.37 -16.53 1.25e+00 6.40e-01 1.75e+02 angle pdb=" C ALA N 22 " pdb=" N PRO N 23 " pdb=" CA PRO N 23 " ideal model delta sigma weight residual 119.84 133.34 -13.50 1.25e+00 6.40e-01 1.17e+02 angle pdb=" N MET K 3 " pdb=" CA MET K 3 " pdb=" C MET K 3 " ideal model delta sigma weight residual 108.25 97.67 10.58 1.16e+00 7.43e-01 8.33e+01 angle pdb=" N VAL Y 47 " pdb=" CA VAL Y 47 " pdb=" C VAL Y 47 " ideal model delta sigma weight residual 113.53 105.36 8.17 9.80e-01 1.04e+00 6.95e+01 ... (remaining 113473 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.99: 43996 35.99 - 71.98: 4576 71.98 - 107.97: 481 107.97 - 143.96: 38 143.96 - 179.95: 54 Dihedral angle restraints: 49145 sinusoidal: 36140 harmonic: 13005 Sorted by residual: dihedral pdb=" CA GLU Q 40 " pdb=" C GLU Q 40 " pdb=" N PRO Q 41 " pdb=" CA PRO Q 41 " ideal model delta harmonic sigma weight residual 180.00 57.62 122.38 0 5.00e+00 4.00e-02 5.99e+02 dihedral pdb=" CA ALA N 22 " pdb=" C ALA N 22 " pdb=" N PRO N 23 " pdb=" CA PRO N 23 " ideal model delta harmonic sigma weight residual 180.00 82.78 97.22 0 5.00e+00 4.00e-02 3.78e+02 dihedral pdb=" CA ASN V 81 " pdb=" C ASN V 81 " pdb=" N VAL V 82 " pdb=" CA VAL V 82 " ideal model delta harmonic sigma weight residual -180.00 -107.75 -72.25 0 5.00e+00 4.00e-02 2.09e+02 ... (remaining 49142 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.108: 13176 0.108 - 0.216: 954 0.216 - 0.324: 77 0.324 - 0.432: 23 0.432 - 0.539: 8 Chirality restraints: 14238 Sorted by residual: chirality pdb=" CG LEU G 68 " pdb=" CB LEU G 68 " pdb=" CD1 LEU G 68 " pdb=" CD2 LEU G 68 " both_signs ideal model delta sigma weight residual False -2.59 -2.05 -0.54 2.00e-01 2.50e+01 7.27e+00 chirality pdb=" C3' C 2 131 " pdb=" C4' C 2 131 " pdb=" O3' C 2 131 " pdb=" C2' C 2 131 " both_signs ideal model delta sigma weight residual False -2.74 -2.21 -0.53 2.00e-01 2.50e+01 7.05e+00 chirality pdb=" C1' C 2 827 " pdb=" O4' C 2 827 " pdb=" C2' C 2 827 " pdb=" N1 C 2 827 " both_signs ideal model delta sigma weight residual False 2.47 1.94 0.52 2.00e-01 2.50e+01 6.88e+00 ... (remaining 14235 not shown) Planarity restraints: 7955 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL R 85 " 0.075 5.00e-02 4.00e+02 1.14e-01 2.09e+01 pdb=" N PRO R 86 " -0.197 5.00e-02 4.00e+02 pdb=" CA PRO R 86 " 0.053 5.00e-02 4.00e+02 pdb=" CD PRO R 86 " 0.069 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA SER F 57 " -0.020 2.00e-02 2.50e+03 4.14e-02 1.72e+01 pdb=" C SER F 57 " 0.072 2.00e-02 2.50e+03 pdb=" O SER F 57 " -0.027 2.00e-02 2.50e+03 pdb=" N LEU F 58 " -0.024 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C VAL H 64 " -0.067 5.00e-02 4.00e+02 1.01e-01 1.65e+01 pdb=" N PRO H 65 " 0.175 5.00e-02 4.00e+02 pdb=" CA PRO H 65 " -0.053 5.00e-02 4.00e+02 pdb=" CD PRO H 65 " -0.056 5.00e-02 4.00e+02 ... (remaining 7952 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.76: 11741 2.76 - 3.29: 66141 3.29 - 3.83: 151374 3.83 - 4.36: 174643 4.36 - 4.90: 245457 Nonbonded interactions: 649356 Sorted by model distance: nonbonded pdb=" OP2 C 21284 " pdb=" O2' C 21623 " model vdw 2.220 2.440 nonbonded pdb=" O2' A 2 992 " pdb=" O2 U 21785 " model vdw 2.221 2.440 nonbonded pdb=" OG SER Q 34 " pdb=" O ARG T 7 " model vdw 2.228 2.440 nonbonded pdb=" O2' U 2 886 " pdb=" O VAL O 121 " model vdw 2.232 2.440 nonbonded pdb=" OP1 U 21561 " pdb=" O2' C 21599 " model vdw 2.232 2.440 ... (remaining 649351 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=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 9.850 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: 0.080 Extract box with map and model: 14.140 Check model and map are aligned: 0.810 Set scattering table: 0.500 Process input model: 174.860 Find NCS groups from input model: 1.460 Set up NCS constraints: 0.170 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.140 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 204.020 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7873 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 0.136 77723 Z= 0.416 Angle : 1.267 29.695 113478 Z= 0.676 Chirality : 0.061 0.539 14238 Planarity : 0.008 0.114 7955 Dihedral : 23.457 179.954 40747 Min Nonbonded Distance : 2.220 Molprobity Statistics. All-atom Clashscore : 9.10 Ramachandran Plot: Outliers : 1.24 % Allowed : 11.92 % Favored : 86.84 % Rotamer: Outliers : 1.35 % Allowed : 6.37 % Favored : 92.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.81 % Cis-general : 0.07 % Twisted Proline : 7.30 % Twisted General : 1.63 % 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: -4.17 (0.10), residues: 4438 helix: -2.48 (0.11), residues: 1356 sheet: -2.10 (0.17), residues: 717 loop : -3.24 (0.11), residues: 2365 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.046 0.004 TRP M 126 HIS 0.020 0.003 HIS g 195 PHE 0.044 0.004 PHE I 21 TYR 0.038 0.004 TYR J 19 ARG 0.035 0.001 ARG C 91 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8876 Ramachandran restraints generated. 4438 Oldfield, 0 Emsley, 4438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8876 Ramachandran restraints generated. 4438 Oldfield, 0 Emsley, 4438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 541 residues out of total 3832 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 490 time to evaluate : 3.989 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 81 MET cc_start: 0.8976 (mmt) cc_final: 0.8670 (mmm) REVERT: E 206 ASP cc_start: 0.7857 (OUTLIER) cc_final: 0.7382 (m-30) REVERT: H 20 VAL cc_start: 0.8962 (t) cc_final: 0.8384 (m) REVERT: H 85 PHE cc_start: 0.5004 (t80) cc_final: 0.4759 (m-10) REVERT: I 159 GLN cc_start: 0.9164 (mt0) cc_final: 0.8893 (mt0) REVERT: J 96 VAL cc_start: 0.8659 (m) cc_final: 0.8441 (t) REVERT: L 101 GLU cc_start: 0.8472 (pt0) cc_final: 0.8223 (pt0) REVERT: N 33 VAL cc_start: 0.9216 (m) cc_final: 0.8985 (p) REVERT: N 50 ILE cc_start: 0.8583 (OUTLIER) cc_final: 0.8381 (mp) REVERT: N 83 GLU cc_start: 0.7091 (pt0) cc_final: 0.6773 (pm20) REVERT: R 16 LEU cc_start: 0.8749 (mt) cc_final: 0.8458 (mt) REVERT: R 59 LYS cc_start: 0.4252 (tttm) cc_final: 0.4049 (mttp) REVERT: R 108 ASP cc_start: 0.7986 (m-30) cc_final: 0.6947 (m-30) REVERT: W 92 ASN cc_start: 0.8184 (m-40) cc_final: 0.7863 (m-40) REVERT: X 62 LYS cc_start: 0.7872 (mttt) cc_final: 0.7453 (mttm) REVERT: Y 125 LEU cc_start: 0.8884 (tp) cc_final: 0.8683 (tp) REVERT: e 25 GLU cc_start: 0.7133 (tt0) cc_final: 0.6407 (tm-30) REVERT: F 84 LYS cc_start: -0.2945 (OUTLIER) cc_final: -0.4312 (mmtm) REVERT: F 98 MET cc_start: -0.3155 (ptt) cc_final: -0.4004 (ptp) REVERT: K 1 MET cc_start: -0.3005 (ttt) cc_final: -0.3210 (ttt) REVERT: K 3 MET cc_start: 0.3912 (ptp) cc_final: 0.3666 (ptp) REVERT: M 29 LYS cc_start: 0.8369 (ttpt) cc_final: 0.8142 (tptt) REVERT: P 36 LEU cc_start: 0.4927 (OUTLIER) cc_final: 0.3914 (pt) REVERT: P 49 MET cc_start: 0.7859 (mtt) cc_final: 0.7624 (mmm) REVERT: S 72 ILE cc_start: 0.5706 (mt) cc_final: 0.5505 (tt) REVERT: S 91 ASP cc_start: 0.5605 (t0) cc_final: 0.5235 (t0) REVERT: T 67 MET cc_start: 0.7904 (mtt) cc_final: 0.7529 (mtt) REVERT: Z 42 LEU cc_start: -0.0016 (OUTLIER) cc_final: -0.0489 (pp) REVERT: Z 58 ARG cc_start: 0.7502 (tpt170) cc_final: 0.6802 (mmt180) REVERT: c 57 MET cc_start: 0.3311 (ttt) cc_final: 0.2681 (mtp) REVERT: f 123 ASN cc_start: 0.5536 (OUTLIER) cc_final: 0.5090 (t0) REVERT: g 111 MET cc_start: 0.3334 (mmm) cc_final: 0.3076 (mtm) REVERT: g 231 MET cc_start: 0.5392 (mtp) cc_final: 0.4876 (mtm) outliers start: 51 outliers final: 9 residues processed: 536 average time/residue: 0.8187 time to fit residues: 699.3399 Evaluate side-chains 228 residues out of total 3832 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 213 time to evaluate : 3.926 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 181 VAL Chi-restraints excluded: chain E residue 206 ASP Chi-restraints excluded: chain J residue 99 LEU Chi-restraints excluded: chain N residue 50 ILE Chi-restraints excluded: chain N residue 125 LEU Chi-restraints excluded: chain V residue 82 VAL Chi-restraints excluded: chain Y residue 35 VAL Chi-restraints excluded: chain d residue 28 THR Chi-restraints excluded: chain D residue 175 VAL Chi-restraints excluded: chain F residue 84 LYS Chi-restraints excluded: chain P residue 36 LEU Chi-restraints excluded: chain T residue 135 ILE Chi-restraints excluded: chain Z residue 42 LEU Chi-restraints excluded: chain Z residue 69 LEU Chi-restraints excluded: chain f residue 123 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 613 random chunks: chunk 517 optimal weight: 7.9990 chunk 464 optimal weight: 0.1980 chunk 257 optimal weight: 10.0000 chunk 158 optimal weight: 50.0000 chunk 313 optimal weight: 0.7980 chunk 248 optimal weight: 3.9990 chunk 480 optimal weight: 8.9990 chunk 185 optimal weight: 2.9990 chunk 292 optimal weight: 2.9990 chunk 357 optimal weight: 0.2980 chunk 556 optimal weight: 2.9990 overall best weight: 1.4584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 23 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 46 HIS A 49 ASN ** A 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 94 GLN C 209 ASN E 98 ASN E 188 ASN ** G 139 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 185 GLN G 190 GLN G 201 GLN H 29 ASN ** H 71 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 122 HIS I 32 GLN I 64 ASN I 103 GLN I 159 GLN L 14 GLN L 18 HIS ** N 5 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 58 HIS N 105 ASN ** R 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 7 GLN ** V 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 80 ASN X 10 ASN X 27 ASN X 79 ASN ** Y 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 77 ASN d 48 ASN e 5 HIS e 17 GLN D 67 ASN D 111 ASN F 34 GLN F 104 ASN K 9 ASN M 70 ASN M 125 ASN P 103 ASN ** Q 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 44 ASN S 78 HIS ** T 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 33 GLN ** Z 95 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Z 98 GLN f 123 ASN f 135 HIS ** g 174 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** g 182 ASN g 187 GLN Total number of N/Q/H flips: 44 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7823 moved from start: 0.1891 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 77723 Z= 0.176 Angle : 0.734 11.993 113478 Z= 0.381 Chirality : 0.041 0.417 14238 Planarity : 0.006 0.096 7955 Dihedral : 24.914 179.785 31985 Min Nonbonded Distance : 2.032 Molprobity Statistics. All-atom Clashscore : 17.42 Ramachandran Plot: Outliers : 0.74 % Allowed : 11.29 % Favored : 87.97 % Rotamer: Outliers : 2.55 % Allowed : 11.34 % Favored : 86.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.81 % Cis-general : 0.07 % Twisted Proline : 3.93 % Twisted General : 0.61 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.02 (0.11), residues: 4438 helix: -0.97 (0.13), residues: 1406 sheet: -1.55 (0.19), residues: 685 loop : -2.90 (0.12), residues: 2347 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP V 83 HIS 0.011 0.001 HIS J 133 PHE 0.018 0.002 PHE I 21 TYR 0.021 0.002 TYR J 19 ARG 0.008 0.001 ARG J 175 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8876 Ramachandran restraints generated. 4438 Oldfield, 0 Emsley, 4438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8876 Ramachandran restraints generated. 