Starting phenix.real_space_refine on Tue Jul 7 03:37:47 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7y8r_33684/07_2026/7y8r_33684_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/7y8r_33684/07_2026/7y8r_33684.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7y8r_33684/07_2026/7y8r_33684.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7y8r_33684/07_2026/7y8r_33684.map" model { file = "/net/cci-nas-00/data/ceres_data/7y8r_33684/07_2026/7y8r_33684_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7y8r_33684/07_2026/7y8r_33684_neut.cif" } resolution = 4.4 write_initial_geo_file = False refinement { macro_cycles = 10 } 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= 0.053 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: 8 Type Number sf(0) Gaussians P 332 5.49 5 Mg 1 5.21 5 S 174 5.16 5 Be 1 3.05 5 C 26136 2.51 5 N 7753 2.21 5 O 8709 1.98 5 F 3 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 66 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 43109 Number of models: 1 Model: "" Number of chains: 28 Chain: "A" Number of atoms: 815 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 815 Classifications: {'peptide': 99} Link IDs: {'PTRANS': 4, 'TRANS': 94} Chain: "B" Number of atoms: 741 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 741 Classifications: {'peptide': 94} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 92} Chain: "C" Number of atoms: 799 Number of conformers: 1 Conformer: "" Number of residues, atoms: 104, 799 Classifications: {'peptide': 104} Link IDs: {'PTRANS': 5, 'TRANS': 98} Chain: "D" Number of atoms: 755 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 755 Classifications: {'peptide': 96} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 93} Chain: "E" Number of atoms: 806 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 806 Classifications: {'peptide': 98} Link IDs: {'PTRANS': 3, 'TRANS': 94} Chain: "F" Number of atoms: 702 Number of conformers: 1 Conformer: "" Number of residues, atoms: 87, 702 Classifications: {'peptide': 87} Link IDs: {'PTRANS': 1, 'TRANS': 85} Chain: "G" Number of atoms: 833 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 833 Classifications: {'peptide': 108} Link IDs: {'PTRANS': 5, 'TRANS': 102} Chain: "H" Number of atoms: 736 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 736 Classifications: {'peptide': 94} Link IDs: {'PTRANS': 2, 'TRANS': 91} Chain: "Z" Number of atoms: 141 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 141 Classifications: {'peptide': 29} Incomplete info: {'backbone_only': 4, 'truncation_to_alanine': 25} Link IDs: {'TRANS': 28} Unresolved non-hydrogen bonds: 62 Unresolved non-hydrogen angles: 95 Unresolved non-hydrogen dihedrals: 29 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'UNK:plan-1': 29} Unresolved non-hydrogen planarities: 29 Chain: "I" Number of atoms: 6051 Number of conformers: 1 Conformer: "" Number of residues, atoms: 732, 6051 Classifications: {'peptide': 732} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 20, 'TRANS': 711} Chain breaks: 6 Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 17 Unresolved non-hydrogen dihedrals: 13 Planarities with less than four sites: {'ASP:plan': 1, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 7 Chain: "J" Number of atoms: 2821 Number of conformers: 1 Conformer: "" Number of residues, atoms: 360, 2821 Classifications: {'peptide': 360} Link IDs: {'PTRANS': 19, 'TRANS': 340} Chain breaks: 2 Chain: "K" Number of atoms: 2787 Number of conformers: 1 Conformer: "" Number of residues, atoms: 356, 2787 Classifications: {'peptide': 356} Link IDs: {'PTRANS': 18, 'TRANS': 337} Chain breaks: 3 Chain: "L" Number of atoms: 4151 Number of conformers: 1 Conformer: "" Number of residues, atoms: 521, 4151 Classifications: {'peptide': 521} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 18, 'TRANS': 502} Chain breaks: 3 Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "M" Number of atoms: 2918 Number of conformers: 1 Conformer: "" Number of residues, atoms: 362, 2918 Classifications: {'peptide': 362} Link IDs: {'PTRANS': 18, 'TRANS': 343} Chain breaks: 1 Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 5 Chain: "N" Number of atoms: 2085 Number of conformers: 1 Conformer: "" Number of residues, atoms: 255, 2085 Classifications: {'peptide': 255} Link IDs: {'PTRANS': 8, 'TRANS': 246} Chain breaks: 3 Chain: "a" Number of atoms: 58 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 58 Classifications: {'peptide': 12} Incomplete info: {'backbone_only': 2, 'truncation_to_alanine': 10} Link IDs: {'TRANS': 11} Unresolved non-hydrogen bonds: 26 Unresolved non-hydrogen angles: 40 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'UNK:plan-1': 12} Unresolved non-hydrogen planarities: 12 Chain: "O" Number of atoms: 2354 Number of conformers: 1 Conformer: "" Number of residues, atoms: 297, 2354 Classifications: {'peptide': 297} Incomplete info: {'truncation_to_alanine': 16} Link IDs: {'PTRANS': 15, 'TRANS': 281} Chain breaks: 3 Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 64 Unresolved non-hydrogen angles: 86 Unresolved non-hydrogen dihedrals: 55 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'ARG:plan': 1, 'GLU:plan': 2, 'TRP:plan': 1, 'ASP:plan': 1, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 32 Chain: "P" Number of atoms: 3174 Number of conformers: 1 Conformer: "" Number of residues, atoms: 385, 3174 Classifications: {'peptide': 385} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 19, 'TRANS': 365} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 17 Unresolved non-hydrogen dihedrals: 10 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'TYR:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "Q" Number of atoms: 739 Number of conformers: 1 Conformer: "" Number of residues, atoms: 91, 739 Classifications: {'peptide': 91} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 1, 'TRANS': 89} Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 17 Unresolved non-hydrogen dihedrals: 15 Planarities with less than four sites: {'PHE:plan': 1} Unresolved non-hydrogen planarities: 6 Chain: "R" Number of atoms: 366 Number of conformers: 1 Conformer: "" Number of residues, atoms: 44, 366 Classifications: {'peptide': 44} Link IDs: {'PTRANS': 2, 'TRANS': 41} Chain: "S" Number of atoms: 1738 Number of conformers: 1 Conformer: "" Number of residues, atoms: 213, 1738 Classifications: {'peptide': 213} Link IDs: {'PTRANS': 13, 'TRANS': 199} Chain breaks: 2 Chain: "T" Number of atoms: 110 Number of conformers: 1 Conformer: "" Number of residues, atoms: 22, 110 Classifications: {'peptide': 22} Incomplete info: {'truncation_to_alanine': 22} Link IDs: {'TRANS': 21} Unresolved non-hydrogen bonds: 44 Unresolved non-hydrogen angles: 66 Unresolved non-hydrogen dihedrals: 22 Planarities with less than four sites: {'UNK:plan-1': 22} Unresolved non-hydrogen planarities: 22 Chain: "U" Number of atoms: 92 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 92 Classifications: {'peptide': 11} Link IDs: {'TRANS': 10} Chain: "V" Number of atoms: 420 Number of conformers: 1 Conformer: "" Number of residues, atoms: 84, 420 Classifications: {'peptide': 84} Incomplete info: {'truncation_to_alanine': 84} Link IDs: {'TRANS': 83} Chain breaks: 3 Unresolved non-hydrogen bonds: 168 Unresolved non-hydrogen angles: 252 Unresolved non-hydrogen dihedrals: 84 Planarities with less than four sites: {'UNK:plan-1': 84} Unresolved non-hydrogen planarities: 84 Chain: "X" Number of atoms: 3360 Number of conformers: 1 Conformer: "" Number of residues, atoms: 165, 3360 Classifications: {'DNA': 165} Link IDs: {'rna3p': 164} Chain: "Y" Number of atoms: 3405 Number of conformers: 1 Conformer: "" Number of residues, atoms: 165, 3405 Classifications: {'DNA': 165} Link IDs: {'rna3p': 164} Chain: "W" Number of atoms: 120 Number of conformers: 1 Conformer: "" Number of residues, atoms: 24, 120 Classifications: {'peptide': 24} Incomplete info: {'truncation_to_alanine': 24} Link IDs: {'TRANS': 23} Unresolved non-hydrogen bonds: 48 Unresolved non-hydrogen angles: 72 Unresolved non-hydrogen dihedrals: 24 Planarities with less than four sites: {'UNK:plan-1': 24} Unresolved non-hydrogen planarities: 24 Chain: "I" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 32 Unusual residues: {' MG': 1, 'ADP': 1, 'BEF': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Time building chain proxies: 7.91, per 1000 atoms: 0.18 Number of scatterers: 43109 At special positions: 0 Unit cell: (160.08, 188.094, 249.458, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 8 Type Number sf(0) S 174 16.00 P 332 15.00 Mg 1 11.99 F 3 9.00 O 8709 8.00 N 7753 7.00 C 26136 6.00 Be 1 4.00 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=2, symmetry=0 Number of additional bonds: simple=2, symmetry=0 Coordination: Other bonds: Time building additional restraints: 3.24 Conformation dependent library (CDL) restraints added in 1.5 seconds 8642 Ramachandran restraints generated. 4321 Oldfield, 0 Emsley, 4321 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8742 Finding SS restraints... Secondary structure from input PDB file: 201 helices and 23 sheets defined 62.8% alpha, 4.2% beta 153 base pairs and 247 stacking pairs defined. Time for finding SS restraints: 5.22 Creating SS restraints... Processing helix chain 'A' and resid 44 through 57 Processing helix chain 'A' and resid 63 through 76 Processing helix chain 'A' and resid 85 through 114 Processing helix chain 'A' and resid 120 through 132 Processing helix chain 'B' and resid 30 through 41 Processing helix chain 'B' and resid 49 through 76 Processing helix chain 'B' and resid 82 through 93 Processing helix chain 'C' and resid 16 through 21 removed outlier: 3.797A pdb=" N ARG C 20 " --> pdb=" O SER C 16 " (cutoff:3.500A) Processing helix chain 'C' and resid 26 through 37 Processing helix chain 'C' and resid 45 through 72 removed outlier: 4.488A pdb=" N VAL C 49 " --> pdb=" O ALA C 45 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N ASP C 72 " --> pdb=" O ASN C 68 " (cutoff:3.500A) Processing helix chain 'C' and resid 79 through 90 Processing helix chain 'C' and resid 90 through 97 Processing helix chain 'D' and resid 37 through 49 Processing helix chain 'D' and resid 55 through 84 Processing helix chain 'D' and resid 90 through 102 removed outlier: 3.600A pdb=" N ILE D 94 " --> pdb=" O THR D 90 " (cutoff:3.500A) Processing helix chain 'D' and resid 103 through 124 removed outlier: 3.685A pdb=" N SER D 124 " --> pdb=" O LYS D 120 " (cutoff:3.500A) Processing helix chain 'E' and resid 44 through 57 removed outlier: 3.687A pdb=" N ARG E 49 " --> pdb=" O THR E 45 " (cutoff:3.500A) Processing helix chain 'E' and resid 63 through 79 removed outlier: 3.599A pdb=" N PHE E 67 " --> pdb=" O ARG E 63 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N PHE E 78 " --> pdb=" O ILE E 74 " (cutoff:3.500A) Processing helix chain 'E' and resid 85 through 114 Processing helix chain 'E' and resid 120 through 132 removed outlier: 3.501A pdb=" N ILE E 124 " --> pdb=" O MET E 120 " (cutoff:3.500A) Processing helix chain 'F' and resid 24 through 29 removed outlier: 3.535A pdb=" N GLN F 27 " --> pdb=" O ASP F 24 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N ILE F 29 " --> pdb=" O ILE F 26 " (cutoff:3.500A) Processing helix chain 'F' and resid 30 through 41 Processing helix chain 'F' and resid 49 through 76 removed outlier: 4.109A pdb=" N ARG F 55 " --> pdb=" O TYR F 51 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N ASP F 68 " --> pdb=" O ASN F 64 " (cutoff:3.500A) Processing helix chain 'F' and resid 82 through 94 removed outlier: 3.571A pdb=" N VAL F 86 " --> pdb=" O THR F 82 " (cutoff:3.500A) Processing helix chain 'G' and resid 16 through 22 Processing helix chain 'G' and resid 26 through 37 Processing helix chain 'G' and resid 45 through 73 removed outlier: 4.118A pdb=" N VAL G 49 " --> pdb=" O ALA G 45 " (cutoff:3.500A) Processing helix chain 'G' and resid 79 through 90 Processing helix chain 'G' and resid 90 through 97 Processing helix chain 'G' and resid 112 through 116 Processing helix chain 'H' and resid 37 through 49 Processing helix chain 'H' and resid 55 through 84 Processing helix chain 'H' and resid 90 through 102 Processing helix chain 'H' and resid 104 through 124 removed outlier: 3.836A pdb=" N LYS H 108 " --> pdb=" O GLY H 104 " (cutoff:3.500A) Processing helix chain 'Z' and resid 115 through 125 removed outlier: 4.195A pdb=" N UNK Z 125 " --> pdb=" O UNK Z 121 " (cutoff:3.500A) Processing helix chain 'Z' and resid 129 through 140 Processing helix chain 'I' and resid 366 through 386 removed outlier: 3.514A pdb=" N ALA I 379 " --> pdb=" O GLN I 375 " (cutoff:3.500A) Processing helix chain 'I' and resid 394 through 423 removed outlier: 4.171A pdb=" N PHE I 412 " --> pdb=" O ARG I 408 " (cutoff:3.500A) removed outlier: 4.249A pdb=" N GLN I 415 " --> pdb=" O ASN I 411 " (cutoff:3.500A) Processing helix chain 'I' and resid 445 through 532 Processing helix chain 'I' and resid 549 through 570 removed outlier: 3.548A pdb=" N GLN I 555 " --> pdb=" O ALA I 551 " (cutoff:3.500A) Processing helix chain 'I' and resid 755 through 771 Processing helix chain 'I' and resid 784 through 799 Processing helix chain 'I' and resid 811 through 826 removed outlier: 4.494A pdb=" N SER I 816 " --> pdb=" O LEU I 812 " (cutoff:3.500A) removed outlier: 4.654A pdb=" N ASN I 817 " --> pdb=" O SER I 813 " (cutoff:3.500A) Processing helix chain 'I' and resid 837 through 843 Processing helix chain 'I' and resid 844 through 851 Processing helix chain 'I' and resid 859 through 866 removed outlier: 3.503A pdb=" N ILE I 863 " --> pdb=" O THR I 859 " (cutoff:3.500A) Processing helix chain 'I' and resid 866 through 872 Processing helix chain 'I' and resid 883 through 887 Processing helix chain 'I' and resid 891 through 899 removed outlier: 3.793A pdb=" N GLN I 895 " --> pdb=" O CYS I 891 " (cutoff:3.500A) Processing helix chain 'I' and resid 917 through 929 removed outlier: 4.084A pdb=" N LEU I 921 " --> pdb=" O LYS I 917 " (cutoff:3.500A) Processing helix chain 'I' and resid 936 through 941 removed outlier: 3.813A pdb=" N GLU I 940 " --> pdb=" O CYS I 936 " (cutoff:3.500A) Processing helix chain 'I' and resid 959 through 971 removed outlier: 3.841A pdb=" N LEU I 963 " --> pdb=" O GLU I 959 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N VAL I 971 " --> pdb=" O ARG I 967 " (cutoff:3.500A) Processing helix chain 'I' and resid 980 through 985 Processing helix chain 'I' and resid 1001 through 1012 Processing helix chain 'I' and resid 1039 through 1048 Processing helix chain 'I' and resid 1049 through 1051 No H-bonds generated for 'chain 'I' and resid 1049 through 1051' Processing helix chain 'I' and resid 1052 through 1061 Processing helix chain 'I' and resid 1079 through 1095 Proline residue: I1090 - end of helix removed outlier: 3.831A pdb=" N THR I1095 " --> pdb=" O LYS I1091 " (cutoff:3.500A) Processing helix chain 'I' and resid 1105 through 1120 removed outlier: 4.007A pdb=" N ILE I1111 " --> pdb=" O SER I1107 " (cutoff:3.500A) Processing helix chain 'I' and resid 1131 through 1144 removed outlier: 3.983A pdb=" N GLY I1136 " --> pdb=" O ALA I1132 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N MET I1137 " --> pdb=" O GLU I1133 " (cutoff:3.500A) Processing helix