Starting phenix.real_space_refine on Tue Feb 20 20:52:06 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zq6_14865/02_2024/7zq6_14865.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zq6_14865/02_2024/7zq6_14865.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.75 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zq6_14865/02_2024/7zq6_14865.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zq6_14865/02_2024/7zq6_14865.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zq6_14865/02_2024/7zq6_14865.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zq6_14865/02_2024/7zq6_14865.pdb" } resolution = 2.75 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= 0.026 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 3095 5.49 5 S 74 5.16 5 C 44734 2.51 5 N 16862 2.21 5 O 25742 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 GLU 8": "OE1" <-> "OE2" Residue "1 GLU 12": "OE1" <-> "OE2" Residue "1 GLU 13": "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 GLU 7": "OE1" <-> "OE2" 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 GLU 35": "OE1" <-> "OE2" Residue "c ARG 52": "NH1" <-> "NH2" Residue "c ARG 63": "NH1" <-> "NH2" Residue "c GLU 79": "OE1" <-> "OE2" Residue "c ARG 80": "NH1" <-> "NH2" 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 GLU 185": "OE1" <-> "OE2" Residue "c ARG 189": "NH1" <-> "NH2" Residue "c GLU 194": "OE1" <-> "OE2" Residue "c GLU 199": "OE1" <-> "OE2" Residue "c ARG 203": "NH1" <-> "NH2" Residue "c ARG 212": "NH1" <-> "NH2" 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 GLU 64": "OE1" <-> "OE2" Residue "d ARG 77": "NH1" <-> "NH2" Residue "d ARG 83": "NH1" <-> "NH2" Residue "d GLU 88": "OE1" <-> "OE2" Residue "d GLU 99": "OE1" <-> "OE2" Residue "d ARG 169": "NH1" <-> "NH2" Residue "d GLU 183": "OE1" <-> "OE2" Residue "d ARG 184": "NH1" <-> "NH2" Residue "e GLU 2": "OE1" <-> "OE2" Residue "e GLU 16": "OE1" <-> "OE2" 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 GLU 111": "OE1" <-> "OE2" Residue "e GLU 122": "OE1" <-> "OE2" Residue "e GLU 152": "OE1" <-> "OE2" Residue "e ARG 162": "NH1" <-> "NH2" Residue "e ARG 170": "NH1" <-> "NH2" Residue "e ASP 176": "OD1" <-> "OD2" Residue "e GLU 197": "OE1" <-> "OE2" Residue "f GLU 42": "OE1" <-> "OE2" Residue "f ARG 71": "NH1" <-> "NH2" Residue "f ARG 80": "NH1" <-> "NH2" Residue "f ARG 92": "NH1" <-> "NH2" Residue "f GLU 94": "OE1" <-> "OE2" Residue "f GLU 101": "OE1" <-> "OE2" 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 "f GLU 134": "OE1" <-> "OE2" Residue "f GLU 165": "OE1" <-> "OE2" Residue "g ARG 3": "NH1" <-> "NH2" Residue "g GLU 42": "OE1" <-> "OE2" Residue "g GLU 81": "OE1" <-> "OE2" Residue "g ARG 153": "NH1" <-> "NH2" Residue "g GLU 155": "OE1" <-> "OE2" Residue "g ARG 163": "NH1" <-> "NH2" Residue "g GLU 167": "OE1" <-> "OE2" Residue "g ARG 170": "NH1" <-> "NH2" Residue "h ARG 27": "NH1" <-> "NH2" Residue "j GLU 9": "OE1" <-> "OE2" Residue "j ARG 13": "NH1" <-> "NH2" Residue "j GLU 31": "OE1" <-> "OE2" Residue "j ARG 37": "NH1" <-> "NH2" Residue "j GLU 43": "OE1" <-> "OE2" Residue "j GLU 90": "OE1" <-> "OE2" Residue "j ARG 96": "NH1" <-> "NH2" Residue "j GLU 102": "OE1" <-> "OE2" Residue "j ARG 120": "NH1" <-> "NH2" Residue "k GLU 4": "OE1" <-> "OE2" Residue "k GLU 106": "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 GLU 86": "OE1" <-> "OE2" Residue "l GLU 115": "OE1" <-> "OE2" Residue "l ARG 126": "NH1" <-> "NH2" 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 110": "OE1" <-> "OE2" Residue "m ARG 114": "NH1" <-> "NH2" Residue "m GLU 115": "OE1" <-> "OE2" 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 43": "OE1" <-> "OE2" Residue "n ARG 46": "NH1" <-> "NH2" Residue "n GLU 49": "OE1" <-> "OE2" 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 ARG 96": "NH1" <-> "NH2" Residue "n ARG 118": "NH1" <-> "NH2" Residue "n GLU 120": "OE1" <-> "OE2" 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 GLU 46": "OE1" <-> "OE2" Residue "o GLU 55": "OE1" <-> "OE2" Residue "o GLU 60": "OE1" <-> "OE2" 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 9": "OE1" <-> "OE2" Residue "p GLU 11": "OE1" <-> "OE2" Residue "p ARG 21": "NH1" <-> "NH2" Residue "p GLU 27": "OE1" <-> "OE2" Residue "p GLU 34": "OE1" <-> "OE2" Residue "p ARG 39": "NH1" <-> "NH2" Residue "p ARG 51": "NH1" <-> "NH2" Residue "p ARG 62": "NH1" <-> "NH2" Residue "p GLU 68": "OE1" <-> "OE2" Residue "p ARG 89": "NH1" <-> "NH2" Residue "p ARG 101": "NH1" <-> "NH2" 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 GLU 46": "OE1" <-> "OE2" Residue "r ARG 68": "NH1" <-> "NH2" Residue "r GLU 70": "OE1" <-> "OE2" Residue "r ARG 78": "NH1" <-> "NH2" Residue "r ARG 79": "NH1" <-> "NH2" Residue "r ARG 84": "NH1" <-> "NH2" Residue "s GLU 59": "OE1" <-> "OE2" Residue "s PHE 75": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "s ARG 84": "NH1" <-> "NH2" Residue "s ARG 88": "NH1" <-> "NH2" Residue "s ARG 95": "NH1" <-> "NH2" Residue "t ARG 12": "NH1" <-> "NH2" Residue "t GLU 25": "OE1" <-> "OE2" Residue "t GLU 56": "OE1" <-> "OE2" Residue "t ARG 69": "NH1" <-> "NH2" Residue "u ARG 6": "NH1" <-> "NH2" Residue "u ARG 7": "NH1" <-> "NH2" Residue "u GLU 49": "OE1" <-> "OE2" Residue "u GLU 51": "OE1" <-> "OE2" Residue "u ARG 71": "NH1" <-> "NH2" Residue "u ARG 75": "NH1" <-> "NH2" Residue "u GLU 77": "OE1" <-> "OE2" Residue "u ARG 83": "NH1" <-> "NH2" Residue "u PHE 84": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "w GLU 7": "OE1" <-> "OE2" Residue "w GLU 35": "OE1" <-> "OE2" Residue "w GLU 41": "OE1" <-> "OE2" Residue "w GLU 59": "OE1" <-> "OE2" Residue "y ARG 11": "NH1" <-> "NH2" Residue "y GLU 17": "OE1" <-> "OE2" 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: 90507 Number of models: 1 Model: "" Number of chains: 32 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: 62281 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2901, 62281 Classifications: {'RNA': 2901} Modifications used: {'rna2p_pur': 282, 'rna2p_pyr': 148, 'rna3p_pur': 1393, 'rna3p_pyr': 1078} Link IDs: {'rna2p': 430, 'rna3p': 2470} 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} Chain: "M" Number of atoms: 1621 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 1621 Classifications: {'RNA': 76} Modifications used: {'rna2p_pur': 8, 'rna2p_pyr': 4, 'rna3p_pur': 30, 'rna3p_pyr': 34} Link IDs: {'rna2p': 11, 'rna3p': 64} Chain: "z" Number of atoms: 16 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 16 Classifications: {'peptide': 3} Link IDs: {'PTRANS': 1, 'TRANS': 1} Time building chain proxies: 36.28, per 1000 atoms: 0.40 Number of scatterers: 90507 At special positions: 0 Unit cell: (200.725, 209.405, 224.595, 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 3095 15.00 O 25742 8.00 N 16862 7.00 C 44734 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=2.04 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: 36.86 Conformation dependent library (CDL) restraints added in 3.7 seconds 6066 Ramachandran restraints generated. 3033 Oldfield, 0 Emsley, 3033 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5632 Finding SS restraints... Secondary structure from input PDB file: 89 helices and 45 sheets defined 30.1% alpha, 21.9% beta 1017 base pairs and 1627 stacking pairs defined. Time for finding SS restraints: 36.00 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 9 Processing helix chain '1' and resid 10 through 34 Processing helix chain '1' and resid 41 through 61 removed outlier: 3.576A pdb=" N GLN 1 45 " --> pdb=" O HIS 1 41 " (cutoff:3.500A) Processing helix chain '2' and resid 17 through 28 Processing helix chain '2' and resid 41 through 51 removed outlier: 3.601A pdb=" N VAL 2 51 " --> pdb=" O MET 2 47 " (cutoff:3.500A) 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 22 Processing helix chain '6' and resid 24 through 38 Processing helix chain '7' and resid 7 through 12 removed outlier: 3.556A pdb=" N LYS 7 12 " --> pdb=" O ARG 7 8 " (cutoff:3.500A) Processing helix chain '7' and resid 37 through 44 Processing helix chain '7' and resid 51 through 62 removed outlier: 4.320A pdb=" N GLY 7 56 " --> pdb=" O LYS 7 52 " (cutoff:3.500A) removed outlier: 4.582A 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 133 through 135 No H-bonds generated for 'chain 'c' and resid 133 through 135' Processing helix chain 'c' and resid 197 through 203 removed outlier: 4.132A pdb=" N MET c 201 " --> pdb=" O ALA c 198 " (cutoff:3.500A) Processing helix chain 'c' and resid 207 through 213 removed outlier: 3.841A 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 61 through 72 removed outlier: 3.700A 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 38 Processing helix chain 'e' and resid 97 through 115 Processing helix chain 'e' and resid 130 through 141 removed outlier: 3.521A 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 removed outlier: 3.501A pdb=" N PHE e 183 " --> pdb=" O SER e 179 " (cutoff:3.500A) Processing helix chain 'e' and resid 190 through 201 Processing helix chain 'f' and resid 3 through 12 Processing helix chain 'f' and resid 12 through 21 Processing helix chain 'f' and resid 24 through 28 Processing helix chain 'f' and resid 40 through 45 removed outlier: 3.960A pdb=" N ILE f 44 " --> pdb=" O GLY f 41 " (cutoff:3.500A) Processing helix chain 'f' and resid 47 through 61 Processing helix chain 'f' and resid 93 through 106 Processing helix chain 'f' and resid 107 through 111 Processing helix chain 'f' and resid 134 through 138 removed outlier: 3.999A 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 removed outlier: 3.527A pdb=" N GLN g 64 " --> pdb=" O ASP g 60 " (cutoff:3.500A) Processing helix chain 'g' and resid 137 through 151 removed outlier: 3.756A pdb=" N TYR g 151 " --> pdb=" O ASP g 147 " (cutoff:3.500A) Processing helix chain 'j' and resid 24 through 38 removed outlier: 3.904A pdb=" N GLU j 31 " --> pdb=" O ARG j 27 " (cutoff:3.500A) Processing helix chain 'j' and resid 58 through 62 removed outlier: 3.666A 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 108 removed outlier: 4.369A pdb=" N VAL j 100 " --> pdb=" O ARG j 96 " (cutoff:3.500A) removed outlier: 4.336A pdb=" N ILE j 101 " --> pdb=" O PRO j 97 " (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: 3.545A 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: 3.995A pdb=" N ALA l 83 " --> pdb=" O SER l 80 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N VAL l 85 " --> pdb=" O LEU l 82 " (cutoff:3.500A) removed outlier: 4.239A 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 43 through 57 removed outlier: 3.576A pdb=" N VAL m 57 " --> pdb=" O MET m 53 " (cutoff:3.500A) Processing helix chain 'm' and resid 109 through 122 removed outlier: 3.579A pdb=" N ALA m 122 " --> pdb=" O LYS m 118 " (cutoff:3.500A) 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 82 Processing helix chain 'n' and resid 82 through 87 Processing helix chain 'o' and resid 3 through 22 removed outlier: 4.498A pdb=" N ARG o 13 " --> pdb=" O ARG o 9 " (cutoff:3.500A) removed outlier: 5.187A pdb=" N ALA o 14 " --> pdb=" O ARG o 10 " (cutoff:3.500A) Processing helix chain 'o' and resid 55 through 62 removed outlier: 4.115A pdb=" N GLN o 61 " --> pdb=" O ALA o 57 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N LEU o 62 " --> pdb=" O ILE o 58 " (cutoff:3.500A) Processing helix chain 'o' and resid 67 through 85 removed outlier: 3.576A 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 21 removed outlier: 3.744A 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 71 removed outlier: 3.821A pdb=" N GLN q 37 " --> pdb=" O ARG q 33 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N ARG q 51 " --> pdb=" O TYR q 47 " (cutoff:3.500A) removed outlier: 4.231A 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 removed outlier: 3.581A pdb=" N VAL q 100 " --> pdb=" O ALA q 96 " (cutoff:3.500A) Processing helix chain 'q' and resid 102 through 118 Processing helix chain 's' and resid 13 through 25 removed outlier: 3.777A pdb=" N VAL s 20 " --> pdb=" O LYS s 16 " (cutoff:3.500A) removed outlier: 4.173A pdb=" N LEU s 23 " --> pdb=" O LEU s 19 " (cutoff:3.500A) removed outlier: 4.076A pdb=" N ILE s 24 " --> pdb=" O VAL s 20 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N ARG s 25 " --> pdb=" O ALA s 21 " (cutoff:3.500A) Processing helix chain 's' and resid 28 through 38 Processing helix chain 's' and resid 41 through 62 removed outlier: 4.003A pdb=" N VAL s 45 " --> pdb=" O LYS s 41 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N LEU s 46 " --> pdb=" O LYS s 42 " (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 9 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 helix chain 'w' and resid 52 through 58 removed outlier: 6.495A pdb=" N GLU w 55 " --> pdb=" O ALA w 52 " (cutoff:3.500A) 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: 3.668A pdb=" N LYS 2 6 " --> pdb=" O GLU 2 58 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain '3' and resid 29 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 4 removed outlier: 5.961A pdb=" N LYS 8 2 " --> pdb=" O ARG 8 36 " (cutoff:3.500A) removed outlier: 5.181A pdb=" N ILE 8 23 " --> pdb=" O GLN 8 37 " (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 36 Processing sheet with id=AB2, first strand: chain 'c' and resid 101 through 105 removed outlier: 6.741A pdb=" N ILE c 91 " --> pdb=" O LEU c 81 " (cutoff:3.500A) removed outlier: 4.669A pdb=" N LEU c 81 " --> pdb=" O ILE c 91 " (cutoff:3.500A) removed outlier: 6.782A 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: 5.932A pdb=" N ILE c 164 " --> pdb=" O ARG c 175 " (cutoff:3.500A) removed outlier: 6.655A pdb=" N ARG c 175 " --> pdb=" O ILE c 164 " (cutoff:3.500A) removed outlier: 6.884A pdb=" N LYS c 183 " --> pdb=" O ILE c 267 " (cutoff:3.500A) removed outlier: 6.158A 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: 5.893A pdb=" N VAL c 144 " --> pdb=" O GLN c 153 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'd' and resid 4 through 15 removed outlier: 6.601A pdb=" N VAL d 26 " --> pdb=" O VAL d 9 " (cutoff:3.500A) removed outlier: 4.566A pdb=" N MET d 11 " --> pdb=" O VAL d 24 " (cutoff:3.500A) removed outlier: 6.786A pdb=" N VAL d 24 " --> pdb=" O MET d 11 " (cutoff:3.500A) removed outlier: 4.396A pdb=" N ARG d 13 " --> pdb=" O ILE d 22 " (cutoff:3.500A) removed outlier: 6.324A pdb=" N ILE d 22 " --> pdb=" O ARG d 13 " (cutoff:3.500A) removed outlier: 6.894A pdb=" N LEU d 186 " --> pdb=" O VAL d 180 " (cutoff:3.500A) removed outlier: 4.745A pdb=" N VAL d 180 " --> pdb=" O LEU d 186 " (cutoff:3.500A) removed outlier: 6.631A pdb=" N LEU d 188 " --> pdb=" O VAL d 178 " (cutoff:3.500A) removed outlier: 4.487A pdb=" N ASP d 176 " --> pdb=" O LYS d 190 " (cutoff:3.500A) removed outlier: 5.772A pdb=" N VAL d 107 " --> pdb=" O SER d 174 " (cutoff:3.500A) removed outlier: 4.676A pdb=" N THR d 112 " --> pdb=" O ASP d 200 " (cutoff:3.500A) removed outlier: 7.159A pdb=" N ASP d 200 " --> pdb=" O THR d 112 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'd' and resid 80 through 83 removed outlier: 6.559A pdb=" N ALA d 47 " --> pdb=" O VAL d 37 " (cutoff:3.500A) removed outlier: 4.737A pdb=" N VAL d 37 " --> pdb=" O ALA d 47 " (cutoff:3.500A) removed outlier: 6.567A pdb=" N GLN d 49 " --> pdb=" O THR d 35 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'd' and resid 117 through 119 removed outlier: 3.601A pdb=" N GLY d 117 " --> pdb=" O MET d 165 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'e' and resid 2 through 4 Processing sheet with id=AB9, first strand: chain 'e' and resid 118 through 121 removed outlier: 6.088A pdb=" N ILE e 119 " --> pdb=" O MET e 188 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'f' and resid 66 through 69 removed outlier: 3.684A pdb=" N GLY f 86 " --> pdb=" O THR f 68 " (cutoff:3.500A) removed outlier: 6.998A pdb=" N THR f 157 " --> pdb=" O GLU f 32 " (cutoff:3.500A) removed outlier: 4.359A pdb=" N ILE f 34 " --> pdb=" O THR f 155 " (cutoff:3.500A) removed outlier: 6.433A pdb=" N