Starting phenix.real_space_refine on Wed Feb 21 01:16:58 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wnt_21856/02_2024/6wnt_21856.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wnt_21856/02_2024/6wnt_21856.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wnt_21856/02_2024/6wnt_21856.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wnt_21856/02_2024/6wnt_21856.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wnt_21856/02_2024/6wnt_21856.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wnt_21856/02_2024/6wnt_21856.pdb" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.774 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 3024 5.49 5 S 87 5.16 5 C 45409 2.51 5 N 16964 2.21 5 O 25680 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "b GLU 22": "OE1" <-> "OE2" Residue "b ASP 65": "OD1" <-> "OD2" Residue "b TYR 82": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b ASP 83": "OD1" <-> "OD2" Residue "b TYR 95": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b ASP 120": "OD1" <-> "OD2" Residue "b ASP 167": "OD1" <-> "OD2" Residue "b PHE 265": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "c ARG 13": "NH1" <-> "NH2" Residue "c GLU 17": "OE1" <-> "OE2" Residue "c ARG 33": "NH1" <-> "NH2" Residue "c ARG 59": "NH1" <-> "NH2" Residue "c ARG 77": "NH1" <-> "NH2" Residue "c PHE 82": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "c ARG 83": "NH1" <-> "NH2" Residue "c GLU 88": "OE1" <-> "OE2" Residue "c PHE 118": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "c ASP 131": "OD1" <-> "OD2" Residue "c ARG 169": "NH1" <-> "NH2" Residue "c ASP 176": "OD1" <-> "OD2" Residue "c ARG 184": "NH1" <-> "NH2" Residue "d GLU 16": "OE1" <-> "OE2" Residue "d ARG 21": "NH1" <-> "NH2" Residue "d GLU 25": "OE1" <-> "OE2" Residue "d ARG 44": "NH1" <-> "NH2" Residue "d ARG 49": "NH1" <-> "NH2" Residue "d ARG 61": "NH1" <-> "NH2" Residue "d ARG 88": "NH1" <-> "NH2" Residue "d ASP 91": "OD1" <-> "OD2" Residue "d ARG 102": "NH1" <-> "NH2" Residue "d ARG 162": "NH1" <-> "NH2" Residue "d ARG 170": "NH1" <-> "NH2" Residue "d ASP 176": "OD1" <-> "OD2" Residue "d ASP 191": "OD1" <-> "OD2" Residue "e ASP 5": "OD1" <-> "OD2" Residue "e GLU 10": "OE1" <-> "OE2" Residue "e ASP 55": "OD1" <-> "OD2" Residue "e ARG 70": "NH1" <-> "NH2" Residue "e ARG 79": "NH1" <-> "NH2" Residue "e ARG 91": "NH1" <-> "NH2" Residue "e GLU 100": "OE1" <-> "OE2" Residue "e ARG 101": "NH1" <-> "NH2" Residue "e ARG 109": "NH1" <-> "NH2" Residue "e ARG 111": "NH1" <-> "NH2" Residue "e ARG 114": "NH1" <-> "NH2" Residue "e PHE 121": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "e ASP 122": "OD1" <-> "OD2" Residue "e ARG 132": "NH1" <-> "NH2" Residue "e GLU 133": "OE1" <-> "OE2" Residue "e ASP 146": "OD1" <-> "OD2" Residue "e ASP 162": "OD1" <-> "OD2" Residue "f ARG 2": "NH1" <-> "NH2" Residue "f ASP 38": "OD1" <-> "OD2" Residue "f ASP 146": "OD1" <-> "OD2" Residue "f ARG 152": "NH1" <-> "NH2" Residue "f ARG 162": "NH1" <-> "NH2" Residue "f ASP 165": "OD1" <-> "OD2" Residue "f ARG 169": "NH1" <-> "NH2" Residue "g ASP 7": "OD1" <-> "OD2" Residue "g ASP 17": "OD1" <-> "OD2" Residue "g PHE 47": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "h PHE 76": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "h GLU 116": "OE1" <-> "OE2" Residue "i ASP 120": "OD1" <-> "OD2" Residue "i GLU 122": "OE1" <-> "OE2" Residue "j GLU 9": "OE1" <-> "OE2" Residue "j ARG 13": "NH1" <-> "NH2" Residue "j ARG 37": "NH1" <-> "NH2" Residue "j ASP 60": "OD1" <-> "OD2" Residue "j ARG 96": "NH1" <-> "NH2" Residue "j GLU 102": "OE1" <-> "OE2" Residue "j ARG 120": "NH1" <-> "NH2" Residue "k GLU 45": "OE1" <-> "OE2" Residue "k ASP 73": "OD1" <-> "OD2" Residue "k ASP 80": "OD1" <-> "OD2" 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 ASP 81": "OD1" <-> "OD2" Residue "l ARG 126": "NH1" <-> "NH2" Residue "n ARG 8": "NH1" <-> "NH2" Residue "n ARG 12": "NH1" <-> "NH2" Residue "n ARG 17": "NH1" <-> "NH2" Residue "n ARG 22": "NH1" <-> "NH2" Residue "n GLU 43": "OE1" <-> "OE2" Residue "n ARG 46": "NH1" <-> "NH2" Residue "n ARG 63": "NH1" <-> "NH2" Residue "n ARG 64": "NH1" <-> "NH2" Residue "n ARG 69": "NH1" <-> "NH2" Residue "n ARG 71": "NH1" <-> "NH2" Residue "n ASP 72": "OD1" <-> "OD2" Residue "n ARG 96": "NH1" <-> "NH2" Residue "n ASP 117": "OD1" <-> "OD2" Residue "n ARG 118": "NH1" <-> "NH2" Residue "o ARG 10": "NH1" <-> "NH2" Residue "o ARG 16": "NH1" <-> "NH2" Residue "o ARG 25": "NH1" <-> "NH2" Residue "o GLU 60": "OE1" <-> "OE2" Residue "o ARG 81": "NH1" <-> "NH2" Residue "o GLU 84": "OE1" <-> "OE2" Residue "o ASP 93": "OD1" <-> "OD2" Residue "o ARG 94": "NH1" <-> "NH2" Residue "o ARG 102": "NH1" <-> "NH2" Residue "o ARG 111": "NH1" <-> "NH2" Residue "p ASP 15": "OD1" <-> "OD2" Residue "p ARG 20": "NH1" <-> "NH2" Residue "p GLU 33": "OE1" <-> "OE2" Residue "p ARG 38": "NH1" <-> "NH2" Residue "p PHE 42": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "p GLU 43": "OE1" <-> "OE2" Residue "p ARG 61": "NH1" <-> "NH2" Residue "p ARG 88": "NH1" <-> "NH2" Residue "p TYR 98": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "p ARG 100": "NH1" <-> "NH2" Residue "p ARG 108": "NH1" <-> "NH2" Residue "p GLU 111": "OE1" <-> "OE2" Residue "q ARG 2": "NH1" <-> "NH2" Residue "q ARG 5": "NH1" <-> "NH2" Residue "q ARG 12": "NH1" <-> "NH2" Residue "q ARG 32": "NH1" <-> "NH2" Residue "q ARG 47": "NH1" <-> "NH2" Residue "q ARG 69": "NH1" <-> "NH2" Residue "q GLU 88": "OE1" <-> "OE2" Residue "q GLU 110": "OE1" <-> "OE2" Residue "r TYR 2": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "r ARG 21": "NH1" <-> "NH2" Residue "r GLU 37": "OE1" <-> "OE2" Residue "r ARG 68": "NH1" <-> "NH2" Residue "r ARG 78": "NH1" <-> "NH2" Residue "r ARG 79": "NH1" <-> "NH2" Residue "r ARG 84": "NH1" <-> "NH2" Residue "s GLU 59": "OE1" <-> "OE2" Residue "s ASP 68": "OD1" <-> "OD2" 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 "s ARG 110": "NH1" <-> "NH2" Residue "t GLU 25": "OE1" <-> "OE2" Residue "t GLU 54": "OE1" <-> "OE2" Residue "t GLU 56": "OE1" <-> "OE2" Residue "t ARG 73": "NH1" <-> "NH2" Residue "t ASP 79": "OD1" <-> "OD2" Residue "u ARG 5": "NH1" <-> "NH2" Residue "u ARG 6": "NH1" <-> "NH2" Residue "u ARG 81": "NH1" <-> "NH2" Residue "u ARG 85": "NH1" <-> "NH2" Residue "u ARG 93": "NH1" <-> "NH2" Residue "v GLU 7": "OE1" <-> "OE2" Residue "v TYR 31": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "v GLU 35": "OE1" <-> "OE2" Residue "w GLU 25": "OE1" <-> "OE2" Residue "w ASP 52": "OD1" <-> "OD2" Residue "w PHE 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "w GLU 66": "OE1" <-> "OE2" Residue "y ARG 29": "NH1" <-> "NH2" Residue "y ARG 47": "NH1" <-> "NH2" Residue "y ARG 52": "NH1" <-> "NH2" Residue "z ARG 10": "NH1" <-> "NH2" Residue "z ARG 29": "NH1" <-> "NH2" Residue "z ARG 44": "NH1" <-> "NH2" Residue "A ASP 4": "OD1" <-> "OD2" Residue "B ARG 9": "NH1" <-> "NH2" Residue "B ARG 15": "NH1" <-> "NH2" Residue "B ARG 39": "NH1" <-> "NH2" Residue "B ARG 51": "NH1" <-> "NH2" Residue "D ARG 3": "NH1" <-> "NH2" Residue "D ARG 12": "NH1" <-> "NH2" Residue "D ARG 14": "NH1" <-> "NH2" Residue "D ARG 19": "NH1" <-> "NH2" Residue "D ARG 21": "NH1" <-> "NH2" Residue "D ARG 33": "NH1" <-> "NH2" Residue "D ARG 41": "NH1" <-> "NH2" Residue "E ARG 12": "NH1" <-> "NH2" Residue "E ARG 29": "NH1" <-> "NH2" Residue "E ARG 39": "NH1" <-> "NH2" Residue "E ARG 41": "NH1" <-> "NH2" Residue "F ARG 12": "NH1" <-> "NH2" Residue "F ASP 20": "OD1" <-> "OD2" Residue "F ARG 24": "NH1" <-> "NH2" Residue "a ARG 7": "NH1" <-> "NH2" Residue "a ARG 12": "NH1" <-> "NH2" Residue "a ASP 56": "OD1" <-> "OD2" Residue "a ARG 162": "NH1" <-> "NH2" Residue "a ASP 179": "OD1" <-> "OD2" Residue "a ASP 183": "OD1" <-> "OD2" 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: 91164 Number of models: 1 Model: "" Number of chains: 31 Chain: "b" 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: "c" Number of atoms: 1564 Number of conformers: 1 Conformer: "" Number of residues, atoms: 209, 1564 Classifications: {'peptide': 209} Link IDs: {'PTRANS': 6, 'TRANS': 202} Chain: "d" Number of atoms: 1551 Number of conformers: 1 Conformer: "" Number of residues, atoms: 201, 1551 Classifications: {'peptide': 201} Link IDs: {'PTRANS': 5, 'TRANS': 195} Chain: "e" 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: "f" Number of atoms: 1322 Number of conformers: 1 Conformer: "" Number of residues, atoms: 176, 1322 Classifications: {'peptide': 176} Link IDs: {'PTRANS': 8, 'TRANS': 167} Chain: "g" Number of atoms: 409 Number of conformers: 1 Conformer: "" Number of residues, atoms: 53, 409 Classifications: {'peptide': 53} Link IDs: {'PTRANS': 2, 'TRANS': 50} Chain: "h" Number of atoms: 988 Number of conformers: 1 Conformer: "" Number of residues, atoms: 131, 988 Classifications: {'peptide': 131} Link IDs: {'PTRANS': 5, 'TRANS': 125} Chain: "i" Number of atoms: 1031 Number of conformers: 1 Conformer: "" Number of residues, atoms: 141, 1031 Classifications: {'peptide': 141} Link IDs: {'PTRANS': 9, 'TRANS': 131} Chain: "j" Number of atoms: 1128 Number of conformers: 1 Conformer: "" Number of residues, atoms: 142, 1128 Classifications: {'peptide': 142} 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: 1044 Number of conformers: 1 Conformer: "" Number of residues, atoms: 143, 1044 Classifications: {'peptide': 143} Link IDs: {'PTRANS': 4, 'TRANS': 138} 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: 891 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 891 Classifications: {'peptide': 116} Link IDs: {'PTRANS': 2, 'TRANS': 113} Chain: "p" Number of atoms: 916 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 916 Classifications: {'peptide': 114} Link IDs: {'PTRANS': 3, 'TRANS': 110} Chain: "q" Number of atoms: 946 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 946 Classifications: {'peptide': 117} Link IDs: {'TRANS': 116} Chain: "r" Number of atoms: 815 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 815 Classifications: {'peptide': 103} Link IDs: {'PTRANS': 1, 'TRANS': 101} Chain: "s" Number of atoms: 856 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 856 Classifications: {'peptide': 110} Link IDs: {'PTRANS': 2, 'TRANS': 107} Chain: "t" Number of atoms: 738 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 738 Classifications: {'peptide': 93} Link IDs: {'PTRANS': 1, 'TRANS': 91} Chain: "u" Number of atoms: 779 Number of conformers: 1 Conformer: "" Number of residues, atoms: 102, 779 Classifications: {'peptide': 102} Link IDs: {'PTRANS': 3, 'TRANS': 98} Chain: "v" Number of atoms: 752 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 752 Classifications: {'peptide': 94} Link IDs: {'PTRANS': 4, 'TRANS': 89} Chain: "w" Number of atoms: 574 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 574 Classifications: {'peptide': 75} Link IDs: {'PTRANS': 1, 'TRANS': 73} Chain: "x" Number of atoms: 624 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 624 Classifications: {'peptide': 77} Link IDs: {'PTRANS': 2, 'TRANS': 74} Chain: "y" Number of atoms: 508 Number of conformers: 1 Conformer: "" Number of residues, atoms: 63, 508 Classifications: {'peptide': 63} Link IDs: {'TRANS': 62} Chain: "z" Number of atoms: 448 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 448 Classifications: {'peptide': 58} Link IDs: {'PTRANS': 2, 'TRANS': 55} Chain: "A" Number of atoms: 315 Number of conformers: 1 Conformer: "" Number of residues, atoms: 41, 315 Classifications: {'peptide': 41} Link IDs: {'PTRANS': 1, 'TRANS': 39} Chain: "B" Number of atoms: 443 Number of conformers: 1 Conformer: "" Number of residues, atoms: 56, 443 Classifications: {'peptide': 56} Link IDs: {'PTRANS': 1, 'TRANS': 54} Chain: "D" Number of atoms: 376 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 376 Classifications: {'peptide': 46} Link IDs: {'PTRANS': 1, 'TRANS': 44} Chain: "E" Number of atoms: 503 Number of conformers: 1 Conformer: "" Number of residues, atoms: 64, 503 Classifications: {'peptide': 64} Link IDs: {'PTRANS': 2, 'TRANS': 61} Chain: "F" Number of atoms: 302 Number of conformers: 1 Conformer: "" Number of residues, atoms: 38, 302 Classifications: {'peptide': 38} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 36} Chain: "a" Number of atoms: 1026 Number of conformers: 1 Conformer: "" Number of residues, atoms: 134, 1026 Classifications: {'peptide': 134} Link IDs: {'PTRANS': 2, 'TRANS': 131} Chain breaks: 1 Chain: "4" Number of atoms: 64925 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3025, 64925 Classifications: {'RNA': 3025} Modifications used: {'5*END': 1, 'rna2p_pur': 220, 'rna2p_pyr': 105, 'rna3p_pur': 1517, 'rna3p_pyr': 1183} Link IDs: {'rna2p': 325, 'rna3p': 2699} Chain breaks: 1 Time building chain proxies: 36.02, per 1000 atoms: 0.40 Number of scatterers: 91164 At special positions: 0 Unit cell: (223.59, 201.84, 245.34, 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 87 16.00 P 3024 15.00 O 25680 8.00 N 16964 7.00 C 45409 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 38.12 Conformation dependent library (CDL) restraints added in 5.7 seconds 6650 Ramachandran restraints generated. 3325 Oldfield, 0 Emsley, 3325 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6190 Finding SS restraints... Secondary structure from input PDB file: 98 helices and 47 sheets defined 29.7% alpha, 18.1% beta 921 base pairs and 1674 stacking pairs defined. Time for finding SS restraints: 36.09 Creating SS restraints... Processing helix chain 'b' and resid 29 through 31 No H-bonds generated for 'chain 'b' and resid 29 through 31' Processing helix chain 'b' and resid 132 through 134 No H-bonds generated for 'chain 'b' and resid 132 through 134' Processing helix chain 'b' and resid 206 through 212 removed outlier: 4.228A pdb=" N ALA b 210 " --> pdb=" O LYS b 206 " (cutoff:3.500A) Processing helix chain 'c' and resid 61 through 72 Processing helix chain 'c' and resid 97 through 104 removed outlier: 3.931A pdb=" N LEU c 100 " --> pdb=" O SER c 97 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N ASP c 103 " --> pdb=" O LEU c 100 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N VAL c 104 " --> pdb=" O PHE c 101 " (cutoff:3.500A) Processing helix chain 'c' and resid 120 through 126 Processing helix chain 'd' and resid 15 through 20 Processing helix chain 'd' and resid 24 through 38 removed outlier: 3.536A pdb=" N GLN d 30 " --> pdb=" O ALA d 26 " (cutoff:3.500A) Processing helix chain 'd' and resid 97 through 115 Processing helix chain 'd' and resid 130 through 139 removed outlier: 3.514A pdb=" N LEU d 134 " --> pdb=" O LYS d 130 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N LYS d 139 " --> pdb=" O ALA d 135 " (cutoff:3.500A) Processing helix chain 'd' and resid 154 through 161 removed outlier: 3.585A pdb=" N PHE d 158 " --> pdb=" O ASP d 154 " (cutoff:3.500A) Processing helix chain 'd' and resid 173 through 175 No H-bonds generated for 'chain 'd' and resid 173 through 175' Processing helix chain 'd' and resid 176 through 183 removed outlier: 3.527A pdb=" N ILE d 181 " --> pdb=" O PRO d 177 " (cutoff:3.500A) Processing helix chain 'd' and resid 190 through 200 Processing helix chain 'e' and resid 2 through 19 removed outlier: 3.670A pdb=" N VAL e 11 " --> pdb=" O TYR e 7 " (cutoff:3.500A) removed outlier: 5.486A pdb=" N VAL e 12 " --> pdb=" O LYS e 8 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N LYS e 13 " --> pdb=" O ASP e 9 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N THR e 17 " --> pdb=" O LYS e 13 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N GLU e 18 " --> pdb=" O LYS e 14 " (cutoff:3.500A) Processing helix chain 'e' and resid 40 through 44 removed outlier: 3.870A pdb=" N ILE e 43 " --> pdb=" O GLY e 40 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N ALA e 44 " --> pdb=" O GLU e 41 " (cutoff:3.500A) No H-bonds generated for 'chain 'e' and resid 40 through 44' Processing helix chain 'e' and resid 45 through 60 removed outlier: 4.180A pdb=" N LEU e 49 " --> pdb=" O ASP e 45 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N ASP e 50 " --> pdb=" O LYS e 46 " (cutoff:3.500A) Processing helix chain 'e' and resid 92 through 106 removed outlier: 3.623A pdb=" N TRP e 96 " --> pdb=" O GLY e 92 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ILE e 103 " --> pdb=" O PHE e 99 " (cutoff:3.500A) Processing helix chain 'e' and resid 107 through 110 Processing helix chain 'e' and resid 161 through 170 removed outlier: 3.572A pdb=" N GLY e 165 " --> pdb=" O SER e 161 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N LEU e 168 " --> pdb=" O GLU e 164 " (cutoff:3.500A) Processing helix chain 'e' and resid 171 through 173 No H-bonds generated for 'chain 'e' and resid 171 through 173' Processing helix chain 'f' and resid 59 through 81 removed outlier: 3.660A pdb=" N ILE f 76 " --> pdb=" O ASN f 72 " (cutoff:3.500A) Processing helix chain 'f' and resid 136 through 150 Processing helix chain 'g' and resid 22 through 29 removed outlier: 3.532A pdb=" N PHE g 29 " --> pdb=" O TYR g 25 " (cutoff:3.500A) Processing helix chain 'g' and resid 40 through 49 removed outlier: 3.780A pdb=" N GLU g 48 " --> pdb=" O ILE g 44 " (cutoff:3.500A) removed outlier: 4.587A pdb=" N ALA g 49 " --> pdb=" O GLU g 45 " (cutoff:3.500A) Processing helix chain 'h' and resid 3 through 19 removed outlier: 3.557A pdb=" N ILE h 11 " --> pdb=" O ASP h 7 " (cutoff:3.500A) Processing helix chain 'h' and resid 33 through 38 removed outlier: 3.806A pdb=" N LYS h 37 " --> pdb=" O VAL h 33 " (cutoff:3.500A) Processing helix chain 'h' and resid 39 through 46 Processing helix chain 'h' and resid 71 through 78 removed outlier: 3.614A pdb=" N ALA h 75 " --> pdb=" O LEU h 72 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N PHE h 76 " --> pdb=" O LYS h 73 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N VAL h 77 " --> pdb=" O ASP h 74 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N GLY h 78 " --> pdb=" O ALA h 75 " (cutoff:3.500A) Processing helix chain 'h' and resid 96 through 101 removed outlier: 3.798A pdb=" N LYS h 101 " --> pdb=" O LYS h 97 " (cutoff:3.500A) Processing helix chain 'i' and resid 19 through 24 Processing helix chain 'i' and resid 35 through 43 removed outlier: 3.628A pdb=" N LYS i 39 " --> pdb=" O MET i 35 " (cutoff:3.500A) Processing helix chain 'i' and resid 74 through 84 removed outlier: 3.695A pdb=" N LEU i 79 " --> pdb=" O ALA i 75 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N LYS i 80 " --> pdb=" O ALA i 76 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N LYS i 81 " --> pdb=" O VAL i 77 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N ALA i 82 " --> pdb=" O LEU i 78 " (cutoff:3.500A) Processing helix chain 'i' and resid 101 through 113 removed outlier: 4.100A pdb=" N ILE i 108 " --> pdb=" O GLN i 104 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N THR i 111 " --> pdb=" O GLU i 107 " (cutoff:3.500A) Processing helix chain 'i' and resid 120 through 134 removed outlier: 3.519A pdb=" N ILE i 128 " --> pdb=" O MET i 124 " (cutoff:3.500A) Processing helix chain 'j' and resid 24 through 38 removed outlier: 3.525A pdb=" N GLU j 31 " --> pdb=" O ARG j 27 " (cutoff:3.500A) Processing helix chain 'j' and resid 58 through 62 Processing helix chain 'j' and resid 67 through 72 Processing helix chain 'j' and resid 88 through 96 Processing helix chain 'j' and resid 98 through 108 removed outlier: 3.668A pdb=" N MET j 108 " --> pdb=" O ALA j 104 " (cutoff:3.500A) Processing helix chain 'j' and resid 112 through 121 removed outlier: 3.593A pdb=" N ARG j 120 " --> pdb=" O ARG j 116 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N LYS j 121 " --> pdb=" O ALA j 117 " (cutoff:3.500A) Processing helix chain 'j' and resid 132 through 136 Processing helix chain 'k' and resid 112 through 118 Processing helix chain 'l' and resid 2 through 6 removed outlier: 3.962A pdb=" N LEU l 6 " --> pdb=" O LEU l 3 " (cutoff:3.500A) Processing helix chain 'l' and resid 56 through 61 removed outlier: 3.522A pdb=" N LEU l 61 " --> pdb=" O LEU l 57 " (cutoff:3.500A) Processing helix chain 'l' and resid 68 through 72 Processing helix chain 'l' and resid 80 through 85 removed outlier: 3.536A pdb=" N ALA l 83 " --> pdb=" O SER l 80 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N VAL l 85 " --> pdb=" O LEU l 82 " (cutoff:3.500A) Processing helix chain 'l' and resid 128 through 138 removed outlier: 3.533A pdb=" N ALA l 133 " --> pdb=" O LYS l 129 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N ALA l 138 " --> pdb=" O ALA l 134 " (cutoff:3.500A) Processing helix chain 'n' and resid 13 through 32 Processing helix chain 'n' and resid 38 through 55 removed outlier: 3.600A pdb=" N ARG n 45 " --> pdb=" O ALA n 41 " (cutoff:3.500A) removed outlier: 4.740A pdb=" N ARG n 46 " --> pdb=" O LYS n 42 " (cutoff:3.500A) removed outlier: 4.312A pdb=" N VAL n 47 " --> pdb=" O GLU n 43 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N GLU n 49 " --> pdb=" O ARG n 45 " (cutoff:3.500A) Proline residue: n 50 - end of helix Processing helix chain 'n' and resid 59 through 69 Processing helix chain 'n' and resid 72 through 79 Processing helix chain 'n' and resid 82 through 87 