Starting phenix.real_space_refine on Sun Sep 13 23:02:08 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8dej_27393/09_2026/8dej_27393.cif Found real_map, /net/cci-nas-00/data/ceres_data/8dej_27393/09_2026/8dej_27393.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.86 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8dej_27393/09_2026/8dej_27393.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8dej_27393/09_2026/8dej_27393.map" restraint_files = "/net/cci-nas-00/data/ceres_data/8dej_27393/09_2026/8dej_27393.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8dej_27393/09_2026/8dej_27393.cif" model { file = "/net/cci-nas-00/data/ceres_data/8dej_27393/09_2026/8dej_27393.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8dej_27393/09_2026/8dej_27393.cif" } resolution = 2.86 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 sd= 0.209 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 134 5.49 5 S 133 5.16 5 C 16026 2.51 5 N 4704 2.21 5 O 5200 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 19 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 26197 Number of models: 1 Model: "" Number of chains: 14 Chain: "A" Number of atoms: 1778 Number of conformers: 1 Conformer: "" Number of residues, atoms: 220, 1778 Classifications: {'peptide': 220} Link IDs: {'PTRANS': 16, 'TRANS': 203} Chain: "B" Number of atoms: 2112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 270, 2112 Classifications: {'peptide': 270} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 12, 'TRANS': 257} Chain breaks: 2 Chain: "C" Number of atoms: 2238 Number of conformers: 1 Conformer: "" Number of residues, atoms: 286, 2238 Classifications: {'peptide': 286} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 15, 'TRANS': 270} Chain breaks: 1 Chain: "D" Number of atoms: 2238 Number of conformers: 1 Conformer: "" Number of residues, atoms: 286, 2238 Classifications: {'peptide': 286} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 15, 'TRANS': 270} Chain breaks: 1 Chain: "E" Number of atoms: 2238 Number of conformers: 1 Conformer: "" Number of residues, atoms: 286, 2238 Classifications: {'peptide': 286} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 15, 'TRANS': 270} Chain breaks: 1 Chain: "F" Number of atoms: 2238 Number of conformers: 1 Conformer: "" Number of residues, atoms: 286, 2238 Classifications: {'peptide': 286} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 15, 'TRANS': 270} Chain breaks: 1 Chain: "G" Number of atoms: 2238 Number of conformers: 1 Conformer: "" Number of residues, atoms: 286, 2238 Classifications: {'peptide': 286} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 15, 'TRANS': 270} Chain breaks: 1 Chain: "H" Number of atoms: 2238 Number of conformers: 1 Conformer: "" Number of residues, atoms: 286, 2238 Classifications: {'peptide': 286} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 15, 'TRANS': 270} Chain breaks: 1 Chain: "I" Number of atoms: 4207 Number of conformers: 1 Conformer: "" Number of residues, atoms: 535, 4207 Classifications: {'peptide': 535} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 30, 'TRANS': 504} Chain breaks: 4 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Chain: "J" Number of atoms: 930 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 930 Classifications: {'peptide': 117} Link IDs: {'PTRANS': 6, 'TRANS': 110} Chain breaks: 1 Chain: "K" Number of atoms: 930 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 930 Classifications: {'peptide': 117} Link IDs: {'PTRANS': 6, 'TRANS': 110} Chain breaks: 1 Chain: "L" Number of atoms: 1002 Number of conformers: 1 Conformer: "" Number of residues, atoms: 47, 1002 Classifications: {'RNAv2': 47} Modifications used: {'rna2p_pur': 11, 'rna2p_pyr': 11, 'rna3p_pur': 14, 'rna3p_pyr': 11} Link IDs: {'rna2p': 22, 'rna3p': 24} Chain breaks: 1 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "M" Number of atoms: 824 Number of conformers: 1 Conformer: "" Number of residues, atoms: 40, 824 Classifications: {'DNA': 40} Link IDs: {'rna3p': 39} Chain: "N" Number of atoms: 986 Number of conformers: 1 Conformer: "" Number of residues, atoms: 48, 986 Classifications: {'DNA': 46, 'RNAv2': 2} Modifications used: {'rna2p_pyr': 1, 'rna3p_pur': 1} Link IDs: {'rna2p': 1, 'rna3p': 46} Time building chain proxies: 5.62, per 1000 atoms: 0.21 Number of scatterers: 26197 At special positions: 0 Unit cell: (110, 115.5, 232.1, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 133 16.00 P 134 15.00 O 5200 8.00 N 4704 7.00 C 16026 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.76 Conformation dependent library (CDL) restraints added in 981.0 milliseconds 5850 Ramachandran restraints generated. 2925 Oldfield, 0 Emsley, 2925 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5570 Finding SS restraints... Secondary structure from input PDB file: 105 helices and 34 sheets defined 38.0% alpha, 23.6% beta 40 base pairs and 65 stacking pairs defined. Time for finding SS restraints: 3.19 Creating SS restraints... Processing helix chain 'A' and resid 24 through 28 removed outlier: 3.829A pdb=" N LYS A 28 " --> pdb=" O PRO A 25 " (cutoff:3.500A) Processing helix chain 'A' and resid 38 through 48 removed outlier: 3.554A pdb=" N ALA A 42 " --> pdb=" O PRO A 38 " (cutoff:3.500A) Processing helix chain 'A' and resid 86 through 93 Processing helix chain 'A' and resid 103 through 105 No H-bonds generated for 'chain 'A' and resid 103 through 105' Processing helix chain 'A' and resid 137 through 152 removed outlier: 3.583A pdb=" N HIS A 141 " --> pdb=" O ASN A 137 " (cutoff:3.500A) Processing helix chain 'A' and resid 222 through 227 Processing helix chain 'B' and resid 43 through 60 removed outlier: 4.107A pdb=" N LEU B 47 " --> pdb=" O THR B 43 " (cutoff:3.500A) Processing helix chain 'B' and resid 102 through 111 Processing helix chain 'B' and resid 113 through 120 Processing helix chain 'B' and resid 193 through 198 Processing helix chain 'B' and resid 203 through 216 Processing helix chain 'B' and resid 217 through 221 removed outlier: 3.817A pdb=" N HIS B 220 " --> pdb=" O MET B 217 " (cutoff:3.500A) Processing helix chain 'B' and resid 247 through 255 removed outlier: 3.631A pdb=" N LEU B 251 " --> pdb=" O PRO B 247 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N ASP B 253 " --> pdb=" O HIS B 249 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N LEU B 254 " --> pdb=" O LYS B 250 " (cutoff:3.500A) removed outlier: 4.263A pdb=" N VAL B 255 " --> pdb=" O LEU B 251 " (cutoff:3.500A) Processing helix chain 'B' and resid 269 through 271 No H-bonds generated for 'chain 'B' and resid 269 through 271' Processing helix chain 'C' and resid 43 through 60 removed outlier: 3.923A pdb=" N LEU C 47 " --> pdb=" O THR C 43 " (cutoff:3.500A) Processing helix chain 'C' and resid 74 through 87 removed outlier: 3.693A pdb=" N THR C 78 " --> pdb=" O ILE C 74 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N ALA C 82 " --> pdb=" O THR C 78 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N TYR C 83 " --> pdb=" O HIS C 79 " (cutoff:3.500A) Processing helix chain 'C' and resid 97 through 101 Processing helix chain 'C' and resid 102 through 112 removed outlier: 3.871A pdb=" N ASN C 112 " --> pdb=" O TRP C 108 " (cutoff:3.500A) Processing helix chain 'C' and resid 113 through 120 Processing helix chain 'C' and resid 193 through 201 removed outlier: 3.698A pdb=" N LYS C 199 " --> pdb=" O PRO C 195 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N THR C 200 " --> pdb=" O LEU C 196 " (cutoff:3.500A) Processing helix chain 'C' and resid 203 through 217 Processing helix chain 'C' and resid 218 through 221 Processing helix chain 'C' and resid 247 through 253 removed outlier: 3.607A pdb=" N LEU C 251 " --> pdb=" O PRO C 247 " (cutoff:3.500A) Processing helix chain 'C' and resid 269 through 271 No H-bonds generated for 'chain 'C' and resid 269 through 271' Processing helix chain 'D' and resid 43 through 60 removed outlier: 3.991A pdb=" N LEU D 47 " --> pdb=" O THR D 43 " (cutoff:3.500A) Processing helix chain 'D' and resid 75 through 86 removed outlier: 3.889A pdb=" N ARG D 81 " --> pdb=" O GLU D 77 " (cutoff:3.500A) Processing helix chain 'D' and resid 98 through 113 removed outlier: 3.575A pdb=" N VAL D 105 " --> pdb=" O ASP D 101 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N THR D 106 " --> pdb=" O ALA D 102 " (cutoff:3.500A) Processing helix chain 'D' and resid 113 through 120 Processing helix chain 'D' and resid 193 through 201 removed outlier: 3.546A pdb=" N ALA D 197 " --> pdb=" O SER D 193 " (cutoff:3.500A) Processing helix chain 'D' and resid 203 through 216 Processing helix chain 'D' and resid 217 through 221 removed outlier: 4.171A pdb=" N HIS D 220 " --> pdb=" O MET D 217 " (cutoff:3.500A) Processing helix chain 'D' and resid 247 through 253 removed outlier: 3.567A pdb=" N LEU D 251 " --> pdb=" O PRO D 247 " (cutoff:3.500A) Processing helix chain 'D' and resid 269 through 271 No H-bonds generated for 'chain 'D' and resid 269 through 271' Processing helix chain 'E' and resid 43 through 60 removed outlier: 3.694A pdb=" N LEU E 47 " --> pdb=" O THR E 43 " (cutoff:3.500A) Processing helix chain 'E' and resid 74 through 87 removed outlier: 3.729A pdb=" N THR E 78 " --> pdb=" O ILE E 74 " (cutoff:3.500A) Processing helix chain 'E' and resid 98 through 113 Processing helix chain 'E' and resid 113 through 120 removed outlier: 3.518A pdb=" N ARG E 117 " --> pdb=" O PHE E 113 " (cutoff:3.500A) Processing helix chain 'E' and resid 193 through 201 removed outlier: 3.836A pdb=" N LYS E 199 " --> pdb=" O PRO E 195 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N THR E 200 " --> pdb=" O LEU E 196 " (cutoff:3.500A) Processing helix chain 'E' and resid 203 through 216 Processing helix chain 'E' and resid 217 through 220 removed outlier: 4.235A pdb=" N HIS E 220 " --> pdb=" O MET E 217 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 217 through 220' Processing helix chain 'E' and resid 247 through 254 removed outlier: 3.701A pdb=" N LEU E 251 " --> pdb=" O PRO E 247 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N LEU E 254 " --> pdb=" O LYS E 250 " (cutoff:3.500A) Processing helix chain 'E' and resid 269 through 271 No H-bonds generated for 'chain 'E' and resid 269 through 271' Processing helix chain 'F' and resid 43 through 60 removed outlier: 3.892A pdb=" N LEU F 47 " --> pdb=" O THR F 43 " (cutoff:3.500A) Processing helix chain 'F' and resid 74 through 87 removed outlier: 3.754A pdb=" N ALA F 82 " --> pdb=" O THR F 78 " (cutoff:3.500A) Processing helix chain 'F' and resid 98 through 113 removed outlier: 3.825A pdb=" N ASN F 112 " --> pdb=" O TRP F 108 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N PHE F 113 " --> pdb=" O MET F 109 " (cutoff:3.500A) Processing helix chain 'F' and resid 113 through 120 Processing helix chain 'F' and resid 193 through 201 removed outlier: 3.546A pdb=" N ALA F 197 " --> pdb=" O SER F 193 " (cutoff:3.500A) Processing helix chain 'F' and resid 203 through 216 Processing helix chain 'F' and resid 217 through 221 removed outlier: 4.098A pdb=" N HIS F 220 " --> pdb=" O MET F 217 " (cutoff:3.500A) Processing helix chain 'F' and resid 247 through 253 removed outlier: 3.634A pdb=" N LEU F 251 " --> pdb=" O PRO F 247 " (cutoff:3.500A) Processing helix chain 'F' and resid 269 through 271 No H-bonds generated for 'chain 'F' and resid 269 through 271' Processing helix chain 'G' and resid 43 through 60 removed outlier: 3.970A pdb=" N LEU G 47 " --> pdb=" O THR G 43 " (cutoff:3.500A) Processing helix chain 'G' and resid 74 through 87 removed outlier: 3.685A pdb=" N ARG G 81 " --> pdb=" O GLU G 77 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N ALA G 82 " --> pdb=" O THR G 78 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N TYR G 83 " --> pdb=" O HIS G 79 " (cutoff:3.500A) Processing helix chain 'G' and resid 98 through 113 removed outlier: 3.846A pdb=" N ASN G 112 " --> pdb=" O TRP G 108 " (cutoff:3.500A) Processing helix chain 'G' and resid 113 through 120 Processing helix chain 'G' and resid 193 through 201 removed outlier: 3.605A pdb=" N ALA G 197 " --> pdb=" O SER G 193 " (cutoff:3.500A) Processing helix chain 'G' and resid 203 through 216 Processing helix chain 'G' and resid 217 through 221 removed outlier: 3.975A pdb=" N HIS G 220 " --> pdb=" O MET G 217 " (cutoff:3.500A) Processing helix chain 'G' and resid 247 through 254 removed outlier: 3.529A pdb=" N LEU G 251 " --> pdb=" O PRO G 247 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N LEU G 254 " --> pdb=" O LYS G 250 " (cutoff:3.500A) Processing helix chain 'G' and resid 269 through 271 No H-bonds generated for 'chain 'G' and resid 269 through 271' Processing helix chain 'H' and resid 43 through 60 removed outlier: 3.826A pdb=" N LEU H 47 " --> pdb=" O THR H 43 " (cutoff:3.500A) Processing helix chain 'H' and resid 74 through 