Starting phenix.real_space_refine on Fri Dec 27 06:19:25 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8dfa_27403/12_2024/8dfa_27403.cif Found real_map, /net/cci-nas-00/data/ceres_data/8dfa_27403/12_2024/8dfa_27403.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8dfa_27403/12_2024/8dfa_27403.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8dfa_27403/12_2024/8dfa_27403.map" model { file = "/net/cci-nas-00/data/ceres_data/8dfa_27403/12_2024/8dfa_27403.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8dfa_27403/12_2024/8dfa_27403.cif" } resolution = 2.8 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.002 sd= 0.171 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: 6 Type Number sf(0) Gaussians P 63 5.49 5 S 132 5.16 5 C 14740 2.51 5 N 4256 2.21 5 O 4599 1.98 5 H 23023 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 206 residue(s): 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/chem_data/mon_lib" Total number of atoms: 46813 Number of models: 1 Model: "" Number of chains: 13 Chain: "A" Number of atoms: 3535 Number of conformers: 1 Conformer: "" Number of residues, atoms: 220, 3535 Classifications: {'peptide': 220} Link IDs: {'PTRANS': 16, 'TRANS': 203} Chain: "B" Number of atoms: 4193 Number of conformers: 1 Conformer: "" Number of residues, atoms: 270, 4193 Classifications: {'peptide': 270} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 12, 'TRANS': 257} Chain breaks: 2 Chain: "C" Number of atoms: 4462 Number of conformers: 1 Conformer: "" Number of residues, atoms: 286, 4462 Classifications: {'peptide': 286} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 15, 'TRANS': 270} Chain breaks: 1 Chain: "D" Number of atoms: 4462 Number of conformers: 1 Conformer: "" Number of residues, atoms: 286, 4462 Classifications: {'peptide': 286} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 15, 'TRANS': 270} Chain breaks: 1 Chain: "E" Number of atoms: 4462 Number of conformers: 1 Conformer: "" Number of residues, atoms: 286, 4462 Classifications: {'peptide': 286} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 15, 'TRANS': 270} Chain breaks: 1 Chain: "F" Number of atoms: 4462 Number of conformers: 1 Conformer: "" Number of residues, atoms: 286, 4462 Classifications: {'peptide': 286} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 15, 'TRANS': 270} Chain breaks: 1 Chain: "G" Number of atoms: 4462 Number of conformers: 1 Conformer: "" Number of residues, atoms: 286, 4462 Classifications: {'peptide': 286} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 15, 'TRANS': 270} Chain breaks: 1 Chain: "H" Number of atoms: 4462 Number of conformers: 1 Conformer: "" Number of residues, atoms: 286, 4462 Classifications: {'peptide': 286} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 15, 'TRANS': 270} Chain breaks: 1 Chain: "I" Number of atoms: 6536 Number of conformers: 1 Conformer: "" Number of residues, atoms: 415, 6536 Classifications: {'peptide': 415} Link IDs: {'PTRANS': 26, 'TRANS': 388} Chain breaks: 4 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 2 Chain: "J" Number of atoms: 1863 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 1863 Classifications: {'peptide': 117} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 6, 'TRANS': 110} Chain breaks: 2 Chain: "K" Number of atoms: 1863 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 1863 Classifications: {'peptide': 117} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 6, 'TRANS': 110} Chain breaks: 1 Chain: "L" Number of atoms: 1480 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 1480 Classifications: {'RNA': 46} Modifications used: {'3*END': 1, '5*END': 1, 'rna2p_pur': 11, 'rna2p_pyr': 10, 'rna3p_pur': 