Starting phenix.real_space_refine on Mon Feb 19 15:57:17 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ppk_20441/02_2024/6ppk_20441_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ppk_20441/02_2024/6ppk_20441.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ppk_20441/02_2024/6ppk_20441.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ppk_20441/02_2024/6ppk_20441.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ppk_20441/02_2024/6ppk_20441_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ppk_20441/02_2024/6ppk_20441_updated.pdb" } resolution = 4.4 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.005 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 2773 5.49 5 S 65 5.16 5 C 39667 2.51 5 N 14963 2.21 5 O 22983 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "C ARG 63": "NH1" <-> "NH2" Residue "C ARG 221": "NH1" <-> "NH2" Residue "D PHE 16": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 29": "OE1" <-> "OE2" Residue "E PHE 34": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 177": "OE1" <-> "OE2" Residue "F GLU 32": "OE1" <-> "OE2" Residue "F ARG 92": "NH1" <-> "NH2" Residue "G GLU 123": "OE1" <-> "OE2" Residue "G GLU 125": "OE1" <-> "OE2" Residue "J GLU 130": "OE1" <-> "OE2" Residue "J GLU 134": "OE1" <-> "OE2" Residue "K GLU 18": "OE1" <-> "OE2" Residue "K GLU 81": "OE1" <-> "OE2" Residue "L GLU 87": "OE1" <-> "OE2" Residue "N TYR 98": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O ARG 11": "NH1" <-> "NH2" Residue "P ARG 42": "NH1" <-> "NH2" Residue "P PHE 62": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P GLU 115": "OE1" <-> "OE2" Residue "Q ARG 13": "NH1" <-> "NH2" Residue "Q PHE 25": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R ARG 89": "NH1" <-> "NH2" Residue "S ARG 86": "NH1" <-> "NH2" Residue "V ARG 28": "NH1" <-> "NH2" Residue "Y GLU 45": "OE1" <-> "OE2" Residue "W ARG 53": "NH1" <-> "NH2" Residue "W GLU 168": "OE1" <-> "OE2" Residue "W GLU 243": "OE1" <-> "OE2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 80451 Number of models: 1 Model: "" Number of chains: 24 Chain: "A" Number of atoms: 57112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2658, 57112 Classifications: {'RNA': 2658} Modifications used: {'rna2p_pur': 253, 'rna2p_pyr': 132, 'rna3p_pur': 1302, 'rna3p_pyr': 971} Link IDs: {'rna2p': 385, 'rna3p': 2272} Chain breaks: 14 Chain: "B" Number of atoms: 2395 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 2395 Classifications: {'RNA': 112} Modifications used: {'rna2p_pur': 7, 'rna2p_pyr': 8, 'rna3p_pur': 53, 'rna3p_pyr': 44} Link IDs: {'rna2p': 15, 'rna3p': 96} Chain: "C" Number of atoms: 2010 Number of conformers: 1 Conformer: "" Number of residues, atoms: 260, 2010 Classifications: {'peptide': 260} Link IDs: {'PTRANS': 16, 'TRANS': 243} Chain breaks: 1 Chain: "D" Number of atoms: 1569 Number of conformers: 1 Conformer: "" Number of residues, atoms: 206, 1569 Classifications: {'peptide': 206} Link IDs: {'PTRANS': 10, 'TRANS': 195} Chain: "E" Number of atoms: 1511 Number of conformers: 1 Conformer: "" Number of residues, atoms: 197, 1511 Classifications: {'peptide': 197} Link IDs: {'PTRANS': 7, 'TRANS': 189} Chain breaks: 1 Chain: "F" Number of atoms: 1090 Number of conformers: 1 Conformer: "" Number of residues, atoms: 139, 1090 Classifications: {'peptide': 139} Link IDs: {'PTRANS': 6, 'TRANS': 132} Chain breaks: 3 Chain: "G" Number of atoms: 829 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 829 Classifications: {'peptide': 109} Link IDs: {'PTRANS': 5, 'TRANS': 103} Chain: "J" Number of atoms: 1119 Number of conformers: 1 Conformer: "" Number of residues, atoms: 141, 1119 Classifications: {'peptide': 141} Link IDs: {'PTRANS': 8, 'TRANS': 132} Chain: "K" Number of atoms: 920 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 920 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 4, 'TRANS': 117} Chain: "L" Number of atoms: 904 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 904 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 2, 'TRANS': 119} Chain breaks: 1 Chain: "N" Number of atoms: 947 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 947 Classifications: {'peptide': 118} Link IDs: {'PTRANS': 2, 'TRANS': 115} Chain: "O" Number of atoms: 775 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 775 Classifications: {'peptide': 100} Link IDs: {'PTRANS': 1, 'TRANS': 98} Chain breaks: 3 Chain: "P" Number of atoms: 936 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 936 Classifications: {'peptide': 114} Link IDs: {'PTRANS': 4, 'TRANS': 109} Chain: "Q" Number of atoms: 940 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 940 Classifications: {'peptide': 117} Link IDs: {'TRANS': 116} Chain: "R" Number of atoms: 781 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 781 Classifications: {'peptide': 100} Link IDs: {'PTRANS': 3, 'TRANS': 96} Chain: "S" Number of atoms: 842 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 842 Classifications: {'peptide': 109} Link IDs: {'PTRANS': 5, 'TRANS': 103} Chain: "T" Number of atoms: 724 Number of conformers: 1 Conformer: "" Number of residues, atoms: 90, 724 Classifications: {'peptide': 90} Link IDs: {'PTRANS': 2, 'TRANS': 87} Chain: "U" Number of atoms: 691 Number of conformers: 1 Conformer: "" Number of residues, atoms: 91, 691 Classifications: {'peptide': 91} Link IDs: {'PTRANS': 5, 'TRANS': 85} Chain breaks: 2 Chain: "V" Number of atoms: 604 Number of conformers: 1 Conformer: "" Number of residues, atoms: 78, 604 Classifications: {'peptide': 78} Link IDs: {'PTRANS': 2, 'TRANS': 75} Chain breaks: 1 Chain: "Z" Number of atoms: 455 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 455 Classifications: {'peptide': 58} Link IDs: {'PTRANS': 1, 'TRANS': 56} Chain: "b" Number of atoms: 418 Number of conformers: 1 Conformer: "" Number of residues, atoms: 53, 418 Classifications: {'peptide': 53} Link IDs: {'PTRANS': 3, 'TRANS': 49} Chain: "Y" Number of atoms: 530 Number of conformers: 1 Conformer: "" Number of residues, atoms: 65, 530 Classifications: {'peptide': 65} Link IDs: {'TRANS': 64} Chain: "d" Number of atoms: 359 Number of conformers: 1 Conformer: "" Number of residues, atoms: 43, 359 Classifications: {'peptide': 43} Link IDs: {'PTRANS': 1, 'TRANS': 41} Chain: "W" Number of atoms: 1990 Number of conformers: 1 Conformer: "" Number of residues, atoms: 253, 1990 Unusual residues: {'GNP': 1} Classifications: {'peptide': 252, 'undetermined': 1} Incomplete info: {'truncation_to_alanine': 13} Link IDs: {'PTRANS': 12, 'TRANS': 239, None: 1} Not linked: pdbres="GLN W 279 " pdbres="GNP W 301 " Chain breaks: 4 Unresolved non-hydrogen bonds: 52 Unresolved non-hydrogen angles: 60 Unresolved non-hydrogen dihedrals: 44 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 3, 'ASN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 25 Time building chain proxies: 31.38, per 1000 atoms: 0.39 Number of scatterers: 80451 At special positions: 0 Unit cell: (203, 210.25, 217.5, 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 65 16.00 P 2773 15.00 O 22983 8.00 N 14963 7.00 C 39667 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 Atom "ATOM 58212 O4' U B 54 .*. O " rejected from bonding due to valence issues. Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 43.26 Conformation dependent library (CDL) restraints added in 3.2 seconds 5216 Ramachandran restraints generated. 2608 Oldfield, 0 Emsley, 2608 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4890 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 75 helices and 27 sheets defined 23.7% alpha, 10.5% beta 645 base pairs and 1304 stacking pairs defined. Time for finding SS restraints: 37.87 Creating SS restraints... Processing helix chain 'C' and resid 31 through 33 No H-bonds generated for 'chain 'C' and resid 31 through 33' Processing helix chain 'C' and resid 132 through 134 No H-bonds generated for 'chain 'C' and resid 132 through 134' Processing helix chain 'C' and resid 177 through 179 No H-bonds generated for 'chain 'C' and resid 177 through 179' Processing helix chain 'C' and resid 198 through 202 removed outlier: 3.785A pdb=" N GLU C 201 " --> pdb=" O GLU C 198 " (cutoff:3.500A) Processing helix chain 'C' and resid 208 through 214 removed outlier: 4.300A pdb=" N LYS C 214 " --> pdb=" O ARG C 210 " (cutoff:3.500A) Processing helix chain 'C' and resid 222 through 224 No H-bonds generated for 'chain 'C' and resid 222 through 224' Processing helix chain 'C' and resid 265 through 269 removed outlier: 3.703A pdb=" N LYS C 268 " --> pdb=" O LYS C 265 " (cutoff:3.500A) Processing helix chain 'D' and resid 41 through 44 No H-bonds generated for 'chain 'D' and resid 41 through 44' Processing helix chain 'D' and resid 63 through 67 removed outlier: 3.591A pdb=" N GLY D 67 " --> pdb=" O LYS D 63 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 63 through 67' Processing helix chain 'D' and resid 122 through 126 Processing helix chain 'E' and resid 30 through 41 removed outlier: 3.609A pdb=" N MET E 39 " --> pdb=" O ASP E 35 " (cutoff:3.500A) Processing helix chain 'E' and resid 103 through 119 removed outlier: 3.625A pdb=" N ILE E 110 " --> pdb=" O ARG E 106 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N LYS E 111 " --> pdb=" O ARG E 107 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N SER E 115 " --> pdb=" O LYS E 111 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N ILE E 119 " --> pdb=" O SER E 115 " (cutoff:3.500A) Processing helix chain 'E' and resid 137 through 145 removed outlier: 4.268A pdb=" N GLY E 145 " --> pdb=" O ALA E 141 " (cutoff:3.500A) Processing helix chain 'E' and resid 161 through 164 No H-bonds generated for 'chain 'E' and resid 161 through 164' Processing helix chain 'E' and resid 178 through 180 No H-bonds generated for 'chain 'E' and resid 178 through 180' Processing helix chain 'E' and resid 183 through 189 removed outlier: 4.150A pdb=" N VAL E 187 " --> pdb=" O VAL E 183 " (cutoff:3.500A) Processing helix chain 'E' and resid 196 through 205 Processing helix chain 'F' and resid 12 through 15 No H-bonds generated for 'chain 'F' and resid 12 through 15' Processing helix chain 'F' and resid 95 through 106 removed outlier: 3.526A pdb=" N ILE F 104 " --> pdb=" O LEU F 100 " (cutoff:3.500A) removed outlier: 4.352A pdb=" N SER F 105 " --> pdb=" O ASP F 101 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N VAL F 106 " --> pdb=" O LYS F 102 " (cutoff:3.500A) Processing helix chain 'F' and resid 163 through 171 Processing helix chain 'G' and resid 61 through 81 Processing helix chain 'G' and resid 139 through 150 removed outlier: 3.737A pdb=" N ALA G 144 " --> pdb=" O GLU G 140 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N ILE G 145 " --> pdb=" O ARG G 141 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N ALA G 146 " --> pdb=" O VAL G 142 " (cutoff:3.500A) Processing helix chain 'J' and resid 26 through 37 Processing helix chain 'J' and resid 90 through 96 Processing helix chain 'J' and resid 98 through 109 removed outlier: 3.860A pdb=" N ALA J 105 " --> pdb=" O MET J 101 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N ILE J 106 " --> pdb=" O LEU J 102 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N GLY J 108 " --> pdb=" O LEU J 104 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N MET J 109 " --> pdb=" O ALA J 105 " (cutoff:3.500A) Processing helix chain 'J' and resid 115 through 120 Processing helix chain 'J' and resid 134 through 136 No H-bonds generated for 'chain 'J' and resid 134 through 136' Processing helix chain 'L' and resid 95 through 98 No H-bonds generated for 'chain 'L' and resid 95 through 98' Processing helix chain 'L' and resid 130 through 136 removed outlier: 3.783A pdb=" N GLU L 134 " --> pdb=" O ALA L 130 " (cutoff:3.500A) Processing helix chain 'N' and resid 10 through 27 removed outlier: 3.624A pdb=" N ALA N 15 " --> pdb=" O ALA N 11 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N LEU N 17 " --> pdb=" O ARG N 13 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N ARG N 18 " --> pdb=" O LYS N 14 " (cutoff:3.500A) removed outlier: 4.162A pdb=" N ASP N 19 " --> pdb=" O ALA N 15 " (cutoff:3.500A) removed outlier: 4.408A pdb=" N LEU N 20 " --> pdb=" O MET N 16 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N ASN N 27 " --> pdb=" O ASP N 23 " (cutoff:3.500A) Processing helix chain 'N' and resid 34 through 51 removed outlier: 4.832A pdb=" N SER N 42 " --> pdb=" O LYS N 38 " (cutoff:3.500A) removed outlier: 4.146A pdb=" N VAL N 43 " --> pdb=" O GLU N 39 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N GLU N 45 " --> pdb=" O ARG N 41 " (cutoff:3.500A) removed outlier: 5.204A pdb=" N LYS N 46 " --> pdb=" O SER N 42 " (cutoff:3.500A) Processing helix chain 'N' and resid 56 through 63 removed outlier: 3.523A pdb=" N GLN N 61 " --> pdb=" O HIS N 57 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N ALA N 62 " --> pdb=" O ALA N 58 " (cutoff:3.500A) Processing helix chain 'N' and resid 79 through 91 removed outlier: 3.623A pdb=" N LEU N 83 " --> pdb=" O ALA N 79 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N PHE N 84 " --> pdb=" O LEU N 80 " (cutoff:3.500A) removed outlier: 4.423A