Starting phenix.real_space_refine on Sat Dec 28 03:23:52 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8byv_16334/12_2024/8byv_16334.cif Found real_map, /net/cci-nas-00/data/ceres_data/8byv_16334/12_2024/8byv_16334.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.89 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8byv_16334/12_2024/8byv_16334.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8byv_16334/12_2024/8byv_16334.map" model { file = "/net/cci-nas-00/data/ceres_data/8byv_16334/12_2024/8byv_16334.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8byv_16334/12_2024/8byv_16334.cif" } resolution = 2.89 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.036 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 1533 5.49 5 S 55 5.16 5 C 26590 2.51 5 N 9550 2.21 5 O 14138 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 58 residue(s): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/chem_data/mon_lib" Total number of atoms: 51866 Number of models: 1 Model: "" Number of chains: 21 Chain: "a" Number of atoms: 32835 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1533, 32835 Classifications: {'RNA': 1533} Modifications used: {'rna2p_pur': 125, 'rna2p_pyr': 86, 'rna3p_pur': 737, 'rna3p_pyr': 585} Link IDs: {'rna2p': 211, 'rna3p': 1321} Chain breaks: 2 Chain: "b" Number of atoms: 1774 Number of conformers: 1 Conformer: "" Number of residues, atoms: 222, 1774 Classifications: {'peptide': 222} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 7, 'TRANS': 214} Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 13 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'TYR:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 10 Chain: "c" Number of atoms: 1609 Number of conformers: 1 Conformer: "" Number of residues, atoms: 204, 1609 Classifications: {'peptide': 204} Link IDs: {'PTRANS': 3, 'TRANS': 200} Chain: "d" Number of atoms: 1600 Number of conformers: 1 Conformer: "" Number of residues, atoms: 197, 1600 Classifications: {'peptide': 197} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 8, 'TRANS': 188} Chain breaks: 1 Chain: "e" Number of atoms: 1154 Number of conformers: 1 Conformer: "" Number of residues, atoms: 154, 1154 Classifications: {'peptide': 154} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 146} Chain breaks: 1 Chain: "f" Number of atoms: 781 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 781 Classifications: {'peptide': 94} Link IDs: {'PTRANS': 1, 'TRANS': 92} Chain: "g" Number of atoms: 1120 Number of conformers: 1 Conformer: "" Number of residues, atoms: 140, 1120 Classifications: {'peptide': 140} Link IDs: {'PTRANS': 6, 'TRANS': 133} Chain breaks: 1 Chain: "h" Number of atoms: 1032 Number of conformers: 1 Conformer: "" Number of residues, atoms: 131, 1032 Classifications: {'peptide': 131} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 126} Chain: "i" Number of atoms: 1017 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 1017 Classifications: {'peptide': 128} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 120} Chain: "j" Number of atoms: 791 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 791 Classifications: {'peptide': 99} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 92} Chain: "k" Number of atoms: 880 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 880 Classifications: {'peptide': 118} Link IDs: {'PTRANS': 7, 'TRANS': 110} Chain: "l" Number of atoms: 1058 Number of conformers: 1 Conformer: "" Number of residues, atoms: 135, 1058 Classifications: {'peptide': 135} Link IDs: {'PTRANS': 8, 'TRANS': 126} Chain: "m" Number of atoms: 877 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 877 Classifications: {'peptide': 110} Link IDs: {'PTRANS': 2, 'TRANS': 107} Chain: "n" Number of atoms: 502 Number of conformers: 1 Conformer: "" Number of residues, atoms: 60, 502 Classifications: {'peptide': 60} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 57} Chain: "o" Number of atoms: 738 Number of conformers: 1 Conformer: "" Number of residues, atoms: 88, 738 Classifications: {'peptide': 88} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 86} Chain: "p" Number of atoms: 712 Number of conformers: 1 Conformer: "" Number of residues, atoms: 90, 712 Classifications: {'peptide': 90} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 84} Chain: "q" Number of atoms: 698 Number of conformers: 1 Conformer: "" Number of residues, atoms: 85, 698 Classifications: {'peptide': 85} Link IDs: {'PTRANS': 1, 'TRANS': 83} Chain: "r" Number of atoms: 478 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 478 Classifications: {'peptide': 58} Link IDs: {'PTRANS': 2, 'TRANS': 55} Chain: "s" Number of atoms: 661 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 661 Classifications: {'peptide': 82} Link IDs: {'PTRANS': 4, 'TRANS': 77} Chain: "t" Number of atoms: 606 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 606 Classifications: {'peptide': 80} Link IDs: {'TRANS': 79} Chain: "A" Number of atoms: 943 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 943 Classifications: {'peptide': 116} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 113} Time building chain proxies: 21.52, per 1000 atoms: 0.41 Number of scatterers: 51866 At special positions: 0 Unit cell: (133.882, 198.268, 251.412, 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 55 16.00 P 1533 15.00 O 14138 8.00 N 9550 7.00 C 26590 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 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: 9.24 Conformation dependent library (CDL) restraints added in 2.3 seconds 4690 Ramachandran restraints generated. 2345 Oldfield, 0 Emsley, 2345 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4446 Finding SS restraints... Secondary structure from input PDB file: 80 helices and 25 sheets defined 42.0% alpha, 15.9% beta 498 base pairs and 813 stacking pairs defined. Time for finding SS restraints: 17.70 Creating SS restraints... Processing helix chain 'b' and resid 8 through 15 Processing helix chain 'b' and resid 27 through 31 removed outlier: 3.730A pdb=" N ILE b 31 " --> pdb=" O LYS b 28 " (cutoff:3.500A) Processing helix chain 'b' and resid 42 through 63 removed outlier: 3.593A pdb=" N THR b 46 " --> pdb=" O ASP b 42 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N LYS b 48 " --> pdb=" O GLN b 44 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N ASP b 63 " --> pdb=" O GLN b 59 " (cutoff:3.500A) Processing helix chain 'b' and resid 76 through 88 Processing helix chain 'b' and resid 106 through 125 removed outlier: 3.959A pdb=" N ARG b 110 " --> pdb=" O THR b 106 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N GLU b 121 " --> pdb=" O ILE b 117 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N GLU b 122 " --> pdb=" O GLU b 118 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N LEU b 125 " --> pdb=" O GLU b 121 " (cutoff:3.500A) Processing helix chain 'b' and resid 130 through 148 removed outlier: 3.661A pdb=" N VAL b 134 " --> pdb=" O PRO b 130 " (cutoff:3.500A) removed outlier: 4.776A pdb=" N GLU b 136 " --> pdb=" O LYS b 132 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N LYS b 139 " --> pdb=" O VAL b 135 " (cutoff:3.500A) Processing helix chain 'b' and resid 169 through 180 Processing helix chain 'b' and resid 206 through 227 Processing helix chain 'c' and resid 6 through 12 removed outlier: 4.203A pdb=" N LEU c 10 " --> pdb=" O ASN c 6 " (cutoff:3.500A) Processing helix chain 'c' and resid 27 through 42 removed outlier: 3.712A pdb=" N LEU c 31 " --> pdb=" O ASP c 27 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N LYS c 37 " --> pdb=" O HIS c 33 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ILE c 38 " --> pdb=" O GLU c 34 " (cutoff:3.500A) Processing helix chain 'c' and resid 42 through 50 removed outlier: 4.193A pdb=" N GLU c 48 " --> pdb=" O ASN c 44 " (cutoff:3.500A) Processing helix chain 'c' and resid 71 through 76 removed outlier: 4.368A pdb=" N VAL c 75 " --> pdb=" O LYS c 71 " (cutoff:3.500A) Processing helix chain 'c' and resid 82 through 95 Processing helix chain 'c' and resid 112 through 125 Processing helix chain 'c' and resid 128 through 144 Processing helix chain 'd' and resid 9 through 16 Processing helix chain 'd' and resid 45 through 62 Processing helix chain 'd' and resid 64 through 78 removed outlier: 3.638A pdb=" N LYS d 77 " --> pdb=" O ASP d 73 " (cutoff:3.500A) removed outlier: 4.166A pdb=" N LYS d 78 " --> pdb=" O ILE d 74 " (cutoff:3.500A) Processing helix chain 'd' and resid 81 through 92 Processing helix chain 'd' and resid 93 through 101 Processing helix chain 'd' and resid 106 through 117 Processing helix chain 'd' and resid 143 through 146 removed outlier: 3.614A pdb=" N GLN d 146 " --> pdb=" O GLU d 143 " (cutoff:3.500A) No H-bonds generated for 'chain 'd' and resid 143 through 146' Processing helix chain 'd' and resid 148 through 156 Processing helix chain 'd' and resid 191 through 198 removed outlier: 3.519A pdb=" N VAL d 195 " --> pdb=" O GLU d 191 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N GLU d 196 " --> pdb=" O GLN d 192 " (cutoff:3.500A) Processing helix chain 'e' and resid 55 through 70 removed outlier: 3.908A pdb=" N ASP e 70 " --> pdb=" O ALA e 66 " (cutoff:3.500A) Processing helix chain 'e' and resid 108 through 118 Processing helix chain 'e' and resid 132 through 146 Processing helix chain 'e' and resid 149 through 157 Processing helix chain 'f' and resid 15 through 32 Processing helix chain 'f' and resid 72 through 83 removed outlier: 4.002A pdb=" N PHE f 76 " --> pdb=" O ALA f 72 " (cutoff:3.500A) removed outlier: 4.144A pdb=" N ARG f 78 " --> pdb=" O ASP f 74 " (cutoff:3.500A) removed outlier: 4.454A pdb=" N LYS f 81 " --> pdb=" O GLN f 77 " (cutoff:3.500A) Processing helix chain 'g' and resid 21 through 30 removed outlier: 4.042A pdb=" N LYS g 25 " --> pdb=" O LYS g 21 " (cutoff:3.500A) Processing helix chain 'g' and resid 31 through 35 removed outlier: 4.302A pdb=" N GLY g 34 " --> pdb=" O MET g 31 " (cutoff:3.500A) Processing helix chain 'g' and resid 36 through 53 Processing helix chain 'g' and resid 57 through 69 removed outlier: 3.788A pdb=" N VAL g 61 " --> pdb=" O ASP g 57 " (cutoff:3.500A) Processing helix chain 'g' and resid 92 through 112 removed outlier: 4.023A pdb=" N GLY g 112 " --> pdb=" O ALA g 108 " (cutoff:3.500A) Processing helix chain 'g' and resid 117 through 129 Processing helix chain 'g' and resid 132 through 148 removed outlier: 3.554A pdb=" N ASN g 148 " --> pdb=" O MET g 144 " (cutoff:3.500A) Processing helix chain 'g' and resid 149 through 152 Processing helix chain 'h' and resid 5 through 20 Processing helix chain 'h' and resid 30 through 44 Processing helix chain 'h' and resid 96 through 101 removed outlier: 3.502A pdb=" N ASN h 99 " --> pdb=" O LYS h 96 " (cutoff:3.500A) Processing helix chain 'h' and resid 114 through 121 removed outlier: 3.676A pdb=" N ARG h 119 " --> pdb=" O ASP h 115 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N ARG h 121 " --> pdb=" O GLU h 117 " (cutoff:3.500A) Processing helix chain 'i' and resid 36 through 41 removed outlier: 3.687A pdb=" N TYR i 40 " --> pdb=" O ASP i 36 " (cutoff:3.500A) Processing helix chain 'i' and resid 46 through 57 removed outlier: 3.713A pdb=" N LEU i 50 " --> pdb=" O LEU i 46 " (cutoff:3.500A) Proline residue: i 53 - end of helix Processing helix chain 'i' and resid 73 through 93 removed outlier: 3.680A pdb=" N ARG i 82 " --> pdb=" O ALA i 78 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N HIS i 83 " --> pdb=" O GLN i 79 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N ASP i 93 " --> pdb=" O LEU i 89 " (cutoff:3.500A) Processing helix chain 'i' and resid 96 through 104 Processing helix chain 'j' and resid 14 through 32 removed outlier: 4.247A pdb=" N SER j 32 " --> pdb=" O THR j 28 " (cutoff:3.500A) Processing helix chain 'j' and resid 80 through 88 Processing helix chain 'k' and resid 54 through 59 removed outlier: 3.850A pdb=" N SER k 58 " --> pdb=" O GLY k 54 " (cutoff:3.500A) Processing helix chain 'k' and resid 59 through 77 removed outlier: 3.638A pdb=" N ALA k 63 " --> pdb=" O THR k 59 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N SER k 73 " --> pdb=" O THR k 69 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N HIS k 77 " --> pdb=" O SER k 73 " (cutoff:3.500A) Processing helix chain 'k' and resid 95 through 103 Processing helix chain 'l' and resid 3 through 9 Processing helix chain 'l' and resid 127 through 131 Processing helix chain 'm' and resid 14 through 19 Processing helix chain 'm' and resid 29 through 37 Processing helix chain 'm' and resid 55 through 60 Processing helix chain 'm' and resid 67 through 83 Processing helix chain 'm' and resid 87 through 93 removed outlier: 3.522A pdb=" N ARG m 92 " --> pdb=" O GLY m 88 " (cutoff:3.500A) removed outlier: 4.246A pdb=" N ARG m 93 " --> pdb=" O ILE m 89 " (cutoff:3.500A) Processing helix chain 'n' and resid 3 through 10 removed outlier: 4.575A pdb=" N ALA n 8 " --> pdb=" O THR n 4 " (cutoff:3.500A) Processing helix chain 'n' and resid 41 through 51 Processing helix chain 'o' and resid 4 through 15 Processing helix chain 'o' and resid 24 through 46 Processing helix chain 'o' and resid 49 through 74 Processing helix chain 'o' and resid 74 through 85 removed outlier: 3.631A pdb=" N TYR o 78 " --> pdb=" O ASP o 74 " (cutoff:3.500A) removed outlier: 4.165A pdb=" N LYS o 83 " --> pdb=" O ARG o 79 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N LEU o 85 " --> pdb=" O LEU o 81 " (cutoff:3.500A) Processing helix chain 'p' and resid 55 through 64 Processing helix chain 'p' and resid 68 through 79 Processing helix chain 