Starting phenix.real_space_refine on Thu Dec 26 06:00:19 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7y8r_33684/12_2024/7y8r_33684_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/7y8r_33684/12_2024/7y8r_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_33684/12_2024/7y8r_33684.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7y8r_33684/12_2024/7y8r_33684.map" model { file = "/net/cci-nas-00/data/ceres_data/7y8r_33684/12_2024/7y8r_33684_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7y8r_33684/12_2024/7y8r_33684_neut.cif" } resolution = 4.4 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.002 sd= 0.053 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): 0.12s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/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: {'GLN:plan1': 1, 'ASP:plan': 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: {'TYR:plan': 1, 'GLU:plan': 2, 'ARG:plan': 1, 'TRP:plan': 1, 'ASP: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: 23.22, per 1000 atoms: 0.54 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: 11.73 Conformation dependent library (CDL) restraints added in 4.7 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: 17.34 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: 22.72 Time building geometry restraints manager: 13.52 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=" F3 BEF I1703 " pdb="BE BEF I1703 " ideal model delta sigma weight residual 1.476 1.544 -0.068 2.00e-02 2.50e+03 1.16e+01 bond pdb=" F1 BEF I1703 " pdb="BE BEF I1703 " ideal model delta sigma weight residual 1.476 1.533 -0.057 2.00e-02 2.50e+03 8.12e+00 bond pdb=" N GLY B 9 " pdb=" CA GLY B 9 " ideal model delta sigma weight residual 1.451 1.492 -0.041 1.60e-02 3.91e+03 6.47e+00 bond pdb=" N GLY K 12 " pdb=" CA GLY K 12 " ideal model delta sigma weight residual 1.451 1.491 -0.040 1.60e-02 3.91e+03 6.22e+00 ... (remaining 44560 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.44: 61153 2.44 - 4.87: 417 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=" F2 BEF I1703 " pdb="BE BEF I1703 " pdb=" F3 BEF I1703 " ideal model delta sigma weight residual 119.96 107.78 12.18 3.00e+00 1.11e-01 1.65e+01 angle pdb=" N HIS O 439 " pdb=" CA HIS O 439 " pdb=" C HIS O 439 " ideal model delta sigma weight residual 109.69 115.29 -5.60 1.44e+00 4.82e-01 1.51e+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: 6228 0.062 - 0.125: 677 0.125 - 0.187: 12 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: 0.010 Normalize map: mean=0, sd=1: 3.100 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.070 Extract box with map and model: 1.780 Check model and map are aligned: 0.300 Set scattering table: 0.420 Process input model: 107.520 Find NCS groups from input model: 1.120 Set up NCS constraints: 0.210 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.530 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 118.080 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5469 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.088 44565 Z= 0.163 Angle : 0.544 12.178 61592 Z= 0.335 Chirality : 0.036 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 : 4.56 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.79 (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 TRP 0.006 0.001 TRP P 320 HIS 0.006 0.000 HIS L 27 PHE 0.015 0.001 PHE I1313 TYR 0.023 0.001 TYR R 225 ARG 0.004 0.000 ARG I1318 *********************** 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 : 4.751 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 104 PHE cc_start: 0.7191 (m-80) cc_final: 0.6739 (m-10) REVERT: B 84 MET cc_start: 0.6083 (mmm) cc_final: 0.5835 (mmm) REVERT: D 98 VAL cc_start: 0.9347 (m) cc_final: 0.8860 (p) REVERT: E 78 PHE cc_start: 0.7475 (m-10) cc_final: 0.7166 (m-10) REVERT: F 22 LEU cc_start: 0.7509 (mp) cc_final: 0.7298 (pt) REVERT: F 60 VAL cc_start: 0.8898 (t) cc_final: 0.8451 (t) REVERT: F 66 ILE cc_start: 0.9130 (mt) cc_final: 0.8693 (tp) REVERT: K 376 MET cc_start: -0.0219 (ptt) cc_final: -0.1248 (ppp) REVERT: L 162 VAL cc_start: 0.9546 (t) cc_final: 0.9282 (t) REVERT: L 211 ASP cc_start: 0.6417 (t0) cc_final: 0.6186 (t70) REVERT: L 332 LEU cc_start: 0.9278 (mm) cc_final: 0.8819 (tp) REVERT: L 372 MET cc_start: 0.8974 (mtt) cc_final: 0.8503 (mtp) REVERT: L 393 GLU cc_start: 0.9036 (pt0) cc_final: 0.8635 (tm-30) REVERT: L 445 MET cc_start: 0.8861 (mtp) cc_final: 0.8459 (mtt) REVERT: M 217 MET cc_start: 0.7688 (mtp) cc_final: 0.7451 (mtp) REVERT: M 301 LEU cc_start: 0.7184 (mm) cc_final: 0.6982 (mm) REVERT: N 936 MET cc_start: 0.8867 (mmp) cc_final: 0.8562 (tmm) REVERT: P 157 LEU cc_start: 0.8797 (tt) cc_final: 0.8569 (tp) REVERT: P 164 LYS cc_start: 0.9043 (mmmt) cc_final: 0.8797 (tmtt) REVERT: P 258 TRP cc_start: 0.2453 (t60) cc_final: 0.0852 (m-10) REVERT: U 1521 TYR cc_start: 0.7383 (t80) cc_final: 0.7101 (m-10) outliers start: 2 outliers final: 1 residues processed: 715 average time/residue: 0.6809 time to fit residues: 762.1866 Evaluate side-chains 385 residues out of total 3874 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 384 time to evaluate : 4.858 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 479 random chunks: chunk 404 optimal weight: 5.9990 chunk 363 optimal weight: 0.9990 chunk 201 optimal weight: 20.0000 chunk 124 optimal weight: 8.9990 chunk 244 optimal weight: 0.7980 chunk 193 optimal weight: 20.0000 chunk 375 optimal weight: 10.0000 chunk 145 optimal weight: 5.9990 chunk 228 optimal weight: 3.9990 chunk 279 optimal weight: 30.0000 chunk 434 optimal weight: 40.0000 overall best weight: 3.