Starting phenix.real_space_refine on Tue Feb 20 16:23:20 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zq5_14864/02_2024/7zq5_14864.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zq5_14864/02_2024/7zq5_14864.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zq5_14864/02_2024/7zq5_14864.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zq5_14864/02_2024/7zq5_14864.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zq5_14864/02_2024/7zq5_14864.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zq5_14864/02_2024/7zq5_14864.pdb" } resolution = 2.7 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.009 sd= 0.028 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 3018 5.49 5 S 74 5.16 5 C 43992 2.51 5 N 16567 2.21 5 O 25197 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "0 ARG 3": "NH1" <-> "NH2" Residue "0 ARG 11": "NH1" <-> "NH2" Residue "0 ARG 18": "NH1" <-> "NH2" Residue "0 ARG 37": "NH1" <-> "NH2" Residue "0 ARG 50": "NH1" <-> "NH2" Residue "0 ARG 57": "NH1" <-> "NH2" Residue "0 ARG 74": "NH1" <-> "NH2" Residue "0 GLU 76": "OE1" <-> "OE2" Residue "1 ARG 29": "NH1" <-> "NH2" Residue "1 ARG 47": "NH1" <-> "NH2" Residue "1 ARG 52": "NH1" <-> "NH2" Residue "2 ARG 11": "NH1" <-> "NH2" Residue "2 ARG 30": "NH1" <-> "NH2" Residue "2 ARG 45": "NH1" <-> "NH2" Residue "3 ARG 10": "NH1" <-> "NH2" Residue "3 ARG 16": "NH1" <-> "NH2" Residue "3 ARG 52": "NH1" <-> "NH2" Residue "4 ARG 44": "NH1" <-> "NH2" Residue "6 ARG 3": "NH1" <-> "NH2" Residue "6 ARG 12": "NH1" <-> "NH2" Residue "6 ARG 14": "NH1" <-> "NH2" Residue "6 ARG 19": "NH1" <-> "NH2" Residue "6 ARG 21": "NH1" <-> "NH2" Residue "6 ARG 33": "NH1" <-> "NH2" Residue "6 ARG 41": "NH1" <-> "NH2" Residue "7 ARG 13": "NH1" <-> "NH2" Residue "7 ARG 30": "NH1" <-> "NH2" Residue "7 ARG 40": "NH1" <-> "NH2" Residue "7 ARG 42": "NH1" <-> "NH2" Residue "8 ARG 24": "NH1" <-> "NH2" Residue "c ARG 52": "NH1" <-> "NH2" Residue "c ARG 63": "NH1" <-> "NH2" Residue "c ARG 80": "NH1" <-> "NH2" Residue "c GLU 82": "OE1" <-> "OE2" Residue "c TYR 96": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "c ARG 133": "NH1" <-> "NH2" Residue "c ARG 167": "NH1" <-> "NH2" Residue "c ARG 177": "NH1" <-> "NH2" Residue "c ARG 182": "NH1" <-> "NH2" Residue "c ARG 189": "NH1" <-> "NH2" Residue "c GLU 194": "OE1" <-> "OE2" Residue "c ARG 203": "NH1" <-> "NH2" Residue "c ARG 212": "NH1" <-> "NH2" Residue "c GLU 236": "OE1" <-> "OE2" Residue "d ARG 13": "NH1" <-> "NH2" Residue "d GLU 30": "OE1" <-> "OE2" Residue "d ARG 33": "NH1" <-> "NH2" Residue "d ARG 59": "NH1" <-> "NH2" Residue "d ARG 77": "NH1" <-> "NH2" Residue "d ARG 83": "NH1" <-> "NH2" Residue "d GLU 88": "OE1" <-> "OE2" Residue "d ARG 169": "NH1" <-> "NH2" Residue "d ARG 184": "NH1" <-> "NH2" Residue "e ARG 21": "NH1" <-> "NH2" Residue "e ARG 44": "NH1" <-> "NH2" Residue "e ARG 49": "NH1" <-> "NH2" Residue "e GLU 51": "OE1" <-> "OE2" Residue "e ARG 61": "NH1" <-> "NH2" Residue "e ARG 67": "NH1" <-> "NH2" Residue "e ARG 88": "NH1" <-> "NH2" Residue "e ARG 102": "NH1" <-> "NH2" Residue "e ARG 162": "NH1" <-> "NH2" Residue "e ARG 170": "NH1" <-> "NH2" Residue "e GLU 198": "OE1" <-> "OE2" Residue "f ARG 71": "NH1" <-> "NH2" Residue "f ARG 80": "NH1" <-> "NH2" Residue "f ARG 92": "NH1" <-> "NH2" Residue "f ARG 102": "NH1" <-> "NH2" Residue "f ARG 110": "NH1" <-> "NH2" Residue "f ARG 112": "NH1" <-> "NH2" Residue "f ARG 115": "NH1" <-> "NH2" Residue "f ARG 133": "NH1" <-> "NH2" Residue "g ARG 3": "NH1" <-> "NH2" Residue "g GLU 32": "OE1" <-> "OE2" Residue "g ARG 153": "NH1" <-> "NH2" Residue "g ARG 163": "NH1" <-> "NH2" Residue "g ARG 170": "NH1" <-> "NH2" Residue "g GLU 173": "OE1" <-> "OE2" Residue "h ARG 27": "NH1" <-> "NH2" Residue "j ARG 13": "NH1" <-> "NH2" Residue "j ARG 37": "NH1" <-> "NH2" Residue "j ARG 96": "NH1" <-> "NH2" Residue "j GLU 98": "OE1" <-> "OE2" Residue "j GLU 102": "OE1" <-> "OE2" Residue "j ARG 120": "NH1" <-> "NH2" Residue "k GLU 4": "OE1" <-> "OE2" Residue "k GLU 92": "OE1" <-> "OE2" Residue "l ARG 21": "NH1" <-> "NH2" Residue "l ARG 33": "NH1" <-> "NH2" Residue "l ARG 41": "NH1" <-> "NH2" Residue "l ARG 47": "NH1" <-> "NH2" Residue "l ARG 60": "NH1" <-> "NH2" Residue "l ARG 78": "NH1" <-> "NH2" Residue "l ARG 126": "NH1" <-> "NH2" Residue "l GLU 136": "OE1" <-> "OE2" Residue "m ARG 10": "NH1" <-> "NH2" Residue "m ARG 18": "NH1" <-> "NH2" Residue "m ARG 40": "NH1" <-> "NH2" Residue "m ARG 44": "NH1" <-> "NH2" Residue "m GLU 47": "OE1" <-> "OE2" Residue "m ARG 50": "NH1" <-> "NH2" Residue "m ARG 55": "NH1" <-> "NH2" Residue "m ARG 59": "NH1" <-> "NH2" Residue "m GLU 104": "OE1" <-> "OE2" Residue "m ARG 114": "NH1" <-> "NH2" Residue "n ARG 8": "NH1" <-> "NH2" Residue "n ARG 12": "NH1" <-> "NH2" Residue "n ARG 17": "NH1" <-> "NH2" Residue "n ARG 22": "NH1" <-> "NH2" Residue "n GLU 32": "OE1" <-> "OE2" Residue "n ARG 46": "NH1" <-> "NH2" Residue "n ARG 63": "NH1" <-> "NH2" Residue "n ARG 64": "NH1" <-> "NH2" Residue "n ARG 69": "NH1" <-> "NH2" Residue "n ARG 71": "NH1" <-> "NH2" Residue "n GLU 74": "OE1" <-> "OE2" Residue "n ARG 96": "NH1" <-> "NH2" Residue "n ARG 118": "NH1" <-> "NH2" Residue "o ARG 10": "NH1" <-> "NH2" Residue "o ARG 13": "NH1" <-> "NH2" Residue "o ARG 16": "NH1" <-> "NH2" Residue "o ARG 25": "NH1" <-> "NH2" Residue "o ARG 81": "NH1" <-> "NH2" Residue "o ARG 94": "NH1" <-> "NH2" Residue "o ARG 102": "NH1" <-> "NH2" Residue "o ARG 111": "NH1" <-> "NH2" Residue "p GLU 11": "OE1" <-> "OE2" Residue "p ARG 21": "NH1" <-> "NH2" Residue "p ARG 39": "NH1" <-> "NH2" Residue "p ARG 51": "NH1" <-> "NH2" Residue "p ARG 62": "NH1" <-> "NH2" Residue "p GLU 71": "OE1" <-> "OE2" Residue "p ARG 89": "NH1" <-> "NH2" Residue "p ARG 101": "NH1" <-> "NH2" Residue "p GLU 102": "OE1" <-> "OE2" Residue "p ARG 109": "NH1" <-> "NH2" Residue "p GLU 112": "OE1" <-> "OE2" Residue "q ARG 3": "NH1" <-> "NH2" Residue "q ARG 6": "NH1" <-> "NH2" Residue "q ARG 13": "NH1" <-> "NH2" Residue "q ARG 33": "NH1" <-> "NH2" Residue "q ARG 48": "NH1" <-> "NH2" Residue "q ARG 70": "NH1" <-> "NH2" Residue "r ARG 21": "NH1" <-> "NH2" Residue "r GLU 23": "OE1" <-> "OE2" Residue "r GLU 34": "OE1" <-> "OE2" Residue "r ARG 68": "NH1" <-> "NH2" Residue "r ARG 78": "NH1" <-> "NH2" Residue "r ARG 79": "NH1" <-> "NH2" Residue "r ARG 84": "NH1" <-> "NH2" Residue "s GLU 2": "OE1" <-> "OE2" Residue "s GLU 78": "OE1" <-> "OE2" Residue "s ARG 84": "NH1" <-> "NH2" Residue "s ARG 88": "NH1" <-> "NH2" Residue "s ARG 95": "NH1" <-> "NH2" Residue "t GLU 5": "OE1" <-> "OE2" Residue "t ARG 12": "NH1" <-> "NH2" Residue "t GLU 18": "OE1" <-> "OE2" Residue "u ARG 6": "NH1" <-> "NH2" Residue "u ARG 7": "NH1" <-> "NH2" Residue "u GLU 51": "OE1" <-> "OE2" Residue "u ARG 71": "NH1" <-> "NH2" Residue "u ARG 75": "NH1" <-> "NH2" Residue "u ARG 83": "NH1" <-> "NH2" Residue "u PHE 84": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "w PHE 56": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "w PHE 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "y ARG 11": "NH1" <-> "NH2" Time to flip residues: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 88848 Number of models: 1 Model: "" Number of chains: 30 Chain: "0" Number of atoms: 625 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 625 Classifications: {'peptide': 77} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 74} Chain: "1" Number of atoms: 495 Number of conformers: 1 Conformer: "" Number of residues, atoms: 61, 495 Classifications: {'peptide': 61} Link IDs: {'TRANS': 60} Chain: "2" Number of atoms: 439 Number of conformers: 1 Conformer: "" Number of residues, atoms: 57, 439 Classifications: {'peptide': 57} Link IDs: {'PTRANS': 2, 'TRANS': 54} Chain: "3" Number of atoms: 434 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 434 Classifications: {'peptide': 55} Link IDs: {'PTRANS': 1, 'TRANS': 53} Chain: "4" Number of atoms: 409 Number of conformers: 1 Conformer: "" Number of residues, atoms: 50, 409 Classifications: {'peptide': 50} Link IDs: {'PTRANS': 2, 'TRANS': 47} Chain: "6" Number of atoms: 377 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 377 Classifications: {'peptide': 46} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 44} Chain: "7" Number of atoms: 504 Number of conformers: 1 Conformer: "" Number of residues, atoms: 64, 504 Classifications: {'peptide': 64} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 61} Chain: "8" Number of atoms: 301 Number of conformers: 1 Conformer: "" Number of residues, atoms: 38, 301 Classifications: {'peptide': 38} Link IDs: {'PTRANS': 1, 'TRANS': 36} Chain: "a" Number of atoms: 2529 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 2529 Classifications: {'RNA': 118} Modifications used: {'rna2p_pur': 7, 'rna2p_pyr': 5, 'rna3p_pur': 57, 'rna3p_pyr': 49} Link IDs: {'rna2p': 12, 'rna3p': 105} Chain: "b" Number of atoms: 62259 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2900, 62259 Classifications: {'RNA': 2900} Modifications used: {'rna2p_pur': 277, 'rna2p_pyr': 154, 'rna3p_pur': 1397, 'rna3p_pyr': 1072} Link IDs: {'rna2p': 431, 'rna3p': 2468} Chain breaks: 1 Chain: "c" Number of atoms: 2082 Number of conformers: 1 Conformer: "" Number of residues, atoms: 271, 2082 Classifications: {'peptide': 271} Link IDs: {'PTRANS': 17, 'TRANS': 253} Chain: "d" Number of atoms: 1565 Number of conformers: 1 Conformer: "" Number of residues, atoms: 209, 1565 Classifications: {'peptide': 209} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 202} Chain: "e" Number of atoms: 1552 Number of conformers: 1 Conformer: "" Number of residues, atoms: 201, 1552 Classifications: {'peptide': 201} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 195} Chain: "f" Number of atoms: 1410 Number of conformers: 1 Conformer: "" Number of residues, atoms: 177, 1410 Classifications: {'peptide': 177} Link IDs: {'PTRANS': 6, 'TRANS': 170} Chain: "g" Number of atoms: 1323 Number of conformers: 1 Conformer: "" Number of residues, atoms: 176, 1323 Classifications: {'peptide': 176} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 8, 'TRANS': 167} Chain: "h" Number of atoms: 287 Number of conformers: 1 Conformer: "" Number of residues, atoms: 39, 287 Classifications: {'peptide': 39} Link IDs: {'PTRANS': 2, 'TRANS': 36} Chain: "j" Number of atoms: 1129 Number of conformers: 1 Conformer: "" Number of residues, atoms: 142, 1129 Classifications: {'peptide': 142} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 135} Chain: "k" Number of atoms: 938 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 938 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 5, 'TRANS': 116} Chain: "l" Number of atoms: 1043 Number of conformers: 1 Conformer: "" Number of residues, atoms: 143, 1043 Classifications: {'peptide': 143} Link IDs: {'PTRANS': 4, 'TRANS': 138} Chain: "m" Number of atoms: 1074 Number of conformers: 1 Conformer: "" Number of residues, atoms: 136, 1074 Classifications: {'peptide': 136} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 128} Chain: "n" Number of atoms: 960 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 960 Classifications: {'peptide': 120} Link IDs: {'PTRANS': 4, 'TRANS': 115} Chain: "o" Number of atoms: 892 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 892 Classifications: {'peptide': 116} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 113} Chain: "p" Number of atoms: 908 Number of conformers: 1 Conformer: "" Number of residues, atoms: 113, 908 Classifications: {'peptide': 113} Link IDs: {'PTRANS': 3, 'TRANS': 109} Chain: "q" Number of atoms: 947 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 947 Classifications: {'peptide': 117} Modifications used: {'COO': 1} Link IDs: {'TRANS': 116} Chain: "r" Number of atoms: 810 Number of conformers: 1 Conformer: "" Number of residues, atoms: 102, 810 Classifications: {'peptide': 102} Link IDs: {'PTRANS': 1, 'TRANS': 100} Chain: "s" Number of atoms: 845 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 845 Classifications: {'peptide': 109} Link IDs: {'PTRANS': 2, 'TRANS': 106} Chain: "t" Number of atoms: 681 Number of conformers: 1 Conformer: "" Number of residues, atoms: 86, 681 Classifications: {'peptide': 86} Link IDs: {'PTRANS': 1, 'TRANS': 84} Chain: "u" Number of atoms: 699 Number of conformers: 1 Conformer: "" Number of residues, atoms: 91, 699 Classifications: {'peptide': 91} Link IDs: {'TRANS': 90} Chain: "w" Number of atoms: 753 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 753 Classifications: {'peptide': 94} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 89} Chain: "y" Number of atoms: 578 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 578 Classifications: {'peptide': 76} Link IDs: {'PTRANS': 1, 'TRANS': 74} Time building chain proxies: 35.88, per 1000 atoms: 0.40 Number of scatterers: 88848 At special positions: 0 Unit cell: (199.64, 210.49, 223.51, 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 74 16.00 P 3018 15.00 O 25197 8.00 N 16567 7.00 C 43992 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS 8 14 " - pdb=" SG CYS 8 27 " distance=2.05 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 35.21 Conformation dependent library (CDL) restraints added in 4.3 seconds 6064 Ramachandran restraints generated. 