Processing helix chain 'o' and resid 3 through 20 removed outlier: 4.935A pdb=" N ARG o 13 " --> pdb=" O ARG o 9 " (cutoff:3.500A) removed outlier: 5.316A pdb=" N ALA o 14 " --> pdb=" O ARG o 10 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N LEU o 18 " --> pdb=" O ALA o 14 " (cutoff:3.500A) Processing helix chain 'o' and resid 55 through 60 removed outlier: 3.688A pdb=" N ALA o 59 " --> pdb=" O GLU o 55 " (cutoff:3.500A) Processing helix chain 'o' and resid 67 through 86 Processing helix chain 'o' and resid 101 through 114 removed outlier: 3.550A pdb=" N ALA o 109 " --> pdb=" O ALA o 105 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ALA o 110 " --> pdb=" O LEU o 106 " (cutoff:3.500A) Processing helix chain 'p' and resid 2 through 10 Processing helix chain 'p' and resid 52 through 55 Processing helix chain 'p' and resid 96 through 100 removed outlier: 3.603A pdb=" N ARG p 100 " --> pdb=" O TYR p 97 " (cutoff:3.500A) Processing helix chain 'p' and resid 103 through 108 removed outlier: 3.579A pdb=" N ALA p 107 " --> pdb=" O GLY p 104 " (cutoff:3.500A) Processing helix chain 'q' and resid 6 through 20 removed outlier: 3.723A pdb=" N ALA q 11 " --> pdb=" O VAL q 7 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N ILE q 16 " --> pdb=" O ARG q 12 " (cutoff:3.500A) Processing helix chain 'q' and resid 24 through 29 Processing helix chain 'q' and resid 30 through 71 removed outlier: 3.840A pdb=" N GLN q 36 " --> pdb=" O ARG q 32 " (cutoff:3.500A) removed outlier: 4.284A pdb=" N ARG q 50 " --> pdb=" O TYR q 46 " (cutoff:3.500A) removed outlier: 4.762A pdb=" N LYS q 53 " --> pdb=" O ARG q 49 " (cutoff:3.500A) Processing helix chain 'q' and resid 74 through 85 Processing helix chain 'q' and resid 90 through 100 Processing helix chain 'q' and resid 101 through 117 Processing helix chain 's' and resid 13 through 22 removed outlier: 3.829A pdb=" N VAL s 20 " --> pdb=" O LYS s 16 " (cutoff:3.500A) Processing helix chain 's' and resid 28 through 37 Processing helix chain 's' and resid 41 through 62 removed outlier: 3.556A pdb=" N VAL s 45 " --> pdb=" O LYS s 41 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N LEU s 46 " --> pdb=" O LYS s 42 " (cutoff:3.500A) 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 2 through 10 Processing helix chain 't' and resid 17 through 24 Processing helix chain 't' and resid 39 through 50 Processing helix chain 'u' and resid 14 through 18 removed outlier: 3.798A pdb=" N ASP u 17 " --> pdb=" O THR u 14 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N LYS u 18 " --> pdb=" O GLY u 15 " (cutoff:3.500A) No H-bonds generated for 'chain 'u' and resid 14 through 18' Processing helix chain 'v' and resid 13 through 23 Processing helix chain 'v' and resid 44 through 49 Processing helix chain 'v' and resid 54 through 59 Processing helix chain 'x' and resid 52 through 62 removed outlier: 3.535A pdb=" N ARG x 56 " --> pdb=" O ALA x 52 " (cutoff:3.500A) Processing helix chain 'x' and resid 62 through 74 removed outlier: 3.732A pdb=" N GLU x 69 " --> pdb=" O THR x 65 " (cutoff:3.500A) Processing helix chain 'y' and resid 11 through 23 removed outlier: 3.633A pdb=" N ASN y 15 " --> pdb=" O VAL y 11 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N THR y 16 " --> pdb=" O GLU y 12 " (cutoff:3.500A) Processing helix chain 'y' and resid 24 through 33 removed outlier: 3.702A pdb=" N ARG y 29 " --> pdb=" O GLN y 25 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N ALA y 33 " --> pdb=" O ARG y 29 " (cutoff:3.500A) Processing helix chain 'y' and resid 40 through 61 removed outlier: 3.925A pdb=" N LYS y 44 " --> pdb=" O SER y 40 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N ASN y 58 " --> pdb=" O LYS y 54 " (cutoff:3.500A) Processing helix chain 'z' and resid 16 through 27 Processing helix chain 'z' and resid 40 through 50 removed outlier: 3.586A pdb=" N VAL z 50 " --> pdb=" O MET z 46 " (cutoff:3.500A) Processing helix chain 'B' and resid 8 through 16 Processing helix chain 'D' and resid 8 through 17 Processing helix chain 'D' and resid 17 through 24 removed outlier: 4.136A pdb=" N THR D 24 " --> pdb=" O ALA D 20 " (cutoff:3.500A) Processing helix chain 'D' and resid 24 through 38 Processing helix chain 'E' and resid 6 through 13 removed outlier: 3.592A pdb=" N LYS E 11 " --> pdb=" O ARG E 7 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N ARG E 12 " --> pdb=" O GLY E 8 " (cutoff:3.500A) Processing helix chain 'E' and resid 36 through 43 Processing helix chain 'E' and resid 50 through 52 No H-bonds generated for 'chain 'E' and resid 50 through 52' Processing helix chain 'E' and resid 53 through 59 removed outlier: 3.753A pdb=" N VAL E 57 " --> pdb=" O ASP E 53 " (cutoff:3.500A) Processing helix chain 'F' and resid 18 through 22 removed outlier: 3.518A pdb=" N GLY F 21 " --> pdb=" O LYS F 18 " (cutoff:3.500A) Processing helix chain 'F' and resid 30 through 34 Processing helix chain 'a' and resid 5 through 12 removed outlier: 3.568A pdb=" N ARG a 9 " --> pdb=" O THR a 5 " (cutoff:3.500A) Processing helix chain 'a' and resid 22 through 34 removed outlier: 4.278A pdb=" N ALA a 28 " --> pdb=" O ASN a 24 " (cutoff:3.500A) removed outlier: 4.293A pdb=" N LYS a 31 " --> pdb=" O ILE a 27 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N GLU a 32 " --> pdb=" O ALA a 28 " (cutoff:3.500A) Processing helix chain 'a' and resid 181 through 198 removed outlier: 3.551A pdb=" N ASN a 188 " --> pdb=" O LYS a 184 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N GLU a 190 " --> pdb=" O LYS a 186 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N ALA a 195 " --> pdb=" O ALA a 191 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'b' and resid 2 through 4 Processing sheet with id=AA2, first strand: chain 'b' and resid 33 through 35 Processing sheet with id=AA3, first strand: chain 'b' and resid 99 through 104 removed outlier: 3.529A pdb=" N GLU b 99 " --> pdb=" O TYR b 95 " (cutoff:3.500A) removed outlier: 6.697A pdb=" N ILE b 90 " --> pdb=" O LEU b 80 " (cutoff:3.500A) removed outlier: 4.626A pdb=" N LEU b 80 " --> pdb=" O ILE b 90 " (cutoff:3.500A) removed outlier: 6.889A pdb=" N LEU b 92 " --> pdb=" O GLU b 78 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'b' and resid 128 through 130 removed outlier: 7.137A pdb=" N THR b 172 " --> pdb=" O VAL b 164 " (cutoff:3.500A) removed outlier: 6.282A pdb=" N LYS b 182 " --> pdb=" O ILE b 266 " (cutoff:3.500A) removed outlier: 5.764A pdb=" N ILE b 266 " --> pdb=" O LYS b 182 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'c' and resid 4 through 5 removed outlier: 3.529A pdb=" N LYS c 204 " --> pdb=" O ASP c 108 " (cutoff:3.500A) removed outlier: 5.504A pdb=" N VAL c 107 " --> pdb=" O SER c 174 " (cutoff:3.500A) removed outlier: 4.694A pdb=" N ASP c 176 " --> pdb=" O LYS c 190 " (cutoff:3.500A) removed outlier: 6.608A pdb=" N LEU c 188 " --> pdb=" O VAL c 178 " (cutoff:3.500A) removed outlier: 4.574A pdb=" N VAL c 180 " --> pdb=" O LEU c 186 " (cutoff:3.500A) removed outlier: 6.615A pdb=" N LEU c 186 " --> pdb=" O VAL c 180 " (cutoff:3.500A) removed outlier: 4.246A pdb=" N GLY c 10 " --> pdb=" O VAL c 26 " (cutoff:3.500A) removed outlier: 6.679A pdb=" N GLU c 28 " --> pdb=" O LYS c 8 " (cutoff:3.500A) removed outlier: 5.957A pdb=" N LYS c 8 " --> pdb=" O GLU c 28 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'c' and resid 32 through 33 Processing sheet with id=AA7, first strand: chain 'c' and resid 36 through 38 Processing sheet with id=AA8, first strand: chain 'c' and resid 115 through 119 Processing sheet with id=AA9, first strand: chain 'd' and resid 2 through 4 Processing sheet with id=AB1, first strand: chain 'd' and resid 118 through 121 removed outlier: 6.158A pdb=" N ILE d 119 " --> pdb=" O MET d 188 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N THR d 189 " --> pdb=" O ILE d 149 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N ASP d 168 " --> pdb=" O VAL d 146 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'e' and resid 65 through 67 Processing sheet with id=AB3, first strand: chain 'f' and resid 8 through 9 Processing sheet with id=AB4, first strand: chain 'f' and resid 15 through 19 removed outlier: 3.635A pdb=" N VAL f 22 " --> pdb=" O ASN f 19 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'f' and resid 120 through 126 removed outlier: 6.750A pdb=" N GLU f 129 " --> pdb=" O PRO f 125 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'f' and resid 94 through 98 removed outlier: 3.722A pdb=" N ARG f 94 " --> pdb=" O SER f 105 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'g' and resid 18 through 20 Processing sheet with id=AB8, first strand: chain 'h' and resid 26 through 27 Processing sheet with id=AB9, first strand: chain 'i' and resid 8 through 10 removed outlier: 4.308A pdb=" N VAL i 8 " --> pdb=" O ILE i 58 " (cutoff:3.500A) removed outlier: 4.136A pdb=" N ILE i 58 " --> pdb=" O VAL i 8 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N LEU i 10 " --> pdb=" O VAL i 56 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N VAL i 56 " --> pdb=" O LEU i 10 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N THR i 59 " --> pdb=" O THR i 67 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'j' and resid 122 through 124 removed outlier: 6.125A pdb=" N ILE j 54 " --> pdb=" O LYS j 123 " (cutoff:3.500A) removed outlier: 6.277A pdb=" N TYR j 16 " --> pdb=" O ILE j 55 " (cutoff:3.500A) removed outlier: 7.259A pdb=" N LEU j 57 " --> pdb=" O TYR j 16 " (cutoff:3.500A) removed outlier: 6.817A pdb=" N VAL j 18 " --> pdb=" O LEU j 57 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'j' and resid 74 through 77 Processing sheet with id=AC3, first strand: chain 'k' and resid 92 through 94 removed outlier: 7.627A pdb=" N LEU k 86 " --> pdb=" O PRO k 94 " (cutoff:3.500A) removed outlier: 6.577A pdb=" N ALA k 83 " --> pdb=" O VAL k 63 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N LYS k 59 " --> pdb=" O LEU k 87 " (cutoff:3.500A) removed outlier: 7.017A pdb=" N ILE k 41 " --> pdb=" O ILE k 22 " (cutoff:3.500A) removed outlier: 5.618A pdb=" N ILE k 22 " --> pdb=" O ILE k 41 " (cutoff:3.500A) removed outlier: 5.365A pdb=" N ILE k 43 " --> pdb=" O MET k 20 " (cutoff:3.500A) removed outlier: 6.667A pdb=" N MET k 20 " --> pdb=" O ILE k 43 " (cutoff:3.500A) removed outlier: 6.924A pdb=" N ARG k 17 " --> pdb=" O VAL k 10 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N VAL k 10 " --> pdb=" O ARG k 17 " (cutoff:3.500A) removed outlier: 8.185A pdb=" N CYS k 84 " --> pdb=" O MET k 7 " (cutoff:3.500A) removed outlier: 6.441A pdb=" N ASN k 9 " --> pdb=" O CYS k 84 " (cutoff:3.500A) removed outlier: 7.710A pdb=" N LEU k 86 " --> pdb=" O ASN k 9 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'k' and resid 69 through 70 removed outlier: 4.288A pdb=" N VAL k 76 " --> pdb=" O VAL p 72 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N ALA p 48 " --> pdb=" O THR p 59 " (cutoff:3.500A) removed outlier: 6.625A pdb=" N ARG p 61 " --> pdb=" O VAL p 46 " (cutoff:3.500A) removed outlier: 5.701A pdb=" N VAL p 46 " --> pdb=" O ARG p 61 " (cutoff:3.500A) removed outlier: 8.267A pdb=" N ILE p 63 " --> pdb=" O GLY p 44 " (cutoff:3.500A) removed outlier: 8.584A pdb=" N GLY p 44 " --> pdb=" O ILE p 63 " (cutoff:3.500A) removed outlier: 7.446A pdb=" N THR p 24 " --> pdb=" O VAL p 85 " (cutoff:3.500A) removed outlier: 5.564A pdb=" N VAL p 85 " --> pdb=" O THR p 24 " (cutoff:3.500A) removed outlier: 6.191A pdb=" N GLU p 26 " --> pdb=" O ILE p 83 " (cutoff:3.500A) removed outlier: 4.783A pdb=" N ILE p 83 " --> pdb=" O GLU p 26 " (cutoff:3.500A) removed outlier: 6.975A pdb=" N LYS p 28 " --> pdb=" O ASP p 81 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'l' and resid 74 through 78 Processing sheet with id=AC6, first strand: chain 'l' and resid 89 through 90 removed outlier: 5.674A pdb=" N VAL l 90 " --> pdb=" O ARG l 123 " (cutoff:3.500A) removed outlier: 5.819A pdb=" N VAL l 122 " --> pdb=" O GLU l 143 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC6 Processing sheet with id=AC7, first strand: chain 'n' and resid 33 through 37 removed outlier: 6.966A pdb=" N MET n 110 " --> pdb=" O CYS n 100 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'o' and resid 25 through 29 removed outlier: 7.209A pdb=" N ALA o 37 " --> pdb=" O ALA o 50 " (cutoff:3.500A) removed outlier: 4.689A pdb=" N ALA o 50 " --> pdb=" O ALA o 37 " (cutoff:3.500A) removed outlier: 6.753A pdb=" N VAL o 39 " --> pdb=" O LEU o 48 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'r' and resid 11 through 14 removed outlier: 7.025A pdb=" N TYR r 2 " --> pdb=" O ILE r 41 " (cutoff:3.500A) removed outlier: 4.646A pdb=" N ILE r 41 " --> pdb=" O TYR r 2 " (cutoff:3.500A) removed outlier: 6.627A pdb=" N VAL r 4 " --> pdb=" O LEU r 39 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'r' and resid 19 through 22 removed outlier: 6.679A pdb=" N ASP r 95 " --> pdb=" O VAL r 64 " (cutoff:3.500A) removed outlier: 6.721A pdb=" N LYS r 60 " --> pdb=" O THR r 99 " (cutoff:3.500A) removed outlier: 4.726A pdb=" N ILE r 101 " --> pdb=" O VAL r 58 " (cutoff:3.500A) removed outlier: 7.072A pdb=" N VAL r 58 " --> pdb=" O ILE r 101 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'r' and resid 72 through 78 removed outlier: 3.913A pdb=" N TYR r 83 " --> pdb=" O ARG r 78 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 's' and resid 4 through 10 removed outlier: 5.431A pdb=" N SER s 101 " --> pdb=" O HIS s 9 " (cutoff:3.500A) removed outlier: 6.807A pdb=" N ASP s 94 " --> pdb=" O ILE s 85 " (cutoff:3.500A) removed outlier: 5.380A pdb=" N ILE s 85 " --> pdb=" O ASP s 94 " (cutoff:3.500A) removed outlier: 6.929A pdb=" N ILE s 96 " --> pdb=" O LYS s 83 " (cutoff:3.500A) removed outlier: 5.035A pdb=" N LYS s 83 " --> pdb=" O ILE s 96 " (cutoff:3.500A) removed outlier: 5.550A pdb=" N LYS s 98 " --> pdb=" O SER s 81 " (cutoff:3.500A) removed outlier: 4.747A pdb=" N SER s 81 " --> pdb=" O LYS s 98 " (cutoff:3.500A) removed outlier: 4.718A pdb=" N THR s 100 " --> pdb=" O GLY s 79 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 't' and resid 11 through 14 removed outlier: 3.545A pdb=" N LYS t 81 " --> pdb=" O VAL t 34 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N TRP t 80 " --> pdb=" O VAL t 63 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N VAL t 57 " --> pdb=" O THR t 86 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 't' and resid 69 through 70 Processing sheet with id=AD6, first strand: chain 'u' and resid 64 through 65 removed outlier: 5.411A pdb=" N GLU u 9 " --> pdb=" O PHE u 72 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N ILE u 71 " --> pdb=" O ASP u 80 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'u' and resid 39 through 43 removed outlier: 4.524A pdb=" N ASN u 39 " --> pdb=" O ALA u 62 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'u' and resid 82 through 86 Processing sheet with id=AD9, first strand: chain 'v' and resid 7 through 8 removed outlier: 5.635A pdb=" N ALA v 36 " --> pdb=" O GLY v 32 " (cutoff:3.500A) removed outlier: 5.753A pdb=" N GLY v 32 " --> pdb=" O ALA v 36 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N LEU v 42 " --> pdb=" O PHE v 26 " (cutoff:3.500A) removed outlier: 8.418A pdb=" N LYS v 25 " --> pdb=" O GLN v 87 " (cutoff:3.500A) removed outlier: 9.536A pdb=" N ILE v 89 " --> pdb=" O LYS v 25 " (cutoff:3.500A) removed outlier: 8.059A pdb=" N PHE v 91 " --> pdb=" O PRO v 27 " (cutoff:3.500A) removed outlier: 6.038A pdb=" N ILE v 29 " --> pdb=" O PHE v 91 " (cutoff:3.500A) removed outlier: 6.654A pdb=" N ARG v 93 " --> pdb=" O ILE v 29 " (cutoff:3.500A) removed outlier: 6.668A pdb=" N TYR v 31 " --> pdb=" O ARG v 93 " (cutoff:3.500A) removed outlier: 6.274A pdb=" N VAL v 92 " --> pdb=" O ALA v 74 " (cutoff:3.500A) removed outlier: 5.343A pdb=" N ALA v 74 " --> pdb=" O VAL v 92 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N LYS v 68 " --> pdb=" O VAL v 65 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'w' and resid 18 through 19 removed outlier: 6.949A pdb=" N LEU w 55 " --> pdb=" O ILE w 33 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'w' and resid 26 through 27 removed outlier: 3.584A pdb=" N LYS w 62 " --> pdb=" O GLU w 79 " (cutoff:3.500A) removed outlier: 6.737A pdb=" N HIS w 42 " --> pdb=" O ILE w 76 " (cutoff:3.500A) removed outlier: 8.795A pdb=" N ILE w 78 " --> pdb=" O HIS w 42 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'x' and resid 12 through 15 Processing sheet with id=AE4, first strand: chain 'x' and resid 32 through 39 Processing sheet with id=AE5, first strand: chain 'z' and resid 34 through 37 removed outlier: 3.505A pdb=" N LYS z 5 " --> pdb=" O GLU z 57 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'A' and resid 10 through 14 Processing sheet with id=AE7, first strand: chain 'B' and resid 28 through 29 Processing sheet with id=AE8, first strand: chain 'E' and resid 14 through 15 Processing sheet with id=AE9, first strand: chain 'F' and resid 14 through 17 Processing sheet with id=AF1, first strand: chain 'a' and resid 170 through 177 removed outlier: 3.523A pdb=" N VAL a 44 " --> pdb=" O THR a 173 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N ILE a 175 " --> pdb=" O VAL a 42 " (cutoff:3.500A) removed outlier: 6.281A pdb=" N VAL a 42 " --> pdb=" O ILE a 175 " (cutoff:3.500A) removed outlier: 4.095A pdb=" N LYS a 211 " --> pdb=" O ASN a 47 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'a' and resid 60 through 64 removed outlier: 3.837A pdb=" N VAL a 161 " --> pdb=" O THR a 63 " (cutoff:3.500A) 881 hydrogen bonds defined for protein. 2430 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 2310 hydrogen bonds 3700 hydrogen bond angles 0 basepair planarities 921 basepair parallelities 1674 stacking parallelities Total time for adding SS restraints: 161.58 Time building geometry restraints manager: 41.02 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 20255 1.34 - 1.47: 41288 1.47 - 1.60: 33665 1.60 - 1.72: 3929 1.72 - 1.85: 155 Bond restraints: 99292 Sorted by residual: bond pdb=" CA PRO i 73 " pdb=" C PRO i 73 " ideal model delta sigma weight residual 1.514 1.540 -0.026 5.50e-03 3.31e+04 2.18e+01 bond pdb=" CA ILE i 54 " pdb=" CB ILE i 54 " ideal model delta sigma weight residual 1.538 1.567 -0.029 8.80e-03 1.29e+04 1.10e+01 bond pdb=" CA ILE h 123 " pdb=" CB ILE h 123 " ideal model delta sigma weight residual 1.530 1.564 -0.035 1.11e-02 8.12e+03 9.75e+00 bond pdb=" CA VAL i 139 " pdb=" CB VAL i 139 " ideal model delta sigma weight residual 1.530 1.563 -0.032 1.05e-02 9.07e+03 9.52e+00 bond pdb=" CA THR h 128 " pdb=" CB THR h 128 " ideal model delta sigma weight residual 1.524 1.564 -0.041 1.33e-02 5.65e+03 9.39e+00 ... (remaining 99287 not shown) Histogram of bond angle deviations from ideal: 99.79 - 106.62: 18493 106.62 - 113.46: 58727 113.46 - 120.29: 36615 120.29 - 127.12: 27849 127.12 - 133.95: 7373 Bond angle restraints: 149057 Sorted by residual: angle pdb=" N ALA g 10 " pdb=" CA ALA g 10 " pdb=" C ALA g 10 " ideal model delta sigma weight residual 110.43 121.15 -10.72 1.31e+00 5.83e-01 6.70e+01 angle pdb=" N ASN f 47 " pdb=" CA ASN f 47 " pdb=" C ASN f 47 " ideal model delta sigma weight residual 112.88 102.37 10.51 1.29e+00 6.01e-01 6.64e+01 angle pdb=" N ALA n 68 " pdb=" CA ALA n 68 " pdb=" C ALA n 68 " ideal model delta sigma weight residual 111.28 103.12 8.16 1.09e+00 8.42e-01 5.60e+01 angle pdb=" N LEU l 95 " pdb=" CA LEU l 95 " pdb=" C LEU l 95 " ideal model delta sigma weight residual 113.41 104.28 9.13 1.22e+00 6.72e-01 5.60e+01 angle pdb=" N THR h 58 " pdb=" CA THR h 58 " pdb=" C THR h 58 " ideal model delta sigma weight residual 112.72 121.19 -8.47 1.14e+00 7.69e-01 5.52e+01 ... (remaining 149052 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.73: 56142 35.73 - 71.45: 6651 71.45 - 107.18: 821 107.18 - 142.91: 11 142.91 - 178.63: 11 Dihedral angle restraints: 63636 sinusoidal: 54029 harmonic: 9607 Sorted by residual: dihedral pdb=" C4' U 42632 " pdb=" C3' U 42632 " pdb=" C2' U 42632 " pdb=" C1' U 42632 " ideal model delta sinusoidal sigma weight residual -35.00 33.77 -68.77 1 8.00e+00 1.56e-02 9.57e+01 dihedral pdb=" C5' U 42632 " pdb=" C4' U 42632 " pdb=" C3' U 42632 " pdb=" O3' U 42632 " ideal model delta sinusoidal sigma weight residual 147.00 81.02 65.98 1 8.00e+00 1.56e-02 8.89e+01 dihedral pdb=" O4' U 42680 " pdb=" C1' U 42680 " pdb=" N1 U 42680 " pdb=" C2 U 42680 " ideal model delta sinusoidal sigma weight residual 200.00 39.81 160.19 1 1.50e+01 4.44e-03 8.28e+01 ... (remaining 63633 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.104: 15874 0.104 - 0.208: 3022 0.208 - 0.312: 242 0.312 - 0.416: 13 0.416 - 0.520: 2 Chirality restraints: 19153 Sorted by residual: chirality pdb=" C3' G 41025 " pdb=" C4' G 41025 " pdb=" O3' G 41025 " pdb=" C2' G 41025 " both_signs ideal model delta sigma weight residual False -2.74 -2.23 -0.52 2.00e-01 2.50e+01 6.75e+00 chirality pdb=" C3' A 41020 " pdb=" C4' A 41020 " pdb=" O3' A 41020 " pdb=" C2' A 41020 " both_signs ideal model delta sigma weight residual False -2.74 -2.26 -0.48 2.00e-01 2.50e+01 5.84e+00 chirality