4438 Oldfield, 0 Emsley, 4438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 381 residues out of total 3832 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 96 poor density : 285 time to evaluate : 4.002 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 196 GLU cc_start: 0.8907 (mt-10) cc_final: 0.8622 (pt0) REVERT: C 79 GLU cc_start: 0.7777 (mm-30) cc_final: 0.7426 (mp0) REVERT: C 81 MET cc_start: 0.8923 (mmt) cc_final: 0.8706 (mmm) REVERT: H 46 ILE cc_start: 0.8269 (tp) cc_final: 0.7946 (tp) REVERT: H 67 LEU cc_start: 0.5961 (mt) cc_final: 0.5529 (mt) REVERT: I 159 GLN cc_start: 0.9074 (mt0) cc_final: 0.8863 (mt0) REVERT: L 55 ASP cc_start: 0.7803 (t0) cc_final: 0.7496 (t0) REVERT: N 138 ASN cc_start: 0.8115 (p0) cc_final: 0.7774 (p0) REVERT: W 65 LEU cc_start: 0.7891 (OUTLIER) cc_final: 0.7546 (pp) REVERT: X 18 HIS cc_start: 0.8343 (OUTLIER) cc_final: 0.8100 (t-90) REVERT: X 60 GLU cc_start: 0.7780 (tp30) cc_final: 0.7575 (tp30) REVERT: X 112 LYS cc_start: 0.7620 (mmtm) cc_final: 0.7396 (tttm) REVERT: Y 35 VAL cc_start: 0.6540 (OUTLIER) cc_final: 0.6328 (p) REVERT: b 43 ILE cc_start: 0.5109 (mp) cc_final: 0.4851 (mm) REVERT: e 25 GLU cc_start: 0.6793 (tt0) cc_final: 0.6140 (tm-30) REVERT: F 84 LYS cc_start: -0.2738 (OUTLIER) cc_final: -0.4257 (mmtm) REVERT: F 98 MET cc_start: -0.3443 (ptt) cc_final: -0.4493 (ptp) REVERT: K 1 MET cc_start: -0.3793 (ttt) cc_final: -0.4030 (ttt) REVERT: K 3 MET cc_start: 0.4278 (ptp) cc_final: 0.3934 (ptp) REVERT: P 49 MET cc_start: 0.7946 (mtt) cc_final: 0.7666 (mmm) REVERT: Q 8 GLN cc_start: 0.4901 (tt0) cc_final: 0.4453 (tm-30) REVERT: S 21 ASN cc_start: 0.6962 (t0) cc_final: 0.6654 (t0) REVERT: S 91 ASP cc_start: 0.5923 (t0) cc_final: 0.5543 (m-30) REVERT: Z 102 THR cc_start: 0.7104 (t) cc_final: 0.6812 (m) REVERT: c 57 MET cc_start: 0.3629 (ttt) cc_final: 0.3009 (mtp) REVERT: g 231 MET cc_start: 0.5393 (mtp) cc_final: 0.4805 (mtm) outliers start: 96 outliers final: 37 residues processed: 367 average time/residue: 0.7627 time to fit residues: 466.3495 Evaluate side-chains 234 residues out of total 3832 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 193 time to evaluate : 3.944 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 180 THR Chi-restraints excluded: chain B residue 207 LEU Chi-restraints excluded: chain B residue 215 VAL Chi-restraints excluded: chain C residue 111 VAL Chi-restraints excluded: chain C residue 156 THR Chi-restraints excluded: chain C residue 226 THR Chi-restraints excluded: chain E residue 180 LEU Chi-restraints excluded: chain E residue 181 VAL Chi-restraints excluded: chain E residue 236 ILE Chi-restraints excluded: chain G residue 29 ASP Chi-restraints excluded: chain G residue 43 ASP Chi-restraints excluded: chain G residue 68 LEU Chi-restraints excluded: chain G residue 170 THR Chi-restraints excluded: chain J residue 46 SER Chi-restraints excluded: chain J residue 99 LEU Chi-restraints excluded: chain J residue 147 MET Chi-restraints excluded: chain R residue 40 THR Chi-restraints excluded: chain V residue 69 LEU Chi-restraints excluded: chain V residue 82 VAL Chi-restraints excluded: chain W residue 65 LEU Chi-restraints excluded: chain W residue 93 LEU Chi-restraints excluded: chain X residue 18 HIS Chi-restraints excluded: chain Y residue 35 VAL Chi-restraints excluded: chain Y residue 64 PHE Chi-restraints excluded: chain b residue 30 SER Chi-restraints excluded: chain b residue 46 VAL Chi-restraints excluded: chain e residue 26 LYS Chi-restraints excluded: chain D residue 39 VAL Chi-restraints excluded: chain D residue 175 VAL Chi-restraints excluded: chain F residue 25 LEU Chi-restraints excluded: chain F residue 69 PHE Chi-restraints excluded: chain F residue 84 LYS Chi-restraints excluded: chain K residue 55 VAL Chi-restraints excluded: chain K residue 74 GLU Chi-restraints excluded: chain P residue 14 THR Chi-restraints excluded: chain S residue 93 THR Chi-restraints excluded: chain S residue 98 TYR Chi-restraints excluded: chain T residue 135 ILE Chi-restraints excluded: chain Z residue 69 LEU Chi-restraints excluded: chain f residue 117 LEU Chi-restraints excluded: chain g residue 283 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 613 random chunks: chunk 309 optimal weight: 1.9990 chunk 172 optimal weight: 50.0000 chunk 463 optimal weight: 9.9990 chunk 379 optimal weight: 3.9990 chunk 153 optimal weight: 50.0000 chunk 557 optimal weight: 8.9990 chunk 602 optimal weight: 6.9990 chunk 496 optimal weight: 40.0000 chunk 553 optimal weight: 9.9990 chunk 190 optimal weight: 5.9990 chunk 447 optimal weight: 20.0000 overall best weight: 5.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 211 HIS ** C 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 209 ASN ** E 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 258 GLN ** H 71 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 88 ASN I 159 GLN J 74 ASN J 155 HIS L 14 GLN ** N 5 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 79 ASN e 5 HIS D 74 GLN D 165 ASN D 179 GLN F 103 ASN F 127 GLN K 9 ASN ** M 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 8 GLN Q 21 HIS ** Q 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 48 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 95 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** g 174 ASN g 187 GLN ** g 268 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7939 moved from start: 0.2664 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.094 77723 Z= 0.323 Angle : 0.792 14.071 113478 Z= 0.404 Chirality : 0.044 0.383 14238 Planarity : 0.006 0.096 7955 Dihedral : 24.870 178.819 31972 Min Nonbonded Distance : 2.031 Molprobity Statistics. All-atom Clashscore : 23.54 Ramachandran Plot: Outliers : 0.68 % Allowed : 12.84 % Favored : 86.48 % Rotamer: Outliers : 4.04 % Allowed : 12.18 % Favored : 83.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.81 % Cis-general : 0.07 % Twisted Proline : 4.49 % Twisted General : 0.58 % 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: -2.82 (0.12), residues: 4438 helix: -0.63 (0.13), residues: 1412 sheet: -1.65 (0.19), residues: 700 loop : -2.84 (0.12), residues: 2326 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP N 139 HIS 0.008 0.002 HIS K 32 PHE 0.032 0.002 PHE H 24 TYR 0.020 0.002 TYR L 93 ARG 0.012 0.001 ARG U 85 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8876 Ramachandran restraints generated. 4438 Oldfield, 0 Emsley, 4438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8876 Ramachandran restraints generated. 4438 Oldfield, 0 Emsley, 4438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 356 residues out of total 3832 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 152 poor density : 204 time to evaluate : 4.043 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 79 GLU cc_start: 0.7844 (mm-30) cc_final: 0.7486 (mm-30) REVERT: C 113 LEU cc_start: 0.9257 (OUTLIER) cc_final: 0.9011 (tm) REVERT: E 38 LEU cc_start: 0.9209 (OUTLIER) cc_final: 0.8984 (tt) REVERT: E 164 LEU cc_start: 0.9090 (OUTLIER) cc_final: 0.8740 (tp) REVERT: E 200 ARG cc_start: 0.6879 (OUTLIER) cc_final: 0.6159 (tpm170) REVERT: H 67 LEU cc_start: 0.5655 (mt) cc_final: 0.5168 (mt) REVERT: I 103 GLN cc_start: 0.7691 (OUTLIER) cc_final: 0.7487 (mm110) REVERT: N 90 TYR cc_start: 0.7727 (m-10) cc_final: 0.7496 (m-10) REVERT: N 138 ASN cc_start: 0.8278 (p0) cc_final: 0.7781 (p0) REVERT: R 63 LYS cc_start: 0.5498 (pptt) cc_final: 0.5088 (pttm) REVERT: X 18 HIS cc_start: 0.8373 (OUTLIER) cc_final: 0.8059 (t-90) REVERT: Y 29 HIS cc_start: 0.8063 (OUTLIER) cc_final: 0.7663 (p90) REVERT: Y 102 LYS cc_start: 0.8457 (OUTLIER) cc_final: 0.8189 (pttm) REVERT: b 32 PHE cc_start: 0.6814 (OUTLIER) cc_final: 0.6333 (m-10) REVERT: e 25 GLU cc_start: 0.6970 (tt0) cc_final: 0.6246 (tm-30) REVERT: e 55 ARG cc_start: 0.7099 (tpm170) cc_final: 0.6256 (mmm160) REVERT: D 150 MET cc_start: -0.0949 (mtt) cc_final: -0.1324 (tpt) REVERT: D 177 MET cc_start: 0.0955 (mmm) cc_final: 0.0603 (mmt) REVERT: F 84 LYS cc_start: -0.2400 (OUTLIER) cc_final: -0.4162 (mmtm) REVERT: K 1 MET cc_start: -0.2336 (ttt) cc_final: -0.2657 (ttp) REVERT: P 34 VAL cc_start: -0.0270 (OUTLIER) cc_final: -0.1033 (t) REVERT: P 35 LYS cc_start: 0.8166 (pttm) cc_final: 0.7858 (mmtm) REVERT: P 57 MET cc_start: 0.4447 (mtt) cc_final: 0.4126 (mmt) REVERT: P 61 ARG cc_start: 0.7090 (ttm110) cc_final: 0.6830 (mmp80) REVERT: P 88 GLU cc_start: 0.4111 (OUTLIER) cc_final: 0.3860 (pt0) REVERT: Q 8 GLN cc_start: 0.5470 (tt0) cc_final: 0.4665 (tm-30) REVERT: S 21 ASN cc_start: 0.7030 (t0) cc_final: 0.6756 (t0) REVERT: S 91 ASP cc_start: 0.5836 (t0) cc_final: 0.5622 (m-30) REVERT: c 57 MET cc_start: 0.3889 (ttt) cc_final: 0.3320 (mtp) REVERT: f 148 TYR cc_start: 0.8317 (t80) cc_final: 0.8094 (t80) REVERT: g 111 MET cc_start: 0.4082 (mmm) cc_final: 0.3391 (mtp) REVERT: g 165 ASP cc_start: 0.3652 (OUTLIER) cc_final: 0.3420 (t70) REVERT: g 231 MET cc_start: 0.5184 (mtp) cc_final: 0.4395 (mtm) outliers start: 152 outliers final: 74 residues processed: 337 average time/residue: 0.7299 time to fit residues: 414.9548 Evaluate side-chains 261 residues out of total 3832 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 87 poor density : 174 time to evaluate : 4.050 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 THR Chi-restraints excluded: chain A residue 32 HIS Chi-restraints excluded: chain A residue 172 LEU Chi-restraints excluded: chain B residue 180 THR Chi-restraints excluded: chain B residue 207 LEU Chi-restraints excluded: chain B residue 215 VAL Chi-restraints excluded: chain C residue 86 VAL Chi-restraints excluded: chain C residue 108 ASN Chi-restraints excluded: chain C residue 111 VAL Chi-restraints excluded: chain C residue 113 LEU Chi-restraints excluded: chain C residue 156 THR Chi-restraints excluded: chain C residue 196 VAL Chi-restraints excluded: chain C residue 226 THR Chi-restraints excluded: chain C residue 245 ASP Chi-restraints excluded: chain E residue 38 LEU Chi-restraints excluded: chain E residue 65 LEU Chi-restraints excluded: chain E residue 96 ASN Chi-restraints excluded: chain E residue 164 LEU Chi-restraints excluded: chain E residue 180 LEU Chi-restraints excluded: chain E residue 181 VAL Chi-restraints excluded: chain E residue 200 ARG Chi-restraints excluded: chain E residue 222 LEU Chi-restraints excluded: chain G residue 29 ASP Chi-restraints excluded: chain G residue 43 ASP Chi-restraints excluded: chain G residue 68 LEU Chi-restraints excluded: chain G residue 96 SER Chi-restraints excluded: chain G residue 170 THR Chi-restraints excluded: chain H residue 25 VAL Chi-restraints excluded: chain H residue 147 ASN Chi-restraints excluded: chain H residue 154 LEU Chi-restraints excluded: chain I residue 58 LEU Chi-restraints excluded: chain I residue 103 GLN Chi-restraints excluded: chain I residue 193 LEU Chi-restraints excluded: chain R residue 8 THR Chi-restraints excluded: chain R residue 40 THR Chi-restraints excluded: chain V residue 79 LEU Chi-restraints excluded: chain W residue 26 LEU Chi-restraints excluded: chain W residue 65 LEU Chi-restraints excluded: chain W residue 93 LEU Chi-restraints excluded: chain X residue 18 HIS Chi-restraints excluded: chain X residue 76 LEU Chi-restraints excluded: chain X residue 90 ASP Chi-restraints excluded: chain Y residue 29 HIS Chi-restraints excluded: chain Y residue 47 VAL Chi-restraints excluded: chain Y residue 53 ASP Chi-restraints excluded: chain Y residue 64 PHE Chi-restraints excluded: chain Y residue 102 LYS Chi-restraints excluded: chain Y residue 118 ILE Chi-restraints excluded: chain b residue 7 LEU Chi-restraints excluded: chain b residue 8 LEU Chi-restraints excluded: chain b residue 15 GLU Chi-restraints excluded: chain b residue 30 SER Chi-restraints excluded: chain b residue 32 PHE Chi-restraints excluded: chain b residue 46 VAL Chi-restraints excluded: chain b residue 61 THR Chi-restraints excluded: chain b residue 67 THR Chi-restraints excluded: chain e residue 51 ASN Chi-restraints excluded: chain D residue 39 VAL Chi-restraints excluded: chain D residue 175 VAL