86 removed outlier: 3.909A pdb=" N THR H 78 " --> pdb=" O ILE H 74 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N HIS H 79 " --> pdb=" O LEU H 75 " (cutoff:3.500A) Processing helix chain 'H' and resid 98 through 113 removed outlier: 3.944A pdb=" N ASN H 112 " --> pdb=" O TRP H 108 " (cutoff:3.500A) Processing helix chain 'H' and resid 113 through 120 Processing helix chain 'H' and resid 193 through 201 removed outlier: 3.503A pdb=" N ALA H 197 " --> pdb=" O SER H 193 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N LYS H 199 " --> pdb=" O PRO H 195 " (cutoff:3.500A) Processing helix chain 'H' and resid 203 through 216 Processing helix chain 'H' and resid 217 through 220 removed outlier: 3.658A pdb=" N HIS H 220 " --> pdb=" O MET H 217 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 217 through 220' Processing helix chain 'H' and resid 247 through 254 removed outlier: 3.511A pdb=" N LEU H 251 " --> pdb=" O PRO H 247 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N LEU H 254 " --> pdb=" O LYS H 250 " (cutoff:3.500A) Processing helix chain 'H' and resid 269 through 271 No H-bonds generated for 'chain 'H' and resid 269 through 271' Processing helix chain 'I' and resid 4 through 15 removed outlier: 3.754A pdb=" N ALA I 15 " --> pdb=" O GLN I 11 " (cutoff:3.500A) Processing helix chain 'I' and resid 83 through 88 Processing helix chain 'I' and resid 94 through 111 removed outlier: 3.641A pdb=" N THR I 98 " --> pdb=" O LYS I 94 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N ILE I 109 " --> pdb=" O PHE I 105 " (cutoff:3.500A) removed outlier: 4.079A pdb=" N LYS I 110 " --> pdb=" O ILE I 106 " (cutoff:3.500A) removed outlier: 4.348A pdb=" N ALA I 111 " --> pdb=" O ALA I 107 " (cutoff:3.500A) Processing helix chain 'I' and resid 117 through 127 Processing helix chain 'I' and resid 140 through 144 Processing helix chain 'I' and resid 158 through 161 Processing helix chain 'I' and resid 162 through 177 Processing helix chain 'I' and resid 222 through 226 Processing helix chain 'I' and resid 231 through 236 Processing helix chain 'I' and resid 239 through 255 Processing helix chain 'I' and resid 276 through 281 removed outlier: 3.535A pdb=" N ASP I 281 " --> pdb=" O SER I 277 " (cutoff:3.500A) Processing helix chain 'I' and resid 281 through 288 Processing helix chain 'I' and resid 377 through 388 removed outlier: 3.994A pdb=" N ARG I 383 " --> pdb=" O ASP I 379 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N LEU I 388 " --> pdb=" O HIS I 384 " (cutoff:3.500A) Processing helix chain 'I' and resid 402 through 410 removed outlier: 3.870A pdb=" N THR I 410 " --> pdb=" O LEU I 406 " (cutoff:3.500A) Processing helix chain 'I' and resid 415 through 419 Processing helix chain 'I' and resid 420 through 434 removed outlier: 3.711A pdb=" N PHE I 428 " --> pdb=" O ALA I 424 " (cutoff:3.500A) Processing helix chain 'I' and resid 440 through 452 Processing helix chain 'I' and resid 468 through 482 Processing helix chain 'I' and resid 497 through 517 removed outlier: 3.636A pdb=" N ALA I 507 " --> pdb=" O GLY I 503 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N VAL I 508 " --> pdb=" O ARG I 504 " (cutoff:3.500A) Processing helix chain 'I' and resid 523 through 527 Processing helix chain 'I' and resid 528 through 535 Processing helix chain 'I' and resid 536 through 538 No H-bonds generated for 'chain 'I' and resid 536 through 538' Processing helix chain 'I' and resid 539 through 556 removed outlier: 3.880A pdb=" N ASN I 549 " --> pdb=" O LYS I 545 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N LEU I 554 " --> pdb=" O HIS I 550 " (cutoff:3.500A) Processing helix chain 'I' and resid 564 through 576 Processing helix chain 'I' and resid 586 through 604 Processing helix chain 'J' and resid 9 through 29 Processing helix chain 'J' and resid 35 through 47 removed outlier: 5.870A pdb=" N ALA J 42 " --> pdb=" O ASP J 38 " (cutoff:3.500A) removed outlier: 5.795A pdb=" N SER J 43 " --> pdb=" O ARG J 39 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N SER J 45 " --> pdb=" O LEU J 41 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N ALA J 46 " --> pdb=" O ALA J 42 " (cutoff:3.500A) Processing helix chain 'J' and resid 48 through 50 No H-bonds generated for 'chain 'J' and resid 48 through 50' Processing helix chain 'J' and resid 51 through 68 removed outlier: 4.051A pdb=" N LYS J 57 " --> pdb=" O HIS J 53 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N ASN J 58 " --> pdb=" O MET J 54 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N LYS J 65 " --> pdb=" O ASN J 61 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N LEU J 66 " --> pdb=" O HIS J 62 " (cutoff:3.500A) Processing helix chain 'J' and resid 77 through 88 Processing helix chain 'J' and resid 98 through 117 removed outlier: 3.645A pdb=" N ALA J 115 " --> pdb=" O HIS J 111 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N LEU J 116 " --> pdb=" O GLN J 112 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N PHE J 117 " --> pdb=" O ARG J 113 " (cutoff:3.500A) Processing helix chain 'K' and resid 9 through 29 Processing helix chain 'K' and resid 35 through 47 removed outlier: 6.840A pdb=" N ALA K 42 " --> pdb=" O ASP K 38 " (cutoff:3.500A) removed outlier: 6.149A pdb=" N SER K 43 " --> pdb=" O ARG K 39 " (cutoff:3.500A) Processing helix chain 'K' and resid 47 through 67 removed outlier: 4.207A pdb=" N VAL K 51 " --> pdb=" O ASN K 47 " (cutoff:3.500A) removed outlier: 5.473A pdb=" N HIS K 53 " --> pdb=" O GLY K 49 " (cutoff:3.500A) removed outlier: 5.982A pdb=" N MET K 54 " --> pdb=" O GLN K 50 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N SER K 60 " --> pdb=" O LEU K 56 " (cutoff:3.500A) removed outlier: 4.382A pdb=" N ASN K 61 " --> pdb=" O LYS K 57 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N HIS K 62 " --> pdb=" O ASN K 58 " (cutoff:3.500A) Processing helix chain 'K' and resid 77 through 90 removed outlier: 3.977A pdb=" N ASN K 89 " --> pdb=" O GLU K 85 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N ILE K 90 " --> pdb=" O ILE K 86 " (cutoff:3.500A) Processing helix chain 'K' and resid 98 through 117 removed outlier: 3.518A pdb=" N ALA K 115 " --> pdb=" O HIS K 111 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N LEU K 116 " --> pdb=" O GLN K 112 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N PHE K 117 " --> pdb=" O ARG K 113 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 168 through 171 removed outlier: 3.535A pdb=" N ALA A 124 " --> pdb=" O ILE A 11 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N GLY A 17 " --> pdb=" O VAL A 118 " (cutoff:3.500A) removed outlier: 7.795A pdb=" N ASP A 119 " --> pdb=" O VAL A 64 " (cutoff:3.500A) removed outlier: 4.977A pdb=" N VAL A 64 " --> pdb=" O ASP A 119 " (cutoff:3.500A) removed outlier: 6.417A pdb=" N VAL A 121 " --> pdb=" O ILE A 62 " (cutoff:3.500A) removed outlier: 4.312A pdb=" N ILE A 62 " --> pdb=" O VAL A 121 " (cutoff:3.500A) removed outlier: 6.790A pdb=" N GLU A 123 " --> pdb=" O ASP A 60 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N ILE A 62 " --> pdb=" O ILE A 215 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 31 through 32 removed outlier: 6.566A pdb=" N ARG A 31 " --> pdb=" O THR A 113 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 99 through 100 removed outlier: 5.977A pdb=" N PHE A 99 " --> pdb=" O GLN B 70 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'A' and resid 185 through 196 removed outlier: 6.212A pdb=" N ALA A 208 " --> pdb=" O LEU A 188 " (cutoff:3.500A) removed outlier: 4.463A pdb=" N TYR A 190 " --> pdb=" O PHE A 206 " (cutoff:3.500A) removed outlier: 6.637A pdb=" N PHE A 206 " --> pdb=" O TYR A 190 " (cutoff:3.500A) removed outlier: 4.884A pdb=" N LEU A 192 " --> pdb=" O LEU A 204 " (cutoff:3.500A) removed outlier: 7.469A pdb=" N LEU A 204 " --> pdb=" O LEU A 192 " (cutoff:3.500A) removed outlier: 7.052A pdb=" N ASP A 194 " --> pdb=" O THR A 202 " (cutoff:3.500A) removed outlier: 6.931A pdb=" N THR A 202 " --> pdb=" O ASP A 194 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 41 through 42 removed outlier: 3.520A pdb=" N ARG B 142 " --> pdb=" O VAL B 187 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N THR B 174 " --> pdb=" O ARG B 156 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 136 through 138 removed outlier: 3.532A pdb=" N GLY B 190 " --> pdb=" O PHE B 10 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N PHE B 10 " --> pdb=" O GLY B 190 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N TYR B 8 " --> pdb=" O ILE B 192 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N LYS B 233 " --> pdb=" O LEU B 13 " (cutoff:3.500A) removed outlier: 6.644A pdb=" N ASP B 15 " --> pdb=" O SER B 231 " (cutoff:3.500A) removed outlier: 5.781A pdb=" N SER B 231 " --> pdb=" O ASP B 15 " (cutoff:3.500A) removed outlier: 7.650A pdb=" N GLU B 17 " --> pdb=" O MET B 229 " (cutoff:3.500A) removed outlier: 5.973A pdb=" N MET B 229 " --> pdb=" O GLU B 17 " (cutoff:3.500A) removed outlier: 5.988A pdb=" N LEU B 234 " --> pdb=" O MET B 289 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 256 through 259 Processing sheet with id=AA8, first strand: chain 'C' and resid 41 through 42 Processing sheet with id=AA9, first strand: chain 'C' and resid 136 through 138 removed outlier: 3.552A pdb=" N PHE C 14 " --> pdb=" O TYR C 186 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N GLY C 190 " --> pdb=" O PHE C 10 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N PHE C 10 " --> pdb=" O GLY C 190 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N LYS C 233 " --> pdb=" O LEU C 13 " (cutoff:3.500A) removed outlier: 6.386A pdb=" N ASP C 15 " --> pdb=" O SER C 231 " (cutoff:3.500A) removed outlier: 6.141A pdb=" N SER C 231 " --> pdb=" O ASP C 15 " (cutoff:3.500A) removed outlier: 7.662A pdb=" N GLU C 17 " --> pdb=" O MET C 229 " (cutoff:3.500A) removed outlier: 5.940A pdb=" N MET C 229 " --> pdb=" O GLU C 17 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 122 through 124 removed outlier: 6.378A pdb=" N MET C 123 " --> pdb=" O CYS C 129 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 255 through 259 Processing sheet with id=AB3, first strand: chain 'D' and resid 41 through 42 removed outlier: 3.797A pdb=" N THR D 174 " --> pdb=" O ARG D 156 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 136 through 138 removed outlier: 3.505A pdb=" N ASN D 18 " --> pdb=" O PRO D 182 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N GLY D 184 " --> pdb=" O VAL D 16 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N PHE D 14 " --> pdb=" O TYR D 186 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N PHE D 10 " --> pdb=" O GLY D 190 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N TYR D 8 " --> pdb=" O ILE D 192 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N LYS D 233 " --> pdb=" O LEU D 13 " (cutoff:3.500A) removed outlier: 6.761A pdb=" N ASP D 15 " --> pdb=" O SER D 231 " (cutoff:3.500A) removed outlier: 5.937A pdb=" N SER D 231 " --> pdb=" O ASP D 15 " (cutoff:3.500A) removed outlier: 7.665A pdb=" N GLU D 17 " --> pdb=" O MET D 229 " (cutoff:3.500A) removed outlier: 5.972A pdb=" N MET D 229 " --> pdb=" O GLU D 17 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 122 through 124 removed outlier: 4.129A pdb=" N GLY D 130 " --> pdb=" O MET D 123 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 255 through 259 Processing sheet with id=AB7, first strand: chain 'E' and resid 41 through 42 Processing sheet with id=AB8, first strand: chain 'E' and resid 136 through 138 removed outlier: 3.599A pdb=" N GLN E 137 " --> pdb=" O PHE E 191 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N PHE E 10 " --> pdb=" O GLY E 190 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N LYS E 233 " --> pdb=" O LEU E 13 " (cutoff:3.500A) removed outlier: 6.786A pdb=" N ASP E 15 " --> pdb=" O SER E 231 " (cutoff:3.500A) removed outlier: 5.907A pdb=" N SER E 231 " --> pdb=" O ASP E 15 " (cutoff:3.500A) removed outlier: 7.554A pdb=" N GLU E 17 " --> pdb=" O MET E 229 " (cutoff:3.500A) removed outlier: 5.949A pdb=" N MET E 229 " --> pdb=" O GLU E 17 " (cutoff:3.500A) removed outlier: 6.281A pdb=" N LEU E 234 " --> pdb=" O MET E 289 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'E' and resid 255 through 259 Processing sheet with id=AC1, first strand: chain 'F' and resid 41 through 42 Processing sheet with id=AC2, first strand: chain 'F' and resid 136 through 138 removed outlier: 3.535A pdb=" N PHE F 14 " --> pdb=" O TYR F 186 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N PHE F 10 " --> pdb=" O GLY F 190 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N TYR F 8 " --> pdb=" O ILE F 192 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N LYS F 233 " --> pdb=" O LEU F 13 " (cutoff:3.500A) removed outlier: 6.272A pdb=" N ASP F 15 " --> pdb=" O SER F 231 " (cutoff:3.500A) removed outlier: 5.598A pdb=" N SER F 231 " --> pdb=" O ASP F 15 " (cutoff:3.500A) removed outlier: 7.355A pdb=" N GLU F 17 " --> pdb=" O MET F 229 " (cutoff:3.500A) removed outlier: 5.624A pdb=" N MET F 229 " --> pdb=" O GLU F 17 " (cutoff:3.500A) removed outlier: 5.955A pdb=" N LEU F 234 " --> pdb=" O MET F 289 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'F' and resid 256 through 259 Processing sheet with id=AC4, first strand: chain 'G' and resid 41 through 42 removed outlier: 3.808A pdb=" N THR G 174 " --> pdb=" O ARG G 156 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'G' and resid 136 through 138 removed outlier: 3.598A pdb=" N PHE G 14 " --> pdb=" O TYR G 186 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N PHE G 10 " --> pdb=" O GLY G 190 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N TYR G 8 " --> pdb=" O ILE G 192 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N LYS G 233 " --> pdb=" O LEU G 13 " (cutoff:3.500A) removed outlier: 6.268A pdb=" N ASP G 15 " --> pdb=" O SER G 231 " (cutoff:3.500A) removed outlier: 6.059A pdb=" N SER G 231 " --> pdb=" O ASP G 15 " (cutoff:3.500A) removed outlier: 7.666A pdb=" N GLU G 17 " --> pdb=" O MET G 229 " (cutoff:3.500A) removed outlier: 5.975A pdb=" N MET G 229 " --> pdb=" O GLU G 17 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'G' and resid 122 through 124 removed outlier: 4.490A pdb=" N GLY G 130 " --> pdb=" O MET G 123 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'G' and resid 255 through 259 Processing sheet with id=AC8, first strand: chain 'H' and resid 41 through 42 Processing sheet with id=AC9, first strand: chain 'H' and resid 136 through 138 removed outlier: 6.409A pdb=" N TYR H 183 " --> pdb=" O GLU H 17 " (cutoff:3.500A) removed outlier: 6.503A pdb=" N GLU H 17 " --> pdb=" O TYR H 183 " (cutoff:3.500A) removed outlier: 6.841A pdb=" N LEU H 185 " --> pdb=" O ASP H 15 " (cutoff:3.500A) removed outlier: 6.987A pdb=" N ASP H 15 " --> pdb=" O LEU H 185 " (cutoff:3.500A) removed outlier: 7.183A pdb=" N VAL H 187 " --> pdb=" O LEU H 13 " (cutoff:3.500A) removed outlier: 7.003A pdb=" N LEU H 13 " --> pdb=" O VAL H 187 " (cutoff:3.500A) removed outlier: 7.203A pdb=" N HIS H 189 " --> pdb=" O VAL H 11 " (cutoff:3.500A) removed outlier: 6.996A pdb=" N VAL H 11 " --> pdb=" O HIS H 189 " (cutoff:3.500A) removed outlier: 7.137A pdb=" N PHE H 191 " --> pdb=" O GLU H 9 " (cutoff:3.500A) removed outlier: 6.763A pdb=" N GLU H 9 " --> pdb=" O PHE H 191 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N LYS H 233 " --> pdb=" O LEU H 13 " (cutoff:3.500A) removed outlier: 6.196A pdb=" N ASP H 15 " --> pdb=" O SER H 231 " (cutoff:3.500A) removed outlier: 5.758A pdb=" N SER H 231 " --> pdb=" O ASP H 15 " (cutoff:3.500A) removed outlier: 7.458A pdb=" N GLU H 17 " --> pdb=" O MET H 229 " (cutoff:3.500A) removed outlier: 5.884A pdb=" N MET H 229 " --> pdb=" O GLU H 17 " (cutoff:3.500A) removed outlier: 6.050A pdb=" N LEU H 234 " --> pdb=" O MET H 289 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'H' and resid 122 through 124 removed outlier: 6.816A pdb=" N MET H 123 " --> pdb=" O CYS H 129 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'H' and resid 255 through 259 Processing sheet with id=AD3, first strand: chain 'I' and resid 26 through 31 Processing sheet with id=AD4, first strand: chain 'I' and resid 43 through 48 removed outlier: 3.677A pdb=" N GLY I 45 " --> pdb=" O VAL I 36 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N GLU I 81 " --> pdb=" O ILE I 148 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'I' and resid 51 through 52 Processing sheet with id=AD6, first strand: chain 'I' and resid 201 through 202 Processing sheet with id=AD7, first strand: chain 'I' and resid 261 through 264 removed outlier: 6.040A pdb=" N SER I 358 " --> pdb=" O VAL I 366 " (cutoff:3.500A) removed outlier: 5.242A pdb=" N VAL I 366 " --> pdb=" O SER I 358 " (cutoff:3.500A) 942 hydrogen bonds defined for protein. 2670 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 103 hydrogen bonds 206 hydrogen bond angles 0 basepair planarities 40 basepair parallelities 65 stacking parallelities Total time for adding SS restraints: 5.39 Time building geometry restraints manager: 3.45 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 7891 1.33 - 1.45: 4661 1.45 - 1.57: 13963 1.57 - 1.69: 265 1.69 - 1.82: 231 Bond restraints: 27011 Sorted by residual: bond pdb=" C3' DC N 42 " pdb=" C2' DC N 42 " ideal model delta sigma weight residual 1.516 1.542 -0.026 8.00e-03 1.56e+04 1.05e+01 bond pdb=" C3' DA N 1 " pdb=" C2' DA N 1 " ideal model delta sigma weight residual 1.516 1.541 -0.025 8.00e-03 1.56e+04 9.92e+00 bond pdb=" C1' DT N 44 " pdb=" N1 DT N 44 " ideal model delta sigma weight residual 1.468 1.511 -0.043 1.40e-02 5.10e+03 9.32e+00 bond pdb=" C1' DC M 2 " pdb=" N1 DC M 2 " ideal model delta sigma weight residual 1.468 1.507 -0.039 1.40e-02 5.10e+03 7.90e+00 bond pdb=" C3' DC N 13 " pdb=" C2' DC N 13 " ideal model delta sigma weight residual 1.516 1.538 -0.022 8.00e-03 1.56e+04 7.44e+00 ... (remaining 27006 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.36: 36379 2.36 - 4.71: 639 4.71 - 7.07: 44 7.07 - 9.43: 19 9.43 - 11.79: 33 Bond angle restraints: 37114 Sorted by residual: angle pdb=" O4' DG N 10 " pdb=" C4' DG N 10 " pdb=" C3' DG N 10 " ideal model delta sigma weight residual 106.00 103.12 2.88 6.00e-01 2.78e+00 2.31e+01 angle pdb=" C ASN B 128 " pdb=" CA ASN B 128 " pdb=" CB ASN B 128 " ideal model delta sigma weight residual 116.54 111.30 5.24 1.15e+00 7.56e-01 2.07e+01 angle pdb=" N3 DT M 36 " pdb=" C4 DT M 36 " pdb=" O4 DT M 36 " ideal model delta sigma weight residual 119.90 122.55 -2.65 6.00e-01 2.78e+00 1.95e+01 angle pdb=" N3 DT M 12 " pdb=" C4 DT M 12 " pdb=" O4 DT M 12 " ideal model delta sigma weight residual 119.90 122.43 -2.53 6.00e-01 2.78e+00 1.78e+01 angle pdb=" N3 DT M 11 " pdb=" C4 DT M 11 " pdb=" O4 DT M 11 " ideal model delta sigma weight residual 119.90 122.41 -2.51 6.00e-01 2.78e+00 1.75e+01 ... (remaining 37109 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 32.81: 15173 32.81 - 65.63: 796 65.63 - 98.44: 74 98.44 - 131.26: 0 131.26 - 164.07: 4 Dihedral angle restraints: 16047 sinusoidal: 7443 harmonic: 8604 Sorted by residual: dihedral pdb=" C4' C L 45 " pdb=" C3' C L 45 " pdb=" C2' C L 45 " pdb=" C1' C L 45 " ideal model delta sinusoidal sigma weight residual 36.34 -38.80 75.15 1 3.10e+00 1.04e-01 7.43e+02 dihedral pdb=" C4' G L 33 " pdb=" C3' G L 33 " pdb=" C2' G L 33 " pdb=" C1' G L 33 " ideal model delta sinusoidal sigma weight residual 36.34 -37.86 74.21 1 3.10e+00 1.04e-01 7.27e+02 dihedral pdb=" C4' G L 2 " pdb=" C3' G L 2 " pdb=" C2' G L 2 " pdb=" C1' G L 2 " ideal model delta sinusoidal sigma weight residual 36.34 -37.76 74.11 1 3.10e+00 1.04e-01 7.25e+02 ... (remaining 16044 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.104: 3768 0.104 - 0.209: 260 0.209 - 0.313: 73 0.313 - 0.417: 20 0.417 - 0.522: 8 Chirality restraints: 4129 Sorted by residual: chirality pdb=" P A L 48 " pdb=" OP1 A L 48 " pdb=" OP2 A L 48 " pdb=" O5' A L 48 " both_signs ideal model delta sigma weight residual True 2.17 -2.69 -0.52 2.00e-01 2.50e+01 6.80e+00 chirality pdb=" P C N 29 " pdb=" OP1 C N 29 " pdb=" OP2 C N 29 " pdb=" O5' C N 29 " both_signs ideal model delta sigma weight residual True 2.17 -2.68 -0.50 2.00e-01 2.50e+01 6.36e+00 chirality pdb=" P G N 26 " pdb=" OP1 G N 26 " pdb=" OP2 G N 26 " pdb=" O5' G N 26 " both_signs ideal model delta sigma weight residual True 2.17 -2.68 -0.50 2.00e-01 2.50e+01 6.35e+00 ... (remaining 4126 not shown) Planarity restraints: 4384 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA THR I 606 " 0.024 2.00e-02 2.50e+03 4.82e-02 2.32e+01 pdb=" C THR I 606 " -0.083 2.00e-02 2.50e+03 pdb=" O THR I 606 " 0.032 2.00e-02 2.50e+03 pdb=" N LYS I 607 " 0.028 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' G L 22 " 0.032 2.00e-02 2.50e+03 1.41e-02 5.97e+00 pdb=" N9 G L 22 " -0.034 2.00e-02 2.50e+03 pdb=" C8 G L 22 " -0.003 2.00e-02 2.50e+03 pdb=" N7 G L 22 " 0.000 2.00e-02 2.50e+03 pdb=" C5 G L 22 " -0.000 2.00e-02 2.50e+03 pdb=" C6 G L 22 " 0.000 2.00e-02 2.50e+03 pdb=" O6 G L 22 " 0.012 2.00e-02 2.50e+03 pdb=" N1 G L 22 " 0.002 2.00e-02 2.50e+03 pdb=" C2 G L 22 " 0.001 2.00e-02 2.50e+03 pdb=" N2 G L 22 " -0.003 2.00e-02 2.50e+03 pdb=" N3 G L 22 " -0.004 2.00e-02 2.50e+03 pdb=" C4 G L 22 " -0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' C L 28 " 0.031 2.00e-02 2.50e+03 1.56e-02 5.45e+00 pdb=" N1 C L 28 " -0.032 2.00e-02 2.50e+03 pdb=" C2 C L 28 " 0.002 2.00e-02 2.50e+03 pdb=" O2 C L 28 " -0.007 2.00e-02 2.50e+03 pdb=" N3 C L 28 " 0.002 2.00e-02 2.50e+03 pdb=" C4 C L 28 " 0.002 2.00e-02 2.50e+03 pdb=" N4 C L 28 " 0.011 2.00e-02 2.50e+03 pdb=" C5 C L 28 " -0.001 2.00e-02 2.50e+03 pdb=" C6 C L 28 " -0.007 2.00e-02 2.50e+03 ... (remaining 4381 not shown) Histogram of nonbonded interaction distances: 1.83 - 2.44: 107 2.44 - 3.06: 17618 3.06 - 3.67: 37924 3.67 - 4.29: 54730 4.29 - 4.90: 94728 Nonbonded interactions: 205107 Sorted by model distance: nonbonded pdb=" O2' C L 45 " pdb=" OP2 C L 46 " model vdw 1.829 3.040 nonbonded pdb=" O2' G N 26 " pdb=" O5' DA N 27 " model vdw 1.965 3.040 nonbonded pdb=" O2' C N 29 " pdb=" OP2 DA N 30 " model vdw 2.011 3.040 nonbonded pdb=" O2' G L 12 " pdb=" OP2 C L 13 " model vdw 2.097 3.040 nonbonded pdb=" OD2 ASP I 90 " pdb=" OG1 THR I 98 " model vdw 2.105 3.040 ... (remaining 205102 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 'B' selection = (chain 'C' and (resid 1 through 84 or resid 101 through 290)) selection = (chain 'D' and (resid 1 through 84 or resid 101 through 290)) selection = (chain 'E' and (resid 1 through 84 or resid 101 through 290)) selection = (chain 'F' and (resid 1 through 84 or resid 101 through 290)) selection = (chain 'G' and (resid 1 through 84 or resid 101 through 290)) selection = (chain 'H' and (resid 1 through 84 or resid 101 through 290)) } ncs_group { reference = chain 'J' selection = chain 'K' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.00 max=1.00 mean=0.99 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 7.650 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.020 Construct map_model_manager: 0.030 Extract box with map and model: 0.460 Check model and map are aligned: 0.090 Set scattering table: 0.060 Process input model: 27.170 Find NCS groups from input model: 0.420 Set up NCS constraints: 0.050 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:9.230 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 45.200 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7025 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 : 0.005 0.043 27011 Z= 0.285 Angle : 0.788 11.786 37114 Z= 0.445 Chirality : 0.068 0.522 4129 Planarity : 0.004 0.048 4384 Dihedral : 17.889 164.071 10477 Min Nonbonded Distance : 1.829 Molprobity Statistics. All-atom Clashscore : 4.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.00 % Favored : 96.00 % Rotamer: Outliers : 0.36 % Allowed : 8.84 % Favored : 90.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.19 (0.15), residues: 2925 helix: 1.33 (0.18), residues: 895 sheet: -0.20 (0.20), residues: 611 loop : -1.04 (0.16), residues: 1419 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 177 TYR 0.012 0.001 TYR J 12 PHE 0.010 0.001 PHE J 105 TRP 0.009 0.001 TRP B 108 HIS 0.009 0.001 HIS H 179 Details of bonding type rmsd/Z covalent geometry : bond 0.00468 / 0.28 (27011) covalent geometry : angle 0.78827 / 0.44 (37114) hydrogen bonds : bond 0.21720 / 14.73 ( 1045) hydrogen bonds : angle 7.98542 / 5.58 ( 2876) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5850 Ramachandran restraints generated. 2925 Oldfield, 0 Emsley, 2925 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5850 Ramachandran restraints generated. 