Starting phenix.real_space_refine on Tue Sep 15 18:28:40 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7y8r_33684/09_2026/7y8r_33684_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/7y8r_33684/09_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_33684/09_2026/7y8r_33684.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7y8r_33684/09_2026/7y8r_33684.map" model { file = "/net/cci-nas-00/data/ceres_data/7y8r_33684/09_2026/7y8r_33684_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7y8r_33684/09_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): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/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: 8.97, per 1000 atoms: 0.21 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: 3.84 Conformation dependent library (CDL) restraints added in 1.6 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: 4.21 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: 10.97 Time building geometry restraints manager: 4.98 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: 60803 2.44 - 4.87: 767 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: 5.420 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: 0.020 Extract box with map and model: 0.760 Check model and map are aligned: 0.130 Set scattering table: 0.110 Process input model: 42.150 Find NCS groups from input model: 0.350 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:1.290 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 50.340 ------------------------------------------------------------------------------- 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 : 0.613 12.178 61592 Z= 0.464 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 0.61282 / 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 : 1.413 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: symmetry clash REVERT: A 104 PHE cc_start: 0.7191 (m-80) cc_final: 0.6741 (m-10) REVERT: D 98 VAL cc_start: 0.9347 (m) cc_final: 0.8866 (p) REVERT: E 78 PHE cc_start: 0.7475 (m-10) cc_final: 0.7155 (m-10) REVERT: E 93 GLN cc_start: 0.8328 (tt0) cc_final: 0.7919 (tt0) REVERT: F 22 LEU cc_start: 0.7509 (mp) cc_final: 0.7305 (pt) REVERT: F 60 VAL cc_start: 0.8898 (t) cc_final: 0.8461 (t) REVERT: F 66 ILE cc_start: 0.9130 (mt) cc_final: 0.8701 (tp) REVERT: K 376 MET cc_start: -0.0219 (ptt) cc_final: -0.1262 (ppp) REVERT: L 162 VAL cc_start: 0.9546 (t) cc_final: 0.9283 (t) REVERT: L 211 ASP cc_start: 0.6416 (t0) cc_final: 0.6182 (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: 0.8634 (tm-30) REVERT: L 445 MET cc_start: 0.8861 (mtp) cc_final: 0.8456 (mtt) REVERT: M 217 MET cc_start: 0.7688 (mtp) cc_final: 0.7452 (mtp) REVERT: M 301 LEU cc_start: 0.7184 (mm) cc_final: 0.6981 (mm) REVERT: N 936 MET cc_start: 0.8867 (mmp) cc_final: 0.8564 (tmm) REVERT: P 157 LEU cc_start: 0.8797 (tt) cc_final: 0.8566 (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: 0.0848 (m-10) REVERT: U 1521 TYR cc_start: 0.7383 (t80) cc_final: 0.7099 (m-10) outliers start: 2 outliers final: 1 residues processed: 715 average time/residue: 0.2783 time to fit residues: 312.6513 Evaluate side-chains 387 residues out of total 3874 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 386 time to evaluate : 1.485 ------------------------------------------------------------------------------- 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: 30.0000 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 B 75 HIS C 38 ASN C 94 ASN ** D 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 94 ASN G 104 GLN H 63 ASN H 84 ASN I 570 GLN I 745 GLN I 847 GLN I 888 ASN ** 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 105 HIS L 159 ASN ** L 309 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 406 HIS M 103 ASN M 123 GLN M 140 HIS ** N 422 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 439 HIS ** N 513 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 935 HIS ** O 467 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 604 GLN P 145 GLN P 326 HIS R 231 HIS S 206 ASN S 394 ASN Total number of N/Q/H flips: 33 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3866 r_free = 0.3866 target = 0.068163 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.048505 restraints weight = 453198.386| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 56)----------------| | r_work = 0.3490 r_free = 0.3490 target = 0.049576 restraints weight = 248494.186| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 53)----------------| | r_work = 0.3510 r_free = 0.3510 target = 0.050365 restraints weight = 166341.305| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3521 r_free = 0.3521 target = 0.050761 restraints weight = 127364.737| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 55)----------------| | r_work = 0.3528 r_free = 0.3528 target = 0.051184 restraints weight = 109224.652| |-----------------------------------------------------------------------------| r_work (final): 0.3411 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3412 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3412 r_free = 0.3412 target_work(ls_wunit_k1) = 0.045 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3412 r_free = 0.3412 target_work(ls_wunit_k1) = 0.045 | | occupancies: max = 1.00 min = 0.04 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (7 function evaluations) r_final: 0.3412 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7750 moved from start: 0.2779 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.080 44567 Z= 0.256 Angle : 0.796 11.834 61592 Z= 0.422 Chirality : 0.044 0.365 6923 Planarity : 0.007 0.152 6764 Dihedral : 22.699 168.190 8596 Min Nonbonded Distance : 2.260 Molprobity Statistics. All-atom Clashscore : 12.29 Ramachandran Plot: Outliers : 0.07 % Allowed : 6.53 % Favored : 93.40 % Rotamer: Outliers : 0.42 % Allowed : 5.39 % Favored : 94.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -1.04 (0.12), residues: 4321 helix: 0.35 (0.10), residues: 2475 sheet: -2.27 (0.35), residues: 165 loop : -2.09 (0.15), residues: 1681 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.035 0.001 ARG C 99 TYR 0.033 0.002 TYR D 83 PHE 0.025 0.002 PHE N 468 TRP 0.043 0.002 TRP M 321 HIS 0.017 0.002 HIS O 638 Details of bonding type rmsd/Z covalent geometry : bond 0.00500 / 0.26 (44565) covalent geometry : angle 0.79593 / 0.42 (61592) hydrogen bonds : bond 0.07778 / 5.24 ( 2339) hydrogen bonds : angle 4.82429 / 3.41 ( 6495) Misc. bond : bond 0.03225 / 1.62 ( 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 462 residues out of total 3874 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 446 time to evaluate : 1.270 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: A 90 MET cc_start: 0.9057 (mmp) cc_final: 0.8820 (mmm) REVERT: A 100 LEU cc_start: 0.9758 (mm) cc_final: 0.9548 (mm) REVERT: B 37 LEU cc_start: 0.9733 (mt) cc_final: 0.9518 (mt) REVERT: B 84 MET cc_start: 0.9217 (mmm) cc_final: 0.8336 (mmm) REVERT: C 64 GLU cc_start: 0.9431 (tt0) cc_final: 0.8907 (tm-30) REVERT: D 59 MET cc_start: 0.9483 (tmm) cc_final: 0.9235 (tmm) REVERT: D 106 LEU cc_start: 0.9320 (mt) cc_final: 0.9091 (mt) REVERT: E 59 GLU cc_start: 0.9008 (pm20) cc_final: 0.8756 (pm20) REVERT: E 62 ILE cc_start: 0.9602 (tt) cc_final: 0.9263 (tp) REVERT: E 67 PHE cc_start: 0.9532 (t80) cc_final: 0.9171 (t80) REVERT: E 93 GLN cc_start: 0.9317 (tt0) cc_final: 0.8809 (tp40) REVERT: F 22 LEU cc_start: 0.8771 (mp) cc_final: 0.8499 (pt) REVERT: F 64 ASN cc_start: 0.9533 (t0) cc_final: 0.9292 (t0) REVERT: G 36 LYS cc_start: 0.9476 (mmmt) cc_final: 0.9017 (mmtm) REVERT: G 39 TYR cc_start: 0.8772 (m-10) cc_final: 0.8484 (m-80) REVERT: G 51 LEU cc_start: 0.9768 (tp) cc_final: 0.9506 (tp) REVERT: G 56 GLU cc_start: 0.8676 (tt0) cc_final: 0.7958 (mt-10) REVERT: G 64 GLU cc_start: 0.8986 (tp30) cc_final: 0.8308 (tp30) REVERT: G 95 LYS cc_start: 0.9634 (tptp) cc_final: 0.9196 (tppt) REVERT: H 59 MET cc_start: 0.9113 (tpp) cc_final: 0.8691 (tpp) REVERT: H 79 ARG cc_start: 0.9387 (mtt90) cc_final: 0.9177 (ttm-80) REVERT: H 82 HIS cc_start: 0.8851 (m90) cc_final: 0.8420 (m90) REVERT: H 95 GLN cc_start: 0.9519 (tt0) cc_final: 0.9301 (tm-30) REVERT: I 424 MET cc_start: 0.6527 (ppp) cc_final: 0.6257 (ppp) REVERT: I 886 MET cc_start: 0.7848 (mtt) cc_final: 0.7282 (mmt) REVERT: I 1040 MET cc_start: 0.9472 (tpt) cc_final: 0.9149 (tpt) REVERT: I 1109 MET cc_start: 0.8757 (tpp) cc_final: 0.8368 (tpp) REVERT: I 1112 MET cc_start: 0.9305 (mmt) cc_final: 0.8984 (mmm) REVERT: I 1154 LEU cc_start: 0.9196 (mp) cc_final: 0.8904 (mp) REVERT: J 240 TYR cc_start: 0.9193 (t80) cc_final: 0.8851 (p90) REVERT: J 247 VAL cc_start: 0.6189 (OUTLIER) cc_final: 0.5952 (m) REVERT: K 376 MET cc_start: 0.0031 (ptt) cc_final: -0.0900 (ppp) REVERT: L 78 PHE cc_start: 0.8046 (m-80) cc_final: 0.7787 (m-80) REVERT: L 327 LEU cc_start: 0.9503 (tp) cc_final: 0.9265 (tp) REVERT: L 332 LEU cc_start: 0.9559 (mm) cc_final: 0.8935 (tp) REVERT: L 372 MET cc_start: 0.9557 (mtt) cc_final: 0.9218 (mpp) REVERT: M 38 MET cc_start: 0.5304 (ttt) cc_final: 0.5037 (ttm) REVERT: M 166 LEU cc_start: 0.9422 (mm) cc_final: 0.8782 (tt) REVERT: M 193 MET cc_start: 0.8823 (ptp) cc_final: 0.8383 (ppp) REVERT: M 200 LEU cc_start: 0.9601 (tt) cc_final: 0.9060 (tt) REVERT: M 208 MET cc_start: 0.8870 (mtm) cc_final: 0.8638 (mtt) REVERT: M 217 MET cc_start: 0.9571 (mtp) cc_final: 0.9285 (mtp) REVERT: