Starting phenix.real_space_refine on Mon Nov 18 23:21:55 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5o5j_3748/11_2024/5o5j_3748.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5o5j_3748/11_2024/5o5j_3748.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.45 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5o5j_3748/11_2024/5o5j_3748.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5o5j_3748/11_2024/5o5j_3748.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5o5j_3748/11_2024/5o5j_3748.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5o5j_3748/11_2024/5o5j_3748.cif" } resolution = 3.45 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= 0.002 sd= 0.031 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: 7 Type Number sf(0) Gaussians Zn 2 6.06 5 P 1535 5.49 5 Mg 217 5.21 5 S 45 5.16 5 C 26565 2.51 5 N 9697 2.21 5 O 14102 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 8 residue(s): 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/chem_data/mon_lib" Total number of atoms: 52163 Number of models: 1 Model: "" Number of chains: 28 Chain: "A" Number of atoms: 32439 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1511, 32439 Classifications: {'RNA': 1511} Modifications used: {'rna2p_pur': 112, 'rna2p_pyr': 85, 'rna3p_pur': 737, 'rna3p_pyr': 577} Link IDs: {'rna2p': 197, 'rna3p': 1313} Chain: "B" Number of atoms: 280 Number of conformers: 1 Conformer: "" Number of residues, atoms: 32, 280 Classifications: {'peptide': 32} Link IDs: {'TRANS': 31} Chain: "C" Number of atoms: 1660 Number of conformers: 1 Conformer: "" Number of residues, atoms: 208, 1660 Classifications: {'peptide': 208} Link IDs: {'PTRANS': 5, 'TRANS': 202} Chain: "D" Number of atoms: 1641 Number of conformers: 1 Conformer: "" Number of residues, atoms: 200, 1641 Classifications: {'peptide': 200} Link IDs: {'PTRANS': 11, 'TRANS': 188} Chain: "E" Number of atoms: 1296 Number of conformers: 1 Conformer: "" Number of residues, atoms: 180, 1296 Classifications: {'peptide': 180} Link IDs: {'PTRANS': 8, 'TRANS': 171} Chain: "F" Number of atoms: 771 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 771 Classifications: {'peptide': 96} Link IDs: {'PTRANS': 4, 'TRANS': 91} Chain: "G" Number of atoms: 1232 Number of conformers: 1 Conformer: "" Number of residues, atoms: 155, 1232 Classifications: {'peptide': 155} Link IDs: {'PTRANS': 8, 'TRANS': 146} Chain: "H" Number of atoms: 1010 Number of conformers: 1 Conformer: "" Number of residues, atoms: 131, 1010 Classifications: {'peptide': 131} Link IDs: {'PTRANS': 5, 'TRANS': 125} Chain: "I" Number of atoms: 994 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 994 Classifications: {'peptide': 126} Link IDs: {'PTRANS': 8, 'TRANS': 117} Chain: "J" Number of atoms: 788 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 788 Classifications: {'peptide': 99} Link IDs: {'PTRANS': 7, 'TRANS': 91} Chain: "K" Number of atoms: 855 Number of conformers: 1 Conformer: "" Number of residues, atoms: 115, 855 Classifications: {'peptide': 115} Link IDs: {'PTRANS': 8, 'TRANS': 106} Chain: "L" Number of atoms: 958 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 958 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 5, 'TRANS': 116} Chain: "M" Number of atoms: 935 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 935 Classifications: {'peptide': 116} Link IDs: {'PTRANS': 3, 'TRANS': 112} Chain: "N" Number of atoms: 477 Number of conformers: 1 Conformer: "" Number of residues, atoms: 60, 477 Classifications: {'peptide': 60} Link IDs: {'PTRANS': 3, 'TRANS': 56} Chain: "O" Number of atoms: 720 Number of conformers: 1 Conformer: "" Number of residues, atoms: 88, 720 Classifications: {'peptide': 88} Link IDs: {'PTRANS': 1, 'TRANS': 86} Chain: "P" Number of atoms: 891 Number of conformers: 1 Conformer: "" Number of residues, atoms: 113, 891 Classifications: {'peptide': 113} Link IDs: {'PTRANS': 8, 'TRANS': 104} Chain: "Q" Number of atoms: 748 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 748 Classifications: {'peptide': 94} Link IDs: {'PTRANS': 5, 'TRANS': 88} Chain: "R" Number of atoms: 513 Number of conformers: 1 Conformer: "" Number of residues, atoms: 65, 513 Classifications: {'peptide': 65} Link IDs: {'PTRANS': 1, 'TRANS': 63} Chain: "S" Number of atoms: 662 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 662 Classifications: {'peptide': 82} Link IDs: {'PTRANS': 4, 'TRANS': 77} Chain: "T" Number of atoms: 660 Number of conformers: 1 Conformer: "" Number of residues, atoms: 85, 660 Classifications: {'peptide': 85} Link IDs: {'PTRANS': 1, 'TRANS': 83} Chain: "V" Number of atoms: 1793 Number of conformers: 1 Conformer: "" Number of residues, atoms: 228, 1793 Classifications: {'peptide': 228} Link IDs: {'PTRANS': 7, 'TRANS': 220} Chain: "W" Number of atoms: 410 Number of conformers: 1 Conformer: "" Number of residues, atoms: 19, 410 Classifications: {'RNA': 19} Modifications used: {'rna3p_pur': 12, 'rna3p_pyr': 7} Link IDs: {'rna3p': 18} Chain: "X" Number of atoms: 117 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 117 Classifications: {'RNA': 6} Modifications used: {'5*END': 1, 'rna3p_pyr': 6} Link IDs: {'rna3p': 5} Chain: "g" Number of atoms: 94 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 94 Classifications: {'peptide': 11} Link IDs: {'TRANS': 10} Chain: "A" Number of atoms: 215 Number of conformers: 1 Conformer: "" Number of residues, atoms: 215, 215 Unusual residues: {' MG': 215} Classifications: {'undetermined': 215} Link IDs: {None: 214} Chain: "F" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "N" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "R" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MG': 1, ' ZN': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 45043 SG CYS N 24 57.685 122.311 115.050 1.00 34.82 S ATOM 45066 SG CYS N 27 61.429 120.802 115.181 1.00 47.23 S ATOM 45172 SG CYS N 40 60.843 122.916 112.320 1.00 52.70 S ATOM 45197 SG CYS N 43 59.422 119.634 112.537 1.00 50.43 S ATOM 47728 SG CYS R 20 115.128 98.193 30.398 1.00 69.69 S ATOM 47752 SG CYS R 23 116.081 94.621 30.826 1.00 84.90 S ATOM 48024 SG CYS R 57 117.174 96.819 33.816 1.00 52.35 S Time building chain proxies: 27.56, per 1000 atoms: 0.53 Number of scatterers: 52163 At special positions: 0 Unit cell: (216.84, 207.11, 189.04, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 2 29.99 S 45 16.00 P 1535 15.00 Mg 217 11.99 O 14102 8.00 N 9697 7.00 C 26565 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: 11.55 Conformation dependent library (CDL) restraints added in 2.9 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN N 101 " pdb="ZN ZN N 101 " - pdb=" SG CYS N 27 " pdb="ZN ZN N 101 " - pdb=" SG CYS N 43 " pdb="ZN ZN N 101 " - pdb=" SG CYS N 40 " pdb="ZN ZN N 101 " - pdb=" SG CYS N 24 " pdb=" ZN R 102 " pdb="ZN ZN R 102 " - pdb=" ND1 HIS R 60 " pdb="ZN ZN R 102 " - pdb=" SG CYS R 23 " pdb="ZN ZN R 102 " - pdb=" SG CYS R 57 " pdb="ZN ZN R 102 " - pdb=" SG CYS R 20 " Number of angles added : 9 4728 Ramachandran restraints generated. 2364 Oldfield, 0 Emsley, 2364 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4434 Finding SS restraints... Secondary structure from input PDB file: 88 helices and 20 sheets defined 45.9% alpha, 16.6% beta 502 base pairs and 824 stacking pairs defined. Time for finding SS restraints: 23.67 Creating SS restraints... Processing helix chain 'B' and resid 3 through 24 removed outlier: 4.685A pdb=" N LYS B 7 " --> pdb=" O SER B 3 " (cutoff:3.500A) Processing helix chain 'B' and resid 24 through 33 Processing helix chain 'C' and resid 6 through 11 Processing helix chain 'C' and resid 27 through 46 removed outlier: 3.914A pdb=" N LEU C 46 " --> pdb=" O LEU C 42 " (cutoff:3.500A) Processing helix chain 'C' and resid 71 through 75 removed outlier: 3.605A pdb=" N ILE C 74 " --> pdb=" O ARG C 71 " (cutoff:3.500A) Processing helix chain 'C' and resid 80 through 93 Processing helix chain 'C' and resid 111 through 125 Processing helix chain 'C' and resid 128 through 143 removed outlier: 3.889A pdb=" N GLN C 143 " --> pdb=" O SER C 139 " (cutoff:3.500A) Processing helix chain 'D' and resid 7 through 16 removed outlier: 4.329A pdb=" N LYS D 11 " --> pdb=" O PRO D 7 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N SER D 12 " --> pdb=" O ALA D 8 " (cutoff:3.500A) Processing helix chain 'D' and resid 23 through 29 removed outlier: 3.791A pdb=" N GLU D 27 " --> pdb=" O ASP D 23 " (cutoff:3.500A) Processing helix chain 'D' and resid 44 through 61 removed outlier: 3.873A pdb=" N LEU D 50 " --> pdb=" O TYR D 46 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N LYS D 53 " --> pdb=" O GLN D 49 " (cutoff:3.500A) Processing helix chain 'D' and resid 63 through 77 Processing helix chain 'D' and resid 80 through 91 Processing helix chain 'D' and resid 92 through 100 Processing helix chain 'D' and resid 105 through 115 Processing helix chain 'D' and resid 141 through 146 removed outlier: 3.770A pdb=" N ASN D 146 " --> pdb=" O GLU D 142 " (cutoff:3.500A) Processing helix chain 'D' and resid 147 through 156 Processing helix chain 'D' and resid 182 through 187 removed outlier: 3.683A pdb=" N ASP D 187 " --> pdb=" O ARG D 183 " (cutoff:3.500A) Processing helix chain 'D' and resid 192 through 201 removed outlier: 3.599A pdb=" N TYR D 199 " --> pdb=" O ILE D 195 " (cutoff:3.500A) Processing helix chain 'E' and resid 80 through 95 Processing helix chain 'E' and resid 133 through 143 Processing helix chain 'E' and resid 157 through 172 removed outlier: 3.621A pdb=" N LEU E 172 " --> pdb=" O ALA E 168 " (cutoff:3.500A) Processing helix chain 'E' and resid 174 through 183 Processing helix chain 'E' and resid 185 through 190 removed outlier: 3.815A pdb=" N VAL E 189 " --> pdb=" O PRO E 185 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ALA E 190 " --> pdb=" O ILE E 186 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 185 through 190' Processing helix chain 'E' and resid 191 through 214 removed outlier: 3.506A pdb=" N ALA E 214 " --> pdb=" O ARG E 210 " (cutoff:3.500A) Processing helix chain 'F' and resid 15 through 17 No H-bonds generated for 'chain 'F' and resid 15 through 17' Processing helix chain 'F' and resid 18 through 34 removed outlier: 3.844A pdb=" N VAL F 29 " --> pdb=" O THR F 25 " (cutoff:3.500A) removed outlier: 4.414A pdb=" N ILE F 30 " --> pdb=" O PHE F 26 " (cutoff:3.500A) Processing helix chain 'F' and resid 68 through 80 removed outlier: 3.531A pdb=" N SER F 73 " --> pdb=" O PRO F 69 " (cutoff:3.500A) Processing helix chain 'G' and resid 20 through 31 removed outlier: 3.847A pdb=" N THR G 24 " --> pdb=" O SER G 20 " (cutoff:3.500A) Processing helix chain 'G' and resid 35 through 55 removed outlier: 3.575A pdb=" N ALA G 39 " --> pdb=" O LYS G 35 " (cutoff:3.500A) Processing helix chain 'G' and resid 57 through 69 Processing helix chain 'G' and resid 92 through 109 removed outlier: 3.578A pdb=" N SER G 96 " --> pdb=" O ARG G 92 " (cutoff:3.500A) Processing helix chain 'G' and resid 115 through 129 removed outlier: 3.720A pdb=" N ALA G 121 " --> pdb=" O VAL G 117 " (cutoff:3.500A) Processing helix chain 'G' and resid 132 through 148 removed outlier: 3.945A pdb=" N ASN G 148 " --> pdb=" O MET G 144 " (cutoff:3.500A) Processing helix chain 'G' and resid 149 through 155 Processing helix chain 'H' and resid 5 through 20 Processing helix chain 'H' and resid 30 through 43 Processing helix chain 'H' and resid 115 through 121 Processing helix chain 'I' and resid 61 through 76 Proline residue: I 71 - end of helix Processing helix chain 'I' and resid 91 through 111 removed outlier: 3.687A pdb=" N ILE I 108 " --> pdb=" O ALA I 104 " (cutoff:3.500A) Processing helix chain 'I' and resid 114 through 119 Processing helix chain 'J' and resid 14 through 32 removed outlier: 3.734A pdb=" N ILE J 18 " --> pdb=" O ASP J 14 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N THR 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 62 through 67 removed outlier: 3.748A pdb=" N ARG K 65 " --> pdb=" O LYS K 62 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N SER K 67 " --> pdb=" O SER K 64 " (cutoff:3.500A) Processing helix chain 'K' and resid 68 through 85 Processing helix chain 'K' and resid 101 through 112 Processing helix chain 'L' and resid 3 through 11 Processing helix chain 'L' and resid 21 through 25 removed outlier: 3.709A pdb=" N LEU L 24 " --> pdb=" O THR L 21 " (cutoff:3.500A) Processing helix chain 'M' and resid 14 through 19 Processing helix chain 'M' and resid 20 through 22 No H-bonds generated for 'chain 'M' and resid 20 through 22' Processing helix chain 'M' and resid 26 through 38 removed outlier: 3.883A pdb=" N ALA M 35 " --> pdb=" O ASN M 31 " (cutoff:3.500A) Processing helix chain 'M' and resid 49 through 64 Processing helix chain 'M' and resid 66 through 84 removed outlier: 3.762A pdb=" N LEU M 70 " --> pdb=" O VAL M 66 " (cutoff:3.500A) Processing helix chain 'M' and resid 86 through 95 Processing helix chain 'M' and resid 107 through 112 Processing helix chain 'N' and resid 3 through 11 removed outlier: 3.539A pdb=" N ASN N 11 " --> pdb=" O VAL N 7 " (cutoff:3.500A) Processing helix chain 'N' and resid 16 through 20 removed outlier: 3.623A pdb=" N ALA N 20 " --> pdb=" O ALA N 17 " (cutoff:3.500A) Processing helix chain 'N' and resid 40 through 51 Processing helix chain 'O' and resid 4 through 16 Processing helix chain 'O' and resid 24 through 46 removed outlier: 3.663A pdb=" N VAL O 45 " --> pdb=" O GLU O 41 " (cutoff:3.500A) Processing helix chain 'O' and resid 49 through 74 removed outlier: 3.557A pdb=" N ARG O 53 " --> pdb=" O ASP O 49 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N GLY O 55 " --> pdb=" O HIS O 51 " (cutoff:3.500A) Processing helix chain 'O' and resid 74 through 86 Processing helix chain 'P' and resid 52 through 62 Processing helix chain 'P' and resid 