2925 Oldfield, 0 Emsley, 2925 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 405 residues out of total 2489 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 396 time to evaluate : 0.954 Fit side-chains REVERT: A 131 LYS cc_start: 0.7330 (ptpt) cc_final: 0.6466 (ptmm) REVERT: A 140 LYS cc_start: 0.7837 (mmpt) cc_final: 0.7314 (ttpm) REVERT: A 191 MET cc_start: 0.6173 (ptp) cc_final: 0.5909 (ptp) REVERT: A 210 MET cc_start: 0.6059 (ttp) cc_final: 0.5657 (ttp) REVERT: B 30 MET cc_start: 0.7361 (OUTLIER) cc_final: 0.6893 (mmp) REVERT: B 240 GLN cc_start: 0.7770 (tp40) cc_final: 0.7191 (tt0) REVERT: B 256 LYS cc_start: 0.7603 (mttp) cc_final: 0.6999 (tmtt) REVERT: B 285 GLU cc_start: 0.7274 (mt-10) cc_final: 0.6860 (mp0) REVERT: C 123 MET cc_start: 0.7247 (mtm) cc_final: 0.6889 (mtm) REVERT: C 138 MET cc_start: 0.8008 (ptm) cc_final: 0.7656 (ptm) REVERT: C 287 LYS cc_start: 0.7354 (ptmt) cc_final: 0.7032 (pttt) REVERT: D 1 MET cc_start: 0.2452 (mtt) cc_final: 0.1915 (mtp) REVERT: D 156 ARG cc_start: 0.7594 (ttt180) cc_final: 0.7365 (ttt180) REVERT: E 80 GLU cc_start: 0.7697 (tt0) cc_final: 0.7396 (mt-10) REVERT: F 89 LYS cc_start: 0.7614 (tppt) cc_final: 0.6960 (tptm) REVERT: F 109 MET cc_start: 0.6329 (tpp) cc_final: 0.5924 (mmp) REVERT: F 125 THR cc_start: 0.7675 (m) cc_final: 0.7446 (p) REVERT: F 180 ILE cc_start: 0.7750 (mt) cc_final: 0.7478 (pt) REVERT: F 256 LYS cc_start: 0.7847 (mttt) cc_final: 0.7564 (mttm) REVERT: F 279 GLN cc_start: 0.7828 (mm110) cc_final: 0.7284 (tt0) REVERT: G 89 LYS cc_start: 0.7257 (mppt) cc_final: 0.6686 (tptm) REVERT: G 221 ASP cc_start: 0.8421 (t0) cc_final: 0.8098 (t0) REVERT: G 256 LYS cc_start: 0.7925 (mttm) cc_final: 0.7536 (mtpp) REVERT: G 287 LYS cc_start: 0.6999 (ptmt) cc_final: 0.6618 (ptpt) REVERT: H 261 GLU cc_start: 0.5349 (pm20) cc_final: 0.4186 (tp30) REVERT: I 58 ARG cc_start: 0.4962 (mmt180) cc_final: 0.4506 (mmm160) REVERT: I 80 TRP cc_start: 0.6359 (p-90) cc_final: 0.6058 (p-90) REVERT: I 202 LYS cc_start: 0.6909 (mptt) cc_final: 0.6475 (mmmt) REVERT: I 231 GLU cc_start: 0.6794 (pt0) cc_final: 0.6417 (pt0) REVERT: I 399 GLU cc_start: 0.7372 (tt0) cc_final: 0.6643 (tm-30) REVERT: I 452 GLU cc_start: 0.7168 (mm-30) cc_final: 0.6949 (mm-30) REVERT: I 594 MET cc_start: 0.6311 (mmt) cc_final: 0.6022 (mmp) REVERT: J 58 ASN cc_start: 0.6568 (m-40) cc_final: 0.6113 (t0) REVERT: K 2 SER cc_start: 0.6958 (p) cc_final: 0.6701 (m) REVERT: K 26 GLU cc_start: 0.6598 (tp30) cc_final: 0.6027 (tt0) outliers start: 9 outliers final: 5 residues processed: 402 average time/residue: 0.8463 time to fit residues: 382.6504 Evaluate side-chains 212 residues out of total 2489 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 206 time to evaluate : 0.948 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 30 MET Chi-restraints excluded: chain D residue 127 VAL Chi-restraints excluded: chain D residue 152 VAL Chi-restraints excluded: chain E residue 171 ASP Chi-restraints excluded: chain H residue 87 ASP Chi-restraints excluded: chain I residue 390 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 304 random chunks: chunk 197 optimal weight: 10.0000 chunk 215 optimal weight: 9.9990 chunk 20 optimal weight: 0.9990 chunk 132 optimal weight: 7.9990 chunk 261 optimal weight: 0.7980 chunk 248 optimal weight: 4.9990 chunk 207 optimal weight: 3.9990 chunk 155 optimal weight: 3.9990 chunk 244 optimal weight: 0.0040 chunk 183 optimal weight: 8.9990 chunk 298 optimal weight: 20.0000 overall best weight: 1.9598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 141 HIS B 70 GLN B 79 HIS D 216 ASN D 279 GLN E 22 ASN E 216 ASN F 79 HIS I 572 GLN K 58 ASN K 89 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3845 r_free = 0.3845 target = 0.133108 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3436 r_free = 0.3436 target = 0.102998 restraints weight = 43022.706| |-----------------------------------------------------------------------------| r_work (start): 0.3402 rms_B_bonded: 1.95 r_work: 0.3221 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.3112 rms_B_bonded: 4.30 restraints_weight: 0.2500 r_work (final): 0.3112 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8584 moved from start: 0.1940 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.082 27011 Z= 0.220 Angle : 1.010 22.218 37114 Z= 0.476 Chirality : 0.097 2.288 4129 Planarity : 0.005 0.046 4384 Dihedral : 18.313 168.022 4760 Min Nonbonded Distance : 2.103 Molprobity Statistics. All-atom Clashscore : 2.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer: Outliers : 2.73 % Allowed : 12.06 % Favored : 85.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.02 (0.15), residues: 2925 helix: 1.40 (0.17), residues: 923 sheet: 0.55 (0.20), residues: 587 loop : -1.18 (0.15), residues: 1415 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG I 205 TYR 0.021 0.002 TYR H 83 PHE 0.015 0.002 PHE K 105 TRP 0.018 0.002 TRP H 108 HIS 0.007 0.002 HIS E 39 Details of bonding type rmsd/Z covalent geometry : bond 0.00468 / 0.22 (27011) covalent geometry : angle 1.01027 / 0.48 (37114) hydrogen bonds : bond 0.07395 / 4.97 ( 1045) hydrogen bonds : angle 5.77546 / 4.03 ( 2876) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5850 Ramachandran restraints generated. 2925 Oldfield, 0 Emsley, 2925 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5850 Ramachandran restraints generated. 2925 Oldfield, 0 Emsley, 2925 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 283 residues out of total 2489 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 215 time to evaluate : 0.983 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 131 LYS cc_start: 0.8199 (ptpt) cc_final: 0.7484 (ptmm) REVERT: C 126 GLU cc_start: 0.8807 (OUTLIER) cc_final: 0.8266 (tt0) REVERT: D 9 GLU cc_start: 0.8356 (OUTLIER) cc_final: 0.7531 (mm-30) REVERT: D 221 ASP cc_start: 0.8595 (OUTLIER) cc_final: 0.8241 (t0) REVERT: E 9 GLU cc_start: 0.8572 (OUTLIER) cc_final: 0.8005 (mp0) REVERT: E 109 MET cc_start: 0.6409 (mtm) cc_final: 0.6203 (mtm) REVERT: E 137 GLN cc_start: 0.8295 (OUTLIER) cc_final: 0.8081 (mt0) REVERT: E 255 VAL cc_start: 0.9148 (OUTLIER) cc_final: 0.8943 (t) REVERT: F 89 LYS cc_start: 0.7956 (tppt) cc_final: 0.7541 (tmtt) REVERT: G 30 MET cc_start: 0.8415 (OUTLIER) cc_final: 0.7772 (mtm) REVERT: G 89 LYS cc_start: 0.7586 (mppt) cc_final: 0.7289 (tptm) REVERT: G 109 MET cc_start: 0.8051 (mmm) cc_final: 0.7745 (mmm) REVERT: H 30 MET cc_start: 0.6806 (mmt) cc_final: 0.6314 (mmm) REVERT: H 261 GLU cc_start: 0.5216 (pm20) cc_final: 0.4451 (tp30) REVERT: I 58 ARG cc_start: 0.5908 (mmt180) cc_final: 0.5138 (mmm160) REVERT: I 94 LYS cc_start: 0.6426 (OUTLIER) cc_final: 0.5942 (mttt) REVERT: I 286 MET cc_start: 0.5207 (pp-130) cc_final: 0.3960 (mmp) REVERT: I 570 MET cc_start: 0.8974 (mtp) cc_final: 0.8712 (mtt) REVERT: J 50 GLN cc_start: 0.8220 (OUTLIER) cc_final: 0.7990 (mp10) REVERT: J 82 MET cc_start: 0.8731 (mtt) cc_final: 0.8373 (mtp) outliers start: 68 outliers final: 20 residues processed: 255 average time/residue: 0.8060 time to fit residues: 232.9831 Evaluate side-chains 209 residues out of total 2489 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 180 time to evaluate : 0.954 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 ILE Chi-restraints excluded: chain A residue 40 SER Chi-restraints excluded: chain A residue 136 ASP Chi-restraints excluded: chain A residue 170 GLU Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain C residue 126 GLU Chi-restraints excluded: chain D residue 9 GLU Chi-restraints excluded: chain D residue 148 VAL Chi-restraints excluded: chain D residue 152 VAL Chi-restraints excluded: chain D residue 221 ASP Chi-restraints excluded: chain D residue 269 SER Chi-restraints excluded: chain E residue 9 GLU Chi-restraints excluded: chain E residue 26 ASP Chi-restraints excluded: chain E residue 58 THR Chi-restraints excluded: chain E residue 137 GLN Chi-restraints excluded: chain E residue 171 ASP Chi-restraints excluded: chain E residue 255 VAL Chi-restraints excluded: chain F residue 257 VAL Chi-restraints excluded: chain F residue 258 SER Chi-restraints excluded: chain G residue 30 MET Chi-restraints excluded: chain G residue 264 SER Chi-restraints excluded: chain H residue 138 MET Chi-restraints excluded: chain I residue 94 LYS Chi-restraints excluded: chain I residue 149 VAL Chi-restraints excluded: chain I residue 390 ILE Chi-restraints excluded: chain J residue 50 GLN Chi-restraints excluded: chain K residue 68 LYS Chi-restraints excluded: chain K residue 91 SER Chi-restraints excluded: chain K residue 95 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 304 random chunks: chunk 283 optimal weight: 2.9990 chunk 156 optimal weight: 0.9980 chunk 94 optimal weight: 0.5980 chunk 12 optimal weight: 10.0000 chunk 74 optimal weight: 7.9990 chunk 56 optimal weight: 7.9990 chunk 121 optimal weight: 4.9990 chunk 118 optimal weight: 0.0870 chunk 263 optimal weight: 4.9990 chunk 180 optimal weight: 0.5980 chunk 152 optimal weight: 2.9990 overall best weight: 1.0560 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 79 HIS E 39 HIS H 22 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3868 r_free = 0.3868 target = 0.134854 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3467 r_free = 0.3467 target = 0.105136 restraints weight = 43011.554| |-----------------------------------------------------------------------------| r_work (start): 0.3434 rms_B_bonded: 1.85 r_work: 0.3267 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.3161 rms_B_bonded: 4.13 restraints_weight: 0.2500 r_work (final): 0.3161 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8537 moved from start: 0.2415 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 27011 Z= 0.156 Angle : 0.798 16.234 37114 Z= 0.387 Chirality : 0.071 0.995 4129 Planarity : 0.005 0.053 4384 Dihedral : 17.935 171.236 4754 Min Nonbonded Distance : 2.209 Molprobity Statistics. All-atom Clashscore : 2.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer: Outliers : 2.89 % Allowed : 13.22 % Favored : 83.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.07 (0.15), residues: 2925 helix: 1.52 (0.17), residues: 918 sheet: 0.37 (0.20), residues: 600 loop : -1.11 (0.16), residues: 1407 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG I 205 TYR 0.017 0.002 TYR I 246 PHE 0.017 0.001 PHE I 283 TRP 0.030 0.002 TRP H 108 HIS 0.006 0.001 HIS H 54 Details of bonding type rmsd/Z covalent geometry : bond 0.00311 / 0.16 (27011) covalent geometry : angle 0.79808 / 0.39 (37114) hydrogen bonds : bond 0.05631 / 3.80 ( 1045) hydrogen bonds : angle 5.29179 / 3.71 ( 2876) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5850 Ramachandran restraints generated. 2925 Oldfield, 0 Emsley, 2925 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5850 Ramachandran restraints generated. 2925 Oldfield, 0 Emsley, 2925 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 267 residues out of total 2489 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 195 time to evaluate : 0.994 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 131 LYS cc_start: 0.8237 (ptpt) cc_final: 0.7531 (ptmm) REVERT: B 83 TYR cc_start: 0.5038 (OUTLIER) cc_final: 0.4715 (t80) REVERT: C 103 LYS cc_start: 0.7456 (OUTLIER) cc_final: 0.6939 (ttpt) REVERT: C 126 GLU cc_start: 0.8785 (OUTLIER) cc_final: 0.8261 (tt0) REVERT: C 173 ARG cc_start: 0.7978 (OUTLIER) cc_final: 0.7448 (mpt-90) REVERT: D 9 GLU cc_start: 0.8328 (OUTLIER) cc_final: 0.7463 (mm-30) REVERT: D 221 ASP cc_start: 0.8594 (OUTLIER) cc_final: 0.8182 (t0) REVERT: E 9 GLU cc_start: 0.8487 (OUTLIER) cc_final: 0.8123 (mp0) REVERT: E 109 MET cc_start: 0.6471 (mtm) cc_final: 0.6191 (mtm) REVERT: F 89 LYS cc_start: 0.7892 (tppt) cc_final: 0.7550 (tmtt) REVERT: G 89 LYS cc_start: 0.7526 (mppt) cc_final: 0.7299 (tptm) REVERT: H 30 MET cc_start: 0.6887 (mmt) cc_final: 0.6403 (mmm) REVERT: H 123 MET cc_start: 0.7839 (mtm) cc_final: 0.7380 (mtp) REVERT: H 261 GLU cc_start: 0.5961 (pm20) cc_final: 0.4891 (tp30) REVERT: I 58 ARG cc_start: 0.5786 (mmt180) cc_final: 0.5099 (mmm160) REVERT: I 94 LYS cc_start: 0.6397 (OUTLIER) cc_final: 0.5912 (mttt) REVERT: I 282 ILE cc_start: 0.3261 (OUTLIER) cc_final: 0.3037 (mp) REVERT: I 286 MET cc_start: 0.4725 (pp-130) cc_final: 0.3811 (mmp) REVERT: I 396 ASN cc_start: 0.4503 (p0) cc_final: 0.2474 (t0) REVERT: I 568 GLU cc_start: 0.8145 (OUTLIER) cc_final: 0.7862 (mt-10) REVERT: J 82 MET cc_start: 0.8624 (mtt) cc_final: 0.8304 (mtp) outliers start: 72 outliers final: 28 residues processed: 236 average time/residue: 0.8472 time to fit residues: 225.9166 Evaluate side-chains 223 residues out of total 2489 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 185 time to evaluate : 0.952 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 ILE Chi-restraints excluded: chain A residue 40 SER Chi-restraints excluded: chain A residue 170 GLU Chi-restraints excluded: chain A residue 191 MET Chi-restraints excluded: chain B residue 83 TYR Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 279 GLN Chi-restraints excluded: chain C residue 45 VAL Chi-restraints excluded: chain C residue 103 LYS Chi-restraints excluded: chain C residue 126 GLU Chi-restraints excluded: chain C residue 138 MET Chi-restraints excluded: chain C residue 173 ARG Chi-restraints excluded: chain C residue 287 LYS Chi-restraints excluded: chain D residue 9 GLU Chi-restraints excluded: chain D residue 148 VAL Chi-restraints excluded: chain D residue 152 VAL Chi-restraints excluded: chain D residue 221 ASP Chi-restraints excluded: chain D residue 286 VAL Chi-restraints excluded: chain D residue 288 GLU Chi-restraints excluded: chain E residue 9 GLU Chi-restraints excluded: chain E residue 26 ASP Chi-restraints excluded: chain E residue 32 ARG Chi-restraints excluded: chain E residue 58 THR Chi-restraints excluded: chain E residue 171 ASP Chi-restraints excluded: chain F residue 290 LEU Chi-restraints excluded: chain