Starting phenix.real_space_refine on Sat Apr 13 18:39:26 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zp8_14850/04_2024/7zp8_14850.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zp8_14850/04_2024/7zp8_14850.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zp8_14850/04_2024/7zp8_14850.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zp8_14850/04_2024/7zp8_14850.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zp8_14850/04_2024/7zp8_14850.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zp8_14850/04_2024/7zp8_14850.pdb" } resolution = 2.2 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= 0.000 sd= 0.006 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 3095 5.49 5 S 74 5.16 5 C 45021 2.51 5 N 16949 2.21 5 O 25812 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "0 ARG 3": "NH1" <-> "NH2" Residue "0 ARG 11": "NH1" <-> "NH2" Residue "0 ARG 18": "NH1" <-> "NH2" Residue "0 ARG 37": "NH1" <-> "NH2" Residue "0 ARG 50": "NH1" <-> "NH2" Residue "0 ARG 57": "NH1" <-> "NH2" Residue "0 GLU 70": "OE1" <-> "OE2" Residue "0 ARG 74": "NH1" <-> "NH2" Residue "0 GLU 76": "OE1" <-> "OE2" Residue "1 ARG 29": "NH1" <-> "NH2" Residue "1 ARG 47": "NH1" <-> "NH2" Residue "1 ARG 52": "NH1" <-> "NH2" Residue "2 ARG 11": "NH1" <-> "NH2" Residue "2 ARG 30": "NH1" <-> "NH2" Residue "2 ARG 45": "NH1" <-> "NH2" Residue "3 ARG 10": "NH1" <-> "NH2" Residue "3 ARG 16": "NH1" <-> "NH2" Residue "3 ARG 52": "NH1" <-> "NH2" Residue "4 GLU 32": "OE1" <-> "OE2" Residue "4 GLU 35": "OE1" <-> "OE2" Residue "4 ARG 44": "NH1" <-> "NH2" Residue "6 ARG 3": "NH1" <-> "NH2" Residue "6 ARG 12": "NH1" <-> "NH2" Residue "6 ARG 14": "NH1" <-> "NH2" Residue "6 ARG 19": "NH1" <-> "NH2" Residue "6 ARG 21": "NH1" <-> "NH2" Residue "6 ARG 33": "NH1" <-> "NH2" Residue "6 ARG 41": "NH1" <-> "NH2" Residue "7 ARG 13": "NH1" <-> "NH2" Residue "7 ARG 30": "NH1" <-> "NH2" Residue "7 ARG 40": "NH1" <-> "NH2" Residue "7 ARG 42": "NH1" <-> "NH2" Residue "8 ARG 24": "NH1" <-> "NH2" Residue "c ARG 52": "NH1" <-> "NH2" Residue "c ARG 63": "NH1" <-> "NH2" Residue "c ARG 80": "NH1" <-> "NH2" Residue "c ARG 133": "NH1" <-> "NH2" Residue "c ARG 167": "NH1" <-> "NH2" Residue "c ARG 177": "NH1" <-> "NH2" Residue "c ARG 182": "NH1" <-> "NH2" Residue "c ARG 189": "NH1" <-> "NH2" Residue "c ARG 203": "NH1" <-> "NH2" Residue "c ARG 212": "NH1" <-> "NH2" Residue "c GLU 236": "OE1" <-> "OE2" Residue "d ARG 13": "NH1" <-> "NH2" Residue "d GLU 28": "OE1" <-> "OE2" Residue "d ARG 33": "NH1" <-> "NH2" Residue "d ARG 59": "NH1" <-> "NH2" Residue "d ARG 77": "NH1" <-> "NH2" Residue "d ARG 83": "NH1" <-> "NH2" Residue "d GLU 99": "OE1" <-> "OE2" Residue "d GLU 168": "OE1" <-> "OE2" Residue "d ARG 169": "NH1" <-> "NH2" Residue "d ARG 184": "NH1" <-> "NH2" Residue "e ARG 21": "NH1" <-> "NH2" Residue "e ARG 44": "NH1" <-> "NH2" Residue "e ARG 49": "NH1" <-> "NH2" Residue "e ARG 61": "NH1" <-> "NH2" Residue "e ARG 67": "NH1" <-> "NH2" Residue "e ARG 88": "NH1" <-> "NH2" Residue "e ARG 102": "NH1" <-> "NH2" Residue "e GLU 111": "OE1" <-> "OE2" Residue "e ARG 162": "NH1" <-> "NH2" Residue "e ARG 170": "NH1" <-> "NH2" Residue "f ARG 71": "NH1" <-> "NH2" Residue "f ARG 80": "NH1" <-> "NH2" Residue "f ARG 92": "NH1" <-> "NH2" Residue "f GLU 101": "OE1" <-> "OE2" Residue "f ARG 102": "NH1" <-> "NH2" Residue "f ARG 110": "NH1" <-> "NH2" Residue "f ARG 112": "NH1" <-> "NH2" Residue "f ARG 115": "NH1" <-> "NH2" Residue "f ARG 133": "NH1" <-> "NH2" Residue "g ARG 3": "NH1" <-> "NH2" Residue "g ARG 153": "NH1" <-> "NH2" Residue "g ARG 163": "NH1" <-> "NH2" Residue "g GLU 167": "OE1" <-> "OE2" Residue "g ARG 170": "NH1" <-> "NH2" Residue "h ARG 27": "NH1" <-> "NH2" Residue "j ARG 13": "NH1" <-> "NH2" Residue "j GLU 31": "OE1" <-> "OE2" Residue "j ARG 37": "NH1" <-> "NH2" Residue "j TYR 75": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "j ARG 96": "NH1" <-> "NH2" Residue "j GLU 98": "OE1" <-> "OE2" Residue "j GLU 102": "OE1" <-> "OE2" Residue "j ARG 120": "NH1" <-> "NH2" Residue "j GLU 129": "OE1" <-> "OE2" Residue "k GLU 4": "OE1" <-> "OE2" Residue "l ARG 21": "NH1" <-> "NH2" Residue "l ARG 33": "NH1" <-> "NH2" Residue "l ARG 41": "NH1" <-> "NH2" Residue "l ARG 47": "NH1" <-> "NH2" Residue "l ARG 60": "NH1" <-> "NH2" Residue "l ARG 78": "NH1" <-> "NH2" Residue "l GLU 86": "OE1" <-> "OE2" Residue "l ARG 126": "NH1" <-> "NH2" Residue "m ARG 10": "NH1" <-> "NH2" Residue "m ARG 18": "NH1" <-> "NH2" Residue "m ARG 40": "NH1" <-> "NH2" Residue "m ARG 44": "NH1" <-> "NH2" Residue "m ARG 50": "NH1" <-> "NH2" Residue "m ARG 55": "NH1" <-> "NH2" Residue "m ARG 59": "NH1" <-> "NH2" Residue "m GLU 75": "OE1" <-> "OE2" Residue "m GLU 90": "OE1" <-> "OE2" Residue "m ARG 114": "NH1" <-> "NH2" Residue "n ARG 8": "NH1" <-> "NH2" Residue "n ARG 12": "NH1" <-> "NH2" Residue "n ARG 17": "NH1" <-> "NH2" Residue "n ARG 22": "NH1" <-> "NH2" Residue "n ARG 46": "NH1" <-> "NH2" Residue "n ARG 63": "NH1" <-> "NH2" Residue "n ARG 64": "NH1" <-> "NH2" Residue "n ARG 69": "NH1" <-> "NH2" Residue "n ARG 71": "NH1" <-> "NH2" Residue "n GLU 82": "OE1" <-> "OE2" Residue "n ARG 96": "NH1" <-> "NH2" Residue "n GLU 114": "OE1" <-> "OE2" Residue "n ARG 118": "NH1" <-> "NH2" Residue "o ARG 10": "NH1" <-> "NH2" Residue "o ARG 13": "NH1" <-> "NH2" Residue "o ARG 16": "NH1" <-> "NH2" Residue "o GLU 20": "OE1" <-> "OE2" Residue "o ARG 25": "NH1" <-> "NH2" Residue "o GLU 80": "OE1" <-> "OE2" Residue "o ARG 81": "NH1" <-> "NH2" Residue "o ARG 94": "NH1" <-> "NH2" Residue "o ARG 102": "NH1" <-> "NH2" Residue "o ARG 111": "NH1" <-> "NH2" Residue "o PHE 117": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "p GLU 11": "OE1" <-> "OE2" Residue "p ARG 21": "NH1" <-> "NH2" Residue "p ARG 39": "NH1" <-> "NH2" Residue "p GLU 44": "OE1" <-> "OE2" Residue "p ARG 51": "NH1" <-> "NH2" Residue "p ARG 62": "NH1" <-> "NH2" Residue "p ARG 89": "NH1" <-> "NH2" Residue "p ARG 101": "NH1" <-> "NH2" Residue "p ARG 109": "NH1" <-> "NH2" Residue "q ARG 3": "NH1" <-> "NH2" Residue "q ARG 6": "NH1" <-> "NH2" Residue "q ARG 13": "NH1" <-> "NH2" Residue "q ARG 33": "NH1" <-> "NH2" Residue "q ARG 48": "NH1" <-> "NH2" Residue "q ARG 70": "NH1" <-> "NH2" Residue "q GLU 89": "OE1" <-> "OE2" Residue "r ARG 21": "NH1" <-> "NH2" Residue "r GLU 23": "OE1" <-> "OE2" Residue "r ARG 68": "NH1" <-> "NH2" Residue "r ARG 78": "NH1" <-> "NH2" Residue "r ARG 79": "NH1" <-> "NH2" Residue "r ARG 84": "NH1" <-> "NH2" Residue "s GLU 2": "OE1" <-> "OE2" Residue "s ARG 84": "NH1" <-> "NH2" Residue "s ARG 88": "NH1" <-> "NH2" Residue "s ARG 95": "NH1" <-> "NH2" Residue "t ARG 12": "NH1" <-> "NH2" Residue "t GLU 52": "OE1" <-> "OE2" Residue "t GLU 54": "OE1" <-> "OE2" Residue "u ARG 6": "NH1" <-> "NH2" Residue "u ARG 7": "NH1" <-> "NH2" Residue "u GLU 62": "OE1" <-> "OE2" Residue "u ARG 82": "NH1" <-> "NH2" Residue "u ARG 86": "NH1" <-> "NH2" Residue "u GLU 88": "OE1" <-> "OE2" Residue "u ARG 94": "NH1" <-> "NH2" Residue "u PHE 95": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "w GLU 41": "OE1" <-> "OE2" Residue "w GLU 69": "OE1" <-> "OE2" Residue "y ARG 11": "NH1" <-> "NH2" Residue "y GLU 29": "OE1" <-> "OE2" Residue "z GLU 149": "OE1" <-> "OE2" Time to flip residues: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 90951 Number of models: 1 Model: "" Number of chains: 32 Chain: "0" Number of atoms: 625 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 625 Classifications: {'peptide': 77} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 74} Chain: "1" Number of atoms: 495 Number of conformers: 1 Conformer: "" Number of residues, atoms: 61, 495 Classifications: {'peptide': 61} Link IDs: {'TRANS': 60} Chain: "2" Number of atoms: 439 Number of conformers: 1 Conformer: "" Number of residues, atoms: 57, 439 Classifications: {'peptide': 57} Link IDs: {'PTRANS': 2, 'TRANS': 54} Chain: "3" Number of atoms: 434 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 434 Classifications: {'peptide': 55} Link IDs: {'PTRANS': 1, 'TRANS': 53} Chain: "4" Number of atoms: 409 Number of conformers: 1 Conformer: "" Number of residues, atoms: 50, 409 Classifications: {'peptide': 50} Link IDs: {'PTRANS': 2, 'TRANS': 47} Chain: "6" Number of atoms: 377 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 377 Classifications: {'peptide': 46} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 44} Chain: "7" Number of atoms: 504 Number of conformers: 1 Conformer: "" Number of residues, atoms: 64, 504 Classifications: {'peptide': 64} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 61} Chain: "8" Number of atoms: 301 Number of conformers: 1 Conformer: "" Number of residues, atoms: 38, 301 Classifications: {'peptide': 38} Link IDs: {'PTRANS': 1, 'TRANS': 36} Chain: "a" Number of atoms: 2529 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 2529 Classifications: {'RNA': 118} Modifications used: {'rna2p_pur': 7, 'rna2p_pyr': 5, 'rna3p_pur': 57, 'rna3p_pyr': 49} Link IDs: {'rna2p': 12, 'rna3p': 105} Chain: "b" Number of atoms: 62281 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2901, 62281 Classifications: {'RNA': 2901} Modifications used: {'rna2p_pur': 281, 'rna2p_pyr': 151, 'rna3p_pur': 1394, 'rna3p_pyr': 1075} Link IDs: {'rna2p': 432, 'rna3p': 2468} Chain: "c" Number of atoms: 2082 Number of conformers: 1 Conformer: "" Number of residues, atoms: 271, 2082 Classifications: {'peptide': 271} Link IDs: {'PTRANS': 17, 'TRANS': 253} Chain: "d" Number of atoms: 1565 Number of conformers: 1 Conformer: "" Number of residues, atoms: 209, 1565 Classifications: {'peptide': 209} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 202} Chain: "e" Number of atoms: 1552 Number of conformers: 1 Conformer: "" Number of residues, atoms: 201, 1552 Classifications: {'peptide': 201} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 195} Chain: "f" Number of atoms: 1410 Number of conformers: 1 Conformer: "" Number of residues, atoms: 177, 1410 Classifications: {'peptide': 177} Link IDs: {'PTRANS': 6, 'TRANS': 170} Chain: "g" Number of atoms: 1323 Number of conformers: 1 Conformer: "" Number of residues, atoms: 176, 1323 Classifications: {'peptide': 176} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 8, 'TRANS': 167} Chain: "h" Number of atoms: 287 Number of conformers: 1 Conformer: "" Number of residues, atoms: 39, 287 Classifications: {'peptide': 39} Link IDs: {'PTRANS': 2, 'TRANS': 36} Chain: "j" Number of atoms: 1129 Number of conformers: 1 Conformer: "" Number of residues, atoms: 142, 1129 Classifications: {'peptide': 142} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 135} Chain: "k" Number of atoms: 938 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 938 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 5, 'TRANS': 116} Chain: "l" Number of atoms: 1043 Number of conformers: 1 Conformer: "" Number of residues, atoms: 143, 1043 Classifications: {'peptide': 143} Link IDs: {'PTRANS': 4, 'TRANS': 138} Chain: "m" Number of atoms: 1074 Number of conformers: 1 Conformer: "" Number of residues, atoms: 136, 1074 Classifications: {'peptide': 136} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 128} Chain: "n" Number of atoms: 960 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 960 Classifications: {'peptide': 120} Link IDs: {'PTRANS': 4, 'TRANS': 115} Chain: "o" Number of atoms: 892 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 892 Classifications: {'peptide': 116} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 113} Chain: "p" Number of atoms: 908 Number of conformers: 1 Conformer: "" Number of residues, atoms: 113, 908 Classifications: {'peptide': 113} Link IDs: {'PTRANS': 3, 'TRANS': 109} Chain: "q" Number of atoms: 947 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 947 Classifications: {'peptide': 117} Modifications used: {'COO': 1} Link IDs: {'TRANS': 116} Chain: "r" Number of atoms: 810 Number of conformers: 1 Conformer: "" Number of residues, atoms: 102, 810 Classifications: {'peptide': 102} Link IDs: {'PTRANS': 1, 'TRANS': 100} Chain: "s" Number of atoms: 845 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 845 Classifications: {'peptide': 109} Link IDs: {'PTRANS': 2, 'TRANS': 106} Chain: "t" Number of atoms: 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: "w" Number of atoms: 753 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 753 Classifications: {'peptide': 94} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 89} Chain: "y" Number of atoms: 619 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 619 Classifications: {'peptide': 82} Link IDs: {'PTRANS': 1, 'TRANS': 80} Chain: "v" Number of atoms: 1626 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 1626 Classifications: {'RNA': 76} Modifications used: {'rna2p_pur': 6, 'rna2p_pyr': 4, 'rna3p_pur': 34, 'rna3p_pyr': 32} Link IDs: {'rna2p': 9, 'rna3p': 66} Chain: "z" Number of atoms: 277 Number of conformers: 1 Conformer: "" Number of residues, atoms: 33, 277 Classifications: {'peptide': 33} Link IDs: {'PTRANS': 3, 'TRANS': 29} Time building chain proxies: 35.61, per 1000 atoms: 0.39 Number of scatterers: 90951 At special positions: 0 Unit cell: (202.608, 207.968, 224.048, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 74 16.00 P 3095 15.00 O 25812 8.00 N 16949 7.00 C 45021 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS 8 14 " - pdb=" SG CYS 8 27 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 36.24 Conformation dependent library (CDL) restraints added in 3.8 seconds 6174 Ramachandran restraints generated. 