pdb=" CA THR h 80 " pdb=" N THR h 80 " pdb=" C THR h 80 " pdb=" CB THR h 80 " both_signs ideal model delta sigma weight residual False 2.53 2.13 0.39 2.00e-01 2.50e+01 3.83e+00 ... (remaining 19150 not shown) Planarity restraints: 7608 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' A 41216 " -0.098 2.00e-02 2.50e+03 4.35e-02 5.20e+01 pdb=" N9 A 41216 " 0.005 2.00e-02 2.50e+03 pdb=" C8 A 41216 " 0.040 2.00e-02 2.50e+03 pdb=" N7 A 41216 " 0.039 2.00e-02 2.50e+03 pdb=" C5 A 41216 " 0.021 2.00e-02 2.50e+03 pdb=" C6 A 41216 " -0.014 2.00e-02 2.50e+03 pdb=" N6 A 41216 " -0.072 2.00e-02 2.50e+03 pdb=" N1 A 41216 " -0.003 2.00e-02 2.50e+03 pdb=" C2 A 41216 " 0.020 2.00e-02 2.50e+03 pdb=" N3 A 41216 " 0.031 2.00e-02 2.50e+03 pdb=" C4 A 41216 " 0.030 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' G 41029 " -0.094 2.00e-02 2.50e+03 4.05e-02 4.92e+01 pdb=" N9 G 41029 " 0.005 2.00e-02 2.50e+03 pdb=" C8 G 41029 " 0.046 2.00e-02 2.50e+03 pdb=" N7 G 41029 " 0.047 2.00e-02 2.50e+03 pdb=" C5 G 41029 " 0.016 2.00e-02 2.50e+03 pdb=" C6 G 41029 " -0.020 2.00e-02 2.50e+03 pdb=" O6 G 41029 " -0.063 2.00e-02 2.50e+03 pdb=" N1 G 41029 " -0.014 2.00e-02 2.50e+03 pdb=" C2 G 41029 " 0.009 2.00e-02 2.50e+03 pdb=" N2 G 41029 " 0.028 2.00e-02 2.50e+03 pdb=" N3 G 41029 " 0.019 2.00e-02 2.50e+03 pdb=" C4 G 41029 " 0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' C 41027 " -0.093 2.00e-02 2.50e+03 4.67e-02 4.91e+01 pdb=" N1 C 41027 " 0.007 2.00e-02 2.50e+03 pdb=" C2 C 41027 " 0.017 2.00e-02 2.50e+03 pdb=" O2 C 41027 " 0.041 2.00e-02 2.50e+03 pdb=" N3 C 41027 " 0.003 2.00e-02 2.50e+03 pdb=" C4 C 41027 " -0.003 2.00e-02 2.50e+03 pdb=" N4 C 41027 " -0.067 2.00e-02 2.50e+03 pdb=" C5 C 41027 " 0.043 2.00e-02 2.50e+03 pdb=" C6 C 41027 " 0.051 2.00e-02 2.50e+03 ... (remaining 7605 not shown) Histogram of nonbonded interaction distances: 2.28 - 2.80: 19723 2.80 - 3.33: 80987 3.33 - 3.85: 195522 3.85 - 4.38: 233765 4.38 - 4.90: 305277 Nonbonded interactions: 835274 Sorted by model distance: nonbonded pdb=" O ASN l 93 " pdb=" OG1 THR l 94 " model vdw 2.278 2.440 nonbonded pdb=" O ALA o 105 " pdb=" OD1 ASP o 108 " model vdw 2.287 3.040 nonbonded pdb=" O LYS l 29 " pdb=" OG1 THR l 30 " model vdw 2.297 2.440 nonbonded pdb=" O ARG i 126 " pdb=" O2' A 41208 " model vdw 2.332 2.440 nonbonded pdb=" OG SER u 67 " pdb=" O2 C 4 335 " model vdw 2.337 2.440 ... (remaining 835269 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: 11.800 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.060 Extract box with map and model: 47.360 Check model and map are aligned: 1.030 Set scattering table: 1.150 Process input model: 337.510 Find NCS groups from input model: 1.470 Set up NCS constraints: 0.200 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:2.600 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 403.210 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8485 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.057 99292 Z= 0.426 Angle : 0.926 12.273 149057 Z= 0.616 Chirality : 0.080 0.520 19153 Planarity : 0.008 0.070 7608 Dihedral : 22.750 178.632 57446 Min Nonbonded Distance : 2.278 Molprobity Statistics. All-atom Clashscore : 12.12 Ramachandran Plot: Outliers : 1.59 % Allowed : 10.44 % Favored : 87.97 % Rotamer: Outliers : 0.69 % Allowed : 6.46 % Favored : 92.84 % 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: -4.65 (0.11), residues: 3325 helix: -3.43 (0.11), residues: 884 sheet: -2.71 (0.19), residues: 601 loop : -3.10 (0.12), residues: 1840 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.051 0.008 TRP b 212 HIS 0.002 0.000 HIS x 19 PHE 0.040 0.006 PHE r 53 TYR 0.048 0.008 TYR e 82 ARG 0.009 0.001 ARG b 86 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6650 Ramachandran restraints generated. 3325 Oldfield, 0 Emsley, 3325 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6650 Ramachandran restraints generated. 3325 Oldfield, 0 Emsley, 3325 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 861 residues out of total 2739 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 842 time to evaluate : 4.055 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: d 100 MET cc_start: 0.8217 (mtp) cc_final: 0.7973 (mtp) REVERT: d 101 TYR cc_start: 0.9175 (t80) cc_final: 0.8975 (t80) REVERT: e 41 GLU cc_start: 0.7886 (mp0) cc_final: 0.7422 (tm-30) REVERT: f 41 GLU cc_start: 0.8529 (tt0) cc_final: 0.8256 (tt0) REVERT: f 68 ARG cc_start: 0.8528 (tmt170) cc_final: 0.7790 (tpt90) REVERT: f 72 ASN cc_start: 0.9053 (t0) cc_final: 0.8706 (t0) REVERT: f 82 PHE cc_start: 0.7867 (m-80) cc_final: 0.7559 (m-80) REVERT: f 102 ILE cc_start: 0.8996 (mt) cc_final: 0.8784 (tp) REVERT: f 113 ASP cc_start: 0.8757 (m-30) cc_final: 0.8474 (m-30) REVERT: f 172 GLU cc_start: 0.8454 (mm-30) cc_final: 0.8115 (mm-30) REVERT: g 2 GLN cc_start: 0.8064 (mm-40) cc_final: 0.7825 (mm110) REVERT: g 6 LEU cc_start: 0.7977 (tt) cc_final: 0.7719 (tt) REVERT: g 25 TYR cc_start: 0.8690 (t80) cc_final: 0.8394 (t80) REVERT: h 52 MET cc_start: -0.0889 (mmp) cc_final: -0.1797 (mpp) REVERT: i 135 MET cc_start: 0.3687 (mmt) cc_final: 0.2817 (mmt) REVERT: j 14 ASP cc_start: 0.7721 (t70) cc_final: 0.7009 (t0) REVERT: j 31 GLU cc_start: 0.8744 (tp30) cc_final: 0.8386 (tp30) REVERT: j 90 GLU cc_start: 0.7979 (pp20) cc_final: 0.7778 (pp20) REVERT: j 91 GLU cc_start: 0.8539 (mt-10) cc_final: 0.8281 (mt-10) REVERT: j 118 MET cc_start: 0.8752 (mtt) cc_final: 0.8446 (mtm) REVERT: j 125 TYR cc_start: 0.8548 (m-80) cc_final: 0.8084 (m-80) REVERT: k 37 ASP cc_start: 0.8485 (t70) cc_final: 0.7946 (t0) REVERT: k 56 ASP cc_start: 0.8287 (t0) cc_final: 0.8032 (t70) REVERT: k 111 LYS cc_start: 0.9216 (ttmt) cc_final: 0.9001 (ttmm) REVERT: l 58 TYR cc_start: 0.8382 (p90) cc_final: 0.7998 (p90) REVERT: l 64 PHE cc_start: 0.8704 (p90) cc_final: 0.7972 (p90) REVERT: n 56 LYS cc_start: 0.8877 (mtpp) cc_final: 0.8624 (mtpm) REVERT: o 17 LYS cc_start: 0.9053 (tppp) cc_final: 0.8776 (tptm) REVERT: o 83 LEU cc_start: 0.9189 (mt) cc_final: 0.8928 (mt) REVERT: o 108 ASP cc_start: 0.9239 (p0) cc_final: 0.8988 (p0) REVERT: p 26 GLU cc_start: 0.7958 (tm-30) cc_final: 0.7724 (tm-30) REVERT: p 39 LEU cc_start: 0.9142 (tp) cc_final: 0.8934 (tp) REVERT: q 46 TYR cc_start: 0.8973 (t80) cc_final: 0.8726 (t80) REVERT: q 65 ASN cc_start: 0.8798 (t0) cc_final: 0.8480 (t0) REVERT: q 75 TYR cc_start: 0.9038 (t80) cc_final: 0.8811 (t80) REVERT: q 96 ASP cc_start: 0.8458 (t70) cc_final: 0.7897 (t0) REVERT: r 11 GLN cc_start: 0.8654 (mp10) cc_final: 0.8309 (mp10) REVERT: r 31 GLU cc_start: 0.7405 (tm-30) cc_final: 0.7163 (tm-30) REVERT: r 60 LYS cc_start: 0.8592 (mtmm) cc_final: 0.8355 (mttm) REVERT: r 78 ARG cc_start: 0.8963 (tpp-160) cc_final: 0.8436 (tpp80) REVERT: r 97 LYS cc_start: 0.9249 (tttt) cc_final: 0.8851 (ttpt) REVERT: s 34 ASP cc_start: 0.8811 (p0) cc_final: 0.8585 (p0) REVERT: s 48 LYS cc_start: 0.9390 (tttt) cc_final: 0.9168 (ttpp) REVERT: s 109 ASP cc_start: 0.8483 (p0) cc_final: 0.8225 (p0) REVERT: t 24 MET cc_start: 0.8107 (tpt) cc_final: 0.7885 (ttp) REVERT: t 73 ARG cc_start: 0.7802 (mmt180) cc_final: 0.7524 (mmm160) REVERT: u 17 ASP cc_start: 0.8032 (m-30) cc_final: 0.7679 (m-30) REVERT: u 30 SER cc_start: 0.9375 (p) cc_final: 0.9152 (p) REVERT: u 38 ILE cc_start: 0.9028 (mm) cc_final: 0.8805 (mm) REVERT: u 72 PHE cc_start: 0.8421 (t80) cc_final: 0.8185 (t80) REVERT: u 85 ARG cc_start: 0.8046 (ptp-170) cc_final: 0.7749 (ptm160) REVERT: v 11 GLU cc_start: 0.7485 (tt0) cc_final: 0.6074 (tt0) REVERT: v 59 GLU cc_start: 0.6994 (mt-10) cc_final: 0.6715 (mt-10) REVERT: w 17 LEU cc_start: 0.9097 (mt) cc_final: 0.8871 (mp) REVERT: w 26 SER cc_start: 0.9278 (t) cc_final: 0.8950 (t) REVERT: w 52 ASP cc_start: 0.8239 (t0) cc_final: 0.8028 (t0) REVERT: w 62 LYS cc_start: 0.9348 (ttmm) cc_final: 0.8990 (mtpp) REVERT: w 64 LYS cc_start: 0.8169 (tptt) cc_final: 0.7813 (tptt) REVERT: y 4 LYS cc_start: 0.8892 (mptt) cc_final: 0.8579 (mmtp) REVERT: y 14 LEU cc_start: 0.9414 (mt) cc_final: 0.9208 (mt) REVERT: A 11 GLU cc_start: 0.8907 (tt0) cc_final: 0.8649 (tp30) REVERT: A 24 ILE cc_start: 0.7985 (tp) cc_final: 0.7702 (tt) REVERT: A 27 THR cc_start: 0.7575 (m) cc_final: 0.7138 (m) REVERT: A 35 ASP cc_start: 0.8379 (OUTLIER) cc_final: 0.7517 (t0) REVERT: E 16 THR cc_start: 0.8206 (p) cc_final: 0.8001 (p) REVERT: E 27 ASN cc_start: 0.9155 (m-40) cc_final: 0.8953 (m-40) REVERT: E 28 LEU cc_start: 0.9451 (tp) cc_final: 0.9208 (tt) REVERT: F 10 LEU cc_start: 0.8369 (mt) cc_final: 0.7968 (mt) REVERT: F 30 GLU cc_start: 0.8522 (mp0) cc_final: 0.7921 (mp0) REVERT: F 36 ARG cc_start: 0.8811 (OUTLIER) cc_final: 0.8116 (tmm-80) outliers start: 19 outliers final: 10 residues processed: 859 average time/residue: 0.8992 time to fit residues: 1300.5819 Evaluate side-chains 655 residues out of total 2739 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 643 time to evaluate : 3.712 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain d residue 187 VAL Chi-restraints excluded: chain e residue 34 THR Chi-restraints excluded: chain e residue 168 LEU Chi-restraints excluded: chain f residue 22 VAL Chi-restraints excluded: chain i residue 61 TYR Chi-restraints excluded: chain j residue 81 ILE Chi-restraints excluded: chain k residue 58 LEU Chi-restraints excluded: chain w residue 67 VAL Chi-restraints excluded: chain A residue 35 ASP Chi-restraints excluded: chain D residue 44 VAL Chi-restraints excluded: chain F residue 36 ARG Chi-restraints excluded: chain a residue 214 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 629 random chunks: chunk 531 optimal weight: 20.0000 chunk 476 optimal weight: 10.0000 chunk 264 optimal weight: 6.9990 chunk 162 optimal weight: 9.9990 chunk 321 optimal weight: 30.0000 chunk 254 optimal weight: 3.9990 chunk 493 optimal weight: 20.0000 chunk 190 optimal weight: 0.1980 chunk 299 optimal weight: 9.9990 chunk 366 optimal weight: 10.0000 chunk 571 optimal weight: 10.0000 overall best weight: 6.2388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: b 127 ASN b 162 GLN b 259 ASN ** c 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** c 49 GLN c 126 ASN c 164 GLN ** c 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 9 GLN d 30 GLN d 41 GLN d 90 GLN d 97 ASN f 138 GLN g 11 ASN ** g 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** g 43 ASN h 122 GLN ** i 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** i 42 ASN j 58 ASN l 38 GLN n 3 HIS n 9 GLN n 62 ASN o 29 HIS p 11 GLN p 65 ASN p 114 ASN q 19 GLN q 36 GLN q 43 GLN r 6 GLN s 7 HIS t 15 HIS t 59 ASN u 44 HIS u 68 ASN u 73 ASN v 24 ASN ** v 80 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** v 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** x 22 ASN ** y 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** y 20 ASN y 36 GLN y 38 GLN z 19 HIS A 20 ASN A 41 HIS ** B 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 4 GLN B 5 ASN D 6 GLN ** E 25 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 42 HIS F 35 GLN a 47 ASN ** a 57 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 49 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8519 moved from start: 0.1880 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.104 99292 Z= 0.362 Angle : 0.708 10.304 149057 Z= 0.367 Chirality : 0.042 0.305 19153 Planarity : 0.005 0.067 7608 Dihedral : 23.416 178.036 50904 Min Nonbonded Distance : 2.098 Molprobity Statistics. All-atom Clashscore : 15.32 Ramachandran Plot: Outliers : 0.21 % Allowed : 7.97 % Favored : 91.82 % Rotamer: Outliers : 4.31 % Allowed : 15.59 % Favored : 80.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.32 (0.13), residues: 3325 helix: -1.54 (0.16), residues: 941 sheet: -2.29 (0.19), residues: 627 loop : -2.57 (0.13), residues: 1757 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP b 212 HIS 0.009 0.002 HIS n 31 PHE 0.021 0.002 PHE v 26 TYR 0.017 0.002 TYR b 61 ARG 0.013 0.001 ARG y 7 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6650 Ramachandran restraints generated. 3325 Oldfield, 0 Emsley, 3325 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6650 Ramachandran restraints generated. 3325 Oldfield, 0 Emsley, 3325 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 807 residues out of total 2739 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 118 poor density : 689 time to evaluate : 3.864 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: b 224 MET cc_start: 0.8772 (mtt) cc_final: 0.8471 (mmt) REVERT: d 24 ASN cc_start: 0.8923 (t0) cc_final: 0.8650 (t0) REVERT: d 195 GLN cc_start: 0.8489 (mt0) cc_final: 0.8051 (mt0) REVERT: e 41 GLU cc_start: 0.7996 (mp0) cc_final: 0.7497 (tm-30) REVERT: e 95 MET cc_start: 0.9017 (ttp) cc_final: 0.8552 (ttp) REVERT: f 19 ASN cc_start: 0.7968 (t0) cc_final: 0.7680 (t0) REVERT: f 41 GLU cc_start: 0.8356 (tt0) cc_final: 0.8144 (tt0) REVERT: f 68 ARG cc_start: 0.8575 (tmt170) cc_final: 0.8299 (tpt90) REVERT: f 72 ASN cc_start: 0.8976 (t0) cc_final: 0.8047 (t0) REVERT: f 82 PHE cc_start: 0.7873 (m-80) cc_final: 0.7503 (m-80) REVERT: f 111 PRO cc_start: 0.8897 (Cg_exo) cc_final: 0.8650 (Cg_endo) REVERT: f 129 GLU cc_start: 0.8413 (tm-30) cc_final: 0.8024 (tp30) REVERT: h 52 MET cc_start: -0.0986 (mmp) cc_final: -0.1642 (mpp) REVERT: i 135 MET cc_start: 0.3781 (mmt) cc_final: 0.3027 (mmt) REVERT: j 125 TYR cc_start: 0.8485 (m-80) cc_final: 0.8050 (m-80) REVERT: k 37 ASP cc_start: 0.8450 (t70) cc_final: 0.7882 (t0) REVERT: l 58 TYR cc_start: 0.8451 (p90) cc_final: 0.8182 (p90) REVERT: l 91 ASP cc_start: 0.8532 (p0) cc_final: 0.7961 (p0) REVERT: n 56 LYS cc_start: 0.8954 (mtpp) cc_final: 0.8658 (mtpm) REVERT: n 72 ASP cc_start: 0.8582 (t0) cc_final: 0.8341 (t0) REVERT: o 83 LEU cc_start: 0.9229 (mt) cc_final: 0.8970 (mt) REVERT: p 26 GLU cc_start: 0.7933 (tm-30) cc_final: 0.7609 (tm-30) REVERT: q 46 TYR cc_start: 0.9083 (t80) cc_final: 0.8794 (t80) REVERT: q 65 ASN cc_start: 0.8807 (t0) cc_final: 0.8428 (t0) REVERT: q 96 ASP cc_start: 0.8254 (t70) cc_final: 0.7852 (t0) REVERT: r 11 GLN cc_start: 0.8933 (mp10) cc_final: 0.8552 (mp10) REVERT: r 31 GLU cc_start: 0.7468 (tm-30) cc_final: 0.7017 (tm-30) REVERT: r 60 LYS cc_start: 0.8401 (mtmm) cc_final: 0.8091 (mttm) REVERT: r 78 ARG cc_start: 0.8989 (tpp-160) cc_final: 0.8408 (tpp80) REVERT: r 97 LYS cc_start: 0.9294 (tttt) cc_final: 0.8783 (tmmt) REVERT: s 34 ASP cc_start: 0.8808 (p0) cc_final: 0.8520 (p0) REVERT: s 69 LEU cc_start: 0.9103 (mt) cc_final: 0.8595 (mt) REVERT: t 5 GLU cc_start: 0.8168 (mp0) cc_final: 0.7850 (mp0) REVERT: t 42 GLU cc_start: 0.8121 (mt-10) cc_final: 0.7910 (mt-10) REVERT: u 17 ASP cc_start: 0.8014 (m-30) cc_final: 0.7644 (m-30) REVERT: u 30 SER cc_start: 0.9365 (p) cc_final: 0.9146 (p) REVERT: u 72 PHE cc_start: 0.8355 (t80) cc_final: 0.7736 (t80) REVERT: v 10 LYS cc_start: 0.7502 (OUTLIER) cc_final: 0.6706 (pptt) REVERT: w 17 LEU cc_start: 0.9087 (mt) cc_final: 0.8604 (mt) REVERT: w 52 ASP cc_start: 0.8104 (t0) cc_final: 0.7808 (t0) REVERT: w 58 LYS cc_start: 0.9119 (OUTLIER) cc_final: 0.8758 (mtmm) REVERT: y 5 GLU cc_start: 0.7929 (tp30) cc_final: 0.7520 (tp30) REVERT: y 20 ASN cc_start: 0.9411 (m-40) cc_final: 0.9144 (m-40) REVERT: y 36 GLN cc_start: 0.8775 (mt0) cc_final: 0.8559 (mp10) REVERT: y 38 GLN cc_start: 0.8392 (tp-100) cc_final: 0.8181 (tp-100) REVERT: z 5 LYS cc_start: 0.8376 (mmmt) cc_final: 0.8112 (mmmt) REVERT: A 11 GLU cc_start: 0.8905 (tt0) cc_final: 0.8616 (tp30) REVERT: D 3 ARG cc_start: 0.8318 (mmm-85) cc_final: 0.8055 (mmm160) REVERT: D 25 LYS cc_start: 0.8387 (tmmt) cc_final: 0.7780 (tmmt) REVERT: E 5 THR cc_start: 0.8848 (m) cc_final: 0.8559 (p) REVERT: E 28 LEU cc_start: 0.9465 (tp) cc_final: 0.9244 (tt) REVERT: F 15 LYS cc_start: 0.8743 (mmmt) cc_final: 0.8261 (mppt) REVERT: F 24 ARG cc_start: 0.8499 (mtt90) cc_final: 0.8223 (ttm110) REVERT: F 35 GLN cc_start: 0.8739 (OUTLIER) cc_final: 0.8234 (pt0) REVERT: a 50 ILE cc_start: -0.0675 (OUTLIER) cc_final: -0.0971 (mm) outliers start: 118 outliers final: 80 residues processed: 751 average time/residue: 0.8870 time to fit residues: 1140.7905 Evaluate side-chains 698 residues out of total 2739 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 84 poor density : 614 time to evaluate : 3.737 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain b residue 5 CYS Chi-restraints excluded: chain b residue 18 VAL Chi-restraints excluded: chain b residue 19 VAL Chi-restraints excluded: chain b residue 117 SER Chi-restraints excluded: chain b residue 203 VAL Chi-restraints excluded: chain c residue 122 VAL Chi-restraints excluded: chain d residue 4 VAL Chi-restraints excluded: chain d residue 73 ILE Chi-restraints excluded: chain d residue 120 VAL Chi-restraints excluded: chain d residue 149 ILE Chi-restraints excluded: chain d residue 187 VAL Chi-restraints excluded: chain e residue 34 THR Chi-restraints excluded: chain e residue 156 THR Chi-restraints excluded: chain e residue 168 LEU Chi-restraints excluded: chain f residue 9 VAL Chi-restraints excluded: chain f residue 10 VAL Chi-restraints excluded: chain f residue 16 VAL Chi-restraints excluded: chain f residue 22 VAL Chi-restraints excluded: chain f residue 130 ILE Chi-restraints excluded: chain f residue 161 VAL Chi-restraints excluded: chain g residue 4 ILE Chi-restraints excluded: chain g residue 12 LEU Chi-restraints excluded: chain g residue 37 VAL Chi-restraints excluded: chain h residue 5 LEU Chi-restraints excluded: chain h residue 26 VAL Chi-restraints excluded: chain h residue 33 VAL Chi-restraints excluded: chain h residue 57 ASN Chi-restraints excluded: chain h residue 95 LEU Chi-restraints excluded: chain i residue 61 TYR Chi-restraints excluded: chain j residue 81 ILE Chi-restraints excluded: chain k residue 35 VAL Chi-restraints excluded: chain k residue 57 VAL Chi-restraints excluded: chain k residue 58 LEU Chi-restraints excluded: chain l residue 101 ILE Chi-restraints excluded: chain n residue 15 SER Chi-restraints excluded: chain n residue 36 THR Chi-restraints excluded: chain n residue 37 THR Chi-restraints excluded: chain n residue 57 THR Chi-restraints excluded: chain n residue 74 GLU Chi-restraints excluded: chain n residue 97 ILE Chi-restraints excluded: chain o residue 35 ILE Chi-restraints excluded: chain o residue 49 VAL Chi-restraints excluded: chain o residue 74 VAL Chi-restraints excluded: chain p residue 8 GLU Chi-restraints excluded: chain p residue 23 ASP Chi-restraints excluded: chain p residue 65 ASN Chi-restraints excluded: chain p residue 109 ILE Chi-restraints excluded: chain q residue 87 VAL Chi-restraints excluded: chain q residue 90 ASP Chi-restraints excluded: chain r residue 4 VAL Chi-restraints excluded: chain r residue 27 ILE Chi-restraints excluded: chain r residue 29 THR Chi-restraints excluded: chain r residue 53 PHE Chi-restraints excluded: chain r residue 63 VAL Chi-restraints excluded: chain r residue 86 GLN Chi-restraints excluded: chain s residue 65 ASP Chi-restraints excluded: chain s residue 66 ILE Chi-restraints excluded: chain t residue 10 VAL Chi-restraints excluded: chain t residue 39 THR Chi-restraints excluded: chain u residue 11 ILE Chi-restraints excluded: chain v residue 10 LYS Chi-restraints excluded: chain v residue 43 ASP Chi-restraints excluded: chain v residue 45 ASP Chi-restraints excluded: chain v residue 71 LYS Chi-restraints excluded: chain w residue 27 VAL Chi-restraints excluded: chain w residue 31 SER Chi-restraints excluded: chain w residue 58 LYS Chi-restraints excluded: chain w residue 67 VAL Chi-restraints excluded: chain x residue 70 LEU Chi-restraints excluded: chain y residue 17 GLU Chi-restraints excluded: chain y residue 19 LEU Chi-restraints excluded: chain y residue 21 LEU Chi-restraints excluded: chain z residue 31 ILE Chi-restraints excluded: chain A residue 9 TYR Chi-restraints excluded: chain A residue 35 ASP Chi-restraints excluded: chain B residue 4 GLN Chi-restraints excluded: chain D residue 4 THR Chi-restraints excluded: chain D residue 30 VAL Chi-restraints excluded: chain D residue 44 VAL Chi-restraints excluded: chain F residue 8 LYS Chi-restraints excluded: chain F residue 35 GLN Chi-restraints excluded: chain a residue 47 ASN Chi-restraints excluded: chain a residue 50 ILE Chi-restraints excluded: chain a residue 214 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 629 random chunks: chunk 317 optimal weight: 9.9990 chunk 177 optimal weight: 0.8980 chunk 475 optimal weight: 8.9990 chunk 388 optimal weight: 10.0000 chunk 157 optimal weight: 1.9990 chunk 572 optimal weight: 10.0000 chunk 618 optimal weight: 20.0000 chunk 509 optimal weight: 10.0000 chunk 567 optimal weight: 10.0000 chunk 195 optimal weight: 5.9990 chunk 459 optimal weight: 10.0000 overall best weight: 5.