67 through 78 Processing helix chain 'P' and resid 78 through 85 Processing helix chain 'P' and resid 101 through 114 Processing helix chain 'R' and resid 34 through 41 removed outlier: 3.903A pdb=" N LEU R 38 " --> pdb=" O ASP R 34 " (cutoff:3.500A) removed outlier: 4.317A pdb=" N TYR R 41 " --> pdb=" O LEU R 37 " (cutoff:3.500A) Processing helix chain 'R' and resid 50 through 55 Processing helix chain 'R' and resid 57 through 74 Processing helix chain 'S' and resid 4 through 8 removed outlier: 3.520A pdb=" N LYS S 7 " --> pdb=" O SER S 4 " (cutoff:3.500A) Processing helix chain 'S' and resid 12 through 25 Processing helix chain 'S' and resid 41 through 45 Processing helix chain 'S' and resid 70 through 75 Processing helix chain 'T' and resid 4 through 42 removed outlier: 3.560A pdb=" N ILE T 8 " --> pdb=" O ILE T 4 " (cutoff:3.500A) Processing helix chain 'T' and resid 43 through 63 removed outlier: 3.522A pdb=" N ALA T 53 " --> pdb=" O GLU T 49 " (cutoff:3.500A) Processing helix chain 'T' and resid 68 through 86 Processing helix chain 'V' and resid 5 through 12 Processing helix chain 'V' and resid 24 through 28 Processing helix chain 'V' and resid 42 through 63 Processing helix chain 'V' and resid 73 through 88 removed outlier: 4.680A pdb=" N GLU V 78 " --> pdb=" O LYS V 74 " (cutoff:3.500A) removed outlier: 4.666A pdb=" N SER V 79 " --> pdb=" O GLN V 75 " (cutoff:3.500A) Processing helix chain 'V' and resid 103 through 108 removed outlier: 4.041A pdb=" N VAL V 107 " --> pdb=" O ASN V 103 " (cutoff:3.500A) Processing helix chain 'V' and resid 108 through 123 removed outlier: 3.590A pdb=" N THR V 123 " --> pdb=" O ALA V 119 " (cutoff:3.500A) Processing helix chain 'V' and resid 130 through 148 removed outlier: 3.772A pdb=" N LEU V 135 " --> pdb=" O LYS V 131 " (cutoff:3.500A) Processing helix chain 'V' and resid 149 through 155 removed outlier: 3.537A pdb=" N ASP V 153 " --> pdb=" O GLY V 149 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N GLN V 155 " --> pdb=" O ILE V 151 " (cutoff:3.500A) Processing helix chain 'V' and resid 169 through 179 removed outlier: 3.738A pdb=" N VAL V 173 " --> pdb=" O GLU V 169 " (cutoff:3.500A) Processing helix chain 'V' and resid 192 through 196 removed outlier: 3.618A pdb=" N VAL V 195 " --> pdb=" O ASP V 192 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N VAL V 196 " --> pdb=" O PRO V 193 " (cutoff:3.500A) No H-bonds generated for 'chain 'V' and resid 192 through 196' Processing helix chain 'V' and resid 206 through 227 Processing helix chain 'g' and resid 57 through 65 removed outlier: 3.650A pdb=" N ARG g 64 " --> pdb=" O ARG g 60 " (cutoff:3.500A) Processing sheet with id=A, first strand: chain 'C' and resid 98 through 104 removed outlier: 6.781A pdb=" N VAL C 63 " --> pdb=" O GLN C 99 " (cutoff:3.500A) removed outlier: 7.764A pdb=" N ASN C 101 " --> pdb=" O VAL C 63 " (cutoff:3.500A) removed outlier: 6.385A pdb=" N VAL C 65 " --> pdb=" O ASN C 101 " (cutoff:3.500A) removed outlier: 7.405A pdb=" N LEU C 103 " --> pdb=" O VAL C 65 " (cutoff:3.500A) removed outlier: 6.198A pdb=" N ILE C 67 " --> pdb=" O LEU C 103 " (cutoff:3.500A) Processing sheet with id=B, first strand: chain 'C' and resid 164 through 170 removed outlier: 6.800A pdb=" N TYR C 203 " --> pdb=" O LYS C 147 " (cutoff:3.500A) removed outlier: 4.347A pdb=" N ILE C 149 " --> pdb=" O TRP C 201 " (cutoff:3.500A) removed outlier: 6.619A pdb=" N TRP C 201 " --> pdb=" O ILE C 149 " (cutoff:3.500A) removed outlier: 4.555A pdb=" N VAL C 151 " --> pdb=" O LYS C 199 " (cutoff:3.500A) removed outlier: 6.724A pdb=" N LYS C 199 " --> pdb=" O VAL C 151 " (cutoff:3.500A) removed outlier: 4.412A pdb=" N CYS C 153 " --> pdb=" O GLY C 197 " (cutoff:3.500A) removed outlier: 6.788A pdb=" N GLY C 197 " --> pdb=" O CYS C 153 " (cutoff:3.500A) removed outlier: 5.867A pdb=" N GLY C 155 " --> pdb=" O ARG C 195 " (cutoff:3.500A) removed outlier: 8.852A pdb=" N ARG C 195 " --> pdb=" O GLY C 155 " (cutoff:3.500A) Processing sheet with id=C, first strand: chain 'D' and resid 118 through 120 Processing sheet with id=D, first strand: chain 'E' and resid 71 through 78 removed outlier: 3.830A pdb=" N SER E 42 " --> pdb=" O LEU E 61 " (cutoff:3.500A) removed outlier: 7.083A pdb=" N ILE E 63 " --> pdb=" O VAL E 40 " (cutoff:3.500A) removed outlier: 5.538A pdb=" N VAL E 40 " --> pdb=" O ILE E 63 " (cutoff:3.500A) removed outlier: 7.557A pdb=" N GLY E 65 " --> pdb=" O GLU E 38 " (cutoff:3.500A) removed outlier: 5.302A pdb=" N GLU E 38 " --> pdb=" O GLY E 65 " (cutoff:3.500A) Processing sheet with id=E, first strand: chain 'E' and resid 110 through 114 removed outlier: 3.726A pdb=" N VAL E 118 " --> pdb=" O GLY E 154 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N GLY E 154 " --> pdb=" O VAL E 118 " (cutoff:3.500A) removed outlier: 6.960A pdb=" N MET E 120 " --> pdb=" O SER E 152 " (cutoff:3.500A) removed outlier: 5.730A pdb=" N SER E 152 " --> pdb=" O MET E 120 " (cutoff:3.500A) removed outlier: 7.347A pdb=" N ARG E 122 " --> pdb=" O ALA E 150 " (cutoff:3.500A) removed outlier: 5.037A pdb=" N ALA E 150 " --> pdb=" O ARG E 122 " (cutoff:3.500A) Processing sheet with id=F, first strand: chain 'F' and resid 37 through 43 removed outlier: 6.741A pdb=" N ASP F 11 " --> pdb=" O VAL F 85 " (cutoff:3.500A) removed outlier: 7.710A pdb=" N VAL F 85 " --> pdb=" O ASP F 11 " (cutoff:3.500A) Processing sheet with id=G, first strand: chain 'G' and resid 73 through 80 Processing sheet with id=H, first strand: chain 'H' and resid 24 through 28 Processing sheet with id=I, first strand: chain 'H' and resid 76 through 79 removed outlier: 6.607A pdb=" N ILE H 105 " --> pdb=" O LEU H 128 " (cutoff:3.500A) removed outlier: 4.786A pdb=" N TYR H 130 " --> pdb=" O VAL H 103 " (cutoff:3.500A) removed outlier: 6.923A pdb=" N VAL H 103 " --> pdb=" O TYR H 130 " (cutoff:3.500A) Processing sheet with id=J, first strand: chain 'I' and resid 28 through 31 Processing sheet with id=K, first strand: chain 'J' and resid 70 through 77 Processing sheet with id=L, first strand: chain 'J' and resid 45 through 52 Processing sheet with id=M, first strand: chain 'K' and resid 50 through 55 removed outlier: 6.845A pdb=" N ILE K 43 " --> pdb=" O ILE K 51 " (cutoff:3.500A) removed outlier: 4.483A pdb=" N TRP K 53 " --> pdb=" O VAL K 41 " (cutoff:3.500A) removed outlier: 6.937A pdb=" N VAL K 41 " --> pdb=" O TRP K 53 " (cutoff:3.500A) removed outlier: 5.010A pdb=" N SER K 55 " --> pdb=" O THR K 39 " (cutoff:3.500A) removed outlier: 7.155A pdb=" N THR K 39 " --> pdb=" O SER K 55 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N ASN K 38 " --> pdb=" O THR K 35 " (cutoff:3.500A) removed outlier: 6.644A pdb=" N LYS K 90 " --> pdb=" O GLY K 28 " (cutoff:3.500A) removed outlier: 7.290A pdb=" N ALA K 30 " --> pdb=" O LYS K 90 " (cutoff:3.500A) removed outlier: 6.226A pdb=" N ASP K 92 " --> pdb=" O ALA K 30 " (cutoff:3.500A) removed outlier: 7.519A pdb=" N ILE K 32 " --> pdb=" O ASP K 92 " (cutoff:3.500A) removed outlier: 6.232A pdb=" N PHE K 94 " --> pdb=" O ILE K 32 " (cutoff:3.500A) removed outlier: 7.384A pdb=" N SER K 34 " --> pdb=" O PHE K 94 " (cutoff:3.500A) removed outlier: 6.319A pdb=" N LYS K 96 " --> pdb=" O SER K 34 " (cutoff:3.500A) removed outlier: 5.736A pdb=" N GLU K 115 " --> pdb=" O VAL K 91 " (cutoff:3.500A) removed outlier: 6.836A pdb=" N VAL K 93 " --> pdb=" O GLU K 115 " (cutoff:3.500A) removed outlier: 7.654A pdb=" N GLY K 117 " --> pdb=" O VAL K 93 " (cutoff:3.500A) removed outlier: 11.573A pdb=" N VAL K 95 " --> pdb=" O GLY K 117 " (cutoff:3.500A) removed outlier: 9.169A pdb=" N ILE K 119 " --> pdb=" O VAL K 95 " (cutoff:3.500A) Processing sheet with id=N, first strand: chain 'L' and resid 29 through 33 removed outlier: 4.063A pdb=" N TYR L 95 " --> pdb=" O THR L 64 " (cutoff:3.500A) removed outlier: 5.277A pdb=" N LYS L 51 " --> pdb=" O ILE L 67 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N ARG L 36 " --> pdb=" O ARG L 54 " (cutoff:3.500A) removed outlier: 5.915A pdb=" N LYS L 56 " --> pdb=" O CYS L 34 " (cutoff:3.500A) removed outlier: 5.098A pdb=" N CYS L 34 " --> pdb=" O LYS L 56 " (cutoff:3.500A) Processing sheet with id=O, first strand: chain 'P' and resid 3 through 10 removed outlier: 6.704A pdb=" N VAL P 22 " --> pdb=" O VAL P 36 " (cutoff:3.500A) removed outlier: 5.760A pdb=" N VAL P 36 " --> pdb=" O VAL P 22 " (cutoff:3.500A) Processing sheet with id=P, first strand: chain 'Q' and resid 22 through 26 removed outlier: 8.899A pdb=" N ARG Q 87 " --> pdb=" O LYS Q 58 " (cutoff:3.500A) removed outlier: 8.107A pdb=" N LYS Q 60 " --> pdb=" O ARG Q 87 " (cutoff:3.500A) removed outlier: 6.012A pdb=" N ARG Q 89 " --> pdb=" O LYS Q 60 " (cutoff:3.500A) removed outlier: 5.757A pdb=" N HIS Q 62 " --> pdb=" O ARG Q 89 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N SER Q 29 " --> pdb=" O VAL Q 37 " (cutoff:3.500A) removed outlier: 6.647A pdb=" N GLU Q 39 " --> pdb=" O VAL Q 27 " (cutoff:3.500A) removed outlier: 6.173A pdb=" N VAL Q 27 " --> pdb=" O GLU Q 39 " (cutoff:3.500A) Processing sheet with id=Q, first strand: chain 'Q' and resid 73 through 75 removed outlier: 6.442A pdb=" N SER Q 75 " --> pdb=" O ILE Q 93 " (cutoff:3.500A) removed outlier: 5.513A pdb=" N ILE Q 93 " --> pdb=" O SER Q 75 " (cutoff:3.500A) Processing sheet with id=R, first strand: chain 'S' and resid 30 through 33 removed outlier: 7.229A pdb=" N THR S 48 " --> pdb=" O ILE S 31 " (cutoff:3.500A) removed outlier: 7.763A pdb=" N THR S 33 " --> pdb=" O THR S 48 " (cutoff:3.500A) removed outlier: 5.991A pdb=" N ALA S 50 " --> pdb=" O THR S 33 " (cutoff:3.500A) Processing sheet with id=S, first strand: chain 'V' and resid 67 through 70 removed outlier: 7.328A pdb=" N ALA V 160 " --> pdb=" O LEU V 68 " (cutoff:3.500A) removed outlier: 8.233A pdb=" N VAL V 70 " --> pdb=" O ALA V 160 " (cutoff:3.500A) removed outlier: 6.930A pdb=" N TRP V 162 " --> pdb=" O VAL V 70 " (cutoff:3.500A) removed outlier: 7.559A pdb=" N VAL V 163 " --> pdb=" O PRO V 182 " (cutoff:3.500A) removed outlier: 6.557A pdb=" N ILE V 184 " --> pdb=" O VAL V 163 " (cutoff:3.500A) removed outlier: 6.713A pdb=" N TYR V 198 " --> pdb=" O ALA V 185 " (cutoff:3.500A) removed outlier: 7.608A pdb=" N LEU V 187 " --> pdb=" O TYR V 198 " (cutoff:3.500A) removed outlier: 6.719A pdb=" N ILE V 200 " --> pdb=" O LEU V 187 " (cutoff:3.500A) No H-bonds generated for sheet with id=S Processing sheet with id=T, first strand: chain 'V' and resid 31 through 34 removed outlier: 6.681A pdb=" N ILE V 40 " --> pdb=" O PHE V 32 " (cutoff:3.500A) 918 hydrogen bonds defined for protein. 2649 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 1271 hydrogen bonds 1996 hydrogen bond angles 0 basepair planarities 502 basepair parallelities 824 stacking parallelities Total time for adding SS restraints: 53.64 Time building geometry restraints manager: 13.76 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 6033 1.32 - 1.45: 24329 1.45 - 1.58: 22683 1.58 - 1.71: 3042 1.71 - 1.84: 76 Bond restraints: 56163 Sorted by residual: bond pdb=" CA VAL V 157 " pdb=" CB VAL V 157 " ideal model delta sigma weight residual 1.537 1.602 -0.065 1.29e-02 6.01e+03 2.51e+01 bond pdb=" CA VAL R 58 " pdb=" CB VAL R 58 " ideal model delta sigma weight residual 1.539 1.491 0.048 1.11e-02 8.12e+03 1.83e+01 bond pdb=" CA ILE E 63 " pdb=" CB ILE E 63 " ideal model delta sigma weight residual 1.540 1.489 0.052 1.23e-02 6.61e+03 1.76e+01 bond pdb=" CA VAL H 123 " pdb=" CB VAL H 123 " ideal model delta sigma weight residual 1.540 1.484 0.056 1.36e-02 5.41e+03 1.68e+01 bond pdb=" CA ILE C 202 " pdb=" CB ILE C 202 " ideal model delta sigma weight residual 1.537 1.491 0.046 1.26e-02 6.30e+03 1.35e+01 ... (remaining 56158 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.65: 80154 2.65 - 5.29: 2963 5.29 - 7.94: 300 7.94 - 10.59: 38 10.59 - 13.24: 10 Bond angle restraints: 83465 Sorted by residual: angle pdb=" C GLY K 97 " pdb=" N PRO K 98 " pdb=" CA PRO K 98 " ideal model delta sigma weight residual 119.89 128.98 -9.09 1.02e+00 9.61e-01 7.95e+01 angle pdb=" C LYS J 57 " pdb=" CA LYS J 57 " pdb=" CB LYS J 57 " ideal model delta sigma weight residual 115.89 104.29 11.60 1.32e+00 5.74e-01 7.72e+01 angle pdb=" C PRO D 32 " pdb=" N PRO D 33 " pdb=" CA PRO D 33 " ideal model delta sigma weight residual 120.03 127.41 -7.38 9.90e-01 1.02e+00 5.55e+01 angle pdb=" C3' U A1482 " pdb=" O3' U A1482 " pdb=" P A A1483 " ideal model delta sigma weight residual 120.20 131.16 -10.96 1.50e+00 4.44e-01 5.34e+01 angle pdb=" C VAL E 99 " pdb=" N PRO E 100 " pdb=" CA PRO E 100 " ideal model delta sigma weight residual 119.84 128.95 -9.11 1.25e+00 6.40e-01 5.31e+01 ... (remaining 83460 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.62: 31543 35.62 - 71.24: 4213 71.24 - 106.85: 458 106.85 - 142.47: 17 142.47 - 178.09: 20 Dihedral angle restraints: 36251 sinusoidal: 29366 harmonic: 6885 Sorted by residual: dihedral pdb=" O4' U A 328 " pdb=" C1' U A 328 " pdb=" N1 U A 328 " pdb=" C2 U A 328 " ideal model delta sinusoidal sigma weight residual -160.00 18.09 -178.09 1 1.50e+01 4.44e-03 8.53e+01 dihedral pdb=" O4' C A 415 " pdb=" C1' C A 415 " pdb=" N1 C A 415 " pdb=" C2 C A 415 " ideal model delta sinusoidal sigma weight residual -160.00 15.14 -175.14 1 1.50e+01 4.44e-03 8.52e+01 dihedral pdb=" O4' C A 179 " pdb=" C1' C A 179 " pdb=" N1 C A 179 " pdb=" C2 C A 179 " ideal model delta sinusoidal sigma weight residual 200.00 28.03 171.97 1 1.50e+01 4.44e-03 8.49e+01 ... (remaining 36248 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.125: 10321 0.125 - 0.250: 245 0.250 - 0.374: 7 0.374 - 0.499: 2 0.499 - 0.624: 1 Chirality restraints: 10576 Sorted by residual: chirality pdb=" C3' U A1482 " pdb=" C4' U A1482 " pdb=" O3' U A1482 " pdb=" C2' U A1482 " both_signs ideal model delta sigma weight residual False -2.74 -2.12 -0.62 2.00e-01 2.50e+01 9.73e+00 chirality