G residue 70 GLN Chi-restraints excluded: chain G residue 203 SER Chi-restraints excluded: chain G residue 264 SER Chi-restraints excluded: chain H residue 127 VAL Chi-restraints excluded: chain I residue 94 LYS Chi-restraints excluded: chain I residue 149 VAL Chi-restraints excluded: chain I residue 175 ARG Chi-restraints excluded: chain I residue 282 ILE Chi-restraints excluded: chain I residue 390 ILE Chi-restraints excluded: chain I residue 568 GLU Chi-restraints excluded: chain J residue 2 SER Chi-restraints excluded: chain K residue 68 LYS Chi-restraints excluded: chain K residue 91 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 304 random chunks: chunk 76 optimal weight: 3.9990 chunk 83 optimal weight: 0.0770 chunk 113 optimal weight: 7.9990 chunk 242 optimal weight: 9.9990 chunk 106 optimal weight: 3.9990 chunk 240 optimal weight: 3.9990 chunk 121 optimal weight: 4.9990 chunk 143 optimal weight: 1.9990 chunk 139 optimal weight: 5.9990 chunk 84 optimal weight: 0.9980 chunk 286 optimal weight: 0.8980 overall best weight: 1.5942 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 79 HIS D 79 HIS D 279 GLN E 137 GLN H 220 HIS I 52 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3843 r_free = 0.3843 target = 0.133125 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.103236 restraints weight = 42777.109| |-----------------------------------------------------------------------------| r_work (start): 0.3400 rms_B_bonded: 1.80 r_work: 0.3236 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.3129 rms_B_bonded: 3.98 restraints_weight: 0.2500 r_work (final): 0.3129 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8572 moved from start: 0.2758 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 27011 Z= 0.176 Angle : 0.796 14.270 37114 Z= 0.392 Chirality : 0.070 0.795 4129 Planarity : 0.005 0.050 4384 Dihedral : 17.957 168.199 4754 Min Nonbonded Distance : 2.374 Molprobity Statistics. All-atom Clashscore : 2.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.79 % Favored : 96.21 % Rotamer: Outliers : 3.26 % Allowed : 13.63 % Favored : 83.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.01 (0.15), residues: 2925 helix: 1.30 (0.17), residues: 930 sheet: 0.74 (0.20), residues: 599 loop : -1.26 (0.15), residues: 1396 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG I 560 TYR 0.016 0.002 TYR H 83 PHE 0.015 0.002 PHE J 105 TRP 0.024 0.002 TRP H 108 HIS 0.006 0.002 HIS B 189 Details of bonding type rmsd/Z covalent geometry : bond 0.00377 / 0.18 (27011) covalent geometry : angle 0.79596 / 0.39 (37114) hydrogen bonds : bond 0.06098 / 4.12 ( 1045) hydrogen bonds : angle 5.11670 / 3.58 ( 2876) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5850 Ramachandran restraints generated. 2925 Oldfield, 0 Emsley, 2925 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5850 Ramachandran restraints generated. 2925 Oldfield, 0 Emsley, 2925 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 268 residues out of total 2489 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 187 time to evaluate : 1.025 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 77 GLU cc_start: 0.8351 (OUTLIER) cc_final: 0.7349 (mt-10) REVERT: A 131 LYS cc_start: 0.8219 (ptpt) cc_final: 0.7531 (ptmm) REVERT: B 83 TYR cc_start: 0.5359 (OUTLIER) cc_final: 0.5042 (t80) REVERT: C 126 GLU cc_start: 0.8674 (OUTLIER) cc_final: 0.8234 (tt0) REVERT: C 173 ARG cc_start: 0.8080 (OUTLIER) cc_final: 0.7678 (mpt-90) REVERT: C 226 ARG cc_start: 0.9023 (OUTLIER) cc_final: 0.8811 (ttp-110) REVERT: D 9 GLU cc_start: 0.8358 (OUTLIER) cc_final: 0.7484 (mm-30) REVERT: E 9 GLU cc_start: 0.8540 (OUTLIER) cc_final: 0.8117 (mp0) REVERT: E 109 MET cc_start: 0.6625 (mtm) cc_final: 0.6271 (mtm) REVERT: F 89 LYS cc_start: 0.7847 (tppt) cc_final: 0.7498 (tmtt) REVERT: G 89 LYS cc_start: 0.7585 (mppt) cc_final: 0.7325 (tptm) REVERT: H 30 MET cc_start: 0.6928 (mmt) cc_final: 0.6483 (mmm) REVERT: H 123 MET cc_start: 0.7956 (mtm) cc_final: 0.7591 (mtp) REVERT: H 127 VAL cc_start: 0.4874 (OUTLIER) cc_final: 0.4535 (m) REVERT: H 261 GLU cc_start: 0.6291 (pm20) cc_final: 0.5197 (tp30) REVERT: I 3 LEU cc_start: 0.7003 (OUTLIER) cc_final: 0.6423 (mp) REVERT: I 58 ARG cc_start: 0.5818 (mmt180) cc_final: 0.5216 (mmp-170) REVERT: I 63 LEU cc_start: 0.8025 (OUTLIER) cc_final: 0.7453 (tp) REVERT: I 94 LYS cc_start: 0.6519 (OUTLIER) cc_final: 0.5979 (mttt) REVERT: I 231 GLU cc_start: 0.7758 (OUTLIER) cc_final: 0.7446 (pt0) REVERT: I 286 MET cc_start: 0.4713 (pp-130) cc_final: 0.3832 (mmp) REVERT: I 568 GLU cc_start: 0.8158 (OUTLIER) cc_final: 0.7869 (mt-10) REVERT: J 50 GLN cc_start: 0.8212 (OUTLIER) cc_final: 0.7849 (mm110) REVERT: J 82 MET cc_start: 0.8615 (OUTLIER) cc_final: 0.8336 (mtp) outliers start: 81 outliers final: 32 residues processed: 244 average time/residue: 0.8085 time to fit residues: 223.6854 Evaluate side-chains 228 residues out of total 2489 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 181 time to evaluate : 0.965 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 ILE Chi-restraints excluded: chain A residue 40 SER Chi-restraints excluded: chain A residue 77 GLU Chi-restraints excluded: chain A residue 170 GLU Chi-restraints excluded: chain A residue 191 MET Chi-restraints excluded: chain B residue 83 TYR Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 257 VAL Chi-restraints excluded: chain B residue 279 GLN Chi-restraints excluded: chain C residue 45 VAL Chi-restraints excluded: chain C residue 126 GLU Chi-restraints excluded: chain C residue 138 MET Chi-restraints excluded: chain C residue 159 VAL Chi-restraints excluded: chain C residue 173 ARG Chi-restraints excluded: chain C residue 226 ARG Chi-restraints excluded: chain D residue 9 GLU Chi-restraints excluded: chain D residue 148 VAL Chi-restraints excluded: chain D residue 152 VAL Chi-restraints excluded: chain D residue 174 THR Chi-restraints excluded: chain D residue 250 LYS Chi-restraints excluded: chain D residue 269 SER Chi-restraints excluded: chain D residue 288 GLU Chi-restraints excluded: chain E residue 9 GLU Chi-restraints excluded: chain E residue 26 ASP Chi-restraints excluded: chain E residue 58 THR Chi-restraints excluded: chain E residue 171 ASP Chi-restraints excluded: chain E residue 257 VAL Chi-restraints excluded: chain E residue 279 GLN Chi-restraints excluded: chain F residue 257 VAL Chi-restraints excluded: chain F residue 290 LEU Chi-restraints excluded: chain G residue 264 SER Chi-restraints excluded: chain H residue 127 VAL Chi-restraints excluded: chain I residue 3 LEU Chi-restraints excluded: chain I residue 63 LEU Chi-restraints excluded: chain I residue 94 LYS Chi-restraints excluded: chain I residue 148 ILE Chi-restraints excluded: chain I residue 149 VAL Chi-restraints excluded: chain I residue 175 ARG Chi-restraints excluded: chain I residue 231 GLU Chi-restraints excluded: chain I residue 390 ILE Chi-restraints excluded: chain I residue 568 GLU Chi-restraints excluded: chain J residue 50 GLN Chi-restraints excluded: chain J residue 82 MET Chi-restraints excluded: chain K residue 43 SER Chi-restraints excluded: chain K residue 68 LYS Chi-restraints excluded: chain K residue 91 SER Chi-restraints excluded: chain K residue 100 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 304 random chunks: chunk 22 optimal weight: 6.9990 chunk 297 optimal weight: 20.0000 chunk 166 optimal weight: 4.9990 chunk 143 optimal weight: 0.0870 chunk 12 optimal weight: 8.9990 chunk 244 optimal weight: 10.0000 chunk 301 optimal weight: 8.9990 chunk 243 optimal weight: 8.9990 chunk 196 optimal weight: 20.0000 chunk 229 optimal weight: 0.1980 chunk 203 optimal weight: 4.9990 overall best weight: 3.4564 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 79 HIS D 39 HIS D 279 GLN E 66 ASN H 29 ASN H 220 HIS J 111 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3780 r_free = 0.3780 target = 0.128773 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3354 r_free = 0.3354 target = 0.098102 restraints weight = 42507.121| |-----------------------------------------------------------------------------| r_work (start): 0.3312 rms_B_bonded: 2.04 r_work: 0.3124 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.3015 rms_B_bonded: 4.24 restraints_weight: 0.2500 r_work (final): 0.3015 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8669 moved from start: 0.3165 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.083 27011 Z= 0.292 Angle : 0.974 16.875 37114 Z= 0.482 Chirality : 0.083 0.879 4129 Planarity : 0.007 0.056 4384 Dihedral : 18.255 159.353 4754 Min Nonbonded Distance : 2.179 Molprobity Statistics. All-atom Clashscore : 3.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.97 % Favored : 96.03 % Rotamer: Outliers : 4.10 % Allowed : 14.19 % Favored : 81.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.63 (0.14), residues: 2925 helix: 0.75 (0.17), residues: 930 sheet: 1.00 (0.22), residues: 506 loop : -1.77 (0.14), residues: 1489 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG E 117 TYR 0.026 0.003 TYR F 8 PHE 0.026 0.003 PHE I 605 TRP 0.019 0.002 TRP H 108 HIS 0.010 0.002 HIS G 189 Details of bonding type rmsd/Z covalent geometry : bond 0.00682 / 0.29 (27011) covalent geometry : angle 0.97407 / 0.48 (37114) hydrogen bonds : bond 0.08799 / 5.90 ( 1045) hydrogen bonds : angle 5.41143 / 3.79 ( 2876) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5850 Ramachandran restraints generated. 2925 Oldfield, 0 Emsley, 2925 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5850 Ramachandran restraints generated. 2925 Oldfield, 0 Emsley, 2925 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 282 residues out of total 2489 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 102 poor density : 180 time to evaluate : 0.982 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 114 LEU cc_start: 0.8860 (OUTLIER) cc_final: 0.8639 (pp) REVERT: A 131 LYS cc_start: 0.8242 (ptpt) cc_final: 0.7607 (ptmm) REVERT: A 137 ASN cc_start: 0.5785 (OUTLIER) cc_final: 0.5473 (p0) REVERT: B 83 TYR cc_start: 0.5637 (OUTLIER) cc_final: 0.5348 (t80) REVERT: C 126 GLU cc_start: 0.8753 (OUTLIER) cc_final: 0.8314 (tt0) REVERT: C 226 ARG cc_start: 0.9110 (OUTLIER) cc_final: 0.8833 (ttp-170) REVERT: D 9 GLU cc_start: 0.8532 (OUTLIER) cc_final: 0.7517 (mm-30) REVERT: E 109 MET cc_start: 0.7009 (mtm) cc_final: 0.6528 (mtm) REVERT: E 123 MET cc_start: 0.9000 (mtp) cc_final: 0.8743 (mtm) REVERT: F 89 LYS cc_start: 0.7916 (tppt) cc_final: 0.7506 (tmtt) REVERT: G 89 LYS cc_start: 0.7532 (mppt) cc_final: 0.7221 (tptm) REVERT: G 289 MET cc_start: 0.6504 (pmt) cc_final: 0.6298 (pmm) REVERT: H 29 ASN cc_start: 0.6187 (OUTLIER) cc_final: 0.5972 (t0) REVERT: H 30 MET cc_start: 0.7176 (mmt) cc_final: 0.6734 (mmm) REVERT: H 123 MET cc_start: 0.8202 (mtm) cc_final: 0.7442 (ttm) REVERT: H 127 VAL cc_start: 0.5203 (OUTLIER) cc_final: 0.4815 (m) REVERT: I 63 LEU cc_start: 0.7743 (OUTLIER) cc_final: 0.7158 (tp) REVERT: I 231 GLU cc_start: 0.7961 (OUTLIER) cc_final: 0.7595 (pt0) REVERT: I 286 MET cc_start: 0.5051 (pp-130) cc_final: 0.4101 (mmp) REVERT: I 568 GLU cc_start: 0.8204 (OUTLIER) cc_final: 0.7901 (mt-10) REVERT: J 50 GLN cc_start: 0.8395 (OUTLIER) cc_final: 0.8156 (mm-40) REVERT: J 82 MET cc_start: 0.8724 (OUTLIER) cc_final: 0.8414 (mtp) outliers start: 102 outliers final: 43 residues processed: 247 average time/residue: 0.8097 time to fit residues: 226.8349 Evaluate side-chains 229 residues out of total 2489 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 173 time to evaluate : 1.007 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 TYR Chi-restraints excluded: chain A residue 11 ILE Chi-restraints excluded: chain A residue 40 SER Chi-restraints excluded: chain A residue 55 ILE Chi-restraints excluded: chain A residue 114 LEU Chi-restraints excluded: chain A residue 137 ASN Chi-restraints excluded: chain A residue 170 GLU Chi-restraints excluded: chain A residue 191 MET Chi-restraints excluded: chain A residue 213 ASP Chi-restraints excluded: chain B residue 45 VAL Chi-restraints excluded: chain B residue 83 TYR Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 257 VAL Chi-restraints excluded: chain B residue 279 GLN Chi-restraints excluded: chain C residue 45 VAL Chi-restraints excluded: chain C residue 126 GLU Chi-restraints excluded: chain C residue 138 MET Chi-restraints excluded: chain C residue 159 VAL Chi-restraints excluded: chain C residue 226 ARG Chi-restraints excluded: chain D residue 9 GLU Chi-restraints excluded: chain D residue 148 VAL Chi-restraints excluded: chain D residue 152 VAL Chi-restraints excluded: chain D residue 174 THR Chi-restraints excluded: chain D residue 269 SER Chi-restraints excluded: chain D residue 276 THR Chi-restraints excluded: chain D residue 286 VAL Chi-restraints excluded: chain D residue 288 GLU Chi-restraints excluded: chain E residue 26 ASP Chi-restraints excluded: chain E residue 58 THR Chi-restraints excluded: chain E residue 171 ASP Chi-restraints excluded: chain E residue 257 VAL Chi-restraints excluded: chain F residue 257 VAL Chi-restraints excluded: chain F residue 286 VAL Chi-restraints excluded: chain F residue 290 LEU Chi-restraints excluded: chain G residue 2 THR Chi-restraints excluded: chain G residue 264 SER Chi-restraints excluded: chain H residue 29 ASN Chi-restraints excluded: chain H residue 69 ILE Chi-restraints excluded: chain H residue 127 VAL Chi-restraints excluded: chain I residue 3 LEU Chi-restraints excluded: chain I residue 49 LEU Chi-restraints excluded: chain I residue 50 ARG Chi-restraints excluded: chain I residue 63 LEU Chi-restraints excluded: chain I residue 94 LYS Chi-restraints excluded: chain I residue 148 ILE Chi-restraints excluded: chain I residue 149 VAL Chi-restraints excluded: chain I residue 175 ARG Chi-restraints excluded: chain I residue 231 GLU Chi-restraints excluded: chain I residue 390 ILE Chi-restraints excluded: chain I residue 568 GLU Chi-restraints excluded: chain J residue 50 GLN Chi-restraints excluded: chain J residue 82 MET Chi-restraints excluded: chain K residue 36 ILE Chi-restraints excluded: chain K residue 43 SER Chi-restraints excluded: chain K residue 68 LYS Chi-restraints excluded: chain K residue 91 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 304 random chunks: chunk 156 optimal weight: 3.9990 chunk 292 optimal weight: 2.9990 chunk 25 optimal weight: 3.9990 chunk 162 optimal weight: 3.9990 chunk 303 optimal weight: 9.9990 chunk 214 optimal weight: 0.9980 chunk 233 optimal weight: 0.8980 chunk 248 optimal weight: 4.9990 chunk 241 optimal weight: 6.9990 chunk 44 optimal weight: 4.9990 chunk 225 optimal weight: 10.0000 overall best weight: 2.