Chi-restraints excluded: chain D residue 189 MET Chi-restraints excluded: chain F residue 25 LEU Chi-restraints excluded: chain F residue 69 PHE Chi-restraints excluded: chain F residue 84 LYS Chi-restraints excluded: chain K residue 74 GLU Chi-restraints excluded: chain M residue 66 VAL Chi-restraints excluded: chain M residue 71 ILE Chi-restraints excluded: chain M residue 91 VAL Chi-restraints excluded: chain M residue 97 LEU Chi-restraints excluded: chain P residue 14 THR Chi-restraints excluded: chain P residue 22 LEU Chi-restraints excluded: chain P residue 34 VAL Chi-restraints excluded: chain P residue 88 GLU Chi-restraints excluded: chain P residue 121 ILE Chi-restraints excluded: chain Q residue 97 VAL Chi-restraints excluded: chain Q residue 136 SER Chi-restraints excluded: chain S residue 3 LEU Chi-restraints excluded: chain S residue 93 THR Chi-restraints excluded: chain S residue 98 TYR Chi-restraints excluded: chain T residue 6 VAL Chi-restraints excluded: chain T residue 135 ILE Chi-restraints excluded: chain Z residue 57 TYR Chi-restraints excluded: chain Z residue 69 LEU Chi-restraints excluded: chain c residue 15 VAL Chi-restraints excluded: chain f residue 117 LEU Chi-restraints excluded: chain g residue 79 TYR Chi-restraints excluded: chain g residue 165 ASP Chi-restraints excluded: chain g residue 283 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 613 random chunks: chunk 550 optimal weight: 30.0000 chunk 419 optimal weight: 4.9990 chunk 289 optimal weight: 20.0000 chunk 61 optimal weight: 8.9990 chunk 266 optimal weight: 0.5980 chunk 374 optimal weight: 1.9990 chunk 559 optimal weight: 7.9990 chunk 592 optimal weight: 20.0000 chunk 292 optimal weight: 6.9990 chunk 530 optimal weight: 0.0030 chunk 159 optimal weight: 40.0000 overall best weight: 2.9196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 49 ASN ** B 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 77 GLN C 209 ASN ** E 258 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 139 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 71 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 159 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 5 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** e 5 HIS F 103 ASN ** Q 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 129 GLN ** U 48 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 159 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** g 196 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7879 moved from start: 0.3034 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 77723 Z= 0.200 Angle : 0.679 11.287 113478 Z= 0.347 Chirality : 0.040 0.338 14238 Planarity : 0.005 0.094 7955 Dihedral : 24.652 179.995 31968 Min Nonbonded Distance : 2.050 Molprobity Statistics. All-atom Clashscore : 20.21 Ramachandran Plot: Outliers : 0.54 % Allowed : 12.10 % Favored : 87.36 % Rotamer: Outliers : 3.24 % Allowed : 14.15 % Favored : 82.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.81 % Cis-general : 0.09 % Twisted Proline : 3.93 % Twisted General : 0.42 % 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: -2.44 (0.12), residues: 4438 helix: -0.11 (0.13), residues: 1418 sheet: -1.49 (0.19), residues: 710 loop : -2.74 (0.12), residues: 2310 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP X 24 HIS 0.008 0.001 HIS J 133 PHE 0.036 0.002 PHE H 24 TYR 0.014 0.001 TYR b 31 ARG 0.006 0.000 ARG P 61 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8876 Ramachandran restraints generated. 4438 Oldfield, 0 Emsley, 4438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8876 Ramachandran restraints generated. 4438 Oldfield, 0 Emsley, 4438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 319 residues out of total 3832 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 122 poor density : 197 time to evaluate : 3.972 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 87 MET cc_start: 0.8477 (tpp) cc_final: 0.8060 (tpp) REVERT: E 164 LEU cc_start: 0.9062 (OUTLIER) cc_final: 0.8790 (tp) REVERT: E 200 ARG cc_start: 0.6749 (OUTLIER) cc_final: 0.5970 (tpm170) REVERT: G 76 LEU cc_start: 0.9016 (OUTLIER) cc_final: 0.8728 (tm) REVERT: H 67 LEU cc_start: 0.6144 (mt) cc_final: 0.5917 (mt) REVERT: N 83 GLU cc_start: 0.6878 (pt0) cc_final: 0.6468 (pm20) REVERT: N 138 ASN cc_start: 0.8280 (p0) cc_final: 0.7828 (p0) REVERT: R 58 MET cc_start: -0.1671 (mmm) cc_final: -0.1936 (mmm) REVERT: R 63 LYS cc_start: 0.5882 (pptt) cc_final: 0.5421 (pttm) REVERT: X 18 HIS cc_start: 0.8245 (OUTLIER) cc_final: 0.7960 (t-90) REVERT: X 95 PHE cc_start: 0.8093 (OUTLIER) cc_final: 0.7682 (m-80) REVERT: Y 29 HIS cc_start: 0.7958 (OUTLIER) cc_final: 0.7651 (p90) REVERT: b 47 PHE cc_start: 0.7830 (t80) cc_final: 0.7602 (t80) REVERT: e 25 GLU cc_start: 0.6904 (tt0) cc_final: 0.6196 (tm-30) REVERT: D 127 MET cc_start: 0.7704 (mmp) cc_final: 0.7238 (mmm) REVERT: D 150 MET cc_start: -0.0972 (mtt) cc_final: -0.1664 (tpt) REVERT: D 177 MET cc_start: 0.1152 (mmm) cc_final: 0.0815 (mmt) REVERT: F 84 LYS cc_start: -0.2168 (OUTLIER) cc_final: -0.3911 (mmtm) REVERT: P 36 LEU cc_start: 0.4733 (OUTLIER) cc_final: 0.3970 (pt) REVERT: Q 8 GLN cc_start: 0.5398 (tt0) cc_final: 0.4909 (tm-30) REVERT: S 21 ASN cc_start: 0.6890 (t0) cc_final: 0.6612 (t0) REVERT: c 57 MET cc_start: 0.3677 (ttt) cc_final: 0.3258 (mtp) REVERT: f 148 TYR cc_start: 0.8350 (t80) cc_final: 0.7962 (t80) REVERT: g 111 MET cc_start: 0.4400 (mmm) cc_final: 0.3927 (mtp) REVERT: g 165 ASP cc_start: 0.3530 (OUTLIER) cc_final: 0.3314 (t70) REVERT: g 231 MET cc_start: 0.5197 (mtp) cc_final: 0.4538 (mtm) outliers start: 122 outliers final: 72 residues processed: 302 average time/residue: 0.7135 time to fit residues: 364.9651 Evaluate side-chains 246 residues out of total 3832 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 81 poor density : 165 time to evaluate : 3.950 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 180 THR Chi-restraints excluded: chain B residue 207 LEU Chi-restraints excluded: chain B residue 215 VAL Chi-restraints excluded: chain C residue 86 VAL Chi-restraints excluded: chain C residue 108 ASN Chi-restraints excluded: chain C residue 111 VAL Chi-restraints excluded: chain C residue 137 ILE Chi-restraints excluded: chain C residue 156 THR Chi-restraints excluded: chain C residue 196 VAL Chi-restraints excluded: chain C residue 226 THR Chi-restraints excluded: chain E residue 164 LEU Chi-restraints excluded: chain E residue 181 VAL Chi-restraints excluded: chain E residue 195 ILE Chi-restraints excluded: chain E residue 200 ARG Chi-restraints excluded: chain E residue 215 ASP Chi-restraints excluded: chain G residue 29 ASP Chi-restraints excluded: chain G residue 43 ASP Chi-restraints excluded: chain G residue 63 MET Chi-restraints excluded: chain G residue 68 LEU Chi-restraints excluded: chain G residue 76 LEU Chi-restraints excluded: chain G residue 170 THR Chi-restraints excluded: chain H residue 20 VAL Chi-restraints excluded: chain H residue 49 ILE Chi-restraints excluded: chain H residue 147 ASN Chi-restraints excluded: chain I residue 58 LEU Chi-restraints excluded: chain I residue 193 LEU Chi-restraints excluded: chain J residue 99 LEU Chi-restraints excluded: chain L residue 21 ASN Chi-restraints excluded: chain R residue 8 THR Chi-restraints excluded: chain R residue 40 THR Chi-restraints excluded: chain W residue 65 LEU Chi-restraints excluded: chain W residue 74 VAL Chi-restraints excluded: chain W residue 93 LEU Chi-restraints excluded: chain X residue 18 HIS Chi-restraints excluded: chain X residue 90 ASP Chi-restraints excluded: chain X residue 95 PHE Chi-restraints excluded: chain X residue 103 LEU Chi-restraints excluded: chain Y residue 29 HIS Chi-restraints excluded: chain Y residue 53 ASP Chi-restraints excluded: chain Y residue 64 PHE Chi-restraints excluded: chain b residue 3 LEU Chi-restraints excluded: chain b residue 7 LEU Chi-restraints excluded: chain b residue 15 GLU Chi-restraints excluded: chain b residue 30 SER Chi-restraints excluded: chain b residue 46 VAL Chi-restraints excluded: chain b residue 67 THR Chi-restraints excluded: chain D residue 39 VAL Chi-restraints excluded: chain D residue 142 LEU Chi-restraints excluded: chain D residue 175 VAL Chi-restraints excluded: chain D residue 189 MET Chi-restraints excluded: chain F residue 25 LEU Chi-restraints excluded: chain F residue 69 PHE Chi-restraints excluded: chain F residue 84 LYS Chi-restraints excluded: chain K residue 55 VAL Chi-restraints excluded: chain K residue 74 GLU Chi-restraints excluded: chain M residue 28 LEU Chi-restraints excluded: chain M residue 66 VAL Chi-restraints excluded: chain M residue 71 ILE Chi-restraints excluded: chain M residue 91 VAL Chi-restraints excluded: chain M residue 97 LEU Chi-restraints excluded: chain P residue 14 THR Chi-restraints excluded: chain P residue 22 LEU Chi-restraints excluded: chain P residue 36 LEU Chi-restraints excluded: chain P residue 121 ILE Chi-restraints excluded: chain P residue 126 VAL Chi-restraints excluded: chain Q residue 97 VAL Chi-restraints excluded: chain Q residue 136 SER Chi-restraints excluded: chain S residue 3 LEU Chi-restraints excluded: chain S residue 35 ILE Chi-restraints excluded: chain S residue 98 TYR Chi-restraints excluded: chain T residue 6 VAL Chi-restraints excluded: chain T residue 35 ASP Chi-restraints excluded: chain T residue 135 ILE Chi-restraints excluded: chain Z residue 57 TYR Chi-restraints excluded: chain Z residue 69 LEU Chi-restraints excluded: chain f residue 117 LEU Chi-restraints excluded: chain g residue 79 TYR Chi-restraints excluded: chain g residue 165 ASP Chi-restraints excluded: chain g residue 193 ILE Chi-restraints excluded: chain g residue 283 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 613 random chunks: chunk 493 optimal weight: 30.0000 chunk 336 optimal weight: 5.9990 chunk 8 optimal weight: 10.0000 chunk 441 optimal weight: 20.0000 chunk 244 optimal weight: 10.0000 chunk 505 optimal weight: 9.9990 chunk 409 optimal weight: 5.9990 chunk 0 optimal weight: 10.0000 chunk 302 optimal weight: 9.9990 chunk 531 optimal weight: 6.9990 chunk 149 optimal weight: 50.0000 overall best weight: 7.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 33 GLN ** B 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 59 HIS C 87 GLN C 209 ASN ** E 258 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 71 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 110 GLN ** I 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 74 ASN ** L 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 81 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 5 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 74 GLN R 83 GLN e 5 HIS F 103 ASN ** F 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 32 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 70 ASN M 139 HIS ** P 128 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 74 HIS ** Q 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 19 ASN ** T 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 48 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 159 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7986 moved from start: 0.3627 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.064 77723 Z= 0.410 Angle : 0.825 13.959 113478 Z= 0.418 Chirality : 0.045 0.305 14238 Planarity : 0.006 0.099 7955 Dihedral : 24.884 179.971 31968 Min Nonbonded Distance : 1.993 Molprobity Statistics. All-atom Clashscore : 27.97 Ramachandran Plot: Outliers : 0.61 % Allowed : 13.90 % Favored : 85.49 % Rotamer: Outliers : 3.90 % Allowed : 14.95 % Favored : 81.