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 39 HIS A 85 GLN B 75 HIS C 38 ASN ** C 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 94 ASN G 104 GLN H 63 ASN H 84 ASN ** I 510 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 570 GLN I 745 GLN I 847 GLN I 888 ASN I1230 GLN ** J 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 296 ASN K 73 ASN K 105 HIS K 189 GLN ** K 205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 263 GLN K 294 ASN L 48 HIS L 105 HIS L 159 ASN L 406 HIS M 103 ASN M 123 GLN M 140 HIS ** N 422 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 439 HIS N 513 GLN N 935 HIS O 604 GLN ** O 638 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 145 GLN P 326 HIS R 231 HIS S 206 ASN Total number of N/Q/H flips: 34 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5789 moved from start: 0.2656 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 44565 Z= 0.279 Angle : 0.689 15.288 61592 Z= 0.366 Chirality : 0.041 0.276 6923 Planarity : 0.006 0.131 6764 Dihedral : 22.542 170.110 8596 Min Nonbonded Distance : 2.220 Molprobity Statistics. All-atom Clashscore : 10.09 Ramachandran Plot: Outliers : 0.07 % Allowed : 6.18 % Favored : 93.75 % Rotamer: Outliers : 0.29 % Allowed : 4.97 % Favored : 94.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.79 (0.13), residues: 4321 helix: 0.57 (0.10), residues: 2472 sheet: -2.32 (0.34), residues: 176 loop : -1.99 (0.15), residues: 1673 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.042 0.002 TRP M 321 HIS 0.022 0.001 HIS O 638 PHE 0.023 0.002 PHE O 951 TYR 0.026 0.002 TYR H 40 ARG 0.016 0.001 ARG C 99 *********************** 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 472 residues out of total 3874 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 461 time to evaluate : 4.659 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 104 PHE cc_start: 0.7152 (m-80) cc_final: 0.6819 (m-10) REVERT: D 83 TYR cc_start: 0.7945 (m-10) cc_final: 0.7617 (m-80) REVERT: E 93 GLN cc_start: 0.7437 (tp40) cc_final: 0.7020 (tp40) REVERT: G 95 LYS cc_start: 0.8371 (tptp) cc_final: 0.8154 (tppt) REVERT: H 59 MET cc_start: 0.7339 (tpp) cc_final: 0.7010 (tpp) REVERT: I 886 MET cc_start: 0.6705 (mtt) cc_final: 0.6303 (mmp) REVERT: I 960 GLU cc_start: 0.5273 (tt0) cc_final: 0.5027 (tt0) REVERT: I 1011 MET cc_start: 0.6257 (mmt) cc_final: 0.5779 (mmt) REVERT: I 1109 MET cc_start: 0.7148 (tpp) cc_final: 0.6809 (tpt) REVERT: J 123 MET cc_start: 0.4397 (mmm) cc_final: 0.3876 (mmm) REVERT: J 132 MET cc_start: -0.0485 (ppp) cc_final: -0.0972 (ttp) REVERT: J 305 MET cc_start: 0.6566 (mmt) cc_final: 0.5535 (mmt) REVERT: K 376 MET cc_start: 0.0012 (ptt) cc_final: -0.1005 (ppp) REVERT: L 287 LEU cc_start: 0.8655 (mm) cc_final: 0.8300 (mm) REVERT: L 332 LEU cc_start: 0.9222 (mm) cc_final: 0.8666 (tp) REVERT: L 372 MET cc_start: 0.9004 (mtt) cc_final: 0.8601 (mtt) REVERT: L 445 MET cc_start: 0.8666 (mtp) cc_final: 0.8450 (mtt) REVERT: M 275 LEU cc_start: 0.6206 (tp) cc_final: 0.5731 (tp) REVERT: N 906 PHE cc_start: 0.7903 (t80) cc_final: 0.7670 (t80) REVERT: O 615 MET cc_start: 0.7955 (mtt) cc_final: 0.7651 (mmp) REVERT: P 161 ILE cc_start: 0.9370 (mt) cc_final: 0.9156 (mt) REVERT: P 164 LYS cc_start: 0.9166 (mmmt) cc_final: 0.8905 (tmtt) REVERT: P 441 MET cc_start: 0.8775 (mpp) cc_final: 0.8456 (mpp) REVERT: P 474 GLU cc_start: 0.6871 (tm-30) cc_final: 0.6620 (tm-30) REVERT: S 572 MET cc_start: -0.0518 (mmm) cc_final: -0.1474 (mtp) outliers start: 11 outliers final: 3 residues processed: 470 average time/residue: 0.6141 time to fit residues: 467.3131 Evaluate side-chains 323 residues out of total 3874 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 320 time to evaluate : 4.915 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 479 random chunks: chunk 241 optimal weight: 2.9990 chunk 135 optimal weight: 3.9990 chunk 362 optimal weight: 10.0000 chunk 296 optimal weight: 20.0000 chunk 119 optimal weight: 3.9990 chunk 435 optimal weight: 30.0000 chunk 470 optimal weight: 5.9990 chunk 388 optimal weight: 8.9990 chunk 432 optimal weight: 30.0000 chunk 148 optimal weight: 0.3980 chunk 349 optimal weight: 9.9990 overall best weight: 3.4788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 39 HIS ** C 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 76 GLN ** E 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 313 ASN L1796 ASN ** M 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 140 HIS N 422 HIS N 439 HIS ** O 436 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 638 HIS ** P 345 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 252 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S 584 HIS Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5907 moved from start: 0.3537 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.072 44565 Z= 0.264 Angle : 0.650 9.727 61592 Z= 0.348 Chirality : 0.040 0.209 6923 Planarity : 0.005 0.086 6764 Dihedral : 22.969 169.024 8596 Min Nonbonded Distance : 2.214 Molprobity Statistics. All-atom Clashscore : 11.68 Ramachandran Plot: Outliers : 0.07 % Allowed : 6.09 % Favored : 93.84 % Rotamer: Outliers : 0.13 % Allowed : 4.16 % Favored : 95.