THR f 155 " --> pdb=" O ILE f 34 " (cutoff:3.500A) removed outlier: 4.376A pdb=" N LEU f 36 " --> pdb=" O ASP f 153 " (cutoff:3.500A) removed outlier: 6.381A pdb=" N ASP f 153 " --> pdb=" O LEU f 36 " (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: 4.010A pdb=" N VAL g 23 " --> pdb=" O ASN g 20 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'g' and resid 122 through 124 Processing sheet with id=AC5, first strand: chain 'g' and resid 95 through 99 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 Processing sheet with id=AC8, first strand: chain 'j' and resid 73 through 77 Processing sheet with id=AC9, first strand: chain 'k' and resid 7 through 10 removed outlier: 3.684A pdb=" N VAL k 10 " --> pdb=" O ARG k 17 " (cutoff:3.500A) removed outlier: 6.657A pdb=" N ARG k 17 " --> pdb=" O VAL k 10 " (cutoff:3.500A) removed outlier: 6.572A pdb=" N ALA k 16 " --> pdb=" O ALA k 46 " (cutoff:3.500A) removed outlier: 6.205A pdb=" N ALA k 46 " --> pdb=" O ALA k 16 " (cutoff:3.500A) removed outlier: 6.180A pdb=" N ARG k 18 " --> pdb=" O LYS k 44 " (cutoff:3.500A) removed outlier: 6.527A pdb=" N LYS k 40 " --> pdb=" O ILE k 22 " (cutoff:3.500A) removed outlier: 5.854A pdb=" N VAL k 24 " --> pdb=" O ILE k 38 " (cutoff:3.500A) removed outlier: 8.364A pdb=" N ILE k 38 " --> pdb=" O VAL k 24 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N LYS k 59 " --> pdb=" O LEU k 87 " (cutoff:3.500A) removed outlier: 6.485A pdb=" N ALA k 83 " --> pdb=" O VAL k 63 " (cutoff:3.500A) removed outlier: 8.219A pdb=" N CYS k 84 " --> pdb=" O MET k 7 " (cutoff:3.500A) removed outlier: 6.486A pdb=" N ASN k 9 " --> pdb=" O CYS k 84 " (cutoff:3.500A) removed outlier: 7.466A 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: 3.747A pdb=" N ALA p 49 " --> pdb=" O THR p 60 " (cutoff:3.500A) removed outlier: 6.617A pdb=" N ARG p 62 " --> pdb=" O VAL p 47 " (cutoff:3.500A) removed outlier: 5.675A pdb=" N VAL p 47 " --> pdb=" O ARG p 62 " (cutoff:3.500A) removed outlier: 8.603A pdb=" N ILE p 64 " --> pdb=" O GLY p 45 " (cutoff:3.500A) removed outlier: 8.412A pdb=" N GLY p 45 " --> pdb=" O ILE p 64 " (cutoff:3.500A) removed outlier: 6.514A pdb=" N THR p 25 " --> pdb=" O LYS p 87 " (cutoff:3.500A) removed outlier: 6.565A pdb=" N TRP p 31 " --> pdb=" O VAL p 81 " (cutoff:3.500A) removed outlier: 6.789A 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 removed outlier: 6.314A pdb=" N VAL l 90 " --> pdb=" O ARG l 123 " (cutoff:3.500A) removed outlier: 7.507A pdb=" N VAL l 122 " --> pdb=" O GLU l 143 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD3 Processing sheet with id=AD4, first strand: chain 'm' and resid 62 through 65 removed outlier: 6.600A pdb=" N LEU m 33 " --> pdb=" O LEU m 102 " (cutoff:3.500A) removed outlier: 4.397A pdb=" N GLU m 104 " --> pdb=" O PHE m 31 " (cutoff:3.500A) removed outlier: 6.639A pdb=" N PHE m 31 " --> pdb=" O GLU m 104 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'm' and resid 39 through 42 removed outlier: 6.888A pdb=" N ILE m 73 " --> pdb=" O GLU m 90 " (cutoff:3.500A) removed outlier: 4.521A pdb=" N TRP m 92 " --> pdb=" O LYS m 71 " (cutoff:3.500A) removed outlier: 6.188A pdb=" N LYS m 71 " --> pdb=" O TRP m 92 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'n' and resid 33 through 37 removed outlier: 5.570A 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: 6.752A pdb=" N VAL o 39 " --> pdb=" O LEU o 48 " (cutoff:3.500A) removed outlier: 4.558A pdb=" N ALA o 50 " --> pdb=" O ALA o 37 " (cutoff:3.500A) removed outlier: 6.921A pdb=" N ALA o 37 " --> pdb=" O ALA o 50 " (cutoff:3.500A) removed outlier: 4.677A pdb=" N SER o 52 " --> pdb=" O ILE o 35 " (cutoff:3.500A) removed outlier: 7.001A pdb=" N ILE o 35 " --> pdb=" O SER o 52 " (cutoff:3.500A) removed outlier: 6.172A pdb=" N LEU o 26 " --> pdb=" O ASP o 93 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'r' and resid 11 through 15 removed outlier: 3.770A pdb=" N MET r 40 " --> pdb=" O VAL r 4 " (cutoff:3.500A) removed outlier: 7.680A pdb=" N GLN r 6 " --> pdb=" O VAL r 38 " (cutoff:3.500A) removed outlier: 7.103A pdb=" N VAL r 38 " --> pdb=" O GLN r 6 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'r' and resid 19 through 23 removed outlier: 6.733A pdb=" N PHE r 93 " --> pdb=" O HIS r 66 " (cutoff:3.500A) removed outlier: 4.652A pdb=" N HIS r 66 " --> pdb=" O PHE r 93 " (cutoff:3.500A) removed outlier: 6.587A pdb=" N ASP r 95 " --> pdb=" O VAL r 64 " (cutoff:3.500A) removed outlier: 6.525A pdb=" N LYS r 60 " --> pdb=" O THR r 99 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'r' and resid 72 through 78 removed outlier: 4.267A pdb=" N TYR r 83 " --> pdb=" O ARG r 78 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 's' and resid 2 through 10 removed outlier: 5.607A pdb=" N SER s 101 " --> pdb=" O HIS s 9 " (cutoff:3.500A) removed outlier: 6.296A pdb=" N HIS s 102 " --> pdb=" O VAL s 76 " (cutoff:3.500A) removed outlier: 4.405A pdb=" N VAL s 76 " --> pdb=" O HIS s 102 " (cutoff:3.500A) removed outlier: 7.018A pdb=" N THR s 104 " --> pdb=" O ILE s 74 " (cutoff:3.500A) removed outlier: 4.449A pdb=" N ILE s 74 " --> pdb=" O THR s 104 " (cutoff:3.500A) removed outlier: 6.821A pdb=" N VAL s 106 " --> pdb=" O THR s 72 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 's' and resid 82 through 87 Processing sheet with id=AE4, first strand: chain 't' and resid 11 through 14 removed outlier: 3.828A pdb=" N LYS t 74 " --> pdb=" O VAL t 34 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'u' and resid 54 through 55 removed outlier: 6.616A pdb=" N LYS u 33 " --> pdb=" O VAL u 28 " (cutoff:3.500A) removed outlier: 4.791A pdb=" N VAL u 28 " --> pdb=" O LYS u 33 " (cutoff:3.500A) removed outlier: 6.546A pdb=" N ILE u 35 " --> pdb=" O LYS u 26 " (cutoff:3.500A) removed outlier: 5.950A pdb=" N GLU u 10 " --> pdb=" O PHE u 62 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N ILE u 61 " --> pdb=" O ASP u 70 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'u' and resid 72 through 76 Processing sheet with id=AE7, first strand: chain 'w' and resid 3 through 8 removed outlier: 7.932A pdb=" N ASN w 5 " --> pdb=" O ASP w 43 " (cutoff:3.500A) removed outlier: 4.919A pdb=" N ASP w 43 " --> pdb=" O ASN w 5 " (cutoff:3.500A) removed outlier: 8.990A pdb=" N LYS w 25 " --> pdb=" O GLN w 87 " (cutoff:3.500A) removed outlier: 9.856A pdb=" N ILE w 89 " --> pdb=" O LYS w 25 " (cutoff:3.500A) removed outlier: 8.471A pdb=" N PHE w 91 " --> pdb=" O PRO w 27 " (cutoff:3.500A) removed outlier: 6.303A pdb=" N ILE w 29 " --> pdb=" O PHE w 91 " (cutoff:3.500A) removed outlier: 7.272A pdb=" N ARG w 93 " --> pdb=" O ILE w 29 " (cutoff:3.500A) removed outlier: 7.377A pdb=" N TYR w 31 " --> pdb=" O ARG w 93 " (cutoff:3.500A) removed outlier: 6.566A pdb=" N GLN w 78 " --> pdb=" O GLN w 87 " (cutoff:3.500A) removed outlier: 4.451A pdb=" N ILE w 89 " --> pdb=" O ASP w 76 " (cutoff:3.500A) removed outlier: 6.407A pdb=" N ASP w 76 " --> pdb=" O ILE w 89 " (cutoff:3.500A) removed outlier: 6.695A pdb=" N PHE w 91 " --> pdb=" O ALA w 74 " (cutoff:3.500A) removed outlier: 6.897A pdb=" N ALA w 74 " --> pdb=" O PHE w 91 " (cutoff:3.500A) removed outlier: 6.842A pdb=" N ARG w 93 " --> pdb=" O VAL w 72 " (cutoff:3.500A) removed outlier: 6.357A pdb=" N VAL w 72 " --> pdb=" O ARG w 93 " (cutoff:3.500A) removed outlier: 6.735A pdb=" N ILE w 4 " --> pdb=" O VAL w 64 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'y' and resid 22 through 23 removed outlier: 6.787A pdb=" N LEU y 59 " --> pdb=" O ILE y 37 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'y' and resid 30 through 31 935 hydrogen bonds defined for protein. 2529 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 2548 hydrogen bonds 3974 hydrogen bond angles 0 basepair planarities 1017 basepair parallelities 1627 stacking parallelities Total time for adding SS restraints: 172.51 Time building geometry restraints manager: 39.89 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 10498 1.32 - 1.44: 42908 1.44 - 1.57: 39068 1.57 - 1.69: 6187 1.69 - 1.81: 135 Bond restraints: 98796 Sorted by residual: bond pdb=" O3' G b1737 " pdb=" P G b1738 " ideal model delta sigma weight residual 1.607 1.667 -0.060 1.50e-02 4.44e+03 1.60e+01 bond pdb=" O3' C b1072 " pdb=" P A b1073 " ideal model delta sigma weight residual 1.607 1.661 -0.054 1.50e-02 4.44e+03 1.28e+01 bond pdb=" O3' C M 74 " pdb=" P C M 75 " ideal model delta sigma weight residual 1.607 1.658 -0.051 1.50e-02 4.44e+03 1.15e+01 bond pdb=" O3' U b 702 " pdb=" P U b 703 " ideal model delta sigma weight residual 1.607 1.657 -0.050 1.50e-02 4.44e+03 1.12e+01 bond pdb=" N ILE q 90 " pdb=" CA ILE q 90 " ideal model delta sigma weight residual 1.458 1.497 -0.039 1.17e-02 7.31e+03 1.11e+01 ... (remaining 98791 not shown) Histogram of bond angle deviations from ideal: 96.93 - 104.38: 13132 104.38 - 111.84: 54270 111.84 - 119.29: 34959 119.29 - 126.74: 37657 126.74 - 134.19: 8724 Bond angle restraints: 148742 Sorted by residual: angle pdb=" O3' G b2864 " pdb=" C3' G b2864 " pdb=" C2' G b2864 " ideal model delta sigma weight residual 113.70 127.20 -13.50 1.50e+00 4.44e-01 8.10e+01 angle pdb=" O3' U b2832 " pdb=" C3' U b2832 " pdb=" C2' U b2832 " ideal model delta sigma weight residual 109.50 121.60 -12.10 1.50e+00 4.44e-01 6.51e+01 angle pdb=" O3' A b1626 " pdb=" C3' A b1626 " pdb=" C2' A b1626 " ideal model delta sigma weight residual 113.70 125.36 -11.66 1.50e+00 4.44e-01 6.05e+01 angle pdb=" O3' U b 390 " pdb=" C3' U b 390 " pdb=" C2' U b 390 " ideal model delta sigma weight residual 109.50 121.06 -11.56 1.50e+00 4.44e-01 5.94e+01 angle pdb=" C4' G b2375 " pdb=" C3' G b2375 " pdb=" O3' G b2375 " ideal model delta sigma weight residual 109.40 120.18 -10.78 1.50e+00 4.44e-01 5.16e+01 ... (remaining 148737 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.78: 54301 35.78 - 71.56: 8162 71.56 - 107.34: 867 107.34 - 143.12: 17 143.12 - 178.90: 23 Dihedral angle restraints: 63370 sinusoidal: 54619 harmonic: 8751 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 25.72 174.28 1 1.50e+01 4.44e-03 8.51e+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 34.03 165.97 1 1.50e+01 4.44e-03 8.41e+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 52.39 147.61 1 1.50e+01 4.44e-03 7.87e+01 ... (remaining 63367 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.161: 17565 0.161 - 0.322: 1549 0.322 - 0.482: 20 0.482 - 0.643: 6 0.643 - 0.804: 3 Chirality restraints: 19143 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 -1.94 -0.80 2.00e-01 2.50e+01 1.62e+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 -2.02 -0.72 2.00e-01 2.50e+01 1.31e+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 19140 not shown) Planarity restraints: 7297 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' C b 417 " 0.046 2.00e-02 2.50e+03 2.29e-02 1.18e+01 pdb=" N1 C b 417 " -0.045 2.00e-02 2.50e+03 pdb=" C2 C b 417 " -0.013 2.00e-02 2.50e+03 pdb=" O2 C b 417 " -0.001 2.00e-02 2.50e+03 pdb=" N3 C b 417 " 0.001 2.00e-02 2.50e+03 pdb=" C4 C b 417 " 0.012 2.00e-02 2.50e+03 pdb=" N4 C b 417 " 0.012 2.00e-02 2.50e+03 pdb=" C5 C b 417 " -0.001 2.00e-02 2.50e+03 pdb=" C6 C b 417 " -0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLU g 81 " 0.016 2.00e-02 2.50e+03 3.35e-02 1.12e+01 pdb=" CD GLU g 81 " -0.058 2.00e-02 2.50e+03 pdb=" OE1 GLU g 81 " 0.021 2.00e-02 2.50e+03 pdb=" OE2 GLU g 81 " 0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' G b2405 " -0.045 2.00e-02 2.50e+03 1.93e-02 1.11e+01 pdb=" N9 G b2405 " 0.045 2.00e-02 2.50e+03 pdb=" C8 G b2405 " 0.005 2.00e-02 2.50e+03 pdb=" N7 G b2405 " -0.003 2.00e-02 2.50e+03 pdb=" C5 G b2405 " 0.003 2.00e-02 2.50e+03 pdb=" C6 G b2405 " -0.004 2.00e-02 2.50e+03 pdb=" O6 G b2405 " -0.011 2.00e-02 2.50e+03 pdb=" N1 G b2405 " -0.009 2.00e-02 2.50e+03 pdb=" C2 G b2405 " 0.004 2.00e-02 2.50e+03 pdb=" N2 G b2405 " -0.001 2.00e-02 2.50e+03 pdb=" N3 G b2405 " 0.010 2.00e-02 2.50e+03 pdb=" C4 G b2405 " 0.005 2.00e-02 2.50e+03 ... (remaining 7294 not shown) Histogram of nonbonded interaction distances: 2.14 - 2.69: 7098 2.69 - 3.24: 73354 3.24 - 3.80: 193890 3.80 - 4.35: 255968 4.35 - 4.90: 325001 Nonbonded interactions: 855311 Sorted by model distance: nonbonded pdb=" OD1 ASN d 149 " pdb=" N GLN d 150 " model vdw 2.140 2.520 nonbonded pdb=" N GLU e 122 " pdb=" OE1 GLU e 122 " model vdw 2.166 2.520 nonbonded pdb=" O SER n 119 " pdb=" OG SER n 119 " model vdw 2.181 2.440 nonbonded pdb=" OD1 ASP h 7 " pdb=" N LYS h 8 " model vdw 2.185 2.520 nonbonded pdb=" O2' G b2304 " pdb=" OD1 ASP f 153 " model vdw 2.201 2.440 ... (remaining 855306 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: 4.230 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: 0.090 Extract box with map and model: 13.220 Check model and map are aligned: 1.070 Set scattering table: 0.650 Process input model: 343.790 Find NCS groups from input model: 1.460 Set up NCS constraints: 0.210 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: 0.020 Load rotamer database and sin/cos tables:12.290 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 377.030 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8377 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 : 0.009 0.066 98796 Z= 0.555 Angle : 0.934 13.499 148742 Z= 0.574 Chirality : 0.083 0.804 19143 Planarity : 0.005 0.052 7297 Dihedral : 24.803 178.899 57735 Min Nonbonded Distance : 2.140 Molprobity Statistics. All-atom Clashscore : 5.42 Ramachandran Plot: Outliers : 0.23 % Allowed : 5.01 % Favored : 94.76 % Rotamer: Outliers : 3.67 % Allowed : 37.38 % Favored : 58.95 % Cbeta Deviations : 0.07 % 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: -0.70 (0.15), residues: 3033 helix: 0.50 (0.18), residues: 802 sheet: -0.48 (0.20), residues: 673 loop : -0.92 (0.15), residues: 1558 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.003 TRP p 31 HIS 0.011 0.002 HIS c 53 PHE 0.030 0.003 PHE q 57 TYR 0.021 0.002 TYR s 38 ARG 0.016 0.002 ARG f 178 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6066 Ramachandran restraints generated. 3033 Oldfield, 0 Emsley, 3033 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6066 Ramachandran restraints generated. 