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.81 % Cis-general : 0.09 % Twisted Proline : 2.81 % Twisted General : 0.40 % 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: -2.66 (0.12), residues: 4438 helix: -0.37 (0.13), residues: 1413 sheet: -1.74 (0.19), residues: 693 loop : -2.76 (0.12), residues: 2332 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP N 139 HIS 0.008 0.002 HIS P 128 PHE 0.036 0.002 PHE J 164 TYR 0.021 0.002 TYR L 93 ARG 0.009 0.001 ARG f 119 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8876 Ramachandran restraints generated. 4438 Oldfield, 0 Emsley, 4438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8876 Ramachandran restraints generated. 4438 Oldfield, 0 Emsley, 4438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 318 residues out of total 3832 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 147 poor density : 171 time to evaluate : 4.228 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 87 MET cc_start: 0.8539 (tpp) cc_final: 0.8186 (tpp) REVERT: E 164 LEU cc_start: 0.9070 (OUTLIER) cc_final: 0.8730 (tp) REVERT: E 200 ARG cc_start: 0.6730 (OUTLIER) cc_final: 0.6051 (tpm170) REVERT: G 76 LEU cc_start: 0.9025 (OUTLIER) cc_final: 0.8762 (tm) REVERT: N 138 ASN cc_start: 0.8342 (p0) cc_final: 0.8017 (p0) REVERT: W 26 LEU cc_start: 0.9088 (OUTLIER) cc_final: 0.8865 (tp) REVERT: X 18 HIS cc_start: 0.8426 (OUTLIER) cc_final: 0.8010 (t-90) REVERT: X 95 PHE cc_start: 0.8097 (OUTLIER) cc_final: 0.7658 (m-80) REVERT: Y 29 HIS cc_start: 0.8030 (OUTLIER) cc_final: 0.7692 (p90) REVERT: b 32 PHE cc_start: 0.6394 (OUTLIER) cc_final: 0.5912 (m-10) REVERT: e 25 GLU cc_start: 0.6948 (tt0) cc_final: 0.6218 (tm-30) REVERT: D 150 MET cc_start: -0.0090 (mtt) cc_final: -0.0697 (tpt) REVERT: F 84 LYS cc_start: -0.2018 (OUTLIER) cc_final: -0.4389 (mmtm) REVERT: P 36 LEU cc_start: 0.4599 (OUTLIER) cc_final: 0.4396 (pt) REVERT: P 49 MET cc_start: 0.8019 (mtt) cc_final: 0.7706 (mpp) REVERT: S 21 ASN cc_start: 0.6732 (t0) cc_final: 0.6480 (t0) REVERT: c 57 MET cc_start: 0.4059 (ttt) cc_final: 0.3535 (mtp) REVERT: f 148 TYR cc_start: 0.8326 (OUTLIER) cc_final: 0.8077 (t80) REVERT: g 111 MET cc_start: 0.4730 (mmm) cc_final: 0.4358 (mtp) REVERT: g 165 ASP cc_start: 0.3779 (OUTLIER) cc_final: 0.3569 (t70) REVERT: g 231 MET cc_start: 0.5265 (mtp) cc_final: 0.4773 (mtm) outliers start: 147 outliers final: 99 residues processed: 296 average time/residue: 0.7419 time to fit residues: 378.0995 Evaluate side-chains 263 residues out of total 3832 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 111 poor density : 152 time to evaluate : 4.056 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 HIS Chi-restraints excluded: chain A residue 172 LEU Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 180 THR Chi-restraints excluded: chain B residue 192 VAL Chi-restraints excluded: chain B residue 207 LEU Chi-restraints excluded: chain B residue 215 VAL Chi-restraints excluded: chain C residue 78 ASP Chi-restraints excluded: chain C residue 86 VAL Chi-restraints excluded: chain C residue 95 ARG Chi-restraints excluded: chain C residue 108 ASN Chi-restraints excluded: chain C residue 111 VAL Chi-restraints excluded: chain C residue 137 ILE Chi-restraints excluded: chain C residue 156 THR Chi-restraints excluded: chain C residue 196 VAL Chi-restraints excluded: chain C residue 226 THR Chi-restraints excluded: chain C residue 245 ASP Chi-restraints excluded: chain E residue 21 ASP Chi-restraints excluded: chain E residue 96 ASN Chi-restraints excluded: chain E residue 164 LEU Chi-restraints excluded: chain E residue 181 VAL Chi-restraints excluded: chain E residue 200 ARG Chi-restraints excluded: chain E residue 215 ASP Chi-restraints excluded: chain E residue 223 ASN Chi-restraints excluded: chain G residue 29 ASP Chi-restraints excluded: chain G residue 43 ASP Chi-restraints excluded: chain G residue 63 MET Chi-restraints excluded: chain G residue 68 LEU Chi-restraints excluded: chain G residue 76 LEU Chi-restraints excluded: chain G residue 96 SER Chi-restraints excluded: chain G residue 170 THR Chi-restraints excluded: chain H residue 20 VAL Chi-restraints excluded: chain H residue 49 ILE Chi-restraints excluded: chain H residue 143 LEU Chi-restraints excluded: chain H residue 154 LEU Chi-restraints excluded: chain I residue 58 LEU Chi-restraints excluded: chain I residue 193 LEU Chi-restraints excluded: chain J residue 99 LEU Chi-restraints excluded: chain L residue 21 ASN Chi-restraints excluded: chain N residue 72 MET Chi-restraints excluded: chain N residue 87 ASP Chi-restraints excluded: chain R residue 8 THR Chi-restraints excluded: chain R residue 40 THR Chi-restraints excluded: chain V residue 67 ASP Chi-restraints excluded: chain W residue 26 LEU Chi-restraints excluded: chain W residue 49 GLU Chi-restraints excluded: chain W residue 53 ILE Chi-restraints excluded: chain W residue 65 LEU Chi-restraints excluded: chain W residue 74 VAL Chi-restraints excluded: chain W residue 93 LEU Chi-restraints excluded: chain X residue 18 HIS Chi-restraints excluded: chain X residue 59 ILE Chi-restraints excluded: chain X residue 76 LEU Chi-restraints excluded: chain X residue 90 ASP Chi-restraints excluded: chain X residue 95 PHE Chi-restraints excluded: chain X residue 101 GLU Chi-restraints excluded: chain X residue 103 LEU Chi-restraints excluded: chain Y residue 22 GLN Chi-restraints excluded: chain Y residue 29 HIS Chi-restraints excluded: chain Y residue 47 VAL Chi-restraints excluded: chain Y residue 53 ASP Chi-restraints excluded: chain Y residue 64 PHE Chi-restraints excluded: chain Y residue 118 ILE Chi-restraints excluded: chain b residue 4 VAL Chi-restraints excluded: chain b residue 7 LEU Chi-restraints excluded: chain b residue 8 LEU Chi-restraints excluded: chain b residue 15 GLU Chi-restraints excluded: chain b residue 30 SER Chi-restraints excluded: chain b residue 32 PHE Chi-restraints excluded: chain b residue 46 VAL Chi-restraints excluded: chain b residue 67 THR Chi-restraints excluded: chain e residue 51 ASN Chi-restraints excluded: chain D residue 39 VAL Chi-restraints excluded: chain D residue 137 VAL Chi-restraints excluded: chain D residue 175 VAL Chi-restraints excluded: chain D residue 189 MET Chi-restraints excluded: chain F residue 25 LEU Chi-restraints excluded: chain F residue 69 PHE Chi-restraints excluded: chain F residue 84 LYS Chi-restraints excluded: chain F residue 194 LEU Chi-restraints excluded: chain K residue 55 VAL Chi-restraints excluded: chain K residue 74 GLU Chi-restraints excluded: chain M residue 28 LEU Chi-restraints excluded: chain M residue 38 HIS Chi-restraints excluded: chain M residue 71 ILE Chi-restraints excluded: chain M residue 91 VAL Chi-restraints excluded: chain P residue 14 THR Chi-restraints excluded: chain P residue 22 LEU Chi-restraints excluded: chain P residue 36 LEU Chi-restraints excluded: chain Q residue 97 VAL Chi-restraints excluded: chain Q residue 117 LEU Chi-restraints excluded: chain Q residue 136 SER Chi-restraints excluded: chain S residue 3 LEU Chi-restraints excluded: chain S residue 98 TYR Chi-restraints excluded: chain S residue 133 VAL Chi-restraints excluded: chain T residue 6 VAL Chi-restraints excluded: chain T residue 36 ILE Chi-restraints excluded: chain T residue 135 ILE Chi-restraints excluded: chain Z residue 57 TYR Chi-restraints excluded: chain Z residue 60 VAL Chi-restraints excluded: chain Z residue 69 LEU Chi-restraints excluded: chain f residue 117 LEU Chi-restraints excluded: chain f residue 148 TYR Chi-restraints excluded: chain g residue 79 TYR Chi-restraints excluded: chain g residue 104 VAL Chi-restraints excluded: chain g residue 165 ASP Chi-restraints excluded: chain g residue 193 ILE Chi-restraints excluded: chain g residue 196 ASN Chi-restraints excluded: chain g residue 221 MET Chi-restraints excluded: chain g residue 283 LYS Chi-restraints excluded: chain g residue 306 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 613 random chunks: chunk 199 optimal weight: 4.9990 chunk 533 optimal weight: 4.9990 chunk 117 optimal weight: 50.0000 chunk 347 optimal weight: 6.9990 chunk 146 optimal weight: 50.0000 chunk 593 optimal weight: 20.0000 chunk 492 optimal weight: 7.9990 chunk 274 optimal weight: 5.9990 chunk 49 optimal weight: 30.0000 chunk 196 optimal weight: 0.9980 chunk 311 optimal weight: 2.9990 overall best weight: 3.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 87 GLN C 94 GLN ** E 258 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 139 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 71 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 159 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 81 HIS ** N 5 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** e 5 HIS e 17 GLN ** F 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 32 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 103 ASN ** Q 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 55 HIS ** T 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 48 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 95 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** g 29 GLN ** g 159 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7926 moved from start: 0.3846 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.074 77723 Z= 0.234 Angle : 0.690 12.429 113478 Z= 0.351 Chirality : 0.040 0.296 14238 Planarity : 0.005 0.096 7955 Dihedral : 24.715 179.896 31968 Min Nonbonded Distance : 2.058 Molprobity Statistics. All-atom Clashscore : 22.40 Ramachandran Plot: Outliers : 0.52 % Allowed : 12.51 % Favored : 86.98 % Rotamer: Outliers : 3.72 % Allowed : 15.95 % Favored : 80.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.81 % Cis-general : 0.09 % Twisted Proline : 2.81 % Twisted General : 0.40 % 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: -2.38 (0.12), residues: 4438 helix: 0.02 (0.13), residues: 1414 sheet: -1.77 (0.19), residues: 690 loop : -2.63 (0.12), residues: 2334 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP X 24 HIS 0.007 0.001 HIS P 128 PHE 0.031 0.002 PHE b 47 TYR 0.018 0.002 TYR d 14 ARG 0.010 0.001 ARG Q 123 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8876 Ramachandran restraints generated. 4438 Oldfield, 0 Emsley, 4438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8876 Ramachandran restraints generated. 