pdb=" C3' A A 895 " pdb=" C4' A A 895 " pdb=" O3' A A 895 " pdb=" C2' A A 895 " both_signs ideal model delta sigma weight residual False -2.74 -2.34 -0.40 2.00e-01 2.50e+01 4.08e+00 chirality pdb=" C1' G A 713 " pdb=" O4' G A 713 " pdb=" C2' G A 713 " pdb=" N9 G A 713 " both_signs ideal model delta sigma weight residual False 2.46 2.05 0.40 2.00e-01 2.50e+01 4.08e+00 ... (remaining 10573 not shown) Planarity restraints: 4881 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' G A 953 " -0.048 2.00e-02 2.50e+03 2.41e-02 1.74e+01 pdb=" N9 G A 953 " 0.066 2.00e-02 2.50e+03 pdb=" C8 G A 953 " 0.003 2.00e-02 2.50e+03 pdb=" N7 G A 953 " -0.002 2.00e-02 2.50e+03 pdb=" C5 G A 953 " -0.007 2.00e-02 2.50e+03 pdb=" C6 G A 953 " -0.007 2.00e-02 2.50e+03 pdb=" O6 G A 953 " -0.008 2.00e-02 2.50e+03 pdb=" N1 G A 953 " -0.003 2.00e-02 2.50e+03 pdb=" C2 G A 953 " 0.004 2.00e-02 2.50e+03 pdb=" N2 G A 953 " 0.004 2.00e-02 2.50e+03 pdb=" N3 G A 953 " 0.001 2.00e-02 2.50e+03 pdb=" C4 G A 953 " -0.005 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' U A 110 " 0.050 2.00e-02 2.50e+03 2.47e-02 1.37e+01 pdb=" N1 U A 110 " -0.046 2.00e-02 2.50e+03 pdb=" C2 U A 110 " -0.019 2.00e-02 2.50e+03 pdb=" O2 U A 110 " 0.003 2.00e-02 2.50e+03 pdb=" N3 U A 110 " -0.005 2.00e-02 2.50e+03 pdb=" C4 U A 110 " 0.009 2.00e-02 2.50e+03 pdb=" O4 U A 110 " 0.018 2.00e-02 2.50e+03 pdb=" C5 U A 110 " 0.002 2.00e-02 2.50e+03 pdb=" C6 U A 110 " -0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' C A 67 " -0.039 2.00e-02 2.50e+03 2.24e-02 1.13e+01 pdb=" N1 C A 67 " 0.053 2.00e-02 2.50e+03 pdb=" C2 C A 67 " 0.000 2.00e-02 2.50e+03 pdb=" O2 C A 67 " 0.003 2.00e-02 2.50e+03 pdb=" N3 C A 67 " -0.006 2.00e-02 2.50e+03 pdb=" C4 C A 67 " -0.007 2.00e-02 2.50e+03 pdb=" N4 C A 67 " -0.005 2.00e-02 2.50e+03 pdb=" C5 C A 67 " -0.005 2.00e-02 2.50e+03 pdb=" C6 C A 67 " 0.005 2.00e-02 2.50e+03 ... (remaining 4878 not shown) Histogram of nonbonded interaction distances: 1.74 - 2.37: 153 2.37 - 3.00: 26062 3.00 - 3.64: 87320 3.64 - 4.27: 150925 4.27 - 4.90: 203922 Nonbonded interactions: 468382 Sorted by model distance: nonbonded pdb=" OP2 A A 540 " pdb="MG MG A1615 " model vdw 1.740 2.170 nonbonded pdb=" OP1 G A 455 " pdb="MG MG A1710 " model vdw 1.818 2.170 nonbonded pdb=" OP2 A A 513 " pdb="MG MG A1765 " model vdw 1.824 2.170 nonbonded pdb=" OP1 C A 961 " pdb="MG MG A1669 " model vdw 1.849 2.170 nonbonded pdb=" OP1 U A1205 " pdb="MG MG A1639 " model vdw 1.867 2.170 ... (remaining 468377 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=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.420 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.030 Extract box with map and model: 1.860 Check model and map are aligned: 0.340 Set scattering table: 0.450 Process input model: 156.580 Find NCS groups from input model: 0.530 Set up NCS constraints: 0.150 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:2.650 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 163.030 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8569 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.077 56163 Z= 0.495 Angle : 1.198 13.237 83465 Z= 0.687 Chirality : 0.050 0.624 10576 Planarity : 0.006 0.069 4881 Dihedral : 24.367 178.090 31817 Min Nonbonded Distance : 1.740 Molprobity Statistics. All-atom Clashscore : 9.43 Ramachandran Plot: Outliers : 0.13 % Allowed : 5.41 % Favored : 94.46 % Rotamer: Outliers : 11.65 % Allowed : 12.35 % Favored : 76.00 % 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: -3.62 (0.13), residues: 2364 helix: -3.17 (0.11), residues: 1012 sheet: -0.76 (0.22), residues: 399 loop : -2.03 (0.16), residues: 953 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP P 59 HIS 0.015 0.002 HIS J 56 PHE 0.027 0.003 PHE V 32 TYR 0.029 0.003 TYR I 58 ARG 0.006 0.001 ARG K 102 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4728 Ramachandran restraints generated. 2364 Oldfield, 0 Emsley, 2364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4728 Ramachandran restraints generated. 2364 Oldfield, 0 Emsley, 2364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1098 residues out of total 2000 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 233 poor density : 865 time to evaluate : 3.199 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 8 ARG cc_start: 0.8433 (OUTLIER) cc_final: 0.7942 (ptm160) REVERT: B 10 LYS cc_start: 0.8539 (OUTLIER) cc_final: 0.7736 (mmtm) REVERT: B 11 ARG cc_start: 0.8620 (OUTLIER) cc_final: 0.8034 (tmm-80) REVERT: B 14 LYS cc_start: 0.8507 (tttt) cc_final: 0.8245 (tptm) REVERT: B 15 LYS cc_start: 0.8439 (mttt) cc_final: 0.8202 (mttt) REVERT: B 24 THR cc_start: 0.8799 (OUTLIER) cc_final: 0.8495 (p) REVERT: B 30 LYS cc_start: 0.7037 (OUTLIER) cc_final: 0.6333 (mmtt) REVERT: C 26 LYS cc_start: 0.8565 (mmtt) cc_final: 0.8223 (ptpt) REVERT: C 34 GLU cc_start: 0.8464 (mm-30) cc_final: 0.7678 (mt-10) REVERT: C 55 GLU cc_start: 0.7788 (tt0) cc_final: 0.7552 (mp0) REVERT: C 133 MET cc_start: 0.8619 (mmm) cc_final: 0.8337 (mmm) REVERT: C 135 LYS cc_start: 0.8897 (tttt) cc_final: 0.8657 (tttm) REVERT: C 177 THR cc_start: 0.9289 (m) cc_final: 0.9029 (p) REVERT: C 192 THR cc_start: 0.8616 (m) cc_final: 0.8398 (t) REVERT: D 63 MET cc_start: 0.8222 (mmp) cc_final: 0.7942 (mmm) REVERT: D 64 GLU cc_start: 0.8116 (tp30) cc_final: 0.7715 (tp30) REVERT: D 130 TYR cc_start: 0.9165 (t80) cc_final: 0.8887 (t80) REVERT: D 147 THR cc_start: 0.8642 (m) cc_final: 0.8249 (p) REVERT: D 166 LEU cc_start: 0.8452 (mt) cc_final: 0.8132 (tp) REVERT: D 186 ILE cc_start: 0.8540 (mt) cc_final: 0.8270 (mt) REVERT: D 199 TYR cc_start: 0.8468 (m-80) cc_final: 0.8140 (m-10) REVERT: E 77 LYS cc_start: 0.9018 (pttt) cc_final: 0.8715 (pttm) REVERT: E 85 ILE cc_start: 0.9367 (OUTLIER) cc_final: 0.8979 (mt) REVERT: E 94 LYS cc_start: 0.8640 (mttt) cc_final: 0.8274 (mttp) REVERT: E 186 ILE cc_start: 0.8929 (OUTLIER) cc_final: 0.8485 (mp) REVERT: E 200 GLU cc_start: 0.8930 (mm-30) cc_final: 0.8401 (mp0) REVERT: F 5 GLU cc_start: 0.8623 (tt0) cc_final: 0.8356 (tt0) REVERT: F 80 ASN cc_start: 0.8018 (m110) cc_final: 0.7134 (m-40) REVERT: F 89 LYS cc_start: 0.9080 (tptt) cc_final: 0.8794 (tppt) REVERT: G 35 LYS cc_start: 0.8853 (OUTLIER) cc_final: 0.8452 (mttp) REVERT: G 67 ASP cc_start: 0.8730 (m-30) cc_final: 0.8452 (p0) REVERT: G 106 ASN cc_start: 0.8612 (m110) cc_final: 0.8355 (m-40) REVERT: G 114 LYS cc_start: 0.8396 (mmtt) cc_final: 0.8003 (mtpp) REVERT: G 123 GLU cc_start: 0.6828 (tp30) cc_final: 0.6156 (tp30) REVERT: G 136 LYS cc_start: 0.8499 (tttt) cc_final: 0.8137 (ttmt) REVERT: G 140 ASP cc_start: 0.7630 (m-30) cc_final: 0.7260 (m-30) REVERT: H 70 ARG cc_start: 0.7315 (OUTLIER) cc_final: 0.6944 (tpp80) REVERT: H 72 ARG cc_start: 0.8071 (OUTLIER) cc_final: 0.7608 (ptp90) REVERT: H 113 LEU cc_start: 0.9445 (OUTLIER) cc_final: 0.9211 (mt) REVERT: H 131 VAL cc_start: 0.9446 (t) cc_final: 0.9170 (m) REVERT: I 39 VAL cc_start: 0.9384 (t) cc_final: 0.8949 (p) REVERT: I 48 PHE cc_start: 0.8431 (m-80) cc_final: 0.8217 (m-80) REVERT: I 81 PHE cc_start: 0.7775 (m-80) cc_final: 0.7551 (m-80) REVERT: I 140 LYS cc_start: 0.8857 (pttt) cc_final: 0.8655 (pttp) REVERT: I 149 LYS cc_start: 0.7751 (pttt) cc_final: 0.7291 (ptmt) REVERT: J 13 TYR cc_start: 0.8868 (m-80) cc_final: 0.8657 (m-80) REVERT: J 99 ASN cc_start: 0.8250 (OUTLIER) cc_final: 0.7671 (t0) REVERT: K 106 ILE cc_start: 0.8921 (mm) cc_final: 0.8696 (mp) REVERT: K 123 THR cc_start: 0.8891 (m) cc_final: 0.8504 (p) REVERT: K 136 ARG cc_start: 0.8710 (mtp-110) cc_final: 0.8304 (mtp85) REVERT: L 13 ARG cc_start: 0.8816 (ttt180) cc_final: 0.8460 (tpp-160) REVERT: L 29 GLN cc_start: 0.9142 (OUTLIER) cc_final: 0.8818 (mp10) REVERT: L 86 ARG cc_start: 0.7164 (tpt-90) cc_final: 0.6909 (tpt90) REVERT: M 15 MET cc_start: 0.8422 (mmp) cc_final: 0.8213 (tpp) REVERT: M 20 THR cc_start: 0.9167 (m) cc_final: 0.8864 (p) REVERT: M 31 ASN cc_start: 0.8543 (m110) cc_final: 0.7867 (m110) REVERT: M 40 ASP cc_start: 0.7718 (t0) cc_final: 0.7513 (t70) REVERT: M 52 GLN cc_start: 0.8314 (mt0) cc_final: 0.7743 (mt0) REVERT: M 63 ASN cc_start: 0.8402 (OUTLIER) cc_final: 0.8202 (m-40) REVERT: M 77 ASP cc_start: 0.7288 (m-30) cc_final: 0.6739 (m-30) REVERT: M 104 LYS cc_start: 0.9202 (tttt) cc_final: 0.8116 (ttmt) REVERT: M 115 ARG cc_start: 0.8103 (ptt180) cc_final: 0.7852 (ptt90) REVERT: N 11 ASN cc_start: 0.8884 (m-40) cc_final: 0.8648 (m110) REVERT: N 29 ARG cc_start: 0.9049 (ttt-90) cc_final: 0.8523 (ttt-90) REVERT: N 46 GLU cc_start: 0.8643 (mm-30) cc_final: 0.8418 (mm-30) REVERT: O 8 LYS cc_start: 0.8073 (mttt) cc_final: 0.7554 (mmmm) REVERT: O 68 LYS cc_start: 0.9241 (tttt) cc_final: 0.8994 (ttmt) REVERT: P 15 ASN cc_start: 0.9211 (p0) cc_final: 0.8232 (p0) REVERT: P 20 ILE cc_start: 0.9243 (mt) cc_final: 0.9009 (mt) REVERT: P 32 ARG cc_start: 0.8744 (ttt180) cc_final: 0.8528 (ttt180) REVERT: P 107 ASN cc_start: 0.8308 (m-40) cc_final: 0.8039 (m-40) REVERT: Q 21 LYS cc_start: 0.8798 (mmtp) cc_final: 0.8349 (mmmt) REVERT: Q 48 LEU cc_start: 0.8984 (OUTLIER) cc_final: 0.8657 (tp) REVERT: Q 79 THR cc_start: 0.8637 (t) cc_final: 0.8403 (p) REVERT: Q 92 GLU cc_start: 0.8133 (OUTLIER) cc_final: 0.7214 (tp30) REVERT: Q 95 GLU cc_start: 0.8089 (tt0) cc_final: 0.7720 (mt-10) REVERT: R 33 LYS cc_start: 0.7271 (mmtt) cc_final: 0.6717 (mmtm) REVERT: S 7 LYS cc_start: 0.9031 (mttt) cc_final: 0.8773 (mtmm) REVERT: S 12 ASP cc_start: 0.8298 (OUTLIER) cc_final: 0.8052 (p0) REVERT: S 36 ARG cc_start: 0.8738 (OUTLIER) cc_final: 0.8185 (mmt180) REVERT: S 44 PHE cc_start: 0.7975 (m-80) cc_final: 0.7731 (m-10) REVERT: S 47 HIS cc_start: 0.8229 (m-70) cc_final: 0.7662 (m-70) REVERT: S 53 ASP cc_start: 0.8566 (OUTLIER) cc_final: 0.8098 (p0) REVERT: S 56 LYS cc_start: 0.9163 (pttt) cc_final: 0.8880 (pttp) REVERT: T 75 LYS cc_start: 0.8922 (OUTLIER) cc_final: 0.8626 (mmtp) REVERT: V 24 ASN cc_start: 0.7940 (OUTLIER) cc_final: 0.7569 (t0) REVERT: V 72 THR cc_start: 0.6624 (m) cc_final: 0.6098 (m) REVERT: V 73 LYS cc_start: 0.8211 (OUTLIER) cc_final: 0.7137 (ttpp) REVERT: V 90 PRO cc_start: 0.6423 (Cg_exo) cc_final: 0.6137 (Cg_endo) REVERT: V 107 VAL cc_start: 0.6696 (m) cc_final: 0.6462 (t) REVERT: V 109 LYS cc_start: 0.7758 (mttt) cc_final: 0.7174 (tttt) REVERT: V 169 GLU cc_start: 0.8467 (OUTLIER) cc_final: 0.8237 (mm-30) REVERT: V 184 ILE cc_start: 0.7394 (OUTLIER) cc_final: 0.7066 (tp) outliers start: 233 outliers final: 75 residues processed: 1017 average time/residue: 0.8589 time to fit residues: 1351.8586 Evaluate side-chains 718 residues out of total 2000 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 99 poor density : 619 time to evaluate : 3.273 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 6 LYS Chi-restraints excluded: chain B residue 8 ARG Chi-restraints excluded: chain B residue 10 LYS Chi-restraints excluded: chain B residue 11 ARG Chi-restraints excluded: chain B residue 24 THR Chi-restraints excluded: chain B residue 30 LYS Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 46 LEU Chi-restraints excluded: chain C residue 66 ASP Chi-restraints excluded: chain C residue 82 GLU Chi-restraints excluded: chain C residue 167 PHE Chi-restraints excluded: chain C residue 169 ARG Chi-restraints excluded: chain C residue 182 ILE Chi-restraints excluded: chain C residue 191 THR Chi-restraints excluded: chain D residue 86 LEU Chi-restraints excluded: chain D residue 123 VAL Chi-restraints excluded: chain D residue 154 ARG Chi-restraints excluded: chain D residue 177 VAL Chi-restraints excluded: chain D residue 190 LEU Chi-restraints excluded: chain E residue 71 VAL Chi-restraints excluded: chain E residue 85 ILE Chi-restraints excluded: chain E residue 95 ASN Chi-restraints excluded: chain E residue 148 ILE Chi-restraints excluded: chain E residue 186 ILE Chi-restraints excluded: chain F residue 15 ASP Chi-restraints excluded: chain F residue 18 THR Chi-restraints excluded: chain F residue 43 TRP Chi-restraints excluded: chain G residue 24 THR Chi-restraints excluded: chain G residue 27 VAL Chi-restraints excluded: chain G residue 35 LYS Chi-restraints excluded: chain G residue 80 VAL Chi-restraints excluded: chain G residue 99 LEU Chi-restraints excluded: chain G residue 102 ARG Chi-restraints excluded: chain H residue 36 ILE Chi-restraints excluded: chain H residue 70 ARG Chi-restraints excluded: chain H residue 72 ARG Chi-restraints excluded: chain H residue 92 THR Chi-restraints excluded: chain H residue 113 LEU Chi-restraints excluded: chain I residue 42 VAL Chi-restraints excluded: chain I residue 78 VAL Chi-restraints excluded: chain I residue 147 TYR Chi-restraints excluded: chain J residue 18 ILE Chi-restraints excluded: chain J residue 44 THR Chi-restraints excluded: chain J residue 50 CYS Chi-restraints excluded: chain J residue 57 LYS Chi-restraints excluded: chain J residue 99 ASN Chi-restraints excluded: chain K residue 25 VAL Chi-restraints excluded: chain K residue 40 ILE Chi-restraints excluded: chain K residue 91 VAL Chi-restraints excluded: chain K residue 95 VAL Chi-restraints excluded: chain L residue 8 VAL Chi-restraints excluded: chain L residue 27 SER Chi-restraints excluded: chain L residue 29 GLN Chi-restraints excluded: chain L residue 38 TYR Chi-restraints excluded: chain L residue 52 VAL Chi-restraints excluded: chain L residue 73 ASN Chi-restraints excluded: chain L residue 104 THR Chi-restraints excluded: chain M residue 63 ASN Chi-restraints excluded: chain M residue 70 LEU Chi-restraints excluded: chain M residue 103 THR Chi-restraints excluded: chain M residue 109 THR Chi-restraints excluded: chain N residue 24 CYS Chi-restraints excluded: chain N residue 32 SER Chi-restraints excluded: chain O residue 60 VAL Chi-restraints excluded: chain O residue 75 VAL Chi-restraints excluded: chain P residue 9 ARG Chi-restraints excluded: chain P residue 28 ARG Chi-restraints excluded: chain P residue 50 GLN Chi-restraints excluded: chain P residue 67 THR Chi-restraints excluded: chain P residue 86 LEU Chi-restraints excluded: chain P residue 90 GLU Chi-restraints excluded: chain Q residue 28 VAL Chi-restraints excluded: chain Q residue 35 THR Chi-restraints excluded: chain Q residue 48 LEU Chi-restraints excluded: chain Q residue 65 ASN Chi-restraints excluded: chain Q residue 74 VAL Chi-restraints excluded: chain Q residue 92 GLU Chi-restraints excluded: chain Q residue 93 ILE Chi-restraints excluded: chain S residue 11 VAL Chi-restraints excluded: chain S residue 12 ASP Chi-restraints excluded: chain S residue 15 LEU Chi-restraints excluded: chain S residue 31 ILE Chi-restraints excluded: chain S residue 36 ARG Chi-restraints excluded: chain S residue 53 ASP Chi-restraints excluded: chain S residue 78 ARG Chi-restraints excluded: chain T residue 23 SER Chi-restraints excluded: chain T residue 50 LEU Chi-restraints excluded: chain T residue 70 ASN Chi-restraints excluded: chain T residue 75 LYS Chi-restraints excluded: chain T residue 81 LEU Chi-restraints excluded: chain V residue 24 ASN Chi-restraints excluded: chain V residue 32 PHE Chi-restraints excluded: chain V residue 38 ILE Chi-restraints excluded: chain V residue 73 LYS Chi-restraints excluded: chain V residue 155 GLN Chi-restraints excluded: chain V residue 169 GLU Chi-restraints excluded: chain V residue 184 ILE Chi-restraints excluded: chain V residue 186 ILE Chi-restraints excluded: chain g residue 58 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 324 optimal weight: 6.9990 chunk 291 optimal weight: 5.9990 chunk 161 optimal weight: 3.9990 chunk 99 optimal weight: 30.0000 chunk 196 optimal weight: 5.9990 chunk 155 optimal weight: 8.9990 chunk 300 optimal weight: 20.0000 chunk 116 optimal weight: 10.0000 chunk 183 optimal weight: 5.9990 chunk 224 optimal weight: 0.9980 chunk 348 optimal weight: 20.0000 overall best weight: 4.