3033 Oldfield, 0 Emsley, 3033 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 903 residues out of total 2507 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 92 poor density : 811 time to evaluate : 3.779 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 49 ASP cc_start: 0.8155 (m-30) cc_final: 0.7912 (m-30) REVERT: c 111 LYS cc_start: 0.8781 (pttp) cc_final: 0.7940 (pttp) REVERT: c 114 ASP cc_start: 0.8441 (m-30) cc_final: 0.8220 (m-30) REVERT: c 187 ASP cc_start: 0.8371 (m-30) cc_final: 0.8122 (m-30) REVERT: f 34 ILE cc_start: 0.9098 (mt) cc_final: 0.8873 (mm) REVERT: f 38 MET cc_start: 0.8630 (mtp) cc_final: 0.8059 (mtp) REVERT: f 40 VAL cc_start: 0.8741 (t) cc_final: 0.8498 (p) REVERT: f 64 LYS cc_start: 0.8297 (ptmt) cc_final: 0.7078 (pttt) REVERT: f 81 GLN cc_start: 0.8677 (tm-30) cc_final: 0.8296 (tm-30) REVERT: f 112 ARG cc_start: 0.8859 (ttm-80) cc_final: 0.8406 (tpt170) REVERT: f 133 ARG cc_start: 0.8078 (ttm-80) cc_final: 0.7764 (mpt180) REVERT: f 159 THR cc_start: 0.8968 (m) cc_final: 0.8376 (p) REVERT: f 161 LYS cc_start: 0.8896 (ptpp) cc_final: 0.8656 (ptpp) REVERT: g 6 LYS cc_start: 0.9103 (mmtp) cc_final: 0.8738 (mptt) REVERT: g 158 LYS cc_start: 0.9028 (mtpt) cc_final: 0.8820 (mttt) REVERT: j 52 ASP cc_start: 0.8863 (m-30) cc_final: 0.8646 (m-30) REVERT: j 58 ASN cc_start: 0.9140 (m-40) cc_final: 0.8865 (m-40) REVERT: j 95 ARG cc_start: 0.8171 (ttp-110) cc_final: 0.7638 (mtm110) REVERT: j 103 ILE cc_start: 0.9039 (OUTLIER) cc_final: 0.8816 (mt) REVERT: k 56 ASP cc_start: 0.8184 (m-30) cc_final: 0.7928 (m-30) REVERT: k 73 ASP cc_start: 0.8763 (p0) cc_final: 0.8370 (p0) REVERT: k 100 PHE cc_start: 0.9124 (m-80) cc_final: 0.8888 (m-80) REVERT: k 104 THR cc_start: 0.9285 (p) cc_final: 0.8965 (m) REVERT: k 106 GLU cc_start: 0.8622 (mp0) cc_final: 0.7615 (mp0) REVERT: p 11 GLU cc_start: 0.8006 (mt-10) cc_final: 0.7736 (mt-10) REVERT: p 13 MET cc_start: 0.8563 (mtm) cc_final: 0.8158 (mtm) REVERT: p 38 LYS cc_start: 0.8789 (ttpt) cc_final: 0.8460 (ttpp) REVERT: p 66 ASN cc_start: 0.8972 (m110) cc_final: 0.8762 (m-40) REVERT: q 109 LEU cc_start: 0.9189 (mt) cc_final: 0.8925 (mt) REVERT: t 42 GLU cc_start: 0.8617 (OUTLIER) cc_final: 0.8403 (mt-10) REVERT: y 68 LYS cc_start: 0.8919 (tttm) cc_final: 0.8564 (mmmm) outliers start: 92 outliers final: 10 residues processed: 857 average time/residue: 1.7445 time to fit residues: 2013.2516 Evaluate side-chains 664 residues out of total 2507 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 652 time to evaluate : 3.988 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 12 GLU Chi-restraints excluded: chain 1 residue 13 GLU Chi-restraints excluded: chain g residue 24 ILE Chi-restraints excluded: chain h residue 15 LEU Chi-restraints excluded: chain j residue 21 THR Chi-restraints excluded: chain j residue 30 THR Chi-restraints excluded: chain j residue 103 ILE Chi-restraints excluded: chain l residue 77 ILE Chi-restraints excluded: chain l residue 121 THR Chi-restraints excluded: chain r residue 49 ILE Chi-restraints excluded: chain t residue 42 GLU Chi-restraints excluded: chain y residue 43 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 604 random chunks: chunk 510 optimal weight: 9.9990 chunk 457 optimal weight: 1.9990 chunk 254 optimal weight: 10.0000 chunk 156 optimal weight: 30.0000 chunk 308 optimal weight: 10.0000 chunk 244 optimal weight: 10.0000 chunk 473 optimal weight: 5.9990 chunk 183 optimal weight: 10.0000 chunk 287 optimal weight: 10.0000 chunk 352 optimal weight: 5.9990 chunk 548 optimal weight: 6.9990 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 3 4 GLN 3 42 HIS 4 26 ASN ** 6 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 6 29 GLN c 226 ASN c 251 GLN d 36 GLN d 42 ASN e 115 GLN e 165 HIS h 20 ASN ** j 77 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** k 93 GLN l 35 HIS ** o 34 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** o 38 GLN o 43 ASN o 67 ASN p 12 GLN p 75 GLN q 20 GLN ** q 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** r 18 GLN u 27 ASN w 12 GLN y 76 ASN Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8507 moved from start: 0.2419 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.059 98796 Z= 0.291 Angle : 0.623 8.515 148742 Z= 0.324 Chirality : 0.038 0.318 19143 Planarity : 0.005 0.046 7297 Dihedral : 24.113 179.438 51707 Min Nonbonded Distance : 2.037 Molprobity Statistics. All-atom Clashscore : 9.58 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.48 % Favored : 95.42 % Rotamer: Outliers : 7.10 % Allowed : 31.55 % Favored : 61.35 % 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: 3033 helix: 0.93 (0.18), residues: 821 sheet: -0.31 (0.20), residues: 660 loop : -0.68 (0.15), residues: 1552 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP 0 39 HIS 0.006 0.001 HIS o 34 PHE 0.024 0.002 PHE u 85 TYR 0.018 0.002 TYR f 83 ARG 0.016 0.001 ARG f 167 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6066 Ramachandran restraints generated. 3033 Oldfield, 0 Emsley, 3033 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6066 Ramachandran restraints generated. 3033 Oldfield, 0 Emsley, 3033 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 867 residues out of total 2507 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 178 poor density : 689 time to evaluate : 3.786 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: 0 77 LYS cc_start: 0.8827 (mmmt) cc_final: 0.8568 (tptp) REVERT: 1 16 THR cc_start: 0.9448 (p) cc_final: 0.9147 (p) REVERT: 1 45 GLN cc_start: 0.8700 (tt0) cc_final: 0.8448 (tt0) REVERT: 1 49 ASP cc_start: 0.8242 (m-30) cc_final: 0.8033 (m-30) REVERT: 3 53 LYS cc_start: 0.9160 (tptt) cc_final: 0.8930 (tptp) REVERT: c 114 ASP cc_start: 0.8514 (m-30) cc_final: 0.8249 (m-30) REVERT: d 1 MET cc_start: 0.6901 (OUTLIER) cc_final: 0.6528 (tmm) REVERT: e 111 GLU cc_start: 0.8797 (tp30) cc_final: 0.8557 (tp30) REVERT: e 115 GLN cc_start: 0.9046 (mt0) cc_final: 0.8643 (mt0) REVERT: e 136 GLN cc_start: 0.8192 (tp40) cc_final: 0.7614 (tp-100) REVERT: e 140 ASP cc_start: 0.8658 (m-30) cc_final: 0.7974 (m-30) REVERT: f 34 ILE cc_start: 0.9299 (mt) cc_final: 0.9083 (mm) REVERT: f 38 MET cc_start: 0.8633 (mtp) cc_final: 0.8227 (mtp) REVERT: f 64 LYS cc_start: 0.8826 (ptmt) cc_final: 0.7605 (pttt) REVERT: f 81 GLN cc_start: 0.8692 (tm-30) cc_final: 0.8341 (tm-30) REVERT: f 112 ARG cc_start: 0.8894 (ttm-80) cc_final: 0.8423 (tpt170) REVERT: f 133 ARG cc_start: 0.8115 (ttm-80) cc_final: 0.7819 (mpt180) REVERT: g 6 LYS cc_start: 0.9096 (mmtp) cc_final: 0.8704 (mmtt) REVERT: g 158 LYS cc_start: 0.9054 (mtpt) cc_final: 0.8718 (mttt) REVERT: j 53 TYR cc_start: 0.9270 (m-80) cc_final: 0.8910 (m-80) REVERT: j 58 ASN cc_start: 0.9298 (m-40) cc_final: 0.9082 (m-40) REVERT: k 20 MET cc_start: 0.8981 (ttm) cc_final: 0.8649 (ttm) REVERT: k 106 GLU cc_start: 0.9014 (mp0) cc_final: 0.8613 (mp0) REVERT: m 22 GLN cc_start: 0.8421 (OUTLIER) cc_final: 0.8200 (mm-40) REVERT: m 115 GLU cc_start: 0.8254 (OUTLIER) cc_final: 0.8033 (tm-30) REVERT: o 34 HIS cc_start: 0.8850 (m170) cc_final: 0.8593 (m90) REVERT: p 6 LYS cc_start: 0.9122 (OUTLIER) cc_final: 0.8203 (mtmt) REVERT: p 10 GLN cc_start: 0.8519 (tp40) cc_final: 0.8191 (mp10) REVERT: p 52 ASN cc_start: 0.8963 (OUTLIER) cc_final: 0.8725 (p0) REVERT: p 68 GLU cc_start: 0.8220 (OUTLIER) cc_final: 0.7190 (pm20) REVERT: q 84 LYS cc_start: 0.8502 (ttmm) cc_final: 0.8236 (mttt) REVERT: q 89 GLU cc_start: 0.6941 (tm-30) cc_final: 0.6481 (tm-30) REVERT: r 11 GLN cc_start: 0.8890 (mt0) cc_final: 0.8129 (mt0) REVERT: t 56 GLU cc_start: 0.7908 (mm-30) cc_final: 0.7602 (mm-30) REVERT: u 37 GLU cc_start: 0.7485 (mt-10) cc_final: 0.6725 (mm-30) REVERT: u 83 ARG cc_start: 0.9241 (OUTLIER) cc_final: 0.7361 (mtm-85) REVERT: y 25 ARG cc_start: 0.8460 (mmt-90) cc_final: 0.8228 (mmp80) outliers start: 178 outliers final: 74 residues processed: 791 average time/residue: 1.6810 time to fit residues: 1816.3641 Evaluate side-chains 728 residues out of total 2507 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 81 poor density : 647 time to evaluate : 3.703 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 35 SER Chi-restraints excluded: chain 1 residue 12 GLU Chi-restraints excluded: chain 1 residue 56 LEU Chi-restraints excluded: chain 2 residue 12 SER Chi-restraints excluded: chain 2 residue 41 THR Chi-restraints excluded: chain 3 residue 27 SER Chi-restraints excluded: chain 7 residue 55 LEU Chi-restraints excluded: chain 8 residue 13 ASN Chi-restraints excluded: chain 8 residue 24 ARG Chi-restraints excluded: chain 8 residue 25 VAL Chi-restraints excluded: chain 8 residue 27 CYS Chi-restraints excluded: chain c residue 88 SER Chi-restraints excluded: chain c residue 90 ASN Chi-restraints excluded: chain d residue 1 MET Chi-restraints excluded: chain d residue 40 LEU Chi-restraints excluded: chain d residue 86 GLU Chi-restraints excluded: chain d residue 94 GLN Chi-restraints excluded: chain d residue 98 VAL Chi-restraints excluded: chain d residue 151 THR Chi-restraints excluded: chain d residue 202 ILE Chi-restraints excluded: chain e residue 4 VAL Chi-restraints excluded: chain e residue 72 SER Chi-restraints excluded: chain e residue 150 THR Chi-restraints excluded: chain f residue 25 VAL Chi-restraints excluded: chain f residue 31 VAL Chi-restraints excluded: chain f residue 73 SER Chi-restraints excluded: chain f residue 74 VAL Chi-restraints excluded: chain f residue 132 VAL Chi-restraints excluded: chain g residue 9 VAL Chi-restraints excluded: chain g residue 15 VAL Chi-restraints excluded: chain g residue 34 THR Chi-restraints excluded: chain g residue 36 THR Chi-restraints excluded: chain g residue 37 LEU Chi-restraints excluded: chain g residue 44 LYS Chi-restraints excluded: chain g residue 55 ARG Chi-restraints excluded: chain g residue 127 THR Chi-restraints excluded: chain h residue 15 LEU Chi-restraints excluded: chain h residue 37 VAL Chi-restraints excluded: chain j residue 17 VAL Chi-restraints excluded: chain j residue 30 THR Chi-restraints excluded: chain j residue 43 GLU Chi-restraints excluded: chain j residue 131 ASN Chi-restraints excluded: chain k residue 76 VAL Chi-restraints excluded: chain l residue 82 LEU Chi-restraints excluded: chain l residue 121 THR Chi-restraints excluded: chain m residue 7 THR Chi-restraints excluded: chain m residue 22 GLN Chi-restraints excluded: chain m residue 115 GLU Chi-restraints excluded: chain n residue 6 SER Chi-restraints excluded: chain n residue 65 LEU Chi-restraints excluded: chain o residue 36 TYR Chi-restraints excluded: chain o residue 40 ILE Chi-restraints excluded: chain o residue 52 SER Chi-restraints excluded: chain o residue 60 GLU Chi-restraints excluded: chain o residue 90 VAL Chi-restraints excluded: chain p residue 5 ILE Chi-restraints excluded: chain p residue 6 LYS Chi-restraints excluded: chain p residue 52 ASN Chi-restraints excluded: chain p residue 68 GLU Chi-restraints excluded: chain p residue 70 VAL Chi-restraints excluded: chain p residue 76 THR Chi-restraints excluded: chain q residue 77 SER Chi-restraints excluded: chain r residue 22 LEU Chi-restraints excluded: chain r residue 49 ILE Chi-restraints excluded: chain r residue 94 THR Chi-restraints excluded: chain s residue 109 ASP Chi-restraints excluded: chain t residue 9 LYS Chi-restraints excluded: chain t residue 78 VAL Chi-restraints excluded: chain u residue 44 LYS Chi-restraints excluded: chain u residue 57 SER Chi-restraints excluded: chain u residue 72 VAL Chi-restraints excluded: chain u residue 78 ASP Chi-restraints excluded: chain u residue 83 ARG Chi-restraints excluded: chain u residue 88 ASN Chi-restraints excluded: chain u residue 92 ILE Chi-restraints excluded: chain w residue 1 MET Chi-restraints excluded: chain w residue 12 GLN Chi-restraints excluded: chain w residue 65 VAL Chi-restraints excluded: chain y residue 9 SER Chi-restraints excluded: chain y residue 10 THR Chi-restraints excluded: chain y residue 17 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 604 random chunks: chunk 304 optimal weight: 10.0000 chunk 170 optimal weight: 10.0000 chunk 456 optimal weight: 6.9990 chunk 373 optimal weight: 20.0000 chunk 151 optimal weight: 10.0000 chunk 549 optimal weight: 5.9990 chunk 593 optimal weight: 9.9990 chunk 489 optimal weight: 9.9990 chunk 544 optimal weight: 9.9990 chunk 187 optimal weight: 10.0000 chunk 440 optimal weight: 20.0000 overall best weight: 8.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 6 6 GLN ** 6 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 8 35 GLN g 38 ASN g 48 ASN ** j 77 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** k 93 GLN ** n 16 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** o 19 GLN ** o 34 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** o 38 GLN o 43 ASN p 12 GLN p 52 ASN p 75 GLN q 72 ASN ** q 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** s 57 ASN t 59 ASN w 24 ASN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8566 moved from start: 0.3300 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.066 98796 Z= 0.370 Angle : 0.621 10.076 148742 Z= 0.328 Chirality : 0.040 0.311 19143 Planarity : 0.005 0.045 7297 Dihedral : 23.954 179.808 51693 Min Nonbonded Distance : 1.994 Molprobity Statistics. All-atom Clashscore : 8.69 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.62 % Favored : 95.29 % Rotamer: Outliers : 6.86 % Allowed : 30.55 % Favored : 62.58 % 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: -0.15 (0.15), residues: 3033 helix: 1.09 (0.18), residues: 824 sheet: -0.14 (0.20), residues: 659 loop : -0.70 (0.15), residues: 1550 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.044 0.002 TRP 0 39 HIS 0.010 0.002 HIS e 165 PHE 0.022 0.002 PHE u 85 TYR 0.017 0.002 TYR m 103 ARG 0.008 0.001 ARG y 11 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6066 Ramachandran restraints generated. 3033 Oldfield, 0 Emsley, 3033 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6066 Ramachandran restraints generated. 3033 Oldfield, 0 Emsley, 3033 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 829 residues out of total 2507 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 172 poor density : 657 time to evaluate : 4.005 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 0 77 LYS cc_start: 0.8888 (mmmt) cc_final: 0.8566 (tptp) REVERT: 1 23 ARG cc_start: 0.9136 (mtt90) cc_final: 0.8656 (mtt-85) REVERT: 1 27 ASN cc_start: 0.9100 (m110) cc_final: 0.8757 (m110) REVERT: 1 45 GLN cc_start: 0.8854 (tt0) cc_final: 0.8644 (tt0) REVERT: c 157 SER cc_start: 0.9090 (m) cc_final: 0.8862 (m) REVERT: d 1 MET cc_start: 0.6959 (OUTLIER) cc_final: 0.6529 (tmm) REVERT: e 6 LYS cc_start: 0.7449 (OUTLIER) cc_final: 0.7130 (pptt) REVERT: e 69 ARG cc_start: 0.8376 (OUTLIER) cc_final: 0.6425 (ptp-170) REVERT: e 111 GLU cc_start: 0.8943 (tp30) cc_final: 0.8676 (tp30) REVERT: e 115 GLN cc_start: 0.9016 (mt0) cc_final: 0.8729 (mt0) REVERT: e 136 GLN cc_start: 0.8501 (tp40) cc_final: 0.8134 (tp40) REVERT: f 38 MET cc_start: 0.8566 (mtp) cc_final: 0.8211 (mtp) REVERT: f 42 GLU cc_start: 0.8563 (pm20) cc_final: 0.8231 (pm20) REVERT: f 64 LYS cc_start: 0.9034 (OUTLIER) cc_final: 0.7890 (pttt) REVERT: f 69 LYS cc_start: 0.9396 (mptm) cc_final: 0.9192 (mmtm) REVERT: f 81 GLN cc_start: 0.8948 (tm-30) cc_final: 0.8698 (tm-30) REVERT: f 112 ARG cc_start: 0.8890 (ttm-80) cc_final: 0.8293 (tpt170) REVERT: f 129 SER cc_start: 0.8697 (OUTLIER) cc_final: 0.8496 (t) REVERT: f 133 ARG cc_start: 0.8131 (ttm-80) cc_final: 0.7896 (tpt170) REVERT: g 6 LYS cc_start: 0.9192 (mmtp) cc_final: 0.8821 (mmtt) REVERT: g 25 THR cc_start: 0.9197 (m) cc_final: 0.8971 (m) REVERT: g 158 LYS cc_start: 0.9113 (mtpt) cc_final: 0.8892 (mttt) REVERT: j 53 TYR cc_start: 0.9320 (m-80) cc_final: 0.8907 (m-80) REVERT: k 106 GLU cc_start: 0.9180 (mp0) cc_final: 0.8917 (mp0) REVERT: k 108 ARG cc_start: 0.8664 (mtp85) cc_final: 0.8406 (ptp-110) REVERT: m 22 GLN cc_start: 0.8507 (OUTLIER) cc_final: 0.8155 (mm-40) REVERT: m 115 GLU cc_start: 0.8256 (OUTLIER) cc_final: 0.8038 (tm-30) REVERT: n 35 LYS cc_start: 0.9314 (OUTLIER) cc_final: 0.8989 (tttp) REVERT: n 110 MET cc_start: 0.8934 (mmp) cc_final: 0.8639 (mmp) REVERT: o 104 GLN cc_start: 0.8827 (tt0) cc_final: 0.8306 (tp40) REVERT: p 6 LYS cc_start: 0.9160 (OUTLIER) cc_final: 0.8277 (ttpp) REVERT: p 10 GLN cc_start: 0.8511 (tp40) cc_final: 0.8118 (mp10) REVERT: p 68 GLU cc_start: 0.8291 (OUTLIER) cc_final: 0.7478 (pm20) REVERT: s 92 ARG cc_start: 0.7895 (OUTLIER) cc_final: 0.7613 (ttp80) REVERT: t 36 LYS cc_start: 0.8779 (OUTLIER) cc_final: 0.8428 (ttmp) REVERT: u 26 LYS cc_start: 0.9046 (mmtp) cc_final: 0.8628 (mmtm) REVERT: u 51 GLU cc_start: 0.8709 (mp0) cc_final: 0.8394 (mp0) REVERT: y 25 ARG cc_start: 0.8585 (mmt-90) cc_final: 0.8311 (mmp80) outliers start: 172 outliers final: 85 residues processed: 759 average time/residue: 1.7183 time to fit residues: 1788.6457 Evaluate side-chains 721 residues out of total 2507 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 97 poor density : 624 time to evaluate : 3.746 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 35 SER Chi-restraints excluded: chain 0 residue 51 VAL Chi-restraints excluded: chain 1 residue 54 LYS Chi-restraints excluded: chain 2 residue 12 SER Chi-restraints excluded: chain 2 residue 36 VAL Chi-restraints excluded: chain 2 residue 41 THR Chi-restraints excluded: chain 3 residue 23 THR Chi-restraints excluded: chain 3 residue 27 SER Chi-restraints excluded: chain 8 residue 13 ASN Chi-restraints excluded: chain 8 residue 24 ARG Chi-restraints excluded: chain 8 residue 25 VAL Chi-restraints excluded: chain c residue 53 HIS Chi-restraints excluded: chain c residue 88 SER Chi-restraints excluded: chain c residue 90 ASN Chi-restraints