4438 Oldfield, 0 Emsley, 4438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 309 residues out of total 3832 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 140 poor density : 169 time to evaluate : 4.038 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 87 MET cc_start: 0.8498 (tpp) cc_final: 0.8169 (tpp) REVERT: E 164 LEU cc_start: 0.8999 (OUTLIER) cc_final: 0.8714 (tp) REVERT: E 200 ARG cc_start: 0.6650 (OUTLIER) cc_final: 0.5983 (tpm170) REVERT: G 76 LEU cc_start: 0.9077 (OUTLIER) cc_final: 0.8805 (tm) REVERT: N 83 GLU cc_start: 0.6832 (pt0) cc_final: 0.6418 (pm20) REVERT: N 127 ARG cc_start: 0.8605 (OUTLIER) cc_final: 0.8262 (mmt-90) REVERT: N 138 ASN cc_start: 0.8260 (p0) cc_final: 0.7742 (p0) REVERT: R 58 MET cc_start: -0.1263 (mmm) cc_final: -0.2327 (ttm) REVERT: X 18 HIS cc_start: 0.8275 (OUTLIER) cc_final: 0.7989 (t-90) REVERT: X 95 PHE cc_start: 0.8053 (OUTLIER) cc_final: 0.7561 (m-80) REVERT: Y 108 ARG cc_start: 0.8034 (OUTLIER) cc_final: 0.7762 (mtm-85) REVERT: b 32 PHE cc_start: 0.6487 (OUTLIER) cc_final: 0.5920 (m-10) REVERT: e 25 GLU cc_start: 0.6908 (tt0) cc_final: 0.6204 (tm-30) REVERT: D 150 MET cc_start: 0.0499 (mtt) cc_final: -0.0249 (tpt) REVERT: F 84 LYS cc_start: -0.1871 (OUTLIER) cc_final: -0.4132 (mmtm) REVERT: F 98 MET cc_start: -0.4192 (mtt) cc_final: -0.4451 (mtt) REVERT: K 1 MET cc_start: -0.2575 (ttt) cc_final: -0.2845 (ttt) REVERT: Q 117 LEU cc_start: 0.3617 (OUTLIER) cc_final: 0.3222 (tp) REVERT: S 21 ASN cc_start: 0.6758 (t0) cc_final: 0.6478 (t0) REVERT: c 57 MET cc_start: 0.4078 (ttt) cc_final: 0.3596 (mtp) REVERT: f 148 TYR cc_start: 0.8128 (OUTLIER) cc_final: 0.7841 (t80) REVERT: g 111 MET cc_start: 0.4588 (mmm) cc_final: 0.4215 (mtp) REVERT: g 165 ASP cc_start: 0.3446 (OUTLIER) cc_final: 0.3126 (t70) REVERT: g 231 MET cc_start: 0.5388 (mtp) cc_final: 0.4838 (mtm) outliers start: 140 outliers final: 93 residues processed: 292 average time/residue: 0.6757 time to fit residues: 341.3104 Evaluate side-chains 257 residues out of total 3832 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 105 poor density : 152 time to evaluate : 3.914 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 172 LEU Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 180 THR Chi-restraints excluded: chain B residue 207 LEU Chi-restraints excluded: chain B residue 215 VAL Chi-restraints excluded: chain C residue 86 VAL Chi-restraints excluded: chain C residue 108 ASN Chi-restraints excluded: chain C residue 111 VAL Chi-restraints excluded: chain C residue 137 ILE Chi-restraints excluded: chain C residue 156 THR Chi-restraints excluded: chain C residue 196 VAL Chi-restraints excluded: chain C residue 226 THR Chi-restraints excluded: chain C residue 245 ASP Chi-restraints excluded: chain E residue 21 ASP Chi-restraints excluded: chain E residue 96 ASN Chi-restraints excluded: chain E residue 164 LEU Chi-restraints excluded: chain E residue 180 LEU Chi-restraints excluded: chain E residue 181 VAL Chi-restraints excluded: chain E residue 195 ILE Chi-restraints excluded: chain E residue 200 ARG Chi-restraints excluded: chain E residue 215 ASP Chi-restraints excluded: chain G residue 29 ASP Chi-restraints excluded: chain G residue 43 ASP Chi-restraints excluded: chain G residue 63 MET Chi-restraints excluded: chain G residue 68 LEU Chi-restraints excluded: chain G residue 76 LEU Chi-restraints excluded: chain G residue 96 SER Chi-restraints excluded: chain G residue 170 THR Chi-restraints excluded: chain H residue 20 VAL Chi-restraints excluded: chain H residue 49 ILE Chi-restraints excluded: chain H residue 154 LEU Chi-restraints excluded: chain I residue 58 LEU Chi-restraints excluded: chain I residue 193 LEU Chi-restraints excluded: chain J residue 99 LEU Chi-restraints excluded: chain L residue 21 ASN Chi-restraints excluded: chain N residue 72 MET Chi-restraints excluded: chain N residue 87 ASP Chi-restraints excluded: chain N residue 127 ARG Chi-restraints excluded: chain R residue 8 THR Chi-restraints excluded: chain R residue 40 THR Chi-restraints excluded: chain V residue 9 VAL Chi-restraints excluded: chain V residue 67 ASP Chi-restraints excluded: chain W residue 65 LEU Chi-restraints excluded: chain W residue 74 VAL Chi-restraints excluded: chain W residue 93 LEU Chi-restraints excluded: chain X residue 18 HIS Chi-restraints excluded: chain X residue 59 ILE Chi-restraints excluded: chain X residue 90 ASP Chi-restraints excluded: chain X residue 95 PHE Chi-restraints excluded: chain X residue 101 GLU Chi-restraints excluded: chain X residue 103 LEU Chi-restraints excluded: chain Y residue 47 VAL Chi-restraints excluded: chain Y residue 53 ASP Chi-restraints excluded: chain Y residue 64 PHE Chi-restraints excluded: chain Y residue 108 ARG Chi-restraints excluded: chain Y residue 121 THR Chi-restraints excluded: chain b residue 3 LEU Chi-restraints excluded: chain b residue 4 VAL Chi-restraints excluded: chain b residue 7 LEU Chi-restraints excluded: chain b residue 8 LEU Chi-restraints excluded: chain b residue 15 GLU Chi-restraints excluded: chain b residue 30 SER Chi-restraints excluded: chain b residue 32 PHE Chi-restraints excluded: chain b residue 46 VAL Chi-restraints excluded: chain D residue 39 VAL Chi-restraints excluded: chain D residue 175 VAL Chi-restraints excluded: chain D residue 189 MET Chi-restraints excluded: chain F residue 25 LEU Chi-restraints excluded: chain F residue 69 PHE Chi-restraints excluded: chain F residue 84 LYS Chi-restraints excluded: chain F residue 194 LEU Chi-restraints excluded: chain K residue 55 VAL Chi-restraints excluded: chain K residue 74 GLU Chi-restraints excluded: chain M residue 38 HIS Chi-restraints excluded: chain M residue 71 ILE Chi-restraints excluded: chain M residue 91 VAL Chi-restraints excluded: chain P residue 14 THR Chi-restraints excluded: chain P residue 22 LEU Chi-restraints excluded: chain P residue 121 ILE Chi-restraints excluded: chain P residue 126 VAL Chi-restraints excluded: chain Q residue 97 VAL Chi-restraints excluded: chain Q residue 117 LEU Chi-restraints excluded: chain Q residue 136 SER Chi-restraints excluded: chain S residue 3 LEU Chi-restraints excluded: chain S residue 85 PHE Chi-restraints excluded: chain S residue 93 THR Chi-restraints excluded: chain S residue 98 TYR Chi-restraints excluded: chain S residue 133 VAL Chi-restraints excluded: chain T residue 6 VAL Chi-restraints excluded: chain T residue 28 LEU Chi-restraints excluded: chain T residue 35 ASP Chi-restraints excluded: chain T residue 36 ILE Chi-restraints excluded: chain T residue 135 ILE Chi-restraints excluded: chain U residue 27 THR Chi-restraints excluded: chain Z residue 57 TYR Chi-restraints excluded: chain Z residue 60 VAL Chi-restraints excluded: chain Z residue 69 LEU Chi-restraints excluded: chain f residue 117 LEU Chi-restraints excluded: chain f residue 148 TYR Chi-restraints excluded: chain g residue 79 TYR Chi-restraints excluded: chain g residue 104 VAL Chi-restraints excluded: chain g residue 165 ASP Chi-restraints excluded: chain g residue 193 ILE Chi-restraints excluded: chain g residue 283 LYS Chi-restraints excluded: chain g residue 306 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 613 random chunks: chunk 571 optimal weight: 20.0000 chunk 66 optimal weight: 30.0000 chunk 337 optimal weight: 7.9990 chunk 433 optimal weight: 9.9990 chunk 335 optimal weight: 1.9990 chunk 499 optimal weight: 9.9990 chunk 331 optimal weight: 6.9990 chunk 590 optimal weight: 8.9990 chunk 369 optimal weight: 40.0000 chunk 360 optimal weight: 6.9990 chunk 272 optimal weight: 7.9990 overall best weight: 6.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 109 ASN ** B 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 87 GLN ** E 258 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 139 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 71 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 5 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** e 5 HIS ** F 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 128 ASN ** K 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 128 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 48 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 95 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 159 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** g 299 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7983 moved from start: 0.4324 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.060 77723 Z= 0.345 Angle : 0.770 14.405 113478 Z= 0.390 Chirality : 0.043 0.301 14238 Planarity : 0.006 0.098 7955 Dihedral : 24.843 178.576 31968 Min Nonbonded Distance : 1.960 Molprobity Statistics. All-atom Clashscore : 27.48 Ramachandran Plot: Outliers : 0.43 % Allowed : 14.20 % Favored : 85.38 % Rotamer: Outliers : 3.74 % Allowed : 16.46 % Favored : 79.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.81 % Cis-general : 0.09 % Twisted Proline : 1.69 % Twisted General : 0.37 % 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: -2.50 (0.12), residues: 4438 helix: -0.14 (0.13), residues: 1409 sheet: -1.84 (0.19), residues: 644 loop : -2.65 (0.12), residues: 2385 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP N 139 HIS 0.008 0.002 HIS K 32 PHE 0.027 0.002 PHE b 47 TYR 0.020 0.002 TYR K 14 ARG 0.016 0.001 ARG P 61 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8876 Ramachandran restraints generated. 4438 Oldfield, 0 Emsley, 4438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8876 Ramachandran restraints generated. 4438 Oldfield, 0 Emsley, 4438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 296 residues out of total 3832 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 141 poor density : 155 time to evaluate : 4.046 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 203 ASP cc_start: 0.8179 (m-30) cc_final: 0.7771 (t70) REVERT: E 87 MET cc_start: 0.8504 (tpp) cc_final: 0.8188 (tpp) REVERT: E 164 LEU cc_start: 0.9073 (OUTLIER) cc_final: 0.8725 (tp) REVERT: E 200 ARG cc_start: 0.6873 (OUTLIER) cc_final: 0.6518 (tpt170) REVERT: G 76 LEU cc_start: 0.9041 (OUTLIER) cc_final: 0.8738 (tm) REVERT: H 50 ASP cc_start: 0.8565 (p0) cc_final: 0.7807 (t0) REVERT: N 138 ASN cc_start: 0.8336 (p0) cc_final: 0.7979 (p0) REVERT: W 26 LEU cc_start: 0.9064 (OUTLIER) cc_final: 0.8854 (tp) REVERT: X 18 HIS cc_start: 0.8419 (OUTLIER) cc_final: 0.8072 (t-90) REVERT: X 95 PHE cc_start: 0.8184 (OUTLIER) cc_final: 0.7676 (m-80) REVERT: Y 108 ARG cc_start: 0.8139 (OUTLIER) cc_final: 0.7931 (mtm-85) REVERT: b 32 PHE cc_start: 0.6352 (OUTLIER) cc_final: 0.5984 (m-10) REVERT: e 25 GLU cc_start: 0.6954 (tt0) cc_final: 0.6273 (tm-30) REVERT: D 177 MET cc_start: 0.1097 (mmt) cc_final: 0.0403 (mmt) REVERT: F 84 LYS cc_start: -0.1936 (OUTLIER) cc_final: -0.4458 (mmtm) REVERT: K 1 MET cc_start: -0.2887 (ttt) cc_final: -0.3344 (ttt) REVERT: P 49 MET cc_start: 0.7953 (mtt) cc_final: 0.7642 (mpp) REVERT: Q 117 LEU cc_start: 0.3920 (OUTLIER) cc_final: 0.3525 (tp) REVERT: S 21 ASN cc_start: 0.6728 (t0) cc_final: 0.6483 (t0) REVERT: T 67 MET cc_start: 0.8341 (mtt) cc_final: 0.8064 (mtt) REVERT: c 57 MET cc_start: 0.4114 (ttt) cc_final: 0.3562 (mtp) REVERT: f 139 LEU cc_start: 0.9151 (OUTLIER) cc_final: 0.8811 (mm) REVERT: f 148 TYR cc_start: 0.8109 (OUTLIER) cc_final: 0.7790 (t80) REVERT: g 111 MET cc_start: 0.4683 (mmm) cc_final: 0.4316 (mtp) REVERT: g 121 MET cc_start: 0.1817 (ttm) cc_final: 0.1581 (ptm) REVERT: g 165 ASP cc_start: 0.3648 (OUTLIER) cc_final: 0.3444 (t70) REVERT: g 221 MET cc_start: -0.3675 (ptt) cc_final: -0.4053 (ptt) outliers start: 141 outliers final: 100 residues processed: 277 average time/residue: 0.6953 time to fit residues: 334.5291 Evaluate side-chains 256 residues out of total 3832 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 113 poor density : 143 time to evaluate : 3.973 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 THR Chi-restraints excluded: chain A residue 32 HIS Chi-restraints excluded: chain A residue 172 LEU Chi-restraints excluded: chain B residue 110 LEU Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 192 VAL Chi-restraints excluded: chain B residue 207 LEU Chi-restraints excluded: chain B residue 215 VAL Chi-restraints excluded: chain C residue 69 ILE Chi-restraints excluded: chain C residue 78 ASP Chi-restraints excluded: chain C residue 86 VAL Chi-restraints excluded: chain C residue 108 ASN Chi-restraints excluded: chain C residue 111 VAL Chi-restraints excluded: chain C residue 137 ILE Chi-restraints excluded: chain C residue 156 THR Chi-restraints excluded: chain C residue 196 VAL Chi-restraints excluded: chain C residue 226 THR Chi-restraints excluded: chain C residue 245 ASP Chi-restraints excluded: chain E residue 21 ASP Chi-restraints excluded: chain E residue 96 ASN Chi-restraints excluded: chain E residue 164 LEU Chi-restraints excluded: chain E residue 181 VAL Chi-restraints excluded: chain E residue 200 ARG Chi-restraints excluded: chain E residue 215 ASP Chi-restraints excluded: chain G residue 29 ASP Chi-restraints excluded: chain G