Starting phenix.real_space_refine on Sun May 25 05:44:24 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8dej_27393/05_2025/8dej_27393.cif Found real_map, /net/cci-nas-00/data/ceres_data/8dej_27393/05_2025/8dej_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_27393/05_2025/8dej_27393.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8dej_27393/05_2025/8dej_27393.map" model { file = "/net/cci-nas-00/data/ceres_data/8dej_27393/05_2025/8dej_27393.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8dej_27393/05_2025/8dej_27393.cif" } resolution = 2.86 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 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): 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/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: {'RNA': 47} Modifications used: {'5*END': 1, 'rna2p_pur': 11, 'rna2p_pyr': 11, 'rna3p_pur': 14, 'rna3p_pyr': 11} Link IDs: {'rna2p': 22, 'rna3p': 24} Chain breaks: 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, 'RNA': 2} Modifications used: {'rna2p_pyr': 1, 'rna3p_pur': 1} Link IDs: {'rna2p': 1, 'rna3p': 46} Time building chain proxies: 16.89, per 1000 atoms: 0.64 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: 7.19 Conformation dependent library (CDL) restraints added in 3.2 seconds 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: 9.44 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: 9.58 Time building geometry restraints manager: 8.28 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=" N MET B 1 " pdb=" CA MET B 1 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.90e-02 2.77e+03 3.08e+00 bond pdb=" N MET D 1 " pdb=" CA MET D 1 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.90e-02 2.77e+03 2.96e+00 bond pdb=" N LEU I 3 " pdb=" CA LEU I 3 " ideal model delta sigma weight residual 1.458 1.490 -0.032 1.90e-02 2.77e+03 2.92e+00 bond pdb=" N THR A 8 " pdb=" CA THR A 8 " ideal model delta sigma weight residual 1.458 1.490 -0.032 1.90e-02 2.77e+03 2.90e+00 bond pdb=" N MET G 1 " pdb=" CA MET G 1 " ideal model delta sigma weight residual 1.458 1.490 -0.032 1.90e-02 2.77e+03 2.88e+00 ... (remaining 27006 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.36: 36628 2.36 - 4.71: 423 4.71 - 7.07: 21 7.07 - 9.43: 21 9.43 - 11.79: 33 Bond angle restraints: 37126 Sorted by residual: 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=" C4' C N 29 " pdb=" C3' C N 29 " pdb=" O3' C N 29 " ideal model delta sigma weight residual 109.40 115.67 -6.27 1.50e+00 4.44e-01 1.75e+01 angle pdb=" C2' C L 46 " pdb=" C1' C L 46 " pdb=" N1 C L 46 " ideal model delta sigma weight residual 112.00 118.00 -6.00 1.50e+00 4.44e-01 1.60e+01 angle pdb=" O3' DT M 37 " pdb=" P DC M 38 " pdb=" OP1 DC M 38 " ideal model delta sigma weight residual 108.00 119.79 -11.79 3.00e+00 1.11e-01 1.54e+01 angle pdb=" OP1 DC M 38 " pdb=" P DC M 38 " pdb=" OP2 DC M 38 " ideal model delta sigma weight residual 120.00 108.96 11.04 3.00e+00 1.11e-01 1.36e+01 ... (remaining 37121 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.95: 15493 35.95 - 71.91: 690 71.91 - 107.86: 50 107.86 - 143.81: 1 143.81 - 179.77: 7 Dihedral angle restraints: 16241 sinusoidal: 7637 harmonic: 8604 Sorted by residual: dihedral pdb=" C4' C N 29 " pdb=" C3' C N 29 " pdb=" C2' C N 29 " pdb=" C1' C N 29 " ideal model delta sinusoidal sigma weight residual -35.00 35.66 -70.66 1 8.00e+00 1.56e-02 1.00e+02 dihedral pdb=" C5' C N 29 " pdb=" C4' C N 29 " pdb=" C3' C N 29 " pdb=" O3' C N 29 " ideal model delta sinusoidal sigma weight residual 147.00 78.67 68.33 1 8.00e+00 1.56e-02 9.46e+01 dihedral pdb=" O4' C N 29 " pdb=" C4' C N 29 " pdb=" C3' C N 29 " pdb=" C2' C N 29 " ideal model delta sinusoidal sigma weight residual 24.00 -36.02 60.02 1 8.00e+00 1.56e-02 7.50e+01 ... (remaining 16238 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.087: 3759 0.087 - 0.175: 339 0.175 - 0.262: 4 0.262 - 0.349: 11 0.349 - 0.437: 16 Chirality restraints: 4129 Sorted by residual: chirality pdb=" P DC M 38 " pdb=" OP1 DC M 38 " pdb=" OP2 DC M 38 " pdb=" O5' DC M 38 " both_signs ideal model delta sigma weight residual True 2.35 -2.78 -0.44 2.00e-01 2.50e+01 4.77e+00 chirality pdb=" P DC M 18 " pdb=" OP1 DC M 18 " pdb=" OP2 DC M 18 " pdb=" O5' DC M 18 " both_signs ideal model delta sigma weight residual True 2.35 -2.77 -0.42 2.00e-01 2.50e+01 4.44e+00 chirality pdb=" P DA M 19 " pdb=" OP1 DA M 19 " pdb=" OP2 DA M 19 " pdb=" O5' DA M 19 " both_signs ideal model delta sigma weight residual True 2.35 -2.77 -0.42 2.00e-01 2.50e+01 4.42e+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: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.570 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.020 Extract box with map and model: 1.080 Check model and map are aligned: 0.190 Set scattering table: 0.250 Process input model: 66.440 Find NCS groups from input model: 1.020 Set up NCS constraints: 0.120 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:11.170 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 84.880 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6815 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 : 0.004 0.040 27011 Z= 0.208 Angle : 0.728 11.786 37126 Z= 0.386 Chirality : 0.053 0.437 4129 Planarity : 0.004 0.048 4384 Dihedral : 17.950 179.768 10671 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.19 (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 TRP 0.009 0.001 TRP B 108 HIS 0.009 0.001 HIS H 179 PHE 0.010 0.001 PHE J 105 TYR 0.012 0.001 TYR J 12 ARG 0.004 0.000 ARG E 177 Details of bonding type rmsd hydrogen bonds : bond 0.21720 ( 1045) hydrogen bonds : angle 7.98542 ( 2876) covalent geometry : bond 0.00437 (27011) covalent geometry : angle 0.72829 (37126) *********************** 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 : 2.860 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: 0.6678 (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: 0.6112 (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: 1.7022 time to fit residues: 769.2579 Evaluate side-chains 210 residues out of total 2489 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 204 time to evaluate : 2.597 ------------------------------------------------------------------------------- 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 256 optimal weight: 0.9980 chunk 230 optimal weight: 1.9990 chunk 127 optimal weight: 5.9990 chunk 78 optimal weight: 3.9990 chunk 155 optimal weight: 3.9990 chunk 123 optimal weight: 4.9990 chunk 238 optimal weight: 4.9990 chunk 92 optimal weight: 0.4980 chunk 144 optimal weight: 3.9990 chunk 177 optimal weight: 30.0000 chunk 276 optimal weight: 1.9990 overall best weight: 1.