pdb=" N SER N 85 " --> pdb=" O GLN N 81 " (cutoff:3.500A) removed outlier: 5.217A pdb=" N ALA N 88 " --> pdb=" O PHE N 84 " (cutoff:3.500A) removed outlier: 5.285A pdb=" N THR N 89 " --> pdb=" O SER N 85 " (cutoff:3.500A) Processing helix chain 'O' and resid 8 through 20 Processing helix chain 'O' and resid 80 through 83 No H-bonds generated for 'chain 'O' and resid 80 through 83' Processing helix chain 'O' and resid 85 through 87 No H-bonds generated for 'chain 'O' and resid 85 through 87' Processing helix chain 'O' and resid 105 through 115 Processing helix chain 'P' and resid 6 through 15 removed outlier: 4.234A pdb=" N ASP P 10 " --> pdb=" O LYS P 6 " (cutoff:3.500A) removed outlier: 5.545A pdb=" N ILE P 11 " --> pdb=" O LEU P 7 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N THR P 12 " --> pdb=" O ILE P 8 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N LYS P 13 " --> pdb=" O GLU P 9 " (cutoff:3.500A) removed outlier: 4.266A pdb=" N GLU P 14 " --> pdb=" O ASP P 10 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N GLN P 15 " --> pdb=" O ILE P 11 " (cutoff:3.500A) No H-bonds generated for 'chain 'P' and resid 6 through 15' Processing helix chain 'P' and resid 57 through 59 No H-bonds generated for 'chain 'P' and resid 57 through 59' Processing helix chain 'P' and resid 101 through 104 Processing helix chain 'P' and resid 113 through 115 No H-bonds generated for 'chain 'P' and resid 113 through 115' Processing helix chain 'Q' and resid 9 through 21 removed outlier: 3.868A pdb=" N LYS Q 16 " --> pdb=" O LYS Q 12 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N VAL Q 17 " --> pdb=" O ARG Q 13 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N LEU Q 20 " --> pdb=" O LYS Q 16 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N ALA Q 21 " --> pdb=" O VAL Q 17 " (cutoff:3.500A) Processing helix chain 'Q' and resid 26 through 29 removed outlier: 4.048A pdb=" N HIS Q 29 " --> pdb=" O GLY Q 26 " (cutoff:3.500A) No H-bonds generated for 'chain 'Q' and resid 26 through 29' Processing helix chain 'Q' and resid 32 through 35 No H-bonds generated for 'chain 'Q' and resid 32 through 35' Processing helix chain 'Q' and resid 39 through 72 removed outlier: 3.849A pdb=" N ASN Q 44 " --> pdb=" O MET Q 40 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N ARG Q 51 " --> pdb=" O PHE Q 47 " (cutoff:3.500A) removed outlier: 4.448A pdb=" N LYS Q 54 " --> pdb=" O ARG Q 50 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N ARG Q 58 " --> pdb=" O LYS Q 54 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N ILE Q 62 " --> pdb=" O ARG Q 58 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N THR Q 63 " --> pdb=" O LYS Q 59 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N ALA Q 68 " --> pdb=" O ARG Q 64 " (cutoff:3.500A) Processing helix chain 'Q' and resid 76 through 85 removed outlier: 3.918A pdb=" N LEU Q 85 " --> pdb=" O HIS Q 81 " (cutoff:3.500A) Processing helix chain 'Q' and resid 93 through 98 Processing helix chain 'Q' and resid 107 through 114 removed outlier: 4.196A pdb=" N ASP Q 111 " --> pdb=" O ASN Q 107 " (cutoff:3.500A) removed outlier: 4.508A pdb=" N ALA Q 112 " --> pdb=" O GLN Q 108 " (cutoff:3.500A) Processing helix chain 'S' and resid 17 through 23 removed outlier: 3.603A pdb=" N VAL S 20 " --> pdb=" O ALA S 17 " (cutoff:3.500A) removed outlier: 5.491A pdb=" N ASP S 22 " --> pdb=" O LEU S 19 " (cutoff:3.500A) Processing helix chain 'S' and resid 29 through 35 removed outlier: 4.104A pdb=" N SER S 34 " --> pdb=" O GLY S 30 " (cutoff:3.500A) Processing helix chain 'S' and resid 44 through 62 removed outlier: 3.768A pdb=" N VAL S 50 " --> pdb=" O ILE S 46 " (cutoff:3.500A) Processing helix chain 'S' and resid 66 through 68 No H-bonds generated for 'chain 'S' and resid 66 through 68' Processing helix chain 'S' and resid 89 through 91 No H-bonds generated for 'chain 'S' and resid 89 through 91' Processing helix chain 'T' and resid 15 through 21 Processing helix chain 'T' and resid 36 through 46 removed outlier: 3.542A pdb=" N GLU T 44 " --> pdb=" O LYS T 40 " (cutoff:3.500A) Processing helix chain 'U' and resid 14 through 16 No H-bonds generated for 'chain 'U' and resid 14 through 16' Processing helix chain 'U' and resid 65 through 67 No H-bonds generated for 'chain 'U' and resid 65 through 67' Processing helix chain 'Z' and resid 17 through 26 removed outlier: 3.532A pdb=" N VAL Z 21 " --> pdb=" O GLU Z 17 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N THR Z 22 " --> pdb=" O ASP Z 18 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N VAL Z 23 " --> pdb=" O GLN Z 19 " (cutoff:3.500A) Processing helix chain 'Z' and resid 41 through 49 removed outlier: 4.258A pdb=" N MET Z 46 " --> pdb=" O ALA Z 42 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N ILE Z 47 " --> pdb=" O ILE Z 43 " (cutoff:3.500A) Processing helix chain 'b' and resid 18 through 20 No H-bonds generated for 'chain 'b' and resid 18 through 20' Processing helix chain 'Y' and resid 11 through 34 removed outlier: 4.978A pdb=" N GLN Y 16 " --> pdb=" O ALA Y 12 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N LYS Y 17 " --> pdb=" O GLU Y 13 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N LYS Y 19 " --> pdb=" O GLU Y 15 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N SER Y 20 " --> pdb=" O GLN Y 16 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N PHE Y 30 " --> pdb=" O PHE Y 26 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N GLN Y 31 " --> pdb=" O ASN Y 27 " (cutoff:3.500A) Processing helix chain 'Y' and resid 40 through 64 removed outlier: 3.994A pdb=" N ARG Y 47 " --> pdb=" O ILE Y 43 " (cutoff:3.500A) removed outlier: 4.354A pdb=" N VAL Y 56 " --> pdb=" O ARG Y 52 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N ILE Y 57 " --> pdb=" O MET Y 53 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N GLU Y 59 " --> pdb=" O THR Y 55 " (cutoff:3.500A) Processing helix chain 'd' and resid 9 through 15 Processing helix chain 'd' and resid 25 through 37 removed outlier: 3.597A pdb=" N LEU d 31 " --> pdb=" O GLY d 27 " (cutoff:3.500A) Processing helix chain 'W' and resid 11 through 20 removed outlier: 3.509A pdb=" N GLU W 16 " --> pdb=" O LYS W 12 " (cutoff:3.500A) removed outlier: 4.250A pdb=" N GLU W 19 " --> pdb=" O ARG W 15 " (cutoff:3.500A) removed outlier: 4.872A pdb=" N LYS W 20 " --> pdb=" O GLU W 16 " (cutoff:3.500A) Processing helix chain 'W' and resid 37 through 39 No H-bonds generated for 'chain 'W' and resid 37 through 39' Processing helix chain 'W' and resid 44 through 47 No H-bonds generated for 'chain 'W' and resid 44 through 47' Processing helix chain 'W' and resid 66 through 78 Processing helix chain 'W' and resid 99 through 102 No H-bonds generated for 'chain 'W' and resid 99 through 102' Processing helix chain 'W' and resid 105 through 107 No H-bonds generated for 'chain 'W' and resid 105 through 107' Processing helix chain 'W' and resid 190 through 192 No H-bonds generated for 'chain 'W' and resid 190 through 192' Processing helix chain 'W' and resid 203 through 215 removed outlier: 4.092A pdb=" N LEU W 210 " --> pdb=" O ALA W 206 " (cutoff:3.500A) removed outlier: 4.819A pdb=" N ARG W 211 " --> pdb=" O VAL W 207 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N PHE W 212 " --> pdb=" O PHE W 208 " (cutoff:3.500A) Processing helix chain 'W' and resid 218 through 224 removed outlier: 3.926A pdb=" N LEU W 221 " --> pdb=" O PRO W 218 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N LYS W 222 " --> pdb=" O GLU W 219 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N GLU W 223 " --> pdb=" O ARG W 220 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N ARG W 224 " --> pdb=" O LEU W 221 " (cutoff:3.500A) No H-bonds generated for 'chain 'W' and resid 218 through 224' Processing helix chain 'W' and resid 236 through 245 removed outlier: 3.710A pdb=" N LYS W 244 " --> pdb=" O ALA W 240 " (cutoff:3.500A) Processing helix chain 'W' and resid 256 through 267 removed outlier: 3.717A pdb=" N ILE W 263 " --> pdb=" O THR W 259 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N ASP W 266 " --> pdb=" O VAL W 262 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'C' and resid 34 through 36 Processing sheet with id= B, first strand: chain 'C' and resid 115 through 117 removed outlier: 4.687A pdb=" N ASN C 90 " --> pdb=" O ALA C 106 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N ARG C 102 " --> pdb=" O ILE C 94 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'C' and resid 129 through 131 Processing sheet with id= D, first strand: chain 'C' and resid 172 through 175 removed outlier: 3.564A pdb=" N ARG C 182 " --> pdb=" O VAL C 174 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'D' and resid 4 through 8 removed outlier: 7.038A pdb=" N LEU D 199 " --> pdb=" O VAL D 113 " (cutoff:3.500A) removed outlier: 4.338A pdb=" N VAL D 113 " --> pdb=" O LEU D 199 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'D' and resid 12 through 15 Processing sheet with id= G, first strand: chain 'D' and resid 175 through 180 removed outlier: 4.515A pdb=" N GLU D 175 " --> pdb=" O LYS D 189 " (cutoff:3.500A) removed outlier: 7.200A pdb=" N LEU D 187 " --> pdb=" O VAL D 177 " (cutoff:3.500A) removed outlier: 4.753A pdb=" N VAL D 179 " --> pdb=" O LEU D 185 " (cutoff:3.500A) removed outlier: 6.825A pdb=" N LEU D 185 " --> pdb=" O VAL D 179 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'E' and resid 123 through 125 removed outlier: 6.134A pdb=" N LEU E 192 " --> pdb=" O ILE E 124 " (cutoff:3.500A) removed outlier: 6.543A pdb=" N LEU E 153 " --> pdb=" O LEU E 193 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N THR E 174 " --> pdb=" O ALA E 152 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'F' and resid 89 through 91 removed outlier: 4.156A pdb=" N LEU F 91 " --> pdb=" O ILE F 34 " (cutoff:3.500A) removed outlier: 4.351A pdb=" N ILE F 34 " --> pdb=" O LEU F 91 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'G' and resid 162 through 165 removed outlier: 4.306A pdb=" N VAL G 91 " --> pdb=" O GLY G 162 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'G' and resid 103 through 105 removed outlier: 3.512A pdb=" N LEU G 104 " --> pdb=" O ILE G 116 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'J' and resid 18 through 20 removed outlier: 6.126A pdb=" N ILE J 56 " --> pdb=" O VAL J 19 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N ASN J 124 " --> pdb=" O VAL J 55 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'K' and resid 7 through 9 removed outlier: 7.235A pdb=" N VAL K 40 " --> pdb=" O ILE K 22 " (cutoff:3.500A) removed outlier: 5.476A pdb=" N VAL K 24 " --> pdb=" O VAL K 38 " (cutoff:3.500A) removed outlier: 7.393A pdb=" N VAL K 38 " --> pdb=" O VAL K 24 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'L' and resid 75 through 77 removed outlier: 3.955A pdb=" N LYS L 110 " --> pdb=" O ALA L 75 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N VAL L 77 " --> pdb=" O LYS L 110 " (cutoff:3.500A) No H-bonds generated for sheet with id= N Processing sheet with id= O, first strand: chain 'N' and resid 29 through 33 removed outlier: 4.485A pdb=" N GLY N 105 " --> pdb=" O MET N 114 " (cutoff:3.500A) removed outlier: 6.178A pdb=" N ILE N 116 " --> pdb=" O LYS N 103 " (cutoff:3.500A) removed outlier: 5.632A pdb=" N LYS N 103 " --> pdb=" O ILE N 116 " (cutoff:3.500A) removed outlier: 8.395A pdb=" N GLU N 118 " --> pdb=" O ILE N 101 " (cutoff:3.500A) removed outlier: 6.705A pdb=" N ILE N 101 " --> pdb=" O GLU N 118 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'P' and resid 44 through 49 removed outlier: 3.667A pdb=" N THR P 28 " --> pdb=" O ARG P 91 " (cutoff:3.500A) removed outlier: 5.242A pdb=" N ARG P 30 " --> pdb=" O VAL P 89 " (cutoff:3.500A) removed outlier: 5.210A pdb=" N VAL P 89 " --> pdb=" O ARG P 30 " (cutoff:3.500A) removed outlier: 7.552A pdb=" N HIS P 32 " --> pdb=" O ILE P 87 " (cutoff:3.500A) removed outlier: 6.357A pdb=" N ILE P 87 " --> pdb=" O HIS P 32 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'P' and resid 64 through 68 Processing sheet with id= R, first strand: chain 'R' and resid 3 through 5 Processing sheet with id= S, first strand: chain 'R' and resid 19 through 22 removed outlier: 4.108A pdb=" N GLY R 66 " --> pdb=" O TYR R 92 " (cutoff:3.500A) removed outlier: 6.402A pdb=" N THR R 96 " --> pdb=" O VAL R 62 " (cutoff:3.500A) removed outlier: 5.274A pdb=" N VAL R 62 " --> pdb=" O THR R 96 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'R' and resid 71 through 76 removed outlier: 3.687A pdb=" N ILE R 71 " --> pdb=" O HIS R 88 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'S' and resid 3 through 6 removed outlier: 3.721A pdb=" N GLN S 73 " --> pdb=" O VAL S 106 " (cutoff:3.500A) removed outlier: 6.645A pdb=" N SER S 108 " --> pdb=" O ILE S 71 " (cutoff:3.500A) removed outlier: 5.110A pdb=" N ILE S 71 " --> pdb=" O SER S 108 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'S' and resid 84 through 86 removed outlier: 3.681A pdb=" N ARG S 86 " --> pdb=" O SER S 94 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N SER S 94 " --> pdb=" O ARG S 86 " (cutoff:3.500A) Processing sheet with id= W, first strand: chain 'T' and resid 25 through 29 removed outlier: 3.581A pdb=" N LYS T 53 " --> pdb=" O LYS T 82 " (cutoff:3.500A) Processing sheet with id= X, first strand: chain 'U' and resid 23 through 27 removed outlier: 6.671A pdb=" N LEU U 34 " --> pdb=" O LEU U 24 " (cutoff:3.500A) removed outlier: 4.904A pdb=" N ALA U 26 " --> pdb=" O ARG U 32 " (cutoff:3.500A) removed outlier: 6.636A pdb=" N ARG U 32 " --> pdb=" O ALA U 26 " (cutoff:3.500A) Processing sheet with id= Y, first strand: chain 'V' and resid 74 through 80 Processing sheet with id= Z, first strand: chain 'Z' and resid 34 through 38 removed outlier: 3.768A pdb=" N THR Z 7 " --> pdb=" O SER Z 55 " (cutoff:3.500A) Processing sheet with id= AA, first strand: chain 'W' and resid 123 through 125 removed outlier: 7.307A pdb=" N ILE W 26 " --> pdb=" O LEU W 124 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N ASN W 58 " --> pdb=" O VAL W 31 " (cutoff:3.500A) 406 hydrogen bonds defined for protein. 