chain 'I' and resid 1179 through 1189 removed outlier: 3.606A pdb=" N ASP I1183 " --> pdb=" O ASN I1179 " (cutoff:3.500A) Processing helix chain 'I' and resid 1209 through 1230 removed outlier: 3.822A pdb=" N LYS I1213 " --> pdb=" O SER I1209 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N VAL I1228 " --> pdb=" O VAL I1224 " (cutoff:3.500A) Processing helix chain 'I' and resid 1241 through 1243 No H-bonds generated for 'chain 'I' and resid 1241 through 1243' Processing helix chain 'I' and resid 1244 through 1253 Processing helix chain 'I' and resid 1298 through 1307 Processing helix chain 'I' and resid 1309 through 1330 removed outlier: 3.980A pdb=" N ASP I1314 " --> pdb=" O GLU I1310 " (cutoff:3.500A) removed outlier: 4.174A pdb=" N ARG I1329 " --> pdb=" O ARG I1325 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N ASN I1330 " --> pdb=" O GLU I1326 " (cutoff:3.500A) Processing helix chain 'J' and resid 2 through 6 Processing helix chain 'J' and resid 55 through 61 Processing helix chain 'J' and resid 62 through 64 No H-bonds generated for 'chain 'J' and resid 62 through 64' Processing helix chain 'J' and resid 81 through 97 removed outlier: 4.578A pdb=" N ASN J 92 " --> pdb=" O HIS J 88 " (cutoff:3.500A) removed outlier: 4.728A pdb=" N GLU J 93 " --> pdb=" O THR J 89 " (cutoff:3.500A) Processing helix chain 'J' and resid 112 through 128 removed outlier: 4.189A pdb=" N THR J 120 " --> pdb=" O ARG J 116 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N THR J 126 " --> pdb=" O ILE J 122 " (cutoff:3.500A) Processing helix chain 'J' and resid 137 through 146 Processing helix chain 'J' and resid 181 through 197 removed outlier: 3.529A pdb=" N LEU J 185 " --> pdb=" O ALA J 181 " (cutoff:3.500A) Processing helix chain 'J' and resid 202 through 213 removed outlier: 5.272A pdb=" N ARG J 210 " --> pdb=" O ARG J 206 " (cutoff:3.500A) Processing helix chain 'J' and resid 222 through 229 Processing helix chain 'J' and resid 233 through 237 Processing helix chain 'J' and resid 252 through 257 Processing helix chain 'J' and resid 258 through 261 Processing helix chain 'J' and resid 274 through 284 Processing helix chain 'J' and resid 288 through 295 removed outlier: 3.557A pdb=" N ASP J 292 " --> pdb=" O ASP J 288 " (cutoff:3.500A) Processing helix chain 'J' and resid 308 through 321 Processing helix chain 'J' and resid 337 through 347 Processing helix chain 'J' and resid 352 through 356 removed outlier: 4.134A pdb=" N TRP J 356 " --> pdb=" O GLN J 353 " (cutoff:3.500A) Processing helix chain 'J' and resid 358 through 363 Processing helix chain 'J' and resid 366 through 371 removed outlier: 3.502A pdb=" N VAL J 370 " --> pdb=" O GLY J 366 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N HIS J 371 " --> pdb=" O PRO J 367 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 366 through 371' Processing helix chain 'K' and resid 71 through 75 Processing helix chain 'K' and resid 95 through 111 Processing helix chain 'K' and resid 129 through 145 Processing helix chain 'K' and resid 153 through 162 Processing helix chain 'K' and resid 189 through 192 Processing helix chain 'K' and resid 198 through 208 removed outlier: 4.012A pdb=" N ILE K 202 " --> pdb=" O ALA K 198 " (cutoff:3.500A) Processing helix chain 'K' and resid 252 through 264 Processing helix chain 'K' and resid 325 through 334 Processing helix chain 'K' and resid 340 through 346 Processing helix chain 'K' and resid 353 through 357 removed outlier: 4.137A pdb=" N LEU K 356 " --> pdb=" O GLY K 353 " (cutoff:3.500A) Processing helix chain 'K' and resid 361 through 372 Processing helix chain 'K' and resid 382 through 386 removed outlier: 4.339A pdb=" N THR K 385 " --> pdb=" O ALA K 382 " (cutoff:3.500A) Processing helix chain 'K' and resid 387 through 399 removed outlier: 5.200A pdb=" N SER K 393 " --> pdb=" O ARG K 389 " (cutoff:3.500A) removed outlier: 5.409A pdb=" N TRP K 394 " --> pdb=" O ARG K 390 " (cutoff:3.500A) Processing helix chain 'K' and resid 400 through 402 No H-bonds generated for 'chain 'K' and resid 400 through 402' Processing helix chain 'K' and resid 403 through 409 removed outlier: 4.492A pdb=" N GLN K 408 " --> pdb=" O GLY K 404 " (cutoff:3.500A) Processing helix chain 'K' and resid 412 through 416 Processing helix chain 'L' and resid 10 through 16 Processing helix chain 'L' and resid 16 through 31 removed outlier: 3.803A pdb=" N GLY L 31 " --> pdb=" O HIS L 27 " (cutoff:3.500A) Processing helix chain 'L' and resid 46 through 57 removed outlier: 3.772A pdb=" N LEU L 50 " --> pdb=" O ASP L 46 " (cutoff:3.500A) Processing helix chain 'L' and resid 59 through 67 removed outlier: 4.551A pdb=" N GLU L 65 " --> pdb=" O ALA L 61 " (cutoff:3.500A) Processing helix chain 'L' and resid 68 through 76 removed outlier: 4.146A pdb=" N GLU L 74 " --> pdb=" O GLY L 70 " (cutoff:3.500A) removed outlier: 4.404A pdb=" N GLU L 75 " --> pdb=" O GLU L 71 " (cutoff:3.500A) Processing helix chain 'L' and resid 85 through 97 Processing helix chain 'L' and resid 100 through 105 Processing helix chain 'L' and resid 140 through 146 removed outlier: 4.070A pdb=" N GLN L 144 " --> pdb=" O ASP L 140 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N SER L 145 " --> pdb=" O TYR L 141 " (cutoff:3.500A) Processing helix chain 'L' and resid 156 through 167 Processing helix chain 'L' and resid 169 through 184 Processing helix chain 'L' and resid 192 through 196 Processing helix chain 'L' and resid 197 through 206 removed outlier: 4.108A pdb=" N THR L 201 " --> pdb=" O PRO L 197 " (cutoff:3.500A) Processing helix chain 'L' and resid 217 through 224 removed outlier: 3.561A pdb=" N PHE L 221 " --> pdb=" O PHE L 217 " (cutoff:3.500A) Processing helix chain 'L' and resid 233 through 240 Processing helix chain 'L' and resid 243 through 251 Processing helix chain 'L' and resid 280 through 297 Processing helix chain 'L' and resid 299 through 309 removed outlier: 4.287A pdb=" N LYS L 304 " --> pdb=" O GLU L 300 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N LEU L 305 " --> pdb=" O GLY L 301 " (cutoff:3.500A) Processing helix chain 'L' and resid 310 through 322 Processing helix chain 'L' and resid 324 through 339 Processing helix chain 'L' and resid 340 through 342 No H-bonds generated for 'chain 'L' and resid 340 through 342' Processing helix chain 'L' and resid 349 through 364 removed outlier: 3.570A pdb=" N HIS L 353 " --> pdb=" O PHE L 349 " (cutoff:3.500A) Processing helix chain 'L' and resid 367 through 382 removed outlier: 3.754A pdb=" N CYS L 382 " --> pdb=" O LEU L 378 " (cutoff:3.500A) Processing helix chain 'L' and resid 387 through 395 removed outlier: 3.662A pdb=" N VAL L 395 " --> pdb=" O ILE L 391 " (cutoff:3.500A) Processing helix chain 'L' and resid 396 through 406 removed outlier: 3.983A pdb=" N TYR L 400 " --> pdb=" O ASP L 396 " (cutoff:3.500A) Processing helix chain 'L' and resid 411 through 427 Processing helix chain 'L' and resid 429 through 438 removed outlier: 3.618A pdb=" N CYS L 433 " --> pdb=" O GLY L 429 " (cutoff:3.500A) Processing helix chain 'L' and resid 441 through 452 removed outlier: 3.550A pdb=" N VAL L 450 " --> pdb=" O LEU L 446 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N SER L 451 " --> pdb=" O VAL L 447 " (cutoff:3.500A) Processing helix chain 'L' and resid 453 through 457 Processing helix chain 'L' and resid 468 through 479 Processing helix chain 'L' and resid 1762 through 1783 removed outlier: 3.925A pdb=" N LEU L1770 " --> pdb=" O LYS L1766 " (cutoff:3.500A) Processing helix chain 'L' and resid 1783 through 1793 Processing helix chain 'L' and resid 1793 through 1803 removed outlier: 4.061A pdb=" N VAL L1799 " --> pdb=" O ASN L1795 " (cutoff:3.500A) Processing helix chain 'L' and resid 1808 through 1821 removed outlier: 3.874A pdb=" N ALA L1812 " --> pdb=" O SER L1808 " (cutoff:3.500A) Processing helix chain 'M' and resid 29 through 37 Processing helix chain 'M' and resid 41 through 46 removed outlier: 3.514A pdb=" N LYS M 45 " --> pdb=" O GLY M 41 " (cutoff:3.500A) Processing helix chain 'M' and resid 56 through 67 Processing helix chain 'M' and resid 83 through 87 removed outlier: 3.629A pdb=" N SER M 87 " --> pdb=" O LEU M 84 " (cutoff:3.500A) Processing helix chain 'M' and resid 93 through 102 Processing helix chain 'M' and resid 172 through 182 Processing helix chain 'M' and resid 214 through 227 removed outlier: 3.535A pdb=" N PHE M 218 " --> pdb=" O THR M 214 " (cutoff:3.500A) Processing helix chain 'M' and resid 229 through 247 Proline residue: M 235 - end of helix Processing helix chain 'M' and resid 289 through 302 Processing helix chain 'M' and resid 306 through 323 removed outlier: 3.508A pdb=" N THR M 310 " --> pdb=" O GLU M 306 " (cutoff:3.500A) Processing helix chain 'M' and resid 344 through 350 Processing helix chain 'M' and resid 357 through 381 removed outlier: 3.542A pdb=" N THR M 381 " --> pdb=" O ARG M 377 " (cutoff:3.500A) Processing helix chain 'N' and resid 439 through 446 Processing helix chain 'N' and resid 447 through 452 removed outlier: 4.585A pdb=" N GLY N 452 " --> pdb=" O GLU N 448 " (cutoff:3.500A) Processing helix chain 'N' and resid 458 through 476 removed outlier: 4.141A pdb=" N ASN N 476 " --> pdb=" O THR N 472 " (cutoff:3.500A) Processing helix chain 'N' and resid 482 through 491 removed outlier: 3.772A pdb=" N CYS N 486 " --> pdb=" O THR N 482 " (cutoff:3.500A) Processing helix chain 'N' and resid 493 through 507 removed outlier: 3.705A pdb=" N TRP N 507 " --> pdb=" O PHE N 503 " (cutoff:3.500A) Processing helix chain 'N' and resid 603 through 616 Processing helix chain 'N' and resid 622 through 627 Processing helix chain 'N' and resid 631 through 640 Processing helix chain 'N' and resid 672 through 684 removed outlier: 3.571A pdb=" N SER N 682 " --> pdb=" O ALA N 678 " (cutoff:3.500A) Processing helix chain 'N' and resid 859 through 951 Processing helix chain 'O' and resid 440 through 446 Processing helix chain 'O' and resid 446 through 451 removed outlier: 3.686A pdb=" N ASN O 451 " --> pdb=" O PRO O 447 " (cutoff:3.500A) Processing helix chain 'O' and resid 458 through 476 removed outlier: 3.879A pdb=" N ALA O 464 " --> pdb=" O GLU O 460 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N ASN O 467 " --> pdb=" O LEU O 463 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N TYR O 473 " --> pdb=" O MET O 469 " (cutoff:3.500A) Processing helix chain 'O' and resid 484 through 489 removed outlier: 3.688A pdb=" N ASN O 489 " --> pdb=" O ALA O 485 " (cutoff:3.500A) Processing helix chain 'O' and resid 493 through 507 removed outlier: 3.634A pdb=" N ILE O 497 " --> pdb=" O ASP O 493 " (cutoff:3.500A) Processing helix chain 'O' and resid 536 through 540 Processing helix chain 'O' and resid 606 through 613 Processing helix chain 'O' and resid 620 through 628 removed outlier: 3.508A pdb=" N GLU O 625 " --> pdb=" O ASN O 621 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N HIS O 626 " --> pdb=" O LYS O 622 " (cutoff:3.500A) Processing helix chain 'O' and resid 633 through 642 Processing helix chain 'O' and resid 671 through 682 Processing helix chain 'O' and resid 685 through 705 Processing helix chain 'O' and resid 868 through 952 Processing helix chain 'P' and resid 143 through 174 removed outlier: 3.791A pdb=" N TYR P 147 " --> pdb=" O GLU P 143 " (cutoff:3.500A) Processing helix chain 'P' and resid 218 through 225 Processing helix chain 'P' and resid 232 through 236 Processing helix chain 'P' and resid 245 through 250 removed outlier: 3.814A pdb=" N TYR P 249 " --> pdb=" O ASP P 245 " (cutoff:3.500A) Processing helix chain 'P' and resid 298 through 306 Processing helix chain 'P' and resid 312 through 327 Processing helix chain 'P' and resid 340 through 348 removed outlier: 3.582A pdb=" N GLN P 345 " --> pdb=" O LYS P 341 " (cutoff:3.500A) Processing helix chain 'P' and resid 353 through 355 No H-bonds generated for 'chain 'P' and resid 353 through 355' Processing helix chain 'P' and resid 356 through 365 removed outlier: 3.604A pdb=" N ARG P 360 " --> pdb=" O GLU P 356 " (cutoff:3.500A) removed outlier: 4.833A pdb=" N ALA P 363 " --> pdb=" O GLN P 359 " (cutoff:3.500A) Processing helix chain 'P' and resid 380 through 384 removed outlier: 3.624A pdb=" N ASP P 383 " --> pdb=" O ASP P 380 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N GLN P 384 " --> pdb=" O PRO P 381 " (cutoff:3.500A) No H-bonds generated for 'chain 'P' and resid 380 through 384' Processing helix chain 'P' and resid 399 through 447 removed outlier: 3.567A pdb=" N THR P 411 " --> pdb=" O PHE P 407 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N ALA P 418 " --> pdb=" O GLN P 414 " (cutoff:3.500A) removed outlier: 5.076A pdb=" N THR P 419 " --> pdb=" O GLN P 415 " (cutoff:3.500A) removed outlier: 5.035A pdb=" N LEU P 420 " --> pdb=" O GLU P 416 " (cutoff:3.500A) Processing helix chain 'P' and resid 447 through 465 Processing helix chain 'P' and resid 483 through 511 removed outlier: 4.480A pdb=" N GLN P 488 " --> pdb=" O GLN P 484 " (cutoff:3.500A) removed outlier: 5.193A pdb=" N GLU P 489 " --> pdb=" O PRO P 485 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N CYS P 492 " --> pdb=" O GLN P 488 " (cutoff:3.500A) Processing helix chain 'Q' and resid 188 through 195 removed outlier: 3.541A pdb=" N THR Q 191 " --> pdb=" O MET Q 188 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N ARG Q 195 " --> pdb=" O ALA Q 192 " (cutoff:3.500A) Processing helix chain 'Q' and resid 196 through 207 removed outlier: 3.947A pdb=" N LEU Q 202 " --> pdb=" O ARG Q 198 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N GLU Q 205 " --> pdb=" O ARG Q 201 " (cutoff:3.500A) Processing helix chain 'Q' and resid 221 through 275 removed outlier: 3.576A pdb=" N GLN Q 225 " --> pdb=" O THR Q 221 " (cutoff:3.500A) Processing helix chain 'R' and resid 197 through 222 Processing helix chain 'S' and resid 134 through 150 removed outlier: 3.619A pdb=" N LYS S 150 " --> pdb=" O GLN S 146 " (cutoff:3.500A) Processing helix chain 'S' and resid 167 through 172 Processing helix chain 'S' and resid 177 through 187 Processing helix chain 'S' and resid 192 through 211 removed outlier: 3.744A pdb=" N LEU S 196 " --> pdb=" O SER S 192 " (cutoff:3.500A) Processing helix chain 'S' and resid 215 through 232 removed outlier: 3.725A pdb=" N LYS S 219 " --> pdb=" O THR S 215 " (cutoff:3.500A) Processing helix chain 'S' and resid 405 through 409 removed outlier: 3.649A pdb=" N SER S 409 " --> pdb=" O PRO S 406 " (cutoff:3.500A) Processing helix chain 'S' and resid 422 through 433 Processing helix chain 'S' and resid 537 through 565 Processing helix chain 'S' and resid 579 through 599 Processing helix chain 'U' and resid 1516 through 1524 removed outlier: 3.813A pdb=" N LYS U1520 " --> pdb=" O GLU U1516 " (cutoff:3.500A) Processing helix chain 'V' and resid 3 through 11 Processing helix chain 'V' and resid 19 through 33 Processing helix chain 'V' and resid 1003 through 1017 Processing helix chain 'V' and resid 1032 through 1034 No H-bonds generated for 'chain 'V' and resid 1032 through 1034' Processing helix chain 'V' and resid 1035 through 1042 Processing helix chain 'W' and resid 3 through 10 removed outlier: 3.766A pdb=" N UNK W 8 " --> pdb=" O UNK W 4 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 118 through 119 removed outlier: 3.595A pdb=" N ILE A 119 " --> pdb=" O ARG B 45 