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.60 (0.13), residues: 4321 helix: 0.70 (0.10), residues: 2469 sheet: -2.00 (0.34), residues: 184 loop : -1.89 (0.15), residues: 1668 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.046 0.002 TRP M 321 HIS 0.012 0.002 HIS O 638 PHE 0.020 0.002 PHE O 951 TYR 0.028 0.002 TYR R 225 ARG 0.013 0.001 ARG Q 251 *********************** 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 428 residues out of total 3874 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 423 time to evaluate : 4.434 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: A 104 PHE cc_start: 0.7060 (m-80) cc_final: 0.6817 (m-10) REVERT: A 120 MET cc_start: 0.7224 (mmm) cc_final: 0.6873 (mmm) REVERT: D 76 GLU cc_start: 0.6847 (mm-30) cc_final: 0.6382 (mm-30) REVERT: D 83 TYR cc_start: 0.7739 (m-10) cc_final: 0.7397 (m-80) REVERT: E 74 ILE cc_start: 0.8640 (pt) cc_final: 0.8096 (pt) REVERT: E 126 LEU cc_start: 0.8388 (tt) cc_final: 0.8129 (tt) REVERT: F 59 LYS cc_start: 0.8502 (tmtt) cc_final: 0.8169 (tptp) REVERT: H 59 MET cc_start: 0.7040 (tpp) cc_final: 0.6837 (tpp) REVERT: I 1011 MET cc_start: 0.6656 (mmt) cc_final: 0.6090 (mmt) REVERT: I 1109 MET cc_start: 0.7348 (tpp) cc_final: 0.6920 (tpp) REVERT: J 305 MET cc_start: 0.6793 (mmt) cc_final: 0.5754 (mmp) REVERT: K 376 MET cc_start: -0.0085 (ptt) cc_final: -0.0500 (ppp) REVERT: L 287 LEU cc_start: 0.8857 (mm) cc_final: 0.8619 (mm) REVERT: L 445 MET cc_start: 0.8900 (mtp) cc_final: 0.8499 (mtt) REVERT: M 275 LEU cc_start: 0.6110 (tp) cc_final: 0.5785 (tp) REVERT: M 352 LEU cc_start: 0.6895 (mt) cc_final: 0.6625 (mp) REVERT: P 149 ASP cc_start: 0.9057 (t0) cc_final: 0.8637 (t0) REVERT: P 164 LYS cc_start: 0.9286 (mmmt) cc_final: 0.8968 (tmtt) REVERT: P 494 TYR cc_start: 0.8759 (t80) cc_final: 0.8458 (t80) REVERT: Q 205 GLU cc_start: 0.5516 (tp30) cc_final: 0.4832 (pp20) REVERT: S 572 MET cc_start: -0.0625 (mmm) cc_final: -0.1511 (mtt) outliers start: 5 outliers final: 1 residues processed: 427 average time/residue: 0.6141 time to fit residues: 425.2185 Evaluate side-chains 313 residues out of total 3874 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 312 time to evaluate : 8.721 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 479 random chunks: chunk 430 optimal weight: 8.9990 chunk 327 optimal weight: 0.9980 chunk 226 optimal weight: 8.9990 chunk 48 optimal weight: 8.9990 chunk 207 optimal weight: 0.0040 chunk 292 optimal weight: 0.0470 chunk 437 optimal weight: 20.0000 chunk 463 optimal weight: 6.9990 chunk 228 optimal weight: 30.0000 chunk 414 optimal weight: 30.0000 chunk 124 optimal weight: 0.8980 overall best weight: 1.7892 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 25 ASN B 93 GLN ** C 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 63 ASN ** I 915 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I1253 HIS ** J 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 296 ASN ** L 288 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** ** P 437 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 200 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 252 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S 394 ASN S 584 HIS Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5886 moved from start: 0.3879 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 44565 Z= 0.192 Angle : 0.607 11.447 61592 Z= 0.323 Chirality : 0.039 0.168 6923 Planarity : 0.004 0.044 6764 Dihedral : 22.968 159.711 8596 Min Nonbonded Distance : 2.234 Molprobity Statistics. All-atom Clashscore : 10.02 Ramachandran Plot: Outliers : 0.07 % Allowed : 6.34 % Favored : 93.59 % Rotamer: Outliers : 0.10 % Allowed : 3.33 % Favored : 96.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.36 (0.13), residues: 4321 helix: 0.87 (0.10), residues: 2475 sheet: -1.68 (0.34), residues: 201 loop : -1.78 (0.15), residues: 1645 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP P 207 HIS 0.014 0.001 HIS S 584 PHE 0.025 0.001 PHE K 160 TYR 0.048 0.002 TYR R 225 ARG 0.010 0.001 ARG F 92 *********************** 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 414 residues out of total 3874 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 410 time to evaluate : 4.861 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: A 104 PHE cc_start: 0.7075 (m-80) cc_final: 0.6796 (m-10) REVERT: E 74 ILE cc_start: 0.8473 (pt) cc_final: 0.8035 (pt) REVERT: F 60 VAL cc_start: 0.8858 (t) cc_final: 0.8561 (t) REVERT: H 59 MET cc_start: 0.6937 (tpp) cc_final: 0.6724 (tpp) REVERT: I 1011 MET cc_start: 0.6667 (mmt) cc_final: 0.6155 (mmt) REVERT: I 1109 MET cc_start: 0.7606 (tpp) cc_final: 0.7319 (tpt) REVERT: J 123 MET cc_start: 0.4981 (mmm) cc_final: 0.4451 (mmm) REVERT: J 305 MET cc_start: 0.6579 (mmt) cc_final: 0.5549 (mmp) REVERT: K 376 MET cc_start: 0.0018 (ptt) cc_final: -0.0443 (ppp) REVERT: L 287 LEU cc_start: 0.8696 (mm) cc_final: 0.8358 (mm) REVERT: L 445 MET cc_start: 0.8762 (mtp) cc_final: 0.8437 (mtt) REVERT: O 896 MET cc_start: 0.7192 (mtp) cc_final: 0.6621 (mtp) REVERT: P 149 ASP cc_start: 0.8787 (t0) cc_final: 0.8022 (t0) REVERT: P 161 ILE cc_start: 0.9404 (mt) cc_final: 0.9180 (pt) REVERT: P 162 MET cc_start: 0.9000 (mmp) cc_final: 0.8334 (mmm) REVERT: P 164 LYS cc_start: 0.9350 (mmmt) cc_final: 0.9119 (tmtt) REVERT: P 404 MET cc_start: 0.8835 (mtm) cc_final: 0.8587 (mtp) REVERT: P 441 MET cc_start: 0.8893 (mpp) cc_final: 0.8638 (mpp) REVERT: P 494 TYR cc_start: 0.8769 (t80) cc_final: 0.8403 (t80) REVERT: Q 205 GLU cc_start: 0.5538 (tp30) cc_final: 0.4827 (pp20) REVERT: S 572 MET cc_start: -0.0629 (mmm) cc_final: -0.1474 (mtt) outliers start: 4 outliers final: 2 residues processed: 413 average time/residue: 0.5948 time to fit residues: 404.2229 Evaluate side-chains 308 residues out of total 3874 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 306 time to evaluate : 4.574 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 479 random chunks: chunk 385 optimal weight: 0.1980 chunk 262 optimal weight: 0.0570 chunk 6 optimal weight: 0.9980 chunk 344 optimal weight: 20.0000 chunk 191 optimal weight: 0.0060 chunk 395 optimal weight: 8.9990 chunk 320 optimal weight: 2.9990 chunk 0 optimal weight: 10.0000 chunk 236 optimal weight: 7.9990 chunk 415 optimal weight: 0.0470 chunk 116 optimal weight: 10.0000 overall best weight: 0.2612 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 38 ASN ** I 915 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 296 ASN ** K 313 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L1778 ASN M 140 HIS M 318 GLN N 439 HIS N 454 ASN ** O 436 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 345 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 403 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 200 HIS ** Q 252 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5808 moved from start: 0.3978 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 44565 Z= 0.164 Angle : 0.600 11.636 61592 Z= 0.317 Chirality : 0.039 0.217 6923 Planarity : 0.004 0.081 6764 Dihedral : 22.815 156.924 8596 Min Nonbonded Distance : 2.210 Molprobity Statistics. All-atom Clashscore : 8.92 Ramachandran Plot: Outliers : 0.07 % Allowed : 6.29 % Favored : 93.64 % Rotamer: Outliers : 0.03 % Allowed : 2.86 % Favored : 97.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.25 (0.13), residues: 4321 helix: 0.92 (0.10), residues: 2477 sheet: -1.58 (0.36), residues: 191 loop : -1.67 (0.15), residues: 1653 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.044 0.001 TRP O 620 HIS 0.007 0.001 HIS P 362 PHE 0.023 0.001 PHE K 289 TYR 0.024 0.001 TYR R 225 ARG 0.008 0.000 ARG L 95 *********************** 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 408 residues out of total 3874 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 407 time to evaluate : 4.948 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 104 PHE cc_start: 0.7036 (m-80) cc_final: 0.6598 (m-10) REVERT: E 74 ILE cc_start: 0.8477 (pt) cc_final: 0.8047 (pt) REVERT: G 87 ILE cc_start: 0.8976 (pt) cc_final: 0.8774 (pt) REVERT: H 59 MET cc_start: 0.6847 (tpp) cc_final: 0.6617 (tpp) REVERT: H 100 LEU cc_start: 0.8289 (tp) cc_final: 0.7953 (tp) REVERT: I 1011 MET cc_start: 0.6685 (mmt) cc_final: 0.6183 (mmt) REVERT: I 1051 MET cc_start: 0.8239 (tpp) cc_final: 0.8009 (tpp) REVERT: I 1109 MET cc_start: 0.7710 (tpp) cc_final: 0.7367 (tpt) REVERT: J 123 MET cc_start: 0.4854 (mmm) cc_final: 0.4479 (mmm) REVERT: J 305 MET cc_start: 0.6179 (mmt) cc_final: 0.5161 (mmp) REVERT: K 376 MET cc_start: -0.0107 (ptt) cc_final: -0.0509 (ppp) REVERT: L 287 LEU cc_start: 0.8763 (mm) cc_final: 0.8457 (mm) REVERT: L 372 MET cc_start: 0.9206 (mpp) cc_final: 0.8964 (mpp) REVERT: L 445 MET cc_start: 0.8819 (mtp) cc_final: 0.8490 (mtt) REVERT: M 275 LEU cc_start: 0.5866 (tp) cc_final: 0.5615 (tp) REVERT: O 620 TRP cc_start: -0.2820 (m-10) cc_final: -0.3023 (m-10) REVERT: P 149 ASP cc_start: 0.8939 (t0) cc_final: 0.8173 (t0) REVERT: P 162 MET cc_start: 0.9077 (mmp) cc_final: 0.8377 (mmm) REVERT: P 164 LYS cc_start: 0.9323 (mmmt) cc_final: 0.9099 (tmtt) REVERT: P 441 MET cc_start: 0.8871 (mpp) cc_final: 0.8666 (mpp) REVERT: P 494 TYR cc_start: 0.8675 (t80) cc_final: 0.8325 (t80) REVERT: Q 205 GLU cc_start: 0.5919 (tp30) cc_final: 0.5192 (pp20) REVERT: S 572 MET cc_start: -0.0746 (mmm) cc_final: -0.1535 (mtt) outliers start: 1 outliers final: 1 residues processed: 408 average time/residue: 0.5802 time to fit residues: 389.7326 Evaluate side-chains 311 residues out of total 3874 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 310 time to evaluate : 5.027 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 479 random chunks: chunk 155 optimal weight: 5.9990 chunk 416 optimal weight: 8.9990 chunk 91 optimal weight: 10.0000 chunk 271 optimal weight: 0.9980 chunk 114 optimal weight: 10.0000 chunk 463 optimal weight: 7.9990 chunk 384 optimal weight: 8.9990 chunk 214 optimal weight: 8.9990 chunk 38 optimal weight: 3.9990 chunk 153 optimal weight: 6.9990 chunk 243 optimal weight: 5.9990 overall best weight: 4.