1155 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 1520 hydrogen bonds 2308 hydrogen bond angles 0 basepair planarities 645 basepair parallelities 1304 stacking parallelities Total time for adding SS restraints: 98.60 Time building geometry restraints manager: 45.98 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: 38759 1.44 - 1.56: 34598 1.56 - 1.69: 5530 1.69 - 1.81: 124 Bond restraints: 87845 Sorted by residual: bond pdb=" C GLN d 6 " pdb=" N PRO d 7 " ideal model delta sigma weight residual 1.335 1.285 0.050 8.70e-03 1.32e+04 3.25e+01 bond pdb=" O2B GNP W 301 " pdb=" PB GNP W 301 " ideal model delta sigma weight residual 1.505 1.610 -0.105 2.00e-02 2.50e+03 2.76e+01 bond pdb=" C4 GNP W 301 " pdb=" C5 GNP W 301 " ideal model delta sigma weight residual 1.382 1.470 -0.088 2.00e-02 2.50e+03 1.94e+01 bond pdb=" O2G GNP W 301 " pdb=" PG GNP W 301 " ideal model delta sigma weight residual 1.528 1.610 -0.082 2.00e-02 2.50e+03 1.67e+01 bond pdb=" O3G GNP W 301 " pdb=" PG GNP W 301 " ideal model delta sigma weight residual 1.532 1.610 -0.078 2.00e-02 2.50e+03 1.52e+01 ... (remaining 87840 not shown) Histogram of bond angle deviations from ideal: 92.19 - 101.26: 874 101.26 - 110.34: 45707 110.34 - 119.41: 45907 119.41 - 128.48: 36100 128.48 - 137.56: 3754 Bond angle restraints: 132342 Sorted by residual: angle pdb=" C ILE K 2 " pdb=" CA ILE K 2 " pdb=" CB ILE K 2 " ideal model delta sigma weight residual 111.49 137.56 -26.07 1.38e+00 5.25e-01 3.57e+02 angle pdb=" C ARG V 82 " pdb=" CA ARG V 82 " pdb=" CB ARG V 82 " ideal model delta sigma weight residual 111.26 134.21 -22.95 1.66e+00 3.63e-01 1.91e+02 angle pdb=" N ARG V 82 " pdb=" CA ARG V 82 " pdb=" C ARG V 82 " ideal model delta sigma weight residual 112.12 95.34 16.78 1.34e+00 5.57e-01 1.57e+02 angle pdb=" N ILE K 2 " pdb=" CA ILE K 2 " pdb=" C ILE K 2 " ideal model delta sigma weight residual 109.45 92.19 17.26 1.39e+00 5.18e-01 1.54e+02 angle pdb=" N LYS U 84 " pdb=" CA LYS U 84 " pdb=" C LYS U 84 " ideal model delta sigma weight residual 112.93 127.69 -14.76 1.33e+00 5.65e-01 1.23e+02 ... (remaining 132337 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.96: 47655 35.96 - 71.93: 7660 71.93 - 107.89: 891 107.89 - 143.86: 31 143.86 - 179.82: 51 Dihedral angle restraints: 56288 sinusoidal: 48692 harmonic: 7596 Sorted by residual: dihedral pdb=" O4' C A1281 " pdb=" C1' C A1281 " pdb=" N1 C A1281 " pdb=" C2 C A1281 " ideal model delta sinusoidal sigma weight residual -160.00 19.45 -179.45 1 1.50e+01 4.44e-03 8.53e+01 dihedral pdb=" O4' C A1515 " pdb=" C1' C A1515 " pdb=" N1 C A1515 " pdb=" C2 C A1515 " ideal model delta sinusoidal sigma weight residual 200.00 46.15 153.85 1 1.50e+01 4.44e-03 8.10e+01 dihedral pdb=" O4' C A 482 " pdb=" C1' C A 482 " pdb=" N1 C A 482 " pdb=" C2 C A 482 " ideal model delta sinusoidal sigma weight residual 200.00 47.90 152.10 1 1.50e+01 4.44e-03 8.04e+01 ... (remaining 56285 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.123: 16497 0.123 - 0.247: 521 0.247 - 0.370: 36 0.370 - 0.493: 7 0.493 - 0.617: 5 Chirality restraints: 17066 Sorted by residual: chirality pdb=" CA ILE K 2 " pdb=" N ILE K 2 " pdb=" C ILE K 2 " pdb=" CB ILE K 2 " both_signs ideal model delta sigma weight residual False 2.43 1.82 0.62 2.00e-01 2.50e+01 9.51e+00 chirality pdb=" CA SER D 103 " pdb=" N SER D 103 " pdb=" C SER D 103 " pdb=" CB SER D 103 " both_signs ideal model delta sigma weight residual False 2.51 3.09 -0.58 2.00e-01 2.50e+01 8.37e+00 chirality pdb=" CA LEU P 29 " pdb=" N LEU P 29 " pdb=" C LEU P 29 " pdb=" CB LEU P 29 " both_signs ideal model delta sigma weight residual False 2.51 1.97 0.54 2.00e-01 2.50e+01 7.33e+00 ... (remaining 17063 not shown) Planarity restraints: 6406 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASN R 50 " 0.052 5.00e-02 4.00e+02 7.90e-02 9.99e+00 pdb=" N PRO R 51 " -0.137 5.00e-02 4.00e+02 pdb=" CA PRO R 51 " 0.040 5.00e-02 4.00e+02 pdb=" CD PRO R 51 " 0.044 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR J 4 " -0.051 5.00e-02 4.00e+02 7.65e-02 9.36e+00 pdb=" N PRO J 5 " 0.132 5.00e-02 4.00e+02 pdb=" CA PRO J 5 " -0.038 5.00e-02 4.00e+02 pdb=" CD PRO J 5 " -0.043 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER C 248 " 0.049 5.00e-02 4.00e+02 7.30e-02 8.53e+00 pdb=" N PRO C 249 " -0.126 5.00e-02 4.00e+02 pdb=" CA PRO C 249 " 0.037 5.00e-02 4.00e+02 pdb=" CD PRO C 249 " 0.040 5.00e-02 4.00e+02 ... (remaining 6403 not shown) Histogram of nonbonded interaction distances: 1.15 - 1.90: 36 1.90 - 2.65: 5166 2.65 - 3.40: 110790 3.40 - 4.15: 268701 4.15 - 4.90: 353518 Nonbonded interactions: 738211 Sorted by model distance: nonbonded pdb=" CD LYS F 33 " pdb=" NH2 ARG F 92 " model vdw 1.150 3.520 nonbonded pdb=" O4' A B 55 " pdb=" OE1 GLN F 27 " model vdw 1.152 3.040 nonbonded pdb=" OD2 ASP D 54 " pdb=" NH1 ARG D 78 " model vdw 1.177 2.520 nonbonded pdb=" OD1 ASP U 72 " pdb=" NE2 GLN U 99 " model vdw 1.245 2.520 nonbonded pdb=" O2 C B 41 " pdb=" CD ARG F 92 " model vdw 1.329 3.440 ... (remaining 738206 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: 0.620 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: 0.060 Extract box with map and model: 6.010 Check model and map are aligned: 0.870 Set scattering table: 0.530 Process input model: 261.900 Find NCS groups from input model: 1.240 Set up NCS constraints: 0.190 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:2.290 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 273.720 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8225 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.134 87845 Z= 0.500 Angle : 1.080 26.069 132342 Z= 0.548 Chirality : 0.054 0.617 17066 Planarity : 0.006 0.079 6406 Dihedral : 26.185 179.820 51398 Min Nonbonded Distance : 1.150 Molprobity Statistics. All-atom Clashscore : 22.61 Ramachandran Plot: Outliers : 0.65 % Allowed : 11.81 % Favored : 87.54 % Rotamer: Outliers : 8.03 % Allowed : 13.19 % Favored : 78.78 % Cbeta Deviations : 0.61 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: -4.28 (0.13), residues: 2608 helix: -3.33 (0.14), residues: 587 sheet: -2.46 (0.24), residues: 396 loop : -2.87 (0.13), residues: 1625 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP J 16 HIS 0.014 0.002 HIS J 54 PHE 0.044 0.002 PHE Q 57 TYR 0.022 0.002 TYR J 97 ARG 0.023 0.001 ARG Q 92 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5216 Ramachandran restraints generated. 2608 Oldfield, 0 Emsley, 2608 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5216 Ramachandran restraints generated. 2608 Oldfield, 0 Emsley, 2608 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 964 residues out of total 2242 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 179 poor density : 785 time to evaluate : 3.251 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: C 16 MET cc_start: 0.8494 (ppp) cc_final: 0.7536 (ppp) REVERT: C 156 ARG cc_start: 0.8409 (OUTLIER) cc_final: 0.7427 (ttm110) REVERT: C 188 CYS cc_start: 0.8253 (m) cc_final: 0.8001 (m) REVERT: C 247 MET cc_start: 0.5812 (ttm) cc_final: 0.5172 (ttm) REVERT: D 36 LEU cc_start: 0.9147 (mt) cc_final: 0.8713 (mp) REVERT: D 95 GLN cc_start: 0.8920 (OUTLIER) cc_final: 0.8556 (tt0) REVERT: D 153 ARG cc_start: 0.8473 (ptt90) cc_final: 0.8022 (ptm-80) REVERT: D 155 PHE cc_start: 0.8370 (m-10) cc_final: 0.8163 (m-80) REVERT: D 159 LEU cc_start: 0.8339 (OUTLIER) cc_final: 0.8072 (mt) REVERT: D 201 THR cc_start: 0.8701 (m) cc_final: 0.8406 (p) REVERT: E 35 ASP cc_start: 0.8656 (t70) cc_final: 0.8251 (t70) REVERT: E 48 THR cc_start: 0.8957 (p) cc_final: 0.8564 (p) REVERT: E 150 LYS cc_start: 0.9179 (mppt) cc_final: 0.8729 (mttp) REVERT: E 158 ASP cc_start: 0.8530 (p0) cc_final: 0.7950 (p0) REVERT: E 165 LEU cc_start: 0.8891 (mm) cc_final: 0.8463 (tp) REVERT: F 12 ILE cc_start: 0.4784 (OUTLIER) cc_final: 0.4550 (mp) REVERT: G 66 HIS cc_start: 0.5839 (t-90) cc_final: 0.5230 (t70) REVERT: G 73 LEU cc_start: 0.8615 (mt) cc_final: 0.8227 (mt) REVERT: G 78 GLU cc_start: 0.6615 (OUTLIER) cc_final: 0.6346 (mm-30) REVERT: G 90 LEU cc_start: 0.6201 (mt) cc_final: 0.5940 (mp) REVERT: J 50 ASP cc_start: 0.8131 (t70) cc_final: 0.6784 (t70) REVERT: J 109 MET cc_start: 0.8600 (mmp) cc_final: 0.8205 (mmp) REVERT: J 121 LYS cc_start: 0.7940 (OUTLIER) cc_final: 0.7618 (pttm) REVERT: J 139 GLU cc_start: 0.8584 (mt-10) cc_final: 0.7928 (mp0) REVERT: K 7 ARG cc_start: 0.8752 (ttm170) cc_final: 0.8269 (mmt90) REVERT: K 122 ILE cc_start: 0.8142 (mt) cc_final: 0.7646 (mt) REVERT: L 36 LYS cc_start: 0.7607 (OUTLIER) cc_final: 0.7202 (mmtm) REVERT: L 74 TYR cc_start: 0.6348 (OUTLIER) cc_final: 0.4058 (m-80) REVERT: L 89 THR cc_start: 0.6165 (OUTLIER) cc_final: 0.5438 (p) REVERT: L 90 GLU cc_start: 0.8093 (OUTLIER) cc_final: 0.7772 (mp0) REVERT: L 106 ASN cc_start: 0.9019 (m-40) cc_final: 0.8788 (t0) REVERT: L 109 VAL cc_start: 0.7722 (OUTLIER) cc_final: 0.7267 (p) REVERT: L 120 LYS cc_start: 0.7090 (OUTLIER) cc_final: 0.6728 (pttp) REVERT: L 137 GLU cc_start: 0.6344 (OUTLIER) cc_final: 0.6092 (mm-30) REVERT: N 26 ILE cc_start: 0.9021 (mt) cc_final: 0.8511 (mt) REVERT: N 92 GLU cc_start: 0.9145 (tm-30) cc_final: 0.8877 (tm-30) REVERT: O 41 TYR cc_start: 0.8121 (m-10) cc_final: 0.7905 (m-10) REVERT: O 61 LYS cc_start: 0.6919 (OUTLIER) cc_final: 0.5703 (ptmm) REVERT: O 96 ASP cc_start: 0.8751 (m-30) cc_final: 0.8433 (m-30) REVERT: O 102 TYR cc_start: 0.5664 (OUTLIER) cc_final: 0.5200 (t80) REVERT: O 107 LYS cc_start: 0.8376 (OUTLIER) cc_final: 0.7925 (mtpp) REVERT: O 111 ASP cc_start: 0.7506 (m-30) cc_final: 0.7176 (m-30) REVERT: P 6 LYS cc_start: 0.8623 (tttt) cc_final: 0.8355 (tttt) REVERT: P 28 THR cc_start: 0.8830 (p) cc_final: 0.8189 (p) REVERT: P 44 GLN cc_start: 0.7962 (pt0) cc_final: 0.7421 (pp30) REVERT: P 51 ILE cc_start: 0.9624 (mt) cc_final: 0.9391 (mm) REVERT: P 52 LYS cc_start: 0.8825 (mtmt) cc_final: 0.8164 (mmmt) REVERT: P 87 ILE cc_start: 0.9133 (mt) cc_final: 0.8686 (mm) REVERT: Q 40 MET cc_start: 0.9261 (ttm) cc_final: 0.8926 (ttm) REVERT: Q 41 LYS cc_start: 0.9516 (tptt) cc_final: 0.9139 (tppp) REVERT: Q 49 ASP cc_start: 0.8882 (t0) cc_final: 0.8422 (t0) REVERT: Q 92 ARG cc_start: 0.8349 (tpt90) cc_final: 0.8008 (tpp80) REVERT: R 11 GLN cc_start: 0.7130 (mm-40) cc_final: 0.6290 (mt0) REVERT: R 16 GLU cc_start: 0.7448 (tt0) cc_final: 0.6687 (mt-10) REVERT: R 36 GLU cc_start: 0.8538 (tp30) cc_final: 0.8230 (tp30) REVERT: R 63 GLU cc_start: 0.8538 (tt0) cc_final: 0.8165 (mm-30) REVERT: R 76 TYR cc_start: 0.9123 (p90) cc_final: 0.8352 (p90) REVERT: S 31 GLU cc_start: 0.7890 (mm-30) cc_final: 0.7662 (mm-30) REVERT: S 63 GLU cc_start: 0.7753 (mp0) cc_final: 0.7252 (mp0) REVERT: S 64 MET cc_start: 0.5899 (mmt) cc_final: 0.5441 (mtt) REVERT: S 78 GLU cc_start: 0.8554 (pt0) cc_final: 0.8132 (pt0) REVERT: S 100 THR cc_start: 0.9152 (m) cc_final: 0.8906 (p) REVERT: T 33 ARG cc_start: 0.8442 (ptp90) cc_final: 0.7977 (tpt170) REVERT: T 35 ASN cc_start: 0.9232 (m-40) cc_final: 0.8917 (m-40) REVERT: T 56 ILE cc_start: 0.9365 (mt) cc_final: 0.8916 (tt) REVERT: T 60 LYS cc_start: 0.8968 (mttt) cc_final: 0.8718 (mtpt) REVERT: U 31 ASP cc_start: 0.8534 (m-30) cc_final: 0.8145 (m-30) REVERT: U 59 GLN cc_start: 0.8641 (mt0) cc_final: 0.8084 (mt0) REVERT: V 27 LYS cc_start: 0.8418 (mttt) cc_final: 0.8147 (pttt) REVERT: V 28 ARG cc_start: 0.8192 (mmt90) cc_final: 0.7740 (mmt-90) REVERT: V 46 TYR cc_start: 0.8233 (t80) cc_final: 0.7888 (t80) REVERT: V 48 GLN cc_start: 0.8941 (OUTLIER) cc_final: 0.8295 (mt0) REVERT: V 65 ASP cc_start: 0.8630 (t0) cc_final: 0.8415 (t0) REVERT: Z 6 ILE cc_start: 0.8249 (mm) cc_final: 0.7387 (tp) REVERT: Z 8 LEU cc_start: 0.8825 (mt) cc_final: 0.8057 (mp) REVERT: Z 17 GLU cc_start: 0.6960 (pm20) cc_final: 0.6481 (pm20) REVERT: Z 20 ARG cc_start: 0.8581 (mtt180) cc_final: 0.8362 (mtp180) REVERT: Z 24 ARG cc_start: 0.8880 (tpt170) cc_final: 0.8206 (tpt90) REVERT: Z 25 THR cc_start: 0.9033 (p) cc_final: 0.8813 (p) REVERT: Z 28 LEU cc_start: 0.7850 (mt) cc_final: 0.7632 (mt) REVERT: b 6 ARG cc_start: 0.9214 (mmm-85) cc_final: 0.8430 (mmm-85) REVERT: b 11 MET cc_start: 0.8921 (ttt) cc_final: 0.8703 (ttt) REVERT: b 14 ARG cc_start: 0.9488 (mtt180) cc_final: 0.9145 (mtp85) REVERT: b 27 MET cc_start: 0.8579 (mtm) cc_final: 0.7694 (mtm) REVERT: b 42 VAL cc_start: 0.8528 (t) cc_final: 0.8250 (t) REVERT: Y 5 GLU cc_start: 0.7262 (OUTLIER) cc_final: 0.6612 (mm-30) REVERT: Y 28 LEU cc_start: 0.9394 (tp) cc_final: 0.9156 (tp) REVERT: Y 31 GLN cc_start: 0.9247 (mm-40) cc_final: 0.8805 (mp10) REVERT: Y 43 ILE cc_start: 0.8908 (mt) cc_final: 0.8574 (mt) REVERT: Y 53 MET cc_start: 0.8946 (mtm) cc_final: 0.8702 (mmm) REVERT: Y 65 ASN cc_start: 0.7978 (t0) cc_final: 0.7455 (m110) REVERT: W 15 ARG cc_start: 0.5446 (ttt90) cc_final: 0.4986 (tpt-90) REVERT: W 58 ASN cc_start: 0.7473 (p0) cc_final: 0.7086 (p0) REVERT: W 177 TRP cc_start: 0.6139 (OUTLIER) cc_final: 0.5546 (m-10) REVERT: W 201 ASN cc_start: 0.6302 (t0) cc_final: 0.5685 (m-40) REVERT: W 271 LYS cc_start: 0.7911 (mttt) cc_final: 0.7209 (ttmt) REVERT: W 277 PHE cc_start: 0.7152 (OUTLIER) cc_final: 0.6155 (m-80) outliers start: 179 outliers final: 39 residues processed: 890 average time/residue: 0.8292 time to fit residues: 1216.8815 Evaluate side-chains 578 residues out of total 2242 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 519 time to evaluate : 3.096 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 535 random chunks: chunk 451 optimal weight: 3.9990 chunk 405 optimal weight: 7.9990 chunk 225 optimal weight: 20.0000 chunk 138 optimal weight: 9.9990 chunk 273 optimal weight: 20.0000 chunk 216 optimal weight: 20.0000 chunk 419 optimal weight: 9.9990 chunk 162 optimal weight: 7.9990 chunk 254 optimal weight: 10.0000 chunk 312 optimal weight: 4.9990 chunk 485 optimal weight: 6.9990 overall best weight: 6.