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 101 ASN C 111 GLN C 138 GLN E 157 ASN E 160 ASN F 96 HIS G 28 ASN G 106 ASN G 142 HIS H 121 GLN I 64 HIS I 146 GLN J 56 HIS J 70 HIS J 99 ASN ** K 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 128 ASN L 29 GLN L 73 ASN ** O 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 41 HIS Q 46 HIS S 14 HIS S 52 HIS S 57 HIS T 68 HIS T 70 ASN T 74 ASN V 24 ASN V 167 ASN Total number of N/Q/H flips: 28 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8461 moved from start: 0.2541 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 56163 Z= 0.241 Angle : 0.698 9.712 83465 Z= 0.357 Chirality : 0.040 0.323 10576 Planarity : 0.006 0.069 4881 Dihedral : 24.390 179.751 27195 Min Nonbonded Distance : 1.471 Molprobity Statistics. All-atom Clashscore : 9.97 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.68 % Favored : 96.28 % Rotamer: Outliers : 7.05 % Allowed : 20.00 % Favored : 72.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.00 (0.16), residues: 2364 helix: -0.16 (0.15), residues: 1008 sheet: -0.14 (0.24), residues: 392 loop : -1.32 (0.18), residues: 964 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP F 43 HIS 0.010 0.001 HIS G 153 PHE 0.023 0.002 PHE V 32 TYR 0.020 0.002 TYR C 203 ARG 0.008 0.001 ARG V 208 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4728 Ramachandran restraints generated. 2364 Oldfield, 0 Emsley, 2364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4728 Ramachandran restraints generated. 2364 Oldfield, 0 Emsley, 2364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 843 residues out of total 2000 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 141 poor density : 702 time to evaluate : 2.989 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 10 LYS cc_start: 0.8832 (OUTLIER) cc_final: 0.7805 (mmtm) REVERT: B 21 LEU cc_start: 0.8339 (mt) cc_final: 0.8104 (mt) REVERT: B 24 THR cc_start: 0.8433 (OUTLIER) cc_final: 0.8138 (p) REVERT: B 30 LYS cc_start: 0.6108 (OUTLIER) cc_final: 0.5611 (mmtt) REVERT: C 3 GLN cc_start: 0.7876 (mm-40) cc_final: 0.7288 (mt0) REVERT: C 34 GLU cc_start: 0.8476 (mm-30) cc_final: 0.7996 (tt0) REVERT: C 68 HIS cc_start: 0.7892 (m170) cc_final: 0.7557 (m90) REVERT: C 97 GLN cc_start: 0.6544 (tt0) cc_final: 0.6067 (tp40) REVERT: C 162 MET cc_start: 0.7511 (mmp) cc_final: 0.7301 (mmp) REVERT: C 167 PHE cc_start: 0.8441 (OUTLIER) cc_final: 0.8096 (p90) REVERT: C 177 THR cc_start: 0.9286 (m) cc_final: 0.8947 (p) REVERT: D 43 GLU cc_start: 0.8011 (mt-10) cc_final: 0.7762 (mm-30) REVERT: D 63 MET cc_start: 0.8395 (mmp) cc_final: 0.7991 (mmm) REVERT: D 64 GLU cc_start: 0.7914 (tp30) cc_final: 0.7698 (tp30) REVERT: D 130 TYR cc_start: 0.9031 (t80) cc_final: 0.8776 (t80) REVERT: D 147 THR cc_start: 0.8634 (m) cc_final: 0.8279 (p) REVERT: D 199 TYR cc_start: 0.7958 (m-80) cc_final: 0.7598 (m-10) REVERT: E 58 PHE cc_start: 0.9008 (m-80) cc_final: 0.8694 (m-80) REVERT: E 77 LYS cc_start: 0.8764 (pttt) cc_final: 0.8509 (pttm) REVERT: E 80 GLU cc_start: 0.8577 (tp30) cc_final: 0.8105 (tt0) REVERT: E 200 GLU cc_start: 0.8931 (mm-30) cc_final: 0.8196 (mp0) REVERT: F 42 ILE cc_start: 0.9199 (mt) cc_final: 0.8998 (mp) REVERT: F 46 ARG cc_start: 0.8249 (tpp-160) cc_final: 0.8009 (mmt180) REVERT: F 54 LYS cc_start: 0.8541 (mmtt) cc_final: 0.8332 (mmtt) REVERT: F 80 ASN cc_start: 0.8343 (m110) cc_final: 0.7984 (m-40) REVERT: F 89 LYS cc_start: 0.8937 (tptt) cc_final: 0.8686 (tppt) REVERT: G 10 ARG cc_start: 0.6917 (mmt90) cc_final: 0.6665 (mtt-85) REVERT: G 102 ARG cc_start: 0.8330 (OUTLIER) cc_final: 0.7437 (ttp-110) REVERT: G 114 LYS cc_start: 0.8405 (mmtt) cc_final: 0.8008 (ptmm) REVERT: G 124 ILE cc_start: 0.9116 (mt) cc_final: 0.8907 (tt) REVERT: H 7 ILE cc_start: 0.8983 (mm) cc_final: 0.8769 (mp) REVERT: H 72 ARG cc_start: 0.8093 (OUTLIER) cc_final: 0.7709 (mtt180) REVERT: I 39 VAL cc_start: 0.9287 (t) cc_final: 0.8812 (p) REVERT: I 75 VAL cc_start: 0.8005 (p) cc_final: 0.7692 (p) REVERT: I 146 GLN cc_start: 0.8781 (OUTLIER) cc_final: 0.8491 (tt0) REVERT: I 149 LYS cc_start: 0.7572 (pttt) cc_final: 0.7059 (ptmt) REVERT: J 6 ILE cc_start: 0.8341 (mt) cc_final: 0.8124 (mm) REVERT: J 7 ARG cc_start: 0.7893 (ttm110) cc_final: 0.7686 (mtp180) REVERT: J 13 TYR cc_start: 0.8754 (m-80) cc_final: 0.8518 (m-80) REVERT: J 71 LYS cc_start: 0.9039 (mttt) cc_final: 0.8832 (mttp) REVERT: K 89 LYS cc_start: 0.8686 (mmmm) cc_final: 0.8462 (mmmt) REVERT: K 136 ARG cc_start: 0.8884 (mtp-110) cc_final: 0.8569 (mtp85) REVERT: L 13 ARG cc_start: 0.8737 (ttt180) cc_final: 0.8430 (tpp-160) REVERT: L 38 TYR cc_start: 0.7898 (OUTLIER) cc_final: 0.7617 (p90) REVERT: L 94 ARG cc_start: 0.8481 (mmt-90) cc_final: 0.8069 (mmt-90) REVERT: M 15 MET cc_start: 0.8570 (mmp) cc_final: 0.8329 (tpp) REVERT: M 31 ASN cc_start: 0.8400 (m110) cc_final: 0.7970 (m110) REVERT: M 52 GLN cc_start: 0.8382 (mt0) cc_final: 0.7960 (mt0) REVERT: M 73 GLU cc_start: 0.8752 (tm-30) cc_final: 0.8469 (tm-30) REVERT: O 8 LYS cc_start: 0.7880 (mttt) cc_final: 0.7447 (mmmm) REVERT: O 68 LYS cc_start: 0.9216 (tttt) cc_final: 0.8934 (ttmt) REVERT: P 9 ARG cc_start: 0.8894 (OUTLIER) cc_final: 0.8575 (ttt-90) REVERT: P 15 ASN cc_start: 0.9036 (p0) cc_final: 0.8086 (p0) REVERT: P 26 ARG cc_start: 0.9048 (mtm-85) cc_final: 0.8728 (mtm-85) REVERT: Q 28 VAL cc_start: 0.7861 (OUTLIER) cc_final: 0.7642 (m) REVERT: Q 39 GLU cc_start: 0.8744 (mt-10) cc_final: 0.8521 (mt-10) REVERT: Q 73 ARG cc_start: 0.8220 (ttt180) cc_final: 0.7874 (ttp-170) REVERT: R 41 TYR cc_start: 0.9356 (m-80) cc_final: 0.9130 (m-80) REVERT: R 49 ARG cc_start: 0.9075 (ttm-80) cc_final: 0.8696 (mtm-85) REVERT: S 73 GLU cc_start: 0.9006 (mt-10) cc_final: 0.8744 (mt-10) REVERT: T 29 ARG cc_start: 0.7840 (ttm110) cc_final: 0.7482 (ttm110) REVERT: T 81 LEU cc_start: 0.8543 (OUTLIER) cc_final: 0.8315 (tp) REVERT: V 48 THR cc_start: 0.7534 (m) cc_final: 0.7185 (p) REVERT: V 72 THR cc_start: 0.6480 (m) cc_final: 0.6226 (m) REVERT: V 73 LYS cc_start: 0.8060 (mtpt) cc_final: 0.7394 (mmmm) REVERT: V 109 LYS cc_start: 0.7688 (mttt) cc_final: 0.7156 (tttt) REVERT: V 136 MET cc_start: 0.6043 (tmm) cc_final: 0.5552 (tmm) REVERT: V 169 GLU cc_start: 0.8192 (OUTLIER) cc_final: 0.7976 (mm-30) outliers start: 141 outliers final: 68 residues processed: 780 average time/residue: 0.7341 time to fit residues: 903.6580 Evaluate side-chains 680 residues out of total 2000 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 600 time to evaluate : 3.201 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 4 VAL Chi-restraints excluded: chain B residue 6 LYS Chi-restraints excluded: chain B residue 10 LYS Chi-restraints excluded: chain B residue 24 THR Chi-restraints excluded: chain B residue 30 LYS Chi-restraints excluded: chain C residue 46 LEU Chi-restraints excluded: chain C residue 69 THR Chi-restraints excluded: chain C residue 101 ASN Chi-restraints excluded: chain C residue 111 GLN Chi-restraints excluded: chain C residue 117 GLN Chi-restraints excluded: chain C residue 163 SER Chi-restraints excluded: chain C residue 167 PHE Chi-restraints excluded: chain C residue 182 ILE Chi-restraints excluded: chain C residue 191 THR Chi-restraints excluded: chain D residue 20 VAL Chi-restraints excluded: chain D residue 44 SER Chi-restraints excluded: chain D residue 88 ILE Chi-restraints excluded: chain D residue 133 SER Chi-restraints excluded: chain D residue 177 VAL Chi-restraints excluded: chain D residue 190 LEU Chi-restraints excluded: chain E residue 42 SER Chi-restraints excluded: chain E residue 51 LYS Chi-restraints excluded: chain E residue 59 THR Chi-restraints excluded: chain E residue 71 VAL Chi-restraints excluded: chain E residue 81 VAL Chi-restraints excluded: chain E residue 148 ILE Chi-restraints excluded: chain F residue 43 TRP Chi-restraints excluded: chain G residue 24 THR Chi-restraints excluded: chain G residue 27 VAL Chi-restraints excluded: chain G residue 80 VAL Chi-restraints excluded: chain G residue 84 THR Chi-restraints excluded: chain G residue 102 ARG Chi-restraints excluded: chain G residue 128 SER Chi-restraints excluded: chain G residue 153 HIS Chi-restraints excluded: chain H residue 72 ARG Chi-restraints excluded: chain H residue 92 THR Chi-restraints excluded: chain I residue 78 VAL Chi-restraints excluded: chain I residue 146 GLN Chi-restraints excluded: chain J residue 18 ILE Chi-restraints excluded: chain K residue 40 ILE Chi-restraints excluded: chain K residue 91 VAL Chi-restraints excluded: chain L residue 27 SER Chi-restraints excluded: chain L residue 38 TYR Chi-restraints excluded: chain L residue 39 THR Chi-restraints excluded: chain L residue 49 LEU Chi-restraints excluded: chain L residue 63 VAL Chi-restraints excluded: chain L residue 73 ASN Chi-restraints excluded: chain L residue 104 THR Chi-restraints excluded: chain L residue 108 LYS Chi-restraints excluded: chain M residue 4 LEU Chi-restraints excluded: chain M residue 5 VAL Chi-restraints excluded: chain M residue 45 THR Chi-restraints excluded: chain N residue 9 LYS Chi-restraints excluded: chain N residue 22 THR Chi-restraints excluded: chain N residue 24 CYS Chi-restraints excluded: chain N residue 59 SER Chi-restraints excluded: chain O residue 38 ASP Chi-restraints excluded: chain O residue 80 SER Chi-restraints excluded: chain P residue 9 ARG Chi-restraints excluded: chain P residue 30 ASP Chi-restraints excluded: chain P residue 67 THR Chi-restraints excluded: chain P residue 86 LEU Chi-restraints excluded: chain P residue 92 THR Chi-restraints excluded: chain P residue 95 VAL Chi-restraints excluded: chain Q residue 28 VAL Chi-restraints excluded: chain Q residue 35 THR Chi-restraints excluded: chain Q residue 55 THR Chi-restraints excluded: chain Q residue 65 ASN Chi-restraints excluded: chain S residue 11 VAL Chi-restraints excluded: chain S residue 14 HIS Chi-restraints excluded: chain S residue 27 THR Chi-restraints excluded: chain S residue 71 LEU Chi-restraints excluded: chain S residue 78 ARG Chi-restraints excluded: chain T residue 39 VAL Chi-restraints excluded: chain T residue 50 LEU Chi-restraints excluded: chain T residue 51 LEU Chi-restraints excluded: chain T residue 81 LEU Chi-restraints excluded: chain V residue 169 GLU Chi-restraints excluded: chain V residue 186 ILE Chi-restraints excluded: chain g residue 58 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 193 optimal weight: 6.9990 chunk 108 optimal weight: 10.0000 chunk 290 optimal weight: 2.9990 chunk 237 optimal weight: 2.9990 chunk 96 optimal weight: 20.0000 chunk 349 optimal weight: 9.9990 chunk 377 optimal weight: 5.9990 chunk 311 optimal weight: 8.9990 chunk 346 optimal weight: 20.0000 chunk 119 optimal weight: 10.0000 chunk 280 optimal weight: 4.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 111 GLN C 138 GLN G 25 GLN G 129 ASN G 142 HIS G 153 HIS ** H 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 146 GLN ** K 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 110 GLN ** K 128 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 42 ASN M 75 GLN N 11 ASN P 57 GLN R 28 GLN S 14 HIS Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8451 moved from start: 0.3197 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 56163 Z= 0.236 Angle : 0.638 10.498 83465 Z= 0.328 Chirality : 0.038 0.269 10576 Planarity : 0.005 0.069 4881 Dihedral : 24.121 179.230 27068 Min Nonbonded Distance : 0.890 Molprobity Statistics. All-atom Clashscore : 9.13 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.51 % Favored : 96.45 % Rotamer: Outliers : 6.80 % Allowed : 23.10 % Favored : 70.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.09 (0.17), residues: 2364 helix: 0.86 (0.16), residues: 1020 sheet: 0.02 (0.24), residues: 398 loop : -1.06 (0.19), residues: 946 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP D 165 HIS 0.009 0.001 HIS G 153 PHE 0.017 0.002 PHE V 32 TYR 0.024 0.002 TYR C 187 ARG 0.010 0.001 ARG C 85 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4728 Ramachandran restraints generated. 