M 361 MET cc_start: 0.8684 (mmp) cc_final: 0.8295 (mmm) REVERT: N 506 GLN cc_start: 0.9436 (tt0) cc_final: 0.9228 (tm-30) REVERT: N 906 PHE cc_start: 0.8577 (t80) cc_final: 0.8235 (t80) REVERT: O 469 MET cc_start: 0.8744 (mmt) cc_final: 0.8271 (mmt) REVERT: O 498 MET cc_start: 0.8006 (mmp) cc_final: 0.7231 (mtp) REVERT: O 523 MET cc_start: 0.9163 (tpt) cc_final: 0.8898 (tpt) REVERT: O 897 LYS cc_start: 0.9612 (tptp) cc_final: 0.9322 (tppt) REVERT: P 164 LYS cc_start: 0.9448 (mmmt) cc_final: 0.9099 (tmtt) REVERT: P 441 MET cc_start: 0.9095 (mpp) cc_final: 0.8695 (mpp) REVERT: P 474 GLU cc_start: 0.7469 (tm-30) cc_final: 0.7166 (tm-30) REVERT: P 494 TYR cc_start: 0.9366 (t80) cc_final: 0.8990 (t80) REVERT: Q 205 GLU cc_start: 0.5248 (tp30) cc_final: 0.4726 (pp20) REVERT: R 196 VAL cc_start: 0.8050 (t) cc_final: 0.7810 (t) REVERT: R 216 ARG cc_start: 0.9613 (tmt170) cc_final: 0.9375 (ttp80) REVERT: S 144 MET cc_start: -0.5248 (ttt) cc_final: -0.5729 (ttt) REVERT: S 572 MET cc_start: -0.1481 (mmm) cc_final: -0.2017 (mtp) REVERT: U 1521 TYR cc_start: 0.8304 (t80) cc_final: 0.7655 (m-80) outliers start: 16 outliers final: 3 residues processed: 460 average time/residue: 0.2629 time to fit residues: 197.2275 Evaluate side-chains 336 residues out of total 3874 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 332 time to evaluate : 1.450 ------------------------------------------------------------------------------- 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: 2.9990 chunk 228 optimal weight: 8.9990 chunk 304 optimal weight: 6.9990 chunk 183 optimal weight: 0.0980 chunk 92 optimal weight: 7.9990 chunk 78 optimal weight: 0.3980 chunk 424 optimal weight: 4.9990 chunk 138 optimal weight: 0.8980 chunk 440 optimal weight: 30.0000 chunk 43 optimal weight: 3.9990 chunk 307 optimal weight: 2.9990 overall best weight: 1.4784 ------------------------------------------------------------------------------- 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** H 84 ASN ** I 915 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I1230 GLN ** J 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 296 ASN ** K 205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 140 HIS N 422 HIS N 439 HIS N 513 GLN ** O 467 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 638 HIS ** P 437 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 252 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3885 r_free = 0.3885 target = 0.069198 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3488 r_free = 0.3488 target = 0.049356 restraints weight = 442550.772| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 53)----------------| | r_work = 0.3513 r_free = 0.3513 target = 0.050448 restraints weight = 241528.690| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 52)----------------| | r_work = 0.3533 r_free = 0.3533 target = 0.051296 restraints weight = 159899.879| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3545 r_free = 0.3545 target = 0.051796 restraints weight = 122124.209| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 53)----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.052233 restraints weight = 104091.138| |-----------------------------------------------------------------------------| r_work (final): 0.3433 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3432 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3432 r_free = 0.3432 target_work(ls_wunit_k1) = 0.046 | | occupancies: max = 1.00 min = 0.04 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3432 r_free = 0.3432 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: 0.3432 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7701 moved from start: 0.2953 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 44567 Z= 0.144 Angle : 0.631 10.821 61592 Z= 0.339 Chirality : 0.041 0.331 6923 Planarity : 0.004 0.069 6764 Dihedral : 22.804 165.983 8596 Min Nonbonded Distance : 2.231 Molprobity Statistics. All-atom Clashscore : 9.91 Ramachandran Plot: Outliers : 0.07 % Allowed : 6.20 % Favored : 93.73 % Rotamer: Outliers : 0.05 % Allowed : 2.60 % Favored : 97.35 % 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: -0.67 (0.13), residues: 4321 helix: 0.66 (0.10), residues: 2488 sheet: -2.19 (0.33), residues: 188 loop : -1.97 (0.15), residues: 1645 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG E 128 TYR 0.039 0.001 TYR B 51 PHE 0.020 0.001 PHE O 951 TRP 0.032 0.001 TRP M 321 HIS 0.014 0.001 HIS Q 200 Details of bonding type rmsd/Z covalent geometry : bond 0.00285 / 0.14 (44565) covalent geometry : angle 0.63050 / 0.34 (61592) hydrogen bonds : bond 0.04599 / 3.08 ( 2339) hydrogen bonds : angle 4.53341 / 3.21 ( 6495) Misc. bond : bond 0.00572 / 0.28 ( 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 430 residues out of total 3874 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 428 time to evaluate : 1.521 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 90 MET cc_start: 0.9040 (mmp) cc_final: 0.8752 (mmm) REVERT: A 92 LEU cc_start: 0.9834 (mm) cc_final: 0.9570 (mm) REVERT: B 49 LEU cc_start: 0.9399 (mm) cc_final: 0.9197 (mm) REVERT: B 84 MET cc_start: 0.9169 (mmm) cc_final: 0.8293 (mmm) REVERT: C 64 GLU cc_start: 0.9367 (tt0) cc_final: 0.8860 (tm-30) REVERT: D 42 TYR cc_start: 0.8179 (t80) cc_final: 0.7967 (t80) REVERT: D 59 MET cc_start: 0.9514 (tmm) cc_final: 0.9259 (tmm) REVERT: D 83 TYR cc_start: 0.9130 (m-10) cc_final: 0.8902 (m-80) REVERT: D 106 LEU cc_start: 0.9390 (mt) cc_final: 0.9135 (mt) REVERT: E 67 PHE cc_start: 0.9578 (t80) cc_final: 0.9115 (t80) REVERT: E 74 ILE cc_start: 0.9672 (pt) cc_final: 0.9330 (pt) REVERT: E 77 ASP cc_start: 0.9382 (m-30) cc_final: 0.9176 (m-30) REVERT: E 90 MET cc_start: 0.9454 (mmp) cc_final: 0.9212 (mmp) REVERT: E 93 GLN cc_start: 0.9343 (tt0) cc_final: 0.8767 (tp40) REVERT: E 105 GLU cc_start: 0.9067 (tm-30) cc_final: 0.8848 (tm-30) REVERT: F 22 LEU cc_start: 0.8791 (mp) cc_final: 0.8545 (pt) REVERT: F 59 LYS cc_start: 0.9689 (tmtt) cc_final: 0.9404 (tmtt) REVERT: F 64 ASN cc_start: 0.9466 (t0) cc_final: 0.9205 (t0) REVERT: F 91 LYS cc_start: 0.9598 (tmmt) cc_final: 0.9360 (ptmm) REVERT: G 36 LYS cc_start: 0.9457 (mmmt) cc_final: 0.8975 (mmtm) REVERT: G 51 LEU cc_start: 0.9758 (tp) cc_final: 0.9516 (tp) REVERT: G 56 GLU cc_start: 0.8470 (tt0) cc_final: 0.7855 (mt-10) REVERT: G 64 GLU cc_start: 0.8991 (tp30) cc_final: 0.8338 (tp30) REVERT: G 95 LYS cc_start: 0.9566 (tptp) cc_final: 0.9332 (tppt) REVERT: H 59 MET cc_start: 0.9032 (tpp) cc_final: 0.8623 (tpp) REVERT: H 82 HIS cc_start: 0.8865 (m90) cc_final: 0.8380 (m90) REVERT: H 95 GLN cc_start: 0.9505 (tt0) cc_final: 0.9055 (tm-30) REVERT: H 99 ARG cc_start: 0.9078 (tpp80) cc_final: 0.8571 (tpp-160) REVERT: H 106 LEU cc_start: 0.9469 (tp) cc_final: 0.9213 (tt) REVERT: I 424 MET cc_start: 0.6231 (ppp) cc_final: 0.5858 (ppp) REVERT: I 527 MET cc_start: 0.8073 (tpt) cc_final: 0.7671 (mtt) REVERT: I 886 MET cc_start: 0.7824 (mtt) cc_final: 0.7167 (mmt) REVERT: I 960 GLU cc_start: 0.6411 (tt0) cc_final: 0.5657 (mm-30) REVERT: I 1011 MET cc_start: 0.5543 (mmt) cc_final: 0.5282 (mmt) REVERT: I 1109 MET cc_start: 0.8798 (tpp) cc_final: 0.8228 (tpt) REVERT: I 1112 MET cc_start: 0.9317 (mmt) cc_final: 0.9019 (mmm) REVERT: I 1154 LEU cc_start: 0.9256 (mp) cc_final: 0.8876 (mp) REVERT: I 1233 MET cc_start: 0.2482 (tpp) cc_final: 0.1992 (tpp) REVERT: J 240 TYR cc_start: 0.9132 (t80) cc_final: 0.8786 (p90) REVERT: K 376 MET cc_start: 0.0168 (ptt) cc_final: -0.0663 (ppp) REVERT: L 287 LEU cc_start: 0.9014 (mt) cc_final: 0.8759 (mm) REVERT: L 372 MET cc_start: 0.9552 (mtt) cc_final: 0.9230 (mpp) REVERT: M 38 MET cc_start: 0.4978 (ttt) cc_final: 0.4667 (ttm) REVERT: M 166 LEU cc_start: 0.9483 (mm) cc_final: 0.8975 (tt) REVERT: M 208 MET cc_start: 0.8829 (mtm) cc_final: 0.8613 (mtt) REVERT: M 213 MET cc_start: 0.8801 (tpp) cc_final: 0.8561 (tpp) REVERT: M 217 MET cc_start: 0.9619 (mtp) cc_final: 0.9344 (mtp) REVERT: M 361 MET cc_start: 0.8611 (mmp) cc_final: 0.8284 (mmm) REVERT: N 896 MET cc_start: 0.9307 (mmp) cc_final: 0.9092 (mmm) REVERT: O 469 MET cc_start: 0.8412 (mmt) cc_final: 0.7754 (mmm) REVERT: O 498 MET cc_start: 0.7925 (mmp) cc_final: 0.6935 (mtp) REVERT: O 900 GLU cc_start: 0.9510 (OUTLIER) cc_final: 0.9146 (pm20) REVERT: P 149 ASP cc_start: 0.9283 (t70) cc_final: 0.8578 (t0) REVERT: P 161 ILE cc_start: 0.9479 (mt) cc_final: 0.9262 (mt) REVERT: P 164 LYS cc_start: 0.9433 (mmmt) cc_final: 0.9090 (tmtt) REVERT: P 441 MET cc_start: 0.9058 (mpp) cc_final: 0.8636 (mpp) REVERT: P 474 GLU cc_start: 0.7587 (tm-30) cc_final: 0.7350 (tm-30) REVERT: Q 205 GLU cc_start: 0.5263 (tp30) cc_final: 0.4724 (pp20) REVERT: R 196 VAL cc_start: 0.8031 (t) cc_final: 0.7790 (t) REVERT: R 216 ARG cc_start: 0.9594 (tmt170) cc_final: 0.9232 (mmt-90) REVERT: R 228 LEU cc_start: 0.7384 (pp) cc_final: 0.6982 (mp) REVERT: S 572 MET cc_start: -0.1510 (mmm) cc_final: -0.2059 (mtp) REVERT: U 1521 TYR cc_start: 0.8186 (t80) cc_final: 0.7542 (m-80) outliers start: 2 outliers final: 0 residues processed: 430 average time/residue: 0.2551 time to fit residues: 179.6511 Evaluate side-chains 331 residues out of total 3874 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 330 time to evaluate : 1.315 ------------------------------------------------------------------------------- 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: 