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 375 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 380 HIS I 788 GLN I 847 GLN ** I 915 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 173 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 296 ASN ** K 190 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 313 ASN L 144 GLN L 192 GLN L1778 ASN M 140 HIS M 141 HIS M 152 ASN M 198 GLN M 209 ASN M 380 ASN ** N 422 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 439 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 875 HIS ** O 436 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 145 GLN ** P 308 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 345 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 403 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 437 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 501 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 504 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 252 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S 142 GLN S 584 HIS ** U1514 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6114 moved from start: 0.4998 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.093 44565 Z= 0.341 Angle : 0.716 11.257 61592 Z= 0.384 Chirality : 0.042 0.280 6923 Planarity : 0.005 0.100 6764 Dihedral : 23.231 156.807 8596 Min Nonbonded Distance : 2.233 Molprobity Statistics. All-atom Clashscore : 18.19 Ramachandran Plot: Outliers : 0.07 % Allowed : 6.85 % Favored : 93.08 % Rotamer: Outliers : 0.03 % Allowed : 2.24 % Favored : 97.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.57 (0.13), residues: 4321 helix: 0.64 (0.10), residues: 2479 sheet: -1.62 (0.35), residues: 208 loop : -1.78 (0.16), residues: 1634 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP O 620 HIS 0.008 0.002 HIS S 584 PHE 0.022 0.002 PHE K 289 TYR 0.043 0.002 TYR R 225 ARG 0.014 0.001 ARG H 79 *********************** 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 365 residues out of total 3874 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 364 time to evaluate : 4.703 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: E 74 ILE cc_start: 0.8846 (pt) cc_final: 0.8339 (pt) REVERT: H 44 VAL cc_start: 0.8628 (m) cc_final: 0.8392 (m) REVERT: H 73 ILE cc_start: 0.8855 (mm) cc_final: 0.8645 (mm) REVERT: H 100 LEU cc_start: 0.8433 (tp) cc_final: 0.7985 (tp) REVERT: I 1051 MET cc_start: 0.8198 (tpp) cc_final: 0.7989 (tpp) REVERT: I 1109 MET cc_start: 0.7780 (tpp) cc_final: 0.7435 (tpt) REVERT: I 1317 MET cc_start: 0.7813 (mmm) cc_final: 0.7494 (mmm) REVERT: J 305 MET cc_start: 0.6797 (mmt) cc_final: 0.5811 (mmp) REVERT: L 287 LEU cc_start: 0.9098 (mm) cc_final: 0.8849 (mm) REVERT: L 445 MET cc_start: 0.8951 (mtp) cc_final: 0.8599 (mtt) REVERT: M 275 LEU cc_start: 0.5925 (tp) cc_final: 0.5571 (tp) REVERT: N 615 MET cc_start: 0.8441 (ptt) cc_final: 0.8088 (ptt) REVERT: N 936 MET cc_start: 0.9292 (mmm) cc_final: 0.8902 (tmm) REVERT: P 149 ASP cc_start: 0.8834 (t0) cc_final: 0.8309 (t0) REVERT: P 161 ILE cc_start: 0.9506 (tt) cc_final: 0.8875 (pt) REVERT: P 162 MET cc_start: 0.9173 (mmp) cc_final: 0.8460 (mmm) REVERT: P 494 TYR cc_start: 0.8774 (t80) cc_final: 0.8440 (t80) REVERT: Q 205 GLU cc_start: 0.5739 (tp30) cc_final: 0.4987 (pp20) REVERT: S 572 MET cc_start: -0.0535 (mmm) cc_final: -0.1638 (mtp) outliers start: 1 outliers final: 0 residues processed: 365 average time/residue: 0.5820 time to fit residues: 348.1128 Evaluate side-chains 279 residues out of total 3874 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 279 time to evaluate : 4.381 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 479 random chunks: chunk 446 optimal weight: 10.0000 chunk 52 optimal weight: 2.9990 chunk 264 optimal weight: 0.9980 chunk 338 optimal weight: 8.9990 chunk 262 optimal weight: 0.7980 chunk 390 optimal weight: 0.4980 chunk 258 optimal weight: 5.9990 chunk 461 optimal weight: 20.0000 chunk 288 optimal weight: 9.9990 chunk 281 optimal weight: 0.9990 chunk 213 optimal weight: 0.0670 overall best weight: 0.6720 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 375 GLN ** I 915 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 969 HIS I1010 HIS J 73 HIS ** J 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 173 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 81 ASN M 140 HIS ** M 141 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 152 ASN ** M 368 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 422 HIS N 439 HIS N 467 ASN ** N 632 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 ** P 437 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 252 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5953 moved from start: 0.4962 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 44565 Z= 0.175 Angle : 0.620 12.515 61592 Z= 0.326 Chirality : 0.039 0.252 6923 Planarity : 0.004 0.067 6764 Dihedral : 23.286 155.290 8596 Min Nonbonded Distance : 2.300 Molprobity Statistics. All-atom Clashscore : 11.22 Ramachandran Plot: Outliers : 0.07 % Allowed : 6.09 % Favored : 93.84 % Rotamer: Outliers : 0.08 % Allowed : 1.74 % Favored : 98.