'p' and resid 79 through 89 removed outlier: 3.867A pdb=" N LYS p 83 " --> pdb=" O GLY p 79 " (cutoff:3.500A) Processing helix chain 'r' and resid 30 through 37 removed outlier: 3.622A pdb=" N LEU r 34 " --> pdb=" O ASP r 30 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N PHE r 37 " --> pdb=" O LEU r 33 " (cutoff:3.500A) Processing helix chain 'r' and resid 46 through 51 Processing helix chain 'r' and resid 53 through 70 Processing helix chain 's' and resid 14 through 25 removed outlier: 4.631A pdb=" N SER s 25 " --> pdb=" O ALA s 21 " (cutoff:3.500A) Processing helix chain 's' and resid 41 through 45 removed outlier: 3.611A pdb=" N ILE s 45 " --> pdb=" O PRO s 42 " (cutoff:3.500A) Processing helix chain 's' and resid 78 through 83 removed outlier: 3.688A pdb=" N GLY s 82 " --> pdb=" O THR s 79 " (cutoff:3.500A) Processing helix chain 't' and resid 6 through 38 removed outlier: 3.811A pdb=" N ARG t 10 " --> pdb=" O SER t 6 " (cutoff:3.500A) Processing helix chain 't' and resid 46 through 63 Processing helix chain 't' and resid 67 through 80 Processing helix chain 'A' and resid 3 through 24 Processing helix chain 'A' and resid 58 through 82 removed outlier: 4.030A pdb=" N LYS A 69 " --> pdb=" O LYS A 65 " (cutoff:3.500A) removed outlier: 5.301A pdb=" N GLY A 72 " --> pdb=" O ASP A 68 " (cutoff:3.500A) removed outlier: 5.176A pdb=" N PHE A 73 " --> pdb=" O LYS A 69 " (cutoff:3.500A) Processing helix chain 'A' and resid 96 through 105 Processing helix chain 'A' and resid 107 through 116 Processing sheet with id=AA1, first strand: chain 'b' and resid 69 through 70 removed outlier: 7.485A pdb=" N PHE b 69 " --> pdb=" O ILE b 92 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'b' and resid 161 through 163 removed outlier: 3.726A pdb=" N VAL b 184 " --> pdb=" O LEU b 161 " (cutoff:3.500A) removed outlier: 6.226A pdb=" N ILE b 183 " --> pdb=" O TYR b 198 " (cutoff:3.500A) removed outlier: 7.337A pdb=" N ILE b 200 " --> pdb=" O ILE b 183 " (cutoff:3.500A) removed outlier: 6.349A pdb=" N GLY b 185 " --> pdb=" O ILE b 200 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'c' and resid 54 through 58 removed outlier: 6.655A pdb=" N ILE c 63 " --> pdb=" O HIS c 99 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'c' and resid 54 through 58 removed outlier: 6.827A pdb=" N ILE c 103 " --> pdb=" O ILE c 65 " (cutoff:3.500A) removed outlier: 5.245A pdb=" N ILE c 67 " --> pdb=" O ILE c 103 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'c' and resid 163 through 167 removed outlier: 3.510A pdb=" N GLY c 154 " --> pdb=" O ARG c 163 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N TYR c 167 " --> pdb=" O THR c 150 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N THR c 150 " --> pdb=" O TYR c 167 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'c' and resid 163 through 167 removed outlier: 3.510A pdb=" N GLY c 154 " --> pdb=" O ARG c 163 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N TYR c 167 " --> pdb=" O THR c 150 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N THR c 150 " --> pdb=" O TYR c 167 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'd' and resid 124 through 125 Processing sheet with id=AA8, first strand: chain 'e' and resid 12 through 21 removed outlier: 6.438A pdb=" N LEU e 36 " --> pdb=" O VAL e 16 " (cutoff:3.500A) removed outlier: 4.339A pdb=" N ILE e 18 " --> pdb=" O THR e 34 " (cutoff:3.500A) removed outlier: 6.568A pdb=" N THR e 34 " --> pdb=" O ILE e 18 " (cutoff:3.500A) removed outlier: 4.123A pdb=" N ARG e 20 " --> pdb=" O ARG e 32 " (cutoff:3.500A) removed outlier: 5.762A pdb=" N ARG e 32 " --> pdb=" O ARG e 20 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'e' and resid 85 through 89 Processing sheet with id=AB1, first strand: chain 'f' and resid 36 through 45 removed outlier: 3.521A pdb=" N GLU f 36 " --> pdb=" O LYS f 66 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N LYS f 66 " --> pdb=" O GLU f 36 " (cutoff:3.500A) removed outlier: 6.646A pdb=" N ARG f 64 " --> pdb=" O LEU f 38 " (cutoff:3.500A) removed outlier: 4.306A pdb=" N ALA f 40 " --> pdb=" O ILE f 62 " (cutoff:3.500A) removed outlier: 6.588A pdb=" N ILE f 62 " --> pdb=" O ALA f 40 " (cutoff:3.500A) removed outlier: 5.324A pdb=" N ASP f 42 " --> pdb=" O TYR f 60 " (cutoff:3.500A) removed outlier: 7.249A pdb=" N TYR f 60 " --> pdb=" O ASP f 42 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N VAL f 10 " --> pdb=" O PHE f 59 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N ASN f 61 " --> pdb=" O TYR f 8 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N VAL f 65 " --> pdb=" O TYR f 4 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N ARG f 88 " --> pdb=" O ILE f 9 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'g' and resid 74 through 76 removed outlier: 4.104A pdb=" N GLU g 74 " --> pdb=" O VAL g 89 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N LYS g 76 " --> pdb=" O VAL g 87 " (cutoff:3.500A) removed outlier: 4.457A pdb=" N VAL g 87 " --> pdb=" O LYS g 76 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'h' and resid 24 through 28 removed outlier: 3.515A pdb=" N ASN h 48 " --> pdb=" O PHE h 63 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'h' and resid 76 through 79 Processing sheet with id=AB5, first strand: chain 'h' and resid 76 through 79 removed outlier: 6.392A pdb=" N LEU h 105 " --> pdb=" O ILE h 128 " (cutoff:3.500A) removed outlier: 4.646A pdb=" N TYR h 130 " --> pdb=" O ILE h 103 " (cutoff:3.500A) removed outlier: 6.795A pdb=" N ILE h 103 " --> pdb=" O TYR h 130 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'i' and resid 8 through 14 removed outlier: 3.846A pdb=" N VAL i 18 " --> pdb=" O HIS i 70 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'j' and resid 36 through 41 removed outlier: 6.214A pdb=" N VAL j 36 " --> pdb=" O VAL j 77 " (cutoff:3.500A) removed outlier: 7.166A pdb=" N VAL j 77 " --> pdb=" O VAL j 36 " (cutoff:3.500A) removed outlier: 4.978A pdb=" N GLY j 38 " --> pdb=" O ASP j 75 " (cutoff:3.500A) removed outlier: 4.437A pdb=" N ASP j 75 " --> pdb=" O GLY j 38 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'j' and resid 49 through 52 Processing sheet with id=AB9, first strand: chain 'k' and resid 43 through 46 removed outlier: 3.912A pdb=" N SER k 43 " --> pdb=" O ILE k 34 " (cutoff:3.500A) removed outlier: 8.683A pdb=" N THR k 85 " --> pdb=" O GLY k 19 " (cutoff:3.500A) removed outlier: 6.805A pdb=" N ALA k 21 " --> pdb=" O THR k 85 " (cutoff:3.500A) removed outlier: 7.682A pdb=" N LYS k 87 " --> pdb=" O ALA k 21 " (cutoff:3.500A) removed outlier: 7.159A pdb=" N ILE k 23 " --> pdb=" O LYS k 87 " (cutoff:3.500A) removed outlier: 5.796A pdb=" N VAL k 84 " --> pdb=" O ARG k 111 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'l' and resid 27 through 29 Processing sheet with id=AC2, first strand: chain 'l' and resid 92 through 95 removed outlier: 5.931A pdb=" N CYS l 47 " --> pdb=" O ARG l 69 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N ARG l 69 " --> pdb=" O CYS l 47 " (cutoff:3.500A) removed outlier: 9.305A pdb=" N VAL l 106 " --> pdb=" O GLU l 75 " (cutoff:3.500A) removed outlier: 7.510A pdb=" N ASN l 77 " --> pdb=" O VAL l 106 " (cutoff:3.500A) removed outlier: 4.202A pdb=" N TYR l 108 " --> pdb=" O ASN l 77 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'n' and resid 33 through 34 Processing sheet with id=AC4, first strand: chain 'p' and resid 35 through 36 removed outlier: 6.762A pdb=" N VAL p 3 " --> pdb=" O LYS p 66 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'q' and resid 9 through 14 removed outlier: 16.546A pdb=" N VAL q 9 " --> pdb=" O TYR q 30 " (cutoff:3.500A) removed outlier: 13.393A pdb=" N TYR q 30 " --> pdb=" O VAL q 9 " (cutoff:3.500A) removed outlier: 8.108A pdb=" N VAL q 11 " --> pdb=" O GLU q 28 " (cutoff:3.500A) removed outlier: 5.205A pdb=" N GLU q 28 " --> pdb=" O VAL q 11 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N LYS q 13 " --> pdb=" O LEU q 26 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N VAL q 40 " --> pdb=" O LYS q 31 " (cutoff:3.500A) removed outlier: 15.475A pdb=" N LYS q 73 " --> pdb=" O SER q 43 " (cutoff:3.500A) removed outlier: 13.085A pdb=" N LYS q 45 " --> pdb=" O LYS q 73 " (cutoff:3.500A) removed outlier: 9.183A pdb=" N PHE q 75 " --> pdb=" O LYS q 45 " (cutoff:3.500A) removed outlier: 7.090A pdb=" N LYS q 47 " --> pdb=" O PHE q 75 " (cutoff:3.500A) removed outlier: 7.541A pdb=" N LEU q 77 " --> pdb=" O LYS q 47 " (cutoff:3.500A) removed outlier: 6.655A pdb=" N HIS q 49 " --> pdb=" O LEU q 77 " (cutoff:3.500A) removed outlier: 8.314A pdb=" N GLU q 79 " --> pdb=" O HIS q 49 " (cutoff:3.500A) removed outlier: 8.506A pdb=" N ARG q 74 " --> pdb=" O THR q 66 " (cutoff:3.500A) removed outlier: 7.424A pdb=" N LYS q 62 " --> pdb=" O VAL q 78 " (cutoff:3.500A) removed outlier: 5.277A pdb=" N ILE q 80 " --> pdb=" O ILE q 60 " (cutoff:3.500A) removed outlier: 7.209A pdb=" N ILE q 60 " --> pdb=" O ILE q 80 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 's' and resid 48 through 51 removed outlier: 3.754A pdb=" N VAL s 51 " --> pdb=" O VAL s 58 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N VAL s 58 " --> pdb=" O VAL s 51 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'A' and resid 35 through 40 removed outlier: 4.013A pdb=" N ILE A 35 " --> pdb=" O THR A 52 " (cutoff:3.500A) removed outlier: 7.213A pdb=" N ALA A 47 " --> pdb=" O MET A 91 " (cutoff:3.500A) removed outlier: 8.101A pdb=" N GLU A 93 " --> pdb=" O ALA A 47 " (cutoff:3.500A) removed outlier: 6.090A pdb=" N VAL A 49 " --> pdb=" O GLU A 93 " (cutoff:3.500A) 833 hydrogen bonds defined for protein. 2376 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 1237 hydrogen bonds 1984 hydrogen bond angles 0 basepair planarities 498 basepair parallelities 813 stacking parallelities Total time for adding SS restraints: 42.77 Time building geometry restraints manager: 11.16 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: 7654 1.33 - 1.45: 23440 1.45 - 1.58: 21797 1.58 - 1.70: 3063 1.70 - 1.83: 103 Bond restraints: 56057 Sorted by residual: bond pdb=" CA VAL e 56 " pdb=" CB VAL e 56 " ideal model delta sigma weight residual 1.539 1.550 -0.011 5.40e-03 3.43e+04 4.45e+00 bond pdb=" C HIS k 118 " pdb=" N ASN k 119 " ideal model delta sigma weight residual 1.333 1.309 0.023 1.29e-02 6.01e+03 3.27e+00 bond pdb=" C LYS l 10 " pdb=" N PRO l 11 " ideal model delta sigma weight residual 1.334 1.315 0.019 1.11e-02 8.12e+03 2.98e+00 bond pdb=" CA HIS k 118 " pdb=" C HIS k 118 " ideal model delta sigma weight residual 1.530 1.511 0.019 1.14e-02 7.69e+03 2.84e+00 bond pdb=" C LEU d 185 " pdb=" N PRO d 186 " ideal model delta sigma weight residual 1.326 1.349 -0.023 1.44e-02 4.82e+03 2.46e+00 ... (remaining 56052 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.93: 82018 1.93 - 3.85: 1063 3.85 - 5.78: 114 5.78 - 7.70: 14 7.70 - 9.63: 6 Bond angle restraints: 83215 Sorted by residual: angle pdb=" N PRO d 186 " pdb=" CA PRO d 186 " pdb=" C PRO d 186 " ideal model delta sigma weight residual 110.40 119.24 -8.84 1.61e+00 3.86e-01 3.01e+01 angle pdb=" C2' G a1232 " pdb=" C1' G a1232 " pdb=" N9 G a1232 " ideal model delta sigma weight residual 112.00 117.63 -5.63 1.50e+00 4.44e-01 1.41e+01 angle pdb=" N VAL g 72 " pdb=" CA VAL g 72 " pdb=" C VAL g 72 " ideal model delta sigma weight residual 113.47 109.78 3.69 1.01e+00 9.80e-01 1.34e+01 angle pdb=" C ASP f 74 " pdb=" N GLU f 75 " pdb=" CA GLU f 75 " ideal model delta sigma weight residual 121.52 114.84 6.68 1.84e+00 2.95e-01 1.32e+01 angle pdb=" N VAL A 30 " pdb=" CA VAL A 30 " pdb=" C VAL A 30 " ideal model delta sigma weight residual 106.21 110.05 -3.84 1.07e+00 8.73e-01 1.29e+01 ... (remaining 83210 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.85: 31645 35.85 - 71.70: 3731 71.70 - 107.56: 413 107.56 - 143.41: 7 143.41 - 179.26: 6 Dihedral angle restraints: 35802 sinusoidal: 28917 harmonic: 6885 Sorted by residual: dihedral pdb=" O4' U a 463 " pdb=" C1' U a 463 " pdb=" N1 U a 463 " pdb=" C2 U a 463 " ideal model delta sinusoidal sigma weight residual 200.00 29.80 170.20 1 1.50e+01 4.44e-03 8.47e+01 dihedral pdb=" O4' C a1169 " pdb=" C1' C a1169 " pdb=" N1 C a1169 " pdb=" C2 C a1169 " ideal model delta sinusoidal sigma weight residual 200.00 46.29 153.71 1 1.50e+01 4.44e-03 8.09e+01 dihedral pdb=" O4' C a 762 " pdb=" C1' C a 762 " pdb=" N1 C a 762 " pdb=" C2 C a 762 " ideal model delta sinusoidal sigma weight residual 200.00 58.79 141.21 1 1.50e+01 4.44e-03 7.59e+01 ... (remaining 35799 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.069: 9894 0.069 - 0.139: 592 0.139 - 0.208: 65 0.208 - 0.277: 5 0.277 - 0.347: 1 Chirality restraints: 10557 Sorted by residual: chirality pdb=" C1' G a1232 " pdb=" O4' G a1232 " pdb=" C2' G a1232 " pdb=" N9 G a1232 " both_signs ideal model delta sigma weight residual False 2.46 2.11 0.35 2.00e-01 2.50e+01 3.00e+00 chirality pdb=" C1' U a1012 " pdb=" O4' U a1012 " pdb=" C2' U a1012 " pdb=" N1 U a1012 " both_signs ideal model delta sigma weight residual False 2.47 2.22 0.25 2.00e-01 2.50e+01 1.57e+00 chirality pdb=" C3' U a1391 " pdb=" C4' U a1391 " pdb=" O3' U a1391 " pdb=" C2' U a1391 " both_signs ideal model delta sigma weight residual False -2.74 -2.52 -0.23 2.00e-01 2.50e+01 1.32e+00 ... (remaining 10554 not shown) Planarity restraints: 4874 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' G a1232 " -0.036 2.00e-02 2.50e+03 1.76e-02 9.34e+00 pdb=" N9 G a1232 " 0.045 2.00e-02 2.50e+03 pdb=" C8 G a1232 " 0.005 2.00e-02 2.50e+03 pdb=" N7 G a1232 " -0.004 2.00e-02 2.50e+03 pdb=" C5 G a1232 " -0.002 2.00e-02 2.50e+03 pdb=" C6 G a1232 " -0.017 2.00e-02 