2364 Oldfield, 0 Emsley, 2364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4728 Ramachandran restraints generated. 2364 Oldfield, 0 Emsley, 2364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 763 residues out of total 2000 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 136 poor density : 627 time to evaluate : 3.014 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 10 LYS cc_start: 0.8820 (OUTLIER) cc_final: 0.7838 (mmtm) REVERT: B 21 LEU cc_start: 0.8441 (mt) cc_final: 0.8135 (mt) REVERT: B 24 THR cc_start: 0.8609 (OUTLIER) cc_final: 0.8163 (p) REVERT: B 30 LYS cc_start: 0.6005 (OUTLIER) cc_final: 0.5516 (mmtt) REVERT: C 3 GLN cc_start: 0.7916 (mm-40) cc_final: 0.7440 (mt0) REVERT: C 34 GLU cc_start: 0.8607 (mm-30) cc_final: 0.8027 (tt0) REVERT: C 66 ASP cc_start: 0.7821 (t0) cc_final: 0.7343 (t0) REVERT: C 121 GLU cc_start: 0.8118 (mm-30) cc_final: 0.7902 (mm-30) REVERT: C 126 ARG cc_start: 0.7676 (mmt180) cc_final: 0.7358 (mmt180) REVERT: C 135 LYS cc_start: 0.8921 (ttpt) cc_final: 0.8555 (ttpt) REVERT: C 167 PHE cc_start: 0.8563 (OUTLIER) cc_final: 0.8319 (p90) REVERT: C 177 THR cc_start: 0.9194 (m) cc_final: 0.8751 (p) REVERT: D 43 GLU cc_start: 0.8117 (mt-10) cc_final: 0.7783 (mm-30) REVERT: D 44 SER cc_start: 0.8259 (OUTLIER) cc_final: 0.7944 (m) REVERT: D 63 MET cc_start: 0.8337 (mmp) cc_final: 0.8058 (mmp) REVERT: D 64 GLU cc_start: 0.7851 (tp30) cc_final: 0.7529 (tp30) REVERT: D 199 TYR cc_start: 0.8146 (m-80) cc_final: 0.7883 (m-10) REVERT: E 58 PHE cc_start: 0.8937 (m-80) cc_final: 0.8680 (m-80) REVERT: E 77 LYS cc_start: 0.8683 (pttt) cc_final: 0.8385 (pttm) REVERT: E 80 GLU cc_start: 0.8789 (tp30) cc_final: 0.8216 (tt0) REVERT: E 97 PHE cc_start: 0.7984 (OUTLIER) cc_final: 0.7363 (t80) REVERT: E 177 GLU cc_start: 0.8371 (pm20) cc_final: 0.8123 (mp0) REVERT: F 42 ILE cc_start: 0.9300 (mt) cc_final: 0.8976 (mp) REVERT: F 51 GLU cc_start: 0.9031 (mm-30) cc_final: 0.8652 (tt0) REVERT: F 89 LYS cc_start: 0.8964 (tptt) cc_final: 0.8718 (tppt) REVERT: F 95 LYS cc_start: 0.7121 (tttm) cc_final: 0.6899 (tttm) REVERT: G 108 SER cc_start: 0.8735 (m) cc_final: 0.8452 (m) REVERT: H 7 ILE cc_start: 0.8957 (mm) cc_final: 0.8734 (mp) REVERT: H 58 LYS cc_start: 0.8854 (mtmm) cc_final: 0.8601 (mtpp) REVERT: H 63 GLN cc_start: 0.8659 (tt0) cc_final: 0.8375 (mp-120) REVERT: I 39 VAL cc_start: 0.9265 (t) cc_final: 0.8827 (p) REVERT: I 83 ILE cc_start: 0.8082 (pt) cc_final: 0.7697 (pt) REVERT: I 127 ASP cc_start: 0.7937 (t0) cc_final: 0.7686 (t0) REVERT: I 149 LYS cc_start: 0.7447 (pttt) cc_final: 0.7077 (ptmt) REVERT: J 13 TYR cc_start: 0.8763 (m-80) cc_final: 0.8550 (m-80) REVERT: J 27 GLU cc_start: 0.8080 (pp20) cc_final: 0.7639 (tm-30) REVERT: K 134 LYS cc_start: 0.8691 (ptpp) cc_final: 0.8374 (pttm) REVERT: K 136 ARG cc_start: 0.8821 (mtp-110) cc_final: 0.8581 (mtp85) REVERT: L 76 GLU cc_start: 0.8380 (mt-10) cc_final: 0.8135 (pm20) REVERT: L 105 GLN cc_start: 0.8646 (mm-40) cc_final: 0.8420 (mm-40) REVERT: M 15 MET cc_start: 0.8695 (mmp) cc_final: 0.8355 (tpp) REVERT: M 42 ASN cc_start: 0.8320 (t0) cc_final: 0.8026 (t0) REVERT: M 52 GLN cc_start: 0.8474 (mt0) cc_final: 0.8090 (mt0) REVERT: M 73 GLU cc_start: 0.8825 (tm-30) cc_final: 0.8525 (tm-30) REVERT: N 29 ARG cc_start: 0.9070 (ttt-90) cc_final: 0.8609 (ttt-90) REVERT: O 8 LYS cc_start: 0.8014 (mttt) cc_final: 0.7507 (mmmm) REVERT: O 81 LEU cc_start: 0.9351 (OUTLIER) cc_final: 0.9041 (mp) REVERT: P 15 ASN cc_start: 0.8943 (p0) cc_final: 0.8095 (p0) REVERT: P 26 ARG cc_start: 0.9037 (mtm-85) cc_final: 0.8804 (mtm-85) REVERT: Q 73 ARG cc_start: 0.8093 (ttt180) cc_final: 0.7710 (tmm-80) REVERT: Q 93 ILE cc_start: 0.7689 (mt) cc_final: 0.7423 (mt) REVERT: R 19 LYS cc_start: 0.6696 (mmtm) cc_final: 0.6357 (mtmm) REVERT: R 41 TYR cc_start: 0.9389 (m-80) cc_final: 0.9168 (m-80) REVERT: R 49 ARG cc_start: 0.9104 (ttm-80) cc_final: 0.8605 (mtm180) REVERT: V 68 LEU cc_start: 0.8397 (mt) cc_final: 0.8011 (mp) REVERT: V 73 LYS cc_start: 0.8385 (mtpt) cc_final: 0.7446 (mmmm) REVERT: V 83 GLU cc_start: 0.5221 (pt0) cc_final: 0.4989 (pt0) REVERT: V 109 LYS cc_start: 0.7690 (mttt) cc_final: 0.7097 (tttt) REVERT: V 141 LYS cc_start: 0.7615 (mtpp) cc_final: 0.7329 (mttm) REVERT: V 208 ARG cc_start: 0.7340 (mmm-85) cc_final: 0.7071 (mtp180) REVERT: V 215 LYS cc_start: 0.7232 (mtmm) cc_final: 0.6907 (mtmm) REVERT: g 62 GLU cc_start: 0.8643 (mt-10) cc_final: 0.8426 (mp0) outliers start: 136 outliers final: 82 residues processed: 700 average time/residue: 0.7016 time to fit residues: 788.5939 Evaluate side-chains 679 residues out of total 2000 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 590 time to evaluate : 3.044 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 4 VAL Chi-restraints excluded: chain B residue 6 LYS Chi-restraints excluded: chain B residue 10 LYS Chi-restraints excluded: chain B residue 24 THR Chi-restraints excluded: chain B residue 30 LYS Chi-restraints excluded: chain C residue 32 VAL Chi-restraints excluded: chain C residue 46 LEU Chi-restraints excluded: chain C residue 69 THR Chi-restraints excluded: chain C residue 101 ASN Chi-restraints excluded: chain C residue 163 SER Chi-restraints excluded: chain C residue 167 PHE Chi-restraints excluded: chain C residue 191 THR Chi-restraints excluded: chain D residue 20 VAL Chi-restraints excluded: chain D residue 44 SER Chi-restraints excluded: chain D residue 177 VAL Chi-restraints excluded: chain D residue 190 LEU Chi-restraints excluded: chain E residue 42 SER Chi-restraints excluded: chain E residue 47 SER Chi-restraints excluded: chain E residue 50 VAL Chi-restraints excluded: chain E residue 51 LYS Chi-restraints excluded: chain E residue 59 THR Chi-restraints excluded: chain E residue 71 VAL Chi-restraints excluded: chain E residue 81 VAL Chi-restraints excluded: chain E residue 97 PHE Chi-restraints excluded: chain E residue 130 VAL Chi-restraints excluded: chain E residue 146 HIS Chi-restraints excluded: chain F residue 27 LEU Chi-restraints excluded: chain F residue 43 TRP Chi-restraints excluded: chain F residue 72 VAL Chi-restraints excluded: chain F residue 79 LEU Chi-restraints excluded: chain G residue 27 VAL Chi-restraints excluded: chain G residue 74 GLU Chi-restraints excluded: chain G residue 75 VAL Chi-restraints excluded: chain G residue 80 VAL Chi-restraints excluded: chain G residue 84 THR Chi-restraints excluded: chain G residue 153 HIS Chi-restraints excluded: chain H residue 92 THR Chi-restraints excluded: chain H residue 108 THR Chi-restraints excluded: chain I residue 78 VAL Chi-restraints excluded: chain I residue 148 SER Chi-restraints excluded: chain J residue 44 THR Chi-restraints excluded: chain J residue 97 ASP Chi-restraints excluded: chain K residue 32 ILE Chi-restraints excluded: chain K residue 40 ILE Chi-restraints excluded: chain K residue 91 VAL Chi-restraints excluded: chain K residue 120 SER Chi-restraints excluded: chain L residue 27 SER Chi-restraints excluded: chain L residue 39 THR Chi-restraints excluded: chain L residue 49 LEU Chi-restraints excluded: chain L residue 52 VAL Chi-restraints excluded: chain L residue 58 THR Chi-restraints excluded: chain L residue 63 VAL Chi-restraints excluded: chain L residue 73 ASN Chi-restraints excluded: chain L residue 104 THR Chi-restraints excluded: chain M residue 4 LEU Chi-restraints excluded: chain M residue 5 VAL Chi-restraints excluded: chain M residue 45 THR Chi-restraints excluded: chain M residue 109 THR Chi-restraints excluded: chain N residue 22 THR Chi-restraints excluded: chain N residue 24 CYS Chi-restraints excluded: chain N residue 59 SER Chi-restraints excluded: chain O residue 20 THR Chi-restraints excluded: chain O residue 38 ASP Chi-restraints excluded: chain O residue 75 VAL Chi-restraints excluded: chain O residue 80 SER Chi-restraints excluded: chain O residue 81 LEU Chi-restraints excluded: chain P residue 20 ILE Chi-restraints excluded: chain P residue 30 ASP Chi-restraints excluded: chain P residue 67 THR Chi-restraints excluded: chain P residue 86 LEU Chi-restraints excluded: chain P residue 92 THR Chi-restraints excluded: chain P residue 95 VAL Chi-restraints excluded: chain Q residue 22 THR Chi-restraints excluded: chain Q residue 28 VAL Chi-restraints excluded: chain Q residue 55 THR Chi-restraints excluded: chain Q residue 65 ASN Chi-restraints excluded: chain Q residue 79 THR Chi-restraints excluded: chain S residue 11 VAL Chi-restraints excluded: chain S residue 27 THR Chi-restraints excluded: chain S residue 78 ARG Chi-restraints excluded: chain T residue 39 VAL Chi-restraints excluded: chain T residue 50 LEU Chi-restraints excluded: chain T residue 83 LEU Chi-restraints excluded: chain V residue 4 VAL Chi-restraints excluded: chain V residue 32 PHE Chi-restraints excluded: chain V residue 80 ILE Chi-restraints excluded: chain V residue 100 MET Chi-restraints excluded: chain V residue 186 ILE Chi-restraints excluded: chain g residue 58 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 345 optimal weight: 7.9990 chunk 262 optimal weight: 5.9990 chunk 181 optimal weight: 9.9990 chunk 38 optimal weight: 10.0000 chunk 166 optimal weight: 4.9990 chunk 234 optimal weight: 20.0000 chunk 350 optimal weight: 20.0000 chunk 371 optimal weight: 4.9990 chunk 183 optimal weight: 0.9990 chunk 332 optimal weight: 5.9990 chunk 100 optimal weight: 50.0000 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 101 ASN G 25 GLN G 142 HIS ** H 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 146 GLN ** K 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 128 ASN R 28 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8436 moved from start: 0.3579 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 56163 Z= 0.221 Angle : 0.612 14.224 83465 Z= 0.313 Chirality : 0.036 0.263 10576 Planarity : 0.005 0.072 4881 Dihedral : 24.002 178.666 27041 Min Nonbonded Distance : 0.986 Molprobity Statistics. All-atom Clashscore : 9.06 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.68 % Favored : 96.24 % Rotamer: Outliers : 6.70 % Allowed : 23.65 % Favored : 69.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.13 (0.17), residues: 2364 helix: 1.08 (0.16), residues: 1013 sheet: 0.09 (0.24), residues: 406 loop : -0.95 (0.20), residues: 945 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP F 43 HIS 0.030 0.001 HIS G 153 PHE 0.014 0.002 PHE I 59 TYR 0.023 0.002 TYR g 65 ARG 0.007 0.000 ARG L 83 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4728 Ramachandran restraints generated. 2364 Oldfield, 0 Emsley, 2364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4728 Ramachandran restraints generated. 2364 Oldfield, 0 Emsley, 2364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 753 residues out of total 2000 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 134 poor density : 619 time to evaluate : 3.287 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 10 LYS cc_start: 0.8861 (OUTLIER) cc_final: 0.7804 (mmtm) REVERT: B 16 LYS cc_start: 0.8681 (mmmt) cc_final: 0.8384 (mmmt) REVERT: B 21 LEU cc_start: 0.8482 (mt) cc_final: 0.8247 (mt) REVERT: B 24 THR cc_start: 0.8652 (OUTLIER) cc_final: 0.8233 (p) REVERT: B 30 LYS cc_start: 0.5876 (OUTLIER) cc_final: 0.5395 (mmtt) REVERT: C 3 GLN cc_start: 0.7739 (mm-40) cc_final: 0.7360 (mt0) REVERT: C 34 GLU cc_start: 0.8715 (mm-30) cc_final: 0.8045 (tt0) REVERT: C 64 ARG cc_start: 0.8274 (ttm-80) cc_final: 0.7904 (ttm-80) REVERT: C 68 HIS cc_start: 0.8111 (m170) cc_final: 0.7653 (m-70) REVERT: C 121 GLU cc_start: 0.8291 (mm-30) cc_final: 0.8051 (mm-30) REVERT: C 126 ARG cc_start: 0.7766 (mmt180) cc_final: 0.7472 (mmt180) REVERT: C 135 LYS cc_start: 0.8863 (ttpt) cc_final: 0.8578 (ttpt) REVERT: C 177 THR cc_start: 0.9142 (m) cc_final: 0.8679 (p) REVERT: D 43 GLU cc_start: 0.8164 (mt-10) cc_final: 0.7842 (mm-30) REVERT: D 44 SER cc_start: 0.8170 (OUTLIER) cc_final: 0.7958 (m) REVERT: D 63 MET cc_start: 0.8377 (mmp) cc_final: 0.8135 (mmp) REVERT: D 64 GLU cc_start: 0.7716 (tp30) cc_final: 0.7392 (tp30) REVERT: D 147 THR cc_start: 0.8663 (m) cc_final: 0.8352 (p) REVERT: D 165 TRP cc_start: 0.8287 (p-90) cc_final: 0.7816 (p-90) REVERT: D 199 TYR cc_start: 0.8140 (m-80) cc_final: 0.7934 (m-10) REVERT: E 58 PHE cc_start: 0.8926 (m-80) cc_final: 0.8656 (m-80) REVERT: E 80 GLU cc_start: 0.8623 (tp30) cc_final: 0.8021 (tt0) REVERT: E 97 PHE cc_start: 0.7906 (OUTLIER) cc_final: 0.7343 (t80) REVERT: E 177 GLU cc_start: 0.8314 (OUTLIER) cc_final: 0.8038 (mp0) REVERT: F 42 ILE cc_start: 0.9340 (mt) cc_final: 0.9026 (mp) REVERT: F 46 ARG cc_start: 0.8343 (tpp-160) cc_final: 0.7981 (mpt90) REVERT: F 51 GLU cc_start: 0.9066 (mm-30) cc_final: 0.8653 (tt0) REVERT: F 89 LYS cc_start: 0.8959 (tptt) cc_final: 0.8701 (tppt) REVERT: G 108 SER cc_start: 0.8808 (m) cc_final: 0.8535 (m) REVERT: H 7 ILE cc_start: 0.8894 (mm) cc_final: 0.8665 (mp) REVERT: H 63 GLN cc_start: 0.8738 (tt0) cc_final: 0.8381 (mp-120) REVERT: H 70 ARG cc_start: 0.7030 (OUTLIER) cc_final: 0.6645 (tpp-160) REVERT: I 39 VAL cc_start: 0.9275 (t) cc_final: 0.8990 (p) REVERT: I 53 ARG cc_start: 0.7051 (mtp180) cc_final: 0.6586 (mtm-85) REVERT: I 149 LYS cc_start: 0.7559 (pttt) cc_final: 0.7215 (ptmt) REVERT: J 27 GLU cc_start: 0.8106 (pp20) cc_final: 0.7734 (tm-30) REVERT: J 71 LYS cc_start: 0.8957 (mttp) cc_final: 0.8619 (mttp) REVERT: K 134 LYS cc_start: 0.8757 (ptpp) cc_final: 0.8521 (pttm) REVERT: L 76 GLU cc_start: 0.8371 (mt-10) cc_final: 0.8131 (pm20) REVERT: M 15 MET cc_start: 0.8812 (mmp) cc_final: 0.8447 (tpp) REVERT: M 30 SER cc_start: 0.9059 (m) cc_final: 0.8834 (p) REVERT: M 31 ASN cc_start: 0.8577 (m110) cc_final: 0.7888 (m110) REVERT: M 42 ASN cc_start: 0.8245 (t0) cc_final: 0.7903 (t0) REVERT: M 73 GLU cc_start: 0.8775 (tm-30) cc_final: 