13, 'rna3p_pyr': 12} Link IDs: {'rna2p': 21, 'rna3p': 24} Chain: "N" Number of atoms: 571 Number of conformers: 1 Conformer: "" Number of residues, atoms: 18, 571 Classifications: {'DNA': 18} Modifications used: {'3*END': 1} Link IDs: {'rna3p': 17} Time building chain proxies: 16.78, per 1000 atoms: 0.36 Number of scatterers: 46813 At special positions: 0 Unit cell: (119.9, 119.9, 211.2, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 132 16.00 P 63 15.00 O 4599 8.00 N 4256 7.00 C 14740 6.00 H 23023 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 9.18 Conformation dependent library (CDL) restraints added in 2.8 seconds 5596 Ramachandran restraints generated. 2798 Oldfield, 0 Emsley, 2798 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5350 Finding SS restraints... Secondary structure from input PDB file: 102 helices and 35 sheets defined 37.6% alpha, 21.8% beta 13 base pairs and 23 stacking pairs defined. Time for finding SS restraints: 16.06 Creating SS restraints... Processing helix chain 'A' and resid 38 through 48 removed outlier: 3.622A pdb=" N ALA A 48 " --> pdb=" O GLY A 44 " (cutoff:3.500A) Processing helix chain 'A' and resid 86 through 93 removed outlier: 3.576A pdb=" N MET A 91 " --> pdb=" O PRO A 87 " (cutoff:3.500A) 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: 3.608A pdb=" N HIS A 141 " --> pdb=" O ASN A 137 " (cutoff:3.500A) Processing helix chain 'A' and resid 222 through 227 removed outlier: 3.539A pdb=" N ALA A 227 " --> pdb=" O GLU A 224 " (cutoff:3.500A) Processing helix chain 'B' and resid 44 through 60 removed outlier: 3.661A pdb=" N LYS B 50 " --> pdb=" O CYS B 46 " (cutoff:3.500A) Processing helix chain 'B' and resid 102 through 113 removed outlier: 3.724A pdb=" N ASN B 112 " --> pdb=" O TRP B 108 " (cutoff:3.500A) Processing helix chain 'B' and resid 113 through 120 Processing helix chain 'B' and resid 193 through 199 removed outlier: 3.758A pdb=" N LYS B 199 " --> pdb=" O PRO B 195 " (cutoff:3.500A) Processing helix chain 'B' and resid 203 through 217 Processing helix chain 'B' and resid 218 through 221 Processing helix chain 'B' and resid 247 through 254 removed outlier: 3.551A pdb=" N LEU B 251 " --> pdb=" O PRO B 247 " (cutoff:3.500A) removed outlier: 4.097A pdb=" N ASP B 253 " --> pdb=" O HIS B 249 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N LEU B 254 " --> pdb=" O LYS B 250 " (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: 3.885A pdb=" N LEU C 47 " --> pdb=" O THR C 43 " (cutoff:3.500A) Processing helix chain 'C' and resid 74 through 86 removed outlier: 4.418A pdb=" N THR C 78 " --> pdb=" O ILE C 74 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N HIS C 79 " --> pdb=" O LEU C 75 " (cutoff:3.500A) Processing helix chain 'C' and resid 101 through 113 removed outlier: 3.524A 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 199 removed outlier: 3.687A pdb=" N LYS C 199 " --> pdb=" O PRO C 195 " (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: 3.602A 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: 3.889A pdb=" N LEU D 47 " --> pdb=" O THR D 43 " (cutoff:3.500A) Processing helix chain 'D' and resid 74 through 86 removed outlier: 4.356A pdb=" N THR D 78 " --> pdb=" O ILE D 74 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N HIS D 79 " --> pdb=" O LEU D 75 " (cutoff:3.500A) Processing helix chain 'D' and resid 98 through 113 removed outlier: 4.126A pdb=" N THR D 106 " --> pdb=" O ALA D 102 " (cutoff:3.500A) removed outlier: 4.591A pdb=" N MET D 109 " --> pdb=" O VAL D 105 " (cutoff:3.500A) Processing helix chain 'D' and resid 113 through 120 Processing helix chain 'D' and resid 193 through 199 removed outlier: 3.809A pdb=" N LYS D 199 " --> pdb=" O PRO D 195 " (cutoff:3.500A) Processing helix chain 'D' and resid 203 through 216 Processing helix chain 'D' and resid 217 through 221 removed outlier: 3.985A pdb=" N HIS D 220 " --> pdb=" O MET D 217 " (cutoff:3.500A) Processing helix chain 'D' and resid 247 through 253 removed outlier: 3.644A 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: 3.836A pdb=" N LEU E 47 " --> pdb=" O THR E 43 " (cutoff:3.500A) Processing helix chain 'E' and resid 74 through 86 removed outlier: 3.774A 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 Processing helix chain 'E' and resid 193 through 201 removed outlier: 3.669A pdb=" N LYS E 199 " --> pdb=" O PRO E 195 " (cutoff:3.500A) removed outlier: 3.616A 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 221 removed outlier: 3.920A pdb=" N HIS E 220 " --> pdb=" O MET E 217 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N ASP E 221 " --> pdb=" O PHE E 218 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 217 through 221' Processing helix chain 'E' and resid 247 through 253 removed outlier: 3.626A pdb=" N LEU E 251 " --> pdb=" O PRO E 247 " (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: 3.937A pdb=" N LEU F 47 " --> pdb=" O THR F 43 " (cutoff:3.500A) Processing helix chain 'F' and resid 74 through 86 Processing helix chain 'F' and resid 99 through 113 Processing helix chain 'F' and resid 113 through 120 Processing helix chain 'F' and resid 193 through 201 removed outlier: 3.535A 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: 3.981A pdb=" N HIS F 220 " --> pdb=" O MET F 217 " (cutoff:3.500A) Processing helix chain 'F' and resid 247 through 254 removed outlier: 3.537A pdb=" N LEU F 254 " --> pdb=" O LYS F 250 " (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: 4.069A pdb=" N LEU G 47 " --> pdb=" O THR G 43 " (cutoff:3.500A) Processing helix chain 'G' and resid 74 through 85 removed outlier: 3.562A pdb=" N ALA G 85 " --> pdb=" O ARG G 81 " (cutoff:3.500A) Processing helix chain 'G' and resid 98 through 111 Processing helix chain 'G' and resid 113 through 119 Processing helix chain 'G' and resid 193 through 201 Processing helix chain 'G' and resid 203 through 217 Processing helix chain 'G' and resid 218 through 221 Processing helix chain 'G' and resid 247 through 254 removed outlier: 3.557A pdb=" N LEU G 251 " --> pdb=" O PRO G 247 " (cutoff:3.500A) removed outlier: 3.555A 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 25 through 28 Processing helix chain 'H' and resid 45 through 59 removed outlier: 4.294A pdb=" N ARG H 49 " --> pdb=" O VAL H 45 " (cutoff:3.500A) removed outlier: 4.457A pdb=" N LYS H 50 " --> pdb=" O CYS H 46 " (cutoff:3.500A) Processing helix chain 'H' and resid 62 through 66 removed outlier: 3.607A pdb=" N ASN H 66 " --> pdb=" O GLU H 63 " (cutoff:3.500A) Processing helix chain 'H' and resid 75 through 86 removed outlier: 4.202A pdb=" N HIS H 79 " --> pdb=" O LEU H 75 " (cutoff:3.500A) Processing helix chain 'H' and resid 98 through 113 Processing helix chain 'H' and resid 113 through 119 Processing helix chain 'H' and resid 193 through 201 removed outlier: 3.671A pdb=" N LYS H 199 " --> pdb=" O PRO H 195 " (cutoff:3.500A) Processing helix chain 'H' and resid 203 through 217 Processing helix chain 'H' and resid 218 through 221 Processing helix chain 'H' and resid 247 through 254 removed outlier: 3.532A pdb=" N LEU H 251 " --> pdb=" O PRO H 247 " (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: 3.549A pdb=" N MET I 13 " --> pdb=" O TYR I 9 " (cutoff:3.500A) removed outlier: 4.261A pdb=" N ALA I 15 " --> pdb=" O GLN I 11 " (cutoff:3.500A) 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 254 Processing helix chain 'I' and