3032 Oldfield, 0 Emsley, 3032 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5628 Finding SS restraints... Secondary structure from input PDB file: 88 helices and 46 sheets defined 30.1% alpha, 20.9% beta 966 base pairs and 1662 stacking pairs defined. Time for finding SS restraints: 34.32 Creating SS restraints... Processing helix chain '0' and resid 53 through 63 Processing helix chain '0' and resid 63 through 74 Processing helix chain '1' and resid 3 through 8 Processing helix chain '1' and resid 10 through 35 Processing helix chain '1' and resid 41 through 61 removed outlier: 3.649A pdb=" N ALA 1 61 " --> pdb=" O LEU 1 57 " (cutoff:3.500A) Processing helix chain '2' and resid 17 through 28 Processing helix chain '2' and resid 41 through 51 Processing helix chain '3' and resid 9 through 18 Processing helix chain '6' and resid 8 through 17 Processing helix chain '6' and resid 17 through 24 removed outlier: 4.270A pdb=" N THR 6 24 " --> pdb=" O ALA 6 20 " (cutoff:3.500A) Processing helix chain '6' and resid 24 through 38 Processing helix chain '7' and resid 7 through 12 Processing helix chain '7' and resid 37 through 44 Processing helix chain '7' and resid 51 through 62 removed outlier: 4.549A pdb=" N GLY 7 56 " --> pdb=" O LYS 7 52 " (cutoff:3.500A) removed outlier: 5.378A pdb=" N LEU 7 57 " --> pdb=" O GLY 7 53 " (cutoff:3.500A) Processing helix chain '8' and resid 30 through 33 Processing helix chain 'c' and resid 30 through 32 No H-bonds generated for 'chain 'c' and resid 30 through 32' Processing helix chain 'c' and resid 197 through 203 removed outlier: 4.001A pdb=" N MET c 201 " --> pdb=" O ALA c 198 " (cutoff:3.500A) Processing helix chain 'c' and resid 207 through 213 removed outlier: 3.647A pdb=" N ALA c 211 " --> pdb=" O LYS c 207 " (cutoff:3.500A) Processing helix chain 'c' and resid 221 through 225 Processing helix chain 'c' and resid 263 through 265 No H-bonds generated for 'chain 'c' and resid 263 through 265' Processing helix chain 'd' and resid 39 through 44 Processing helix chain 'd' and resid 56 through 60 Processing helix chain 'd' and resid 61 through 72 removed outlier: 3.564A pdb=" N ALA d 71 " --> pdb=" O HIS d 67 " (cutoff:3.500A) Processing helix chain 'd' and resid 97 through 102 Processing helix chain 'd' and resid 120 through 126 Processing helix chain 'e' and resid 15 through 20 Processing helix chain 'e' and resid 24 through 39 Processing helix chain 'e' and resid 97 through 115 Processing helix chain 'e' and resid 130 through 141 removed outlier: 3.731A pdb=" N LEU e 134 " --> pdb=" O LYS e 130 " (cutoff:3.500A) Processing helix chain 'e' and resid 154 through 162 Processing helix chain 'e' and resid 176 through 183 Processing helix chain 'e' and resid 190 through 201 Processing helix chain 'f' and resid 3 through 9 Processing helix chain 'f' and resid 11 through 20 Processing helix chain 'f' and resid 24 through 28 removed outlier: 3.744A pdb=" N VAL f 28 " --> pdb=" O VAL f 25 " (cutoff:3.500A) Processing helix chain 'f' and resid 41 through 45 removed outlier: 3.593A pdb=" N ILE f 44 " --> pdb=" O GLY f 41 " (cutoff:3.500A) Processing helix chain 'f' and resid 46 through 62 removed outlier: 4.010A pdb=" N LEU f 50 " --> pdb=" O ASP f 46 " (cutoff:3.500A) Processing helix chain 'f' and resid 93 through 107 Processing helix chain 'f' and resid 108 through 111 removed outlier: 4.109A pdb=" N ILE f 111 " --> pdb=" O VAL f 108 " (cutoff:3.500A) No H-bonds generated for 'chain 'f' and resid 108 through 111' Processing helix chain 'f' and resid 134 through 138 removed outlier: 4.088A pdb=" N ILE f 137 " --> pdb=" O GLU f 134 " (cutoff:3.500A) Processing helix chain 'f' and resid 162 through 172 Processing helix chain 'g' and resid 60 through 80 Processing helix chain 'g' and resid 137 through 151 removed outlier: 3.803A pdb=" N TYR g 151 " --> pdb=" O ASP g 147 " (cutoff:3.500A) Processing helix chain 'h' and resid 30 through 34 Processing helix chain 'j' and resid 24 through 38 removed outlier: 3.913A pdb=" N GLU j 31 " --> pdb=" O ARG j 27 " (cutoff:3.500A) Processing helix chain 'j' and resid 58 through 62 removed outlier: 3.671A pdb=" N VAL j 62 " --> pdb=" O ALA j 59 " (cutoff:3.500A) Processing helix chain 'j' and resid 67 through 72 Processing helix chain 'j' and resid 89 through 96 Processing helix chain 'j' and resid 96 through 109 removed outlier: 3.996A pdb=" N VAL j 100 " --> pdb=" O ARG j 96 " (cutoff:3.500A) removed outlier: 4.234A pdb=" N ILE j 101 " --> pdb=" O PRO j 97 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N MET j 108 " --> pdb=" O ALA j 104 " (cutoff:3.500A) Processing helix chain 'j' and resid 112 through 120 Processing helix chain 'j' and resid 132 through 136 Processing helix chain 'k' and resid 104 through 108 Processing helix chain 'k' and resid 112 through 119 Processing helix chain 'l' and resid 56 through 61 removed outlier: 3.519A pdb=" N LEU l 61 " --> pdb=" O LEU l 57 " (cutoff:3.500A) Processing helix chain 'l' and resid 70 through 72 No H-bonds generated for 'chain 'l' and resid 70 through 72' Processing helix chain 'l' and resid 80 through 86 removed outlier: 3.873A pdb=" N ALA l 83 " --> pdb=" O SER l 80 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N VAL l 85 " --> pdb=" O LEU l 82 " (cutoff:3.500A) removed outlier: 4.312A pdb=" N GLU l 86 " --> pdb=" O ALA l 83 " (cutoff:3.500A) Processing helix chain 'l' and resid 91 through 98 Processing helix chain 'l' and resid 128 through 138 Processing helix chain 'm' and resid 42 through 57 removed outlier: 3.562A pdb=" N VAL m 57 " --> pdb=" O MET m 53 " (cutoff:3.500A) Processing helix chain 'm' and resid 109 through 122 Processing helix chain 'n' and resid 13 through 32 Processing helix chain 'n' and resid 44 through 56 Proline residue: n 50 - end of helix Processing helix chain 'n' and resid 59 through 70 Processing helix chain 'n' and resid 72 through 87 removed outlier: 4.776A pdb=" N GLY n 84 " --> pdb=" O PHE n 80 " (cutoff:3.500A) Proline residue: n 85 - end of helix Processing helix chain 'o' and resid 3 through 22 removed outlier: 4.813A pdb=" N ARG o 13 " --> pdb=" O ARG o 9 " (cutoff:3.500A) removed outlier: 5.035A pdb=" N ALA o 14 " --> pdb=" O ARG o 10 " (cutoff:3.500A) Processing helix chain 'o' and resid 55 through 60 Processing helix chain 'o' and resid 67 through 85 removed outlier: 3.714A pdb=" N LYS o 85 " --> pdb=" O ARG o 81 " (cutoff:3.500A) Processing helix chain 'o' and resid 101 through 114 Processing helix chain 'p' and resid 3 through 11 Processing helix chain 'p' and resid 53 through 56 Processing helix chain 'p' and resid 97 through 103 Processing helix chain 'p' and resid 104 through 109 Processing helix chain 'q' and resid 6 through 20 removed outlier: 3.594A pdb=" N GLN q 20 " --> pdb=" O LYS q 16 " (cutoff:3.500A) Processing helix chain 'q' and resid 25 through 30 Processing helix chain 'q' and resid 31 through 72 removed outlier: 3.649A pdb=" N GLN q 37 " --> pdb=" O ARG q 33 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N ARG q 51 " --> pdb=" O TYR q 47 " (cutoff:3.500A) removed outlier: 4.381A pdb=" N LYS q 54 " --> pdb=" O ARG q 50 " (cutoff:3.500A) Processing helix chain 'q' and resid 75 through 86 Processing helix chain 'q' and resid 91 through 102 Processing helix chain 'q' and resid 102 through 118 Processing helix chain 's' and resid 13 through 25 removed outlier: 3.680A pdb=" N VAL s 20 " --> pdb=" O LYS s 16 " (cutoff:3.500A) removed outlier: 4.585A pdb=" N LEU s 23 " --> pdb=" O LEU s 19 " (cutoff:3.500A) removed outlier: 4.064A pdb=" N ILE s 24 " --> pdb=" O VAL s 20 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N ARG s 25 " --> pdb=" O ALA s 21 " (cutoff:3.500A) Processing helix chain 's' and resid 28 through 38 removed outlier: 3.501A pdb=" N TYR s 38 " --> pdb=" O ASP s 34 " (cutoff:3.500A) Processing helix chain 's' and resid 41 through 62 removed outlier: 3.661A pdb=" N VAL s 45 " --> pdb=" O LYS s 41 " (cutoff:3.500A) Processing helix chain 's' and resid 65 through 69 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 3 through 10 removed outlier: 3.531A pdb=" N LEU t 7 " --> pdb=" O ARG t 3 " (cutoff:3.500A) Processing helix chain 't' and resid 17 through 28 Processing helix chain 't' and resid 39 through 51 Processing helix chain 'w' and resid 13 through 23 Processing helix chain 'w' and resid 44 through 51 Processing sheet with id=AA1, first strand: chain '0' and resid 13 through 18 Processing sheet with id=AA2, first strand: chain '0' and resid 33 through 40 Processing sheet with id=AA3, first strand: chain '2' and resid 35 through 38 removed outlier: 4.364A pdb=" N LYS 2 6 " --> pdb=" O GLU 2 58 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain '3' and resid 28 through 30 Processing sheet with id=AA5, first strand: chain '3' and resid 48 through 49 Processing sheet with id=AA6, first strand: chain '4' and resid 20 through 25 Processing sheet with id=AA7, first strand: chain '7' and resid 15 through 16 Processing sheet with id=AA8, first strand: chain '8' and resid 2 through 3 removed outlier: 6.078A pdb=" N LYS 8 2 " --> pdb=" O ARG 8 36 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'c' and resid 3 through 5 Processing sheet with id=AB1, first strand: chain 'c' and resid 34 through 35 Processing sheet with id=AB2, first strand: chain 'c' and resid 101 through 105 removed outlier: 6.695A pdb=" N ILE c 91 " --> pdb=" O LEU c 81 " (cutoff:3.500A) removed outlier: 4.596A pdb=" N LEU c 81 " --> pdb=" O ILE c 91 " (cutoff:3.500A) removed outlier: 6.664A pdb=" N LEU c 93 " --> pdb=" O GLU c 79 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'c' and resid 129 through 131 removed outlier: 3.618A pdb=" N GLN c 163 " --> pdb=" O ARG c 175 " (cutoff:3.500A) removed outlier: 6.303A pdb=" N THR c 173 " --> pdb=" O VAL c 165 " (cutoff:3.500A) removed outlier: 4.680A pdb=" N ARG c 167 " --> pdb=" O TYR c 171 " (cutoff:3.500A) removed outlier: 6.884A pdb=" N TYR c 171 " --> pdb=" O ARG c 167 " (cutoff:3.500A) removed outlier: 6.874A pdb=" N LYS c 183 " --> pdb=" O ILE c 267 " (cutoff:3.500A) removed outlier: 6.169A pdb=" N ILE c 267 " --> pdb=" O LYS c 183 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'c' and resid 144 through 145 removed outlier: 6.097A pdb=" N VAL c 144 " --> pdb=" O GLN c 153 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'd' and resid 169 through 175 removed outlier: 5.235A pdb=" N THR d 171 " --> pdb=" O GLY d 111 " (cutoff:3.500A) removed outlier: 7.249A pdb=" N GLY d 111 " --> pdb=" O THR d 171 " (cutoff:3.500A) removed outlier: 5.381A pdb=" N GLN d 173 " --> pdb=" O VAL d 109 " (cutoff:3.500A) removed outlier: 6.709A pdb=" N VAL d 109 " --> pdb=" O GLN d 173 " (cutoff:3.500A) removed outlier: 4.621A pdb=" N THR d 112 " --> pdb=" O ASP d 200 " (cutoff:3.500A) removed outlier: 7.167A pdb=" N ASP d 200 " --> pdb=" O THR d 112 " (cutoff:3.500A) removed outlier: 5.714A pdb=" N LYS d 8 " --> pdb=" O GLU d 28 " (cutoff:3.500A) removed outlier: 6.450A pdb=" N GLU d 28 " --> pdb=" O LYS d 8 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N GLY d 10 " --> pdb=" O VAL d 26 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N VAL d 20 " --> pdb=" O THR d 16 " (cutoff:3.500A) removed outlier: 6.532A pdb=" N LYS d 190 " --> pdb=" O VAL d 177 " (cutoff:3.500A) removed outlier: 6.732A pdb=" N VAL d 177 " --> pdb=" O LYS d 190 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'd' and resid 79 through 83 removed outlier: 6.491A pdb=" N ALA d 47 " --> pdb=" O VAL d 37 " (cutoff:3.500A) removed outlier: 4.661A pdb=" N VAL d 37 " --> pdb=" O ALA d 47 " (cutoff:3.500A) removed outlier: 6.489A pdb=" N GLN d 49 " --> pdb=" O THR d 35 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'd' and resid 118 through 119 Processing sheet with id=AB8, first strand: chain 'e' and resid 2 through 3 Processing sheet with id=AB9, first strand: chain 'e' and resid 118 through 121 Processing sheet with id=AC1, first strand: chain 'f' and resid 66 through 68 removed outlier: 3.601A pdb=" N VAL f 89 " --> pdb=" O LEU f 36 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N LYS f 33 " --> pdb=" O THR f 157 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N LEU f 152 " --> pdb=" O VAL f 132 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'g' and resid 9 through 10 Processing sheet with id=AC3, first strand: chain 'g' and resid 16 through 20 removed outlier: 3.555A pdb=" N ASP g 16 " --> pdb=" O LYS g 27 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N VAL g 23 " --> pdb=" O ASN g 20 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'g' and resid 121 through 124 removed outlier: 3.752A pdb=" N VAL g 90 " --> pdb=" O GLY g 161 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'g' and resid 98 through 99 removed outlier: 3.697A pdb=" N VAL g 113 " --> pdb=" O LEU g 105 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'h' and resid 18 through 20 Processing sheet with id=AC7, first strand: chain 'j' and resid 122 through 124 removed outlier: 6.702A pdb=" N TRP j 15 " --> pdb=" O GLN j 138 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'j' and resid 73 through 76 Processing sheet with id=AC9, first strand: chain 'k' and resid 7 through 10 removed outlier: 3.812A pdb=" N VAL k 10 " --> pdb=" O ARG k 17 " (cutoff:3.500A) removed outlier: 6.428A pdb=" N ARG k 17 " --> pdb=" O VAL k 10 " (cutoff:3.500A) removed outlier: 6.425A pdb=" N GLU k 45 " --> pdb=" O ARG k 17 " (cutoff:3.500A) removed outlier: 6.657A pdb=" N VAL k 19 " --> pdb=" O ILE k 43 " (cutoff:3.500A) removed outlier: 6.960A pdb=" N ILE k 43 " --> pdb=" O VAL k 19 " (cutoff:3.500A) removed outlier: 6.780A pdb=" N CYS k 21 " --> pdb=" O ILE k 41 " (cutoff:3.500A) removed outlier: 6.319A pdb=" N ILE k 41 " --> pdb=" O CYS k 21 " (cutoff:3.500A) removed outlier: 6.624A pdb=" N LYS k 23 " --> pdb=" O ILE k 39 " (cutoff:3.500A) removed outlier: 4.984A pdb=" N ILE k 39 " --> pdb=" O LYS k 23 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N LYS k 59 " --> pdb=" O LEU k 87 " (cutoff:3.500A) removed outlier: 6.456A pdb=" N ALA k 83 " --> pdb=" O VAL k 63 " (cutoff:3.500A) removed outlier: 8.119A pdb=" N CYS k 84 " --> pdb=" O MET k 7 " (cutoff:3.500A) removed outlier: 6.430A pdb=" N ASN k 9 " --> pdb=" O CYS k 84 " (cutoff:3.500A) removed outlier: 7.245A pdb=" N LEU k 86 " --> pdb=" O ASN k 9 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'k' and resid 69 through 70 removed outlier: 3.600A pdb=" N ALA p 49 " --> pdb=" O THR p 60 " (cutoff:3.500A) removed outlier: 6.440A pdb=" N ARG p 62 " --> pdb=" O VAL p 47 " (cutoff:3.500A) removed outlier: 5.692A pdb=" N VAL p 47 " --> pdb=" O ARG p 62 " (cutoff:3.500A) removed outlier: 8.569A pdb=" N ILE p 64 " --> pdb=" O GLY p 45 " (cutoff:3.500A) removed outlier: 8.585A pdb=" N GLY p 45 " --> pdb=" O ILE p 64 " (cutoff:3.500A) removed outlier: 6.536A pdb=" N THR p 25 " --> pdb=" O LYS p 87 " (cutoff:3.500A) removed outlier: 6.503A pdb=" N TRP p 31 " --> pdb=" O VAL p 81 " (cutoff:3.500A) removed outlier: 6.693A pdb=" N VAL p 81 " --> pdb=" O TRP p 31 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'l' and resid 74 through 78 Processing sheet with id=AD3, first strand: chain 'l' and resid 89 through 90 Processing sheet with id=AD4, first strand: chain 'm' and resid 62 through 65 removed outlier: 6.560A pdb=" N LEU m 33 " --> pdb=" O LEU m 102 " (cutoff:3.500A) removed outlier: 4.405A pdb=" N GLU m 104 " --> pdb=" O PHE m 31 " (cutoff:3.500A) removed outlier: 6.733A pdb=" N PHE m 31 " --> pdb=" O GLU m 104 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'm' and resid 71 through 75 removed outlier: 3.631A pdb=" N TYR m 91 " --> pdb=" O ILE m 73 " (cutoff:3.500A) removed outlier: 6.071A pdb=" N GLU m 75 " --> pdb=" O VAL m 89 " (cutoff:3.500A) removed outlier: 6.017A pdb=" N VAL m 89 " --> pdb=" O GLU m 75 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'n' and resid 33 through 37 removed outlier: 5.780A pdb=" N MET n 110 " --> pdb=" O CYS n 100 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'o' and resid 47 through 52 removed outlier: 6.705A pdb=" N VAL o 39 " --> pdb=" O LEU o 48 " (cutoff:3.500A) removed outlier: 4.714A pdb=" N ALA o 50 " --> pdb=" O ALA o 37 " (cutoff:3.500A) removed outlier: 7.060A pdb=" N ALA o 37 " --> pdb=" O ALA o 50 " (cutoff:3.500A) removed outlier: 5.007A pdb=" N SER o 52 " --> pdb=" O ILE o 35 " (cutoff:3.500A) removed outlier: 7.235A pdb=" N ILE o 35 " --> pdb=" O SER o 52 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'p' and