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 79 HIS B 131 GLN D 279 GLN G 6 ASN H 29 ASN H 220 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3797 r_free = 0.3797 target = 0.130025 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.100010 restraints weight = 42630.941| |-----------------------------------------------------------------------------| r_work (start): 0.3343 rms_B_bonded: 2.00 r_work: 0.3156 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.3047 rms_B_bonded: 4.24 restraints_weight: 0.2500 r_work (final): 0.3047 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8647 moved from start: 0.3273 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.067 27011 Z= 0.230 Angle : 0.871 15.889 37114 Z= 0.431 Chirality : 0.076 0.818 4129 Planarity : 0.006 0.050 4384 Dihedral : 18.196 160.744 4754 Min Nonbonded Distance : 2.285 Molprobity Statistics. All-atom Clashscore : 3.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.83 % Favored : 96.17 % Rotamer: Outliers : 3.50 % Allowed : 15.15 % Favored : 81.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.63 (0.15), residues: 2925 helix: 0.82 (0.17), residues: 930 sheet: 0.99 (0.22), residues: 500 loop : -1.82 (0.14), residues: 1495 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG I 560 TYR 0.022 0.002 TYR F 8 PHE 0.018 0.002 PHE I 605 TRP 0.020 0.002 TRP H 108 HIS 0.007 0.002 HIS G 189 Details of bonding type rmsd/Z covalent geometry : bond 0.00524 / 0.23 (27011) covalent geometry : angle 0.87129 / 0.43 (37114) hydrogen bonds : bond 0.07327 / 4.91 ( 1045) hydrogen bonds : angle 5.23876 / 3.67 ( 2876) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5850 Ramachandran restraints generated. 2925 Oldfield, 0 Emsley, 2925 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5850 Ramachandran restraints generated. 2925 Oldfield, 0 Emsley, 2925 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 264 residues out of total 2489 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 177 time to evaluate : 0.968 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 43 ARG cc_start: 0.8677 (OUTLIER) cc_final: 0.8296 (tmm-80) REVERT: A 84 LYS cc_start: 0.8423 (tptm) cc_final: 0.8215 (tptt) REVERT: A 114 LEU cc_start: 0.8803 (OUTLIER) cc_final: 0.8580 (pp) REVERT: A 131 LYS cc_start: 0.8251 (ptpt) cc_final: 0.7622 (ptmm) REVERT: A 137 ASN cc_start: 0.5805 (OUTLIER) cc_final: 0.5501 (p0) REVERT: B 83 TYR cc_start: 0.5605 (OUTLIER) cc_final: 0.5349 (t80) REVERT: C 126 GLU cc_start: 0.8734 (OUTLIER) cc_final: 0.8263 (tt0) REVERT: C 226 ARG cc_start: 0.9106 (OUTLIER) cc_final: 0.8875 (ttp-170) REVERT: D 9 GLU cc_start: 0.8476 (OUTLIER) cc_final: 0.7539 (mm-30) REVERT: D 103 LYS cc_start: 0.7664 (OUTLIER) cc_final: 0.7272 (tttm) REVERT: E 9 GLU cc_start: 0.8636 (OUTLIER) cc_final: 0.8276 (mp0) REVERT: E 109 MET cc_start: 0.7205 (mtm) cc_final: 0.6677 (mtm) REVERT: E 123 MET cc_start: 0.8945 (mtp) cc_final: 0.8620 (mtm) REVERT: E 285 GLU cc_start: 0.7808 (OUTLIER) cc_final: 0.7566 (mt-10) REVERT: F 63 GLU cc_start: 0.8087 (OUTLIER) cc_final: 0.7432 (tt0) REVERT: F 89 LYS cc_start: 0.7897 (tppt) cc_final: 0.7425 (tmtt) REVERT: G 89 LYS cc_start: 0.7468 (mppt) cc_final: 0.7132 (tptm) REVERT: H 29 ASN cc_start: 0.6094 (OUTLIER) cc_final: 0.5655 (t0) REVERT: H 30 MET cc_start: 0.7120 (mmt) cc_final: 0.6740 (mmt) REVERT: H 123 MET cc_start: 0.8126 (mtm) cc_final: 0.7661 (mtp) REVERT: H 127 VAL cc_start: 0.5370 (OUTLIER) cc_final: 0.5026 (m) REVERT: H 229 MET cc_start: 0.7776 (OUTLIER) cc_final: 0.7306 (mtm) REVERT: I 63 LEU cc_start: 0.7736 (OUTLIER) cc_final: 0.7143 (tp) REVERT: I 205 ARG cc_start: 0.5969 (ptp-170) cc_final: 0.5434 (ttp-110) REVERT: I 231 GLU cc_start: 0.7918 (OUTLIER) cc_final: 0.7554 (pt0) REVERT: I 282 ILE cc_start: 0.3833 (OUTLIER) cc_final: 0.3622 (mp) REVERT: I 286 MET cc_start: 0.5006 (pp-130) cc_final: 0.4110 (mmp) REVERT: I 483 ARG cc_start: 0.8835 (OUTLIER) cc_final: 0.7766 (mmp-170) REVERT: I 568 GLU cc_start: 0.8214 (OUTLIER) cc_final: 0.7918 (mt-10) REVERT: J 82 MET cc_start: 0.8711 (OUTLIER) cc_final: 0.8429 (mtp) REVERT: K 106 MET cc_start: 0.9020 (OUTLIER) cc_final: 0.8041 (mmm) outliers start: 87 outliers final: 46 residues processed: 238 average time/residue: 0.7844 time to fit residues: 212.2022 Evaluate side-chains 240 residues out of total 2489 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 173 time to evaluate : 1.058 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 ILE Chi-restraints excluded: chain A residue 40 SER Chi-restraints excluded: chain A residue 43 ARG Chi-restraints excluded: chain A residue 55 ILE Chi-restraints excluded: chain A residue 114 LEU Chi-restraints excluded: chain A residue 137 ASN Chi-restraints excluded: chain A residue 170 GLU Chi-restraints excluded: chain A residue 179 SER Chi-restraints excluded: chain A residue 191 MET Chi-restraints excluded: chain B residue 83 TYR Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 257 VAL Chi-restraints excluded: chain B residue 279 GLN Chi-restraints excluded: chain B residue 284 VAL Chi-restraints excluded: chain C residue 45 VAL Chi-restraints excluded: chain C residue 126 GLU Chi-restraints excluded: chain C residue 138 MET Chi-restraints excluded: chain C residue 159 VAL Chi-restraints excluded: chain C residue 226 ARG Chi-restraints excluded: chain C residue 287 LYS Chi-restraints excluded: chain D residue 9 GLU Chi-restraints excluded: chain D residue 103 LYS Chi-restraints excluded: chain D residue 148 VAL Chi-restraints excluded: chain D residue 152 VAL Chi-restraints excluded: chain D residue 174 THR Chi-restraints excluded: chain D residue 269 SER Chi-restraints excluded: chain D residue 286 VAL Chi-restraints excluded: chain D residue 288 GLU Chi-restraints excluded: chain E residue 9 GLU Chi-restraints excluded: chain E residue 26 ASP Chi-restraints excluded: chain E residue 58 THR Chi-restraints excluded: chain E residue 171 ASP Chi-restraints excluded: chain E residue 174 THR Chi-restraints excluded: chain E residue 257 VAL Chi-restraints excluded: chain E residue 279 GLN Chi-restraints excluded: chain E residue 285 GLU Chi-restraints excluded: chain F residue 63 GLU Chi-restraints excluded: chain F residue 257 VAL Chi-restraints excluded: chain F residue 286 VAL Chi-restraints excluded: chain F residue 290 LEU Chi-restraints excluded: chain G residue 2 THR Chi-restraints excluded: chain G residue 240 GLN Chi-restraints excluded: chain G residue 264 SER Chi-restraints excluded: chain H residue 29 ASN Chi-restraints excluded: chain H residue 69 ILE Chi-restraints excluded: chain H residue 127 VAL Chi-restraints excluded: chain H residue 229 MET Chi-restraints excluded: chain I residue 3 LEU Chi-restraints excluded: chain I residue 49 LEU Chi-restraints excluded: chain I residue 63 LEU Chi-restraints excluded: chain I residue 94 LYS Chi-restraints excluded: chain I residue 148 ILE Chi-restraints excluded: chain I residue 149 VAL Chi-restraints excluded: chain I residue 159 VAL Chi-restraints excluded: chain I residue 175 ARG Chi-restraints excluded: chain I residue 231 GLU Chi-restraints excluded: chain I residue 282 ILE Chi-restraints excluded: chain I residue 390 ILE Chi-restraints excluded: chain I residue 483 ARG Chi-restraints excluded: chain I residue 568 GLU Chi-restraints excluded: chain J residue 2 SER Chi-restraints excluded: chain J residue 82 MET Chi-restraints excluded: chain K residue 36 ILE Chi-restraints excluded: chain K residue 43 SER Chi-restraints excluded: chain K residue 68 LYS Chi-restraints excluded: chain K residue 91 SER Chi-restraints excluded: chain K residue 106 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 304 random chunks: chunk 94 optimal weight: 0.9980 chunk 176 optimal weight: 7.9990 chunk 292 optimal weight: 3.9990 chunk 275 optimal weight: 3.9990 chunk 158 optimal weight: 8.9990 chunk 296 optimal weight: 40.0000 chunk 199 optimal weight: 10.0000 chunk 226 optimal weight: 4.9990 chunk 92 optimal weight: 0.9980 chunk 169 optimal weight: 7.9990 chunk 37 optimal weight: 0.8980 overall best weight: 2.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 79 HIS B 131 GLN D 279 GLN H 29 ASN H 220 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3804 r_free = 0.3804 target = 0.130558 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.100201 restraints weight = 42545.237| |-----------------------------------------------------------------------------| r_work (start): 0.3348 rms_B_bonded: 1.99 r_work: 0.3178 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.3070 rms_B_bonded: 4.03 restraints_weight: 0.2500 r_work (final): 0.3070 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8618 moved from start: 0.3368 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.063 27011 Z= 0.206 Angle : 0.835 14.136 37114 Z= 0.413 Chirality : 0.072 0.801 4129 Planarity : 0.006 0.047 4384 Dihedral : 18.162 163.449 4754 Min Nonbonded Distance : 2.347 Molprobity Statistics. All-atom Clashscore : 3.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.97 % Favored : 96.03 % Rotamer: Outliers : 3.62 % Allowed : 15.23 % Favored : 81.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.59 (0.15), residues: 2925 helix: 0.91 (0.17), residues: 932 sheet: 0.96 (0.22), residues: 510 loop : -1.83 (0.14), residues: 1483 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG I 205 TYR 0.020 0.002 TYR F 8 PHE 0.022 0.002 PHE I 283 TRP 0.014 0.002 TRP H 108 HIS 0.006 0.001 HIS G 189 Details of bonding type rmsd/Z covalent geometry : bond 0.00462 / 0.21 (27011) covalent geometry : angle 0.83526 / 0.41 (37114) hydrogen bonds : bond 0.06816 / 4.57 ( 1045) hydrogen bonds : angle 5.14864 / 3.61 ( 2876) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5850 Ramachandran restraints generated. 2925 Oldfield, 0 Emsley, 2925 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5850 Ramachandran restraints generated. 