10.0000 chunk 40 optimal weight: 6.9990 chunk 298 optimal weight: 0.9990 chunk 243 optimal weight: 9.9990 chunk 277 optimal weight: 0.3980 chunk 138 optimal weight: 7.9990 chunk 475 optimal weight: 20.0000 chunk 280 optimal weight: 0.0970 chunk 395 optimal weight: 7.9990 chunk 430 optimal weight: 8.9990 chunk 305 optimal weight: 3.9990 overall best weight: 2.4984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 38 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 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 140 HIS N 439 HIS ** O 436 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 135 GLN P 145 GLN ** P 345 GLN ** 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 = 0.3862 r_free = 0.3862 target = 0.068113 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.048279 restraints weight = 444642.893| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.3486 r_free = 0.3486 target = 0.049418 restraints weight = 240933.078| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 55)----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.050176 restraints weight = 160877.061| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 52)----------------| | r_work = 0.3517 r_free = 0.3517 target = 0.050765 restraints weight = 124941.818| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3523 r_free = 0.3523 target = 0.050993 restraints weight = 105625.736| |-----------------------------------------------------------------------------| r_work (final): 0.3403 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3403 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3403 r_free = 0.3403 target_work(ls_wunit_k1) = 0.045 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3403 r_free = 0.3403 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 (8 function evaluations) r_final: 0.3403 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7762 moved from start: 0.3349 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.087 44567 Z= 0.157 Angle : 0.628 10.407 61592 Z= 0.339 Chirality : 0.040 0.340 6923 Planarity : 0.005 0.126 6764 Dihedral : 22.926 159.836 8596 Min Nonbonded Distance : 2.196 Molprobity Statistics. All-atom Clashscore : 10.45 Ramachandran Plot: Outliers : 0.07 % Allowed : 6.48 % Favored : 93.45 % Rotamer: Outliers : 0.03 % Allowed : 3.59 % Favored : 96.38 % 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: -0.44 (0.13), residues: 4321 helix: 0.82 (0.10), residues: 2479 sheet: -2.00 (0.34), residues: 182 loop : -1.82 (0.15), residues: 1660 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG M 366 TYR 0.033 0.001 TYR B 51 PHE 0.029 0.002 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 0.00306 / 0.16 (44565) covalent geometry : angle 0.62813 / 0.34 (61592) hydrogen bonds : bond 0.04706 / 3.15 ( 2339) hydrogen bonds : angle 4.43132 / 3.14 ( 6495) Misc. bond : bond 0.00351 / 0.17 ( 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 415 residues out of total 3874 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 414 time to evaluate : 1.569 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 90 MET cc_start: 0.9154 (mmp) cc_final: 0.8840 (mmm) REVERT: A 92 LEU cc_start: 0.9828 (mm) cc_final: 0.9618 (mm) REVERT: B 84 MET cc_start: 0.9177 (mmm) cc_final: 0.8306 (mmm) REVERT: C 36 LYS cc_start: 0.9648 (mptt) cc_final: 0.9401 (mmtm) REVERT: C 64 GLU cc_start: 0.9461 (tt0) cc_final: 0.8871 (tm-30) REVERT: D 59 MET cc_start: 0.9533 (tmm) cc_final: 0.9282 (tmm) REVERT: D 68 ASP cc_start: 0.9376 (t70) cc_final: 0.8570 (t0) REVERT: D 106 LEU cc_start: 0.9371 (mt) cc_final: 0.9036 (mt) REVERT: E 50 GLU cc_start: 0.9656 (mm-30) cc_final: 0.9455 (mm-30) REVERT: E 67 PHE cc_start: 0.9494 (t80) cc_final: 0.9004 (t80) REVERT: E 74 ILE cc_start: 0.9691 (pt) cc_final: 0.9370 (pt) REVERT: E 77 ASP cc_start: 0.9396 (m-30) cc_final: 0.9169 (m-30) REVERT: E 90 MET cc_start: 0.9480 (mmp) cc_final: 0.9258 (mmp) REVERT: E 93 GLN cc_start: 0.9405 (tt0) cc_final: 0.8486 (tp40) REVERT: E 97 GLU cc_start: 0.9151 (mm-30) cc_final: 0.8936 (mm-30) REVERT: E 105 GLU cc_start: 0.9038 (tm-30) cc_final: 0.8820 (tm-30) REVERT: F 22 LEU cc_start: 0.8837 (mp) cc_final: 0.8598 (pt) REVERT: F 60 VAL cc_start: 0.9683 (t) cc_final: 0.9365 (t) REVERT: F 91 LYS cc_start: 0.9656 (tmmt) cc_final: 0.9318 (ptmm) REVERT: G 36 LYS cc_start: 0.9468 (mmmt) cc_final: 0.8851 (mmtm) REVERT: G 51 LEU cc_start: 0.9767 (tp) cc_final: 0.9507 (tp) REVERT: G 56 GLU cc_start: 0.8531 (tt0) cc_final: 0.8036 (mt-10) REVERT: G 64 GLU cc_start: 0.8980 (tp30) cc_final: 0.8292 (tp30) REVERT: G 95 LYS cc_start: 0.9585 (tptp) cc_final: 0.9185 (tppt) REVERT: H 59 MET cc_start: 0.9067 (tpp) cc_final: 0.8663 (tpp) REVERT: H 95 GLN cc_start: 0.9528 (tt0) cc_final: 0.9163 (tm-30) REVERT: I 372 TYR cc_start: 0.9353 (m-10) cc_final: 0.9031 (t80) REVERT: I 424 MET cc_start: 0.6396 (ppp) cc_final: 0.5910 (ppp) REVERT: I 527 MET cc_start: 0.8072 (tpt) cc_final: 0.7662 (mtt) REVERT: I 886 MET cc_start: 0.7845 (mtt) cc_final: 0.7134 (mmt) REVERT: I 960 GLU cc_start: 0.6256 (tt0) cc_final: 0.5522 (mm-30) REVERT: I 1011 MET cc_start: 0.5796 (mmt) cc_final: 0.5548 (mmt) REVERT: I 1109 MET cc_start: 0.8902 (tpp) cc_final: 0.8429 (tpt) REVERT: I 1112 MET cc_start: 0.9352 (mmt) cc_final: 0.9030 (mmm) REVERT: I 1154 LEU cc_start: 0.9306 (mp) cc_final: 0.8953 (mp) REVERT: I 1233 MET cc_start: 0.2949 (tpp) cc_final: 0.2393 (tpp) REVERT: J 240 TYR cc_start: 0.9104 (t80) cc_final: 0.8752 (p90) REVERT: K 376 MET cc_start: 0.0653 (ptt) cc_final: -0.0106 (ppp) REVERT: L 78 PHE cc_start: 0.7958 (m-80) cc_final: 0.7698 (m-80) REVERT: L 191 MET cc_start: 0.8864 (tpp) cc_final: 0.8648 (tpp) REVERT: L 287 LEU cc_start: 0.9095 (mt) cc_final: 0.8879 (mm) REVERT: L 372 MET cc_start: 0.9586 (mtt) cc_final: 0.9214 (mtt) REVERT: M 38 MET cc_start: 0.4939 (ttt) cc_final: 0.4713 (ttm) REVERT: M 166 LEU cc_start: 0.9446 (mm) cc_final: 0.8920 (tt) REVERT: M 208 MET cc_start: 0.8890 (mtm) cc_final: 0.8678 (mtt) REVERT: M 217 MET cc_start: 0.9603 (mtp) cc_final: 0.9316 (mtp) REVERT: M 361 MET cc_start: 0.8620 (mmp) cc_final: 0.8379 (mmm) REVERT: N 896 MET cc_start: 0.9329 (mmp) cc_final: 0.9070 (mmm) REVERT: O 469 MET cc_start: 0.8414 (mmt) cc_final: 0.7800 (mmt) REVERT: O 498 MET cc_start: 0.7948 (mmp) cc_final: 0.7234 (mtp) REVERT: O 523 MET cc_start: 0.8740 (tpt) cc_final: 0.8179 (tpt) REVERT: O 896 MET cc_start: 0.9204 (mtp) cc_final: 0.8845 (mtp) REVERT: P 164 LYS cc_start: 0.9449 (mmmt) cc_final: 0.9104 (tmtt) REVERT: P 441 MET cc_start: 0.8985 (mpp) cc_final: 0.8742 (mpp) REVERT: P 494 TYR cc_start: 0.9308 (t80) cc_final: 0.8924 (t80) REVERT: Q 205 GLU cc_start: 0.5220 (tp30) cc_final: 0.4808 (pp20) REVERT: R 216 ARG cc_start: 0.9623 (tmt170) cc_final: 0.9267 (mmt-90) REVERT: R 228 LEU cc_start: 0.7719 (pp) cc_final: 0.7297 (mp) REVERT: S 572 MET cc_start: -0.1593 (mmm) cc_final: -0.2102 (mtp) REVERT: U 1521 TYR cc_start: 0.8195 (t80) cc_final: 0.7573 (m-80) outliers start: 1 outliers final: 0 residues processed: 415 average time/residue: 0.2419 time to fit residues: 165.8898 Evaluate side-chains 320 residues out of total 3874 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 320 time to evaluate : 1.204 ------------------------------------------------------------------------------- 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: 8.9990 chunk 354 optimal weight: 20.0000 chunk 149 optimal weight: 20.0000 chunk 187 optimal weight: 1.9990 chunk 95 optimal weight: 20.0000 chunk 35 optimal weight: 3.9990 chunk 45 optimal weight: 0.8980 chunk 73 optimal weight: 30.0000 chunk 461 optimal weight: 50.0000 chunk 50 optimal weight: 0.6980 chunk 326 optimal weight: 3.9990 overall best weight: 2.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 915 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 969 HIS I1253 HIS ** J 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 296 ASN ** K 205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L1796 ASN ** M 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 140 HIS M 380 ASN N 422 HIS N 439 HIS ** O 436 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 345 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 437 GLN ** 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 = 0.3851 r_free = 0.3851 target = 0.067630 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3446 r_free = 0.3446 target = 0.047783 restraints weight = 444754.257| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.3472 r_free = 0.3472 target = 0.048882 restraints weight = 242079.664| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 73)----------------| | r_work = 0.3491 r_free = 0.3491 target = 0.049686 restraints weight = 160464.069| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.050076 restraints weight = 123527.728| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3509 r_free = 0.3509 target = 0.050386 restraints weight = 106568.541| |-----------------------------------------------------------------------------| r_work (final): 0.3387 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3388 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3388 r_free = 0.3388 target_work(ls_wunit_k1) = 0.044 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3388 r_free = 0.3388 target_work(ls_wunit_k1) = 0.044 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3388 