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'B' and resid 96 through 97 removed outlier: 6.807A pdb=" N THR B 96 " --> pdb=" O THR C 101 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'C' and resid 42 through 43 removed outlier: 8.014A pdb=" N ARG C 42 " --> pdb=" O ILE D 89 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'E' and resid 118 through 119 Processing sheet with id=AA5, first strand: chain 'G' and resid 42 through 43 removed outlier: 7.246A pdb=" N ARG G 42 " --> pdb=" O ILE H 89 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'G' and resid 77 through 78 removed outlier: 3.559A pdb=" N ILE G 78 " --> pdb=" O GLY H 53 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'I' and resid 831 through 833 removed outlier: 7.181A pdb=" N VAL I 832 " --> pdb=" O LEU I 857 " (cutoff:3.500A) removed outlier: 6.819A pdb=" N PHE I 806 " --> pdb=" O LEU I 856 " (cutoff:3.500A) removed outlier: 7.419A pdb=" N THR I 858 " --> pdb=" O PHE I 806 " (cutoff:3.500A) removed outlier: 6.144A pdb=" N ILE I 808 " --> pdb=" O THR I 858 " (cutoff:3.500A) removed outlier: 6.388A pdb=" N LEU I 807 " --> pdb=" O ILE I 879 " (cutoff:3.500A) removed outlier: 7.914A pdb=" N ASP I 881 " --> pdb=" O LEU I 807 " (cutoff:3.500A) removed outlier: 6.883A pdb=" N ILE I 809 " --> pdb=" O ASP I 881 " (cutoff:3.500A) removed outlier: 7.244A pdb=" N LEU I 909 " --> pdb=" O MET I 878 " (cutoff:3.500A) removed outlier: 7.197A pdb=" N VAL I 880 " --> pdb=" O LEU I 909 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'I' and resid 992 through 998 removed outlier: 6.328A pdb=" N VAL I 992 " --> pdb=" O VAL I1201 " (cutoff:3.500A) removed outlier: 7.753A pdb=" N ARG I1203 " --> pdb=" O VAL I 992 " (cutoff:3.500A) removed outlier: 6.573A pdb=" N TYR I 994 " --> pdb=" O ARG I1203 " (cutoff:3.500A) removed outlier: 7.876A pdb=" N CYS I1205 " --> pdb=" O TYR I 994 " (cutoff:3.500A) removed outlier: 6.661A pdb=" N ILE I 996 " --> pdb=" O CYS I1205 " (cutoff:3.500A) removed outlier: 6.768A pdb=" N VAL I1099 " --> pdb=" O PHE I1152 " (cutoff:3.500A) removed outlier: 7.476A pdb=" N LEU I1154 " --> pdb=" O VAL I1099 " (cutoff:3.500A) removed outlier: 6.467A pdb=" N LEU I1101 " --> pdb=" O LEU I1154 " (cutoff:3.500A) removed outlier: 6.808A pdb=" N LEU I1124 " --> pdb=" O LEU I1153 " (cutoff:3.500A) removed outlier: 8.612A pdb=" N SER I1155 " --> pdb=" O LEU I1124 " (cutoff:3.500A) removed outlier: 8.296A pdb=" N LEU I1126 " --> pdb=" O SER I1155 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'J' and resid 19 through 21 removed outlier: 6.380A pdb=" N LEU J 8 " --> pdb=" O LEU J 104 " (cutoff:3.500A) removed outlier: 7.871A pdb=" N THR J 106 " --> pdb=" O LEU J 8 " (cutoff:3.500A) removed outlier: 8.454A pdb=" N VAL J 10 " --> pdb=" O THR J 106 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'J' and resid 176 through 177 removed outlier: 3.853A pdb=" N LEU J 176 " --> pdb=" O THR J 162 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N THR J 162 " --> pdb=" O LEU J 176 " (cutoff:3.500A) removed outlier: 5.993A pdb=" N ILE J 151 " --> pdb=" O VAL J 298 " (cutoff:3.500A) removed outlier: 7.356A pdb=" N SER J 300 " --> pdb=" O ILE J 151 " (cutoff:3.500A) removed outlier: 5.798A pdb=" N MET J 153 " --> pdb=" O SER J 300 " (cutoff:3.500A) removed outlier: 7.308A pdb=" N THR J 297 " --> pdb=" O ILE J 330 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'J' and resid 239 through 240 Processing sheet with id=AB3, first strand: chain 'K' and resid 14 through 17 Processing sheet with id=AB4, first strand: chain 'K' and resid 88 through 89 Processing sheet with id=AB5, first strand: chain 'K' and resid 186 through 187 Processing sheet with id=AB6, first strand: chain 'K' and resid 186 through 187 removed outlier: 3.901A pdb=" N THR K 178 " --> pdb=" O ASP K 171 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N ASP K 171 " --> pdb=" O THR K 178 " (cutoff:3.500A) removed outlier: 5.597A pdb=" N LEU K 168 " --> pdb=" O ILE K 349 " (cutoff:3.500A) removed outlier: 7.191A pdb=" N ALA K 351 " --> pdb=" O LEU K 168 " (cutoff:3.500A) removed outlier: 5.816A pdb=" N LEU K 170 " --> pdb=" O ALA K 351 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'M' and resid 16 through 20 removed outlier: 3.664A pdb=" N LEU M 19 " --> pdb=" O GLU M 24 " (cutoff:3.500A) removed outlier: 7.671A pdb=" N GLU M 24 " --> pdb=" O LEU M 19 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'M' and resid 186 through 191 Processing sheet with id=AB9, first strand: chain 'M' and resid 194 through 195 Processing sheet with id=AC1, first strand: chain 'M' and resid 262 through 267 Processing sheet with id=AC2, first strand: chain 'P' and resid 178 through 180 removed outlier: 6.375A pdb=" N GLN P 178 " --> pdb=" O VAL P 396 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'P' and resid 185 through 188 removed outlier: 4.488A pdb=" N TRP P 207 " --> pdb=" O ARG P 274 " (cutoff:3.500A) removed outlier: 4.464A pdb=" N ARG P 274 " --> pdb=" O TRP P 207 " (cutoff:3.500A) removed outlier: 4.175A pdb=" N VAL P 272 " --> pdb=" O LEU P 209 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'P' and resid 257 through 259 removed outlier: 3.770A pdb=" N TRP P 258 " --> pdb=" O LEU P 240 " (cutoff:3.500A) removed outlier: 4.278A pdb=" N SER P 239 " --> pdb=" O MET P 287 " (cutoff:3.500A) removed outlier: 4.338A pdb=" N MET P 287 " --> pdb=" O SER P 239 " (cutoff:3.500A) removed outlier: 4.111A pdb=" N VAL P 241 " --> pdb=" O LEU P 285 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N GLU P 243 " --> pdb=" O THR P 283 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N VAL P 280 " --> pdb=" O ILE P 377 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'P' and resid 294 through 296 1948 hydrogen bonds defined for protein. 5709 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 393 hydrogen bonds 786 hydrogen bond angles 0 basepair planarities 153 basepair parallelities 247 stacking parallelities Total time for adding SS restraints: 11.35 Time building geometry restraints manager: 4.32 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.33: 10817 1.33 - 1.45: 9261 1.45 - 1.57: 23531 1.57 - 1.69: 661 1.69 - 1.81: 295 Bond restraints: 44565 Sorted by residual: bond pdb=" F2 BEF I1703 " pdb="BE BEF I1703 " ideal model delta sigma weight residual 1.476 1.564 -0.088 2.00e-02 2.50e+03 1.93e+01 bond pdb=" C1' DC Y 65 " pdb=" N1 DC Y 65 " ideal model delta sigma weight residual 1.468 1.522 -0.054 1.40e-02 5.10e+03 1.51e+01 bond pdb=" C1' DC X 149 " pdb=" N1 DC X 149 " ideal model delta sigma weight residual 1.468 1.521 -0.053 1.40e-02 5.10e+03 1.43e+01 bond pdb=" C1' DT Y 89 " pdb=" N1 DT Y 89 " ideal model delta sigma weight residual 1.468 1.518 -0.050 1.40e-02 5.10e+03 1.27e+01 bond pdb=" C1' DC Y -9 " pdb=" N1 DC Y -9 " ideal model delta sigma weight residual 1.468 1.517 -0.049 1.40e-02 5.10e+03 1.23e+01 ... (remaining 44560 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.44: 60804 2.44 - 4.87: 766 4.87 - 7.31: 16 7.31 - 9.74: 5 9.74 - 12.18: 1 Bond angle restraints: 61592 Sorted by residual: angle pdb=" N PRO O 543 " pdb=" CA PRO O 543 " pdb=" CB PRO O 543 " ideal model delta sigma weight residual 103.25 111.67 -8.42 1.05e+00 9.07e-01 6.43e+01 angle pdb=" N PRO O 643 " pdb=" CA PRO O 643 " pdb=" CB PRO O 643 " ideal model delta sigma weight residual 103.25 110.82 -7.57 1.05e+00 9.07e-01 5.20e+01 angle pdb=" N PRO O 647 " pdb=" CA PRO O 647 " pdb=" CB PRO O 647 " ideal model delta sigma weight residual 103.25 110.49 -7.24 1.05e+00 9.07e-01 4.75e+01 angle pdb=" N3 DT Y -3 " pdb=" C4 DT Y -3 " pdb=" O4 DT Y -3 " ideal model delta sigma weight residual 119.90 122.66 -2.76 6.00e-01 2.78e+00 2.12e+01 angle pdb=" N3 DT Y 143 " pdb=" C4 DT Y 143 " pdb=" O4 DT Y 143 " ideal model delta sigma weight residual 119.90 122.65 -2.75 6.00e-01 2.78e+00 2.10e+01 ... (remaining 61587 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.44: 24580 33.44 - 66.88: 1645 66.88 - 100.31: 54 100.31 - 133.75: 1 133.75 - 167.19: 3 Dihedral angle restraints: 26283 sinusoidal: 12859 harmonic: 13424 Sorted by residual: dihedral pdb=" O1B ADP I1701 " pdb=" O3A ADP I1701 " pdb=" PB ADP I1701 " pdb=" PA ADP I1701 " ideal model delta sinusoidal sigma weight residual -60.00 -177.48 117.48 1 2.00e+01 2.50e-03 3.51e+01 dihedral pdb=" CA ARG M 341 " pdb=" C ARG M 341 " pdb=" N ASN M 342 " pdb=" CA ASN M 342 " ideal model delta harmonic sigma weight residual -180.00 -155.80 -24.20 0 5.00e+00 4.00e-02 2.34e+01 dihedral pdb=" CA LYS M 73 " pdb=" C LYS M 73 " pdb=" N PRO M 74 " pdb=" CA PRO M 74 " ideal model delta harmonic sigma weight residual -180.00 -157.15 -22.85 0 5.00e+00 4.00e-02 2.09e+01 ... (remaining 26280 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.062: 6063 0.062 - 0.125: 624 0.125 - 0.187: 230 0.187 - 0.250: 4 0.250 - 0.312: 2 Chirality restraints: 6923 Sorted by residual: chirality pdb=" CA SER O 437 " pdb=" N SER O 437 " pdb=" C SER O 437 " pdb=" CB SER O 437 " both_signs ideal model delta sigma weight residual False 2.51 2.20 0.31 2.00e-01 2.50e+01 2.44e+00 chirality pdb=" CA VAL O 542 " pdb=" N VAL O 542 " pdb=" C VAL O 542 " pdb=" CB VAL O 542 " both_signs ideal model delta sigma weight residual False 2.44 2.16 0.28 2.00e-01 2.50e+01 1.94e+00 chirality pdb=" CA PRO O 643 " pdb=" N PRO O 643 " pdb=" C PRO O 643 " pdb=" CB PRO O 643 " both_signs ideal model delta sigma weight residual False 2.72 2.48 0.24 2.00e-01 2.50e+01 1.39e+00 ... (remaining 6920 not shown) Planarity restraints: 6764 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASN O 436 " -0.013 2.00e-02 2.50e+03 2.62e-02 6.85e+00 pdb=" C ASN O 436 " 0.045 2.00e-02 2.50e+03 pdb=" O ASN O 436 " -0.018 2.00e-02 2.50e+03 pdb=" N SER O 437 " -0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DA X 60 " 0.021 2.00e-02 2.50e+03 9.94e-03 2.72e+00 pdb=" N9 DA X 60 " -0.023 2.00e-02 2.50e+03 pdb=" C8 DA X 60 " -0.004 2.00e-02 2.50e+03 pdb=" N7 DA X 60 " 0.002 2.00e-02 2.50e+03 pdb=" C5 DA X 60 " -0.000 2.00e-02 2.50e+03 pdb=" C6 DA X 60 " 0.004 2.00e-02 2.50e+03 pdb=" N6 DA X 60 " 0.007 2.00e-02 2.50e+03 pdb=" N1 DA X 60 " -0.004 2.00e-02 2.50e+03 pdb=" C2 DA X 60 " 0.001 2.00e-02 2.50e+03 pdb=" N3 DA X 60 " -0.003 2.00e-02 2.50e+03 pdb=" C4 DA X 60 " -0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C HIS L 470 " -0.027 5.00e-02 4.00e+02 4.03e-02 2.60e+00 pdb=" N PRO L 471 " 0.070 5.00e-02 4.00e+02 pdb=" CA PRO L 471 " -0.020 5.00e-02 4.00e+02 pdb=" CD PRO L 471 " -0.023 5.00e-02 4.00e+02 ... (remaining 6761 not shown) Histogram of nonbonded interaction distances: 1.92 - 2.52: 211 2.52 - 3.11: 33979 3.11 - 3.71: 69844 3.71 - 4.30: 94491 4.30 - 4.90: 147172 Nonbonded interactions: 345697 Sorted by model distance: nonbonded pdb=" OG1 THR J 186 " pdb=" O ARG J 206 " model vdw 1.920 3.040 nonbonded pdb=" OE1 GLU I 365 " pdb=" OG1 THR Q 191 " model vdw 1.973 3.040 nonbonded pdb=" OH TYR O 473 " pdb=" OD2 ASP O 515 " model vdw 2.001 3.040 nonbonded pdb=" OH TYR G 39 " pdb=" OE1 GLU H 71 " model vdw 2.048 3.040 nonbonded pdb=" OG1 THR J 149 " pdb=" OD2 ASP J 292 " model vdw 2.066 3.040 ... (remaining 345692 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 Found NCS groups: ncs_group { reference = (chain 'A' and resid 38 through 135) selection = chain 'E' } ncs_group { reference = (chain 'B' and (resid 16 through 101 or (resid 102 and (name N or name CA or nam \ e C or name O )))) selection = chain 'F' } ncs_group { reference = chain 'C' selection = (chain 'G' and resid 14 through 117) } ncs_group { reference = (chain 'D' and resid 31 through 124) selection = chain 'H' } ncs_group { reference = (chain 'N' and (resid 423 through 641 or (resid 642 through 647 and (name N or n \ ame CA or name C or name O or name CB )) or resid 671 through 686 or resid 862 t \ hrough 952)) selection = (chain 'O' and (resid 423 through 515 or resid 602 through 647 or resid 671 thro \ ugh 686 or resid 691 through 693 or resid 696 through 697 or resid 867 through 9 \ 52)) } ncs_group { reference = chain 'T' selection = (chain 'W' and resid 3 through 24) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.21 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.830 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.060 Extract box with map and model: 0.510 Check model and map are aligned: 0.090 Set scattering table: 0.100 Process input model: 40.930 Find NCS groups from input model: 0.550 Set up NCS constraints: 0.100 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:1.200 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 48.380 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5333 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 : 0.006 0.900 44567 Z= 0.613 Angle : 0.611 12.178 61592 Z= 0.462 Chirality : 0.044 0.312 6923 Planarity : 0.002 0.040 6764 Dihedral : 18.475 167.188 17541 Min Nonbonded Distance : 1.920 Molprobity Statistics. All-atom Clashscore : 4.53 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.05 % Favored : 94.86 % Rotamer: Outliers : 0.05 % Allowed : 1.14 % Favored : 98.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.79 (0.12), residues: 4321 helix: -0.11 (0.10), residues: 2408 sheet: -3.01 (0.30), residues: 200 loop : -2.53 (0.14), residues: 1713 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG I1318 TYR 0.023 0.001 TYR R 225 PHE 0.015 0.001 PHE I1313 TRP 0.006 0.001 TRP P 320 HIS 0.006 0.000 HIS L 27 Details of bonding type rmsd/Z covalent geometry : bond 0.00381 / 0.32 (44565) covalent geometry : angle 0.61069 / 0.46 (61592) hydrogen bonds : bond 0.12907 / 8.61 ( 2339) hydrogen bonds : angle 5.27757 / 3.74 ( 6495) Misc. bond : bond 0.78407 / 38.72 ( 2) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8642 Ramachandran restraints generated. 4321 Oldfield, 0 Emsley, 4321 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8642 Ramachandran restraints generated. 4321 Oldfield, 0 Emsley, 4321 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 715 residues out of total 3874 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 713 time to evaluate : 1.589 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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: A 104 PHE cc_start: 0.7191 (m-80) cc_final: 0.6739 (m-10) REVERT: B 84 MET cc_start: 0.6083 (mmm) cc_final: 0.5835 (mmm) REVERT: D 98 VAL cc_start: 0.9347 (m) cc_final: 0.8860 (p) REVERT: E 78 PHE cc_start: 0.7475 (m-10) cc_final: 0.7166 (m-10) REVERT: F 22 LEU cc_start: 0.7509 (mp) cc_final: 0.7298 (pt) REVERT: F 60 VAL cc_start: 0.8898 (t) cc_final: 0.8451 (t) REVERT: F 66 ILE cc_start: 0.9130 (mt) cc_final: 0.8693 (tp) REVERT: K 376 MET cc_start: -0.0219 (ptt) cc_final: -0.1248 (ppp) REVERT: L 162 VAL cc_start: 0.9546 (t) cc_final: 0.9282 (t) REVERT: L 211 ASP cc_start: 0.6416 (t0) cc_final: 0.6186 (t70) REVERT: L 332 LEU cc_start: 0.9278 (mm) cc_final: 0.8819 (tp) REVERT: L 372 MET cc_start: 0.8974 (mtt) cc_final: 0.8503 (mtp) REVERT: L 393 GLU cc_start: 0.9036 (pt0) cc_final: 0.8635 (tm-30) REVERT: L 445 MET cc_start: 0.8861 (mtp) cc_final: 0.8459 (mtt) REVERT: M 217 MET cc_start: 0.7688 (mtp) cc_final: 0.7451 (mtp) REVERT: M 301 LEU cc_start: 0.7184 (mm) cc_final: 0.6982 (mm) REVERT: N 936 MET cc_start: 0.8867 (mmp) cc_final: 0.8562 (tmm) REVERT: P 157 LEU cc_start: 0.8797 (tt) cc_final: 0.8569 (tp) REVERT: P 164 LYS cc_start: 0.9043 (mmmt) cc_final: 0.8797 (tmtt) REVERT: P 258 TRP cc_start: 0.2453 (t60) cc_final: 0.0852 (m-10) REVERT: U 1521 TYR cc_start: 0.7383 (t80) cc_final: 0.7101 (m-10) outliers start: 2 outliers final: 1 residues processed: 715 average time/residue: 0.3003 time to fit residues: 336.3732 Evaluate side-chains 385 residues out of total 3874 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 384 time to evaluate : 1.431 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 479 random chunks: chunk 432 optimal weight: 7.9990 chunk 197 optimal weight: 9.9990 chunk 388 optimal weight: 6.9990 chunk 455 optimal weight: 20.0000 chunk 215 optimal weight: 30.0000 chunk 20 optimal weight: 7.9990 chunk 132 optimal weight: 8.9990 chunk 261 optimal weight: 2.9990 chunk 248 optimal weight: 6.9990 chunk 207 optimal weight: 0.8980 chunk 470 optimal weight: 20.0000 overall best weight: 5.