excluded: chain c residue 205 LEU Chi-restraints excluded: chain d residue 1 MET Chi-restraints excluded: chain d residue 2 ILE Chi-restraints excluded: chain d residue 40 LEU Chi-restraints excluded: chain d residue 86 GLU Chi-restraints excluded: chain d residue 88 GLU Chi-restraints excluded: chain d residue 98 VAL Chi-restraints excluded: chain d residue 151 THR Chi-restraints excluded: chain d residue 181 ASP Chi-restraints excluded: chain e residue 4 VAL Chi-restraints excluded: chain e residue 6 LYS Chi-restraints excluded: chain e residue 10 SER Chi-restraints excluded: chain e residue 15 SER Chi-restraints excluded: chain e residue 69 ARG Chi-restraints excluded: chain e residue 150 THR Chi-restraints excluded: chain f residue 25 VAL Chi-restraints excluded: chain f residue 64 LYS Chi-restraints excluded: chain f residue 88 LYS Chi-restraints excluded: chain f residue 104 ILE Chi-restraints excluded: chain f residue 121 SER Chi-restraints excluded: chain f residue 129 SER Chi-restraints excluded: chain f residue 132 VAL Chi-restraints excluded: chain g residue 3 ARG Chi-restraints excluded: chain g residue 10 VAL Chi-restraints excluded: chain g residue 15 VAL Chi-restraints excluded: chain g residue 23 VAL Chi-restraints excluded: chain g residue 34 THR Chi-restraints excluded: chain g residue 36 THR Chi-restraints excluded: chain g residue 44 LYS Chi-restraints excluded: chain g residue 48 ASN Chi-restraints excluded: chain g residue 55 ARG Chi-restraints excluded: chain g residue 67 THR Chi-restraints excluded: chain g residue 92 VAL Chi-restraints excluded: chain g residue 106 SER Chi-restraints excluded: chain g residue 122 THR Chi-restraints excluded: chain g residue 127 THR Chi-restraints excluded: chain h residue 11 ASN Chi-restraints excluded: chain h residue 15 LEU Chi-restraints excluded: chain h residue 37 VAL Chi-restraints excluded: chain j residue 30 THR Chi-restraints excluded: chain j residue 131 ASN Chi-restraints excluded: chain k residue 22 ILE Chi-restraints excluded: chain k residue 76 VAL Chi-restraints excluded: chain k residue 110 GLU Chi-restraints excluded: chain l residue 82 LEU Chi-restraints excluded: chain l residue 121 THR Chi-restraints excluded: chain m residue 7 THR Chi-restraints excluded: chain m residue 22 GLN Chi-restraints excluded: chain m residue 30 SER Chi-restraints excluded: chain m residue 41 LEU Chi-restraints excluded: chain m residue 112 LEU Chi-restraints excluded: chain m residue 115 GLU Chi-restraints excluded: chain m residue 135 VAL Chi-restraints excluded: chain n residue 1 MET Chi-restraints excluded: chain n residue 6 SER Chi-restraints excluded: chain n residue 35 LYS Chi-restraints excluded: chain n residue 57 THR Chi-restraints excluded: chain n residue 98 LEU Chi-restraints excluded: chain o residue 28 VAL Chi-restraints excluded: chain o residue 95 SER Chi-restraints excluded: chain p residue 5 ILE Chi-restraints excluded: chain p residue 6 LYS Chi-restraints excluded: chain p residue 52 ASN Chi-restraints excluded: chain p residue 68 GLU Chi-restraints excluded: chain p residue 70 VAL Chi-restraints excluded: chain p residue 76 THR Chi-restraints excluded: chain q residue 77 SER Chi-restraints excluded: chain r residue 22 LEU Chi-restraints excluded: chain r residue 49 ILE Chi-restraints excluded: chain s residue 53 SER Chi-restraints excluded: chain s residue 67 ASP Chi-restraints excluded: chain s residue 92 ARG Chi-restraints excluded: chain s residue 109 ASP Chi-restraints excluded: chain t residue 36 LYS Chi-restraints excluded: chain t residue 78 VAL Chi-restraints excluded: chain t residue 79 THR Chi-restraints excluded: chain u residue 25 VAL Chi-restraints excluded: chain u residue 42 VAL Chi-restraints excluded: chain u residue 57 SER Chi-restraints excluded: chain u residue 78 ASP Chi-restraints excluded: chain w residue 65 VAL Chi-restraints excluded: chain y residue 9 SER Chi-restraints excluded: chain y residue 10 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 604 random chunks: chunk 542 optimal weight: 7.9990 chunk 413 optimal weight: 30.0000 chunk 285 optimal weight: 10.0000 chunk 60 optimal weight: 20.0000 chunk 262 optimal weight: 60.0000 chunk 368 optimal weight: 0.4980 chunk 551 optimal weight: 8.9990 chunk 583 optimal weight: 0.4980 chunk 288 optimal weight: 10.0000 chunk 522 optimal weight: 1.9990 chunk 157 optimal weight: 50.0000 overall best weight: 3.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 6 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** c 243 HIS f 127 ASN ** j 77 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** k 93 GLN o 19 GLN ** o 34 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** o 38 GLN o 43 ASN p 12 GLN p 75 GLN q 81 ASN t 48 GLN w 12 GLN w 24 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8523 moved from start: 0.3492 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 98796 Z= 0.192 Angle : 0.530 8.805 148742 Z= 0.281 Chirality : 0.034 0.275 19143 Planarity : 0.004 0.042 7297 Dihedral : 23.898 178.569 51690 Min Nonbonded Distance : 2.094 Molprobity Statistics. All-atom Clashscore : 9.20 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.09 % Favored : 95.81 % Rotamer: Outliers : 5.38 % Allowed : 30.83 % Favored : 63.78 % 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: 0.08 (0.15), residues: 3033 helix: 1.37 (0.19), residues: 820 sheet: -0.16 (0.20), residues: 634 loop : -0.51 (0.15), residues: 1579 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP 0 39 HIS 0.007 0.001 HIS e 165 PHE 0.020 0.001 PHE u 85 TYR 0.017 0.001 TYR m 103 ARG 0.007 0.000 ARG d 184 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6066 Ramachandran restraints generated. 3033 Oldfield, 0 Emsley, 3033 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6066 Ramachandran restraints generated. 3033 Oldfield, 0 Emsley, 3033 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 785 residues out of total 2507 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 135 poor density : 650 time to evaluate : 3.733 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 0 77 LYS cc_start: 0.8894 (mmmt) cc_final: 0.8582 (tptp) REVERT: 1 23 ARG cc_start: 0.9085 (mtt90) cc_final: 0.8627 (mtt-85) REVERT: 1 27 ASN cc_start: 0.9093 (m110) cc_final: 0.8722 (m110) REVERT: 1 45 GLN cc_start: 0.8744 (tt0) cc_final: 0.8476 (tt0) REVERT: 1 49 ASP cc_start: 0.8225 (m-30) cc_final: 0.7938 (m-30) REVERT: 2 56 LYS cc_start: 0.9181 (ptmm) cc_final: 0.8907 (ptpp) REVERT: 3 50 ARG cc_start: 0.9125 (OUTLIER) cc_final: 0.8449 (mtt180) REVERT: c 114 ASP cc_start: 0.8402 (m-30) cc_final: 0.7975 (m-30) REVERT: d 1 MET cc_start: 0.6803 (OUTLIER) cc_final: 0.6400 (tmm) REVERT: e 6 LYS cc_start: 0.7261 (OUTLIER) cc_final: 0.6934 (pptt) REVERT: e 69 ARG cc_start: 0.8277 (OUTLIER) cc_final: 0.6349 (ptp-170) REVERT: e 111 GLU cc_start: 0.8911 (tp30) cc_final: 0.8532 (tp30) REVERT: e 115 GLN cc_start: 0.9060 (mt0) cc_final: 0.8673 (mt0) REVERT: e 136 GLN cc_start: 0.8477 (tp40) cc_final: 0.8245 (tp40) REVERT: e 162 ARG cc_start: 0.9002 (OUTLIER) cc_final: 0.8732 (ttp-170) REVERT: f 3 LYS cc_start: 0.8733 (OUTLIER) cc_final: 0.8531 (ttmm) REVERT: f 64 LYS cc_start: 0.9019 (OUTLIER) cc_final: 0.7885 (pttt) REVERT: f 112 ARG cc_start: 0.8895 (ttm-80) cc_final: 0.8306 (tpt170) REVERT: f 133 ARG cc_start: 0.8178 (ttm-80) cc_final: 0.7899 (mmt180) REVERT: g 3 ARG cc_start: 0.8032 (OUTLIER) cc_final: 0.6860 (tmt90) REVERT: g 6 LYS cc_start: 0.9146 (mmtp) cc_final: 0.8768 (mmtt) REVERT: g 158 LYS cc_start: 0.9105 (mtpt) cc_final: 0.8882 (mttt) REVERT: j 53 TYR cc_start: 0.9294 (m-80) cc_final: 0.8815 (m-80) REVERT: m 22 GLN cc_start: 0.8483 (OUTLIER) cc_final: 0.8223 (mm-40) REVERT: m 115 GLU cc_start: 0.8238 (OUTLIER) cc_final: 0.8016 (tm-30) REVERT: n 35 LYS cc_start: 0.9225 (OUTLIER) cc_final: 0.8927 (tttp) REVERT: n 110 MET cc_start: 0.8894 (mmp) cc_final: 0.8575 (mmp) REVERT: o 104 GLN cc_start: 0.8767 (OUTLIER) cc_final: 0.8253 (tp40) REVERT: p 6 LYS cc_start: 0.9129 (OUTLIER) cc_final: 0.8237 (ttpp) REVERT: p 10 GLN cc_start: 0.8444 (tp40) cc_final: 0.8019 (mp10) REVERT: p 102 GLU cc_start: 0.8438 (OUTLIER) cc_final: 0.7811 (mp0) REVERT: q 84 LYS cc_start: 0.8548 (ttmm) cc_final: 0.8228 (mttt) REVERT: q 107 THR cc_start: 0.9391 (m) cc_final: 0.9148 (p) REVERT: s 92 ARG cc_start: 0.7814 (OUTLIER) cc_final: 0.7524 (ttp-170) REVERT: t 1 MET cc_start: 0.8196 (ttp) cc_final: 0.7936 (ttm) REVERT: t 22 THR cc_start: 0.9069 (m) cc_final: 0.8868 (m) REVERT: u 51 GLU cc_start: 0.8641 (mp0) cc_final: 0.8440 (mp0) REVERT: y 25 ARG cc_start: 0.8537 (mmt-90) cc_final: 0.8272 (mmp80) outliers start: 135 outliers final: 72 residues processed: 728 average time/residue: 1.7277 time to fit residues: 1709.5608 Evaluate side-chains 710 residues out of total 2507 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 87 poor density : 623 time to evaluate : 3.811 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 35 SER Chi-restraints excluded: chain 2 residue 36 VAL Chi-restraints excluded: chain 3 residue 23 THR Chi-restraints excluded: chain 3 residue 27 SER Chi-restraints excluded: chain 3 residue 50 ARG Chi-restraints excluded: chain 8 residue 13 ASN Chi-restraints excluded: chain 8 residue 25 VAL Chi-restraints excluded: chain c residue 90 ASN Chi-restraints excluded: chain c residue 120 VAL Chi-restraints excluded: chain d residue 1 MET Chi-restraints excluded: chain d residue 40 LEU Chi-restraints excluded: chain d residue 86 GLU Chi-restraints excluded: chain d residue 88 GLU Chi-restraints excluded: chain d residue 94 GLN Chi-restraints excluded: chain d residue 98 VAL Chi-restraints excluded: chain d residue 151 THR Chi-restraints excluded: chain e residue 4 VAL Chi-restraints excluded: chain e residue 6 LYS Chi-restraints excluded: chain e residue 15 SER Chi-restraints excluded: chain e residue 69 ARG Chi-restraints excluded: chain e residue 162 ARG Chi-restraints excluded: chain f residue 3 LYS Chi-restraints excluded: chain f residue 25 VAL Chi-restraints excluded: chain f residue 64 LYS Chi-restraints excluded: chain f residue 101 GLU Chi-restraints excluded: chain f residue 132 VAL Chi-restraints excluded: chain g residue 3 ARG Chi-restraints excluded: chain g residue 15 VAL Chi-restraints excluded: chain g residue 34 THR Chi-restraints excluded: chain g residue 36 THR Chi-restraints excluded: chain g residue 44 LYS Chi-restraints excluded: chain g residue 71 LEU Chi-restraints excluded: chain g residue 92 VAL Chi-restraints excluded: chain g residue 106 SER Chi-restraints excluded: chain g residue 127 THR Chi-restraints excluded: chain g residue 168 VAL Chi-restraints excluded: chain h residue 15 LEU Chi-restraints excluded: chain h residue 37 VAL Chi-restraints excluded: chain j residue 30 THR Chi-restraints excluded: chain j residue 43 GLU Chi-restraints excluded: chain j residue 101 ILE Chi-restraints excluded: chain j residue 131 ASN Chi-restraints excluded: chain k residue 25 LEU Chi-restraints excluded: chain k residue 76 VAL Chi-restraints excluded: chain l residue 82 LEU Chi-restraints excluded: chain l residue 121 THR Chi-restraints excluded: chain m residue 7 THR Chi-restraints excluded: chain m residue 22 GLN Chi-restraints excluded: chain m residue 30 SER Chi-restraints excluded: chain m residue 41 LEU Chi-restraints excluded: chain m residue 112 LEU Chi-restraints excluded: chain m residue 115 GLU Chi-restraints excluded: chain m residue 135 VAL Chi-restraints excluded: chain n residue 1 MET Chi-restraints excluded: chain n residue 6 SER Chi-restraints excluded: chain n residue 35 LYS Chi-restraints excluded: chain n residue 57 THR Chi-restraints excluded: chain o residue 54 VAL Chi-restraints excluded: chain o residue 60 GLU Chi-restraints excluded: chain o residue 90 VAL Chi-restraints excluded: chain o residue 104 GLN Chi-restraints excluded: chain p residue 5 ILE Chi-restraints excluded: chain p residue 6 LYS Chi-restraints excluded: chain p residue 8 LEU Chi-restraints excluded: chain p residue 70 VAL Chi-restraints excluded: chain p residue 76 THR Chi-restraints excluded: chain p residue 102 GLU Chi-restraints excluded: chain q residue 22 LYS Chi-restraints excluded: chain q residue 77 SER Chi-restraints excluded: chain q residue 83 LEU Chi-restraints excluded: chain r residue 22 LEU Chi-restraints excluded: chain r residue 49 ILE Chi-restraints excluded: chain r residue 70 GLU Chi-restraints excluded: chain s residue 67 ASP Chi-restraints excluded: chain s residue 92 ARG Chi-restraints excluded: chain s residue 109 ASP Chi-restraints excluded: chain t residue 11 LEU Chi-restraints excluded: chain t residue 78 VAL Chi-restraints excluded: chain u residue 42 VAL Chi-restraints excluded: chain u residue 57 SER Chi-restraints excluded: chain u residue 72 VAL Chi-restraints excluded: chain u residue 78 ASP Chi-restraints excluded: chain w residue 12 GLN Chi-restraints excluded: chain w residue 65 VAL Chi-restraints excluded: chain y residue 9 SER Chi-restraints excluded: chain y residue 10 THR Chi-restraints excluded: chain y residue 17 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 604 random chunks: chunk 486 optimal weight: 0.9980 chunk 331 optimal weight: 40.0000 chunk 8 optimal weight: 7.9990 chunk 434 optimal weight: 30.0000 chunk 240 optimal weight: 20.0000 chunk 498 optimal weight: 9.9990 chunk 403 optimal weight: 8.9990 chunk 0 optimal weight: 10.0000 chunk 298 optimal weight: 20.0000 chunk 524 optimal weight: 5.9990 chunk 147 optimal weight: 10.0000 overall best weight: 6.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 15 ASN ** 6 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 8 35 GLN f 127 ASN ** j 77 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** k 93 GLN o 19 GLN ** o 34 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** o 38 GLN o 43 ASN p 12 GLN p 52 ASN p 75 GLN ** q 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** t 48 GLN t 84 GLN ** w 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** w 24 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8551 moved from start: 0.3618 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.097 98796 Z= 0.300 Angle : 0.563 9.472 148742 Z= 0.297 Chirality : 0.036 0.290 19143 Planarity : 0.004 0.043 7297 Dihedral : 23.824 179.569 51690 Min Nonbonded Distance : 2.073 Molprobity Statistics. All-atom Clashscore : 8.81 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.45 % Favored : 95.48 % Rotamer: Outliers : 5.98 % Allowed : 30.47 % Favored : 63.54 % 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: 0.13 (0.15), residues: 3033 helix: 1.43 (0.18), residues: 823 sheet: -0.06 (0.21), residues: 618 loop : -0.53 (0.15), residues: 1592 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP c 213 HIS 0.007 0.001 HIS e 165 PHE 0.022 0.001 PHE u 85 TYR 0.015 0.001 TYR s 38 ARG 0.008 0.001 ARG k 105 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6066 Ramachandran restraints generated. 3033 Oldfield, 0 Emsley, 3033 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6066 Ramachandran restraints generated. 