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 90 ASN C 197 ASN C 228 ASN C 264 ASN ** D 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 135 HIS D 152 ASN D 184 ASN ** E 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 96 ASN J 124 ASN L 78 ASN N 61 GLN N 81 GLN P 15 GLN P 32 HIS P 44 GLN ** P 80 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 37 GLN Q 44 ASN ** Q 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 118 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 86 GLN S 60 HIS U 20 GLN U 67 ASN ** V 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 33 GLN ** Z 52 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Y 36 GLN Y 39 ASN ** d 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 9 HIS W 78 GLN W 130 ASN Total number of N/Q/H flips: 27 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8234 moved from start: 0.2096 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.126 87845 Z= 0.325 Angle : 0.795 9.309 132342 Z= 0.394 Chirality : 0.041 0.315 17066 Planarity : 0.006 0.073 6406 Dihedral : 26.513 179.334 46042 Min Nonbonded Distance : 1.928 Molprobity Statistics. All-atom Clashscore : 24.88 Ramachandran Plot: Outliers : 0.12 % Allowed : 9.51 % Favored : 90.38 % Rotamer: Outliers : 0.22 % Allowed : 6.01 % Favored : 93.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.43 (0.15), residues: 2608 helix: -2.09 (0.18), residues: 633 sheet: -2.07 (0.24), residues: 436 loop : -2.50 (0.14), residues: 1539 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP C 213 HIS 0.013 0.002 HIS J 54 PHE 0.028 0.002 PHE Q 47 TYR 0.023 0.002 TYR C 171 ARG 0.023 0.001 ARG F 92 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5216 Ramachandran restraints generated. 2608 Oldfield, 0 Emsley, 2608 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5216 Ramachandran restraints generated. 2608 Oldfield, 0 Emsley, 2608 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 664 residues out of total 2242 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 659 time to evaluate : 3.233 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: C 16 MET cc_start: 0.8609 (ppp) cc_final: 0.7821 (ppp) REVERT: C 197 ASN cc_start: 0.8626 (OUTLIER) cc_final: 0.7964 (t0) REVERT: C 247 MET cc_start: 0.5709 (ttm) cc_final: 0.4994 (ttm) REVERT: D 36 LEU cc_start: 0.9132 (mt) cc_final: 0.8718 (mp) REVERT: D 154 VAL cc_start: 0.9292 (t) cc_final: 0.8979 (p) REVERT: D 201 THR cc_start: 0.8632 (m) cc_final: 0.8240 (p) REVERT: E 35 ASP cc_start: 0.8594 (t70) cc_final: 0.8153 (t70) REVERT: E 158 ASP cc_start: 0.8277 (p0) cc_final: 0.7944 (p0) REVERT: E 165 LEU cc_start: 0.8610 (mm) cc_final: 0.8107 (tp) REVERT: G 90 LEU cc_start: 0.6979 (mt) cc_final: 0.6532 (mp) REVERT: J 76 TYR cc_start: 0.8497 (m-80) cc_final: 0.7828 (m-10) REVERT: J 92 GLU cc_start: 0.9078 (tp30) cc_final: 0.8730 (tp30) REVERT: J 109 MET cc_start: 0.8648 (mmp) cc_final: 0.8175 (mmp) REVERT: J 139 GLU cc_start: 0.8530 (mt-10) cc_final: 0.7976 (mp0) REVERT: K 18 GLU cc_start: 0.7637 (mt-10) cc_final: 0.7160 (mt-10) REVERT: K 22 ILE cc_start: 0.9224 (mt) cc_final: 0.8510 (mp) REVERT: K 112 MET cc_start: 0.8905 (mpp) cc_final: 0.8671 (mpp) REVERT: L 10 GLU cc_start: 0.8601 (tm-30) cc_final: 0.8299 (tm-30) REVERT: L 106 ASN cc_start: 0.8791 (m-40) cc_final: 0.8464 (t0) REVERT: O 32 ASN cc_start: 0.8095 (p0) cc_final: 0.7815 (p0) REVERT: P 6 LYS cc_start: 0.8623 (tttt) cc_final: 0.8318 (tttt) REVERT: P 19 ASP cc_start: 0.6875 (t0) cc_final: 0.6641 (t0) REVERT: Q 40 MET cc_start: 0.8963 (ttm) cc_final: 0.8679 (ttm) REVERT: Q 44 ASN cc_start: 0.9172 (OUTLIER) cc_final: 0.7871 (t0) REVERT: Q 49 ASP cc_start: 0.8678 (t0) cc_final: 0.8201 (t0) REVERT: Q 65 ILE cc_start: 0.9500 (mt) cc_final: 0.9260 (tt) REVERT: Q 94 MET cc_start: 0.8887 (ttt) cc_final: 0.8478 (ttt) REVERT: R 31 GLU cc_start: 0.5954 (mp0) cc_final: 0.5718 (mp0) REVERT: R 36 GLU cc_start: 0.8333 (tp30) cc_final: 0.7919 (tp30) REVERT: R 50 ASN cc_start: 0.8603 (p0) cc_final: 0.8329 (p0) REVERT: R 52 THR cc_start: 0.8984 (m) cc_final: 0.8627 (t) REVERT: R 63 GLU cc_start: 0.8754 (tt0) cc_final: 0.8263 (mm-30) REVERT: R 76 TYR cc_start: 0.9063 (p90) cc_final: 0.8015 (p90) REVERT: R 96 THR cc_start: 0.8514 (t) cc_final: 0.8291 (t) REVERT: S 63 GLU cc_start: 0.7736 (mp0) cc_final: 0.7524 (mp0) REVERT: S 78 GLU cc_start: 0.8442 (pt0) cc_final: 0.8097 (pt0) REVERT: S 95 GLN cc_start: 0.8043 (mp10) cc_final: 0.7749 (mp10) REVERT: S 102 HIS cc_start: 0.7798 (m170) cc_final: 0.7374 (m170) REVERT: T 33 ARG cc_start: 0.8613 (ptp90) cc_final: 0.8053 (tpt170) REVERT: T 56 ILE cc_start: 0.9351 (mt) cc_final: 0.8887 (tt) REVERT: U 31 ASP cc_start: 0.8397 (m-30) cc_final: 0.7882 (m-30) REVERT: V 22 ARG cc_start: 0.7664 (ptp-170) cc_final: 0.7448 (ptp-170) REVERT: V 28 ARG cc_start: 0.8343 (mmt90) cc_final: 0.7859 (mmt-90) REVERT: V 65 ASP cc_start: 0.8357 (t0) cc_final: 0.7994 (t0) REVERT: Z 8 LEU cc_start: 0.9283 (mt) cc_final: 0.8983 (mp) REVERT: Z 9 LYS cc_start: 0.9347 (mmpt) cc_final: 0.8988 (mmmm) REVERT: Z 19 GLN cc_start: 0.7950 (mp10) cc_final: 0.7435 (mp10) REVERT: Z 20 ARG cc_start: 0.8899 (mtt180) cc_final: 0.8602 (mtp180) REVERT: Z 26 LEU cc_start: 0.8940 (tt) cc_final: 0.8662 (tt) REVERT: Z 46 MET cc_start: 0.9026 (mtp) cc_final: 0.7980 (mmt) REVERT: b 6 ARG cc_start: 0.9140 (mmm-85) cc_final: 0.8536 (mmm-85) REVERT: b 27 MET cc_start: 0.8535 (mtm) cc_final: 0.7752 (mtm) REVERT: Y 15 GLU cc_start: 0.7476 (tp30) cc_final: 0.7242 (tp30) REVERT: Y 22 LYS cc_start: 0.8890 (mtpp) cc_final: 0.8202 (mtmm) REVERT: Y 28 LEU cc_start: 0.9440 (tp) cc_final: 0.9207 (tp) REVERT: Y 31 GLN cc_start: 0.9150 (mm-40) cc_final: 0.8921 (mm-40) REVERT: Y 53 MET cc_start: 0.9271 (mtm) cc_final: 0.8797 (mmm) REVERT: Y 65 ASN cc_start: 0.8034 (t0) cc_final: 0.7440 (m110) REVERT: d 22 MET cc_start: 0.9331 (mmm) cc_final: 0.9074 (mmm) REVERT: W 15 ARG cc_start: 0.5420 (ttt180) cc_final: 0.4835 (tpt-90) REVERT: W 81 ARG cc_start: 0.7762 (mtt180) cc_final: 0.7378 (ttt180) REVERT: W 201 ASN cc_start: 0.6139 (t0) cc_final: 0.5407 (m-40) REVERT: W 277 PHE cc_start: 0.6658 (m-10) cc_final: 0.6351 (m-80) outliers start: 5 outliers final: 0 residues processed: 663 average time/residue: 0.8506 time to fit residues: 954.2685 Evaluate side-chains 488 residues out of total 2242 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 486 time to evaluate : 3.152 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 535 random chunks: chunk 270 optimal weight: 40.0000 chunk 150 optimal weight: 20.0000 chunk 404 optimal weight: 0.9990 chunk 330 optimal weight: 3.9990 chunk 134 optimal weight: 10.0000 chunk 486 optimal weight: 9.9990 chunk 525 optimal weight: 9.9990 chunk 433 optimal weight: 0.0870 chunk 482 optimal weight: 20.0000 chunk 165 optimal weight: 10.0000 chunk 390 optimal weight: 5.9990 overall best weight: 4.2166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 264 ASN D 33 ASN D 50 GLN ** D 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 191 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 67 GLN F 172 GLN G 66 HIS J 96 ASN K 4 GLN N 12 GLN N 75 ASN O 43 GLN O 103 HIS P 15 GLN ** P 80 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 116 GLN ** Q 118 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 81 ASN ** S 61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 33 GLN Z 37 HIS ** Z 52 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** b 40 HIS Y 4 ASN Y 39 ASN ** d 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 89 ASN W 216 HIS Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8195 moved from start: 0.2853 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.100 87845 Z= 0.231 Angle : 0.688 10.442 132342 Z= 0.345 Chirality : 0.038 0.379 17066 Planarity : 0.006 0.208 6406 Dihedral : 26.282 179.175 46042 Min Nonbonded Distance : 1.990 Molprobity Statistics. All-atom Clashscore : 21.72 Ramachandran Plot: Outliers : 0.08 % Allowed : 8.40 % Favored : 91.53 % Rotamer: Outliers : 0.36 % Allowed : 5.02 % Favored : 94.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.78 (0.15), residues: 2608 helix: -1.46 (0.19), residues: 633 sheet: -1.72 (0.24), residues: 432 loop : -2.10 (0.15), residues: 1543 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP J 16 HIS 0.009 0.002 HIS R 88 PHE 0.037 0.002 PHE E 90 TYR 0.027 0.002 TYR S 62 ARG 0.034 0.001 ARG F 3 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5216 Ramachandran restraints generated. 2608 Oldfield, 0 Emsley, 2608 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5216 Ramachandran restraints generated. 2608 Oldfield, 0 Emsley, 2608 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 613 residues out of total 2242 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 605 time to evaluate : 3.175 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 247 MET cc_start: 0.5839 (ttm) cc_final: 0.5122 (ttm) REVERT: D 140 HIS cc_start: 0.8959 (p90) cc_final: 0.8726 (p90) REVERT: D 146 MET cc_start: 0.7989 (mmp) cc_final: 0.7601 (mmp) REVERT: D 154 VAL cc_start: 0.9435 (t) cc_final: 0.9069 (p) REVERT: D 168 GLN cc_start: 0.9104 (mt0) cc_final: 0.8835 (pt0) REVERT: D 201 THR cc_start: 0.8572 (m) cc_final: 0.8232 (p) REVERT: E 35 ASP cc_start: 0.8726 (t70) cc_final: 0.8256 (t70) REVERT: E 83 TRP cc_start: 0.9395 (m-10) cc_final: 0.9163 (m-10) REVERT: E 158 ASP cc_start: 0.8270 (p0) cc_final: 0.7930 (p0) REVERT: E 165 LEU cc_start: 0.8625 (mm) cc_final: 0.8130 (tp) REVERT: F 9 ASN cc_start: 0.4957 (m110) cc_final: 0.4681 (t0) REVERT: F 89 VAL cc_start: 0.7229 (t) cc_final: 0.6757 (t) REVERT: F 90 THR cc_start: 0.6269 (m) cc_final: 0.6030 (p) REVERT: F 96 MET cc_start: 0.7352 (mpp) cc_final: 0.6919 (mpp) REVERT: J 89 THR cc_start: 0.8562 (t) cc_final: 0.6543 (m) REVERT: J 93 MET cc_start: 0.8702 (ttm) cc_final: 0.8005 (ttm) REVERT: J 101 MET cc_start: 0.7993 (tmm) cc_final: 0.7336 (ttm) REVERT: J 109 MET cc_start: 0.8814 (mmp) cc_final: 0.8463 (mmp) REVERT: J 139 GLU cc_start: 0.8624 (mt-10) cc_final: 0.8188 (mp0) REVERT: K 7 ARG cc_start: 0.8942 (ttm170) cc_final: 0.8539 (mmt90) REVERT: K 41 CYS cc_start: 0.7844 (p) cc_final: 0.7517 (m) REVERT: K 112 MET cc_start: 0.8877 (mpp) cc_final: 0.8494 (mpp) REVERT: L 106 ASN cc_start: 0.8893 (m-40) cc_final: 0.8320 (t0) REVERT: N 26 ILE cc_start: 0.9376 (mt) cc_final: 0.9082 (tt) REVERT: N 59 ARG cc_start: 0.8964 (mtt180) cc_final: 0.8549 (mtt90) REVERT: P 6 LYS cc_start: 0.8551 (tttt) cc_final: 0.8271 (tttt) REVERT: P 19 ASP cc_start: 0.6733 (t0) cc_final: 0.6508 (t0) REVERT: P 102 TYR cc_start: 0.8938 (p90) cc_final: 0.8477 (p90) REVERT: Q 40 MET cc_start: 0.8812 (ttm) cc_final: 0.8263 (ttm) REVERT: Q 49 ASP cc_start: 0.8713 (t0) cc_final: 0.8099 (t0) REVERT: Q 65 ILE cc_start: 0.9400 (mt) cc_final: 0.9110 (mm) REVERT: Q 94 MET cc_start: 0.8892 (ttt) cc_final: 0.8436 (ttt) REVERT: R 11 GLN cc_start: 0.8223 (mm-40) cc_final: 0.7777 (mt0) REVERT: R 31 GLU cc_start: 0.6158 (mp0) cc_final: 0.5884 (mp0) REVERT: R 36 GLU cc_start: 0.8247 (tp30) cc_final: 0.7797 (tp30) REVERT: R 50 ASN cc_start: 0.8551 (p0) cc_final: 0.8288 (p0) REVERT: R 52 THR cc_start: 0.8815 (m) cc_final: 0.8446 (t) REVERT: R 63 GLU cc_start: 0.8828 (tt0) cc_final: 0.8319 (mm-30) REVERT: R 76 TYR cc_start: 0.8171 (p90) cc_final: 0.7795 (p90) REVERT: R 89 ARG cc_start: 0.9118 (ttt180) cc_final: 0.8772 (ttt180) REVERT: S 48 GLU cc_start: 0.6852 (tm-30) cc_final: 0.6446 (tm-30) REVERT: S 60 HIS cc_start: 0.8519 (t70) cc_final: 0.8263 (t-170) REVERT: S 78 GLU cc_start: 0.8130 (pt0) cc_final: 0.7833 (pt0) REVERT: S 102 HIS cc_start: 0.7824 (m170) cc_final: 0.7340 (m170) REVERT: T 9 LYS