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 39 HIS A 85 GLN B 75 HIS C 38 ASN C 94 ASN ** D 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 104 GLN ** H 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 84 ASN ** I 510 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 570 GLN I 745 GLN I 847 GLN I 888 ASN I1230 GLN ** J 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 296 ASN K 73 ASN K 105 HIS K 189 GLN K 205 GLN K 263 GLN K 294 ASN L 48 HIS L 105 HIS L 159 ASN L 406 HIS M 103 ASN M 123 GLN M 140 HIS M 152 ASN M 318 GLN ** N 422 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 439 HIS N 513 GLN N 935 HIS ** O 467 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 604 GLN ** O 638 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 145 GLN P 326 HIS R 231 HIS S 206 ASN S 394 ASN Total number of N/Q/H flips: 37 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3874 r_free = 0.3874 target = 0.068599 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3475 r_free = 0.3475 target = 0.048872 restraints weight = 452480.396| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.049997 restraints weight = 249027.475| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 52)----------------| | r_work = 0.3520 r_free = 0.3520 target = 0.050787 restraints weight = 166431.026| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.051021 restraints weight = 128121.866| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 54)----------------| | r_work = 0.3537 r_free = 0.3537 target = 0.051554 restraints weight = 113548.731| |-----------------------------------------------------------------------------| r_work (final): 0.3420 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3419 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3419 r_free = 0.3419 target_work(ls_wunit_k1) = 0.046 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3419 r_free = 0.3419 target_work(ls_wunit_k1) = 0.046 | | occupancies: max = 1.00 min = 0.03 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (7 function evaluations) r_final: 0.3419 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7732 moved from start: 0.2640 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.121 44567 Z= 0.252 Angle : 0.757 12.399 61592 Z= 0.405 Chirality : 0.043 0.314 6923 Planarity : 0.006 0.127 6764 Dihedral : 22.698 169.971 8596 Min Nonbonded Distance : 2.267 Molprobity Statistics. All-atom Clashscore : 11.90 Ramachandran Plot: Outliers : 0.07 % Allowed : 6.25 % Favored : 93.68 % Rotamer: Outliers : 0.31 % Allowed : 5.23 % Favored : 94.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.01 (0.12), residues: 4321 helix: 0.37 (0.10), residues: 2467 sheet: -2.38 (0.34), residues: 176 loop : -2.05 (0.15), residues: 1678 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.020 0.001 ARG P 274 TYR 0.037 0.002 TYR A 54 PHE 0.025 0.002 PHE M 39 TRP 0.039 0.002 TRP M 321 HIS 0.015 0.002 HIS O 638 Details of bonding type rmsd/Z covalent geometry : bond 0.00492 / 0.25 (44565) covalent geometry : angle 0.75720 / 0.40 (61592) hydrogen bonds : bond 0.07348 / 4.95 ( 2339) hydrogen bonds : angle 4.79630 / 3.39 ( 6495) Misc. bond : bond 0.01646 / 0.82 ( 2) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8642 Ramachandran restraints generated. 4321 Oldfield, 0 Emsley, 4321 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8642 Ramachandran restraints generated. 4321 Oldfield, 0 Emsley, 4321 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 457 residues out of total 3874 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 445 time to evaluate : 1.595 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 100 LEU cc_start: 0.9740 (mm) cc_final: 0.9527 (mm) REVERT: B 37 LEU cc_start: 0.9726 (mt) cc_final: 0.9477 (mt) REVERT: B 84 MET cc_start: 0.9290 (mmm) cc_final: 0.8403 (mmm) REVERT: C 64 GLU cc_start: 0.9425 (tt0) cc_final: 0.8898 (tm-30) REVERT: D 59 MET cc_start: 0.9507 (tmm) cc_final: 0.9296 (tmm) REVERT: D 106 LEU cc_start: 0.9301 (mt) cc_final: 0.9072 (mt) REVERT: E 59 GLU cc_start: 0.9037 (pm20) cc_final: 0.8750 (pm20) REVERT: E 90 MET cc_start: 0.9586 (mmp) cc_final: 0.9298 (mmp) REVERT: E 93 GLN cc_start: 0.8536 (tp40) cc_final: 0.7918 (tp-100) REVERT: F 22 LEU cc_start: 0.8772 (mp) cc_final: 0.8494 (pt) REVERT: F 68 ASP cc_start: 0.9342 (m-30) cc_final: 0.9136 (m-30) REVERT: G 36 LYS cc_start: 0.9455 (mmmt) cc_final: 0.8989 (mmtm) REVERT: G 39 TYR cc_start: 0.8762 (m-10) cc_final: 0.8485 (m-80) REVERT: G 51 LEU cc_start: 0.9766 (tp) cc_final: 0.9511 (tp) REVERT: G 56 GLU cc_start: 0.8686 (tt0) cc_final: 0.7981 (mt-10) REVERT: G 64 GLU cc_start: 0.8963 (tp30) cc_final: 0.8176 (tp30) REVERT: G 95 LYS cc_start: 0.9600 (tptp) cc_final: 0.9159 (tppt) REVERT: H 59 MET cc_start: 0.9130 (tpp) cc_final: 0.8755 (tpp) REVERT: H 82 HIS cc_start: 0.8819 (m90) cc_final: 0.8413 (m90) REVERT: H 95 GLN cc_start: 0.9511 (tt0) cc_final: 0.9288 (tm-30) REVERT: I 424 MET cc_start: 0.6481 (ppp) cc_final: 0.6232 (ppp) REVERT: I 886 MET cc_start: 0.7908 (mtt) cc_final: 0.7309 (mmt) REVERT: I 960 GLU cc_start: 0.6172 (tt0) cc_final: 0.5368 (pm20) REVERT: I 1011 MET cc_start: 0.5536 (mmt) cc_final: 0.5247 (mmt) REVERT: I 1109 MET cc_start: 0.8771 (tpp) cc_final: 0.8305 (tpp) REVERT: I 1112 MET cc_start: 0.9338 (mmt) cc_final: 0.9027 (mmm) REVERT: I 1154 LEU cc_start: 0.9195 (mp) cc_final: 0.8884 (mp) REVERT: J 240 TYR cc_start: 0.9199 (t80) cc_final: 0.8913 (t80) REVERT: K 376 MET cc_start: -0.0024 (ptt) cc_final: -0.0925 (ppp) REVERT: L 78 PHE cc_start: 0.7954 (m-80) cc_final: 0.7704 (m-80) REVERT: L 287 LEU cc_start: 0.9001 (mm) cc_final: 0.8674 (mm) REVERT: L 332 LEU cc_start: 0.9563 (mm) cc_final: 0.8945 (tp) REVERT: L 372 MET cc_start: 0.9549 (mtt) cc_final: 0.9213 (mpp) REVERT: M 166 LEU cc_start: 0.9364 (mm) cc_final: 0.8885 (tt) REVERT: M 200 LEU cc_start: 0.9600 (tt) cc_final: 0.9038 (tt) REVERT: M 208 MET cc_start: 0.8829 (mtm) cc_final: 0.8552 (mtt) REVERT: M 217 MET cc_start: 0.9595 (mtp) cc_final: 0.9371 (mtp) REVERT: M 361 MET cc_start: 0.8669 (mmp) cc_final: 0.8140 (mmm) REVERT: M 366 ARG cc_start: 0.9702 (mpp80) cc_final: 0.9400 (mtt-85) REVERT: N 906 PHE cc_start: 0.8558 (t80) cc_final: 0.8149 (t80) REVERT: O 469 MET cc_start: 0.8853 (mmt) cc_final: 0.8413 (mmt) REVERT: O 498 MET cc_start: 0.7999 (mmp) cc_final: 0.7255 (mtp) REVERT: O 523 MET cc_start: 0.9204 (tpt) cc_final: 0.8888 (tpt) REVERT: O 897 LYS cc_start: 0.9607 (tptp) cc_final: 0.9318 (tppt) REVERT: P 161 ILE cc_start: 0.9617 (mt) cc_final: 0.9386 (mt) REVERT: P 164 LYS cc_start: 0.9441 (mmmt) cc_final: 0.9161 (pptt) REVERT: P 441 MET cc_start: 0.9086 (mpp) cc_final: 0.8704 (mpp) REVERT: P 474 GLU cc_start: 0.7591 (tm-30) cc_final: 0.7304 (tm-30) REVERT: Q 205 GLU cc_start: 0.4994 (tp30) cc_final: 0.4492 (pp20) REVERT: R 196 VAL cc_start: 0.8046 (t) cc_final: 0.7811 (t) REVERT: R 216 ARG cc_start: 0.9603 (tmt170) cc_final: 0.9386 (ttp80) REVERT: S 144 MET cc_start: -0.5370 (ttt) cc_final: -0.5827 (ttt) REVERT: S 572 MET cc_start: -0.1474 (mmm) cc_final: -0.2014 (mtp) REVERT: S 584 HIS cc_start: 0.7079 (t-90) cc_final: 0.6426 (m-70) REVERT: U 1521 TYR cc_start: 0.8308 (t80) cc_final: 0.7650 (m-80) outliers start: 12 outliers final: 3 residues processed: 455 average time/residue: 0.2679 time to fit residues: 197.9128 Evaluate side-chains 332 residues out of total 3874 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 329 time to evaluate : 1.522 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 479 random chunks: chunk 363 optimal weight: 0.9980 chunk 228 optimal weight: 20.0000 chunk 304 optimal weight: 6.9990 chunk 183 optimal weight: 0.0870 chunk 92 optimal weight: 8.9990 chunk 78 optimal weight: 6.9990 chunk 424 optimal weight: 9.9990 chunk 138 optimal weight: 0.5980 chunk 440 optimal weight: 30.0000 chunk 43 optimal weight: 0.8980 chunk 307 optimal weight: 5.9990 overall best weight: 1.7160 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 39 HIS ** C 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 63 ASN H 84 ASN ** I 915 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 296 ASN ** K 205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 140 HIS ** M 318 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 422 HIS N 439 HIS ** O 467 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 638 HIS ** Q 200 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 252 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3885 r_free = 0.3885 target = 0.069222 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3485 r_free = 0.3485 target = 0.049400 restraints weight = 443793.176| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.3513 r_free = 0.3513 target = 0.050573 restraints weight = 241206.565| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 52)----------------| | r_work = 0.3533 r_free = 0.3533 target = 0.051369 restraints weight = 160127.370| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 54)----------------| | r_work = 0.3544 r_free = 0.3544 target = 0.051909 restraints weight = 123087.321| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3550 r_free = 0.3550 target = 0.052139 restraints weight = 104327.439| |-----------------------------------------------------------------------------| r_work (final): 0.3431 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3431 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3431 r_free = 0.3431 target_work(ls_wunit_k1) = 0.046 | | occupancies: max = 1.00 min = 0.03 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3431 r_free = 0.3431 target_work(ls_wunit_k1) = 0.046 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3431 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7706 moved from start: 0.2895 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 44567 Z= 0.150 Angle : 0.625 10.665 61592 Z= 0.339 Chirality : 0.041 0.301 6923 Planarity : 0.005 0.073 6764 Dihedral : 22.834 166.958 8596 Min Nonbonded Distance : 2.237 Molprobity Statistics. All-atom Clashscore : 10.39 Ramachandran Plot: Outliers : 0.07 % Allowed : 6.25 % Favored : 93.68 % Rotamer: Outliers : 0.08 % Allowed : 2.68 % Favored : 97.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.70 (0.13), residues: 4321 helix: 0.66 (0.10), residues: 2491 sheet: -2.19 (0.34), residues: 184 loop : -2.01 (0.15), residues: 1646 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.019 0.001 ARG P 136 TYR 0.027 0.001 TYR B 51 PHE 0.020 0.002 PHE O 951 TRP 0.033 0.001 TRP M 321 HIS 0.015 0.001 HIS O 638 Details of bonding type rmsd/Z covalent geometry : bond 0.00294 / 0.15 (44565) covalent geometry : angle 0.62540 / 0.34 (61592) hydrogen bonds : bond 0.04665 / 3.14 ( 2339) hydrogen bonds : angle 4.54793 / 3.22 ( 6495) Misc. bond : bond 0.01242 / 0.61 ( 2) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8642 Ramachandran restraints generated. 4321 Oldfield, 0 Emsley, 4321 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8642 Ramachandran restraints generated. 4321 Oldfield, 0 Emsley, 4321 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 427 residues out of total 3874 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 424 time to evaluate : 1.276 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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: A 92 LEU cc_start: 0.9835 (mm) cc_final: 0.9550 (mm) REVERT: B 84 MET cc_start: 0.9244 (mmm) cc_final: 0.8376 (mmm) REVERT: C 64 GLU cc_start: 0.9373 (tt0) cc_final: 0.8863 (tm-30) REVERT: D 42 TYR cc_start: 0.8157 (t80) cc_final: 0.7936 (t80) REVERT: D 59 MET cc_start: 0.9512 (tmm) cc_final: 0.9268 (tmm) REVERT: D 106 LEU cc_start: 0.9391 (mt) cc_final: 0.9138 (mt) REVERT: E 74 ILE cc_start: 0.9677 (pt) cc_final: 0.9320 (pt) REVERT: E 77 ASP cc_start: 0.9387 (m-30) cc_final: 0.9159 (m-30) REVERT: E 90 MET cc_start: 0.9566 (mmp) cc_final: 0.9298 (mmp) REVERT: E 120 MET cc_start: 0.9217 (tpt) cc_final: 0.8863 (mmm) REVERT: F 22 LEU cc_start: 0.8808 (mp) cc_final: 0.8562 (pt) REVERT: F 59 LYS cc_start: 0.9685 (tmtt) cc_final: 0.9420 (tmtt) REVERT: G 36 LYS cc_start: 0.9439 (mmmt) cc_final: 0.8952 (mmtm) REVERT: G 51 LEU cc_start: 0.9757 (tp) cc_final: 0.9512 (tp) REVERT: G 56 GLU cc_start: 0.8487 (tt0) cc_final: 0.7870 (mt-10) REVERT: G 64 GLU cc_start: 0.8982 (tp30) cc_final: 0.8351 (tp30) REVERT: G 95 LYS cc_start: 0.9551 (tptp) cc_final: 0.9330 (tppt) REVERT: H 59 MET cc_start: 0.9118 (tpp) cc_final: 0.8670 (tpp) REVERT: H 82 HIS cc_start: 0.8755 (m90) cc_final: 0.8349 (m-70) REVERT: H 95 GLN cc_start: 0.9493 (tt0) cc_final: 0.9071 (tm-30) REVERT: H 106 LEU cc_start: 0.9452 (tp) cc_final: 0.9001 (tp) REVERT: I 424 MET cc_start: 0.6166 (ppp) cc_final: 0.5784 (ppp) REVERT: I 886 MET cc_start: 0.7921 (mtt) cc_final: 0.7278 (mmt) REVERT: I 960 GLU cc_start: 0.5866 (tt0) cc_final: 0.5033 (mm-30) REVERT: I 1011 MET cc_start: 0.5483 (mmt) cc_final: 0.5222 (mmt) REVERT: I 1109 MET cc_start: 0.8805 (tpp) cc_final: 0.8291 (tpt) REVERT: I 1112 MET cc_start: 0.9320 (mmt) cc_final: 0.9028 (mmm) REVERT: I 1154 LEU cc_start: 0.9230 (mp) cc_final: 0.8853 (mp) REVERT: I 1233 MET cc_start: 0.2650 (tpp) cc_final: 0.2211 (tpp) REVERT: J 240 TYR cc_start: 0.9106 (t80) cc_final: 0.8756 (p90) REVERT: K 376 MET cc_start: 0.0106 (ptt) cc_final: -0.0842 (ppp) REVERT: L 287 LEU cc_start: 0.8829 (mm) cc_final: 0.8490 (mm) REVERT: L 372 MET cc_start: 0.9536 (mtt) cc_final: 0.9205 (mpp) REVERT: M 166 LEU cc_start: 0.9500 (mm) cc_final: 0.8997 (tt) REVERT: M 208 MET cc_start: 0.8801 (mtm) cc_final: 0.8593 (mtt) REVERT: M 213 MET cc_start: 0.8743 (tpp) cc_final: 0.8481 (tpp) REVERT: M 217 MET cc_start: 0.9621 (mtp) cc_final: 0.9329 (mtp) REVERT: M 361 MET cc_start: 0.8351 (mmp) cc_final: 0.8002 (mmm) REVERT: M 366 ARG cc_start: 0.9680 (mpp80) cc_final: 0.8839 (mtt-85) REVERT: O 469 MET cc_start: 0.8416 (mmt) cc_final: 0.7756 (mmm) REVERT: O 498 MET cc_start: 0.7942 (mmp) cc_final: 0.6992 (mtp) REVERT: O 523 MET cc_start: 0.9141 (tpt) cc_final: 0.8908 (tpt) REVERT: O 900 GLU cc_start: 0.9501 (OUTLIER) cc_final: 0.9122 (pm20) REVERT: P 149 ASP cc_start: 0.9283 (t70) cc_final: 0.8743 (t0) REVERT: P 161 ILE cc_start: 0.9590 (mt) cc_final: 0.9381 (mt) REVERT: P 164 LYS cc_start: 0.9433 (mmmt) cc_final: 0.9097 (tmtt) REVERT: P 366 MET cc_start: 0.8049 (mmt) cc_final: 0.7610 (mmp) REVERT: P 441 MET cc_start: 0.9095 (mpp) cc_final: 0.8672 (mpp) REVERT: P 474 GLU cc_start: 0.7565 (tm-30) cc_final: 0.7329 (tm-30) REVERT: Q 205 GLU cc_start: 0.5238 (tp30) cc_final: 0.4709 (pp20) REVERT: R 196 VAL cc_start: 0.8047 (t) cc_final: 0.7805 (t) REVERT: R 216 ARG cc_start: 0.9594 (tmt170) cc_final: 0.9230 (mmt-90) REVERT: R 228 LEU cc_start: 0.7332 (pp) cc_final: 0.7015 (mp) REVERT: S 572 MET cc_start: -0.1626 (mmm) cc_final: -0.2170 (mtp) REVERT: U 1521 TYR cc_start: 0.8219 (t80) cc_final: 0.7571 (m-80) outliers start: 3 outliers final: 0 residues processed: 427 average time/residue: 0.2627 time to fit residues: 183.8802 Evaluate side-chains 327 residues out of total 3874 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 326 time to evaluate : 1.527 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 479 random chunks: chunk 355 optimal weight: 4.9990 chunk 40 optimal weight: 0.8980 chunk 298 optimal weight: 0.9990 chunk 243 optimal weight: 3.9990 chunk 277 optimal weight: 0.0010 chunk 138 optimal weight: 8.9990 chunk 475 optimal weight: 20.0000 chunk 280 optimal weight: 7.9990 chunk 395 optimal weight: 2.9990 chunk 430 optimal weight: 9.9990 chunk 305 optimal weight: 0.7980 overall best weight: 1.1390 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 84 ASN I 519 ASN ** I 915 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 92 ASN ** J 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 296 ASN ** K 205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 140 HIS ** M 318 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 439 HIS ** O 436 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 135 GLN P 145 GLN ** P 437 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 252 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3891 r_free = 0.3891 target = 0.069387 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3492 r_free = 0.3492 target = 0.049548 restraints weight = 442032.743| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 53)----------------| | r_work = 0.3522 r_free = 0.3522 target = 0.050704 restraints weight = 241362.813| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 52)----------------| | r_work = 0.3542 r_free = 0.3542 target = 0.051553 restraints weight = 159548.745| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 49)----------------| | r_work = 0.3555 r_free = 0.3555 target = 0.052078 restraints weight = 121962.592| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3560 r_free = 0.3560 target = 0.052294 restraints weight = 104006.361| |-----------------------------------------------------------------------------| r_work (final): 0.3440 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3440 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3440 r_free = 0.3440 target_work(ls_wunit_k1) = 0.046 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3440 r_free = 0.3440 target_work(ls_wunit_k1) = 0.046 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3440 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7714 moved from start: 0.3128 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 44567 Z= 0.135 Angle : 0.609 10.968 61592 Z= 0.329 Chirality : 0.040 0.313 6923 Planarity : 0.004 0.049 6764 Dihedral : 22.867 160.827 8596 Min Nonbonded Distance : 2.222 Molprobity Statistics. All-atom Clashscore : 9.59 Ramachandran Plot: Outliers : 0.07 % Allowed : 6.48 % Favored : 93.45 % Rotamer: Outliers : 0.03 % Allowed : 3.04 % Favored : 96.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.50 (0.13), residues: 4321 helix: 0.78 (0.10), residues: 2491 sheet: -1.98 (0.35), residues: 183 loop : -1.88 (0.15), residues: 1647 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG K 248 TYR 0.024 0.001 TYR R 225 PHE 0.026 0.001 PHE K 160 TRP 0.021 0.001 TRP M 321 HIS 0.010 0.001 HIS Q 200 Details of bonding type rmsd/Z covalent geometry : bond 0.00266 / 0.14 (44565) covalent geometry : angle 0.60945 / 0.33 (61592) hydrogen bonds : bond 0.04178 / 2.81 ( 2339) hydrogen bonds : angle 4.39861 / 3.11 ( 6495) Misc. bond : bond 0.00389 / 0.20 ( 2) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8642 Ramachandran restraints generated. 4321 Oldfield, 0 Emsley, 4321 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8642 Ramachandran restraints generated. 4321 Oldfield, 0 Emsley, 4321 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 420 residues out of total 3874 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 419 time to evaluate : 1.431 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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: A 92 LEU cc_start: 0.9806 (mm) cc_final: 0.9588 (mm) REVERT: B 84 MET cc_start: 0.9315 (mmm) cc_final: 0.8554 (mmm) REVERT: C 36 LYS cc_start: 0.9324 (mppt) cc_final: 0.9037 (mmtm) REVERT: C 64 GLU cc_start: 0.9363 (tt0) cc_final: 0.8851 (tm-30) REVERT: D 59 MET cc_start: 0.9502 (tmm) cc_final: 0.9278 (tmm) REVERT: D 68 ASP cc_start: 0.9340 (t70) cc_final: 0.8514 (t0) REVERT: D 106 LEU cc_start: 0.9372 (mt) cc_final: 0.9124 (mt) REVERT: E 60 LEU cc_start: 0.9348 (tp) cc_final: 0.9066 (tp) REVERT: E 74 ILE cc_start: 0.9683 (pt) cc_final: 0.9252 (pt) REVERT: E 77 ASP cc_start: 0.9403 (m-30) cc_final: 0.9176 (m-30) REVERT: E 90 MET cc_start: 0.9577 (mmp) cc_final: 0.9314 (mmm) REVERT: F 22 LEU cc_start: 0.8804 (mp) cc_final: 0.8571 (pt) REVERT: F 59 LYS cc_start: 0.9806 (tttm) cc_final: 0.9001 (tptp) REVERT: F 60 VAL cc_start: 0.9663 (t) cc_final: 0.9449 (t) REVERT: F 63 GLU cc_start: 0.9443 (pt0) cc_final: 0.9163 (pt0) REVERT: G 36 LYS cc_start: 0.9406 (mmmt) cc_final: 0.8768 (mmtm) REVERT: G 51 LEU cc_start: 0.9755 (tp) cc_final: 0.9536 (tp) REVERT: G 56 GLU cc_start: 0.8494 (tt0) cc_final: 0.7828 (mt-10) REVERT: G 64 GLU cc_start: 0.9003 (tp30) cc_final: 0.8354 (tp30) REVERT: G 95 LYS cc_start: 0.9570 (tptp) cc_final: 0.9187 (tppt) REVERT: H 59 MET cc_start: 0.9144 (tpp) cc_final: 0.8689 (tpp) REVERT: H 82 HIS cc_start: 0.8755 (m90) cc_final: 0.8303 (m90) REVERT: H 95 GLN cc_start: 0.9510 (tt0) cc_final: 0.9120 (tm-30) REVERT: H 99 ARG cc_start: 0.9040 (tpp80) cc_final: 0.8259 (tpp80) REVERT: I 424 MET cc_start: 0.6217 (ppp) cc_final: 0.5738 (ppp) REVERT: I 886 MET cc_start: 0.8007 (mtt) cc_final: 0.7316 (mmt) REVERT: I 960 GLU cc_start: 0.6023 (tt0) cc_final: 0.5237 (mm-30) REVERT: I 1011 MET cc_start: 0.5730 (mmt) cc_final: 0.5433 (mmt) REVERT: I 1109 MET cc_start: 0.8824 (tpp) cc_final: 0.8304 (tpt) REVERT: I 1112 MET cc_start: 0.9350 (mmt) cc_final: 0.9055 (mmm) REVERT: I 1154 LEU cc_start: 0.9363 (mp) cc_final: 0.9035 (mp) REVERT: I 1233 MET cc_start: 0.2899 (tpp) cc_final: 0.2294 (tpp) REVERT: J 240 TYR cc_start: 0.9053 (t80) cc_final: 0.8704 (p90) REVERT: K 376 MET cc_start: 0.0598 (ptt) cc_final: -0.0375 (ppp) REVERT: L 78 PHE cc_start: 0.7859 (m-80) cc_final: 0.7617 (m-80) REVERT: L 191 MET cc_start: 0.8785 (tpp) cc_final: 0.8578 (tpp) REVERT: L 287 LEU cc_start: 0.8837 (mm) cc_final: 0.8470 (mm) REVERT: L 372 MET cc_start: 0.9565 (mtt) cc_final: 0.9135 (mtt) REVERT: M 166 LEU cc_start: 0.9423 (mm) cc_final: 0.8879 (tt) REVERT: M 208 MET cc_start: 0.8843 (mtm) cc_final: 0.8594 (mtt) REVERT: M 217 MET cc_start: 0.9604 (mtp) cc_final: 0.9334 (mtp) REVERT: M 361 MET cc_start: 0.8479 (mmp) cc_final: 0.8177 (mmm) REVERT: M 366 ARG cc_start: 0.9635 (mpp80) cc_final: 0.9122 (mtt-85) REVERT: N 896 MET cc_start: 0.9310 (mmp) cc_final: 0.9079 (mmm) REVERT: O 469 MET cc_start: 0.8368 (mmt) cc_final: 0.7760 (mmt) REVERT: O 498 MET cc_start: 0.8000 (mmp) cc_final: 0.7258 (mtp) REVERT: P 149 ASP cc_start: 0.8942 (t70) cc_final: 0.8635 (t0) REVERT: P 164 LYS cc_start: 0.9443 (mmmt) cc_final: 0.9114 (tmtt) REVERT: P 366 MET cc_start: 0.8186 (mmt) cc_final: 0.7770 (mmp) REVERT: P 441 MET cc_start: 0.9015 (mpp) cc_final: 0.8731 (mpp) REVERT: P 474 GLU cc_start: 0.7569 (tm-30) cc_final: 0.7337 (tm-30) REVERT: P 494 TYR cc_start: 0.9337 (t80) cc_final: 0.8924 (t80) REVERT: Q 205 GLU cc_start: 0.5197 (tp30) cc_final: 0.4707 (pp20) REVERT: R 216 ARG cc_start: 0.9602 (tmt170) cc_final: 0.9227 (mmt-90) REVERT: R 228 LEU cc_start: 0.7680 (pp) cc_final: 0.7289 (mp) REVERT: S 176 MET cc_start: 0.3421 (ttp) cc_final: 0.3126 (ttp) REVERT: S 572 MET cc_start: -0.1616 (mmm) cc_final: -0.2133 (mtp) REVERT: U 1521 TYR cc_start: 0.8159 (t80) cc_final: 0.7560 (m-80) outliers start: 1 outliers final: 0 residues processed: 420 average time/residue: 0.2671 time to fit residues: 184.4126 Evaluate side-chains 325 residues out of total 3874 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 325 time to evaluate : 1.556 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 479 random chunks: chunk 170 optimal weight: 5.9990 chunk 354 optimal weight: 20.0000 chunk 149 optimal weight: 30.0000 chunk 187 optimal weight: 0.0970 chunk 95 optimal weight: 20.0000 chunk 35 optimal weight: 3.9990 chunk 45 optimal weight: 3.9990 chunk 73 optimal weight: 30.0000 chunk 461 optimal weight: 50.0000 chunk 50 optimal weight: 2.9990 chunk 326 optimal weight: 2.9990 overall best weight: 2.8186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 375 GLN ** I 915 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I1253 HIS ** J 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 296 ASN ** K 205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 140 HIS M 318 GLN M 380 ASN N 422 HIS N 439 HIS ** P 345 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 437 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 501 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 504 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 252 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3854 r_free = 0.3854 target = 0.067680 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3445 r_free = 0.3445 target = 0.047821 restraints weight = 446641.505| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.3472 r_free = 0.3472 target = 0.048947 restraints weight = 243966.988| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 55)----------------| | r_work = 0.3491 r_free = 0.3491 target = 0.049737 restraints weight = 162694.215| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 53)----------------| | r_work = 0.3503 r_free = 0.3503 target = 0.050273 restraints weight = 125260.829| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 53)----------------| | r_work = 0.3509 r_free = 0.3509 target = 0.050607 restraints weight = 107073.376| |-----------------------------------------------------------------------------| r_work (final): 0.3388 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3389 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3389 r_free = 0.3389 target_work(ls_wunit_k1) = 0.045 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3389 r_free = 0.3389 target_work(ls_wunit_k1) = 0.045 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3389 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7780 moved from start: 0.3576 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.109 44567 Z= 0.166 Angle : 0.628 10.271 61592 Z= 0.340 Chirality : 0.040 0.312 6923 Planarity : 0.005 0.084 6764 Dihedral : 23.027 157.858 8596 Min Nonbonded Distance : 2.213 Molprobity Statistics. All-atom Clashscore : 11.15 Ramachandran Plot: Outliers : 0.07 % Allowed : 6.39 % Favored : 93.54 % Rotamer: Outliers : 0.05 % Allowed : 3.04 % Favored : 96.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.41 (0.13), residues: 4321 helix: 0.82 (0.10), residues: 2484 sheet: -1.86 (0.35), residues: 186 loop : -1.78 (0.15), residues: 1651 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG C 99 TYR 0.022 0.002 TYR N 922 PHE 0.020 0.002 PHE O 951 TRP 0.046 0.002 TRP O 620 HIS 0.013 0.001 HIS I1253 Details of bonding type rmsd/Z covalent geometry : bond 0.00329 / 0.17 (44565) covalent geometry : angle 0.62846 / 0.34 (61592) hydrogen bonds : bond 0.04924 / 3.28 ( 2339) hydrogen bonds : angle 4.40916 / 3.13 ( 6495) Misc. bond : bond 0.00050 / 0.03 ( 2) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8642 Ramachandran restraints generated. 4321 Oldfield, 0 Emsley, 4321 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8642 Ramachandran restraints generated. 4321 Oldfield, 0 Emsley, 4321 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 409 residues out of total 3874 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 407 time to evaluate : 1.555 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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: A 92 LEU cc_start: 0.9831 (mm) cc_final: 0.9623 (mm) REVERT: A 105 GLU cc_start: 0.8908 (mp0) cc_final: 0.8581 (mm-30) REVERT: A 125 GLN cc_start: 0.9718 (mt0) cc_final: 0.9466 (mp10) REVERT: B 84 MET cc_start: 0.9333 (mmm) cc_final: 0.8532 (mmm) REVERT: C 64 GLU cc_start: 0.9424 (tt0) cc_final: 0.8884 (tm-30) REVERT: D 59 MET cc_start: 0.9545 (tmm) cc_final: 0.9278 (tmm) REVERT: D 106 LEU cc_start: 0.9362 (mt) cc_final: 0.9068 (mt) REVERT: E 74 ILE cc_start: 0.9666 (pt) cc_final: 0.9328 (pt) REVERT: E 90 MET cc_start: 0.9583 (mmp) cc_final: 0.9329 (mmm) REVERT: F 22 LEU cc_start: 0.8833 (mp) cc_final: 0.8596 (pt) REVERT: F 59 LYS cc_start: 0.9813 (tttm) cc_final: 0.9396 (ttmm) REVERT: F 60 VAL cc_start: 0.9648 (t) cc_final: 0.9425 (t) REVERT: G 36 LYS cc_start: 0.9495 (mmmt) cc_final: 0.8904 (mmtm) REVERT: G 51 LEU cc_start: 0.9758 (tp) cc_final: 0.9511 (tp) REVERT: G 56 GLU cc_start: 0.8464 (tt0) cc_final: 0.7865 (mt-10) REVERT: G 64 GLU cc_start: 0.9026 (tp30) cc_final: 0.8378 (tp30) REVERT: G 95 LYS cc_start: 0.9589 (tptp) cc_final: 0.9186 (tppt) REVERT: H 59 MET cc_start: 0.9120 (tpp) cc_final: 0.8652 (tpp) REVERT: H 82 HIS cc_start: 0.8785 (m90) cc_final: 0.8380 (m90) REVERT: H 95 GLN cc_start: 0.9493 (tt0) cc_final: 0.9124 (tm-30) REVERT: H 99 ARG cc_start: 0.9085 (tpp80) cc_final: 0.8217 (tpp80) REVERT: I 424 MET cc_start: 0.6382 (ppp) cc_final: 0.5575 (ppp) REVERT: I 886 MET cc_start: 0.8160 (mtt) cc_final: 0.7414 (mmt) REVERT: I 1011 MET cc_start: 0.5908 (mmt) cc_final: 0.5607 (mmt) REVERT: I 1109 MET cc_start: 0.8928 (tpp) cc_final: 0.8594 (tpp) REVERT: I 1112 MET cc_start: 0.9359 (mmt) cc_final: 0.9061 (mmm) REVERT: I 1154 LEU cc_start: 0.9305 (mp) cc_final: 0.9091 (mp) REVERT: I 1233 MET cc_start: 0.3063 (tpp) cc_final: 0.2531 (tpp) REVERT: J 240 TYR cc_start: 0.9047 (t80) cc_final: 0.8667 (p90) REVERT: K 376 MET cc_start: 0.0895 (ptt) cc_final: 0.0081 (ppp) REVERT: L 287 LEU cc_start: 0.8936 (mm) cc_final: 0.8691 (mm) REVERT: L 372 MET cc_start: 0.9591 (mtt) cc_final: 0.9201 (mtt) REVERT: L 445 MET cc_start: 0.9075 (mpp) cc_final: 0.8732 (mpp) REVERT: M 166 LEU cc_start: 0.9430 (mm) cc_final: 0.8875 (tt) REVERT: M 361 MET cc_start: 0.8609 (mmp) cc_final: 0.8307 (mmm) REVERT: N 896 MET cc_start: 0.9338 (mmp) cc_final: 0.9102 (mmm) REVERT: N 936 MET cc_start: 0.8969 (mmp) cc_final: 0.8704 (tmm) REVERT: O 469 MET cc_start: 0.8297 (mmt) cc_final: 0.7795 (mmt) REVERT: O 498 MET cc_start: 0.7835 (mmp) cc_final: 0.7034 (mtp) REVERT: O 523 MET cc_start: 0.8846 (tpt) cc_final: 0.8272 (tpt) REVERT: P 149 ASP cc_start: 0.9053 (t70) cc_final: 0.8824 (t0) REVERT: P 161 ILE cc_start: 0.9479 (tt) cc_final: 0.8976 (pt) REVERT: P 164 LYS cc_start: 0.9500 (mmmt) cc_final: 0.9192 (tmtt) REVERT: P 366 MET cc_start: 0.8331 (mmt) cc_final: 0.7952 (mmp) REVERT: P 441 MET cc_start: 0.9059 (mpp) cc_final: 0.8765 (mpp) REVERT: P 494 TYR cc_start: 0.9315 (t80) cc_final: 0.8930 (t80) REVERT: Q 205 GLU cc_start: 0.5259 (tp30) cc_final: 0.4841 (pp20) REVERT: R 196 VAL cc_start: 0.7818 (t) cc_final: 0.7530 (t) REVERT: R 216 ARG cc_start: 0.9622 (tmt170) cc_final: 0.9269 (mmt-90) REVERT: R 219 MET cc_start: 0.9295 (mmp) cc_final: 0.9021 (mmm) REVERT: R 228 LEU cc_start: 0.7662 (pp) cc_final: 0.7283 (mp) REVERT: S 572 MET cc_start: -0.1609 (mmm) cc_final: -0.2136 (mtt) REVERT: U 1521 TYR cc_start: 0.8218 (t80) cc_final: 0.7603 (m-80) outliers start: 2 outliers final: 1 residues processed: 408 average time/residue: 0.2560 time to fit residues: 173.0053 Evaluate side-chains 320 residues out of total 3874 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 319 time to evaluate : 1.546 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 479 random chunks: chunk 141 optimal weight: 10.0000 chunk 186 optimal weight: 0.6980 chunk 193 optimal weight: 6.9990 chunk 332 optimal weight: 50.0000 chunk 445 optimal weight: 50.0000 chunk 37 optimal weight: 10.0000 chunk 81 optimal weight: 4.9990 chunk 209 optimal weight: 7.9990 chunk 430 optimal weight: 0.2980 chunk 103 optimal weight: 8.9990 chunk 412 optimal weight: 10.0000 overall best weight: 4.