resid 278 through 287 removed outlier: 3.601A pdb=" N ALA I 284 " --> pdb=" O GLU I 280 " (cutoff:3.500A) removed outlier: 4.335A pdb=" N GLY I 285 " --> pdb=" O ASP I 281 " (cutoff:3.500A) Processing helix chain 'I' and resid 327 through 336 Processing helix chain 'I' and resid 338 through 342 Processing helix chain 'I' and resid 373 through 389 removed outlier: 3.595A pdb=" N ASP I 379 " --> pdb=" O GLY I 375 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N GLU I 387 " --> pdb=" O ARG I 383 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N LEU I 388 " --> pdb=" O HIS I 384 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N GLU I 389 " --> pdb=" O TYR I 385 " (cutoff:3.500A) Processing helix chain 'I' and resid 402 through 409 removed outlier: 3.695A pdb=" N GLN I 409 " --> pdb=" O THR I 405 " (cutoff:3.500A) Processing helix chain 'I' and resid 420 through 434 Processing helix chain 'I' and resid 440 through 452 removed outlier: 3.676A pdb=" N ALA I 444 " --> pdb=" O SER I 440 " (cutoff:3.500A) Processing helix chain 'I' and resid 455 through 459 Processing helix chain 'I' and resid 468 through 482 removed outlier: 3.531A pdb=" N ALA I 473 " --> pdb=" O TYR I 469 " (cutoff:3.500A) Processing helix chain 'I' and resid 497 through 517 removed outlier: 4.022A pdb=" N GLN I 513 " --> pdb=" O LEU I 509 " (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 557 removed outlier: 3.585A pdb=" N LYS I 545 " --> pdb=" O HIS I 541 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N ASN I 549 " --> pdb=" O LYS I 545 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N HIS I 550 " --> pdb=" O ASN I 546 " (cutoff:3.500A) Processing helix chain 'I' and resid 561 through 561 No H-bonds generated for 'chain 'I' and resid 561 through 561' Processing helix chain 'I' and resid 565 through 577 removed outlier: 3.511A pdb=" N MET I 570 " --> pdb=" O HIS I 566 " (cutoff:3.500A) removed outlier: 4.164A pdb=" N ASN I 577 " --> pdb=" O GLU I 573 " (cutoff:3.500A) Processing helix chain 'I' and resid 592 through 608 removed outlier: 3.976A pdb=" N LYS I 607 " --> pdb=" O ALA I 603 " (cutoff:3.500A) Processing helix chain 'J' and resid 9 through 29 Processing helix chain 'J' and resid 35 through 47 removed outlier: 3.526A pdb=" N ARG J 39 " --> pdb=" O THR J 35 " (cutoff:3.500A) removed outlier: 6.192A pdb=" N ALA J 42 " --> pdb=" O ASP J 38 " (cutoff:3.500A) removed outlier: 5.824A pdb=" N SER J 43 " --> pdb=" O ARG J 39 " (cutoff:3.500A) Processing helix chain 'J' and resid 47 through 68 removed outlier: 3.903A pdb=" N VAL J 51 " --> pdb=" O ASN J 47 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N PHE J 52 " --> pdb=" O PRO J 48 " (cutoff:3.500A) removed outlier: 5.390A pdb=" N HIS J 53 " --> pdb=" O GLY J 49 " (cutoff:3.500A) removed outlier: 4.957A pdb=" N MET J 54 " --> pdb=" O GLN J 50 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N LYS J 57 " --> pdb=" O HIS J 53 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N ASN J 58 " --> pdb=" O MET J 54 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N LYS J 68 " --> pdb=" O ALA J 64 " (cutoff:3.500A) Processing helix chain 'J' and resid 77 through 89 removed outlier: 3.948A pdb=" N ASN J 89 " --> pdb=" O GLU J 85 " (cutoff:3.500A) Processing helix chain 'J' and resid 98 through 100 No H-bonds generated for 'chain 'J' and resid 98 through 100' Processing helix chain 'J' and resid 102 through 118 Processing helix chain 'K' and resid 9 through 29 Processing helix chain 'K' and resid 35 through 47 removed outlier: 6.462A pdb=" N ALA K 42 " --> pdb=" O ASP K 38 " (cutoff:3.500A) removed outlier: 5.933A pdb=" N SER K 43 " --> pdb=" O ARG K 39 " (cutoff:3.500A) Processing helix