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: b 225 ASN ** c 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** c 49 GLN c 136 ASN d 30 GLN d 90 GLN f 87 GLN g 11 ASN ** g 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** g 43 ASN ** i 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** l 38 GLN l 104 GLN ** p 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** p 114 ASN ** q 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** s 15 GLN ** t 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** t 70 HIS ** v 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** y 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 13 ASN E 25 HIS F 35 GLN ** F 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 47 ASN ** a 57 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8514 moved from start: 0.2409 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.093 99292 Z= 0.331 Angle : 0.653 14.485 149057 Z= 0.339 Chirality : 0.039 0.308 19153 Planarity : 0.005 0.055 7608 Dihedral : 23.590 175.859 50900 Min Nonbonded Distance : 2.096 Molprobity Statistics. All-atom Clashscore : 15.69 Ramachandran Plot: Outliers : 0.15 % Allowed : 8.54 % Favored : 91.31 % Rotamer: Outliers : 5.81 % Allowed : 17.45 % Favored : 76.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.81 (0.13), residues: 3325 helix: -0.95 (0.16), residues: 936 sheet: -1.95 (0.19), residues: 627 loop : -2.37 (0.13), residues: 1762 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP b 212 HIS 0.005 0.001 HIS E 25 PHE 0.040 0.002 PHE g 46 TYR 0.017 0.002 TYR b 61 ARG 0.011 0.001 ARG v 19 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6650 Ramachandran restraints generated. 3325 Oldfield, 0 Emsley, 3325 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6650 Ramachandran restraints generated. 3325 Oldfield, 0 Emsley, 3325 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 814 residues out of total 2739 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 159 poor density : 655 time to evaluate : 5.070 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: b 86 ARG cc_start: 0.8314 (OUTLIER) cc_final: 0.7605 (mmt90) REVERT: b 224 MET cc_start: 0.8788 (mtt) cc_final: 0.8482 (mmt) REVERT: d 24 ASN cc_start: 0.8962 (t0) cc_final: 0.8624 (t0) REVERT: d 195 GLN cc_start: 0.8480 (mt0) cc_final: 0.8089 (mp10) REVERT: e 26 GLN cc_start: 0.7960 (tt0) cc_final: 0.7711 (tt0) REVERT: e 41 GLU cc_start: 0.8006 (mp0) cc_final: 0.7502 (tm-30) REVERT: e 95 MET cc_start: 0.9086 (ttp) cc_final: 0.8848 (ttp) REVERT: f 41 GLU cc_start: 0.8266 (tt0) cc_final: 0.8048 (tt0) REVERT: f 72 ASN cc_start: 0.8879 (t0) cc_final: 0.8444 (t0) REVERT: f 82 PHE cc_start: 0.7864 (m-80) cc_final: 0.7484 (m-80) REVERT: f 123 GLU cc_start: 0.8351 (tp30) cc_final: 0.8124 (pm20) REVERT: f 129 GLU cc_start: 0.8341 (tm-30) cc_final: 0.7743 (tm-30) REVERT: g 2 GLN cc_start: 0.8235 (mm110) cc_final: 0.7822 (mm110) REVERT: h 52 MET cc_start: -0.1329 (mmp) cc_final: -0.1873 (mpp) REVERT: i 135 MET cc_start: 0.3926 (mmt) cc_final: 0.2786 (mmt) REVERT: j 125 TYR cc_start: 0.8426 (m-80) cc_final: 0.7967 (m-80) REVERT: k 37 ASP cc_start: 0.8435 (t70) cc_final: 0.7869 (t0) REVERT: l 58 TYR cc_start: 0.8474 (p90) cc_final: 0.8250 (p90) REVERT: l 91 ASP cc_start: 0.8492 (OUTLIER) cc_final: 0.8105 (p0) REVERT: n 56 LYS cc_start: 0.8939 (mtpp) cc_final: 0.8663 (mtpm) REVERT: n 72 ASP cc_start: 0.8710 (t0) cc_final: 0.8476 (t0) REVERT: o 17 LYS cc_start: 0.9238 (tptp) cc_final: 0.9020 (tptp) REVERT: o 83 LEU cc_start: 0.9221 (mt) cc_final: 0.8981 (mt) REVERT: p 12 MET cc_start: 0.8039 (OUTLIER) cc_final: 0.7529 (mpp) REVERT: p 26 GLU cc_start: 0.7983 (tm-30) cc_final: 0.7577 (tm-30) REVERT: q 65 ASN cc_start: 0.8857 (t0) cc_final: 0.8655 (t0) REVERT: q 96 ASP cc_start: 0.8218 (t70) cc_final: 0.7916 (t0) REVERT: r 11 GLN cc_start: 0.8944 (mp10) cc_final: 0.8616 (mp10) REVERT: r 31 GLU cc_start: 0.7376 (tm-30) cc_final: 0.7090 (tm-30) REVERT: r 78 ARG cc_start: 0.9001 (tpp-160) cc_final: 0.8457 (tpp80) REVERT: r 97 LYS cc_start: 0.9252 (tttt) cc_final: 0.8958 (ttpt) REVERT: s 34 ASP cc_start: 0.8824 (p0) cc_final: 0.8551 (p0) REVERT: s 69 LEU cc_start: 0.9147 (mt) cc_final: 0.8764 (mt) REVERT: t 5 GLU cc_start: 0.8226 (mp0) cc_final: 0.7853 (mp0) REVERT: t 12 ARG cc_start: 0.8348 (mmm-85) cc_final: 0.8114 (mmm-85) REVERT: u 17 ASP cc_start: 0.8075 (m-30) cc_final: 0.7698 (m-30) REVERT: u 21 ARG cc_start: 0.8501 (ptm-80) cc_final: 0.7866 (mtp-110) REVERT: u 30 SER cc_start: 0.9341 (p) cc_final: 0.9125 (p) REVERT: u 38 ILE cc_start: 0.8997 (mm) cc_final: 0.8784 (mm) REVERT: u 72 PHE cc_start: 0.8515 (t80) cc_final: 0.8091 (t80) REVERT: v 10 LYS cc_start: 0.7653 (OUTLIER) cc_final: 0.6928 (pptt) REVERT: v 11 GLU cc_start: 0.7835 (tm-30) cc_final: 0.7588 (tm-30) REVERT: w 17 LEU cc_start: 0.9076 (mt) cc_final: 0.8609 (mt) REVERT: w 52 ASP cc_start: 0.8180 (t0) cc_final: 0.7834 (t0) REVERT: w 58 LYS cc_start: 0.9086 (mtmm) cc_final: 0.8787 (mtmm) REVERT: y 8 GLU cc_start: 0.8300 (mp0) cc_final: 0.7787 (mp0) REVERT: y 9 LYS cc_start: 0.9340 (tmmt) cc_final: 0.8072 (pttp) REVERT: y 20 ASN cc_start: 0.9350 (m-40) cc_final: 0.9109 (m-40) REVERT: z 5 LYS cc_start: 0.8374 (mmmt) cc_final: 0.8140 (mmmt) REVERT: A 11 GLU cc_start: 0.8814 (tt0) cc_final: 0.8481 (tp30) REVERT: D 1 MET cc_start: 0.8352 (pmm) cc_final: 0.7431 (pmm) REVERT: D 25 LYS cc_start: 0.8278 (tmmt) cc_final: 0.7404 (ttpp) REVERT: D 29 GLN cc_start: 0.8553 (OUTLIER) cc_final: 0.8037 (mp10) REVERT: E 5 THR cc_start: 0.8870 (m) cc_final: 0.8600 (p) REVERT: E 28 LEU cc_start: 0.9490 (tp) cc_final: 0.9261 (tt) REVERT: F 15 LYS cc_start: 0.8739 (mmmt) cc_final: 0.8254 (mppt) REVERT: F 24 ARG cc_start: 0.8554 (mtt90) cc_final: 0.8181 (ttm110) REVERT: F 35 GLN cc_start: 0.8888 (OUTLIER) cc_final: 0.8617 (pt0) REVERT: F 36 ARG cc_start: 0.8817 (OUTLIER) cc_final: 0.7750 (tmm-80) REVERT: a 47 ASN cc_start: 0.4536 (OUTLIER) cc_final: 0.4258 (p0) REVERT: a 50 ILE cc_start: -0.0368 (OUTLIER) cc_final: -0.0702 (mm) outliers start: 159 outliers final: 109 residues processed: 745 average time/residue: 0.8610 time to fit residues: 1108.2359 Evaluate side-chains 732 residues out of total 2739 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 118 poor density : 614 time to evaluate : 3.855 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain b residue 5 CYS Chi-restraints excluded: chain b residue 18 VAL Chi-restraints excluded: chain b residue 19 VAL Chi-restraints excluded: chain b residue 86 ARG Chi-restraints excluded: chain b residue 117 SER Chi-restraints excluded: chain b residue 183 VAL Chi-restraints excluded: chain b residue 203 VAL Chi-restraints excluded: chain b residue 256 THR Chi-restraints excluded: chain c residue 9 VAL Chi-restraints excluded: chain c residue 60 VAL Chi-restraints excluded: chain c residue 91 THR Chi-restraints excluded: chain c residue 136 ASN Chi-restraints excluded: chain d residue 4 VAL Chi-restraints excluded: chain d residue 73 ILE Chi-restraints excluded: chain d residue 120 VAL Chi-restraints excluded: chain d residue 149 ILE Chi-restraints excluded: chain d residue 187 VAL Chi-restraints excluded: chain e residue 34 THR Chi-restraints excluded: chain e residue 39 VAL Chi-restraints excluded: chain e residue 131 VAL Chi-restraints excluded: chain e residue 151 LEU Chi-restraints excluded: chain e residue 156 THR Chi-restraints excluded: chain e residue 168 LEU Chi-restraints excluded: chain f residue 9 VAL Chi-restraints excluded: chain f residue 10 VAL Chi-restraints excluded: chain f residue 15 ASP Chi-restraints excluded: chain f residue 16 VAL Chi-restraints excluded: chain f residue 22 VAL Chi-restraints excluded: chain f residue 130 ILE Chi-restraints excluded: chain f residue 161 VAL Chi-restraints excluded: chain g residue 4 ILE Chi-restraints excluded: chain g residue 12 LEU Chi-restraints excluded: chain g residue 37 VAL Chi-restraints excluded: chain h residue 5 LEU Chi-restraints excluded: chain h residue 26 VAL Chi-restraints excluded: chain h residue 57 ASN Chi-restraints excluded: chain h residue 64 VAL Chi-restraints excluded: chain h residue 95 LEU Chi-restraints excluded: chain i residue 61 TYR Chi-restraints excluded: chain j residue 70 THR Chi-restraints excluded: chain j residue 81 ILE Chi-restraints excluded: chain j residue 86 GLN Chi-restraints excluded: chain j residue 140 LEU Chi-restraints excluded: chain k residue 35 VAL Chi-restraints excluded: chain k residue 42 THR Chi-restraints excluded: chain k residue 56 ASP Chi-restraints excluded: chain k residue 57 VAL Chi-restraints excluded: chain k residue 58 LEU Chi-restraints excluded: chain k residue 88 ASN Chi-restraints excluded: chain l residue 91 ASP Chi-restraints excluded: chain l residue 101 ILE Chi-restraints excluded: chain l residue 128 THR Chi-restraints excluded: chain n residue 1 MET Chi-restraints excluded: chain n residue 9 GLN Chi-restraints excluded: chain n residue 15 SER Chi-restraints excluded: chain n residue 33 ILE Chi-restraints excluded: chain n residue 36 THR Chi-restraints excluded: chain n residue 57 THR Chi-restraints excluded: chain n residue 113 ILE Chi-restraints excluded: chain o residue 49 VAL Chi-restraints excluded: chain o residue 74 VAL Chi-restraints excluded: chain p residue 3 ILE Chi-restraints excluded: chain p residue 11 GLN Chi-restraints excluded: chain p residue 12 MET Chi-restraints excluded: chain p residue 23 ASP Chi-restraints excluded: chain p residue 65 ASN Chi-restraints excluded: chain p residue 72 VAL Chi-restraints excluded: chain p residue 109 ILE Chi-restraints excluded: chain p residue 114 ASN Chi-restraints excluded: chain q residue 87 VAL Chi-restraints excluded: chain q residue 90 ASP Chi-restraints excluded: chain r residue 4 VAL Chi-restraints excluded: chain r residue 27 ILE Chi-restraints excluded: chain r residue 29 THR Chi-restraints excluded: chain r residue 63 VAL Chi-restraints excluded: chain s residue 20 VAL Chi-restraints excluded: chain s residue 65 ASP Chi-restraints excluded: chain s residue 66 ILE Chi-restraints excluded: chain s residue 74 ILE Chi-restraints excluded: chain t residue 39 THR Chi-restraints excluded: chain u residue 11 ILE Chi-restraints excluded: chain u residue 33 VAL Chi-restraints excluded: chain u residue 64 ILE Chi-restraints excluded: chain v residue 8 VAL Chi-restraints excluded: chain v residue 10 LYS Chi-restraints excluded: chain v residue 45 ASP Chi-restraints excluded: chain v residue 63 ILE Chi-restraints excluded: chain w residue 27 VAL Chi-restraints excluded: chain w residue 31 SER Chi-restraints excluded: chain w residue 63 VAL Chi-restraints excluded: chain w residue 67 VAL Chi-restraints excluded: chain x residue 19 HIS Chi-restraints excluded: chain x residue 39 VAL Chi-restraints excluded: chain x residue 70 LEU Chi-restraints excluded: chain y residue 17 GLU Chi-restraints excluded: chain y residue 19 LEU Chi-restraints excluded: chain y residue 21 LEU Chi-restraints excluded: chain y residue 50 VAL Chi-restraints excluded: chain z residue 3 THR Chi-restraints excluded: chain z residue 31 ILE Chi-restraints excluded: chain A residue 9 TYR Chi-restraints excluded: chain A residue 30 HIS Chi-restraints excluded: chain A residue 35 ASP Chi-restraints excluded: chain A residue 37 CYS Chi-restraints excluded: chain B residue 21 LEU Chi-restraints excluded: chain D residue 4 THR Chi-restraints excluded: chain D residue 29 GLN Chi-restraints excluded: chain D residue 30 VAL Chi-restraints excluded: chain D residue 44 VAL Chi-restraints excluded: chain E residue 53 ASP Chi-restraints excluded: chain F residue 8 LYS Chi-restraints excluded: chain F residue 23 ILE Chi-restraints excluded: chain F residue 35 GLN Chi-restraints excluded: chain F residue 36 ARG Chi-restraints excluded: chain a residue 35 THR Chi-restraints excluded: chain a residue 47 ASN Chi-restraints excluded: chain a residue 50 ILE Chi-restraints excluded: chain a residue 214 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 629 random chunks: chunk 565 optimal weight: 10.0000 chunk 430 optimal weight: 10.0000 chunk 296 optimal weight: 4.9990 chunk 63 optimal weight: 9.9990 chunk 273 optimal weight: 7.9990 chunk 384 optimal weight: 10.0000 chunk 574 optimal weight: 10.0000 chunk 607 optimal weight: 10.0000 chunk 300 optimal weight: 8.9990 chunk 544 optimal weight: 8.9990 chunk 163 optimal weight: 6.9990 overall best weight: 7.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: b 114 GLN b 133 ASN c 67 HIS d 30 GLN d 90 GLN d 115 GLN ** f 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** g 11 ASN ** g 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** g 43 ASN ** i 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** n 18 GLN p 65 ASN ** p 114 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** s 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** s 61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** t 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** v 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** y 25 GLN A 20 ASN B 4 GLN E 25 HIS F 35 GLN ** F 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 47 ASN ** a 57 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8544 moved from start: 0.3037 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.117 99292 Z= 0.444 Angle : 0.741 12.937 149057 Z= 0.379 Chirality : 0.042 0.299 19153 Planarity : 0.005 0.055 7608 Dihedral : 23.874 175.631 50900 Min Nonbonded Distance : 1.780 Molprobity Statistics. All-atom Clashscore : 19.97 Ramachandran Plot: Outliers : 0.15 % Allowed : 9.71 % Favored : 90.14 % Rotamer: Outliers : 6.79 % Allowed : 18.77 % Favored : 74.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.68 (0.14), residues: 3325 helix: -0.88 (0.16), residues: 935 sheet: -1.66 (0.20), residues: 597 loop : -2.37 (0.14), residues: 1793 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP b 212 HIS 0.006 0.002 HIS B 18 PHE 0.037 0.002 PHE g 46 TYR 0.019 0.002 TYR d 101 ARG 0.009 0.001 ARG c 184 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6650 Ramachandran restraints generated. 3325 Oldfield, 0 Emsley, 3325 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6650 Ramachandran restraints generated. 3325 Oldfield, 0 Emsley, 3325 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 823 residues out of total 2739 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 186 poor density : 637 time to evaluate : 3.823 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: b 86 ARG cc_start: 0.8437 (OUTLIER) cc_final: 0.7612 (mmt90) REVERT: d 24 ASN cc_start: 0.9045 (t0) cc_final: 0.8639 (t0) REVERT: d 195 GLN cc_start: 0.8445 (mt0) cc_final: 0.8066 (mp10) REVERT: e 26 GLN cc_start: 0.8183 (tt0) cc_final: 0.7929 (tt0) REVERT: e 95 MET cc_start: 0.9122 (ttp) cc_final: 0.8914 (ttp) REVERT: f 129 GLU cc_start: 0.8461 (tm-30) cc_final: 0.7683 (tm-30) REVERT: g 7 ASP cc_start: 0.7673 (m-30) cc_final: 0.7469 (m-30) REVERT: g 35 LYS cc_start: 0.8699 (mptt) cc_final: 0.8449 (mptt) REVERT: h 52 MET cc_start: -0.1002 (mmp) cc_final: -0.1646 (mpp) REVERT: i 16 MET cc_start: 0.1018 (ptt) cc_final: 0.0330 (ptm) REVERT: i 135 MET cc_start: 0.4132 (mmt) cc_final: 0.3222 (mmt) REVERT: j 125 TYR cc_start: 0.8381 (m-80) cc_final: 0.7894 (m-80) REVERT: k 37 ASP cc_start: 0.8357 (t70) cc_final: 0.7810 (t0) REVERT: l 58 TYR cc_start: 0.8563 (p90) cc_final: 0.8256 (p90) REVERT: l 91 ASP cc_start: 0.8570 (OUTLIER) cc_final: 0.8246 (p0) REVERT: n 32 GLU cc_start: 0.8693 (mp0) cc_final: 0.8467 (mp0) REVERT: n 49 GLU cc_start: 0.8324 (mp0) cc_final: 0.7796 (mp0) REVERT: n 56 LYS cc_start: 0.8869 (mtpp) cc_final: 0.8638 (mtpm) REVERT: o 84 GLU cc_start: 0.8132 (pt0) cc_final: 0.6563 (pt0) REVERT: p 4 ILE cc_start: 0.9361 (pt) cc_final: 0.8920 (mm) REVERT: p 8 GLU cc_start: 0.8533 (mp0) cc_final: 0.8234 (mp0) REVERT: p 11 GLN cc_start: 0.8765 (OUTLIER) cc_final: 0.8481 (mt0) REVERT: p 12 MET cc_start: 0.8005 (OUTLIER) cc_final: 0.7412 (mpp) REVERT: p 26 GLU cc_start: 0.7949 (tm-30) cc_final: 0.7365 (tm-30) REVERT: q 65 ASN cc_start: 0.8897 (t0) cc_final: 0.8674 (t0) REVERT: q 96 ASP cc_start: 0.8362 (t70) cc_final: 0.7753 (t0) REVERT: r 6 GLN cc_start: 0.9004 (tt0) cc_final: 0.8743 (pt0) REVERT: r 11 GLN cc_start: 0.8935 (mp10) cc_final: 0.8658 (mp10) REVERT: r 31 GLU cc_start: 0.7457 (tm-30) cc_final: 0.7137 (tm-30) REVERT: r 78 ARG cc_start: 0.9072 (tpp-160) cc_final: 0.8546 (tpp80) REVERT: r 81 LYS cc_start: 0.9161 (mmtt) cc_final: 0.8913 (mmtp) REVERT: r 97 LYS cc_start: 0.9283 (tttt) cc_final: 0.8864 (ttpt) REVERT: s 4 ILE cc_start: 0.8957 (OUTLIER) cc_final: 0.8436 (mp) REVERT: s 34 ASP cc_start: 0.8858 (p0) cc_final: 0.8556 (p0) REVERT: s 52 GLU cc_start: 0.8632 (mm-30) cc_final: 0.8315 (mm-30) REVERT: s 69 LEU cc_start: 0.9178 (mt) cc_final: 0.8804 (mt) REVERT: t 1 MET cc_start: 0.3680 (mmt) cc_final: 0.3332 (tpt) REVERT: t 5 GLU cc_start: 0.8258 (mp0) cc_final: 0.7867 (mp0) REVERT: t 48 GLN cc_start: 0.8772 (OUTLIER) cc_final: 0.7960 (mp10) REVERT: u 17 ASP cc_start: 0.8080 (m-30) cc_final: 0.7653 (m-30) REVERT: u 30 SER cc_start: 0.9328 (p) cc_final: 0.9103 (p) REVERT: v 19 ARG cc_start: 0.8909 (mtm-85) cc_final: 0.8305 (mtm-85) REVERT: v 83 LYS cc_start: 0.8775 (tppt) cc_final: 0.8478 (tptp) REVERT: w 17 LEU cc_start: 0.9133 (mt) cc_final: 0.8643 (mt) REVERT: w 52 ASP cc_start: 0.8253 (t0) cc_final: 0.7879 (t0) REVERT: w 58 LYS cc_start: 0.9060 (mtmm) cc_final: 0.8758 (mtmm) REVERT: w 64 LYS cc_start: 0.8502 (OUTLIER) cc_final: 0.8246 (mtpp) REVERT: y 20 ASN cc_start: 0.9290 (m-40) cc_final: 0.9053 (m-40) REVERT: y 36 GLN cc_start: 0.8800 (mt0) cc_final: 0.8448 (mt0) REVERT: A 11 GLU cc_start: 0.8863 (tt0) cc_final: 0.8523 (tp30) REVERT: B 52 LYS cc_start: 0.8198 (tppt) cc_final: 0.7830 (tptp) REVERT: E 5 THR cc_start: 0.8841 (m) cc_final: 0.8577 (p) REVERT: E 15 LYS cc_start: 0.8489 (OUTLIER) cc_final: 0.8200 (tmtt) REVERT: E 28 LEU cc_start: 0.9490 (tp) cc_final: 0.9279 (tt) REVERT: F 15 LYS cc_start: 0.8728 (mmmt) cc_final: 0.8250 (mppt) REVERT: F 36 ARG cc_start: 0.8656 (OUTLIER) cc_final: 0.7613 (tmm-80) REVERT: a 50 ILE cc_start: -0.0447 (OUTLIER) cc_final: -0.0809 (mm) REVERT: a 218 MET cc_start: 0.1476 (mmm) cc_final: 0.1250 (mmt) outliers start: 186 outliers final: 138 residues processed: 743 average time/residue: 0.8428 time to fit residues: 1083.9366 Evaluate side-chains 752 residues out of total 2739 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 148 poor density : 604 time to evaluate : 3.812 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain b residue 5 CYS Chi-restraints excluded: chain b residue 18 VAL Chi-restraints excluded: chain b residue 19 VAL Chi-restraints excluded: chain b residue 86 ARG Chi-restraints excluded: chain b residue 89 ASN Chi-restraints excluded: chain b residue 117 SER Chi-restraints excluded: chain b residue 183 VAL Chi-restraints excluded: chain b residue 200 MET Chi-restraints excluded: chain b residue 203 VAL Chi-restraints excluded: chain b residue 218 THR Chi-restraints excluded: chain b residue 256 THR Chi-restraints excluded: chain c residue 9 VAL Chi-restraints excluded: chain c residue 60 VAL Chi-restraints excluded: chain c residue 91 THR Chi-restraints excluded: chain c residue 96 ILE Chi-restraints excluded: chain c residue 100 LEU Chi-restraints excluded: chain c residue 122 VAL Chi-restraints excluded: chain c residue 138 LEU Chi-restraints excluded: chain d residue 4 VAL Chi-restraints excluded: chain d residue 73 ILE Chi-restraints excluded: chain d residue 100 MET Chi-restraints excluded: chain d residue 120 VAL Chi-restraints excluded: chain d residue 133 LEU Chi-restraints excluded: chain d residue 167 VAL Chi-restraints excluded: chain d residue 176 ASP Chi-restraints excluded: chain d residue 187 VAL Chi-restraints excluded: chain e residue 34 THR Chi-restraints excluded: chain e residue 39 VAL Chi-restraints excluded: chain e residue 43 ILE Chi-restraints excluded: chain e residue 131 VAL Chi-restraints excluded: chain e residue 156 THR Chi-restraints excluded: chain e residue 168 LEU Chi-restraints excluded: chain f residue 9 VAL Chi-restraints excluded: chain f residue 10 VAL Chi-restraints excluded: chain f residue 15 ASP Chi-restraints excluded: chain f residue 16 VAL Chi-restraints excluded: chain f residue 22 VAL Chi-restraints excluded: chain f residue 102 ILE Chi-restraints excluded: chain f residue 130 ILE Chi-restraints excluded: chain f residue 161 VAL Chi-restraints excluded: chain g residue 4 ILE Chi-restraints excluded: chain g residue 12 LEU Chi-restraints excluded: chain g residue 37 VAL Chi-restraints excluded: chain g residue 46 PHE Chi-restraints excluded: chain h residue 5 LEU Chi-restraints excluded: chain h residue 26 VAL Chi-restraints excluded: chain h residue 57 ASN Chi-restraints excluded: chain h residue 64 VAL Chi-restraints excluded: chain h residue 88 HIS Chi-restraints excluded: chain h residue 95 LEU Chi-restraints excluded: chain i residue 23 VAL Chi-restraints excluded: chain i residue 61 TYR Chi-restraints excluded: chain i residue 70 THR Chi-restraints excluded: chain i residue 141 ASP Chi-restraints excluded: chain j residue 60 ASP Chi-restraints excluded: chain j residue 70 THR Chi-restraints excluded: chain j residue 81 ILE Chi-restraints excluded: chain j residue 86 GLN Chi-restraints excluded: chain j residue 140 LEU Chi-restraints excluded: chain k residue 35 VAL Chi-restraints excluded: chain k residue 42 THR Chi-restraints excluded: chain k residue 53 LYS Chi-restraints excluded: chain k residue 56 ASP Chi-restraints excluded: chain k residue 57 