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7792 moved from start: 0.3657 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 44567 Z= 0.149 Angle : 0.622 10.465 61592 Z= 0.336 Chirality : 0.041 0.345 6923 Planarity : 0.004 0.062 6764 Dihedral : 23.019 156.317 8596 Min Nonbonded Distance : 2.182 Molprobity Statistics. All-atom Clashscore : 10.53 Ramachandran Plot: Outliers : 0.07 % Allowed : 6.09 % Favored : 93.84 % Rotamer: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % 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: -0.35 (0.13), residues: 4321 helix: 0.88 (0.10), residues: 2482 sheet: -1.84 (0.35), residues: 180 loop : -1.78 (0.15), residues: 1659 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.031 0.001 ARG C 99 TYR 0.027 0.001 TYR B 51 PHE 0.021 0.001 PHE O 951 TRP 0.044 0.002 TRP O 620 HIS 0.013 0.001 HIS O 905 Details of bonding type rmsd/Z covalent geometry : bond 0.00288 / 0.15 (44565) covalent geometry : angle 0.62171 / 0.34 (61592) hydrogen bonds : bond 0.04340 / 2.89 ( 2339) hydrogen bonds : angle 4.38486 / 3.12 ( 6495) Misc. bond : bond 0.00350 / 0.18 ( 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 412 residues out of total 3874 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 412 time to evaluate : 1.247 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 90 MET cc_start: 0.9085 (mmp) cc_final: 0.8817 (mmm) REVERT: B 50 ILE cc_start: 0.8812 (mm) cc_final: 0.8553 (mm) REVERT: B 84 MET cc_start: 0.9150 (mmm) cc_final: 0.8404 (mmm) REVERT: C 36 LYS cc_start: 0.9624 (mptt) cc_final: 0.9393 (mmtm) REVERT: C 64 GLU cc_start: 0.9425 (tt0) cc_final: 0.8877 (tm-30) REVERT: D 59 MET cc_start: 0.9520 (tmm) cc_final: 0.9281 (tmm) REVERT: D 80 LEU cc_start: 0.9757 (mt) cc_final: 0.9471 (mt) REVERT: D 106 LEU cc_start: 0.9360 (mt) cc_final: 0.9008 (mt) REVERT: E 50 GLU cc_start: 0.9661 (mm-30) cc_final: 0.9436 (mm-30) REVERT: E 67 PHE cc_start: 0.9521 (t80) cc_final: 0.9279 (t80) REVERT: E 74 ILE cc_start: 0.9643 (pt) cc_final: 0.9334 (pt) REVERT: E 97 GLU cc_start: 0.9225 (mm-30) cc_final: 0.8914 (mm-30) REVERT: F 22 LEU cc_start: 0.8858 (mp) cc_final: 0.8617 (pt) REVERT: F 59 LYS cc_start: 0.9809 (tttm) cc_final: 0.8945 (tptp) REVERT: F 60 VAL cc_start: 0.9638 (t) cc_final: 0.9413 (t) REVERT: F 63 GLU cc_start: 0.9444 (pt0) cc_final: 0.8970 (pt0) REVERT: G 36 LYS cc_start: 0.9512 (mmmt) cc_final: 0.8913 (mmtm) REVERT: G 51 LEU cc_start: 0.9755 (tp) cc_final: 0.9526 (tp) REVERT: G 56 GLU cc_start: 0.8582 (tt0) cc_final: 0.7996 (mt-10) REVERT: G 64 GLU cc_start: 0.8975 (tp30) cc_final: 0.8341 (tp30) REVERT: G 95 LYS cc_start: 0.9574 (tptp) cc_final: 0.9216 (tppt) REVERT: H 59 MET cc_start: 0.9042 (tpp) cc_final: 0.8614 (tpp) REVERT: H 95 GLN cc_start: 0.9485 (tt0) cc_final: 0.8951 (pt0) REVERT: I 372 TYR cc_start: 0.9368 (m-10) cc_final: 0.9034 (t80) REVERT: I 424 MET cc_start: 0.6322 (ppp) cc_final: 0.5450 (ppp) REVERT: I 527 MET cc_start: 0.8053 (tpt) cc_final: 0.7623 (mtt) REVERT: I 886 MET cc_start: 0.7886 (mtt) cc_final: 0.7211 (mmt) REVERT: I 960 GLU cc_start: 0.5959 (tt0) cc_final: 0.5113 (mm-30) REVERT: I 1011 MET cc_start: 0.5786 (mmt) cc_final: 0.5521 (mmt) REVERT: I 1109 MET cc_start: 0.8880 (tpp) cc_final: 0.8456 (mmm) REVERT: I 1112 MET cc_start: 0.9348 (mmt) cc_final: 0.9015 (mmm) REVERT: I 1154 LEU cc_start: 0.9315 (mp) cc_final: 0.8927 (mp) REVERT: I 1233 MET cc_start: 0.2831 (tpp) cc_final: 0.2174 (tpp) REVERT: J 153 MET cc_start: -0.1080 (tpt) cc_final: -0.1534 (tpp) REVERT: J 240 TYR cc_start: 0.9051 (t80) cc_final: 0.8689 (p90) REVERT: K 114 GLU cc_start: 0.8274 (tp30) cc_final: 0.7946 (pm20) REVERT: K 376 MET cc_start: 0.0894 (ptt) cc_final: 0.0093 (ppp) REVERT: L 287 LEU cc_start: 0.9080 (mt) cc_final: 0.8716 (mt) REVERT: L 372 MET cc_start: 0.9592 (mtt) cc_final: 0.9218 (mtt) REVERT: L 445 MET cc_start: 0.8893 (mtt) cc_final: 0.8479 (tpp) REVERT: L 449 LEU cc_start: 0.9352 (mt) cc_final: 0.8868 (mt) REVERT: L 470 HIS cc_start: 0.8383 (m-70) cc_final: 0.8076 (t-90) REVERT: M 166 LEU cc_start: 0.9424 (mm) cc_final: 0.8875 (tp) REVERT: N 462 TYR cc_start: 0.8939 (t80) cc_final: 0.8707 (t80) REVERT: O 469 MET cc_start: 0.8337 (mmt) cc_final: 0.7702 (mmt) REVERT: O 498 MET cc_start: 0.8051 (mmp) cc_final: 0.7206 (mtp) REVERT: O 523 MET cc_start: 0.8795 (tpt) cc_final: 0.8080 (tpt) REVERT: O 896 MET cc_start: 0.9296 (mtp) cc_final: 0.9062 (mmm) REVERT: P 161 ILE cc_start: 0.9475 (tt) cc_final: 0.9118 (pt) REVERT: P 162 MET cc_start: 0.9089 (tpt) cc_final: 0.8777 (tpt) REVERT: P 164 LYS cc_start: 0.9441 (mmmt) cc_final: 0.9083 (tmtt) REVERT: P 366 MET cc_start: 0.8242 (mmt) cc_final: 0.7896 (mmp) REVERT: P 441 MET cc_start: 0.9082 (mpp) cc_final: 0.8796 (mpp) REVERT: P 494 TYR cc_start: 0.9302 (t80) cc_final: 0.8924 (t80) REVERT: Q 205 GLU cc_start: 0.5259 (tp30) cc_final: 0.4844 (pp20) REVERT: R 196 VAL cc_start: 0.7816 (t) cc_final: 0.7531 (t) REVERT: R 216 ARG cc_start: 0.9625 (tmt170) cc_final: 0.9270 (mmt-90) REVERT: R 219 MET cc_start: 0.9325 (mmp) cc_final: 0.9026 (mmm) REVERT: R 228 LEU cc_start: 0.7658 (pp) cc_final: 0.7262 (mp) REVERT: S 176 MET cc_start: 0.3958 (ttp) cc_final: 0.3625 (ttp) REVERT: S 572 MET cc_start: -0.1605 (mmm) cc_final: -0.2121 (mtt) REVERT: U 1521 TYR cc_start: 0.8176 (t80) cc_final: 0.7584 (m-80) outliers start: 0 outliers final: 0 residues processed: 412 average time/residue: 0.2411 time to fit residues: 165.1217 Evaluate side-chains 323 residues out of total 3874 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 323 time to evaluate : 1.432 ------------------------------------------------------------------------------- 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: 4.9990 chunk 186 optimal weight: 30.0000 chunk 193 optimal weight: 5.9990 chunk 332 optimal weight: 50.0000 chunk 445 optimal weight: 50.0000 chunk 37 optimal weight: 10.0000 chunk 81 optimal weight: 8.9990 chunk 209 optimal weight: 0.0570 chunk 430 optimal weight: 8.9990 chunk 103 optimal weight: 8.9990 chunk 412 optimal weight: 0.0060 overall best weight: 4.0120 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 375 GLN ** I 915 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 73 HIS ** J 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 296 ASN K 110 HIS ** K 205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 144 GLN M 140 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** S 142 GLN S 561 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3800 r_free = 0.3800 target = 0.065566 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.045909 restraints weight = 455908.506| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.046894 restraints weight = 248972.359| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 53)----------------| | r_work = 0.3428 r_free = 0.3428 target = 0.047642 restraints weight = 166237.353| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 66)----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.048105 restraints weight = 128517.917| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3442 r_free = 0.3442 target = 0.048222 restraints weight = 110741.694| |-----------------------------------------------------------------------------| r_work (final): 0.3316 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3316 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3316 r_free = 0.3316 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 = 0.3316 r_free = 0.3316 target_work(ls_wunit_k1) = 0.042 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3316 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7870 moved from start: 0.4172 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 44567 Z= 0.199 Angle : 0.667 10.694 61592 Z= 0.359 Chirality : 0.041 0.342 6923 Planarity : 0.005 0.062 6764 Dihedral : 23.222 155.430 8596 Min Nonbonded Distance : 2.180 Molprobity Statistics. All-atom Clashscore : 13.92 Ramachandran Plot: Outliers : 0.07 % Allowed : 6.71 % Favored : 93.22 % Rotamer: Outliers : 0.05 % Allowed : 1.95 % 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: -0.43 (0.13), residues: 4321 helix: 0.79 (0.10), residues: 2480 sheet: -1.70 (0.36), residues: 191 loop : -1.77 (0.15), residues: 1650 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG M 366 TYR 0.032 0.002 TYR B 51 PHE 0.023 0.002 PHE L 217 TRP 0.040 0.002 TRP O 620 HIS 0.008 0.001 HIS P 362 Details of bonding type rmsd/Z covalent geometry : bond 0.00381 / 0.20 (44565) covalent geometry : angle 0.66654 / 0.36 (61592) hydrogen bonds : bond 0.05579 / 3.73 ( 2339) hydrogen bonds : angle 4.51463 / 3.21 ( 6495) Misc. bond : bond 0.00196 / 0.09 ( 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 382 residues out of total 3874 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 380 time to evaluate : 1.485 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 90 MET cc_start: 0.9135 (mmp) cc_final: 0.8860 (mmm) REVERT: A 92 LEU cc_start: 0.9862 (mm) cc_final: 0.9646 (mm) REVERT: B 84 MET cc_start: 0.9231 (mmm) cc_final: 0.8584 (mmm) REVERT: C 36 LYS cc_start: 0.9630 (mptt) cc_final: 0.9412 (mmtm) REVERT: C 64 GLU cc_start: 0.9465 (tt0) cc_final: 0.8888 (tm-30) REVERT: D 59 MET cc_start: 0.9502 (tmm) cc_final: 0.9251 (tmm) REVERT: E 74 ILE cc_start: 0.9614 (pt) cc_final: 0.9270 (pt) REVERT: E 97 GLU cc_start: 0.9220 (mm-30) cc_final: 0.8939 (mm-30) REVERT: E 105 GLU cc_start: 0.9077 (tm-30) cc_final: 0.8851 (tm-30) REVERT: F 22 LEU cc_start: 0.8897 (mp) cc_final: 0.8661 (pt) REVERT: F 59 LYS cc_start: 0.9816 (tttm) cc_final: 0.8959 (tptp) REVERT: F 60 VAL cc_start: 0.9641 (t) cc_final: 0.9386 (t) REVERT: F 63 GLU cc_start: 0.9424 (pt0) cc_final: 0.8981 (pt0) REVERT: G 36 LYS cc_start: 0.9657 (mmmt) cc_final: 0.9116 (mmtm) REVERT: G 51 LEU cc_start: 0.9762 (tp) cc_final: 0.9514 (tp) REVERT: G 56 GLU cc_start: 0.8830 (tt0) cc_final: 0.8465 (mt-10) REVERT: G 64 GLU cc_start: 0.8962 (tp30) cc_final: 0.8326 (tp30) REVERT: G 95 LYS cc_start: 0.9636 (tptp) cc_final: 0.9285 (tppt) REVERT: H 59 MET cc_start: 0.9029 (tpp) cc_final: 0.8649 (tpp) REVERT: I 375 GLN cc_start: 0.7512 (OUTLIER) cc_final: 0.7168 (pp30) REVERT: I 424 MET cc_start: 0.6388 (ppp) cc_final: 0.5466 (ppp) REVERT: I 527 MET cc_start: 0.7912 (tpt) cc_final: 0.7534 (mtt) REVERT: I 886 MET cc_start: 0.7837 (mtt) cc_final: 0.7161 (mmt) REVERT: I 1000 MET cc_start: 0.9119 (ptm) cc_final: 0.8908 (ptm) REVERT: I 1011 MET cc_start: 0.5921 (mmt) cc_final: 0.5673 (mmt) REVERT: I 1109 MET cc_start: 0.8940 (tpp) cc_final: 0.8538 (mmm) REVERT: I 1112 MET cc_start: 0.9356 (mmt) cc_final: 0.9029 (mmm) REVERT: I 1154 LEU cc_start: 0.9367 (mp) cc_final: 0.9016 (mp) REVERT: I 1233 MET cc_start: 0.3594 (tpp) cc_final: 0.2970 (tpp) REVERT: J 240 TYR cc_start: 0.9067 (t80) cc_final: 0.8705 (p90) REVERT: K 114 GLU cc_start: 0.8253 (tp30) cc_final: 0.8010 (pm20) REVERT: K 376 MET cc_start: 0.2172 (ptp) cc_final: 0.1496 (ppp) REVERT: L 78 PHE cc_start: 0.7693 (m-80) cc_final: 0.7439 (m-80) REVERT: L 191 MET cc_start: 0.8944 (tpp) cc_final: 0.8705 (tpp) REVERT: L 287 LEU cc_start: 0.9240 (mt) cc_final: 0.8923 (mt) REVERT: L 372 MET cc_start: 0.9605 (mtt) cc_final: 0.9161 (mtt) REVERT: L 393 GLU cc_start: 0.9461 (tm-30) cc_final: 0.9253 (pt0) REVERT: L 445 MET cc_start: 0.8899 (mtt) cc_final: 0.8382 (mtt) REVERT: L 470 HIS cc_start: 0.8397 (m-70) cc_final: 0.8124 (t-90) REVERT: N 462 TYR cc_start: 0.9039 (t80) cc_final: 0.8781 (t80) REVERT: N 896 MET cc_start: 0.9364 (mmp) cc_final: 0.9154 (mmm) REVERT: O 469 MET cc_start: 0.8402 (mmt) cc_final: 0.7941 (mmm) REVERT: O 523 MET cc_start: 0.8958 (tpt) cc_final: 0.8553 (tpt) REVERT: P 149 ASP cc_start: 0.9048 (t0) cc_final: 0.8814 (t0) REVERT: P 161 ILE cc_start: 0.9537 (tt) cc_final: 0.9201 (pt) REVERT: P 164 LYS cc_start: 0.9488 (mmmt) cc_final: 0.9205 (tmtt) REVERT: P 366 MET cc_start: 0.8341 (mmt) cc_final: 0.8013 (mmp) REVERT: P 441 MET cc_start: 0.9086 (mpp) cc_final: 0.8877 (mpp) REVERT: P 494 TYR cc_start: 0.9322 (t80) cc_final: 0.8869 (t80) REVERT: Q 205 GLU cc_start: 0.5270 (tp30) cc_final: 0.4855 (pp20) REVERT: R 196 VAL cc_start: 0.7605 (t) cc_final: 0.7235 (t) REVERT: R 216 ARG cc_start: 0.9645 (tmt170) cc_final: 0.9335 (mmt-90) REVERT: R 219 MET cc_start: 0.9384 (mmp) cc_final: 0.9101 (mmm) REVERT: R 228 LEU cc_start: 0.8117 (pp) cc_final: 0.7794 (mp) REVERT: S 176 MET cc_start: 0.4125 (ttp) cc_final: 0.3884 (ttp) REVERT: S 572 MET cc_start: -0.1550 (mmm) cc_final: -0.2049 (mtt) REVERT: U 1521 TYR cc_start: 0.8271 (t80) cc_final: 0.7756 (m-80) outliers start: 2 outliers final: 1 residues processed: 382 average time/residue: 0.2475 time to fit residues: 157.0847 Evaluate side-chains 303 residues out of total 3874 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 301 time to evaluate : 1.030 ------------------------------------------------------------------------------- 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: 2.9990 chunk 378 optimal weight: 7.9990 chunk 37 optimal weight: 9.9990 chunk 219 optimal weight: 4.9990 chunk 374 optimal weight: 10.0000 chunk 340 optimal weight: 6.9990 chunk 420 optimal weight: 5.9990 chunk 289 optimal weight: 8.9990 chunk 240 optimal weight: 9.9990 chunk 91 optimal weight: 7.9990 chunk 350 optimal weight: 20.0000 overall best weight: 5.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 25 ASN ** E 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 85 GLN I 380 HIS I 788 GLN I 847 GLN I 915 GLN ** 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 ** L 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 192 GLN M 140 HIS ** M 141 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 152 ASN M 198 GLN M 288 ASN N 422 HIS N 875 HIS ** O 423 HIS ** 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 422 ASN ** 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 190 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 247 GLN S 592 ASN ** U1514 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3732 r_free = 0.3732 target = 0.062573 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3290 r_free = 0.3290 target = 0.042820 restraints weight = 467684.234| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.3315 r_free = 0.3315 target = 0.043820 restraints weight = 253279.070| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 52)----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.044503 restraints weight = 169528.268| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 55)----------------| | r_work = 0.3345 r_free = 0.3345 target = 0.044983 restraints weight = 133095.613| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 61)----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.045193 restraints weight = 114995.137| |-----------------------------------------------------------------------------| r_work (final): 0.3225 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3226 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3226 r_free = 0.3226 target_work(ls_wunit_k1) = 0.039 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3226 r_free = 0.3226 target_work(ls_wunit_k1) = 0.039 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3226 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7984 moved from start: 0.5133 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.123 44567 Z= 0.265 Angle : 0.769 18.215 61592 Z= 0.413 Chirality : 0.045 0.325 6923 Planarity : 0.006 0.084 6764 Dihedral : 23.747 154.619 8596 Min Nonbonded Distance : 2.253 Molprobity Statistics. All-atom Clashscore : 19.42 Ramachandran Plot: Outliers : 0.07 % Allowed : 7.20 % Favored : 92.73 % Rotamer: Outliers : 0.10 % Allowed : 2.73 % Favored : 97.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % 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: -0.87 (0.12), residues: 4321 helix: 0.38 (0.10), residues: 2492 sheet: -1.87 (0.34), residues: 212 loop : -1.87 (0.15), residues: 1617 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG N 499 TYR 0.072 0.002 TYR O 922 PHE 0.030 0.002 PHE K 289 TRP 0.030 0.002 TRP O 620 HIS 0.013 0.002 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00513 / 0.27 (44565) covalent geometry : angle 0.76868 / 0.41 (61592) hydrogen bonds : bond 0.07048 / 4.69 ( 2339) hydrogen bonds : angle 4.88394 / 3.48 ( 6495) Misc. bond : bond 0.00076 / 0.04 ( 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 366 residues out of total 3874 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 362 time to evaluate : 1.308 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: A 90 MET cc_start: 0.9153 (mmp) cc_final: 0.8890 (mmm) REVERT: A 125 GLN cc_start: 0.9712 (mt0) cc_final: 0.9448 (mp10) REVERT: B 84 MET cc_start: 0.9225 (mmm) cc_final: 0.8554 (mmm) REVERT: C 39 TYR cc_start: 0.9194 (m-80) cc_final: 0.8930 (m-80) REVERT: C 64 GLU cc_start: 0.9499 (tt0) cc_final: 0.8909 (tm-30) REVERT: D 59 MET cc_start: 0.9568 (tmm) cc_final: 0.9333 (tmm) REVERT: E 74 ILE cc_start: 0.9691 (pt) cc_final: 0.9357 (pt) REVERT: E 97 GLU cc_start: 0.9323 (mm-30) cc_final: 0.8952 (mm-30) REVERT: E 103 LEU cc_start: 0.9654 (mt) cc_final: 0.9432 (mt) REVERT: E 105 GLU cc_start: 0.9084 (tm-30) cc_final: 0.8795 (tm-30) REVERT: E 106 ASP cc_start: 0.9545 (t70) cc_final: 0.9341 (t0) REVERT: E 120 MET cc_start: 0.9258 (tpt) cc_final: 0.8999 (mmm) REVERT: F 22 LEU cc_start: 0.8952 (mp) cc_final: 0.8723 (pt) REVERT: F 59 LYS cc_start: 0.9795 (tttm) cc_final: 0.9354 (ttmm) REVERT: G 36 LYS cc_start: 0.9717 (mmmt) cc_final: 0.9252 (mmtm) REVERT: G 56 GLU cc_start: 0.8809 (tt0) cc_final: 0.8357 (mt-10) REVERT: G 64 GLU cc_start: 0.8995 (tp30) cc_final: 0.8418 (tp30) REVERT: G 95 LYS cc_start: 0.9665 (tptp) cc_final: 0.9296 (tppt) REVERT: G 112 GLN cc_start: 0.9276 (mp10) cc_final: 0.8982 (mp10) REVERT: H 59 MET cc_start: 0.9036 (tpp) cc_final: 0.8659 (tpp) REVERT: H 62 MET cc_start: 0.9569 (mmp) cc_final: 0.9341 (mmm) REVERT: H 108 LYS cc_start: 0.9784 (ptpp) cc_final: 0.9510 (ptpp) REVERT: I 409 LEU cc_start: 0.7557 (tp) cc_final: 0.6897 (tp) REVERT: I 424 MET cc_start: 0.6672 (ppp) cc_final: 0.6336 (ppp) REVERT: I 527 MET cc_start: 0.7780 (tpt) cc_final: 0.7365 (mtt) REVERT: I 886 MET cc_start: 0.8217 (mtt) cc_final: 0.7415 (mmt) REVERT: I 1000 MET cc_start: 0.9182 (ptm) cc_final: 0.8757 (ptm) REVERT: I 1109 MET cc_start: 0.9036 (tpp) cc_final: 0.8694 (tpp) REVERT: I 1112 MET cc_start: 0.9288 (mmt) cc_final: 0.8977 (mmm) REVERT: I 1154 LEU cc_start: 0.9366 (mp) cc_final: 0.9129 (mp) REVERT: I 1233 MET cc_start: 0.3997 (tpp) cc_final: 0.3367 (tpp) REVERT: J 240 TYR cc_start: 0.9080 (t80) cc_final: 0.8701 (p90) REVERT: K 114 GLU cc_start: 0.8296 (tp30) cc_final: 0.7972 (pm20) REVERT: K 376 MET cc_start: 0.2782 (ptp) cc_final: 0.2048 (ppp) REVERT: L 78 PHE cc_start: 0.7968 (m-80) cc_final: 0.7749 (m-80) REVERT: L 191 MET cc_start: 0.9021 (tpp) cc_final: 