chain 'K' and resid 47 through 67 removed outlier: 3.599A pdb=" N VAL K 51 " --> pdb=" O ASN K 47 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N HIS K 53 " --> pdb=" O GLY K 49 " (cutoff:3.500A) removed outlier: 4.270A pdb=" N MET K 54 " --> pdb=" O GLN K 50 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N LYS K 57 " --> pdb=" O HIS K 53 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N ASN K 58 " --> pdb=" O MET K 54 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N ARG K 67 " --> pdb=" O THR K 63 " (cutoff:3.500A) Processing helix chain 'K' and resid 77 through 90 Processing helix chain 'K' and resid 98 through 100 No H-bonds generated for 'chain 'K' and resid 98 through 100' Processing helix chain 'K' and resid 102 through 118 removed outlier: 3.571A pdb=" N ILE K 107 " --> pdb=" O GLY K 103 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N ALA K 115 " --> pdb=" O HIS K 111 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 168 through 171 removed outlier: 3.648A pdb=" N GLY A 17 " --> pdb=" O VAL A 118 " (cutoff:3.500A) removed outlier: 7.708A pdb=" N ASP A 119 " --> pdb=" O VAL A 64 " (cutoff:3.500A) removed outlier: 4.932A pdb=" N VAL A 64 " --> pdb=" O ASP A 119 " (cutoff:3.500A) removed outlier: 6.533A pdb=" N VAL A 121 " --> pdb=" O ILE A 62 " (cutoff:3.500A) removed outlier: 4.523A pdb=" N ILE A 62 " --> pdb=" O VAL A 121 " (cutoff:3.500A) removed outlier: 6.722A pdb=" N GLU A 123 " --> pdb=" O ASP A 60 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 31 through 32 removed outlier: 6.636A 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: 6.393A 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: 7.283A pdb=" N LEU A 188 " --> pdb=" O MET A 210 " (cutoff:3.500A) removed outlier: 8.736A pdb=" N MET A 210 " --> pdb=" O LEU A 188 " (cutoff:3.500A) removed outlier: 5.802A pdb=" N TYR A 190 " --> pdb=" O ALA A 208 " (cutoff:3.500A) removed outlier: 6.244A pdb=" N ALA A 208 " --> pdb=" O TYR A 190 " (cutoff:3.500A) removed outlier: 5.461A pdb=" N LEU A 192 " --> pdb=" O PHE A 206 " (cutoff:3.500A) removed outlier: 5.907A pdb=" N PHE A 206 " --> pdb=" O LEU A 192 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N ASP A 194 " --> pdb=" O LEU A 204 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 41 through 42 Processing sheet with id=AA6, first strand: chain 'B' and resid 136 through 138 removed outlier: 3.500A pdb=" N TYR B 8 " --> pdb=" O ILE B 192 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N LYS B 233 " --> pdb=" O LEU B 13 " (cutoff:3.500A) removed outlier: 6.716A pdb=" N ASP B 15 " --> pdb=" O SER B 231 " (cutoff:3.500A) removed outlier: 5.864A pdb=" N SER B 231 " --> pdb=" O ASP B 15 " (cutoff:3.500A) removed outlier: 7.492A pdb=" N GLU B 17 " --> pdb=" O MET B 229 " (cutoff:3.500A) removed outlier: 5.825A pdb=" N MET B 229 " --> pdb=" O GLU B 17 " (cutoff:3.500A) removed outlier: 5.974A pdb=" N LEU B 234 " --> pdb=" O MET B 289 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 255 through 259 Processing sheet with id=AA8, first strand: chain 'C' and resid 41 through 42 removed outlier: 3.506A pdb=" N VAL C 187 " --> pdb=" O ARG C 142 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 41 through 42 removed outlier: 3.506A pdb=" N VAL C 187 " --> pdb=" O ARG C 142 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N PHE C 14 " --> pdb=" O TYR C 186 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N PHE C 10 " --> pdb=" O GLY C 190 " (cutoff:3.500A) removed outlier: 3.740A 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: 6.189A pdb=" N SER C 231 " --> pdb=" O ASP C 15 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N LEU C 290 " --> pdb=" O