Starting phenix.real_space_refine on Mon Feb 19 23:55:33 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dej_27393/02_2024/8dej_27393.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dej_27393/02_2024/8dej_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dej_27393/02_2024/8dej_27393.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dej_27393/02_2024/8dej_27393.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dej_27393/02_2024/8dej_27393.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dej_27393/02_2024/8dej_27393.pdb" } 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 Residue "B TYR 8": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 10": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 191": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 202": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 8": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 9": "OE1" <-> "OE2" Residue "D PHE 14": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 44": "OD1" <-> "OD2" Residue "D TYR 83": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 202": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 14": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 191": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ASP 87": "OD1" <-> "OD2" Residue "H TYR 8": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 191": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 202": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 33": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K GLU 26": "OE1" <-> "OE2" Residue "K ASP 69": "OD1" <-> "OD2" Time to flip residues: 0.17s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/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: 15.39, per 1000 atoms: 0.59 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 - 3.50 Amino acid : False - 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: 10.88 Conformation dependent library (CDL) restraints added in 4.3 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: 9.37 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: 9.60 Time building geometry restraints manager: 11.58 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: 95.38 - 103.11: 419 103.11 - 110.85: 10657 110.85 - 118.58: 11060 118.58 - 126.31: 14280 126.31 - 134.05: 710 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 2.440 nonbonded pdb=" O2' G N 26 " pdb=" O5' DA N 27 " model vdw 1.965 2.440 nonbonded pdb=" O2' C N 29 " pdb=" OP2 DA N 30 " model vdw 2.011 2.440 nonbonded pdb=" O2' G L 12 " pdb=" OP2 C L 13 " model vdw 2.097 2.440 nonbonded pdb=" OD2 ASP I 90 " pdb=" OG1 THR I 98 " model vdw 2.105 2.440 ... (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 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: 4.850 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 16.850 Check model and map are aligned: 0.370 Set scattering table: 0.210 Process input model: 75.810 Find NCS groups from input model: 1.460 Set up NCS constraints: 0.110 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:13.410 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 113.090 ------------------------------------------------------------------------------- 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= 0.284 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 *********************** 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 fitting. rotamer outliers: 9 poor density : 396 time to evaluate : 3.015 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: 1.6926 time to fit residues: 765.3414 Evaluate side-chains 210 residues out of total 2489 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 204 time to evaluate : 2.754 ------------------------------------------------------------------------------- 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: 0.8980 chunk 230 optimal weight: 5.9990 chunk 127 optimal weight: 5.9990 chunk 78 optimal weight: 3.9990 chunk 155 optimal weight: 0.3980 chunk 123 optimal weight: 4.9990 chunk 238 optimal weight: 4.9990 chunk 92 optimal weight: 0.5980 chunk 144 optimal weight: 3.9990 chunk 177 optimal weight: 30.0000 chunk 276 optimal weight: 2.9990 overall best weight: 1.7784 ------------------------------------------------------------------------------- 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 216 ASN D 279 GLN E 22 ASN F 79 HIS H 150 GLN I 572 GLN K 58 ASN K 89 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6908 moved from start: 0.2113 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 27011 Z= 0.272 Angle : 0.661 13.102 37126 Z= 0.364 Chirality : 0.048 0.271 4129 Planarity : 0.005 0.042 4384 Dihedral : 19.085 177.426 4954 Min Nonbonded Distance : 2.147 Molprobity Statistics. All-atom Clashscore : 3.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % Rotamer: Outliers : 2.77 % Allowed : 12.58 % Favored : 84.65 % 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: 0.08 (0.15), residues: 2925 helix: 1.56 (0.17), residues: 923 sheet: 0.45 (0.20), residues: 582 loop : -1.17 (0.15), residues: 1420 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP H 108 HIS 0.007 0.002 HIS D 39 PHE 0.017 0.002 PHE J 105 TYR 0.018 0.002 TYR I 246 ARG 0.006 0.001 ARG G 177 *********************** 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 284 residues out of total 2489 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 215 time to evaluate : 3.224 Fit side-chains revert: symmetry clash REVERT: A 131 LYS cc_start: 0.7437 (ptpt) cc_final: 0.6611 (ptmm) REVERT: A 140 LYS cc_start: 0.7931 (mmpt) cc_final: 0.7552 (ptmt) REVERT: B 30 MET cc_start: 0.7548 (mmt) cc_final: 0.7046 (mmp) REVERT: B 83 TYR cc_start: 0.5297 (OUTLIER) cc_final: 0.5046 (t80) REVERT: B 240 GLN cc_start: 0.7694 (tp40) cc_final: 0.7423 (tt0) REVERT: B 256 LYS cc_start: 0.7655 (mttp) cc_final: 0.7011 (tmtt) REVERT: B 285 GLU cc_start: 0.7270 (mt-10) cc_final: 0.6850 (mp0) REVERT: C 123 MET cc_start: 0.7285 (mtm) cc_final: 0.7057 (mtm) REVERT: C 126 GLU cc_start: 0.7866 (OUTLIER) cc_final: 0.7560 (tt0) REVERT: C 138 MET cc_start: 0.8005 (OUTLIER) cc_final: 0.7680 (ptm) REVERT: D 1 MET cc_start: 0.2224 (mtt) cc_final: 0.1444 (mtp) REVERT: D 9 GLU cc_start: 0.8185 (OUTLIER) cc_final: 0.6973 (mm-30) REVERT: D 156 ARG cc_start: 0.7675 (ttt180) cc_final: 0.7323 (ttt180) REVERT: D 240 GLN cc_start: 0.8463 (tm-30) cc_final: 0.8241 (tp40) REVERT: E 9 GLU cc_start: 0.8316 (OUTLIER) cc_final: 0.7835 (mp0) REVERT: E 80 GLU cc_start: 0.7912 (tt0) cc_final: 0.7589 (mt-10) REVERT: E 109 MET cc_start: 0.4195 (mtm) cc_final: 0.3967 (mtm) REVERT: E 123 MET cc_start: 0.7643 (OUTLIER) cc_final: 0.7250 (mtp) REVERT: E 282 GLU cc_start: 0.6485 (pm20) cc_final: 0.5982 (tt0) REVERT: F 89 LYS cc_start: 0.7654 (tppt) cc_final: 0.7034 (tmtt) REVERT: F 125 THR cc_start: 0.7872 (OUTLIER) cc_final: 0.7585 (p) REVERT: F 180 ILE cc_start: 0.7925 (OUTLIER) cc_final: 0.7687 (pt) REVERT: F 240 GLN cc_start: 0.7608 (mm110) cc_final: 0.7369 (mm110) REVERT: F 279 GLN cc_start: 0.7902 (mm110) cc_final: 0.7453 (tt0) REVERT: G 89 LYS cc_start: 0.7213 (mppt) cc_final: 0.6679 (tptm) REVERT: H 30 MET cc_start: 0.5793 (mmt) cc_final: 