resid 90 through 91 removed outlier: 4.382A pdb=" N LYS p 111 " --> pdb=" O ALA p 91 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'r' and resid 11 through 14 removed outlier: 6.770A pdb=" N TYR r 2 " --> pdb=" O ILE r 41 " (cutoff:3.500A) removed outlier: 4.566A pdb=" N ILE r 41 " --> pdb=" O TYR r 2 " (cutoff:3.500A) removed outlier: 6.263A pdb=" N VAL r 4 " --> pdb=" O LEU r 39 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N ILE r 41 " --> pdb=" O VAL r 47 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'r' and resid 19 through 22 removed outlier: 6.617A pdb=" N PHE r 93 " --> pdb=" O HIS r 66 " (cutoff:3.500A) removed outlier: 4.529A pdb=" N HIS r 66 " --> pdb=" O PHE r 93 " (cutoff:3.500A) removed outlier: 6.497A pdb=" N ASP r 95 " --> pdb=" O VAL r 64 " (cutoff:3.500A) removed outlier: 6.502A pdb=" N LYS r 60 " --> pdb=" O THR r 99 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'r' and resid 72 through 78 removed outlier: 4.042A pdb=" N TYR r 83 " --> pdb=" O ARG r 78 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 's' and resid 3 through 10 removed outlier: 5.294A pdb=" N ILE s 4 " --> pdb=" O VAL s 107 " (cutoff:3.500A) removed outlier: 6.871A pdb=" N VAL s 107 " --> pdb=" O ILE s 4 " (cutoff:3.500A) removed outlier: 5.553A pdb=" N LYS s 6 " --> pdb=" O VAL s 105 " (cutoff:3.500A) removed outlier: 7.074A pdb=" N VAL s 105 " --> pdb=" O LYS s 6 " (cutoff:3.500A) removed outlier: 5.131A pdb=" N ARG s 8 " --> pdb=" O ILE s 103 " (cutoff:3.500A) removed outlier: 6.490A pdb=" N ILE s 103 " --> pdb=" O ARG s 8 " (cutoff:3.500A) removed outlier: 6.812A pdb=" N SER s 108 " --> pdb=" O VAL s 71 " (cutoff:3.500A) removed outlier: 5.459A pdb=" N VAL s 71 " --> pdb=" O SER s 108 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 's' and resid 82 through 87 Processing sheet with id=AE5, first strand: chain 't' and resid 11 through 14 removed outlier: 4.044A pdb=" N LYS t 74 " --> pdb=" O VAL t 34 " (cutoff:3.500A) removed outlier: 6.408A pdb=" N TRP t 73 " --> pdb=" O VAL t 62 " (cutoff:3.500A) removed outlier: 4.647A pdb=" N VAL t 62 " --> pdb=" O TRP t 73 " (cutoff:3.500A) removed outlier: 6.594A pdb=" N LYS t 75 " --> pdb=" O THR t 60 " (cutoff:3.500A) removed outlier: 4.402A pdb=" N THR t 60 " --> pdb=" O LYS t 75 " (cutoff:3.500A) removed outlier: 6.355A pdb=" N TYR t 77 " --> pdb=" O VAL t 58 " (cutoff:3.500A) removed outlier: 4.303A pdb=" N VAL t 58 " --> pdb=" O TYR t 77 " (cutoff:3.500A) removed outlier: 6.756A pdb=" N THR t 79 " --> pdb=" O GLU t 56 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'u' and resid 54 through 55 removed outlier: 3.579A pdb=" N LYS u 33 " --> pdb=" O LEU u 29 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'u' and resid 72 through 77 Processing sheet with id=AE8, first strand: chain 'w' and resid 3 through 8 removed outlier: 7.843A pdb=" N ASN w 5 " --> pdb=" O ASP w 43 " (cutoff:3.500A) removed outlier: 4.699A pdb=" N ASP w 43 " --> pdb=" O ASN w 5 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N GLU w 7 " --> pdb=" O GLU w 41 " (cutoff:3.500A) removed outlier: 9.130A pdb=" N LYS w 25 " --> pdb=" O GLN w 87 " (cutoff:3.500A) removed outlier: 9.757A pdb=" N ILE w 89 " --> pdb=" O LYS w 25 " (cutoff:3.500A) removed outlier: 8.474A pdb=" N PHE w 91 " --> pdb=" O PRO w 27 " (cutoff:3.500A) removed outlier: 6.154A pdb=" N ILE w 29 " --> pdb=" O PHE w 91 " (cutoff:3.500A) removed outlier: 7.242A pdb=" N ARG w 93 " --> pdb=" O ILE w 29 " (cutoff:3.500A) removed outlier: 7.639A pdb=" N TYR w 31 " --> pdb=" O ARG w 93 " (cutoff:3.500A) removed outlier: 6.019A pdb=" N VAL w 92 " --> pdb=" O ALA w 74 " (cutoff:3.500A) removed outlier: 5.598A pdb=" N ALA w 74 " --> pdb=" O VAL w 92 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'y' and resid 22 through 23 removed outlier: 6.898A pdb=" N LEU y 59 " --> pdb=" O ILE y 37 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'y' and resid 30 through 31 930 hydrogen bonds defined for protein. 2538 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 2394 hydrogen bonds 3722 hydrogen bond angles 0 basepair planarities 966 basepair parallelities 1662 stacking parallelities Total time for adding SS restraints: 164.96 Time building geometry restraints manager: 38.48 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 9454 1.32 - 1.44: 42069 1.44 - 1.56: 39251 1.56 - 1.69: 6035 1.69 - 1.81: 135 Bond restraints: 96944 Sorted by residual: bond pdb=" C LEU m 124 " pdb=" N PRO m 125 " ideal model delta sigma weight residual 1.333 1.368 -0.035 7.80e-03 1.64e+04 1.98e+01 bond pdb=" N VAL h 21 " pdb=" CA VAL h 21 " ideal model delta sigma weight residual 1.456 1.501 -0.044 1.14e-02 7.69e+03 1.52e+01 bond pdb=" CB ARG c 156 " pdb=" CG ARG c 156 " ideal model delta sigma weight residual 1.520 1.411 0.109 3.00e-02 1.11e+03 1.31e+01 bond pdb=" CG1 ILE k 41 " pdb=" CD1 ILE k 41 " ideal model delta sigma weight residual 1.513 1.377 0.136 3.90e-02 6.57e+02 1.22e+01 bond pdb=" CG ARG c 87 " pdb=" CD ARG c 87 " ideal model delta sigma weight residual 1.520 1.417 0.103 3.00e-02 1.11e+03 1.19e+01 ... (remaining 96939 not shown) Histogram of bond angle deviations from ideal: 96.29 - 104.05: 11391 104.05 - 111.81: 54433 111.81 - 119.57: 38224 119.57 - 127.33: 34872 127.33 - 135.10: 6938 Bond angle restraints: 145858 Sorted by residual: angle pdb=" O3' G b2864 " pdb=" C3' G b2864 " pdb=" C2' G b2864 " ideal model delta sigma weight residual 113.70 127.45 -13.75 1.50e+00 4.44e-01 8.41e+01 angle pdb=" O3' U b 390 " pdb=" C3' U b 390 " pdb=" C2' U b 390 " ideal model delta sigma weight residual 109.50 121.70 -12.20 1.50e+00 4.44e-01 6.62e+01 angle pdb=" C4' A b2820 " pdb=" C3' A b2820 " pdb=" O3' A b2820 " ideal model delta sigma weight residual 113.00 101.28 11.72 1.50e+00 4.44e-01 6.10e+01 angle pdb=" O3' C b1595 " pdb=" C3' C b1595 " pdb=" C2' C b1595 " ideal model delta sigma weight residual 113.70 125.29 -11.59 1.50e+00 4.44e-01 5.97e+01 angle pdb=" O3' C b1704 " pdb=" C3' C b1704 " pdb=" C2' C b1704 " ideal model delta sigma weight residual 113.70 125.01 -11.31 1.50e+00 4.44e-01 5.69e+01 ... (remaining 145853 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.81: 53095 35.81 - 71.61: 8164 71.61 - 107.42: 838 107.42 - 143.23: 15 143.23 - 179.04: 23 Dihedral angle restraints: 62135 sinusoidal: 53390 harmonic: 8745 Sorted by residual: dihedral pdb=" O4' U b 99 " pdb=" C1' U b 99 " pdb=" N1 U b 99 " pdb=" C2 U b 99 " ideal model delta sinusoidal sigma weight residual 200.00 30.95 169.05 1 1.50e+01 4.44e-03 8.46e+01 dihedral pdb=" O4' U b2884 " pdb=" C1' U b2884 " pdb=" N1 U b2884 " pdb=" C2 U b2884 " ideal model delta sinusoidal sigma weight residual 200.00 42.88 157.12 1 1.50e+01 4.44e-03 8.20e+01 dihedral pdb=" O4' C b2573 " pdb=" C1' C b2573 " pdb=" N1 C b2573 " pdb=" C2 C b2573 " ideal model delta sinusoidal sigma weight residual 200.00 52.08 147.92 1 1.50e+01 4.44e-03 7.88e+01 ... (remaining 62132 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.157: 15562 0.157 - 0.313: 3158 0.313 - 0.470: 22 0.470 - 0.626: 11 0.626 - 0.783: 3 Chirality restraints: 18756 Sorted by residual: chirality pdb=" C3' U b 390 " pdb=" C4' U b 390 " pdb=" O3' U b 390 " pdb=" C2' U b 390 " both_signs ideal model delta sigma weight residual False -2.74 -1.96 -0.78 2.00e-01 2.50e+01 1.53e+01 chirality pdb=" C3' G b2655 " pdb=" C4' G b2655 " pdb=" O3' G b2655 " pdb=" C2' G b2655 " both_signs ideal model delta sigma weight residual False -2.74 -2.03 -0.71 2.00e-01 2.50e+01 1.27e+01 chirality pdb=" C3' U b2832 " pdb=" C4' U b2832 " pdb=" O3' U b2832 " pdb=" C2' U b2832 " both_signs ideal model delta sigma weight residual False -2.74 -2.10 -0.64 2.00e-01 2.50e+01 1.04e+01 ... (remaining 18753 not shown) Planarity restraints: 7217 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP c 213 " -0.042 2.00e-02 2.50e+03 3.49e-02 3.04e+01 pdb=" CG TRP c 213 " 0.095 2.00e-02 2.50e+03 pdb=" CD1 TRP c 213 " -0.035 2.00e-02 2.50e+03 pdb=" CD2 TRP c 213 " -0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP c 213 " -0.002 2.00e-02 2.50e+03 pdb=" CE2 TRP c 213 " -0.003 2.00e-02 2.50e+03 pdb=" CE3 TRP c 213 " -0.006 2.00e-02 2.50e+03 pdb=" CZ2 TRP c 213 " 0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP c 213 " -0.002 2.00e-02 2.50e+03 pdb=" CH2 TRP c 213 " -0.005 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE d 127 " -0.033 2.00e-02 2.50e+03 3.53e-02 2.18e+01 pdb=" CG PHE d 127 " 0.081 2.00e-02 2.50e+03 pdb=" CD1 PHE d 127 " -0.024 2.00e-02 2.50e+03 pdb=" CD2 PHE d 127 " -0.017 2.00e-02 2.50e+03 pdb=" CE1 PHE d 127 " 0.004 2.00e-02 2.50e+03 pdb=" CE2 PHE d 127 " -0.002 2.00e-02 2.50e+03 pdb=" CZ PHE d 127 " -0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR 4 49 " -0.021 2.00e-02 2.50e+03 2.86e-02 1.64e+01 pdb=" CG TYR 4 49 " 0.067 2.00e-02 2.50e+03 pdb=" CD1 TYR 4 49 " -0.035 2.00e-02 2.50e+03 pdb=" CD2 TYR 4 49 " -0.009 2.00e-02 2.50e+03 pdb=" CE1 TYR 4 49 " 0.014 2.00e-02 2.50e+03 pdb=" CE2 TYR 4 49 " -0.013 2.00e-02 2.50e+03 pdb=" CZ TYR 4 49 " -0.007 2.00e-02 2.50e+03 pdb=" OH TYR 4 49 " 0.004 2.00e-02 2.50e+03 ... (remaining 7214 not shown) Histogram of nonbonded interaction distances: 2.10 - 2.66: 5000 2.66 - 3.22: 70597 3.22 - 3.78: 194804 3.78 - 4.34: 258893 4.34 - 4.90: 328880 Nonbonded interactions: 858174 Sorted by model distance: nonbonded pdb=" OP2 A b 362 " pdb=" C8 A b 362 " model vdw 2.104 3.260 nonbonded pdb=" O VAL 3 25 " pdb=" OG1 THR 3 26 " model vdw 2.168 2.440 nonbonded pdb=" OP1 G a 51 " pdb=" NZ LYS o 63 " model vdw 2.213 2.520 nonbonded pdb=" O ASN 1 27 " pdb=" NE2 GLN 1 31 " model vdw 2.220 2.520 nonbonded pdb=" NH1 ARG k 105 " pdb=" OE2 GLU p 34 " model vdw 2.221 2.520 ... (remaining 858169 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.070 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: 0.050 Extract box with map and model: 13.110 Check model and map are aligned: 0.970 Set scattering table: 0.590 Process input model: 333.840 Find NCS groups from input model: 1.370 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:13.630 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 367.830 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8613 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 : 0.012 0.136 96944 Z= 0.729 Angle : 1.134 13.755 145858 Z= 0.724 Chirality : 0.106 0.783 18756 Planarity : 0.005 0.054 7217 Dihedral : 25.199 179.035 56504 Min Nonbonded Distance : 2.104 Molprobity Statistics. All-atom Clashscore : 6.00 Ramachandran Plot: Outliers : 0.36 % Allowed : 5.80 % Favored : 93.83 % Rotamer: Outliers : 4.15 % Allowed : 1.84 % Favored : 94.01 % Cbeta Deviations : 0.04 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.31 (0.14), residues: 3032 helix: -0.02 (0.18), residues: 803 sheet: -0.70 (0.20), residues: 600 loop : -1.37 (0.14), residues: 1629 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.095 0.005 TRP c 213 HIS 0.037 0.005 HIS n 16 PHE 0.081 0.005 PHE d 127 TYR 0.067 0.004 TYR 4 49 ARG 0.046 0.003 ARG 3 50 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6064 Ramachandran restraints generated. 3032 Oldfield, 0 Emsley, 3032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6064 Ramachandran restraints generated. 3032 Oldfield, 0 Emsley, 3032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 805 residues out of total 2506 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 104 poor density : 701 time to evaluate : 3.470 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: 1 20 ASN cc_start: 0.9117 (m-40) cc_final: 0.8768 (m110) REVERT: e 110 SER cc_start: 0.9170 (m) cc_final: 0.8968 (m) REVERT: e 125 SER cc_start: 0.9286 (p) cc_final: 0.8962 (p) REVERT: e 136 GLN cc_start: 0.8986 (tp-100) cc_final: 0.8223 (mm-40) REVERT: e 140 ASP cc_start: 0.8989 (m-30) cc_final: 0.8640 (m-30) REVERT: f 24 SER cc_start: 0.7081 (OUTLIER) cc_final: 0.6860 (t) REVERT: f 27 GLN cc_start: 0.8940 (OUTLIER) cc_final: 0.8706 (tp40) REVERT: f 56 ASP cc_start: 0.8795 (m-30) cc_final: 0.8400 (m-30) REVERT: f 64 LYS cc_start: 0.9299 (OUTLIER) cc_final: 0.8647 (mptt) REVERT: f 94 GLU cc_start: 0.8538 (pp20) cc_final: 0.8289 (pp20) REVERT: f 98 GLU cc_start: 0.8207 (tt0) cc_final: 0.7604 (tt0) REVERT: f 142 ASP cc_start: 0.8939 (p0) cc_final: 0.8659 (p0) REVERT: g 67 THR cc_start: 0.9323 (m) cc_final: 0.8845 (m) REVERT: g 71 LEU cc_start: 0.9467 (mt) cc_final: 0.9134 (mp) REVERT: g 75 MET cc_start: 0.8959 (mtt) cc_final: 0.8561 (mtt) REVERT: h 37 VAL cc_start: 0.9500 (t) cc_final: 0.9187 (m) REVERT: j 58 ASN cc_start: 0.9298 (m-40) cc_final: 0.9077 (m110) REVERT: j 108 MET cc_start: 0.9332 (mtt) cc_final: 0.9037 (mtt) REVERT: k 53 LYS cc_start: 0.8585 (ptpp) cc_final: 0.8209 (ptpp) REVERT: k 56 ASP cc_start: 0.8055 (m-30) cc_final: 0.7818 (m-30) REVERT: m 82 MET cc_start: 0.9379 (mmp) cc_final: 0.8831 (mmp) REVERT: o 30 ARG cc_start: 0.8692 (ptt90) cc_final: 0.8402 (ptt90) REVERT: p 9 GLU cc_start: 0.8267 (mt-10) cc_final: 0.8065 (mt-10) REVERT: q 72 ASN cc_start: 0.9238 (m110) cc_final: 0.9033 (m110) REVERT: u 10 GLU cc_start: 0.7771 (tm-30) cc_final: 0.7391 (tm-30) REVERT: w 43 ASP cc_start: 0.8524 (t0) cc_final: 0.8269 (t0) REVERT: w 85 LYS cc_start: 0.9436 (mmmm) cc_final: 0.9013 (mttm) outliers start: 104 outliers final: 19 residues processed: 756 average time/residue: 1.9182 time to fit residues: 1896.6499 Evaluate side-chains 603 residues out of total 2506 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 581 time to evaluate : 3.443 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 7 residue 32 ILE Chi-restraints excluded: chain f residue 9 LYS Chi-restraints excluded: chain f residue 12 VAL Chi-restraints excluded: chain f residue 14 LYS Chi-restraints excluded: chain f residue 24 SER Chi-restraints excluded: chain f residue 27 GLN Chi-restraints excluded: chain f residue 64 LYS Chi-restraints excluded: chain f residue 66 LEU Chi-restraints excluded: chain f residue 158 THR Chi-restraints excluded: chain g residue 29 LYS Chi-restraints excluded: chain g residue 32 GLU Chi-restraints excluded: chain g residue 128 GLN Chi-restraints excluded: chain g residue 130 GLU Chi-restraints excluded: chain l residue 143 GLU Chi-restraints excluded: chain m residue 128 THR Chi-restraints excluded: chain r residue 48 LYS Chi-restraints excluded: chain r residue 51 VAL Chi-restraints excluded: chain s residue 13 SER Chi-restraints excluded: chain t residue 16 VAL Chi-restraints excluded: chain t residue 62 VAL Chi-restraints excluded: chain w residue 10 LYS Chi-restraints excluded: chain y residue 43 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 597 random chunks: chunk 504 optimal weight: 4.9990 chunk 452 optimal weight: 6.9990 chunk 251 optimal weight: 7.9990 chunk 154 optimal weight: 10.0000 chunk 305 optimal weight: 10.0000 chunk 241 optimal weight: 10.0000 chunk 467 optimal weight: 6.9990 chunk 181 optimal weight: 10.0000 chunk 284 optimal weight: 10.0000 chunk 348 optimal weight: 5.9990 chunk 542 optimal weight: 5.9990 overall best weight: 6.