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 79 HIS D 79 HIS D 279 GLN E 22 ASN E 39 HIS F 79 HIS H 22 ASN H 150 GLN 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 = 0.3820 r_free = 0.3820 target = 0.131517 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.101016 restraints weight = 42374.228| |-----------------------------------------------------------------------------| r_work (start): 0.3363 rms_B_bonded: 2.15 r_work: 0.3162 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.3053 rms_B_bonded: 4.51 restraints_weight: 0.2500 r_work (final): 0.3053 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8462 moved from start: 0.2288 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 27011 Z= 0.194 Angle : 0.686 13.155 37126 Z= 0.378 Chirality : 0.050 0.320 4129 Planarity : 0.005 0.043 4384 Dihedral : 19.069 177.255 4954 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 2.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.21 % Favored : 96.79 % Rotamer: Outliers : 2.81 % Allowed : 12.42 % Favored : 84.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.05 (0.15), residues: 2925 helix: 1.53 (0.17), residues: 921 sheet: 0.49 (0.20), residues: 581 loop : -1.21 (0.15), residues: 1423 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP H 108 HIS 0.007 0.002 HIS B 189 PHE 0.018 0.002 PHE J 105 TYR 0.023 0.002 TYR H 83 ARG 0.007 0.001 ARG G 177 Details of bonding type rmsd hydrogen bonds : bond 0.06617 ( 1045) hydrogen bonds : angle 5.53139 ( 2876) covalent geometry : bond 0.00437 (27011) covalent geometry : angle 0.68604 (37126) *********************** 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 292 residues out of total 2489 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 222 time to evaluate : 2.637 Fit side-chains revert: symmetry clash REVERT: A 131 LYS cc_start: 0.8197 (ptpt) cc_final: 0.7484 (ptmm) REVERT: B 83 TYR cc_start: 0.5145 (OUTLIER) cc_final: 0.4878 (t80) REVERT: C 126 GLU cc_start: 0.8772 (OUTLIER) cc_final: 0.8266 (tt0) REVERT: D 1 MET cc_start: 0.2097 (mtt) cc_final: 0.1807 (mtp) REVERT: D 9 GLU cc_start: 0.8453 (OUTLIER) cc_final: 0.7673 (mm-30) REVERT: E 9 GLU cc_start: 0.8610 (OUTLIER) cc_final: 0.8178 (mp0) REVERT: E 123 MET cc_start: 0.8952 (OUTLIER) cc_final: 0.8602 (mtm) REVERT: F 89 LYS cc_start: 0.8033 (tppt) cc_final: 0.7582 (tmtt) REVERT: G 89 LYS cc_start: 0.7552 (mppt) cc_final: 0.7256 (tptm) REVERT: H 30 MET cc_start: 0.6957 (mmt) cc_final: 0.6557 (mmm) REVERT: H 127 VAL cc_start: 0.5177 (OUTLIER) cc_final: 0.4883 (m) REVERT: H 261 GLU cc_start: 0.5695 (pm20) cc_final: 0.4835 (tp30) REVERT: I 58 ARG cc_start: 0.5890 (mmt180) cc_final: 0.5276 (mmt180) REVERT: I 94 LYS cc_start: 0.6399 (OUTLIER) cc_final: 0.5863 (mttt) REVERT: I 282 ILE cc_start: 0.3243 (OUTLIER) cc_final: 0.2955 (mp) REVERT: I 286 MET cc_start: 0.4754 (pp-130) cc_final: 0.3831 (mmp) REVERT: J 82 MET cc_start: 0.8660 (mtt) cc_final: 0.8459 (mtp) REVERT: K 26 GLU cc_start: 0.8217 (tp30) cc_final: 0.7987 (mt-10) outliers start: 70 outliers final: 20 residues processed: 268 average time/residue: 1.5683 time to fit residues: 478.7257 Evaluate side-chains 211 residues out of total 2489 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 183 time to evaluate : 2.735 ------------------------------------------------------------------------------- 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 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 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 276 THR 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 123 MET Chi-restraints excluded: chain E residue 171 ASP Chi-restraints excluded: chain F residue 257 VAL Chi-restraints excluded: chain G residue 2 THR 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 282 ILE Chi-restraints excluded: chain I residue 390 ILE 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 287 optimal weight: 5.9990 chunk 228 optimal weight: 20.0000 chunk 268 optimal weight: 3.9990 chunk 80 optimal weight: 2.9990 chunk 225 optimal weight: 10.0000 chunk 7 optimal weight: 2.9990 chunk 274 optimal weight: 0.6980 chunk 208 optimal weight: 0.4980 chunk 135 optimal weight: 2.9990 chunk 150 optimal weight: 0.9990 chunk 66 optimal weight: 1.9990 overall best weight: 1.4386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 79 HIS D 216 ASN D 279 GLN E 137 GLN H 150 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3824 r_free = 0.3824 target = 0.131928 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.101918 restraints weight = 42310.799| |-----------------------------------------------------------------------------| r_work (start): 0.3377 rms_B_bonded: 2.09 r_work: 0.3183 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.3075 rms_B_bonded: 4.30 restraints_weight: 0.2500 r_work (final): 0.3075 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8420 moved from start: 0.2818 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 27011 Z= 0.158 Angle : 0.607 14.100 37126 Z= 0.334 Chirality : 0.046 0.253 4129 Planarity : 0.005 0.040 4384 Dihedral : 19.005 178.838 4948 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 2.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer: Outliers : 3.01 % Allowed : 13.50 % Favored : 83.