2.50e+03 pdb=" O6 G a1232 " 0.002 2.00e-02 2.50e+03 pdb=" N1 G a1232 " -0.002 2.00e-02 2.50e+03 pdb=" C2 G a1232 " -0.003 2.00e-02 2.50e+03 pdb=" N2 G a1232 " 0.006 2.00e-02 2.50e+03 pdb=" N3 G a1232 " 0.004 2.00e-02 2.50e+03 pdb=" C4 G a1232 " 0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' G a1045 " 0.035 2.00e-02 2.50e+03 1.69e-02 8.53e+00 pdb=" N9 G a1045 " -0.028 2.00e-02 2.50e+03 pdb=" C8 G a1045 " -0.010 2.00e-02 2.50e+03 pdb=" N7 G a1045 " 0.002 2.00e-02 2.50e+03 pdb=" C5 G a1045 " 0.001 2.00e-02 2.50e+03 pdb=" C6 G a1045 " -0.000 2.00e-02 2.50e+03 pdb=" O6 G a1045 " 0.017 2.00e-02 2.50e+03 pdb=" N1 G a1045 " 0.001 2.00e-02 2.50e+03 pdb=" C2 G a1045 " -0.028 2.00e-02 2.50e+03 pdb=" N2 G a1045 " 0.015 2.00e-02 2.50e+03 pdb=" N3 G a1045 " -0.004 2.00e-02 2.50e+03 pdb=" C4 G a1045 " -0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' G a 10 " 0.039 2.00e-02 2.50e+03 1.64e-02 8.02e+00 pdb=" N9 G a 10 " -0.037 2.00e-02 2.50e+03 pdb=" C8 G a 10 " -0.004 2.00e-02 2.50e+03 pdb=" N7 G a 10 " 0.000 2.00e-02 2.50e+03 pdb=" C5 G a 10 " 0.001 2.00e-02 2.50e+03 pdb=" C6 G a 10 " 0.005 2.00e-02 2.50e+03 pdb=" O6 G a 10 " 0.010 2.00e-02 2.50e+03 pdb=" N1 G a 10 " 0.003 2.00e-02 2.50e+03 pdb=" C2 G a 10 " -0.001 2.00e-02 2.50e+03 pdb=" N2 G a 10 " -0.001 2.00e-02 2.50e+03 pdb=" N3 G a 10 " -0.006 2.00e-02 2.50e+03 pdb=" C4 G a 10 " -0.009 2.00e-02 2.50e+03 ... (remaining 4871 not shown) Histogram of nonbonded interaction distances: 2.16 - 2.71: 4186 2.71 - 3.25: 49201 3.25 - 3.80: 107147 3.80 - 4.35: 135290 4.35 - 4.90: 180816 Nonbonded interactions: 476640 Sorted by model distance: nonbonded pdb=" O ASN h 99 " pdb=" ND2 ASN h 99 " model vdw 2.158 3.120 nonbonded pdb=" O2' C a 990 " pdb=" NZ LYS n 9 " model vdw 2.195 3.120 nonbonded pdb=" O6 G a1084 " pdb=" N2 G a1096 " model vdw 2.201 3.120 nonbonded pdb=" O LEU l 24 " pdb=" OG SER l 40 " model vdw 2.206 3.040 nonbonded pdb=" OG SER h 92 " pdb=" OE1 GLU h 93 " model vdw 2.207 3.040 ... (remaining 476635 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== 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=0.00 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: 2.410 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.050 Extract box with map and model: 1.640 Check model and map are aligned: 0.300 Set scattering table: 0.400 Process input model: 116.890 Find NCS groups from input model: 0.440 Set up NCS constraints: 0.130 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:10.380 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 132.650 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7937 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 : 0.003 0.038 56057 Z= 0.193 Angle : 0.569 9.628 83215 Z= 0.301 Chirality : 0.035 0.347 10557 Planarity : 0.004 0.052 4874 Dihedral : 22.866 179.261 31356 Min Nonbonded Distance : 2.158 Molprobity Statistics. All-atom Clashscore : 15.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.18 % Favored : 95.82 % Rotamer: Outliers : 0.88 % Allowed : 28.56 % Favored : 70.56 % 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: -1.29 (0.17), residues: 2345 helix: 0.30 (0.17), residues: 889 sheet: -0.88 (0.27), residues: 387 loop : -1.84 (0.18), residues: 1069 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP d 9 HIS 0.010 0.001 HIS d 116 PHE 0.017 0.002 PHE f 55 TYR 0.023 0.002 TYR b 141 ARG 0.015 0.001 ARG d 182 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4690 Ramachandran restraints generated. 2345 Oldfield, 0 Emsley, 2345 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4690 Ramachandran restraints generated. 2345 Oldfield, 0 Emsley, 2345 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 261 residues out of total 2049 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 243 time to evaluate : 2.523 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: b 24 ASN cc_start: 0.5954 (m110) cc_final: 0.5182 (m110) REVERT: b 156 SER cc_start: 0.6675 (t) cc_final: 0.6247 (t) REVERT: b 157 MET cc_start: 0.7664 (tpp) cc_final: 0.7268 (tpp) REVERT: c 151 GLN cc_start: 0.4782 (pp30) cc_final: 0.4565 (pp30) REVERT: f 2 ARG cc_start: 0.6686 (mtt180) cc_final: 0.6273 (mtt180) REVERT: f 33 GLU cc_start: 0.7782 (tm-30) cc_final: 0.7367 (mp0) REVERT: f 70 ASN cc_start: 0.7454 (m-40) cc_final: 0.6979 (m-40) REVERT: g 11 ASP cc_start: 0.2922 (p0) cc_final: 0.2283 (p0) REVERT: g 144 MET cc_start: 0.7717 (mmm) cc_final: 0.6887 (ppp) REVERT: h 99 ASN cc_start: 0.8788 (OUTLIER) cc_final: 0.8404 (t0) REVERT: h 115 ASP cc_start: 0.7067 (t0) cc_final: 0.6535 (p0) REVERT: j 58 TYR cc_start: 0.5312 (m-80) cc_final: 0.5080 (m-80) REVERT: j 88 MET cc_start: 0.1758 (mmt) cc_final: 0.0226 (pmt) REVERT: o 20 THR cc_start: 0.8532 (m) cc_final: 0.8102 (m) REVERT: r 41 ARG cc_start: 0.8903 (mmt180) cc_final: 0.8650 (mmm-85) REVERT: A 62 ASN cc_start: 0.7160 (t0) cc_final: 0.6927 (t0) REVERT: A 65 LYS cc_start: 0.6620 (mttt) cc_final: 0.6410 (pptt) REVERT: A 85 ARG cc_start: 0.4250 (ptp90) cc_final: 0.3761 (ptp-170) REVERT: A 107 MET cc_start: 0.5680 (mpp) cc_final: 0.5280 (mpm) outliers start: 18 outliers final: 6 residues processed: 256 average time/residue: 1.2824 time to fit residues: 416.5168 Evaluate side-chains 185 residues out of total 2049 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 178 time to evaluate : 2.535 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain c residue 171 THR Chi-restraints excluded: chain d residue 116 HIS Chi-restraints excluded: chain h residue 99 ASN Chi-restraints excluded: chain h residue 127 ILE Chi-restraints excluded: chain k residue 116 VAL Chi-restraints excluded: chain l residue 115 LEU Chi-restraints excluded: chain p residue 46 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 324 optimal weight: 20.0000 chunk 291 optimal weight: 10.0000 chunk 161 optimal weight: 6.9990 chunk 99 optimal weight: 50.0000 chunk 196 optimal weight: 5.9990 chunk 155 optimal weight: 30.0000 chunk 300 optimal weight: 8.9990 chunk 116 optimal weight: 40.0000 chunk 183 optimal weight: 10.0000 chunk 224 optimal weight: 8.9990 chunk 348 optimal weight: 6.9990 overall best weight: 7.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** b 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 171 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 180 ASN ** c 68 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** f 61 ASN g 153 HIS ** j 15 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** p 62 ASN p 87 GLN ** q 5 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** t 69 ASN ** t 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 22 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8033 moved from start: 0.1437 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.075 56057 Z= 0.465 Angle : 0.745 8.165 83215 Z= 0.379 Chirality : 0.042 0.335 10557 Planarity : 0.006 0.096 4874 Dihedral : 22.928 178.425 26449 Min Nonbonded Distance : 2.137 Molprobity Statistics. All-atom Clashscore : 15.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.04 % Favored : 92.96 % Rotamer: Outliers : 6.60 % Allowed : 28.36 % Favored : 65.04 % 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: -1.39 (0.17), residues: 2345 helix: 0.11 (0.17), residues: 912 sheet: -0.86 (0.27), residues: 386 loop : -1.86 (0.18), residues: 1047 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP c 22 HIS 0.024 0.002 HIS d 116 PHE 0.032 0.003 PHE e 31 TYR 0.019 0.002 TYR d 198 ARG 0.013 0.001 ARG j 16 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4690 Ramachandran restraints generated. 2345 Oldfield, 0 Emsley, 2345 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4690 Ramachandran restraints generated. 2345 Oldfield, 0 Emsley, 2345 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 319 residues out of total 2049 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 135 poor density : 184 time to evaluate : 2.521 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: b 24 ASN cc_start: 0.5741 (m110) cc_final: 0.5380 (m110) REVERT: b 27 MET cc_start: 0.5713 (OUTLIER) cc_final: 0.4513 (tmm) REVERT: b 30 TYR cc_start: 0.6385 (m-80) cc_final: 0.5713 (m-80) REVERT: b 128 VAL cc_start: 0.4871 (OUTLIER) cc_final: 0.4646 (t) REVERT: b 139 LYS cc_start: 0.7328 (OUTLIER) cc_final: 0.6957 (tppt) REVERT: b 157 MET cc_start: 0.7803 (tpp) cc_final: 0.7342 (tpp) REVERT: c 23 TYR cc_start: 0.8126 (OUTLIER) cc_final: 0.7481 (p90) REVERT: c 141 MET cc_start: 0.7063 (mpm) cc_final: 0.6838 (mpm) REVERT: c 151 GLN cc_start: 0.5211 (pp30) cc_final: 0.4940 (pp30) REVERT: e 54 GLN cc_start: 0.8251 (mm-40) cc_final: 0.7767 (mm110) REVERT: f 2 ARG cc_start: 0.6644 (mtt180) cc_final: 0.5912 (mtp85) REVERT: f 70 ASN cc_start: 0.8148 (m-40) cc_final: 0.7863 (m-40) REVERT: f 94 GLU cc_start: 0.8046 (OUTLIER) cc_final: 0.7553 (pp20) REVERT: g 11 ASP cc_start: 0.3323 (p0) cc_final: 0.3012 (p0) REVERT: g 144 MET cc_start: 0.7679 (mmm) cc_final: 0.6859 (tmt) REVERT: h 24 LYS cc_start: 0.8933 (OUTLIER) cc_final: 0.8728 (ptpp) REVERT: h 34 LYS cc_start: 0.8513 (OUTLIER) cc_final: 0.8216 (ptmm) REVERT: h 68 GLN cc_start: 0.8531 (pm20) cc_final: 0.8257 (pp30) REVERT: h 99 ASN cc_start: 0.8686 (OUTLIER) cc_final: 0.7944 (t0) REVERT: j 14 ASP cc_start: 0.7096 (t70) cc_final: 0.6851 (t70) REVERT: j 88 MET cc_start: 0.1601 (mmt) cc_final: 0.0084 (pmt) REVERT: k 40 ASN cc_start: 0.7773 (OUTLIER) cc_final: 0.7543 (t0) REVERT: k 83 GLU cc_start: 0.7858 (mp0) cc_final: 0.7504 (mp0) REVERT: m 28 SER cc_start: -0.0872 (OUTLIER) cc_final: -0.1395 (m) REVERT: o 80 GLU cc_start: 0.8335 (pp20) cc_final: 0.8106 (pp20) REVERT: r 41 ARG cc_start: 0.8985 (mmt180) cc_final: 0.8747 (mmm160) REVERT: A 82 MET cc_start: 0.5688 (OUTLIER) cc_final: 0.5402 (mtt) REVERT: A 85 ARG cc_start: 0.4255 (ptp90) cc_final: 0.4040 (ptp-170) REVERT: A 104 ILE cc_start: 0.6618 (OUTLIER) cc_final: 0.6244 (mm) outliers start: 135 outliers final: 51 residues processed: 289 average time/residue: 1.1460 time to fit residues: 430.8823 Evaluate side-chains 235 residues out of total 2049 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 172 time to evaluate : 2.489 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain b residue 27 MET Chi-restraints excluded: chain b residue 43 LEU Chi-restraints excluded: chain b residue 128 VAL Chi-restraints excluded: chain b residue 139 LYS Chi-restraints excluded: chain b residue 190 ASN Chi-restraints excluded: chain c residue 23 TYR Chi-restraints excluded: chain c residue 150 THR Chi-restraints excluded: chain c residue 197 VAL Chi-restraints excluded: chain d residue 3 ARG Chi-restraints excluded: chain d residue 63 MET Chi-restraints excluded: chain d residue 64 THR Chi-restraints excluded: chain d residue 100 SER Chi-restraints excluded: chain d residue 116 HIS Chi-restraints excluded: chain d residue 141 VAL Chi-restraints excluded: chain d residue 184 GLU Chi-restraints excluded: chain e residue 17 THR Chi-restraints excluded: chain e residue 18 ILE Chi-restraints excluded: chain e residue 114 VAL Chi-restraints excluded: chain e residue 153 VAL Chi-restraints excluded: chain f residue 3 THR Chi-restraints excluded: chain f residue 6 VAL Chi-restraints excluded: chain f residue 10 VAL Chi-restraints excluded: chain f residue 53 ASN Chi-restraints excluded: chain f residue 91 VAL Chi-restraints excluded: chain f residue 94 GLU Chi-restraints excluded: chain g residue 115 THR Chi-restraints excluded: chain h residue 24 LYS Chi-restraints excluded: chain h residue 34 LYS Chi-restraints excluded: chain h residue 36 ILE Chi-restraints excluded: chain h residue 74 ILE Chi-restraints excluded: chain h residue 75 THR Chi-restraints excluded: chain h residue 99 ASN Chi-restraints excluded: chain h residue 116 LYS Chi-restraints excluded: chain h residue 127 ILE Chi-restraints excluded: chain i residue 24 VAL Chi-restraints excluded: chain i residue 67 VAL Chi-restraints excluded: chain k residue 20 VAL Chi-restraints excluded: chain k residue 40 ASN Chi-restraints excluded: chain k residue 82 VAL Chi-restraints excluded: chain k residue 116 VAL Chi-restraints excluded: chain l residue 30 SER Chi-restraints excluded: chain l residue 74 ILE Chi-restraints excluded: chain l residue 109 HIS Chi-restraints excluded: chain l residue 115 LEU Chi-restraints excluded: chain m residue 15 VAL Chi-restraints excluded: chain m residue 28 SER Chi-restraints excluded: chain n residue 4 THR Chi-restraints excluded: chain n residue 31 HIS Chi-restraints excluded: chain p residue 22 VAL Chi-restraints excluded: chain q residue 28 GLU Chi-restraints excluded: chain q residue 57 LEU Chi-restraints excluded: chain q residue 78 VAL Chi-restraints excluded: chain r residue 61 THR Chi-restraints excluded: chain s residue 84 VAL Chi-restraints excluded: chain t residue 4 ILE Chi-restraints excluded: chain t residue 18 GLU Chi-restraints excluded: chain t residue 32 VAL Chi-restraints excluded: chain t residue 37 THR Chi-restraints excluded: chain t residue 41 ASN Chi-restraints excluded: chain t residue 50 VAL Chi-restraints excluded: chain A residue 20 ILE Chi-restraints excluded: chain A residue 82 MET Chi-restraints excluded: chain A residue 104 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 193 optimal weight: 7.9990 chunk 108 optimal weight: 7.9990 chunk 290 optimal weight: 10.0000 chunk 237 optimal weight: 2.9990 chunk 96 optimal weight: 50.0000 chunk 349 optimal weight: 8.9990 chunk 377 optimal weight: 7.9990 chunk 311 optimal weight: 20.0000 chunk 346 optimal weight: 10.0000 chunk 119 optimal weight: 30.0000 chunk 280 optimal weight: 50.0000 overall best weight: 7.