3033 Oldfield, 0 Emsley, 3033 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 778 residues out of total 2507 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 150 poor density : 628 time to evaluate : 4.752 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 0 77 LYS cc_start: 0.8910 (mmmt) cc_final: 0.8583 (tptp) REVERT: 1 23 ARG cc_start: 0.9089 (mtt90) cc_final: 0.8780 (mtt-85) REVERT: 1 27 ASN cc_start: 0.9094 (m110) cc_final: 0.8631 (m110) REVERT: 1 45 GLN cc_start: 0.8740 (tt0) cc_final: 0.8451 (tt0) REVERT: 1 49 ASP cc_start: 0.8268 (m-30) cc_final: 0.8034 (m-30) REVERT: 2 56 LYS cc_start: 0.9168 (ptmm) cc_final: 0.8891 (ptpp) REVERT: c 114 ASP cc_start: 0.8418 (m-30) cc_final: 0.7982 (m-30) REVERT: d 1 MET cc_start: 0.6855 (OUTLIER) cc_final: 0.6473 (tmm) REVERT: e 6 LYS cc_start: 0.7294 (OUTLIER) cc_final: 0.6966 (pptt) REVERT: e 22 ASP cc_start: 0.8185 (OUTLIER) cc_final: 0.7931 (p0) REVERT: e 69 ARG cc_start: 0.8358 (OUTLIER) cc_final: 0.6409 (ptp-170) REVERT: e 111 GLU cc_start: 0.8971 (tp30) cc_final: 0.8533 (tp30) REVERT: e 115 GLN cc_start: 0.9114 (mt0) cc_final: 0.8736 (mt0) REVERT: e 140 ASP cc_start: 0.8559 (m-30) cc_final: 0.8347 (m-30) REVERT: e 162 ARG cc_start: 0.9055 (OUTLIER) cc_final: 0.8782 (ttp-170) REVERT: f 64 LYS cc_start: 0.9066 (OUTLIER) cc_final: 0.7942 (pttt) REVERT: f 112 ARG cc_start: 0.8959 (ttm-80) cc_final: 0.8291 (tpt170) REVERT: f 133 ARG cc_start: 0.8215 (ttm-80) cc_final: 0.7932 (mmt180) REVERT: g 3 ARG cc_start: 0.8042 (OUTLIER) cc_final: 0.6872 (tmt90) REVERT: g 6 LYS cc_start: 0.9167 (mmtp) cc_final: 0.8778 (mmtt) REVERT: g 106 SER cc_start: 0.9287 (OUTLIER) cc_final: 0.9036 (p) REVERT: g 158 LYS cc_start: 0.9136 (mtpt) cc_final: 0.8908 (mttt) REVERT: j 53 TYR cc_start: 0.9313 (m-80) cc_final: 0.8874 (m-80) REVERT: k 93 GLN cc_start: 0.8639 (mm110) cc_final: 0.7932 (mm-40) REVERT: m 22 GLN cc_start: 0.8462 (OUTLIER) cc_final: 0.8182 (mm-40) REVERT: m 115 GLU cc_start: 0.8240 (OUTLIER) cc_final: 0.8019 (tm-30) REVERT: m 133 LYS cc_start: 0.8884 (OUTLIER) cc_final: 0.8234 (ttmm) REVERT: n 35 LYS cc_start: 0.9270 (OUTLIER) cc_final: 0.8973 (tttp) REVERT: n 110 MET cc_start: 0.8916 (mmp) cc_final: 0.8559 (mmp) REVERT: o 104 GLN cc_start: 0.8812 (tt0) cc_final: 0.8317 (tp40) REVERT: p 6 LYS cc_start: 0.9157 (OUTLIER) cc_final: 0.8268 (ttpp) REVERT: p 10 GLN cc_start: 0.8484 (tp40) cc_final: 0.8095 (mp10) REVERT: p 38 LYS cc_start: 0.8911 (ttpt) cc_final: 0.8616 (ttpt) REVERT: p 68 GLU cc_start: 0.8215 (OUTLIER) cc_final: 0.7354 (pm20) REVERT: p 102 GLU cc_start: 0.8476 (OUTLIER) cc_final: 0.7885 (mp0) REVERT: q 6 ARG cc_start: 0.9288 (OUTLIER) cc_final: 0.9085 (mtp180) REVERT: q 22 LYS cc_start: 0.8900 (OUTLIER) cc_final: 0.8696 (ttmm) REVERT: q 84 LYS cc_start: 0.8625 (ttmm) cc_final: 0.8232 (mttt) REVERT: q 107 THR cc_start: 0.9393 (m) cc_final: 0.9147 (p) REVERT: s 92 ARG cc_start: 0.7916 (OUTLIER) cc_final: 0.7658 (ttp80) REVERT: t 1 MET cc_start: 0.8266 (ttp) cc_final: 0.8011 (ttm) REVERT: y 25 ARG cc_start: 0.8549 (mmt-90) cc_final: 0.8277 (mmp80) REVERT: y 55 ARG cc_start: 0.9026 (OUTLIER) cc_final: 0.8023 (ttp80) outliers start: 150 outliers final: 92 residues processed: 708 average time/residue: 1.7207 time to fit residues: 1661.3084 Evaluate side-chains 732 residues out of total 2507 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 111 poor density : 621 time to evaluate : 3.925 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 2 SER Chi-restraints excluded: chain 0 residue 35 SER Chi-restraints excluded: chain 0 residue 51 VAL Chi-restraints excluded: chain 2 residue 21 LYS Chi-restraints excluded: chain 2 residue 36 VAL Chi-restraints excluded: chain 3 residue 23 THR Chi-restraints excluded: chain 3 residue 27 SER Chi-restraints excluded: chain 3 residue 34 SER Chi-restraints excluded: chain 4 residue 12 VAL Chi-restraints excluded: chain 7 residue 51 SER Chi-restraints excluded: chain 8 residue 13 ASN Chi-restraints excluded: chain 8 residue 25 VAL Chi-restraints excluded: chain c residue 88 SER Chi-restraints excluded: chain c residue 90 ASN Chi-restraints excluded: chain c residue 120 VAL Chi-restraints excluded: chain d residue 1 MET Chi-restraints excluded: chain d residue 2 ILE Chi-restraints excluded: chain d residue 40 LEU Chi-restraints excluded: chain d residue 86 GLU Chi-restraints excluded: chain d residue 88 GLU Chi-restraints excluded: chain d residue 94 GLN Chi-restraints excluded: chain d residue 98 VAL Chi-restraints excluded: chain d residue 151 THR Chi-restraints excluded: chain d residue 181 ASP Chi-restraints excluded: chain e residue 4 VAL Chi-restraints excluded: chain e residue 6 LYS Chi-restraints excluded: chain e residue 15 SER Chi-restraints excluded: chain e residue 17 THR Chi-restraints excluded: chain e residue 22 ASP Chi-restraints excluded: chain e residue 69 ARG Chi-restraints excluded: chain e residue 72 SER Chi-restraints excluded: chain e residue 113 VAL Chi-restraints excluded: chain e residue 150 THR Chi-restraints excluded: chain e residue 162 ARG Chi-restraints excluded: chain f residue 25 VAL Chi-restraints excluded: chain f residue 64 LYS Chi-restraints excluded: chain f residue 88 LYS Chi-restraints excluded: chain f residue 101 GLU Chi-restraints excluded: chain f residue 132 VAL Chi-restraints excluded: chain g residue 3 ARG Chi-restraints excluded: chain g residue 10 VAL Chi-restraints excluded: chain g residue 15 VAL Chi-restraints excluded: chain g residue 36 THR Chi-restraints excluded: chain g residue 44 LYS Chi-restraints excluded: chain g residue 67 THR Chi-restraints excluded: chain g residue 71 LEU Chi-restraints excluded: chain g residue 84 THR Chi-restraints excluded: chain g residue 92 VAL Chi-restraints excluded: chain g residue 106 SER Chi-restraints excluded: chain g residue 107 LEU Chi-restraints excluded: chain g residue 122 THR Chi-restraints excluded: chain g residue 127 THR Chi-restraints excluded: chain g residue 168 VAL Chi-restraints excluded: chain h residue 11 ASN Chi-restraints excluded: chain h residue 15 LEU Chi-restraints excluded: chain h residue 37 VAL Chi-restraints excluded: chain j residue 30 THR Chi-restraints excluded: chain j residue 43 GLU Chi-restraints excluded: chain j residue 131 ASN Chi-restraints excluded: chain k residue 25 LEU Chi-restraints excluded: chain k residue 76 VAL Chi-restraints excluded: chain l residue 7 SER Chi-restraints excluded: chain l residue 82 LEU Chi-restraints excluded: chain l residue 121 THR Chi-restraints excluded: chain m residue 7 THR Chi-restraints excluded: chain m residue 22 GLN Chi-restraints excluded: chain m residue 30 SER Chi-restraints excluded: chain m residue 41 LEU Chi-restraints excluded: chain m residue 112 LEU Chi-restraints excluded: chain m residue 115 GLU Chi-restraints excluded: chain m residue 133 LYS Chi-restraints excluded: chain m residue 135 VAL Chi-restraints excluded: chain n residue 1 MET Chi-restraints excluded: chain n residue 6 SER Chi-restraints excluded: chain n residue 35 LYS Chi-restraints excluded: chain n residue 57 THR Chi-restraints excluded: chain n residue 98 LEU Chi-restraints excluded: chain o residue 49 VAL Chi-restraints excluded: chain o residue 54 VAL Chi-restraints excluded: chain o residue 60 GLU Chi-restraints excluded: chain o residue 90 VAL Chi-restraints excluded: chain p residue 5 ILE Chi-restraints excluded: chain p residue 6 LYS Chi-restraints excluded: chain p residue 52 ASN Chi-restraints excluded: chain p residue 68 GLU Chi-restraints excluded: chain p residue 70 VAL Chi-restraints excluded: chain p residue 76 THR Chi-restraints excluded: chain p residue 102 GLU Chi-restraints excluded: chain p residue 114 LEU Chi-restraints excluded: chain q residue 6 ARG Chi-restraints excluded: chain q residue 22 LYS Chi-restraints excluded: chain q residue 77 SER Chi-restraints excluded: chain q residue 83 LEU Chi-restraints excluded: chain r residue 22 LEU Chi-restraints excluded: chain r residue 49 ILE Chi-restraints excluded: chain s residue 67 ASP Chi-restraints excluded: chain s residue 92 ARG Chi-restraints excluded: chain s residue 109 ASP Chi-restraints excluded: chain t residue 11 LEU Chi-restraints excluded: chain t residue 27 SER Chi-restraints excluded: chain t residue 58 VAL Chi-restraints excluded: chain t residue 78 VAL Chi-restraints excluded: chain t residue 79 THR Chi-restraints excluded: chain u residue 57 SER Chi-restraints excluded: chain u residue 78 ASP Chi-restraints excluded: chain w residue 17 SER Chi-restraints excluded: chain w residue 65 VAL Chi-restraints excluded: chain y residue 9 SER Chi-restraints excluded: chain y residue 10 THR Chi-restraints excluded: chain y residue 17 GLU Chi-restraints excluded: chain y residue 55 ARG Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 604 random chunks: chunk 196 optimal weight: 20.0000 chunk 525 optimal weight: 8.9990 chunk 115 optimal weight: 10.0000 chunk 342 optimal weight: 0.3980 chunk 144 optimal weight: 10.0000 chunk 584 optimal weight: 9.9990 chunk 485 optimal weight: 20.0000 chunk 270 optimal weight: 60.0000 chunk 48 optimal weight: 10.0000 chunk 193 optimal weight: 40.0000 chunk 306 optimal weight: 10.0000 overall best weight: 7.8792 ------------------------------------------------------------------------------- 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** ** 6 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 8 35 GLN f 127 ASN ** h 2 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 77 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** k 93 GLN o 19 GLN ** o 34 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** o 38 GLN o 43 ASN p 52 ASN q 81 ASN r 89 HIS t 48 GLN w 24 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8561 moved from start: 0.3744 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.086 98796 Z= 0.339 Angle : 0.581 9.996 148742 Z= 0.306 Chirality : 0.038 0.298 19143 Planarity : 0.005 0.049 7297 Dihedral : 23.812 179.105 51690 Min Nonbonded Distance : 2.070 Molprobity Statistics. All-atom Clashscore : 8.88 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.48 % Favored : 95.45 % Rotamer: Outliers : 6.38 % Allowed : 29.92 % Favored : 63.70 % 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: 0.09 (0.15), residues: 3033 helix: 1.43 (0.18), residues: 823 sheet: -0.16 (0.20), residues: 631 loop : -0.53 (0.15), residues: 1579 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP c 213 HIS 0.007 0.001 HIS e 165 PHE 0.012 0.001 PHE n 21 TYR 0.023 0.001 TYR m 103 ARG 0.011 0.001 ARG f 148 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6066 Ramachandran restraints generated. 3033 Oldfield, 0 Emsley, 3033 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6066 Ramachandran restraints generated. 3033 Oldfield, 0 Emsley, 3033 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 783 residues out of total 2507 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 160 poor density : 623 time to evaluate : 3.831 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 1 23 ARG cc_start: 0.9087 (mtt90) cc_final: 0.8755 (mtt-85) REVERT: 1 27 ASN cc_start: 0.9077 (m110) cc_final: 0.8625 (m110) REVERT: 1 45 GLN cc_start: 0.8765 (tt0) cc_final: 0.8489 (tt0) REVERT: 1 49 ASP cc_start: 0.8273 (m-30) cc_final: 0.8057 (m-30) REVERT: c 114 ASP cc_start: 0.8423 (m-30) cc_final: 0.7962 (m-30) REVERT: d 1 MET cc_start: 0.6909 (OUTLIER) cc_final: 0.6550 (tmm) REVERT: e 6 LYS cc_start: 0.7305 (OUTLIER) cc_final: 0.6979 (pptt) REVERT: e 69 ARG cc_start: 0.8365 (OUTLIER) cc_final: 0.6375 (ptp-170) REVERT: e 84 THR cc_start: 0.9175 (OUTLIER) cc_final: 0.8972 (t) REVERT: e 111 GLU cc_start: 0.8968 (tp30) cc_final: 0.8440 (tp30) REVERT: e 115 GLN cc_start: 0.9133 (mt0) cc_final: 0.8661 (mt0) REVERT: e 136 GLN cc_start: 0.8408 (tp40) cc_final: 0.8143 (tp40) REVERT: e 140 ASP cc_start: 0.8566 (m-30) cc_final: 0.8248 (m-30) REVERT: e 162 ARG cc_start: 0.9093 (OUTLIER) cc_final: 0.8804 (ttp-170) REVERT: f 64 LYS cc_start: 0.9079 (OUTLIER) cc_final: 0.7966 (pttt) REVERT: f 101 GLU cc_start: 0.8644 (OUTLIER) cc_final: 0.8383 (tt0) REVERT: f 112 ARG cc_start: 0.9019 (ttm-80) cc_final: 0.8283 (tpt170) REVERT: f 134 GLU cc_start: 0.7562 (OUTLIER) cc_final: 0.7299 (pp20) REVERT: f 148 ARG cc_start: 0.8674 (mtp-110) cc_final: 0.8447 (ttm110) REVERT: g 3 ARG cc_start: 0.8027 (OUTLIER) cc_final: 0.6722 (tmt90) REVERT: g 6 LYS cc_start: 0.9197 (mmtp) cc_final: 0.8789 (mmtt) REVERT: g 27 LYS cc_start: 0.7897 (OUTLIER) cc_final: 0.7487 (mmpt) REVERT: g 106 SER cc_start: 0.9313 (OUTLIER) cc_final: 0.9056 (p) REVERT: g 158 LYS cc_start: 0.9144 (mtpt) cc_final: 0.8883 (mttt) REVERT: j 53 TYR cc_start: 0.9318 (m-80) cc_final: 0.8831 (m-80) REVERT: l 123 ARG cc_start: 0.8865 (ttm-80) cc_final: 0.8625 (ttm-80) REVERT: m 22 GLN cc_start: 0.8438 (OUTLIER) cc_final: 0.8182 (mm-40) REVERT: m 115 GLU cc_start: 0.8243 (OUTLIER) cc_final: 0.8030 (tm-30) REVERT: m 133 LYS cc_start: 0.8899 (OUTLIER) cc_final: 0.8237 (ttmm) REVERT: n 35 LYS cc_start: 0.9266 (OUTLIER) cc_final: 0.8980 (tttp) REVERT: n 110 MET cc_start: 0.8920 (mmp) cc_final: 0.8577 (mmp) REVERT: p 6 LYS cc_start: 0.9175 (OUTLIER) cc_final: 0.8273 (ttpp) REVERT: p 10 GLN cc_start: 0.8496 (tp40) cc_final: 0.8053 (mp10) REVERT: p 38 LYS cc_start: 0.8934 (ttpt) cc_final: 0.8633 (ttpt) REVERT: p 68 GLU cc_start: 0.8225 (OUTLIER) cc_final: 0.7403 (pm20) REVERT: p 102 GLU cc_start: 0.8513 (OUTLIER) cc_final: 0.7933 (mp0) REVERT: q 6 ARG cc_start: 0.9298 (OUTLIER) cc_final: 0.9088 (mtp180) REVERT: q 84 LYS cc_start: 0.8610 (ttmm) cc_final: 0.8213 (mttt) REVERT: q 107 THR cc_start: 0.9354 (m) cc_final: 0.9090 (p) REVERT: r 79 ARG cc_start: 0.9329 (OUTLIER) cc_final: 0.8900 (ptt180) REVERT: s 92 ARG cc_start: 0.7963 (OUTLIER) cc_final: 0.7617 (ttp80) REVERT: t 36 LYS cc_start: 0.8885 (OUTLIER) cc_final: 0.8583 (ttmp) REVERT: u 26 LYS cc_start: 0.8304 (mmtm) cc_final: 0.7963 (mmtm) REVERT: y 25 ARG cc_start: 0.8564 (mmt-90) cc_final: 0.8291 (mmp80) REVERT: y 55 ARG cc_start: 0.9039 (OUTLIER) cc_final: 0.7996 (ttp80) outliers start: 160 outliers final: 92 residues processed: 711 average time/residue: 1.7296 time to fit residues: 1674.6139 Evaluate side-chains 721 residues out of total 2507 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 115 poor density : 606 time to evaluate : 3.706 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 2 SER Chi-restraints excluded: chain 0 residue 35 SER Chi-restraints excluded: chain 0 residue 51 VAL Chi-restraints excluded: chain 2 residue 21 LYS Chi-restraints excluded: chain 2 residue 36 VAL Chi-restraints excluded: chain 3 residue 23 THR Chi-restraints excluded: chain 3 residue 27 SER Chi-restraints excluded: chain 3 residue 34 SER Chi-restraints excluded: chain 4 residue 12 VAL Chi-restraints excluded: chain 7 residue 51 SER Chi-restraints excluded: chain 8 residue 13 ASN Chi-restraints excluded: chain 8 residue 25 VAL Chi-restraints excluded: chain c residue 88 SER Chi-restraints excluded: chain c residue 90 ASN Chi-restraints excluded: chain c residue 120 VAL Chi-restraints excluded: chain d residue 1 MET Chi-restraints excluded: chain d residue 2 ILE Chi-restraints excluded: chain d residue 40 LEU Chi-restraints excluded: chain d residue 86 GLU Chi-restraints excluded: chain d residue 88 GLU Chi-restraints excluded: chain d residue 94 GLN Chi-restraints excluded: chain d residue 98 VAL Chi-restraints excluded: chain d residue 100 LEU Chi-restraints excluded: chain d residue 151 THR Chi-restraints excluded: chain e residue 4 VAL Chi-restraints excluded: chain e residue 6 LYS Chi-restraints excluded: chain e residue 17 THR Chi-restraints excluded: chain e residue 69 ARG Chi-restraints excluded: chain e residue 72 SER Chi-restraints excluded: chain e residue 84 THR Chi-restraints excluded: chain e residue 113 VAL Chi-restraints excluded: chain e residue 150 THR Chi-restraints excluded: chain e residue 162 ARG Chi-restraints excluded: chain e residue 191 ASP Chi-restraints excluded: chain e residue 199 MET Chi-restraints excluded: chain f residue 25 VAL Chi-restraints excluded: chain f residue 64 LYS Chi-restraints excluded: chain f residue 88 LYS Chi-restraints excluded: chain f residue 101 GLU Chi-restraints excluded: chain f residue 132 VAL Chi-restraints excluded: chain f residue 134 GLU Chi-restraints excluded: chain g residue 3 ARG Chi-restraints excluded: chain g residue 10 VAL Chi-restraints excluded: chain g residue 15 VAL Chi-restraints excluded: chain g residue 27 LYS Chi-restraints excluded: chain g residue 34 THR Chi-restraints excluded: chain g residue 36 THR Chi-restraints excluded: chain g residue 44 LYS Chi-restraints excluded: chain g residue 67 THR Chi-restraints excluded: chain g residue 71 LEU Chi-restraints excluded: chain g residue 84 THR Chi-restraints excluded: chain g