0.5535 (mmm) REVERT: H 261 GLU cc_start: 0.5393 (pm20) cc_final: 0.4472 (tp30) REVERT: I 58 ARG cc_start: 0.5483 (mmt180) cc_final: 0.4794 (mmm160) REVERT: I 94 LYS cc_start: 0.5947 (OUTLIER) cc_final: 0.5691 (mttt) REVERT: I 202 LYS cc_start: 0.7040 (mptt) cc_final: 0.6625 (mmmt) REVERT: I 231 GLU cc_start: 0.6589 (pt0) cc_final: 0.6105 (pt0) REVERT: I 399 GLU cc_start: 0.7120 (tt0) cc_final: 0.6698 (tm-30) REVERT: I 452 GLU cc_start: 0.7007 (mm-30) cc_final: 0.6670 (mm-30) REVERT: J 58 ASN cc_start: 0.6668 (m-40) cc_final: 0.6302 (t0) REVERT: J 82 MET cc_start: 0.5976 (mtt) cc_final: 0.5731 (mtp) REVERT: K 26 GLU cc_start: 0.6768 (tp30) cc_final: 0.6185 (mt-10) outliers start: 69 outliers final: 22 residues processed: 260 average time/residue: 1.6570 time to fit residues: 489.0788 Evaluate side-chains 222 residues out of total 2489 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 191 time to evaluate : 2.709 ------------------------------------------------------------------------------- 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 C residue 138 MET 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 58 THR Chi-restraints excluded: chain E residue 123 MET Chi-restraints excluded: chain E residue 171 ASP Chi-restraints excluded: chain F residue 125 THR Chi-restraints excluded: chain F residue 180 ILE 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 I residue 94 LYS Chi-restraints excluded: chain I residue 149 VAL Chi-restraints excluded: chain I residue 390 ILE Chi-restraints excluded: chain J residue 38 ASP 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 153 optimal weight: 3.9990 chunk 85 optimal weight: 10.0000 chunk 229 optimal weight: 8.9990 chunk 187 optimal weight: 4.9990 chunk 76 optimal weight: 6.9990 chunk 276 optimal weight: 0.8980 chunk 298 optimal weight: 8.9990 chunk 246 optimal weight: 8.9990 chunk 274 optimal weight: 0.0370 chunk 94 optimal weight: 0.9990 chunk 221 optimal weight: 5.9990 overall best weight: 2.1864 ------------------------------------------------------------------------------- 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 E 39 HIS E 137 GLN H 150 GLN H 220 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6937 moved from start: 0.2731 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 27011 Z= 0.310 Angle : 0.670 13.789 37126 Z= 0.367 Chirality : 0.049 0.237 4129 Planarity : 0.005 0.056 4384 Dihedral : 19.016 176.999 4948 Min Nonbonded Distance : 2.140 Molprobity Statistics. All-atom Clashscore : 3.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.69 % Favored : 96.31 % Rotamer: Outliers : 3.42 % Allowed : 13.34 % Favored : 83.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.32 (0.17), residues: 921 sheet: 0.91 (0.21), residues: 549 loop : -1.37 (0.15), residues: 1455 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP H 108 HIS 0.007 0.002 HIS G 189 PHE 0.019 0.002 PHE I 283 TYR 0.024 0.002 TYR H 83 ARG 0.012 0.001 ARG I 205 *********************** 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 276 residues out of total 2489 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 85 poor density : 191 time to evaluate : 3.088 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 131 LYS cc_start: 0.7553 (ptpt) cc_final: 0.6816 (ptmm) REVERT: A 143 ASP cc_start: 0.7973 (m-30) cc_final: 0.7497 (t0) REVERT: B 30 MET cc_start: 0.7517 (mmt) cc_final: 0.7139 (mtp) REVERT: B 83 TYR cc_start: 0.5375 (OUTLIER) cc_final: 0.5161 (t80) REVERT: B 112 ASN cc_start: 0.8272 (OUTLIER) cc_final: 0.7974 (p0) REVERT: B 240 GLN cc_start: 0.7834 (tp40) cc_final: 0.7393 (tt0) REVERT: C 30 MET cc_start: 0.8135 (mtt) cc_final: 0.7851 (mtp) REVERT: C 126 GLU cc_start: 0.7910 (OUTLIER) cc_final: 0.7652 (tt0) REVERT: C 175 MET cc_start: 0.8674 (OUTLIER) cc_final: 0.8385 (mtm) REVERT: C 226 ARG cc_start: 0.7927 (OUTLIER) cc_final: 0.7559 (ttp-170) REVERT: D 9 GLU cc_start: 0.8211 (OUTLIER) cc_final: 0.6872 (mm-30) REVERT: D 63 GLU cc_start: 0.7580 (tp30) cc_final: 0.7366 (tm-30) REVERT: D 156 ARG cc_start: 0.7699 (ttt180) cc_final: 0.7271 (ttt180) REVERT: D 240 GLN cc_start: 0.8444 (tm-30) cc_final: 0.8193 (tp40) REVERT: E 32 ARG cc_start: 0.5952 (tpm170) cc_final: 0.5675 (tpt170) REVERT: E 80 GLU cc_start: 0.7841 (tt0) cc_final: 0.7404 (mt-10) REVERT: E 109 MET cc_start: 0.4457 (mtm) cc_final: 0.4143 (mtm) REVERT: E 123 MET cc_start: 0.7748 (OUTLIER) cc_final: 0.7248 (mtm) REVERT: E 282 GLU cc_start: 0.6582 (pm20) cc_final: 0.6207 (tt0) REVERT: F 89 LYS cc_start: 0.7579 (tppt) cc_final: 0.6982 (tmtt) REVERT: F 180 ILE cc_start: 0.7831 (OUTLIER) cc_final: 0.7560 (pt) REVERT: F 240 GLN cc_start: 0.7661 (mm110) cc_final: 0.7398 (mm110) REVERT: F 279 GLN cc_start: 0.7893 (mm110) cc_final: 0.7499 (tt0) REVERT: F 290 LEU cc_start: 0.6417 (OUTLIER) cc_final: 0.5925 (tt) REVERT: G 89 LYS cc_start: 0.7191 (mppt) cc_final: 0.6656 (tptm) REVERT: G 138 MET cc_start: 0.8346 (OUTLIER) cc_final: 0.7727 (ptm) REVERT: H 30 MET cc_start: 0.5804 (mmt) cc_final: 0.5535 (mmm) REVERT: I 58 ARG cc_start: 0.5409 (mmt180) cc_final: 0.4780 (mmm160) REVERT: I 94 LYS cc_start: 0.6227 (OUTLIER) cc_final: 0.5971 (mttt) REVERT: I 202 LYS cc_start: 0.7098 (mptt) cc_final: 0.6674 (mmmt) REVERT: I 231 GLU cc_start: 0.6467 (pt0) cc_final: 0.6216 (pt0) REVERT: I 286 MET cc_start: 0.3559 (pp-130) cc_final: 0.3197 (mmp) REVERT: I 399 GLU cc_start: 0.7093 (tt0) cc_final: 0.6584 (tm-30) REVERT: I 452 GLU cc_start: 0.7033 (mm-30) cc_final: 0.6654 (mm-30) REVERT: J 50 GLN cc_start: 0.7726 (OUTLIER) cc_final: 0.7000 (mp10) REVERT: J 58 ASN cc_start: 0.6633 (m-40) cc_final: 0.6355 (t0) REVERT: J 82 MET cc_start: 0.6067 (mtt) cc_final: 0.5744 (mtp) REVERT: K 26 GLU cc_start: 0.6765 (tp30) cc_final: 0.6186 (mt-10) outliers start: 85 outliers final: 31 residues processed: 247 average time/residue: 1.6407 time to fit residues: 459.8286 Evaluate side-chains 229 residues out of total 2489 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 186 time to evaluate : 2.628 ------------------------------------------------------------------------------- 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 A residue 213 ASP Chi-restraints excluded: chain B residue 83 TYR Chi-restraints excluded: chain B residue 112 ASN 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 159 VAL Chi-restraints excluded: chain C residue 175 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 276 THR 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 123 MET Chi-restraints excluded: chain E residue 171 ASP Chi-restraints excluded: chain E residue 257 VAL Chi-restraints excluded: chain F residue 180 ILE 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 203 SER Chi-restraints excluded: chain H residue 70 GLN Chi-restraints excluded: chain H residue 127 VAL Chi-restraints excluded: chain I residue 3 LEU Chi-restraints excluded: chain I residue 94 LYS Chi-restraints excluded: chain I residue 149 VAL Chi-restraints excluded: chain I residue 258 ASN Chi-restraints excluded: chain I residue 379 ASP Chi-restraints excluded: chain I residue 390 ILE Chi-restraints excluded: chain J residue 38 ASP Chi-restraints excluded: chain J residue 50 GLN 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 273 optimal weight: 4.9990 chunk 207 optimal weight: 2.9990 chunk 143 optimal weight: 6.9990 chunk 30 optimal weight: 5.9990 chunk 131 optimal weight: 0.9990 chunk 185 optimal weight: 5.9990 chunk 277 optimal weight: 0.3980 chunk 293 optimal weight: 4.9990 chunk 145 optimal weight: 4.9990 chunk 263 optimal weight: 4.9990 chunk 79 optimal weight: 0.4980 overall best weight: 1.