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** b 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 171 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** f 61 ASN ** j 15 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 70 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** p 62 ASN p 87 GLN ** q 5 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** t 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 22 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8031 moved from start: 0.1840 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.071 56057 Z= 0.437 Angle : 0.709 8.828 83215 Z= 0.363 Chirality : 0.042 0.335 10557 Planarity : 0.005 0.072 4874 Dihedral : 22.916 176.986 26446 Min Nonbonded Distance : 2.081 Molprobity Statistics. All-atom Clashscore : 14.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.99 % Favored : 93.01 % Rotamer: Outliers : 7.78 % Allowed : 27.63 % Favored : 64.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.49 (0.17), residues: 2345 helix: 0.05 (0.17), residues: 907 sheet: -0.94 (0.27), residues: 380 loop : -1.92 (0.18), residues: 1058 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP h 132 HIS 0.022 0.002 HIS d 116 PHE 0.019 0.002 PHE f 76 TYR 0.016 0.002 TYR p 40 ARG 0.010 0.001 ARG g 138 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4690 Ramachandran restraints generated. 2345 Oldfield, 0 Emsley, 2345 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4690 Ramachandran restraints generated. 2345 Oldfield, 0 Emsley, 2345 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 344 residues out of total 2049 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 159 poor density : 185 time to evaluate : 2.534 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: b 24 ASN cc_start: 0.5843 (m110) cc_final: 0.5540 (m110) REVERT: b 27 MET cc_start: 0.5520 (OUTLIER) cc_final: 0.4469 (tmm) REVERT: b 30 TYR cc_start: 0.6354 (m-80) cc_final: 0.5642 (m-80) REVERT: b 128 VAL cc_start: 0.4901 (OUTLIER) cc_final: 0.4651 (t) REVERT: b 139 LYS cc_start: 0.7389 (OUTLIER) cc_final: 0.6992 (tppt) REVERT: b 154 MET cc_start: 0.0778 (OUTLIER) cc_final: 0.0566 (tmt) REVERT: b 156 SER cc_start: 0.6631 (t) cc_final: 0.4927 (p) REVERT: b 157 MET cc_start: 0.7799 (tpp) cc_final: 0.7037 (tmm) REVERT: c 23 TYR cc_start: 0.8217 (OUTLIER) cc_final: 0.7627 (p90) REVERT: c 141 MET cc_start: 0.6967 (mpm) cc_final: 0.6580 (mpm) REVERT: c 151 GLN cc_start: 0.5141 (pp30) cc_final: 0.4855 (pp30) REVERT: c 156 LEU cc_start: 0.2131 (OUTLIER) cc_final: 0.1436 (mp) REVERT: d 166 ASN cc_start: 0.7778 (OUTLIER) cc_final: 0.7456 (t0) REVERT: d 178 ARG cc_start: 0.7583 (OUTLIER) cc_final: 0.6446 (pmt-80) REVERT: e 76 ARG cc_start: 0.6954 (OUTLIER) cc_final: 0.6360 (mmm160) REVERT: f 2 ARG cc_start: 0.6706 (mtt180) cc_final: 0.5931 (mtp85) REVERT: f 36 GLU cc_start: 0.7970 (pm20) cc_final: 0.7726 (pm20) REVERT: f 66 LYS cc_start: 0.7238 (ptpp) cc_final: 0.7028 (ptpp) REVERT: f 94 GLU cc_start: 0.8087 (OUTLIER) cc_final: 0.7594 (pp20) REVERT: g 11 ASP cc_start: 0.2905 (p0) cc_final: 0.2534 (p0) REVERT: g 116 MET cc_start: 0.4161 (mmt) cc_final: 0.3761 (mpm) REVERT: g 144 MET cc_start: 0.7710 (mmm) cc_final: 0.6839 (tmt) REVERT: h 34 LYS cc_start: 0.8497 (OUTLIER) cc_final: 0.8129 (ptmm) REVERT: h 99 ASN cc_start: 0.8714 (OUTLIER) cc_final: 0.8033 (t0) REVERT: i 67 VAL cc_start: 0.6571 (OUTLIER) cc_final: 0.6338 (t) REVERT: j 14 ASP cc_start: 0.7056 (t70) cc_final: 0.6842 (t70) REVERT: j 88 MET cc_start: 0.1594 (mmt) cc_final: -0.0021 (pmt) REVERT: k 26 THR cc_start: 0.7515 (OUTLIER) cc_final: 0.7289 (p) REVERT: k 36 ASP cc_start: 0.9040 (m-30) cc_final: 0.8601 (p0) REVERT: k 40 ASN cc_start: 0.8038 (OUTLIER) cc_final: 0.7812 (t0) REVERT: o 77 ARG cc_start: 0.7796 (OUTLIER) cc_final: 0.7110 (ptm160) REVERT: o 80 GLU cc_start: 0.8392 (pp20) cc_final: 0.8087 (pp20) REVERT: t 49 LEU cc_start: 0.8144 (OUTLIER) cc_final: 0.7726 (mp) REVERT: t 63 SER cc_start: 0.8918 (m) cc_final: 0.8507 (p) REVERT: A 16 GLU cc_start: 0.7071 (mp0) cc_final: 0.6431 (mp0) REVERT: A 61 GLU cc_start: 0.8489 (mm-30) cc_final: 0.8152 (tm-30) REVERT: A 85 ARG cc_start: 0.4015 (ptp90) cc_final: 0.3673 (ptp-170) REVERT: A 104 ILE cc_start: 0.6589 (OUTLIER) cc_final: 0.6360 (mm) outliers start: 159 outliers final: 63 residues processed: 314 average time/residue: 1.1540 time to fit residues: 468.9142 Evaluate side-chains 255 residues out of total 2049 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 174 time to evaluate : 2.528 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain b residue 27 MET Chi-restraints excluded: chain b residue 43 LEU Chi-restraints excluded: chain b residue 128 VAL Chi-restraints excluded: chain b residue 139 LYS Chi-restraints excluded: chain b residue 154 MET Chi-restraints excluded: chain b residue 190 ASN Chi-restraints excluded: chain c residue 23 TYR Chi-restraints excluded: chain c residue 150 THR Chi-restraints excluded: chain c residue 156 LEU Chi-restraints excluded: chain c residue 197 VAL Chi-restraints excluded: chain d residue 3 ARG Chi-restraints excluded: chain d residue 8 ASN Chi-restraints excluded: chain d residue 45 SER Chi-restraints excluded: chain d residue 81 VAL Chi-restraints excluded: chain d residue 100 SER Chi-restraints excluded: chain d residue 114 VAL Chi-restraints excluded: chain d residue 141 VAL Chi-restraints excluded: chain d residue 166 ASN Chi-restraints excluded: chain d residue 178 ARG Chi-restraints excluded: chain d residue 184 GLU Chi-restraints excluded: chain e residue 17 THR Chi-restraints excluded: chain e residue 18 ILE Chi-restraints excluded: chain e residue 52 LYS Chi-restraints excluded: chain e residue 76 ARG Chi-restraints excluded: chain e residue 84 THR Chi-restraints excluded: chain e residue 114 VAL Chi-restraints excluded: chain e residue 153 VAL Chi-restraints excluded: chain e residue 161 VAL Chi-restraints excluded: chain f residue 3 THR Chi-restraints excluded: chain f residue 6 VAL Chi-restraints excluded: chain f residue 7 MET Chi-restraints excluded: chain f residue 10 VAL Chi-restraints excluded: chain f residue 43 TRP Chi-restraints excluded: chain f residue 91 VAL Chi-restraints excluded: chain f residue 94 GLU Chi-restraints excluded: chain g residue 115 THR Chi-restraints excluded: chain h residue 34 LYS Chi-restraints excluded: chain h residue 36 ILE Chi-restraints excluded: chain h residue 62 LEU Chi-restraints excluded: chain h residue 74 ILE Chi-restraints excluded: chain h residue 99 ASN Chi-restraints excluded: chain h residue 127 ILE Chi-restraints excluded: chain i residue 67 VAL Chi-restraints excluded: chain k residue 20 VAL Chi-restraints excluded: chain k residue 26 THR Chi-restraints excluded: chain k residue 40 ASN Chi-restraints excluded: chain k residue 82 VAL Chi-restraints excluded: chain k residue 110 ILE Chi-restraints excluded: chain k residue 116 VAL Chi-restraints excluded: chain l residue 30 SER Chi-restraints excluded: chain l residue 74 ILE Chi-restraints excluded: chain l residue 100 VAL Chi-restraints excluded: chain l residue 109 HIS Chi-restraints excluded: chain l residue 121 ASP Chi-restraints excluded: chain m residue 15 VAL Chi-restraints excluded: chain n residue 4 THR Chi-restraints excluded: chain o residue 77 ARG Chi-restraints excluded: chain p residue 3 VAL Chi-restraints excluded: chain p residue 22 VAL Chi-restraints excluded: chain p residue 43 THR Chi-restraints excluded: chain p residue 80 ILE Chi-restraints excluded: chain q residue 28 GLU Chi-restraints excluded: chain q residue 40 VAL Chi-restraints excluded: chain q residue 57 LEU Chi-restraints excluded: chain q residue 78 VAL Chi-restraints excluded: chain r residue 61 THR Chi-restraints excluded: chain s residue 84 VAL Chi-restraints excluded: chain t residue 4 ILE Chi-restraints excluded: chain t residue 13 THR Chi-restraints excluded: chain t residue 18 GLU Chi-restraints excluded: chain t residue 32 VAL Chi-restraints excluded: chain t residue 37 THR Chi-restraints excluded: chain t residue 41 ASN Chi-restraints excluded: chain t residue 49 LEU Chi-restraints excluded: chain t residue 50 VAL Chi-restraints excluded: chain A residue 17 LEU Chi-restraints excluded: chain A residue 20 ILE Chi-restraints excluded: chain A residue 30 VAL Chi-restraints excluded: chain A residue 34 THR Chi-restraints excluded: chain A residue 78 LEU Chi-restraints excluded: chain A residue 104 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 345 optimal weight: 3.9990 chunk 262 optimal weight: 0.9990 chunk 181 optimal weight: 5.9990 chunk 38 optimal weight: 5.9990 chunk 166 optimal weight: 6.9990 chunk 234 optimal weight: 7.9990 chunk 350 optimal weight: 3.9990 chunk 371 optimal weight: 0.7980 chunk 183 optimal weight: 20.0000 chunk 332 optimal weight: 1.9990 chunk 100 optimal weight: 50.0000 overall best weight: 2.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** b 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 171 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** g 153 HIS h 16 ASN ** j 15 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 70 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** o 46 HIS ** q 5 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** t 24 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7966 moved from start: 0.1855 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.066 56057 Z= 0.192 Angle : 0.566 8.840 83215 Z= 0.293 Chirality : 0.034 0.327 10557 Planarity : 0.004 0.050 4874 Dihedral : 22.783 177.540 26442 Min Nonbonded Distance : 2.130 Molprobity Statistics. All-atom Clashscore : 12.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.84 % Favored : 94.16 % Rotamer: Outliers : 5.33 % Allowed : 29.68 % Favored : 64.99 % 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: -1.18 (0.17), residues: 2345 helix: 0.42 (0.17), residues: 907 sheet: -0.99 (0.26), residues: 380 loop : -1.77 (0.18), residues: 1058 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP s 34 HIS 0.005 0.001 HIS l 109 PHE 0.011 0.001 PHE b 56 TYR 0.020 0.002 TYR A 100 ARG 0.007 0.000 ARG j 16 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4690 Ramachandran restraints generated. 2345 Oldfield, 0 Emsley, 2345 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4690 Ramachandran restraints generated. 2345 Oldfield, 0 Emsley, 2345 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 305 residues out of total 2049 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 109 poor density : 196 time to evaluate : 2.544 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: b 24 ASN cc_start: 0.5818 (m110) cc_final: 0.5443 (m110) REVERT: b 27 MET cc_start: 0.5449 (OUTLIER) cc_final: 0.4449 (tmm) REVERT: b 30 TYR cc_start: 0.6428 (m-80) cc_final: 0.5727 (m-80) REVERT: b 139 LYS cc_start: 0.7390 (OUTLIER) cc_final: 0.7014 (tppt) REVERT: b 156 SER cc_start: 0.6629 (t) cc_final: 0.4650 (p) REVERT: b 157 MET cc_start: 0.7739 (tpp) cc_final: 0.7150 (tmm) REVERT: c 76 ILE cc_start: 0.0497 (tp) cc_final: 0.0202 (mp) REVERT: c 141 MET cc_start: 0.6978 (mpm) cc_final: 0.6681 (mpm) REVERT: c 151 GLN cc_start: 0.5582 (pp30) cc_final: 0.4945 (pp30) REVERT: c 156 LEU cc_start: 0.2226 (OUTLIER) cc_final: 0.1861 (mp) REVERT: c 200 TRP cc_start: 0.5372 (m-90) cc_final: 0.5097 (m-90) REVERT: d 178 ARG cc_start: 0.7634 (OUTLIER) cc_final: 0.6541 (pmt-80) REVERT: d 181 GLU cc_start: 0.6508 (OUTLIER) cc_final: 0.6301 (tm-30) REVERT: f 2 ARG cc_start: 0.6752 (mtt180) cc_final: 0.6040 (mtp85) REVERT: f 70 ASN cc_start: 0.7730 (m-40) cc_final: 0.7386 (m-40) REVERT: f 94 GLU cc_start: 0.7994 (OUTLIER) cc_final: 0.7454 (pp20) REVERT: g 11 ASP cc_start: 0.2759 (p0) cc_final: 0.2363 (p0) REVERT: g 116 MET cc_start: 0.4357 (mmt) cc_final: 0.4107 (mpm) REVERT: g 144 MET cc_start: 0.7684 (mmm) cc_final: 0.6883 (ppp) REVERT: h 68 GLN cc_start: 0.8640 (pm20) cc_final: 0.8140 (pp30) REVERT: h 99 ASN cc_start: 0.8726 (OUTLIER) cc_final: 0.7911 (t0) REVERT: i 67 VAL cc_start: 0.6585 (OUTLIER) cc_final: 0.6349 (t) REVERT: j 14 ASP cc_start: 0.6986 (t70) cc_final: 0.6775 (t70) REVERT: k 34 ILE cc_start: 0.7346 (tp) cc_final: 0.6853 (pp) REVERT: k 36 ASP cc_start: 0.8991 (m-30) cc_final: 0.8552 (p0) REVERT: k 40 ASN cc_start: 0.7968 (OUTLIER) cc_final: 0.7687 (t0) REVERT: l 75 GLU cc_start: 0.8651 (OUTLIER) cc_final: 0.8412 (mt-10) REVERT: o 80 GLU cc_start: 0.8372 (pp20) cc_final: 0.8015 (pp20) REVERT: r 32 GLU cc_start: 0.8770 (mm-30) cc_final: 0.8391 (pp20) REVERT: A 16 GLU cc_start: 0.7108 (OUTLIER) cc_final: 0.6511 (mp0) REVERT: A 61 GLU cc_start: 0.8468 (mm-30) cc_final: 0.8208 (tm-30) REVERT: A 99 GLU cc_start: 0.7277 (pp20) cc_final: 0.6735 (pm20) outliers start: 109 outliers final: 41 residues processed: 279 average time/residue: 1.1158 time to fit residues: 407.3258 Evaluate side-chains 226 residues out of total 2049 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 174 time to evaluate : 2.510 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain b residue 27 MET Chi-restraints excluded: chain b residue 139 LYS Chi-restraints excluded: chain b residue 190 ASN Chi-restraints excluded: chain c residue 156 LEU Chi-restraints excluded: chain c residue 197 VAL Chi-restraints excluded: chain d residue 64 THR Chi-restraints excluded: chain d residue 81 VAL Chi-restraints excluded: chain d residue 178 ARG Chi-restraints excluded: chain d residue 181 GLU Chi-restraints excluded: chain e residue 17 THR Chi-restraints excluded: chain e residue 18 ILE Chi-restraints excluded: chain e residue 52 LYS Chi-restraints excluded: chain e residue 161 VAL Chi-restraints excluded: chain f residue 10 VAL Chi-restraints excluded: chain f residue 26 PHE Chi-restraints excluded: chain f residue 86 ILE Chi-restraints excluded: chain f residue 91 VAL Chi-restraints excluded: chain f residue 94 GLU Chi-restraints excluded: chain g residue 115 THR Chi-restraints excluded: chain g residue 126 ASP Chi-restraints excluded: chain h residue 62 LEU Chi-restraints excluded: chain h residue 99 ASN Chi-restraints excluded: chain h residue 127 ILE Chi-restraints excluded: chain i residue 67 VAL Chi-restraints excluded: chain j residue 69 THR Chi-restraints excluded: chain k residue 35 THR Chi-restraints excluded: chain k residue 40 ASN Chi-restraints excluded: chain k residue 82 VAL Chi-restraints excluded: chain k residue 116 VAL Chi-restraints excluded: chain l residue 75 GLU Chi-restraints excluded: chain l residue 100 VAL Chi-restraints excluded: chain l residue 109 HIS Chi-restraints excluded: chain l residue 121 ASP Chi-restraints excluded: chain m residue 15 VAL Chi-restraints excluded: chain p residue 12 SER Chi-restraints excluded: chain p residue 22 VAL Chi-restraints excluded: chain p residue 43 THR Chi-restraints excluded: chain p residue 46 ASN Chi-restraints excluded: chain p residue 80 ILE Chi-restraints excluded: chain q residue 27 VAL Chi-restraints excluded: chain q residue 28 GLU Chi-restraints excluded: chain q residue 57 LEU Chi-restraints excluded: chain q residue 78 VAL Chi-restraints excluded: chain s residue 71 LEU Chi-restraints excluded: chain s residue 84 VAL Chi-restraints excluded: chain t residue 4 ILE Chi-restraints excluded: chain t residue 18 GLU Chi-restraints excluded: chain t residue 32 VAL Chi-restraints excluded: chain t residue 37 THR Chi-restraints excluded: chain t residue 51 SER Chi-restraints excluded: chain A residue 16 GLU Chi-restraints excluded: chain A residue 78 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 309 optimal weight: 0.7980 chunk 210 optimal weight: 9.9990 chunk 5 optimal weight: 8.9990 chunk 276 optimal weight: 30.0000 chunk 153 optimal weight: 8.9990 chunk 316 optimal weight: 0.7980 chunk 256 optimal weight: 0.6980 chunk 0 optimal weight: 10.0000 chunk 189 optimal weight: 20.0000 chunk 333 optimal weight: 7.9990 chunk 93 optimal weight: 30.0000 overall best weight: 3.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** b 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 77 GLN ** b 171 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** j 15 HIS ** j 70 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7997 moved from start: 0.2025 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 56057 Z= 0.262 Angle : 0.599 8.714 83215 Z= 0.308 Chirality : 0.036 0.334 10557 Planarity : 0.004 0.050 4874 Dihedral : 22.735 177.117 26442 Min Nonbonded Distance : 2.135 Molprobity Statistics. All-atom Clashscore : 12.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.57 % Favored : 93.43 % Rotamer: Outliers : 5.92 % Allowed : 30.12 % Favored : 63.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.06 (0.17), residues: 2345 helix: 0.51 (0.17), residues: 905 sheet: -0.88 (0.27), residues: 368 loop : -1.71 (0.18), residues: 1072 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP s 34 HIS 0.008 0.001 HIS l 109 PHE 0.015 0.002 PHE f 76 TYR 0.014 0.002 TYR d 61 ARG 0.005 0.000 ARG d 5 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4690 Ramachandran restraints generated. 2345 Oldfield, 0 Emsley, 2345 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4690 Ramachandran restraints generated. 2345 Oldfield, 0 Emsley, 2345 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 302 residues out of total 2049 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 121 poor density : 181 time to evaluate : 2.519 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: b 24 ASN cc_start: 0.5875 (m110) cc_final: 0.5550 (m110) REVERT: b 27 MET cc_start: 0.5359 (OUTLIER) cc_final: 0.4447 (tmm) REVERT: b 30 TYR cc_start: 0.6406 (m-80) cc_final: 0.5792 (m-80) REVERT: b 128 VAL cc_start: 0.4714 (OUTLIER) cc_final: 0.4446 (t) REVERT: b 139 LYS cc_start: 0.7394 (OUTLIER) cc_final: 0.7010 (tppt) REVERT: b 156 SER cc_start: 0.6170 (t) cc_final: 0.5649 (p) REVERT: b 157 MET cc_start: 0.7750 (tpp) cc_final: 0.7424 (tmm) REVERT: c 76 ILE cc_start: 0.0506 (tp) cc_final: 0.0206 (mp) REVERT: c 141 MET cc_start: 0.6969 (mpm) cc_final: 0.6667 (mpm) REVERT: c 151 GLN cc_start: 0.5678 (pp30) cc_final: 0.5052 (pp30) REVERT: c 200 TRP cc_start: 0.5444 (m-90) cc_final: 0.5096 (m-90) REVERT: d 166 ASN cc_start: 0.7716 (OUTLIER) cc_final: 0.7512 (t0) REVERT: d 178 ARG cc_start: 0.7655 (OUTLIER) cc_final: 0.6592 (pmt-80) REVERT: f 2 ARG cc_start: 0.6660 (mtt180) cc_final: 0.6154 (mtt90) REVERT: f 70 ASN cc_start: 0.7877 (m-40) cc_final: 0.7561 (m-40) REVERT: f 94 GLU cc_start: 0.8034 (OUTLIER) cc_final: 0.7510 (pp20) REVERT: g 11 ASP cc_start: 0.2579 (p0) cc_final: 0.2196 (p0) REVERT: g 144 MET cc_start: 0.7647 (mmm) cc_final: 0.6890 (ppp) REVERT: h 68 GLN cc_start: 0.8739 (pm20) cc_final: 0.8426 (pm20) REVERT: h 69 ASN cc_start: 0.8524 (p0) cc_final: 0.8233 (p0) REVERT: h 99 ASN cc_start: 0.8778 (OUTLIER) cc_final: 0.8040 (t0) REVERT: i 67 VAL cc_start: 0.6586 (OUTLIER) cc_final: 0.6332 (t) REVERT: k 26 THR cc_start: 0.7546 (OUTLIER) cc_final: 0.7316 (p) REVERT: k 34 ILE cc_start: 0.7142 (tp) cc_final: 0.6729 (pp) REVERT: k 40 ASN cc_start: 0.8018 (OUTLIER) cc_final: 0.7677 (t0) REVERT: l 75 GLU cc_start: 0.8640 (OUTLIER) cc_final: 0.8413 (mt-10) REVERT: o 80 GLU cc_start: 0.8451 (pp20) cc_final: 0.8115 (pp20) REVERT: s 12 ASP cc_start: 0.1067 (OUTLIER) cc_final: 0.0696 (m-30) REVERT: t 45 ASN cc_start: 0.8391 (p0) cc_final: 0.7927 (p0) REVERT: t 49 LEU cc_start: 0.8149 (OUTLIER) cc_final: 0.7758 (mp) REVERT: A 16 GLU cc_start: 0.7104 (OUTLIER) cc_final: 0.6507 (mp0) REVERT: A 61 GLU cc_start: 0.8469 (mm-30) cc_final: 0.8236 (tm-30) REVERT: A 86 ILE cc_start: 0.8048 (pt) cc_final: 0.7845 (pp) REVERT: A 99 GLU cc_start: 0.7420 (pp20) cc_final: 0.6968 (pm20) outliers start: 121 outliers final: 58 residues processed: 278 average time/residue: 1.1382 time to fit residues: 415.2124 Evaluate side-chains 241 residues out of total 2049 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 169 time to evaluate : 2.492 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain b residue 27 MET Chi-restraints excluded: chain b residue 128 VAL Chi-restraints excluded: chain b residue 139 LYS Chi-restraints excluded: chain b residue 154 MET Chi-restraints excluded: chain b residue 190 ASN Chi-restraints excluded: chain c residue 150 THR Chi-restraints excluded: chain c residue 172 VAL Chi-restraints excluded: chain c residue 197 VAL Chi-restraints excluded: chain d residue 64 THR Chi-restraints excluded: chain d residue 81 VAL Chi-restraints excluded: chain d residue 100 SER Chi-restraints excluded: chain d residue 141 VAL Chi-restraints excluded: chain d residue 166 ASN Chi-restraints excluded: chain d residue 178 ARG Chi-restraints excluded: chain e residue 17 THR Chi-restraints excluded: chain e residue 18 ILE Chi-restraints excluded: chain e residue 52 LYS Chi-restraints excluded: chain e residue 84 THR Chi-restraints excluded: chain e residue 125 SER Chi-restraints excluded: chain e residue 161 VAL Chi-restraints excluded: chain f residue 3 THR Chi-restraints excluded: chain f residue 6 VAL Chi-restraints excluded: chain f residue 7 MET Chi-restraints excluded: chain f residue 53 ASN Chi-restraints excluded: chain f residue 86 ILE Chi-restraints excluded: chain f residue 91 VAL Chi-restraints excluded: chain f residue 94 GLU Chi-restraints excluded: chain g residue 115 THR Chi-restraints excluded: chain g residue 126 ASP Chi-restraints excluded: chain h residue 62 LEU Chi-restraints excluded: chain h residue 74 ILE Chi-restraints excluded: chain h residue 99 ASN Chi-restraints excluded: chain h residue 127 ILE Chi-restraints excluded: chain i residue 24 VAL Chi-restraints excluded: chain i residue 67 VAL Chi-restraints excluded: chain j residue 69 THR Chi-restraints excluded: chain k residue 26 THR Chi-restraints excluded: chain k residue 40 ASN Chi-restraints excluded: chain k residue 55 SER Chi-restraints excluded: chain k residue 82 VAL Chi-restraints excluded: chain k residue 116 VAL Chi-restraints excluded: chain l residue 40 SER Chi-restraints excluded: chain l residue 53 MET Chi-restraints excluded: chain l residue 74 ILE Chi-restraints excluded: chain l residue 75 GLU Chi-restraints excluded: chain l residue 100 VAL Chi-restraints excluded: chain l residue 109 HIS Chi-restraints excluded: chain l residue 121 ASP Chi-restraints excluded: chain m residue 15 VAL Chi-restraints excluded: chain p residue 12 SER Chi-restraints excluded: chain p residue 22 VAL Chi-restraints excluded: chain p residue 43 THR Chi-restraints excluded: chain p residue 46 ASN Chi-restraints excluded: chain p residue 80 ILE Chi-restraints excluded: chain q residue 27 VAL Chi-restraints excluded: chain q residue 28 GLU Chi-restraints excluded: chain q residue 57 LEU Chi-restraints excluded: chain q residue 78 VAL Chi-restraints excluded: chain r residue 59 MET Chi-restraints excluded: chain s residue 12 ASP Chi-restraints excluded: chain s residue 84 VAL Chi-restraints excluded: chain t residue 4 ILE Chi-restraints excluded: chain t residue 18 GLU Chi-restraints excluded: chain t residue 32 VAL Chi-restraints excluded: chain t residue 37 THR Chi-restraints excluded: chain t residue 41 ASN Chi-restraints excluded: chain t residue 49 LEU Chi-restraints excluded: chain t residue 50 VAL Chi-restraints excluded: chain t residue 51 SER Chi-restraints excluded: chain t residue 54 VAL Chi-restraints excluded: chain A residue 16 GLU Chi-restraints excluded: chain A residue 78 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 124 optimal weight: 50.0000 chunk 334 optimal weight: 0.9990 chunk 73 optimal weight: 10.0000 chunk 217 optimal weight: 9.9990 chunk 91 optimal weight: 10.0000 chunk 371 optimal weight: 4.9990 chunk 308 optimal weight: 6.9990 chunk 172 optimal weight: 1.9990 chunk 30 optimal weight: 8.9990 chunk 122 optimal weight: 50.0000 chunk 195 optimal weight: 0.7980 overall best weight: 3.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** b 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 171 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 70 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7980 moved from start: 0.2194 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 56057 Z= 0.223 Angle : 0.569 9.778 83215 Z= 0.293 Chirality : 0.034 0.333 10557 Planarity : 0.004 0.051 4874 Dihedral : 22.678 177.132 26442 Min Nonbonded Distance : 2.149 Molprobity Statistics. All-atom Clashscore : 12.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.31 % Favored : 93.69 % Rotamer: Outliers : 5.13 % Allowed : 31.64 % Favored : 63.23 % 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: -1.02 (0.17), residues: 2345 helix: 0.60 (0.17), residues: 911 sheet: -0.93 (0.27), residues: 356 loop : -1.70 (0.18), residues: 1078 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP s 34 HIS 0.018 0.001 HIS j 15 PHE 0.014 0.001 PHE f 76 TYR 0.022 0.002 TYR f 8 ARG 0.009 0.000 ARG e 76 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4690 Ramachandran restraints generated. 2345 Oldfield, 0 Emsley, 2345 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4690 Ramachandran restraints generated. 2345 Oldfield, 0 Emsley, 2345 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 292 residues out of total 2049 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 105 poor density : 187 time to evaluate : 2.552 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: b 24 ASN cc_start: 0.5810 (m110) cc_final: 0.5508 (m110) REVERT: b 27 MET cc_start: 0.5385 (OUTLIER) cc_final: 0.4683 (tmm) REVERT: b 30 TYR cc_start: 0.6406 (m-80) cc_final: 0.5883 (m-80) REVERT: b 139 LYS cc_start: 0.7442 (OUTLIER) cc_final: 0.7050 (tppt) REVERT: b 157 MET cc_start: 0.7668 (tpp) cc_final: 0.7357 (tmm) REVERT: c 76 ILE cc_start: 0.0493 (tp) cc_final: 0.0195 (mp) REVERT: c 141 MET cc_start: 0.6953 (mpm) cc_final: 0.6649 (mpm) REVERT: c 151 GLN cc_start: 0.5661 (pp30) cc_final: 0.4844 (pp30) REVERT: c 163 ARG cc_start: 0.7478 (tmm-80) cc_final: 0.7083 (pmm-80) REVERT: c 200 TRP cc_start: 0.5579 (m-90) cc_final: 0.5132 (m-90) REVERT: d 178 ARG cc_start: 0.7665 (OUTLIER) cc_final: 0.6627 (pmt-80) REVERT: d 181 GLU cc_start: 0.6510 (OUTLIER) cc_final: 0.6304 (tm-30) REVERT: e 54 GLN cc_start: 0.8198 (mm-40) cc_final: 0.7728 (mm110) REVERT: f 2 ARG cc_start: 0.6657 (mtt180) cc_final: 0.6173 (mtt90) REVERT: f 11 ARG cc_start: 0.6567 (ptt180) cc_final: 0.6319 (ptt180) REVERT: f 70 ASN cc_start: 0.7646 (m-40) cc_final: 0.7289 (m-40) REVERT: f 94 GLU cc_start: 0.7988 (OUTLIER) cc_final: 0.7444 (pp20) REVERT: g 11 ASP cc_start: 0.2577 (p0) cc_final: 0.2227 (p0) REVERT: g 144 MET cc_start: 0.7756 (mmm) cc_final: 0.6956 (pp-130) REVERT: h 99 ASN cc_start: 0.8829 (OUTLIER) cc_final: 0.7956 (t0) REVERT: i 50 LEU cc_start: 0.3955 (OUTLIER) cc_final: 0.3726 (mm) REVERT: i 67 VAL cc_start: 0.6551 (OUTLIER) cc_final: 0.6289 (t) REVERT: j 88 MET cc_start: 0.1899 (mmt) cc_final: 0.0273 (pmm) REVERT: k 26 THR cc_start: 0.7477 (OUTLIER) cc_final: 0.7252 (p) REVERT: k 34 ILE cc_start: 0.7138 (tp) cc_final: 0.6799 (pp) REVERT: k 36 ASP cc_start: 0.8940 (m-30) cc_final: 0.8535 (p0) REVERT: k 40 ASN cc_start: 0.8041 (OUTLIER) cc_final: 0.7822 (t0) REVERT: l 75 GLU cc_start: 0.8643 (OUTLIER) cc_final: 0.8401 (mt-10) REVERT: o 80 GLU cc_start: 0.8415 (pp20) cc_final: 0.8064 (pp20) REVERT: s 12 ASP cc_start: 0.0881 (OUTLIER) cc_final: 0.0436 (m-30) REVERT: t 18 GLU cc_start: 0.7742 (OUTLIER) cc_final: 0.7367 (tt0) REVERT: t 45 ASN cc_start: 