3087 Oldfield, 0 Emsley, 3087 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5726 Finding SS restraints... Secondary structure from input PDB file: 89 helices and 47 sheets defined 29.9% alpha, 21.4% beta 967 base pairs and 1744 stacking pairs defined. Time for finding SS restraints: 34.92 Creating SS restraints... Processing helix chain '0' and resid 53 through 63 Processing helix chain '0' and resid 63 through 75 Processing helix chain '1' and resid 3 through 9 Processing helix chain '1' and resid 10 through 35 Processing helix chain '1' and resid 41 through 61 Processing helix chain '2' and resid 17 through 28 Processing helix chain '2' and resid 41 through 51 removed outlier: 3.523A pdb=" N VAL 2 51 " --> pdb=" O MET 2 47 " (cutoff:3.500A) Processing helix chain '3' and resid 9 through 17 Processing helix chain '3' and resid 18 through 20 No H-bonds generated for 'chain '3' and resid 18 through 20' Processing helix chain '6' and resid 8 through 17 Processing helix chain '6' and resid 17 through 24 removed outlier: 4.313A pdb=" N THR 6 24 " --> pdb=" O ALA 6 20 " (cutoff:3.500A) Processing helix chain '6' and resid 24 through 38 Processing helix chain '7' and resid 7 through 12 Processing helix chain '7' and resid 37 through 45 Processing helix chain '7' and resid 51 through 62 removed outlier: 4.246A pdb=" N GLY 7 56 " --> pdb=" O LYS 7 52 " (cutoff:3.500A) removed outlier: 4.542A pdb=" N LEU 7 57 " --> pdb=" O GLY 7 53 " (cutoff:3.500A) Processing helix chain '8' and resid 30 through 33 Processing helix chain 'c' and resid 30 through 32 No H-bonds generated for 'chain 'c' and resid 30 through 32' Processing helix chain 'c' and resid 133 through 135 No H-bonds generated for 'chain 'c' and resid 133 through 135' Processing helix chain 'c' and resid 197 through 203 removed outlier: 4.226A pdb=" N MET c 201 " --> pdb=" O ALA c 198 " (cutoff:3.500A) Processing helix chain 'c' and resid 207 through 213 removed outlier: 4.031A pdb=" N ALA c 211 " --> pdb=" O LYS c 207 " (cutoff:3.500A) Processing helix chain 'c' and resid 221 through 225 Processing helix chain 'c' and resid 263 through 265 No H-bonds generated for 'chain 'c' and resid 263 through 265' Processing helix chain 'd' and resid 39 through 44 Processing helix chain 'd' and resid 56 through 60 removed outlier: 3.693A pdb=" N VAL d 60 " --> pdb=" O ALA d 57 " (cutoff:3.500A) Processing helix chain 'd' and resid 61 through 72 removed outlier: 3.633A pdb=" N ALA d 71 " --> pdb=" O HIS d 67 " (cutoff:3.500A) Processing helix chain 'd' and resid 97 through 102 Processing helix chain 'd' and resid 120 through 126 Processing helix chain 'e' and resid 15 through 20 Processing helix chain 'e' and resid 24 through 39 Processing helix chain 'e' and resid 97 through 115 Processing helix chain 'e' and resid 130 through 141 removed outlier: 3.649A pdb=" N LEU e 134 " --> pdb=" O LYS e 130 " (cutoff:3.500A) Processing helix chain 'e' and resid 154 through 163 removed outlier: 4.493A pdb=" N ASN e 163 " --> pdb=" O LEU e 159 " (cutoff:3.500A) Processing helix chain 'e' and resid 176 through 183 Processing helix chain 'e' and resid 190 through 201 Processing helix chain 'f' and resid 3 through 21 removed outlier: 5.507A pdb=" N VAL f 13 " --> pdb=" O LYS f 9 " (cutoff:3.500A) removed outlier: 6.179A pdb=" N LYS f 14 " --> pdb=" O ASP f 10 " (cutoff:3.500A) Processing helix chain 'f' and resid 24 through 28 Processing helix chain 'f' and resid 40 through 45 removed outlier: 3.961A pdb=" N ILE f 44 " --> pdb=" O GLY f 41 " (cutoff:3.500A) Processing helix chain 'f' and resid 46 through 61 removed outlier: 4.300A pdb=" N LEU f 50 " --> pdb=" O ASP f 46 " (cutoff:3.500A) Processing helix chain 'f' and resid 93 through 106 Processing helix chain 'f' and resid 107 through 111 Processing helix chain 'f' and resid 134 through 138 removed outlier: 4.032A pdb=" N ILE f 137 " --> pdb=" O GLU f 134 " (cutoff:3.500A) Processing helix chain 'f' and resid 162 through 172 Processing helix chain 'g' and resid 60 through 80 removed outlier: 3.550A pdb=" N GLN g 64 " --> pdb=" O ASP g 60 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N THR g 80 " --> pdb=" O VAL g 76 " (cutoff:3.500A) Processing helix chain 'g' and resid 137 through 151 removed outlier: 3.807A pdb=" N TYR g 151 " --> pdb=" O ASP g 147 " (cutoff:3.500A) Processing helix chain 'j' and resid 24 through 38 removed outlier: 3.953A pdb=" N GLU j 31 " --> pdb=" O ARG j 27 " (cutoff:3.500A) Processing helix chain 'j' and resid 58 through 62 removed outlier: 3.672A pdb=" N VAL j 62 " --> pdb=" O ALA j 59 " (cutoff:3.500A) Processing helix chain 'j' and resid 67 through 72 Processing helix chain 'j' and resid 89 through 96 Processing helix chain 'j' and resid 96 through 108 removed outlier: 4.150A pdb=" N VAL j 100 " --> pdb=" O ARG j 96 " (cutoff:3.500A) removed outlier: 4.536A pdb=" N ILE j 101 " --> pdb=" O PRO j 97 " (cutoff:3.500A) Processing helix chain 'j' and resid 112 through 120 Processing helix chain 'j' and resid 132 through 136 Processing helix chain 'k' and resid 104 through 108 Processing helix chain 'k' and resid 112 through 119 Processing helix chain 'l' and resid 56 through 61 Processing helix chain 'l' and resid 82 through 86 removed outlier: 4.052A pdb=" N GLU l 86 " --> pdb=" O ALA l 83 " (cutoff:3.500A) Processing helix chain 'l' and resid 91 through 98 Processing helix chain 'l' and resid 128 through 138 Processing helix chain 'm' and resid 43 through 57 Processing helix chain 'm' and resid 109 through 122 removed outlier: 3.505A pdb=" N ALA m 122 " --> pdb=" O LYS m 118 " (cutoff:3.500A) Processing helix chain 'n' and resid 13 through 32 Processing helix chain 'n' and resid 44 through 56 Proline residue: n 50 - end of helix Processing helix chain 'n' and resid 59 through 70 Processing helix chain 'n' and resid 72 through 87 removed outlier: 4.989A pdb=" N GLY n 84 " --> pdb=" O PHE n 80 " (cutoff:3.500A) Proline residue: n 85 - end of helix Processing helix chain 'o' and resid 3 through 22 removed outlier: 4.453A pdb=" N ARG o 13 " --> pdb=" O ARG o 9 " (cutoff:3.500A) removed outlier: 4.995A pdb=" N ALA o 14 " --> pdb=" O ARG o 10 " (cutoff:3.500A) Processing helix chain 'o' and resid 55 through 60 Processing helix chain 'o' and resid 67 through 85 removed outlier: 3.855A pdb=" N LYS o 85 " --> pdb=" O ARG o 81 " (cutoff:3.500A) Processing helix chain 'o' and resid 101 through 114 Processing helix chain 'p' and resid 3 through 11 Processing helix chain 'p' and resid 53 through 56 Processing helix chain 'p' and resid 97 through 103 Processing helix chain 'p' and resid 104 through 109 Processing helix chain 'q' and resid 6 through 21 removed outlier: 3.667A pdb=" N GLN q 20 " --> pdb=" O LYS q 16 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ALA q 21 " --> pdb=" O ILE q 17 " (cutoff:3.500A) Processing helix chain 'q' and resid 25 through 30 Processing helix chain 'q' and resid 31 through 72 removed outlier: 3.722A pdb=" N GLN q 37 " --> pdb=" O ARG q 33 " (cutoff:3.500A) removed outlier: 4.121A pdb=" N ARG q 51 " --> pdb=" O TYR q 47 " (cutoff:3.500A) removed outlier: 4.484A pdb=" N LYS q 54 " --> pdb=" O ARG q 50 " (cutoff:3.500A) Processing helix chain 'q' and resid 75 through 86 Processing helix chain 'q' and resid 91 through 102 Processing helix chain 'q' and resid 102 through 118 Processing helix chain 's' and resid 13 through 22 removed outlier: 3.842A pdb=" N VAL s 20 " --> pdb=" O LYS s 16 " (cutoff:3.500A) Processing helix chain 's' and resid 28 through 38 Processing helix chain 's' and resid 41 through 62 removed outlier: 3.879A pdb=" N VAL s 45 " --> pdb=" O LYS s 41 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N LEU s 46 " --> pdb=" O LYS s 42 " (cutoff:3.500A) Processing helix chain 's' and resid 65 through 69 Processing helix chain 's' and resid 89 through 91 No H-bonds generated for 'chain 's' and resid 89 through 91' Processing helix chain 't' and resid 3 through 10 Processing helix chain 't' and resid 17 through 28 Processing helix chain 't' and resid 39 through 51 Processing helix chain 'w' and resid 12 through 23 removed outlier: 4.340A pdb=" N ALA w 16 " --> pdb=" O GLN w 12 " (cutoff:3.500A) Processing helix chain 'w' and resid 44 through 51 Processing helix chain 'w' and resid 52 through 58 removed outlier: 6.465A pdb=" N GLU w 55 " --> pdb=" O ALA w 52 " (cutoff:3.500A) Processing helix chain 'z' and resid 159 through 163 Processing sheet with id=AA1, first strand: chain '0' and resid 13 through 18 Processing sheet with id=AA2, first strand: chain '0' and resid 33 through 40 removed outlier: 3.531A pdb=" N ARG 0 45 " --> pdb=" O VAL 0 40 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain '2' and resid 35 through 37 removed outlier: 4.066A pdb=" N LYS 2 6 " --> pdb=" O GLU 2 58 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain '3' and resid 29 through 30 Processing sheet with id=AA5, first strand: chain '3' and resid 48 through 49 Processing sheet with id=AA6, first strand: chain '4' and resid 20 through 25 Processing sheet with id=AA7, first strand: chain '7' and resid 15 through 16 Processing sheet with id=AA8, first strand: chain '8' and resid 2 through 4 removed outlier: 5.960A pdb=" N LYS 8 2 " --> pdb=" O ARG 8 36 " (cutoff:3.500A) removed outlier: 5.203A pdb=" N ILE 8 23 " --> pdb=" O GLN 8 37 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'c' and resid 3 through 5 Processing sheet with id=AB1, first strand: chain 'c' and resid 34 through 36 Processing sheet with id=AB2, first strand: chain 'c' and resid 101 through 105 removed outlier: 6.852A pdb=" N ILE c 91 " --> pdb=" O LEU c 81 " (cutoff:3.500A) removed outlier: 4.778A pdb=" N LEU c 81 " --> pdb=" O ILE c 91 " (cutoff:3.500A) removed outlier: 6.767A pdb=" N LEU c 93 " --> pdb=" O GLU c 79 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'c' and resid 129 through 131 removed outlier: 5.935A pdb=" N ILE c 164 " --> pdb=" O ARG c 175 " (cutoff:3.500A) removed outlier: 6.637A pdb=" N ARG c 175 " --> pdb=" O ILE c 164 " (cutoff:3.500A) removed outlier: 6.609A pdb=" N MET c 181 " --> pdb=" O VAL c 268 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'c' and resid 144 through 145 removed outlier: 6.002A pdb=" N VAL c 144 " --> pdb=" O GLN c 153 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'd' and resid 4 through 16 removed outlier: 6.027A pdb=" N LYS d 8 " --> pdb=" O GLU d 28 " (cutoff:3.500A) removed outlier: 6.599A pdb=" N GLU d 28 " --> pdb=" O LYS d 8 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N GLY d 10 " --> pdb=" O VAL d 26 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N VAL d 20 " --> pdb=" O THR d 16 " (cutoff:3.500A) removed outlier: 7.002A pdb=" N LEU d 186 " --> pdb=" O VAL d 180 " (cutoff:3.500A) removed outlier: 4.831A pdb=" N VAL d 180 " --> pdb=" O LEU d 186 " (cutoff:3.500A) removed outlier: 6.659A pdb=" N LEU d 188 " --> pdb=" O VAL d 178 " (cutoff:3.500A) removed outlier: 4.433A pdb=" N ASP d 176 " --> pdb=" O LYS d 190 " (cutoff:3.500A) removed outlier: 5.837A pdb=" N VAL d 107 " --> pdb=" O SER d 174 " (cutoff:3.500A) removed outlier: 4.673A pdb=" N THR d 112 " --> pdb=" O ASP d 200 " (cutoff:3.500A) removed outlier: 7.132A pdb=" N ASP d 200 " --> pdb=" O THR d 112 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'd' and resid 80 through 83 removed outlier: 6.368A pdb=" N THR d 51 " --> pdb=" O VAL d 34 " (cutoff:3.500A) removed outlier: 5.409A pdb=" N VAL d 34 " --> pdb=" O THR d 51 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'd' and resid 117 through 119 removed outlier: 3.578A pdb=" N GLY d 117 " --> pdb=" O MET d 165 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'e' and resid 2 through 3 Processing sheet with id=AB9, first strand: chain 'e' and resid 118 through 121 Processing sheet with id=AC1, first strand: chain 'f' and resid 87 through 92 removed outlier: 3.745A pdb=" N LYS f 33 " --> pdb=" O THR f 157 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N LEU f 152 " --> pdb=" O VAL f 132 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'g' and resid 9 through 10 Processing sheet with id=AC3, first strand: chain 'g' and resid 16 through 20 removed outlier: 4.179A pdb=" N VAL g 23 " --> pdb=" O ASN g 20 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'g' and resid 122 through 124 Processing sheet with id=AC5, first strand: chain 'g' and resid 95 through 99 Processing sheet with id=AC6, first strand: chain 'h' and resid 18 through 20 Processing sheet with id=AC7, first strand: chain 'j' and resid 122 through 124 Processing sheet with id=AC8, first strand: chain 'j' and resid 73 through 77 Processing sheet with id=AC9, first strand: chain 'k' and resid 7 through 10 removed outlier: 3.783A pdb=" N VAL k 10 " --> pdb=" O ARG k 17 " (cutoff:3.500A) removed outlier: 6.623A pdb=" N ARG k 17 " --> pdb=" O VAL k 10 " (cutoff:3.500A) removed outlier: 6.622A pdb=" N ALA k 16 " --> pdb=" O ALA k 46 " (cutoff:3.500A) removed outlier: 6.135A pdb=" N ALA k 46 " --> pdb=" O ALA k 16 " (cutoff:3.500A) removed outlier: 6.137A pdb=" N ARG k 18 " --> pdb=" O LYS k 44 " (cutoff:3.500A) removed outlier: 6.618A pdb=" N LYS k 40 " --> pdb=" O ILE k 22 " (cutoff:3.500A) removed outlier: 5.972A pdb=" N VAL k 24 " --> pdb=" O ILE k 38 " (cutoff:3.500A) removed outlier: 8.328A pdb=" N ILE k 38 " --> pdb=" O VAL k 24 " (cutoff:3.500A) removed outlier: 5.024A pdb=" N ALA k 60 " --> pdb=" O LEU k 87 " (cutoff:3.500A) removed outlier: 6.184A pdb=" N LEU k 87 " --> pdb=" O ALA k 60 " (cutoff:3.500A) removed outlier: 5.717A pdb=" N VAL k 62 " --> pdb=" O VAL k 85 " (cutoff:3.500A) removed outlier: 6.536A pdb=" N VAL k 85 " --> pdb=" O VAL k 62 " (cutoff:3.500A) removed outlier: 7.997A pdb=" N CYS k 84 " --> pdb=" O MET k 7 " (cutoff:3.500A) removed outlier: 6.481A pdb=" N ASN k 9 " --> pdb=" O CYS k 84 " (cutoff:3.500A) removed outlier: 7.474A pdb=" N LEU k 86 " --> pdb=" O ASN k 9 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'k' and resid 69 through 70 removed outlier: 3.760A pdb=" N ALA p 49 " --> pdb=" O THR p 60 " (cutoff:3.500A) removed outlier: 6.690A pdb=" N ARG p 62 " --> pdb=" O VAL p 47 " (cutoff:3.500A) removed outlier: 5.778A pdb=" N VAL p 47 " --> pdb=" O ARG p 62 " (cutoff:3.500A) removed outlier: 8.605A pdb=" N ILE p 64 " --> pdb=" O GLY p 45 " (cutoff:3.500A) removed outlier: 8.641A pdb=" N GLY p 45 " --> pdb=" O ILE p 64 " (cutoff:3.500A) removed outlier: 6.408A pdb=" N THR p 25 " --> pdb=" O LYS p 87 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N SER p 83 " --> pdb=" O LYS p 29 " (cutoff:3.500A) removed outlier: 6.600A pdb=" N TRP p 31 " --> pdb=" O VAL p 81 " (cutoff:3.500A) removed outlier: 6.855A pdb=" N VAL p 81 " --> pdb=" O TRP p 31 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'l' and resid 77 through 78 removed outlier: 6.575A pdb=" N ILE l 77 " --> pdb=" O ILE l 111 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'l' and resid 89 through 90 Processing sheet with id=AD4, first strand: chain 'm' and resid 62 through 65 removed outlier: 6.587A pdb=" N LEU m 33 " --> pdb=" O LEU m 102 " (cutoff:3.500A) removed outlier: 4.439A pdb=" N GLU m 104 " --> pdb=" O PHE m 31 " (cutoff:3.500A) removed outlier: 6.701A pdb=" N PHE m 31 " --> pdb=" O GLU m 104 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'm' and resid 39 through 42 removed outlier: 6.842A pdb=" N ILE m 73 " --> pdb=" O GLU m 90 " (cutoff:3.500A) removed outlier: 4.486A pdb=" N TRP m 92 " --> pdb=" O LYS m 71 " (cutoff:3.500A) removed outlier: 6.128A pdb=" N LYS m 71 " --> pdb=" O TRP m 92 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'n' and resid 33 through 37 removed outlier: 5.697A pdb=" N MET n 110 " --> pdb=" O CYS n 100 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'o' and resid 47 through 52 removed outlier: 6.797A pdb=" N VAL o 39 " --> pdb=" O LEU o 48 " (cutoff:3.500A) removed outlier: 4.635A pdb=" N ALA o 50 " --> pdb=" O ALA o 37 " (cutoff:3.500A) removed outlier: 7.097A pdb=" N ALA o 37 " --> pdb=" O ALA o 50 " (cutoff:3.500A) removed outlier: 4.817A pdb=" N SER o 52 " --> pdb=" O ILE o 35 " (cutoff:3.500A) removed outlier: 7.027A pdb=" N ILE o 35 " --> pdb=" O SER o 52 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'r' and resid 11 through 14 removed outlier: 3.759A pdb=" N MET r 40 " --> pdb=" O VAL r 4 " (cutoff:3.500A) removed outlier: 7.308A pdb=" N GLN r 6 " --> pdb=" O VAL r 38 " (cutoff:3.500A) removed outlier: 6.977A pdb=" N VAL r 38 " --> pdb=" O GLN r 6 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'r' and resid 19 through 23 removed outlier: 6.797A pdb=" N PHE r 93 " --> pdb=" O HIS r 66 " (cutoff:3.500A) removed outlier: 4.782A pdb=" N HIS r 66 " --> pdb=" O PHE r 93 " (cutoff:3.500A) removed outlier: 6.653A pdb=" N ASP r 95 " --> pdb=" O VAL r 64 " (cutoff:3.500A) removed outlier: 6.516A pdb=" N LYS r 60 " --> pdb=" O THR r 99 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'r' and resid 72 through 78 removed outlier: 3.502A pdb=" N ARG r 78 " --> pdb=" O TYR r 83 " (cutoff:3.500A) removed outlier: 4.227A pdb=" N TYR r 83 " --> pdb=" O ARG r 78 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 's' and resid 3 through 10 removed outlier: 5.587A pdb=" N ILE s 4 " --> pdb=" O VAL s 107 " (cutoff:3.500A) removed outlier: 7.135A pdb=" N VAL s 107 " --> pdb=" O ILE s 4 " (cutoff:3.500A) removed outlier: 5.524A pdb=" N LYS s 6 " --> pdb=" O VAL s 105 " (cutoff:3.500A) removed outlier: 7.239A pdb=" N VAL s 105 " --> pdb=" O LYS s 6 " (cutoff:3.500A) removed outlier: 5.106A pdb=" N ARG s 8 " --> pdb=" O ILE s 103 " (cutoff:3.500A) removed outlier: 6.648A pdb=" N ILE s 103 " --> pdb=" O ARG s 8 " (cutoff:3.500A) removed outlier: 6.741A pdb=" N SER s 108 " --> pdb=" O VAL s 71 " (cutoff:3.500A) removed outlier: 5.393A pdb=" N VAL s 71 " --> pdb=" O SER s 108 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 's' and resid 82 through 87 Processing sheet with id=AE4, first strand: chain 't' and resid 11 through 14 removed outlier: 4.071A pdb=" N LYS t 81 " --> pdb=" O VAL t 34 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 't' and resid 67 through 69 Processing sheet with id=AE6, first strand: chain 'u' and resid 65 through 66 removed outlier: 6.387A pdb=" N LYS u 33 " --> pdb=" O VAL u 28 " (cutoff:3.500A) removed outlier: 4.560A pdb=" N VAL u 28 " --> pdb=" O LYS u 33 " (cutoff:3.500A) removed outlier: 6.456A pdb=" N ILE u 35 " --> pdb=" O LYS u 26 " (cutoff:3.500A) removed outlier: 5.940A pdb=" N GLU u 10 " --> pdb=" O PHE u 73 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N ILE u 72 " --> pdb=" O ASP u 81 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'u' and resid 41 through 45 Processing sheet with id=AE8, first strand: chain 'u' and resid 83 through 88 Processing sheet with id=AE9, first strand: chain 'w' and resid 3 through 8 removed outlier: 8.059A pdb=" N ASN w 5 " --> pdb=" O ASP w 43 " (cutoff:3.500A) removed outlier: 5.105A pdb=" N ASP w 43 " --> pdb=" O ASN w 5 " (cutoff:3.500A) removed outlier: 8.688A pdb=" N LYS w 25 " --> pdb=" O GLN w 87 " (cutoff:3.500A) removed outlier: 9.801A pdb=" N ILE w 89 " --> pdb=" O LYS w 25 " (cutoff:3.500A) removed outlier: 8.485A pdb=" N PHE w 91 " --> pdb=" O PRO w 27 " (cutoff:3.500A) removed outlier: 6.187A pdb=" N ILE w 29 " --> pdb=" O PHE w 91 " (cutoff:3.500A) removed outlier: 7.292A pdb=" N ARG w 93 " --> pdb=" O ILE w 29 " (cutoff:3.500A) removed outlier: 7.473A pdb=" N TYR w 31 " --> pdb=" O ARG w 93 " (cutoff:3.500A) removed outlier: 6.591A pdb=" N GLN w 78 " --> pdb=" O GLN w 87 " (cutoff:3.500A) removed outlier: 4.503A pdb=" N ILE w 89 " --> pdb=" O ASP w 76 " (cutoff:3.500A) removed outlier: 6.519A pdb=" N ASP w 76 " --> pdb=" O ILE w 89 " (cutoff:3.500A) removed outlier: 6.809A pdb=" N PHE w 91 " --> pdb=" O ALA w 74 " (cutoff:3.500A) removed outlier: 7.023A pdb=" N ALA w 74 " --> pdb=" O PHE w 91 " (cutoff:3.500A) removed outlier: 6.631A pdb=" N ARG w 93 " --> pdb=" O VAL w 72 " (cutoff:3.500A) removed outlier: 6.162A pdb=" N VAL w 72 " --> pdb=" O ARG w 93 " (cutoff:3.500A) removed outlier: 6.421A pdb=" N ILE w 4 " --> pdb=" O VAL w 64 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'y' and resid 22 through 23 removed outlier: 6.895A pdb=" N LEU y 59 " --> pdb=" O ILE y 37 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'y' and resid 30 through 31 953 hydrogen bonds defined for protein. 2574 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 2374 hydrogen bonds 3684 hydrogen bond angles 0 basepair planarities 967 basepair parallelities 1744 stacking parallelities Total time for adding SS restraints: 161.25 Time building geometry restraints manager: 39.55 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 14516 1.33 - 1.46: 44570 1.46 - 1.58: 33853 1.58 - 1.70: 6187 1.70 - 1.83: 135 Bond restraints: 99261 Sorted by residual: bond pdb=" N GLN j 136 " pdb=" CA GLN j 136 " ideal model delta sigma weight residual 1.458 1.494 -0.036 7.40e-03 1.83e+04 2.41e+01 bond pdb=" N VAL z 148 " pdb=" CA VAL z 148 " ideal model delta sigma weight residual 1.459 1.505 -0.046 1.25e-02 6.40e+03 1.37e+01 bond pdb=" O3' G b 551 " pdb=" P U b 552 " ideal model delta sigma weight residual 1.607 1.661 -0.054 1.50e-02 4.44e+03 1.30e+01 bond pdb=" N ILE z 157 " pdb=" CA ILE z 157 " ideal model delta sigma weight residual 1.457 1.494 -0.037 1.11e-02 8.12e+03 1.13e+01 bond pdb=" C THR z 153 " pdb=" N PRO z 154 " ideal model delta sigma weight residual 1.331 1.372 -0.040 1.20e-02 6.94e+03 1.13e+01 ... (remaining 99256 not shown) Histogram of bond angle deviations from ideal: 97.63 - 104.97: 13964 104.97 - 112.32: 56787 112.32 - 119.66: 35993 119.66 - 127.00: 34681 127.00 - 134.34: 7953 Bond angle restraints: 149378 Sorted by residual: angle pdb=" O3' G b2864 " pdb=" C3' G b2864 " pdb=" C2' G b2864 " ideal model delta sigma weight residual 113.70 126.69 -12.99 1.50e+00 4.44e-01 7.50e+01 angle pdb=" O3' U b 390 " pdb=" C3' U b 390 " pdb=" C2' U b 390 " ideal model delta sigma weight residual 109.50 122.01 -12.51 1.50e+00 4.44e-01 6.96e+01 angle pdb=" O3' C b1595 " pdb=" C3' C b1595 " pdb=" C2' C b1595 " ideal model delta sigma weight residual 113.70 125.58 -11.88 1.50e+00 4.44e-01 6.27e+01 angle pdb=" C4' U b2832 " pdb=" C3' U b2832 " pdb=" O3' U b2832 " ideal model delta sigma weight residual 109.40 121.01 -11.61 1.50e+00 4.44e-01 5.99e+01 angle pdb=" O3' A b1626 " pdb=" C3' A b1626 " pdb=" C2' A b1626 " ideal model delta sigma weight residual 113.70 124.33 -10.63 1.50e+00 4.44e-01 5.02e+01 ... (remaining 149373 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.80: 54143 35.80 - 71.59: 8557 71.59 - 107.39: 883 107.39 - 143.18: 17 143.18 - 178.98: 24 Dihedral angle restraints: 63624 sinusoidal: 