0.8436 (tm-30) REVERT: N 29 ARG cc_start: 0.9013 (ttt-90) cc_final: 0.8754 (ttt-90) REVERT: O 8 LYS cc_start: 0.8053 (mttt) cc_final: 0.7635 (mmmm) REVERT: O 75 VAL cc_start: 0.9086 (OUTLIER) cc_final: 0.8758 (t) REVERT: O 81 LEU cc_start: 0.9390 (OUTLIER) cc_final: 0.9107 (mp) REVERT: P 15 ASN cc_start: 0.8849 (p0) cc_final: 0.7958 (p0) REVERT: P 26 ARG cc_start: 0.9021 (mtm-85) cc_final: 0.8771 (mtm-85) REVERT: Q 73 ARG cc_start: 0.8078 (ttt180) cc_final: 0.7811 (ttp80) REVERT: Q 92 GLU cc_start: 0.7992 (pp20) cc_final: 0.7548 (pp20) REVERT: R 41 TYR cc_start: 0.9408 (m-80) cc_final: 0.9192 (m-80) REVERT: R 49 ARG cc_start: 0.9058 (ttm-80) cc_final: 0.8647 (mtm180) REVERT: R 61 GLN cc_start: 0.9116 (tp40) cc_final: 0.7992 (tp40) REVERT: V 48 THR cc_start: 0.7474 (m) cc_final: 0.7123 (p) REVERT: V 68 LEU cc_start: 0.8372 (mt) cc_final: 0.7929 (mp) REVERT: V 73 LYS cc_start: 0.8403 (mtpt) cc_final: 0.7429 (mmmm) REVERT: V 109 LYS cc_start: 0.7773 (mttt) cc_final: 0.7053 (tttt) REVERT: V 208 ARG cc_start: 0.7464 (mmm-85) cc_final: 0.7173 (mtp180) REVERT: g 58 VAL cc_start: 0.9161 (OUTLIER) cc_final: 0.8617 (p) outliers start: 134 outliers final: 77 residues processed: 688 average time/residue: 0.6996 time to fit residues: 775.8106 Evaluate side-chains 670 residues out of total 2000 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 583 time to evaluate : 3.338 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 4 VAL Chi-restraints excluded: chain B residue 6 LYS Chi-restraints excluded: chain B residue 10 LYS Chi-restraints excluded: chain B residue 24 THR Chi-restraints excluded: chain B residue 30 LYS Chi-restraints excluded: chain C residue 32 VAL Chi-restraints excluded: chain C residue 41 LEU Chi-restraints excluded: chain C residue 69 THR Chi-restraints excluded: chain C residue 163 SER Chi-restraints excluded: chain C residue 191 THR Chi-restraints excluded: chain D residue 17 VAL Chi-restraints excluded: chain D residue 44 SER Chi-restraints excluded: chain D residue 177 VAL Chi-restraints excluded: chain E residue 42 SER Chi-restraints excluded: chain E residue 47 SER Chi-restraints excluded: chain E residue 51 LYS Chi-restraints excluded: chain E residue 59 THR Chi-restraints excluded: chain E residue 71 VAL Chi-restraints excluded: chain E residue 81 VAL Chi-restraints excluded: chain E residue 97 PHE Chi-restraints excluded: chain E residue 107 THR Chi-restraints excluded: chain E residue 130 VAL Chi-restraints excluded: chain E residue 146 HIS Chi-restraints excluded: chain E residue 177 GLU Chi-restraints excluded: chain F residue 43 TRP Chi-restraints excluded: chain F residue 72 VAL Chi-restraints excluded: chain F residue 74 GLU Chi-restraints excluded: chain G residue 24 THR Chi-restraints excluded: chain G residue 27 VAL Chi-restraints excluded: chain G residue 75 VAL Chi-restraints excluded: chain G residue 80 VAL Chi-restraints excluded: chain G residue 84 THR Chi-restraints excluded: chain H residue 70 ARG Chi-restraints excluded: chain H residue 92 THR Chi-restraints excluded: chain H residue 108 THR Chi-restraints excluded: chain I residue 42 VAL Chi-restraints excluded: chain I residue 78 VAL Chi-restraints excluded: chain I residue 114 ASP Chi-restraints excluded: chain I residue 146 GLN Chi-restraints excluded: chain J residue 18 ILE Chi-restraints excluded: chain J residue 44 THR Chi-restraints excluded: chain J residue 97 ASP Chi-restraints excluded: chain K residue 25 VAL Chi-restraints excluded: chain K residue 32 ILE Chi-restraints excluded: chain K residue 91 VAL Chi-restraints excluded: chain K residue 120 SER Chi-restraints excluded: chain L residue 39 THR Chi-restraints excluded: chain L residue 49 LEU Chi-restraints excluded: chain L residue 52 VAL Chi-restraints excluded: chain L residue 58 THR Chi-restraints excluded: chain L residue 63 VAL Chi-restraints excluded: chain L residue 73 ASN Chi-restraints excluded: chain L residue 104 THR Chi-restraints excluded: chain M residue 4 LEU Chi-restraints excluded: chain M residue 5 VAL Chi-restraints excluded: chain M residue 45 THR Chi-restraints excluded: chain M residue 109 THR Chi-restraints excluded: chain N residue 24 CYS Chi-restraints excluded: chain N residue 59 SER Chi-restraints excluded: chain O residue 20 THR Chi-restraints excluded: chain O residue 38 ASP Chi-restraints excluded: chain O residue 41 GLU Chi-restraints excluded: chain O residue 75 VAL Chi-restraints excluded: chain O residue 80 SER Chi-restraints excluded: chain O residue 81 LEU Chi-restraints excluded: chain P residue 20 ILE Chi-restraints excluded: chain P residue 30 ASP Chi-restraints excluded: chain P residue 67 THR Chi-restraints excluded: chain P residue 86 LEU Chi-restraints excluded: chain P residue 92 THR Chi-restraints excluded: chain Q residue 22 THR Chi-restraints excluded: chain Q residue 55 THR Chi-restraints excluded: chain Q residue 65 ASN Chi-restraints excluded: chain Q residue 79 THR Chi-restraints excluded: chain S residue 11 VAL Chi-restraints excluded: chain S residue 60 VAL Chi-restraints excluded: chain T residue 39 VAL Chi-restraints excluded: chain T residue 50 LEU Chi-restraints excluded: chain T residue 51 LEU Chi-restraints excluded: chain T residue 83 LEU Chi-restraints excluded: chain V residue 4 VAL Chi-restraints excluded: chain V residue 32 PHE Chi-restraints excluded: chain V residue 80 ILE Chi-restraints excluded: chain V residue 100 MET Chi-restraints excluded: chain V residue 108 HIS Chi-restraints excluded: chain V residue 186 ILE Chi-restraints excluded: chain g residue 58 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 309 optimal weight: 10.0000 chunk 210 optimal weight: 6.9990 chunk 5 optimal weight: 20.0000 chunk 276 optimal weight: 9.9990 chunk 153 optimal weight: 5.9990 chunk 316 optimal weight: 3.9990 chunk 256 optimal weight: 10.0000 chunk 0 optimal weight: 20.0000 chunk 189 optimal weight: 30.0000 chunk 333 optimal weight: 9.9990 chunk 93 optimal weight: 10.0000 overall best weight: 7.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 8 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 138 GLN ** D 115 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 185 GLN G 142 HIS ** H 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8469 moved from start: 0.3783 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 56163 Z= 0.318 Angle : 0.676 9.945 83465 Z= 0.343 Chirality : 0.039 0.305 10576 Planarity : 0.005 0.066 4881 Dihedral : 24.011 179.120 27027 Min Nonbonded Distance : 0.983 Molprobity Statistics. All-atom Clashscore : 9.61 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.19 % Favored : 95.73 % Rotamer: Outliers : 6.40 % Allowed : 25.00 % Favored : 68.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.01 (0.17), residues: 2364 helix: 1.02 (0.16), residues: 1011 sheet: -0.04 (0.24), residues: 399 loop : -1.03 (0.19), residues: 954 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP F 43 HIS 0.009 0.001 HIS J 15 PHE 0.017 0.002 PHE E 97 TYR 0.022 0.002 TYR C 187 ARG 0.010 0.001 ARG D 10 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4728 Ramachandran restraints generated. 2364 Oldfield, 0 Emsley, 2364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4728 Ramachandran restraints generated. 2364 Oldfield, 0 Emsley, 2364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 717 residues out of total 2000 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 128 poor density : 589 time to evaluate : 3.228 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 10 LYS cc_start: 0.8962 (OUTLIER) cc_final: 0.7869 (mmtm) REVERT: B 21 LEU cc_start: 0.8536 (mt) cc_final: 0.8199 (mt) REVERT: B 24 THR cc_start: 0.8669 (OUTLIER) cc_final: 0.8307 (p) REVERT: B 25 ARG cc_start: 0.8410 (ttm170) cc_final: 0.8155 (ttm-80) REVERT: C 34 GLU cc_start: 0.8879 (mm-30) cc_final: 0.8066 (tt0) REVERT: C 64 ARG cc_start: 0.8298 (ttm-80) cc_final: 0.7691 (ttm-80) REVERT: C 121 GLU cc_start: 0.8406 (mm-30) cc_final: 0.8151 (mm-30) REVERT: C 135 LYS cc_start: 0.8846 (ttpt) cc_final: 0.8585 (ttpt) REVERT: C 177 THR cc_start: 0.9266 (m) cc_final: 0.8905 (p) REVERT: D 43 GLU cc_start: 0.8109 (mt-10) cc_final: 0.7729 (mm-30) REVERT: D 44 SER cc_start: 0.8227 (OUTLIER) cc_final: 0.7903 (m) REVERT: D 64 GLU cc_start: 0.7854 (tp30) cc_final: 0.7540 (tp30) REVERT: D 86 LEU cc_start: 0.8635 (tp) cc_final: 0.8240 (pp) REVERT: D 147 THR cc_start: 0.8694 (m) cc_final: 0.8387 (p) REVERT: D 165 TRP cc_start: 0.8485 (p-90) cc_final: 0.8261 (p-90) REVERT: E 58 PHE cc_start: 0.8945 (m-80) cc_final: 0.8720 (m-80) REVERT: E 97 PHE cc_start: 0.8085 (OUTLIER) cc_final: 0.7485 (t80) REVERT: E 141 GLU cc_start: 0.7728 (OUTLIER) cc_final: 0.7324 (mm-30) REVERT: E 177 GLU cc_start: 0.8336 (pm20) cc_final: 0.8023 (mp0) REVERT: F 42 ILE cc_start: 0.9341 (mt) cc_final: 0.8967 (mp) REVERT: F 51 GLU cc_start: 0.9120 (mm-30) cc_final: 0.8725 (tt0) REVERT: F 89 LYS cc_start: 0.8979 (tptt) cc_final: 0.8716 (tppt) REVERT: G 108 SER cc_start: 0.8818 (m) cc_final: 0.8489 (m) REVERT: G 144 MET cc_start: 0.8631 (OUTLIER) cc_final: 0.8343 (tmm) REVERT: H 7 ILE cc_start: 0.8887 (mm) cc_final: 0.8645 (mp) REVERT: H 63 GLN cc_start: 0.8733 (tt0) cc_final: 0.8272 (mp10) REVERT: H 70 ARG cc_start: 0.7014 (OUTLIER) cc_final: 0.6584 (tpp-160) REVERT: I 39 VAL cc_start: 0.9274 (t) cc_final: 0.9010 (p) REVERT: I 149 LYS cc_start: 0.7652 (pttt) cc_final: 0.7386 (ptmt) REVERT: J 27 GLU cc_start: 0.8164 (pp20) cc_final: 0.7849 (tm-30) REVERT: J 71 LYS cc_start: 0.9043 (mttp) cc_final: 0.8663 (mttp) REVERT: K 36 PHE cc_start: 0.8729 (m-80) cc_final: 0.8524 (m-80) REVERT: K 45 ASP cc_start: 0.8290 (t0) cc_final: 0.8061 (t0) REVERT: K 81 ARG cc_start: 0.8683 (OUTLIER) cc_final: 0.8419 (mpp80) REVERT: K 114 LEU cc_start: 0.8700 (OUTLIER) cc_final: 0.8435 (tp) REVERT: L 76 GLU cc_start: 0.8501 (mt-10) cc_final: 0.8203 (pm20) REVERT: M 15 MET cc_start: 0.8864 (mmp) cc_final: 0.8578 (tpp) REVERT: M 22 ILE cc_start: 0.8983 (mp) cc_final: 0.8713 (mm) REVERT: M 42 ASN cc_start: 0.8198 (t0) cc_final: 0.7919 (t0) REVERT: M 73 GLU cc_start: 0.8760 (tm-30) cc_final: 0.8394 (tm-30) REVERT: M 104 LYS cc_start: 0.9047 (tttt) cc_final: 0.8611 (ttmp) REVERT: N 29 ARG cc_start: 0.9000 (ttt-90) cc_final: 0.8472 (ttt-90) REVERT: O 8 LYS cc_start: 0.8110 (mttt) cc_final: 0.7594 (mmmm) REVERT: O 75 VAL cc_start: 0.9085 (m) cc_final: 0.8736 (t) REVERT: P 15 ASN cc_start: 0.8945 (p0) cc_final: 0.8140 (p0) REVERT: P 26 ARG cc_start: 0.9037 (mtm-85) cc_final: 0.8830 (mtm-85) REVERT: Q 73 ARG cc_start: 0.8058 (ttt180) cc_final: 0.7823 (ttp80) REVERT: R 41 TYR cc_start: 0.9430 (m-80) cc_final: 0.9185 (m-80) REVERT: R 49 ARG cc_start: 0.9086 (ttm-80) cc_final: 0.8682 (mtm180) REVERT: T 50 LEU cc_start: 0.8446 (OUTLIER) cc_final: 0.8205 (pt) REVERT: V 48 THR cc_start: 0.7489 (m) cc_final: 0.7121 (p) REVERT: V 68 LEU cc_start: 0.8363 (mt) cc_final: 0.7881 (mp) REVERT: V 73 LYS cc_start: 0.7909 (mtpt) cc_final: 0.7123 (mmmm) REVERT: V 109 LYS cc_start: 0.7853 (mttt) cc_final: 0.7126 (tttt) REVERT: V 129 ARG cc_start: 0.4979 (mpt180) cc_final: 0.4448 (mtt90) REVERT: V 208 ARG cc_start: 0.7427 (mmm-85) cc_final: 0.7125 (mtp180) outliers start: 128 outliers final: 98 residues processed: 653 average time/residue: 0.6977 time to fit residues: 735.3634 Evaluate side-chains 683 residues out of total 2000 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 108 poor density : 575 time to evaluate : 3.390 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 4 VAL Chi-restraints excluded: chain B residue 6 LYS Chi-restraints excluded: chain B residue 10 LYS Chi-restraints excluded: chain B residue 13 SER Chi-restraints excluded: chain B residue 24 THR Chi-restraints excluded: chain B residue 26 VAL Chi-restraints excluded: chain C residue 32 VAL Chi-restraints excluded: chain C residue 41 LEU Chi-restraints excluded: chain C residue 69 THR Chi-restraints excluded: chain C residue 103 LEU Chi-restraints excluded: chain C residue 163 SER Chi-restraints excluded: chain C residue 191 THR Chi-restraints excluded: chain D residue 17 VAL Chi-restraints excluded: chain D residue 20 VAL Chi-restraints excluded: chain D residue 44 SER Chi-restraints excluded: chain D residue 120 VAL Chi-restraints excluded: chain D residue 133 SER Chi-restraints excluded: chain D residue 177 VAL Chi-restraints excluded: chain E residue 42 SER Chi-restraints excluded: chain E residue 47 SER Chi-restraints excluded: chain E residue 51 LYS Chi-restraints excluded: chain E residue 59 THR Chi-restraints excluded: chain E residue 71 VAL Chi-restraints excluded: chain E residue 81 VAL Chi-restraints excluded: chain E residue 97 PHE Chi-restraints excluded: chain E residue 107 THR Chi-restraints excluded: chain E residue 130 VAL Chi-restraints excluded: chain E residue 140 LEU Chi-restraints excluded: chain E residue 141 GLU Chi-restraints excluded: chain E residue 146 HIS Chi-restraints excluded: chain F residue 43 TRP Chi-restraints excluded: chain F residue 74 GLU Chi-restraints excluded: chain F residue 93 THR Chi-restraints excluded: chain G residue 24 THR Chi-restraints excluded: chain G residue 27 VAL Chi-restraints excluded: chain G residue 75 VAL Chi-restraints excluded: chain G residue 80 VAL Chi-restraints excluded: chain G residue 84 THR Chi-restraints excluded: chain G residue 144 MET Chi-restraints excluded: chain G residue 153 HIS Chi-restraints excluded: chain H residue 27 LEU Chi-restraints excluded: chain H residue 36 ILE Chi-restraints excluded: chain H residue 70 ARG Chi-restraints excluded: chain H residue 92 THR Chi-restraints excluded: chain H residue 108 THR Chi-restraints excluded: chain I residue 42 VAL Chi-restraints excluded: chain I residue 78 VAL Chi-restraints excluded: chain I residue 114 ASP Chi-restraints excluded: chain I residue 148 SER Chi-restraints excluded: chain