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 79 HIS D 279 GLN H 220 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6934 moved from start: 0.3016 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 27011 Z= 0.281 Angle : 0.642 13.047 37126 Z= 0.353 Chirality : 0.047 0.221 4129 Planarity : 0.005 0.045 4384 Dihedral : 19.049 178.799 4948 Min Nonbonded Distance : 2.154 Molprobity Statistics. All-atom Clashscore : 3.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.83 % Favored : 96.17 % Rotamer: Outliers : 3.66 % Allowed : 13.99 % Favored : 82.36 % 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: 1.28 (0.18), residues: 921 sheet: 0.91 (0.22), residues: 537 loop : -1.52 (0.14), residues: 1467 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP H 108 HIS 0.006 0.001 HIS G 189 PHE 0.017 0.002 PHE J 105 TYR 0.018 0.002 TYR F 8 ARG 0.004 0.001 ARG F 52 *********************** 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 279 residues out of total 2489 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 91 poor density : 188 time to evaluate : 2.691 Fit side-chains revert: symmetry clash REVERT: A 43 ARG cc_start: 0.6962 (OUTLIER) cc_final: 0.6723 (tmm-80) REVERT: A 131 LYS cc_start: 0.7600 (ptpt) cc_final: 0.6887 (ptmm) REVERT: A 140 LYS cc_start: 0.7950 (mmpt) cc_final: 0.7491 (pttt) REVERT: A 143 ASP cc_start: 0.7920 (m-30) cc_final: 0.7568 (t0) REVERT: B 30 MET cc_start: 0.7541 (mmt) cc_final: 0.7174 (mtp) REVERT: B 112 ASN cc_start: 0.8212 (OUTLIER) cc_final: 0.7995 (p0) REVERT: B 240 GLN cc_start: 0.7839 (tp40) cc_final: 0.7457 (tt0) REVERT: C 15 ASP cc_start: 0.8711 (OUTLIER) cc_final: 0.8359 (m-30) REVERT: C 30 MET cc_start: 0.8137 (mtt) cc_final: 0.7861 (mtp) REVERT: C 126 GLU cc_start: 0.7932 (OUTLIER) cc_final: 0.7710 (tt0) REVERT: C 175 MET cc_start: 0.8657 (OUTLIER) cc_final: 0.8377 (mtm) REVERT: C 226 ARG cc_start: 0.7957 (OUTLIER) cc_final: 0.7630 (ttp-170) REVERT: D 9 GLU cc_start: 0.8317 (OUTLIER) cc_final: 0.7012 (mm-30) REVERT: D 63 GLU cc_start: 0.7609 (tp30) cc_final: 0.7384 (tm-30) REVERT: D 240 GLN cc_start: 0.8304 (tm-30) cc_final: 0.8030 (tp40) REVERT: E 80 GLU cc_start: 0.7745 (tt0) cc_final: 0.7270 (mt-10) REVERT: E 109 MET cc_start: 0.4750 (mtm) cc_final: 0.4253 (mtm) REVERT: E 123 MET cc_start: 0.7566 (OUTLIER) cc_final: 0.7094 (mtm) REVERT: E 282 GLU cc_start: 0.6623 (pm20) cc_final: 0.6371 (tt0) REVERT: F 89 LYS cc_start: 0.7570 (tppt) cc_final: 0.6912 (tmtt) REVERT: F 180 ILE cc_start: 0.7906 (OUTLIER) cc_final: 0.7567 (pt) REVERT: F 240 GLN cc_start: 0.7753 (mm110) cc_final: 0.7483 (mm110) REVERT: F 279 GLN cc_start: 0.7855 (mm110) cc_final: 0.7474 (tt0) REVERT: G 36 GLU cc_start: 0.7805 (OUTLIER) cc_final: 0.6594 (mp0) REVERT: G 88 LEU cc_start: 0.5369 (mt) cc_final: 0.5031 (mt) REVERT: G 89 LYS cc_start: 0.7056 (mppt) cc_final: 0.6408 (tptp) REVERT: G 138 MET cc_start: 0.8358 (OUTLIER) cc_final: 0.7710 (ptm) REVERT: H 30 MET cc_start: 0.5960 (mmt) cc_final: 0.5664 (mmm) REVERT: I 58 ARG cc_start: 0.5475 (mmt180) cc_final: 0.4844 (mmm160) REVERT: I 94 LYS cc_start: 0.6269 (OUTLIER) cc_final: 0.6025 (mttt) REVERT: I 202 LYS cc_start: 0.7180 (mptt) cc_final: 0.6726 (mmmt) REVERT: I 231 GLU cc_start: 0.6453 (pt0) cc_final: 0.6169 (pt0) REVERT: I 399 GLU cc_start: 0.6985 (tt0) cc_final: 0.6453 (tm-30) REVERT: I 452 GLU cc_start: 0.7027 (mm-30) cc_final: 0.6698 (mm-30) REVERT: J 50 GLN cc_start: 0.7749 (OUTLIER) cc_final: 0.7295 (mm-40) REVERT: J 58 ASN cc_start: 0.6630 (m-40) cc_final: 0.6407 (t0) REVERT: J 82 MET cc_start: 0.5979 (OUTLIER) cc_final: 0.5697 (mtp) REVERT: K 26 GLU cc_start: 0.6771 (tp30) cc_final: 0.6180 (mt-10) outliers start: 91 outliers final: 38 residues processed: 251 average time/residue: 1.6616 time to fit residues: 474.0870 Evaluate side-chains 231 residues out of total 2489 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 179 time to evaluate : 3.140 ------------------------------------------------------------------------------- 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 A residue 213 ASP Chi-restraints excluded: chain B residue 103 LYS Chi-restraints excluded: chain B residue 112 ASN 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 15 ASP Chi-restraints excluded: chain C residue 126 GLU Chi-restraints excluded: chain C residue 138 MET Chi-restraints excluded: chain C residue 173 ARG Chi-restraints excluded: chain C residue 175 MET 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 44 ASP 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 123 MET Chi-restraints excluded: chain E residue 171 ASP Chi-restraints excluded: chain E residue 279 GLN Chi-restraints excluded: chain F residue 180 ILE Chi-restraints excluded: chain F residue 257 VAL Chi-restraints excluded: chain G residue 2 THR Chi-restraints excluded: chain G residue 36 GLU Chi-restraints excluded: chain G residue 138 MET Chi-restraints excluded: chain G residue 203 SER Chi-restraints excluded: chain H residue 44 ASP Chi-restraints excluded: chain H residue 69 ILE 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 175 ARG Chi-restraints excluded: chain I residue 379 ASP Chi-restraints excluded: chain I residue 390 ILE Chi-restraints excluded: chain J residue 38 ASP Chi-restraints excluded: chain J residue 50 GLN Chi-restraints excluded: chain J residue 82 MET 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 244 optimal weight: 6.9990 chunk 166 optimal weight: 4.9990 chunk 4 optimal weight: 3.9990 chunk 218 optimal weight: 9.9990 chunk 121 optimal weight: 3.9990 chunk 250 optimal weight: 5.9990 chunk 203 optimal weight: 9.9990 chunk 0 optimal weight: 7.9990 chunk 150 optimal weight: 1.9990 chunk 263 optimal weight: 5.9990 chunk 74 optimal weight: 6.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 141 HIS B 79 HIS B 131 GLN D 39 HIS D 279 GLN G 6 ASN H 29 ASN H 220 HIS J 111 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6991 moved from start: 0.3431 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.079 27011 Z= 0.543 Angle : 0.837 14.801 37126 Z= 0.456 Chirality : 0.055 0.273 4129 Planarity : 0.007 0.068 4384 Dihedral : 19.159 176.872 4948 Min Nonbonded Distance : 2.076 Molprobity Statistics. All-atom Clashscore : 4.