residue 92 VAL Chi-restraints excluded: chain g residue 106 SER Chi-restraints excluded: chain g residue 122 THR Chi-restraints excluded: chain g residue 127 THR Chi-restraints excluded: chain g residue 168 VAL Chi-restraints excluded: chain h residue 11 ASN Chi-restraints excluded: chain h residue 15 LEU Chi-restraints excluded: chain h residue 37 VAL Chi-restraints excluded: chain j residue 30 THR Chi-restraints excluded: chain j residue 131 ASN Chi-restraints excluded: chain k residue 25 LEU Chi-restraints excluded: chain k residue 76 VAL Chi-restraints excluded: chain l residue 7 SER Chi-restraints excluded: chain l residue 30 THR Chi-restraints excluded: chain l residue 82 LEU Chi-restraints excluded: chain l residue 121 THR Chi-restraints excluded: chain m residue 2 LEU Chi-restraints excluded: chain m residue 7 THR Chi-restraints excluded: chain m residue 22 GLN Chi-restraints excluded: chain m residue 30 SER Chi-restraints excluded: chain m residue 41 LEU Chi-restraints excluded: chain m residue 112 LEU Chi-restraints excluded: chain m residue 115 GLU Chi-restraints excluded: chain m residue 133 LYS Chi-restraints excluded: chain m residue 135 VAL Chi-restraints excluded: chain n residue 1 MET Chi-restraints excluded: chain n residue 6 SER Chi-restraints excluded: chain n residue 35 LYS Chi-restraints excluded: chain n residue 57 THR Chi-restraints excluded: chain o residue 49 VAL Chi-restraints excluded: chain o residue 54 VAL Chi-restraints excluded: chain o residue 60 GLU Chi-restraints excluded: chain o residue 87 ILE Chi-restraints excluded: chain o residue 90 VAL Chi-restraints excluded: chain p residue 5 ILE Chi-restraints excluded: chain p residue 6 LYS Chi-restraints excluded: chain p residue 68 GLU Chi-restraints excluded: chain p residue 70 VAL Chi-restraints excluded: chain p residue 76 THR Chi-restraints excluded: chain p residue 102 GLU Chi-restraints excluded: chain p residue 114 LEU Chi-restraints excluded: chain q residue 6 ARG Chi-restraints excluded: chain q residue 22 LYS Chi-restraints excluded: chain q residue 77 SER Chi-restraints excluded: chain q residue 83 LEU Chi-restraints excluded: chain r residue 22 LEU Chi-restraints excluded: chain r residue 49 ILE Chi-restraints excluded: chain r residue 79 ARG Chi-restraints excluded: chain s residue 67 ASP Chi-restraints excluded: chain s residue 92 ARG Chi-restraints excluded: chain s residue 109 ASP Chi-restraints excluded: chain t residue 11 LEU Chi-restraints excluded: chain t residue 36 LYS Chi-restraints excluded: chain t residue 58 VAL Chi-restraints excluded: chain t residue 78 VAL Chi-restraints excluded: chain t residue 79 THR Chi-restraints excluded: chain u residue 57 SER Chi-restraints excluded: chain u residue 78 ASP Chi-restraints excluded: chain w residue 17 SER Chi-restraints excluded: chain w residue 65 VAL Chi-restraints excluded: chain y residue 9 SER Chi-restraints excluded: chain y residue 10 THR Chi-restraints excluded: chain y residue 17 GLU Chi-restraints excluded: chain y residue 55 ARG Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 604 random chunks: chunk 563 optimal weight: 9.9990 chunk 65 optimal weight: 20.0000 chunk 332 optimal weight: 30.0000 chunk 426 optimal weight: 30.0000 chunk 330 optimal weight: 10.0000 chunk 491 optimal weight: 2.9990 chunk 326 optimal weight: 20.0000 chunk 582 optimal weight: 5.9990 chunk 364 optimal weight: 9.9990 chunk 354 optimal weight: 9.9990 chunk 268 optimal weight: 110.0000 overall best weight: 7.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 1 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** f 127 ASN ** h 2 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 77 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** o 19 GLN ** o 34 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** o 38 GLN o 43 ASN p 52 ASN q 81 ASN t 48 GLN w 24 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8563 moved from start: 0.3884 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.081 98796 Z= 0.335 Angle : 0.582 10.415 148742 Z= 0.306 Chirality : 0.038 0.299 19143 Planarity : 0.004 0.047 7297 Dihedral : 23.808 179.057 51690 Min Nonbonded Distance : 2.072 Molprobity Statistics. All-atom Clashscore : 9.04 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.62 % Favored : 95.32 % Rotamer: Outliers : 6.22 % Allowed : 30.16 % Favored : 63.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.07 (0.15), residues: 3033 helix: 1.40 (0.18), residues: 821 sheet: -0.16 (0.20), residues: 624 loop : -0.56 (0.15), residues: 1588 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP c 213 HIS 0.006 0.001 HIS e 165 PHE 0.012 0.001 PHE n 21 TYR 0.029 0.001 TYR m 103 ARG 0.011 0.001 ARG k 105 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6066 Ramachandran restraints generated. 3033 Oldfield, 0 Emsley, 3033 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6066 Ramachandran restraints generated. 3033 Oldfield, 0 Emsley, 3033 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 774 residues out of total 2507 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 156 poor density : 618 time to evaluate : 3.841 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 1 45 GLN cc_start: 0.8776 (tt0) cc_final: 0.8557 (tt0) REVERT: 2 21 LYS cc_start: 0.9427 (OUTLIER) cc_final: 0.9178 (mtmm) REVERT: c 114 ASP cc_start: 0.8443 (m-30) cc_final: 0.7968 (m-30) REVERT: d 1 MET cc_start: 0.6775 (OUTLIER) cc_final: 0.6479 (tmm) REVERT: e 69 ARG cc_start: 0.8357 (OUTLIER) cc_final: 0.6373 (ptp-170) REVERT: e 84 THR cc_start: 0.9186 (OUTLIER) cc_final: 0.8985 (t) REVERT: e 111 GLU cc_start: 0.8953 (tp30) cc_final: 0.8434 (tp30) REVERT: e 115 GLN cc_start: 0.9131 (mt0) cc_final: 0.8666 (mt0) REVERT: e 162 ARG cc_start: 0.9088 (OUTLIER) cc_final: 0.8795 (ttp-170) REVERT: f 33 LYS cc_start: 0.9372 (pttm) cc_final: 0.9163 (pttt) REVERT: f 42 GLU cc_start: 0.8717 (pm20) cc_final: 0.8417 (pm20) REVERT: f 64 LYS cc_start: 0.9092 (OUTLIER) cc_final: 0.8001 (pttt) REVERT: f 101 GLU cc_start: 0.8625 (OUTLIER) cc_final: 0.8375 (tt0) REVERT: f 112 ARG cc_start: 0.9037 (ttm-80) cc_final: 0.8305 (tpt170) REVERT: g 3 ARG cc_start: 0.8048 (OUTLIER) cc_final: 0.6883 (tmt90) REVERT: g 6 LYS cc_start: 0.9206 (mmtp) cc_final: 0.8814 (mmtt) REVERT: g 106 SER cc_start: 0.9353 (OUTLIER) cc_final: 0.9110 (p) REVERT: g 158 LYS cc_start: 0.9152 (mtpt) cc_final: 0.8949 (mttt) REVERT: j 53 TYR cc_start: 0.9329 (m-80) cc_final: 0.8830 (m-80) REVERT: j 128 ASN cc_start: 0.8551 (p0) cc_final: 0.7993 (t0) REVERT: m 22 GLN cc_start: 0.8380 (OUTLIER) cc_final: 0.8122 (mm-40) REVERT: m 47 GLU cc_start: 0.8025 (tp30) cc_final: 0.7756 (tp30) REVERT: m 115 GLU cc_start: 0.8228 (OUTLIER) cc_final: 0.8021 (tm-30) REVERT: m 133 LYS cc_start: 0.8895 (OUTLIER) cc_final: 0.8238 (ttmm) REVERT: n 35 LYS cc_start: 0.9261 (OUTLIER) cc_final: 0.8976 (tttp) REVERT: n 110 MET cc_start: 0.8950 (mmp) cc_final: 0.8630 (mmp) REVERT: p 6 LYS cc_start: 0.9204 (OUTLIER) cc_final: 0.8471 (ttpp) REVERT: p 10 GLN cc_start: 0.8478 (tp40) cc_final: 0.8103 (mp10) REVERT: p 38 LYS cc_start: 0.8934 (ttpt) cc_final: 0.8629 (ttpt) REVERT: p 68 GLU cc_start: 0.8253 (OUTLIER) cc_final: 0.7469 (pm20) REVERT: p 89 ARG cc_start: 0.7953 (mtp-110) cc_final: 0.7718 (mtp-110) REVERT: p 102 GLU cc_start: 0.8549 (OUTLIER) cc_final: 0.7949 (mp0) REVERT: q 22 LYS cc_start: 0.8898 (OUTLIER) cc_final: 0.8697 (ttmm) REVERT: q 84 LYS cc_start: 0.8616 (ttmm) cc_final: 0.8414 (tttp) REVERT: r 79 ARG cc_start: 0.9332 (OUTLIER) cc_final: 0.8897 (ptt180) REVERT: s 92 ARG cc_start: 0.7990 (OUTLIER) cc_final: 0.7642 (ttp80) REVERT: u 80 LYS cc_start: 0.8729 (mtpt) cc_final: 0.8491 (mmmm) REVERT: y 25 ARG cc_start: 0.8552 (mmt-90) cc_final: 0.8273 (mmp80) REVERT: y 55 ARG cc_start: 0.9043 (OUTLIER) cc_final: 0.7987 (ttp80) outliers start: 156 outliers final: 96 residues processed: 709 average time/residue: 1.7298 time to fit residues: 1669.0965 Evaluate side-chains 725 residues out of total 2507 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 116 poor density : 609 time to evaluate : 3.737 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 2 SER Chi-restraints excluded: chain 0 residue 35 SER Chi-restraints excluded: chain 2 residue 21 LYS Chi-restraints excluded: chain 2 residue 36 VAL Chi-restraints excluded: chain 3 residue 23 THR Chi-restraints excluded: chain 3 residue 27 SER Chi-restraints excluded: chain 3 residue 33 THR Chi-restraints excluded: chain 4 residue 12 VAL Chi-restraints excluded: chain 7 residue 51 SER Chi-restraints excluded: chain 8 residue 13 ASN Chi-restraints excluded: chain 8 residue 25 VAL Chi-restraints excluded: chain c residue 88 SER Chi-restraints excluded: chain c residue 90 ASN Chi-restraints excluded: chain c residue 120 VAL Chi-restraints excluded: chain d residue 1 MET Chi-restraints excluded: chain d residue 2 ILE Chi-restraints excluded: chain d residue 40 LEU Chi-restraints excluded: chain d residue 86 GLU Chi-restraints excluded: chain d residue 88 GLU Chi-restraints excluded: chain d residue 94 GLN Chi-restraints excluded: chain d residue 98 VAL Chi-restraints excluded: chain d residue 151 THR Chi-restraints excluded: chain d residue 181 ASP Chi-restraints excluded: chain e residue 4 VAL Chi-restraints excluded: chain e residue 17 THR Chi-restraints excluded: chain e residue 69 ARG Chi-restraints excluded: chain e residue 72 SER Chi-restraints excluded: chain e residue 84 THR Chi-restraints excluded: chain e residue 113 VAL Chi-restraints excluded: chain e residue 150 THR Chi-restraints excluded: chain e residue 162 ARG Chi-restraints excluded: chain e residue 191 ASP Chi-restraints excluded: chain e residue 199 MET Chi-restraints excluded: chain f residue 25 VAL Chi-restraints excluded: chain f residue 64 LYS Chi-restraints excluded: chain f residue 101 GLU Chi-restraints excluded: chain f residue 132 VAL Chi-restraints excluded: chain g residue 3 ARG Chi-restraints excluded: chain g residue 10 VAL Chi-restraints excluded: chain g residue 15 VAL Chi-restraints excluded: chain g residue 17 VAL Chi-restraints excluded: chain g residue 34 THR Chi-restraints excluded: chain g residue 36 THR Chi-restraints excluded: chain g residue 44 LYS Chi-restraints excluded: chain g residue 67 THR Chi-restraints excluded: chain g residue 71 LEU Chi-restraints excluded: chain g residue 84 THR Chi-restraints excluded: chain g residue 92 VAL Chi-restraints excluded: chain g residue 106 SER Chi-restraints excluded: chain g residue 122 THR Chi-restraints excluded: chain g residue 127 THR Chi-restraints excluded: chain g residue 168 VAL Chi-restraints excluded: chain g residue 171 THR Chi-restraints excluded: chain h residue 11 ASN Chi-restraints excluded: chain h residue 15 LEU Chi-restraints excluded: chain h residue 37 VAL Chi-restraints excluded: chain j residue 30 THR Chi-restraints excluded: chain j residue 131 ASN Chi-restraints excluded: chain k residue 25 LEU Chi-restraints excluded: chain k residue 76 VAL Chi-restraints excluded: chain k residue 110 GLU Chi-restraints excluded: chain l residue 7 SER Chi-restraints excluded: chain l residue 30 THR Chi-restraints excluded: chain l residue 69 ARG Chi-restraints excluded: chain l residue 82 LEU Chi-restraints excluded: chain l residue 89 VAL Chi-restraints excluded: chain l residue 121 THR Chi-restraints excluded: chain m residue 7 THR Chi-restraints excluded: chain m residue 22 GLN Chi-restraints excluded: chain m residue 30 SER Chi-restraints excluded: chain m residue 41 LEU Chi-restraints excluded: chain m residue 112 LEU Chi-restraints excluded: chain m residue 115 GLU Chi-restraints excluded: chain m residue 133 LYS Chi-restraints excluded: chain m residue 135 VAL Chi-restraints excluded: chain n residue 1 MET Chi-restraints excluded: chain n residue 6 SER Chi-restraints excluded: chain n residue 35 LYS Chi-restraints excluded: chain n residue 57 THR Chi-restraints excluded: chain n residue 98 LEU Chi-restraints excluded: chain o residue 49 VAL Chi-restraints excluded: chain o residue 54 VAL Chi-restraints excluded: chain o residue 60 GLU Chi-restraints excluded: chain o residue 87 ILE Chi-restraints excluded: chain o residue 90 VAL Chi-restraints excluded: chain p residue 4 ILE Chi-restraints excluded: chain p residue 5 ILE Chi-restraints excluded: chain p residue 6 LYS Chi-restraints excluded: chain p residue 37 LYS Chi-restraints excluded: chain p residue 68 GLU Chi-restraints excluded: chain p residue 70 VAL Chi-restraints excluded: chain p residue 76 THR Chi-restraints excluded: chain p residue 102 GLU Chi-restraints excluded: chain p residue 114 LEU Chi-restraints excluded: chain q residue 22 LYS Chi-restraints excluded: chain q residue 77 SER Chi-restraints excluded: chain q residue 83 LEU Chi-restraints excluded: chain r residue 22 LEU Chi-restraints excluded: chain r residue 49 ILE Chi-restraints excluded: chain r residue 79 ARG Chi-restraints excluded: chain s residue 67 ASP Chi-restraints excluded: chain s residue 92 ARG Chi-restraints excluded: chain s residue 109 ASP Chi-restraints excluded: chain t residue 11 LEU Chi-restraints excluded: chain t residue 27 SER Chi-restraints excluded: chain t residue 58 VAL Chi-restraints excluded: chain t residue 78 VAL Chi-restraints excluded: chain u residue 5 ILE Chi-restraints excluded: chain u residue 54 ILE Chi-restraints excluded: chain u residue 57 SER Chi-restraints excluded: chain u residue 78 ASP Chi-restraints excluded: chain w residue 65 VAL Chi-restraints excluded: chain y residue 9 SER Chi-restraints excluded: chain y residue 10 THR Chi-restraints excluded: chain y residue 17 GLU Chi-restraints excluded: chain y residue 55 ARG Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 604 random chunks: chunk 360 optimal weight: 9.9990 chunk 232 optimal weight: 10.0000 chunk 347 optimal weight: 6.9990 chunk 175 optimal weight: 10.0000 chunk 114 optimal weight: 10.0000 chunk 112 optimal weight: 10.0000 chunk 370 optimal weight: 1.9990 chunk 396 optimal weight: 4.9990 chunk 287 optimal weight: 10.0000 chunk 54 optimal weight: 10.0000 chunk 457 optimal weight: 3.9990 overall best weight: 5.5990 ------------------------------------------------------------------------------- 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** ** 6 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 8 35 GLN h 2 GLN ** j 77 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** o 19 GLN ** o 34 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** o 38 GLN o 43 ASN p 52 ASN ** q 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** t 48 GLN ** w 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** w 24 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8551 moved from start: 0.3917 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 98796 Z= 0.258 Angle : 0.564 11.331 148742 Z= 0.297 Chirality : 0.036 0.290 19143 Planarity : 0.004 0.061 7297 Dihedral : 23.828 179.800 51690 Min Nonbonded Distance : 2.081 Molprobity Statistics. All-atom Clashscore : 9.21 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.39 % Favored : 95.55 % Rotamer: Outliers : 5.62 % Allowed : 31.59 % Favored : 62.78 % 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: 0.07 (0.15), residues: 3033 helix: 1.43 (0.18), residues: 820 sheet: -0.21 (0.20), residues: 629 loop : -0.53 (0.16), residues: 1584 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP c 213 HIS 0.006 0.001 HIS e 165 PHE 0.009 0.001 PHE w 26 TYR 0.029 0.001 TYR m 103 ARG 0.011 0.000 ARG k 105 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6066 Ramachandran restraints generated. 3033 Oldfield, 0 Emsley, 3033 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6066 Ramachandran restraints generated. 