54725 harmonic: 8899 Sorted by residual: dihedral pdb=" O4' U b 99 " pdb=" C1' U b 99 " pdb=" N1 U b 99 " pdb=" C2 U b 99 " ideal model delta sinusoidal sigma weight residual 200.00 36.35 163.65 1 1.50e+01 4.44e-03 8.36e+01 dihedral pdb=" O4' U b2884 " pdb=" C1' U b2884 " pdb=" N1 U b2884 " pdb=" C2 U b2884 " ideal model delta sinusoidal sigma weight residual 200.00 37.96 162.04 1 1.50e+01 4.44e-03 8.33e+01 dihedral pdb=" O4' C b2573 " pdb=" C1' C b2573 " pdb=" N1 C b2573 " pdb=" C2 C b2573 " ideal model delta sinusoidal sigma weight residual 200.00 53.15 146.85 1 1.50e+01 4.44e-03 7.84e+01 ... (remaining 63621 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.148: 15183 0.148 - 0.297: 3965 0.297 - 0.445: 43 0.445 - 0.594: 7 0.594 - 0.742: 3 Chirality restraints: 19201 Sorted by residual: chirality pdb=" C3' U b 390 " pdb=" C4' U b 390 " pdb=" O3' U b 390 " pdb=" C2' U b 390 " both_signs ideal model delta sigma weight residual False -2.74 -2.00 -0.74 2.00e-01 2.50e+01 1.38e+01 chirality pdb=" C3' G b2655 " pdb=" C4' G b2655 " pdb=" O3' G b2655 " pdb=" C2' G b2655 " both_signs ideal model delta sigma weight residual False -2.74 -2.07 -0.68 2.00e-01 2.50e+01 1.14e+01 chirality pdb=" C3' G v 1 " pdb=" C4' G v 1 " pdb=" O3' G v 1 " pdb=" C2' G v 1 " both_signs ideal model delta sigma weight residual False -2.48 -1.87 -0.61 2.00e-01 2.50e+01 9.16e+00 ... (remaining 19198 not shown) Planarity restraints: 7378 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR f 83 " -0.031 2.00e-02 2.50e+03 2.27e-02 1.03e+01 pdb=" CG TYR f 83 " 0.054 2.00e-02 2.50e+03 pdb=" CD1 TYR f 83 " -0.008 2.00e-02 2.50e+03 pdb=" CD2 TYR f 83 " 0.002 2.00e-02 2.50e+03 pdb=" CE1 TYR f 83 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 TYR f 83 " -0.010 2.00e-02 2.50e+03 pdb=" CZ TYR f 83 " -0.007 2.00e-02 2.50e+03 pdb=" OH TYR f 83 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLN j 135 " 0.015 2.00e-02 2.50e+03 3.00e-02 8.97e+00 pdb=" C GLN j 135 " -0.052 2.00e-02 2.50e+03 pdb=" O GLN j 135 " 0.019 2.00e-02 2.50e+03 pdb=" N GLN j 136 " 0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP c 213 " -0.028 2.00e-02 2.50e+03 1.77e-02 7.86e+00 pdb=" CG TRP c 213 " 0.047 2.00e-02 2.50e+03 pdb=" CD1 TRP c 213 " -0.010 2.00e-02 2.50e+03 pdb=" CD2 TRP c 213 " -0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP c 213 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP c 213 " -0.002 2.00e-02 2.50e+03 pdb=" CE3 TRP c 213 " 0.003 2.00e-02 2.50e+03 pdb=" CZ2 TRP c 213 " -0.005 2.00e-02 2.50e+03 pdb=" CZ3 TRP c 213 " 0.001 2.00e-02 2.50e+03 pdb=" CH2 TRP c 213 " -0.004 2.00e-02 2.50e+03 ... (remaining 7375 not shown) Histogram of nonbonded interaction distances: 1.81 - 2.43: 71 2.43 - 3.05: 48633 3.05 - 3.67: 170055 3.67 - 4.28: 286378 4.28 - 4.90: 363651 Nonbonded interactions: 868788 Sorted by model distance: nonbonded pdb=" OP2 G b 370 " pdb=" C8 G b 370 " model vdw 1.813 3.260 nonbonded pdb=" O2' C b2601 " pdb=" OP1 A b2602 " model vdw 1.876 2.440 nonbonded pdb=" C8 A b 892 " pdb=" C6 C b 893 " model vdw 1.958 3.560 nonbonded pdb=" OP2 G b 370 " pdb=" N7 G b 370 " model vdw 2.097 3.120 nonbonded pdb=" C2' A b 368 " pdb=" O5' U b 369 " model vdw 2.108 3.470 ... (remaining 868783 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: 3.430 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: 0.080 Extract box with map and model: 14.850 Check model and map are aligned: 1.040 Set scattering table: 0.670 Process input model: 333.550 Find NCS groups from input model: 1.450 Set up NCS constraints: 0.210 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:11.730 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 367.030 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8574 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.072 99261 Z= 0.504 Angle : 1.046 12.994 149378 Z= 0.673 Chirality : 0.106 0.742 19201 Planarity : 0.004 0.068 7378 Dihedral : 25.348 178.977 57895 Min Nonbonded Distance : 1.813 Molprobity Statistics. All-atom Clashscore : 5.05 Ramachandran Plot: Outliers : 0.19 % Allowed : 4.66 % Favored : 95.14 % Rotamer: Outliers : 1.68 % Allowed : 1.49 % Favored : 96.83 % Cbeta Deviations : 0.07 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.45 (0.15), residues: 3087 helix: 0.85 (0.19), residues: 795 sheet: -0.36 (0.19), residues: 699 loop : -0.82 (0.15), residues: 1593 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.047 0.003 TRP c 213 HIS 0.023 0.002 HIS n 16 PHE 0.030 0.002 PHE f 77 TYR 0.054 0.003 TYR f 83 ARG 0.020 0.002 ARG r 21 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6174 Ramachandran restraints generated. 3087 Oldfield, 0 Emsley, 3087 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6174 Ramachandran restraints generated. 3087 Oldfield, 0 Emsley, 3087 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 485 residues out of total 2552 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 442 time to evaluate : 3.842 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: 0 44 LYS cc_start: 0.9031 (mmtm) cc_final: 0.8782 (mmmt) REVERT: 1 24 GLU cc_start: 0.8624 (tp30) cc_final: 0.8213 (tp30) REVERT: 1 49 ASP cc_start: 0.8734 (m-30) cc_final: 0.8247 (m-30) REVERT: 2 37 GLU cc_start: 0.8034 (tp30) cc_final: 0.7803 (tp30) REVERT: d 181 ASP cc_start: 0.8537 (t0) cc_final: 0.8337 (t0) REVERT: e 136 GLN cc_start: 0.9077 (tp-100) cc_final: 0.8841 (tp-100) REVERT: g 130 GLU cc_start: 0.8055 (OUTLIER) cc_final: 0.7661 (mp0) REVERT: n 72 ASP cc_start: 0.8524 (t70) cc_final: 0.8313 (t0) REVERT: o 61 GLN cc_start: 0.8616 (mp10) cc_final: 0.8367 (mp10) REVERT: o 67 ASN cc_start: 0.7570 (OUTLIER) cc_final: 0.7324 (t0) REVERT: o 76 LYS cc_start: 0.9486 (tttm) cc_final: 0.9165 (tttm) REVERT: o 80 GLU cc_start: 0.8600 (mt-10) cc_final: 0.8076 (mt-10) REVERT: s 65 ASP cc_start: 0.7671 (t0) cc_final: 0.6927 (t0) REVERT: s 68 ASP cc_start: 0.8929 (p0) cc_final: 0.8483 (p0) REVERT: t 56 GLU cc_start: 0.8542 (tp30) cc_final: 0.8313 (tp30) REVERT: u 10 GLU cc_start: 0.8446 (tp30) cc_final: 0.8205 (tp30) outliers start: 43 outliers final: 0 residues processed: 468 average time/residue: 2.0837 time to fit residues: 1276.9504 Evaluate side-chains 351 residues out of total 2552 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 349 time to evaluate : 3.783 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain g residue 130 GLU Chi-restraints excluded: chain o residue 67 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 610 random chunks: chunk 515 optimal weight: 7.9990 chunk 462 optimal weight: 10.0000 chunk 256 optimal weight: 10.0000 chunk 157 optimal weight: 40.0000 chunk 311 optimal weight: 10.0000 chunk 247 optimal weight: 10.0000 chunk 478 optimal weight: 9.9990 chunk 185 optimal weight: 10.0000 chunk 290 optimal weight: 10.0000 chunk 355 optimal weight: 9.9990 chunk 553 optimal weight: 6.9990 overall best weight: 8.9992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 1 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 5 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** f 23 ASN ** f 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** g 22 GLN ** g 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** h 33 GLN j 138 GLN k 29 HIS ** m 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** m 22 GLN ** m 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** o 67 ASN ** p 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** r 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** s 31 GLN ** u 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** u 99 ASN w 12 GLN y 76 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8866 moved from start: 0.2504 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.098 99261 Z= 0.427 Angle : 0.700 12.402 149378 Z= 0.359 Chirality : 0.043 0.298 19201 Planarity : 0.006 0.070 7378 Dihedral : 24.479 179.584 51745 Min Nonbonded Distance : 2.042 Molprobity Statistics. All-atom Clashscore : 7.38 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.47 % Favored : 95.43 % Rotamer: Outliers : 1.61 % Allowed : 9.05 % Favored : 89.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.19 (0.15), residues: 3087 helix: 1.13 (0.18), residues: 812 sheet: -0.27 (0.20), residues: 699 loop : -0.68 (0.15), residues: 1576 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP c 213 HIS 0.017 0.002 HIS n 16 PHE 0.019 0.002 PHE f 77 TYR 0.036 0.002 TYR f 83 ARG 0.015 0.001 ARG 8 12 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6174 Ramachandran restraints generated. 3087 Oldfield, 0 Emsley, 3087 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6174 Ramachandran restraints generated. 3087 Oldfield, 0 Emsley, 3087 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 416 residues out of total 2552 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 375 time to evaluate : 3.809 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 0 41 GLU cc_start: 0.8682 (tp30) cc_final: 0.8271 (tp30) REVERT: 0 44 LYS cc_start: 0.9182 (mmtm) cc_final: 0.8782 (mmtm) REVERT: 1 24 GLU cc_start: 0.8626 (tp30) cc_final: 0.8220 (tp30) REVERT: 1 49 ASP cc_start: 0.8772 (m-30) cc_final: 0.8270 (m-30) REVERT: 2 4 THR cc_start: 0.8680 (t) cc_final: 0.8270 (t) REVERT: 3 37 LYS cc_start: 0.9349 (OUTLIER) cc_final: 0.9029 (mmmm) REVERT: 8 30 GLU cc_start: 0.8562 (tp30) cc_final: 0.8305 (tp30) REVERT: e 136 GLN cc_start: 0.8996 (tp-100) cc_final: 0.8790 (tp-100) REVERT: f 83 TYR cc_start: 0.9032 (m-80) cc_final: 0.8495 (m-80) REVERT: g 130 GLU cc_start: 0.8105 (OUTLIER) cc_final: 0.7732 (mp0) REVERT: g 170 ARG cc_start: 0.8490 (OUTLIER) cc_final: 0.7986 (ttp-170) REVERT: h 7 ASP cc_start: 0.8868 (t0) cc_final: 0.8577 (t0) REVERT: h 20 ASN cc_start: 0.8638 (t0) cc_final: 0.8422 (t0) REVERT: j 108 MET cc_start: 0.9178 (mtt) cc_final: 0.8797 (mtt) REVERT: l 69 ARG cc_start: 0.9351 (OUTLIER) cc_final: 0.8766 (ptm-80) REVERT: n 72 ASP cc_start: 0.8480 (t70) cc_final: 0.8119 (t0) REVERT: o 19 GLN cc_start: 0.9339 (tm-30) cc_final: 0.8705 (tm-30) REVERT: o 76 LYS cc_start: 0.9470 (tttm) cc_final: 0.9153 (tttm) REVERT: p 11 GLU cc_start: 0.8011 (mt-10) cc_final: 0.7787 (mt-10) REVERT: s 65 ASP cc_start: 0.7397 (t0) cc_final: 0.6417 (t0) REVERT: s 68 ASP cc_start: 0.8887 (p0) cc_final: 0.8165 (p0) REVERT: t 56 GLU cc_start: 0.8555 (tp30) cc_final: 0.8328 (tp30) REVERT: u 10 GLU cc_start: 0.8509 (tp30) cc_final: 0.8301 (tp30) REVERT: w 25 LYS cc_start: 0.9172 (OUTLIER) cc_final: 0.8757 (mttp) outliers start: 41 outliers final: 22 residues processed: 393 average time/residue: 1.9957 time to fit residues: 1026.7843 Evaluate side-chains 385 residues out of total 2552 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 358 time to evaluate : 3.738 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 56 MET Chi-restraints excluded: chain 3 residue 37 LYS Chi-restraints excluded: chain 4 residue 30 LYS Chi-restraints excluded: chain 4 residue 36 LEU Chi-restraints excluded: chain d residue 103 ASP Chi-restraints excluded: chain f residue 90 THR Chi-restraints excluded: chain g residue 2 SER Chi-restraints excluded: chain g residue 26 ILE Chi-restraints excluded: chain g residue 74 SER Chi-restraints excluded: chain g residue 130 GLU Chi-restraints excluded: chain g residue 170 ARG Chi-restraints excluded: chain h residue 15 LEU Chi-restraints excluded: chain h residue 30 LEU Chi-restraints excluded: chain l residue 69 ARG Chi-restraints excluded: chain l residue 115 GLU Chi-restraints excluded: chain m residue 126 ILE Chi-restraints excluded: chain o residue 54 VAL Chi-restraints excluded: chain o residue 69 ASP Chi-restraints excluded: chain o residue 83 LEU Chi-restraints excluded: chain p residue 5 ILE Chi-restraints excluded: chain r residue 15 SER Chi-restraints excluded: chain r residue 29 THR Chi-restraints excluded: chain r residue 34 GLU Chi-restraints excluded: chain s residue 67 ASP Chi-restraints excluded: chain w residue 12 GLN Chi-restraints excluded: chain w residue 25 LYS Chi-restraints excluded: chain z residue 140 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 610 random chunks: chunk 307 optimal weight: 10.0000 chunk 171 optimal weight: 10.0000 chunk 461 optimal weight: 6.9990 chunk 377 optimal weight: 6.9990 chunk 152 optimal weight: 10.0000 chunk 554 optimal weight: 1.9990 chunk 599 optimal weight: 4.9990 chunk 494 optimal weight: 10.0000 chunk 550 optimal weight: 8.9990 chunk 189 optimal weight: 10.0000 chunk 445 optimal weight: 9.9990 overall best weight: 5.