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.26 (0.13), residues: 4321 helix: 0.88 (0.10), residues: 2490 sheet: -1.51 (0.36), residues: 196 loop : -1.63 (0.16), residues: 1635 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP O 620 HIS 0.009 0.001 HIS J 73 PHE 0.021 0.002 PHE O 951 TYR 0.053 0.002 TYR O 922 ARG 0.014 0.000 ARG M 366 *********************** 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 392 residues out of total 3874 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 389 time to evaluate : 4.930 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: A 104 PHE cc_start: 0.7367 (m-80) cc_final: 0.7072 (m-10) REVERT: D 83 TYR cc_start: 0.7669 (m-80) cc_final: 0.7278 (m-80) REVERT: E 74 ILE cc_start: 0.8587 (pt) cc_final: 0.8227 (pt) REVERT: H 59 MET cc_start: 0.6691 (tpp) cc_final: 0.6482 (tpp) REVERT: H 73 ILE cc_start: 0.8570 (mm) cc_final: 0.8300 (mm) REVERT: H 100 LEU cc_start: 0.8167 (tp) cc_final: 0.7337 (tp) REVERT: I 1036 MET cc_start: 0.3626 (pmm) cc_final: 0.3274 (pmm) REVERT: I 1109 MET cc_start: 0.7865 (tpp) cc_final: 0.7547 (tpt) REVERT: I 1233 MET cc_start: 0.1193 (tpp) cc_final: 0.0870 (tpp) REVERT: J 123 MET cc_start: 0.5083 (mmm) cc_final: 0.4882 (mmm) REVERT: J 153 MET cc_start: 0.0944 (tpt) cc_final: 0.0187 (tpp) REVERT: J 305 MET cc_start: 0.6540 (mmt) cc_final: 0.5662 (mmp) REVERT: K 97 ASP cc_start: 0.7771 (t0) cc_final: 0.7279 (p0) REVERT: L 287 LEU cc_start: 0.8969 (mm) cc_final: 0.8663 (mm) REVERT: L 445 MET cc_start: 0.8888 (mtp) cc_final: 0.8547 (mtt) REVERT: M 156 MET cc_start: 0.7374 (tmm) cc_final: 0.6927 (tmm) REVERT: M 275 LEU cc_start: 0.5754 (tp) cc_final: 0.5177 (tp) REVERT: M 301 LEU cc_start: 0.8117 (tt) cc_final: 0.7692 (mm) REVERT: N 615 MET cc_start: 0.8388 (ptt) cc_final: 0.7974 (ptt) REVERT: N 674 MET cc_start: 0.4755 (mpp) cc_final: 0.3001 (ttt) REVERT: N 936 MET cc_start: 0.9319 (mmm) cc_final: 0.8942 (tmm) REVERT: P 161 ILE cc_start: 0.9431 (tt) cc_final: 0.8818 (pt) REVERT: P 162 MET cc_start: 0.9129 (mmp) cc_final: 0.8523 (mmm) REVERT: P 494 TYR cc_start: 0.8678 (t80) cc_final: 0.8270 (t80) REVERT: Q 205 GLU cc_start: 0.5960 (tp30) cc_final: 0.5258 (pp20) REVERT: Q 257 ARG cc_start: 0.9329 (mmp80) cc_final: 0.8946 (ptm-80) REVERT: S 572 MET cc_start: -0.0679 (mmm) cc_final: -0.1687 (mtp) outliers start: 3 outliers final: 0 residues processed: 392 average time/residue: 0.5792 time to fit residues: 374.0720 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 : 4.837 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 479 random chunks: chunk 285 optimal weight: 0.0970 chunk 184 optimal weight: 50.0000 chunk 275 optimal weight: 0.9990 chunk 139 optimal weight: 4.9990 chunk 90 optimal weight: 3.9990 chunk 89 optimal weight: 10.0000 chunk 293 optimal weight: 0.8980 chunk 314 optimal weight: 2.9990 chunk 228 optimal weight: 20.0000 chunk 43 optimal weight: 0.7980 chunk 362 optimal weight: 4.9990 overall best weight: 1.1582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 81 ASN M 140 HIS M 368 GLN ** N 632 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 437 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 500 GLN ** Q 252 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S 584 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5963 moved from start: 0.5067 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 44565 Z= 0.184 Angle : 0.629 12.588 61592 Z= 0.334 Chirality : 0.039 0.254 6923 Planarity : 0.004 0.082 6764 Dihedral : 23.125 154.205 8596 Min Nonbonded Distance : 2.275 Molprobity Statistics. All-atom Clashscore : 11.86 Ramachandran Plot: Outliers : 0.07 % Allowed : 6.27 % Favored : 93.66 % Rotamer: Outliers : 0.03 % Allowed : 1.09 % Favored : 98.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.20 (0.13), residues: 4321 helix: 0.90 (0.10), residues: 2492 sheet: -1.39 (0.38), residues: 190 loop : -1.59 (0.16), residues: 1639 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP P 320 HIS 0.011 0.001 HIS S 584 PHE 0.028 0.001 PHE G 25 TYR 0.035 0.002 TYR O 922 ARG 0.009 0.000 ARG L 95 *********************** 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 373 residues out of total 3874 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 372 time to evaluate : 4.564 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: E 74 ILE cc_start: 0.8682 (pt) cc_final: 0.8225 (pt) REVERT: G 87 ILE cc_start: 0.8902 (pt) cc_final: 0.8699 (pt) REVERT: H 59 MET cc_start: 0.6772 (tpp) cc_final: 0.6545 (tpp) REVERT: H 100 LEU cc_start: 0.8164 (tp) cc_final: 0.7643 (tp) REVERT: I 1036 MET cc_start: 0.3500 (pmm) cc_final: 0.3025 (pmm) REVERT: I 1109 MET cc_start: 0.7885 (tpp) cc_final: 0.7551 (tpt) REVERT: J 123 MET cc_start: 0.5149 (mmm) cc_final: 0.4818 (mmm) REVERT: J 305 MET cc_start: 0.6438 (mmt) cc_final: 0.5616 (mmp) REVERT: K 92 MET cc_start: 0.4227 (tpt) cc_final: 0.3724 (mmm) REVERT: K 97 ASP cc_start: 0.7802 (t0) cc_final: 0.7291 (p0) REVERT: L 287 LEU cc_start: 0.8998 (mm) cc_final: 0.8665 (mm) REVERT: L 445 MET cc_start: 0.8849 (mtp) cc_final: 0.8541 (mtt) REVERT: M 275 LEU cc_start: 0.5628 (tp) cc_final: 0.5123 (tp) REVERT: N 615 MET cc_start: 0.8311 (ptt) cc_final: 0.7796 (ptt) REVERT: N 674 MET cc_start: 0.4772 (mpp) cc_final: 0.3060 (ttt) REVERT: N 936 MET cc_start: 0.9328 (mmm) cc_final: 0.8946 (tmm) REVERT: P 161 ILE cc_start: 0.9430 (tt) cc_final: 