LEU C 234 " (cutoff:3.500A) removed outlier: 6.980A pdb=" N VAL C 236 " --> pdb=" O GLU C 288 " (cutoff:3.500A) removed outlier: 5.422A pdb=" N GLU C 288 " --> pdb=" O VAL C 236 " (cutoff:3.500A) removed outlier: 7.266A pdb=" N LYS C 238 " --> pdb=" O VAL C 286 " (cutoff:3.500A) removed outlier: 5.849A pdb=" N VAL C 286 " --> pdb=" O LYS C 238 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 150 through 156 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 Processing sheet with id=AB4, first strand: chain 'D' and resid 136 through 138 removed outlier: 3.650A pdb=" N GLY D 184 " --> pdb=" O VAL D 16 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N PHE D 10 " --> pdb=" O GLY D 190 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N TYR D 8 " --> pdb=" O ILE D 192 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N LYS D 233 " --> pdb=" O LEU D 13 " (cutoff:3.500A) removed outlier: 6.876A pdb=" N ASP D 15 " --> pdb=" O SER D 231 " (cutoff:3.500A) removed outlier: 5.948A pdb=" N SER D 231 " --> pdb=" O ASP D 15 " (cutoff:3.500A) removed outlier: 7.628A pdb=" N GLU D 17 " --> pdb=" O MET D 229 " (cutoff:3.500A) removed outlier: 5.865A 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: 6.415A pdb=" N MET D 123 " --> pdb=" O CYS D 129 " (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 removed outlier: 4.152A pdb=" N THR E 174 " --> pdb=" O ARG E 156 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'E' and resid 136 through 138 removed outlier: 3.609A pdb=" N GLY E 184 " --> pdb=" O VAL E 16 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N GLY E 190 " --> pdb=" O PHE E 10 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N PHE E 10 " --> pdb=" O GLY E 190 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N LYS E 233 " --> pdb=" O LEU E 13 " (cutoff:3.500A) removed outlier: 6.969A pdb=" N ASP E 15 " --> pdb=" O SER E 231 " (cutoff:3.500A) removed outlier: 5.698A pdb=" N SER E 231 " --> pdb=" O ASP E 15 " (cutoff:3.500A) removed outlier: 7.529A pdb=" N GLU E 17 " --> pdb=" O MET E 229 " (cutoff:3.500A) removed outlier: 5.806A pdb=" N MET E 229 " --> pdb=" O GLU E 17 " (cutoff:3.500A) removed outlier: 6.499A pdb=" N LEU E 234 " --> pdb=" O MET E 289 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'E' and resid 122 through 123 removed outlier: 3.718A pdb=" N GLY E 130 " --> pdb=" O MET E 123 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'E' and resid 255 through 259 Processing sheet with id=AC2, first strand: chain 'F' and resid 41 through 42 Processing sheet with id=AC3, first strand: chain 'F' and resid 136 through 138 removed outlier: 3.531A pdb=" N GLN F 137 " --> pdb=" O PHE F 191 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N PHE F 14 " --> pdb=" O TYR F 186 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N LYS F 233 " --> pdb=" O LEU F 13 " (cutoff:3.500A) removed outlier: 6.561A pdb=" N ASP F 15 " --> pdb=" O SER F 231 " (cutoff:3.500A) removed outlier: 5.583A pdb=" N SER F 231 " --> pdb=" O ASP F 15 " (cutoff:3.500A) removed outlier: 7.601A pdb=" N GLU F 17 " --> pdb=" O MET F 229 " (cutoff:3.500A) removed outlier: 5.755A pdb=" N MET F 229 " --> pdb=" O GLU F 17 " (cutoff:3.500A) removed outlier: 6.066A pdb=" N LEU F 234 " --> pdb=" O MET F 289 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'F' and resid 255 through 259 Processing sheet with id=AC5, first strand: chain 'G' and resid 41 through 42 Processing sheet with id=AC6, first strand: chain 'G' and resid 136 through 138 removed outlier: 3.506A pdb=" N GLY G 190 " --> pdb=" O PHE G 10 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N PHE G 10 " --> pdb=" O GLY G 190 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N