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 1 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 5 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** f 23 ASN ** f 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** g 30 ASN ** g 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** h 33 GLN ** m 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** q 71 GLN ** r 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** s 31 GLN ** u 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8890 moved from start: 0.3312 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.079 99261 Z= 0.288 Angle : 0.571 12.075 149378 Z= 0.305 Chirality : 0.037 0.277 19201 Planarity : 0.005 0.073 7378 Dihedral : 23.914 179.439 51743 Min Nonbonded Distance : 2.046 Molprobity Statistics. All-atom Clashscore : 7.50 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.47 % Favored : 95.43 % Rotamer: Outliers : 1.96 % Allowed : 10.58 % Favored : 87.46 % 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: 0.00 (0.15), residues: 3087 helix: 1.34 (0.18), residues: 825 sheet: -0.13 (0.20), residues: 697 loop : -0.61 (0.15), residues: 1565 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP c 213 HIS 0.012 0.001 HIS n 16 PHE 0.015 0.001 PHE f 77 TYR 0.022 0.001 TYR f 83 ARG 0.010 0.001 ARG t 69 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6174 Ramachandran restraints generated. 3087 Oldfield, 0 Emsley, 3087 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6174 Ramachandran restraints generated. 3087 Oldfield, 0 Emsley, 3087 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 432 residues out of total 2552 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 382 time to evaluate : 3.865 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: 0 41 GLU cc_start: 0.8635 (tp30) cc_final: 0.7945 (tp30) REVERT: 0 44 LYS cc_start: 0.9165 (mmtm) cc_final: 0.8594 (mmtm) REVERT: 1 24 GLU cc_start: 0.8596 (tp30) cc_final: 0.8166 (tp30) REVERT: 1 49 ASP cc_start: 0.8758 (m-30) cc_final: 0.8229 (m-30) REVERT: 2 4 THR cc_start: 0.8510 (t) cc_final: 0.7988 (t) REVERT: 3 37 LYS cc_start: 0.9301 (OUTLIER) cc_final: 0.8969 (mmmm) REVERT: 4 27 LYS cc_start: 0.8926 (mmmm) cc_final: 0.8609 (mmtm) REVERT: 8 30 GLU cc_start: 0.8558 (tp30) cc_final: 0.8301 (tp30) REVERT: f 83 TYR cc_start: 0.9057 (m-10) cc_final: 0.8617 (m-80) REVERT: g 130 GLU cc_start: 0.7959 (mp0) cc_final: 0.7467 (mp0) REVERT: h 7 ASP cc_start: 0.9023 (t0) cc_final: 0.8666 (t0) REVERT: j 108 MET cc_start: 0.9211 (mtt) cc_final: 0.8887 (mtt) REVERT: k 106 GLU cc_start: 0.8788 (mp0) cc_final: 0.8576 (mp0) REVERT: l 69 ARG cc_start: 0.9307 (OUTLIER) cc_final: 0.8664 (ptm-80) REVERT: l 70 LYS cc_start: 0.9371 (OUTLIER) cc_final: 0.9120 (tptt) REVERT: n 72 ASP cc_start: 0.8476 (t70) cc_final: 0.8068 (t0) REVERT: o 19 GLN cc_start: 0.9346 (tm-30) cc_final: 0.8749 (tm-30) REVERT: o 60 GLU cc_start: 0.8271 (pm20) cc_final: 0.7729 (pm20) REVERT: o 76 LYS cc_start: 0.9385 (tttm) cc_final: 0.8961 (tttm) REVERT: q 71 GLN cc_start: 0.8892 (tp40) cc_final: 0.8640 (tm-30) REVERT: r 34 GLU cc_start: 0.8330 (OUTLIER) cc_final: 0.7936 (mp0) REVERT: s 65 ASP cc_start: 0.7271 (t0) cc_final: 0.6490 (t0) REVERT: s 68 ASP cc_start: 0.8959 (p0) cc_final: 0.8185 (p0) REVERT: t 56 GLU cc_start: 0.8515 (tp30) cc_final: 0.8309 (tp30) REVERT: u 10 GLU cc_start: 0.8506 (tp30) cc_final: 0.8284 (tp30) REVERT: u 99 ASN cc_start: 0.8690 (t0) cc_final: 0.7904 (t0) REVERT: w 25 LYS cc_start: 0.9103 (OUTLIER) cc_final: 0.8658 (mttp) outliers start: 50 outliers final: 19 residues processed: 407 average time/residue: 1.9279 time to fit residues: 1034.9365 Evaluate side-chains 384 residues out of total 2552 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 360 time to evaluate : 3.778 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 3 residue 37 LYS Chi-restraints excluded: chain 4 residue 30 LYS Chi-restraints excluded: chain 4 residue 36 LEU Chi-restraints excluded: chain d residue 96 ILE Chi-restraints excluded: chain f residue 90 THR Chi-restraints excluded: chain g residue 2 SER Chi-restraints excluded: chain h residue 4 ILE Chi-restraints excluded: chain h residue 15 LEU Chi-restraints excluded: chain h residue 30 LEU Chi-restraints excluded: chain l residue 69 ARG Chi-restraints excluded: chain l residue 70 LYS Chi-restraints excluded: chain m residue 126 ILE Chi-restraints excluded: chain o residue 54 VAL Chi-restraints excluded: chain o residue 58 ILE Chi-restraints excluded: chain o residue 69 ASP Chi-restraints excluded: chain p residue 4 ILE Chi-restraints excluded: chain p residue 5 ILE Chi-restraints excluded: chain r residue 15 SER Chi-restraints excluded: chain r residue 29 THR Chi-restraints excluded: chain r residue 34 GLU Chi-restraints excluded: chain s residue 66 ILE Chi-restraints excluded: chain s residue 67 ASP Chi-restraints excluded: chain w residue 25 LYS Chi-restraints excluded: chain z residue 140 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 610 random chunks: chunk 548 optimal weight: 10.0000 chunk 417 optimal weight: 10.0000 chunk 288 optimal weight: 10.0000 chunk 61 optimal weight: 20.0000 chunk 264 optimal weight: 70.0000 chunk 372 optimal weight: 7.9990 chunk 556 optimal weight: 6.9990 chunk 589 optimal weight: 7.9990 chunk 290 optimal weight: 10.0000 chunk 527 optimal weight: 8.9990 chunk 158 optimal weight: 50.0000 overall best weight: 8.3992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: e 62 GLN f 23 ASN ** f 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** g 101 ASN g 116 GLN ** h 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** h 33 GLN ** m 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** o 43 ASN ** p 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** r 11 GLN s 31 GLN ** u 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** w 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8934 moved from start: 0.3662 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.078 99261 Z= 0.388 Angle : 0.616 15.125 149378 Z= 0.325 Chirality : 0.040 0.307 19201 Planarity : 0.005 0.075 7378 Dihedral : 23.785 179.916 51740 Min Nonbonded Distance : 2.020 Molprobity Statistics. All-atom Clashscore : 7.48 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.63 % Favored : 95.27 % Rotamer: Outliers : 2.04 % Allowed : 11.40 % Favored : 86.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.02 (0.15), residues: 3087 helix: 1.31 (0.18), residues: 814 sheet: -0.03 (0.20), residues: 685 loop : -0.61 (0.15), residues: 1588 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP c 213 HIS 0.013 0.001 HIS n 16 PHE 0.019 0.002 PHE f 77 TYR 0.018 0.002 TYR f 7 ARG 0.013 0.001 ARG 8 12 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6174 Ramachandran restraints generated. 3087 Oldfield, 0 Emsley, 3087 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6174 Ramachandran restraints generated. 3087 Oldfield, 0 Emsley, 3087 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 420 residues out of total 2552 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 368 time to evaluate : 3.957 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 0 41 GLU cc_start: 0.8652 (tp30) cc_final: 0.7996 (tp30) REVERT: 0 44 LYS cc_start: 0.9160 (mmtm) cc_final: 0.8577 (mmtm) REVERT: 1 24 GLU cc_start: 0.8594 (tp30) cc_final: 0.8176 (tp30) REVERT: 1 45 GLN cc_start: 0.8833 (mt0) cc_final: 0.8324 (mt0) REVERT: 1 49 ASP cc_start: 0.8793 (m-30) cc_final: 0.8277 (m-30) REVERT: 3 37 LYS cc_start: 0.9336 (OUTLIER) cc_final: 0.8993 (mmmm) REVERT: 3 46 ASP cc_start: 0.8497 (t0) cc_final: 0.8041 (t0) REVERT: 8 30 GLU cc_start: 0.8593 (tp30) cc_final: 0.8272 (tp30) REVERT: c 90 ASN cc_start: 0.9080 (OUTLIER) cc_final: 0.8792 (p0) REVERT: c 225 MET cc_start: 0.9294 (mtt) cc_final: 0.8997 (mtt) REVERT: f 83 TYR cc_start: 0.9031 (m-10) cc_final: 0.8641 (m-80) REVERT: g 130 GLU cc_start: 0.7910 (mp0) cc_final: 0.7478 (mp0) REVERT: h 7 ASP cc_start: 0.9050 (t0) cc_final: 0.8618 (t0) REVERT: j 108 MET cc_start: 0.9205 (mtt) cc_final: 0.8902 (mtt) REVERT: l 69 ARG cc_start: 0.9362 (OUTLIER) cc_final: 0.8672 (ptm-80) REVERT: l 70 LYS cc_start: 0.9376 (OUTLIER) cc_final: 0.9103 (ttpt) REVERT: o 19 GLN cc_start: 0.9366 (tm-30) cc_final: 0.8769 (tm-30) REVERT: o 60 GLU cc_start: 0.8372 (pm20) cc_final: 0.8085 (pm20) REVERT: o 76 LYS cc_start: 0.9431 (tttm) cc_final: 0.9130 (tttm) REVERT: q 71 GLN cc_start: 0.8927 (tp40) cc_final: 0.8682 (tm-30) REVERT: r 34 GLU cc_start: 0.8337 (OUTLIER) cc_final: 0.7978 (mp0) REVERT: s 65 ASP cc_start: 0.7524 (t0) cc_final: 0.7001 (t0) REVERT: s 68 ASP cc_start: 0.8911 (p0) cc_final: 0.8261 (p0) REVERT: t 56 GLU cc_start: 0.8543 (tp30) cc_final: 0.8323 (tp30) REVERT: u 99 ASN cc_start: 0.8601 (t0) cc_final: 0.8179 (t0) REVERT: w 25 LYS cc_start: 0.9190 (OUTLIER) cc_final: 0.8756 (mttp) outliers start: 52 outliers final: 22 residues processed: 397 average time/residue: 1.9375 time to fit residues: 1018.6428 Evaluate side-chains 390 residues out of total 2552 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 362 time to evaluate : 3.811 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 3 residue 37 LYS Chi-restraints excluded: chain 4 residue 30 LYS Chi-restraints excluded: chain 4 residue 36 LEU Chi-restraints excluded: chain 4 residue 37 LYS Chi-restraints excluded: chain c residue 90 ASN Chi-restraints excluded: chain f residue 90 THR Chi-restraints excluded: chain g residue 2 SER Chi-restraints excluded: chain h residue 4 ILE Chi-restraints excluded: chain h residue 15 LEU Chi-restraints excluded: chain h residue 30 LEU Chi-restraints excluded: chain j residue 131 ASN Chi-restraints excluded: chain l residue 69 ARG Chi-restraints excluded: chain l residue 70 LYS Chi-restraints excluded: chain l residue 120 VAL Chi-restraints excluded: chain m residue 126 ILE Chi-restraints excluded: chain n residue 57 THR Chi-restraints excluded: chain o residue 54 VAL Chi-restraints excluded: chain o residue 69 ASP Chi-restraints excluded: chain p residue 4 ILE Chi-restraints excluded: chain p residue 5 ILE Chi-restraints excluded: chain r residue 29 THR Chi-restraints excluded: chain r residue 34 GLU Chi-restraints excluded: chain s residue 66 ILE Chi-restraints excluded: chain s residue 67 ASP Chi-restraints excluded: chain w residue 25 LYS Chi-restraints excluded: chain z residue 140 SER Chi-restraints excluded: chain z residue 146 PHE Chi-restraints excluded: chain z residue 150 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 610 random chunks: chunk 491 optimal weight: 8.9990 chunk 334 optimal weight: 10.0000 chunk 8 optimal weight: 5.9990 chunk 439 optimal weight: 10.0000 chunk 243 optimal weight: 20.0000 chunk 503 optimal weight: 6.9990 chunk 407 optimal weight: 9.9990 chunk 0 optimal weight: 10.0000 chunk 301 optimal weight: 10.0000 chunk 529 optimal weight: 6.9990 chunk 148 optimal weight: 10.0000 overall best weight: 7.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: e 115 GLN f 23 ASN ** f 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** h 33 GLN j 138 GLN ** m 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** r 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** s 31 GLN ** u 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** w 12 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8929 moved from start: 0.3855 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.068 99261 Z= 0.352 Angle : 0.585 14.975 149378 Z= 0.310 Chirality : 0.039 0.299 19201 Planarity : 0.005 0.075 7378 Dihedral : 23.689 179.974 51740 Min Nonbonded Distance : 2.040 Molprobity Statistics. All-atom Clashscore : 7.31 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.60 % Favored : 95.30 % Rotamer: Outliers : 2.08 % Allowed : 12.34 % Favored : 85.