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 1 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 1 39 GLN 8 35 GLN c 226 ASN ** g 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** g 48 ASN g 104 ASN g 128 GLN ** g 143 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** h 33 GLN ** j 77 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** j 136 GLN k 89 ASN l 93 ASN l 104 GLN ** n 16 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** o 29 HIS ** o 100 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** p 12 GLN r 66 HIS r 86 GLN ** s 7 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** s 15 GLN t 28 ASN u 88 ASN w 78 GLN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8676 moved from start: 0.1998 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 96944 Z= 0.319 Angle : 0.630 8.922 145858 Z= 0.331 Chirality : 0.040 0.331 18756 Planarity : 0.005 0.054 7217 Dihedral : 24.430 179.974 50508 Min Nonbonded Distance : 2.065 Molprobity Statistics. All-atom Clashscore : 9.21 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.32 % Favored : 95.58 % Rotamer: Outliers : 3.51 % Allowed : 13.77 % Favored : 82.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.74 (0.15), residues: 3032 helix: 0.73 (0.18), residues: 804 sheet: -0.72 (0.19), residues: 673 loop : -1.00 (0.15), residues: 1555 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.002 TRP c 213 HIS 0.017 0.002 HIS n 16 PHE 0.031 0.002 PHE d 127 TYR 0.017 0.002 TYR 4 49 ARG 0.011 0.001 ARG f 115 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6064 Ramachandran restraints generated. 3032 Oldfield, 0 Emsley, 3032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6064 Ramachandran restraints generated. 3032 Oldfield, 0 Emsley, 3032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 701 residues out of total 2506 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 88 poor density : 613 time to evaluate : 3.504 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: 1 20 ASN cc_start: 0.9022 (m-40) cc_final: 0.8440 (m110) REVERT: 2 6 LYS cc_start: 0.8717 (mmmm) cc_final: 0.8484 (mtpp) REVERT: 3 52 ARG cc_start: 0.8183 (OUTLIER) cc_final: 0.7560 (ptt-90) REVERT: 8 36 ARG cc_start: 0.8938 (OUTLIER) cc_final: 0.8578 (ptm160) REVERT: e 123 LYS cc_start: 0.8208 (pptt) cc_final: 0.7937 (tmtt) REVERT: e 156 ASN cc_start: 0.9003 (OUTLIER) cc_final: 0.8507 (t0) REVERT: e 194 LYS cc_start: 0.8996 (mmmt) cc_final: 0.8569 (tppt) REVERT: f 56 ASP cc_start: 0.8792 (m-30) cc_final: 0.8421 (m-30) REVERT: f 64 LYS cc_start: 0.9186 (tmmt) cc_final: 0.8539 (mptt) REVERT: f 78 LYS cc_start: 0.8528 (mmpt) cc_final: 0.8255 (mmpt) REVERT: f 98 GLU cc_start: 0.8186 (tt0) cc_final: 0.7668 (tt0) REVERT: f 112 ARG cc_start: 0.4537 (OUTLIER) cc_final: 0.2861 (tpt170) REVERT: f 142 ASP cc_start: 0.9059 (p0) cc_final: 0.8826 (p0) REVERT: g 72 LEU cc_start: 0.9060 (OUTLIER) cc_final: 0.8836 (mm) REVERT: g 75 MET cc_start: 0.8955 (mtt) cc_final: 0.8688 (mtt) REVERT: g 130 GLU cc_start: 0.8322 (OUTLIER) cc_final: 0.7888 (mp0) REVERT: g 158 LYS cc_start: 0.9214 (mttt) cc_final: 0.8956 (mtpt) REVERT: j 108 MET cc_start: 0.9283 (mtt) cc_final: 0.8878 (mtt) REVERT: j 128 ASN cc_start: 0.8584 (p0) cc_final: 0.7745 (t0) REVERT: k 53 LYS cc_start: 0.8500 (ptpp) cc_final: 0.8191 (ptpp) REVERT: k 56 ASP cc_start: 0.8023 (m-30) cc_final: 0.7823 (m-30) REVERT: k 59 LYS cc_start: 0.9136 (mttp) cc_final: 0.8919 (mttp) REVERT: m 5 LYS cc_start: 0.8938 (mmtm) cc_final: 0.8634 (mppt) REVERT: m 82 MET cc_start: 0.9332 (mmp) cc_final: 0.8920 (mmp) REVERT: n 35 LYS cc_start: 0.9279 (tttm) cc_final: 0.9017 (tppp) REVERT: n 103 ARG cc_start: 0.9116 (OUTLIER) cc_final: 0.8706 (ttm170) REVERT: t 18 GLU cc_start: 0.7813 (OUTLIER) cc_final: 0.7311 (tt0) REVERT: u 40 ASN cc_start: 0.8037 (OUTLIER) cc_final: 0.7574 (t0) REVERT: w 85 LYS cc_start: 0.9337 (mmmm) cc_final: 0.9063 (mtpp) outliers start: 88 outliers final: 37 residues processed: 656 average time/residue: 1.8582 time to fit residues: 1613.8091 Evaluate side-chains 623 residues out of total 2506 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 577 time to evaluate : 3.456 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 35 THR Chi-restraints excluded: chain 2 residue 36 VAL Chi-restraints excluded: chain 3 residue 52 ARG Chi-restraints excluded: chain 7 residue 44 LEU Chi-restraints excluded: chain 8 residue 36 ARG Chi-restraints excluded: chain c residue 120 VAL Chi-restraints excluded: chain d residue 151 THR Chi-restraints excluded: chain e residue 156 ASN Chi-restraints excluded: chain f residue 23 ASN Chi-restraints excluded: chain f residue 31 VAL Chi-restraints excluded: chain f residue 49 LEU Chi-restraints excluded: chain f residue 112 ARG Chi-restraints excluded: chain f residue 130 MET Chi-restraints excluded: chain g residue 15 VAL Chi-restraints excluded: chain g residue 32 GLU Chi-restraints excluded: chain g residue 34 THR Chi-restraints excluded: chain g residue 43 VAL Chi-restraints excluded: chain g residue 48 ASN Chi-restraints excluded: chain g residue 51 THR Chi-restraints excluded: chain g residue 72 LEU Chi-restraints excluded: chain g residue 92 VAL Chi-restraints excluded: chain g residue 128 GLN Chi-restraints excluded: chain g residue 130 GLU Chi-restraints excluded: chain g residue 148 LEU Chi-restraints excluded: chain j residue 131 ASN Chi-restraints excluded: chain l residue 143 GLU Chi-restraints excluded: chain m residue 30 SER Chi-restraints excluded: chain m residue 78 LEU Chi-restraints excluded: chain m residue 135 VAL Chi-restraints excluded: chain n residue 70 THR Chi-restraints excluded: chain n residue 103 ARG Chi-restraints excluded: chain p residue 4 ILE Chi-restraints excluded: chain p residue 114 LEU Chi-restraints excluded: chain r residue 48 LYS Chi-restraints excluded: chain r residue 51 VAL Chi-restraints excluded: chain s residue 13 SER Chi-restraints excluded: chain s residue 108 SER Chi-restraints excluded: chain t residue 18 GLU Chi-restraints excluded: chain t residue 29 THR Chi-restraints excluded: chain t residue 62 VAL Chi-restraints excluded: chain u residue 40 ASN Chi-restraints excluded: chain w residue 10 LYS Chi-restraints excluded: chain w residue 58 SER Chi-restraints excluded: chain y residue 30 SER Chi-restraints excluded: chain y residue 43 THR Chi-restraints excluded: chain y residue 62 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 597 random chunks: chunk 301 optimal weight: 20.0000 chunk 168 optimal weight: 10.0000 chunk 451 optimal weight: 10.0000 chunk 369 optimal weight: 9.9990 chunk 149 optimal weight: 10.0000 chunk 543 optimal weight: 6.9990 chunk 586 optimal weight: 20.0000 chunk 483 optimal weight: 7.9990 chunk 538 optimal weight: 10.0000 chunk 185 optimal weight: 10.0000 chunk 435 optimal weight: 30.0000 overall best weight: 8.9994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 31 GLN ** 1 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 8 35 GLN c 37 ASN c 117 GLN ** g 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** g 143 GLN ** h 2 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** h 33 GLN ** j 77 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** j 136 GLN k 89 ASN l 93 ASN ** n 16 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** o 61 GLN p 12 GLN q 14 HIS r 66 HIS s 15 GLN t 28 ASN t 48 GLN u 88 ASN w 78 GLN y 50 ASN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8721 moved from start: 0.2447 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.069 96944 Z= 0.441 Angle : 0.650 9.015 145858 Z= 0.342 Chirality : 0.042 0.313 18756 Planarity : 0.005 0.055 7217 Dihedral : 24.084 179.866 50480 Min Nonbonded Distance : 2.015 Molprobity Statistics. All-atom Clashscore : 8.63 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.72 % Favored : 95.15 % Rotamer: Outliers : 4.55 % Allowed : 15.92 % Favored : 79.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.60 (0.15), residues: 3032 helix: 0.89 (0.19), residues: 810 sheet: -0.67 (0.19), residues: 685 loop : -0.92 (0.15), residues: 1537 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP c 213 HIS 0.018 0.002 HIS s 7 PHE 0.026 0.002 PHE d 127 TYR 0.020 0.002 TYR c 161 ARG 0.008 0.001 ARG y 41 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6064 Ramachandran restraints generated. 3032 Oldfield, 0 Emsley, 3032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6064 Ramachandran restraints generated. 3032 Oldfield, 0 Emsley, 3032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 690 residues out of total 2506 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 114 poor density : 576 time to evaluate : 3.517 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: 1 20 ASN cc_start: 0.8989 (m-40) cc_final: 0.8511 (m110) REVERT: 1 39 GLN cc_start: 0.8661 (OUTLIER) cc_final: 0.8444 (mm110) REVERT: 2 6 LYS cc_start: 0.8747 (OUTLIER) cc_final: 0.8499 (mtpp) REVERT: 3 52 ARG cc_start: 0.8240 (OUTLIER) cc_final: 0.7360 (ptt-90) REVERT: d 97 SER cc_start: 0.9058 (t) cc_final: 0.8405 (p) REVERT: d 99 GLU cc_start: 0.8294 (pm20) cc_final: 0.7545 (pm20) REVERT: e 194 LYS cc_start: 0.9038 (mmmt) cc_final: 0.8625 (tppt) REVERT: f 56 ASP cc_start: 0.8786 (m-30) cc_final: 0.8376 (m-30) REVERT: f 64 LYS cc_start: 0.9057 (tmmt) cc_final: 0.8431 (mptt) REVERT: f 98 GLU cc_start: 0.8115 (tt0) cc_final: 0.7672 (tt0) REVERT: f 112 ARG cc_start: 0.4641 (OUTLIER) cc_final: 0.2905 (tpt170) REVERT: f 142 ASP cc_start: 0.9078 (p0) cc_final: 0.8787 (p0) REVERT: g 30 ASN cc_start: 0.8858 (OUTLIER) cc_final: 0.8408 (t0) REVERT: g 72 LEU cc_start: 0.9051 (OUTLIER) cc_final: 0.8848 (mm) REVERT: g 75 MET cc_start: 0.9013 (mtt) cc_final: 0.8724 (mtt) REVERT: g 130 GLU cc_start: 0.8175 (OUTLIER) cc_final: 0.7775 (mp0) REVERT: g 160 LYS cc_start: 0.9105 (mtpm) cc_final: 0.8767 (mtpm) REVERT: j 108 MET cc_start: 0.9294 (mtt) cc_final: 0.8913 (mtt) REVERT: j 128 ASN cc_start: 0.8573 (p0) cc_final: 0.7758 (t0) REVERT: k 53 LYS cc_start: 0.8498 (ptpp) cc_final: 0.8244 (ptpp) REVERT: k 56 ASP cc_start: 0.8059 (m-30) cc_final: 0.7848 (m-30) REVERT: m 6 ARG cc_start: 0.8135 (pmt-80) cc_final: 0.7890 (ppt170) REVERT: m 82 MET cc_start: 0.9339 (mmp) cc_final: 0.9106 (mmp) REVERT: n 35 LYS cc_start: 0.9250 (tttm) cc_final: 0.8995 (tppp) REVERT: n 86 ARG cc_start: 0.9024 (ttp80) cc_final: 0.8798 (ttp80) REVERT: n 103 ARG cc_start: 0.9181 (OUTLIER) cc_final: 0.8872 (ttm170) REVERT: o 38 GLN cc_start: 0.9501 (mt0) cc_final: 0.9267 (mt0) REVERT: w 85 LYS cc_start: 0.9311 (mmmm) cc_final: 0.9033 (mtpp) outliers start: 114 outliers final: 58 residues processed: 626 average time/residue: 1.8447 time to fit residues: 1532.9441 Evaluate side-chains 625 residues out of total 2506 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 559 time to evaluate : 3.457 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 39 GLN Chi-restraints excluded: chain 2 residue 6 LYS Chi-restraints excluded: chain 2 residue 35 THR Chi-restraints excluded: chain 2 residue 36 VAL Chi-restraints excluded: chain 3 residue 25 VAL Chi-restraints excluded: chain 3 residue 52 ARG Chi-restraints excluded: chain 7 residue 44 LEU Chi-restraints excluded: chain 8 residue 4 ARG Chi-restraints excluded: chain c residue 120 VAL Chi-restraints excluded: chain c residue 139 SER Chi-restraints excluded: chain d residue 74 GLU Chi-restraints excluded: chain d residue 92 VAL Chi-restraints excluded: chain d residue 151 THR Chi-restraints excluded: chain e residue 12 LEU Chi-restraints excluded: chain e residue 133 LEU Chi-restraints excluded: chain f residue 12 VAL Chi-restraints excluded: chain f residue 23 ASN Chi-restraints excluded: chain f residue 31 VAL Chi-restraints excluded: chain f residue 33 LYS Chi-restraints excluded: chain f residue 44 ILE Chi-restraints excluded: chain f residue 49 LEU Chi-restraints excluded: chain f residue 94 GLU Chi-restraints excluded: chain f residue 108 VAL Chi-restraints excluded: chain f residue 112 ARG Chi-restraints excluded: chain g residue 9 VAL Chi-restraints excluded: chain g residue 15 VAL Chi-restraints excluded: chain g residue 30 ASN Chi-restraints excluded: chain g residue 32 GLU Chi-restraints excluded: chain g residue 34 THR Chi-restraints excluded: chain g residue 43 VAL Chi-restraints excluded: chain g residue 51 THR Chi-restraints excluded: chain g residue 72 LEU Chi-restraints excluded: chain g residue 86 LYS Chi-restraints excluded: chain g residue 92 VAL Chi-restraints excluded: chain g residue 127 THR Chi-restraints excluded: chain g residue 130 GLU Chi-restraints excluded: chain g residue 148 LEU Chi-restraints excluded: chain j residue 96 ARG Chi-restraints excluded: chain j residue 131 ASN Chi-restraints excluded: chain k residue 17 ARG Chi-restraints excluded: chain k residue 114 LYS Chi-restraints excluded: chain l residue 7 SER Chi-restraints excluded: chain l residue 121 THR Chi-restraints excluded: chain l residue 143 GLU Chi-restraints excluded: chain m residue 30 SER Chi-restraints excluded: chain m residue 135 VAL Chi-restraints excluded: chain n residue 52 ILE Chi-restraints excluded: chain n residue 70 THR Chi-restraints excluded: chain n residue 103 ARG Chi-restraints excluded: chain o residue 81 ARG Chi-restraints excluded: chain o residue 95 SER Chi-restraints excluded: chain p residue 4 ILE Chi-restraints excluded: chain p residue 5 ILE Chi-restraints excluded: chain p residue 63 LYS Chi-restraints excluded: chain p residue 114 LEU Chi-restraints excluded: chain s residue 13 SER Chi-restraints excluded: chain s residue 86 MET Chi-restraints excluded: chain s residue 108 SER Chi-restraints excluded: chain t residue 7 LEU Chi-restraints excluded: chain t residue 29 THR Chi-restraints excluded: chain t residue 30 ILE Chi-restraints excluded: chain t residue 62 VAL Chi-restraints excluded: chain u residue 35 ILE Chi-restraints excluded: chain w residue 10 LYS Chi-restraints excluded: chain y residue 43 THR Chi-restraints excluded: chain y residue 62 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 597 random chunks: chunk 536 optimal weight: 7.9990 chunk 408 optimal weight: 8.9990 chunk 281 optimal weight: 10.0000 chunk 60 optimal weight: 10.0000 chunk 259 optimal weight: 10.0000 chunk 364 optimal weight: 3.9990 chunk 545 optimal weight: 6.9990 chunk 577 optimal weight: 9.9990 chunk 284 optimal weight: 10.0000 chunk 516 optimal weight: 1.9990 chunk 155 optimal weight: 10.0000 overall best weight: 5.