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.05 (0.15), residues: 2925 helix: 1.49 (0.17), residues: 932 sheet: 0.60 (0.21), residues: 581 loop : -1.25 (0.15), residues: 1412 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP H 108 HIS 0.005 0.001 HIS G 189 PHE 0.021 0.002 PHE I 283 TYR 0.014 0.002 TYR F 8 ARG 0.009 0.001 ARG C 104 Details of bonding type rmsd hydrogen bonds : bond 0.05552 ( 1045) hydrogen bonds : angle 5.06308 ( 2876) covalent geometry : bond 0.00348 (27011) covalent geometry : angle 0.60672 (37126) *********************** 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 263 residues out of total 2489 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 188 time to evaluate : 2.967 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 131 LYS cc_start: 0.8216 (ptpt) cc_final: 0.7589 (ptmm) REVERT: B 83 TYR cc_start: 0.5221 (OUTLIER) cc_final: 0.4974 (t80) REVERT: C 94 LYS cc_start: 0.8065 (mttt) cc_final: 0.7765 (mmtt) REVERT: C 126 GLU cc_start: 0.8769 (OUTLIER) cc_final: 0.8320 (tt0) REVERT: C 226 ARG cc_start: 0.9091 (OUTLIER) cc_final: 0.8849 (ttp-170) REVERT: D 9 GLU cc_start: 0.8436 (OUTLIER) cc_final: 0.7591 (mm-30) REVERT: F 1 MET cc_start: 0.5423 (mtm) cc_final: 0.4966 (ttm) REVERT: F 89 LYS cc_start: 0.7876 (tppt) cc_final: 0.7472 (tmtt) REVERT: G 89 LYS cc_start: 0.7551 (mppt) cc_final: 0.7275 (tptp) REVERT: H 30 MET cc_start: 0.6749 (mmt) cc_final: 0.6378 (mmm) REVERT: I 29 GLU cc_start: 0.6747 (mm-30) cc_final: 0.6541 (mm-30) REVERT: I 58 ARG cc_start: 0.5858 (mmt180) cc_final: 0.5263 (mmm160) REVERT: I 94 LYS cc_start: 0.6396 (OUTLIER) cc_final: 0.6064 (mttp) REVERT: I 231 GLU cc_start: 0.7814 (OUTLIER) cc_final: 0.7513 (pt0) REVERT: I 286 MET cc_start: 0.4876 (pp-130) cc_final: 0.3993 (mmp) REVERT: J 82 MET cc_start: 0.8583 (mtt) cc_final: 0.8292 (mtp) REVERT: K 26 GLU cc_start: 0.8103 (tp30) cc_final: 0.7865 (mt-10) REVERT: K 84 GLN cc_start: 0.8069 (tp40) cc_final: 0.7856 (tp40) outliers start: 75 outliers final: 26 residues processed: 235 average time/residue: 1.6956 time to fit residues: 451.7669 Evaluate side-chains 209 residues out of total 2489 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 177 time to evaluate : 2.863 ------------------------------------------------------------------------------- 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 257 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 148 VAL Chi-restraints excluded: chain D residue 152 VAL Chi-restraints excluded: chain D residue 269 SER 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 E residue 279 GLN 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 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 231 GLU Chi-restraints excluded: chain I residue 282 ILE Chi-restraints excluded: chain I residue 390 ILE 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 6 optimal weight: 1.9990 chunk 48 optimal weight: 6.9990 chunk 45 optimal weight: 3.9990 chunk 104 optimal weight: 0.0370 chunk 153 optimal weight: 4.9990 chunk 244 optimal weight: 0.7980 chunk 147 optimal weight: 3.9990 chunk 291 optimal weight: 2.9990 chunk 115 optimal weight: 6.9990 chunk 92 optimal weight: 1.9990 chunk 105 optimal weight: 4.9990 overall best weight: 1.5664 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3812 r_free = 0.3812 target = 0.131120 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3397 r_free = 0.3397 target = 0.100820 restraints weight = 42730.166| |-----------------------------------------------------------------------------| r_work (start): 0.3357 rms_B_bonded: 2.09 r_work: 0.3157 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.3049 rms_B_bonded: 4.54 restraints_weight: 0.2500 r_work (final): 0.3049 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8467 moved from start: 0.3057 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 27011 Z= 0.165 Angle : 0.614 12.764 37126 Z= 0.337 Chirality : 0.046 0.255 4129 Planarity : 0.005 0.040 4384 Dihedral : 19.006 178.235 4948 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 2.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.69 % Favored : 96.31 % Rotamer: Outliers : 3.22 % Allowed : 14.15 % Favored : 82.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.06 (0.15), residues: 2925 helix: 1.38 (0.17), residues: 930 sheet: 0.77 (0.21), residues: 561 loop : -1.39 (0.15), residues: 1434 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP H 108 HIS 0.005 0.001 HIS I 541 PHE 0.015 0.002 PHE J 105 TYR 0.015 0.002 TYR F 8 ARG 0.005 0.000 ARG I 560 Details of bonding type rmsd hydrogen bonds : bond 0.05749 ( 1045) hydrogen bonds : angle 4.96648 ( 2876) covalent geometry : bond 0.00367 (27011) covalent geometry : angle 0.61369 (37126) *********************** 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 261 residues out of total 2489 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 181 time to evaluate : 2.798 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 43 ARG cc_start: 0.8606 (OUTLIER) cc_final: 0.8244 (tmm-80) REVERT: A 131 LYS cc_start: 0.8224 (ptpt) cc_final: 0.7667 (ptmm) REVERT: B 83 TYR cc_start: 0.5483 (OUTLIER) cc_final: 0.5113 (t80) REVERT: C 94 LYS cc_start: 0.8115 (mttt) cc_final: 0.7854 (mmtt) REVERT: C 126 GLU cc_start: 0.8765 (OUTLIER) cc_final: 0.8344 (tt0) REVERT: C 226 ARG cc_start: 0.9113 (OUTLIER) cc_final: 0.8887 (ttp-170) REVERT: D 1 MET cc_start: 0.2420 (mtp) cc_final: 0.2039 (mtp) REVERT: D 9 GLU cc_start: 0.8475 (OUTLIER) cc_final: 0.7647 (mm-30) REVERT: F 1 MET cc_start: 0.5534 (mtm) cc_final: 0.4722 (ttm) REVERT: F 89 LYS cc_start: 0.7877 (tppt) cc_final: 0.7472 (tmtt) REVERT: G 89 LYS cc_start: 0.7485 (mppt) cc_final: 0.7270 (tptp) REVERT: G 138 MET cc_start: 0.8607 (OUTLIER) cc_final: 0.8013 (ptm) REVERT: H 30 MET cc_start: 0.6960 (mmt) cc_final: 0.6529 (mmm) REVERT: H 175 MET cc_start: 0.2953 (OUTLIER) cc_final: 0.0643 (tpp) REVERT: I 29 GLU cc_start: 0.6821 (mm-30) cc_final: 0.6583 (mm-30) REVERT: I 58 ARG cc_start: 0.5842 (mmt180) cc_final: 0.5365 (mmp-170) REVERT: I 94 LYS cc_start: 0.6512 (OUTLIER) cc_final: 0.5945 (mttt) REVERT: I 286 MET cc_start: 0.4877 (pp-130) cc_final: 0.4105 (mmp) REVERT: J 50 GLN cc_start: 0.8300 (OUTLIER) cc_final: 0.7924 (mm-40) REVERT: J 82 MET cc_start: 0.8730 (OUTLIER) cc_final: 0.8470 (mtp) outliers start: 80 outliers final: 38 residues processed: 241 average time/residue: 1.6840 time to fit residues: 460.9195 Evaluate side-chains 218 residues out of total 2489 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 170 time to