2925 Oldfield, 0 Emsley, 2925 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 266 residues out of total 2489 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 176 time to evaluate : 0.926 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 43 ARG cc_start: 0.8673 (OUTLIER) cc_final: 0.8279 (tmm-80) REVERT: A 77 GLU cc_start: 0.8441 (OUTLIER) cc_final: 0.7493 (mt-10) REVERT: A 114 LEU cc_start: 0.8790 (OUTLIER) cc_final: 0.8574 (pp) REVERT: A 131 LYS cc_start: 0.8246 (ptpt) cc_final: 0.7613 (ptmm) REVERT: A 172 LEU cc_start: 0.8568 (OUTLIER) cc_final: 0.8217 (mp) REVERT: B 83 TYR cc_start: 0.5675 (OUTLIER) cc_final: 0.5396 (t80) REVERT: C 126 GLU cc_start: 0.8735 (OUTLIER) cc_final: 0.8299 (tt0) REVERT: C 226 ARG cc_start: 0.9101 (OUTLIER) cc_final: 0.8870 (ttp-170) REVERT: D 9 GLU cc_start: 0.8450 (OUTLIER) cc_final: 0.7482 (mm-30) REVERT: D 103 LYS cc_start: 0.7628 (OUTLIER) cc_final: 0.7218 (tttm) REVERT: E 9 GLU cc_start: 0.8627 (OUTLIER) cc_final: 0.8257 (mp0) REVERT: E 109 MET cc_start: 0.7323 (mtm) cc_final: 0.6962 (mtm) REVERT: E 123 MET cc_start: 0.8973 (mtp) cc_final: 0.8607 (mtm) REVERT: E 285 GLU cc_start: 0.7724 (OUTLIER) cc_final: 0.7477 (mt-10) REVERT: F 63 GLU cc_start: 0.8090 (OUTLIER) cc_final: 0.7406 (tt0) REVERT: F 89 LYS cc_start: 0.7922 (tppt) cc_final: 0.7424 (tmtt) REVERT: G 36 GLU cc_start: 0.8245 (OUTLIER) cc_final: 0.7873 (mp0) REVERT: G 89 LYS cc_start: 0.7450 (mppt) cc_final: 0.7152 (tptm) REVERT: G 289 MET cc_start: 0.6621 (pmt) cc_final: 0.6357 (pmm) REVERT: H 123 MET cc_start: 0.8005 (mtm) cc_final: 0.7486 (mtp) REVERT: H 127 VAL cc_start: 0.5742 (OUTLIER) cc_final: 0.5449 (m) REVERT: H 229 MET cc_start: 0.7827 (OUTLIER) cc_final: 0.7408 (mtm) REVERT: I 3 LEU cc_start: 0.7121 (OUTLIER) cc_final: 0.6395 (mp) REVERT: I 63 LEU cc_start: 0.7582 (OUTLIER) cc_final: 0.7002 (tp) REVERT: I 205 ARG cc_start: 0.5970 (ptp-170) cc_final: 0.5452 (ttp-110) REVERT: I 231 GLU cc_start: 0.7864 (OUTLIER) cc_final: 0.7470 (pt0) REVERT: I 286 MET cc_start: 0.4994 (pp-130) cc_final: 0.4188 (mmp) REVERT: I 568 GLU cc_start: 0.8202 (OUTLIER) cc_final: 0.7902 (mt-10) REVERT: J 82 MET cc_start: 0.8663 (OUTLIER) cc_final: 0.8344 (mtp) outliers start: 90 outliers final: 44 residues processed: 242 average time/residue: 0.7987 time to fit residues: 219.9105 Evaluate side-chains 235 residues out of total 2489 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 171 time to evaluate : 1.092 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 ILE Chi-restraints excluded: chain A residue 40 SER Chi-restraints excluded: chain A residue 43 ARG Chi-restraints excluded: chain A residue 55 ILE Chi-restraints excluded: chain A residue 77 GLU Chi-restraints excluded: chain A residue 114 LEU Chi-restraints excluded: chain A residue 170 GLU Chi-restraints excluded: chain A residue 172 LEU Chi-restraints excluded: chain A residue 179 SER Chi-restraints excluded: chain A residue 191 MET Chi-restraints excluded: chain B residue 45 VAL Chi-restraints excluded: chain B residue 83 TYR Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 257 VAL Chi-restraints excluded: chain B residue 279 GLN Chi-restraints excluded: chain C residue 45 VAL Chi-restraints excluded: chain C residue 126 GLU Chi-restraints excluded: chain C residue 138 MET Chi-restraints excluded: chain C residue 159 VAL Chi-restraints excluded: chain C residue 226 ARG Chi-restraints excluded: chain C residue 287 LYS Chi-restraints excluded: chain D residue 9 GLU Chi-restraints excluded: chain D residue 103 LYS Chi-restraints excluded: chain D residue 148 VAL Chi-restraints excluded: chain D residue 152 VAL Chi-restraints excluded: chain D residue 174 THR Chi-restraints excluded: chain D residue 269 SER Chi-restraints excluded: chain D residue 286 VAL Chi-restraints excluded: chain D residue 288 GLU Chi-restraints excluded: chain E residue 9 GLU Chi-restraints excluded: chain E residue 26 ASP Chi-restraints excluded: chain E residue 58 THR Chi-restraints excluded: chain E residue 171 ASP Chi-restraints excluded: chain E residue 174 THR Chi-restraints excluded: chain E residue 257 VAL Chi-restraints excluded: chain E residue 279 GLN Chi-restraints excluded: chain E residue 285 GLU Chi-restraints excluded: chain F residue 63 GLU Chi-restraints excluded: chain F residue 257 VAL Chi-restraints excluded: chain F residue 286 VAL Chi-restraints excluded: chain F residue 290 LEU Chi-restraints excluded: chain G residue 2 THR Chi-restraints excluded: chain G residue 36 GLU Chi-restraints excluded: chain G residue 264 SER Chi-restraints excluded: chain H residue 69 ILE Chi-restraints excluded: chain H residue 127 VAL Chi-restraints excluded: chain H residue 229 MET Chi-restraints excluded: chain I residue 3 LEU Chi-restraints excluded: chain I residue 49 LEU Chi-restraints excluded: chain I residue 63 LEU Chi-restraints excluded: chain I residue 94 LYS Chi-restraints excluded: chain I residue 148 ILE Chi-restraints excluded: chain I residue 149 VAL Chi-restraints excluded: chain I residue 175 ARG Chi-restraints excluded: chain I residue 214 VAL Chi-restraints excluded: chain I residue 231 GLU Chi-restraints excluded: chain I residue 390 ILE Chi-restraints excluded: chain I residue 568 GLU Chi-restraints excluded: chain J residue 2 SER Chi-restraints excluded: chain J residue 82 MET Chi-restraints excluded: chain K residue 36 ILE Chi-restraints excluded: chain K residue 43 SER Chi-restraints excluded: chain K residue 68 LYS Chi-restraints excluded: chain K residue 91 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 304 random chunks: chunk 154 optimal weight: 4.9990 chunk 26 optimal weight: 0.0070 chunk 242 optimal weight: 10.0000 chunk 94 optimal weight: 0.7980 chunk 285 optimal weight: 2.9990 chunk 127 optimal weight: 1.9990 chunk 161 optimal weight: 8.9990 chunk 301 optimal weight: 5.9990 chunk 118 optimal weight: 0.7980 chunk 181 optimal weight: 0.8980 chunk 64 optimal weight: 0.5980 overall best weight: 0.6198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 70 GLN B 79 HIS B 131 GLN D 279 GLN H 66 ASN H 220 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3864 r_free = 0.3864 target = 0.134905 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3461 r_free = 0.3461 target = 0.105073 restraints weight = 42746.897| |-----------------------------------------------------------------------------| r_work (start): 0.3426 rms_B_bonded: 1.83 r_work: 0.3270 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.3164 rms_B_bonded: 4.02 restraints_weight: 0.2500 r_work (final): 0.3164 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8526 moved from start: 0.3459 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 27011 Z= 0.129 Angle : 0.707 16.568 37114 Z= 0.349 Chirality : 0.060 0.667 4129 Planarity : 0.005 0.040 4384 Dihedral : 18.063 168.478 4754 Min Nonbonded Distance : 2.400 Molprobity Statistics. All-atom Clashscore : 3.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.18 % Favored : 96.82 % Rotamer: Outliers : 2.29 % Allowed : 16.48 % Favored : 81.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.25 (0.15), residues: 2925 helix: 1.33 (0.18), residues: 925 sheet: 0.85 (0.22), residues: 534 loop : -1.63 (0.14), residues: 1466 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG K 67 TYR 0.014 0.001 TYR I 246 PHE 0.010 0.001 PHE I 593 TRP 0.017 0.002 TRP H 108 HIS 0.004 0.001 HIS H 220 Details of bonding type rmsd/Z covalent geometry : bond 0.00247 / 0.13 (27011) covalent geometry : angle 0.70691 / 0.35 (37114) hydrogen bonds : bond 0.04470 / 3.00 ( 1045) hydrogen bonds : angle 4.82462 / 3.40 ( 2876) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5850 Ramachandran restraints generated. 2925 Oldfield, 0 Emsley, 2925 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5850 Ramachandran restraints generated. 2925 Oldfield, 0 Emsley, 2925 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 237 residues out of total 2489 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 180 time to evaluate : 0.955 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 43 ARG cc_start: 0.8615 (OUTLIER) cc_final: 0.8247 (tmm-80) REVERT: A 77 GLU cc_start: 0.8425 (OUTLIER) cc_final: 0.7414 (mt-10) REVERT: A 131 LYS cc_start: 0.8203 (ptpt) cc_final: 0.7600 (ptmm) REVERT: B 83 TYR cc_start: 0.5419 (OUTLIER) cc_final: 0.5155 (t80) REVERT: C 126 GLU cc_start: 0.8658 (OUTLIER) cc_final: 0.8244 (tt0) REVERT: D 9 GLU cc_start: 0.8358 (OUTLIER) cc_final: 0.7452 (mm-30) REVERT: D 103 LYS cc_start: 0.7769 (OUTLIER) cc_final: 0.7376 (tttm) REVERT: E 9 GLU cc_start: 0.8537 (OUTLIER) cc_final: 0.8185 (mp0) REVERT: E 109 MET cc_start: 0.7269 (mtm) cc_final: 0.5736 (mmm) REVERT: F 1 MET cc_start: 0.5376 (mtm) cc_final: 0.4871 (ttm) REVERT: F 63 GLU cc_start: 0.7984 (OUTLIER) cc_final: 0.7319 (tt0) REVERT: F 89 LYS cc_start: 0.7797 (tppt) cc_final: 0.7353 (tmtt) REVERT: G 36 GLU cc_start: 0.8199 (OUTLIER) cc_final: 0.7898 (mp0) REVERT: G 89 LYS cc_start: 0.7441 (mppt) cc_final: 0.7169 (tptp) REVERT: G 289 MET cc_start: 0.6455 (pmt) cc_final: 0.6177 (pmm) REVERT: H 127 VAL cc_start: 0.5813 (OUTLIER) cc_final: 0.5468 (m) REVERT: H 175 MET cc_start: 0.2899 (mtt) cc_final: 0.0766 (tpp) REVERT: I 94 LYS cc_start: 0.6640 (OUTLIER) cc_final: 0.6117 (mttt) REVERT: I 286 MET cc_start: 0.4807 (pp-130) cc_final: 0.4136 (mmp) REVERT: J 50 GLN cc_start: 0.8201 (mm-40) cc_final: 0.7902 (mm-40) outliers start: 57 outliers final: 29 residues processed: 224 average time/residue: 0.8071 time to fit residues: 204.7114 Evaluate side-chains 209 residues out of total 2489 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 169 time to evaluate : 0.961 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 SER Chi-restraints excluded: chain A residue 43 ARG Chi-restraints excluded: chain A residue 55 ILE Chi-restraints excluded: chain A residue 77 GLU Chi-restraints excluded: chain A residue 170 GLU Chi-restraints excluded: chain A residue 179 SER Chi-restraints excluded: chain B residue 83 TYR Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 257 VAL Chi-restraints excluded: chain B residue 279 GLN Chi-restraints excluded: chain C residue 45 VAL Chi-restraints excluded: chain C residue 126 GLU Chi-restraints excluded: chain C residue 138 MET Chi-restraints excluded: chain D residue 9 GLU Chi-restraints excluded: chain D residue 103 LYS Chi-restraints excluded: chain D residue 148 VAL Chi-restraints excluded: chain D residue 152 VAL Chi-restraints excluded: chain D residue 269 SER Chi-restraints excluded: chain D residue 286 VAL Chi-restraints excluded: chain D residue 288 GLU Chi-restraints excluded: chain E residue 9 GLU Chi-restraints excluded: chain E residue 171 ASP Chi-restraints excluded: chain E residue 174 THR Chi-restraints excluded: chain F residue 63 GLU Chi-restraints excluded: chain F residue 257 VAL Chi-restraints excluded: chain F residue 286 VAL Chi-restraints excluded: chain F residue 290 LEU Chi-restraints excluded: chain G residue 36 GLU Chi-restraints excluded: chain G residue 264 SER Chi-restraints excluded: chain H residue 127 VAL Chi-restraints excluded: chain I residue 50 ARG Chi-restraints excluded: chain I residue 94 LYS Chi-restraints excluded: chain I residue 148 ILE Chi-restraints excluded: chain I residue 149 VAL Chi-restraints excluded: chain I residue 214 VAL Chi-restraints excluded: chain I residue 238 VAL Chi-restraints excluded: chain I residue 390 ILE Chi-restraints excluded: chain J residue 2 SER Chi-restraints excluded: chain K residue 43 SER Chi-restraints excluded: chain K residue 68 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 304 random chunks: chunk 292 optimal weight: 4.9990 chunk 287 optimal weight: 1.9990 chunk 176 optimal weight: 1.9990 chunk 182 optimal weight: 5.9990 chunk 44 optimal weight: 0.0470 chunk 273 optimal weight: 0.5980 chunk 3 optimal weight: 1.9990 chunk 242 optimal weight: 10.0000 chunk 154 optimal weight: 4.9990 chunk 212 optimal weight: 5.9990 chunk 110 optimal weight: 3.9990 overall best weight: 1.3284 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 79 HIS B 131 GLN D 279 GLN H 220 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3841 r_free = 0.3841 target = 0.133258 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3436 r_free = 0.3436 target = 0.103485 restraints weight = 42772.756| |-----------------------------------------------------------------------------| r_work (start): 0.3403 rms_B_bonded: 1.84 r_work: 0.3236 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.3130 rms_B_bonded: 3.99 restraints_weight: 0.2500 r_work (final): 0.3130 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8558 moved from start: 0.3495 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 27011 Z= 0.154 Angle : 0.738 14.668 37114 Z= 0.364 Chirality : 0.063 0.732 4129 Planarity : 0.005 0.039 4384 Dihedral : 18.060 168.138 4754 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 3.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.76 % Favored : 96.24 % Rotamer: Outliers : 2.21 % Allowed : 16.92 % Favored : 80.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.23 (0.15), residues: 2925 helix: 1.32 (0.17), residues: 925 sheet: 0.92 (0.22), residues: 535 loop : -1.63 (0.14), residues: 1465 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG I 205 TYR 0.022 0.002 TYR A 9 PHE 0.026 0.001 PHE I 283 TRP 0.025 0.002 TRP H 108 HIS 0.005 0.001 HIS I 541 Details of bonding type rmsd/Z covalent geometry : bond 0.00327 / 0.15 (27011) covalent geometry : angle 0.73753 / 0.36 (37114) hydrogen bonds : bond 0.05272 / 3.55 ( 1045) hydrogen bonds : angle 4.82326 / 3.39 ( 2876) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5850 Ramachandran restraints generated. 2925 Oldfield, 0 Emsley, 2925 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5850 Ramachandran restraints generated. 