cc_start: 0.8487 (mptt) cc_final: 0.8093 (mmtp) REVERT: T 33 ARG cc_start: 0.8095 (ptp90) cc_final: 0.7645 (tpt170) REVERT: T 56 ILE cc_start: 0.9126 (mt) cc_final: 0.8698 (tt) REVERT: U 31 ASP cc_start: 0.8387 (m-30) cc_final: 0.7755 (m-30) REVERT: U 78 VAL cc_start: 0.7113 (OUTLIER) cc_final: 0.5689 (p) REVERT: V 22 ARG cc_start: 0.7812 (ptp-170) cc_final: 0.7600 (ptp-170) REVERT: V 28 ARG cc_start: 0.8369 (mmt90) cc_final: 0.7703 (mmt-90) REVERT: V 48 GLN cc_start: 0.8474 (mm-40) cc_final: 0.7535 (mm-40) REVERT: V 65 ASP cc_start: 0.8247 (t0) cc_final: 0.7998 (t0) REVERT: V 85 LYS cc_start: 0.7912 (mttm) cc_final: 0.7078 (tptp) REVERT: Z 8 LEU cc_start: 0.9245 (mt) cc_final: 0.8674 (mt) REVERT: Z 9 LYS cc_start: 0.9296 (mmpt) cc_final: 0.8602 (mmtm) REVERT: Z 19 GLN cc_start: 0.8124 (mp10) cc_final: 0.7577 (mp-120) REVERT: Z 20 ARG cc_start: 0.8863 (mtt180) cc_final: 0.8467 (mtp180) REVERT: b 27 MET cc_start: 0.8453 (mtm) cc_final: 0.7765 (mtm) REVERT: Y 15 GLU cc_start: 0.7179 (tp30) cc_final: 0.6740 (tp30) REVERT: Y 22 LYS cc_start: 0.8726 (mtpp) cc_final: 0.8242 (mtmm) REVERT: Y 29 ARG cc_start: 0.9050 (mtt180) cc_final: 0.8642 (tpp80) REVERT: Y 31 GLN cc_start: 0.9221 (mm-40) cc_final: 0.8941 (mm-40) REVERT: Y 53 MET cc_start: 0.9237 (mtm) cc_final: 0.8797 (mmp) REVERT: Y 65 ASN cc_start: 0.7980 (t0) cc_final: 0.7668 (m110) REVERT: W 15 ARG cc_start: 0.5632 (ttt180) cc_final: 0.5083 (ttt90) REVERT: W 71 TRP cc_start: 0.5094 (m100) cc_final: 0.4707 (m100) REVERT: W 77 ASN cc_start: 0.8708 (m110) cc_final: 0.8490 (m110) REVERT: W 81 ARG cc_start: 0.7784 (mtt180) cc_final: 0.7430 (ttt180) REVERT: W 138 ASN cc_start: 0.8969 (p0) cc_final: 0.8698 (p0) REVERT: W 147 LYS cc_start: 0.7150 (mttt) cc_final: 0.6446 (pttt) REVERT: W 201 ASN cc_start: 0.6526 (t0) cc_final: 0.5766 (m-40) REVERT: W 271 LYS cc_start: 0.8123 (mttt) cc_final: 0.7787 (ttmt) outliers start: 8 outliers final: 1 residues processed: 611 average time/residue: 0.8463 time to fit residues: 885.8246 Evaluate side-chains 485 residues out of total 2242 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 483 time to evaluate : 3.182 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 535 random chunks: chunk 480 optimal weight: 4.9990 chunk 365 optimal weight: 20.0000 chunk 252 optimal weight: 20.0000 chunk 53 optimal weight: 10.0000 chunk 232 optimal weight: 30.0000 chunk 326 optimal weight: 4.9990 chunk 488 optimal weight: 10.0000 chunk 517 optimal weight: 8.9990 chunk 255 optimal weight: 20.0000 chunk 462 optimal weight: 4.9990 chunk 139 optimal weight: 10.0000 overall best weight: 6.7992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 11 ASN ** D 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 191 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 49 HIS ** E 182 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 66 HIS J 96 ASN N 12 GLN ** P 80 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 61 ASN U 58 ASN Z 37 HIS ** Z 52 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Y 39 ASN ** d 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 89 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8241 moved from start: 0.3214 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 87845 Z= 0.319 Angle : 0.765 10.138 132342 Z= 0.380 Chirality : 0.040 0.463 17066 Planarity : 0.005 0.072 6406 Dihedral : 26.379 179.495 46042 Min Nonbonded Distance : 1.980 Molprobity Statistics. All-atom Clashscore : 27.33 Ramachandran Plot: Outliers : 0.04 % Allowed : 10.05 % Favored : 89.92 % Rotamer: Outliers : 0.09 % Allowed : 6.24 % Favored : 93.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.71 (0.15), residues: 2608 helix: -1.29 (0.19), residues: 649 sheet: -1.73 (0.25), residues: 413 loop : -2.10 (0.15), residues: 1546 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.003 TRP J 16 HIS 0.021 0.002 HIS J 54 PHE 0.035 0.002 PHE Q 57 TYR 0.018 0.002 TYR J 141 ARG 0.016 0.001 ARG Q 92 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5216 Ramachandran restraints generated. 2608 Oldfield, 0 Emsley, 2608 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5216 Ramachandran restraints generated. 2608 Oldfield, 0 Emsley, 2608 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 570 residues out of total 2242 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 568 time to evaluate : 3.136 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: C 16 MET cc_start: 0.8689 (ppp) cc_final: 0.7655 (ppp) REVERT: C 24 ILE cc_start: 0.9329 (mp) cc_final: 0.9077 (mt) REVERT: C 117 MET cc_start: 0.8421 (tmm) cc_final: 0.7951 (tmm) REVERT: C 247 MET cc_start: 0.5757 (ttm) cc_final: 0.5204 (ttm) REVERT: D 140 HIS cc_start: 0.9019 (p90) cc_final: 0.8599 (p90) REVERT: D 146 MET cc_start: 0.8269 (mmp) cc_final: 0.8001 (mmp) REVERT: D 158 LYS cc_start: 0.9085 (tptm) cc_final: 0.8868 (tptm) REVERT: D 168 GLN cc_start: 0.9163 (mt0) cc_final: 0.8915 (pt0) REVERT: D 201 THR cc_start: 0.8287 (m) cc_final: 0.7897 (p) REVERT: E 158 ASP cc_start: 0.8351 (p0) cc_final: 0.7955 (p0) REVERT: E 165 LEU cc_start: 0.8642 (mm) cc_final: 0.8020 (tp) REVERT: F 9 ASN cc_start: 0.5790 (m110) cc_final: 0.5425 (t0) REVERT: G 150 ARG cc_start: 0.8080 (ttt-90) cc_final: 0.7705 (ttm-80) REVERT: J 33 VAL cc_start: 0.9749 (t) cc_final: 0.9498 (p) REVERT: J 89 THR cc_start: 0.8582 (t) cc_final: 0.7760 (p) REVERT: J 92 GLU cc_start: 0.8800 (mp0) cc_final: 0.8563 (mp0) REVERT: J 93 MET cc_start: 0.8760 (ttm) cc_final: 0.8187 (ttm) REVERT: J 101 MET cc_start: 0.8146 (tmm) cc_final: 0.7388 (ttm) REVERT: J 109 MET cc_start: 0.8769 (mmp) cc_final: 0.8383 (mmp) REVERT: J 121 LYS cc_start: 0.8888 (mtmt) cc_final: 0.8109 (pttm) REVERT: J 139 GLU cc_start: 0.8602 (mt-10) cc_final: 0.7994 (mp0) REVERT: K 18 GLU cc_start: 0.7660 (mt-10) cc_final: 0.7331 (mt-10) REVERT: K 112 MET cc_start: 0.8767 (mpp) cc_final: 0.8408 (mpp) REVERT: L 91 VAL cc_start: 0.7619 (t) cc_final: 0.7204 (p) REVERT: L 106 ASN cc_start: 0.8904 (m-40) cc_final: 0.8230 (t0) REVERT: N 26 ILE cc_start: 0.9308 (mt) cc_final: 0.9014 (tt) REVERT: N 65 TYR cc_start: 0.8985 (t80) cc_final: 0.8583 (t80) REVERT: N 114 MET cc_start: 0.7890 (tpt) cc_final: 0.7679 (tpt) REVERT: O 32 ASN cc_start: 0.8305 (p0) cc_final: 0.8094 (p0) REVERT: O 41 TYR cc_start: 0.7914 (m-10) cc_final: 0.7680 (m-10) REVERT: P 6 LYS cc_start: 0.8609 (tttt) cc_final: 0.8293 (tttt) REVERT: P 19 ASP cc_start: 0.6699 (t0) cc_final: 0.6441 (t0) REVERT: P 29 LEU cc_start: 0.8346 (pp) cc_final: 0.7764 (pp) REVERT: P 102 TYR cc_start: 0.9058 (p90) cc_final: 0.8585 (p90) REVERT: Q 40 MET cc_start: 0.8926 (ttm) cc_final: 0.8394 (ttm) REVERT: Q 49 ASP cc_start: 0.8777 (t0) cc_final: 0.8332 (t0) REVERT: R 31 GLU cc_start: 0.6111 (mp0) cc_final: 0.5845 (mp0) REVERT: R 36 GLU cc_start: 0.8438 (tp30) cc_final: 0.7978 (tp30) REVERT: R 50 ASN cc_start: 0.8532 (p0) cc_final: 0.8262 (p0) REVERT: R 52 THR cc_start: 0.8865 (m) cc_final: 0.8480 (t) REVERT: R 63 GLU cc_start: 0.8782 (tt0) cc_final: 0.8249 (mm-30) REVERT: R 76 TYR cc_start: 0.8497 (p90) cc_final: 0.8047 (p90) REVERT: R 89 ARG cc_start: 0.9171 (ttt180) cc_final: 0.8512 (ttt180) REVERT: S 36 LEU cc_start: 0.8831 (tp) cc_final: 0.8581 (tt) REVERT: S 48 GLU cc_start: 0.7026 (tm-30) cc_final: 0.6630 (tm-30) REVERT: S 60 HIS cc_start: 0.8652 (t70) cc_final: 0.7996 (t-170) REVERT: S 78 GLU cc_start: 0.8153 (pt0) cc_final: 0.7908 (pt0) REVERT: S 82 LEU cc_start: 0.9407 (mt) cc_final: 0.9053 (mm) REVERT: S 102 HIS cc_start: 0.7680 (m170) cc_final: 0.7279 (m170) REVERT: T 33 ARG cc_start: 0.8364 (ptp90) cc_final: 0.8112 (tpt170) REVERT: T 56 ILE cc_start: 0.9168 (mt) cc_final: 0.8666 (tt) REVERT: U 5 LYS cc_start: 0.8246 (ttpt) cc_final: 0.7971 (tptp) REVERT: U 10 MET cc_start: 0.8957 (tpp) cc_final: 0.8731 (tpp) REVERT: U 31 ASP cc_start: 0.8484 (m-30) cc_final: 0.7866 (m-30) REVERT: U 58 ASN cc_start: 0.8687 (m-40) cc_final: 0.8447 (m-40) REVERT: V 28 ARG cc_start: 0.8443 (mmt90) cc_final: 0.7879 (mmt-90) REVERT: V 48 GLN cc_start: 0.8583 (mm-40) cc_final: 0.7552 (mm-40) REVERT: V 49 ARG cc_start: 0.8266 (mmt180) cc_final: 0.7425 (mmt180) REVERT: Z 8 LEU cc_start: 0.9363 (mt) cc_final: 0.8860 (mt) REVERT: Z 9 LYS cc_start: 0.9350 (mmpt) cc_final: 0.8642 (mmtm) REVERT: Z 19 GLN cc_start: 0.7996 (mp10) cc_final: 0.7417 (mp-120) REVERT: Z 29 LYS cc_start: 0.8667 (ptpt) cc_final: 0.8134 (ptpt) REVERT: b 6 ARG cc_start: 0.9219 (mmm-85) cc_final: 0.8639 (mmm-85) REVERT: b 27 MET cc_start: 0.8315 (mtm) cc_final: 0.7752 (mtm) REVERT: Y 15 GLU cc_start: 0.7228 (tp30) cc_final: 0.6827 (tp30) REVERT: Y 22 LYS cc_start: 0.8940 (mtpp) cc_final: 0.8341 (mtmm) REVERT: Y 31 GLN cc_start: 0.9205 (mm-40) cc_final: 0.8924 (mm-40) REVERT: Y 53 MET cc_start: 0.9282 (mtm) cc_final: 0.8903 (mmp) REVERT: Y 65 ASN cc_start: 0.8003 (t0) cc_final: 0.7692 (m110) REVERT: d 22 MET cc_start: 0.9479 (mmm) cc_final: 0.9170 (mmm) REVERT: W 15 ARG cc_start: 0.5716 (ttt180) cc_final: 0.5024 (ttt90) REVERT: W 81 ARG cc_start: 0.7956 (mtt180) cc_final: 0.7545 (ttt180) REVERT: W 138 ASN cc_start: 0.8987 (p0) cc_final: 0.8748 (p0) REVERT: W 147 LYS cc_start: 0.7746 (mttt) cc_final: 0.6724 (pttt) REVERT: W 201 ASN cc_start: 0.6552 (t0) cc_final: 0.5848 (m-40) REVERT: W 231 PRO cc_start: 0.7913 (Cg_exo) cc_final: 0.7538 (Cg_exo) outliers start: 2 outliers final: 1 residues processed: 568 average time/residue: 0.7838 time to fit residues: 756.8217 Evaluate side-chains 452 residues out of total 2242 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 451 time to evaluate : 3.163 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 535 random chunks: chunk 430 optimal weight: 8.9990 chunk 293 optimal weight: 10.0000 chunk 7 optimal weight: 10.0000 chunk 385 optimal weight: 3.9990 chunk 213 optimal weight: 40.0000 chunk 441 optimal weight: 10.0000 chunk 357 optimal weight: 30.0000 chunk 0 optimal weight: 10.0000 chunk 264 optimal weight: 10.0000 chunk 464 optimal weight: 9.9990 chunk 130 optimal weight: 9.9990 overall best weight: 8.5992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 11 ASN ** D 50 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 126 HIS ** D 191 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 182 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 66 HIS G 129 GLN J 96 ASN K 45 GLN N 68 ASN ** P 80 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 52 GLN Q 72 ASN V 20 ASN d 6 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8266 moved from start: 0.3568 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.078 87845 Z= 0.381 Angle : 0.818 9.104 132342 Z= 0.405 Chirality : 0.043 0.370 17066 Planarity : 0.006 0.069 6406 Dihedral : 26.496 179.339 46042 Min Nonbonded Distance : 1.993 Molprobity Statistics. All-atom Clashscore : 30.55 Ramachandran Plot: Outliers : 0.04 % Allowed : 11.00 % Favored : 88.96 % Rotamer: Outliers : 0.04 % Allowed : 4.53 % Favored : 95.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.65 (0.15), residues: 2608 helix: -1.18 (0.19), residues: 629 sheet: -1.65 (0.25), residues: 428 loop : -2.10 (0.15), residues: 1551 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.003 TRP E 65 HIS 0.036 0.002 HIS J 54 PHE 0.039 0.003 PHE Q 57 TYR 0.021 0.002 TYR Q 32 ARG 0.020 0.001 ARG Q 92 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5216 Ramachandran restraints generated. 2608 Oldfield, 0 Emsley, 2608 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5216 Ramachandran restraints generated. 