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.09 (0.15), residues: 3087 helix: 1.39 (0.18), residues: 814 sheet: 0.01 (0.20), residues: 688 loop : -0.58 (0.15), residues: 1585 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP c 213 HIS 0.011 0.001 HIS n 16 PHE 0.016 0.001 PHE f 77 TYR 0.018 0.001 TYR f 143 ARG 0.014 0.001 ARG j 96 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6174 Ramachandran restraints generated. 3087 Oldfield, 0 Emsley, 3087 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6174 Ramachandran restraints generated. 3087 Oldfield, 0 Emsley, 3087 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 426 residues out of total 2552 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 373 time to evaluate : 3.816 Fit side-chains revert: symmetry clash REVERT: 0 41 GLU cc_start: 0.8653 (tp30) cc_final: 0.7958 (tp30) REVERT: 0 44 LYS cc_start: 0.9159 (mmtm) cc_final: 0.8570 (mmtm) REVERT: 1 24 GLU cc_start: 0.8533 (tp30) cc_final: 0.8109 (tp30) REVERT: 1 49 ASP cc_start: 0.8772 (m-30) cc_final: 0.8244 (m-30) REVERT: 3 37 LYS cc_start: 0.9338 (OUTLIER) cc_final: 0.9035 (mmmm) REVERT: 3 46 ASP cc_start: 0.8510 (t0) cc_final: 0.8043 (t0) REVERT: 4 50 LYS cc_start: 0.8874 (OUTLIER) cc_final: 0.8235 (mtpp) REVERT: 8 30 GLU cc_start: 0.8622 (tp30) cc_final: 0.8315 (tp30) REVERT: c 90 ASN cc_start: 0.9128 (OUTLIER) cc_final: 0.8866 (p0) REVERT: f 83 TYR cc_start: 0.8996 (m-10) cc_final: 0.8636 (m-80) REVERT: g 130 GLU cc_start: 0.7894 (mp0) cc_final: 0.7513 (mp0) REVERT: h 7 ASP cc_start: 0.9065 (t0) cc_final: 0.8658 (t0) REVERT: j 108 MET cc_start: 0.9204 (mtt) cc_final: 0.8931 (mtt) REVERT: l 69 ARG cc_start: 0.9350 (OUTLIER) cc_final: 0.8649 (ptm-80) REVERT: l 70 LYS cc_start: 0.9400 (OUTLIER) cc_final: 0.8858 (ttpp) REVERT: o 19 GLN cc_start: 0.9368 (tm-30) cc_final: 0.8780 (tm-30) REVERT: o 60 GLU cc_start: 0.8533 (pm20) cc_final: 0.7964 (pm20) REVERT: o 76 LYS cc_start: 0.9463 (tttm) cc_final: 0.9164 (tttm) REVERT: o 80 GLU cc_start: 0.8612 (mt-10) cc_final: 0.8110 (mt-10) REVERT: q 71 GLN cc_start: 0.8916 (tp40) cc_final: 0.8678 (tm-30) REVERT: r 34 GLU cc_start: 0.8347 (OUTLIER) cc_final: 0.7973 (mp0) REVERT: s 65 ASP cc_start: 0.7552 (t0) cc_final: 0.5877 (t0) REVERT: s 68 ASP cc_start: 0.8927 (p0) cc_final: 0.8219 (p0) REVERT: t 56 GLU cc_start: 0.8545 (tp30) cc_final: 0.8330 (tp30) REVERT: u 99 ASN cc_start: 0.8642 (t0) cc_final: 0.8355 (t0) REVERT: w 25 LYS cc_start: 0.9142 (OUTLIER) cc_final: 0.8690 (mttp) outliers start: 53 outliers final: 24 residues processed: 407 average time/residue: 1.9249 time to fit residues: 1038.8320 Evaluate side-chains 398 residues out of total 2552 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 367 time to evaluate : 3.757 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 57 VAL Chi-restraints excluded: chain 3 residue 37 LYS Chi-restraints excluded: chain 4 residue 29 THR Chi-restraints excluded: chain 4 residue 36 LEU Chi-restraints excluded: chain 4 residue 50 LYS Chi-restraints excluded: chain c residue 90 ASN Chi-restraints excluded: chain f residue 90 THR Chi-restraints excluded: chain g residue 2 SER Chi-restraints excluded: chain g residue 15 VAL Chi-restraints excluded: chain h residue 4 ILE Chi-restraints excluded: chain h residue 15 LEU Chi-restraints excluded: chain h residue 22 LYS Chi-restraints excluded: chain h residue 30 LEU Chi-restraints excluded: chain j residue 131 ASN Chi-restraints excluded: chain l residue 69 ARG Chi-restraints excluded: chain l residue 70 LYS Chi-restraints excluded: chain l residue 76 GLU Chi-restraints excluded: chain m residue 126 ILE Chi-restraints excluded: chain n residue 57 THR Chi-restraints excluded: chain o residue 54 VAL Chi-restraints excluded: chain o residue 69 ASP Chi-restraints excluded: chain p residue 4 ILE Chi-restraints excluded: chain p residue 5 ILE Chi-restraints excluded: chain r residue 15 SER Chi-restraints excluded: chain r residue 29 THR Chi-restraints excluded: chain r residue 34 GLU Chi-restraints excluded: chain s residue 66 ILE Chi-restraints excluded: chain u residue 83 VAL Chi-restraints excluded: chain w residue 12 GLN Chi-restraints excluded: chain w residue 25 LYS Chi-restraints excluded: chain z residue 146 PHE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 610 random chunks: chunk 198 optimal weight: 10.0000 chunk 530 optimal weight: 0.8980 chunk 116 optimal weight: 10.0000 chunk 346 optimal weight: 2.9990 chunk 145 optimal weight: 10.0000 chunk 590 optimal weight: 7.9990 chunk 489 optimal weight: 20.0000 chunk 273 optimal weight: 20.0000 chunk 49 optimal weight: 10.0000 chunk 195 optimal weight: 10.0000 chunk 309 optimal weight: 10.0000 overall best weight: 6.3792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: f 23 ASN ** f 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** g 30 ASN ** g 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** g 101 ASN g 116 GLN h 20 ASN ** m 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** o 61 GLN ** o 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** r 11 GLN r 12 HIS r 43 ASN s 31 GLN ** u 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8924 moved from start: 0.3948 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.058 99261 Z= 0.297 Angle : 0.568 14.971 149378 Z= 0.301 Chirality : 0.037 0.296 19201 Planarity : 0.005 0.072 7378 Dihedral : 23.653 179.653 51740 Min Nonbonded Distance : 2.054 Molprobity Statistics. All-atom Clashscore : 7.39 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.63 % Favored : 95.27 % Rotamer: Outliers : 2.19 % Allowed : 12.97 % Favored : 84.84 % 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: 0.16 (0.15), residues: 3087 helix: 1.49 (0.19), residues: 816 sheet: 0.02 (0.20), residues: 694 loop : -0.55 (0.15), residues: 1577 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP c 213 HIS 0.009 0.001 HIS n 16 PHE 0.015 0.001 PHE f 77 TYR 0.021 0.001 TYR f 143 ARG 0.017 0.001 ARG 8 12 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6174 Ramachandran restraints generated. 3087 Oldfield, 0 Emsley, 3087 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6174 Ramachandran restraints generated. 3087 Oldfield, 0 Emsley, 3087 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 426 residues out of total 2552 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 370 time to evaluate : 4.009 Fit side-chains revert: symmetry clash REVERT: 0 41 GLU cc_start: 0.8625 (tp30) cc_final: 0.7920 (tp30) REVERT: 0 44 LYS cc_start: 0.9158 (mmtm) cc_final: 0.8558 (mmtm) REVERT: 1 24 GLU cc_start: 0.8529 (tp30) cc_final: 0.8130 (tp30) REVERT: 1 49 ASP cc_start: 0.8769 (m-30) cc_final: 0.8235 (m-30) REVERT: 3 37 LYS cc_start: 0.9306 (OUTLIER) cc_final: 0.8956 (mmmm) REVERT: 3 46 ASP cc_start: 0.8507 (t0) cc_final: 0.8017 (t0) REVERT: 4 7 GLU cc_start: 0.7873 (pp20) cc_final: 0.7576 (pp20) REVERT: 4 27 LYS cc_start: 0.8950 (mmmm) cc_final: 0.8567 (mmtm) REVERT: 4 50 LYS cc_start: 0.8858 (OUTLIER) cc_final: 0.8131 (mtpp) REVERT: c 90 ASN cc_start: 0.9139 (OUTLIER) cc_final: 0.8868 (p0) REVERT: f 83 TYR cc_start: 0.8993 (m-10) cc_final: 0.8739 (m-80) REVERT: g 130 GLU cc_start: 0.7877 (mp0) cc_final: 0.7538 (mp0) REVERT: h 7 ASP cc_start: 0.9060 (t0) cc_final: 0.8608 (t0) REVERT: j 108 MET cc_start: 0.9215 (mtt) cc_final: 0.8935 (mtt) REVERT: k 20 MET cc_start: 0.8789 (ttm) cc_final: 0.8337 (ttt) REVERT: l 69 ARG cc_start: 0.9337 (OUTLIER) cc_final: 0.8608 (ptm-80) REVERT: m 110 GLU cc_start: 0.8852 (OUTLIER) cc_final: 0.8646 (tt0) REVERT: o 19 GLN cc_start: 0.9368 (tm-30) cc_final: 0.8783 (tm-30) REVERT: o 76 LYS cc_start: 0.9468 (tttm) cc_final: 0.9155 (tttm) REVERT: o 116 GLN cc_start: 0.8699 (mm-40) cc_final: 0.8302 (mp10) REVERT: q 71 GLN cc_start: 0.8939 (tp40) cc_final: 0.8689 (tm-30) REVERT: r 34 GLU cc_start: 0.8344 (OUTLIER) cc_final: 0.7927 (mp0) REVERT: s 65 ASP cc_start: 0.7179 (t70) cc_final: 0.6644 (t70) REVERT: t 56 GLU cc_start: 0.8547 (tp30) cc_final: 0.8309 (tp30) REVERT: t 69 ARG cc_start: 0.8354 (OUTLIER) cc_final: 0.7862 (tpt90) REVERT: u 9 ASP cc_start: 0.8899 (m-30) cc_final: 0.8673 (m-30) REVERT: u 99 ASN cc_start: 0.8626 (t0) cc_final: 0.8351 (t0) REVERT: w 25 LYS cc_start: 0.9140 (OUTLIER) cc_final: 0.8692 (mttp) outliers start: 56 outliers final: 27 residues processed: 402 average time/residue: 1.9431 time to fit residues: 1036.3794 Evaluate side-chains 402 residues out of total 2552 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 367 time to evaluate : 3.765 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 57 VAL Chi-restraints excluded: chain 3 residue 37 LYS Chi-restraints excluded: chain 4 residue 30 LYS Chi-restraints excluded: chain 4 residue 36 LEU Chi-restraints excluded: chain 4 residue 37 LYS Chi-restraints excluded: chain 4 residue 50 LYS Chi-restraints excluded: chain c residue 90 ASN Chi-restraints excluded: chain d residue 60 VAL Chi-restraints excluded: chain f residue 90 THR Chi-restraints excluded: chain g residue 2 SER Chi-restraints excluded: chain g residue 15 VAL Chi-restraints excluded: chain h residue 4 ILE Chi-restraints excluded: chain h residue 15 LEU Chi-restraints excluded: chain h residue 30 LEU Chi-restraints excluded: chain j residue 131 ASN Chi-restraints excluded: chain l residue 69 ARG Chi-restraints excluded: chain l residue 76 GLU Chi-restraints excluded: chain l residue 121 THR Chi-restraints excluded: chain m residue 1 MET Chi-restraints excluded: chain m residue 110 GLU Chi-restraints excluded: chain m residue 126 ILE Chi-restraints excluded: chain n residue 57 THR Chi-restraints excluded: chain o residue 24 THR Chi-restraints excluded: chain o residue 54 VAL Chi-restraints excluded: chain o residue 55 GLU Chi-restraints excluded: chain o residue 69 ASP Chi-restraints excluded: chain p residue 4 ILE Chi-restraints excluded: chain p residue 5 ILE Chi-restraints excluded: chain r residue 34 GLU Chi-restraints excluded: chain s residue 66 ILE Chi-restraints excluded: chain t residue 69 ARG Chi-restraints excluded: chain u residue 83 VAL Chi-restraints excluded: chain w residue 25 LYS Chi-restraints excluded: chain z residue 146 PHE Chi-restraints excluded: chain z residue 150 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 610 random chunks: chunk 569 optimal weight: 9.9990 chunk 66 optimal weight: 20.0000 chunk 336 optimal weight: 10.0000 chunk 431 optimal weight: 20.0000 chunk 333 optimal weight: 10.0000 chunk 496 optimal weight: 9.9990 chunk 329 optimal weight: 10.0000 chunk 587 optimal weight: 3.9990 chunk 367 optimal weight: 9.9990 chunk 358 optimal weight: 10.0000 chunk 271 optimal weight: 20.0000 overall best weight: 8.7992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** f 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** g 101 ASN ** h 2 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** r 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** s 31 GLN ** u 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** w 12 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8945 moved from start: 0.4007 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.084 99261 Z= 0.398 Angle : 0.612 16.672 149378 Z= 0.323 Chirality : 0.040 0.310 19201 Planarity : 0.005 0.075 7378 Dihedral : 23.624 179.799 51740 Min Nonbonded Distance : 2.024 Molprobity Statistics. All-atom Clashscore : 7.33 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.63 % Favored : 95.30 % Rotamer: Outliers : 2.31 % Allowed : 13.40 % Favored : 84.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.08 (0.15), residues: 3087 helix: 1.43 (0.18), residues: 815 sheet: -0.06 (0.20), residues: 698 loop : -0.58 (0.15), residues: 1574 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP c 213 HIS 0.011 0.001 HIS n 16 PHE 0.018 0.001 PHE f 77 TYR 0.021 0.002 TYR f 143 ARG 0.013 0.001 ARG y 11 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6174 Ramachandran restraints generated. 