VAL Chi-restraints excluded: chain k residue 58 LEU Chi-restraints excluded: chain k residue 88 ASN Chi-restraints excluded: chain l residue 91 ASP Chi-restraints excluded: chain l residue 101 ILE Chi-restraints excluded: chain l residue 128 THR Chi-restraints excluded: chain n residue 1 MET Chi-restraints excluded: chain n residue 9 GLN Chi-restraints excluded: chain n residue 36 THR Chi-restraints excluded: chain n residue 37 THR Chi-restraints excluded: chain n residue 57 THR Chi-restraints excluded: chain n residue 97 ILE Chi-restraints excluded: chain n residue 113 ILE Chi-restraints excluded: chain o residue 8 ILE Chi-restraints excluded: chain o residue 49 VAL Chi-restraints excluded: chain o residue 74 VAL Chi-restraints excluded: chain o residue 103 VAL Chi-restraints excluded: chain p residue 3 ILE Chi-restraints excluded: chain p residue 11 GLN Chi-restraints excluded: chain p residue 12 MET Chi-restraints excluded: chain p residue 23 ASP Chi-restraints excluded: chain p residue 59 THR Chi-restraints excluded: chain p residue 69 VAL Chi-restraints excluded: chain p residue 72 VAL Chi-restraints excluded: chain p residue 109 ILE Chi-restraints excluded: chain q residue 87 VAL Chi-restraints excluded: chain q residue 90 ASP Chi-restraints excluded: chain q residue 94 LEU Chi-restraints excluded: chain r residue 4 VAL Chi-restraints excluded: chain r residue 27 ILE Chi-restraints excluded: chain r residue 29 THR Chi-restraints excluded: chain r residue 53 PHE Chi-restraints excluded: chain r residue 63 VAL Chi-restraints excluded: chain s residue 4 ILE Chi-restraints excluded: chain s residue 19 LEU Chi-restraints excluded: chain s residue 20 VAL Chi-restraints excluded: chain s residue 24 ILE Chi-restraints excluded: chain s residue 65 ASP Chi-restraints excluded: chain s residue 66 ILE Chi-restraints excluded: chain s residue 74 ILE Chi-restraints excluded: chain t residue 39 THR Chi-restraints excluded: chain t residue 48 GLN Chi-restraints excluded: chain u residue 11 ILE Chi-restraints excluded: chain u residue 27 VAL Chi-restraints excluded: chain u residue 33 VAL Chi-restraints excluded: chain u residue 64 ILE Chi-restraints excluded: chain v residue 8 VAL Chi-restraints excluded: chain v residue 10 LYS Chi-restraints excluded: chain v residue 45 ASP Chi-restraints excluded: chain v residue 71 LYS Chi-restraints excluded: chain v residue 77 VAL Chi-restraints excluded: chain w residue 63 VAL Chi-restraints excluded: chain w residue 64 LYS Chi-restraints excluded: chain w residue 67 VAL Chi-restraints excluded: chain x residue 6 VAL Chi-restraints excluded: chain x residue 19 HIS Chi-restraints excluded: chain x residue 29 LEU Chi-restraints excluded: chain x residue 39 VAL Chi-restraints excluded: chain x residue 70 LEU Chi-restraints excluded: chain y residue 17 GLU Chi-restraints excluded: chain y residue 19 LEU Chi-restraints excluded: chain y residue 21 LEU Chi-restraints excluded: chain y residue 50 VAL Chi-restraints excluded: chain z residue 31 ILE Chi-restraints excluded: chain A residue 9 TYR Chi-restraints excluded: chain A residue 30 HIS Chi-restraints excluded: chain A residue 35 ASP Chi-restraints excluded: chain A residue 37 CYS Chi-restraints excluded: chain B residue 4 GLN Chi-restraints excluded: chain B residue 21 LEU Chi-restraints excluded: chain B residue 51 ARG Chi-restraints excluded: chain D residue 4 THR Chi-restraints excluded: chain D residue 30 VAL Chi-restraints excluded: chain D residue 44 VAL Chi-restraints excluded: chain E residue 15 LYS Chi-restraints excluded: chain E residue 16 THR Chi-restraints excluded: chain E residue 32 LEU Chi-restraints excluded: chain E residue 49 VAL Chi-restraints excluded: chain E residue 53 ASP Chi-restraints excluded: chain F residue 23 ILE Chi-restraints excluded: chain F residue 36 ARG Chi-restraints excluded: chain a residue 35 THR Chi-restraints excluded: chain a residue 50 ILE Chi-restraints excluded: chain a residue 54 LYS Chi-restraints excluded: chain a residue 214 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 629 random chunks: chunk 506 optimal weight: 6.9990 chunk 345 optimal weight: 8.9990 chunk 8 optimal weight: 3.9990 chunk 452 optimal weight: 10.0000 chunk 250 optimal weight: 6.9990 chunk 518 optimal weight: 7.9990 chunk 420 optimal weight: 10.0000 chunk 0 optimal weight: 10.0000 chunk 310 optimal weight: 1.9990 chunk 545 optimal weight: 8.9990 chunk 153 optimal weight: 2.9990 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** c 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 9 GLN d 30 GLN d 90 GLN g 11 ASN ** g 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** p 6 GLN p 114 ASN ** q 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** q 55 GLN q 80 ASN s 61 ASN ** t 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** v 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** y 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 57 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8499 moved from start: 0.3137 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.085 99292 Z= 0.281 Angle : 0.620 12.621 149057 Z= 0.321 Chirality : 0.037 0.301 19153 Planarity : 0.005 0.050 7608 Dihedral : 23.833 176.597 50900 Min Nonbonded Distance : 2.064 Molprobity Statistics. All-atom Clashscore : 16.87 Ramachandran Plot: Outliers : 0.12 % Allowed : 7.85 % Favored : 92.03 % Rotamer: Outliers : 6.06 % Allowed : 20.74 % Favored : 73.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.42 (0.14), residues: 3325 helix: -0.56 (0.17), residues: 933 sheet: -1.58 (0.20), residues: 624 loop : -2.24 (0.14), residues: 1768 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP b 212 HIS 0.005 0.001 HIS o 100 PHE 0.040 0.002 PHE g 46 TYR 0.018 0.002 TYR d 101 ARG 0.016 0.001 ARG f 152 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6650 Ramachandran restraints generated. 3325 Oldfield, 0 Emsley, 3325 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6650 Ramachandran restraints generated. 3325 Oldfield, 0 Emsley, 3325 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 806 residues out of total 2739 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 166 poor density : 640 time to evaluate : 3.916 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: b 86 ARG cc_start: 0.8251 (OUTLIER) cc_final: 0.7509 (mmt90) REVERT: b 224 MET cc_start: 0.8710 (OUTLIER) cc_final: 0.8493 (mmm) REVERT: d 24 ASN cc_start: 0.8969 (t0) cc_final: 0.8543 (t0) REVERT: d 195 GLN cc_start: 0.8459 (mt0) cc_final: 0.8107 (mp10) REVERT: e 37 MET cc_start: 0.7442 (tpp) cc_final: 0.7051 (tpp) REVERT: e 95 MET cc_start: 0.9054 (ttp) cc_final: 0.8793 (ttp) REVERT: f 59 ASP cc_start: 0.8442 (p0) cc_final: 0.8115 (p0) REVERT: f 82 PHE cc_start: 0.7823 (m-80) cc_final: 0.7452 (m-80) REVERT: f 123 GLU cc_start: 0.8416 (tp30) cc_final: 0.8026 (pm20) REVERT: f 129 GLU cc_start: 0.8470 (tm-30) cc_final: 0.8051 (tm-30) REVERT: g 7 ASP cc_start: 0.7714 (m-30) cc_final: 0.7512 (m-30) REVERT: g 35 LYS cc_start: 0.8652 (mptt) cc_final: 0.8450 (mptt) REVERT: h 52 MET cc_start: -0.0908 (mmp) cc_final: -0.1699 (mpp) REVERT: h 116 GLU cc_start: 0.3006 (tt0) cc_final: 0.2711 (pt0) REVERT: h 117 LEU cc_start: -0.0833 (OUTLIER) cc_final: -0.1100 (tt) REVERT: i 135 MET cc_start: 0.3641 (mmt) cc_final: 0.2884 (mmt) REVERT: j 125 TYR cc_start: 0.8422 (m-80) cc_final: 0.7933 (m-80) REVERT: k 37 ASP cc_start: 0.8313 (t70) cc_final: 0.7747 (t0) REVERT: k 53 LYS cc_start: 0.8971 (OUTLIER) cc_final: 0.8610 (ptpp) REVERT: l 58 TYR cc_start: 0.8525 (p90) cc_final: 0.8224 (p90) REVERT: l 91 ASP cc_start: 0.8631 (OUTLIER) cc_final: 0.8305 (p0) REVERT: n 49 GLU cc_start: 0.8089 (mp0) cc_final: 0.7541 (mp0) REVERT: n 56 LYS cc_start: 0.8853 (mtpp) cc_final: 0.8634 (mtpm) REVERT: o 115 LEU cc_start: 0.8848 (OUTLIER) cc_final: 0.8601 (mm) REVERT: p 4 ILE cc_start: 0.9311 (pt) cc_final: 0.8645 (mm) REVERT: p 11 GLN cc_start: 0.8704 (OUTLIER) cc_final: 0.8495 (mt0) REVERT: p 12 MET cc_start: 0.8021 (OUTLIER) cc_final: 0.7340 (mpp) REVERT: p 26 GLU cc_start: 0.7948 (tm-30) cc_final: 0.7362 (tm-30) REVERT: q 60 TRP cc_start: 0.9222 (m-10) cc_final: 0.8858 (m-10) REVERT: q 65 ASN cc_start: 0.8858 (t0) cc_final: 0.8617 (t0) REVERT: q 96 ASP cc_start: 0.8336 (t70) cc_final: 0.7455 (t0) REVERT: r 6 GLN cc_start: 0.8918 (tt0) cc_final: 0.8534 (pt0) REVERT: r 11 GLN cc_start: 0.8924 (mp10) cc_final: 0.8628 (mp10) REVERT: r 78 ARG cc_start: 0.8988 (tpp-160) cc_final: 0.8442 (tpp80) REVERT: r 81 LYS cc_start: 0.9154 (mmtt) cc_final: 0.8870 (mmtp) REVERT: r 97 LYS cc_start: 0.9183 (tttt) cc_final: 0.8918 (tmmt) REVERT: s 34 ASP cc_start: 0.8794 (p0) cc_final: 0.8527 (p0) REVERT: s 69 LEU cc_start: 0.9159 (mt) cc_final: 0.8840 (mt) REVERT: t 4 GLU cc_start: 0.8448 (mt-10) cc_final: 0.8192 (mt-10) REVERT: t 5 GLU cc_start: 0.8232 (mp0) cc_final: 0.7842 (mp0) REVERT: t 24 MET cc_start: 0.8413 (tpp) cc_final: 0.7769 (ttp) REVERT: t 91 GLN cc_start: 0.7014 (pm20) cc_final: 0.6796 (pm20) REVERT: u 17 ASP cc_start: 0.7946 (m-30) cc_final: 0.7554 (m-30) REVERT: u 21 ARG cc_start: 0.8320 (ptm-80) cc_final: 0.8060 (mtp-110) REVERT: u 38 ILE cc_start: 0.8861 (mm) cc_final: 0.8598 (mm) REVERT: u 72 PHE cc_start: 0.8545 (t80) cc_final: 0.8188 (t80) REVERT: v 19 ARG cc_start: 0.8900 (mtm-85) cc_final: 0.8495 (mtm-85) REVERT: v 83 LYS cc_start: 0.8762 (tppt) cc_final: 0.8503 (tptp) REVERT: w 17 LEU cc_start: 0.9062 (mt) cc_final: 0.8604 (mt) REVERT: w 52 ASP cc_start: 0.8130 (t0) cc_final: 0.7816 (t0) REVERT: w 58 LYS cc_start: 0.9087 (mtmm) cc_final: 0.8797 (mtmm) REVERT: w 77 SER cc_start: 0.8789 (m) cc_final: 0.8556 (m) REVERT: x 69 GLU cc_start: 0.8995 (mp0) cc_final: 0.8710 (mp0) REVERT: y 20 ASN cc_start: 0.9257 (m-40) cc_final: 0.9038 (m-40) REVERT: y 36 GLN cc_start: 0.8759 (mt0) cc_final: 0.8434 (mt0) REVERT: z 5 LYS cc_start: 0.8473 (mmmm) cc_final: 0.8172 (mmmt) REVERT: A 11 GLU cc_start: 0.8904 (tt0) cc_final: 0.8580 (tp30) REVERT: B 52 LYS cc_start: 0.8259 (tppt) cc_final: 0.7857 (tptp) REVERT: D 25 LYS cc_start: 0.8287 (tmmt) cc_final: 0.7770 (tmmt) REVERT: D 29 GLN cc_start: 0.8623 (OUTLIER) cc_final: 0.8412 (mp10) REVERT: E 5 THR cc_start: 0.8806 (m) cc_final: 0.8553 (p) REVERT: E 28 LEU cc_start: 0.9481 (tp) cc_final: 0.9267 (tt) REVERT: F 15 LYS cc_start: 0.8680 (mmmt) cc_final: 0.8212 (mppt) REVERT: F 36 ARG cc_start: 0.8545 (OUTLIER) cc_final: 0.7654 (tmm-80) REVERT: a 218 MET cc_start: 0.1576 (mmm) cc_final: 0.1134 (mmt) outliers start: 166 outliers final: 122 residues processed: 736 average time/residue: 0.8783 time to fit residues: 1118.1605 Evaluate side-chains 737 residues out of total 2739 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 132 poor density : 605 time to evaluate : 3.743 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain b residue 5 CYS Chi-restraints excluded: chain b residue 18 VAL Chi-restraints excluded: chain b residue 19 VAL Chi-restraints excluded: chain b residue 52 HIS Chi-restraints excluded: chain b residue 86 ARG Chi-restraints excluded: chain b residue 89 ASN Chi-restraints excluded: chain b residue 117 SER Chi-restraints excluded: chain b residue 183 VAL Chi-restraints excluded: chain b residue 203 VAL Chi-restraints excluded: chain b residue 224 MET Chi-restraints excluded: chain b residue 256 THR Chi-restraints excluded: chain c residue 60 VAL Chi-restraints excluded: chain c residue 91 THR Chi-restraints excluded: chain c residue 96 ILE Chi-restraints excluded: chain c residue 138 LEU Chi-restraints excluded: chain d residue 4 VAL Chi-restraints excluded: chain d residue 13 THR Chi-restraints excluded: chain d residue 73 ILE Chi-restraints excluded: chain d residue 120 VAL Chi-restraints excluded: chain d residue 150 THR Chi-restraints excluded: chain d residue 167 VAL Chi-restraints excluded: chain e residue 34 THR Chi-restraints excluded: chain e residue 39 VAL Chi-restraints excluded: chain e residue 73 VAL Chi-restraints excluded: chain e residue 151 LEU Chi-restraints excluded: chain e residue 152 ASP Chi-restraints excluded: chain e residue 156 THR Chi-restraints excluded: chain e residue 168 LEU Chi-restraints excluded: chain f residue 9 VAL Chi-restraints excluded: chain f residue 10 VAL Chi-restraints excluded: chain f residue 15 ASP Chi-restraints excluded: chain f residue 16 VAL Chi-restraints excluded: chain f residue 22 VAL Chi-restraints excluded: chain f residue 100 ASN Chi-restraints excluded: chain f residue 130 ILE Chi-restraints excluded: chain f residue 161 VAL Chi-restraints excluded: chain g residue 5 LEU Chi-restraints excluded: chain g residue 12 LEU Chi-restraints excluded: chain g residue 37 VAL Chi-restraints excluded: chain g residue 46 PHE Chi-restraints excluded: chain h residue 5 LEU Chi-restraints excluded: chain h residue 55 VAL Chi-restraints excluded: chain h residue 57 ASN Chi-restraints excluded: chain h residue 64 VAL Chi-restraints excluded: chain h residue 88 HIS Chi-restraints excluded: chain h residue 95 LEU Chi-restraints excluded: chain h residue 117 LEU Chi-restraints excluded: chain i residue 8 VAL Chi-restraints excluded: chain i residue 61 TYR Chi-restraints excluded: chain i residue 72 THR Chi-restraints excluded: chain i residue 141 ASP Chi-restraints excluded: chain j residue 70 THR Chi-restraints excluded: chain j residue 86 GLN Chi-restraints excluded: chain k residue 35 VAL Chi-restraints excluded: chain k residue 53 LYS Chi-restraints excluded: chain k residue 56 ASP Chi-restraints excluded: chain k residue 57 VAL Chi-restraints excluded: chain k residue 58 LEU Chi-restraints excluded: chain k residue 88 ASN Chi-restraints excluded: chain l residue 91 ASP Chi-restraints excluded: chain l residue 101 ILE Chi-restraints excluded: chain l residue 128 THR Chi-restraints excluded: chain n residue 1 MET Chi-restraints excluded: chain n residue 9 GLN Chi-restraints excluded: chain n residue 36 THR Chi-restraints excluded: chain n residue 37 THR Chi-restraints excluded: chain n residue 57 THR Chi-restraints excluded: chain n residue 97 ILE Chi-restraints excluded: chain o residue 49 VAL Chi-restraints excluded: chain o residue 74 VAL Chi-restraints excluded: chain o residue 103 VAL Chi-restraints excluded: chain o residue 115 LEU Chi-restraints excluded: chain p residue 3 ILE Chi-restraints excluded: chain p residue 11 GLN Chi-restraints excluded: chain p residue 12 MET Chi-restraints excluded: chain p residue 59 THR Chi-restraints excluded: chain p residue 65 ASN Chi-restraints excluded: chain p residue 72 VAL Chi-restraints excluded: chain p residue 109 ILE Chi-restraints excluded: chain q residue 87 VAL Chi-restraints excluded: chain q residue 90 ASP Chi-restraints excluded: chain r residue 4 VAL Chi-restraints excluded: chain r residue 27 ILE Chi-restraints excluded: chain r residue 29 THR Chi-restraints excluded: chain r residue 38 VAL Chi-restraints excluded: chain r residue 63 VAL Chi-restraints excluded: chain s residue 19 LEU Chi-restraints excluded: chain s residue 65 ASP Chi-restraints excluded: chain s residue 66 ILE Chi-restraints excluded: chain s residue 74 ILE Chi-restraints excluded: chain t residue 39 THR Chi-restraints excluded: chain t residue 60 THR Chi-restraints excluded: chain t residue 74 ILE Chi-restraints excluded: chain u residue 11 ILE Chi-restraints excluded: chain u residue 27 VAL Chi-restraints excluded: chain u residue 33 VAL Chi-restraints excluded: chain u residue 64 ILE Chi-restraints excluded: chain v residue 8 VAL Chi-restraints excluded: chain v residue 10 LYS Chi-restraints excluded: chain v residue 29 ILE Chi-restraints excluded: chain v residue 63 ILE Chi-restraints excluded: chain v residue 71 LYS Chi-restraints excluded: chain w residue 31 SER Chi-restraints excluded: chain w residue 63 VAL Chi-restraints excluded: chain w residue 67 VAL Chi-restraints excluded: chain w residue 79 GLU Chi-restraints excluded: chain x residue 19 HIS Chi-restraints excluded: chain x residue 29 LEU Chi-restraints excluded: chain x residue 39 VAL Chi-restraints excluded: chain x residue 70 LEU Chi-restraints excluded: chain y residue 17 GLU Chi-restraints excluded: chain y residue 19 LEU Chi-restraints excluded: chain y residue 21 LEU Chi-restraints excluded: chain y residue 50 VAL Chi-restraints excluded: chain z residue 3 THR Chi-restraints excluded: chain z residue 31 ILE Chi-restraints excluded: chain z residue 40 THR Chi-restraints excluded: chain A residue 9 TYR Chi-restraints excluded: chain A residue 30 HIS Chi-restraints excluded: chain A residue 35 ASP Chi-restraints excluded: chain B residue 21 LEU Chi-restraints excluded: chain D residue 4 THR Chi-restraints excluded: chain D residue 29 GLN Chi-restraints excluded: chain D residue 30 VAL Chi-restraints excluded: chain D residue 44 VAL Chi-restraints excluded: chain E residue 53 ASP Chi-restraints excluded: chain F residue 8 LYS Chi-restraints excluded: chain F residue 23 ILE Chi-restraints excluded: chain F residue 36 ARG Chi-restraints excluded: chain a residue 35 THR Chi-restraints excluded: chain a residue 54 LYS Chi-restraints excluded: chain a residue 214 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 629 random chunks: chunk 204 optimal weight: 0.7980 chunk 547 optimal weight: 10.0000 chunk 120 optimal weight: 30.0000 chunk 356 optimal weight: 10.0000 chunk 150 optimal weight: 10.0000 chunk 608 optimal weight: 10.0000 chunk 505 optimal weight: 10.0000 chunk 281 optimal weight: 0.5980 chunk 50 optimal weight: 0.7980 chunk 201 optimal weight: 5.9990 chunk 319 optimal weight: 30.0000 overall best weight: 3.6386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: b 162 GLN d 9 GLN d 30 GLN e 26 GLN g 11 ASN ** g 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 114 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** q 43 GLN q 55 GLN q 58 GLN ** s 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** t 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** v 12 GLN ** v 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** y 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 57 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8477 moved from start: 0.3303 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.072 99292 Z= 0.236 Angle : 0.589 12.361 149057 Z= 0.305 Chirality : 0.035 0.300 19153 Planarity : 0.004 0.050 7608 Dihedral : 23.793 176.942 50897 Min Nonbonded Distance : 2.066 Molprobity Statistics. All-atom Clashscore : 15.89 Ramachandran Plot: Outliers : 0.12 % Allowed : 7.79 % Favored : 92.09 % Rotamer: Outliers : 6.35 % Allowed : 21.69 % Favored : 71.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.25 (0.14), residues: 3325 helix: -0.43 (0.17), residues: 938 sheet: -1.61 (0.20), residues: 639 loop : -2.06 (0.14), residues: 1748 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP b 212 HIS 0.008 0.001 HIS v 44 PHE 0.040 0.002 PHE g 46 TYR 0.018 0.002 TYR d 101 ARG 0.009 0.000 ARG f 68 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6650 Ramachandran restraints generated. 3325 Oldfield, 0 Emsley, 3325 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6650 Ramachandran restraints generated. 