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 1 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 8 35 GLN e 97 ASN ** g 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 2 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** h 33 GLN ** j 77 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** j 136 GLN l 93 ASN m 3 GLN ** n 16 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 100 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** p 10 GLN p 12 GLN p 52 ASN r 66 HIS t 28 ASN t 48 GLN u 40 ASN u 88 ASN w 78 GLN y 50 ASN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8692 moved from start: 0.2626 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 96944 Z= 0.307 Angle : 0.580 9.018 145858 Z= 0.307 Chirality : 0.038 0.273 18756 Planarity : 0.005 0.065 7217 Dihedral : 24.014 179.449 50472 Min Nonbonded Distance : 2.077 Molprobity Statistics. All-atom Clashscore : 8.95 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.35 % Favored : 95.55 % Rotamer: Outliers : 4.35 % Allowed : 17.16 % Favored : 78.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.41 (0.15), residues: 3032 helix: 1.03 (0.19), residues: 802 sheet: -0.56 (0.19), residues: 686 loop : -0.78 (0.15), residues: 1544 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP c 213 HIS 0.008 0.001 HIS s 7 PHE 0.017 0.002 PHE w 91 TYR 0.014 0.001 TYR s 38 ARG 0.008 0.001 ARG l 123 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6064 Ramachandran restraints generated. 3032 Oldfield, 0 Emsley, 3032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6064 Ramachandran restraints generated. 3032 Oldfield, 0 Emsley, 3032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 690 residues out of total 2506 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 109 poor density : 581 time to evaluate : 3.499 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: 0 65 ASP cc_start: 0.7874 (OUTLIER) cc_final: 0.7576 (m-30) REVERT: 1 20 ASN cc_start: 0.8958 (m-40) cc_final: 0.8527 (m110) REVERT: 2 6 LYS cc_start: 0.8740 (OUTLIER) cc_final: 0.8539 (mtpp) REVERT: 3 52 ARG cc_start: 0.8233 (OUTLIER) cc_final: 0.7355 (ptt-90) REVERT: 8 19 ARG cc_start: 0.9046 (mtt180) cc_final: 0.8774 (mtt180) REVERT: 8 36 ARG cc_start: 0.8986 (ptm160) cc_final: 0.8593 (ptm160) REVERT: e 130 LYS cc_start: 0.9239 (mmmm) cc_final: 0.8927 (mmmt) REVERT: f 56 ASP cc_start: 0.8775 (m-30) cc_final: 0.8456 (m-30) REVERT: f 64 LYS cc_start: 0.9055 (tmmt) cc_final: 0.8403 (mptt) REVERT: f 88 LYS cc_start: 0.8389 (ptmt) cc_final: 0.8096 (ptmt) REVERT: f 98 GLU cc_start: 0.8130 (tt0) cc_final: 0.7668 (tt0) REVERT: f 130 MET cc_start: 0.8851 (ptm) cc_final: 0.8566 (ppp) REVERT: f 142 ASP cc_start: 0.9071 (p0) cc_final: 0.8774 (p0) REVERT: g 72 LEU cc_start: 0.9032 (OUTLIER) cc_final: 0.8816 (mm) REVERT: g 75 MET cc_start: 0.9004 (mtt) cc_final: 0.8719 (mtt) REVERT: g 130 GLU cc_start: 0.8160 (OUTLIER) cc_final: 0.7717 (mp0) REVERT: g 160 LYS cc_start: 0.9063 (mtpm) cc_final: 0.8717 (mtpm) REVERT: j 92 MET cc_start: 0.8993 (mmm) cc_final: 0.8667 (mmm) REVERT: j 108 MET cc_start: 0.9274 (mtt) cc_final: 0.8843 (mtt) REVERT: j 128 ASN cc_start: 0.8483 (p0) cc_final: 0.7788 (t0) REVERT: k 53 LYS cc_start: 0.8475 (ptpp) cc_final: 0.8253 (ptpp) REVERT: m 6 ARG cc_start: 0.8079 (pmt-80) cc_final: 0.7859 (ppt170) REVERT: m 82 MET cc_start: 0.9341 (mmp) cc_final: 0.8843 (mmp) REVERT: n 35 LYS cc_start: 0.9225 (tttm) cc_final: 0.8986 (tppp) REVERT: n 103 ARG cc_start: 0.9164 (OUTLIER) cc_final: 0.8798 (ttm170) REVERT: t 3 ARG cc_start: 0.7950 (OUTLIER) cc_final: 0.7720 (ptm-80) REVERT: w 85 LYS cc_start: 0.9269 (mmmm) cc_final: 0.9014 (mtpp) outliers start: 109 outliers final: 61 residues processed: 624 average time/residue: 1.8774 time to fit residues: 1559.1519 Evaluate side-chains 653 residues out of total 2506 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 585 time to evaluate : 3.475 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 65 ASP Chi-restraints excluded: chain 2 residue 6 LYS Chi-restraints excluded: chain 2 residue 35 THR Chi-restraints excluded: chain 3 residue 25 VAL Chi-restraints excluded: chain 3 residue 52 ARG Chi-restraints excluded: chain 7 residue 44 LEU Chi-restraints excluded: chain 8 residue 4 ARG Chi-restraints excluded: chain 8 residue 20 ASP Chi-restraints excluded: chain 8 residue 23 ILE Chi-restraints excluded: chain c residue 120 VAL Chi-restraints excluded: chain c residue 139 SER Chi-restraints excluded: chain d residue 74 GLU Chi-restraints excluded: chain d residue 151 THR Chi-restraints excluded: chain e residue 126 VAL Chi-restraints excluded: chain e residue 133 LEU Chi-restraints excluded: chain f residue 6 ASP Chi-restraints excluded: chain f residue 12 VAL Chi-restraints excluded: chain f residue 23 ASN Chi-restraints excluded: chain f residue 31 VAL Chi-restraints excluded: chain f residue 44 ILE Chi-restraints excluded: chain f residue 49 LEU Chi-restraints excluded: chain f residue 94 GLU Chi-restraints excluded: chain f residue 101 GLU Chi-restraints excluded: chain f residue 108 VAL Chi-restraints excluded: chain f residue 161 LYS Chi-restraints excluded: chain g residue 9 VAL Chi-restraints excluded: chain g residue 15 VAL Chi-restraints excluded: chain g residue 26 ILE Chi-restraints excluded: chain g residue 32 GLU Chi-restraints excluded: chain g residue 34 THR Chi-restraints excluded: chain g residue 43 VAL Chi-restraints excluded: chain g residue 51 THR Chi-restraints excluded: chain g residue 72 LEU Chi-restraints excluded: chain g residue 86 LYS Chi-restraints excluded: chain g residue 92 VAL Chi-restraints excluded: chain g residue 98 VAL Chi-restraints excluded: chain g residue 122 THR Chi-restraints excluded: chain g residue 127 THR Chi-restraints excluded: chain g residue 130 GLU Chi-restraints excluded: chain g residue 148 LEU Chi-restraints excluded: chain g residue 162 VAL Chi-restraints excluded: chain h residue 37 VAL Chi-restraints excluded: chain l residue 7 SER Chi-restraints excluded: chain l residue 121 THR Chi-restraints excluded: chain l residue 143 GLU Chi-restraints excluded: chain m residue 30 SER Chi-restraints excluded: chain m residue 78 LEU Chi-restraints excluded: chain m residue 135 VAL Chi-restraints excluded: chain n residue 70 THR Chi-restraints excluded: chain n residue 103 ARG Chi-restraints excluded: chain o residue 47 VAL Chi-restraints excluded: chain o residue 95 SER Chi-restraints excluded: chain p residue 5 ILE Chi-restraints excluded: chain p residue 52 ASN Chi-restraints excluded: chain p residue 63 LYS Chi-restraints excluded: chain p residue 114 LEU Chi-restraints excluded: chain s residue 13 SER Chi-restraints excluded: chain s residue 19 LEU Chi-restraints excluded: chain s residue 86 MET Chi-restraints excluded: chain t residue 3 ARG Chi-restraints excluded: chain t residue 7 LEU Chi-restraints excluded: chain t residue 30 ILE Chi-restraints excluded: chain t residue 62 VAL Chi-restraints excluded: chain w residue 10 LYS Chi-restraints excluded: chain w residue 64 VAL Chi-restraints excluded: chain y residue 30 SER Chi-restraints excluded: chain y residue 43 THR Chi-restraints excluded: chain y residue 62 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 597 random chunks: chunk 480 optimal weight: 4.9990 chunk 327 optimal weight: 20.0000 chunk 8 optimal weight: 10.0000 chunk 429 optimal weight: 7.9990 chunk 238 optimal weight: 20.0000 chunk 492 optimal weight: 0.0030 chunk 398 optimal weight: 4.9990 chunk 0 optimal weight: 10.0000 chunk 294 optimal weight: 10.0000 chunk 517 optimal weight: 20.0000 chunk 145 optimal weight: 10.0000 overall best weight: 5.6000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 0 17 ASN ** 1 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 8 35 GLN ** g 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 2 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** h 33 GLN ** j 77 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** k 89 ASN l 93 ASN m 3 GLN ** n 16 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** o 38 GLN ** o 100 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** p 10 GLN p 12 GLN p 52 ASN r 66 HIS t 48 GLN u 40 ASN w 78 GLN y 50 ASN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8688 moved from start: 0.2780 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 96944 Z= 0.288 Angle : 0.563 11.006 145858 Z= 0.298 Chirality : 0.037 0.281 18756 Planarity : 0.005 0.064 7217 Dihedral : 23.912 179.111 50472 Min Nonbonded Distance : 2.087 Molprobity Statistics. All-atom Clashscore : 8.71 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.45 % Favored : 95.45 % Rotamer: Outliers : 3.99 % Allowed : 18.99 % Favored : 77.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.28 (0.15), residues: 3032 helix: 1.15 (0.19), residues: 805 sheet: -0.50 (0.19), residues: 672 loop : -0.70 (0.16), residues: 1555 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP c 213 HIS 0.008 0.001 HIS s 7 PHE 0.016 0.001 PHE g 52 TYR 0.013 0.001 TYR q 32 ARG 0.008 0.001 ARG l 123 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6064 Ramachandran restraints generated. 3032 Oldfield, 0 Emsley, 3032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6064 Ramachandran restraints generated. 3032 Oldfield, 0 Emsley, 3032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 691 residues out of total 2506 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 100 poor density : 591 time to evaluate : 3.561 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: 0 65 ASP cc_start: 0.7876 (OUTLIER) cc_final: 0.7586 (m-30) REVERT: 1 31 GLN cc_start: 0.8688 (mp10) cc_final: 0.8421 (mp-120) REVERT: 3 52 ARG cc_start: 0.8246 (OUTLIER) cc_final: 0.7354 (ptt-90) REVERT: 8 36 ARG cc_start: 0.8994 (ptm160) cc_final: 0.8587 (ptm160) REVERT: d 97 SER cc_start: 0.9010 (t) cc_final: 0.8429 (p) REVERT: d 99 GLU cc_start: 0.8358 (pm20) cc_final: 0.7626 (pm20) REVERT: e 130 LYS cc_start: 0.9178 (mmmm) cc_final: 0.8875 (mmmt) REVERT: f 56 ASP cc_start: 0.8798 (m-30) cc_final: 0.8538 (m-30) REVERT: f 64 LYS cc_start: 0.9081 (tmmt) cc_final: 0.8401 (mptt) REVERT: f 88 LYS cc_start: 0.8420 (ptmt) cc_final: 0.8094 (ptmt) REVERT: f 98 GLU cc_start: 0.8143 (tt0) cc_final: 0.7684 (tt0) REVERT: g 30 ASN cc_start: 0.8939 (OUTLIER) cc_final: 0.8323 (t0) REVERT: g 72 LEU cc_start: 0.9012 (OUTLIER) cc_final: 0.8772 (mm) REVERT: g 75 MET cc_start: 0.8975 (mtt) cc_final: 0.8631 (mtt) REVERT: g 130 GLU cc_start: 0.8124 (OUTLIER) cc_final: 0.7663 (mp0) REVERT: g 160 LYS cc_start: 0.9065 (mtpm) cc_final: 0.8704 (mtpm) REVERT: j 85 LYS cc_start: 0.9075 (OUTLIER) cc_final: 0.8625 (mtpp) REVERT: j 92 MET cc_start: 0.9005 (mmm) cc_final: 0.8533 (mmm) REVERT: j 108 MET cc_start: 0.9270 (mtt) cc_final: 0.8815 (mtt) REVERT: m 82 MET cc_start: 0.9333 (mmp) cc_final: 0.8885 (mmp) REVERT: n 35 LYS cc_start: 0.9176 (tttm) cc_final: 0.8919 (tppp) REVERT: n 86 ARG cc_start: 0.8827 (ttp80) cc_final: 0.7978 (mtm-85) REVERT: n 103 ARG cc_start: 0.9169 (OUTLIER) cc_final: 0.8794 (ttm170) REVERT: t 3 ARG cc_start: 0.7968 (OUTLIER) cc_final: 0.7726 (ptm-80) REVERT: t 18 GLU cc_start: 0.7903 (OUTLIER) cc_final: 0.7377 (tm-30) REVERT: w 85 LYS cc_start: 0.9236 (mmmm) cc_final: 0.8958 (mtpp) outliers start: 100 outliers final: 62 residues processed: 636 average time/residue: 1.8502 time to fit residues: 1567.2227 Evaluate side-chains 639 residues out of total 2506 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 568 time to evaluate : 3.532 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 65 ASP Chi-restraints excluded: chain 2 residue 35 THR Chi-restraints excluded: chain 3 residue 25 VAL Chi-restraints excluded: chain 3 residue 52 ARG Chi-restraints excluded: chain 7 residue 44 LEU Chi-restraints excluded: chain 8 residue 4 ARG Chi-restraints excluded: chain 8 residue 20 ASP Chi-restraints excluded: chain 8 residue 23 ILE Chi-restraints excluded: chain c residue 120 VAL Chi-restraints excluded: chain c residue 139 SER Chi-restraints excluded: chain c residue 205 LEU Chi-restraints excluded: chain d residue 74 GLU Chi-restraints excluded: chain d residue 151 THR Chi-restraints excluded: chain e residue 133 LEU Chi-restraints excluded: chain f residue 6 ASP Chi-restraints excluded: chain f residue 12 VAL Chi-restraints excluded: chain f residue 23 ASN Chi-restraints excluded: chain f residue 31 VAL Chi-restraints excluded: chain f residue 33 LYS Chi-restraints excluded: chain f residue 44 ILE Chi-restraints excluded: chain f residue 49 LEU Chi-restraints excluded: chain f residue 94 GLU Chi-restraints excluded: chain f residue 108 VAL Chi-restraints excluded: chain g residue 9 VAL Chi-restraints excluded: chain g residue 15 VAL Chi-restraints excluded: chain g residue 17 VAL Chi-restraints excluded: chain g residue 26 ILE Chi-restraints excluded: chain g residue 30 ASN Chi-restraints excluded: chain g residue 32 GLU Chi-restraints excluded: chain g residue 34 THR Chi-restraints excluded: chain g residue 43 VAL Chi-restraints excluded: chain g residue 72 LEU Chi-restraints excluded: chain g residue 86 LYS Chi-restraints excluded: chain g residue 92 VAL Chi-restraints excluded: chain g residue 98 VAL Chi-restraints excluded: chain g residue 122 THR Chi-restraints excluded: chain g residue 127 THR Chi-restraints excluded: chain g residue 130 GLU Chi-restraints excluded: chain g residue 148 LEU Chi-restraints excluded: chain g residue 153 ARG Chi-restraints excluded: chain g residue 162 VAL Chi-restraints excluded: chain h residue 2 GLN Chi-restraints excluded: chain h residue 12 LEU Chi-restraints excluded: chain h residue 37 VAL Chi-restraints excluded: chain j residue 85 LYS Chi-restraints excluded: chain j residue 131 ASN Chi-restraints excluded: chain k residue 17 ARG Chi-restraints excluded: chain l residue 7 SER Chi-restraints excluded: chain l residue 121 THR Chi-restraints excluded: chain l residue 143 GLU Chi-restraints excluded: chain m residue 30 SER Chi-restraints excluded: chain m residue 135 VAL Chi-restraints excluded: chain n residue 52 ILE Chi-restraints excluded: chain n residue 70 THR Chi-restraints excluded: chain n residue 103 ARG Chi-restraints excluded: chain o residue 95 SER Chi-restraints excluded: chain p residue 5 ILE Chi-restraints excluded: chain p residue 63 LYS Chi-restraints excluded: chain p residue 114 LEU Chi-restraints excluded: chain s residue 13 SER Chi-restraints excluded: chain s residue 19 LEU Chi-restraints excluded: chain s residue 30 SER Chi-restraints excluded: chain s residue 86 MET Chi-restraints excluded: chain s residue 108 SER Chi-restraints excluded: chain t residue 3 ARG Chi-restraints excluded: chain t residue 7 LEU Chi-restraints excluded: chain t residue 18 GLU Chi-restraints excluded: chain t residue 62 VAL Chi-restraints excluded: chain w residue 10 LYS Chi-restraints excluded: chain w residue 64 VAL Chi-restraints excluded: chain y residue 62 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 597 random chunks: chunk 194 optimal weight: 10.0000 chunk 519 optimal weight: 10.0000 chunk 114 optimal weight: 10.0000 chunk 338 optimal weight: 10.0000 chunk 142 optimal weight: 20.0000 chunk 577 optimal weight: 20.0000 chunk 479 optimal weight: 8.9990 chunk 267 optimal weight: 100.0000 chunk 48 optimal weight: 10.0000 chunk 191 optimal weight: 10.0000 chunk 303 optimal weight: 10.0000 overall best weight: 9.7998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 1 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 8 35 GLN c 117 GLN d 173 GLN ** g 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 2 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 77 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** l 93 ASN m 3 GLN ** n 16 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** p 10 GLN p 12 GLN p 52 ASN r 66 HIS t 48 GLN u 40 ASN w 51 GLN w 78 GLN y 50 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8729 moved from start: 0.2808 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.070 96944 Z= 0.473 Angle : 0.655 9.666 145858 Z= 0.342 Chirality : 0.043 0.320 18756 Planarity : 0.005 0.055 7217 Dihedral : 23.913 179.772 50471 Min Nonbonded Distance : 2.016 Molprobity Statistics. All-atom Clashscore : 8.96 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.68 % Favored : 95.22 % Rotamer: Outliers : 4.79 % Allowed : 19.75 % Favored : 75.46 % 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: -0.39 (0.15), residues: 3032 helix: 1.00 (0.19), residues: 807 sheet: -0.43 (0.19), residues: 681 loop : -0.81 (0.15), residues: 1544 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP c 213 HIS 0.011 0.002 HIS s 7 PHE 0.017 0.002 PHE y 26 TYR 0.020 0.002 TYR c 161 ARG 0.011 0.001 ARG l 123 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6064 Ramachandran restraints generated. 