0.8373 (p0) cc_final: 0.8085 (p0) REVERT: A 16 GLU cc_start: 0.7143 (OUTLIER) cc_final: 0.6581 (mp0) REVERT: A 61 GLU cc_start: 0.8426 (mm-30) cc_final: 0.8208 (tm-30) REVERT: A 99 GLU cc_start: 0.7446 (pp20) cc_final: 0.6882 (pm20) REVERT: A 107 MET cc_start: 0.5396 (mpp) cc_final: 0.5153 (mpm) outliers start: 105 outliers final: 54 residues processed: 268 average time/residue: 1.1224 time to fit residues: 395.1520 Evaluate side-chains 241 residues out of total 2049 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 173 time to evaluate : 2.522 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain b residue 27 MET Chi-restraints excluded: chain b residue 139 LYS Chi-restraints excluded: chain b residue 154 MET Chi-restraints excluded: chain b residue 190 ASN Chi-restraints excluded: chain c residue 150 THR Chi-restraints excluded: chain c residue 172 VAL Chi-restraints excluded: chain c residue 197 VAL Chi-restraints excluded: chain d residue 8 ASN Chi-restraints excluded: chain d residue 64 THR Chi-restraints excluded: chain d residue 81 VAL Chi-restraints excluded: chain d residue 100 SER Chi-restraints excluded: chain d residue 141 VAL Chi-restraints excluded: chain d residue 178 ARG Chi-restraints excluded: chain d residue 181 GLU Chi-restraints excluded: chain e residue 17 THR Chi-restraints excluded: chain e residue 52 LYS Chi-restraints excluded: chain e residue 125 SER Chi-restraints excluded: chain e residue 161 VAL Chi-restraints excluded: chain f residue 3 THR Chi-restraints excluded: chain f residue 6 VAL Chi-restraints excluded: chain f residue 7 MET Chi-restraints excluded: chain f residue 26 PHE Chi-restraints excluded: chain f residue 43 TRP Chi-restraints excluded: chain f residue 86 ILE Chi-restraints excluded: chain f residue 91 VAL Chi-restraints excluded: chain f residue 94 GLU Chi-restraints excluded: chain g residue 115 THR Chi-restraints excluded: chain g residue 126 ASP Chi-restraints excluded: chain h residue 62 LEU Chi-restraints excluded: chain h residue 99 ASN Chi-restraints excluded: chain i residue 50 LEU Chi-restraints excluded: chain i residue 67 VAL Chi-restraints excluded: chain j residue 69 THR Chi-restraints excluded: chain k residue 20 VAL Chi-restraints excluded: chain k residue 26 THR Chi-restraints excluded: chain k residue 40 ASN Chi-restraints excluded: chain k residue 42 LEU Chi-restraints excluded: chain k residue 55 SER Chi-restraints excluded: chain k residue 82 VAL Chi-restraints excluded: chain k residue 116 VAL Chi-restraints excluded: chain l residue 40 SER Chi-restraints excluded: chain l residue 53 MET Chi-restraints excluded: chain l residue 74 ILE Chi-restraints excluded: chain l residue 75 GLU Chi-restraints excluded: chain l residue 100 VAL Chi-restraints excluded: chain l residue 109 HIS Chi-restraints excluded: chain l residue 111 VAL Chi-restraints excluded: chain p residue 12 SER Chi-restraints excluded: chain p residue 22 VAL Chi-restraints excluded: chain p residue 43 THR Chi-restraints excluded: chain p residue 80 ILE Chi-restraints excluded: chain q residue 27 VAL Chi-restraints excluded: chain q residue 28 GLU Chi-restraints excluded: chain q residue 52 ASN Chi-restraints excluded: chain q residue 57 LEU Chi-restraints excluded: chain q residue 78 VAL Chi-restraints excluded: chain r residue 59 MET Chi-restraints excluded: chain s residue 12 ASP Chi-restraints excluded: chain s residue 84 VAL Chi-restraints excluded: chain t residue 4 ILE Chi-restraints excluded: chain t residue 18 GLU Chi-restraints excluded: chain t residue 32 VAL Chi-restraints excluded: chain t residue 37 THR Chi-restraints excluded: chain t residue 41 ASN Chi-restraints excluded: chain t residue 51 SER Chi-restraints excluded: chain A residue 16 GLU Chi-restraints excluded: chain A residue 34 THR Chi-restraints excluded: chain A residue 78 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 358 optimal weight: 10.0000 chunk 41 optimal weight: 10.0000 chunk 211 optimal weight: 7.9990 chunk 271 optimal weight: 9.9990 chunk 210 optimal weight: 0.4980 chunk 312 optimal weight: 10.0000 chunk 207 optimal weight: 5.9990 chunk 370 optimal weight: 3.9990 chunk 231 optimal weight: 5.9990 chunk 225 optimal weight: 0.9990 chunk 170 optimal weight: 30.0000 overall best weight: 3.4988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** b 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 171 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 118 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 116 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 142 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 70 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7991 moved from start: 0.2339 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 56057 Z= 0.243 Angle : 0.583 10.507 83215 Z= 0.300 Chirality : 0.035 0.337 10557 Planarity : 0.004 0.048 4874 Dihedral : 22.654 177.231 26440 Min Nonbonded Distance : 2.155 Molprobity Statistics. All-atom Clashscore : 12.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.44 % Favored : 93.56 % Rotamer: Outliers : 5.48 % Allowed : 31.69 % Favored : 62.84 % 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: -0.96 (0.17), residues: 2345 helix: 0.67 (0.17), residues: 904 sheet: -0.97 (0.27), residues: 365 loop : -1.65 (0.18), residues: 1076 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP s 34 HIS 0.010 0.001 HIS j 15 PHE 0.014 0.002 PHE c 129 TYR 0.019 0.002 TYR q 30 ARG 0.011 0.000 ARG j 16 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4690 Ramachandran restraints generated. 2345 Oldfield, 0 Emsley, 2345 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4690 Ramachandran restraints generated. 2345 Oldfield, 0 Emsley, 2345 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 292 residues out of total 2049 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 112 poor density : 180 time to evaluate : 2.595 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: b 24 ASN cc_start: 0.5549 (m110) cc_final: 0.5156 (m110) REVERT: b 27 MET cc_start: 0.5222 (OUTLIER) cc_final: 0.4459 (tmm) REVERT: b 30 TYR cc_start: 0.6442 (m-80) cc_final: 0.5892 (m-80) REVERT: b 139 LYS cc_start: 0.7429 (OUTLIER) cc_final: 0.7102 (tppt) REVERT: b 156 SER cc_start: 0.6272 (t) cc_final: 0.5821 (p) REVERT: b 157 MET cc_start: 0.7583 (tpp) cc_final: 0.7314 (tmm) REVERT: c 76 ILE cc_start: 0.0473 (tp) cc_final: 0.0177 (mp) REVERT: c 141 MET cc_start: 0.6955 (mpm) cc_final: 0.6649 (mpm) REVERT: c 151 GLN cc_start: 0.5239 (pp30) cc_final: 0.4899 (pp30) REVERT: c 200 TRP cc_start: 0.5659 (m-90) cc_final: 0.5105 (m-90) REVERT: d 50 GLN cc_start: 0.8059 (OUTLIER) cc_final: 0.6339 (mm110) REVERT: d 178 ARG cc_start: 0.7677 (OUTLIER) cc_final: 0.6608 (pmt-80) REVERT: d 181 GLU cc_start: 0.6561 (OUTLIER) cc_final: 0.6352 (tm-30) REVERT: e 54 GLN cc_start: 0.8133 (mm-40) cc_final: 0.7770 (mm110) REVERT: f 2 ARG cc_start: 0.6666 (mtt180) cc_final: 0.6204 (mtt90) REVERT: f 11 ARG cc_start: 0.6547 (ptt180) cc_final: 0.6291 (ptt180) REVERT: f 70 ASN cc_start: 0.7711 (m-40) cc_final: 0.7407 (m-40) REVERT: f 94 GLU cc_start: 0.7976 (OUTLIER) cc_final: 0.7428 (pp20) REVERT: g 11 ASP cc_start: 0.2585 (p0) cc_final: 0.2230 (p0) REVERT: g 144 MET cc_start: 0.7732 (mmm) cc_final: 0.6936 (pp-130) REVERT: h 34 LYS cc_start: 0.8338 (OUTLIER) cc_final: 0.7913 (tttm) REVERT: h 99 ASN cc_start: 0.8817 (OUTLIER) cc_final: 0.8001 (t0) REVERT: i 50 LEU cc_start: 0.3942 (OUTLIER) cc_final: 0.3683 (mm) REVERT: i 67 VAL cc_start: 0.6736 (OUTLIER) cc_final: 0.6490 (t) REVERT: j 88 MET cc_start: 0.1900 (mmt) cc_final: 0.0272 (pmm) REVERT: k 26 THR cc_start: 0.7351 (OUTLIER) cc_final: 0.7102 (p) REVERT: k 34 ILE cc_start: 0.7102 (tp) cc_final: 0.6788 (pp) REVERT: k 36 ASP cc_start: 0.8981 (m-30) cc_final: 0.8604 (p0) REVERT: k 40 ASN cc_start: 0.8055 (OUTLIER) cc_final: 0.7808 (t0) REVERT: l 75 GLU cc_start: 0.8637 (OUTLIER) cc_final: 0.8404 (mt-10) REVERT: o 80 GLU cc_start: 0.8427 (pp20) cc_final: 0.8128 (pp20) REVERT: q 42 TYR cc_start: 0.7636 (OUTLIER) cc_final: 0.7004 (p90) REVERT: s 12 ASP cc_start: 0.0842 (OUTLIER) cc_final: 0.0409 (m-30) REVERT: t 45 ASN cc_start: 0.8412 (p0) cc_final: 0.8174 (p0) REVERT: A 16 GLU cc_start: 0.7107 (OUTLIER) cc_final: 0.6532 (mp0) REVERT: A 61 GLU cc_start: 0.8417 (mm-30) cc_final: 0.8169 (tm-30) REVERT: A 86 ILE cc_start: 0.7219 (OUTLIER) cc_final: 0.6953 (pp) REVERT: A 99 GLU cc_start: 0.7211 (pp20) cc_final: 0.6715 (pm20) outliers start: 112 outliers final: 66 residues processed: 270 average time/residue: 1.0967 time to fit residues: 390.2111 Evaluate side-chains 256 residues out of total 2049 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 173 time to evaluate : 2.527 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain b residue 27 MET Chi-restraints excluded: chain b residue 139 LYS Chi-restraints excluded: chain b residue 154 MET Chi-restraints excluded: chain b residue 190 ASN Chi-restraints excluded: chain c residue 150 THR Chi-restraints excluded: chain c residue 172 VAL Chi-restraints excluded: chain c residue 197 VAL Chi-restraints excluded: chain d residue 8 ASN Chi-restraints excluded: chain d residue 50 GLN Chi-restraints excluded: chain d residue 64 THR Chi-restraints excluded: chain d residue 81 VAL Chi-restraints excluded: chain d residue 100 SER Chi-restraints excluded: chain d residue 138 THR Chi-restraints excluded: chain d residue 141 VAL Chi-restraints excluded: chain d residue 178 ARG Chi-restraints excluded: chain d residue 181 GLU Chi-restraints excluded: chain e residue 17 THR Chi-restraints excluded: chain e residue 52 LYS Chi-restraints excluded: chain e residue 84 THR Chi-restraints excluded: chain e residue 125 SER Chi-restraints excluded: chain e residue 161 VAL Chi-restraints excluded: chain f residue 3 THR Chi-restraints excluded: chain f residue 6 VAL Chi-restraints excluded: chain f residue 7 MET Chi-restraints excluded: chain f residue 26 PHE Chi-restraints excluded: chain f residue 53 ASN Chi-restraints excluded: chain f residue 86 ILE Chi-restraints excluded: chain f residue 91 VAL Chi-restraints excluded: chain f residue 94 GLU Chi-restraints excluded: chain g residue 61 VAL Chi-restraints excluded: chain g residue 115 THR Chi-restraints excluded: chain g residue 126 ASP Chi-restraints excluded: chain h residue 34 LYS Chi-restraints excluded: chain h residue 36 ILE Chi-restraints excluded: chain h residue 62 LEU Chi-restraints excluded: chain h residue 74 ILE Chi-restraints excluded: chain h residue 99 ASN Chi-restraints excluded: chain h residue 127 ILE Chi-restraints excluded: chain i residue 50 LEU Chi-restraints excluded: chain i residue 67 VAL Chi-restraints excluded: chain j residue 69 THR Chi-restraints excluded: chain k residue 20 VAL Chi-restraints excluded: chain k residue 26 THR Chi-restraints excluded: chain k residue 40 ASN Chi-restraints excluded: chain k residue 55 SER Chi-restraints excluded: chain k residue 82 VAL Chi-restraints excluded: chain k residue 116 VAL Chi-restraints excluded: chain l residue 40 SER Chi-restraints excluded: chain l residue 53 MET Chi-restraints excluded: chain l residue 74 ILE Chi-restraints excluded: chain l residue 75 GLU Chi-restraints excluded: chain l residue 100 VAL Chi-restraints excluded: chain l residue 109 HIS Chi-restraints excluded: chain l residue 111 VAL Chi-restraints excluded: chain l residue 121 ASP Chi-restraints excluded: chain m residue 15 VAL Chi-restraints excluded: chain n residue 4 THR Chi-restraints excluded: chain o residue 77 ARG Chi-restraints excluded: chain p residue 12 SER Chi-restraints excluded: chain p residue 22 VAL Chi-restraints excluded: chain p residue 43 THR Chi-restraints excluded: chain p residue 80 ILE Chi-restraints excluded: chain q residue 27 VAL Chi-restraints excluded: chain q residue 28 GLU Chi-restraints excluded: chain q residue 42 TYR Chi-restraints excluded: chain q residue 52 ASN Chi-restraints excluded: chain q residue 57 LEU Chi-restraints excluded: chain q residue 78 VAL Chi-restraints excluded: chain r residue 59 MET Chi-restraints excluded: chain s residue 12 ASP Chi-restraints excluded: chain s residue 71 LEU Chi-restraints excluded: chain s residue 84 VAL Chi-restraints excluded: chain t residue 4 ILE Chi-restraints excluded: chain t residue 18 GLU Chi-restraints excluded: chain t residue 32 VAL Chi-restraints excluded: chain t residue 37 THR Chi-restraints excluded: chain t residue 41 ASN Chi-restraints excluded: chain t residue 51 SER Chi-restraints excluded: chain t residue 63 SER Chi-restraints excluded: chain A residue 16 GLU Chi-restraints excluded: chain A residue 34 THR Chi-restraints excluded: chain A residue 78 LEU Chi-restraints excluded: chain A residue 86 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 228 optimal weight: 0.9990 chunk 147 optimal weight: 20.0000 chunk 221 optimal weight: 8.9990 chunk 111 optimal weight: 30.0000 chunk 72 optimal weight: 10.0000 chunk 71 optimal weight: 10.0000 chunk 235 optimal weight: 20.0000 chunk 252 optimal weight: 3.9990 chunk 182 optimal weight: 0.1980 chunk 34 optimal weight: 10.0000 chunk 290 optimal weight: 9.9990 overall best weight: 4.8388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** b 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 171 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 118 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 116 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 142 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** i 52 GLN ** j 70 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 5 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8018 moved from start: 0.2567 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 56057 Z= 0.313 Angle : 0.633 10.864 83215 Z= 0.325 Chirality : 0.037 0.339 10557 Planarity : 0.005 0.058 4874 Dihedral : 22.704 176.660 26440 Min Nonbonded Distance : 2.127 Molprobity Statistics. All-atom Clashscore : 13.