3325 Oldfield, 0 Emsley, 3325 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 823 residues out of total 2739 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 174 poor density : 649 time to evaluate : 3.859 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: b 86 ARG cc_start: 0.8266 (OUTLIER) cc_final: 0.7455 (mmt90) REVERT: c 99 GLU cc_start: 0.9198 (OUTLIER) cc_final: 0.8818 (mp0) REVERT: d 24 ASN cc_start: 0.8957 (t0) cc_final: 0.8486 (t0) REVERT: e 43 ILE cc_start: 0.8032 (OUTLIER) cc_final: 0.7569 (mt) REVERT: e 95 MET cc_start: 0.9078 (ttp) cc_final: 0.8819 (ttp) REVERT: f 19 ASN cc_start: 0.8054 (t0) cc_final: 0.7716 (t0) REVERT: f 41 GLU cc_start: 0.8220 (tt0) cc_final: 0.7970 (mt-10) REVERT: f 59 ASP cc_start: 0.8496 (p0) cc_final: 0.8183 (p0) REVERT: f 82 PHE cc_start: 0.7803 (m-80) cc_final: 0.7399 (m-80) REVERT: f 129 GLU cc_start: 0.8576 (tm-30) cc_final: 0.8205 (tm-30) REVERT: g 7 ASP cc_start: 0.7747 (m-30) cc_final: 0.7513 (m-30) REVERT: g 35 LYS cc_start: 0.8579 (mptt) cc_final: 0.8253 (mptt) REVERT: g 50 ARG cc_start: 0.7786 (mtm110) cc_final: 0.7455 (ttp-110) REVERT: h 52 MET cc_start: -0.0883 (mmp) cc_final: -0.1685 (mpp) REVERT: i 85 ILE cc_start: 0.4344 (OUTLIER) cc_final: 0.4095 (tp) REVERT: i 135 MET cc_start: 0.3442 (mmt) cc_final: 0.2528 (mmt) REVERT: j 81 ILE cc_start: 0.8617 (OUTLIER) cc_final: 0.8358 (pp) REVERT: j 125 TYR cc_start: 0.8449 (m-80) cc_final: 0.7945 (m-80) REVERT: k 37 ASP cc_start: 0.8305 (t70) cc_final: 0.7735 (t0) REVERT: k 53 LYS cc_start: 0.8968 (OUTLIER) cc_final: 0.8644 (ptpp) REVERT: l 58 TYR cc_start: 0.8504 (p90) cc_final: 0.8236 (p90) REVERT: l 91 ASP cc_start: 0.8592 (OUTLIER) cc_final: 0.8249 (p0) REVERT: l 143 GLU cc_start: 0.8184 (pt0) cc_final: 0.7743 (pm20) REVERT: n 49 GLU cc_start: 0.8091 (mp0) cc_final: 0.7619 (mp0) REVERT: n 56 LYS cc_start: 0.8838 (mtpp) cc_final: 0.8637 (mtpm) REVERT: p 9 GLN cc_start: 0.8746 (tm-30) cc_final: 0.8531 (tm-30) REVERT: p 11 GLN cc_start: 0.8666 (OUTLIER) cc_final: 0.8451 (mt0) REVERT: p 12 MET cc_start: 0.8058 (OUTLIER) cc_final: 0.7349 (mpp) REVERT: p 26 GLU cc_start: 0.8027 (tm-30) cc_final: 0.7477 (tm-30) REVERT: q 60 TRP cc_start: 0.9202 (m-10) cc_final: 0.8865 (m-10) REVERT: q 65 ASN cc_start: 0.8830 (t0) cc_final: 0.8469 (t0) REVERT: q 71 ASN cc_start: 0.8547 (t0) cc_final: 0.8345 (t0) REVERT: q 96 ASP cc_start: 0.8186 (t70) cc_final: 0.7825 (t0) REVERT: r 2 TYR cc_start: 0.8707 (p90) cc_final: 0.7678 (p90) REVERT: r 6 GLN cc_start: 0.8840 (tt0) cc_final: 0.8435 (pt0) REVERT: r 11 GLN cc_start: 0.8857 (mp10) cc_final: 0.8276 (mp10) REVERT: r 13 ARG cc_start: 0.8135 (ttt-90) cc_final: 0.7901 (ptt90) REVERT: r 78 ARG cc_start: 0.8966 (tpp-160) cc_final: 0.8432 (tpp80) REVERT: r 81 LYS cc_start: 0.9138 (mmtt) cc_final: 0.8868 (mmtp) REVERT: r 97 LYS cc_start: 0.9183 (tttt) cc_final: 0.8944 (tmmt) REVERT: s 1 MET cc_start: 0.7404 (tmm) cc_final: 0.7116 (tmm) REVERT: s 34 ASP cc_start: 0.8769 (p0) cc_final: 0.8520 (p0) REVERT: s 69 LEU cc_start: 0.9182 (mt) cc_final: 0.8831 (mt) REVERT: t 4 GLU cc_start: 0.8339 (mt-10) cc_final: 0.8125 (mt-10) REVERT: t 5 GLU cc_start: 0.8210 (mp0) cc_final: 0.7860 (mp0) REVERT: t 24 MET cc_start: 0.8382 (tpp) cc_final: 0.8109 (tpp) REVERT: u 17 ASP cc_start: 0.7986 (m-30) cc_final: 0.7622 (m-30) REVERT: u 21 ARG cc_start: 0.8370 (ptm-80) cc_final: 0.8129 (mtp-110) REVERT: u 72 PHE cc_start: 0.8525 (t80) cc_final: 0.8230 (t80) REVERT: v 9 ARG cc_start: 0.7717 (mmm-85) cc_final: 0.6438 (mmm-85) REVERT: v 19 ARG cc_start: 0.8869 (mtm-85) cc_final: 0.8178 (mtm-85) REVERT: v 83 LYS cc_start: 0.8752 (tppt) cc_final: 0.8548 (tppt) REVERT: w 17 LEU cc_start: 0.9077 (mt) cc_final: 0.8620 (mt) REVERT: w 52 ASP cc_start: 0.8039 (t0) cc_final: 0.7796 (t0) REVERT: w 58 LYS cc_start: 0.9098 (mtmm) cc_final: 0.8797 (mtmm) REVERT: w 77 SER cc_start: 0.8801 (m) cc_final: 0.8466 (m) REVERT: x 69 GLU cc_start: 0.8987 (mp0) cc_final: 0.8728 (mp0) REVERT: y 20 ASN cc_start: 0.9179 (m-40) cc_final: 0.8974 (m-40) REVERT: y 36 GLN cc_start: 0.8762 (mt0) cc_final: 0.8433 (mt0) REVERT: A 11 GLU cc_start: 0.8888 (tt0) cc_final: 0.8556 (tp30) REVERT: B 52 LYS cc_start: 0.8338 (tppt) cc_final: 0.8082 (tptp) REVERT: E 5 THR cc_start: 0.8703 (m) cc_final: 0.8461 (p) REVERT: E 15 LYS cc_start: 0.8432 (OUTLIER) cc_final: 0.8158 (tmtt) REVERT: E 28 LEU cc_start: 0.9465 (tp) cc_final: 0.9185 (tt) REVERT: F 15 LYS cc_start: 0.8655 (mmmt) cc_final: 0.8206 (mppt) REVERT: F 36 ARG cc_start: 0.8563 (OUTLIER) cc_final: 0.7701 (tmm-80) REVERT: a 218 MET cc_start: 0.1802 (mmm) cc_final: 0.1349 (mmt) outliers start: 174 outliers final: 120 residues processed: 749 average time/residue: 0.8462 time to fit residues: 1097.7620 Evaluate side-chains 750 residues out of total 2739 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 131 poor density : 619 time to evaluate : 3.788 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain b residue 5 CYS Chi-restraints excluded: chain b residue 18 VAL Chi-restraints excluded: chain b residue 19 VAL Chi-restraints excluded: chain b residue 71 ASP Chi-restraints excluded: chain b residue 86 ARG Chi-restraints excluded: chain b residue 89 ASN Chi-restraints excluded: chain b residue 117 SER Chi-restraints excluded: chain b residue 203 VAL Chi-restraints excluded: chain b residue 218 THR Chi-restraints excluded: chain b residue 256 THR Chi-restraints excluded: chain c residue 9 VAL Chi-restraints excluded: chain c residue 60 VAL Chi-restraints excluded: chain c residue 91 THR Chi-restraints excluded: chain c residue 96 ILE Chi-restraints excluded: chain c residue 99 GLU Chi-restraints excluded: chain c residue 100 LEU Chi-restraints excluded: chain c residue 138 LEU Chi-restraints excluded: chain d residue 4 VAL Chi-restraints excluded: chain d residue 7 ASP Chi-restraints excluded: chain d residue 13 THR Chi-restraints excluded: chain d residue 73 ILE Chi-restraints excluded: chain d residue 120 VAL Chi-restraints excluded: chain d residue 150 THR Chi-restraints excluded: chain d residue 167 VAL Chi-restraints excluded: chain e residue 12 VAL Chi-restraints excluded: chain e residue 34 THR Chi-restraints excluded: chain e residue 39 VAL Chi-restraints excluded: chain e residue 43 ILE Chi-restraints excluded: chain e residue 105 ILE Chi-restraints excluded: chain e residue 151 LEU Chi-restraints excluded: chain e residue 152 ASP Chi-restraints excluded: chain e residue 156 THR Chi-restraints excluded: chain e residue 168 LEU Chi-restraints excluded: chain f residue 9 VAL Chi-restraints excluded: chain f residue 10 VAL Chi-restraints excluded: chain f residue 15 ASP Chi-restraints excluded: chain f residue 16 VAL Chi-restraints excluded: chain f residue 22 VAL Chi-restraints excluded: chain f residue 102 ILE Chi-restraints excluded: chain f residue 130 ILE Chi-restraints excluded: chain f residue 161 VAL Chi-restraints excluded: chain g residue 5 LEU Chi-restraints excluded: chain g residue 12 LEU Chi-restraints excluded: chain g residue 37 VAL Chi-restraints excluded: chain h residue 5 LEU Chi-restraints excluded: chain h residue 55 VAL Chi-restraints excluded: chain h residue 57 ASN Chi-restraints excluded: chain h residue 88 HIS Chi-restraints excluded: chain i residue 61 TYR Chi-restraints excluded: chain i residue 72 THR Chi-restraints excluded: chain i residue 85 ILE Chi-restraints excluded: chain j residue 70 THR Chi-restraints excluded: chain j residue 81 ILE Chi-restraints excluded: chain j residue 86 GLN Chi-restraints excluded: chain j residue 93 ILE Chi-restraints excluded: chain k residue 35 VAL Chi-restraints excluded: chain k residue 53 LYS Chi-restraints excluded: chain k residue 56 ASP Chi-restraints excluded: chain k residue 57 VAL Chi-restraints excluded: chain k residue 58 LEU Chi-restraints excluded: chain l residue 91 ASP Chi-restraints excluded: chain l residue 101 ILE Chi-restraints excluded: chain l residue 128 THR Chi-restraints excluded: chain n residue 1 MET Chi-restraints excluded: chain n residue 9 GLN Chi-restraints excluded: chain n residue 36 THR Chi-restraints excluded: chain n residue 57 THR Chi-restraints excluded: chain n residue 97 ILE Chi-restraints excluded: chain o residue 74 VAL Chi-restraints excluded: chain p residue 11 GLN Chi-restraints excluded: chain p residue 12 MET Chi-restraints excluded: chain p residue 59 THR Chi-restraints excluded: chain p residue 69 VAL Chi-restraints excluded: chain p residue 72 VAL Chi-restraints excluded: chain p residue 109 ILE Chi-restraints excluded: chain q residue 58 GLN Chi-restraints excluded: chain q residue 87 VAL Chi-restraints excluded: chain q residue 90 ASP Chi-restraints excluded: chain r residue 4 VAL Chi-restraints excluded: chain r residue 27 ILE Chi-restraints excluded: chain r residue 29 THR Chi-restraints excluded: chain r residue 38 VAL Chi-restraints excluded: chain r residue 53 PHE Chi-restraints excluded: chain r residue 63 VAL Chi-restraints excluded: chain r residue 98 ILE Chi-restraints excluded: chain s residue 19 LEU Chi-restraints excluded: chain s residue 24 ILE Chi-restraints excluded: chain s residue 65 ASP Chi-restraints excluded: chain s residue 66 ILE Chi-restraints excluded: chain s residue 74 ILE Chi-restraints excluded: chain s residue 77 ASP Chi-restraints excluded: chain s residue 86 MET Chi-restraints excluded: chain t residue 39 THR Chi-restraints excluded: chain t residue 60 THR Chi-restraints excluded: chain u residue 11 ILE Chi-restraints excluded: chain u residue 27 VAL Chi-restraints excluded: chain u residue 33 VAL Chi-restraints excluded: chain u residue 64 ILE Chi-restraints excluded: chain v residue 8 VAL Chi-restraints excluded: chain v residue 10 LYS Chi-restraints excluded: chain v residue 12 GLN Chi-restraints excluded: chain v residue 63 ILE Chi-restraints excluded: chain v residue 71 LYS Chi-restraints excluded: chain w residue 31 SER Chi-restraints excluded: chain w residue 63 VAL Chi-restraints excluded: chain w residue 67 VAL Chi-restraints excluded: chain w residue 79 GLU Chi-restraints excluded: chain x residue 19 HIS Chi-restraints excluded: chain x residue 39 VAL Chi-restraints excluded: chain y residue 17 GLU Chi-restraints excluded: chain y residue 21 LEU Chi-restraints excluded: chain y residue 50 VAL Chi-restraints excluded: chain z residue 3 THR Chi-restraints excluded: chain z residue 40 THR Chi-restraints excluded: chain A residue 9 TYR Chi-restraints excluded: chain A residue 30 HIS Chi-restraints excluded: chain A residue 35 ASP Chi-restraints excluded: chain B residue 21 LEU Chi-restraints excluded: chain D residue 4 THR Chi-restraints excluded: chain D residue 24 THR Chi-restraints excluded: chain D residue 30 VAL Chi-restraints excluded: chain D residue 44 VAL Chi-restraints excluded: chain E residue 15 LYS Chi-restraints excluded: chain E residue 53 ASP Chi-restraints excluded: chain F residue 8 LYS Chi-restraints excluded: chain F residue 23 ILE Chi-restraints excluded: chain F residue 36 ARG Chi-restraints excluded: chain a residue 35 THR Chi-restraints excluded: chain a residue 44 VAL Chi-restraints excluded: chain a residue 54 LYS Chi-restraints excluded: chain a residue 214 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 629 random chunks: chunk 586 optimal weight: 10.0000 chunk 68 optimal weight: 9.9990 chunk 346 optimal weight: 10.0000 chunk 444 optimal weight: 30.0000 chunk 344 optimal weight: 10.0000 chunk 512 optimal weight: 20.0000 chunk 339 optimal weight: 10.0000 chunk 606 optimal weight: 10.0000 chunk 379 optimal weight: 10.0000 chunk 369 optimal weight: 10.0000 chunk 279 optimal weight: 7.9990 overall best weight: 9.5996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: b 162 GLN d 30 GLN d 90 GLN g 11 ASN ** g 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** l 104 GLN p 6 GLN ** p 114 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** q 55 GLN ** q 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** r 12 HIS ** t 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** v 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** y 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 4 GLN E 25 HIS ** F 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8560 moved from start: 0.3561 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.117 99292 Z= 0.546 Angle : 0.816 12.096 149057 Z= 0.412 Chirality : 0.044 0.291 19153 Planarity : 0.006 0.052 7608 Dihedral : 24.014 175.893 50897 Min Nonbonded Distance : 1.972 Molprobity Statistics. All-atom Clashscore : 23.12 Ramachandran Plot: Outliers : 0.12 % Allowed : 11.19 % Favored : 88.69 % Rotamer: Outliers : 7.12 % Allowed : 22.82 % Favored : 70.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.54 (0.14), residues: 3325 helix: -0.78 (0.17), residues: 924 sheet: -1.60 (0.20), residues: 608 loop : -2.26 (0.14), residues: 1793 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP b 212 HIS 0.006 0.002 HIS B 18 PHE 0.049 0.002 PHE g 46 TYR 0.020 0.002 TYR d 101 ARG 0.008 0.001 ARG t 73 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6650 Ramachandran restraints generated. 3325 Oldfield, 0 Emsley, 3325 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6650 Ramachandran restraints generated. 3325 Oldfield, 0 Emsley, 3325 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 794 residues out of total 2739 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 195 poor density : 599 time to evaluate : 3.866 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: b 224 MET cc_start: 0.8703 (mmm) cc_final: 0.8481 (mmm) REVERT: c 99 GLU cc_start: 0.9211 (OUTLIER) cc_final: 0.8794 (mp0) REVERT: d 24 ASN cc_start: 0.8976 (t0) cc_final: 0.8629 (t0) REVERT: e 25 MET cc_start: 0.8082 (pmm) cc_final: 0.7714 (pmm) REVERT: e 37 MET cc_start: 0.7498 (tpp) cc_final: 0.7000 (tpp) REVERT: e 95 MET cc_start: 0.9102 (ttp) cc_final: 0.8882 (ttp) REVERT: f 19 ASN cc_start: 0.8115 (t0) cc_final: 0.7758 (t0) REVERT: f 59 ASP cc_start: 0.8537 (p0) cc_final: 0.8217 (p0) REVERT: f 82 PHE cc_start: 0.7888 (m-80) cc_final: 0.7498 (m-80) REVERT: f 129 GLU cc_start: 0.8755 (tm-30) cc_final: 0.8313 (tm-30) REVERT: g 7 ASP cc_start: 0.8133 (m-30) cc_final: 0.7863 (m-30) REVERT: g 35 LYS cc_start: 0.8577 (mptt) cc_final: 0.8349 (mptt) REVERT: g 47 PHE cc_start: 0.7610 (t80) cc_final: 0.7031 (t80) REVERT: g 51 ARG cc_start: 0.7446 (OUTLIER) cc_final: 0.5887 (ptt-90) REVERT: h 52 MET cc_start: -0.0697 (mmp) cc_final: -0.1427 (mpp) REVERT: h 116 GLU cc_start: 0.2865 (tt0) cc_final: 0.2470 (pt0) REVERT: i 16 MET cc_start: 0.1073 (ptt) cc_final: 0.0445 (ptm) REVERT: i 85 ILE cc_start: 0.4315 (OUTLIER) cc_final: 0.4030 (tp) REVERT: i 135 MET cc_start: 0.4600 (mmt) cc_final: 0.4345 (mmt) REVERT: j 102 GLU cc_start: 0.8150 (pt0) cc_final: 0.7841 (pt0) REVERT: k 37 ASP cc_start: 0.8381 (t70) cc_final: 0.7853 (t0) REVERT: l 58 TYR cc_start: 0.8635 (p90) cc_final: 0.8298 (p90) REVERT: l 91 ASP cc_start: 0.8701 (OUTLIER) cc_final: 0.8356 (p0) REVERT: l 136 GLU cc_start: 0.8261 (mt-10) cc_final: 0.8026 (mt-10) REVERT: n 49 GLU cc_start: 0.8229 (mp0) cc_final: 0.7690 (mp0) REVERT: n 56 LYS cc_start: 0.8858 (mtpp) cc_final: 0.8648 (mtpm) REVERT: o 115 LEU cc_start: 0.8795 (OUTLIER) cc_final: 0.8591 (mm) REVERT: p 9 GLN cc_start: 0.8842 (tm-30) cc_final: 0.8619 (tm-30) REVERT: p 11 GLN cc_start: 0.8734 (OUTLIER) cc_final: 0.8523 (mt0) REVERT: p 12 MET cc_start: 0.8194 (OUTLIER) cc_final: 0.7639 (mpp) REVERT: p 26 GLU cc_start: 0.8005 (tm-30) cc_final: 0.7494 (tm-30) REVERT: q 65 ASN cc_start: 0.8925 (t0) cc_final: 0.8702 (t0) REVERT: q 96 ASP cc_start: 0.8406 (OUTLIER) cc_final: 0.7743 (t0) REVERT: r 13 ARG cc_start: 0.8228 (ttt-90) cc_final: 0.7933 (ptt90) REVERT: r 24 LYS cc_start: 0.9323 (tttp) cc_final: 0.9002 (ttpp) REVERT: r 78 ARG cc_start: 0.9113 (tpp-160) cc_final: 0.8579 (tpp80) REVERT: r 81 LYS cc_start: 0.9206 (mmtt) cc_final: 0.8959 (mmtp) REVERT: r 97 LYS cc_start: 0.9273 (tttt) cc_final: 0.8770 (tmmt) REVERT: s 34 ASP cc_start: 0.8844 (p0) cc_final: 0.8534 (p0) REVERT: s 69 LEU cc_start: 0.9208 (mt) cc_final: 0.8846 (mt) REVERT: t 5 GLU cc_start: 0.8226 (mp0) cc_final: 0.7965 (mp0) REVERT: t 91 GLN cc_start: 0.7549 (pm20) cc_final: 0.7297 (pm20) REVERT: u 17 ASP cc_start: 0.8089 (m-30) cc_final: 0.7705 (m-30) REVERT: u 21 ARG cc_start: 0.8370 (ptm-80) cc_final: 0.8028 (mtp-110) REVERT: u 72 PHE cc_start: 0.8520 (t80) cc_final: 0.8208 (t80) REVERT: v 83 LYS cc_start: 0.8835 (tppt) cc_final: 0.8614 (tppt) REVERT: w 17 LEU cc_start: 0.9142 (mt) cc_final: 0.8658 (mt) REVERT: w 52 ASP cc_start: 0.8244 (t0) cc_final: 0.7820 (t0) REVERT: w 58 LYS cc_start: 0.9050 (mtmm) cc_final: 0.8761 (mtmm) REVERT: y 7 ARG cc_start: 0.8778 (mmm160) cc_final: 0.8561 (mmm-85) REVERT: y 20 ASN cc_start: 0.9222 (m-40) cc_final: 0.9015 (m-40) REVERT: A 11 GLU cc_start: 0.8941 (tt0) cc_final: 0.8604 (tp30) REVERT: B 52 LYS cc_start: 0.8291 (tppt) cc_final: 0.8090 (tptp) REVERT: E 15 LYS cc_start: 0.8600 (OUTLIER) cc_final: 0.8172 (tmtt) REVERT: E 28 LEU cc_start: 0.9502 (tp) cc_final: 0.9241 (tt) REVERT: F 36 ARG cc_start: 0.8596 (OUTLIER) cc_final: 0.7705 (tmm-80) REVERT: a 218 MET cc_start: 0.2241 (mmm) cc_final: 0.1771 (mmt) outliers start: 195 outliers final: 152 residues processed: 709 average time/residue: 0.9000 time to fit residues: 1111.7155 Evaluate side-chains 744 residues out of total 2739 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 162 poor density : 582 time to evaluate : 3.831 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain b residue 5 CYS Chi-restraints excluded: chain b residue 18 VAL Chi-restraints excluded: chain b residue 19 VAL Chi-restraints excluded: chain b residue 52 HIS Chi-restraints excluded: chain b residue 89 ASN Chi-restraints excluded: chain b residue 117 SER Chi-restraints excluded: chain b residue 183 VAL Chi-restraints excluded: chain b residue 203 VAL Chi-restraints excluded: chain b residue 218 THR Chi-restraints excluded: chain b residue 256 THR Chi-restraints excluded: chain b residue 263 ASP Chi-restraints excluded: chain c residue 9 VAL Chi-restraints excluded: chain c residue 60 VAL Chi-restraints excluded: chain c residue 91 THR Chi-restraints excluded: chain c residue 96 ILE Chi-restraints excluded: chain c residue 99 GLU Chi-restraints excluded: chain c residue 100 LEU Chi-restraints excluded: chain c residue 122 VAL Chi-restraints excluded: chain c residue 138 LEU Chi-restraints excluded: chain d residue 4 VAL Chi-restraints excluded: chain d residue 7 ASP Chi-restraints excluded: chain d residue 13 THR Chi-restraints excluded: chain d residue 73 ILE Chi-restraints excluded: chain d residue 100 MET Chi-restraints excluded: chain d residue 120 VAL Chi-restraints excluded: chain d residue 150 THR Chi-restraints excluded: chain d residue 167 VAL Chi-restraints excluded: chain d residue 176 ASP Chi-restraints excluded: chain e residue 12 VAL Chi-restraints excluded: chain e residue 34 THR Chi-restraints excluded: chain e residue 39 VAL Chi-restraints excluded: chain e residue 105 ILE Chi-restraints excluded: chain e residue 112 ASP Chi-restraints excluded: chain e residue 152 ASP Chi-restraints excluded: chain e residue 156 THR Chi-restraints excluded: chain e residue 168 LEU Chi-restraints excluded: chain f residue 9 VAL Chi-restraints excluded: chain f residue 10 VAL Chi-restraints excluded: chain f residue 16 VAL Chi-restraints excluded: chain f residue 22 VAL Chi-restraints excluded: chain f residue 100 ASN Chi-restraints excluded: chain f residue 102 ILE Chi-restraints excluded: chain f residue 130 ILE Chi-restraints excluded: chain f residue 161 VAL Chi-restraints excluded: chain g residue 5 LEU Chi-restraints excluded: chain g residue 12 LEU Chi-restraints excluded: chain g residue 37 VAL Chi-restraints excluded: chain g residue 43 ASN Chi-restraints excluded: chain g residue 46 PHE Chi-restraints excluded: chain g residue 51 ARG Chi-restraints excluded: chain h residue 5 LEU Chi-restraints excluded: chain h residue 55 VAL Chi-restraints excluded: chain h residue 57 ASN Chi-restraints excluded: chain h residue 88 HIS Chi-restraints excluded: chain h residue 124 ASP Chi-restraints excluded: chain i residue 7 TYR Chi-restraints excluded: chain i residue 8 VAL Chi-restraints excluded: chain i residue 23 VAL Chi-restraints excluded: chain i residue 70 THR Chi-restraints excluded: chain i residue 72 THR Chi-restraints excluded: chain i residue 85 ILE Chi-restraints excluded: chain i residue 141 ASP Chi-restraints excluded: chain j residue 70 THR Chi-restraints excluded: chain j residue 86 GLN Chi-restraints excluded: chain j residue 93 ILE Chi-restraints excluded: chain j residue 131 ASN Chi-restraints excluded: chain j residue 140 LEU Chi-restraints excluded: chain k residue 35 VAL Chi-restraints excluded: chain k residue 42 THR Chi-restraints excluded: chain k residue 53 LYS Chi-restraints excluded: chain k residue 56 ASP Chi-restraints excluded: chain k residue 57 VAL Chi-restraints excluded: chain k residue 58 LEU Chi-restraints excluded: chain k residue 118 LEU Chi-restraints excluded: chain l residue 91 ASP Chi-restraints excluded: chain l residue 101 ILE Chi-restraints excluded: chain l residue 122 VAL Chi-restraints excluded: chain l residue 128 THR Chi-restraints excluded: chain n residue 1 MET Chi-restraints excluded: chain n residue 34 ILE Chi-restraints excluded: chain n residue 57 THR Chi-restraints excluded: chain n residue 97 ILE Chi-restraints excluded: chain n residue 113 ILE Chi-restraints excluded: chain o residue 49 VAL Chi-restraints excluded: chain o residue 74 VAL Chi-restraints excluded: chain o residue 115 LEU Chi-restraints excluded: chain p residue 3 ILE Chi-restraints excluded: chain p residue 11 GLN Chi-restraints excluded: chain p residue 12 MET Chi-restraints excluded: chain p residue 59 THR Chi-restraints excluded: chain p residue 69 VAL Chi-restraints excluded: chain p residue 72 VAL Chi-restraints excluded: chain p residue 109 ILE Chi-restraints excluded: chain q residue 39 ILE Chi-restraints excluded: chain q residue 87 VAL Chi-restraints excluded: chain q residue 90 ASP Chi-restraints excluded: chain q residue 96 ASP Chi-restraints excluded: chain r residue 4 VAL Chi-restraints excluded: chain r residue 27 ILE Chi-restraints excluded: chain r residue 29 THR Chi-restraints excluded: chain r residue 38 VAL Chi-restraints excluded: chain r residue 63 VAL Chi-restraints excluded: chain r residue 86 GLN Chi-restraints excluded: chain s residue 4 ILE Chi-restraints excluded: chain s residue 19 LEU Chi-restraints excluded: chain s residue 24 ILE Chi-restraints excluded: chain s residue 55 ILE Chi-restraints excluded: chain s residue 65 ASP Chi-restraints excluded: chain s residue 66 ILE Chi-restraints excluded: chain s residue 74 ILE Chi-restraints excluded: chain s residue 77 ASP Chi-restraints excluded: chain s residue 86 MET Chi-restraints excluded: chain t residue 39 THR Chi-restraints excluded: chain u residue 11 ILE Chi-restraints excluded: chain u residue 27 VAL Chi-restraints excluded: chain u residue 33 VAL Chi-restraints excluded: chain u residue 64 ILE Chi-restraints excluded: chain v residue 8 VAL Chi-restraints