3032 Oldfield, 0 Emsley, 3032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6064 Ramachandran restraints generated. 3032 Oldfield, 0 Emsley, 3032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 705 residues out of total 2506 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 120 poor density : 585 time to evaluate : 3.772 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: 0 65 ASP cc_start: 0.7884 (OUTLIER) cc_final: 0.7587 (m-30) REVERT: 1 20 ASN cc_start: 0.9063 (m110) cc_final: 0.8832 (m110) REVERT: 3 52 ARG cc_start: 0.8233 (OUTLIER) cc_final: 0.7362 (ptt-90) REVERT: 4 44 ARG cc_start: 0.8878 (mtp180) cc_final: 0.8491 (mtp180) REVERT: 8 36 ARG cc_start: 0.9038 (ptm160) cc_final: 0.8652 (ptm160) REVERT: d 97 SER cc_start: 0.9014 (t) cc_final: 0.8356 (p) REVERT: d 99 GLU cc_start: 0.8343 (pm20) cc_final: 0.7623 (pm20) REVERT: e 122 GLU cc_start: 0.8444 (pm20) cc_final: 0.8206 (pm20) REVERT: e 130 LYS cc_start: 0.9214 (mmmm) cc_final: 0.8968 (mmmt) REVERT: e 194 LYS cc_start: 0.8949 (tptp) cc_final: 0.8577 (tppt) REVERT: f 56 ASP cc_start: 0.8827 (m-30) cc_final: 0.8558 (m-30) REVERT: f 64 LYS cc_start: 0.9046 (tmmt) cc_final: 0.8350 (mptt) REVERT: f 88 LYS cc_start: 0.8490 (ptmt) cc_final: 0.8032 (ptmt) REVERT: f 98 GLU cc_start: 0.8198 (tt0) cc_final: 0.7743 (tt0) REVERT: f 112 ARG cc_start: 0.4380 (OUTLIER) cc_final: 0.2737 (tpm170) REVERT: f 130 MET cc_start: 0.8931 (ptm) cc_final: 0.8406 (ppp) REVERT: g 30 ASN cc_start: 0.8975 (OUTLIER) cc_final: 0.8287 (t0) REVERT: g 75 MET cc_start: 0.8996 (mtt) cc_final: 0.8641 (mtt) REVERT: g 130 GLU cc_start: 0.8175 (OUTLIER) cc_final: 0.7602 (mp0) REVERT: g 160 LYS cc_start: 0.9086 (mtpm) cc_final: 0.8731 (mtpm) REVERT: j 58 ASN cc_start: 0.9270 (m-40) cc_final: 0.8587 (m110) REVERT: j 85 LYS cc_start: 0.9094 (OUTLIER) cc_final: 0.8718 (mtpp) REVERT: j 92 MET cc_start: 0.9012 (mmm) cc_final: 0.8566 (mmm) REVERT: j 108 MET cc_start: 0.9286 (mtt) cc_final: 0.8959 (mtt) REVERT: j 128 ASN cc_start: 0.8514 (p0) cc_final: 0.7739 (t0) REVERT: m 82 MET cc_start: 0.9349 (mmp) cc_final: 0.8867 (mmp) REVERT: n 35 LYS cc_start: 0.9248 (tttm) cc_final: 0.8982 (tppp) REVERT: n 103 ARG cc_start: 0.9212 (OUTLIER) cc_final: 0.8840 (ttm170) REVERT: t 3 ARG cc_start: 0.8039 (OUTLIER) cc_final: 0.7792 (ptm-80) REVERT: t 18 GLU cc_start: 0.7911 (OUTLIER) cc_final: 0.7402 (tm-30) REVERT: w 85 LYS cc_start: 0.9230 (mmmm) cc_final: 0.9023 (mtpp) outliers start: 120 outliers final: 69 residues processed: 638 average time/residue: 1.8829 time to fit residues: 1606.7792 Evaluate side-chains 657 residues out of total 2506 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 78 poor density : 579 time to evaluate : 3.505 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 65 ASP Chi-restraints excluded: chain 1 residue 40 SER Chi-restraints excluded: chain 2 residue 35 THR Chi-restraints excluded: chain 3 residue 25 VAL Chi-restraints excluded: chain 3 residue 52 ARG Chi-restraints excluded: chain 7 residue 44 LEU Chi-restraints excluded: chain 8 residue 4 ARG Chi-restraints excluded: chain 8 residue 20 ASP Chi-restraints excluded: chain c residue 120 VAL Chi-restraints excluded: chain c residue 139 SER Chi-restraints excluded: chain d residue 74 GLU Chi-restraints excluded: chain d residue 92 VAL Chi-restraints excluded: chain d residue 151 THR Chi-restraints excluded: chain e residue 4 VAL Chi-restraints excluded: chain e residue 133 LEU Chi-restraints excluded: chain f residue 12 VAL Chi-restraints excluded: chain f residue 23 ASN Chi-restraints excluded: chain f residue 31 VAL Chi-restraints excluded: chain f residue 33 LYS Chi-restraints excluded: chain f residue 44 ILE Chi-restraints excluded: chain f residue 49 LEU Chi-restraints excluded: chain f residue 94 GLU Chi-restraints excluded: chain f residue 101 GLU Chi-restraints excluded: chain f residue 108 VAL Chi-restraints excluded: chain f residue 112 ARG Chi-restraints excluded: chain f residue 174 ASP Chi-restraints excluded: chain g residue 9 VAL Chi-restraints excluded: chain g residue 15 VAL Chi-restraints excluded: chain g residue 17 VAL Chi-restraints excluded: chain g residue 26 ILE Chi-restraints excluded: chain g residue 30 ASN Chi-restraints excluded: chain g residue 34 THR Chi-restraints excluded: chain g residue 43 VAL Chi-restraints excluded: chain g residue 86 LYS Chi-restraints excluded: chain g residue 92 VAL Chi-restraints excluded: chain g residue 98 VAL Chi-restraints excluded: chain g residue 122 THR Chi-restraints excluded: chain g residue 127 THR Chi-restraints excluded: chain g residue 130 GLU Chi-restraints excluded: chain g residue 148 LEU Chi-restraints excluded: chain g residue 153 ARG Chi-restraints excluded: chain g residue 162 VAL Chi-restraints excluded: chain h residue 12 LEU Chi-restraints excluded: chain h residue 37 VAL Chi-restraints excluded: chain j residue 85 LYS Chi-restraints excluded: chain j residue 90 GLU Chi-restraints excluded: chain j residue 131 ASN Chi-restraints excluded: chain k residue 17 ARG Chi-restraints excluded: chain k residue 118 LEU Chi-restraints excluded: chain l residue 7 SER Chi-restraints excluded: chain l residue 30 THR Chi-restraints excluded: chain l residue 121 THR Chi-restraints excluded: chain m residue 30 SER Chi-restraints excluded: chain m residue 78 LEU Chi-restraints excluded: chain m residue 135 VAL Chi-restraints excluded: chain n residue 52 ILE Chi-restraints excluded: chain n residue 70 THR Chi-restraints excluded: chain n residue 103 ARG Chi-restraints excluded: chain o residue 95 SER Chi-restraints excluded: chain p residue 5 ILE Chi-restraints excluded: chain p residue 63 LYS Chi-restraints excluded: chain p residue 114 LEU Chi-restraints excluded: chain s residue 13 SER Chi-restraints excluded: chain s residue 19 LEU Chi-restraints excluded: chain s residue 30 SER Chi-restraints excluded: chain s residue 31 GLN Chi-restraints excluded: chain s residue 86 MET Chi-restraints excluded: chain s residue 108 SER Chi-restraints excluded: chain t residue 3 ARG Chi-restraints excluded: chain t residue 7 LEU Chi-restraints excluded: chain t residue 18 GLU Chi-restraints excluded: chain t residue 22 THR Chi-restraints excluded: chain t residue 50 LEU Chi-restraints excluded: chain t residue 62 VAL Chi-restraints excluded: chain u residue 11 VAL Chi-restraints excluded: chain w residue 10 LYS Chi-restraints excluded: chain w residue 64 VAL Chi-restraints excluded: chain y residue 62 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 597 random chunks: chunk 556 optimal weight: 9.9990 chunk 65 optimal weight: 10.0000 chunk 329 optimal weight: 10.0000 chunk 421 optimal weight: 8.9990 chunk 326 optimal weight: 10.0000 chunk 486 optimal weight: 5.9990 chunk 322 optimal weight: 10.0000 chunk 575 optimal weight: 5.9990 chunk 360 optimal weight: 9.9990 chunk 350 optimal weight: 6.9990 chunk 265 optimal weight: 70.0000 overall best weight: 7.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 1 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 8 35 GLN c 117 GLN ** g 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 2 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 77 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** k 89 ASN l 93 ASN m 3 GLN ** n 16 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** o 38 GLN p 10 GLN p 12 GLN p 52 ASN r 66 HIS t 48 GLN u 40 ASN w 78 GLN y 50 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8713 moved from start: 0.2861 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.064 96944 Z= 0.378 Angle : 0.611 9.918 145858 Z= 0.321 Chirality : 0.040 0.297 18756 Planarity : 0.005 0.060 7217 Dihedral : 23.905 179.760 50465 Min Nonbonded Distance : 2.043 Molprobity Statistics. All-atom Clashscore : 9.01 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.75 % Favored : 95.15 % Rotamer: Outliers : 4.19 % Allowed : 20.87 % Favored : 74.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.34 (0.15), residues: 3032 helix: 1.03 (0.19), residues: 809 sheet: -0.38 (0.19), residues: 679 loop : -0.79 (0.16), residues: 1544 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP c 213 HIS 0.009 0.001 HIS s 7 PHE 0.015 0.002 PHE y 26 TYR 0.015 0.001 TYR q 32 ARG 0.012 0.001 ARG l 123 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6064 Ramachandran restraints generated. 3032 Oldfield, 0 Emsley, 3032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6064 Ramachandran restraints generated. 3032 Oldfield, 0 Emsley, 3032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 696 residues out of total 2506 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 105 poor density : 591 time to evaluate : 3.886 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: 1 20 ASN cc_start: 0.9019 (m110) cc_final: 0.8121 (m110) REVERT: 1 55 THR cc_start: 0.9136 (OUTLIER) cc_final: 0.8736 (p) REVERT: 3 52 ARG cc_start: 0.8245 (OUTLIER) cc_final: 0.7383 (ptt-90) REVERT: 8 36 ARG cc_start: 0.9039 (ptm160) cc_final: 0.8649 (ptm160) REVERT: d 97 SER cc_start: 0.9018 (t) cc_final: 0.8344 (p) REVERT: d 99 GLU cc_start: 0.8334 (pm20) cc_final: 0.7659 (pm20) REVERT: e 122 GLU cc_start: 0.8429 (pm20) cc_final: 0.8223 (pm20) REVERT: e 130 LYS cc_start: 0.9228 (mmmm) cc_final: 0.8920 (mmmt) REVERT: e 194 LYS cc_start: 0.8928 (tptp) cc_final: 0.8550 (tppt) REVERT: f 19 GLU cc_start: 0.8939 (tt0) cc_final: 0.8726 (tm-30) REVERT: f 56 ASP cc_start: 0.8831 (m-30) cc_final: 0.8563 (m-30) REVERT: f 64 LYS cc_start: 0.9054 (tmmt) cc_final: 0.8350 (mptt) REVERT: f 78 LYS cc_start: 0.8497 (OUTLIER) cc_final: 0.8258 (mmpt) REVERT: f 88 LYS cc_start: 0.8459 (ptmt) cc_final: 0.8017 (ptmt) REVERT: f 98 GLU cc_start: 0.8189 (tt0) cc_final: 0.7679 (tt0) REVERT: f 130 MET cc_start: 0.8885 (ptm) cc_final: 0.8437 (ppp) REVERT: g 30 ASN cc_start: 0.8972 (OUTLIER) cc_final: 0.8282 (t0) REVERT: g 72 LEU cc_start: 0.9029 (mm) cc_final: 0.8786 (mm) REVERT: g 75 MET cc_start: 0.9019 (mtt) cc_final: 0.8626 (mtt) REVERT: g 130 GLU cc_start: 0.8204 (OUTLIER) cc_final: 0.7779 (mp0) REVERT: g 160 LYS cc_start: 0.9108 (mtpm) cc_final: 0.8757 (mtpm) REVERT: h 1 MET cc_start: 0.7944 (ttp) cc_final: 0.7690 (ttm) REVERT: j 85 LYS cc_start: 0.9093 (OUTLIER) cc_final: 0.8703 (mtpp) REVERT: j 92 MET cc_start: 0.9005 (mmm) cc_final: 0.8568 (mmm) REVERT: j 108 MET cc_start: 0.9287 (mtt) cc_final: 0.8995 (mtt) REVERT: j 128 ASN cc_start: 0.8456 (p0) cc_final: 0.7809 (t0) REVERT: m 82 MET cc_start: 0.9354 (mmp) cc_final: 0.8870 (mmp) REVERT: n 35 LYS cc_start: 0.9171 (tttm) cc_final: 0.8911 (tppp) REVERT: n 103 ARG cc_start: 0.9201 (OUTLIER) cc_final: 0.8763 (ttm170) REVERT: t 3 ARG cc_start: 0.7980 (OUTLIER) cc_final: 0.7738 (ptm-80) REVERT: t 18 GLU cc_start: 0.7918 (OUTLIER) cc_final: 0.7409 (tm-30) REVERT: w 85 LYS cc_start: 0.9241 (mmmm) cc_final: 0.9034 (mtpp) outliers start: 105 outliers final: 65 residues processed: 632 average time/residue: 1.8209 time to fit residues: 1540.0010 Evaluate side-chains 657 residues out of total 2506 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 74 poor density : 583 time to evaluate : 3.519 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 55 THR Chi-restraints excluded: chain 2 residue 35 THR Chi-restraints excluded: chain 3 residue 25 VAL Chi-restraints excluded: chain 3 residue 52 ARG Chi-restraints excluded: chain 4 residue 42 VAL Chi-restraints excluded: chain 7 residue 44 LEU Chi-restraints excluded: chain 7 residue 51 SER Chi-restraints excluded: chain 8 residue 4 ARG Chi-restraints excluded: chain c residue 120 VAL Chi-restraints excluded: chain c residue 139 SER Chi-restraints excluded: chain d residue 74 GLU Chi-restraints excluded: chain d residue 151 THR Chi-restraints excluded: chain e residue 4 VAL Chi-restraints excluded: chain e residue 12 LEU Chi-restraints excluded: chain e residue 133 LEU Chi-restraints excluded: chain f residue 12 VAL Chi-restraints excluded: chain f residue 23 ASN Chi-restraints excluded: chain f residue 33 LYS Chi-restraints excluded: chain f residue 42 GLU Chi-restraints excluded: chain f residue 44 ILE Chi-restraints excluded: chain f residue 49 LEU Chi-restraints excluded: chain f residue 78 LYS Chi-restraints excluded: chain f residue 94 GLU Chi-restraints excluded: chain f residue 101 GLU Chi-restraints excluded: chain f residue 108 VAL Chi-restraints excluded: chain f residue 134 GLU Chi-restraints excluded: chain g residue 9 VAL Chi-restraints excluded: chain g residue 15 VAL Chi-restraints excluded: chain g residue 17 VAL Chi-restraints excluded: chain g residue 26 ILE Chi-restraints excluded: chain g residue 30 ASN Chi-restraints excluded: chain g residue 34 THR Chi-restraints excluded: chain g residue 43 VAL Chi-restraints excluded: chain g residue 86 LYS Chi-restraints excluded: chain g residue 92 VAL Chi-restraints excluded: chain g residue 98 VAL Chi-restraints excluded: chain g residue 122 THR Chi-restraints excluded: chain g residue 127 THR Chi-restraints excluded: chain g residue 130 GLU Chi-restraints excluded: chain g residue 148 LEU Chi-restraints excluded: chain g residue 153 ARG Chi-restraints excluded: chain g residue 162 VAL Chi-restraints excluded: chain h residue 37 VAL Chi-restraints excluded: chain j residue 85 LYS Chi-restraints excluded: chain j residue 131 ASN Chi-restraints excluded: chain l residue 7 SER Chi-restraints excluded: chain l residue 30 THR Chi-restraints excluded: chain l residue 121 THR Chi-restraints excluded: chain m residue 5 LYS Chi-restraints excluded: chain m residue 30 SER Chi-restraints excluded: chain m residue 135 VAL Chi-restraints excluded: chain n residue 52 ILE Chi-restraints excluded: chain n residue 70 THR Chi-restraints excluded: chain n residue 103 ARG Chi-restraints excluded: chain o residue 95 SER Chi-restraints excluded: chain p residue 5 ILE Chi-restraints excluded: chain p residue 52 ASN Chi-restraints excluded: chain p residue 63 LYS Chi-restraints excluded: chain p residue 114 LEU Chi-restraints excluded: chain r residue 33 VAL Chi-restraints excluded: chain s residue 13 SER Chi-restraints excluded: chain s residue 19 LEU Chi-restraints excluded: chain s residue 30 SER Chi-restraints excluded: chain s residue 86 MET Chi-restraints excluded: chain s residue 108 SER Chi-restraints excluded: chain t residue 3 ARG Chi-restraints excluded: chain t residue 7 LEU Chi-restraints excluded: chain t residue 18 GLU Chi-restraints excluded: chain t residue 50 LEU Chi-restraints excluded: chain t residue 62 VAL Chi-restraints excluded: chain u residue 11 VAL Chi-restraints excluded: chain w residue 10 LYS Chi-restraints excluded: chain w residue 64 VAL Chi-restraints excluded: chain y residue 62 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 597 random chunks: chunk 355 optimal weight: 2.9990 chunk 229 optimal weight: 10.0000 chunk 343 optimal weight: 5.9990 chunk 173 optimal weight: 10.0000 chunk 113 optimal weight: 10.0000 chunk 111 optimal weight: 10.0000 chunk 365 optimal weight: 7.9990 chunk 392 optimal weight: 0.9980 chunk 284 optimal weight: 10.0000 chunk 53 optimal weight: 10.0000 chunk 452 optimal weight: 7.9990 overall best weight: 5.