3087 Oldfield, 0 Emsley, 3087 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6174 Ramachandran restraints generated. 3087 Oldfield, 0 Emsley, 3087 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 426 residues out of total 2552 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 367 time to evaluate : 3.889 Fit side-chains revert: symmetry clash REVERT: 0 41 GLU cc_start: 0.8611 (tp30) cc_final: 0.7920 (tp30) REVERT: 0 44 LYS cc_start: 0.9133 (mmtm) cc_final: 0.8422 (mmtm) REVERT: 1 24 GLU cc_start: 0.8549 (tp30) cc_final: 0.8097 (tp30) REVERT: 1 49 ASP cc_start: 0.8796 (m-30) cc_final: 0.8276 (m-30) REVERT: 3 37 LYS cc_start: 0.9341 (OUTLIER) cc_final: 0.9056 (mmmm) REVERT: 3 46 ASP cc_start: 0.8485 (t0) cc_final: 0.8002 (t0) REVERT: 4 7 GLU cc_start: 0.7890 (pp20) cc_final: 0.7374 (pp20) REVERT: 4 27 LYS cc_start: 0.8934 (mmmm) cc_final: 0.8597 (mmmm) REVERT: 4 50 LYS cc_start: 0.8884 (OUTLIER) cc_final: 0.8228 (mtpp) REVERT: 8 30 GLU cc_start: 0.8613 (mm-30) cc_final: 0.8190 (tp30) REVERT: c 90 ASN cc_start: 0.9063 (OUTLIER) cc_final: 0.8765 (p0) REVERT: f 83 TYR cc_start: 0.9001 (m-10) cc_final: 0.8780 (m-80) REVERT: g 130 GLU cc_start: 0.7897 (mp0) cc_final: 0.7551 (mp0) REVERT: h 5 LEU cc_start: 0.8536 (OUTLIER) cc_final: 0.8238 (tt) REVERT: h 7 ASP cc_start: 0.9084 (t0) cc_final: 0.8547 (t0) REVERT: j 108 MET cc_start: 0.9225 (mtt) cc_final: 0.8954 (mtt) REVERT: l 69 ARG cc_start: 0.9351 (OUTLIER) cc_final: 0.8636 (ptm-80) REVERT: l 70 LYS cc_start: 0.9412 (OUTLIER) cc_final: 0.9122 (ttpt) REVERT: l 115 GLU cc_start: 0.7749 (pm20) cc_final: 0.7514 (pm20) REVERT: o 19 GLN cc_start: 0.9375 (tm-30) cc_final: 0.8794 (tm-30) REVERT: o 56 LYS cc_start: 0.9052 (mtmm) cc_final: 0.8843 (ttpp) REVERT: o 60 GLU cc_start: 0.8465 (OUTLIER) cc_final: 0.8089 (pm20) REVERT: o 76 LYS cc_start: 0.9481 (tttm) cc_final: 0.9216 (tttm) REVERT: o 116 GLN cc_start: 0.8775 (mm-40) cc_final: 0.8266 (mp10) REVERT: q 71 GLN cc_start: 0.8930 (tp40) cc_final: 0.8682 (tm-30) REVERT: r 60 LYS cc_start: 0.9214 (OUTLIER) cc_final: 0.8904 (mmtp) REVERT: s 65 ASP cc_start: 0.7264 (t70) cc_final: 0.7054 (t0) REVERT: t 56 GLU cc_start: 0.8562 (tp30) cc_final: 0.8321 (tp30) REVERT: t 69 ARG cc_start: 0.8397 (OUTLIER) cc_final: 0.7896 (tpt90) REVERT: u 9 ASP cc_start: 0.8922 (m-30) cc_final: 0.8721 (m-30) REVERT: u 99 ASN cc_start: 0.8661 (t0) cc_final: 0.8336 (t0) REVERT: w 25 LYS cc_start: 0.9172 (OUTLIER) cc_final: 0.8729 (mttp) outliers start: 59 outliers final: 31 residues processed: 404 average time/residue: 1.9223 time to fit residues: 1025.3707 Evaluate side-chains 405 residues out of total 2552 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 364 time to evaluate : 3.820 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 57 VAL Chi-restraints excluded: chain 3 residue 37 LYS Chi-restraints excluded: chain 4 residue 30 LYS Chi-restraints excluded: chain 4 residue 36 LEU Chi-restraints excluded: chain 4 residue 37 LYS Chi-restraints excluded: chain 4 residue 50 LYS Chi-restraints excluded: chain c residue 90 ASN Chi-restraints excluded: chain d residue 60 VAL Chi-restraints excluded: chain f residue 23 ASN Chi-restraints excluded: chain f residue 90 THR Chi-restraints excluded: chain g residue 2 SER Chi-restraints excluded: chain g residue 15 VAL Chi-restraints excluded: chain h residue 5 LEU Chi-restraints excluded: chain h residue 15 LEU Chi-restraints excluded: chain h residue 30 LEU Chi-restraints excluded: chain j residue 131 ASN Chi-restraints excluded: chain l residue 69 ARG Chi-restraints excluded: chain l residue 70 LYS Chi-restraints excluded: chain l residue 76 GLU Chi-restraints excluded: chain l residue 121 THR Chi-restraints excluded: chain m residue 1 MET Chi-restraints excluded: chain m residue 126 ILE Chi-restraints excluded: chain n residue 57 THR Chi-restraints excluded: chain o residue 24 THR Chi-restraints excluded: chain o residue 54 VAL Chi-restraints excluded: chain o residue 55 GLU Chi-restraints excluded: chain o residue 60 GLU Chi-restraints excluded: chain o residue 69 ASP Chi-restraints excluded: chain p residue 4 ILE Chi-restraints excluded: chain p residue 5 ILE Chi-restraints excluded: chain r residue 15 SER Chi-restraints excluded: chain r residue 29 THR Chi-restraints excluded: chain r residue 60 LYS Chi-restraints excluded: chain s residue 66 ILE Chi-restraints excluded: chain s residue 67 ASP Chi-restraints excluded: chain t residue 69 ARG Chi-restraints excluded: chain u residue 83 VAL Chi-restraints excluded: chain w residue 25 LYS Chi-restraints excluded: chain y residue 70 GLU Chi-restraints excluded: chain z residue 146 PHE Chi-restraints excluded: chain z residue 150 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 610 random chunks: chunk 363 optimal weight: 10.0000 chunk 234 optimal weight: 10.0000 chunk 351 optimal weight: 9.9990 chunk 177 optimal weight: 10.0000 chunk 115 optimal weight: 10.0000 chunk 113 optimal weight: 10.0000 chunk 373 optimal weight: 10.0000 chunk 400 optimal weight: 10.0000 chunk 290 optimal weight: 10.0000 chunk 54 optimal weight: 10.0000 chunk 462 optimal weight: 9.9990 overall best weight: 9.9996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** f 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** g 101 ASN g 116 GLN h 2 GLN ** m 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** r 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** r 12 HIS s 31 GLN ** u 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** w 12 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8956 moved from start: 0.4120 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.081 99261 Z= 0.445 Angle : 0.643 18.311 149378 Z= 0.339 Chirality : 0.042 0.316 19201 Planarity : 0.005 0.089 7378 Dihedral : 23.650 179.596 51740 Min Nonbonded Distance : 2.012 Molprobity Statistics. All-atom Clashscore : 7.65 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.79 % Favored : 95.14 % Rotamer: Outliers : 2.00 % Allowed : 14.26 % Favored : 83.74 % 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: -0.03 (0.15), residues: 3087 helix: 1.32 (0.18), residues: 814 sheet: -0.06 (0.20), residues: 686 loop : -0.67 (0.15), residues: 1587 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP c 213 HIS 0.011 0.001 HIS n 16 PHE 0.017 0.002 PHE f 77 TYR 0.022 0.002 TYR f 143 ARG 0.021 0.001 ARG 8 12 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6174 Ramachandran restraints generated. 3087 Oldfield, 0 Emsley, 3087 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6174 Ramachandran restraints generated. 3087 Oldfield, 0 Emsley, 3087 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 418 residues out of total 2552 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 367 time to evaluate : 3.870 Fit side-chains revert: symmetry clash REVERT: 0 41 GLU cc_start: 0.8606 (tp30) cc_final: 0.7941 (tp30) REVERT: 0 44 LYS cc_start: 0.9145 (mmtm) cc_final: 0.8454 (mmtm) REVERT: 1 24 GLU cc_start: 0.8539 (tp30) cc_final: 0.8088 (tp30) REVERT: 1 49 ASP cc_start: 0.8795 (m-30) cc_final: 0.8279 (m-30) REVERT: 3 37 LYS cc_start: 0.9357 (OUTLIER) cc_final: 0.9070 (mmmm) REVERT: 3 46 ASP cc_start: 0.8565 (t0) cc_final: 0.8071 (t0) REVERT: 4 7 GLU cc_start: 0.7856 (pp20) cc_final: 0.7517 (pp20) REVERT: 4 50 LYS cc_start: 0.8912 (OUTLIER) cc_final: 0.8235 (mtpp) REVERT: 8 30 GLU cc_start: 0.8635 (mm-30) cc_final: 0.8190 (tp30) REVERT: c 90 ASN cc_start: 0.9063 (OUTLIER) cc_final: 0.8762 (p0) REVERT: f 83 TYR cc_start: 0.8962 (m-10) cc_final: 0.8760 (m-80) REVERT: g 130 GLU cc_start: 0.7930 (mp0) cc_final: 0.7553 (mp0) REVERT: h 5 LEU cc_start: 0.8466 (OUTLIER) cc_final: 0.8175 (tt) REVERT: h 7 ASP cc_start: 0.9104 (t0) cc_final: 0.8613 (t0) REVERT: j 108 MET cc_start: 0.9204 (mtt) cc_final: 0.8948 (mtt) REVERT: l 69 ARG cc_start: 0.9381 (OUTLIER) cc_final: 0.8716 (ptm-80) REVERT: l 70 LYS cc_start: 0.9393 (OUTLIER) cc_final: 0.9147 (ttpt) REVERT: o 19 GLN cc_start: 0.9382 (tm-30) cc_final: 0.8801 (tm-30) REVERT: o 76 LYS cc_start: 0.9465 (tttm) cc_final: 0.9173 (tttm) REVERT: s 65 ASP cc_start: 0.7108 (t70) cc_final: 0.6627 (t70) REVERT: s 68 ASP cc_start: 0.8448 (p0) cc_final: 0.8004 (p0) REVERT: t 56 GLU cc_start: 0.8577 (tp30) cc_final: 0.8334 (tp30) REVERT: t 69 ARG cc_start: 0.8393 (OUTLIER) cc_final: 0.7944 (tpt90) REVERT: u 9 ASP cc_start: 0.8993 (m-30) cc_final: 0.8680 (m-30) REVERT: u 99 ASN cc_start: 0.8745 (t0) cc_final: 0.8411 (t0) REVERT: w 25 LYS cc_start: 0.9171 (OUTLIER) cc_final: 0.8721 (mttp) outliers start: 51 outliers final: 28 residues processed: 397 average time/residue: 1.9662 time to fit residues: 1034.5822 Evaluate side-chains 401 residues out of total 2552 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 365 time to evaluate : 3.752 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 57 VAL Chi-restraints excluded: chain 3 residue 37 LYS Chi-restraints excluded: chain 4 residue 30 LYS Chi-restraints excluded: chain 4 residue 36 LEU Chi-restraints excluded: chain 4 residue 50 LYS Chi-restraints excluded: chain c residue 90 ASN Chi-restraints excluded: chain f residue 90 THR Chi-restraints excluded: chain g residue 2 SER Chi-restraints excluded: chain g residue 15 VAL Chi-restraints excluded: chain g residue 26 ILE Chi-restraints excluded: chain h residue 5 LEU Chi-restraints excluded: chain h residue 15 LEU Chi-restraints excluded: chain h residue 22 LYS Chi-restraints excluded: chain h residue 30 LEU Chi-restraints excluded: chain j residue 131 ASN Chi-restraints excluded: chain l residue 69 ARG Chi-restraints excluded: chain l residue 70 LYS Chi-restraints excluded: chain l residue 76 GLU Chi-restraints excluded: chain l residue 121 THR Chi-restraints excluded: chain m residue 1 MET Chi-restraints excluded: chain m residue 126 ILE Chi-restraints excluded: chain n residue 57 THR Chi-restraints excluded: chain o residue 24 THR Chi-restraints excluded: chain o residue 54 VAL Chi-restraints excluded: chain o residue 69 ASP Chi-restraints excluded: chain p residue 4 ILE Chi-restraints excluded: chain p residue 5 ILE Chi-restraints excluded: chain r residue 15 SER Chi-restraints excluded: chain r residue 29 THR Chi-restraints excluded: chain s residue 66 ILE Chi-restraints excluded: chain t residue 69 ARG Chi-restraints excluded: chain u residue 83 VAL Chi-restraints excluded: chain w residue 25 LYS Chi-restraints excluded: chain y residue 70 GLU Chi-restraints excluded: chain z residue 146 PHE Chi-restraints excluded: chain z residue 150 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 610 random chunks: chunk 534 optimal weight: 4.9990 chunk 563 optimal weight: 9.9990 chunk 513 optimal weight: 5.9990 chunk 547 optimal weight: 7.9990 chunk 329 optimal weight: 10.0000 chunk 238 optimal weight: 10.0000 chunk 430 optimal weight: 20.0000 chunk 168 optimal weight: 10.0000 chunk 495 optimal weight: 0.9990 chunk 518 optimal weight: 5.9990 chunk 545 optimal weight: 10.0000 overall best weight: 5.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** f 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** g 101 ASN ** h 2 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** j 138 GLN ** m 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** q 71 GLN ** r 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** s 31 GLN ** u 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** w 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8938 moved from start: 0.4130 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 99261 Z= 0.258 Angle : 0.602 16.983 149378 Z= 0.318 Chirality : 0.037 0.304 19201 Planarity : 0.005 0.085 7378 Dihedral : 23.718 179.271 51740 Min Nonbonded Distance : 2.034 Molprobity Statistics. All-atom Clashscore : 8.04 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.70 % Favored : 95.24 % Rotamer: Outliers : 1.80 % Allowed : 14.93 % Favored : 83.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.05 (0.15), residues: 3087 helix: 1.39 (0.18), residues: 813 sheet: -0.02 (0.20), residues: 682 loop : -0.61 (0.15), residues: 1592 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP z 159 HIS 0.007 0.001 HIS n 16 PHE 0.016 0.001 PHE f 77 TYR 0.021 0.001 TYR f 143 ARG 0.014 0.001 ARG y 11 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6174 Ramachandran restraints generated. 