evaluate : 2.652 ------------------------------------------------------------------------------- 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 170 GLU Chi-restraints excluded: chain A residue 191 MET Chi-restraints excluded: chain B residue 83 TYR Chi-restraints excluded: chain B residue 138 MET 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 C residue 159 VAL Chi-restraints excluded: chain C residue 173 ARG 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 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 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 2 THR Chi-restraints excluded: chain G residue 138 MET Chi-restraints excluded: chain G residue 264 SER Chi-restraints excluded: chain H residue 69 ILE Chi-restraints excluded: chain H residue 175 MET Chi-restraints excluded: chain I residue 3 LEU Chi-restraints excluded: chain I residue 50 ARG 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 390 ILE Chi-restraints excluded: chain J residue 50 GLN Chi-restraints excluded: chain J residue 82 MET Chi-restraints excluded: chain J residue 113 ARG 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 304 random chunks: chunk 12 optimal weight: 9.9990 chunk 178 optimal weight: 5.9990 chunk 159 optimal weight: 6.9990 chunk 87 optimal weight: 10.0000 chunk 11 optimal weight: 2.9990 chunk 291 optimal weight: 2.9990 chunk 38 optimal weight: 2.9990 chunk 100 optimal weight: 4.9990 chunk 214 optimal weight: 0.1980 chunk 248 optimal weight: 6.9990 chunk 252 optimal weight: 9.9990 overall best weight: 2.8388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3767 r_free = 0.3767 target = 0.128034 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3344 r_free = 0.3344 target = 0.097537 restraints weight = 42286.950| |-----------------------------------------------------------------------------| r_work (start): 0.3302 rms_B_bonded: 2.12 r_work: 0.3092 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.2982 rms_B_bonded: 4.55 restraints_weight: 0.2500 r_work (final): 0.2982 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8533 moved from start: 0.3378 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.058 27011 Z= 0.248 Angle : 0.729 15.582 37126 Z= 0.399 Chirality : 0.051 0.266 4129 Planarity : 0.006 0.056 4384 Dihedral : 19.063 177.270 4948 Min Nonbonded Distance : 2.393 Molprobity Statistics. All-atom Clashscore : 3.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.79 % Favored : 96.21 % Rotamer: Outliers : 3.66 % Allowed : 14.87 % Favored : 81.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.44 (0.15), residues: 2925 helix: 0.99 (0.17), residues: 923 sheet: 1.10 (0.22), residues: 498 loop : -1.70 (0.14), residues: 1504 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP H 108 HIS 0.007 0.002 HIS J 111 PHE 0.021 0.002 PHE J 105 TYR 0.022 0.002 TYR F 8 ARG 0.006 0.001 ARG I 560 Details of bonding type rmsd hydrogen bonds : bond 0.07853 ( 1045) hydrogen bonds : angle 5.23410 ( 2876) covalent geometry : bond 0.00582 (27011) covalent geometry : angle 0.72850 (37126) *********************** 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 267 residues out of total 2489 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 176 time to evaluate : 2.907 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 43 ARG cc_start: 0.8677 (OUTLIER) cc_final: 0.8251 (tmm-80) REVERT: A 131 LYS cc_start: 0.8258 (ptpt) cc_final: 0.7663 (ptmm) REVERT: A 137 ASN cc_start: 0.5717 (OUTLIER) cc_final: 0.5422 (p0) REVERT: B 112 ASN cc_start: 0.9065 (OUTLIER) cc_final: 0.8744 (OUTLIER) REVERT: C 101 ASP cc_start: 0.4997 (OUTLIER) cc_final: 0.4490 (t0) REVERT: C 126 GLU cc_start: 0.8822 (OUTLIER) cc_final: 0.8379 (tt0) REVERT: C 226 ARG cc_start: 0.9132 (OUTLIER) cc_final: 0.8908 (ttp-170) REVERT: D 9 GLU cc_start: 0.8561 (OUTLIER) cc_final: 0.7573 (mm-30) REVERT: D 103 LYS cc_start: 0.7798 (OUTLIER) cc_final: 0.7388 (ptmm) REVERT: F 30 MET cc_start: 0.8880 (OUTLIER) cc_final: 0.8666 (mtt) REVERT: F 63 GLU cc_start: 0.8147 (OUTLIER) cc_final: 0.7445 (tt0) REVERT: F 89 LYS cc_start: 0.8028 (tppt) cc_final: 0.7482 (tmtt) REVERT: G 89 LYS cc_start: 0.7591 (mppt) cc_final: 0.7353 (tptp) REVERT: G 138 MET cc_start: 0.8647 (OUTLIER) cc_final: 0.8044 (ptm) REVERT: H 30 MET cc_start: 0.7148 (mmt) cc_final: 0.6712 (mmm) REVERT: I 58 ARG cc_start: 0.5943 (mmt180) cc_final: 0.5377 (mmp-170) REVERT: I 63 LEU cc_start: 0.7666 (OUTLIER) cc_final: 0.7103 (tp) REVERT: I 231 GLU cc_start: 0.8002 (OUTLIER) cc_final: 0.7621 (pt0) REVERT: I 286 MET cc_start: 0.5042 (pp-130) cc_final: 0.4232 (mmp) REVERT: I 481 ARG cc_start: 0.8344 (OUTLIER) cc_final: 0.8140 (ttt180) REVERT: J 50 GLN cc_start: 0.8435 (OUTLIER) cc_final: 0.8224 (mm-40) outliers start: 91 outliers final: 44 residues processed: 239 average time/residue: 1.6606 time to fit residues: 450.9649 Evaluate side-chains 229 residues out of total 2489 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 171 time to evaluate : 2.622 ------------------------------------------------------------------------------- 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 137 ASN Chi-restraints excluded: chain A residue 140 LYS Chi-restraints excluded: chain A residue 170 GLU Chi-restraints excluded: chain A residue 191 MET Chi-restraints excluded: chain B residue 45 VAL Chi-restraints excluded: chain B residue 112 ASN Chi-restraints excluded: chain B residue 138 MET 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 101 ASP 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 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 276 THR Chi-restraints excluded: chain D residue 286 VAL 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 229 MET Chi-restraints excluded: chain E residue 257 VAL Chi-restraints excluded: chain F residue 30 MET 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 138 MET Chi-restraints excluded: chain G residue 153 SER Chi-restraints excluded: chain G residue 264 SER 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 231 GLU Chi-restraints excluded: chain I residue 390 ILE Chi-restraints excluded: chain I residue 481 ARG Chi-restraints excluded: chain J residue 