residue 43 ASP Chi-restraints excluded: chain G residue 63 MET Chi-restraints excluded: chain G residue 68 LEU Chi-restraints excluded: chain G residue 76 LEU Chi-restraints excluded: chain G residue 96 SER Chi-restraints excluded: chain G residue 170 THR Chi-restraints excluded: chain H residue 20 VAL Chi-restraints excluded: chain H residue 49 ILE Chi-restraints excluded: chain H residue 143 LEU Chi-restraints excluded: chain H residue 154 LEU Chi-restraints excluded: chain I residue 58 LEU Chi-restraints excluded: chain I residue 193 LEU Chi-restraints excluded: chain J residue 99 LEU Chi-restraints excluded: chain J residue 111 THR Chi-restraints excluded: chain L residue 5 LEU Chi-restraints excluded: chain L residue 21 ASN Chi-restraints excluded: chain N residue 33 VAL Chi-restraints excluded: chain N residue 87 ASP Chi-restraints excluded: chain N residue 127 ARG Chi-restraints excluded: chain R residue 8 THR Chi-restraints excluded: chain R residue 40 THR Chi-restraints excluded: chain V residue 9 VAL Chi-restraints excluded: chain V residue 67 ASP Chi-restraints excluded: chain W residue 26 LEU Chi-restraints excluded: chain W residue 49 GLU Chi-restraints excluded: chain W residue 53 ILE Chi-restraints excluded: chain W residue 55 ASP Chi-restraints excluded: chain W residue 65 LEU Chi-restraints excluded: chain W residue 74 VAL Chi-restraints excluded: chain W residue 93 LEU Chi-restraints excluded: chain X residue 18 HIS Chi-restraints excluded: chain X residue 59 ILE Chi-restraints excluded: chain X residue 76 LEU Chi-restraints excluded: chain X residue 90 ASP Chi-restraints excluded: chain X residue 95 PHE Chi-restraints excluded: chain X residue 103 LEU Chi-restraints excluded: chain Y residue 47 VAL Chi-restraints excluded: chain Y residue 53 ASP Chi-restraints excluded: chain Y residue 64 PHE Chi-restraints excluded: chain Y residue 108 ARG Chi-restraints excluded: chain Y residue 118 ILE Chi-restraints excluded: chain Y residue 121 THR Chi-restraints excluded: chain b residue 4 VAL Chi-restraints excluded: chain b residue 7 LEU Chi-restraints excluded: chain b residue 8 LEU Chi-restraints excluded: chain b residue 15 GLU Chi-restraints excluded: chain b residue 30 SER Chi-restraints excluded: chain b residue 32 PHE Chi-restraints excluded: chain b residue 46 VAL Chi-restraints excluded: chain b residue 67 THR Chi-restraints excluded: chain e residue 24 THR Chi-restraints excluded: chain e residue 51 ASN Chi-restraints excluded: chain D residue 39 VAL Chi-restraints excluded: chain D residue 137 VAL Chi-restraints excluded: chain D residue 189 MET Chi-restraints excluded: chain F residue 25 LEU Chi-restraints excluded: chain F residue 84 LYS Chi-restraints excluded: chain F residue 194 LEU Chi-restraints excluded: chain K residue 55 VAL Chi-restraints excluded: chain K residue 74 GLU Chi-restraints excluded: chain M residue 38 HIS Chi-restraints excluded: chain M residue 71 ILE Chi-restraints excluded: chain M residue 91 VAL Chi-restraints excluded: chain P residue 13 LYS Chi-restraints excluded: chain P residue 14 THR Chi-restraints excluded: chain P residue 22 LEU Chi-restraints excluded: chain Q residue 97 VAL Chi-restraints excluded: chain Q residue 117 LEU Chi-restraints excluded: chain S residue 3 LEU Chi-restraints excluded: chain S residue 93 THR Chi-restraints excluded: chain S residue 98 TYR Chi-restraints excluded: chain S residue 133 VAL Chi-restraints excluded: chain T residue 6 VAL Chi-restraints excluded: chain T residue 35 ASP Chi-restraints excluded: chain T residue 36 ILE Chi-restraints excluded: chain T residue 135 ILE Chi-restraints excluded: chain Z residue 57 TYR Chi-restraints excluded: chain Z residue 60 VAL Chi-restraints excluded: chain f residue 130 VAL Chi-restraints excluded: chain f residue 139 LEU Chi-restraints excluded: chain f residue 148 TYR Chi-restraints excluded: chain g residue 79 TYR Chi-restraints excluded: chain g residue 100 TYR Chi-restraints excluded: chain g residue 104 VAL Chi-restraints excluded: chain g residue 165 ASP Chi-restraints excluded: chain g residue 193 ILE Chi-restraints excluded: chain g residue 283 LYS Chi-restraints excluded: chain g residue 306 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 613 random chunks: chunk 365 optimal weight: 9.9990 chunk 235 optimal weight: 2.9990 chunk 352 optimal weight: 3.9990 chunk 177 optimal weight: 0.8980 chunk 116 optimal weight: 50.0000 chunk 114 optimal weight: 50.0000 chunk 375 optimal weight: 0.9990 chunk 402 optimal weight: 20.0000 chunk 292 optimal weight: 7.9990 chunk 55 optimal weight: 9.9990 chunk 464 optimal weight: 40.0000 overall best weight: 3.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 16 HIS E 17 HIS ** E 258 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 139 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 71 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 159 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 5 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 31 ASN ** W 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** e 5 HIS D 162 GLN ** F 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 128 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 48 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 95 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** f 123 ASN ** g 159 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7926 moved from start: 0.4503 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 77723 Z= 0.211 Angle : 0.678 12.912 113478 Z= 0.343 Chirality : 0.039 0.319 14238 Planarity : 0.005 0.096 7955 Dihedral : 24.646 179.458 31965 Min Nonbonded Distance : 2.059 Molprobity Statistics. All-atom Clashscore : 22.49 Ramachandran Plot: Outliers : 0.47 % Allowed : 12.48 % Favored : 87.04 % Rotamer: Outliers : 3.32 % Allowed : 17.07 % Favored : 79.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.81 % Cis-general : 0.09 % Twisted Proline : 1.69 % Twisted General : 0.33 % 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: -2.21 (0.12), residues: 4438 helix: 0.22 (0.14), residues: 1407 sheet: -1.71 (0.19), residues: 682 loop : -2.55 (0.12), residues: 2349 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP X 24 HIS 0.007 0.001 HIS J 133 PHE 0.024 0.002 PHE b 47 TYR 0.015 0.002 TYR S 30 ARG 0.007 0.001 ARG f 118 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8876 Ramachandran restraints generated. 4438 Oldfield, 0 Emsley, 4438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8876 Ramachandran restraints generated. 4438 Oldfield, 0 Emsley, 4438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 290 residues out of total 3832 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 125 poor density : 165 time to evaluate : 3.986 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 198 MET cc_start: 0.8528 (tpp) cc_final: 0.8290 (tpp) REVERT: B 203 ASP cc_start: 0.8197 (m-30) cc_final: 0.7723 (t70) REVERT: E 87 MET cc_start: 0.8489 (tpp) cc_final: 0.8191 (tpp) REVERT: E 164 LEU cc_start: 0.9011 (OUTLIER) cc_final: 0.8715 (tp) REVERT: E 200 ARG cc_start: 0.6822 (OUTLIER) cc_final: 0.6455 (tpt170) REVERT: G 76 LEU cc_start: 0.9045 (OUTLIER) cc_final: 0.8749 (tm) REVERT: H 50 ASP cc_start: 0.8391 (p0) cc_final: 0.7726 (t0) REVERT: I 8 ARG cc_start: 0.8456 (OUTLIER) cc_final: 0.8062 (tpp80) REVERT: N 83 GLU cc_start: 0.6811 (pt0) cc_final: 0.6395 (pm20) REVERT: N 90 TYR cc_start: 0.7708 (m-10) cc_final: 0.7488 (m-10) REVERT: N 127 ARG cc_start: 0.8571 (OUTLIER) cc_final: 0.8235 (mmt-90) REVERT: N 138 ASN cc_start: 0.8261 (p0) cc_final: 0.7787 (p0) REVERT: R 58 MET cc_start: -0.1782 (mmm) cc_final: -0.2685 (ttp) REVERT: X 18 HIS cc_start: 0.8249 (OUTLIER) cc_final: 0.7976 (t-90) REVERT: X 95 PHE cc_start: 0.8001 (OUTLIER) cc_final: 0.7559 (m-80) REVERT: Y 108 ARG cc_start: 0.8015 (OUTLIER) cc_final: 0.7753 (mtm-85) REVERT: b 32 PHE cc_start: 0.6451 (OUTLIER) cc_final: 0.6233 (m-10) REVERT: e 25 GLU cc_start: 0.6911 (tt0) cc_final: 0.6232 (tm-30) REVERT: D 127 MET cc_start: 0.8072 (mmp) cc_final: 0.7690 (mmm) REVERT: D 177 MET cc_start: 0.0679 (mmt) cc_final: 0.0092 (mmt) REVERT: D 189 MET cc_start: 0.8664 (OUTLIER) cc_final: 0.8449 (tpt) REVERT: F 84 LYS cc_start: -0.1568 (OUTLIER) cc_final: -0.3994 (mmtm) REVERT: M 129 GLU cc_start: 0.8425 (mm-30) cc_final: 0.7994 (pm20) REVERT: P 49 MET cc_start: 0.7950 (mtt) cc_final: 0.7650 (mpp) REVERT: S 21 ASN cc_start: 0.6563 (t0) cc_final: 0.6316 (t0) REVERT: T 67 MET cc_start: 0.8229 (mtt) cc_final: 0.7943 (mtt) REVERT: c 57 MET cc_start: 0.3958 (ttt) cc_final: 0.3544 (mtp) REVERT: f 139 LEU cc_start: 0.9166 (OUTLIER) cc_final: 0.8860 (mm) REVERT: g 111 MET cc_start: 0.4459 (mmm) cc_final: 0.4014 (mtp) REVERT: g 221 MET cc_start: -0.3815 (ptt) cc_final: -0.4026 (ptt) REVERT: g 231 MET cc_start: 0.4735 (OUTLIER) cc_final: 0.4457 (mtm) outliers start: 125 outliers final: 91 residues processed: 274 average time/residue: 0.6983 time to fit residues: 331.6710 Evaluate side-chains 261 residues out of total 3832 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 104 poor density : 157 time to evaluate : 4.286 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 THR Chi-restraints excluded: chain A residue 172 LEU Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 180 THR Chi-restraints excluded: chain B residue 207 LEU Chi-restraints excluded: chain B residue 215 VAL Chi-restraints excluded: chain C residue 78 ASP Chi-restraints excluded: chain C residue 86 VAL Chi-restraints excluded: chain C residue 108 ASN Chi-restraints excluded: chain C residue 111 VAL Chi-restraints excluded: chain C residue 137 ILE Chi-restraints excluded: chain C residue 156 THR Chi-restraints excluded: chain C residue 196 VAL Chi-restraints excluded: chain C residue 226 THR Chi-restraints excluded: chain C residue 245 ASP Chi-restraints excluded: chain E residue 21 ASP Chi-restraints excluded: chain E residue 96 ASN Chi-restraints excluded: chain E residue 164 LEU Chi-restraints excluded: chain E residue 180 LEU Chi-restraints excluded: chain E residue 181 VAL Chi-restraints excluded: chain E residue 195 ILE Chi-restraints excluded: chain E residue 200 ARG Chi-restraints excluded: chain E residue 215 ASP Chi-restraints excluded: chain G residue 29 ASP Chi-restraints excluded: chain G residue 43 ASP Chi-restraints excluded: chain G residue 68 LEU Chi-restraints excluded: chain G residue 76 LEU Chi-restraints excluded: chain G residue 170 THR Chi-restraints excluded: chain H residue 20 VAL Chi-restraints excluded: chain H residue 49 ILE Chi-restraints excluded: chain H residue 91 ILE Chi-restraints excluded: chain H residue 143 LEU Chi-restraints excluded: chain H residue 154 LEU Chi-restraints excluded: chain I residue 8 ARG Chi-restraints excluded: chain I residue 58 LEU Chi-restraints excluded: chain I residue 193 LEU Chi-restraints excluded: chain J residue 99 LEU Chi-restraints excluded: chain J residue 111 THR Chi-restraints excluded: chain J residue 134 ILE Chi-restraints excluded: chain L residue 21 ASN Chi-restraints excluded: chain N residue 72 MET Chi-restraints excluded: chain N residue 87 ASP Chi-restraints excluded: chain N residue 127 ARG Chi-restraints excluded: chain R residue 8 THR Chi-restraints excluded: chain R residue 40 THR Chi-restraints excluded: chain V residue 68 SER Chi-restraints excluded: chain W residue 53 ILE Chi-restraints excluded: chain W residue 55 ASP Chi-restraints excluded: chain W residue 65 LEU Chi-restraints excluded: chain W residue 74 VAL Chi-restraints excluded: chain W residue 93 LEU Chi-restraints excluded: chain X residue 18 HIS Chi-restraints excluded: chain X residue 59 ILE Chi-restraints excluded: chain X