J residue 11 LYS Chi-restraints excluded: chain J residue 18 ILE Chi-restraints excluded: chain J residue 44 THR Chi-restraints excluded: chain J residue 97 ASP Chi-restraints excluded: chain K residue 25 VAL Chi-restraints excluded: chain K residue 32 ILE Chi-restraints excluded: chain K residue 40 ILE Chi-restraints excluded: chain K residue 81 ARG Chi-restraints excluded: chain K residue 91 VAL Chi-restraints excluded: chain K residue 114 LEU Chi-restraints excluded: chain K residue 120 SER Chi-restraints excluded: chain L residue 39 THR Chi-restraints excluded: chain L residue 49 LEU Chi-restraints excluded: chain L residue 52 VAL Chi-restraints excluded: chain L residue 58 THR Chi-restraints excluded: chain L residue 63 VAL Chi-restraints excluded: chain L residue 73 ASN Chi-restraints excluded: chain L residue 104 THR Chi-restraints excluded: chain M residue 4 LEU Chi-restraints excluded: chain M residue 5 VAL Chi-restraints excluded: chain M residue 11 ARG Chi-restraints excluded: chain M residue 45 THR Chi-restraints excluded: chain M residue 90 LEU Chi-restraints excluded: chain M residue 109 THR Chi-restraints excluded: chain N residue 11 ASN Chi-restraints excluded: chain N residue 24 CYS Chi-restraints excluded: chain N residue 59 SER Chi-restraints excluded: chain O residue 20 THR Chi-restraints excluded: chain O residue 38 ASP Chi-restraints excluded: chain O residue 40 THR Chi-restraints excluded: chain O residue 41 GLU Chi-restraints excluded: chain O residue 80 SER Chi-restraints excluded: chain P residue 20 ILE Chi-restraints excluded: chain P residue 30 ASP Chi-restraints excluded: chain P residue 67 THR Chi-restraints excluded: chain P residue 77 THR Chi-restraints excluded: chain P residue 81 GLN Chi-restraints excluded: chain P residue 86 LEU Chi-restraints excluded: chain P residue 92 THR Chi-restraints excluded: chain P residue 95 VAL Chi-restraints excluded: chain Q residue 22 THR Chi-restraints excluded: chain Q residue 35 THR Chi-restraints excluded: chain Q residue 55 THR Chi-restraints excluded: chain Q residue 65 ASN Chi-restraints excluded: chain Q residue 79 THR Chi-restraints excluded: chain S residue 11 VAL Chi-restraints excluded: chain S residue 31 ILE Chi-restraints excluded: chain S residue 60 VAL Chi-restraints excluded: chain S residue 71 LEU Chi-restraints excluded: chain T residue 39 VAL Chi-restraints excluded: chain T residue 50 LEU Chi-restraints excluded: chain T residue 51 LEU Chi-restraints excluded: chain T residue 83 LEU Chi-restraints excluded: chain V residue 4 VAL Chi-restraints excluded: chain V residue 32 PHE Chi-restraints excluded: chain V residue 80 ILE Chi-restraints excluded: chain V residue 100 MET Chi-restraints excluded: chain V residue 108 HIS Chi-restraints excluded: chain V residue 186 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 124 optimal weight: 20.0000 chunk 334 optimal weight: 8.9990 chunk 73 optimal weight: 10.0000 chunk 217 optimal weight: 20.0000 chunk 91 optimal weight: 10.0000 chunk 371 optimal weight: 0.6980 chunk 308 optimal weight: 6.9990 chunk 172 optimal weight: 20.0000 chunk 30 optimal weight: 10.0000 chunk 122 optimal weight: 20.0000 chunk 195 optimal weight: 7.9990 overall best weight: 6.9390 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 115 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 142 HIS I 146 GLN ** K 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 63 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8458 moved from start: 0.4002 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 56163 Z= 0.296 Angle : 0.657 9.401 83465 Z= 0.334 Chirality : 0.038 0.283 10576 Planarity : 0.005 0.068 4881 Dihedral : 23.994 179.083 27022 Min Nonbonded Distance : 0.985 Molprobity Statistics. All-atom Clashscore : 9.20 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.15 % Favored : 95.73 % Rotamer: Outliers : 6.65 % Allowed : 25.90 % Favored : 67.45 % 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: -0.01 (0.17), residues: 2364 helix: 1.02 (0.16), residues: 1017 sheet: -0.04 (0.25), residues: 394 loop : -1.07 (0.19), residues: 953 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP F 43 HIS 0.008 0.001 HIS J 56 PHE 0.018 0.002 PHE E 97 TYR 0.019 0.002 TYR C 187 ARG 0.008 0.001 ARG M 79 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4728 Ramachandran restraints generated. 2364 Oldfield, 0 Emsley, 2364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4728 Ramachandran restraints generated. 2364 Oldfield, 0 Emsley, 2364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 727 residues out of total 2000 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 133 poor density : 594 time to evaluate : 3.266 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 10 LYS cc_start: 0.8968 (OUTLIER) cc_final: 0.7867 (mmtm) REVERT: B 16 LYS cc_start: 0.8593 (mmmt) cc_final: 0.8215 (mmmt) REVERT: B 21 LEU cc_start: 0.8533 (mt) cc_final: 0.8202 (mt) REVERT: B 24 THR cc_start: 0.8644 (OUTLIER) cc_final: 0.8288 (p) REVERT: B 25 ARG cc_start: 0.8425 (ttm170) cc_final: 0.7994 (ttm-80) REVERT: C 34 GLU cc_start: 0.8895 (mm-30) cc_final: 0.8050 (tt0) REVERT: C 64 ARG cc_start: 0.8348 (ttm-80) cc_final: 0.8026 (ttm-80) REVERT: C 121 GLU cc_start: 0.8405 (mm-30) cc_final: 0.8164 (mm-30) REVERT: C 133 MET cc_start: 0.8447 (mtp) cc_final: 0.7832 (mtp) REVERT: C 135 LYS cc_start: 0.8853 (ttpt) cc_final: 0.8591 (ttpt) REVERT: C 166 GLU cc_start: 0.8273 (tm-30) cc_final: 0.8003 (tm-30) REVERT: C 177 THR cc_start: 0.9255 (m) cc_final: 0.8881 (p) REVERT: D 43 GLU cc_start: 0.8125 (mt-10) cc_final: 0.7702 (mm-30) REVERT: D 44 SER cc_start: 0.8231 (OUTLIER) cc_final: 0.7911 (m) REVERT: D 64 GLU cc_start: 0.7866 (tp30) cc_final: 0.7363 (tp30) REVERT: D 165 TRP cc_start: 0.8545 (p-90) cc_final: 0.8327 (p-90) REVERT: E 58 PHE cc_start: 0.8926 (m-80) cc_final: 0.8672 (m-80) REVERT: E 97 PHE cc_start: 0.8143 (OUTLIER) cc_final: 0.7479 (t80) REVERT: E 177 GLU cc_start: 0.8316 (OUTLIER) cc_final: 0.8043 (mp0) REVERT: F 42 ILE cc_start: 0.9396 (mt) cc_final: 0.9062 (mp) REVERT: F 51 GLU cc_start: 0.9120 (mm-30) cc_final: 0.8719 (tt0) REVERT: F 89 LYS cc_start: 0.8908 (tptt) cc_final: 0.8650 (tppt) REVERT: F 95 LYS cc_start: 0.6921 (tttm) cc_final: 0.6456 (mtpt) REVERT: G 108 SER cc_start: 0.8804 (m) cc_final: 0.8512 (m) REVERT: H 7 ILE cc_start: 0.8889 (mm) cc_final: 0.8639 (mp) REVERT: H 41 LYS cc_start: 0.9369 (tttt) cc_final: 0.9156 (mtpt) REVERT: H 70 ARG cc_start: 0.6971 (OUTLIER) cc_final: 0.6521 (tpp-160) REVERT: I 39 VAL cc_start: 0.9278 (t) cc_final: 0.9017 (p) REVERT: I 149 LYS cc_start: 0.7583 (pttt) cc_final: 0.7381 (ptmt) REVERT: J 7 ARG cc_start: 0.8038 (mtp180) cc_final: 0.7814 (mtt90) REVERT: J 27 GLU cc_start: 0.8206 (pp20) cc_final: 0.7953 (tm-30) REVERT: J 71 LYS cc_start: 0.9043 (mttp) cc_final: 0.8654 (mttp) REVERT: K 81 ARG cc_start: 0.8857 (OUTLIER) cc_final: 0.8628 (mpp80) REVERT: K 114 LEU cc_start: 0.8728 (OUTLIER) cc_final: 0.8424 (tp) REVERT: L 62 GLU cc_start: 0.7966 (mm-30) cc_final: 0.7706 (mm-30) REVERT: L 76 GLU cc_start: 0.8510 (mt-10) cc_final: 0.8176 (pm20) REVERT: L 104 THR cc_start: 0.9111 (OUTLIER) cc_final: 0.8869 (p) REVERT: M 15 MET cc_start: 0.8881 (mmp) cc_final: 0.8627 (tpp) REVERT: M 22 ILE cc_start: 0.8942 (mp) cc_final: 0.8675 (mm) REVERT: M 30 SER cc_start: 0.9110 (m) cc_final: 0.8891 (p) REVERT: M 31 ASN cc_start: 0.8407 (m110) cc_final: 0.7626 (m110) REVERT: M 42 ASN cc_start: 0.8248 (t0) cc_final: 0.7883 (t0) REVERT: M 73 GLU cc_start: 0.8753 (tm-30) cc_final: 0.8407 (tm-30) REVERT: M 104 LYS cc_start: 0.9025 (tttt) cc_final: 0.8625 (ttmp) REVERT: N 29 ARG cc_start: 0.8970 (ttt-90) cc_final: 0.8478 (ttt-90) REVERT: O 8 LYS cc_start: 0.8085 (mttt) cc_final: 0.7571 (mmmm) REVERT: O 81 LEU cc_start: 0.9180 (OUTLIER) cc_final: 0.8866 (mm) REVERT: P 26 ARG cc_start: 0.9052 (mtm-85) cc_final: 0.8846 (mtm-85) REVERT: Q 90 LEU cc_start: 0.8959 (tt) cc_final: 0.8677 (mp) REVERT: R 32 TYR cc_start: 0.8541 (p90) cc_final: 0.8314 (p90) REVERT: R 41 TYR cc_start: 0.9423 (m-80) cc_final: 0.9208 (m-80) REVERT: R 49 ARG cc_start: 0.9204 (ttm-80) cc_final: 0.8511 (ttp-170) REVERT: R 61 GLN cc_start: 0.9090 (tp40) cc_final: 0.8751 (tp40) REVERT: T 50 LEU cc_start: 0.8440 (OUTLIER) cc_final: 0.8208 (pt) REVERT: V 48 THR cc_start: 0.7494 (m) cc_final: 0.7142 (t) REVERT: V 68 LEU cc_start: 0.8256 (mt) cc_final: 0.7789 (mp) REVERT: V 73 LYS cc_start: 0.7871 (mtpt) cc_final: 0.7259 (mmmt) REVERT: V 109 LYS cc_start: 0.7774 (mttt) cc_final: 0.7049 (tttt) REVERT: V 129 ARG cc_start: 0.5249 (mpt180) cc_final: 0.4818 (mtt90) REVERT: V 208 ARG cc_start: 0.7506 (mmm-85) cc_final: 0.7271 (mtm180) REVERT: g 62 GLU cc_start: 0.8877 (mp0) cc_final: 0.8609 (mp0) outliers start: 133 outliers final: 99 residues processed: 663 average time/residue: 0.7037 time to fit residues: 753.5583 Evaluate side-chains 682 residues out of total 2000 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 110 poor density : 572 time to evaluate : 3.190 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 4 VAL Chi-restraints excluded: chain B residue 6 LYS Chi-restraints excluded: chain B residue 10 LYS Chi-restraints excluded: chain B residue 13 SER Chi-restraints excluded: chain B residue 24 THR Chi-restraints excluded: chain B residue 26 VAL Chi-restraints excluded: chain C residue 32 VAL Chi-restraints excluded: chain C residue 41 LEU Chi-restraints excluded: chain C residue 69 THR Chi-restraints excluded: chain C residue 103 LEU Chi-restraints excluded: chain C residue 162 MET Chi-restraints excluded: chain C residue 163 SER Chi-restraints excluded: chain C residue 191 THR Chi-restraints excluded: chain D residue 17 VAL Chi-restraints excluded: chain D residue 20 VAL Chi-restraints excluded: chain D residue 44 SER Chi-restraints excluded: chain D residue 120 VAL Chi-restraints excluded: chain D residue 133 SER Chi-restraints excluded: chain D residue 177 VAL Chi-restraints excluded: chain E residue 42 SER Chi-restraints excluded: chain E residue 47 SER Chi-restraints excluded: chain E residue 51 LYS Chi-restraints excluded: chain E residue 59 THR Chi-restraints excluded: chain E residue 71 VAL Chi-restraints excluded: chain E residue 81 VAL Chi-restraints excluded: chain E residue 97 PHE Chi-restraints excluded: chain E residue 107 THR Chi-restraints excluded: chain E residue 130 VAL Chi-restraints excluded: chain E residue 140 LEU Chi-restraints excluded: chain E residue 146 HIS Chi-restraints excluded: chain E residue 177 GLU Chi-restraints excluded: chain F residue 43 TRP Chi-restraints excluded: chain F residue 74 GLU Chi-restraints excluded: chain F residue 93 THR Chi-restraints excluded: chain G residue 24 THR Chi-restraints excluded: chain G residue 27 VAL Chi-restraints excluded: chain G residue 30 VAL Chi-restraints excluded: chain G residue 75 VAL Chi-restraints excluded: chain G residue 80 VAL Chi-restraints excluded: chain G residue 84 THR Chi-restraints excluded: chain G residue 153 HIS Chi-restraints excluded: chain H residue 27 LEU Chi-restraints excluded: chain H residue 36 ILE Chi-restraints excluded: chain H residue 70 ARG Chi-restraints excluded: chain H residue 92 THR Chi-restraints excluded: chain H residue 101 LEU Chi-restraints excluded: chain H residue 108 THR Chi-restraints excluded: chain I residue 42 VAL Chi-restraints excluded: chain I residue 78 VAL Chi-restraints excluded: chain I residue 114 ASP Chi-restraints excluded: chain I residue 146 GLN Chi-restraints excluded: chain J residue 11 LYS Chi-restraints excluded: chain J residue 18 ILE Chi-restraints excluded: chain J residue 44 THR Chi-restraints excluded: chain J residue 50 CYS Chi-restraints excluded: chain K residue 25 VAL Chi-restraints excluded: chain K residue 32 ILE Chi-restraints excluded: chain K residue 40 ILE Chi-restraints excluded: chain K residue 81 ARG Chi-restraints excluded: chain K residue 91 VAL Chi-restraints excluded: chain K residue 114 LEU Chi-restraints excluded: chain K residue 120 SER Chi-restraints excluded: chain L residue 39 THR Chi-restraints excluded: chain L residue 49 LEU Chi-restraints excluded: chain L residue 52 VAL Chi-restraints excluded: chain L residue 63 VAL Chi-restraints excluded: chain L residue 73 ASN Chi-restraints excluded: chain L residue 104 THR Chi-restraints excluded: chain M residue 4 LEU Chi-restraints excluded: chain M residue 5 VAL Chi-restraints excluded: chain M residue 45 THR Chi-restraints excluded: chain M residue 90 LEU Chi-restraints excluded: chain M residue 103 THR Chi-restraints excluded: chain M residue 109 THR Chi-restraints excluded: chain N residue 11 ASN Chi-restraints excluded: chain N residue 24 CYS Chi-restraints excluded: chain N residue 59 SER Chi-restraints excluded: chain O residue 20 THR Chi-restraints excluded: chain O residue 38 ASP Chi-restraints excluded: chain O residue 40 THR Chi-restraints excluded: chain O residue 41 GLU Chi-restraints excluded: chain O residue 80 SER Chi-restraints excluded: chain O residue 81 LEU Chi-restraints excluded: chain P residue 20 ILE Chi-restraints excluded: chain P residue 30 ASP Chi-restraints excluded: chain P residue 67 THR Chi-restraints excluded: chain P residue 86 LEU Chi-restraints excluded: chain P residue 92 THR Chi-restraints excluded: chain Q residue 10 THR Chi-restraints excluded: chain Q residue 22 THR Chi-restraints excluded: chain Q residue 35 THR Chi-restraints excluded: chain Q residue 55 THR Chi-restraints excluded: chain Q residue 65 ASN Chi-restraints excluded: chain Q residue 79 THR Chi-restraints excluded: chain S residue 11 VAL Chi-restraints excluded: chain S residue 31 ILE Chi-restraints excluded: chain S residue 60 VAL Chi-restraints excluded: chain T residue 39 VAL Chi-restraints excluded: chain T residue 50 LEU Chi-restraints excluded: chain T residue 51 LEU Chi-restraints excluded: chain T residue 83 LEU Chi-restraints excluded: chain V residue 4 VAL Chi-restraints excluded: chain V residue 32 PHE Chi-restraints excluded: chain V residue 41 ILE Chi-restraints excluded: chain V residue 80 ILE Chi-restraints excluded: chain V residue 100 MET Chi-restraints excluded: chain V residue 108 HIS Chi-restraints excluded: chain V residue 151 ILE Chi-restraints excluded: chain V residue 186 ILE Chi-restraints excluded: chain g residue 58 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 358 optimal weight: 20.0000 chunk 41 optimal weight: 30.0000 chunk 211 optimal weight: 7.9990 chunk 271 optimal weight: 10.0000 chunk 210 optimal weight: 20.0000 chunk 312 optimal weight: 20.0000 chunk 207 optimal weight: 20.0000 chunk 370 optimal weight: 0.9990 chunk 231 optimal weight: 9.9990 chunk 225 optimal weight: 6.9990 chunk 170 optimal weight: 20.0000 overall best weight: 7.1992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 8 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 142 HIS I 146 GLN ** K 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 38 ASN M 63 ASN ** S 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8461 moved from start: 0.4144 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 56163 Z= 0.307 Angle : 0.669 9.426 83465 Z= 0.340 Chirality : 0.039 0.287 10576 Planarity : 0.005 0.066 4881 Dihedral : 23.989 179.900 27022 Min Nonbonded Distance : 0.981 Molprobity Statistics. All-atom Clashscore : 9.69 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.48 % Favored : 95.39 % Rotamer: Outliers : 6.65 % Allowed : 27.30 % Favored : 66.05 % 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: -0.06 (0.17), residues: 2364 helix: 0.99 (0.16), residues: 1019 sheet: -0.12 (0.25), residues: 394 loop : -1.09 (0.19), residues: 951 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP F 43 HIS 0.008 0.001 HIS J 56 PHE 0.018 0.002 PHE I 48 TYR 0.020 0.002 TYR C 187 ARG 0.010 0.001 ARG L 83 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4728 Ramachandran restraints generated. 