0.8813 (tpp) REVERT: L 287 LEU cc_start: 0.9400 (mt) cc_final: 0.9143 (mm) REVERT: L 372 MET cc_start: 0.9642 (mtt) cc_final: 0.9381 (mpp) REVERT: L 393 GLU cc_start: 0.9567 (tm-30) cc_final: 0.9304 (pt0) REVERT: L 445 MET cc_start: 0.8901 (mtt) cc_final: 0.8412 (mtt) REVERT: M 166 LEU cc_start: 0.9446 (mm) cc_final: 0.9019 (tp) REVERT: M 217 MET cc_start: 0.9606 (mtp) cc_final: 0.9385 (mtp) REVERT: M 361 MET cc_start: 0.8734 (mmp) cc_final: 0.8464 (mmm) REVERT: N 462 TYR cc_start: 0.9196 (t80) cc_final: 0.8851 (t80) REVERT: N 469 MET cc_start: 0.9535 (mtm) cc_final: 0.9277 (ptp) REVERT: N 498 MET cc_start: 0.9433 (mpp) cc_final: 0.9041 (mpp) REVERT: N 896 MET cc_start: 0.9394 (mmp) cc_final: 0.9174 (mmm) REVERT: O 469 MET cc_start: 0.8448 (mmt) cc_final: 0.7944 (mmm) REVERT: O 498 MET cc_start: 0.8214 (mmp) cc_final: 0.7545 (mtp) REVERT: O 523 MET cc_start: 0.9164 (tpt) cc_final: 0.8828 (tpt) REVERT: P 157 LEU cc_start: 0.9584 (tp) cc_final: 0.9299 (tp) REVERT: P 161 ILE cc_start: 0.9635 (tt) cc_final: 0.8819 (pt) REVERT: P 164 LYS cc_start: 0.9557 (mmmt) cc_final: 0.9328 (tmtt) REVERT: P 494 TYR cc_start: 0.9328 (t80) cc_final: 0.8939 (t80) REVERT: Q 205 GLU cc_start: 0.4940 (tp30) cc_final: 0.4483 (pp20) REVERT: R 196 VAL cc_start: 0.7507 (t) cc_final: 0.7049 (t) REVERT: R 216 ARG cc_start: 0.9664 (tmt170) cc_final: 0.9392 (mmt-90) REVERT: R 219 MET cc_start: 0.9519 (mmp) cc_final: 0.9228 (mmm) REVERT: S 176 MET cc_start: 0.4288 (ttp) cc_final: 0.4034 (ttp) REVERT: S 572 MET cc_start: -0.1378 (mmm) cc_final: -0.1952 (mtp) REVERT: U 1521 TYR cc_start: 0.8420 (t80) cc_final: 0.7897 (m-10) outliers start: 4 outliers final: 1 residues processed: 366 average time/residue: 0.2538 time to fit residues: 154.8534 Evaluate side-chains 284 residues out of total 3874 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 283 time to evaluate : 1.434 ------------------------------------------------------------------------------- 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: 9.9990 chunk 263 optimal weight: 5.9990 chunk 68 optimal weight: 0.9980 chunk 247 optimal weight: 4.9990 chunk 97 optimal weight: 1.9990 chunk 323 optimal weight: 6.9990 chunk 146 optimal weight: 0.5980 chunk 40 optimal weight: 0.9980 chunk 244 optimal weight: 2.9990 chunk 25 optimal weight: 0.8980 chunk 369 optimal weight: 7.9990 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 38 ASN ** E 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 817 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 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 M 152 ASN M 318 GLN N 454 ASN N 467 ASN ** N 489 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 632 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 875 HIS O 621 ASN ** P 345 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 403 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 500 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3786 r_free = 0.3786 target = 0.064874 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3354 r_free = 0.3354 target = 0.044902 restraints weight = 455255.950| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.3382 r_free = 0.3382 target = 0.045998 restraints weight = 241733.278| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 52)----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.046784 restraints weight = 160464.498| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 52)----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.047271 restraints weight = 124070.948| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 55)----------------| | r_work = 0.3420 r_free = 0.3420 target = 0.047560 restraints weight = 106605.545| |-----------------------------------------------------------------------------| r_work (final): 0.3291 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3292 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3292 r_free = 0.3292 target_work(ls_wunit_k1) = 0.041 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3292 r_free = 0.3292 target_work(ls_wunit_k1) = 0.041 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (12 function evaluations) r_final: 0.3292 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7890 moved from start: 0.5106 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.077 44567 Z= 0.141 Angle : 0.668 12.583 61592 Z= 0.355 Chirality : 0.042 0.344 6923 Planarity : 0.005 0.059 6764 Dihedral : 23.645 152.458 8596 Min Nonbonded Distance : 2.293 Molprobity Statistics. All-atom Clashscore : 12.74 Ramachandran Plot: Outliers : 0.07 % Allowed : 6.50 % Favored : 93.43 % Rotamer: Outliers : 0.05 % Allowed : 0.88 % Favored : 99.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -0.47 (0.13), residues: 4321 helix: 0.70 (0.10), residues: 2479 sheet: -1.59 (0.37), residues: 197 loop : -1.70 (0.16), residues: 1645 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.028 0.001 ARG H 99 TYR 0.035 0.002 TYR N 435 PHE 0.027 0.002 PHE E 104 TRP 0.028 0.002 TRP P 207 HIS 0.010 0.001 HIS N 905 Details of bonding type rmsd/Z covalent geometry : bond 0.00282 / 0.14 (44565) covalent geometry : angle 0.66810 / 0.35 (61592) hydrogen bonds : bond 0.04291 / 2.87 ( 2339) hydrogen bonds : angle 4.54660 / 3.24 ( 6495) Misc. bond : bond 0.00619 / 0.33 ( 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 387 residues out of total 3874 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 385 time to evaluate : 1.550 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: A 90 MET cc_start: 0.9142 (mmp) cc_final: 0.8851 (mmm) REVERT: A 125 GLN cc_start: 0.9720 (mt0) cc_final: 0.9440 (mp10) REVERT: B 63 GLU cc_start: 0.9349 (mt-10) cc_final: 0.9024 (pt0) REVERT: B 84 MET cc_start: 0.9102 (mmm) cc_final: 0.8442 (mmm) REVERT: C 36 LYS cc_start: 0.9424 (mppt) cc_final: 0.9153 (mmtm) REVERT: C 64 GLU cc_start: 0.9453 (tt0) cc_final: 0.8840 (tm-30) REVERT: D 59 MET cc_start: 0.9532 (tmm) cc_final: 0.9276 (tmm) REVERT: D 106 LEU cc_start: 0.9439 (mt) cc_final: 0.9224 (mt) REVERT: E 50 GLU cc_start: 0.9644 (mm-30) cc_final: 0.9436 (mm-30) REVERT: E 74 ILE cc_start: 0.9633 (pt) cc_final: 0.9294 (pt) REVERT: E 97 GLU cc_start: 0.9185 (mm-30) cc_final: 0.8839 (mm-30) REVERT: E 105 GLU cc_start: 0.9085 (tm-30) cc_final: 0.8834 (tm-30) REVERT: F 22 LEU cc_start: 0.8916 (mp) cc_final: 0.8626 (pt) REVERT: F 59 LYS cc_start: 0.9808 (tttm) cc_final: 0.9320 (tttp) REVERT: F 63 GLU cc_start: 0.9503 (pt0) cc_final: 0.9276 (pt0) REVERT: G 36 LYS cc_start: 0.9674 (mmmt) cc_final: 0.9148 (mmtm) REVERT: G 51 LEU cc_start: 0.9776 (tp) cc_final: 0.9502 (tp) REVERT: G 56 GLU cc_start: 0.8800 (tt0) cc_final: 0.8243 (mt-10) REVERT: G 64 GLU cc_start: 0.9024 (tp30) cc_final: 0.8366 (tp30) REVERT: G 95 LYS cc_start: 0.9611 (tptp) cc_final: 0.9367 (tppt) REVERT: H 37 TYR cc_start: 0.9476 (m-80) cc_final: 0.9202 (m-10) REVERT: H 59 MET cc_start: 0.8994 (tpp) cc_final: 0.8604 (tpp) REVERT: H 62 MET cc_start: 0.9564 (mmp) cc_final: 0.9351 (mmm) REVERT: I 424 MET cc_start: 0.6509 (ppp) cc_final: 0.6147 (ppp) REVERT: I 527 MET cc_start: 0.7948 (tpt) cc_final: 0.7563 (mtt) REVERT: I 886 MET cc_start: 0.8148 (mtt) cc_final: 0.7312 (mmt) REVERT: I 960 GLU cc_start: 0.6276 (tt0) cc_final: 0.5415 (mm-30) REVERT: I 1011 MET cc_start: 0.6021 (mmt) cc_final: 0.5677 (mmt) REVERT: I 1109 MET cc_start: 0.9007 (tpp) cc_final: 0.8536 (tpt) REVERT: I 1112 MET cc_start: 0.9310 (mmt) cc_final: 0.8980 (mmm) REVERT: I 1154 LEU cc_start: 0.9439 (mp) cc_final: 0.9139 (mp) REVERT: I 1233 MET cc_start: 0.3834 (tpp) cc_final: 0.3143 (tpp) REVERT: J 240 TYR cc_start: 0.9074 (t80) cc_final: 0.8708 (p90) REVERT: K 82 MET cc_start: 0.1867 (tpt) cc_final: 0.1642 (tpt) REVERT: K 114 GLU cc_start: 0.8296 (tp30) cc_final: 0.8050 (pm20) REVERT: K 376 MET cc_start: 0.3035 (ptp) cc_final: 0.2417 (ppp) REVERT: L 191 MET cc_start: 0.9029 (tpp) cc_final: 0.8799 (tpp) REVERT: L 287 LEU cc_start: 0.9347 (mt) cc_final: 0.9002 (mt) REVERT: L 372 MET cc_start: 0.9674 (mtt) cc_final: 0.9332 (mtt) REVERT: L 393 GLU cc_start: 0.9492 (tm-30) cc_final: 0.9289 (pt0) REVERT: M 152 ASN cc_start: 0.6098 (OUTLIER) cc_final: 0.5751 (t0) REVERT: M 275 LEU cc_start: 0.9418 (tp) cc_final: 0.9193 (tp) REVERT: N 462 TYR cc_start: 0.9034 (t80) cc_final: 0.8620 (t80) REVERT: N 468 PHE cc_start: 0.9253 (t80) cc_final: 0.9031 (t80) REVERT: N 489 ASN cc_start: 0.7920 (m110) cc_final: 0.7714 (m110) REVERT: N 674 MET cc_start: 0.3865 (mpp) cc_final: 0.2551 (ttt) REVERT: N 896 MET cc_start: 0.9417 (mmp) cc_final: 0.9209 (mmm) REVERT: O 469 MET cc_start: 0.8491 (mmt) cc_final: 0.7889 (mmm) REVERT: O 498 MET cc_start: 0.8017 (mmp) cc_final: 0.7095 (mtp) REVERT: O 523 MET cc_start: 0.8840 (tpt) cc_final: 0.8374 (tpt) REVERT: P 157 LEU cc_start: 0.9512 (tp) cc_final: 0.9258 (tp) REVERT: P 161 ILE cc_start: 0.9571 (tt) cc_final: 0.8898 (pt) REVERT: P 162 MET cc_start: 0.9210 (mmp) cc_final: 0.8461 (mmm) REVERT: P 164 LYS cc_start: 0.9545 (mmmt) cc_final: 0.9310 (tmtt) REVERT: P 366 MET cc_start: 0.7985 (mmt) cc_final: 0.7572 (mmp) REVERT: P 441 MET cc_start: 0.9076 (mpp) cc_final: 0.8802 (mpp) REVERT: Q 205 GLU cc_start: 0.5867 (tp30) cc_final: 0.5374 (pp20) REVERT: Q 257 ARG cc_start: 0.9513 (mmp80) cc_final: 0.8986 (ptm-80) REVERT: R 196 VAL cc_start: 0.7613 (t) cc_final: 0.7199 (t) REVERT: R 216 ARG cc_start: 0.9599 (tmt170) cc_final: 0.9342 (mmt-90) REVERT: R 219 MET cc_start: 0.9384 (mmp) cc_final: 0.9156 (mmm) REVERT: R 228 LEU cc_start: 0.7980 (tt) cc_final: 0.7290 (mp) REVERT: S 176 MET cc_start: 0.4268 (ttp) cc_final: 0.3963 (ttp) REVERT: S 572 MET cc_start: -0.1476 (mmm) cc_final: -0.2016 (mtp) REVERT: U 1521 TYR cc_start: 0.8161 (t80) cc_final: 0.7784 (m-80) outliers start: 2 outliers final: 1 residues processed: 387 average time/residue: 0.2616 time to fit residues: 168.7565 Evaluate side-chains 302 residues out of total 3874 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 300 time to evaluate : 1.546 ------------------------------------------------------------------------------- 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: 0.8980 chunk 85 optimal weight: 4.9990 chunk 475 optimal weight: 30.0000 chunk 330 optimal weight: 5.9990 chunk 10 optimal weight: 0.8980 chunk 172 optimal weight: 2.9990 chunk 320 optimal weight: 8.9990 chunk 235 optimal weight: 0.7980 chunk 336 optimal weight: 9.9990 chunk 396 optimal weight: 7.9990 chunk 467 optimal weight: 20.0000 overall best weight: 2.