2608 Oldfield, 0 Emsley, 2608 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 540 residues out of total 2242 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 539 time to evaluate : 3.233 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: C 16 MET cc_start: 0.8652 (ppp) cc_final: 0.8431 (tmm) REVERT: C 24 ILE cc_start: 0.9326 (mp) cc_final: 0.9071 (mt) REVERT: C 247 MET cc_start: 0.5811 (ttm) cc_final: 0.5370 (ttm) REVERT: D 146 MET cc_start: 0.8427 (mmp) cc_final: 0.8164 (mmp) REVERT: D 160 LEU cc_start: 0.8896 (tp) cc_final: 0.8656 (tp) REVERT: D 168 GLN cc_start: 0.9031 (mt0) cc_final: 0.8729 (pt0) REVERT: D 201 THR cc_start: 0.8468 (m) cc_final: 0.8098 (p) REVERT: E 35 ASP cc_start: 0.8430 (t70) cc_final: 0.8121 (t70) REVERT: E 158 ASP cc_start: 0.8252 (p0) cc_final: 0.7690 (p0) REVERT: E 165 LEU cc_start: 0.8674 (mm) cc_final: 0.8331 (tp) REVERT: F 9 ASN cc_start: 0.6151 (m110) cc_final: 0.5869 (t0) REVERT: G 78 GLU cc_start: 0.8198 (mp0) cc_final: 0.7439 (tp30) REVERT: J 89 THR cc_start: 0.8573 (t) cc_final: 0.8164 (p) REVERT: J 92 GLU cc_start: 0.8915 (mp0) cc_final: 0.8673 (mp0) REVERT: J 93 MET cc_start: 0.8878 (ttm) cc_final: 0.8400 (ttm) REVERT: J 96 ASN cc_start: 0.7028 (OUTLIER) cc_final: 0.6745 (t0) REVERT: J 101 MET cc_start: 0.8105 (tmm) cc_final: 0.7841 (tmm) REVERT: J 102 LEU cc_start: 0.9177 (tp) cc_final: 0.8925 (tp) REVERT: J 109 MET cc_start: 0.8837 (mmp) cc_final: 0.8308 (mmp) REVERT: J 121 LYS cc_start: 0.8927 (mtmt) cc_final: 0.8627 (mtmm) REVERT: K 4 GLN cc_start: 0.8842 (tp-100) cc_final: 0.8511 (tp-100) REVERT: K 18 GLU cc_start: 0.7661 (mt-10) cc_final: 0.7346 (mt-10) REVERT: K 89 ASP cc_start: 0.8093 (p0) cc_final: 0.7848 (p0) REVERT: K 112 MET cc_start: 0.8922 (mpp) cc_final: 0.8459 (mpp) REVERT: L 106 ASN cc_start: 0.8964 (m-40) cc_final: 0.8215 (t0) REVERT: N 26 ILE cc_start: 0.9306 (mt) cc_final: 0.9025 (tt) REVERT: N 114 MET cc_start: 0.7852 (tpt) cc_final: 0.7600 (mmm) REVERT: O 41 TYR cc_start: 0.8148 (m-10) cc_final: 0.7913 (m-10) REVERT: P 6 LYS cc_start: 0.8559 (tttt) cc_final: 0.8343 (tttt) REVERT: P 19 ASP cc_start: 0.6664 (t0) cc_final: 0.6446 (t0) REVERT: Q 40 MET cc_start: 0.9110 (ttm) cc_final: 0.8553 (ttm) REVERT: Q 49 ASP cc_start: 0.8684 (t0) cc_final: 0.8046 (t0) REVERT: Q 94 MET cc_start: 0.8884 (ttt) cc_final: 0.8539 (ttt) REVERT: R 10 LYS cc_start: 0.8995 (ptmt) cc_final: 0.8778 (ptmt) REVERT: R 31 GLU cc_start: 0.6172 (mp0) cc_final: 0.5905 (mp0) REVERT: R 36 GLU cc_start: 0.8547 (tp30) cc_final: 0.8077 (tp30) REVERT: R 50 ASN cc_start: 0.8756 (p0) cc_final: 0.8483 (p0) REVERT: R 52 THR cc_start: 0.8954 (m) cc_final: 0.8587 (t) REVERT: R 63 GLU cc_start: 0.8794 (tt0) cc_final: 0.8337 (mm-30) REVERT: R 76 TYR cc_start: 0.8728 (p90) cc_final: 0.8354 (p90) REVERT: R 89 ARG cc_start: 0.9061 (ttt180) cc_final: 0.8183 (ttt180) REVERT: R 98 GLU cc_start: 0.8773 (tt0) cc_final: 0.8493 (mt-10) REVERT: S 38 LEU cc_start: 0.8865 (mm) cc_final: 0.8563 (mp) REVERT: S 48 GLU cc_start: 0.7014 (tm-30) cc_final: 0.6634 (tm-30) REVERT: S 82 LEU cc_start: 0.9455 (mt) cc_final: 0.9153 (mm) REVERT: T 56 ILE cc_start: 0.9217 (mt) cc_final: 0.8738 (tt) REVERT: U 31 ASP cc_start: 0.8461 (m-30) cc_final: 0.8074 (m-30) REVERT: U 58 ASN cc_start: 0.8348 (m-40) cc_final: 0.8023 (m-40) REVERT: U 69 MET cc_start: 0.8553 (ttm) cc_final: 0.8301 (ttm) REVERT: V 28 ARG cc_start: 0.8490 (mmt90) cc_final: 0.7813 (mmt-90) REVERT: V 48 GLN cc_start: 0.8562 (mm-40) cc_final: 0.7784 (mm-40) REVERT: V 49 ARG cc_start: 0.8351 (mmt180) cc_final: 0.7452 (mmt180) REVERT: Z 8 LEU cc_start: 0.9360 (mt) cc_final: 0.9090 (mp) REVERT: Z 9 LYS cc_start: 0.9413 (mmpt) cc_final: 0.8698 (mmtm) REVERT: Z 19 GLN cc_start: 0.7953 (mp10) cc_final: 0.7438 (mp-120) REVERT: Z 24 ARG cc_start: 0.8629 (mmm160) cc_final: 0.8400 (tpt170) REVERT: Z 29 LYS cc_start: 0.8553 (ptpt) cc_final: 0.8327 (ptmt) REVERT: b 6 ARG cc_start: 0.9207 (mmm-85) cc_final: 0.8671 (mmm-85) REVERT: b 27 MET cc_start: 0.8275 (mtm) cc_final: 0.7751 (mtm) REVERT: Y 15 GLU cc_start: 0.7499 (tp30) cc_final: 0.7033 (tp30) REVERT: Y 31 GLN cc_start: 0.9291 (mm-40) cc_final: 0.8602 (mm110) REVERT: Y 36 GLN cc_start: 0.7792 (mt0) cc_final: 0.7589 (mt0) REVERT: Y 53 MET cc_start: 0.9315 (mtm) cc_final: 0.8929 (mmp) REVERT: Y 65 ASN cc_start: 0.8051 (t0) cc_final: 0.7542 (m110) REVERT: W 15 ARG cc_start: 0.5797 (ttt180) cc_final: 0.5439 (ttt180) REVERT: W 81 ARG cc_start: 0.8087 (mtt180) cc_final: 0.7603 (ttt180) REVERT: W 138 ASN cc_start: 0.8932 (p0) cc_final: 0.8682 (p0) REVERT: W 147 LYS cc_start: 0.7561 (mttt) cc_final: 0.6967 (pttt) REVERT: W 201 ASN cc_start: 0.6641 (t0) cc_final: 0.5958 (m-40) REVERT: W 231 PRO cc_start: 0.7682 (Cg_exo) cc_final: 0.7165 (Cg_exo) REVERT: W 249 MET cc_start: 0.7002 (ptm) cc_final: 0.6799 (ptm) REVERT: W 269 THR cc_start: 0.6778 (t) cc_final: 0.6495 (m) outliers start: 1 outliers final: 0 residues processed: 540 average time/residue: 0.7803 time to fit residues: 717.8190 Evaluate side-chains 425 residues out of total 2242 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 424 time to evaluate : 3.121 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 535 random chunks: chunk 173 optimal weight: 10.0000 chunk 465 optimal weight: 10.0000 chunk 102 optimal weight: 10.0000 chunk 303 optimal weight: 9.9990 chunk 127 optimal weight: 10.0000 chunk 517 optimal weight: 10.0000 chunk 429 optimal weight: 10.0000 chunk 239 optimal weight: 10.0000 chunk 43 optimal weight: 20.0000 chunk 171 optimal weight: 20.0000 chunk 271 optimal weight: 30.0000 overall best weight: 9.9998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 11 ASN ** C 134 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 50 GLN ** D 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 152 ASN E 40 GLN ** E 182 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 66 HIS J 96 ASN N 12 GLN ** P 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 80 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 72 ASN R 45 ASN S 67 ASN Z 37 HIS Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8286 moved from start: 0.3795 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.084 87845 Z= 0.441 Angle : 0.886 8.938 132342 Z= 0.437 Chirality : 0.045 0.375 17066 Planarity : 0.007 0.076 6406 Dihedral : 26.580 179.523 46042 Min Nonbonded Distance : 1.988 Molprobity Statistics. All-atom Clashscore : 34.78 Ramachandran Plot: Outliers : 0.04 % Allowed : 12.00 % Favored : 87.96 % Rotamer: Outliers : 0.09 % Allowed : 4.80 % Favored : 95.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.85 (0.15), residues: 2608 helix: -1.35 (0.18), residues: 643 sheet: -1.74 (0.25), residues: 404 loop : -2.24 (0.15), residues: 1561 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.003 TRP J 16 HIS 0.011 0.002 HIS J 54 PHE 0.044 0.003 PHE Q 57 TYR 0.022 0.003 TYR C 103 ARG 0.016 0.001 ARG Q 92 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5216 Ramachandran restraints generated. 2608 Oldfield, 0 Emsley, 2608 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5216 Ramachandran restraints generated. 2608 Oldfield, 0 Emsley, 2608 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 501 residues out of total 2242 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 499 time to evaluate : 3.232 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: C 16 MET cc_start: 0.8698 (ppp) cc_final: 0.7688 (ppp) REVERT: C 24 ILE cc_start: 0.9337 (mp) cc_final: 0.9090 (mt) REVERT: C 117 MET cc_start: 0.8639 (tmm) cc_final: 0.8168 (tmm) REVERT: C 247 MET cc_start: 0.5780 (ttm) cc_final: 0.5430 (ttm) REVERT: D 140 HIS cc_start: 0.8950 (p90) cc_final: 0.8625 (p-80) REVERT: D 146 MET cc_start: 0.8521 (mmp) cc_final: 0.8320 (mmp) REVERT: D 168 GLN cc_start: 0.8953 (mt0) cc_final: 0.8585 (pt0) REVERT: D 201 THR cc_start: 0.8270 (m) cc_final: 0.7905 (p) REVERT: E 35 ASP cc_start: 0.8531 (t70) cc_final: 0.8215 (t0) REVERT: E 158 ASP cc_start: 0.8427 (p0) cc_final: 0.7855 (p0) REVERT: E 165 LEU cc_start: 0.8696 (mm) cc_final: 0.8220 (tp) REVERT: G 78 GLU cc_start: 0.8219 (mp0) cc_final: 0.7528 (mm-30) REVERT: J 32 GLU cc_start: 0.9447 (tp30) cc_final: 0.9197 (tp30) REVERT: J 93 MET cc_start: 0.8848 (ttm) cc_final: 0.8431 (ttm) REVERT: J 101 MET cc_start: 0.8190 (tmm) cc_final: 0.7763 (tmm) REVERT: J 102 LEU cc_start: 0.9172 (tp) cc_final: 0.8930 (tp) REVERT: J 109 MET cc_start: 0.8843 (mmp) cc_final: 0.8281 (mmp) REVERT: J 139 GLU cc_start: 0.8692 (mt-10) cc_final: 0.7972 (mp0) REVERT: K 8 LEU cc_start: 0.9613 (tp) cc_final: 0.8828 (tp) REVERT: K 18 GLU cc_start: 0.7858 (mt-10) cc_final: 0.7470 (mt-10) REVERT: K 89 ASP cc_start: 0.8327 (p0) cc_final: 0.8000 (p0) REVERT: K 112 MET cc_start: 0.8977 (mpp) cc_final: 0.8519 (mpp) REVERT: L 106 ASN cc_start: 0.9039 (m-40) cc_final: 0.8023 (t0) REVERT: N 26 ILE cc_start: 0.9293 (mt) cc_final: 0.9020 (tt) REVERT: N 102 MET cc_start: 0.7560 (tpp) cc_final: 0.7349 (tpp) REVERT: N 114 MET cc_start: 0.8036 (tpt) cc_final: 0.7798 (tpp) REVERT: P 6 LYS cc_start: 0.8501 (tttt) cc_final: 0.8203 (tttt) REVERT: P 19 ASP cc_start: 0.6701 (t0) cc_final: 0.6429 (t0) REVERT: Q 32 TYR cc_start: 0.9293 (t80) cc_final: 0.9073 (t80) REVERT: Q 40 MET cc_start: 0.9203 (ttm) cc_final: 0.8611 (ttm) REVERT: Q 49 ASP cc_start: 0.8780 (t0) cc_final: 0.8194 (t0) REVERT: Q 94 MET cc_start: 0.8898 (ttt) cc_final: 0.8661 (ttt) REVERT: R 10 LYS cc_start: 0.9113 (ptmt) cc_final: 0.8813 (ptmt) REVERT: R 31 GLU cc_start: 0.6343 (mp0) cc_final: 0.6068 (mp0) REVERT: R 36 GLU cc_start: 0.8536 (tp30) cc_final: 0.8195 (tp30) REVERT: R 50 ASN cc_start: 0.8702 (p0) cc_final: 0.8368 (p0) REVERT: R 52 THR cc_start: 0.8721 (m) cc_final: 0.8332 (t) REVERT: R 63 GLU cc_start: 0.8832 (tt0) cc_final: 0.8376 (mm-30) REVERT: R 76 TYR cc_start: 0.8781 (p90) cc_final: 0.8463 (p90) REVERT: R 89 ARG cc_start: 0.8891 (ttt180) cc_final: 0.8124 (ttt180) REVERT: S 24 ILE cc_start: 0.9462 (mm) cc_final: 0.9209 (mm) REVERT: S 78 GLU cc_start: 0.8338 (pt0) cc_final: 0.8122 (pt0) REVERT: T 56 ILE cc_start: 0.9248 (mt) cc_final: 0.8716 (tt) REVERT: U 31 ASP cc_start: 0.8527 (m-30) cc_final: 0.8224 (m-30) REVERT: U 58 ASN cc_start: 0.8397 (m-40) cc_final: 0.8037 (m-40) REVERT: U 69 MET cc_start: 0.8597 (ttm) cc_final: 0.8346 (ttm) REVERT: V 28 ARG cc_start: 0.8522 (mmt90) cc_final: 0.7784 (mmt-90) REVERT: V 48 GLN cc_start: 0.8460 (mm-40) cc_final: 0.7727 (mm-40) REVERT: V 49 ARG cc_start: 0.8563 (mmt180) cc_final: 0.8002 (mmt180) REVERT: Z 9 LYS cc_start: 0.9432 (mmpt) cc_final: 0.9166 (mmmm) REVERT: Z 19 GLN cc_start: 0.8192 (mp10) cc_final: 0.7810 (mp-120) REVERT: Z 24 ARG cc_start: 0.8682 (mmm160) cc_final: 0.8332 (tpt90) REVERT: Z 29 LYS cc_start: 0.8648 (ptpt) cc_final: 0.8128 (ptmt) REVERT: b 6 ARG cc_start: 0.9266 (mmm-85) cc_final: 0.8738 (mmm-85) REVERT: b 27 MET cc_start: 0.8179 (mtm) cc_final: 0.7674 (mtm) REVERT: Y 15 GLU cc_start: 0.7516 (tp30) cc_final: 0.7122 (tp30) REVERT: Y 22 LYS cc_start: 0.8995 (mtpp) cc_final: 0.8421 (mtmm) REVERT: Y 31 GLN cc_start: 0.9266 (mm-40) cc_final: 0.8534 (mm110) REVERT: Y 53 MET cc_start: 0.9343 (mtm) cc_final: 0.8916 (mmp) REVERT: Y 65 ASN cc_start: 0.8073 (t0) cc_final: 0.7524 (m110) REVERT: W 15 ARG cc_start: 0.5946 (ttt180) cc_final: 0.5628 (ttt180) REVERT: W 81 ARG cc_start: 0.8110 (mtt180) cc_final: 0.7568 (ttt180) REVERT: W 201 ASN cc_start: 0.6556 (t0) cc_final: 0.5904 (m-40) REVERT: W 231 PRO cc_start: 0.7672 (Cg_exo) cc_final: 0.7146 (Cg_exo) outliers start: 2 outliers final: 1 residues processed: 500 average time/residue: 0.7768 time to fit residues: 664.8678 Evaluate side-chains 396 residues out of total 2242 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 395 time to evaluate : 3.138 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 535 random chunks: chunk 499 optimal weight: 6.9990 chunk 58 optimal weight: 10.0000 chunk 294 optimal weight: 9.9990 chunk 378 optimal weight: 6.9990 chunk 292 optimal weight: 8.9990 chunk 435 optimal weight: 0.7980 chunk 289 optimal weight: 8.9990 chunk 515 optimal weight: 30.0000 chunk 322 optimal weight: 2.9990 chunk 314 optimal weight: 6.9990 chunk 238 optimal weight: 10.0000 overall best weight: 4.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 11 ASN C 86 ASN ** C 134 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 126 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 67 GLN G 66 HIS J 96 ASN J 124 ASN N 12 GLN ** P 80 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 45 ASN U 39 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8215 moved from start: 0.3966 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.073 87845 Z= 0.246 Angle : 0.699 9.132 132342 Z= 0.351 Chirality : 0.038 0.372 17066 Planarity : 0.005 0.065 6406 Dihedral : 26.351 179.987 46042 Min Nonbonded Distance : 2.040 Molprobity Statistics. All-atom Clashscore : 24.31 Ramachandran Plot: Outliers : 0.04 % Allowed : 9.66 % Favored : 90.30 % Rotamer: Outliers : 0.09 % Allowed : 2.29 % Favored : 97.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.52 (0.16), residues: 2608 helix: -0.98 (0.19), residues: 664 sheet: -1.66 (0.24), residues: 421 loop : -2.05 (0.15), residues: 1523 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP E 65 HIS 0.017 0.001 HIS J 54 PHE 0.025 0.002 PHE S 75 TYR 0.025 0.002 TYR E 97 ARG 0.011 0.001 ARG Q 92 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5216 Ramachandran restraints generated. 2608 Oldfield, 0 Emsley, 2608 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5216 Ramachandran restraints generated. 