2364 Oldfield, 0 Emsley, 2364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4728 Ramachandran restraints generated. 2364 Oldfield, 0 Emsley, 2364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 722 residues out of total 2000 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 133 poor density : 589 time to evaluate : 3.320 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 10 LYS cc_start: 0.8957 (OUTLIER) cc_final: 0.7838 (mmtm) REVERT: B 16 LYS cc_start: 0.8611 (mmmt) cc_final: 0.8272 (mmmt) REVERT: B 21 LEU cc_start: 0.8537 (mt) cc_final: 0.8207 (mt) REVERT: B 24 THR cc_start: 0.8646 (OUTLIER) cc_final: 0.8279 (p) REVERT: B 25 ARG cc_start: 0.8438 (ttm170) cc_final: 0.8003 (ttm-80) REVERT: C 34 GLU cc_start: 0.8956 (mm-30) cc_final: 0.8098 (tt0) REVERT: C 64 ARG cc_start: 0.8382 (ttm-80) cc_final: 0.8050 (ttm-80) REVERT: C 133 MET cc_start: 0.8503 (mtp) cc_final: 0.8013 (mtp) REVERT: C 135 LYS cc_start: 0.8833 (ttpt) cc_final: 0.8578 (ttpt) REVERT: C 177 THR cc_start: 0.9267 (m) cc_final: 0.8754 (p) REVERT: D 43 GLU cc_start: 0.8126 (mt-10) cc_final: 0.7671 (mm-30) REVERT: D 44 SER cc_start: 0.8235 (OUTLIER) cc_final: 0.7903 (m) REVERT: D 64 GLU cc_start: 0.7908 (tp30) cc_final: 0.7394 (tp30) REVERT: D 165 TRP cc_start: 0.8582 (p-90) cc_final: 0.8321 (p-90) REVERT: E 58 PHE cc_start: 0.8918 (m-80) cc_final: 0.8675 (m-80) REVERT: E 97 PHE cc_start: 0.8149 (OUTLIER) cc_final: 0.7546 (t80) REVERT: E 177 GLU cc_start: 0.8319 (OUTLIER) cc_final: 0.7976 (mp0) REVERT: F 42 ILE cc_start: 0.9378 (mt) cc_final: 0.9059 (mp) REVERT: F 51 GLU cc_start: 0.9102 (mm-30) cc_final: 0.8629 (tt0) REVERT: F 89 LYS cc_start: 0.8930 (tptt) cc_final: 0.8660 (tppt) REVERT: F 95 LYS cc_start: 0.7215 (tttm) cc_final: 0.6785 (mtpt) REVERT: G 108 SER cc_start: 0.8848 (m) cc_final: 0.8536 (m) REVERT: H 7 ILE cc_start: 0.8878 (mm) cc_final: 0.8630 (mp) REVERT: I 39 VAL cc_start: 0.9277 (t) cc_final: 0.8902 (p) REVERT: J 7 ARG cc_start: 0.8034 (mtp180) cc_final: 0.7815 (mtt90) REVERT: J 71 LYS cc_start: 0.9045 (mttp) cc_final: 0.8730 (mttp) REVERT: K 81 ARG cc_start: 0.8811 (OUTLIER) cc_final: 0.8543 (mtp85) REVERT: K 114 LEU cc_start: 0.8689 (OUTLIER) cc_final: 0.8399 (tp) REVERT: L 62 GLU cc_start: 0.7960 (mm-30) cc_final: 0.7729 (mm-30) REVERT: L 76 GLU cc_start: 0.8502 (mt-10) cc_final: 0.8169 (pm20) REVERT: L 104 THR cc_start: 0.9077 (OUTLIER) cc_final: 0.8831 (p) REVERT: M 30 SER cc_start: 0.9126 (m) cc_final: 0.8896 (p) REVERT: M 31 ASN cc_start: 0.8410 (m110) cc_final: 0.7608 (m110) REVERT: M 42 ASN cc_start: 0.8234 (t0) cc_final: 0.7903 (t0) REVERT: M 61 GLU cc_start: 0.8831 (pp20) cc_final: 0.8560 (pp20) REVERT: M 73 GLU cc_start: 0.8782 (tm-30) cc_final: 0.8323 (tm-30) REVERT: M 104 LYS cc_start: 0.9034 (tttt) cc_final: 0.8642 (ttmp) REVERT: N 29 ARG cc_start: 0.8922 (ttt-90) cc_final: 0.8432 (ttt-90) REVERT: O 8 LYS cc_start: 0.8106 (mttt) cc_final: 0.7567 (mmmm) REVERT: O 81 LEU cc_start: 0.9312 (mt) cc_final: 0.9030 (mm) REVERT: P 26 ARG cc_start: 0.9080 (mtm-85) cc_final: 0.8869 (mtm-85) REVERT: R 49 ARG cc_start: 0.9208 (ttm-80) cc_final: 0.8528 (ttp-170) REVERT: T 50 LEU cc_start: 0.8441 (OUTLIER) cc_final: 0.8235 (pt) REVERT: V 48 THR cc_start: 0.7464 (m) cc_final: 0.7077 (t) REVERT: V 68 LEU cc_start: 0.8261 (mt) cc_final: 0.7798 (mp) REVERT: V 73 LYS cc_start: 0.7773 (mtpt) cc_final: 0.7150 (mmmm) REVERT: V 109 LYS cc_start: 0.7796 (mttt) cc_final: 0.7054 (tttt) REVERT: V 129 ARG cc_start: 0.5327 (mpt180) cc_final: 0.4906 (mtt90) REVERT: g 62 GLU cc_start: 0.8926 (mp0) cc_final: 0.8649 (mp0) outliers start: 133 outliers final: 104 residues processed: 652 average time/residue: 0.7083 time to fit residues: 744.6370 Evaluate side-chains 685 residues out of total 2000 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 113 poor density : 572 time to evaluate : 3.038 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 4 VAL Chi-restraints excluded: chain B residue 6 LYS Chi-restraints excluded: chain B residue 10 LYS Chi-restraints excluded: chain B residue 13 SER Chi-restraints excluded: chain B residue 24 THR Chi-restraints excluded: chain B residue 26 VAL Chi-restraints excluded: chain C residue 32 VAL Chi-restraints excluded: chain C residue 69 THR Chi-restraints excluded: chain C residue 103 LEU Chi-restraints excluded: chain C residue 162 MET Chi-restraints excluded: chain C residue 163 SER Chi-restraints excluded: chain C residue 191 THR Chi-restraints excluded: chain C residue 192 THR Chi-restraints excluded: chain D residue 17 VAL Chi-restraints excluded: chain D residue 20 VAL Chi-restraints excluded: chain D residue 44 SER Chi-restraints excluded: chain D residue 120 VAL Chi-restraints excluded: chain D residue 133 SER Chi-restraints excluded: chain D residue 177 VAL Chi-restraints excluded: chain E residue 41 VAL Chi-restraints excluded: chain E residue 42 SER Chi-restraints excluded: chain E residue 47 SER Chi-restraints excluded: chain E residue 51 LYS Chi-restraints excluded: chain E residue 59 THR Chi-restraints excluded: chain E residue 71 VAL Chi-restraints excluded: chain E residue 81 VAL Chi-restraints excluded: chain E residue 97 PHE Chi-restraints excluded: chain E residue 107 THR Chi-restraints excluded: chain E residue 140 LEU Chi-restraints excluded: chain E residue 141 GLU Chi-restraints excluded: chain E residue 146 HIS Chi-restraints excluded: chain E residue 177 GLU Chi-restraints excluded: chain F residue 43 TRP Chi-restraints excluded: chain F residue 74 GLU Chi-restraints excluded: chain F residue 79 LEU Chi-restraints excluded: chain F residue 93 THR Chi-restraints excluded: chain G residue 24 THR Chi-restraints excluded: chain G residue 27 VAL Chi-restraints excluded: chain G residue 30 VAL Chi-restraints excluded: chain G residue 75 VAL Chi-restraints excluded: chain G residue 80 VAL Chi-restraints excluded: chain G residue 84 THR Chi-restraints excluded: chain G residue 153 HIS Chi-restraints excluded: chain H residue 36 ILE Chi-restraints excluded: chain H residue 92 THR Chi-restraints excluded: chain H residue 101 LEU Chi-restraints excluded: chain H residue 108 THR Chi-restraints excluded: chain I residue 42 VAL Chi-restraints excluded: chain I residue 47 GLN Chi-restraints excluded: chain I residue 78 VAL Chi-restraints excluded: chain I residue 83 ILE Chi-restraints excluded: chain I residue 114 ASP Chi-restraints excluded: chain J residue 11 LYS Chi-restraints excluded: chain J residue 18 ILE Chi-restraints excluded: chain J residue 44 THR Chi-restraints excluded: chain K residue 25 VAL Chi-restraints excluded: chain K residue 32 ILE Chi-restraints excluded: chain K residue 40 ILE Chi-restraints excluded: chain K residue 81 ARG Chi-restraints excluded: chain K residue 91 VAL Chi-restraints excluded: chain K residue 114 LEU Chi-restraints excluded: chain K residue 119 ILE Chi-restraints excluded: chain L residue 39 THR Chi-restraints excluded: chain L residue 49 LEU Chi-restraints excluded: chain L residue 52 VAL Chi-restraints excluded: chain L residue 58 THR Chi-restraints excluded: chain L residue 63 VAL Chi-restraints excluded: chain L residue 104 THR Chi-restraints excluded: chain M residue 4 LEU Chi-restraints excluded: chain M residue 5 VAL Chi-restraints excluded: chain M residue 11 ARG Chi-restraints excluded: chain M residue 45 THR Chi-restraints excluded: chain M residue 49 THR Chi-restraints excluded: chain M residue 90 LEU Chi-restraints excluded: chain M residue 103 THR Chi-restraints excluded: chain M residue 109 THR Chi-restraints excluded: chain N residue 11 ASN Chi-restraints excluded: chain N residue 24 CYS Chi-restraints excluded: chain N residue 46 GLU Chi-restraints excluded: chain N residue 59 SER Chi-restraints excluded: chain O residue 20 THR Chi-restraints excluded: chain O residue 38 ASP Chi-restraints excluded: chain O residue 40 THR Chi-restraints excluded: chain O residue 41 GLU Chi-restraints excluded: chain O residue 80 SER Chi-restraints excluded: chain P residue 20 ILE Chi-restraints excluded: chain P residue 30 ASP Chi-restraints excluded: chain P residue 67 THR Chi-restraints excluded: chain P residue 77 THR Chi-restraints excluded: chain P residue 81 GLN Chi-restraints excluded: chain P residue 86 LEU Chi-restraints excluded: chain P residue 92 THR Chi-restraints excluded: chain P residue 95 VAL Chi-restraints excluded: chain Q residue 10 THR Chi-restraints excluded: chain Q residue 22 THR Chi-restraints excluded: chain Q residue 35 THR Chi-restraints excluded: chain Q residue 55 THR Chi-restraints excluded: chain Q residue 65 ASN Chi-restraints excluded: chain Q residue 79 THR Chi-restraints excluded: chain S residue 11 VAL Chi-restraints excluded: chain S residue 14 HIS Chi-restraints excluded: chain S residue 31 ILE Chi-restraints excluded: chain S residue 60 VAL Chi-restraints excluded: chain T residue 39 VAL Chi-restraints excluded: chain T residue 50 LEU Chi-restraints excluded: chain T residue 51 LEU Chi-restraints excluded: chain T residue 79 LEU Chi-restraints excluded: chain T residue 83 LEU Chi-restraints excluded: chain V residue 4 VAL Chi-restraints excluded: chain V residue 32 PHE Chi-restraints excluded: chain V residue 100 MET Chi-restraints excluded: chain V residue 108 HIS Chi-restraints excluded: chain V residue 186 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/cctbx_project/iotbx/cli_parser.py", line 946, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/phenix/phenix/programs/real_space_refine.py", line 213, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 766, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1525, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1427, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1308, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 71.9926 > 50: distance: 95 - 96: 41.574 distance: 95 - 101: 50.910 distance: 96 - 97: 47.991 distance: 96 - 99: 7.055 distance: 97 - 98: 53.121 distance: 97 - 102: 48.230 distance: 99 - 100: 62.490 distance: 100 - 101: 55.948 distance: 102 - 103: 69.300 distance: 103 - 104: 40.823 distance: 103 - 106: 57.924 distance: 104 - 105: 70.101 distance: 104 - 113: 55.731 distance: 106 - 107: 55.906 distance: 107 - 108: 57.436 distance: 108 - 109: 68.386 distance: 109 - 110: 24.810 distance: 110 - 111: 15.930 distance: 110 - 112: 13.222 distance: 113 - 114: 59.607 distance: 114 - 115: 47.095 distance: 114 - 117: 59.132 distance: 115 - 116: 54.884 distance: 115 - 122: 54.839 distance: 117 - 118: 70.583 distance: 118 - 119: 38.633 distance: 119 - 120: 46.933 distance: 120 - 121: 47.422 distance: 122 - 123: 57.135 distance: 123 - 124: 56.581 distance: 124 - 125: 70.291 distance: 124 - 126: 68.932 distance: 126 - 127: 68.280 distance: 126 - 132: 70.586 distance: 127 - 128: 40.083 distance: 127 - 130: 41.414 distance: 128 - 129: 52.232 distance: 128 - 133: 69.378 distance: 130 - 131: 40.451 distance: 131 - 132: 57.263 distance: 133 - 134: 39.976 distance: 134 - 135: 56.880 distance: 134 - 137: 70.345 distance: 135 - 136: 68.171 distance: 135 - 138: 56.780 distance: 138 - 139: 36.027 distance: 138 - 144: 69.109 distance: 139 - 140: 56.403 distance: 139 - 142: 38.935 distance: 140 - 141: 56.647 distance: 140 - 145: 24.624 distance: 142 - 143: 55.654 distance: 143 - 144: 70.731 distance: 145 - 146: 44.294 distance: 146 - 147: 57.461 distance: 146 - 149: 56.705 distance: 147 - 148: 40.413 distance: 147 - 154: 39.451 distance: 149 - 150: 68.930 distance: 150 - 151: 44.837 distance: 151 - 152: 40.717 distance: 152 - 153: 21.097 distance: 154 - 155: 57.930 distance: 155 - 156: 41.240 distance: 155 - 158: 56.189 distance: 156 - 157: 64.309 distance: 156 - 165: 28.478 distance: 158 - 159: 57.752 distance: 159 - 160: 55.952 distance: 161 - 162: 8.439 distance: 162 - 163: 58.318 distance: 162 - 164: 53.808