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 67 ASN ** E 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 817 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 M 152 ASN N 422 HIS ** N 489 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 632 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 875 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** S 142 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3777 r_free = 0.3777 target = 0.064448 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.044449 restraints weight = 457482.614| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.045559 restraints weight = 244194.891| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 68)----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.046313 restraints weight = 162163.872| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 56)----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.046784 restraints weight = 126596.706| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.047013 restraints weight = 109222.271| |-----------------------------------------------------------------------------| r_work (final): 0.3278 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3278 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3278 r_free = 0.3278 target_work(ls_wunit_k1) = 0.041 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3278 r_free = 0.3278 target_work(ls_wunit_k1) = 0.041 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3278 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7915 moved from start: 0.5217 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 44567 Z= 0.148 Angle : 0.656 12.705 61592 Z= 0.350 Chirality : 0.042 0.345 6923 Planarity : 0.004 0.050 6764 Dihedral : 23.570 152.395 8596 Min Nonbonded Distance : 2.286 Molprobity Statistics. All-atom Clashscore : 13.77 Ramachandran Plot: Outliers : 0.07 % Allowed : 6.71 % Favored : 93.22 % Rotamer: Outliers : 0.00 % Allowed : 0.70 % Favored : 99.30 % 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: 0.75 (0.10), residues: 2480 sheet: -1.48 (0.38), residues: 199 loop : -1.68 (0.16), residues: 1642 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG A 49 TYR 0.031 0.002 TYR O 922 PHE 0.022 0.002 PHE K 289 TRP 0.021 0.002 TRP P 207 HIS 0.009 0.001 HIS N 905 Details of bonding type rmsd/Z covalent geometry : bond 0.00291 / 0.15 (44565) covalent geometry : angle 0.65583 / 0.35 (61592) hydrogen bonds : bond 0.04466 / 2.97 ( 2339) hydrogen bonds : angle 4.55466 / 3.24 ( 6495) Misc. bond : bond 0.00495 / 0.26 ( 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 369 residues out of total 3874 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 369 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: A 50 GLU cc_start: 0.9512 (mp0) cc_final: 0.9171 (mp0) REVERT: A 90 MET cc_start: 0.9170 (mmp) cc_final: 0.8898 (mmm) REVERT: A 125 GLN cc_start: 0.9720 (mt0) cc_final: 0.9442 (mp10) REVERT: B 63 GLU cc_start: 0.9377 (mt-10) cc_final: 0.9038 (pt0) REVERT: B 84 MET cc_start: 0.9145 (mmm) cc_final: 0.8527 (mmm) REVERT: C 64 GLU cc_start: 0.9466 (tt0) cc_final: 0.8848 (tm-30) REVERT: D 59 MET cc_start: 0.9527 (tmm) cc_final: 0.9301 (tmm) REVERT: D 106 LEU cc_start: 0.9394 (mt) cc_final: 0.9135 (mt) REVERT: E 50 GLU cc_start: 0.9649 (mm-30) cc_final: 0.9389 (mm-30) REVERT: E 74 ILE cc_start: 0.9666 (pt) cc_final: 0.9371 (pt) REVERT: E 77 ASP cc_start: 0.9361 (m-30) cc_final: 0.9091 (m-30) REVERT: E 97 GLU cc_start: 0.9215 (mm-30) cc_final: 0.8894 (mm-30) REVERT: E 103 LEU cc_start: 0.9694 (mt) cc_final: 0.9487 (mt) REVERT: E 105 GLU cc_start: 0.9096 (tm-30) cc_final: 0.8849 (tm-30) REVERT: F 58 LEU cc_start: 0.9672 (tt) cc_final: 0.9400 (mm) REVERT: F 59 LYS cc_start: 0.9805 (tttm) cc_final: 0.9295 (ttmm) REVERT: G 36 LYS cc_start: 0.9687 (mmmt) cc_final: 0.9178 (mmtm) REVERT: G 56 GLU cc_start: 0.8823 (tt0) cc_final: 0.8364 (mt-10) REVERT: G 64 GLU cc_start: 0.8991 (tp30) cc_final: 0.8393 (tp30) REVERT: G 95 LYS cc_start: 0.9634 (tptp) cc_final: 0.9383 (tppt) REVERT: H 59 MET cc_start: 0.9046 (tpp) cc_final: 0.8579 (tpp) REVERT: H 62 MET cc_start: 0.9592 (mmp) cc_final: 0.9351 (mmm) REVERT: I 424 MET cc_start: 0.6524 (ppp) cc_final: 0.6138 (ppp) REVERT: I 527 MET cc_start: 0.7890 (tpt) cc_final: 0.7495 (mtt) REVERT: I 744 LYS cc_start: 0.7946 (tptp) cc_final: 0.7554 (tppt) REVERT: I 886 MET cc_start: 0.8143 (mtt) cc_final: 0.7319 (mmt) REVERT: I 1000 MET cc_start: 0.9095 (ptm) cc_final: 0.8649 (tmm) REVERT: I 1011 MET cc_start: 0.5983 (mmt) cc_final: 0.5641 (mmt) REVERT: I 1109 MET cc_start: 0.9035 (tpp) cc_final: 0.8640 (tpt) REVERT: I 1112 MET cc_start: 0.9311 (mmt) cc_final: 0.9005 (mmm) REVERT: I 1154 LEU cc_start: 0.9472 (mp) cc_final: 0.9195 (mp) REVERT: I 1233 MET cc_start: 0.3960 (tpp) cc_final: 0.3235 (tpp) REVERT: J 240 TYR cc_start: 0.8988 (t80) cc_final: 0.8608 (p90) REVERT: K 82 MET cc_start: 0.2064 (tpt) cc_final: 0.1708 (tpt) REVERT: K 114 GLU cc_start: 0.8285 (tp30) cc_final: 0.7966 (pm20) REVERT: K 376 MET cc_start: 0.2759 (ptp) cc_final: 0.2237 (ppp) REVERT: L 287 LEU cc_start: 0.9498 (mt) cc_final: 0.9258 (mt) REVERT: L 372 MET cc_start: 0.9652 (mtt) cc_final: 0.9329 (mtt) REVERT: M 275 LEU cc_start: 0.9450 (tp) cc_final: 0.9204 (tp) REVERT: N 462 TYR cc_start: 0.9062 (t80) cc_final: 0.8646 (t80) REVERT: N 468 PHE cc_start: 0.9274 (t80) cc_final: 0.9045 (t80) REVERT: N 674 MET cc_start: 0.3989 (mpp) cc_final: 0.2668 (ttt) REVERT: N 913 MET cc_start: 0.9442 (mmp) cc_final: 0.9214 (mmp) REVERT: O 469 MET cc_start: 0.8524 (mmt) cc_final: 0.7945 (mmm) REVERT: O 523 MET cc_start: 0.8949 (tpt) cc_final: 0.8395 (tpt) REVERT: P 157 LEU cc_start: 0.9511 (tp) cc_final: 0.9273 (tp) REVERT: P 161 ILE cc_start: 0.9610 (tt) cc_final: 0.8952 (pt) REVERT: P 162 MET cc_start: 0.9335 (mmp) cc_final: 0.8513 (mmm) REVERT: P 366 MET cc_start: 0.7969 (mmt) cc_final: 0.7587 (mmm) REVERT: P 441 MET cc_start: 0.9110 (mpp) cc_final: 0.8797 (mpp) REVERT: Q 205 GLU cc_start: 0.6382 (tp30) cc_final: 0.5806 (pp20) REVERT: R 196 VAL cc_start: 0.7611 (t) cc_final: 0.7208 (t) REVERT: R 216 ARG cc_start: 0.9617 (tmt170) cc_final: 0.9365 (ttp80) REVERT: R 219 MET cc_start: 0.9416 (mmp) cc_final: 0.9134 (mmm) REVERT: R 228 LEU cc_start: 0.8041 (tt) cc_final: 0.7320 (mp) REVERT: S 176 MET cc_start: 0.4277 (ttp) cc_final: 0.3956 (ttp) REVERT: S 572 MET cc_start: -0.1454 (mmm) cc_final: -0.2013 (mtp) REVERT: U 1521 TYR cc_start: 0.8318 (t80) cc_final: 0.7911 (m-80) outliers start: 0 outliers final: 0 residues processed: 369 average time/residue: 0.2524 time to fit residues: 156.3577 Evaluate side-chains 291 residues out of total 3874 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 291 time to evaluate : 1.506 ------------------------------------------------------------------------------- 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: 8.9990 chunk 356 optimal weight: 10.0000 chunk 406 optimal weight: 0.7980 chunk 447 optimal weight: 20.0000 chunk 6 optimal weight: 0.6980 chunk 249 optimal weight: 1.9990 chunk 211 optimal weight: 0.9990 chunk 217 optimal weight: 20.0000 chunk 416 optimal weight: 3.9990 chunk 60 optimal weight: 0.9980 chunk 289 optimal weight: 0.9980 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** E 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 63 ASN I 817 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** N 875 HIS O 423 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 500 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3796 r_free = 0.3796 target = 0.065305 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3367 r_free = 0.3367 target = 0.045314 restraints weight = 453769.373| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 53)----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.046466 restraints weight = 240451.632| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 52)----------------| | r_work = 0.3417 r_free = 0.3417 target = 0.047260 restraints weight = 158312.675| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 53)----------------| | r_work = 0.3427 r_free = 0.3427 target = 0.047753 restraints weight = 122581.324| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 54)----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.048075 restraints weight = 