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 915 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 296 ASN K 110 HIS ** K 205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 313 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 144 GLN L1796 ASN M 140 HIS N 422 HIS N 439 HIS ** P 308 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 345 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 501 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 504 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 247 GLN ** Q 252 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3813 r_free = 0.3813 target = 0.065974 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.046122 restraints weight = 452812.007| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.3422 r_free = 0.3422 target = 0.047158 restraints weight = 248216.870| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 53)----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.047905 restraints weight = 166920.331| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3446 r_free = 0.3446 target = 0.048123 restraints weight = 130066.075| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 53)----------------| | r_work = 0.3456 r_free = 0.3456 target = 0.048639 restraints weight = 115887.408| |-----------------------------------------------------------------------------| r_work (final): 0.3332 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3332 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3332 r_free = 0.3332 target_work(ls_wunit_k1) = 0.043 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3332 r_free = 0.3332 target_work(ls_wunit_k1) = 0.043 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3332 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7845 moved from start: 0.4041 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 44567 Z= 0.201 Angle : 0.650 11.276 61592 Z= 0.352 Chirality : 0.041 0.311 6923 Planarity : 0.005 0.064 6764 Dihedral : 23.243 157.129 8596 Min Nonbonded Distance : 2.231 Molprobity Statistics. All-atom Clashscore : 13.03 Ramachandran Plot: Outliers : 0.07 % Allowed : 6.53 % Favored : 93.40 % Rotamer: Outliers : 0.05 % Allowed : 1.93 % Favored : 98.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.46 (0.13), residues: 4321 helix: 0.76 (0.10), residues: 2491 sheet: -1.82 (0.36), residues: 186 loop : -1.79 (0.15), residues: 1644 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG I 414 TYR 0.032 0.002 TYR D 83 PHE 0.022 0.002 PHE G 25 TRP 0.041 0.002 TRP O 620 HIS 0.012 0.001 HIS O 905 Details of bonding type rmsd/Z covalent geometry : bond 0.00387 / 0.20 (44565) covalent geometry : angle 0.64956 / 0.35 (61592) hydrogen bonds : bond 0.05359 / 3.58 ( 2339) hydrogen bonds : angle 4.53842 / 3.22 ( 6495) Misc. bond : bond 0.00051 / 0.02 ( 2) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8642 Ramachandran restraints generated. 4321 Oldfield, 0 Emsley, 4321 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8642 Ramachandran restraints generated. 4321 Oldfield, 0 Emsley, 4321 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 394 residues out of total 3874 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 392 time to evaluate : 1.356 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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: A 92 LEU cc_start: 0.9842 (mm) cc_final: 0.9621 (mm) REVERT: B 63 GLU cc_start: 0.9381 (mt-10) cc_final: 0.9023 (pt0) REVERT: B 84 MET cc_start: 0.9338 (mmm) cc_final: 0.8665 (mmm) REVERT: C 23 LEU cc_start: 0.8855 (mt) cc_final: 0.8648 (mt) REVERT: C 36 LYS cc_start: 0.9647 (mptt) cc_final: 0.9410 (mmtm) REVERT: C 64 GLU cc_start: 0.9461 (tt0) cc_final: 0.8827 (tm-30) REVERT: D 59 MET cc_start: 0.9546 (tmm) cc_final: 0.9304 (tmm) REVERT: D 106 LEU cc_start: 0.9417 (mt) cc_final: 0.9109 (mt) REVERT: E 74 ILE cc_start: 0.9672 (pt) cc_final: 0.9378 (pt) REVERT: E 90 MET cc_start: 0.9537 (mmp) cc_final: 0.9332 (mmm) REVERT: F 22 LEU cc_start: 0.8866 (mp) cc_final: 0.8625 (pt) REVERT: F 58 LEU cc_start: 0.9706 (tt) cc_final: 0.9428 (mm) REVERT: F 59 LYS cc_start: 0.9822 (tttm) cc_final: 0.9351 (ttmm) REVERT: G 36 LYS cc_start: 0.9569 (mmmt) cc_final: 0.9011 (mmtm) REVERT: G 51 LEU cc_start: 0.9759 (tp) cc_final: 0.9529 (tp) REVERT: G 56 GLU cc_start: 0.8805 (tt0) cc_final: 0.8407 (mt-10) REVERT: G 64 GLU cc_start: 0.9049 (tp30) cc_final: 0.8371 (tp30) REVERT: G 95 LYS cc_start: 0.9616 (tptp) cc_final: 0.9236 (tppt) REVERT: H 59 MET cc_start: 0.9034 (tpp) cc_final: 0.8691 (tpp) REVERT: H 82 HIS cc_start: 0.8841 (m90) cc_final: 0.8389 (m-70) REVERT: H 95 GLN cc_start: 0.9499 (tt0) cc_final: 0.8944 (pt0) REVERT: I 424 MET cc_start: 0.6577 (ppp) cc_final: 0.5738 (ppp) REVERT: I 527 MET cc_start: 0.8044 (tpt) cc_final: 0.7624 (mtt) REVERT: I 886 MET cc_start: 0.8228 (mtt) cc_final: 0.7411 (mmt) REVERT: I 960 GLU cc_start: 0.6206 (tt0) cc_final: 0.5326 (mm-30) REVERT: I 1011 MET cc_start: 0.5934 (mmt) cc_final: 0.5669 (mmt) REVERT: I 1109 MET cc_start: 0.8973 (tpp) cc_final: 0.8535 (tpt) REVERT: I 1112 MET cc_start: 0.9316 (mmt) cc_final: 0.8986 (mmm) REVERT: I 1154 LEU cc_start: 0.9320 (mp) cc_final: 0.8990 (mp) REVERT: I 1233 MET cc_start: 0.3529 (tpp) cc_final: 0.2923 (tpp) REVERT: J 132 MET cc_start: -0.3088 (ttp) cc_final: -0.3293 (ptt) REVERT: J 240 TYR cc_start: 0.9068 (t80) cc_final: 0.8716 (p90) REVERT: K 114 GLU cc_start: 0.8251 (tp30) cc_final: 0.8002 (pm20) REVERT: K 376 MET cc_start: 0.1678 (ptt) cc_final: 0.1026 (ppp) REVERT: L 78 PHE cc_start: 0.7768 (m-80) cc_final: 0.7521 (m-80) REVERT: L 191 MET cc_start: 0.8935 (tpp) cc_final: 0.8709 (tpp) REVERT: L 287 LEU cc_start: 0.9101 (mm) cc_final: 0.8794 (mm) REVERT: L 372 MET cc_start: 0.9592 (mtt) cc_final: 0.9202 (mtt) REVERT: L 393 GLU cc_start: 0.9457 (tm-30) cc_final: 0.9249 (pt0) REVERT: L 445 MET cc_start: 0.9149 (mpp) cc_final: 0.8811 (mpp) REVERT: L 470 HIS cc_start: 0.8384 (m-70) cc_final: 0.8090 (t-90) REVERT: M 166 LEU cc_start: 0.9484 (mm) cc_final: 0.8939 (tt) REVERT: M 217 MET cc_start: 0.9588 (mtp) cc_final: 0.9385 (mtp) REVERT: M 361 MET cc_start: 0.8675 (mmp) cc_final: 0.8364 (mmm) REVERT: M 366 ARG cc_start: 0.9674 (mpp80) cc_final: 0.9465 (mtm-85) REVERT: N 462 TYR cc_start: 0.9071 (t80) cc_final: 0.8838 (t80) REVERT: N 498 MET cc_start: 0.9293 (mpp) cc_final: 0.9077 (mpp) REVERT: N 936 MET cc_start: 0.9041 (mmp) cc_final: 0.8780 (tmm) REVERT: O 469 MET cc_start: 0.8311 (mmt) cc_final: 0.7876 (mmm) REVERT: O 523 MET cc_start: 0.8775 (tpt) cc_final: 0.8272 (tpt) REVERT: P 149 ASP cc_start: 0.9024 (t70) cc_final: 0.8750 (t0) REVERT: P 161 ILE cc_start: 0.9547 (tt) cc_final: 0.8718 (pt) REVERT: P 162 MET cc_start: 0.9160 (mmm) cc_final: 0.8533 (mmm) REVERT: P 164 LYS cc_start: 0.9479 (mmmt) cc_final: 0.9137 (tmtt) REVERT: P 366 MET cc_start: 0.8384 (mmt) cc_final: 0.8029 (mmm) REVERT: P 441 MET cc_start: 0.9132 (mpp) cc_final: 0.8874 (mpp) REVERT: P 494 TYR cc_start: 0.9349 (t80) cc_final: 0.8980 (t80) REVERT: Q 205 GLU cc_start: 0.5278 (tp30) cc_final: 0.4856 (pp20) REVERT: R 196 VAL cc_start: 0.7582 (t) cc_final: 0.7237 (t) REVERT: R 216 ARG cc_start: 0.9640 (tmt170) cc_final: 0.9323 (mmt-90) REVERT: R 228 LEU cc_start: 0.7898 (pp) cc_final: 0.7593 (mp) REVERT: S 572 MET cc_start: -0.1581 (mmm) cc_final: -0.2095 (mtt) REVERT: U 1521 TYR cc_start: 0.8300 (t80) cc_final: 0.7773 (m-80) outliers start: 2 outliers final: 1 residues processed: 394 average time/residue: 0.2540 time to fit residues: 165.8418 Evaluate side-chains 311 residues out of total 3874 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 310 time to evaluate : 1.503 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 479 random chunks: chunk 387 optimal weight: 0.1980 chunk 378 optimal weight: 9.9990 chunk 37 optimal weight: 9.9990 chunk 219 optimal weight: 6.9990 chunk 374 optimal weight: 0.0000 chunk 340 optimal weight: 2.9990 chunk 420 optimal weight: 8.9990 chunk 289 optimal weight: 10.0000 chunk 240 optimal weight: 3.9990 chunk 91 optimal weight: 10.0000 chunk 350 optimal weight: 10.0000 overall best weight: 2.8390 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 25 ASN ** C 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 788 GLN ** I 915 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 73 HIS ** J 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 173 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 296 ASN ** K 205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 313 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 140 HIS N 422 HIS N 439 HIS ** O 436 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 308 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 345 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 403 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 437 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 500 GLN ** Q 252 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S 592 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3809 r_free = 0.3809 target = 0.065956 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.046110 restraints weight = 449207.799| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.047217 restraints weight = 244721.245| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 52)----------------| | r_work = 0.3437 r_free = 0.3437 target = 0.047947 restraints weight = 164404.063| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 52)----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.048460 restraints weight = 127994.211| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 54)----------------| | r_work = 0.3456 r_free = 0.3456 target = 0.048771 restraints weight = 110062.885| |-----------------------------------------------------------------------------| r_work (final): 0.3330 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3331 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3331 r_free = 0.3331 target_work(ls_wunit_k1) = 0.043 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3331 r_free = 0.3331 target_work(ls_wunit_k1) = 0.043 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3331 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7850 moved from start: 0.4360 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 44567 Z= 0.157 Angle : 0.632 13.035 61592 Z= 0.341 Chirality : 0.041 0.319 6923 Planarity : 0.005 0.084 6764 Dihedral : 23.348 155.494 8596 Min Nonbonded Distance : 2.257 Molprobity Statistics. All-atom Clashscore : 12.01 Ramachandran Plot: Outliers : 0.07 % Allowed : 6.50 % Favored : 93.43 % Rotamer: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.36 (0.13), residues: 4321 helix: 0.84 (0.10), residues: 2486 sheet: -1.67 (0.35), residues: 209 loop : -1.72 (0.16), residues: 1626 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG K 248 TYR 0.050 0.002 TYR D 83 PHE 0.027 0.002 PHE K 289 TRP 0.029 0.001 TRP P 207 HIS 0.009 0.001 HIS N 905 Details of bonding type rmsd/Z covalent geometry : bond 0.00305 / 0.16 (44565) covalent geometry : angle 0.63224 / 0.34 (61592) hydrogen bonds : bond 0.04398 / 2.93 ( 2339) hydrogen bonds : angle 4.46020 / 3.17 ( 6495) Misc. bond : bond 0.00052 / 0.03 ( 2) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8642 Ramachandran restraints generated. 4321 Oldfield, 0 Emsley, 4321 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8642 Ramachandran restraints generated. 4321 Oldfield, 0 Emsley, 4321 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 399 residues out of total 3874 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 399 time to evaluate : 1.523 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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: A 92 LEU cc_start: 0.9844 (mm) cc_final: 0.9635 (mm) REVERT: B 63 GLU cc_start: 0.9355 (mt-10) cc_final: 0.9039 (pt0) REVERT: B 84 MET cc_start: 0.9321 (mmm) cc_final: 0.8764 (mmp) REVERT: C 36 LYS cc_start: 0.9631 (mptt) cc_final: 0.9379 (mmtm) REVERT: C 64 GLU cc_start: 0.9454 (tt0) cc_final: 0.8823 (tm-30) REVERT: D 59 MET cc_start: 0.9590 (tmm) cc_final: 0.9345 (tmm) REVERT: D 106 LEU cc_start: 0.9442 (mt) cc_final: 0.9113 (mt) REVERT: E 70 LEU cc_start: 0.9862 (tt) cc_final: 0.9626 (tp) REVERT: E 74 ILE cc_start: 0.9665 (pt) cc_final: 0.9339 (pt) REVERT: E 90 MET cc_start: 0.9560 (mmp) cc_final: 0.9284 (mmp) REVERT: E 97 GLU cc_start: 0.9299 (mt-10) cc_final: 0.8854 (mt-10) REVERT: F 22 LEU cc_start: 0.8896 (mp) cc_final: 0.8657 (pt) REVERT: F 58 LEU cc_start: 0.9685 (tt) cc_final: 0.9428 (mm) REVERT: F 60 VAL cc_start: 0.9649 (t) cc_final: 0.9390 (t) REVERT: F 85 ASP cc_start: 0.8867 (m-30) cc_final: 0.8660 (p0) REVERT: F 91 LYS cc_start: 0.9617 (ptmm) cc_final: 0.9225 (pttp) REVERT: G 51 LEU cc_start: 0.9763 (tp) cc_final: 0.9532 (tp) REVERT: G 56 GLU cc_start: 0.8752 (tt0) cc_final: 0.8260 (mt-10) REVERT: G 64 GLU cc_start: 0.9044 (tp30) cc_final: 0.8356 (tp30) REVERT: G 95 LYS cc_start: 0.9636 (tptp) cc_final: 0.9277 (tppt) REVERT: H 59 MET cc_start: 0.9020 (tpp) cc_final: 0.8616 (tpp) REVERT: H 82 HIS cc_start: 0.8822 (m90) cc_final: 0.8310 (m90) REVERT: H 99 ARG cc_start: 0.8963 (mtm-85) cc_final: 0.8740 (mtm110) REVERT: I 424 MET cc_start: 0.6506 (ppp) cc_final: 0.5633 (ppp) REVERT: I 527 MET cc_start: 0.8022 (tpt) cc_final: 0.7614 (mtt) REVERT: I 886 MET cc_start: 0.8270 (mtt) cc_final: 0.7472 (mmt) REVERT: I 960 GLU cc_start: 0.6167 (tt0) cc_final: 0.5245 (mm-30) REVERT: I 1000 MET cc_start: 0.9162 (ptm) cc_final: 0.8826 (ptm) REVERT: I 1011 MET cc_start: 0.6064 (mmt) cc_final: 0.5851 (mmt) REVERT: I 1109 MET cc_start: 0.9006 (tpp) cc_final: 0.8565 (tpt) REVERT: I 1112 MET cc_start: 0.9362 (mmt) cc_final: 0.9059 (mmm) REVERT: I 1154 LEU cc_start: 0.9347 (mp) cc_final: 0.9036 (mp) REVERT: I 1233 MET cc_start: 0.3568 (tpp) cc_final: 0.2910 (tpp) REVERT: J 153 MET cc_start: -0.1254 (tpt) cc_final: -0.1760 (tpp) REVERT: J 240 TYR cc_start: 0.9051 (t80) cc_final: 0.8670 (p90) REVERT: K 114 GLU cc_start: 0.8258 (tp30) cc_final: 0.8012 (pm20) REVERT: K 376 MET cc_start: 0.2156 (ptp) cc_final: 0.1716 (ppp) REVERT: L 78 PHE cc_start: 0.7940 (m-80) cc_final: 0.7709 (m-80) REVERT: L 191 MET cc_start: 0.8956 (tpp) cc_final: 0.8739 (tpp) REVERT: L 372 MET cc_start: 0.9646 (mtt) cc_final: 0.9342 (mtt) REVERT: L 393 GLU cc_start: 0.9463 (tm-30) cc_final: 0.9216 (pt0) REVERT: L 445 MET cc_start: 0.9184 (mpp) cc_final: 0.8797 (mpp) REVERT: L 470 HIS cc_start: 0.8387 (m-70) cc_final: 0.8186 (t-90) REVERT: M 361 MET cc_start: 0.8495 (mmp) cc_final: 0.8220 (mmm) REVERT: N 462 TYR cc_start: 0.9041 (t80) cc_final: 0.8721 (t80) REVERT: N 936 MET cc_start: 0.9017 (mmp) cc_final: 0.8757 (tmm) REVERT: O 469 MET cc_start: 0.8353 (mmt) cc_final: 0.7822 (mmm) REVERT: O 498 MET cc_start: 0.8115 (mmp) cc_final: 0.7466 (mtp) REVERT: O 523 MET cc_start: 0.8784 (tpt) cc_final: 0.8312 (tpt) REVERT: P 149 ASP cc_start: 0.9076 (t70) cc_final: 0.8873 (t0) REVERT: P 161 ILE cc_start: 0.9557 (tt) cc_final: 0.8942 (pt) REVERT: P 162 MET cc_start: 0.9304 (mmm) cc_final: 0.8547 (mmm) REVERT: P 164 LYS cc_start: 0.9534 (mmmt) cc_final: 0.9334 (tmtt) REVERT: P 366 MET cc_start: 0.8391 (mmt) cc_final: 0.8036 (mmm) REVERT: P 441 MET cc_start: 0.9048 (mpp) cc_final: 0.8719 (mpp) REVERT: P 494 TYR cc_start: 0.9306 (t80) cc_final: 0.8957 (t80) REVERT: Q 205 GLU cc_start: 0.5238 (tp30) cc_final: 0.4821 (pp20) REVERT: R 196 VAL cc_start: 0.7603 (t) cc_final: 0.7287 (t) REVERT: R 216 ARG cc_start: 0.9640 (tmt170) cc_final: 0.9348 (mmt-90) REVERT: R 219 MET cc_start: 0.9390 (mmp) cc_final: 0.9128 (mmm) REVERT: R 228 LEU cc_start: 0.8180 (pp) cc_final: 0.7873 (mp) REVERT: S 572 MET cc_start: -0.1567 (mmm) cc_final: -0.2073 (mtp) outliers start: 0 outliers final: 0 residues processed: 399 average time/residue: 0.2479 time to fit residues: 164.0949 Evaluate side-chains 312 residues out of total 3874 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 312 time to evaluate : 1.510 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 479 random chunks: chunk 436 optimal weight: 10.0000 chunk 263 optimal weight: 40.0000 chunk 68 optimal weight: 0.6980 chunk 247 optimal weight: 8.9990 chunk 97 optimal weight: 3.9990 chunk 323 optimal weight: 6.9990 chunk 146 optimal weight: 2.9990 chunk 40 optimal weight: 5.9990 chunk 244 optimal weight: 1.9990 chunk 25 optimal weight: 5.9990 chunk 369 optimal weight: 0.1980 overall best weight: 1.