excluded: chain v residue 10 LYS Chi-restraints excluded: chain v residue 26 PHE Chi-restraints excluded: chain v residue 29 ILE Chi-restraints excluded: chain v residue 38 LEU Chi-restraints excluded: chain v residue 59 GLU Chi-restraints excluded: chain v residue 63 ILE Chi-restraints excluded: chain v residue 71 LYS Chi-restraints excluded: chain v residue 77 VAL Chi-restraints excluded: chain w residue 27 VAL Chi-restraints excluded: chain w residue 31 SER Chi-restraints excluded: chain w residue 34 VAL Chi-restraints excluded: chain w residue 63 VAL Chi-restraints excluded: chain w residue 67 VAL Chi-restraints excluded: chain x residue 6 VAL Chi-restraints excluded: chain x residue 19 HIS Chi-restraints excluded: chain x residue 29 LEU Chi-restraints excluded: chain x residue 39 VAL Chi-restraints excluded: chain y residue 8 GLU Chi-restraints excluded: chain y residue 17 GLU Chi-restraints excluded: chain y residue 21 LEU Chi-restraints excluded: chain y residue 50 VAL Chi-restraints excluded: chain z residue 3 THR Chi-restraints excluded: chain z residue 40 THR Chi-restraints excluded: chain A residue 5 ILE Chi-restraints excluded: chain A residue 9 TYR Chi-restraints excluded: chain A residue 30 HIS Chi-restraints excluded: chain A residue 34 LEU Chi-restraints excluded: chain A residue 35 ASP Chi-restraints excluded: chain A residue 37 CYS Chi-restraints excluded: chain B residue 22 THR Chi-restraints excluded: chain D residue 4 THR Chi-restraints excluded: chain D residue 24 THR Chi-restraints excluded: chain D residue 30 VAL Chi-restraints excluded: chain D residue 44 VAL Chi-restraints excluded: chain E residue 15 LYS Chi-restraints excluded: chain E residue 37 THR Chi-restraints excluded: chain E residue 49 VAL Chi-restraints excluded: chain E residue 53 ASP Chi-restraints excluded: chain F residue 23 ILE Chi-restraints excluded: chain F residue 36 ARG Chi-restraints excluded: chain a residue 35 THR Chi-restraints excluded: chain a residue 44 VAL Chi-restraints excluded: chain a residue 54 LYS Chi-restraints excluded: chain a residue 214 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 629 random chunks: chunk 375 optimal weight: 10.0000 chunk 242 optimal weight: 0.9980 chunk 362 optimal weight: 20.0000 chunk 182 optimal weight: 5.9990 chunk 119 optimal weight: 9.9990 chunk 117 optimal weight: 0.0970 chunk 385 optimal weight: 3.9990 chunk 413 optimal weight: 10.0000 chunk 299 optimal weight: 3.9990 chunk 56 optimal weight: 4.9990 chunk 476 optimal weight: 7.9990 overall best weight: 2.8184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: b 162 GLN b 242 HIS d 30 GLN g 11 ASN ** g 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** k 3 GLN ** p 114 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** q 43 GLN q 55 GLN ** q 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** t 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** v 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** x 22 ASN ** y 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8472 moved from start: 0.3569 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 99292 Z= 0.208 Angle : 0.600 12.072 149057 Z= 0.309 Chirality : 0.035 0.292 19153 Planarity : 0.004 0.053 7608 Dihedral : 23.884 177.574 50895 Min Nonbonded Distance : 2.036 Molprobity Statistics. All-atom Clashscore : 16.58 Ramachandran Plot: Outliers : 0.12 % Allowed : 7.49 % Favored : 92.39 % Rotamer: Outliers : 5.11 % Allowed : 25.37 % Favored : 69.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.27 (0.14), residues: 3325 helix: -0.48 (0.17), residues: 934 sheet: -1.67 (0.20), residues: 650 loop : -2.03 (0.14), residues: 1741 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP p 30 HIS 0.007 0.001 HIS v 44 PHE 0.043 0.002 PHE g 46 TYR 0.016 0.002 TYR d 101 ARG 0.006 0.000 ARG F 24 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6650 Ramachandran restraints generated. 3325 Oldfield, 0 Emsley, 3325 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6650 Ramachandran restraints generated. 3325 Oldfield, 0 Emsley, 3325 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 779 residues out of total 2739 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 140 poor density : 639 time to evaluate : 3.787 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: c 99 GLU cc_start: 0.9196 (OUTLIER) cc_final: 0.8755 (mp0) REVERT: d 24 ASN cc_start: 0.8823 (t0) cc_final: 0.8525 (t0) REVERT: e 25 MET cc_start: 0.8030 (pmm) cc_final: 0.7687 (pmm) REVERT: e 37 MET cc_start: 0.7533 (tpp) cc_final: 0.7095 (tpp) REVERT: e 95 MET cc_start: 0.9087 (ttp) cc_final: 0.8847 (ttp) REVERT: f 59 ASP cc_start: 0.8621 (p0) cc_final: 0.8317 (p0) REVERT: f 82 PHE cc_start: 0.7762 (m-80) cc_final: 0.7360 (m-80) REVERT: f 123 GLU cc_start: 0.8423 (tp30) cc_final: 0.8165 (pm20) REVERT: f 129 GLU cc_start: 0.8580 (tm-30) cc_final: 0.8232 (tm-30) REVERT: g 7 ASP cc_start: 0.7927 (m-30) cc_final: 0.7620 (m-30) REVERT: g 18 GLN cc_start: 0.8669 (tm-30) cc_final: 0.8318 (pp30) REVERT: g 35 LYS cc_start: 0.8574 (mptt) cc_final: 0.8238 (mptt) REVERT: h 52 MET cc_start: -0.0730 (mmp) cc_final: -0.1428 (mpp) REVERT: h 116 GLU cc_start: 0.2728 (tt0) cc_final: 0.2318 (pt0) REVERT: i 16 MET cc_start: 0.1119 (ptt) cc_final: 0.0484 (ptm) REVERT: i 85 ILE cc_start: 0.4296 (OUTLIER) cc_final: 0.4021 (tp) REVERT: i 135 MET cc_start: 0.3812 (mmt) cc_final: 0.3023 (mmt) REVERT: j 125 TYR cc_start: 0.8455 (m-80) cc_final: 0.7887 (m-80) REVERT: k 1 MET cc_start: 0.7268 (ptt) cc_final: 0.7040 (ptt) REVERT: k 37 ASP cc_start: 0.8340 (t70) cc_final: 0.7761 (t0) REVERT: k 53 LYS cc_start: 0.8944 (OUTLIER) cc_final: 0.8635 (ptpp) REVERT: l 58 TYR cc_start: 0.8511 (p90) cc_final: 0.8205 (p90) REVERT: l 91 ASP cc_start: 0.8626 (OUTLIER) cc_final: 0.8091 (p0) REVERT: n 49 GLU cc_start: 0.8149 (mp0) cc_final: 0.7703 (mp0) REVERT: n 56 LYS cc_start: 0.8812 (mtpp) cc_final: 0.8603 (mtpm) REVERT: o 115 LEU cc_start: 0.8834 (OUTLIER) cc_final: 0.8630 (mm) REVERT: p 12 MET cc_start: 0.8121 (OUTLIER) cc_final: 0.7484 (mpp) REVERT: q 60 TRP cc_start: 0.9153 (m-10) cc_final: 0.8794 (m-10) REVERT: q 65 ASN cc_start: 0.8897 (t0) cc_final: 0.8651 (t0) REVERT: q 71 ASN cc_start: 0.8631 (t0) cc_final: 0.8413 (t0) REVERT: q 96 ASP cc_start: 0.8208 (t70) cc_final: 0.7815 (t0) REVERT: r 2 TYR cc_start: 0.8714 (p90) cc_final: 0.7613 (p90) REVERT: r 11 GLN cc_start: 0.8883 (mp10) cc_final: 0.8520 (mp10) REVERT: r 13 ARG cc_start: 0.8138 (ttt-90) cc_final: 0.7742 (ptt90) REVERT: r 24 LYS cc_start: 0.9346 (tttp) cc_final: 0.8831 (ttpp) REVERT: r 78 ARG cc_start: 0.8983 (tpp-160) cc_final: 0.8436 (tpp80) REVERT: r 81 LYS cc_start: 0.9165 (mmtt) cc_final: 0.8930 (mmtp) REVERT: r 97 LYS cc_start: 0.9166 (tttt) cc_final: 0.8240 (ttpt) REVERT: s 34 ASP cc_start: 0.8736 (p0) cc_final: 0.8531 (p0) REVERT: s 69 LEU cc_start: 0.9171 (mt) cc_final: 0.8843 (mt) REVERT: t 5 GLU cc_start: 0.8171 (mp0) cc_final: 0.7886 (mp0) REVERT: t 24 MET cc_start: 0.8350 (tpp) cc_final: 0.7751 (ttp) REVERT: u 17 ASP cc_start: 0.7901 (m-30) cc_final: 0.7543 (m-30) REVERT: u 21 ARG cc_start: 0.8272 (ptm-80) cc_final: 0.7979 (mtp-110) REVERT: u 72 PHE cc_start: 0.8547 (t80) cc_final: 0.8139 (t80) REVERT: v 19 ARG cc_start: 0.8847 (mtm-85) cc_final: 0.8365 (mtm-85) REVERT: v 91 PHE cc_start: 0.7970 (m-10) cc_final: 0.7757 (m-10) REVERT: w 17 LEU cc_start: 0.9034 (mt) cc_final: 0.8592 (mt) REVERT: w 52 ASP cc_start: 0.8057 (t0) cc_final: 0.7778 (t0) REVERT: w 58 LYS cc_start: 0.9052 (mtmm) cc_final: 0.8758 (mtmm) REVERT: w 77 SER cc_start: 0.8852 (m) cc_final: 0.8529 (m) REVERT: x 69 GLU cc_start: 0.9058 (mp0) cc_final: 0.8712 (mp0) REVERT: y 7 ARG cc_start: 0.8736 (mmm160) cc_final: 0.8512 (mmm-85) REVERT: z 5 LYS cc_start: 0.8650 (mmmm) cc_final: 0.8305 (mmmt) REVERT: A 11 GLU cc_start: 0.8862 (tt0) cc_final: 0.8568 (tp30) REVERT: B 52 LYS cc_start: 0.8403 (tppt) cc_final: 0.8149 (tptp) REVERT: D 29 GLN cc_start: 0.8814 (OUTLIER) cc_final: 0.8575 (pm20) REVERT: E 5 THR cc_start: 0.8738 (m) cc_final: 0.8527 (p) REVERT: E 28 LEU cc_start: 0.9476 (tp) cc_final: 0.9207 (tt) REVERT: F 15 LYS cc_start: 0.8680 (mmmt) cc_final: 0.8250 (mppt) REVERT: F 36 ARG cc_start: 0.8561 (OUTLIER) cc_final: 0.7724 (tmm-80) REVERT: a 218 MET cc_start: 0.1991 (mmm) cc_final: 0.1469 (mmt) outliers start: 140 outliers final: 117 residues processed: 724 average time/residue: 0.8432 time to fit residues: 1057.9407 Evaluate side-chains 729 residues out of total 2739 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 125 poor density : 604 time to evaluate : 5.443 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain b residue 5 CYS Chi-restraints excluded: chain b residue 18 VAL Chi-restraints excluded: chain b residue 19 VAL Chi-restraints excluded: chain b residue 89 ASN Chi-restraints excluded: chain b residue 183 VAL Chi-restraints excluded: chain b residue 203 VAL Chi-restraints excluded: chain b residue 218 THR Chi-restraints excluded: chain b residue 256 THR Chi-restraints excluded: chain b residue 263 ASP Chi-restraints excluded: chain c residue 9 VAL Chi-restraints excluded: chain c residue 60 VAL Chi-restraints excluded: chain c residue 91 THR Chi-restraints excluded: chain c residue 96 ILE Chi-restraints excluded: chain c residue 99 GLU Chi-restraints excluded: chain c residue 100 LEU Chi-restraints excluded: chain c residue 122 VAL Chi-restraints excluded: chain d residue 4 VAL Chi-restraints excluded: chain d residue 7 ASP Chi-restraints excluded: chain d residue 13 THR Chi-restraints excluded: chain d residue 53 THR Chi-restraints excluded: chain d residue 73 ILE Chi-restraints excluded: chain d residue 167 VAL Chi-restraints excluded: chain e residue 12 VAL Chi-restraints excluded: chain e residue 34 THR Chi-restraints excluded: chain e residue 39 VAL Chi-restraints excluded: chain e residue 105 ILE Chi-restraints excluded: chain e residue 112 ASP Chi-restraints excluded: chain e residue 151 LEU Chi-restraints excluded: chain e residue 152 ASP Chi-restraints excluded: chain e residue 156 THR Chi-restraints excluded: chain e residue 168 LEU Chi-restraints excluded: chain f residue 9 VAL Chi-restraints excluded: chain f residue 10 VAL Chi-restraints excluded: chain f residue 16 VAL Chi-restraints excluded: chain f residue 22 VAL Chi-restraints excluded: chain f residue 100 ASN Chi-restraints excluded: chain f residue 130 ILE Chi-restraints excluded: chain g residue 5 LEU Chi-restraints excluded: chain g residue 12 LEU Chi-restraints excluded: chain g residue 37 VAL Chi-restraints excluded: chain h residue 5 LEU Chi-restraints excluded: chain h residue 55 VAL Chi-restraints excluded: chain h residue 57 ASN Chi-restraints excluded: chain h residue 88 HIS Chi-restraints excluded: chain h residue 124 ASP Chi-restraints excluded: chain i residue 8 VAL Chi-restraints excluded: chain i residue 70 THR Chi-restraints excluded: chain i residue 72 THR Chi-restraints excluded: chain i residue 85 ILE Chi-restraints excluded: chain i residue 141 ASP Chi-restraints excluded: chain j residue 70 THR Chi-restraints excluded: chain j residue 78 THR Chi-restraints excluded: chain j residue 86 GLN Chi-restraints excluded: chain j residue 131 ASN Chi-restraints excluded: chain k residue 22 ILE Chi-restraints excluded: chain k residue 35 VAL Chi-restraints excluded: chain k residue 53 LYS Chi-restraints excluded: chain k residue 56 ASP Chi-restraints excluded: chain k residue 57 VAL Chi-restraints excluded: chain k residue 58 LEU Chi-restraints excluded: chain l residue 91 ASP Chi-restraints excluded: chain l residue 101 ILE Chi-restraints excluded: chain l residue 128 THR Chi-restraints excluded: chain n residue 1 MET Chi-restraints excluded: chain n residue 34 ILE Chi-restraints excluded: chain n residue 37 THR Chi-restraints excluded: chain n residue 57 THR Chi-restraints excluded: chain n residue 97 ILE Chi-restraints excluded: chain o residue 49 VAL Chi-restraints excluded: chain o residue 74 VAL Chi-restraints excluded: chain o residue 115 LEU Chi-restraints excluded: chain p residue 12 MET Chi-restraints excluded: chain p residue 59 THR Chi-restraints excluded: chain p residue 65 ASN Chi-restraints excluded: chain p residue 69 VAL Chi-restraints excluded: chain p residue 72 VAL Chi-restraints excluded: chain p residue 109 ILE Chi-restraints excluded: chain q residue 87 VAL Chi-restraints excluded: chain r residue 4 VAL Chi-restraints excluded: chain r residue 27 ILE Chi-restraints excluded: chain r residue 38 VAL Chi-restraints excluded: chain r residue 63 VAL Chi-restraints excluded: chain s residue 19 LEU Chi-restraints excluded: chain s residue 65 ASP Chi-restraints excluded: chain s residue 66 ILE Chi-restraints excluded: chain s residue 74 ILE Chi-restraints excluded: chain s residue 77 ASP Chi-restraints excluded: chain s residue 86 MET Chi-restraints excluded: chain t residue 39 THR Chi-restraints excluded: chain u residue 11 ILE Chi-restraints excluded: chain u residue 14 THR Chi-restraints excluded: chain u residue 27 VAL Chi-restraints excluded: chain u residue 33 VAL Chi-restraints excluded: chain u residue 64 ILE Chi-restraints excluded: chain v residue 10 LYS Chi-restraints excluded: chain v residue 26 PHE Chi-restraints excluded: chain v residue 29 ILE Chi-restraints excluded: chain v residue 38 LEU Chi-restraints excluded: chain v residue 63 ILE Chi-restraints excluded: chain v residue 71 LYS Chi-restraints excluded: chain v residue 77 VAL Chi-restraints excluded: chain w residue 34 VAL Chi-restraints excluded: chain w residue 63 VAL Chi-restraints excluded: chain w residue 67 VAL Chi-restraints excluded: chain w residue 79 GLU Chi-restraints excluded: chain x residue 19 HIS Chi-restraints excluded: chain y residue 17 GLU Chi-restraints excluded: chain y residue 21 LEU Chi-restraints excluded: chain z residue 3 THR Chi-restraints excluded: chain z residue 40 THR Chi-restraints excluded: chain A residue 9 TYR Chi-restraints excluded: chain A residue 30 HIS Chi-restraints excluded: chain A residue 34 LEU Chi-restraints excluded: chain A residue 35 ASP Chi-restraints excluded: chain D residue 4 THR Chi-restraints excluded: chain D residue 24 THR Chi-restraints excluded: chain D residue 29 GLN Chi-restraints excluded: chain D residue 44 VAL Chi-restraints excluded: chain E residue 53 ASP Chi-restraints excluded: chain F residue 23 ILE Chi-restraints excluded: chain F residue 36 ARG Chi-restraints excluded: chain a residue 35 THR Chi-restraints excluded: chain a residue 54 LYS Chi-restraints excluded: chain a residue 60 ARG Chi-restraints excluded: chain a residue 214 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 629 random chunks: chunk 551 optimal weight: 50.0000 chunk 580 optimal weight: 10.0000 chunk 529 optimal weight: 10.0000 chunk 564 optimal weight: 10.0000 chunk 340 optimal weight: 10.0000 chunk 246 optimal weight: 9.9990 chunk 443 optimal weight: 10.0000 chunk 173 optimal weight: 9.9990 chunk 510 optimal weight: 10.0000 chunk 534 optimal weight: 10.0000 chunk 562 optimal weight: 10.0000 overall best weight: 9.9996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: b 162 GLN c 136 ASN ** d 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 80 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 2 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** g 11 ASN ** g 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 114 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** q 55 GLN ** q 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** t 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** v 12 GLN ** v 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** y 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8560 moved from start: 0.3779 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.110 99292 Z= 0.560 Angle : 0.829 11.905 149057 Z= 0.417 Chirality : 0.045 0.304 19153 Planarity : 0.006 0.057 7608 Dihedral : 24.088 178.804 50895 Min Nonbonded Distance : 1.951 Molprobity Statistics. All-atom Clashscore : 23.65 Ramachandran Plot: Outliers : 0.12 % Allowed : 11.19 % Favored : 88.69 % Rotamer: Outliers : 6.17 % Allowed : 24.90 % Favored : 68.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.53 (0.14), residues: 3325 helix: -0.76 (0.17), residues: 924 sheet: -1.68 (0.20), residues: 631 loop : -2.20 (0.14), residues: 1770 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP b 212 HIS 0.006 0.002 HIS B 18 PHE 0.052 0.003 PHE g 46 TYR 0.023 0.002 TYR j 75 ARG 0.010 0.001 ARG l 59 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6650 Ramachandran restraints generated. 3325 Oldfield, 0 Emsley, 3325 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6650 Ramachandran restraints generated. 3325 Oldfield, 0 Emsley, 3325 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 752 residues out of total 2739 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 169 poor density : 583 time to evaluate : 3.742 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: c 99 GLU cc_start: 0.9179 (OUTLIER) cc_final: 0.8696 (mp0) REVERT: d 24 ASN cc_start: 0.8956 (t0) cc_final: 0.8622 (t0) REVERT: e 25 MET cc_start: 0.7989 (pmm) cc_final: 0.7724 (pmm) REVERT: e 37 MET cc_start: 0.7611 (tpp) cc_final: 0.7212 (tpp) REVERT: e 95 MET cc_start: 0.9087 (ttp) cc_final: 0.8870 (ttp) REVERT: f 59 ASP cc_start: 0.8553 (p0) cc_final: 0.8239 (p0) REVERT: f 82 PHE cc_start: 0.7866 (m-80) cc_final: 0.7464 (m-80) REVERT: f 129 GLU cc_start: 0.8756 (tm-30) cc_final: 0.8334 (tm-30) REVERT: g 7 ASP cc_start: 0.8316 (m-30) cc_final: 0.7982 (m-30) REVERT: g 35 LYS cc_start: 0.8532 (mptt) cc_final: 0.8134 (mptt) REVERT: h 52 MET cc_start: -0.0789 (mmp) cc_final: -0.1365 (mpp) REVERT: i 16 MET cc_start: 0.1117 (ptt) cc_final: 0.0501 (ptm) REVERT: i 85 ILE cc_start: 0.4387 (OUTLIER) cc_final: 0.4109 (tp) REVERT: i 135 MET cc_start: 0.5001 (mmt) cc_final: 0.4761 (mmt) REVERT: j 102 GLU cc_start: 0.8208 (pt0) cc_final: 0.7939 (pt0) REVERT: k 37 ASP cc_start: 0.8399 (t70) cc_final: 0.7866 (t0) REVERT: l 58 TYR cc_start: 0.8645 (p90) cc_final: 0.8248 (p90) REVERT: l 91 ASP cc_start: 0.8706 (OUTLIER) cc_final: 0.8361 (p0) REVERT: l 136 GLU cc_start: 0.8294 (mt-10) cc_final: 0.8062 (mt-10) REVERT: n 49 GLU cc_start: 0.8234 (mp0) cc_final: 0.7718 (mp0) REVERT: n 56 LYS cc_start: 0.8862 (mtpp) cc_final: 0.8570 (mtpm) REVERT: o 115 LEU cc_start: 0.8790 (OUTLIER) cc_final: 0.8578 (mm) REVERT: p 12 MET cc_start: 0.8279 (OUTLIER) cc_final: 0.7748 (mpp) REVERT: q 10 ARG cc_start: 0.8045 (ttp-170) cc_final: 0.7812 (ttp-170) REVERT: q 65 ASN cc_start: 0.8955 (t0) cc_final: 0.8724 (t0) REVERT: q 71 ASN cc_start: 0.8860 (t0) cc_final: 0.8654 (t0) REVERT: q 96 ASP cc_start: 0.8396 (t70) cc_final: 0.7752 (t0) REVERT: r 6 GLN cc_start: 0.9002 (tt0) cc_final: 0.8661 (pt0) REVERT: r 13 ARG cc_start: 0.8191 (ttt-90) cc_final: 0.7851 (ptt90) REVERT: r 24 LYS cc_start: 0.9343 (tttp) cc_final: 0.8900 (ttpp) REVERT: r 46 GLU cc_start: 0.7782 (tm-30) cc_final: 0.7581 (tm-30) REVERT: r 48 LYS cc_start: 0.8939 (tppp) cc_final: 0.8422 (mmtp) REVERT: r 60 LYS cc_start: 0.8478 (mttp) cc_final: 0.8062 (tmtt) REVERT: r 97 LYS cc_start: 0.9048 (tttt) cc_final: 0.8832 (ttmt) REVERT: s 34 ASP cc_start: 0.8820 (p0) cc_final: 0.8553 (p0) REVERT: s 69 LEU cc_start: 0.9222 (mt) cc_final: 0.8851 (mt) REVERT: t 5 GLU cc_start: 0.8131 (mp0) cc_final: 0.7841 (mp0) REVERT: t 24 MET cc_start: 0.8523 (tpp) cc_final: 0.7888 (ttp) REVERT: u 17 ASP cc_start: 0.8067 (m-30) cc_final: 0.7644 (m-30) REVERT: u 21 ARG cc_start: 0.8295 (ptm-80) cc_final: 0.7922 (mtp-110) REVERT: u 72 PHE cc_start: 0.8483 (t80) cc_final: 0.8154 (t80) REVERT: v 19 ARG cc_start: 0.8885 (mtm-85) cc_final: 0.8429 (mtm-85) REVERT: w 17 LEU cc_start: 0.9139 (mt) cc_final: 0.8685 (mt) REVERT: w 52 ASP cc_start: 0.8276 (t0) cc_final: 0.7796 (t0) REVERT: w 58 LYS cc_start: 0.9053 (mtmm) cc_final: 0.8762 (mtmm) REVERT: z 5 LYS cc_start: 0.8632 (mmmm) cc_final: 0.8174 (mmmt) REVERT: A 11 GLU cc_start: 0.8925 (tt0) cc_final: 0.8606 (tp30) REVERT: B 52 LYS cc_start: 0.8256 (tppt) cc_final: 0.8038 (tptp) REVERT: E 15 LYS cc_start: 0.8578 (OUTLIER) cc_final: 0.8084 (tmtt) REVERT: E 28 LEU cc_start: 0.9500 (tp) cc_final: 0.9239 (tt) REVERT: F 36 ARG cc_start: 0.8602 (OUTLIER) cc_final: 0.7726 (tmm-80) REVERT: a 218 MET cc_start: 0.2301 (mmm) cc_final: 0.2048 (mmm) outliers start: 169 outliers final: 142 residues processed: 683 average time/residue: 0.8503 time to fit residues: 1001.1704 Evaluate side-chains 718 residues out of total 2739 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 149 poor density : 569 time to evaluate : 3.756 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain b residue 5 CYS Chi-restraints excluded: chain b residue 18 VAL Chi-restraints excluded: chain b residue 19 VAL Chi-restraints excluded: chain b residue 52 HIS Chi-restraints excluded: chain b residue 89 ASN Chi-restraints excluded: chain b residue 183 VAL Chi-restraints excluded: chain b residue 203 VAL Chi-restraints excluded: chain b residue 218 THR Chi-restraints excluded: chain b residue 256 THR Chi-restraints excluded: chain b residue 263 ASP Chi-restraints excluded: chain c residue 9 