105446.909| |-----------------------------------------------------------------------------| r_work (final): 0.3306 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3307 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3307 r_free = 0.3307 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 = 0.3307 r_free = 0.3307 target_work(ls_wunit_k1) = 0.042 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3307 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7877 moved from start: 0.5240 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 44567 Z= 0.129 Angle : 0.648 13.505 61592 Z= 0.341 Chirality : 0.041 0.354 6923 Planarity : 0.004 0.050 6764 Dihedral : 23.430 151.633 8596 Min Nonbonded Distance : 2.291 Molprobity Statistics. All-atom Clashscore : 11.80 Ramachandran Plot: Outliers : 0.07 % Allowed : 6.57 % Favored : 93.36 % Rotamer: Outliers : 0.00 % Allowed : 0.29 % Favored : 99.71 % 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: -0.30 (0.13), residues: 4321 helix: 0.83 (0.10), residues: 2482 sheet: -1.53 (0.37), residues: 201 loop : -1.61 (0.16), residues: 1638 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG H 99 TYR 0.033 0.002 TYR O 922 PHE 0.022 0.001 PHE O 951 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 0.00254 / 0.13 (44565) covalent geometry : angle 0.64771 / 0.34 (61592) hydrogen bonds : bond 0.03764 / 2.52 ( 2339) hydrogen bonds : angle 4.43370 / 3.16 ( 6495) Misc. bond : bond 0.00125 / 0.07 ( 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 375 residues out of total 3874 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 375 time to evaluate : 1.581 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: A 50 GLU cc_start: 0.9520 (mp0) cc_final: 0.9232 (mp0) REVERT: A 90 MET cc_start: 0.9186 (mmp) cc_final: 0.8907 (mmm) REVERT: B 63 GLU cc_start: 0.9353 (mt-10) cc_final: 0.9036 (pt0) REVERT: B 84 MET cc_start: 0.9180 (mmm) cc_final: 0.8524 (mmm) REVERT: C 64 GLU cc_start: 0.9444 (tt0) cc_final: 0.8824 (tm-30) REVERT: D 59 MET cc_start: 0.9519 (tmm) cc_final: 0.9266 (tmm) REVERT: D 102 LEU cc_start: 0.9472 (mp) cc_final: 0.9271 (mp) REVERT: D 106 LEU cc_start: 0.9386 (mt) cc_final: 0.9107 (mt) REVERT: E 74 ILE cc_start: 0.9662 (pt) cc_final: 0.9374 (pt) REVERT: E 77 ASP cc_start: 0.9291 (m-30) cc_final: 0.9012 (m-30) REVERT: E 90 MET cc_start: 0.9517 (mmp) cc_final: 0.9253 (mmp) REVERT: E 97 GLU cc_start: 0.9203 (mm-30) cc_final: 0.8891 (mm-30) REVERT: E 105 GLU cc_start: 0.9100 (tm-30) cc_final: 0.8899 (tm-30) REVERT: F 58 LEU cc_start: 0.9649 (tt) cc_final: 0.9412 (mm) REVERT: F 59 LYS cc_start: 0.9775 (tttm) cc_final: 0.9132 (tptp) REVERT: F 60 VAL cc_start: 0.9648 (t) cc_final: 0.9429 (t) REVERT: F 63 GLU cc_start: 0.9489 (mt-10) cc_final: 0.9267 (pt0) REVERT: G 36 LYS cc_start: 0.9688 (mmmt) cc_final: 0.9161 (mmtm) REVERT: G 56 GLU cc_start: 0.8797 (tt0) cc_final: 0.8255 (mt-10) REVERT: G 64 GLU cc_start: 0.8968 (tp30) cc_final: 0.8360 (tp30) REVERT: H 59 MET cc_start: 0.8979 (tpp) cc_final: 0.8597 (tpp) REVERT: H 62 MET cc_start: 0.9554 (mmp) cc_final: 0.9287 (mmm) REVERT: I 424 MET cc_start: 0.5718 (ppp) cc_final: 0.5438 (ppp) REVERT: I 527 MET cc_start: 0.7904 (tpt) cc_final: 0.7505 (mtt) REVERT: I 886 MET cc_start: 0.8105 (mtt) cc_final: 0.7286 (mmt) REVERT: I 1000 MET cc_start: 0.9130 (ptm) cc_final: 0.8696 (tmm) REVERT: I 1011 MET cc_start: 0.6055 (mmt) cc_final: 0.5690 (mmt) REVERT: I 1109 MET cc_start: 0.9104 (tpp) cc_final: 0.8693 (tpt) REVERT: I 1112 MET cc_start: 0.9339 (mmt) cc_final: 0.9032 (mmm) REVERT: I 1154 LEU cc_start: 0.9492 (mp) cc_final: 0.9283 (mp) REVERT: I 1233 MET cc_start: 0.3806 (tpp) cc_final: 0.3086 (tpp) REVERT: J 240 TYR cc_start: 0.9010 (t80) cc_final: 0.8642 (p90) REVERT: K 82 MET cc_start: 0.2140 (tpt) cc_final: 0.1917 (tpt) REVERT: K 114 GLU cc_start: 0.8282 (tp30) cc_final: 0.7966 (pm20) REVERT: K 376 MET cc_start: 0.2843 (ptp) cc_final: 0.1941 (ppp) REVERT: L 287 LEU cc_start: 0.9499 (mt) cc_final: 0.9270 (mt) REVERT: L 315 PHE cc_start: 0.9520 (t80) cc_final: 0.9245 (t80) REVERT: L 372 MET cc_start: 0.9649 (mtt) cc_final: 0.9324 (mtt) REVERT: M 214 THR cc_start: 0.9631 (p) cc_final: 0.9370 (p) REVERT: M 275 LEU cc_start: 0.9441 (tp) cc_final: 0.9200 (tp) REVERT: N 462 TYR cc_start: 0.9031 (t80) cc_final: 0.8555 (t80) REVERT: N 468 PHE cc_start: 0.9256 (t80) cc_final: 0.9017 (t80) REVERT: N 489 ASN cc_start: 0.7952 (m110) cc_final: 0.7678 (m110) REVERT: N 674 MET cc_start: 0.4063 (mpp) cc_final: 0.2816 (ttt) REVERT: N 896 MET cc_start: 0.9431 (mmp) cc_final: 0.9163 (mmm) REVERT: N 906 PHE cc_start: 0.8554 (t80) cc_final: 0.8182 (t80) REVERT: N 913 MET cc_start: 0.9487 (mmp) cc_final: 0.9231 (mmp) REVERT: O 469 MET cc_start: 0.8447 (mmt) cc_final: 0.8238 (mmt) REVERT: O 498 MET cc_start: 0.7926 (mmp) cc_final: 0.7313 (mtp) REVERT: O 523 MET cc_start: 0.8792 (tpt) cc_final: 0.8230 (tpt) REVERT: P 157 LEU cc_start: 0.9485 (tp) cc_final: 0.9246 (tp) REVERT: P 161 ILE cc_start: 0.9584 (tt) cc_final: 0.8958 (pt) REVERT: P 162 MET cc_start: 0.9365 (mmp) cc_final: 0.8530 (mmm) REVERT: P 308 HIS cc_start: 0.6941 (p-80) cc_final: 0.6729 (p-80) REVERT: P 366 MET cc_start: 0.8111 (mmt) cc_final: 0.7781 (mmm) REVERT: P 441 MET cc_start: 0.9067 (mpp) cc_final: 0.8760 (mpp) REVERT: Q 205 GLU cc_start: 0.6351 (tp30) cc_final: 0.5807 (pp20) REVERT: Q 257 ARG cc_start: 0.9512 (mmp80) cc_final: 0.8982 (ptm-80) REVERT: R 196 VAL cc_start: 0.7570 (t) cc_final: 0.7189 (t) REVERT: R 216 ARG cc_start: 0.9626 (tmt170) cc_final: 0.9350 (mmt-90) REVERT: R 219 MET cc_start: 0.9429 (mmp) cc_final: 0.9190 (mmm) REVERT: R 228 LEU cc_start: 0.8021 (tt) cc_final: 0.7258 (mp) REVERT: S 176 MET cc_start: 0.4253 (ttp) cc_final: 0.3935 (ttp) REVERT: S 572 MET cc_start: -0.1495 (mmm) cc_final: -0.2020 (mtp) REVERT: U 1521 TYR cc_start: 0.8280 (t80) cc_final: 0.7909 (m-80) outliers start: 0 outliers final: 0 residues processed: 375 average time/residue: 0.2582 time to fit residues: 162.8450 Evaluate side-chains 297 residues out of total 3874 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 297 time to evaluate : 1.572 ------------------------------------------------------------------------------- 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: 6.9990 chunk 445 optimal weight: 40.0000 chunk 3 optimal weight: 0.9980 chunk 214 optimal weight: 9.9990 chunk 324 optimal weight: 4.9990 chunk 120 optimal weight: 9.9990 chunk 161 optimal weight: 20.0000 chunk 410 optimal weight: 6.9990 chunk 80 optimal weight: 6.9990 chunk 146 optimal weight: 6.9990 chunk 368 optimal weight: 10.0000 overall best weight: 5.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** E 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 63 ASN I 847 GLN I1187 GLN ** 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 ** M 141 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 422 HIS N 454 ASN ** N 489 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 875 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 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** ** U1514 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3727 r_free = 0.3727 target = 0.062228 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.042469 restraints weight = 473036.562| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 53)----------------| | r_work = 0.3309 r_free = 0.3309 target = 0.043522 restraints weight = 255023.999| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.044212 restraints weight = 168922.458| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 52)----------------| | r_work = 0.3339 r_free = 0.3339 target = 0.044681 restraints weight = 132473.679| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.044916 restraints weight = 115032.841| |-----------------------------------------------------------------------------| r_work (final): 0.3217 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3217 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3217 r_free = 0.3217 target_work(ls_wunit_k1) = 0.039 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3217 r_free = 0.3217 target_work(ls_wunit_k1) = 0.039 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3217 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7992 moved from start: 0.5822 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.059 44567 Z= 0.237 Angle : 0.733 12.457 61592 Z= 0.391 Chirality : 0.043 0.325 6923 Planarity : 0.005 0.070 6764 Dihedral : 23.709 154.155 8596 Min Nonbonded Distance : 2.247 Molprobity Statistics. All-atom Clashscore : 18.64 Ramachandran Plot: Outliers : 0.07 % Allowed : 7.10 % Favored : 92.83 % Rotamer: Outliers : 0.00 % Allowed : 0.49 % Favored : 99.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -0.57 (0.13), residues: 4321 helix: 0.59 (0.10), residues: 2500 sheet: -1.57 (0.38), residues: 194 loop : -1.73 (0.16), residues: 1627 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG Q 251 TYR 0.035 0.002 TYR B 51 PHE 0.024 0.002 PHE K 289 TRP 0.023 0.002 TRP O 620 HIS 0.012 0.002 HIS H 109 Details of bonding type rmsd/Z covalent geometry : bond 0.00454 / 0.24 (44565) covalent geometry : angle 0.73259 / 0.39 (61592) hydrogen bonds : bond 0.06667 / 4.45 ( 2339) hydrogen bonds : angle 4.76621 / 3.40 ( 6495) Misc. bond : bond 0.00126 / 0.06 ( 2) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 11433.97 seconds wall clock time: 196 minutes 41.36 seconds (11801.36 seconds total)