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 1 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 8 35 GLN c 117 GLN ** g 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 2 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 77 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** l 93 ASN ** n 16 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 100 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** p 10 GLN p 12 GLN p 52 ASN q 72 ASN r 66 HIS t 48 GLN u 40 ASN w 78 GLN y 50 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8697 moved from start: 0.2903 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.074 96944 Z= 0.274 Angle : 0.579 10.030 145858 Z= 0.306 Chirality : 0.037 0.280 18756 Planarity : 0.005 0.086 7217 Dihedral : 23.922 179.937 50465 Min Nonbonded Distance : 2.056 Molprobity Statistics. All-atom Clashscore : 9.27 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.52 % Favored : 95.38 % Rotamer: Outliers : 3.83 % Allowed : 21.79 % Favored : 74.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.28 (0.15), residues: 3032 helix: 1.06 (0.19), residues: 809 sheet: -0.38 (0.19), residues: 667 loop : -0.72 (0.16), residues: 1556 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP c 213 HIS 0.007 0.001 HIS s 7 PHE 0.013 0.001 PHE e 183 TYR 0.016 0.001 TYR n 112 ARG 0.016 0.001 ARG l 123 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6064 Ramachandran restraints generated. 3032 Oldfield, 0 Emsley, 3032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6064 Ramachandran restraints generated. 3032 Oldfield, 0 Emsley, 3032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 683 residues out of total 2506 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 96 poor density : 587 time to evaluate : 3.991 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: 1 31 GLN cc_start: 0.8682 (mp10) cc_final: 0.8371 (mp-120) REVERT: 1 55 THR cc_start: 0.9100 (OUTLIER) cc_final: 0.8710 (p) REVERT: 3 52 ARG cc_start: 0.8231 (OUTLIER) cc_final: 0.7368 (ptt-90) REVERT: 8 36 ARG cc_start: 0.9018 (ptm160) cc_final: 0.8617 (ptm160) REVERT: d 97 SER cc_start: 0.8998 (t) cc_final: 0.8265 (p) REVERT: d 99 GLU cc_start: 0.8314 (pm20) cc_final: 0.7629 (pm20) REVERT: e 130 LYS cc_start: 0.9188 (mmmm) cc_final: 0.8961 (mmmt) REVERT: e 156 ASN cc_start: 0.9009 (OUTLIER) cc_final: 0.8750 (t0) REVERT: e 194 LYS cc_start: 0.8928 (tptp) cc_final: 0.8538 (tppt) REVERT: f 19 GLU cc_start: 0.8943 (tt0) cc_final: 0.8729 (tm-30) REVERT: f 56 ASP cc_start: 0.8809 (m-30) cc_final: 0.8536 (m-30) REVERT: f 64 LYS cc_start: 0.9056 (tmmt) cc_final: 0.8350 (mptt) REVERT: f 78 LYS cc_start: 0.8512 (OUTLIER) cc_final: 0.8225 (mmpt) REVERT: f 88 LYS cc_start: 0.8470 (ptmt) cc_final: 0.7997 (ptmt) REVERT: f 98 GLU cc_start: 0.8133 (tt0) cc_final: 0.7621 (tt0) REVERT: f 130 MET cc_start: 0.8857 (ptm) cc_final: 0.8422 (ppp) REVERT: g 30 ASN cc_start: 0.8961 (OUTLIER) cc_final: 0.8277 (t0) REVERT: g 72 LEU cc_start: 0.9034 (OUTLIER) cc_final: 0.8813 (mm) REVERT: g 75 MET cc_start: 0.9001 (mtm) cc_final: 0.8651 (mtt) REVERT: g 130 GLU cc_start: 0.8187 (OUTLIER) cc_final: 0.7762 (mp0) REVERT: g 160 LYS cc_start: 0.9074 (mtpm) cc_final: 0.8710 (mtpm) REVERT: h 1 MET cc_start: 0.8061 (ttp) cc_final: 0.7819 (ttm) REVERT: j 92 MET cc_start: 0.8995 (mmm) cc_final: 0.8552 (mmm) REVERT: j 108 MET cc_start: 0.9274 (mtt) cc_final: 0.8895 (mtt) REVERT: l 123 ARG cc_start: 0.8371 (ttm-80) cc_final: 0.8110 (ttm-80) REVERT: m 82 MET cc_start: 0.9348 (mmp) cc_final: 0.8874 (mmp) REVERT: n 35 LYS cc_start: 0.9160 (tttm) cc_final: 0.8916 (tppp) REVERT: n 103 ARG cc_start: 0.9180 (OUTLIER) cc_final: 0.8673 (ttm170) REVERT: t 1 MET cc_start: 0.8278 (OUTLIER) cc_final: 0.7901 (ttp) REVERT: t 3 ARG cc_start: 0.7977 (OUTLIER) cc_final: 0.7746 (ptm-80) REVERT: t 18 GLU cc_start: 0.7926 (OUTLIER) cc_final: 0.7393 (tm-30) REVERT: w 85 LYS cc_start: 0.9232 (mmmm) cc_final: 0.9026 (mtpp) outliers start: 96 outliers final: 66 residues processed: 632 average time/residue: 1.8495 time to fit residues: 1566.4393 Evaluate side-chains 655 residues out of total 2506 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 77 poor density : 578 time to evaluate : 3.511 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 55 THR Chi-restraints excluded: chain 2 residue 35 THR Chi-restraints excluded: chain 3 residue 25 VAL Chi-restraints excluded: chain 3 residue 52 ARG Chi-restraints excluded: chain 4 residue 42 VAL Chi-restraints excluded: chain 7 residue 44 LEU Chi-restraints excluded: chain 7 residue 51 SER Chi-restraints excluded: chain 8 residue 4 ARG Chi-restraints excluded: chain 8 residue 23 ILE Chi-restraints excluded: chain c residue 120 VAL Chi-restraints excluded: chain c residue 139 SER Chi-restraints excluded: chain d residue 74 GLU Chi-restraints excluded: chain d residue 92 VAL Chi-restraints excluded: chain d residue 151 THR Chi-restraints excluded: chain e residue 4 VAL Chi-restraints excluded: chain e residue 126 VAL Chi-restraints excluded: chain e residue 133 LEU Chi-restraints excluded: chain e residue 156 ASN Chi-restraints excluded: chain f residue 12 VAL Chi-restraints excluded: chain f residue 23 ASN Chi-restraints excluded: chain f residue 33 LYS Chi-restraints excluded: chain f residue 42 GLU Chi-restraints excluded: chain f residue 44 ILE Chi-restraints excluded: chain f residue 49 LEU Chi-restraints excluded: chain f residue 78 LYS Chi-restraints excluded: chain f residue 94 GLU Chi-restraints excluded: chain f residue 101 GLU Chi-restraints excluded: chain f residue 108 VAL Chi-restraints excluded: chain f residue 134 GLU Chi-restraints excluded: chain g residue 15 VAL Chi-restraints excluded: chain g residue 26 ILE Chi-restraints excluded: chain g residue 30 ASN Chi-restraints excluded: chain g residue 34 THR Chi-restraints excluded: chain g residue 43 VAL Chi-restraints excluded: chain g residue 72 LEU Chi-restraints excluded: chain g residue 86 LYS Chi-restraints excluded: chain g residue 92 VAL Chi-restraints excluded: chain g residue 98 VAL Chi-restraints excluded: chain g residue 127 THR Chi-restraints excluded: chain g residue 130 GLU Chi-restraints excluded: chain g residue 148 LEU Chi-restraints excluded: chain g residue 153 ARG Chi-restraints excluded: chain g residue 162 VAL Chi-restraints excluded: chain h residue 12 LEU Chi-restraints excluded: chain h residue 37 VAL Chi-restraints excluded: chain j residue 131 ASN Chi-restraints excluded: chain k residue 17 ARG Chi-restraints excluded: chain l residue 7 SER Chi-restraints excluded: chain l residue 30 THR Chi-restraints excluded: chain l residue 121 THR Chi-restraints excluded: chain m residue 30 SER Chi-restraints excluded: chain m residue 78 LEU Chi-restraints excluded: chain m residue 135 VAL Chi-restraints excluded: chain n residue 52 ILE Chi-restraints excluded: chain n residue 70 THR Chi-restraints excluded: chain n residue 103 ARG Chi-restraints excluded: chain o residue 95 SER Chi-restraints excluded: chain p residue 5 ILE Chi-restraints excluded: chain p residue 52 ASN Chi-restraints excluded: chain p residue 63 LYS Chi-restraints excluded: chain p residue 114 LEU Chi-restraints excluded: chain s residue 13 SER Chi-restraints excluded: chain s residue 19 LEU Chi-restraints excluded: chain s residue 30 SER Chi-restraints excluded: chain s residue 86 MET Chi-restraints excluded: chain s residue 108 SER Chi-restraints excluded: chain t residue 1 MET Chi-restraints excluded: chain t residue 3 ARG Chi-restraints excluded: chain t residue 7 LEU Chi-restraints excluded: chain t residue 18 GLU Chi-restraints excluded: chain t residue 50 LEU Chi-restraints excluded: chain t residue 62 VAL Chi-restraints excluded: chain u residue 11 VAL Chi-restraints excluded: chain w residue 10 LYS Chi-restraints excluded: chain w residue 64 VAL Chi-restraints excluded: chain y residue 30 SER Chi-restraints excluded: chain y residue 62 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 597 random chunks: chunk 523 optimal weight: 4.9990 chunk 551 optimal weight: 5.9990 chunk 502 optimal weight: 8.9990 chunk 536 optimal weight: 0.9980 chunk 322 optimal weight: 10.0000 chunk 233 optimal weight: 10.0000 chunk 421 optimal weight: 30.0000 chunk 164 optimal weight: 10.0000 chunk 484 optimal weight: 9.9990 chunk 507 optimal weight: 9.9990 chunk 534 optimal weight: 6.9990 overall best weight: 5.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 1 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 8 35 GLN c 117 GLN ** g 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 2 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 77 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** l 93 ASN ** n 16 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 100 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** p 10 GLN p 12 GLN r 66 HIS t 48 GLN u 40 ASN w 78 GLN y 50 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8694 moved from start: 0.2937 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.058 96944 Z= 0.290 Angle : 0.575 10.080 145858 Z= 0.304 Chirality : 0.037 0.284 18756 Planarity : 0.005 0.066 7217 Dihedral : 23.876 179.664 50465 Min Nonbonded Distance : 2.069 Molprobity Statistics. All-atom Clashscore : 9.21 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.35 % Favored : 95.55 % Rotamer: Outliers : 3.83 % Allowed : 22.23 % Favored : 73.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.27 (0.15), residues: 3032 helix: 1.08 (0.19), residues: 809 sheet: -0.40 (0.19), residues: 672 loop : -0.70 (0.16), residues: 1551 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP c 213 HIS 0.007 0.001 HIS s 7 PHE 0.014 0.001 PHE 4 20 TYR 0.015 0.001 TYR n 112 ARG 0.012 0.001 ARG l 123 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6064 Ramachandran restraints generated. 3032 Oldfield, 0 Emsley, 3032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6064 Ramachandran restraints generated. 3032 Oldfield, 0 Emsley, 3032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 685 residues out of total 2506 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 96 poor density : 589 time to evaluate : 3.627 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: 1 55 THR cc_start: 0.9041 (OUTLIER) cc_final: 0.8644 (p) REVERT: 3 52 ARG cc_start: 0.8234 (OUTLIER) cc_final: 0.7365 (ptt-90) REVERT: 4 7 GLU cc_start: 0.8402 (pm20) cc_final: 0.7899 (pm20) REVERT: 8 36 ARG cc_start: 0.9012 (ptm160) cc_final: 0.8612 (ptm160) REVERT: d 70 LYS cc_start: 0.9384 (tttm) cc_final: 0.9087 (tttp) REVERT: d 97 SER cc_start: 0.9006 (t) cc_final: 0.8263 (p) REVERT: d 99 GLU cc_start: 0.8297 (pm20) cc_final: 0.7619 (pm20) REVERT: e 122 GLU cc_start: 0.8455 (pm20) cc_final: 0.8205 (pm20) REVERT: e 130 LYS cc_start: 0.9182 (mmmm) cc_final: 0.8964 (mmmt) REVERT: e 156 ASN cc_start: 0.9017 (OUTLIER) cc_final: 0.8777 (t0) REVERT: e 194 LYS cc_start: 0.8950 (tptp) cc_final: 0.8557 (tppt) REVERT: f 19 GLU cc_start: 0.8957 (tt0) cc_final: 0.8746 (tm-30) REVERT: f 56 ASP cc_start: 0.8836 (m-30) cc_final: 0.8564 (m-30) REVERT: f 64 LYS cc_start: 0.9062 (tmmt) cc_final: 0.8348 (mptt) REVERT: f 78 LYS cc_start: 0.8514 (OUTLIER) cc_final: 0.8238 (mmpt) REVERT: f 88 LYS cc_start: 0.8467 (ptmt) cc_final: 0.8002 (ptmt) REVERT: f 98 GLU cc_start: 0.8190 (tt0) cc_final: 0.7678 (tt0) REVERT: f 112 ARG cc_start: 0.4421 (OUTLIER) cc_final: 0.2711 (tpt170) REVERT: f 130 MET cc_start: 0.8883 (ptm) cc_final: 0.8393 (ppp) REVERT: g 30 ASN cc_start: 0.8968 (OUTLIER) cc_final: 0.8294 (t0) REVERT: g 72 LEU cc_start: 0.9028 (OUTLIER) cc_final: 0.8794 (mm) REVERT: g 75 MET cc_start: 0.8974 (mtm) cc_final: 0.8621 (mtt) REVERT: g 130 GLU cc_start: 0.8177 (OUTLIER) cc_final: 0.7618 (mp0) REVERT: g 160 LYS cc_start: 0.9077 (mtpm) cc_final: 0.8702 (mtpm) REVERT: j 85 LYS cc_start: 0.9076 (OUTLIER) cc_final: 0.8621 (mtpp) REVERT: j 92 MET cc_start: 0.8987 (mmm) cc_final: 0.8552 (mmm) REVERT: j 108 MET cc_start: 0.9270 (mtt) cc_final: 0.8899 (mtt) REVERT: j 128 ASN cc_start: 0.8400 (p0) cc_final: 0.7849 (t0) REVERT: k 66 LYS cc_start: 0.8865 (OUTLIER) cc_final: 0.8410 (ptmm) REVERT: l 123 ARG cc_start: 0.8355 (ttm-80) cc_final: 0.7812 (ttm-80) REVERT: l 143 GLU cc_start: 0.6209 (pt0) cc_final: 0.5616 (pt0) REVERT: m 82 MET cc_start: 0.9343 (mmp) cc_final: 0.8877 (mmp) REVERT: n 35 LYS cc_start: 0.9160 (tttm) cc_final: 0.8922 (tppp) REVERT: n 103 ARG cc_start: 0.9190 (OUTLIER) cc_final: 0.8744 (ttm170) REVERT: t 1 MET cc_start: 0.8263 (OUTLIER) cc_final: 0.7960 (ttp) REVERT: w 85 LYS cc_start: 0.9230 (mmmm) cc_final: 0.9020 (mtpp) outliers start: 96 outliers final: 68 residues processed: 633 average time/residue: 1.8058 time to fit residues: 1527.2804 Evaluate side-chains 660 residues out of total 2506 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 80 poor density : 580 time to