2 SER Chi-restraints excluded: chain J residue 50 GLN 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 99 optimal weight: 4.9990 chunk 37 optimal weight: 0.9990 chunk 98 optimal weight: 1.9990 chunk 291 optimal weight: 4.9990 chunk 148 optimal weight: 0.7980 chunk 63 optimal weight: 0.9980 chunk 298 optimal weight: 8.9990 chunk 268 optimal weight: 2.9990 chunk 0 optimal weight: 6.9990 chunk 192 optimal weight: 4.9990 chunk 294 optimal weight: 3.9990 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3800 r_free = 0.3800 target = 0.130354 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3381 r_free = 0.3381 target = 0.099818 restraints weight = 42393.498| |-----------------------------------------------------------------------------| r_work (start): 0.3338 rms_B_bonded: 2.05 r_work: 0.3144 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.3035 rms_B_bonded: 4.50 restraints_weight: 0.2500 r_work (final): 0.3035 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8480 moved from start: 0.3453 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 27011 Z= 0.164 Angle : 0.611 12.033 37126 Z= 0.336 Chirality : 0.046 0.243 4129 Planarity : 0.005 0.042 4384 Dihedral : 19.017 179.351 4948 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 2.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.76 % Favored : 96.24 % Rotamer: Outliers : 3.09 % Allowed : 15.76 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.33 (0.15), residues: 2925 helix: 1.18 (0.17), residues: 927 sheet: 1.02 (0.22), residues: 516 loop : -1.67 (0.14), residues: 1482 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP H 108 HIS 0.006 0.001 HIS H 79 PHE 0.013 0.002 PHE J 105 TYR 0.016 0.002 TYR F 8 ARG 0.003 0.000 ARG G 177 Details of bonding type rmsd hydrogen bonds : bond 0.05575 ( 1045) hydrogen bonds : angle 4.91211 ( 2876) covalent geometry : bond 0.00366 (27011) covalent geometry : angle 0.61129 (37126) *********************** 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 257 residues out of total 2489 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 180 time to evaluate : 2.569 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 43 ARG cc_start: 0.8623 (OUTLIER) cc_final: 0.8246 (tmm-80) REVERT: A 131 LYS cc_start: 0.8293 (ptpt) cc_final: 0.7698 (ptmm) REVERT: B 83 TYR cc_start: 0.5791 (OUTLIER) cc_final: 0.5552 (t80) REVERT: C 126 GLU cc_start: 0.8777 (OUTLIER) cc_final: 0.8361 (tt0) REVERT: C 226 ARG cc_start: 0.9126 (OUTLIER) cc_final: 0.8911 (ttp-170) REVERT: D 9 GLU cc_start: 0.8443 (OUTLIER) cc_final: 0.7593 (mm-30) REVERT: E 9 GLU cc_start: 0.8616 (OUTLIER) cc_final: 0.8247 (mp0) REVERT: E 109 MET cc_start: 0.6436 (mtm) cc_final: 0.5528 (mmm) REVERT: F 1 MET cc_start: 0.5319 (mtm) cc_final: 0.4475 (ttm) REVERT: F 63 GLU cc_start: 0.8069 (OUTLIER) cc_final: 0.7401 (tt0) REVERT: F 89 LYS cc_start: 0.7933 (tppt) cc_final: 0.7381 (tmtt) REVERT: G 89 LYS cc_start: 0.7490 (mppt) cc_final: 0.7180 (tptm) REVERT: G 138 MET cc_start: 0.8642 (OUTLIER) cc_final: 0.8078 (ptm) REVERT: G 289 MET cc_start: 0.6622 (pmt) cc_final: 0.6365 (pmm) REVERT: H 30 MET cc_start: 0.7160 (mmt) cc_final: 0.6713 (mmm) REVERT: H 175 MET cc_start: 0.2953 (mtp) cc_final: 0.0645 (tpp) REVERT: I 63 LEU cc_start: 0.7593 (OUTLIER) cc_final: 0.7045 (tp) REVERT: I 94 LYS cc_start: 0.6575 (OUTLIER) cc_final: 0.6029 (mttt) REVERT: I 286 MET cc_start: 0.4938 (pp-130) cc_final: 0.4195 (mmp) REVERT: J 50 GLN cc_start: 0.8352 (OUTLIER) cc_final: 0.8015 (mm-40) outliers start: 77 outliers final: 45 residues processed: 236 average time/residue: 1.5644 time to fit residues: 420.3421 Evaluate side-chains 227 residues out of total 2489 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 171 time to evaluate : 2.686 ------------------------------------------------------------------------------- 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 140 LYS 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 138 MET 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 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 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 9 GLU Chi-restraints excluded: chain E residue 26 ASP Chi-restraints excluded: chain E residue 171 ASP Chi-restraints excluded: chain E residue 279 GLN Chi-restraints excluded: chain F residue 63 GLU Chi-restraints excluded: chain F residue 217 MET 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 138 MET Chi-restraints excluded: chain G residue 153 SER Chi-restraints excluded: chain G residue 264 SER Chi-restraints excluded: chain H residue 70 GLN 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 390 ILE Chi-restraints excluded: chain I residue 606 THR Chi-restraints excluded: chain J residue 50 GLN Chi-restraints excluded: chain J residue 113 ARG 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 304 random chunks: chunk 71 optimal weight: 0.3980 chunk 32 optimal weight: 2.9990 chunk 160 optimal weight: 0.0980 chunk 276 optimal weight: 0.7980 chunk 287 optimal weight: 1.9990 chunk 129 optimal weight: 1.9990 chunk 107 optimal weight: 0.6980 chunk 76 optimal weight: 5.9990 chunk 213 optimal weight: 0.0770 chunk 183 optimal weight: 5.9990 chunk 216 optimal weight: 7.9990 overall best weight: 0.4138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 79 HIS B 131 GLN D 279 GLN F 54 HIS 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 = 0.3870 r_free = 0.3870 target = 0.135338 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3472 r_free = 0.3472 target = 0.105679 restraints weight = 42716.779| |-----------------------------------------------------------------------------| r_work (start): 0.3436 rms_B_bonded: 1.91 r_work: 0.3274 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.3170 rms_B_bonded: 4.15 restraints_weight: 0.2500 r_work (final): 0.3170 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8343 moved from start: 0.3618 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 27011 Z= 0.108 Angle : 0.519 8.633 37126 Z= 0.284 Chirality : 0.042 0.215 4129 Planarity : 0.004 0.036 4384 Dihedral : 19.092 179.050 4948 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 3.