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 67 ASN H 63 ASN ** I 915 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 173 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 296 ASN ** K 190 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 313 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 140 HIS N 454 ASN ** N 489 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 632 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 467 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 308 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 345 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 403 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 437 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 500 GLN ** P 501 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 504 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 252 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3810 r_free = 0.3810 target = 0.066012 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.046178 restraints weight = 451897.291| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 53)----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.047271 restraints weight = 244713.257| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 52)----------------| | r_work = 0.3440 r_free = 0.3440 target = 0.048056 restraints weight = 163286.935| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 52)----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.048559 restraints weight = 126972.282| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 55)----------------| | r_work = 0.3458 r_free = 0.3458 target = 0.048862 restraints weight = 108960.876| |-----------------------------------------------------------------------------| r_work (final): 0.3331 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3331 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3331 r_free = 0.3331 target_work(ls_wunit_k1) = 0.043 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3331 r_free = 0.3331 target_work(ls_wunit_k1) = 0.043 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3331 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7848 moved from start: 0.4507 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 44567 Z= 0.141 Angle : 0.632 15.309 61592 Z= 0.338 Chirality : 0.041 0.325 6923 Planarity : 0.004 0.056 6764 Dihedral : 23.345 154.724 8596 Min Nonbonded Distance : 2.267 Molprobity Statistics. All-atom Clashscore : 11.85 Ramachandran Plot: Outliers : 0.07 % Allowed : 6.50 % Favored : 93.43 % Rotamer: Outliers : 0.00 % Allowed : 0.83 % Favored : 99.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.29 (0.13), residues: 4321 helix: 0.88 (0.10), residues: 2477 sheet: -1.66 (0.35), residues: 202 loop : -1.66 (0.16), residues: 1642 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG L 95 TYR 0.051 0.002 TYR O 922 PHE 0.025 0.001 PHE L 217 TRP 0.022 0.001 TRP O 620 HIS 0.008 0.001 HIS O 905 Details of bonding type rmsd/Z covalent geometry : bond 0.00273 / 0.14 (44565) covalent geometry : angle 0.63225 / 0.34 (61592) hydrogen bonds : bond 0.04281 / 2.87 ( 2339) hydrogen bonds : angle 4.42930 / 3.15 ( 6495) Misc. bond : bond 0.00362 / 0.19 ( 2) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8642 Ramachandran restraints generated. 4321 Oldfield, 0 Emsley, 4321 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8642 Ramachandran restraints generated. 4321 Oldfield, 0 Emsley, 4321 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 394 residues out of total 3874 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 394 time to evaluate : 1.529 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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: A 92 LEU cc_start: 0.9834 (mm) cc_final: 0.9620 (mm) REVERT: B 63 GLU cc_start: 0.9357 (mt-10) cc_final: 0.8982 (mt-10) REVERT: B 84 MET cc_start: 0.9299 (mmm) cc_final: 0.8731 (mmp) REVERT: C 36 LYS cc_start: 0.9616 (mptt) cc_final: 0.9355 (mmtm) REVERT: C 64 GLU cc_start: 0.9450 (tt0) cc_final: 0.8823 (tm-30) REVERT: D 59 MET cc_start: 0.9583 (tmm) cc_final: 0.9347 (tmm) REVERT: D 106 LEU cc_start: 0.9321 (mt) cc_final: 0.9067 (mt) REVERT: E 74 ILE cc_start: 0.9663 (pt) cc_final: 0.9311 (pt) REVERT: E 77 ASP cc_start: 0.9375 (m-30) cc_final: 0.9151 (m-30) REVERT: E 90 MET cc_start: 0.9556 (mmp) cc_final: 0.9289 (mmp) REVERT: E 97 GLU cc_start: 0.9324 (mt-10) cc_final: 0.8852 (mt-10) REVERT: F 22 LEU cc_start: 0.8898 (mp) cc_final: 0.8670 (pt) REVERT: F 85 ASP cc_start: 0.8855 (m-30) cc_final: 0.8635 (p0) REVERT: F 91 LYS cc_start: 0.9597 (ptmm) cc_final: 0.9318 (pttp) REVERT: G 36 LYS cc_start: 0.9637 (mmmt) cc_final: 0.9086 (mmtm) REVERT: G 51 LEU cc_start: 0.9762 (tp) cc_final: 0.9537 (tp) REVERT: G 56 GLU cc_start: 0.8691 (tt0) cc_final: 0.8131 (mt-10) REVERT: G 64 GLU cc_start: 0.9012 (tp30) cc_final: 0.8326 (tp30) REVERT: G 95 LYS cc_start: 0.9629 (tptp) cc_final: 0.9243 (tppt) REVERT: H 59 MET cc_start: 0.9014 (tpp) cc_final: 0.8684 (tpp) REVERT: H 62 MET cc_start: 0.9502 (mmp) cc_final: 0.9297 (mmm) REVERT: H 82 HIS cc_start: 0.8795 (m90) cc_final: 0.8264 (m90) REVERT: I 424 MET cc_start: 0.6497 (ppp) cc_final: 0.5618 (ppp) REVERT: I 527 MET cc_start: 0.8005 (tpt) cc_final: 0.7603 (mtt) REVERT: I 886 MET cc_start: 0.8399 (mtt) cc_final: 0.7482 (mmt) REVERT: I 960 GLU cc_start: 0.5982 (tt0) cc_final: 0.5115 (mm-30) REVERT: I 1000 MET cc_start: 0.9172 (ptm) cc_final: 0.8811 (ptm) REVERT: I 1109 MET cc_start: 0.8954 (tpp) cc_final: 0.8503 (tpt) REVERT: I 1112 MET cc_start: 0.9333 (mmt) cc_final: 0.9022 (mmm) REVERT: I 1154 LEU cc_start: 0.9352 (mp) cc_final: 0.9040 (mp) REVERT: I 1233 MET cc_start: 0.3592 (tpp) cc_final: 0.2907 (tpp) REVERT: J 240 TYR cc_start: 0.9046 (t80) cc_final: 0.8656 (p90) REVERT: K 114 GLU cc_start: 0.8281 (tp30) cc_final: 0.8022 (pm20) REVERT: K 376 MET cc_start: 0.2254 (ptp) cc_final: 0.1724 (ppp) REVERT: L 78 PHE cc_start: 0.7884 (m-80) cc_final: 0.7646 (m-80) REVERT: L 191 MET cc_start: 0.8959 (tpp) cc_final: 0.8751 (tpp) REVERT: L 372 MET cc_start: 0.9637 (mtt) cc_final: 0.9324 (mtt) REVERT: L 393 GLU cc_start: 0.9441 (tm-30) cc_final: 0.9232 (pt0) REVERT: L 445 MET cc_start: 0.9089 (mpp) cc_final: 0.8770 (mpp) REVERT: M 214 THR cc_start: 0.9671 (p) cc_final: 0.9419 (p) REVERT: M 361 MET cc_start: 0.8586 (mmp) cc_final: 0.8285 (mmm) REVERT: N 462 TYR cc_start: 0.9043 (t80) cc_final: 0.8684 (t80) REVERT: N 468 PHE cc_start: 0.9268 (t80) cc_final: 0.9046 (t80) REVERT: N 489 ASN cc_start: 0.8009 (m110) cc_final: 0.7738 (m110) REVERT: N 896 MET cc_start: 0.9346 (mmp) cc_final: 0.9090 (mmm) REVERT: N 936 MET cc_start: 0.9069 (mmp) cc_final: 0.8806 (tmm) REVERT: O 469 MET cc_start: 0.8354 (mmt) cc_final: 0.7819 (mmm) REVERT: O 498 MET cc_start: 0.8040 (mmp) cc_final: 0.7245 (mtp) REVERT: O 523 MET cc_start: 0.8700 (tpt) cc_final: 0.8069 (tpt) REVERT: O 534 LEU cc_start: 0.8953 (mt) cc_final: 0.8726 (mp) REVERT: P 161 ILE cc_start: 0.9582 (tt) cc_final: 0.8998 (pt) REVERT: P 162 MET cc_start: 0.9261 (mmm) cc_final: 0.8461 (mmm) REVERT: P 164 LYS cc_start: 0.9540 (mmmt) cc_final: 0.9334 (tmtt) REVERT: P 366 MET cc_start: 0.8429 (mmt) cc_final: 0.8084 (mmm) REVERT: P 441 MET cc_start: 0.9059 (mpp) cc_final: 0.8729 (mpp) REVERT: P 494 TYR cc_start: 0.9315 (t80) cc_final: 0.8904 (t80) REVERT: Q 205 GLU cc_start: 0.5857 (tp30) cc_final: 0.5353 (pp20) REVERT: R 196 VAL cc_start: 0.7576 (t) cc_final: 0.7254 (t) REVERT: R 216 ARG cc_start: 0.9620 (tmt170) cc_final: 0.9339 (ttp80) REVERT: R 219 MET cc_start: 0.9187 (mmp) cc_final: 0.8886 (mmm) REVERT: R 228 LEU cc_start: 0.8176 (pp) cc_final: 0.7878 (mp) REVERT: S 572 MET cc_start: -0.1351 (mmm) cc_final: -0.1923 (mtp) outliers start: 0 outliers final: 0 residues processed: 394 average time/residue: 0.2461 time to fit residues: 160.7618 Evaluate side-chains 318 residues out of total 3874 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 318 time to evaluate : 1.501 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 479 random chunks: chunk 226 optimal weight: 10.0000 chunk 85 optimal weight: 3.9990 chunk 475 optimal weight: 30.0000 chunk 330 optimal weight: 9.9990 chunk 10 optimal weight: 0.0770 chunk 172 optimal weight: 6.9990 chunk 320 optimal weight: 5.9990 chunk 235 optimal weight: 0.7980 chunk 336 optimal weight: 7.9990 chunk 396 optimal weight: 0.8980 chunk 467 optimal weight: 20.0000 overall best weight: 2.3542 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 95 GLN ** I 915 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 969 HIS ** J 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 173 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 296 ASN ** K 205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 313 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 140 HIS N 422 HIS N 467 ASN ** N 489 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 632 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 423 HIS ** O 436 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 145 GLN ** P 308 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 345 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 403 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 437 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 500 GLN ** P 501 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 504 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 252 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3795 r_free = 0.3795 target = 0.065442 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.045595 restraints weight = 449950.352| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.046682 restraints weight = 245990.510| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 52)----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.047404 restraints weight = 164069.386| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 52)----------------| | r_work = 0.3434 r_free = 0.3434 target = 0.047954 restraints weight = 128251.730| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 60)----------------| | r_work = 0.3440 r_free = 0.3440 target = 0.048232 restraints weight = 109796.415| |-----------------------------------------------------------------------------| r_work (final): 0.3314 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3314 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3314 r_free = 0.3314 target_work(ls_wunit_k1) = 0.042 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3314 r_free = 0.3314 target_work(ls_wunit_k1) = 0.042 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3314 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7871 moved from start: 0.4774 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 44567 Z= 0.149 Angle : 0.634 12.900 61592 Z= 0.340 Chirality : 0.040 0.326 6923 Planarity : 0.004 0.073 6764 Dihedral : 23.368 155.512 8596 Min Nonbonded Distance : 2.277 Molprobity Statistics. All-atom Clashscore : 12.80 Ramachandran Plot: Outliers : 0.07 % Allowed : 6.67 % Favored : 93.27 % Rotamer: Outliers : 0.00 % Allowed : 0.68 % Favored : 99.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.25 (0.13), residues: 4321 helix: 0.87 (0.10), residues: 2492 sheet: -1.43 (0.38), residues: 195 loop : -1.63 (0.16), residues: 1634 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG H 99 TYR 0.034 0.002 TYR O 922 PHE 0.023 0.001 PHE L 217 TRP 0.022 0.001 TRP O 620 HIS 0.008 0.001 HIS N 905 Details of bonding type rmsd/Z covalent geometry : bond 0.00289 / 0.15 (44565) covalent geometry : angle 0.63357 / 0.34 (61592) hydrogen bonds : bond 0.04374 / 2.92 ( 2339) hydrogen bonds : angle 4.46311 / 3.17 ( 6495) Misc. bond : bond 0.00182 / 0.09 ( 2) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8642 Ramachandran restraints generated. 4321 Oldfield, 0 Emsley, 4321 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8642 Ramachandran restraints generated. 