residue 76 LEU Chi-restraints excluded: chain X residue 90 ASP Chi-restraints excluded: chain X residue 95 PHE Chi-restraints excluded: chain X residue 103 LEU Chi-restraints excluded: chain Y residue 22 GLN Chi-restraints excluded: chain Y residue 47 VAL Chi-restraints excluded: chain Y residue 53 ASP Chi-restraints excluded: chain Y residue 64 PHE Chi-restraints excluded: chain Y residue 108 ARG Chi-restraints excluded: chain Y residue 121 THR Chi-restraints excluded: chain b residue 4 VAL Chi-restraints excluded: chain b residue 7 LEU Chi-restraints excluded: chain b residue 8 LEU Chi-restraints excluded: chain b residue 15 GLU Chi-restraints excluded: chain b residue 30 SER Chi-restraints excluded: chain b residue 32 PHE Chi-restraints excluded: chain b residue 46 VAL Chi-restraints excluded: chain b residue 67 THR Chi-restraints excluded: chain e residue 24 THR Chi-restraints excluded: chain e residue 51 ASN Chi-restraints excluded: chain D residue 39 VAL Chi-restraints excluded: chain D residue 189 MET Chi-restraints excluded: chain F residue 25 LEU Chi-restraints excluded: chain F residue 84 LYS Chi-restraints excluded: chain F residue 194 LEU Chi-restraints excluded: chain K residue 51 SER Chi-restraints excluded: chain M residue 38 HIS Chi-restraints excluded: chain M residue 71 ILE Chi-restraints excluded: chain M residue 91 VAL Chi-restraints excluded: chain P residue 13 LYS Chi-restraints excluded: chain P residue 14 THR Chi-restraints excluded: chain P residue 22 LEU Chi-restraints excluded: chain P residue 126 VAL Chi-restraints excluded: chain Q residue 136 SER Chi-restraints excluded: chain S residue 3 LEU Chi-restraints excluded: chain S residue 93 THR Chi-restraints excluded: chain S residue 98 TYR Chi-restraints excluded: chain S residue 133 VAL Chi-restraints excluded: chain T residue 35 ASP Chi-restraints excluded: chain T residue 135 ILE Chi-restraints excluded: chain Z residue 57 TYR Chi-restraints excluded: chain Z residue 60 VAL Chi-restraints excluded: chain f residue 117 LEU Chi-restraints excluded: chain f residue 139 LEU Chi-restraints excluded: chain g residue 79 TYR Chi-restraints excluded: chain g residue 100 TYR Chi-restraints excluded: chain g residue 104 VAL Chi-restraints excluded: chain g residue 193 ILE Chi-restraints excluded: chain g residue 231 MET Chi-restraints excluded: chain g residue 283 LYS Chi-restraints excluded: chain g residue 306 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 613 random chunks: chunk 537 optimal weight: 30.0000 chunk 566 optimal weight: 6.9990 chunk 516 optimal weight: 9.9990 chunk 550 optimal weight: 10.0000 chunk 565 optimal weight: 9.9990 chunk 331 optimal weight: 8.9990 chunk 239 optimal weight: 0.9990 chunk 432 optimal weight: 0.2980 chunk 168 optimal weight: 10.0000 chunk 497 optimal weight: 0.2980 chunk 520 optimal weight: 7.9990 overall best weight: 3.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 199 ASN ** B 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 87 GLN ** E 258 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 139 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 71 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 159 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 5 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** e 5 HIS ** F 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 100 ASN F 122 ASN ** K 32 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 128 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 43 ASN ** U 48 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 95 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** f 123 ASN ** g 159 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 268 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7925 moved from start: 0.4819 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 77723 Z= 0.214 Angle : 0.668 12.315 113478 Z= 0.338 Chirality : 0.038 0.334 14238 Planarity : 0.005 0.096 7955 Dihedral : 24.555 179.637 31965 Min Nonbonded Distance : 2.008 Molprobity Statistics. All-atom Clashscore : 22.14 Ramachandran Plot: Outliers : 0.41 % Allowed : 12.73 % Favored : 86.86 % Rotamer: Outliers : 3.00 % Allowed : 17.49 % Favored : 79.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.81 % Cis-general : 0.09 % Twisted Proline : 1.69 % Twisted General : 0.37 % 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: -2.06 (0.12), residues: 4438 helix: 0.41 (0.14), residues: 1398 sheet: -1.62 (0.20), residues: 653 loop : -2.49 (0.12), residues: 2387 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP X 24 HIS 0.006 0.001 HIS J 133 PHE 0.033 0.002 PHE J 164 TYR 0.014 0.001 TYR S 30 ARG 0.010 0.001 ARG P 81 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8876 Ramachandran restraints generated. 4438 Oldfield, 0 Emsley, 4438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8876 Ramachandran restraints generated. 4438 Oldfield, 0 Emsley, 4438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 286 residues out of total 3832 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 113 poor density : 173 time to evaluate : 4.011 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 198 MET cc_start: 0.8511 (tpp) cc_final: 0.8296 (tpp) REVERT: B 203 ASP cc_start: 0.8202 (m-30) cc_final: 0.7673 (t70) REVERT: E 87 MET cc_start: 0.8519 (tpp) cc_final: 0.8236 (tpp) REVERT: E 164 LEU cc_start: 0.9036 (OUTLIER) cc_final: 0.8711 (tp) REVERT: G 76 LEU cc_start: 0.9076 (OUTLIER) cc_final: 0.8780 (tm) REVERT: H 50 ASP cc_start: 0.8424 (p0) cc_final: 0.7825 (t0) REVERT: I 8 ARG cc_start: 0.8467 (OUTLIER) cc_final: 0.8051 (tpp80) REVERT: N 83 GLU cc_start: 0.6786 (pt0) cc_final: 0.6365 (pm20) REVERT: N 90 TYR cc_start: 0.7672 (m-10) cc_final: 0.7405 (m-10) REVERT: N 138 ASN cc_start: 0.8318 (p0) cc_final: 0.7883 (p0) REVERT: R 58 MET cc_start: -0.1193 (mmm) cc_final: -0.2119 (ttm) REVERT: R 111 LYS cc_start: 0.8391 (ptpt) cc_final: 0.8177 (pttm) REVERT: X 18 HIS cc_start: 0.8258 (OUTLIER) cc_final: 0.8008 (t70) REVERT: X 95 PHE cc_start: 0.7879 (OUTLIER) cc_final: 0.7493 (m-80) REVERT: b 32 PHE cc_start: 0.6338 (OUTLIER) cc_final: 0.6058 (m-10) REVERT: e 25 GLU cc_start: 0.6875 (tt0) cc_final: 0.6227 (tm-30) REVERT: D 127 MET cc_start: 0.8038 (mmp) cc_final: 0.7608 (mmm) REVERT: D 177 MET cc_start: 0.0300 (mmt) cc_final: -0.0243 (mmt) REVERT: D 189 MET cc_start: 0.8827 (OUTLIER) cc_final: 0.8598 (tpt) REVERT: F 84 LYS cc_start: -0.1869 (OUTLIER) cc_final: -0.4226 (mmtm) REVERT: M 129 GLU cc_start: 0.8518 (mm-30) cc_final: 0.8228 (pm20) REVERT: P 49 MET cc_start: 0.8018 (mtt) cc_final: 0.7705 (mpp) REVERT: S 21 ASN cc_start: 0.6646 (t0) cc_final: 0.6409 (t0) REVERT: T 67 MET cc_start: 0.8064 (mtt) cc_final: 0.7808 (mtt) REVERT: Z 49 ARG cc_start: 0.8634 (mmm-85) cc_final: 0.8421 (mmm-85) REVERT: Z 57 TYR cc_start: 0.3891 (OUTLIER) cc_final: 0.3406 (m-10) REVERT: c 57 MET cc_start: 0.3988 (ttt) cc_final: 0.3461 (mtp) REVERT: f 139 LEU cc_start: 0.9119 (OUTLIER) cc_final: 0.8903 (mm) REVERT: g 111 MET cc_start: 0.4460 (mmm) cc_final: 0.3960 (mtp) REVERT: g 165 ASP cc_start: 0.3549 (OUTLIER) cc_final: 0.3287 (t70) REVERT: g 193 ILE cc_start: 0.8719 (OUTLIER) cc_final: 0.8358 (tt) REVERT: g 221 MET cc_start: -0.2904 (ptt) cc_final: -0.3341 (ptt) REVERT: g 231 MET cc_start: 0.5267 (mtp) cc_final: 0.4871 (mtm) outliers start: 113 outliers final: 89 residues processed: 269 average time/residue: 0.6917 time to fit residues: 322.6137 Evaluate side-chains 264 residues out of total 3832 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 101 poor density : 163 time to evaluate : 3.914 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 HIS Chi-restraints excluded: chain A residue 172 LEU Chi-restraints excluded: chain B residue 180 THR Chi-restraints excluded: chain B residue 215 VAL Chi-restraints excluded: chain C residue 69 ILE Chi-restraints excluded: chain C residue 78 ASP Chi-restraints excluded: chain C residue 86 VAL Chi-restraints excluded: chain C residue 108 ASN Chi-restraints excluded: chain C residue 111 VAL Chi-restraints excluded: chain C residue 137 ILE Chi-restraints excluded: chain C residue 156 THR Chi-restraints excluded: chain C residue 196 VAL Chi-restraints excluded: chain C residue 226 THR Chi-restraints excluded: chain C residue 245 ASP Chi-restraints excluded: chain E residue 21 ASP Chi-restraints excluded: chain E residue 96 ASN Chi-restraints excluded: chain E residue 164 LEU Chi-restraints excluded: chain E residue 180 LEU Chi-restraints excluded: chain E residue 181 VAL Chi-restraints excluded: chain E residue 195 ILE Chi-restraints excluded: chain E residue 215 ASP Chi-restraints excluded: chain G residue 29 ASP Chi-restraints excluded: chain G residue 43 ASP Chi-restraints excluded: chain G residue 63 MET Chi-restraints excluded: chain G residue 68 LEU Chi-restraints excluded: chain G residue 76 LEU Chi-restraints excluded: chain G residue 96 SER Chi-restraints excluded: chain G residue 158 ILE Chi-restraints excluded: chain G residue 170 THR Chi-restraints excluded: chain H residue 20 VAL Chi-restraints excluded: chain H residue 49 ILE Chi-restraints excluded: chain H residue 91 ILE Chi-restraints excluded: chain H residue 143 LEU Chi-restraints excluded: chain H residue 154 LEU Chi-restraints excluded: chain I residue 8 ARG Chi-restraints excluded: chain I residue 58 LEU Chi-restraints excluded: chain I residue 193 LEU Chi-restraints excluded: chain J residue 99 LEU Chi-restraints excluded: chain J residue 111 THR Chi-restraints excluded: chain L residue 21 ASN Chi-restraints excluded: chain N residue 72 MET Chi-restraints excluded: chain N residue 87 ASP Chi-restraints excluded: chain N residue 127 ARG Chi-restraints excluded: chain R residue 8 THR Chi-restraints excluded: chain R residue 40 THR Chi-restraints excluded: chain V residue 68 SER Chi-restraints excluded: chain W residue 53 ILE Chi-restraints excluded: chain W residue 65 LEU Chi-restraints excluded: chain W residue 74 VAL Chi-restraints excluded: chain W residue 93 LEU Chi-restraints excluded: chain X residue 18 HIS Chi-restraints excluded: chain X residue 59 ILE Chi-restraints excluded: chain X residue 76 LEU Chi-restraints excluded: chain X residue 90 ASP Chi-restraints excluded: chain X residue 95 PHE Chi-restraints excluded: chain X residue 103 LEU Chi-restraints excluded: chain Y residue 22 GLN Chi-restraints excluded: chain Y residue 47 VAL Chi-restraints excluded: chain Y residue 53 ASP Chi-restraints excluded: chain Y residue 64 PHE Chi-restraints excluded: chain Y residue 121 THR Chi-restraints excluded: chain b residue 4 VAL Chi-restraints excluded: chain b residue 7 LEU Chi-restraints excluded: chain b residue 8 LEU Chi-restraints excluded: chain b residue 30 SER Chi-restraints excluded: chain b residue 32 PHE Chi-restraints excluded: chain b residue 46 VAL Chi-restraints excluded: chain b residue 67 THR Chi-restraints excluded: chain e residue 24 THR Chi-restraints excluded: chain e residue 51 ASN Chi-restraints excluded: chain D residue 39 VAL Chi-restraints excluded: chain D residue 189 MET Chi-restraints excluded: chain F residue 25 LEU Chi-restraints excluded: chain F residue 84 LYS Chi-restraints excluded: chain F residue 194 LEU Chi-restraints excluded: chain K residue 51 SER Chi-restraints excluded: chain M residue 38 HIS Chi-restraints excluded: chain M residue 71 ILE Chi-restraints excluded: chain M residue 91 VAL Chi-restraints excluded: chain P residue 13 LYS Chi-restraints excluded: chain P residue 14 THR Chi-restraints excluded: chain P residue 22 LEU Chi-restraints excluded: chain P residue 126 VAL Chi-restraints excluded: chain S residue 3 LEU Chi-restraints excluded: chain S