VAL Chi-restraints excluded: chain c residue 60 VAL Chi-restraints excluded: chain c residue 91 THR Chi-restraints excluded: chain c residue 96 ILE Chi-restraints excluded: chain c residue 99 GLU Chi-restraints excluded: chain c residue 100 LEU Chi-restraints excluded: chain c residue 122 VAL Chi-restraints excluded: chain c residue 177 VAL Chi-restraints excluded: chain d residue 4 VAL Chi-restraints excluded: chain d residue 7 ASP Chi-restraints excluded: chain d residue 13 THR Chi-restraints excluded: chain d residue 53 THR Chi-restraints excluded: chain d residue 73 ILE Chi-restraints excluded: chain d residue 120 VAL Chi-restraints excluded: chain d residue 150 THR Chi-restraints excluded: chain d residue 167 VAL Chi-restraints excluded: chain e residue 12 VAL Chi-restraints excluded: chain e residue 34 THR Chi-restraints excluded: chain e residue 39 VAL Chi-restraints excluded: chain e residue 105 ILE Chi-restraints excluded: chain e residue 112 ASP Chi-restraints excluded: chain e residue 152 ASP Chi-restraints excluded: chain e residue 156 THR Chi-restraints excluded: chain e residue 168 LEU Chi-restraints excluded: chain f residue 9 VAL Chi-restraints excluded: chain f residue 10 VAL Chi-restraints excluded: chain f residue 16 VAL Chi-restraints excluded: chain f residue 22 VAL Chi-restraints excluded: chain f residue 100 ASN Chi-restraints excluded: chain f residue 102 ILE Chi-restraints excluded: chain f residue 130 ILE Chi-restraints excluded: chain g residue 5 LEU Chi-restraints excluded: chain g residue 12 LEU Chi-restraints excluded: chain g residue 37 VAL Chi-restraints excluded: chain g residue 46 PHE Chi-restraints excluded: chain h residue 5 LEU Chi-restraints excluded: chain h residue 55 VAL Chi-restraints excluded: chain h residue 57 ASN Chi-restraints excluded: chain h residue 88 HIS Chi-restraints excluded: chain h residue 124 ASP Chi-restraints excluded: chain i residue 7 TYR Chi-restraints excluded: chain i residue 8 VAL Chi-restraints excluded: chain i residue 23 VAL Chi-restraints excluded: chain i residue 70 THR Chi-restraints excluded: chain i residue 72 THR Chi-restraints excluded: chain i residue 85 ILE Chi-restraints excluded: chain i residue 141 ASP Chi-restraints excluded: chain j residue 70 THR Chi-restraints excluded: chain j residue 78 THR Chi-restraints excluded: chain j residue 86 GLN Chi-restraints excluded: chain j residue 93 ILE Chi-restraints excluded: chain j residue 131 ASN Chi-restraints excluded: chain j residue 140 LEU Chi-restraints excluded: chain k residue 22 ILE Chi-restraints excluded: chain k residue 35 VAL Chi-restraints excluded: chain k residue 53 LYS Chi-restraints excluded: chain k residue 56 ASP Chi-restraints excluded: chain k residue 57 VAL Chi-restraints excluded: chain k residue 58 LEU Chi-restraints excluded: chain l residue 91 ASP Chi-restraints excluded: chain l residue 101 ILE Chi-restraints excluded: chain l residue 128 THR Chi-restraints excluded: chain n residue 1 MET Chi-restraints excluded: chain n residue 34 ILE Chi-restraints excluded: chain n residue 37 THR Chi-restraints excluded: chain n residue 57 THR Chi-restraints excluded: chain n residue 97 ILE Chi-restraints excluded: chain o residue 49 VAL Chi-restraints excluded: chain o residue 74 VAL Chi-restraints excluded: chain o residue 115 LEU Chi-restraints excluded: chain p residue 12 MET Chi-restraints excluded: chain p residue 59 THR Chi-restraints excluded: chain p residue 65 ASN Chi-restraints excluded: chain p residue 69 VAL Chi-restraints excluded: chain p residue 72 VAL Chi-restraints excluded: chain p residue 109 ILE Chi-restraints excluded: chain q residue 39 ILE Chi-restraints excluded: chain q residue 87 VAL Chi-restraints excluded: chain r residue 4 VAL Chi-restraints excluded: chain r residue 27 ILE Chi-restraints excluded: chain r residue 29 THR Chi-restraints excluded: chain r residue 38 VAL Chi-restraints excluded: chain r residue 86 GLN Chi-restraints excluded: chain s residue 19 LEU Chi-restraints excluded: chain s residue 24 ILE Chi-restraints excluded: chain s residue 65 ASP Chi-restraints excluded: chain s residue 66 ILE Chi-restraints excluded: chain s residue 74 ILE Chi-restraints excluded: chain s residue 77 ASP Chi-restraints excluded: chain s residue 86 MET Chi-restraints excluded: chain t residue 39 THR Chi-restraints excluded: chain t residue 74 ILE Chi-restraints excluded: chain u residue 11 ILE Chi-restraints excluded: chain u residue 14 THR Chi-restraints excluded: chain u residue 27 VAL Chi-restraints excluded: chain u residue 33 VAL Chi-restraints excluded: chain u residue 64 ILE Chi-restraints excluded: chain v residue 8 VAL Chi-restraints excluded: chain v residue 10 LYS Chi-restraints excluded: chain v residue 26 PHE Chi-restraints excluded: chain v residue 29 ILE Chi-restraints excluded: chain v residue 38 LEU Chi-restraints excluded: chain v residue 63 ILE Chi-restraints excluded: chain v residue 64 VAL Chi-restraints excluded: chain v residue 71 LYS Chi-restraints excluded: chain v residue 76 ASP Chi-restraints excluded: chain v residue 77 VAL Chi-restraints excluded: chain w residue 27 VAL Chi-restraints excluded: chain w residue 31 SER Chi-restraints excluded: chain w residue 34 VAL Chi-restraints excluded: chain w residue 63 VAL Chi-restraints excluded: chain w residue 67 VAL Chi-restraints excluded: chain w residue 79 GLU Chi-restraints excluded: chain x residue 19 HIS Chi-restraints excluded: chain y residue 8 GLU Chi-restraints excluded: chain y residue 17 GLU Chi-restraints excluded: chain y residue 21 LEU Chi-restraints excluded: chain z residue 3 THR Chi-restraints excluded: chain z residue 26 LEU Chi-restraints excluded: chain z residue 40 THR Chi-restraints excluded: chain z residue 56 VAL Chi-restraints excluded: chain z residue 57 GLU Chi-restraints excluded: chain A residue 9 TYR Chi-restraints excluded: chain A residue 30 HIS Chi-restraints excluded: chain A residue 34 LEU Chi-restraints excluded: chain A residue 35 ASP Chi-restraints excluded: chain B residue 22 THR Chi-restraints excluded: chain D residue 4 THR Chi-restraints excluded: chain D residue 24 THR Chi-restraints excluded: chain D residue 30 VAL Chi-restraints excluded: chain D residue 44 VAL Chi-restraints excluded: chain E residue 15 LYS Chi-restraints excluded: chain E residue 49 VAL Chi-restraints excluded: chain E residue 53 ASP Chi-restraints excluded: chain F residue 23 ILE Chi-restraints excluded: chain F residue 36 ARG Chi-restraints excluded: chain a residue 35 THR Chi-restraints excluded: chain a residue 60 ARG Chi-restraints excluded: chain a residue 214 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 629 random chunks: chunk 370 optimal weight: 10.0000 chunk 597 optimal weight: 10.0000 chunk 364 optimal weight: 8.9990 chunk 283 optimal weight: 2.9990 chunk 415 optimal weight: 30.0000 chunk 626 optimal weight: 6.9990 chunk 576 optimal weight: 6.9990 chunk 499 optimal weight: 10.0000 chunk 51 optimal weight: 4.9990 chunk 385 optimal weight: 2.9990 chunk 305 optimal weight: 1.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: b 162 GLN d 30 GLN e 80 GLN ** g 2 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** g 11 ASN ** g 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 114 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** q 43 GLN q 55 GLN q 58 GLN ** v 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** v 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** y 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8492 moved from start: 0.3769 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.070 99292 Z= 0.264 Angle : 0.638 15.962 149057 Z= 0.328 Chirality : 0.037 0.281 19153 Planarity : 0.005 0.053 7608 Dihedral : 23.969 179.150 50895 Min Nonbonded Distance : 1.999 Molprobity Statistics. All-atom Clashscore : 17.92 Ramachandran Plot: Outliers : 0.12 % Allowed : 8.03 % Favored : 91.85 % Rotamer: Outliers : 5.04 % Allowed : 26.10 % Favored : 68.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.31 (0.14), residues: 3325 helix: -0.47 (0.17), residues: 922 sheet: -1.72 (0.19), residues: 667 loop : -2.05 (0.14), residues: 1736 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP b 212 HIS 0.007 0.001 HIS v 44 PHE 0.052 0.002 PHE g 46 TYR 0.022 0.002 TYR j 75 ARG 0.010 0.000 ARG s 18 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6650 Ramachandran restraints generated. 3325 Oldfield, 0 Emsley, 3325 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6650 Ramachandran restraints generated. 3325 Oldfield, 0 Emsley, 3325 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 746 residues out of total 2739 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 138 poor density : 608 time to evaluate : 3.885 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: c 99 GLU cc_start: 0.9171 (OUTLIER) cc_final: 0.8757 (mp0) REVERT: d 24 ASN cc_start: 0.8849 (t0) cc_final: 0.8575 (t0) REVERT: e 21 TYR cc_start: 0.6907 (m-10) cc_final: 0.6554 (m-10) REVERT: e 25 MET cc_start: 0.7969 (pmm) cc_final: 0.7727 (pmm) REVERT: e 37 MET cc_start: 0.7690 (tpp) cc_final: 0.7349 (tpp) REVERT: e 95 MET cc_start: 0.9069 (ttp) cc_final: 0.8836 (ttp) REVERT: f 59 ASP cc_start: 0.8606 (p0) cc_final: 0.8297 (p0) REVERT: f 82 PHE cc_start: 0.7738 (m-80) cc_final: 0.7327 (m-80) REVERT: f 87 GLN cc_start: 0.8333 (pp30) cc_final: 0.8050 (pp30) REVERT: g 7 ASP cc_start: 0.8062 (m-30) cc_final: 0.7729 (m-30) REVERT: g 35 LYS cc_start: 0.8515 (mptt) cc_final: 0.8284 (mptt) REVERT: h 52 MET cc_start: -0.0643 (mmp) cc_final: -0.1328 (mpp) REVERT: h 116 GLU cc_start: 0.2783 (tt0) cc_final: 0.2395 (pt0) REVERT: i 16 MET cc_start: 0.1166 (ptt) cc_final: 0.0560 (ptm) REVERT: i 85 ILE cc_start: 0.4340 (OUTLIER) cc_final: 0.4060 (tp) REVERT: i 135 MET cc_start: 0.4345 (mmt) cc_final: 0.3498 (mmt) REVERT: k 37 ASP cc_start: 0.8363 (t70) cc_final: 0.7801 (t0) REVERT: k 53 LYS cc_start: 0.8974 (OUTLIER) cc_final: 0.8636 (ptpp) REVERT: l 91 ASP cc_start: 0.8639 (OUTLIER) cc_final: 0.8257 (p0) REVERT: l 136 GLU cc_start: 0.8189 (mt-10) cc_final: 0.7976 (mt-10) REVERT: n 49 GLU cc_start: 0.8165 (mp0) cc_final: 0.7813 (mp0) REVERT: n 56 LYS cc_start: 0.8834 (mtpp) cc_final: 0.8622 (mtpm) REVERT: o 115 LEU cc_start: 0.8838 (OUTLIER) cc_final: 0.8633 (mm) REVERT: p 12 MET cc_start: 0.8139 (OUTLIER) cc_final: 0.7485 (mpp) REVERT: p 26 GLU cc_start: 0.8055 (tm-30) cc_final: 0.7542 (tm-30) REVERT: q 60 TRP cc_start: 0.9168 (m-10) cc_final: 0.8831 (m-10) REVERT: q 65 ASN cc_start: 0.8910 (t0) cc_final: 0.8653 (t0) REVERT: q 71 ASN cc_start: 0.8658 (t0) cc_final: 0.8447 (t0) REVERT: q 96 ASP cc_start: 0.8227 (t70) cc_final: 0.7775 (t0) REVERT: r 6 GLN cc_start: 0.8803 (tt0) cc_final: 0.8471 (pt0) REVERT: r 11 GLN cc_start: 0.8883 (mp10) cc_final: 0.8510 (mp10) REVERT: r 13 ARG cc_start: 0.8176 (ttt-90) cc_final: 0.7783 (ptt90) REVERT: r 24 LYS cc_start: 0.9274 (tttp) cc_final: 0.8795 (ttpp) REVERT: r 60 LYS cc_start: 0.8482 (mttp) cc_final: 0.8103 (tmtt) REVERT: r 78 ARG cc_start: 0.9010 (tpp-160) cc_final: 0.8451 (tpp80) REVERT: s 69 LEU cc_start: 0.9186 (mt) cc_final: 0.8893 (mt) REVERT: t 5 GLU cc_start: 0.8062 (mp0) cc_final: 0.7725 (mp0) REVERT: t 24 MET cc_start: 0.8350 (tpp) cc_final: 0.7748 (ttp) REVERT: u 17 ASP cc_start: 0.7963 (m-30) cc_final: 0.7588 (m-30) REVERT: u 21 ARG cc_start: 0.8357 (ptm-80) cc_final: 0.7946 (mtp-110) REVERT: u 72 PHE cc_start: 0.8511 (t80) cc_final: 0.8007 (t80) REVERT: v 19 ARG cc_start: 0.8871 (mtm-85) cc_final: 0.8185 (mtm-85) REVERT: w 17 LEU cc_start: 0.9050 (mt) cc_final: 0.8602 (mt) REVERT: w 52 ASP cc_start: 0.8130 (t0) cc_final: 0.7789 (t0) REVERT: w 58 LYS cc_start: 0.9063 (mtmm) cc_final: 0.8764 (mtmm) REVERT: w 77 SER cc_start: 0.8831 (m) cc_final: 0.8524 (m) REVERT: x 69 GLU cc_start: 0.9081 (mp0) cc_final: 0.8697 (mp0) REVERT: y 59 GLU cc_start: 0.8814 (tt0) cc_final: 0.8604 (pt0) REVERT: z 5 LYS cc_start: 0.8629 (mmmm) cc_final: 0.8147 (mmmt) REVERT: A 11 GLU cc_start: 0.8871 (tt0) cc_final: 0.8569 (tp30) REVERT: E 5 THR cc_start: 0.8720 (OUTLIER) cc_final: 0.8503 (p) REVERT: E 15 LYS cc_start: 0.8463 (OUTLIER) cc_final: 0.7992 (tmtt) REVERT: E 28 LEU cc_start: 0.9498 (tp) cc_final: 0.9239 (tt) REVERT: F 15 LYS cc_start: 0.8687 (mmmt) cc_final: 0.8259 (mppt) REVERT: F 36 ARG cc_start: 0.8565 (OUTLIER) cc_final: 0.7709 (tmm-80) outliers start: 138 outliers final: 119 residues processed: 684 average time/residue: 0.8496 time to fit residues: 1008.7150 Evaluate side-chains 720 residues out of total 2739 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 128 poor density : 592 time to evaluate : 3.824 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain b residue 5 CYS Chi-restraints excluded: chain b residue 18 VAL Chi-restraints excluded: chain b residue 19 VAL Chi-restraints excluded: chain b residue 52 HIS Chi-restraints excluded: chain b residue 89 ASN Chi-restraints excluded: chain b residue 183 VAL Chi-restraints excluded: chain b residue 203 VAL Chi-restraints excluded: chain b residue 218 THR Chi-restraints excluded: chain b residue 256 THR Chi-restraints excluded: chain b residue 263 ASP Chi-restraints excluded: chain c residue 9 VAL Chi-restraints excluded: chain c residue 60 VAL Chi-restraints excluded: chain c residue 91 THR Chi-restraints excluded: chain c residue 96 ILE Chi-restraints excluded: chain c residue 99 GLU Chi-restraints excluded: chain c residue 100 LEU Chi-restraints excluded: chain c residue 122 VAL Chi-restraints excluded: chain d residue 4 VAL Chi-restraints excluded: chain d residue 7 ASP Chi-restraints excluded: chain d residue 13 THR Chi-restraints excluded: chain d residue 53 THR Chi-restraints excluded: chain d residue 73 ILE Chi-restraints excluded: chain d residue 150 THR Chi-restraints excluded: chain d residue 167 VAL Chi-restraints excluded: chain e residue 34 THR Chi-restraints excluded: chain e residue 105 ILE Chi-restraints excluded: chain e residue 112 ASP Chi-restraints excluded: chain e residue 152 ASP Chi-restraints excluded: chain e residue 156 THR Chi-restraints excluded: chain e residue 168 LEU Chi-restraints excluded: chain f residue 9 VAL Chi-restraints excluded: chain f residue 10 VAL Chi-restraints excluded: chain f residue 16 VAL Chi-restraints excluded: chain f residue 22 VAL Chi-restraints excluded: chain f residue 100 ASN Chi-restraints excluded: chain f residue 130 ILE Chi-restraints excluded: chain g residue 5 LEU Chi-restraints excluded: chain g residue 12 LEU Chi-restraints excluded: chain g residue 37 VAL Chi-restraints excluded: chain h residue 5 LEU Chi-restraints excluded: chain h residue 55 VAL Chi-restraints excluded: chain h residue 57 ASN Chi-restraints excluded: chain h residue 88 HIS Chi-restraints excluded: chain h residue 124 ASP Chi-restraints excluded: chain i residue 7 TYR Chi-restraints excluded: chain i residue 8 VAL Chi-restraints excluded: chain i residue 72 THR Chi-restraints excluded: chain i residue 85 ILE Chi-restraints excluded: chain i residue 141 ASP Chi-restraints excluded: chain j residue 70 THR Chi-restraints excluded: chain j residue 78 THR Chi-restraints excluded: chain j residue 86 GLN Chi-restraints excluded: chain j residue 93 ILE Chi-restraints excluded: chain j residue 131 ASN Chi-restraints excluded: chain k residue 35 VAL Chi-restraints excluded: chain k residue 53 LYS Chi-restraints excluded: chain k residue 56 ASP Chi-restraints excluded: chain k residue 57 VAL Chi-restraints excluded: chain k residue 58 LEU Chi-restraints excluded: chain l residue 91 ASP Chi-restraints excluded: chain l residue 101 ILE Chi-restraints excluded: chain l residue 128 THR Chi-restraints excluded: chain n residue 1 MET Chi-restraints excluded: chain n residue 34 ILE Chi-restraints excluded: chain n residue 37 THR Chi-restraints excluded: chain n residue 57 THR Chi-restraints excluded: chain n residue 97 ILE Chi-restraints excluded: chain o residue 49 VAL Chi-restraints excluded: chain o residue 74 VAL Chi-restraints excluded: chain o residue 115 LEU Chi-restraints excluded: chain p residue 12 MET Chi-restraints excluded: chain p residue 59 THR Chi-restraints excluded: chain p residue 65 ASN Chi-restraints excluded: chain p residue 69 VAL Chi-restraints excluded: chain p residue 72 VAL Chi-restraints excluded: chain p residue 109 ILE Chi-restraints excluded: chain q residue 58 GLN Chi-restraints excluded: chain q residue 87 VAL Chi-restraints excluded: chain r residue 27 ILE Chi-restraints excluded: chain r residue 29 THR Chi-restraints excluded: chain r residue 38 VAL Chi-restraints excluded: chain s residue 19 LEU Chi-restraints excluded: chain s residue 24 ILE Chi-restraints excluded: chain s residue 65 ASP Chi-restraints excluded: chain s residue 66 ILE Chi-restraints excluded: chain s residue 74 ILE Chi-restraints excluded: chain s residue 77 ASP Chi-restraints excluded: chain s residue 86 MET Chi-restraints excluded: chain t residue 39 THR Chi-restraints excluded: chain u residue 11 ILE Chi-restraints excluded: chain u residue 14 THR Chi-restraints excluded: chain u residue 33 VAL Chi-restraints excluded: chain u residue 64 ILE Chi-restraints excluded: chain v residue 10 LYS Chi-restraints excluded: chain v residue 26 PHE Chi-restraints excluded: chain v residue 29 ILE Chi-restraints excluded: chain v residue 38 LEU Chi-restraints excluded: chain v residue 63 ILE Chi-restraints excluded: chain v residue 71 LYS Chi-restraints excluded: chain w residue 63 VAL Chi-restraints excluded: chain w residue 67 VAL Chi-restraints excluded: chain w residue 79 GLU Chi-restraints excluded: chain x residue 19 HIS Chi-restraints excluded: chain x residue 39 VAL Chi-restraints excluded: chain y residue 17 GLU Chi-restraints excluded: chain y residue 21 LEU Chi-restraints excluded: chain z residue 3 THR Chi-restraints excluded: chain z residue 40 THR Chi-restraints excluded: chain z residue 56 VAL Chi-restraints excluded: chain z residue 57 GLU Chi-restraints excluded: chain A residue 9 TYR Chi-restraints excluded: chain A residue 30 HIS Chi-restraints excluded: chain A residue 34 LEU Chi-restraints excluded: chain A residue 35 ASP Chi-restraints excluded: chain B residue 21 LEU Chi-restraints excluded: chain B residue 22 THR Chi-restraints excluded: chain D residue 4 THR Chi-restraints excluded: chain D residue 24 THR Chi-restraints excluded: chain D residue 29 GLN Chi-restraints excluded: chain D residue 44 VAL Chi-restraints excluded: chain E residue 5 THR Chi-restraints excluded: chain E residue 15 LYS Chi-restraints excluded: chain E residue 53 ASP Chi-restraints excluded: chain F residue 23 ILE Chi-restraints excluded: chain F residue 36 ARG Chi-restraints excluded: chain a residue 35 THR Chi-restraints excluded: chain a residue 60 ARG Chi-restraints excluded: chain a residue 214 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 629 random chunks: chunk 396 optimal weight: 10.0000 chunk 531 optimal weight: 30.0000 chunk 152 optimal weight: 4.9990 chunk 460 optimal weight: 10.0000 chunk 73 optimal weight: 5.9990 chunk 138 optimal weight: 9.9990 chunk 499 optimal weight: 10.0000 chunk 209 optimal weight: 0.1980 chunk 513 optimal weight: 10.0000 chunk 63 optimal weight: 4.9990 chunk 92 optimal weight: 20.0000 overall best weight: 5.2388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: b 162 GLN d 163 ASN ** g 2 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** g 11 ASN ** g 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** l 104 GLN ** p 114 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** q 55 GLN ** q 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** t 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** v 12 GLN ** v 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** y 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3518 r_free = 0.3518 target = 0.055033 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.3115 r_free = 0.3115 target = 0.040159 restraints weight = 515137.955| |-----------------------------------------------------------------------------| r_work (start): 0.3078 rms_B_bonded: 2.11 r_work: 0.2967 rms_B_bonded: 3.57 restraints_weight: 0.5000 r_work (final): 0.2967 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8711 moved from start: 0.3824 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.084 99292 Z= 0.319 Angle : 0.656 11.705 149057 Z= 0.337 Chirality : 0.038 0.276 19153 Planarity : 0.005 0.051 7608 Dihedral : 23.950 178.709 50895 Min Nonbonded Distance : 1.986 Molprobity Statistics. All-atom Clashscore : 19.02 Ramachandran Plot: Outliers : 0.12 % Allowed : 9.20 % Favored : 90.68 % Rotamer: Outliers : 5.40 % Allowed : 25.99 % Favored : 68.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.29 (0.14), residues: 3325 helix: -0.46 (0.17), residues: 912 sheet: -1.70 (0.19), residues: 666 loop : -2.03 (0.14), residues: 1747 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP b 212 HIS 0.006 0.001 HIS v 44 PHE 0.053 0.002 PHE g 46 TYR 0.025 0.002 TYR j 75 ARG 0.008 0.001 ARG q 57 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 20254.66 seconds wall clock time: 359 minutes 32.13 seconds (21572.13 seconds total)