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer: Outliers : 2.53 % Allowed : 16.36 % Favored : 81.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.02 (0.15), residues: 2925 helix: 1.53 (0.17), residues: 945 sheet: 0.72 (0.21), residues: 580 loop : -1.49 (0.15), residues: 1400 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP I 272 HIS 0.004 0.001 HIS H 79 PHE 0.028 0.001 PHE I 283 TYR 0.025 0.001 TYR A 9 ARG 0.003 0.000 ARG G 177 Details of bonding type rmsd hydrogen bonds : bond 0.03418 ( 1045) hydrogen bonds : angle 4.49978 ( 2876) covalent geometry : bond 0.00217 (27011) covalent geometry : angle 0.51868 (37126) *********************** 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 252 residues out of total 2489 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 189 time to evaluate : 2.652 Fit side-chains revert: symmetry clash REVERT: A 131 LYS cc_start: 0.8263 (ptpt) cc_final: 0.7755 (ptmm) REVERT: B 83 TYR cc_start: 0.5275 (OUTLIER) cc_final: 0.5033 (t80) REVERT: C 126 GLU cc_start: 0.8654 (OUTLIER) cc_final: 0.8313 (tt0) REVERT: C 226 ARG cc_start: 0.9068 (OUTLIER) cc_final: 0.8813 (ttp-170) REVERT: D 1 MET cc_start: 0.2189 (mtp) cc_final: 0.1972 (mtp) REVERT: D 9 GLU cc_start: 0.8224 (OUTLIER) cc_final: 0.7378 (mm-30) REVERT: E 123 MET cc_start: 0.8913 (ptp) cc_final: 0.8639 (mtm) REVERT: F 1 MET cc_start: 0.5263 (mtm) cc_final: 0.4302 (ttm) REVERT: F 63 GLU cc_start: 0.7886 (OUTLIER) cc_final: 0.7245 (tt0) REVERT: G 89 LYS cc_start: 0.7438 (mppt) cc_final: 0.7228 (tptm) REVERT: H 30 MET cc_start: 0.7098 (mmt) cc_final: 0.6673 (mmm) REVERT: H 175 MET cc_start: 0.2480 (mtp) cc_final: 0.0411 (tpp) REVERT: I 58 ARG cc_start: 0.5729 (mmt180) cc_final: 0.5014 (mmm160) REVERT: I 286 MET cc_start: 0.4699 (pp-130) cc_final: 0.4095 (mmp) REVERT: J 50 GLN cc_start: 0.8134 (OUTLIER) cc_final: 0.7827 (mm110) outliers start: 63 outliers final: 27 residues processed: 232 average time/residue: 1.6537 time to fit residues: 437.4686 Evaluate side-chains 206 residues out of total 2489 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 173 time to evaluate : 2.694 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 SER Chi-restraints excluded: chain A residue 55 ILE 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 290 LEU 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 269 SER Chi-restraints excluded: chain D residue 276 THR Chi-restraints excluded: chain D residue 286 VAL Chi-restraints excluded: chain E residue 32 ARG Chi-restraints excluded: chain E residue 171 ASP Chi-restraints excluded: chain E residue 257 VAL 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 G residue 153 SER Chi-restraints excluded: chain H residue 70 GLN Chi-restraints excluded: chain I residue 148 ILE 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 J residue 113 ARG Chi-restraints excluded: chain K residue 43 SER 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 33 optimal weight: 3.9990 chunk 132 optimal weight: 4.9990 chunk 50 optimal weight: 2.9990 chunk 269 optimal weight: 4.9990 chunk 153 optimal weight: 5.9990 chunk 151 optimal weight: 2.9990 chunk 134 optimal weight: 0.9990 chunk 281 optimal weight: 6.9990 chunk 254 optimal weight: 6.9990 chunk 129 optimal weight: 3.9990 chunk 244 optimal weight: 8.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 79 HIS D 179 HIS D 279 GLN F 279 GLN G 6 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 = 0.3769 r_free = 0.3769 target = 0.128114 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.097611 restraints weight = 42459.835| |-----------------------------------------------------------------------------| r_work (start): 0.3303 rms_B_bonded: 2.10 r_work: 0.3101 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.2992 rms_B_bonded: 4.32 restraints_weight: 0.2500 r_work (final): 0.2992 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8519 moved from start: 0.3678 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.060 27011 Z= 0.258 Angle : 0.726 13.981 37126 Z= 0.396 Chirality : 0.050 0.260 4129 Planarity : 0.006 0.041 4384 Dihedral : 18.977 177.215 4948 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 3.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.07 % Favored : 95.93 % Rotamer: Outliers : 3.05 % Allowed : 16.28 % Favored : 80.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.41 (0.15), residues: 2925 helix: 1.11 (0.17), residues: 925 sheet: 1.15 (0.23), residues: 496 loop : -1.76 (0.14), residues: 1504 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP H 108 HIS 0.008 0.002 HIS G 189 PHE 0.021 0.002 PHE J 105 TYR 0.021 0.002 TYR F 8 ARG 0.006 0.001 ARG I 50 Details of bonding type rmsd hydrogen bonds : bond 0.07776 ( 1045) hydrogen bonds : angle 5.06817 ( 2876) covalent geometry : bond 0.00606 (27011) covalent geometry : angle 0.72557 (37126) *********************** 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 249 residues out of total 2489 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 173 time to evaluate : 2.758 Fit side-chains revert: symmetry clash REVERT: A 43 ARG cc_start: 0.8676 (OUTLIER) cc_final: 0.8300 (tmm-80) REVERT: A 114 LEU cc_start: 0.8801 (OUTLIER) cc_final: 0.8553 (pp) REVERT: A 131 LYS cc_start: 0.8342 (ptpt) cc_final: 0.7753 (ptmm) REVERT: A 137 ASN cc_start: 0.5693 (OUTLIER) cc_final: 0.5438 (p0) REVERT: A 172 LEU cc_start: 0.8536 (OUTLIER) cc_final: 0.8306 (mp) REVERT: A 199 ARG cc_start: 0.7907 (mmm160) cc_final: 0.7675 (mtt-85) REVERT: B 83 TYR cc_start: 0.5575 (t80) cc_final: 0.5349 (t80) REVERT: C 126 GLU cc_start: 0.8816 (OUTLIER) cc_final: 0.8377 (tt0) REVERT: C 226 ARG cc_start: 0.9134 (OUTLIER) cc_final: 0.8863 (ttp-170) REVERT: D 9 GLU cc_start: 0.8521 (OUTLIER) cc_final: 0.7512 (mm-30) REVERT: F 89 LYS cc_start: 0.7975 (tppt) cc_final: 0.7377 (tmtt) REVERT: G 89 LYS cc_start: 0.7477 (mppt) cc_final: 0.7193 (tptm) REVERT: G 289 MET cc_start: 0.6577 (pmt) cc_final: 0.6323 (pmm) REVERT: H 30 MET cc_start: 0.7285 (mmt) cc_final: 0.6782 (mmm) REVERT: H 175 MET cc_start: 0.2835 (mtp) cc_final: 0.0494 (tpp) REVERT: I 58 ARG cc_start: 0.5894 (mmt180) cc_final: 0.5238 (mmm160) REVERT: I 63 LEU