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.75 % Favored : 95.25 % Rotamer: Outliers : 4.34 % Allowed : 14.23 % Favored : 81.43 % 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: -0.83 (0.14), residues: 2925 helix: 0.68 (0.17), residues: 923 sheet: 0.97 (0.22), residues: 498 loop : -1.98 (0.13), residues: 1504 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.003 TRP H 108 HIS 0.011 0.002 HIS J 111 PHE 0.023 0.003 PHE I 605 TYR 0.027 0.003 TYR F 8 ARG 0.009 0.001 ARG E 32 *********************** 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 296 residues out of total 2489 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 108 poor density : 188 time to evaluate : 2.941 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 43 ARG cc_start: 0.6827 (OUTLIER) cc_final: 0.6568 (tmm-80) REVERT: A 131 LYS cc_start: 0.7724 (ptpt) cc_final: 0.6993 (ptmm) REVERT: A 143 ASP cc_start: 0.7922 (m-30) cc_final: 0.7585 (t0) REVERT: B 30 MET cc_start: 0.7583 (mmt) cc_final: 0.7248 (mtp) REVERT: B 112 ASN cc_start: 0.8373 (OUTLIER) cc_final: 0.8095 (p0) REVERT: B 240 GLN cc_start: 0.7714 (tp40) cc_final: 0.7401 (tt0) REVERT: C 15 ASP cc_start: 0.8974 (OUTLIER) cc_final: 0.8634 (m-30) REVERT: C 126 GLU cc_start: 0.7983 (OUTLIER) cc_final: 0.7744 (tt0) REVERT: C 226 ARG cc_start: 0.7944 (OUTLIER) cc_final: 0.7575 (ttp-170) REVERT: D 9 GLU cc_start: 0.8404 (OUTLIER) cc_final: 0.6967 (mm-30) REVERT: D 63 GLU cc_start: 0.7835 (tp30) cc_final: 0.7418 (tm-30) REVERT: E 80 GLU cc_start: 0.7820 (tt0) cc_final: 0.7325 (mt-10) REVERT: E 109 MET cc_start: 0.5634 (mtm) cc_final: 0.4948 (mtm) REVERT: E 123 MET cc_start: 0.7856 (OUTLIER) cc_final: 0.7365 (mtm) REVERT: E 250 LYS cc_start: 0.7766 (OUTLIER) cc_final: 0.7449 (mttt) REVERT: F 240 GLN cc_start: 0.7402 (mm110) cc_final: 0.7135 (mm110) REVERT: F 279 GLN cc_start: 0.7923 (mm110) cc_final: 0.7500 (tt0) REVERT: G 15 ASP cc_start: 0.8744 (OUTLIER) cc_final: 0.8488 (t0) REVERT: G 88 LEU cc_start: 0.5811 (mt) cc_final: 0.5353 (mt) REVERT: G 89 LYS cc_start: 0.7120 (mppt) cc_final: 0.6846 (tptm) REVERT: G 138 MET cc_start: 0.8424 (OUTLIER) cc_final: 0.7784 (ptm) REVERT: G 289 MET cc_start: 0.6998 (pmm) cc_final: 0.6696 (pmt) REVERT: H 30 MET cc_start: 0.6089 (mmt) cc_final: 0.5664 (mmm) REVERT: I 58 ARG cc_start: 0.5360 (mmt180) cc_final: 0.4749 (mmm160) REVERT: I 63 LEU cc_start: 0.6112 (OUTLIER) cc_final: 0.5836 (tp) REVERT: I 202 LYS cc_start: 0.7230 (mptt) cc_final: 0.6787 (mmmt) REVERT: I 231 GLU cc_start: 0.6826 (pt0) cc_final: 0.6487 (pt0) REVERT: I 399 GLU cc_start: 0.6961 (tt0) cc_final: 0.6422 (tm-30) REVERT: I 452 GLU cc_start: 0.7307 (mm-30) cc_final: 0.6936 (mm-30) REVERT: J 50 GLN cc_start: 0.7858 (OUTLIER) cc_final: 0.7640 (mm-40) REVERT: J 58 ASN cc_start: 0.6471 (m-40) cc_final: 0.6212 (t0) REVERT: J 82 MET cc_start: 0.6256 (OUTLIER) cc_final: 0.5813 (mtp) REVERT: K 26 GLU cc_start: 0.6854 (tp30) cc_final: 0.6309 (mt-10) outliers start: 108 outliers final: 54 residues processed: 266 average time/residue: 1.5638 time to fit residues: 474.7028 Evaluate side-chains 247 residues out of total 2489 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 180 time to evaluate : 2.875 ------------------------------------------------------------------------------- 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 179 SER Chi-restraints excluded: chain A residue 191 MET Chi-restraints excluded: chain A residue 213 ASP Chi-restraints excluded: chain B residue 45 VAL Chi-restraints excluded: chain B residue 103 LYS Chi-restraints excluded: chain B residue 112 ASN Chi-restraints excluded: chain B residue 124 THR Chi-restraints excluded: chain B residue 127 VAL 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 15 ASP Chi-restraints excluded: chain C residue 97 LYS 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 44 ASP Chi-restraints excluded: chain D residue 148 VAL Chi-restraints excluded: chain D residue 152 VAL Chi-restraints excluded: chain D residue 174 THR Chi-restraints excluded: chain D residue 269 SER Chi-restraints excluded: chain D residue 276 THR Chi-restraints excluded: chain D residue 286 VAL Chi-restraints excluded: chain D residue 288 GLU Chi-restraints excluded: chain E residue 26 ASP Chi-restraints excluded: chain E residue 58 THR Chi-restraints excluded: chain E residue 123 MET Chi-restraints excluded: chain E residue 171 ASP Chi-restraints excluded: chain E residue 229 MET Chi-restraints excluded: chain E residue 250 LYS Chi-restraints excluded: chain E residue 257 VAL Chi-restraints excluded: chain F residue 180 ILE Chi-restraints excluded: chain F residue 257 VAL Chi-restraints excluded: chain F residue 286 VAL Chi-restraints excluded: chain G residue 2 THR Chi-restraints excluded: chain G residue 15 ASP Chi-restraints excluded: chain G residue 138 MET Chi-restraints excluded: chain G residue 203 SER Chi-restraints excluded: chain H residue 44 ASP 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 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 258 ASN Chi-restraints excluded: chain I residue 379 ASP Chi-restraints excluded: chain I residue 390 ILE Chi-restraints excluded: chain I residue 606 THR Chi-restraints excluded: chain J residue 2 SER Chi-restraints excluded: chain J residue 38 ASP Chi-restraints excluded: chain J residue 50 GLN Chi-restraints excluded: chain J residue 82 MET 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 98 optimal weight: 1.9990 chunk 264 optimal weight: 0.8980 chunk 58 optimal weight: 4.9990 chunk 172 optimal weight: 0.9980 chunk 72 optimal weight: 1.9990 chunk 294 optimal weight: 0.9990 chunk 244 optimal weight: 6.9990 chunk 136 optimal weight: 1.9990 chunk 24 optimal weight: 0.5980 chunk 97 optimal weight: 2.9990 chunk 154 optimal weight: 0.6980 overall best weight: 0.8382 ------------------------------------------------------------------------------- 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 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 220 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6905 moved from start: 0.3434 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 27011 Z= 0.173 Angle : 0.577 11.518 37126 Z= 0.317 Chirality : 0.044 0.215 4129 Planarity : 0.005 0.042 4384 Dihedral : 19.059 179.491 4948 Min Nonbonded Distance : 2.125 Molprobity Statistics. All-atom Clashscore : 4.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.21 % Favored : 96.79 % Rotamer: Outliers : 2.77 % Allowed : 16.28 % Favored : 80.95 % 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: -0.34 (0.15), residues: 2925 helix: 1.29 (0.18), residues: 922 sheet: 0.79 (0.22), residues: 541 loop : -1.71 (0.14), residues: 1462 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP H 108 HIS 0.004 0.001 HIS I 541 PHE 0.012 0.001 PHE E 113 TYR 0.014 0.001 TYR F 8 ARG 0.004 0.000 ARG G 177 *********************** 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 258 residues out of total 2489 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 189 time to evaluate : 2.868 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 131 LYS cc_start: 0.7679 (ptpt) cc_final: 0.6910 (ptmm) REVERT: A 140 LYS cc_start: 0.7997 (mmpt) cc_final: 0.7479 (pttm) REVERT: A 143 ASP cc_start: 0.7864 (m-30) cc_final: 0.7566 (t0) REVERT: B 30 MET cc_start: 0.7546 (mmt) cc_final: 0.7220 (mtp) REVERT: B 240 GLN cc_start: 0.7699 (tp40) cc_final: 0.7459 (tt0) REVERT: C 30 MET cc_start: 0.8168 (mtt) cc_final: 0.7934 (mtp) REVERT: C 126 GLU cc_start: 0.7919 (OUTLIER) cc_final: 0.7716 (tt0) REVERT: C 226 ARG cc_start: 0.7839 (OUTLIER) cc_final: 0.7494 (ttp-170) REVERT: D 