4321 Oldfield, 0 Emsley, 4321 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 388 residues out of total 3874 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 388 time to evaluate : 1.543 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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: A 50 GLU cc_start: 0.9615 (mp0) cc_final: 0.9407 (mp0) REVERT: A 92 LEU cc_start: 0.9863 (mm) cc_final: 0.9625 (mm) REVERT: B 63 GLU cc_start: 0.9353 (mt-10) cc_final: 0.9032 (mt-10) REVERT: B 84 MET cc_start: 0.9290 (mmm) cc_final: 0.8786 (mmp) REVERT: C 36 LYS cc_start: 0.9609 (mptt) cc_final: 0.9370 (mmtm) REVERT: C 64 GLU cc_start: 0.9469 (tt0) cc_final: 0.8854 (tm-30) REVERT: D 59 MET cc_start: 0.9580 (tmm) cc_final: 0.9344 (tmm) REVERT: D 83 TYR cc_start: 0.9323 (m-80) cc_final: 0.8947 (m-80) REVERT: D 106 LEU cc_start: 0.9341 (mt) cc_final: 0.9022 (mt) REVERT: E 70 LEU cc_start: 0.9874 (tt) cc_final: 0.9644 (tp) REVERT: E 74 ILE cc_start: 0.9662 (pt) cc_final: 0.9340 (pt) REVERT: E 90 MET cc_start: 0.9567 (mmp) cc_final: 0.9295 (mmp) REVERT: E 97 GLU cc_start: 0.9366 (mt-10) cc_final: 0.8829 (mt-10) REVERT: F 22 LEU cc_start: 0.8913 (mp) cc_final: 0.8688 (pt) REVERT: F 60 VAL cc_start: 0.9656 (t) cc_final: 0.9272 (t) REVERT: F 91 LYS cc_start: 0.9653 (ptmm) cc_final: 0.9237 (pttp) REVERT: G 36 LYS cc_start: 0.9672 (mmmt) cc_final: 0.9142 (mmtm) REVERT: G 51 LEU cc_start: 0.9773 (tp) cc_final: 0.9561 (tp) REVERT: G 56 GLU cc_start: 0.8690 (tt0) cc_final: 0.8096 (mt-10) REVERT: G 61 GLU cc_start: 0.8342 (mt-10) cc_final: 0.8028 (mt-10) REVERT: G 64 GLU cc_start: 0.9017 (tp30) cc_final: 0.8370 (tp30) REVERT: G 95 LYS cc_start: 0.9626 (tptp) cc_final: 0.9234 (tppt) REVERT: H 59 MET cc_start: 0.9050 (tpp) cc_final: 0.8639 (tpp) REVERT: H 62 MET cc_start: 0.9531 (mmp) cc_final: 0.9308 (mmm) REVERT: H 82 HIS cc_start: 0.8910 (m90) cc_final: 0.8267 (m90) REVERT: H 99 ARG cc_start: 0.9101 (tpp80) cc_final: 0.8567 (tpp-160) REVERT: H 108 LYS cc_start: 0.9758 (ptpp) cc_final: 0.9338 (ptpp) REVERT: I 424 MET cc_start: 0.6509 (ppp) cc_final: 0.6137 (ppp) REVERT: I 527 MET cc_start: 0.7884 (tpt) cc_final: 0.7449 (mtt) REVERT: I 886 MET cc_start: 0.8416 (mtt) cc_final: 0.7530 (mmt) REVERT: I 960 GLU cc_start: 0.5987 (tt0) cc_final: 0.5100 (mm-30) REVERT: I 1000 MET cc_start: 0.9197 (ptm) cc_final: 0.8788 (ptm) REVERT: I 1011 MET cc_start: 0.5981 (mmt) cc_final: 0.5644 (mmt) REVERT: I 1109 MET cc_start: 0.9062 (tpp) cc_final: 0.8545 (tpt) REVERT: I 1112 MET cc_start: 0.9332 (mmt) cc_final: 0.9012 (mmm) REVERT: I 1154 LEU cc_start: 0.9430 (mp) cc_final: 0.9106 (mp) REVERT: I 1233 MET cc_start: 0.3711 (tpp) cc_final: 0.3013 (tpp) REVERT: J 240 TYR cc_start: 0.9053 (t80) cc_final: 0.8656 (p90) REVERT: K 82 MET cc_start: -0.0726 (ttt) cc_final: -0.1406 (mtp) REVERT: K 97 ASP cc_start: 0.8927 (t0) cc_final: 0.8539 (p0) REVERT: K 114 GLU cc_start: 0.8268 (tp30) cc_final: 0.8023 (pm20) REVERT: K 376 MET cc_start: 0.2312 (ptp) cc_final: 0.1675 (ppp) REVERT: L 372 MET cc_start: 0.9636 (mtt) cc_final: 0.9328 (mtt) REVERT: L 393 GLU cc_start: 0.9485 (tm-30) cc_final: 0.9284 (pt0) REVERT: L 445 MET cc_start: 0.9082 (mpp) cc_final: 0.8761 (mpp) REVERT: M 166 LEU cc_start: 0.9499 (mm) cc_final: 0.8836 (tp) REVERT: M 214 THR cc_start: 0.9658 (p) cc_final: 0.9401 (p) REVERT: M 275 LEU cc_start: 0.9390 (tp) cc_final: 0.9189 (tp) REVERT: M 361 MET cc_start: 0.8631 (mmp) cc_final: 0.8328 (mmm) REVERT: N 462 TYR cc_start: 0.9021 (t80) cc_final: 0.8582 (t80) REVERT: N 468 PHE cc_start: 0.9252 (t80) cc_final: 0.9042 (t80) REVERT: N 489 ASN cc_start: 0.8041 (m110) cc_final: 0.7774 (m110) REVERT: N 896 MET cc_start: 0.9402 (mmp) cc_final: 0.9172 (mmm) REVERT: N 913 MET cc_start: 0.9437 (mmp) cc_final: 0.9232 (mmp) REVERT: O 469 MET cc_start: 0.8352 (mmt) cc_final: 0.7809 (mmm) REVERT: O 498 MET cc_start: 0.7989 (mmp) cc_final: 0.7202 (mtp) REVERT: O 523 MET cc_start: 0.8829 (tpt) cc_final: 0.8474 (tpt) REVERT: P 161 ILE cc_start: 0.9604 (tt) cc_final: 0.9028 (pt) REVERT: P 162 MET cc_start: 0.9306 (mmm) cc_final: 0.8488 (mmm) REVERT: P 366 MET cc_start: 0.8432 (mmt) cc_final: 0.8102 (mmm) REVERT: P 494 TYR cc_start: 0.9335 (t80) cc_final: 0.8860 (t80) REVERT: Q 205 GLU cc_start: 0.5858 (tp30) cc_final: 0.5369 (pp20) REVERT: R 196 VAL cc_start: 0.7604 (t) cc_final: 0.7229 (t) REVERT: R 216 ARG cc_start: 0.9629 (tmt170) cc_final: 0.9346 (mmt-90) REVERT: R 219 MET cc_start: 0.9367 (mmp) cc_final: 0.9160 (mmm) REVERT: S 572 MET cc_start: -0.1572 (mmm) cc_final: -0.2122 (mtp) REVERT: U 1521 TYR cc_start: 0.8211 (t80) cc_final: 0.7792 (m-80) outliers start: 0 outliers final: 0 residues processed: 388 average time/residue: 0.2527 time to fit residues: 163.1939 Evaluate side-chains 308 residues out of total 3874 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 308 time to evaluate : 1.368 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 479 random chunks: chunk 225 optimal weight: 0.8980 chunk 356 optimal weight: 7.9990 chunk 406 optimal weight: 0.8980 chunk 447 optimal weight: 20.0000 chunk 6 optimal weight: 0.9980 chunk 249 optimal weight: 10.0000 chunk 211 optimal weight: 0.9980 chunk 217 optimal weight: 0.8980 chunk 416 optimal weight: 0.5980 chunk 60 optimal weight: 4.9990 chunk 289 optimal weight: 9.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 38 ASN ** I 915 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 173 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 313 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 140 HIS ** N 489 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 632 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 436 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 621 ASN P 145 GLN ** P 308 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 345 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 403 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 500 GLN ** Q 252 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3815 r_free = 0.3815 target = 0.066281 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.046421 restraints weight = 448582.710| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.3428 r_free = 0.3428 target = 0.047509 restraints weight = 242171.651| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 52)----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.048288 restraints weight = 160345.418| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 54)----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.048805 restraints weight = 124072.671| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.049041 restraints weight = 106744.631| |-----------------------------------------------------------------------------| r_work (final): 0.3340 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3341 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3341 r_free = 0.3341 target_work(ls_wunit_k1) = 0.043 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3341 r_free = 0.3341 target_work(ls_wunit_k1) = 0.043 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3341 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7841 moved from start: 0.4832 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 44567 Z= 0.124 Angle : 0.628 12.876 61592 Z= 0.332 Chirality : 0.041 0.335 6923 Planarity : 0.004 0.053 6764 Dihedral : 23.290 154.821 8596 Min Nonbonded Distance : 2.292 Molprobity Statistics. All-atom Clashscore : 11.33 Ramachandran Plot: Outliers : 0.07 % Allowed : 6.39 % Favored : 93.54 % Rotamer: Outliers : 0.03 % Allowed : 0.21 % Favored : 99.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.19 (0.13), residues: 4321 helix: 0.93 (0.10), residues: 2488 sheet: -1.56 (0.36), residues: 203 loop : -1.60 (0.16), residues: 1630 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG L 95 TYR 0.038 0.001 TYR O 922 PHE 0.028 0.001 PHE L 78 TRP 0.019 0.001 TRP O 620 HIS 0.008 0.001 HIS N 905 Details of bonding type rmsd/Z covalent geometry : bond 0.00241 / 0.12 (44565) covalent geometry : angle 0.62781 / 0.33 (61592) hydrogen bonds : bond 0.03637 / 2.45 ( 2339) hydrogen bonds : angle 4.36744 / 3.10 ( 6495) Misc. bond : bond 0.00056 / 0.03 ( 2) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8642 Ramachandran restraints generated. 4321 Oldfield, 0 Emsley, 4321 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8642 Ramachandran restraints generated. 4321 Oldfield, 0 Emsley, 4321 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 390 residues out of total 3874 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 389 time to evaluate : 1.518 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 GLU cc_start: 0.9551 (mp0) cc_final: 0.9253 (pm20) REVERT: A 92 LEU cc_start: 0.9850 (mm) cc_final: 0.9589 (mm) REVERT: B 63 GLU cc_start: 0.9357 (mt-10) cc_final: 0.9038 (mt-10) REVERT: B 84 MET cc_start: 0.9309 (mmm) cc_final: 0.8809 (mmp) REVERT: C 36 LYS cc_start: 0.9597 (mptt) cc_final: 0.9330 (mmtm) REVERT: C 64 GLU cc_start: 0.9449 (tt0) cc_final: 0.8819 (tm-30) REVERT: D 59 MET cc_start: 0.9565 (tmm) cc_final: 0.9333 (tmm) REVERT: D 83 TYR cc_start: 0.9306 (m-80) cc_final: 0.8994 (m-80) REVERT: D 106 LEU cc_start: 0.9353 (mt) cc_final: 0.9023 (mt) REVERT: E 74 ILE cc_start: 0.9677 (pt) cc_final: 0.9317 (pt) REVERT: E 90 MET cc_start: 0.9569 (mmp) cc_final: 0.9282 (mmp) REVERT: E 97 GLU cc_start: 0.9316 (mt-10) cc_final: 0.8785 (mt-10) REVERT: F 21 VAL cc_start: 0.8816 (p) cc_final: 0.8556 (p) REVERT: F 22 LEU cc_start: 0.8860 (mp) cc_final: 0.8596 (pt) REVERT: F 58 LEU cc_start: 0.9714 (tt) cc_final: 0.9404 (mm) REVERT: F 60 VAL cc_start: 0.9614 (t) cc_final: 0.9174 (t) REVERT: F 91 LYS cc_start: 0.9633 (ptmm) cc_final: 0.9261 (pttp) REVERT: G 56 GLU cc_start: 0.8683 (tt0) cc_final: 0.8054 (mt-10) REVERT: G 64 GLU cc_start: 0.9026 (tp30) cc_final: 0.8413 (tp30) REVERT: G 91 GLU cc_start: 0.9385 (pp20) cc_final: 0.9150 (pm20) REVERT: H 59 MET cc_start: 0.9073 (tpp) cc_final: 0.8583 (tpp) REVERT: H 62 MET cc_start: 0.9509 (mmp) cc_final: 0.9277 (mmm) REVERT: H 71 GLU cc_start: 0.9034 (pp20) cc_final: 0.8723 (pp20) REVERT: H 99 ARG cc_start: 0.8953 (tpp80) cc_final: 0.8740 (tpp80) REVERT: I 424 MET cc_start: 0.6392 (ppp) cc_final: 0.6024 (ppp) REVERT: I 527 MET cc_start: 0.7870 (tpt) cc_final: 0.7428 (mtt) REVERT: I 886 MET cc_start: 0.8362 (mtt) cc_final: 0.7468 (mmt) REVERT: I 960 GLU cc_start: 0.5975 (tt0) cc_final: 0.5077 (mm-30) REVERT: I 1000 MET cc_start: 0.9194 (ptm) cc_final: 0.8783 (ptm) REVERT: I 1011 MET cc_start: 0.5889 (mmt) cc_final: 0.5563 (mmt) REVERT: I 1109 MET cc_start: 0.9106 (tpp) cc_final: 0.8634 (tpt) REVERT: I 1112 MET cc_start: 0.9318 (mmt) cc_final: 0.9043 (mmm) REVERT: I 1154 LEU cc_start: 0.9455 (mp) cc_final: 0.9167 (mp) REVERT: I 1233 MET cc_start: 0.3721 (tpp) cc_final: 0.3021 (tpp) REVERT: J 240 TYR cc_start: 0.8983 (t80) cc_final: 0.8610 (p90) REVERT: K 97 ASP cc_start: 0.8939 (t0) cc_final: 0.8546 (p0) REVERT: K 114 GLU cc_start: 0.8260 (tp30) cc_final: 0.8021 (pm20) REVERT: K 376 MET cc_start: 0.2348 (ptp) cc_final: 0.1742 (ppp) REVERT: L 315 PHE cc_start: 0.9496 (t80) cc_final: 0.9211 (t80) REVERT: L 372 MET cc_start: 0.9631 (mtt) cc_final: 0.9319 (mtt) REVERT: L 393 GLU cc_start: 0.9450 (tm-30) cc_final: 0.9227 (pt0) REVERT: L 445 MET cc_start: 0.9096 (mpp) cc_final: 0.8755 (mpp) REVERT: M 166 LEU cc_start: 0.9500 (mm) cc_final: 0.8828 (tp) REVERT: M 214 THR cc_start: 0.9652 (p) cc_final: 0.9395 (p) REVERT: M 275 LEU cc_start: 0.9408 (tp) cc_final: 0.9193 (tp) REVERT: M 366 ARG cc_start: 0.9671 (mpp80) cc_final: 0.9345 (mtt-85) REVERT: N 462 TYR cc_start: 0.8951 (t80) cc_final: 0.8492 (t80) REVERT: N 468 PHE cc_start: 0.9222 (t80) cc_final: 0.8999 (t80) REVERT: N 489 ASN cc_start: 0.8024 (m110) cc_final: 0.7739 (m110) REVERT: N 674 MET cc_start: 0.4227 (mpp) cc_final: 0.3015 (ttt) REVERT: N 896 MET cc_start: 0.9413 (mmp) cc_final: 0.9156 (mmm) REVERT: N 913 MET cc_start: 0.9484 (mmp) cc_final: 0.9229 (mmp) REVERT: O 469 MET cc_start: 0.8442 (mmt) cc_final: 0.7844 (mmm) REVERT: O 498 MET cc_start: 0.7991 (mmp) cc_final: 0.7158 (mtp) REVERT: O 523 MET cc_start: 0.8678 (tpt) cc_final: 0.8309 (tpt) REVERT: O 944 MET cc_start: 0.7430 (tpt) cc_final: 0.6484 (ptt) REVERT: P 161 ILE cc_start: 0.9561 (tt) cc_final: 0.9045 (pt) REVERT: P 162 MET cc_start: 0.9317 (mmm) cc_final: 0.8543 (mmm) REVERT: P 366 MET cc_start: 0.8420 (mmt) cc_final: 0.8095 (mmm) REVERT: P 441 MET cc_start: 0.9080 (mpp) cc_final: 0.8435 (mpp) REVERT: P 494 TYR cc_start: 0.9335 (t80) cc_final: 0.8874 (t80) REVERT: Q 205 GLU cc_start: 0.5860 (tp30) cc_final: 0.5385 (pp20) REVERT: Q 257 ARG cc_start: 0.9516 (mmp80) cc_final: 0.8960 (ptm-80) REVERT: R 196 VAL cc_start: 0.7589 (t) cc_final: 0.7203 (t) REVERT: R 216 ARG cc_start: 0.9622 (tmt170) cc_final: 0.9334 (mmt-90) REVERT: R 219 MET cc_start: 0.9380 (mmp) cc_final: 0.9081 (mmm) REVERT: R 228 LEU cc_start: 0.7945 (tt) cc_final: 0.7034 (mp) REVERT: S 572 MET cc_start: -0.1606 (mmm) cc_final: -0.2199 (mtp) REVERT: U 1521 TYR cc_start: 0.8238 (t80) cc_final: 0.7915 (m-80) outliers start: 1 outliers final: 0 residues processed: 390 average time/residue: 0.2640 time to fit residues: 171.3830 Evaluate side-chains 316 residues out of total 3874 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 316 time to evaluate : 1.602 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 479 random chunks: chunk 162 optimal weight: 1.9990 chunk 445 optimal weight: 40.0000 chunk 3 optimal weight: 1.9990 chunk 214 optimal weight: 6.9990 chunk 324 optimal weight: 6.9990 chunk 120 optimal weight: 2.9990 chunk 161 optimal weight: 20.0000 chunk 410 optimal weight: 1.9990 chunk 80 optimal weight: 0.7980 chunk 146 optimal weight: 10.0000 chunk 368 optimal weight: 9.9990 overall best weight: 1.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** E 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 915 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 313 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 140 HIS N 422 HIS ** N 489 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 436 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 621 ASN ** P 308 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 345 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 403 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 437 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 501 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 504 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 247 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 252 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3804 r_free = 0.3804 target = 0.065631 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.045552 restraints weight = 454304.396| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.046674 restraints weight = 245903.011| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 52)----------------| | r_work = 0.3420 r_free = 0.3420 target = 0.047462 restraints weight = 163333.754| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 52)----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.047993 restraints weight = 126073.749| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 53)----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.048251 restraints weight = 108367.216| |-----------------------------------------------------------------------------| r_work (final): 0.3314 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3313 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3313 r_free = 0.3313 target_work(ls_wunit_k1) = 0.042 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3313 r_free = 0.3313 target_work(ls_wunit_k1) = 0.042 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3313 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7867 moved from start: 0.5004 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 44567 Z= 0.139 Angle : 0.627 12.524 61592 Z= 0.334 Chirality : 0.041 0.332 6923 Planarity : 0.004 0.063 6764 Dihedral : 23.298 156.358 8596 Min Nonbonded Distance : 2.287 Molprobity Statistics. All-atom Clashscore : 12.40 Ramachandran Plot: Outliers : 0.07 % Allowed : 6.43 % Favored : 93.50 % Rotamer: Outliers : 0.03 % Allowed : 0.36 % Favored : 99.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.14 (0.13), residues: 4321 helix: 0.96 (0.10), residues: 2490 sheet: -1.51 (0.38), residues: 194 loop : -1.56 (0.16), residues: 1637 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG L 95 TYR 0.033 0.001 TYR O 922 PHE 0.039 0.001 PHE P 153 TRP 0.020 0.001 TRP O 620 HIS 0.007 0.001 HIS N 905 Details of bonding type rmsd/Z covalent geometry : bond 0.00272 / 0.14 (44565) covalent geometry : angle 0.62664 / 0.33 (61592) hydrogen bonds : bond 0.04104 / 2.76 ( 2339) hydrogen bonds : angle 4.40311 / 3.13 ( 6495) Misc. bond : bond 0.00051 / 0.02 ( 2) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 11529.87 seconds wall clock time: 198 minutes 11.67 seconds (11891.67 seconds total)