2925 Oldfield, 0 Emsley, 2925 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 232 residues out of total 2489 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 177 time to evaluate : 1.103 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 43 ARG cc_start: 0.8655 (OUTLIER) cc_final: 0.8301 (tmm-80) REVERT: A 77 GLU cc_start: 0.8447 (OUTLIER) cc_final: 0.7442 (mt-10) REVERT: A 131 LYS cc_start: 0.8210 (ptpt) cc_final: 0.7614 (ptmm) REVERT: A 137 ASN cc_start: 0.5728 (OUTLIER) cc_final: 0.5500 (p0) REVERT: B 83 TYR cc_start: 0.5400 (OUTLIER) cc_final: 0.5135 (t80) REVERT: C 94 LYS cc_start: 0.8123 (mttt) cc_final: 0.7816 (mmtt) REVERT: C 126 GLU cc_start: 0.8695 (OUTLIER) cc_final: 0.8297 (tt0) REVERT: D 9 GLU cc_start: 0.8406 (OUTLIER) cc_final: 0.7530 (mm-30) REVERT: D 103 LYS cc_start: 0.7680 (OUTLIER) cc_final: 0.7318 (tttm) REVERT: E 9 GLU cc_start: 0.8571 (OUTLIER) cc_final: 0.8220 (mp0) REVERT: F 1 MET cc_start: 0.5353 (mtm) cc_final: 0.4670 (ttm) REVERT: F 63 GLU cc_start: 0.7990 (OUTLIER) cc_final: 0.7330 (tt0) REVERT: F 89 LYS cc_start: 0.7850 (tppt) cc_final: 0.7382 (tmtt) REVERT: G 36 GLU cc_start: 0.8197 (OUTLIER) cc_final: 0.7925 (mp0) REVERT: G 89 LYS cc_start: 0.7475 (mppt) cc_final: 0.7209 (tptp) REVERT: G 289 MET cc_start: 0.6491 (pmt) cc_final: 0.6213 (pmm) REVERT: H 123 MET cc_start: 0.7914 (mtm) cc_final: 0.7552 (mtp) REVERT: H 127 VAL cc_start: 0.5850 (OUTLIER) cc_final: 0.5559 (m) REVERT: H 175 MET cc_start: 0.2738 (OUTLIER) cc_final: 0.0669 (tpp) REVERT: I 94 LYS cc_start: 0.6644 (OUTLIER) cc_final: 0.6118 (mttt) REVERT: I 286 MET cc_start: 0.4814 (pp-130) cc_final: 0.4112 (mmp) REVERT: J 50 GLN cc_start: 0.8235 (mm-40) cc_final: 0.7943 (mm-40) outliers start: 55 outliers final: 34 residues processed: 222 average time/residue: 0.8251 time to fit residues: 207.7434 Evaluate side-chains 220 residues out of total 2489 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 173 time to evaluate : 0.971 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 ILE Chi-restraints excluded: chain A residue 40 SER Chi-restraints excluded: chain A residue 43 ARG Chi-restraints excluded: chain A residue 55 ILE Chi-restraints excluded: chain A residue 77 GLU Chi-restraints excluded: chain A residue 137 ASN Chi-restraints excluded: chain A residue 170 GLU Chi-restraints excluded: chain A residue 179 SER Chi-restraints excluded: chain A residue 191 MET Chi-restraints excluded: chain B residue 45 VAL Chi-restraints excluded: chain B residue 83 TYR Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 257 VAL Chi-restraints excluded: chain B residue 279 GLN Chi-restraints excluded: chain C residue 126 GLU Chi-restraints excluded: chain C residue 138 MET Chi-restraints excluded: chain D residue 9 GLU Chi-restraints excluded: chain D residue 103 LYS Chi-restraints excluded: chain D residue 148 VAL Chi-restraints excluded: chain D residue 152 VAL Chi-restraints excluded: chain D residue 269 SER Chi-restraints excluded: chain D residue 276 THR Chi-restraints excluded: chain D residue 286 VAL Chi-restraints excluded: chain D residue 288 GLU Chi-restraints excluded: chain E residue 9 GLU Chi-restraints excluded: chain E residue 171 ASP Chi-restraints excluded: chain E residue 174 THR Chi-restraints excluded: chain E residue 257 VAL Chi-restraints excluded: chain E residue 279 GLN Chi-restraints excluded: chain F residue 63 GLU Chi-restraints excluded: chain F residue 257 VAL Chi-restraints excluded: chain F residue 286 VAL Chi-restraints excluded: chain F residue 290 LEU Chi-restraints excluded: chain G residue 2 THR Chi-restraints excluded: chain G residue 36 GLU Chi-restraints excluded: chain G residue 264 SER Chi-restraints excluded: chain H residue 127 VAL Chi-restraints excluded: chain H residue 175 MET Chi-restraints excluded: chain I residue 94 LYS Chi-restraints excluded: chain I residue 148 ILE Chi-restraints excluded: chain I residue 149 VAL Chi-restraints excluded: chain I residue 159 VAL Chi-restraints excluded: chain I residue 214 VAL Chi-restraints excluded: chain I residue 390 ILE Chi-restraints excluded: chain J residue 2 SER Chi-restraints excluded: chain K residue 43 SER Chi-restraints excluded: chain K residue 68 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 304 random chunks: chunk 226 optimal weight: 9.9990 chunk 188 optimal weight: 0.6980 chunk 295 optimal weight: 3.9990 chunk 22 optimal weight: 6.9990 chunk 276 optimal weight: 4.9990 chunk 151 optimal weight: 4.9990 chunk 18 optimal weight: 4.9990 chunk 67 optimal weight: 1.9990 chunk 139 optimal weight: 1.9990 chunk 31 optimal weight: 0.9990 chunk 223 optimal weight: 5.9990 overall best weight: 1.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 79 HIS D 179 HIS D 279 GLN H 220 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3817 r_free = 0.3817 target = 0.131556 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.101409 restraints weight = 42395.748| |-----------------------------------------------------------------------------| r_work (start): 0.3369 rms_B_bonded: 1.82 r_work: 0.3201 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.3096 rms_B_bonded: 3.96 restraints_weight: 0.2500 r_work (final): 0.3096 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8609 moved from start: 0.3553 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 27011 Z= 0.189 Angle : 0.793 13.048 37114 Z= 0.392 Chirality : 0.067 0.760 4129 Planarity : 0.005 0.041 4384 Dihedral : 18.105 165.548 4754 Min Nonbonded Distance : 2.399 Molprobity Statistics. All-atom Clashscore : 3.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.00 % Favored : 96.00 % Rotamer: Outliers : 2.25 % Allowed : 16.92 % Favored : 80.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.39 (0.15), residues: 2925 helix: 1.14 (0.17), residues: 928 sheet: 1.04 (0.22), residues: 519 loop : -1.75 (0.14), residues: 1478 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG I 560 TYR 0.017 0.002 TYR F 8 PHE 0.016 0.002 PHE J 105 TRP 0.028 0.002 TRP H 108 HIS 0.006 0.001 HIS I 541 Details of bonding type rmsd/Z covalent geometry : bond 0.00420 / 0.19 (27011) covalent geometry : angle 0.79256 / 0.39 (37114) hydrogen bonds : bond 0.06347 / 4.26 ( 1045) hydrogen bonds : angle 4.93777 / 3.47 ( 2876) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5850 Ramachandran restraints generated. 2925 Oldfield, 0 Emsley, 2925 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5850 Ramachandran restraints generated. 2925 Oldfield, 0 Emsley, 2925 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 230 residues out of total 2489 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 174 time to evaluate : 0.926 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 43 ARG cc_start: 0.8669 (OUTLIER) cc_final: 0.8286 (tmm-80) REVERT: A 77 GLU cc_start: 0.8387 (OUTLIER) cc_final: 0.7413 (mt-10) REVERT: A 114 LEU cc_start: 0.8797 (OUTLIER) cc_final: 0.8596 (pp) REVERT: A 131 LYS cc_start: 0.8219 (ptpt) cc_final: 0.7629 (ptmm) REVERT: A 137 ASN cc_start: 0.5820 (OUTLIER) cc_final: 0.5585 (p0) REVERT: B 83 TYR cc_start: 0.5426 (OUTLIER) cc_final: 0.5166 (t80) REVERT: C 45 VAL cc_start: 0.8610 (OUTLIER) cc_final: 0.8383 (m) REVERT: C 94 LYS cc_start: 0.8108 (mttt) cc_final: 0.7809 (mmtt) REVERT: C 126 GLU cc_start: 0.8744 (OUTLIER) cc_final: 0.8321 (tt0) REVERT: C 226 ARG cc_start: 0.9057 (OUTLIER) cc_final: 0.8819 (ttp-170) REVERT: D 9 GLU cc_start: 0.8370 (OUTLIER) cc_final: 0.7499 (mm-30) REVERT: D 103 LYS cc_start: 0.7758 (OUTLIER) cc_final: 0.7404 (tttm) REVERT: F 1 MET cc_start: 0.5349 (mtm) cc_final: 0.4659 (ttm) REVERT: F 63 GLU cc_start: 0.8007 (OUTLIER) cc_final: 0.7301 (tt0) REVERT: F 89 LYS cc_start: 0.7912 (tppt) cc_final: 0.7402 (tmtt) REVERT: G 36 GLU cc_start: 0.8225 (OUTLIER) cc_final: 0.7922 (mp0) REVERT: G 89 LYS cc_start: 0.7492 (mppt) cc_final: 0.7195 (tptp) REVERT: G 175 MET cc_start: 0.5184 (mmm) cc_final: 0.4956 (mmm) REVERT: G 289 MET cc_start: 0.6519 (pmt) cc_final: 0.6243 (pmm) REVERT: H 109 MET cc_start: 0.6879 (mpt) cc_final: 0.6320 (mpt) REVERT: H 123 MET cc_start: 0.7859 (mtm) cc_final: 0.7614 (mtp) REVERT: H 127 VAL cc_start: 0.5950 (OUTLIER) cc_final: 0.5672 (m) REVERT: H 175 MET cc_start: 0.2767 (mtt) cc_final: 0.0664 (tpp) REVERT: I 94 LYS cc_start: 0.6683 (OUTLIER) cc_final: 0.6193 (mttt) REVERT: I 286 MET cc_start: 0.4886 (pp-130) cc_final: 0.4147 (mmp) outliers start: 56 outliers final: 35 residues processed: 219 average time/residue: 0.8135 time to fit residues: 202.4002 Evaluate side-chains 219 residues out of total 2489 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 170 time to evaluate : 0.999 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 ILE Chi-restraints excluded: chain A residue 40 SER Chi-restraints excluded: chain A residue 43 ARG Chi-restraints excluded: chain A residue 55 ILE Chi-restraints excluded: chain A residue 77 GLU Chi-restraints excluded: chain A residue 114 LEU Chi-restraints excluded: chain A residue 137 ASN Chi-restraints excluded: chain A residue 170 GLU Chi-restraints excluded: chain A residue 179 SER Chi-restraints excluded: chain B residue 45 VAL Chi-restraints excluded: chain B residue 83 TYR Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 257 VAL Chi-restraints excluded: chain B residue 279 GLN Chi-restraints excluded: chain C residue 45 VAL Chi-restraints excluded: chain C residue 126 GLU Chi-restraints excluded: chain C residue 138 MET Chi-restraints excluded: chain C residue 226 ARG Chi-restraints excluded: chain D residue 9 GLU Chi-restraints excluded: chain D residue 103 LYS Chi-restraints excluded: chain D residue 148 VAL Chi-restraints excluded: chain D residue 152 VAL Chi-restraints excluded: chain D residue 269 SER Chi-restraints excluded: chain D residue 276 THR Chi-restraints excluded: chain D residue 286 VAL Chi-restraints excluded: chain D residue 288 GLU Chi-restraints excluded: chain E residue 171 ASP Chi-restraints excluded: chain E residue 174 THR Chi-restraints excluded: chain E residue 257 VAL Chi-restraints excluded: chain E residue 279 GLN Chi-restraints excluded: chain F residue 63 GLU Chi-restraints excluded: chain F residue 257 VAL Chi-restraints excluded: chain F residue 286 VAL Chi-restraints excluded: chain F residue 290 LEU Chi-restraints excluded: chain G residue 2 THR Chi-restraints excluded: chain G residue 36 GLU Chi-restraints excluded: chain G residue 264 SER Chi-restraints excluded: chain H residue 127 VAL Chi-restraints excluded: chain I residue 3 LEU Chi-restraints excluded: chain I residue 94 LYS Chi-restraints excluded: chain I residue 148 ILE Chi-restraints excluded: chain I residue 149 VAL Chi-restraints excluded: chain I residue 159 VAL Chi-restraints excluded: chain I residue 214 VAL Chi-restraints excluded: chain I residue 390 ILE Chi-restraints excluded: chain J residue 2 SER Chi-restraints excluded: chain K residue 43 SER Chi-restraints excluded: chain K residue 68 LYS Chi-restraints excluded: chain K residue 100 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 304 random chunks: chunk 50 optimal weight: 1.9990 chunk 222 optimal weight: 0.9990 chunk 99 optimal weight: 3.9990 chunk 279 optimal weight: 6.9990 chunk 149 optimal weight: 7.9990 chunk 255 optimal weight: 3.9990 chunk 294 optimal weight: 3.9990 chunk 268 optimal weight: 4.9990 chunk 167 optimal weight: 3.9990 chunk 172 optimal weight: 0.8980 chunk 175 optimal weight: 0.8980 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 79 HIS B 131 GLN C 131 GLN D 279 GLN H 220 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3825 r_free = 0.3825 target = 0.132080 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.101567 restraints weight = 42422.352| |-----------------------------------------------------------------------------| r_work (start): 0.3373 rms_B_bonded: 1.85 r_work: 0.3211 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.3104 rms_B_bonded: 4.00 restraints_weight: 0.2500 r_work (final): 0.3104 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8583 moved from start: 0.3636 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 27011 Z= 0.175 Angle : 0.764 14.708 37114 Z= 0.378 Chirality : 0.065 0.753 4129 Planarity : 0.005 0.040 4384 Dihedral : 18.105 165.978 4754 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 3.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.90 % Favored : 96.10 % Rotamer: Outliers : 2.29 % Allowed : 17.00 % Favored : 80.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.38 (0.15), residues: 2925 helix: 1.18 (0.17), residues: 928 sheet: 0.92 (0.22), residues: 540 loop : -1.76 (0.14), residues: 1457 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 104 TYR 0.019 0.002 TYR A 9 PHE 0.029 0.002 PHE I 283 TRP 0.019 0.002 TRP H 108 HIS 0.006 0.001 HIS I 541 Details of bonding type rmsd/Z covalent geometry : bond 0.00385 / 0.18 (27011) covalent geometry : angle 0.76445 / 0.38 (37114) hydrogen bonds : bond 0.05827 / 3.92 ( 1045) hydrogen bonds : angle 4.87513 / 3.43 ( 2876) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9357.20 seconds wall clock time: 159 minutes 51.10 seconds (9591.10 seconds total)