residue 93 THR Chi-restraints excluded: chain S residue 98 TYR Chi-restraints excluded: chain S residue 133 VAL Chi-restraints excluded: chain T residue 35 ASP Chi-restraints excluded: chain T residue 135 ILE Chi-restraints excluded: chain Z residue 57 TYR Chi-restraints excluded: chain Z residue 60 VAL Chi-restraints excluded: chain f residue 117 LEU Chi-restraints excluded: chain f residue 139 LEU Chi-restraints excluded: chain g residue 79 TYR Chi-restraints excluded: chain g residue 100 TYR Chi-restraints excluded: chain g residue 104 VAL Chi-restraints excluded: chain g residue 165 ASP Chi-restraints excluded: chain g residue 178 VAL Chi-restraints excluded: chain g residue 193 ILE Chi-restraints excluded: chain g residue 283 LYS Chi-restraints excluded: chain g residue 306 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 613 random chunks: chunk 548 optimal weight: 20.0000 chunk 361 optimal weight: 10.0000 chunk 582 optimal weight: 50.0000 chunk 355 optimal weight: 6.9990 chunk 276 optimal weight: 2.9990 chunk 404 optimal weight: 0.3980 chunk 610 optimal weight: 1.9990 chunk 562 optimal weight: 0.7980 chunk 486 optimal weight: 7.9990 chunk 50 optimal weight: 20.0000 chunk 375 optimal weight: 1.9990 overall best weight: 1.6386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 30 GLN ** B 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 199 ASN B 208 GLN ** C 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 188 ASN ** G 139 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 71 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 159 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 5 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** e 5 HIS F 86 GLN ** K 32 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 47 GLN ** Q 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 94 GLN ** U 48 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 95 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 159 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 268 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7858 moved from start: 0.5090 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.052 77723 Z= 0.153 Angle : 0.623 11.211 113478 Z= 0.314 Chirality : 0.036 0.342 14238 Planarity : 0.005 0.094 7955 Dihedral : 24.351 179.322 31965 Min Nonbonded Distance : 2.017 Molprobity Statistics. All-atom Clashscore : 19.21 Ramachandran Plot: Outliers : 0.34 % Allowed : 11.42 % Favored : 88.24 % Rotamer: Outliers : 2.39 % Allowed : 18.16 % Favored : 79.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.81 % Cis-general : 0.09 % Twisted Proline : 1.69 % Twisted General : 0.37 % 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 (0.13), residues: 4438 helix: 0.69 (0.14), residues: 1402 sheet: -1.51 (0.20), residues: 669 loop : -2.38 (0.12), residues: 2367 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP V 83 HIS 0.006 0.001 HIS J 133 PHE 0.035 0.002 PHE J 164 TYR 0.017 0.001 TYR J 19 ARG 0.006 0.000 ARG N 55 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8876 Ramachandran restraints generated. 4438 Oldfield, 0 Emsley, 4438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8876 Ramachandran restraints generated. 4438 Oldfield, 0 Emsley, 4438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 275 residues out of total 3832 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 90 poor density : 185 time to evaluate : 4.288 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 109 ASN cc_start: 0.7949 (t0) cc_final: 0.7719 (t0) REVERT: A 198 MET cc_start: 0.8503 (tpp) cc_final: 0.8290 (tpp) REVERT: B 111 ARG cc_start: 0.8679 (mmm160) cc_final: 0.8324 (mmp80) REVERT: B 203 ASP cc_start: 0.8143 (m-30) cc_final: 0.7693 (t70) REVERT: E 87 MET cc_start: 0.8455 (tpp) cc_final: 0.8146 (tpp) REVERT: G 76 LEU cc_start: 0.9053 (OUTLIER) cc_final: 0.8777 (tp) REVERT: H 50 ASP cc_start: 0.8302 (p0) cc_final: 0.7774 (t0) REVERT: I 8 ARG cc_start: 0.8485 (OUTLIER) cc_final: 0.8096 (tpp80) REVERT: J 99 LEU cc_start: 0.5493 (OUTLIER) cc_final: 0.5204 (mm) REVERT: N 83 GLU cc_start: 0.6859 (pt0) cc_final: 0.6528 (pm20) REVERT: N 90 TYR cc_start: 0.7659 (m-10) cc_final: 0.7389 (m-10) REVERT: N 138 ASN cc_start: 0.8148 (p0) cc_final: 0.7742 (p0) REVERT: R 111 LYS cc_start: 0.8386 (ptpt) cc_final: 0.8150 (pttm) REVERT: V 64 GLU cc_start: 0.8351 (mm-30) cc_final: 0.8125 (mm-30) REVERT: e 25 GLU cc_start: 0.6706 (tt0) cc_final: 0.6114 (tm-30) REVERT: D 127 MET cc_start: 0.7960 (mmp) cc_final: 0.7687 (mmm) REVERT: D 177 MET cc_start: -0.0411 (mmt) cc_final: -0.1051 (mmt) REVERT: F 84 LYS cc_start: -0.2092 (OUTLIER) cc_final: -0.4128 (mmtp) REVERT: K 1 MET cc_start: -0.4856 (ttp) cc_final: -0.5420 (ttt) REVERT: M 129 GLU cc_start: 0.8321 (mm-30) cc_final: 0.8068 (pm20) REVERT: P 49 MET cc_start: 0.7931 (mtt) cc_final: 0.7702 (mmm) REVERT: T 67 MET cc_start: 0.8057 (mtt) cc_final: 0.7722 (mtt) REVERT: g 111 MET cc_start: 0.4737 (mmm) cc_final: 0.4250 (mtp) REVERT: g 165 ASP cc_start: 0.3296 (OUTLIER) cc_final: 0.3020 (t70) REVERT: g 221 MET cc_start: -0.3429 (ptt) cc_final: -0.3837 (ttp) REVERT: g 231 MET cc_start: 0.4793 (mtp) cc_final: 0.4390 (mtm) outliers start: 90 outliers final: 62 residues processed: 261 average time/residue: 0.7059 time to fit residues: 317.3285 Evaluate side-chains 235 residues out of total 3832 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 168 time to evaluate : 4.418 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 172 LEU Chi-restraints excluded: chain B residue 215 VAL Chi-restraints excluded: chain C residue 78 ASP Chi-restraints excluded: chain C residue 86 VAL Chi-restraints excluded: chain C residue 108 ASN Chi-restraints excluded: chain C residue 137 ILE Chi-restraints excluded: chain C residue 156 THR Chi-restraints excluded: chain C residue 196 VAL Chi-restraints excluded: chain C residue 226 THR Chi-restraints excluded: chain C residue 245 ASP Chi-restraints excluded: chain E residue 21 ASP Chi-restraints excluded: chain E residue 156 VAL Chi-restraints excluded: chain E residue 180 LEU Chi-restraints excluded: chain E residue 181 VAL Chi-restraints excluded: chain E residue 195 ILE Chi-restraints excluded: chain E residue 215 ASP Chi-restraints excluded: chain G residue 43 ASP Chi-restraints excluded: chain G residue 68 LEU Chi-restraints excluded: chain G residue 76 LEU Chi-restraints excluded: chain G residue 158 ILE Chi-restraints excluded: chain G residue 170 THR Chi-restraints excluded: chain H residue 49 ILE Chi-restraints excluded: chain H residue 91 ILE Chi-restraints excluded: chain I residue 8 ARG Chi-restraints excluded: chain I residue 193 LEU Chi-restraints excluded: chain J residue 99 LEU Chi-restraints excluded: chain J residue 111 THR Chi-restraints excluded: chain L residue 21 ASN Chi-restraints excluded: chain N residue 72 MET Chi-restraints excluded: chain N residue 87 ASP Chi-restraints excluded: chain R residue 40 THR Chi-restraints excluded: chain V residue 68 SER Chi-restraints excluded: chain W residue 53 ILE Chi-restraints excluded: chain W residue 65 LEU Chi-restraints excluded: chain W residue 74 VAL Chi-restraints excluded: chain W residue 93 LEU Chi-restraints excluded: chain X residue 103 LEU Chi-restraints excluded: chain Y residue 53 ASP Chi-restraints excluded: chain Y residue 64 PHE Chi-restraints excluded: chain Y residue 121 THR Chi-restraints excluded: chain b residue 4 VAL Chi-restraints excluded: chain b residue 8 LEU Chi-restraints excluded: chain b residue 46 VAL Chi-restraints excluded: chain b residue 67 THR Chi-restraints excluded: chain e residue 24 THR Chi-restraints excluded: chain e residue 51 ASN Chi-restraints excluded: chain F residue 25 LEU Chi-restraints excluded: chain F residue 69 PHE Chi-restraints excluded: chain F residue 84 LYS Chi-restraints excluded: chain F residue 194 LEU Chi-restraints excluded: chain K residue 51 SER Chi-restraints excluded: chain M residue 38 HIS Chi-restraints excluded: chain M residue 91 VAL Chi-restraints excluded: chain P residue 13 LYS Chi-restraints excluded: chain P residue 14 THR Chi-restraints excluded: chain P residue 22 LEU Chi-restraints excluded: chain S residue 3 LEU Chi-restraints excluded: chain S residue 93 THR Chi-restraints excluded: chain S residue 133 VAL Chi-restraints excluded: chain T residue 35 ASP Chi-restraints excluded: chain T residue 45 MET Chi-restraints excluded: chain T residue 135 ILE Chi-restraints excluded: chain Z residue 60 VAL Chi-restraints excluded: chain f residue 117 LEU Chi-restraints excluded: chain g residue 165 ASP Chi-restraints excluded: chain g residue 193 ILE Chi-restraints excluded: chain g residue 283 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 613 random chunks: chunk 298 optimal weight: 0.7980 chunk 386 optimal weight: 7.9990 chunk 518 optimal weight: 0.2980 chunk 148 optimal weight: 50.0000 chunk 448 optimal weight: 7.9990 chunk 71 optimal weight: 40.0000 chunk 135 optimal weight: 40.0000 chunk 487 optimal weight: 2.9990 chunk 203 optimal weight: 20.0000 chunk 500 optimal weight: 7.9990 chunk 61 optimal weight: 10.0000 overall best weight: 4.0186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 153 HIS ** B 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 87 GLN ** C 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 188 ASN ** E 258 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 139 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 185 GLN ** H 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 5 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 81 ASN ** W 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 22 ASN e 5 HIS ** K 32 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 128 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 19 ASN S 103 ASN ** U 48 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 95 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 159 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 174 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 268 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4163 r_free = 0.4163 target = 0.081002 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3711 r_free = 0.3711 target = 0.064354 restraints weight = 581076.335| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3655 r_free = 0.3655 target = 0.064068 restraints weight = 749721.574| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3671 r_free = 0.3671 target = 0.064473 restraints weight = 430569.644| |-----------------------------------------------------------------------------| r_work (final): 0.3592 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7324 moved from start: 0.5221 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 77723 Z= 0.235 Angle : 0.667 13.245 113478 Z= 0.336 Chirality : 0.038 0.360 14238 Planarity : 0.005 0.089 7955 Dihedral : 24.426 179.739 31965 Min Nonbonded Distance : 1.988 Molprobity Statistics. All-atom Clashscore : 22.21 Ramachandran Plot: Outliers : 0.38 % Allowed : 12.05 % Favored : 87.56 % Rotamer: Outliers : 2.34 % Allowed : 18.29 % Favored : 79.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.81 % Cis-general : 0.09 % Twisted Proline : 1.12 % Twisted General : 0.37 % 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: -1.83 (0.12), residues: 4438 helix: 0.65 (0.14), residues: 1399 sheet: -1.43 (0.20), residues: 627 loop : -2.41 (0.12), residues: 2412 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP C 144 HIS 0.007 0.001 HIS S 99 PHE 0.034 0.002 PHE J 164 TYR 0.015 0.001 TYR L 93 ARG 0.006 0.001 ARG Z 49 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9260.24 seconds wall clock time: 170 minutes 3.71 seconds (10203.71 seconds total)