2608 Oldfield, 0 Emsley, 2608 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 529 residues out of total 2242 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 527 time to evaluate : 3.202 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: C 16 MET cc_start: 0.8745 (ppp) cc_final: 0.7805 (ppp) REVERT: C 24 ILE cc_start: 0.9396 (mp) cc_final: 0.9096 (mt) REVERT: C 117 MET cc_start: 0.8623 (tmm) cc_final: 0.8176 (tmm) REVERT: C 247 MET cc_start: 0.5611 (ttm) cc_final: 0.5384 (ttm) REVERT: D 160 LEU cc_start: 0.8929 (tp) cc_final: 0.8662 (tp) REVERT: D 168 GLN cc_start: 0.8997 (mt0) cc_final: 0.8639 (pt0) REVERT: D 201 THR cc_start: 0.8304 (m) cc_final: 0.7923 (p) REVERT: E 35 ASP cc_start: 0.8559 (t70) cc_final: 0.8154 (t0) REVERT: E 165 LEU cc_start: 0.8754 (mm) cc_final: 0.8248 (tp) REVERT: F 171 THR cc_start: 0.5692 (p) cc_final: 0.5476 (p) REVERT: G 119 GLU cc_start: 0.5719 (mt-10) cc_final: 0.5211 (mp0) REVERT: G 168 GLU cc_start: 0.7790 (tm-30) cc_final: 0.7424 (tm-30) REVERT: J 93 MET cc_start: 0.8620 (ttm) cc_final: 0.8399 (ttm) REVERT: J 109 MET cc_start: 0.8882 (mmp) cc_final: 0.7398 (mmm) REVERT: J 121 LYS cc_start: 0.8974 (mtmt) cc_final: 0.8706 (mtmm) REVERT: J 139 GLU cc_start: 0.8643 (mt-10) cc_final: 0.7973 (mp0) REVERT: K 4 GLN cc_start: 0.8885 (tp-100) cc_final: 0.8549 (tp-100) REVERT: K 8 LEU cc_start: 0.9541 (tp) cc_final: 0.8787 (tp) REVERT: K 66 LYS cc_start: 0.9229 (ttmm) cc_final: 0.8826 (tppp) REVERT: K 89 ASP cc_start: 0.8211 (p0) cc_final: 0.7901 (p0) REVERT: K 112 MET cc_start: 0.8938 (mpp) cc_final: 0.8468 (mpp) REVERT: L 6 LEU cc_start: 0.7996 (tp) cc_final: 0.7713 (tp) REVERT: L 21 ARG cc_start: 0.8443 (mmt180) cc_final: 0.7850 (mmt180) REVERT: L 36 LYS cc_start: 0.8455 (mmtm) cc_final: 0.7312 (pttp) REVERT: L 106 ASN cc_start: 0.8944 (m-40) cc_final: 0.7972 (t0) REVERT: N 114 MET cc_start: 0.8010 (tpt) cc_final: 0.7633 (tpp) REVERT: P 6 LYS cc_start: 0.8464 (tttt) cc_final: 0.8170 (tttt) REVERT: P 19 ASP cc_start: 0.6783 (t0) cc_final: 0.6531 (t0) REVERT: Q 40 MET cc_start: 0.9034 (ttm) cc_final: 0.8370 (ttm) REVERT: Q 49 ASP cc_start: 0.8739 (t0) cc_final: 0.7970 (t0) REVERT: Q 94 MET cc_start: 0.8911 (ttt) cc_final: 0.8553 (ttt) REVERT: R 36 GLU cc_start: 0.8425 (tp30) cc_final: 0.8037 (tp30) REVERT: R 50 ASN cc_start: 0.8872 (p0) cc_final: 0.8567 (p0) REVERT: R 52 THR cc_start: 0.8928 (m) cc_final: 0.8552 (t) REVERT: R 63 GLU cc_start: 0.8727 (tt0) cc_final: 0.8256 (mm-30) REVERT: R 76 TYR cc_start: 0.8566 (p90) cc_final: 0.8096 (p90) REVERT: R 89 ARG cc_start: 0.8954 (ttt180) cc_final: 0.8269 (ttt180) REVERT: R 98 GLU cc_start: 0.9183 (mt-10) cc_final: 0.8836 (mp0) REVERT: S 38 LEU cc_start: 0.8982 (mm) cc_final: 0.8651 (mp) REVERT: T 9 LYS cc_start: 0.8902 (mptt) cc_final: 0.8442 (mmtp) REVERT: T 56 ILE cc_start: 0.9148 (mt) cc_final: 0.8742 (tt) REVERT: U 5 LYS cc_start: 0.8920 (tmtt) cc_final: 0.8596 (tptp) REVERT: U 10 MET cc_start: 0.8742 (tpp) cc_final: 0.8467 (tpp) REVERT: U 31 ASP cc_start: 0.8370 (m-30) cc_final: 0.7975 (m-30) REVERT: U 58 ASN cc_start: 0.8272 (m-40) cc_final: 0.7523 (m-40) REVERT: U 69 MET cc_start: 0.8332 (ttm) cc_final: 0.8132 (ttm) REVERT: V 28 ARG cc_start: 0.8477 (mmt90) cc_final: 0.7771 (mmt-90) REVERT: V 48 GLN cc_start: 0.8607 (mm-40) cc_final: 0.8236 (mt0) REVERT: V 49 ARG cc_start: 0.8564 (mmt180) cc_final: 0.7712 (mmt180) REVERT: V 65 ASP cc_start: 0.7766 (t0) cc_final: 0.7329 (t0) REVERT: Z 9 LYS cc_start: 0.9393 (mmpt) cc_final: 0.9072 (mmmm) REVERT: Z 19 GLN cc_start: 0.8162 (mp10) cc_final: 0.7960 (mp-120) REVERT: Z 24 ARG cc_start: 0.8689 (mmm160) cc_final: 0.8361 (tpt90) REVERT: Y 15 GLU cc_start: 0.7329 (tp30) cc_final: 0.6883 (tp30) REVERT: Y 31 GLN cc_start: 0.9237 (mm-40) cc_final: 0.8756 (mm-40) REVERT: Y 53 MET cc_start: 0.9277 (mtm) cc_final: 0.8878 (mmp) REVERT: Y 65 ASN cc_start: 0.8110 (t0) cc_final: 0.7520 (m110) REVERT: W 15 ARG cc_start: 0.5864 (ttt180) cc_final: 0.5568 (ttt180) REVERT: W 81 ARG cc_start: 0.7974 (mtt180) cc_final: 0.7529 (ttt180) REVERT: W 135 THR cc_start: 0.8235 (t) cc_final: 0.7846 (t) REVERT: W 136 LEU cc_start: 0.8986 (tp) cc_final: 0.8741 (tp) REVERT: W 138 ASN cc_start: 0.8684 (p0) cc_final: 0.8322 (p0) REVERT: W 147 LYS cc_start: 0.7545 (mttt) cc_final: 0.6970 (pttt) REVERT: W 201 ASN cc_start: 0.6497 (t0) cc_final: 0.5882 (m-40) REVERT: W 249 MET cc_start: 0.7138 (ptm) cc_final: 0.6898 (ptm) REVERT: W 269 THR cc_start: 0.6703 (t) cc_final: 0.6412 (m) outliers start: 2 outliers final: 0 residues processed: 528 average time/residue: 0.7827 time to fit residues: 708.7235 Evaluate side-chains 414 residues out of total 2242 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 414 time to evaluate : 3.154 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 535 random chunks: chunk 319 optimal weight: 20.0000 chunk 205 optimal weight: 20.0000 chunk 307 optimal weight: 0.1980 chunk 155 optimal weight: 10.0000 chunk 101 optimal weight: 10.0000 chunk 99 optimal weight: 10.0000 chunk 327 optimal weight: 20.0000 chunk 351 optimal weight: 6.9990 chunk 254 optimal weight: 10.0000 chunk 48 optimal weight: 10.0000 chunk 405 optimal weight: 0.8980 overall best weight: 5.6190 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 11 ASN ** C 134 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 50 GLN ** D 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 126 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 66 HIS J 96 ASN J 124 ASN N 12 GLN N 68 ASN ** P 80 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 45 ASN S 68 ASN T 35 ASN Z 37 HIS Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8220 moved from start: 0.4026 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.074 87845 Z= 0.267 Angle : 0.714 9.085 132342 Z= 0.357 Chirality : 0.039 0.366 17066 Planarity : 0.005 0.068 6406 Dihedral : 26.346 179.382 46042 Min Nonbonded Distance : 2.047 Molprobity Statistics. All-atom Clashscore : 25.29 Ramachandran Plot: Outliers : 0.04 % Allowed : 10.35 % Favored : 89.61 % Rotamer: Outliers : 0.09 % Allowed : 1.57 % Favored : 98.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.45 (0.16), residues: 2608 helix: -0.85 (0.20), residues: 645 sheet: -1.69 (0.24), residues: 422 loop : -2.00 (0.15), residues: 1541 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP C 213 HIS 0.015 0.001 HIS J 54 PHE 0.034 0.002 PHE F 20 TYR 0.020 0.002 TYR O 102 ARG 0.018 0.001 ARG K 7 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5216 Ramachandran restraints generated. 2608 Oldfield, 0 Emsley, 2608 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5216 Ramachandran restraints generated. 2608 Oldfield, 0 Emsley, 2608 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 512 residues out of total 2242 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 510 time to evaluate : 3.193 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: C 16 MET cc_start: 0.8748 (ppp) cc_final: 0.7840 (ppp) REVERT: C 24 ILE cc_start: 0.9385 (mp) cc_final: 0.9069 (mt) REVERT: C 117 MET cc_start: 0.8467 (tmm) cc_final: 0.8073 (tmm) REVERT: C 247 MET cc_start: 0.5628 (ttm) cc_final: 0.5397 (ttm) REVERT: D 140 HIS cc_start: 0.8763 (p90) cc_final: 0.8520 (p-80) REVERT: D 154 VAL cc_start: 0.9172 (t) cc_final: 0.8793 (p) REVERT: D 160 LEU cc_start: 0.9036 (tp) cc_final: 0.8702 (tp) REVERT: D 168 GLN cc_start: 0.9002 (mt0) cc_final: 0.8585 (pt0) REVERT: D 201 THR cc_start: 0.8292 (m) cc_final: 0.7937 (p) REVERT: E 35 ASP cc_start: 0.8533 (t70) cc_final: 0.8191 (t0) REVERT: E 165 LEU cc_start: 0.8551 (mm) cc_final: 0.8204 (tp) REVERT: F 63 GLN cc_start: 0.4586 (mm-40) cc_final: 0.4377 (mm-40) REVERT: F 83 MET cc_start: 0.5566 (pmm) cc_final: 0.5326 (pmm) REVERT: F 89 VAL cc_start: 0.7420 (t) cc_final: 0.7205 (t) REVERT: F 96 MET cc_start: 0.7504 (mpp) cc_final: 0.6931 (mpp) REVERT: G 78 GLU cc_start: 0.8199 (mp0) cc_final: 0.7456 (mm-30) REVERT: J 93 MET cc_start: 0.8660 (ttm) cc_final: 0.8351 (ttm) REVERT: J 102 LEU cc_start: 0.9086 (tp) cc_final: 0.8857 (tp) REVERT: J 109 MET cc_start: 0.8891 (mmp) cc_final: 0.7360 (mmm) REVERT: J 121 LYS cc_start: 0.8947 (mtmt) cc_final: 0.8648 (mtmm) REVERT: J 139 GLU cc_start: 0.8644 (mt-10) cc_final: 0.7973 (mp0) REVERT: K 4 GLN cc_start: 0.8891 (tp-100) cc_final: 0.8545 (tp-100) REVERT: K 8 LEU cc_start: 0.9553 (tp) cc_final: 0.8799 (tp) REVERT: K 66 LYS cc_start: 0.9253 (ttmm) cc_final: 0.8843 (tppp) REVERT: K 89 ASP cc_start: 0.8222 (p0) cc_final: 0.7900 (p0) REVERT: K 112 MET cc_start: 0.8939 (mpp) cc_final: 0.8468 (mpp) REVERT: L 21 ARG cc_start: 0.8475 (mmt180) cc_final: 0.8058 (mmt180) REVERT: L 36 LYS cc_start: 0.8454 (mmtm) cc_final: 0.7304 (pttp) REVERT: L 106 ASN cc_start: 0.8947 (m-40) cc_final: 0.7811 (t0) REVERT: N 26 ILE cc_start: 0.9302 (mm) cc_final: 0.9079 (mm) REVERT: N 102 MET cc_start: 0.7590 (mmm) cc_final: 0.7342 (mmt) REVERT: N 114 MET cc_start: 0.8019 (tpt) cc_final: 0.7777 (tpp) REVERT: O 43 GLN cc_start: 0.5280 (mp10) cc_final: 0.4893 (mp10) REVERT: P 6 LYS cc_start: 0.8457 (tttt) cc_final: 0.8171 (tttt) REVERT: P 19 ASP cc_start: 0.6781 (t0) cc_final: 0.6573 (t0) REVERT: Q 40 MET cc_start: 0.9089 (ttm) cc_final: 0.8467 (ttm) REVERT: Q 49 ASP cc_start: 0.8772 (t0) cc_final: 0.8069 (t0) REVERT: Q 80 MET cc_start: 0.8853 (mtp) cc_final: 0.8372 (mtp) REVERT: R 10 LYS cc_start: 0.8934 (ptmt) cc_final: 0.8580 (ttpt) REVERT: R 36 GLU cc_start: 0.8268 (tp30) cc_final: 0.7950 (tp30) REVERT: R 50 ASN cc_start: 0.8402 (p0) cc_final: 0.8078 (p0) REVERT: R 52 THR cc_start: 0.8872 (m) cc_final: 0.8558 (t) REVERT: R 63 GLU cc_start: 0.8671 (tt0) cc_final: 0.8170 (mm-30) REVERT: R 76 TYR cc_start: 0.8649 (p90) cc_final: 0.8302 (p90) REVERT: R 89 ARG cc_start: 0.8854 (ttt180) cc_final: 0.8216 (ttt180) REVERT: R 98 GLU cc_start: 0.9116 (mt-10) cc_final: 0.8731 (mp0) REVERT: S 38 LEU cc_start: 0.8987 (mm) cc_final: 0.8637 (mp) REVERT: S 48 GLU cc_start: 0.7004 (tm-30) cc_final: 0.6694 (tm-30) REVERT: T 56 ILE cc_start: 0.9167 (mt) cc_final: 0.8761 (tt) REVERT: U 5 LYS cc_start: 0.8959 (tmtt) cc_final: 0.8633 (tptp) REVERT: U 31 ASP cc_start: 0.8314 (m-30) cc_final: 0.7937 (m-30) REVERT: U 58 ASN cc_start: 0.8287 (m-40) cc_final: 0.8003 (m-40) REVERT: U 69 MET cc_start: 0.8494 (ttm) cc_final: 0.8258 (ttm) REVERT: V 28 ARG cc_start: 0.8472 (mmt90) cc_final: 0.7773 (mmt-90) REVERT: V 48 GLN cc_start: 0.8451 (mm-40) cc_final: 0.7799 (mt0) REVERT: V 49 ARG cc_start: 0.8556 (mmt180) cc_final: 0.7754 (mmt180) REVERT: V 65 ASP cc_start: 0.7742 (t0) cc_final: 0.7287 (t0) REVERT: Z 9 LYS cc_start: 0.9419 (mmpt) cc_final: 0.9100 (mmmm) REVERT: Z 24 ARG cc_start: 0.8696 (mmm160) cc_final: 0.8373 (tpt90) REVERT: Y 15 GLU cc_start: 0.7370 (tp30) cc_final: 0.6943 (tp30) REVERT: Y 29 ARG cc_start: 0.9102 (mtt180) cc_final: 0.8710 (tpp80) REVERT: Y 31 GLN cc_start: 0.9233 (mm-40) cc_final: 0.8689 (mm110) REVERT: Y 53 MET cc_start: 0.9289 (mtm) cc_final: 0.8893 (mmp) REVERT: Y 65 ASN cc_start: 0.8072 (t0) cc_final: 0.7546 (m110) REVERT: W 15 ARG cc_start: 0.5860 (ttt180) cc_final: 0.5567 (ttt180) REVERT: W 81 ARG cc_start: 0.7983 (mtt180) cc_final: 0.7522 (ttt180) REVERT: W 136 LEU cc_start: 0.8979 (tp) cc_final: 0.8706 (tp) REVERT: W 138 ASN cc_start: 0.8890 (p0) cc_final: 0.8487 (p0) REVERT: W 147 LYS cc_start: 0.7504 (mttt) cc_final: 0.6957 (pttt) REVERT: W 201 ASN cc_start: 0.6506 (t0) cc_final: 0.5920 (m-40) outliers start: 2 outliers final: 0 residues processed: 511 average time/residue: 0.7829 time to fit residues: 684.6397 Evaluate side-chains 413 residues out of total 2242 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 413 time to evaluate : 3.199 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 535 random chunks: chunk 469 optimal weight: 30.0000 chunk 494 optimal weight: 9.9990 chunk 450 optimal weight: 0.0020 chunk 480 optimal weight: 0.4980 chunk 493 optimal weight: 7.9990 chunk 289 optimal weight: 1.9990 chunk 209 optimal weight: 10.0000 chunk 377 optimal weight: 9.9990 chunk 147 optimal weight: 20.0000 chunk 434 optimal weight: 10.0000 chunk 454 optimal weight: 10.0000 overall best weight: 4.0994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 11 ASN D 50 GLN ** D 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 126 HIS G 66 HIS N 12 GLN ** P 80 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 45 ASN S 68 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8189 moved from start: 0.4227 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.071 87845 Z= 0.214 Angle : 0.664 9.232 132342 Z= 0.333 Chirality : 0.037 0.350 17066 Planarity : 0.005 0.065 6406 Dihedral : 26.239 179.578 46042 Min Nonbonded Distance : 2.051 Molprobity Statistics. All-atom Clashscore : 22.26 Ramachandran Plot: Outliers : 0.04 % Allowed : 9.43 % Favored : 90.53 % Rotamer: Outliers : 0.09 % Allowed : 0.85 % Favored : 99.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.27 (0.16), residues: 2608 helix: -0.62 (0.20), residues: 650 sheet: -1.59 (0.25), residues: 431 loop : -1.93 (0.15), residues: 1527 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP E 83 HIS 0.014 0.001 HIS J 54 PHE 0.027 0.002 PHE Q 106 TYR 0.018 0.002 TYR O 102 ARG 0.010 0.001 ARG Q 92 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5216 Ramachandran restraints generated. 2608 Oldfield, 0 Emsley, 2608 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5216 Ramachandran restraints generated. 