0.8841 (pt) REVERT: P 162 MET cc_start: 0.9145 (mmp) cc_final: 0.8547 (mmm) REVERT: P 494 TYR cc_start: 0.8656 (t80) cc_final: 0.8262 (t80) REVERT: Q 205 GLU cc_start: 0.5945 (tp30) cc_final: 0.5277 (pp20) REVERT: Q 257 ARG cc_start: 0.9335 (mmp80) cc_final: 0.8976 (ptm-80) REVERT: S 572 MET cc_start: -0.0688 (mmm) cc_final: -0.1812 (mtp) outliers start: 1 outliers final: 0 residues processed: 373 average time/residue: 0.5821 time to fit residues: 359.6607 Evaluate side-chains 282 residues out of total 3874 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 282 time to evaluate : 4.522 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 479 random chunks: chunk 419 optimal weight: 7.9990 chunk 442 optimal weight: 20.0000 chunk 403 optimal weight: 0.0870 chunk 430 optimal weight: 10.0000 chunk 258 optimal weight: 3.9990 chunk 187 optimal weight: 3.9990 chunk 337 optimal weight: 10.0000 chunk 132 optimal weight: 9.9990 chunk 388 optimal weight: 20.0000 chunk 406 optimal weight: 0.9980 chunk 428 optimal weight: 0.9980 overall best weight: 2.0162 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 67 ASN ** E 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 375 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 915 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 173 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 81 ASN M 140 HIS N 422 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 500 GLN ** Q 252 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6005 moved from start: 0.5285 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 44565 Z= 0.200 Angle : 0.635 12.617 61592 Z= 0.338 Chirality : 0.039 0.217 6923 Planarity : 0.004 0.066 6764 Dihedral : 23.133 166.735 8596 Min Nonbonded Distance : 2.311 Molprobity Statistics. All-atom Clashscore : 12.73 Ramachandran Plot: Outliers : 0.07 % Allowed : 6.29 % Favored : 93.64 % Rotamer: Outliers : 0.03 % Allowed : 0.65 % Favored : 99.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.20 (0.13), residues: 4321 helix: 0.91 (0.10), residues: 2487 sheet: -1.37 (0.40), residues: 172 loop : -1.59 (0.16), residues: 1662 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP J 356 HIS 0.014 0.001 HIS I 884 PHE 0.028 0.001 PHE L 217 TYR 0.035 0.002 TYR O 922 ARG 0.014 0.000 ARG A 129 *********************** 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 365 residues out of total 3874 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 364 time to evaluate : 4.750 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: D 83 TYR cc_start: 0.7426 (m-80) cc_final: 0.7215 (m-10) REVERT: H 59 MET cc_start: 0.6854 (tpp) cc_final: 0.6601 (tpp) REVERT: H 100 LEU cc_start: 0.8172 (tp) cc_final: 0.7597 (tp) REVERT: H 106 LEU cc_start: 0.7852 (tt) cc_final: 0.7205 (tt) REVERT: I 1109 MET cc_start: 0.7913 (tpp) cc_final: 0.7572 (tpt) REVERT: J 123 MET cc_start: 0.5616 (mmm) cc_final: 0.5221 (mmm) REVERT: J 305 MET cc_start: 0.6493 (mmt) cc_final: 0.5652 (mmp) REVERT: L 287 LEU cc_start: 0.9083 (mm) cc_final: 0.8840 (mm) REVERT: L 445 MET cc_start: 0.8869 (mtp) cc_final: 0.8559 (mtt) REVERT: M 166 LEU cc_start: 0.7692 (mm) cc_final: 0.7386 (tt) REVERT: M 202 ASP cc_start: 0.6232 (p0) cc_final: 0.5995 (p0) REVERT: M 275 LEU cc_start: 0.5587 (tp) cc_final: 0.5291 (tp) REVERT: N 615 MET cc_start: 0.8346 (ptt) cc_final: 0.7837 (ptt) REVERT: N 674 MET cc_start: 0.4802 (mpp) cc_final: 0.3057 (ttt) REVERT: N 936 MET cc_start: 0.9353 (mmm) cc_final: 0.8980 (tmm) REVERT: P 161 ILE cc_start: 0.9455 (tt) cc_final: 0.8871 (pt) REVERT: P 162 MET cc_start: 0.9155 (mmp) cc_final: 0.8573 (mmm) REVERT: P 494 TYR cc_start: 0.8697 (t80) cc_final: 0.8303 (t80) REVERT: Q 205 GLU cc_start: 0.5940 (tp30) cc_final: 0.5291 (pp20) REVERT: R 226 PHE cc_start: 0.6846 (t80) cc_final: 0.6535 (t80) REVERT: S 572 MET cc_start: -0.0654 (mmm) cc_final: -0.1753 (mtp) outliers start: 1 outliers final: 0 residues processed: 365 average time/residue: 0.5924 time to fit residues: 358.4714 Evaluate side-chains 287 residues out of total 3874 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 287 time to evaluate : 5.079 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 479 random chunks: chunk 282 optimal weight: 8.9990 chunk 454 optimal weight: 7.9990 chunk 277 optimal weight: 6.9990 chunk 215 optimal weight: 6.9990 chunk 316 optimal weight: 20.0000 chunk 477 optimal weight: 30.0000 chunk 439 optimal weight: 20.0000 chunk 380 optimal weight: 0.4980 chunk 39 optimal weight: 4.9990 chunk 293 optimal weight: 1.9990 chunk 233 optimal weight: 3.9990 overall best weight: 3.6988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 67 ASN ** E 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 375 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 81 ASN M 140 HIS ** M 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 437 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 501 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 504 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 252 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S 584 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6136 moved from start: 0.5921 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 44565 Z= 0.271 Angle : 0.687 12.850 61592 Z= 0.367 Chirality : 0.041 0.241 6923 Planarity : 0.005 0.071 6764 Dihedral : 23.433 158.039 8596 Min Nonbonded Distance : 2.075 Molprobity Statistics. All-atom Clashscore : 17.06 Ramachandran Plot: Outliers : 0.07 % Allowed : 6.80 % Favored : 93.13 % Rotamer: Outliers : 0.03 % Allowed : 0.44 % Favored : 99.