3087 Oldfield, 0 Emsley, 3087 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6174 Ramachandran restraints generated. 3087 Oldfield, 0 Emsley, 3087 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 416 residues out of total 2552 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 370 time to evaluate : 3.810 Fit side-chains revert: symmetry clash REVERT: 0 41 GLU cc_start: 0.8619 (tp30) cc_final: 0.7959 (tp30) REVERT: 0 44 LYS cc_start: 0.9132 (mmtm) cc_final: 0.8433 (mmtm) REVERT: 1 24 GLU cc_start: 0.8531 (tp30) cc_final: 0.8037 (tp30) REVERT: 1 45 GLN cc_start: 0.8823 (mt0) cc_final: 0.8313 (mt0) REVERT: 1 49 ASP cc_start: 0.8778 (m-30) cc_final: 0.8249 (m-30) REVERT: 3 37 LYS cc_start: 0.9338 (OUTLIER) cc_final: 0.9015 (mmmm) REVERT: 3 46 ASP cc_start: 0.8537 (t0) cc_final: 0.8055 (t0) REVERT: 4 50 LYS cc_start: 0.8902 (OUTLIER) cc_final: 0.8224 (mtpp) REVERT: 8 30 GLU cc_start: 0.8608 (mm-30) cc_final: 0.8160 (tp30) REVERT: c 90 ASN cc_start: 0.9143 (OUTLIER) cc_final: 0.8868 (p0) REVERT: d 97 SER cc_start: 0.9166 (p) cc_final: 0.8966 (p) REVERT: g 130 GLU cc_start: 0.7909 (mp0) cc_final: 0.7538 (mp0) REVERT: h 7 ASP cc_start: 0.9093 (t0) cc_final: 0.8723 (t0) REVERT: j 108 MET cc_start: 0.9180 (mtt) cc_final: 0.8924 (mtt) REVERT: l 69 ARG cc_start: 0.9367 (OUTLIER) cc_final: 0.8683 (ptm-80) REVERT: l 70 LYS cc_start: 0.9382 (OUTLIER) cc_final: 0.8909 (ttpp) REVERT: o 19 GLN cc_start: 0.9372 (tm-30) cc_final: 0.8782 (tm-30) REVERT: o 76 LYS cc_start: 0.9445 (tttm) cc_final: 0.9206 (tttm) REVERT: s 65 ASP cc_start: 0.6986 (t70) cc_final: 0.6620 (t70) REVERT: s 68 ASP cc_start: 0.8560 (p0) cc_final: 0.8189 (p0) REVERT: t 56 GLU cc_start: 0.8565 (tp30) cc_final: 0.8324 (tp30) REVERT: t 69 ARG cc_start: 0.8368 (OUTLIER) cc_final: 0.7923 (tpt90) REVERT: u 9 ASP cc_start: 0.8936 (m-30) cc_final: 0.8734 (m-30) REVERT: u 99 ASN cc_start: 0.8664 (t0) cc_final: 0.8338 (t0) REVERT: w 25 LYS cc_start: 0.9148 (OUTLIER) cc_final: 0.8703 (mttp) outliers start: 46 outliers final: 28 residues processed: 398 average time/residue: 1.9419 time to fit residues: 1022.8191 Evaluate side-chains 400 residues out of total 2552 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 365 time to evaluate : 3.875 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 3 residue 25 VAL Chi-restraints excluded: chain 3 residue 37 LYS Chi-restraints excluded: chain 4 residue 30 LYS Chi-restraints excluded: chain 4 residue 36 LEU Chi-restraints excluded: chain 4 residue 37 LYS Chi-restraints excluded: chain 4 residue 50 LYS Chi-restraints excluded: chain c residue 90 ASN Chi-restraints excluded: chain f residue 66 LEU Chi-restraints excluded: chain f residue 90 THR Chi-restraints excluded: chain g residue 15 VAL Chi-restraints excluded: chain g residue 23 VAL Chi-restraints excluded: chain h residue 4 ILE Chi-restraints excluded: chain h residue 15 LEU Chi-restraints excluded: chain h residue 22 LYS Chi-restraints excluded: chain h residue 30 LEU Chi-restraints excluded: chain j residue 131 ASN Chi-restraints excluded: chain l residue 69 ARG Chi-restraints excluded: chain l residue 70 LYS Chi-restraints excluded: chain l residue 76 GLU Chi-restraints excluded: chain l residue 121 THR Chi-restraints excluded: chain m residue 1 MET Chi-restraints excluded: chain n residue 57 THR Chi-restraints excluded: chain o residue 24 THR Chi-restraints excluded: chain o residue 54 VAL Chi-restraints excluded: chain o residue 69 ASP Chi-restraints excluded: chain p residue 4 ILE Chi-restraints excluded: chain p residue 5 ILE Chi-restraints excluded: chain r residue 29 THR Chi-restraints excluded: chain s residue 66 ILE Chi-restraints excluded: chain t residue 69 ARG Chi-restraints excluded: chain u residue 83 VAL Chi-restraints excluded: chain w residue 25 LYS Chi-restraints excluded: chain y residue 70 GLU Chi-restraints excluded: chain z residue 146 PHE Chi-restraints excluded: chain z residue 150 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 610 random chunks: chunk 359 optimal weight: 4.9990 chunk 579 optimal weight: 3.9990 chunk 353 optimal weight: 10.0000 chunk 274 optimal weight: 10.0000 chunk 402 optimal weight: 6.9990 chunk 607 optimal weight: 20.0000 chunk 559 optimal weight: 6.9990 chunk 483 optimal weight: 7.9990 chunk 50 optimal weight: 10.0000 chunk 373 optimal weight: 10.0000 chunk 296 optimal weight: 10.0000 overall best weight: 6.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** f 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** g 101 ASN ** h 2 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** q 71 GLN r 11 GLN s 31 GLN ** u 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8935 moved from start: 0.4147 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.061 99261 Z= 0.292 Angle : 0.591 15.734 149378 Z= 0.313 Chirality : 0.037 0.300 19201 Planarity : 0.005 0.108 7378 Dihedral : 23.667 179.957 51740 Min Nonbonded Distance : 2.048 Molprobity Statistics. All-atom Clashscore : 8.00 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.63 % Favored : 95.30 % Rotamer: Outliers : 1.68 % Allowed : 15.13 % Favored : 83.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.10 (0.15), residues: 3087 helix: 1.45 (0.18), residues: 818 sheet: -0.02 (0.20), residues: 678 loop : -0.59 (0.15), residues: 1591 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP c 213 HIS 0.008 0.001 HIS n 16 PHE 0.017 0.001 PHE f 77 TYR 0.030 0.002 TYR f 83 ARG 0.020 0.001 ARG 8 12 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6174 Ramachandran restraints generated. 3087 Oldfield, 0 Emsley, 3087 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6174 Ramachandran restraints generated. 3087 Oldfield, 0 Emsley, 3087 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 416 residues out of total 2552 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 373 time to evaluate : 3.822 Fit side-chains revert: symmetry clash REVERT: 0 41 GLU cc_start: 0.8616 (tp30) cc_final: 0.7954 (tp30) REVERT: 0 44 LYS cc_start: 0.9131 (mmtm) cc_final: 0.8432 (mmtm) REVERT: 1 24 GLU cc_start: 0.8531 (tp30) cc_final: 0.8101 (tp30) REVERT: 1 45 GLN cc_start: 0.8832 (mt0) cc_final: 0.8325 (mt0) REVERT: 1 49 ASP cc_start: 0.8780 (m-30) cc_final: 0.8251 (m-30) REVERT: 3 37 LYS cc_start: 0.9325 (OUTLIER) cc_final: 0.9012 (mmmm) REVERT: 3 46 ASP cc_start: 0.8532 (t0) cc_final: 0.8048 (t0) REVERT: 4 50 LYS cc_start: 0.8879 (OUTLIER) cc_final: 0.8171 (mtpp) REVERT: 8 30 GLU cc_start: 0.8623 (mm-30) cc_final: 0.8175 (tp30) REVERT: c 90 ASN cc_start: 0.9137 (OUTLIER) cc_final: 0.8861 (p0) REVERT: f 83 TYR cc_start: 0.8903 (m-80) cc_final: 0.8557 (m-80) REVERT: g 130 GLU cc_start: 0.7907 (mp0) cc_final: 0.7538 (mp0) REVERT: h 7 ASP cc_start: 0.9176 (t0) cc_final: 0.8761 (t0) REVERT: j 108 MET cc_start: 0.9209 (mtt) cc_final: 0.8930 (mtt) REVERT: l 69 ARG cc_start: 0.9356 (OUTLIER) cc_final: 0.8641 (ptm-80) REVERT: l 70 LYS cc_start: 0.9381 (OUTLIER) cc_final: 0.8908 (ttpp) REVERT: o 19 GLN cc_start: 0.9377 (tm-30) cc_final: 0.8795 (tm-30) REVERT: o 76 LYS cc_start: 0.9480 (tttm) cc_final: 0.9215 (tttm) REVERT: s 65 ASP cc_start: 0.7076 (t70) cc_final: 0.6703 (t0) REVERT: t 56 GLU cc_start: 0.8562 (tp30) cc_final: 0.8322 (tp30) REVERT: t 69 ARG cc_start: 0.8344 (OUTLIER) cc_final: 0.7898 (tpt90) REVERT: u 9 ASP cc_start: 0.8916 (m-30) cc_final: 0.8650 (m-30) REVERT: w 25 LYS cc_start: 0.9143 (OUTLIER) cc_final: 0.8691 (mttp) outliers start: 43 outliers final: 30 residues processed: 401 average time/residue: 1.9181 time to fit residues: 1019.0793 Evaluate side-chains 404 residues out of total 2552 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 367 time to evaluate : 3.786 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 3 residue 25 VAL Chi-restraints excluded: chain 3 residue 37 LYS Chi-restraints excluded: chain 4 residue 30 LYS Chi-restraints excluded: chain 4 residue 36 LEU Chi-restraints excluded: chain 4 residue 37 LYS Chi-restraints excluded: chain 4 residue 50 LYS Chi-restraints excluded: chain c residue 90 ASN Chi-restraints excluded: chain f residue 66 LEU Chi-restraints excluded: chain f residue 90 THR Chi-restraints excluded: chain g residue 15 VAL Chi-restraints excluded: chain g residue 23 VAL Chi-restraints excluded: chain g residue 26 ILE Chi-restraints excluded: chain h residue 4 ILE Chi-restraints excluded: chain h residue 15 LEU Chi-restraints excluded: chain h residue 22 LYS Chi-restraints excluded: chain h residue 30 LEU Chi-restraints excluded: chain j residue 131 ASN Chi-restraints excluded: chain l residue 69 ARG Chi-restraints excluded: chain l residue 70 LYS Chi-restraints excluded: chain l residue 76 GLU Chi-restraints excluded: chain l residue 121 THR Chi-restraints excluded: chain l residue 143 GLU Chi-restraints excluded: chain m residue 1 MET Chi-restraints excluded: chain n residue 57 THR Chi-restraints excluded: chain o residue 24 THR Chi-restraints excluded: chain o residue 54 VAL Chi-restraints excluded: chain o residue 69 ASP Chi-restraints excluded: chain p residue 4 ILE Chi-restraints excluded: chain p residue 5 ILE Chi-restraints excluded: chain r residue 29 THR Chi-restraints excluded: chain s residue 66 ILE Chi-restraints excluded: chain t residue 69 ARG Chi-restraints excluded: chain u residue 83 VAL Chi-restraints excluded: chain w residue 25 LYS Chi-restraints excluded: chain y residue 70 GLU Chi-restraints excluded: chain z residue 146 PHE Chi-restraints excluded: chain z residue 150 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 610 random chunks: chunk 384 optimal weight: 10.0000 chunk 515 optimal weight: 0.9990 chunk 148 optimal weight: 10.0000 chunk 446 optimal weight: 7.9990 chunk 71 optimal weight: 10.0000 chunk 134 optimal weight: 10.0000 chunk 484 optimal weight: 20.0000 chunk 202 optimal weight: 20.0000 chunk 497 optimal weight: 9.9990 chunk 61 optimal weight: 20.0000 chunk 89 optimal weight: 10.0000 overall best weight: 7.7994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: f 21 ASN ** f 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** g 101 ASN g 116 GLN ** h 2 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** j 138 GLN ** m 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** q 71 GLN ** r 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** s 31 GLN ** u 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** u 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** w 12 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3272 r_free = 0.3272 target = 0.041511 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.2861 r_free = 0.2861 target = 0.028788 restraints weight = 431710.385| |-----------------------------------------------------------------------------| r_work (start): 0.2822 rms_B_bonded: 1.16 r_work: 0.2739 rms_B_bonded: 2.21 restraints_weight: 0.5000 r_work: 0.2666 rms_B_bonded: 3.32 restraints_weight: 0.2500 r_work (final): 0.2666 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9251 moved from start: 0.4172 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.072 99261 Z= 0.354 Angle : 0.601 16.349 149378 Z= 0.318 Chirality : 0.039 0.305 19201 Planarity : 0.005 0.078 7378 Dihedral : 23.624 179.944 51740 Min Nonbonded Distance : 2.055 Molprobity Statistics. All-atom Clashscore : 7.76 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.70 % Favored : 95.24 % Rotamer: Outliers : 1.72 % Allowed : 15.32 % Favored : 82.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.09 (0.15), residues: 3087 helix: 1.43 (0.18), residues: 818 sheet: -0.04 (0.20), residues: 682 loop : -0.58 (0.15), residues: 1587 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP c 213 HIS 0.009 0.001 HIS n 16 PHE 0.016 0.001 PHE f 77 TYR 0.030 0.002 TYR f 83 ARG 0.013 0.001 ARG y 11 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 22050.95 seconds wall clock time: 386 minutes 19.79 seconds (23179.79 seconds total)