3033 Oldfield, 0 Emsley, 3033 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 761 residues out of total 2507 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 141 poor density : 620 time to evaluate : 3.869 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 0 77 LYS cc_start: 0.8701 (mmmt) cc_final: 0.8400 (tptp) REVERT: 2 21 LYS cc_start: 0.9424 (OUTLIER) cc_final: 0.9170 (mtmm) REVERT: c 114 ASP cc_start: 0.8445 (m-30) cc_final: 0.7972 (m-30) REVERT: e 69 ARG cc_start: 0.8338 (OUTLIER) cc_final: 0.6442 (ptp-170) REVERT: e 84 THR cc_start: 0.9142 (OUTLIER) cc_final: 0.8932 (t) REVERT: e 111 GLU cc_start: 0.8944 (tp30) cc_final: 0.8408 (tp30) REVERT: e 115 GLN cc_start: 0.9134 (mt0) cc_final: 0.8666 (mt0) REVERT: e 140 ASP cc_start: 0.8603 (m-30) cc_final: 0.8384 (m-30) REVERT: e 162 ARG cc_start: 0.9073 (OUTLIER) cc_final: 0.8783 (ttp-170) REVERT: f 27 GLN cc_start: 0.9158 (tt0) cc_final: 0.8802 (tt0) REVERT: f 42 GLU cc_start: 0.8779 (pm20) cc_final: 0.8515 (pm20) REVERT: f 64 LYS cc_start: 0.9086 (OUTLIER) cc_final: 0.7996 (pttt) REVERT: f 112 ARG cc_start: 0.9021 (ttm-80) cc_final: 0.8318 (tpt170) REVERT: g 3 ARG cc_start: 0.8056 (OUTLIER) cc_final: 0.6939 (tmt90) REVERT: g 6 LYS cc_start: 0.9209 (mmtp) cc_final: 0.8823 (mmtt) REVERT: g 106 SER cc_start: 0.9325 (OUTLIER) cc_final: 0.9084 (p) REVERT: g 158 LYS cc_start: 0.9131 (mtpt) cc_final: 0.8910 (mttt) REVERT: j 53 TYR cc_start: 0.9328 (m-80) cc_final: 0.8904 (m-80) REVERT: j 128 ASN cc_start: 0.8504 (p0) cc_final: 0.8042 (t0) REVERT: k 114 LYS cc_start: 0.7973 (OUTLIER) cc_final: 0.7581 (mtmt) REVERT: m 22 GLN cc_start: 0.8328 (OUTLIER) cc_final: 0.8073 (mm-40) REVERT: m 115 GLU cc_start: 0.8222 (OUTLIER) cc_final: 0.8015 (tm-30) REVERT: n 35 LYS cc_start: 0.9247 (OUTLIER) cc_final: 0.8958 (tttp) REVERT: n 110 MET cc_start: 0.8963 (mmp) cc_final: 0.8648 (mmp) REVERT: o 81 ARG cc_start: 0.8878 (mmm-85) cc_final: 0.8615 (mtt180) REVERT: o 104 GLN cc_start: 0.8805 (OUTLIER) cc_final: 0.8403 (tt0) REVERT: p 10 GLN cc_start: 0.8473 (tp40) cc_final: 0.8082 (mp10) REVERT: p 38 LYS cc_start: 0.8930 (ttpt) cc_final: 0.8625 (ttpt) REVERT: p 68 GLU cc_start: 0.8211 (OUTLIER) cc_final: 0.7411 (pm20) REVERT: p 89 ARG cc_start: 0.7945 (mtp-110) cc_final: 0.7706 (mtp-110) REVERT: p 102 GLU cc_start: 0.8552 (OUTLIER) cc_final: 0.7955 (mp0) REVERT: q 22 LYS cc_start: 0.8893 (OUTLIER) cc_final: 0.8691 (ttmm) REVERT: q 84 LYS cc_start: 0.8594 (ttmm) cc_final: 0.8198 (mttt) REVERT: q 107 THR cc_start: 0.9315 (m) cc_final: 0.9066 (p) REVERT: r 79 ARG cc_start: 0.9314 (OUTLIER) cc_final: 0.8896 (ptt180) REVERT: s 92 ARG cc_start: 0.7942 (OUTLIER) cc_final: 0.7588 (ttp80) REVERT: t 1 MET cc_start: 0.8126 (ttp) cc_final: 0.7864 (ttm) REVERT: t 9 LYS cc_start: 0.9002 (OUTLIER) cc_final: 0.8788 (mtpt) REVERT: u 10 GLU cc_start: 0.8375 (mm-30) cc_final: 0.8148 (tp30) REVERT: y 25 ARG cc_start: 0.8538 (mmt-90) cc_final: 0.8267 (mmp80) REVERT: y 55 ARG cc_start: 0.9022 (OUTLIER) cc_final: 0.7980 (ttp80) outliers start: 141 outliers final: 91 residues processed: 698 average time/residue: 1.7353 time to fit residues: 1644.4367 Evaluate side-chains 726 residues out of total 2507 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 110 poor density : 616 time to evaluate : 3.810 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 2 SER Chi-restraints excluded: chain 0 residue 35 SER Chi-restraints excluded: chain 2 residue 21 LYS Chi-restraints excluded: chain 2 residue 36 VAL Chi-restraints excluded: chain 3 residue 23 THR Chi-restraints excluded: chain 3 residue 27 SER Chi-restraints excluded: chain 7 residue 51 SER Chi-restraints excluded: chain 8 residue 13 ASN Chi-restraints excluded: chain 8 residue 25 VAL Chi-restraints excluded: chain c residue 53 HIS Chi-restraints excluded: chain c residue 88 SER Chi-restraints excluded: chain c residue 90 ASN Chi-restraints excluded: chain c residue 98 ASP Chi-restraints excluded: chain c residue 120 VAL Chi-restraints excluded: chain c residue 194 GLU Chi-restraints excluded: chain d residue 2 ILE Chi-restraints excluded: chain d residue 40 LEU Chi-restraints excluded: chain d residue 86 GLU Chi-restraints excluded: chain d residue 88 GLU Chi-restraints excluded: chain d residue 94 GLN Chi-restraints excluded: chain d residue 98 VAL Chi-restraints excluded: chain d residue 100 LEU Chi-restraints excluded: chain d residue 151 THR Chi-restraints excluded: chain e residue 4 VAL Chi-restraints excluded: chain e residue 69 ARG Chi-restraints excluded: chain e residue 84 THR Chi-restraints excluded: chain e residue 113 VAL Chi-restraints excluded: chain e residue 150 THR Chi-restraints excluded: chain e residue 162 ARG Chi-restraints excluded: chain e residue 191 ASP Chi-restraints excluded: chain e residue 199 MET Chi-restraints excluded: chain f residue 25 VAL Chi-restraints excluded: chain f residue 64 LYS Chi-restraints excluded: chain f residue 134 GLU Chi-restraints excluded: chain g residue 3 ARG Chi-restraints excluded: chain g residue 10 VAL Chi-restraints excluded: chain g residue 15 VAL Chi-restraints excluded: chain g residue 17 VAL Chi-restraints excluded: chain g residue 34 THR Chi-restraints excluded: chain g residue 36 THR Chi-restraints excluded: chain g residue 44 LYS Chi-restraints excluded: chain g residue 71 LEU Chi-restraints excluded: chain g residue 84 THR Chi-restraints excluded: chain g residue 92 VAL Chi-restraints excluded: chain g residue 106 SER Chi-restraints excluded: chain g residue 107 LEU Chi-restraints excluded: chain g residue 122 THR Chi-restraints excluded: chain g residue 127 THR Chi-restraints excluded: chain g residue 168 VAL Chi-restraints excluded: chain g residue 171 THR Chi-restraints excluded: chain h residue 15 LEU Chi-restraints excluded: chain h residue 37 VAL Chi-restraints excluded: chain j residue 30 THR Chi-restraints excluded: chain j residue 131 ASN Chi-restraints excluded: chain k residue 25 LEU Chi-restraints excluded: chain k residue 76 VAL Chi-restraints excluded: chain k residue 110 GLU Chi-restraints excluded: chain k residue 114 LYS Chi-restraints excluded: chain l residue 7 SER Chi-restraints excluded: chain l residue 30 THR Chi-restraints excluded: chain l residue 69 ARG Chi-restraints excluded: chain l residue 82 LEU Chi-restraints excluded: chain l residue 89 VAL Chi-restraints excluded: chain l residue 121 THR Chi-restraints excluded: chain m residue 1 MET Chi-restraints excluded: chain m residue 7 THR Chi-restraints excluded: chain m residue 22 GLN Chi-restraints excluded: chain m residue 30 SER Chi-restraints excluded: chain m residue 41 LEU Chi-restraints excluded: chain m residue 112 LEU Chi-restraints excluded: chain m residue 115 GLU Chi-restraints excluded: chain m residue 135 VAL Chi-restraints excluded: chain n residue 1 MET Chi-restraints excluded: chain n residue 6 SER Chi-restraints excluded: chain n residue 35 LYS Chi-restraints excluded: chain n residue 57 THR Chi-restraints excluded: chain o residue 49 VAL Chi-restraints excluded: chain o residue 54 VAL Chi-restraints excluded: chain o residue 60 GLU Chi-restraints excluded: chain o residue 90 VAL Chi-restraints excluded: chain o residue 104 GLN Chi-restraints excluded: chain p residue 4 ILE Chi-restraints excluded: chain p residue 5 ILE Chi-restraints excluded: chain p residue 68 GLU Chi-restraints excluded: chain p residue 70 VAL Chi-restraints excluded: chain p residue 76 THR Chi-restraints excluded: chain p residue 102 GLU Chi-restraints excluded: chain p residue 114 LEU Chi-restraints excluded: chain q residue 22 LYS Chi-restraints excluded: chain q residue 77 SER Chi-restraints excluded: chain q residue 83 LEU Chi-restraints excluded: chain r residue 22 LEU Chi-restraints excluded: chain r residue 49 ILE Chi-restraints excluded: chain r residue 79 ARG Chi-restraints excluded: chain s residue 67 ASP Chi-restraints excluded: chain s residue 92 ARG Chi-restraints excluded: chain s residue 109 ASP Chi-restraints excluded: chain t residue 9 LYS Chi-restraints excluded: chain t residue 11 LEU Chi-restraints excluded: chain t residue 58 VAL Chi-restraints excluded: chain t residue 78 VAL Chi-restraints excluded: chain t residue 79 THR Chi-restraints excluded: chain u residue 5 ILE Chi-restraints excluded: chain u residue 57 SER Chi-restraints excluded: chain u residue 78 ASP Chi-restraints excluded: chain w residue 65 VAL Chi-restraints excluded: chain y residue 9 SER Chi-restraints excluded: chain y residue 10 THR Chi-restraints excluded: chain y residue 17 GLU Chi-restraints excluded: chain y residue 55 ARG Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 604 random chunks: chunk 529 optimal weight: 5.9990 chunk 557 optimal weight: 5.9990 chunk 508 optimal weight: 10.0000 chunk 542 optimal weight: 5.9990 chunk 326 optimal weight: 20.0000 chunk 236 optimal weight: 10.0000 chunk 425 optimal weight: 7.9990 chunk 166 optimal weight: 10.0000 chunk 490 optimal weight: 6.9990 chunk 513 optimal weight: 9.9990 chunk 540 optimal weight: 9.9990 overall best weight: 6.5990 ------------------------------------------------------------------------------- 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** ** 6 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 8 35 GLN f 127 ASN ** j 77 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** o 19 GLN ** o 34 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** o 38 GLN o 43 ASN ** o 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** p 52 ASN ** q 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** t 48 GLN ** w 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** w 24 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8553 moved from start: 0.3975 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.067 98796 Z= 0.291 Angle : 0.568 11.180 148742 Z= 0.298 Chirality : 0.036 0.291 19143 Planarity : 0.004 0.065 7297 Dihedral : 23.789 179.315 51690 Min Nonbonded Distance : 2.082 Molprobity Statistics. All-atom Clashscore : 9.14 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.55 % Favored : 95.38 % Rotamer: Outliers : 5.27 % Allowed : 32.07 % Favored : 62.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.08 (0.15), residues: 3033 helix: 1.44 (0.18), residues: 821 sheet: -0.21 (0.20), residues: 632 loop : -0.53 (0.16), residues: 1580 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP c 213 HIS 0.006 0.001 HIS e 165 PHE 0.010 0.001 PHE n 21 TYR 0.030 0.001 TYR m 103 ARG 0.014 0.001 ARG f 148 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6066 Ramachandran restraints generated. 3033 Oldfield, 0 Emsley, 3033 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6066 Ramachandran restraints generated. 3033 Oldfield, 0 Emsley, 3033 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 745 residues out of total 2507 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 132 poor density : 613 time to evaluate : 3.820 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 2 21 LYS cc_start: 0.9424 (OUTLIER) cc_final: 0.9172 (mtmm) REVERT: c 114 ASP cc_start: 0.8413 (m-30) cc_final: 0.8094 (m-30) REVERT: e 69 ARG cc_start: 0.8346 (OUTLIER) cc_final: 0.6380 (ptp-170) REVERT: e 84 THR cc_start: 0.9152 (OUTLIER) cc_final: 0.8945 (t) REVERT: e 111 GLU cc_start: 0.8950 (tp30) cc_final: 0.8452 (tp30) REVERT: e 115 GLN cc_start: 0.9145 (mt0) cc_final: 0.8689 (mt0) REVERT: e 162 ARG cc_start: 0.9088 (OUTLIER) cc_final: 0.8800 (ttp-170) REVERT: f 64 LYS cc_start: 0.9093 (OUTLIER) cc_final: 0.8006 (pttt) REVERT: f 112 ARG cc_start: 0.9032 (ttm-80) cc_final: 0.8332 (tpt170) REVERT: f 148 ARG cc_start: 0.8706 (ttm110) cc_final: 0.8481 (mtp-110) REVERT: g 3 ARG cc_start: 0.8016 (OUTLIER) cc_final: 0.6720 (tmt90) REVERT: g 6 LYS cc_start: 0.9184 (mmtp) cc_final: 0.8804 (mmtt) REVERT: g 106 SER cc_start: 0.9332 (OUTLIER) cc_final: 0.9094 (p) REVERT: g 158 LYS cc_start: 0.9133 (mtpt) cc_final: 0.8924 (mttt) REVERT: j 53 TYR cc_start: 0.9324 (m-80) cc_final: 0.8895 (m-80) REVERT: j 128 ASN cc_start: 0.8493 (p0) cc_final: 0.8057 (t0) REVERT: m 22 GLN cc_start: 0.8310 (OUTLIER) cc_final: 0.8062 (mm-40) REVERT: m 47 GLU cc_start: 0.8048 (tp30) cc_final: 0.7845 (tp30) REVERT: m 111 GLU cc_start: 0.7460 (OUTLIER) cc_final: 0.7212 (mp0) REVERT: m 115 GLU cc_start: 0.8209 (OUTLIER) cc_final: 0.8005 (tm-30) REVERT: n 35 LYS cc_start: 0.9253 (OUTLIER) cc_final: 0.8968 (tttp) REVERT: n 110 MET cc_start: 0.8969 (mmp) cc_final: 0.8653 (mmp) REVERT: o 81 ARG cc_start: 0.8892 (mmm-85) cc_final: 0.8641 (mtt180) REVERT: o 104 GLN cc_start: 0.8814 (OUTLIER) cc_final: 0.8255 (tp40) REVERT: p 10 GLN cc_start: 0.8498 (tp40) cc_final: 0.8104 (mp10) REVERT: p 38 LYS cc_start: 0.8937 (ttpt) cc_final: 0.8632 (ttpt) REVERT: p 68 GLU cc_start: 0.8251 (OUTLIER) cc_final: 0.7494 (pm20) REVERT: p 89 ARG cc_start: 0.7941 (mtp-110) cc_final: 0.7702 (mtp-110) REVERT: p 102 GLU cc_start: 0.8568 (OUTLIER) cc_final: 0.7974 (mp0) REVERT: q 22 LYS cc_start: 0.8892 (OUTLIER) cc_final: 0.8688 (ttmm) REVERT: q 107 THR cc_start: 0.9314 (m) cc_final: 0.9065 (p) REVERT: r 79 ARG cc_start: 0.9322 (OUTLIER) cc_final: 0.8906 (ptt180) REVERT: s 92 ARG cc_start: 0.7969 (OUTLIER) cc_final: 0.7603 (ttp80) REVERT: t 1 MET cc_start: 0.8034 (ttp) cc_final: 0.7715 (ttm) REVERT: t 9 LYS cc_start: 0.8955 (OUTLIER) cc_final: 0.8718 (mtpt) REVERT: u 10 GLU cc_start: 0.8376 (mm-30) cc_final: 0.8087 (tp30) REVERT: y 25 ARG cc_start: 0.8544 (mmt-90) cc_final: 0.8274 (mmp80) REVERT: y 55 ARG cc_start: 0.9031 (OUTLIER) cc_final: 0.7983 (ttp80) outliers start: 132 outliers final: 90 residues processed: 689 average time/residue: 1.7558 time to fit residues: 1647.8113 Evaluate side-chains 709 residues out of total 2507 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 109 poor density : 600 time to evaluate : 3.684 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 2 SER Chi-restraints excluded: chain 0 residue 35 SER Chi-restraints excluded: chain 2 residue 21 LYS Chi-restraints excluded: chain 2 residue 36 VAL Chi-restraints excluded: chain 3 residue 23 THR Chi-restraints excluded: chain 3 residue 27 SER Chi-restraints excluded: chain 7 residue 51 SER Chi-restraints excluded: chain 7 residue 54 ASP Chi-restraints excluded: chain 8 residue 13 ASN Chi-restraints excluded: chain 8 residue 25 VAL Chi-restraints excluded: chain c residue 88 SER Chi-restraints excluded: chain c residue 90 ASN Chi-restraints excluded: chain c residue 120 VAL Chi-restraints excluded: chain d residue 2 ILE Chi-restraints excluded: chain d residue 40 LEU Chi-restraints excluded: chain d residue 88 GLU Chi-restraints excluded: chain d residue 94 GLN Chi-restraints excluded: chain d residue 98 VAL Chi-restraints excluded: chain d residue 100 LEU Chi-restraints excluded: chain d residue 151 THR Chi-restraints excluded: chain d residue 181 ASP Chi-restraints excluded: chain e residue 4 VAL Chi-restraints excluded: chain e residue 69 ARG Chi-restraints excluded: chain e residue 84 THR Chi-restraints excluded: chain e residue 113 VAL Chi-restraints excluded: chain e residue 150 THR Chi-restraints excluded: chain e residue 162 ARG Chi-restraints excluded: chain e residue 191 ASP Chi-restraints excluded: chain e residue 199 MET Chi-restraints excluded: chain f residue 25 VAL Chi-restraints excluded: chain f residue 64 LYS Chi-restraints excluded: chain f residue 132 VAL Chi-restraints excluded: chain f residue 134 GLU Chi-restraints excluded: chain f residue 146 VAL Chi-restraints excluded: chain g residue 3 ARG Chi-restraints excluded: chain g residue 15 VAL Chi-restraints excluded: chain g residue 17 VAL Chi-restraints excluded: chain g residue 34 THR Chi-restraints excluded: chain g residue 36 THR Chi-restraints excluded: chain g residue 44 LYS Chi-restraints excluded: chain g residue 71 LEU Chi-restraints excluded: chain g residue 84 THR Chi-restraints excluded: chain g residue 92 VAL Chi-restraints excluded: chain g residue 106 SER Chi-restraints excluded: chain g residue 122 THR Chi-restraints excluded: chain g residue 127 THR Chi-restraints excluded: chain g residue 168 VAL Chi-restraints excluded: chain g residue 171 THR Chi-restraints excluded: chain h residue 15 LEU Chi-restraints excluded: chain h residue 37 VAL