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.44 (0.13), residues: 4321 helix: 0.69 (0.10), residues: 2457 sheet: -1.46 (0.37), residues: 204 loop : -1.61 (0.16), residues: 1660 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP M 206 HIS 0.010 0.001 HIS E 39 PHE 0.033 0.002 PHE S 542 TYR 0.069 0.002 TYR R 225 ARG 0.010 0.001 ARG A 129 ********************** 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 347 residues out of total 3874 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 346 time to evaluate : 4.917 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: E 100 LEU cc_start: 0.8931 (pp) cc_final: 0.8552 (pp) REVERT: H 45 LEU cc_start: 0.8582 (pp) cc_final: 0.8231 (pp) REVERT: H 59 MET cc_start: 0.6854 (tpp) cc_final: 0.6603 (tpp) REVERT: H 100 LEU cc_start: 0.8153 (tp) cc_final: 0.7846 (tp) REVERT: I 1011 MET cc_start: 0.7199 (mmt) cc_final: 0.6684 (mmt) REVERT: I 1109 MET cc_start: 0.7823 (tpp) cc_final: 0.7570 (mmt) REVERT: J 123 MET cc_start: 0.5700 (mmm) cc_final: 0.5276 (mmm) REVERT: J 305 MET cc_start: 0.7026 (mmt) cc_final: 0.6092 (mmp) REVERT: K 335 MET cc_start: 0.8163 (pmm) cc_final: 0.7776 (pmm) REVERT: L 287 LEU cc_start: 0.9120 (mm) cc_final: 0.8871 (mm) REVERT: L 375 MET cc_start: 0.8306 (mtm) cc_final: 0.8068 (mtp) REVERT: L 445 MET cc_start: 0.8943 (mtp) cc_final: 0.8615 (mtt) REVERT: M 275 LEU cc_start: 0.6006 (tp) cc_final: 0.5495 (tp) REVERT: N 615 MET cc_start: 0.8302 (ptt) cc_final: 0.7790 (ptt) REVERT: N 936 MET cc_start: 0.9353 (mmm) cc_final: 0.9029 (tmm) REVERT: P 161 ILE cc_start: 0.9495 (tt) cc_final: 0.8928 (pt) REVERT: P 162 MET cc_start: 0.9243 (mmp) cc_final: 0.8635 (mmm) REVERT: P 441 MET cc_start: 0.8717 (mpp) cc_final: 0.8507 (mpp) REVERT: Q 205 GLU cc_start: 0.5929 (tp30) cc_final: 0.5232 (pp20) REVERT: Q 257 ARG cc_start: 0.9389 (mmp80) cc_final: 0.8859 (ttp80) REVERT: R 219 MET cc_start: 0.8849 (mmp) cc_final: 0.8635 (mmt) REVERT: S 572 MET cc_start: -0.0500 (mmm) cc_final: -0.1635 (mtp) outliers start: 1 outliers final: 0 residues processed: 347 average time/residue: 0.5827 time to fit residues: 338.0811 Evaluate side-chains 268 residues out of total 3874 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 268 time to evaluate : 4.873 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 479 random chunks: chunk 301 optimal weight: 5.9990 chunk 404 optimal weight: 6.9990 chunk 116 optimal weight: 6.9990 chunk 350 optimal weight: 0.9990 chunk 56 optimal weight: 1.9990 chunk 105 optimal weight: 8.9990 chunk 380 optimal weight: 7.9990 chunk 159 optimal weight: 8.9990 chunk 390 optimal weight: 0.9990 chunk 48 optimal weight: 5.9990 chunk 70 optimal weight: 0.8980 overall best weight: 2.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 38 ASN ** E 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 375 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 81 ASN K 189 GLN M 140 HIS M 152 ASN N 451 ASN N 454 ASN ** 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** ** Q 252 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S 142 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3758 r_free = 0.3758 target = 0.063711 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3336 r_free = 0.3336 target = 0.044981 restraints weight = 456906.484| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.046366 restraints weight = 254145.088| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.046286 restraints weight = 179070.536| |-----------------------------------------------------------------------------| r_work (final): 0.3230 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3230 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3230 r_free = 0.3230 target_work(ls_wunit_k1) = 0.039 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3230 r_free = 0.3230 target_work(ls_wunit_k1) = 0.039 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.3230 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8056 moved from start: 0.6017 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 44565 Z= 0.207 Angle : 0.653 12.761 61592 Z= 0.345 Chirality : 0.040 0.257 6923 Planarity : 0.004 0.086 6764 Dihedral : 23.442 155.740 8596 Min Nonbonded Distance : 2.109 Molprobity Statistics. All-atom Clashscore : 13.66 Ramachandran Plot: Outliers : 0.07 % Allowed : 6.57 % Favored : 93.36 % Rotamer: Outliers : 0.03 % Allowed : 0.36 % Favored : 99.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.33 (0.13), residues: 4321 helix: 0.79 (0.10), residues: 2463 sheet: -1.50 (0.40), residues: 172 loop : -1.58 (0.15), residues: 1686 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP L 237 HIS 0.009 0.001 HIS B 75 PHE 0.027 0.002 PHE L 217 TYR 0.036 0.002 TYR R 225 ARG 0.013 0.001 ARG A 129 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8858.46 seconds wall clock time: 163 minutes 59.52 seconds (9839.52 seconds total)