9 GLU cc_start: 0.8297 (OUTLIER) cc_final: 0.7006 (mm-30) REVERT: D 63 GLU cc_start: 0.7789 (tp30) cc_final: 0.7392 (tm-30) REVERT: D 156 ARG cc_start: 0.7692 (OUTLIER) cc_final: 0.7279 (ttt180) REVERT: E 9 GLU cc_start: 0.8267 (OUTLIER) cc_final: 0.7890 (mp0) REVERT: E 80 GLU cc_start: 0.7620 (tt0) cc_final: 0.7234 (mt-10) REVERT: E 109 MET cc_start: 0.5401 (mtm) cc_final: 0.4801 (mtm) REVERT: E 123 MET cc_start: 0.7276 (OUTLIER) cc_final: 0.6910 (mtm) REVERT: E 250 LYS cc_start: 0.7672 (OUTLIER) cc_final: 0.7331 (mmtp) REVERT: F 63 GLU cc_start: 0.7520 (OUTLIER) cc_final: 0.7012 (tt0) REVERT: F 180 ILE cc_start: 0.8038 (OUTLIER) cc_final: 0.7665 (pt) REVERT: F 240 GLN cc_start: 0.7448 (mm110) cc_final: 0.7176 (mm110) REVERT: F 279 GLN cc_start: 0.7749 (mm110) cc_final: 0.7176 (tt0) REVERT: G 89 LYS cc_start: 0.7396 (mppt) cc_final: 0.6836 (tptm) REVERT: G 138 MET cc_start: 0.8382 (OUTLIER) cc_final: 0.7743 (ptm) REVERT: G 289 MET cc_start: 0.6865 (pmm) cc_final: 0.6603 (pmt) REVERT: H 30 MET cc_start: 0.6089 (mmt) cc_final: 0.5740 (mmm) REVERT: H 175 MET cc_start: 0.2170 (mtp) cc_final: 0.0601 (tpp) REVERT: I 94 LYS cc_start: 0.6282 (OUTLIER) cc_final: 0.6028 (mttt) REVERT: I 202 LYS cc_start: 0.7191 (mptt) cc_final: 0.6716 (mmmt) REVERT: I 231 GLU cc_start: 0.6619 (pt0) cc_final: 0.6055 (pm20) REVERT: I 399 GLU cc_start: 0.6983 (tt0) cc_final: 0.6449 (tm-30) REVERT: I 452 GLU cc_start: 0.6961 (mm-30) cc_final: 0.6663 (mm-30) REVERT: J 50 GLN cc_start: 0.7726 (OUTLIER) cc_final: 0.7256 (mm110) REVERT: J 58 ASN cc_start: 0.6470 (m-40) cc_final: 0.6164 (t0) REVERT: J 82 MET cc_start: 0.5809 (OUTLIER) cc_final: 0.5535 (mtp) REVERT: K 26 GLU cc_start: 0.6710 (tp30) cc_final: 0.6069 (mt-10) outliers start: 69 outliers final: 36 residues processed: 237 average time/residue: 1.7106 time to fit residues: 458.9262 Evaluate side-chains 226 residues out of total 2489 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 177 time to evaluate : 2.959 ------------------------------------------------------------------------------- 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 136 ASP 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 217 MET Chi-restraints excluded: chain B residue 284 VAL Chi-restraints excluded: chain B residue 290 LEU 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 44 ASP Chi-restraints excluded: chain D residue 148 VAL Chi-restraints excluded: chain D residue 152 VAL Chi-restraints excluded: chain D residue 156 ARG Chi-restraints excluded: chain D residue 174 THR Chi-restraints excluded: chain D residue 269 SER Chi-restraints excluded: chain D residue 286 VAL Chi-restraints excluded: chain D residue 288 GLU Chi-restraints excluded: chain E residue 9 GLU Chi-restraints excluded: chain E residue 123 MET Chi-restraints excluded: chain E residue 171 ASP Chi-restraints excluded: chain E residue 250 LYS Chi-restraints excluded: chain E residue 257 VAL Chi-restraints excluded: chain F residue 63 GLU Chi-restraints excluded: chain F residue 180 ILE Chi-restraints excluded: chain F residue 217 MET Chi-restraints excluded: chain F residue 290 LEU Chi-restraints excluded: chain G residue 138 MET Chi-restraints excluded: chain H residue 44 ASP Chi-restraints excluded: chain H residue 70 GLN 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 379 ASP Chi-restraints excluded: chain I residue 390 ILE Chi-restraints excluded: chain J residue 38 ASP 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 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 283 optimal weight: 3.9990 chunk 33 optimal weight: 3.9990 chunk 167 optimal weight: 0.9980 chunk 214 optimal weight: 9.9990 chunk 166 optimal weight: 0.9990 chunk 247 optimal weight: 9.9990 chunk 164 optimal weight: 0.0470 chunk 293 optimal weight: 5.9990 chunk 183 optimal weight: 4.9990 chunk 178 optimal weight: 3.9990 chunk 135 optimal weight: 0.7980 overall best weight: 1.3682 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 79 HIS D 279 GLN E 70 GLN H 220 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6924 moved from start: 0.3520 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 27011 Z= 0.216 Angle : 0.594 12.247 37126 Z= 0.325 Chirality : 0.045 0.223 4129 Planarity : 0.005 0.039 4384 Dihedral : 18.991 179.457 4948 Min Nonbonded Distance : 2.147 Molprobity Statistics. All-atom Clashscore : 4.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.10 % Favored : 95.90 % Rotamer: Outliers : 3.05 % Allowed : 16.32 % 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: -0.27 (0.15), residues: 2925 helix: 1.37 (0.18), residues: 922 sheet: 0.84 (0.22), residues: 549 loop : -1.71 (0.14), residues: 1454 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP H 108 HIS 0.005 0.001 HIS I 541 PHE 0.025 0.001 PHE I 283 TYR 0.016 0.002 TYR I 246 ARG 0.003 0.000 ARG G 177 *********************** 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 257 residues out of total 2489 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 76 poor density : 181 time to evaluate : 2.755 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 77 GLU cc_start: 0.7509 (OUTLIER) cc_final: 0.6094 (mt-10) REVERT: A 131 LYS cc_start: 0.7762 (ptpt) cc_final: 0.7036 (ptmm) REVERT: A 140 LYS cc_start: 0.8026 (mmpt) cc_final: 0.7606 (ptmt) REVERT: A 143 ASP cc_start: 0.7862 (m-30) cc_final: 0.7573 (t0) REVERT: B 30 MET cc_start: 0.7589 (mmt) cc_final: 0.7241 (mtp) REVERT: B 240 GLN cc_start: 0.7712 (tp40) cc_final: 0.7451 (tt0) REVERT: C 30 MET cc_start: 0.8170 (mtt) cc_final: 0.7940 (mtp) REVERT: C 226 ARG cc_start: 0.7861 (OUTLIER) cc_final: 0.7509 (ttp-170) REVERT: D 9 GLU cc_start: 0.8294 (OUTLIER) cc_final: 0.6979 (mm-30) REVERT: D 156 ARG cc_start: 0.7774 (OUTLIER) cc_final: 0.7355 (ttt180) REVERT: E 9 GLU cc_start: 0.8342 (OUTLIER) cc_final: 0.7905 (mp0) REVERT: E 80 GLU cc_start: 0.7639 (tt0) cc_final: 0.7248 (mt-10) REVERT: E 109 MET cc_start: 0.5489 (mtm) cc_final: 0.5227 (mtm) REVERT: E 123 MET cc_start: 0.7503 (OUTLIER) cc_final: 0.7165 (mtm) REVERT: E 250 LYS cc_start: 0.7684 (OUTLIER) cc_final: 0.7413 (mttt) REVERT: F 1 MET cc_start: 0.4204 (mtm) cc_final: 0.3517 (ttm) REVERT: F 63 GLU cc_start: 0.7540 (OUTLIER) cc_final: 0.6983 (tt0) REVERT: F 180 ILE cc_start: 0.7916 (OUTLIER) cc_final: 0.7681 (pt) REVERT: F 240 GLN cc_start: 0.7448 (mm110) cc_final: 0.7167 (mm110) REVERT: F 279 GLN cc_start: 0.7774 (mm110) cc_final: 0.7177 (tt0) REVERT: G 89 LYS cc_start: 0.7405 (mppt) cc_final: 0.6841 (tptm) REVERT: G 138 MET cc_start: 0.8382 (OUTLIER) cc_final: 0.7763 (ptm) REVERT: G 289 MET cc_start: 0.6799 (pmm) cc_final: 0.6552 (pmt) REVERT: H 30 MET cc_start: 0.6159 (mmt) cc_final: 0.5792 (mmm) REVERT: H 175 MET cc_start: 0.2026 (mtp) cc_final: 0.0540 (tpp) REVERT: I 94 LYS cc_start: 0.6311 (OUTLIER) cc_final: 0.6052 (mttt) REVERT: I 202 LYS cc_start: 0.7217 (mptt) cc_final: 0.6710 (mmmt) REVERT: I 231 GLU cc_start: 0.6555 (pt0) cc_final: 0.6122 (tt0) REVERT: I 399 GLU cc_start: 0.7025 (tt0) cc_final: 0.6474 (tm-30) REVERT: I 452 GLU cc_start: 0.7088 (mm-30) cc_final: 0.6749 (mm-30) REVERT: J 50 GLN cc_start: 0.7733 (OUTLIER) cc_final: 0.7255 (mm-40) REVERT: J 58 