2608 Oldfield, 0 Emsley, 2608 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 517 residues out of total 2242 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 515 time to evaluate : 3.634 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: C 16 MET cc_start: 0.8731 (ppp) cc_final: 0.7833 (ppp) REVERT: C 24 ILE cc_start: 0.9387 (mp) cc_final: 0.9047 (mt) REVERT: C 117 MET cc_start: 0.8458 (tmm) cc_final: 0.8043 (tmm) REVERT: C 156 ARG cc_start: 0.8552 (ttm170) cc_final: 0.8352 (ttp-170) REVERT: C 225 MET cc_start: 0.7667 (tpp) cc_final: 0.7408 (tpp) REVERT: C 247 MET cc_start: 0.5596 (ttm) cc_final: 0.5302 (ttm) REVERT: D 140 HIS cc_start: 0.8952 (p90) cc_final: 0.8712 (p-80) REVERT: D 154 VAL cc_start: 0.8937 (t) cc_final: 0.8541 (p) REVERT: D 160 LEU cc_start: 0.8992 (tp) cc_final: 0.8662 (tp) REVERT: D 168 GLN cc_start: 0.8997 (mt0) cc_final: 0.8582 (pt0) REVERT: D 201 THR cc_start: 0.8499 (m) cc_final: 0.8038 (p) REVERT: E 35 ASP cc_start: 0.8624 (t70) cc_final: 0.8124 (t0) REVERT: E 165 LEU cc_start: 0.8507 (mm) cc_final: 0.8089 (tp) REVERT: F 63 GLN cc_start: 0.4157 (mm-40) cc_final: 0.3869 (mt0) REVERT: F 83 MET cc_start: 0.5720 (pmm) cc_final: 0.5499 (pmm) REVERT: F 89 VAL cc_start: 0.7426 (t) cc_final: 0.7206 (t) REVERT: F 96 MET cc_start: 0.7460 (mpp) cc_final: 0.6962 (mpp) REVERT: G 78 GLU cc_start: 0.8204 (mp0) cc_final: 0.7643 (mm-30) REVERT: J 93 MET cc_start: 0.8541 (ttm) cc_final: 0.8284 (ttm) REVERT: J 102 LEU cc_start: 0.8953 (tp) cc_final: 0.8729 (tp) REVERT: J 109 MET cc_start: 0.8897 (mmp) cc_final: 0.7407 (mmm) REVERT: J 121 LYS cc_start: 0.8780 (mtmt) cc_final: 0.8530 (mtmm) REVERT: J 139 GLU cc_start: 0.8603 (mt-10) cc_final: 0.7966 (mp0) REVERT: K 4 GLN cc_start: 0.8938 (tp-100) cc_final: 0.8606 (tp-100) REVERT: K 8 LEU cc_start: 0.9491 (tp) cc_final: 0.8815 (tp) REVERT: K 66 LYS cc_start: 0.9235 (ttmm) cc_final: 0.8870 (tppp) REVERT: K 89 ASP cc_start: 0.8164 (p0) cc_final: 0.7865 (p0) REVERT: K 112 MET cc_start: 0.8829 (mpp) cc_final: 0.8258 (mpp) REVERT: L 36 LYS cc_start: 0.8433 (mmtm) cc_final: 0.7356 (pttp) REVERT: L 106 ASN cc_start: 0.8946 (m-40) cc_final: 0.7772 (t0) REVERT: N 101 ILE cc_start: 0.9434 (mt) cc_final: 0.9143 (mm) REVERT: N 102 MET cc_start: 0.7829 (mmm) cc_final: 0.7530 (mmt) REVERT: N 114 MET cc_start: 0.8066 (tpt) cc_final: 0.7811 (tpp) REVERT: O 43 GLN cc_start: 0.5130 (mp10) cc_final: 0.4678 (mp10) REVERT: P 6 LYS cc_start: 0.8451 (tttt) cc_final: 0.8146 (tttt) REVERT: P 19 ASP cc_start: 0.6796 (t0) cc_final: 0.6578 (t0) REVERT: Q 49 ASP cc_start: 0.8695 (t0) cc_final: 0.7948 (t0) REVERT: Q 94 MET cc_start: 0.9017 (ttt) cc_final: 0.8529 (ttt) REVERT: R 10 LYS cc_start: 0.8874 (ptmt) cc_final: 0.8668 (ptmt) REVERT: R 36 GLU cc_start: 0.8336 (tp30) cc_final: 0.8030 (tp30) REVERT: R 50 ASN cc_start: 0.8545 (p0) cc_final: 0.8334 (p0) REVERT: R 52 THR cc_start: 0.8792 (m) cc_final: 0.8302 (t) REVERT: R 63 GLU cc_start: 0.8721 (tt0) cc_final: 0.8205 (mm-30) REVERT: R 76 TYR cc_start: 0.8510 (p90) cc_final: 0.8301 (p90) REVERT: R 89 ARG cc_start: 0.8820 (ttt180) cc_final: 0.8010 (ttt180) REVERT: S 38 LEU cc_start: 0.8886 (mm) cc_final: 0.8487 (mp) REVERT: S 48 GLU cc_start: 0.6955 (tm-30) cc_final: 0.6608 (tm-30) REVERT: S 78 GLU cc_start: 0.8380 (pt0) cc_final: 0.8038 (pt0) REVERT: S 90 MET cc_start: 0.8531 (mmt) cc_final: 0.8296 (mmt) REVERT: T 9 LYS cc_start: 0.8872 (mptt) cc_final: 0.8224 (mmtp) REVERT: T 35 ASN cc_start: 0.9287 (m-40) cc_final: 0.8978 (m-40) REVERT: T 38 GLU cc_start: 0.8461 (tt0) cc_final: 0.8098 (tt0) REVERT: T 56 ILE cc_start: 0.9081 (mt) cc_final: 0.8749 (tt) REVERT: U 5 LYS cc_start: 0.9014 (tmtt) cc_final: 0.8643 (tptp) REVERT: U 10 MET cc_start: 0.8808 (tpp) cc_final: 0.8519 (tpp) REVERT: U 31 ASP cc_start: 0.8377 (m-30) cc_final: 0.8014 (m-30) REVERT: U 58 ASN cc_start: 0.8311 (m-40) cc_final: 0.8063 (m-40) REVERT: U 69 MET cc_start: 0.8450 (ttm) cc_final: 0.8244 (ttm) REVERT: V 28 ARG cc_start: 0.8437 (mmt90) cc_final: 0.7595 (mmt-90) REVERT: V 48 GLN cc_start: 0.8414 (mm-40) cc_final: 0.7895 (mt0) REVERT: V 49 ARG cc_start: 0.8556 (mmt180) cc_final: 0.7646 (mmt180) REVERT: V 65 ASP cc_start: 0.7642 (t0) cc_final: 0.7196 (t0) REVERT: Z 9 LYS cc_start: 0.9300 (mmpt) cc_final: 0.9040 (mmmm) REVERT: Z 24 ARG cc_start: 0.8665 (mmm160) cc_final: 0.8316 (tpt90) REVERT: b 18 THR cc_start: 0.8423 (p) cc_final: 0.8221 (p) REVERT: b 27 MET cc_start: 0.8183 (mtp) cc_final: 0.7983 (mtp) REVERT: Y 29 ARG cc_start: 0.9078 (mtt180) cc_final: 0.8676 (tpp80) REVERT: Y 31 GLN cc_start: 0.9225 (mm-40) cc_final: 0.8671 (mm110) REVERT: Y 53 MET cc_start: 0.9231 (mtm) cc_final: 0.8870 (mmp) REVERT: Y 65 ASN cc_start: 0.8046 (t0) cc_final: 0.7523 (m110) REVERT: W 15 ARG cc_start: 0.5825 (ttt180) cc_final: 0.5543 (ttt180) REVERT: W 81 ARG cc_start: 0.7948 (mtt180) cc_final: 0.7397 (ttt180) REVERT: W 136 LEU cc_start: 0.9009 (tp) cc_final: 0.8738 (tp) REVERT: W 201 ASN cc_start: 0.6422 (t0) cc_final: 0.5809 (m-40) REVERT: W 215 GLU cc_start: 0.7554 (pt0) cc_final: 0.6558 (pt0) REVERT: W 269 THR cc_start: 0.6668 (t) cc_final: 0.6356 (m) outliers start: 2 outliers final: 0 residues processed: 516 average time/residue: 0.7957 time to fit residues: 700.9198 Evaluate side-chains 419 residues out of total 2242 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 419 time to evaluate : 3.158 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 535 random chunks: chunk 478 optimal weight: 20.0000 chunk 315 optimal weight: 3.9990 chunk 508 optimal weight: 4.9990 chunk 310 optimal weight: 3.9990 chunk 241 optimal weight: 30.0000 chunk 353 optimal weight: 20.0000 chunk 532 optimal weight: 5.9990 chunk 490 optimal weight: 9.9990 chunk 424 optimal weight: 0.9990 chunk 44 optimal weight: 20.0000 chunk 327 optimal weight: 7.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 11 ASN D 50 GLN ** D 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 67 GLN G 66 HIS N 12 GLN ** P 80 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S 68 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8183 moved from start: 0.4312 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 87845 Z= 0.210 Angle : 0.661 9.871 132342 Z= 0.332 Chirality : 0.036 0.340 17066 Planarity : 0.005 0.086 6406 Dihedral : 26.200 179.535 46042 Min Nonbonded Distance : 2.058 Molprobity Statistics. All-atom Clashscore : 22.64 Ramachandran Plot: Outliers : 0.04 % Allowed : 9.36 % Favored : 90.61 % Rotamer: Outliers : 0.04 % Allowed : 0.67 % Favored : 99.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.23 (0.16), residues: 2608 helix: -0.60 (0.20), residues: 657 sheet: -1.51 (0.25), residues: 430 loop : -1.91 (0.15), residues: 1521 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP W 71 HIS 0.013 0.001 HIS J 54 PHE 0.029 0.002 PHE Q 106 TYR 0.023 0.002 TYR Q 32 ARG 0.009 0.001 ARG Q 92 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5216 Ramachandran restraints generated. 2608 Oldfield, 0 Emsley, 2608 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5216 Ramachandran restraints generated. 2608 Oldfield, 0 Emsley, 2608 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 504 residues out of total 2242 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 503 time to evaluate : 3.799 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: C 16 MET cc_start: 0.8728 (ppp) cc_final: 0.7850 (ppp) REVERT: C 24 ILE cc_start: 0.9391 (mp) cc_final: 0.9046 (mt) REVERT: C 117 MET cc_start: 0.8457 (tmm) cc_final: 0.8049 (tmm) REVERT: C 156 ARG cc_start: 0.8571 (ttm170) cc_final: 0.8346 (ttp-170) REVERT: C 225 MET cc_start: 0.7709 (tpp) cc_final: 0.7448 (tpp) REVERT: C 247 MET cc_start: 0.5570 (ttm) cc_final: 0.5301 (ttm) REVERT: D 140 HIS cc_start: 0.8931 (p90) cc_final: 0.8677 (p-80) REVERT: D 154 VAL cc_start: 0.8951 (t) cc_final: 0.8545 (p) REVERT: D 158 LYS cc_start: 0.8572 (tttt) cc_final: 0.8365 (tttt) REVERT: D 160 LEU cc_start: 0.8879 (tp) cc_final: 0.8506 (tp) REVERT: D 168 GLN cc_start: 0.9100 (mt0) cc_final: 0.8719 (pt0) REVERT: E 35 ASP cc_start: 0.8622 (t70) cc_final: 0.8118 (t0) REVERT: E 165 LEU cc_start: 0.8488 (mm) cc_final: 0.8071 (tp) REVERT: F 89 VAL cc_start: 0.7486 (t) cc_final: 0.7082 (t) REVERT: G 78 GLU cc_start: 0.8206 (mp0) cc_final: 0.7718 (mm-30) REVERT: J 93 MET cc_start: 0.8707 (ttm) cc_final: 0.8317 (ttm) REVERT: J 102 LEU cc_start: 0.9002 (tp) cc_final: 0.8788 (tp) REVERT: J 109 MET cc_start: 0.8882 (mmp) cc_final: 0.7378 (mmm) REVERT: J 139 GLU cc_start: 0.8593 (mt-10) cc_final: 0.8024 (mp0) REVERT: K 4 GLN cc_start: 0.8820 (tp-100) cc_final: 0.8475 (tp-100) REVERT: K 8 LEU cc_start: 0.9529 (tp) cc_final: 0.8831 (tp) REVERT: K 66 LYS cc_start: 0.9251 (ttmm) cc_final: 0.8857 (tppp) REVERT: K 89 ASP cc_start: 0.8193 (p0) cc_final: 0.7845 (p0) REVERT: K 91 LYS cc_start: 0.8288 (mmtm) cc_final: 0.7716 (mmtm) REVERT: K 112 MET cc_start: 0.8810 (mpp) cc_final: 0.8274 (mpp) REVERT: L 36 LYS cc_start: 0.8471 (mmtm) cc_final: 0.7345 (pttp) REVERT: L 106 ASN cc_start: 0.8935 (m-40) cc_final: 0.7744 (t0) REVERT: N 16 MET cc_start: 0.8125 (ttt) cc_final: 0.7502 (ttt) REVERT: N 101 ILE cc_start: 0.9416 (mt) cc_final: 0.9133 (mm) REVERT: N 102 MET cc_start: 0.7788 (mmm) cc_final: 0.7530 (mmt) REVERT: N 114 MET cc_start: 0.8075 (tpt) cc_final: 0.7829 (tpp) REVERT: O 43 GLN cc_start: 0.5113 (mp10) cc_final: 0.4601 (mp10) REVERT: P 6 LYS cc_start: 0.8412 (tttt) cc_final: 0.8179 (tttt) REVERT: P 19 ASP cc_start: 0.6718 (t0) cc_final: 0.6477 (t0) REVERT: P 102 TYR cc_start: 0.8853 (p90) cc_final: 0.8431 (p90) REVERT: Q 49 ASP cc_start: 0.8649 (t0) cc_final: 0.7867 (t0) REVERT: Q 94 MET cc_start: 0.9033 (ttt) cc_final: 0.8509 (ttt) REVERT: R 10 LYS cc_start: 0.8825 (ptmt) cc_final: 0.8602 (ptmt) REVERT: R 36 GLU cc_start: 0.8342 (tp30) cc_final: 0.8038 (tp30) REVERT: R 50 ASN cc_start: 0.8469 (p0) cc_final: 0.8234 (p0) REVERT: R 52 THR cc_start: 0.8750 (m) cc_final: 0.8277 (t) REVERT: R 63 GLU cc_start: 0.8803 (tt0) cc_final: 0.8293 (mm-30) REVERT: R 89 ARG cc_start: 0.8750 (ttt180) cc_final: 0.8007 (ttt180) REVERT: S 48 GLU cc_start: 0.6889 (tm-30) cc_final: 0.6575 (tm-30) REVERT: S 78 GLU cc_start: 0.8377 (pt0) cc_final: 0.8048 (pt0) REVERT: S 90 MET cc_start: 0.8554 (mmt) cc_final: 0.8331 (mmt) REVERT: T 9 LYS cc_start: 0.8875 (mptt) cc_final: 0.8222 (mmtp) REVERT: T 35 ASN cc_start: 0.9272 (m-40) cc_final: 0.8993 (m-40) REVERT: T 38 GLU cc_start: 0.8449 (tt0) cc_final: 0.8173 (tt0) REVERT: T 56 ILE cc_start: 0.9070 (mt) cc_final: 0.8759 (tt) REVERT: U 5 LYS cc_start: 0.9054 (tmtt) cc_final: 0.8711 (tptp) REVERT: U 10 MET cc_start: 0.8749 (tpp) cc_final: 0.8501 (tpp) REVERT: U 31 ASP cc_start: 0.8368 (m-30) cc_final: 0.8012 (m-30) REVERT: U 58 ASN cc_start: 0.8315 (m-40) cc_final: 0.8053 (m-40) REVERT: U 69 MET cc_start: 0.8491 (ttm) cc_final: 0.8265 (ttm) REVERT: V 28 ARG cc_start: 0.8471 (mmt90) cc_final: 0.7696 (mmt-90) REVERT: V 48 GLN cc_start: 0.8387 (mm-40) cc_final: 0.7850 (mt0) REVERT: V 49 ARG cc_start: 0.8548 (mmt180) cc_final: 0.7636 (mmt180) REVERT: Z 9 LYS cc_start: 0.9339 (mmpt) cc_final: 0.9063 (mmmm) REVERT: Z 24 ARG cc_start: 0.8684 (mmm160) cc_final: 0.8350 (tpt90) REVERT: b 18 THR cc_start: 0.8423 (p) cc_final: 0.8218 (p) REVERT: Y 22 LYS cc_start: 0.8874 (mtpp) cc_final: 0.8241 (mtmm) REVERT: Y 29 ARG cc_start: 0.9035 (mtt180) cc_final: 0.8639 (tpp80) REVERT: Y 31 GLN cc_start: 0.9240 (mm-40) cc_final: 0.8933 (mm-40) REVERT: Y 53 MET cc_start: 0.9230 (mtm) cc_final: 0.8856 (mmp) REVERT: Y 65 ASN cc_start: 0.8039 (t0) cc_final: 0.7530 (m110) REVERT: W 15 ARG cc_start: 0.5829 (ttt180) cc_final: 0.5534 (ttt180) REVERT: W 81 ARG cc_start: 0.7962 (mtt180) cc_final: 0.7337 (ttt180) REVERT: W 136 LEU cc_start: 0.9010 (tp) cc_final: 0.8746 (tp) REVERT: W 138 ASN cc_start: 0.8827 (p0) cc_final: 0.8611 (p0) REVERT: W 147 LYS cc_start: 0.7405 (mttt) cc_final: 0.6975 (pttt) REVERT: W 201 ASN cc_start: 0.6402 (t0) cc_final: 0.5793 (m-40) REVERT: W 269 THR cc_start: 0.6663 (t) cc_final: 0.6340 (m) outliers start: 1 outliers final: 0 residues processed: 504 average time/residue: 0.7861 time to fit residues: 678.0240 Evaluate side-chains 411 residues out of total 2242 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 411 time to evaluate : 3.139 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 535 random chunks: chunk 260 optimal weight: 10.0000 chunk 337 optimal weight: 20.0000 chunk 452 optimal weight: 0.0070 chunk 130 optimal weight: 9.9990 chunk 391 optimal weight: 0.0970 chunk 62 optimal weight: 10.0000 chunk 117 optimal weight: 20.0000 chunk 425 optimal weight: 10.0000 chunk 177 optimal weight: 10.0000 chunk 436 optimal weight: 9.9990 chunk 53 optimal weight: 10.0000 overall best weight: 6.0204 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 11 ASN C 134 ASN D 50 GLN ** D 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 67 GLN F 63 GLN G 66 HIS N 12 GLN ** O 39 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 80 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.074624 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2982 r_free = 0.2982 target = 0.059051 restraints weight = 353417.491| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3021 r_free = 0.3021 target = 0.060415 restraints weight = 157758.307| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3032 r_free = 0.3032 target = 0.060922 restraints weight = 94977.006| |-----------------------------------------------------------------------------| r_work (final): 0.3025 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8232 moved from start: 0.4352 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.099 87845 Z= 0.279 Angle : 0.709 9.324 132342 Z= 0.353 Chirality : 0.038 0.327 17066 Planarity : 0.005 0.064 6406 Dihedral : 26.220 179.312 46042 Min Nonbonded Distance : 2.055 Molprobity Statistics. All-atom Clashscore : 25.67 Ramachandran Plot: Outliers : 0.08 % Allowed : 10.74 % Favored : 89.19 % Rotamer: Outliers : 0.00 % Allowed : 0.54 % Favored : 99.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.31 (0.16), residues: 2608 helix: -0.69 (0.20), residues: 657 sheet: -1.58 (0.25), residues: 426 loop : -1.95 (0.15), residues: 1525 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.003 TRP J 16 HIS 0.013 0.001 HIS J 54 PHE 0.027 0.002 PHE Q 106 TYR 0.034 0.002 TYR Q 32 ARG 0.026 0.001 ARG K 7 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 12715.75 seconds wall clock time: 230 minutes 3.74 seconds (13803.74 seconds total)