cc_start: 0.7531 (OUTLIER) cc_final: 0.6978 (tp) REVERT: I 286 MET cc_start: 0.4880 (pp-130) cc_final: 0.4144 (mmp) outliers start: 76 outliers final: 39 residues processed: 228 average time/residue: 1.5958 time to fit residues: 414.2227 Evaluate side-chains 215 residues out of total 2489 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 168 time to evaluate : 2.697 ------------------------------------------------------------------------------- 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 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 217 MET Chi-restraints excluded: chain B residue 257 VAL Chi-restraints excluded: chain B residue 284 VAL Chi-restraints excluded: chain C residue 101 ASP 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 E residue 32 ARG 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 F residue 30 MET 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 H residue 70 GLN Chi-restraints excluded: chain I residue 3 LEU Chi-restraints excluded: chain I residue 63 LEU 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 I residue 606 THR 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 304 random chunks: chunk 113 optimal weight: 6.9990 chunk 159 optimal weight: 0.7980 chunk 240 optimal weight: 3.9990 chunk 220 optimal weight: 0.9980 chunk 11 optimal weight: 0.8980 chunk 114 optimal weight: 0.7980 chunk 5 optimal weight: 2.9990 chunk 259 optimal weight: 0.5980 chunk 126 optimal weight: 3.9990 chunk 65 optimal weight: 0.3980 chunk 88 optimal weight: 1.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 79 HIS B 131 GLN C 179 HIS D 79 HIS D 279 GLN F 279 GLN H 220 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3830 r_free = 0.3830 target = 0.132483 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3417 r_free = 0.3417 target = 0.102175 restraints weight = 42503.188| |-----------------------------------------------------------------------------| r_work (start): 0.3379 rms_B_bonded: 2.05 r_work: 0.3206 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.3098 rms_B_bonded: 4.23 restraints_weight: 0.2500 r_work (final): 0.3098 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8416 moved from start: 0.3720 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 27011 Z= 0.123 Angle : 0.560 10.362 37126 Z= 0.307 Chirality : 0.043 0.228 4129 Planarity : 0.004 0.037 4384 Dihedral : 18.998 179.697 4948 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 2.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.15 % Favored : 96.85 % Rotamer: Outliers : 2.01 % Allowed : 17.36 % Favored : 80.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.15 (0.15), residues: 2925 helix: 1.46 (0.17), residues: 926 sheet: 0.82 (0.22), residues: 555 loop : -1.61 (0.14), residues: 1444 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP H 108 HIS 0.004 0.001 HIS H 79 PHE 0.025 0.001 PHE I 283 TYR 0.021 0.001 TYR A 9 ARG 0.003 0.000 ARG I 50 Details of bonding type rmsd hydrogen bonds : bond 0.04339 ( 1045) hydrogen bonds : angle 4.62611 ( 2876) covalent geometry : bond 0.00255 (27011) covalent geometry : angle 0.56029 (37126) *********************** 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 224 residues out of total 2489 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 174 time to evaluate : 2.637 Fit side-chains revert: symmetry clash REVERT: A 114 LEU cc_start: 0.8768 (OUTLIER) cc_final: 0.8559 (pp) REVERT: A 131 LYS cc_start: 0.8300 (ptpt) cc_final: 0.7790 (ptmm) REVERT: A 137 ASN cc_start: 0.5604 (OUTLIER) cc_final: 0.5390 (p0) REVERT: A 172 LEU cc_start: 0.8512 (OUTLIER) cc_final: 0.8253 (mp) REVERT: B 83 TYR cc_start: 0.5468 (t80) cc_final: 0.5229 (t80) REVERT: C 126 GLU cc_start: 0.8745 (OUTLIER) cc_final: 0.8343 (tt0) REVERT: C 226 ARG cc_start: 0.9077 (OUTLIER) cc_final: 0.8840 (ttp-170) REVERT: D 9 GLU cc_start: 0.8451 (OUTLIER) cc_final: 0.7604 (mm-30) REVERT: F 1 MET cc_start: 0.5128 (mtm) cc_final: 0.4278 (ttm) REVERT: F 63 GLU cc_start: 0.7948 (OUTLIER) cc_final: 0.7290 (tt0) REVERT: G 89 LYS cc_start: 0.7470 (mppt) cc_final: 0.7187 (tptm) REVERT: H 30 MET cc_start: 0.7220 (mmt) cc_final: 0.6706 (mmm) REVERT: H 175 MET cc_start: 0.2710 (mtp) cc_final: 0.0590 (tpp) REVERT: I 58 ARG cc_start: 0.5774 (mmt180) cc_final: 0.5150 (mmm160) REVERT: I 153 GLU cc_start: 0.5112 (mt-10) cc_final: 0.4617 (tp30) REVERT: I 286 MET cc_start: 0.4749 (pp-130) cc_final: 0.4097 (mmp) REVERT: J 50 GLN cc_start: 0.8279 (mm-40) cc_final: 0.7952 (mm-40) outliers start: 50 outliers final: 32 residues processed: 212 average time/residue: 1.4631 time to fit residues: 356.5233 Evaluate side-chains 208 residues out of total 2489 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 169 time to evaluate : 2.714 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 217 MET Chi-restraints excluded: chain B residue 284 VAL Chi-restraints excluded: chain C residue 101 ASP 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 269 SER Chi-restraints excluded: chain D residue 276 THR Chi-restraints excluded: chain D residue 286 VAL Chi-restraints excluded: chain E residue 32 ARG Chi-restraints excluded: chain E residue 171 ASP Chi-restraints excluded: chain E residue 257 VAL Chi-restraints excluded: chain F residue 30 MET 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 H residue 70 GLN Chi-restraints excluded: chain I residue 3 LEU 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 390 ILE Chi-restraints excluded: chain I residue 606 THR Chi-restraints excluded: chain K residue 43 SER Chi-restraints excluded: chain K residue 91 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 304 random chunks: chunk 16 optimal weight: 9.9990 chunk 179 optimal weight: 3.9990 chunk 255 optimal weight: 8.9990 chunk 69 optimal weight: 1.9990 chunk 124 optimal weight: 1.9990 chunk 103 optimal weight: 1.9990 chunk 172 optimal weight: 1.9990 chunk 283 optimal weight: 1.9990 chunk 248 optimal weight: 5.9990 chunk 295 optimal weight: 3.9990 chunk 284 optimal weight: 0.7980 overall best weight: 1.