evaluate : 3.467 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 55 THR Chi-restraints excluded: chain 2 residue 35 THR Chi-restraints excluded: chain 3 residue 25 VAL Chi-restraints excluded: chain 3 residue 52 ARG Chi-restraints excluded: chain 4 residue 42 VAL Chi-restraints excluded: chain 7 residue 44 LEU Chi-restraints excluded: chain 7 residue 51 SER Chi-restraints excluded: chain 8 residue 4 ARG Chi-restraints excluded: chain 8 residue 35 GLN Chi-restraints excluded: chain c residue 120 VAL Chi-restraints excluded: chain c residue 139 SER Chi-restraints excluded: chain d residue 40 LEU Chi-restraints excluded: chain d residue 74 GLU Chi-restraints excluded: chain d residue 92 VAL Chi-restraints excluded: chain d residue 151 THR Chi-restraints excluded: chain e residue 4 VAL Chi-restraints excluded: chain e residue 12 LEU Chi-restraints excluded: chain e residue 14 VAL Chi-restraints excluded: chain e residue 126 VAL Chi-restraints excluded: chain e residue 133 LEU Chi-restraints excluded: chain e residue 156 ASN Chi-restraints excluded: chain f residue 12 VAL Chi-restraints excluded: chain f residue 23 ASN Chi-restraints excluded: chain f residue 33 LYS Chi-restraints excluded: chain f residue 42 GLU Chi-restraints excluded: chain f residue 44 ILE Chi-restraints excluded: chain f residue 49 LEU Chi-restraints excluded: chain f residue 78 LYS Chi-restraints excluded: chain f residue 94 GLU Chi-restraints excluded: chain f residue 101 GLU Chi-restraints excluded: chain f residue 108 VAL Chi-restraints excluded: chain f residue 112 ARG Chi-restraints excluded: chain f residue 134 GLU Chi-restraints excluded: chain g residue 15 VAL Chi-restraints excluded: chain g residue 17 VAL Chi-restraints excluded: chain g residue 26 ILE Chi-restraints excluded: chain g residue 30 ASN Chi-restraints excluded: chain g residue 34 THR Chi-restraints excluded: chain g residue 43 VAL Chi-restraints excluded: chain g residue 72 LEU Chi-restraints excluded: chain g residue 86 LYS Chi-restraints excluded: chain g residue 92 VAL Chi-restraints excluded: chain g residue 98 VAL Chi-restraints excluded: chain g residue 127 THR Chi-restraints excluded: chain g residue 130 GLU Chi-restraints excluded: chain g residue 148 LEU Chi-restraints excluded: chain g residue 153 ARG Chi-restraints excluded: chain h residue 37 VAL Chi-restraints excluded: chain j residue 85 LYS Chi-restraints excluded: chain j residue 131 ASN Chi-restraints excluded: chain k residue 17 ARG Chi-restraints excluded: chain k residue 66 LYS Chi-restraints excluded: chain l residue 7 SER Chi-restraints excluded: chain l residue 30 THR Chi-restraints excluded: chain l residue 121 THR Chi-restraints excluded: chain m residue 30 SER Chi-restraints excluded: chain m residue 78 LEU Chi-restraints excluded: chain m residue 135 VAL Chi-restraints excluded: chain n residue 52 ILE Chi-restraints excluded: chain n residue 70 THR Chi-restraints excluded: chain n residue 103 ARG Chi-restraints excluded: chain o residue 60 GLU Chi-restraints excluded: chain o residue 95 SER Chi-restraints excluded: chain p residue 5 ILE Chi-restraints excluded: chain p residue 63 LYS Chi-restraints excluded: chain p residue 114 LEU Chi-restraints excluded: chain r residue 33 VAL Chi-restraints excluded: chain s residue 13 SER Chi-restraints excluded: chain s residue 19 LEU Chi-restraints excluded: chain s residue 30 SER Chi-restraints excluded: chain s residue 86 MET Chi-restraints excluded: chain s residue 108 SER Chi-restraints excluded: chain t residue 1 MET Chi-restraints excluded: chain t residue 7 LEU Chi-restraints excluded: chain t residue 50 LEU Chi-restraints excluded: chain t residue 62 VAL Chi-restraints excluded: chain u residue 11 VAL Chi-restraints excluded: chain w residue 10 LYS Chi-restraints excluded: chain w residue 64 VAL Chi-restraints excluded: chain y residue 62 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 597 random chunks: chunk 352 optimal weight: 7.9990 chunk 567 optimal weight: 6.9990 chunk 346 optimal weight: 7.9990 chunk 268 optimal weight: 90.0000 chunk 394 optimal weight: 0.0020 chunk 594 optimal weight: 9.9990 chunk 547 optimal weight: 20.0000 chunk 473 optimal weight: 20.0000 chunk 49 optimal weight: 10.0000 chunk 365 optimal weight: 5.9990 chunk 290 optimal weight: 10.0000 overall best weight: 5.7996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 1 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 1 25 GLN ** 1 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 8 35 GLN c 117 GLN f 63 GLN ** g 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 2 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 77 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** l 93 ASN ** n 16 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** o 38 GLN ** o 100 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** p 10 GLN p 12 GLN p 52 ASN r 66 HIS t 48 GLN u 40 ASN w 78 GLN y 50 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8693 moved from start: 0.2990 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.058 96944 Z= 0.297 Angle : 0.573 10.056 145858 Z= 0.302 Chirality : 0.037 0.283 18756 Planarity : 0.005 0.058 7217 Dihedral : 23.840 179.270 50465 Min Nonbonded Distance : 2.077 Molprobity Statistics. All-atom Clashscore : 9.16 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.45 % Favored : 95.48 % Rotamer: Outliers : 3.51 % Allowed : 22.71 % Favored : 73.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.24 (0.15), residues: 3032 helix: 1.11 (0.19), residues: 803 sheet: -0.38 (0.19), residues: 666 loop : -0.68 (0.16), residues: 1563 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP c 213 HIS 0.006 0.001 HIS s 7 PHE 0.015 0.001 PHE 4 20 TYR 0.016 0.001 TYR n 112 ARG 0.011 0.001 ARG l 123 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6064 Ramachandran restraints generated. 3032 Oldfield, 0 Emsley, 3032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6064 Ramachandran restraints generated. 3032 Oldfield, 0 Emsley, 3032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 676 residues out of total 2506 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 88 poor density : 588 time to evaluate : 3.602 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: 1 20 ASN cc_start: 0.8654 (m-40) cc_final: 0.8432 (m110) REVERT: 1 31 GLN cc_start: 0.8615 (mp10) cc_final: 0.8311 (mp-120) REVERT: 3 52 ARG cc_start: 0.8253 (OUTLIER) cc_final: 0.7383 (ptt-90) REVERT: 8 36 ARG cc_start: 0.8894 (ptm160) cc_final: 0.8465 (ptm160) REVERT: d 70 LYS cc_start: 0.9379 (tttm) cc_final: 0.9077 (tttp) REVERT: d 97 SER cc_start: 0.8956 (t) cc_final: 0.8217 (p) REVERT: d 99 GLU cc_start: 0.8271 (pm20) cc_final: 0.7610 (pm20) REVERT: e 122 GLU cc_start: 0.8427 (pm20) cc_final: 0.8224 (pm20) REVERT: e 130 LYS cc_start: 0.9176 (mmmm) cc_final: 0.8848 (mmmt) REVERT: e 194 LYS cc_start: 0.8943 (tptp) cc_final: 0.8526 (tppt) REVERT: f 19 GLU cc_start: 0.8968 (tt0) cc_final: 0.8767 (tm-30) REVERT: f 38 MET cc_start: 0.8625 (mtp) cc_final: 0.8308 (mtm) REVERT: f 56 ASP cc_start: 0.8841 (m-30) cc_final: 0.8602 (m-30) REVERT: f 60 ILE cc_start: 0.9298 (mp) cc_final: 0.9077 (tt) REVERT: f 64 LYS cc_start: 0.9058 (tmmt) cc_final: 0.8344 (mptt) REVERT: f 78 LYS cc_start: 0.8529 (OUTLIER) cc_final: 0.8280 (mmpt) REVERT: f 88 LYS cc_start: 0.8469 (ptmt) cc_final: 0.7974 (ptmt) REVERT: f 98 GLU cc_start: 0.8170 (tt0) cc_final: 0.7671 (tt0) REVERT: f 112 ARG cc_start: 0.4444 (OUTLIER) cc_final: 0.2745 (tpt170) REVERT: f 130 MET cc_start: 0.8891 (ptm) cc_final: 0.8417 (ppp) REVERT: g 30 ASN cc_start: 0.8974 (OUTLIER) cc_final: 0.8313 (t0) REVERT: g 72 LEU cc_start: 0.9019 (OUTLIER) cc_final: 0.8771 (mm) REVERT: g 75 MET cc_start: 0.8975 (mtm) cc_final: 0.8582 (mtt) REVERT: g 130 GLU cc_start: 0.8150 (OUTLIER) cc_final: 0.7594 (mp0) REVERT: g 160 LYS cc_start: 0.9169 (mtpm) cc_final: 0.8742 (mtpm) REVERT: j 92 MET cc_start: 0.8989 (mmm) cc_final: 0.8571 (mmm) REVERT: j 108 MET cc_start: 0.9284 (mtt) cc_final: 0.8915 (mtt) REVERT: j 128 ASN cc_start: 0.8383 (p0) cc_final: 0.7882 (t0) REVERT: k 66 LYS cc_start: 0.8844 (OUTLIER) cc_final: 0.8377 (ptmm) REVERT: l 123 ARG cc_start: 0.8345 (ttm-80) cc_final: 0.8098 (ttm-80) REVERT: m 82 MET cc_start: 0.9344 (mmp) cc_final: 0.8894 (mmp) REVERT: n 35 LYS cc_start: 0.9154 (tttm) cc_final: 0.8928 (tppp) REVERT: n 103 ARG cc_start: 0.9190 (OUTLIER) cc_final: 0.8812 (ttm170) REVERT: t 1 MET cc_start: 0.8196 (OUTLIER) cc_final: 0.7658 (ttm) REVERT: w 85 LYS cc_start: 0.9209 (mmmm) cc_final: 0.8994 (mtpp) outliers start: 88 outliers final: 65 residues processed: 629 average time/residue: 1.8628 time to fit residues: 1571.1329 Evaluate side-chains 653 residues out of total 2506 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 74 poor density : 579 time to evaluate : 3.503 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 35 THR Chi-restraints excluded: chain 3 residue 25 VAL Chi-restraints excluded: chain 3 residue 52 ARG Chi-restraints excluded: chain 4 residue 42 VAL Chi-restraints excluded: chain 7 residue 44 LEU Chi-restraints excluded: chain 7 residue 51 SER Chi-restraints excluded: chain 8 residue 4 ARG Chi-restraints excluded: chain c residue 120 VAL Chi-restraints excluded: chain c residue 139 SER Chi-restraints excluded: chain d residue 40 LEU Chi-restraints excluded: chain d residue 74 GLU Chi-restraints excluded: chain d residue 92 VAL Chi-restraints excluded: chain d residue 151 THR Chi-restraints excluded: chain e residue 4 VAL Chi-restraints excluded: chain e residue 12 LEU Chi-restraints excluded: chain e residue 14 VAL Chi-restraints excluded: chain e residue 126 VAL Chi-restraints excluded: chain e residue 133 LEU Chi-restraints excluded: chain f residue 12 VAL Chi-restraints excluded: chain f residue 23 ASN Chi-restraints excluded: chain f residue 33 LYS Chi-restraints excluded: chain f residue 78 LYS Chi-restraints excluded: chain f residue 94 GLU Chi-restraints excluded: chain f residue 101 GLU Chi-restraints excluded: chain f residue 108 VAL Chi-restraints excluded: chain f residue 112 ARG Chi-restraints excluded: chain g residue 15 VAL Chi-restraints excluded: chain g residue 17 VAL Chi-restraints excluded: chain g residue 26 ILE Chi-restraints excluded: chain g residue 30 ASN Chi-restraints excluded: chain g residue 34 THR Chi-restraints excluded: chain g residue 43 VAL Chi-restraints excluded: chain g residue 51 THR Chi-restraints excluded: chain g residue 72 LEU Chi-restraints excluded: chain g residue 86 LYS Chi-restraints excluded: chain g residue 92 VAL Chi-restraints excluded: chain g residue 98 VAL Chi-restraints excluded: chain g residue 107 LEU Chi-restraints excluded: chain g residue 127 THR Chi-restraints excluded: chain g residue 130 GLU Chi-restraints excluded: chain g residue 148 LEU Chi-restraints excluded: chain g residue 153 ARG Chi-restraints excluded: chain h residue 37 VAL Chi-restraints excluded: chain j residue 131 ASN Chi-restraints excluded: chain k residue 17 ARG Chi-restraints excluded: chain k residue 66 LYS Chi-restraints excluded: chain l residue 7 SER Chi-restraints excluded: chain l residue 30 THR Chi-restraints excluded: chain l residue 121 THR Chi-restraints excluded: chain m residue 30 SER Chi-restraints excluded: chain m residue 78 LEU Chi-restraints excluded: chain m residue 135 VAL Chi-restraints excluded: chain n residue 52 ILE Chi-restraints excluded: chain n residue 70 THR Chi-restraints excluded: chain n residue 103 ARG Chi-restraints excluded: chain o residue 60 GLU Chi-restraints excluded: chain o residue 95 SER Chi-restraints excluded: chain p residue 5 ILE Chi-restraints excluded: chain p residue 63 LYS Chi-restraints excluded: chain p residue 114 LEU Chi-restraints excluded: chain r residue 33 VAL Chi-restraints excluded: chain s residue 13 SER Chi-restraints excluded: chain s residue 19 LEU Chi-restraints excluded: chain s residue 30 SER Chi-restraints excluded: chain s residue 31 GLN Chi-restraints excluded: chain s residue 86 MET Chi-restraints excluded: chain t residue 1 MET Chi-restraints excluded: chain t residue 7 LEU Chi-restraints excluded: chain t residue 62 VAL Chi-restraints excluded: chain u residue 11 VAL Chi-restraints excluded: chain w residue 10 LYS Chi-restraints excluded: chain w residue 64 VAL Chi-restraints excluded: chain y residue 30 SER Chi-restraints excluded: chain y residue 62 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 597 random chunks: chunk 376 optimal weight: 20.0000 chunk 504 optimal weight: 0.9980 chunk 145 optimal weight: 10.0000 chunk 436 optimal weight: 0.5980 chunk 69 optimal weight: 10.0000 chunk 131 optimal weight: 10.0000 chunk 474 optimal weight: 8.9990 chunk 198 optimal weight: 10.0000 chunk 487 optimal weight: 10.0000 chunk 60 optimal weight: 20.0000 chunk 87 optimal weight: 40.0000 overall best weight: 6.1190 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 1 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 1 25 GLN ** 1 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 117 GLN ** g 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 2 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 77 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** l 93 ASN ** n 16 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** p 10 GLN p 12 GLN p 52 ASN q 72 ASN r 66 HIS t 48 GLN u 40 ASN w 78 GLN y 50 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3336 r_free = 0.3336 target = 0.089758 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2775 r_free = 0.2775 target = 0.062992 restraints weight = 205013.553| |-----------------------------------------------------------------------------| r_work (start): 0.2727 rms_B_bonded: 1.13 r_work: 0.2620 rms_B_bonded: 2.05 restraints_weight: 0.5000 r_work: 0.2526 rms_B_bonded: 3.12 restraints_weight: 0.2500 r_work (final): 0.2526 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8916 moved from start: 0.3043 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.061 96944 Z= 0.312 Angle : 0.580 11.648 145858 Z= 0.305 Chirality : 0.037 0.287 18756 Planarity : 0.005 0.054 7217 Dihedral : 23.807 179.036 50465 Min Nonbonded Distance : 2.072 Molprobity Statistics. All-atom Clashscore : 9.26 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.52 % Favored : 95.42 % Rotamer: Outliers : 3.43 % Allowed : 23.06 % Favored : 73.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.23 (0.15), residues: 3032 helix: 1.09 (0.19), residues: 804 sheet: -0.31 (0.19), residues: 666 loop : -0.70 (0.16), residues: 1562 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP c 213 HIS 0.007 0.001 HIS s 7 PHE 0.016 0.001 PHE 4 20 TYR 0.017 0.002 TYR n 112 ARG 0.011 0.001 ARG l 123 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 24673.70 seconds wall clock time: 433 minutes 2.18 seconds (25982.18 seconds total)