ASN cc_start: 0.6552 (m-40) cc_final: 0.6252 (t0) REVERT: J 82 MET cc_start: 0.5793 (OUTLIER) cc_final: 0.5506 (mtp) REVERT: K 26 GLU cc_start: 0.6734 (tp30) cc_final: 0.6087 (mt-10) outliers start: 76 outliers final: 44 residues processed: 233 average time/residue: 1.6403 time to fit residues: 434.0669 Evaluate side-chains 229 residues out of total 2489 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 172 time to evaluate : 2.794 ------------------------------------------------------------------------------- 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 55 ILE Chi-restraints excluded: chain A residue 77 GLU Chi-restraints excluded: chain A residue 136 ASP 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 138 MET Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain C residue 101 ASP 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 44 ASP Chi-restraints excluded: chain D residue 148 VAL Chi-restraints excluded: chain D residue 152 VAL Chi-restraints excluded: chain D residue 156 ARG Chi-restraints excluded: chain D residue 174 THR Chi-restraints excluded: chain D residue 221 ASP Chi-restraints excluded: chain D residue 269 SER Chi-restraints excluded: chain D residue 286 VAL Chi-restraints excluded: chain D residue 288 GLU Chi-restraints excluded: chain E residue 9 GLU Chi-restraints excluded: chain E residue 123 MET Chi-restraints excluded: chain E residue 171 ASP Chi-restraints excluded: chain E residue 229 MET Chi-restraints excluded: chain E residue 250 LYS Chi-restraints excluded: chain E residue 257 VAL Chi-restraints excluded: chain E residue 279 GLN Chi-restraints excluded: chain F residue 63 GLU Chi-restraints excluded: chain F residue 180 ILE 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 138 MET Chi-restraints excluded: chain H residue 44 ASP Chi-restraints excluded: chain H residue 70 GLN 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 214 VAL Chi-restraints excluded: chain I residue 258 ASN Chi-restraints excluded: chain I residue 379 ASP Chi-restraints excluded: chain I residue 390 ILE Chi-restraints excluded: chain I residue 606 THR Chi-restraints excluded: chain J residue 38 ASP 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 304 random chunks: chunk 181 optimal weight: 0.9990 chunk 117 optimal weight: 0.9980 chunk 174 optimal weight: 4.9990 chunk 88 optimal weight: 3.9990 chunk 57 optimal weight: 4.9990 chunk 56 optimal weight: 5.9990 chunk 186 optimal weight: 10.0000 chunk 199 optimal weight: 2.9990 chunk 144 optimal weight: 4.9990 chunk 27 optimal weight: 2.9990 chunk 230 optimal weight: 5.9990 overall best weight: 2.3988 ------------------------------------------------------------------------------- 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 E 70 GLN H 220 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6958 moved from start: 0.3614 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 27011 Z= 0.325 Angle : 0.680 13.461 37126 Z= 0.371 Chirality : 0.048 0.246 4129 Planarity : 0.006 0.044 4384 Dihedral : 19.010 178.594 4948 Min Nonbonded Distance : 2.149 Molprobity Statistics. All-atom Clashscore : 4.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.24 % Favored : 95.76 % Rotamer: Outliers : 3.54 % Allowed : 16.04 % 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: -0.50 (0.15), residues: 2925 helix: 1.12 (0.18), residues: 924 sheet: 1.07 (0.22), residues: 500 loop : -1.87 (0.14), residues: 1501 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP H 108 HIS 0.007 0.001 HIS I 541 PHE 0.018 0.002 PHE J 105 TYR 0.020 0.002 TYR F 8 ARG 0.004 0.001 ARG K 72 *********************** 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 263 residues out of total 2489 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 88 poor density : 175 time to evaluate : 2.880 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 77 GLU cc_start: 0.7518 (OUTLIER) cc_final: 0.6171 (mt-10) REVERT: A 131 LYS cc_start: 0.7839 (ptpt) cc_final: 0.7093 (ptmm) REVERT: A 140 LYS cc_start: 0.8021 (mmpt) cc_final: 0.7574 (pttt) REVERT: A 143 ASP cc_start: 0.7868 (m-30) cc_final: 0.7575 (t0) REVERT: B 30 MET cc_start: 0.7571 (mmt) cc_final: 0.7232 (mtp) REVERT: B 240 GLN cc_start: 0.7816 (tp40) cc_final: 0.7507 (tt0) REVERT: C 30 MET cc_start: 0.8174 (mtt) cc_final: 0.7920 (mtp) REVERT: C 226 ARG cc_start: 0.7987 (OUTLIER) cc_final: 0.7708 (ttp-170) REVERT: D 9 GLU cc_start: 0.8342 (OUTLIER) cc_final: 0.7025 (mm-30) REVERT: D 156 ARG cc_start: 0.7912 (OUTLIER) cc_final: 0.7483 (ttt180) REVERT: E 9 GLU cc_start: 0.8456 (OUTLIER) cc_final: 0.7911 (mp0) REVERT: E 80 GLU cc_start: 0.7649 (tt0) cc_final: 0.7214 (mt-10) REVERT: E 109 MET cc_start: 0.5705 (mtm) cc_final: 0.4227 (mmp) REVERT: E 250 LYS cc_start: 0.7709 (OUTLIER) cc_final: 0.7351 (mmtp) REVERT: F 1 MET cc_start: 0.4218 (mtm) cc_final: 0.3527 (ttm) REVERT: F 63 GLU cc_start: 0.7562 (OUTLIER) cc_final: 0.7042 (tt0) REVERT: F 180 ILE cc_start: 0.7824 (OUTLIER) cc_final: 0.7547 (pt) REVERT: F 240 GLN cc_start: 0.7460 (mm110) cc_final: 0.7179 (mm110) REVERT: F 279 GLN cc_start: 0.7879 (mm110) cc_final: 0.7331 (tt0) REVERT: G 89 LYS cc_start: 0.7547 (mppt) cc_final: 0.6979 (tptp) REVERT: G 138 MET cc_start: 0.8368 (OUTLIER) cc_final: 0.7724 (ptm) REVERT: H 30 MET cc_start: 0.6206 (mmt) cc_final: 0.5834 (mmm) REVERT: H 175 MET cc_start: 0.2038 (mtp) cc_final: 0.0548 (tpp) REVERT: I 63 LEU cc_start: 0.6016 (OUTLIER) cc_final: 0.5737 (tp) REVERT: I 202 LYS cc_start: 0.7302 (mptt) cc_final: 0.6806 (mmmt) REVERT: I 231 GLU cc_start: 0.6625 (pt0) cc_final: 0.6197 (tt0) REVERT: I 399 GLU cc_start: 0.7000 (tt0) cc_final: 0.6470 (tm-30) REVERT: I 452 GLU cc_start: 0.7203 (mm-30) cc_final: 0.6901 (mm-30) REVERT: J 58 ASN cc_start: 0.6589 (m-40) cc_final: 0.6284 (t0) REVERT: J 82 MET cc_start: 0.6013 (OUTLIER) cc_final: 0.5628 (mtp) REVERT: J 113 ARG cc_start: 0.7126 (OUTLIER) cc_final: 0.6881 (ttm-80) REVERT: K 26 GLU cc_start: 0.6859 (tp30) cc_final: 0.6311 (mt-10) outliers start: 88 outliers final: 48 residues processed: 239 average time/residue: 1.5860 time to fit residues: 433.0148 Evaluate side-chains 230 residues out of total 2489 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 170 time to evaluate : 2.576 ------------------------------------------------------------------------------- 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 55 ILE Chi-restraints excluded: chain A residue 77 GLU Chi-restraints excluded: chain A residue 170 GLU Chi-restraints excluded: chain A residue 179 SER Chi-restraints excluded: chain A residue 191 MET Chi-restraints excluded: chain B residue 45 VAL Chi-restraints excluded: chain B residue 124 THR Chi-restraints excluded: chain B residue 127 VAL 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 284 VAL Chi-restraints excluded: chain C residue 101 ASP 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 44 ASP Chi-restraints excluded: chain D residue 148 VAL Chi-restraints excluded: chain D residue 152 VAL Chi-restraints excluded: chain D residue 156 ARG Chi-restraints excluded: chain D residue 174 THR Chi-restraints excluded: chain D residue 269 SER Chi-restraints