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.46 % Favored : 92.54 % Rotamer: Outliers : 5.18 % Allowed : 32.86 % Favored : 61.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.08 (0.17), residues: 2345 helix: 0.52 (0.17), residues: 913 sheet: -1.01 (0.26), residues: 376 loop : -1.70 (0.18), residues: 1056 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP s 34 HIS 0.009 0.001 HIS l 109 PHE 0.016 0.002 PHE c 129 TYR 0.022 0.002 TYR q 30 ARG 0.008 0.001 ARG d 5 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4690 Ramachandran restraints generated. 2345 Oldfield, 0 Emsley, 2345 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4690 Ramachandran restraints generated. 2345 Oldfield, 0 Emsley, 2345 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 290 residues out of total 2049 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 106 poor density : 184 time to evaluate : 2.540 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: b 24 ASN cc_start: 0.5729 (m110) cc_final: 0.5370 (m110) REVERT: b 27 MET cc_start: 0.5312 (OUTLIER) cc_final: 0.4640 (tmm) REVERT: b 30 TYR cc_start: 0.6451 (m-80) cc_final: 0.5917 (m-80) REVERT: b 139 LYS cc_start: 0.7531 (OUTLIER) cc_final: 0.7201 (tppt) REVERT: b 156 SER cc_start: 0.6043 (t) cc_final: 0.5579 (p) REVERT: b 157 MET cc_start: 0.7565 (tpp) cc_final: 0.7296 (tmm) REVERT: c 76 ILE cc_start: 0.0487 (tp) cc_final: 0.0187 (mp) REVERT: c 141 MET cc_start: 0.6990 (mpm) cc_final: 0.6663 (mpm) REVERT: c 151 GLN cc_start: 0.5211 (pp30) cc_final: 0.4894 (pp30) REVERT: c 163 ARG cc_start: 0.7399 (tmm-80) cc_final: 0.6980 (pmm-80) REVERT: c 200 TRP cc_start: 0.5580 (m-90) cc_final: 0.5035 (m-90) REVERT: d 50 GLN cc_start: 0.8184 (OUTLIER) cc_final: 0.6590 (mm-40) REVERT: d 178 ARG cc_start: 0.7646 (OUTLIER) cc_final: 0.6601 (pmt-80) REVERT: d 181 GLU cc_start: 0.6647 (OUTLIER) cc_final: 0.6390 (tm-30) REVERT: e 54 GLN cc_start: 0.8147 (mm-40) cc_final: 0.7727 (mm110) REVERT: f 2 ARG cc_start: 0.6546 (mtt180) cc_final: 0.6084 (mtt90) REVERT: f 8 TYR cc_start: 0.8930 (p90) cc_final: 0.8686 (p90) REVERT: f 11 ARG cc_start: 0.6433 (ptt180) cc_final: 0.6138 (ptt180) REVERT: f 70 ASN cc_start: 0.8063 (m-40) cc_final: 0.7781 (m-40) REVERT: f 94 GLU cc_start: 0.7994 (OUTLIER) cc_final: 0.7499 (pp20) REVERT: g 11 ASP cc_start: 0.2604 (p0) cc_final: 0.2268 (p0) REVERT: g 85 TYR cc_start: 0.1722 (p90) cc_final: 0.1210 (p90) REVERT: g 144 MET cc_start: 0.7685 (mmm) cc_final: 0.6901 (pp-130) REVERT: h 3 MET cc_start: 0.8138 (OUTLIER) cc_final: 0.7801 (tpp) REVERT: h 34 LYS cc_start: 0.8468 (OUTLIER) cc_final: 0.7989 (tttm) REVERT: h 48 ASN cc_start: 0.8274 (OUTLIER) cc_final: 0.7706 (t0) REVERT: h 69 ASN cc_start: 0.8482 (p0) cc_final: 0.8031 (t0) REVERT: h 99 ASN cc_start: 0.8765 (OUTLIER) cc_final: 0.7959 (t0) REVERT: j 88 MET cc_start: 0.1812 (mmt) cc_final: 0.0243 (pmm) REVERT: k 26 THR cc_start: 0.7389 (OUTLIER) cc_final: 0.7094 (p) REVERT: k 36 ASP cc_start: 0.8986 (m-30) cc_final: 0.8589 (p0) REVERT: k 40 ASN cc_start: 0.8112 (OUTLIER) cc_final: 0.7814 (t0) REVERT: l 75 GLU cc_start: 0.8634 (OUTLIER) cc_final: 0.8414 (mt-10) REVERT: n 57 ARG cc_start: 0.5647 (pmt170) cc_final: 0.5329 (pmt170) REVERT: o 80 GLU cc_start: 0.8417 (pp20) cc_final: 0.8101 (pp20) REVERT: q 42 TYR cc_start: 0.7667 (OUTLIER) cc_final: 0.7033 (p90) REVERT: r 32 GLU cc_start: 0.8712 (mm-30) cc_final: 0.8426 (pp20) REVERT: t 45 ASN cc_start: 0.8385 (p0) cc_final: 0.8164 (p0) REVERT: A 16 GLU cc_start: 0.7115 (OUTLIER) cc_final: 0.6377 (mp0) REVERT: A 81 ARG cc_start: 0.8206 (tmt170) cc_final: 0.7680 (tpm-80) REVERT: A 86 ILE cc_start: 0.7249 (OUTLIER) cc_final: 0.7034 (pp) REVERT: A 107 MET cc_start: 0.5386 (mpp) cc_final: 0.5117 (mpm) outliers start: 106 outliers final: 62 residues processed: 268 average time/residue: 1.1375 time to fit residues: 398.7851 Evaluate side-chains 246 residues out of total 2049 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 168 time to evaluate : 2.472 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain b residue 27 MET Chi-restraints excluded: chain b residue 139 LYS Chi-restraints excluded: chain b residue 154 MET Chi-restraints excluded: chain b residue 190 ASN Chi-restraints excluded: chain c residue 150 THR Chi-restraints excluded: chain c residue 172 VAL Chi-restraints excluded: chain c residue 197 VAL Chi-restraints excluded: chain d residue 8 ASN Chi-restraints excluded: chain d residue 50 GLN Chi-restraints excluded: chain d residue 64 THR Chi-restraints excluded: chain d residue 81 VAL Chi-restraints excluded: chain d residue 100 SER Chi-restraints excluded: chain d residue 138 THR Chi-restraints excluded: chain d residue 141 VAL Chi-restraints excluded: chain d residue 178 ARG Chi-restraints excluded: chain d residue 181 GLU Chi-restraints excluded: chain d residue 184 GLU Chi-restraints excluded: chain e residue 17 THR Chi-restraints excluded: chain e residue 18 ILE Chi-restraints excluded: chain e residue 52 LYS Chi-restraints excluded: chain e residue 84 THR Chi-restraints excluded: chain e residue 125 SER Chi-restraints excluded: chain e residue 161 VAL Chi-restraints excluded: chain f residue 3 THR Chi-restraints excluded: chain f residue 6 VAL Chi-restraints excluded: chain f residue 53 ASN Chi-restraints excluded: chain f residue 86 ILE Chi-restraints excluded: chain f residue 91 VAL Chi-restraints excluded: chain f residue 94 GLU Chi-restraints excluded: chain g residue 61 VAL Chi-restraints excluded: chain g residue 115 THR Chi-restraints excluded: chain g residue 126 ASP Chi-restraints excluded: chain h residue 3 MET Chi-restraints excluded: chain h residue 34 LYS Chi-restraints excluded: chain h residue 36 ILE Chi-restraints excluded: chain h residue 48 ASN Chi-restraints excluded: chain h residue 62 LEU Chi-restraints excluded: chain h residue 74 ILE Chi-restraints excluded: chain h residue 99 ASN Chi-restraints excluded: chain h residue 127 ILE Chi-restraints excluded: chain i residue 67 VAL Chi-restraints excluded: chain j residue 69 THR Chi-restraints excluded: chain k residue 20 VAL Chi-restraints excluded: chain k residue 26 THR Chi-restraints excluded: chain k residue 40 ASN Chi-restraints excluded: chain k residue 55 SER Chi-restraints excluded: chain k residue 82 VAL Chi-restraints excluded: chain k residue 116 VAL Chi-restraints excluded: chain l residue 40 SER Chi-restraints excluded: chain l residue 53 MET Chi-restraints excluded: chain l residue 74 ILE Chi-restraints excluded: chain l residue 75 GLU Chi-restraints excluded: chain l residue 100 VAL Chi-restraints excluded: chain l residue 109 HIS Chi-restraints excluded: chain l residue 111 VAL Chi-restraints excluded: chain m residue 15 VAL Chi-restraints excluded: chain m residue 91 HIS Chi-restraints excluded: chain n residue 4 THR Chi-restraints excluded: chain o residue 77 ARG Chi-restraints excluded: chain p residue 3 VAL Chi-restraints excluded: chain p residue 22 VAL Chi-restraints excluded: chain p residue 43 THR Chi-restraints excluded: chain p residue 80 ILE Chi-restraints excluded: chain q residue 28 GLU Chi-restraints excluded: chain q residue 42 TYR Chi-restraints excluded: chain q residue 57 LEU Chi-restraints excluded: chain q residue 78 VAL Chi-restraints excluded: chain r residue 59 MET Chi-restraints excluded: chain s residue 84 VAL Chi-restraints excluded: chain t residue 4 ILE Chi-restraints excluded: chain t residue 18 GLU Chi-restraints excluded: chain t residue 32 VAL Chi-restraints excluded: chain t residue 37 THR Chi-restraints excluded: chain t residue 41 ASN Chi-restraints excluded: chain t residue 63 SER Chi-restraints excluded: chain A residue 16 GLU Chi-restraints excluded: chain A residue 34 THR Chi-restraints excluded: chain A residue 86 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 336 optimal weight: 0.9990 chunk 354 optimal weight: 0.3980 chunk 323 optimal weight: 20.0000 chunk 344 optimal weight: 0.0020 chunk 207 optimal weight: 3.9990 chunk 150 optimal weight: 10.0000 chunk 270 optimal weight: 8.9990 chunk 105 optimal weight: 50.0000 chunk 311 optimal weight: 50.0000 chunk 326 optimal weight: 50.0000 chunk 343 optimal weight: 10.0000 overall best weight: 2.8794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** b 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 116 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 142 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 70 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 5 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7984 moved from start: 0.2638 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 56057 Z= 0.210 Angle : 0.576 11.343 83215 Z= 0.297 Chirality : 0.034 0.339 10557 Planarity : 0.004 0.046 4874 Dihedral : 22.651 177.548 26440 Min Nonbonded Distance : 2.154 Molprobity Statistics. All-atom Clashscore : 12.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.70 % Favored : 93.30 % Rotamer: Outliers : 4.30 % Allowed : 33.74 % Favored : 61.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.98 (0.17), residues: 2345 helix: 0.67 (0.17), residues: 906 sheet: -0.99 (0.27), residues: 365 loop : -1.68 (0.18), residues: 1074 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP p 60 HIS 0.007 0.001 HIS j 15 PHE 0.014 0.001 PHE f 76 TYR 0.021 0.001 TYR q 30 ARG 0.007 0.000 ARG f 25 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4690 Ramachandran restraints generated. 2345 Oldfield, 0 Emsley, 2345 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4690 Ramachandran restraints generated. 2345 Oldfield, 0 Emsley, 2345 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 269 residues out of total 2049 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 181 time to evaluate : 2.515 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: b 24 ASN cc_start: 0.5722 (m110) cc_final: 0.5322 (m110) REVERT: b 27 MET cc_start: 0.5275 (OUTLIER) cc_final: 0.4629 (tmm) REVERT: b 30 TYR cc_start: 0.6432 (m-80) cc_final: 0.5886 (m-80) REVERT: b 139 LYS cc_start: 0.7435 (OUTLIER) cc_final: 0.7096 (tppt) REVERT: b 156 SER cc_start: 0.6132 (t) cc_final: 0.5736 (p) REVERT: b 157 MET cc_start: 0.7556 (tpp) cc_final: 0.7270 (tmm) REVERT: c 76 ILE cc_start: 0.0503 (tp) cc_final: 0.0208 (mp) REVERT: c 141 MET cc_start: 0.6922 (mpm) cc_final: 0.6614 (mpm) REVERT: c 151 GLN cc_start: 0.5299 (pp30) cc_final: 0.4926 (pp30) REVERT: c 163 ARG cc_start: 0.7401 (tmm-80) cc_final: 0.7005 (pmm-80) REVERT: c 200 TRP cc_start: 0.5592 (m-90) cc_final: 0.4979 (m-90) REVERT: d 50 GLN cc_start: 0.8102 (OUTLIER) cc_final: 0.6403 (mm110) REVERT: d 178 ARG cc_start: 0.7725 (OUTLIER) cc_final: 0.6712 (pmt-80) REVERT: d 181 GLU cc_start: 0.6589 (OUTLIER) cc_final: 0.6369 (tm-30) REVERT: f 2 ARG cc_start: 0.6677 (mtt180) cc_final: 0.6214 (mtt90) REVERT: f 11 ARG cc_start: 0.6422 (ptt180) cc_final: 0.6147 (ptt180) REVERT: f 70 ASN cc_start: 0.7654 (m-40) cc_final: 0.7335 (m-40) REVERT: f 94 GLU cc_start: 0.7971 (OUTLIER) cc_final: 0.7443 (pp20) REVERT: g 11 ASP cc_start: 0.2617 (p0) cc_final: 0.2288 (p0) REVERT: g 28 ASN cc_start: 0.6055 (m-40) cc_final: 0.5388 (t0) REVERT: g 85 TYR cc_start: 0.1622 (p90) cc_final: 0.1090 (p90) REVERT: g 144 MET cc_start: 0.7715 (mmm) cc_final: 0.6951 (pp-130) REVERT: h 3 MET cc_start: 0.8089 (OUTLIER) cc_final: 0.7726 (tpp) REVERT: h 34 LYS cc_start: 0.8323 (OUTLIER) cc_final: 0.7911 (tttm) REVERT: h 69 ASN cc_start: 0.8493 (p0) cc_final: 0.7915 (t0) REVERT: h 99 ASN cc_start: 0.8784 (OUTLIER) cc_final: 0.8082 (t0) REVERT: i 7 GLU cc_start: 0.5875 (mp0) cc_final: 0.5521 (tm-30) REVERT: j 88 MET cc_start: 0.1610 (mmt) cc_final: 0.0036 (pmm) REVERT: k 26 THR cc_start: 0.7377 (OUTLIER) cc_final: 0.7087 (p) REVERT: k 36 ASP cc_start: 0.8978 (m-30) cc_final: 0.8586 (p0) REVERT: k 40 ASN cc_start: 0.8110 (OUTLIER) cc_final: 0.7800 (t0) REVERT: l 75 GLU cc_start: 0.8643 (OUTLIER) cc_final: 0.8396 (mt-10) REVERT: m 100 GLN cc_start: -0.0341 (tt0) cc_final: -0.0996 (mt0) REVERT: o 80 GLU cc_start: 0.8426 (pp20) cc_final: 0.8109 (pp20) REVERT: q 42 TYR cc_start: 0.7631 (OUTLIER) cc_final: 0.7062 (p90) REVERT: s 12 ASP cc_start: 0.0920 (OUTLIER) cc_final: 0.0429 (m-30) REVERT: t 45 ASN cc_start: 0.8383 (p0) cc_final: 0.8156 (p0) REVERT: A 16 GLU cc_start: 0.7134 (OUTLIER) cc_final: 0.6480 (mp0) REVERT: A 81 ARG cc_start: 0.8097 (tmt170) cc_final: 0.7722 (tpm-80) REVERT: A 86 ILE cc_start: 0.7147 (OUTLIER) cc_final: 0.6921 (pp) REVERT: A 99 GLU cc_start: 0.7000 (pp20) cc_final: 0.6387 (pm20) REVERT: A 107 MET cc_start: 0.5483 (mpp) cc_final: 0.5176 (mpm) outliers start: 88 outliers final: 57 residues processed: 252 average time/residue: 1.1899 time to fit residues: 388.9818 Evaluate side-chains 247 residues out of total 2049 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 174 time to evaluate : 2.544 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain b residue 27 MET Chi-restraints excluded: chain b residue 139 LYS Chi-restraints excluded: chain b residue 154 MET Chi-restraints excluded: chain b residue 190 ASN Chi-restraints excluded: chain c residue 150 THR Chi-restraints excluded: chain c residue 172 VAL Chi-restraints excluded: chain d residue 50 GLN Chi-restraints excluded: chain d residue 64 THR Chi-restraints excluded: chain d residue 81 VAL Chi-restraints excluded: chain d residue 138 THR Chi-restraints excluded: chain d residue 141 VAL