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 79 HIS B 131 GLN D 279 GLN F 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 = 0.3801 r_free = 0.3801 target = 0.130394 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3381 r_free = 0.3381 target = 0.099925 restraints weight = 42323.568| |-----------------------------------------------------------------------------| r_work (start): 0.3341 rms_B_bonded: 2.06 r_work: 0.3149 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.3042 rms_B_bonded: 4.40 restraints_weight: 0.2500 r_work (final): 0.3042 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8476 moved from start: 0.3739 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 27011 Z= 0.174 Angle : 0.622 11.796 37126 Z= 0.339 Chirality : 0.046 0.245 4129 Planarity : 0.005 0.038 4384 Dihedral : 18.951 178.662 4948 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 3.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.10 % Favored : 95.90 % Rotamer: Outliers : 1.89 % Allowed : 17.68 % Favored : 80.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.29 (0.15), residues: 2925 helix: 1.32 (0.17), residues: 928 sheet: 0.88 (0.22), residues: 549 loop : -1.72 (0.14), residues: 1448 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP H 108 HIS 0.006 0.001 HIS H 79 PHE 0.016 0.002 PHE J 105 TYR 0.016 0.002 TYR F 8 ARG 0.003 0.000 ARG I 560 Details of bonding type rmsd hydrogen bonds : bond 0.05853 ( 1045) hydrogen bonds : angle 4.78765 ( 2876) covalent geometry : bond 0.00395 (27011) covalent geometry : angle 0.62208 (37126) ********************** 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 218 residues out of total 2489 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 171 time to evaluate : 2.656 Fit side-chains revert: symmetry clash REVERT: A 114 LEU cc_start: 0.8814 (OUTLIER) cc_final: 0.8604 (pp) REVERT: A 131 LYS cc_start: 0.8341 (ptpt) cc_final: 0.7810 (ptmm) REVERT: A 137 ASN cc_start: 0.5648 (OUTLIER) cc_final: 0.5419 (p0) REVERT: A 172 LEU cc_start: 0.8524 (OUTLIER) cc_final: 0.8299 (mp) REVERT: B 83 TYR cc_start: 0.5587 (t80) cc_final: 0.5318 (t80) REVERT: C 126 GLU cc_start: 0.8787 (OUTLIER) cc_final: 0.8387 (tt0) REVERT: C 226 ARG cc_start: 0.9135 (OUTLIER) cc_final: 0.8916 (ttp-170) REVERT: D 9 GLU cc_start: 0.8441 (OUTLIER) cc_final: 0.7593 (mm-30) REVERT: F 1 MET cc_start: 0.5335 (mtm) cc_final: 0.4520 (ttm) REVERT: F 63 GLU cc_start: 0.8006 (OUTLIER) cc_final: 0.7302 (tt0) REVERT: F 89 LYS cc_start: 0.7892 (tppt) cc_final: 0.7331 (tmtt) REVERT: G 89 LYS cc_start: 0.7408 (mppt) cc_final: 0.7167 (tptm) REVERT: G 289 MET cc_start: 0.6472 (pmt) cc_final: 0.6234 (pmm) REVERT: H 30 MET cc_start: 0.7286 (mmt) cc_final: 0.6761 (mmm) REVERT: H 175 MET cc_start: 0.2717 (mtp) cc_final: 0.0602 (tpp) REVERT: I 58 ARG cc_start: 0.5738 (mmt180) cc_final: 0.5137 (mmm160) REVERT: I 153 GLU cc_start: 0.5378 (mt-10) cc_final: 0.4566 (tp30) REVERT: I 231 GLU cc_start: 0.8032 (OUTLIER) cc_final: 0.7759 (pt0) REVERT: I 286 MET cc_start: 0.4817 (pp-130) cc_final: 0.4107 (mmp) outliers start: 47 outliers final: 34 residues processed: 208 average time/residue: 1.5538 time to fit residues: 373.7288 Evaluate side-chains 209 residues out of total 2489 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 167 time to evaluate : 2.995 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 217 MET Chi-restraints excluded: chain B residue 284 VAL Chi-restraints excluded: chain C residue 101 ASP 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 269 SER Chi-restraints excluded: chain D residue 276 THR Chi-restraints excluded: chain D residue 286 VAL Chi-restraints excluded: chain E residue 32 ARG 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 F residue 30 MET 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 H residue 70 GLN Chi-restraints excluded: chain I residue 3 LEU 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 231 GLU Chi-restraints excluded: chain I residue 390 ILE Chi-restraints excluded: chain I residue 606 THR Chi-restraints excluded: chain K residue 43 SER Chi-restraints excluded: chain K residue 91 SER 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 228 optimal weight: 9.9990 chunk 104 optimal weight: 2.9990 chunk 64 optimal weight: 0.6980 chunk 49 optimal weight: 5.9990 chunk 98 optimal weight: 2.9990 chunk 224 optimal weight: 5.9990 chunk 127 optimal weight: 1.9990 chunk 33 optimal weight: 3.9990 chunk 100 optimal weight: 4.9990 chunk 44 optimal weight: 0.6980 chunk 243 optimal weight: 6.9990 overall best weight: 1.8786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 79 HIS B 131 GLN C 131 GLN D 279 GLN F 279 GLN H 220 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3789 r_free = 0.3789 target = 0.129337 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3339 r_free = 0.3339 target = 0.097023 restraints weight = 42449.993| |-----------------------------------------------------------------------------| r_work (start): 0.3294 rms_B_bonded: 2.03 r_work: 0.3119 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.3007 rms_B_bonded: 4.31 restraints_weight: 0.2500 r_work (final): 0.3007 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8285 moved from start: 0.3805 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 27011 Z= 0.182 Angle : 0.638 12.218 37126 Z= 0.348 Chirality : 0.047 0.253 4129 Planarity : 0.005 0.037 4384 Dihedral : 18.960 178.766 4948 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 3.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.83 % Favored : 96.17 % Rotamer: Outliers : 2.17 % Allowed : 17.32 % Favored : 80.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.33 (0.15), residues: 2925 helix: 1.21 (0.17), residues: 928 sheet: 1.11 (0.22), residues: 521 loop : -1.76 (0.14), residues: 1476 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP H 108 HIS 0.006 0.001 HIS I 541 PHE 0.025 0.002 PHE I 283 TYR 0.018 0.002 TYR A 9 ARG 0.004 0.000 ARG I 560 Details of bonding type rmsd hydrogen bonds : bond 0.06134 ( 1045) hydrogen bonds : angle 4.84223 ( 2876) covalent geometry : bond 0.00413 (27011) covalent geometry : angle 0.63764 (37126) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 18488.65 seconds wall clock time: 318 minutes 24.54 seconds (19104.54 seconds total)