excluded: chain D residue 286 VAL Chi-restraints excluded: chain D residue 288 GLU Chi-restraints excluded: chain E residue 9 GLU Chi-restraints excluded: chain E residue 58 THR Chi-restraints excluded: chain E residue 171 ASP Chi-restraints excluded: chain E residue 174 THR Chi-restraints excluded: chain E residue 229 MET Chi-restraints excluded: chain E residue 250 LYS Chi-restraints excluded: chain E residue 257 VAL Chi-restraints excluded: chain F residue 63 GLU Chi-restraints excluded: chain F residue 180 ILE Chi-restraints excluded: chain F residue 257 VAL Chi-restraints excluded: chain F residue 286 VAL Chi-restraints excluded: chain G residue 138 MET Chi-restraints excluded: chain G residue 203 SER Chi-restraints excluded: chain H residue 44 ASP 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 94 LYS Chi-restraints excluded: chain I residue 148 ILE Chi-restraints excluded: chain I residue 149 VAL Chi-restraints excluded: chain I residue 214 VAL Chi-restraints excluded: chain I residue 258 ASN Chi-restraints excluded: chain I residue 379 ASP Chi-restraints excluded: chain I residue 390 ILE Chi-restraints excluded: chain I residue 606 THR Chi-restraints excluded: chain J residue 38 ASP 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 304 random chunks: chunk 266 optimal weight: 4.9990 chunk 280 optimal weight: 5.9990 chunk 256 optimal weight: 0.0770 chunk 273 optimal weight: 3.9990 chunk 164 optimal weight: 0.8980 chunk 118 optimal weight: 0.8980 chunk 214 optimal weight: 1.9990 chunk 83 optimal weight: 3.9990 chunk 246 optimal weight: 7.9990 chunk 258 optimal weight: 0.4980 chunk 272 optimal weight: 0.9980 overall best weight: 0.6738 ------------------------------------------------------------------------------- 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 E 70 GLN G 29 ASN G 54 HIS G 220 HIS H 66 ASN ** H 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 220 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6884 moved from start: 0.3676 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 27011 Z= 0.152 Angle : 0.544 10.654 37126 Z= 0.297 Chirality : 0.043 0.214 4129 Planarity : 0.004 0.043 4384 Dihedral : 19.037 179.202 4948 Min Nonbonded Distance : 2.175 Molprobity Statistics. All-atom Clashscore : 4.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % Rotamer: Outliers : 2.21 % Allowed : 17.48 % Favored : 80.31 % 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: -0.17 (0.15), residues: 2925 helix: 1.56 (0.18), residues: 922 sheet: 0.74 (0.21), residues: 577 loop : -1.70 (0.14), residues: 1426 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP H 108 HIS 0.005 0.001 HIS H 220 PHE 0.027 0.001 PHE I 283 TYR 0.014 0.001 TYR I 246 ARG 0.003 0.000 ARG G 177 *********************** 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 238 residues out of total 2489 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 183 time to evaluate : 2.863 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 77 GLU cc_start: 0.7244 (OUTLIER) cc_final: 0.5866 (mt-10) REVERT: A 131 LYS cc_start: 0.7792 (ptpt) cc_final: 0.7072 (ptmm) REVERT: A 140 LYS cc_start: 0.7938 (mmpt) cc_final: 0.7593 (ptmt) REVERT: A 143 ASP cc_start: 0.7850 (m-30) cc_final: 0.7568 (t0) REVERT: B 30 MET cc_start: 0.7536 (mmt) cc_final: 0.7239 (mtp) REVERT: B 240 GLN cc_start: 0.7763 (tp40) cc_final: 0.7485 (tt0) REVERT: C 30 MET cc_start: 0.8148 (mtt) cc_final: 0.7928 (mtp) REVERT: C 226 ARG cc_start: 0.7872 (OUTLIER) cc_final: 0.7510 (ttp-170) REVERT: D 9 GLU cc_start: 0.8254 (OUTLIER) cc_final: 0.6951 (mm-30) REVERT: E 9 GLU cc_start: 0.8273 (OUTLIER) cc_final: 0.7893 (mp0) REVERT: E 80 GLU cc_start: 0.7624 (tt0) cc_final: 0.7247 (mt-10) REVERT: E 109 MET cc_start: 0.5413 (mtm) cc_final: 0.4017 (mmm) REVERT: E 250 LYS cc_start: 0.7608 (OUTLIER) cc_final: 0.7359 (mttt) REVERT: F 63 GLU cc_start: 0.7458 (OUTLIER) cc_final: 0.6948 (tt0) REVERT: F 180 ILE cc_start: 0.7992 (OUTLIER) cc_final: 0.7763 (pt) REVERT: F 240 GLN cc_start: 0.7488 (mm110) cc_final: 0.7212 (mm110) REVERT: F 279 GLN cc_start: 0.7565 (mm110) cc_final: 0.6916 (tt0) REVERT: G 89 LYS cc_start: 0.7562 (mppt) cc_final: 0.7026 (tptp) REVERT: G 138 MET cc_start: 0.8364 (OUTLIER) cc_final: 0.7734 (ptm) REVERT: H 30 MET cc_start: 0.6154 (mmt) cc_final: 0.5787 (mmm) REVERT: H 175 MET cc_start: 0.2059 (mtp) cc_final: 0.0708 (tpp) REVERT: H 240 GLN cc_start: 0.8555 (tt0) cc_final: 0.8109 (mm-40) REVERT: I 94 LYS cc_start: 0.6251 (OUTLIER) cc_final: 0.6007 (mttt) REVERT: I 202 LYS cc_start: 0.7229 (mptt) cc_final: 0.6739 (mmmt) REVERT: I 231 GLU cc_start: 0.6408 (pt0) cc_final: 0.6016 (tt0) REVERT: I 399 GLU cc_start: 0.7002 (tt0) cc_final: 0.6452 (tm-30) REVERT: I 452 GLU cc_start: 0.7068 (mm-30) cc_final: 0.6700 (mm-30) REVERT: J 50 GLN cc_start: 0.7568 (mm-40) cc_final: 0.7256 (mm110) REVERT: J 58 ASN cc_start: 0.6536 (m-40) cc_final: 0.6230 (t0) REVERT: J 82 MET cc_start: 0.5804 (OUTLIER) cc_final: 0.5521 (mtp) REVERT: K 26 GLU cc_start: 0.6684 (tp30) cc_final: 0.6007 (mt-10) outliers start: 55 outliers final: 32 residues processed: 223 average time/residue: 1.6541 time to fit residues: 418.5862 Evaluate side-chains 216 residues out of total 2489 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 174 time to evaluate : 2.663 ------------------------------------------------------------------------------- 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 77 GLU Chi-restraints excluded: chain A residue 170 GLU Chi-restraints excluded: chain A residue 191 MET Chi-restraints excluded: chain A residue 213 ASP Chi-restraints excluded: chain A residue 216 THR 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 C residue 101 ASP 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 174 THR Chi-restraints excluded: chain D residue 286 VAL Chi-restraints excluded: chain D residue 288 GLU Chi-restraints excluded: chain E residue 9 GLU Chi-restraints excluded: chain E residue 171 ASP Chi-restraints excluded: chain E residue 174 THR Chi-restraints excluded: chain E residue 250 LYS Chi-restraints excluded: chain E residue 257 VAL Chi-restraints excluded: chain F residue 63 GLU Chi-restraints excluded: chain F residue 180 ILE Chi-restraints excluded: chain F residue 257 VAL Chi-restraints excluded: chain F residue 286 VAL Chi-restraints excluded: chain G residue 138 MET Chi-restraints excluded: chain H residue 16 VAL Chi-restraints excluded: chain H residue 44 ASP Chi-restraints excluded: chain I residue 94 LYS Chi-restraints excluded: chain I residue 148 ILE Chi-restraints excluded: chain I residue 149 VAL Chi-restraints excluded: chain I residue 214 VAL Chi-restraints excluded: chain I residue 258 ASN Chi-restraints excluded: chain I residue 379 ASP Chi-restraints excluded: chain I residue 390 ILE 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 304 random chunks: chunk 179 optimal weight: 3.9990 chunk 288 optimal weight: 3.9990 chunk 176 optimal weight: 10.0000 chunk 136 optimal weight: 0.7980 chunk 200 optimal weight: 0.9990 chunk 302 optimal weight: 4.9990 chunk 278 optimal weight: 4.9990 chunk 241 optimal weight: 0.9990 chunk 25 optimal weight: 4.9990 chunk 186 optimal weight: 2.9990 chunk 147 optimal weight: 0.0670 overall best weight: 1.1724 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 79 HIS D 279 GLN G 279 GLN ** H 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 220 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6908 moved from start: 0.3703 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= 0.194 Angle : 0.569 11.357 37126 Z= 0.310 Chirality : 0.044 0.222 4129 Planarity : 0.005 0.044 4384 Dihedral : 18.971 179.795 4948 Min Nonbonded Distance : 2.188 Molprobity Statistics. All-atom Clashscore : 4.