Chi-restraints excluded: chain d residue 178 ARG Chi-restraints excluded: chain d residue 181 GLU Chi-restraints excluded: chain e residue 17 THR Chi-restraints excluded: chain e residue 52 LYS Chi-restraints excluded: chain e residue 125 SER Chi-restraints excluded: chain e residue 161 VAL Chi-restraints excluded: chain f residue 3 THR Chi-restraints excluded: chain f residue 6 VAL Chi-restraints excluded: chain f residue 26 PHE Chi-restraints excluded: chain f residue 86 ILE Chi-restraints excluded: chain f residue 91 VAL Chi-restraints excluded: chain f residue 94 GLU Chi-restraints excluded: chain g residue 61 VAL Chi-restraints excluded: chain g residue 115 THR Chi-restraints excluded: chain g residue 126 ASP Chi-restraints excluded: chain h residue 3 MET Chi-restraints excluded: chain h residue 34 LYS Chi-restraints excluded: chain h residue 36 ILE Chi-restraints excluded: chain h residue 62 LEU Chi-restraints excluded: chain h residue 74 ILE Chi-restraints excluded: chain h residue 99 ASN Chi-restraints excluded: chain h residue 127 ILE Chi-restraints excluded: chain i residue 67 VAL Chi-restraints excluded: chain j residue 69 THR Chi-restraints excluded: chain k residue 20 VAL Chi-restraints excluded: chain k residue 26 THR Chi-restraints excluded: chain k residue 40 ASN Chi-restraints excluded: chain k residue 55 SER Chi-restraints excluded: chain k residue 82 VAL Chi-restraints excluded: chain k residue 116 VAL Chi-restraints excluded: chain l residue 40 SER Chi-restraints excluded: chain l residue 53 MET Chi-restraints excluded: chain l residue 74 ILE Chi-restraints excluded: chain l residue 75 GLU Chi-restraints excluded: chain l residue 100 VAL Chi-restraints excluded: chain l residue 109 HIS Chi-restraints excluded: chain l residue 111 VAL Chi-restraints excluded: chain l residue 121 ASP Chi-restraints excluded: chain m residue 15 VAL Chi-restraints excluded: chain m residue 91 HIS Chi-restraints excluded: chain n residue 4 THR Chi-restraints excluded: chain o residue 77 ARG Chi-restraints excluded: chain p residue 22 VAL Chi-restraints excluded: chain p residue 43 THR Chi-restraints excluded: chain p residue 80 ILE Chi-restraints excluded: chain q residue 28 GLU Chi-restraints excluded: chain q residue 42 TYR Chi-restraints excluded: chain q residue 52 ASN Chi-restraints excluded: chain q residue 57 LEU Chi-restraints excluded: chain q residue 78 VAL Chi-restraints excluded: chain r residue 59 MET Chi-restraints excluded: chain s residue 12 ASP Chi-restraints excluded: chain s residue 84 VAL Chi-restraints excluded: chain t residue 4 ILE Chi-restraints excluded: chain t residue 18 GLU Chi-restraints excluded: chain t residue 32 VAL Chi-restraints excluded: chain t residue 37 THR Chi-restraints excluded: chain t residue 41 ASN Chi-restraints excluded: chain t residue 63 SER Chi-restraints excluded: chain A residue 16 GLU Chi-restraints excluded: chain A residue 34 THR Chi-restraints excluded: chain A residue 86 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 226 optimal weight: 1.9990 chunk 364 optimal weight: 10.0000 chunk 222 optimal weight: 2.9990 chunk 173 optimal weight: 2.9990 chunk 253 optimal weight: 5.9990 chunk 382 optimal weight: 5.9990 chunk 352 optimal weight: 10.0000 chunk 304 optimal weight: 0.7980 chunk 31 optimal weight: 8.9990 chunk 235 optimal weight: 20.0000 chunk 186 optimal weight: 8.9990 overall best weight: 2.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** b 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 33 HIS ** c 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 116 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 142 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 5 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7984 moved from start: 0.2755 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 56057 Z= 0.217 Angle : 0.579 15.322 83215 Z= 0.297 Chirality : 0.034 0.340 10557 Planarity : 0.004 0.047 4874 Dihedral : 22.617 177.891 26440 Min Nonbonded Distance : 2.173 Molprobity Statistics. All-atom Clashscore : 11.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.87 % Favored : 93.13 % Rotamer: Outliers : 3.96 % Allowed : 34.28 % Favored : 61.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.94 (0.17), residues: 2345 helix: 0.71 (0.17), residues: 905 sheet: -0.95 (0.27), residues: 362 loop : -1.66 (0.18), residues: 1078 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP p 60 HIS 0.006 0.001 HIS l 109 PHE 0.020 0.002 PHE c 129 TYR 0.025 0.002 TYR f 8 ARG 0.007 0.000 ARG f 25 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4690 Ramachandran restraints generated. 2345 Oldfield, 0 Emsley, 2345 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4690 Ramachandran restraints generated. 2345 Oldfield, 0 Emsley, 2345 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 265 residues out of total 2049 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 184 time to evaluate : 2.577 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: b 24 ASN cc_start: 0.5754 (m110) cc_final: 0.5347 (m110) REVERT: b 27 MET cc_start: 0.5259 (OUTLIER) cc_final: 0.4620 (tmm) REVERT: b 30 TYR cc_start: 0.6404 (m-80) cc_final: 0.5856 (m-80) REVERT: b 139 LYS cc_start: 0.7407 (OUTLIER) cc_final: 0.7080 (tppt) REVERT: b 156 SER cc_start: 0.6098 (t) cc_final: 0.5711 (p) REVERT: b 157 MET cc_start: 0.7532 (tpp) cc_final: 0.7236 (tmm) REVERT: c 76 ILE cc_start: 0.0496 (tp) cc_final: 0.0201 (mp) REVERT: c 141 MET cc_start: 0.6889 (mpm) cc_final: 0.6586 (mpm) REVERT: c 151 GLN cc_start: 0.5370 (pp30) cc_final: 0.5043 (pp30) REVERT: c 200 TRP cc_start: 0.5612 (m-90) cc_final: 0.4956 (m-90) REVERT: d 50 GLN cc_start: 0.8090 (OUTLIER) cc_final: 0.6401 (mm110) REVERT: d 178 ARG cc_start: 0.7750 (OUTLIER) cc_final: 0.6476 (pmt-80) REVERT: d 181 GLU cc_start: 0.6571 (OUTLIER) cc_final: 0.6355 (tm-30) REVERT: f 2 ARG cc_start: 0.6675 (mtt180) cc_final: 0.6231 (mtt90) REVERT: f 11 ARG cc_start: 0.6346 (ptt180) cc_final: 0.6079 (ptt180) REVERT: f 70 ASN cc_start: 0.7588 (m-40) cc_final: 0.7253 (m-40) REVERT: f 94 GLU cc_start: 0.7989 (OUTLIER) cc_final: 0.7443 (pp20) REVERT: g 11 ASP cc_start: 0.2657 (p0) cc_final: 0.2322 (p0) REVERT: g 28 ASN cc_start: 0.6031 (m-40) cc_final: 0.5376 (t0) REVERT: g 85 TYR cc_start: 0.1654 (p90) cc_final: 0.1092 (p90) REVERT: g 144 MET cc_start: 0.7725 (mmm) cc_final: 0.6960 (pp-130) REVERT: h 3 MET cc_start: 0.8088 (OUTLIER) cc_final: 0.7725 (tpp) REVERT: h 69 ASN cc_start: 0.8530 (p0) cc_final: 0.7968 (t0) REVERT: h 99 ASN cc_start: 0.8798 (OUTLIER) cc_final: 0.8105 (t0) REVERT: i 7 GLU cc_start: 0.5879 (mp0) cc_final: 0.5531 (tm-30) REVERT: j 88 MET cc_start: 0.1601 (mmt) cc_final: 0.0030 (pmm) REVERT: k 26 THR cc_start: 0.7364 (OUTLIER) cc_final: 0.7083 (p) REVERT: k 34 ILE cc_start: 0.6926 (tp) cc_final: 0.6468 (pp) REVERT: k 36 ASP cc_start: 0.8944 (m-30) cc_final: 0.8543 (p0) REVERT: k 40 ASN cc_start: 0.8106 (OUTLIER) cc_final: 0.7789 (t0) REVERT: l 75 GLU cc_start: 0.8638 (OUTLIER) cc_final: 0.8392 (mt-10) REVERT: o 80 GLU cc_start: 0.8413 (pp20) cc_final: 0.8096 (pp20) REVERT: q 42 TYR cc_start: 0.7651 (OUTLIER) cc_final: 0.7105 (p90) REVERT: t 45 ASN cc_start: 0.8433 (p0) cc_final: 0.8205 (p0) REVERT: A 16 GLU cc_start: 0.7117 (OUTLIER) cc_final: 0.6479 (mp0) REVERT: A 81 ARG cc_start: 0.8113 (tmt170) cc_final: 0.7732 (tpm-80) REVERT: A 99 GLU cc_start: 0.6983 (pp20) cc_final: 0.6381 (pm20) REVERT: A 107 MET cc_start: 0.5494 (mpp) cc_final: 0.5182 (mpm) outliers start: 81 outliers final: 62 residues processed: 250 average time/residue: 1.1430 time to fit residues: 374.4642 Evaluate side-chains 251 residues out of total 2049 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 176 time to evaluate : 2.492 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain b residue 27 MET Chi-restraints excluded: chain b residue 139 LYS Chi-restraints excluded: chain b residue 154 MET Chi-restraints excluded: chain b residue 190 ASN Chi-restraints excluded: chain c residue 150 THR Chi-restraints excluded: chain c residue 172 VAL Chi-restraints excluded: chain d residue 8 ASN Chi-restraints excluded: chain d residue 50 GLN Chi-restraints excluded: chain d residue 64 THR Chi-restraints excluded: chain d residue 81 VAL Chi-restraints excluded: chain d residue 100 SER Chi-restraints excluded: chain d residue 138 THR Chi-restraints excluded: chain d residue 141 VAL Chi-restraints excluded: chain d residue 178 ARG Chi-restraints excluded: chain d residue 181 GLU Chi-restraints excluded: chain e residue 17 THR Chi-restraints excluded: chain e residue 52 LYS Chi-restraints excluded: chain e residue 84 THR Chi-restraints excluded: chain e residue 125 SER Chi-restraints excluded: chain e residue 161 VAL Chi-restraints excluded: chain f residue 6 VAL Chi-restraints excluded: chain f residue 26 PHE Chi-restraints excluded: chain f residue 43 TRP Chi-restraints excluded: chain f residue 86 ILE Chi-restraints excluded: chain f residue 91 VAL Chi-restraints excluded: chain f residue 94 GLU Chi-restraints excluded: chain g residue 61 VAL Chi-restraints excluded: chain g residue 115 THR Chi-restraints excluded: chain g residue 126 ASP Chi-restraints excluded: chain h residue 3 MET Chi-restraints excluded: chain h residue 36 ILE Chi-restraints excluded: chain h residue 62 LEU Chi-restraints excluded: chain h residue 74 ILE Chi-restraints excluded: chain h residue 75 THR Chi-restraints excluded: chain h residue 99 ASN Chi-restraints excluded: chain h residue 127 ILE Chi-restraints excluded: chain i residue 67 VAL Chi-restraints excluded: chain i residue 112 MET Chi-restraints excluded: chain k residue 20 VAL Chi-restraints excluded: chain k residue 26 THR Chi-restraints excluded: chain k residue 40 ASN Chi-restraints excluded: chain k residue 55 SER Chi-restraints excluded: chain k residue 67 SER Chi-restraints excluded: chain k residue 82 VAL Chi-restraints excluded: chain k residue 116 VAL Chi-restraints excluded: chain l residue 40 SER Chi-restraints excluded: chain l residue 53 MET Chi-restraints excluded: chain l residue 74 ILE Chi-restraints excluded: chain l residue 75 GLU Chi-restraints excluded: chain l residue 100 VAL Chi-restraints excluded: chain l residue 109 HIS Chi-restraints excluded: chain l residue 111 VAL Chi-restraints excluded: chain l residue 121 ASP Chi-restraints excluded: chain m residue 15 VAL Chi-restraints excluded: chain n residue 4 THR Chi-restraints excluded: chain o residue 77 ARG Chi-restraints excluded: chain p residue 22 VAL Chi-restraints excluded: chain p residue 43 THR Chi-restraints excluded: chain p residue 80 ILE Chi-restraints excluded: chain q residue 28 GLU Chi-restraints excluded: chain q residue 42 TYR Chi-restraints excluded: chain q residue 52 ASN Chi-restraints excluded: chain q residue 57 LEU Chi-restraints excluded: chain q residue 78 VAL Chi-restraints excluded: chain r residue 59 MET Chi-restraints excluded: chain s residue 84 VAL Chi-restraints excluded: chain t residue 4 ILE Chi-restraints excluded: chain t residue 18 GLU Chi-restraints excluded: chain t residue 32 VAL Chi-restraints excluded: chain t residue 37 THR Chi-restraints excluded: chain t residue 41 ASN Chi-restraints excluded: chain t residue 63 SER Chi-restraints excluded: chain t residue 68 SER Chi-restraints excluded: chain A residue 16 GLU Chi-restraints excluded: chain A residue 34 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 241 optimal weight: 6.9990 chunk 324 optimal weight: 4.9990 chunk 93 optimal weight: 30.0000 chunk 280 optimal weight: 50.0000 chunk 44 optimal weight: 8.9990 chunk 84 optimal weight: 10.0000 chunk 305 optimal weight: 8.9990 chunk 127 optimal weight: 50.0000 chunk 313 optimal weight: 30.0000 chunk 38 optimal weight: 7.9990 chunk 56 optimal weight: 7.9990 overall best weight: 7.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** b 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 171 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 190 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 116 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** e 145 GLN ** g 142 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** m 100 GLN ** q 5 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** t 24 GLN ** t 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4293 r_free = 0.4293 target = 0.095087 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3512 r_free = 0.3512 target = 0.061411 restraints weight = 211056.789| |-----------------------------------------------------------------------------| r_work (start): 0.3346 rms_B_bonded: 2.54 r_work: 0.3230 rms_B_bonded: 4.00 restraints_weight: 0.5000 r_work (final): 0.3230 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8271 moved from start: 0.3051 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.074 56057 Z= 0.450 Angle : 0.738 14.300 83215 Z= 0.375 Chirality : 0.042 0.349 10557 Planarity : 0.005 0.069 4874 Dihedral : 22.783 176.615 26440 Min Nonbonded Distance : 2.083 Molprobity Statistics. All-atom Clashscore : 15.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.59 % Favored : 92.41 % Rotamer: Outliers : 4.16 % Allowed : 34.43 % Favored : 61.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.24 (0.17), residues: 2345 helix: 0.38 (0.17), residues: 910 sheet: -1.07 (0.26), residues: 373 loop : -1.79 (0.18), residues: 1062 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP d 9 HIS 0.011 0.002 HIS d 116 PHE 0.027 0.002 PHE f 76 TYR 0.028 0.002 TYR q 30 ARG 0.008 0.001 ARG d 5 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10002.49 seconds wall clock time: 177 minutes 23.53 seconds (10643.53 seconds total)