Chi-restraints excluded: chain j residue 30 THR Chi-restraints excluded: chain j residue 131 ASN Chi-restraints excluded: chain k residue 25 LEU Chi-restraints excluded: chain k residue 76 VAL Chi-restraints excluded: chain l residue 7 SER Chi-restraints excluded: chain l residue 30 THR Chi-restraints excluded: chain l residue 69 ARG Chi-restraints excluded: chain l residue 82 LEU Chi-restraints excluded: chain l residue 121 THR Chi-restraints excluded: chain m residue 1 MET Chi-restraints excluded: chain m residue 7 THR Chi-restraints excluded: chain m residue 22 GLN Chi-restraints excluded: chain m residue 30 SER Chi-restraints excluded: chain m residue 41 LEU Chi-restraints excluded: chain m residue 111 GLU Chi-restraints excluded: chain m residue 112 LEU Chi-restraints excluded: chain m residue 115 GLU Chi-restraints excluded: chain m residue 135 VAL Chi-restraints excluded: chain n residue 1 MET Chi-restraints excluded: chain n residue 6 SER Chi-restraints excluded: chain n residue 35 LYS Chi-restraints excluded: chain n residue 57 THR Chi-restraints excluded: chain o residue 49 VAL Chi-restraints excluded: chain o residue 54 VAL Chi-restraints excluded: chain o residue 60 GLU Chi-restraints excluded: chain o residue 87 ILE Chi-restraints excluded: chain o residue 90 VAL Chi-restraints excluded: chain o residue 104 GLN Chi-restraints excluded: chain p residue 4 ILE Chi-restraints excluded: chain p residue 5 ILE Chi-restraints excluded: chain p residue 37 LYS Chi-restraints excluded: chain p residue 68 GLU Chi-restraints excluded: chain p residue 70 VAL Chi-restraints excluded: chain p residue 76 THR Chi-restraints excluded: chain p residue 102 GLU Chi-restraints excluded: chain p residue 114 LEU Chi-restraints excluded: chain q residue 22 LYS Chi-restraints excluded: chain q residue 77 SER Chi-restraints excluded: chain q residue 83 LEU Chi-restraints excluded: chain r residue 22 LEU Chi-restraints excluded: chain r residue 49 ILE Chi-restraints excluded: chain r residue 79 ARG Chi-restraints excluded: chain s residue 67 ASP Chi-restraints excluded: chain s residue 92 ARG Chi-restraints excluded: chain s residue 109 ASP Chi-restraints excluded: chain t residue 9 LYS Chi-restraints excluded: chain t residue 11 LEU Chi-restraints excluded: chain t residue 58 VAL Chi-restraints excluded: chain t residue 78 VAL Chi-restraints excluded: chain t residue 79 THR Chi-restraints excluded: chain u residue 5 ILE Chi-restraints excluded: chain u residue 54 ILE Chi-restraints excluded: chain u residue 57 SER Chi-restraints excluded: chain u residue 78 ASP Chi-restraints excluded: chain w residue 65 VAL Chi-restraints excluded: chain y residue 9 SER Chi-restraints excluded: chain y residue 10 THR Chi-restraints excluded: chain y residue 17 GLU Chi-restraints excluded: chain y residue 55 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 604 random chunks: chunk 356 optimal weight: 3.9990 chunk 573 optimal weight: 3.9990 chunk 350 optimal weight: 7.9990 chunk 272 optimal weight: 20.0000 chunk 398 optimal weight: 10.0000 chunk 601 optimal weight: 50.0000 chunk 553 optimal weight: 9.9990 chunk 479 optimal weight: 9.9990 chunk 49 optimal weight: 10.0000 chunk 370 optimal weight: 7.9990 chunk 293 optimal weight: 10.0000 overall best weight: 6.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 6 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 8 35 GLN e 195 GLN g 22 GLN ** j 77 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** o 19 GLN ** o 34 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** o 38 GLN o 43 ASN ** o 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** p 52 ASN ** q 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** t 48 GLN ** w 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** w 24 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8554 moved from start: 0.4025 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.067 98796 Z= 0.299 Angle : 0.572 11.453 148742 Z= 0.300 Chirality : 0.036 0.290 19143 Planarity : 0.004 0.058 7297 Dihedral : 23.785 179.237 51690 Min Nonbonded Distance : 2.084 Molprobity Statistics. All-atom Clashscore : 9.26 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.48 % Favored : 95.45 % Rotamer: Outliers : 4.87 % Allowed : 32.43 % Favored : 62.70 % 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: 0.08 (0.15), residues: 3033 helix: 1.45 (0.18), residues: 821 sheet: -0.23 (0.20), residues: 632 loop : -0.53 (0.16), residues: 1580 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP c 213 HIS 0.006 0.001 HIS e 165 PHE 0.011 0.001 PHE n 21 TYR 0.029 0.001 TYR m 103 ARG 0.014 0.001 ARG k 105 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6066 Ramachandran restraints generated. 3033 Oldfield, 0 Emsley, 3033 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6066 Ramachandran restraints generated. 3033 Oldfield, 0 Emsley, 3033 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 724 residues out of total 2507 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 122 poor density : 602 time to evaluate : 3.812 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 2 21 LYS cc_start: 0.9423 (OUTLIER) cc_final: 0.9176 (mtmm) REVERT: 8 20 ASP cc_start: 0.8271 (OUTLIER) cc_final: 0.7974 (t70) REVERT: c 114 ASP cc_start: 0.8410 (m-30) cc_final: 0.8091 (m-30) REVERT: e 69 ARG cc_start: 0.8349 (OUTLIER) cc_final: 0.6381 (ptp-170) REVERT: e 84 THR cc_start: 0.9157 (OUTLIER) cc_final: 0.8950 (t) REVERT: e 111 GLU cc_start: 0.8951 (tp30) cc_final: 0.8470 (tp30) REVERT: e 115 GLN cc_start: 0.9154 (mt0) cc_final: 0.8786 (mt0) REVERT: e 162 ARG cc_start: 0.9098 (OUTLIER) cc_final: 0.8685 (ttp-170) REVERT: f 42 GLU cc_start: 0.8843 (pm20) cc_final: 0.8570 (pm20) REVERT: f 64 LYS cc_start: 0.9102 (OUTLIER) cc_final: 0.7998 (pttt) REVERT: f 112 ARG cc_start: 0.9047 (ttm-80) cc_final: 0.8301 (tpt170) REVERT: f 148 ARG cc_start: 0.8729 (ttm110) cc_final: 0.8491 (mtp-110) REVERT: g 3 ARG cc_start: 0.8024 (OUTLIER) cc_final: 0.6808 (tmt90) REVERT: g 6 LYS cc_start: 0.9192 (mmtp) cc_final: 0.8800 (mmtt) REVERT: g 106 SER cc_start: 0.9333 (OUTLIER) cc_final: 0.9089 (p) REVERT: g 158 LYS cc_start: 0.9137 (mtpt) cc_final: 0.8920 (mttt) REVERT: j 53 TYR cc_start: 0.9329 (m-80) cc_final: 0.8902 (m-80) REVERT: j 128 ASN cc_start: 0.8589 (p0) cc_final: 0.8068 (t0) REVERT: m 22 GLN cc_start: 0.8302 (OUTLIER) cc_final: 0.8057 (mm-40) REVERT: m 111 GLU cc_start: 0.7464 (OUTLIER) cc_final: 0.7213 (mp0) REVERT: m 115 GLU cc_start: 0.8198 (OUTLIER) cc_final: 0.7997 (tm-30) REVERT: n 35 LYS cc_start: 0.9254 (OUTLIER) cc_final: 0.8968 (tttp) REVERT: n 110 MET cc_start: 0.8973 (mmp) cc_final: 0.8656 (mmp) REVERT: o 81 ARG cc_start: 0.8874 (mmm-85) cc_final: 0.8606 (mtt180) REVERT: o 104 GLN cc_start: 0.8808 (OUTLIER) cc_final: 0.8248 (tp40) REVERT: p 10 GLN cc_start: 0.8506 (tp40) cc_final: 0.8113 (mp10) REVERT: p 38 LYS cc_start: 0.8941 (ttpt) cc_final: 0.8638 (ttpt) REVERT: p 68 GLU cc_start: 0.8254 (OUTLIER) cc_final: 0.7528 (pm20) REVERT: p 89 ARG cc_start: 0.7939 (mtp-110) cc_final: 0.7701 (mtp-110) REVERT: p 102 GLU cc_start: 0.8563 (OUTLIER) cc_final: 0.7973 (mp0) REVERT: q 22 LYS cc_start: 0.8895 (OUTLIER) cc_final: 0.8692 (ttmm) REVERT: q 107 THR cc_start: 0.9316 (m) cc_final: 0.9066 (p) REVERT: r 79 ARG cc_start: 0.9330 (OUTLIER) cc_final: 0.8903 (ptt180) REVERT: s 92 ARG cc_start: 0.7926 (OUTLIER) cc_final: 0.7573 (ttp80) REVERT: t 9 LYS cc_start: 0.8939 (OUTLIER) cc_final: 0.8702 (mtpt) REVERT: u 10 GLU cc_start: 0.8298 (mm-30) cc_final: 0.8003 (tp30) REVERT: u 27 ASN cc_start: 0.8575 (m110) cc_final: 0.8235 (m-40) REVERT: y 25 ARG cc_start: 0.8547 (mmt-90) cc_final: 0.8274 (mmp80) REVERT: y 55 ARG cc_start: 0.9034 (OUTLIER) cc_final: 0.7984 (ttp80) outliers start: 122 outliers final: 93 residues processed: 676 average time/residue: 1.7178 time to fit residues: 1581.4000 Evaluate side-chains 717 residues out of total 2507 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 113 poor density : 604 time to evaluate : 3.696 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 2 SER Chi-restraints excluded: chain 0 residue 35 SER Chi-restraints excluded: chain 2 residue 21 LYS Chi-restraints excluded: chain 2 residue 36 VAL Chi-restraints excluded: chain 2 residue 41 THR Chi-restraints excluded: chain 3 residue 23 THR Chi-restraints excluded: chain 3 residue 27 SER Chi-restraints excluded: chain 7 residue 51 SER Chi-restraints excluded: chain 8 residue 13 ASN Chi-restraints excluded: chain 8 residue 20 ASP Chi-restraints excluded: chain 8 residue 25 VAL Chi-restraints excluded: chain c residue 88 SER Chi-restraints excluded: chain c residue 90 ASN Chi-restraints excluded: chain c residue 120 VAL Chi-restraints excluded: chain c residue 194 GLU Chi-restraints excluded: chain d residue 2 ILE Chi-restraints excluded: chain d residue 40 LEU Chi-restraints excluded: chain d residue 88 GLU Chi-restraints excluded: chain d residue 94 GLN Chi-restraints excluded: chain d residue 98 VAL Chi-restraints excluded: chain d residue 100 LEU Chi-restraints excluded: chain d residue 151 THR Chi-restraints excluded: chain d residue 183 GLU Chi-restraints excluded: chain e residue 4 VAL Chi-restraints excluded: chain e residue 5 LEU Chi-restraints excluded: chain e residue 6 LYS Chi-restraints excluded: chain e residue 69 ARG Chi-restraints excluded: chain e residue 72 SER Chi-restraints excluded: chain e residue 84 THR Chi-restraints excluded: chain e residue 113 VAL Chi-restraints excluded: chain e residue 150 THR Chi-restraints excluded: chain e residue 162 ARG Chi-restraints excluded: chain e residue 191 ASP Chi-restraints excluded: chain e residue 199 MET Chi-restraints excluded: chain f residue 25 VAL Chi-restraints excluded: chain f residue 35 THR Chi-restraints excluded: chain f residue 64 LYS Chi-restraints excluded: chain f residue 132 VAL Chi-restraints excluded: chain f residue 134 GLU Chi-restraints excluded: chain f residue 146 VAL Chi-restraints excluded: chain g residue 3 ARG Chi-restraints excluded: chain g residue 15 VAL Chi-restraints excluded: chain g residue 17 VAL Chi-restraints excluded: chain g residue 34 THR Chi-restraints excluded: chain g residue 36 THR Chi-restraints excluded: chain g residue 44 LYS Chi-restraints excluded: chain g residue 71 LEU Chi-restraints excluded: chain g residue 84 THR Chi-restraints excluded: chain g residue 92 VAL Chi-restraints excluded: chain g residue 106 SER Chi-restraints excluded: chain g residue 122 THR Chi-restraints excluded: chain g residue 127 THR Chi-restraints excluded: chain g residue 171 THR Chi-restraints excluded: chain h residue 15 LEU Chi-restraints excluded: chain h residue 37 VAL Chi-restraints excluded: chain j residue 30 THR Chi-restraints excluded: chain j residue 131 ASN Chi-restraints excluded: chain k residue 25 LEU Chi-restraints excluded: chain k residue 76 VAL Chi-restraints excluded: chain l residue 7 SER Chi-restraints excluded: chain l residue 30 THR Chi-restraints excluded: chain l residue 69 ARG Chi-restraints excluded: chain l residue 82 LEU Chi-restraints excluded: chain l residue 121 THR Chi-restraints excluded: chain m residue 1 MET Chi-restraints excluded: chain m residue 7 THR Chi-restraints excluded: chain m residue 22 GLN Chi-restraints excluded: chain m residue 30 SER Chi-restraints excluded: chain m residue 41 LEU Chi-restraints excluded: chain m residue 111 GLU Chi-restraints excluded: chain m residue 112 LEU Chi-restraints excluded: chain m residue 115 GLU Chi-restraints excluded: chain m residue 135 VAL Chi-restraints excluded: chain n residue 1 MET Chi-restraints excluded: chain n residue 6 SER Chi-restraints excluded: chain n residue 35 LYS Chi-restraints excluded: chain n residue 57 THR Chi-restraints excluded: chain o residue 49 VAL Chi-restraints excluded: chain o residue 54 VAL Chi-restraints excluded: chain o residue 60 GLU Chi-restraints excluded: chain o residue 87 ILE Chi-restraints excluded: chain o residue 90 VAL Chi-restraints excluded: chain o residue 104 GLN Chi-restraints excluded: chain p residue 4 ILE Chi-restraints excluded: chain p residue 5 ILE Chi-restraints excluded: chain p residue 68 GLU Chi-restraints excluded: chain p residue 70 VAL Chi-restraints excluded: chain p residue 76 THR Chi-restraints excluded: chain p residue 102 GLU Chi-restraints excluded: chain p residue 114 LEU Chi-restraints excluded: chain q residue 22 LYS Chi-restraints excluded: chain q residue 77 SER Chi-restraints excluded: chain q residue 83 LEU Chi-restraints excluded: chain r residue 22 LEU Chi-restraints excluded: chain r residue 49 ILE Chi-restraints excluded: chain r residue 79 ARG Chi-restraints excluded: chain s residue 67 ASP Chi-restraints excluded: chain s residue 92 ARG Chi-restraints excluded: chain s residue 109 ASP Chi-restraints excluded: chain t residue 9 LYS Chi-restraints excluded: chain t residue 11 LEU Chi-restraints excluded: chain t residue 58 VAL Chi-restraints excluded: chain t residue 78 VAL Chi-restraints excluded: chain t residue 79 THR Chi-restraints excluded: chain u residue 5 ILE Chi-restraints excluded: chain u residue 54 ILE Chi-restraints excluded: chain u residue 57 SER Chi-restraints excluded: chain u residue 78 ASP Chi-restraints excluded: chain w residue 65 VAL Chi-restraints excluded: chain y residue 9 SER Chi-restraints excluded: chain y residue 10 THR Chi-restraints excluded: chain y residue 17 GLU Chi-restraints excluded: chain y residue 55 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 604 random chunks: chunk 380 optimal weight: 9.9990 chunk 510 optimal weight: 9.9990 chunk 146 optimal weight: 10.0000 chunk 441 optimal weight: 1.9990 chunk 70 optimal weight: 10.0000 chunk 133 optimal weight: 10.0000 chunk 479 optimal weight: 9.9990 chunk 200 optimal weight: 30.0000 chunk 492 optimal weight: 0.7980 chunk 60 optimal weight: 20.0000 chunk 88 optimal weight: 40.0000 overall best weight: 6.5588 ------------------------------------------------------------------------------- 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** ** 6 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 8 35 GLN e 195 GLN f 127 ASN ** j 77 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** o 19 GLN ** o 34 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** o 38 GLN o 43 ASN ** o 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** p 52 ASN ** q 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** w 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** w 24 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3299 r_free = 0.3299 target = 0.089026 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2757 r_free = 0.2757 target = 0.064817 restraints weight = 227298.361| |-----------------------------------------------------------------------------| r_work (start): 0.2719 rms_B_bonded: 1.22 r_work: 0.2604 rms_B_bonded: 2.21 restraints_weight: 0.5000 r_work: 0.2509 rms_B_bonded: 3.50 restraints_weight: 0.2500 r_work (final): 0.2509 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8860 moved from start: 0.4049 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.067 98796 Z= 0.290 Angle : 0.570 11.430 148742 Z= 0.299 Chirality : 0.036 0.288 19143 Planarity : 0.004 0.058 7297 Dihedral : 23.781 179.329 51690 Min Nonbonded Distance : 2.087 Molprobity Statistics. All-atom Clashscore : 9.38 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.42 % Favored : 95.52 % Rotamer: Outliers : 4.99 % Allowed : 32.39 % Favored : 62.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.05 (0.15), residues: 3033 helix: 1.42 (0.18), residues: 821 sheet: -0.25 (0.20), residues: 627 loop : -0.54 (0.16), residues: 1585 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP c 213 HIS 0.005 0.001 HIS e 165 PHE 0.010 0.001 PHE n 21 TYR 0.029 0.001 TYR m 103 ARG 0.013 0.001 ARG k 105 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 25522.50 seconds wall clock time: 447 minutes 2.27 seconds (26822.27 seconds total)