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.93 % Favored : 96.07 % Rotamer: Outliers : 2.21 % Allowed : 17.56 % Favored : 80.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.16 (0.15), residues: 2925 helix: 1.56 (0.18), residues: 921 sheet: 0.76 (0.21), residues: 579 loop : -1.69 (0.15), residues: 1425 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP H 108 HIS 0.005 0.001 HIS I 541 PHE 0.012 0.001 PHE J 105 TYR 0.015 0.001 TYR I 246 ARG 0.003 0.000 ARG G 177 ********************** 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 234 residues out of total 2489 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 179 time to evaluate : 2.903 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 77 GLU cc_start: 0.7269 (OUTLIER) cc_final: 0.5911 (mt-10) REVERT: A 131 LYS cc_start: 0.7796 (ptpt) cc_final: 0.7079 (ptmm) REVERT: A 140 LYS cc_start: 0.7943 (mmpt) cc_final: 0.7639 (ptmt) REVERT: B 30 MET cc_start: 0.7639 (mmt) cc_final: 0.7249 (mtp) REVERT: B 240 GLN cc_start: 0.7789 (tp40) cc_final: 0.7508 (tt0) REVERT: C 30 MET cc_start: 0.8153 (mtt) cc_final: 0.7930 (mtp) REVERT: C 94 LYS cc_start: 0.7154 (mttt) cc_final: 0.6588 (mmtt) REVERT: C 226 ARG cc_start: 0.7891 (OUTLIER) cc_final: 0.7521 (ttp-170) REVERT: D 9 GLU cc_start: 0.8283 (OUTLIER) cc_final: 0.7012 (mm-30) REVERT: D 156 ARG cc_start: 0.7761 (OUTLIER) cc_final: 0.7340 (ttt180) REVERT: E 9 GLU cc_start: 0.8316 (OUTLIER) cc_final: 0.7930 (mp0) REVERT: E 80 GLU cc_start: 0.7632 (tt0) cc_final: 0.7254 (mt-10) REVERT: E 109 MET cc_start: 0.5460 (mtm) cc_final: 0.3981 (mmm) REVERT: E 250 LYS cc_start: 0.7625 (OUTLIER) cc_final: 0.7372 (mttt) REVERT: F 63 GLU cc_start: 0.7485 (OUTLIER) cc_final: 0.6942 (tt0) REVERT: F 138 MET cc_start: 0.8911 (mtm) cc_final: 0.8638 (mtp) REVERT: F 180 ILE cc_start: 0.8078 (OUTLIER) cc_final: 0.7810 (pt) REVERT: F 240 GLN cc_start: 0.7487 (mm110) cc_final: 0.7219 (mm110) REVERT: F 279 GLN cc_start: 0.7622 (mm110) cc_final: 0.6976 (tt0) REVERT: G 88 LEU cc_start: 0.5487 (mt) cc_final: 0.5145 (mt) REVERT: G 89 LYS cc_start: 0.7434 (mppt) cc_final: 0.7005 (tptp) REVERT: G 138 MET cc_start: 0.8357 (OUTLIER) cc_final: 0.7723 (ptm) REVERT: H 30 MET cc_start: 0.6232 (mmt) cc_final: 0.5821 (mmm) REVERT: H 175 MET cc_start: 0.2026 (mtp) cc_final: 0.0711 (tpp) REVERT: I 94 LYS cc_start: 0.6263 (OUTLIER) cc_final: 0.6014 (mttt) REVERT: I 202 LYS cc_start: 0.7250 (mptt) cc_final: 0.6755 (mmmt) REVERT: I 231 GLU cc_start: 0.6417 (pt0) cc_final: 0.6023 (tt0) REVERT: I 399 GLU cc_start: 0.6989 (tt0) cc_final: 0.6456 (tm-30) REVERT: I 452 GLU cc_start: 0.7146 (mm-30) cc_final: 0.6793 (mm-30) REVERT: J 50 GLN cc_start: 0.7652 (mm-40) cc_final: 0.7355 (mm-40) REVERT: J 58 ASN cc_start: 0.6579 (m-40) cc_final: 0.6271 (t0) REVERT: J 82 MET cc_start: 0.5965 (OUTLIER) cc_final: 0.5675 (mtp) REVERT: K 26 GLU cc_start: 0.6707 (tp30) cc_final: 0.6071 (mt-10) outliers start: 55 outliers final: 35 residues processed: 219 average time/residue: 1.6375 time to fit residues: 409.8333 Evaluate side-chains 224 residues out of total 2489 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 178 time to evaluate : 2.835 ------------------------------------------------------------------------------- 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 77 GLU Chi-restraints excluded: chain A residue 170 GLU Chi-restraints excluded: chain A residue 191 MET Chi-restraints excluded: chain A residue 213 ASP Chi-restraints excluded: chain A residue 216 THR Chi-restraints excluded: chain B residue 45 VAL 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 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 156 ARG Chi-restraints excluded: chain D residue 174 THR Chi-restraints excluded: chain D residue 286 VAL Chi-restraints excluded: chain D residue 288 GLU Chi-restraints excluded: chain E residue 9 GLU Chi-restraints excluded: chain E residue 171 ASP Chi-restraints excluded: chain E residue 174 THR Chi-restraints excluded: chain E residue 250 LYS Chi-restraints excluded: chain E residue 257 VAL Chi-restraints excluded: chain F residue 63 GLU Chi-restraints excluded: chain F residue 180 ILE Chi-restraints excluded: chain F residue 257 VAL Chi-restraints excluded: chain F residue 286 VAL Chi-restraints excluded: chain G residue 138 MET Chi-restraints excluded: chain H residue 16 VAL Chi-restraints excluded: chain H residue 44 ASP 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 214 VAL Chi-restraints excluded: chain I residue 258 ASN Chi-restraints excluded: chain I residue 379 ASP Chi-restraints excluded: chain I residue 390 ILE 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 304 random chunks: chunk 191 optimal weight: 0.0270 chunk 256 optimal weight: 0.5980 chunk 73 optimal weight: 4.9990 chunk 222 optimal weight: 0.5980 chunk 35 optimal weight: 3.9990 chunk 67 optimal weight: 4.9990 chunk 241 optimal weight: 0.9980 chunk 101 optimal weight: 3.9990 chunk 248 optimal weight: 3.9990 chunk 30 optimal weight: 9.9990 chunk 44 optimal weight: 0.9980 overall best weight: 0.6438 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 79 HIS D 279 GLN ** H 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 220 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3854 r_free = 0.3854 target = 0.134339 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.104725 restraints weight = 42536.100| |-----------------------------------------------------------------------------| r_work (start): 0.3421 rms_B_bonded: 1.92 r_work: 0.3245 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.3141 rms_B_bonded: 4.21 restraints_weight: 0.2500 r_work (final): 0.3141 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8374 moved from start: 0.3795 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= 0.148 Angle : 0.525 9.975 37126 Z= 0.285 Chirality : 0.042 0.212 4129 Planarity : 0.004 0.044 4384 Dihedral : 18.990 179.468 4948 Min Nonbonded Distance : 2.183 Molprobity Statistics. All-atom Clashscore : 4.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.32 % Favored : 96.68 % Rotamer: Outliers : 1.93 % Allowed : 17.85 % Favored : 80.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.70 (0.18), residues: 935 sheet: 0.84 (0.21), residues: 589 loop : -1.58 (0.15), residues: 1401 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP H 108 HIS 0.004 0.001 HIS H 220 PHE 0.023 0.001 PHE I 283 TYR 0.013 0.001 TYR I 246 ARG 0.005 0.000 ARG E 32 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8438.50 seconds wall clock time: 155 minutes 37.15 seconds (9337.15 seconds total)