TYR G 8 " --> pdb=" O ILE G 192 " (cutoff:3.500A) removed outlier: 6.454A pdb=" N ASP G 15 " --> pdb=" O SER G 231 " (cutoff:3.500A) removed outlier: 6.146A pdb=" N SER G 231 " --> pdb=" O ASP G 15 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'G' and resid 120 through 121 Processing sheet with id=AC8, first strand: chain 'G' and resid 158 through 159 Processing sheet with id=AC9, first strand: chain 'G' and resid 255 through 259 Processing sheet with id=AD1, first strand: chain 'H' and resid 41 through 42 Processing sheet with id=AD2, first strand: chain 'H' and resid 41 through 42 removed outlier: 5.482A pdb=" N LEU H 234 " --> pdb=" O MET H 289 " (cutoff:3.500A) removed outlier: 4.646A pdb=" N MET H 289 " --> pdb=" O LEU H 234 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'H' and resid 23 through 24 removed outlier: 4.320A pdb=" N MET H 30 " --> pdb=" O ASP H 24 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'H' and resid 150 through 155 removed outlier: 3.577A pdb=" N ILE H 180 " --> pdb=" O GLN H 150 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N ILE H 154 " --> pdb=" O GLY H 176 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N GLY H 176 " --> pdb=" O ILE H 154 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'H' and resid 255 through 259 Processing sheet with id=AD6, first strand: chain 'I' and resid 181 through 182 Processing sheet with id=AD7, first strand: chain 'I' and resid 201 through 202 Processing sheet with id=AD8, first strand: chain 'I' and resid 261 through 264 removed outlier: 3.524A pdb=" N TRP I 272 " --> pdb=" O HIS I 353 " (cutoff:3.500A) removed outlier: 6.801A pdb=" N VAL I 354 " --> pdb=" O TRP I 369 " (cutoff:3.500A) removed outlier: 4.526A pdb=" N TRP I 369 " --> pdb=" O VAL I 354 " (cutoff:3.500A) removed outlier: 6.977A pdb=" N GLY I 356 " --> pdb=" O ARG I 367 " (cutoff:3.500A) 907 hydrogen bonds defined for protein. 2547 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 34 hydrogen bonds 68 hydrogen bond angles 0 basepair planarities 13 basepair parallelities 23 stacking parallelities Total time for adding SS restraints: 15.04 Time building geometry restraints manager: 11.23 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.22: 23085 1.22 - 1.61: 24071 1.61 - 1.99: 271 1.99 - 2.37: 0 2.37 - 2.76: 3 Bond restraints: 47430 Sorted by residual: bond pdb=" C ASP K 100 " pdb=" N GLU K 101 " ideal model delta sigma weight residual 1.335 2.757 -1.422 1.31e-02 5.83e+03 1.18e+04 bond pdb=" C ASP I 588 " pdb=" N GLU I 589 " ideal model delta sigma weight residual 1.334 2.640 -1.306 1.27e-02 6.20e+03 1.06e+04 bond pdb=" C GLN I 590 " pdb=" N GLY I 591 " ideal model delta sigma weight residual 1.331 2.654 -1.323 1.46e-02 4.69e+03 8.21e+03 bond pdb=" CE1 HIS E 189 " pdb=" NE2 HIS E 189 " ideal model delta sigma weight residual 1.321 1.232 0.089 1.00e-02 1.00e+04 7.95e+01 bond pdb=" CE1 HIS G 239 " pdb=" NE2 HIS G 239 " ideal model delta sigma weight residual 1.321 1.232 0.089 1.00e-02 1.00e+04 7.94e+01 ... (remaining 47425 not shown) Histogram of bond angle deviations from ideal: 0.00 - 20.01: 85683 20.01 - 40.03: 5 40.03 - 60.04: 0 60.04 - 80.05: 2 80.05 - 100.06: 4 Bond angle restraints: 85694 Sorted by residual: angle pdb=" O ASP I 588 " pdb=" C ASP I 588 " pdb=" N GLU I 589 " ideal model delta sigma weight residual 122.12 35.21 86.91 1.06e+00 8.90e-01 6.72e+03 angle pdb=" O ASP K 100 " pdb=" C ASP K 100 " pdb=" N GLU K 101 " ideal model delta sigma weight residual 122.11 30.48 91.63 1.15e+00 7.56e-01 6.35e+03 angle pdb=" O GLN I 590 " pdb=" C GLN I 590 " pdb=" N GLY I 591 " ideal model delta sigma weight residual 122.59 28.03 94.56 1.33e+00 5.65e-01 5.06e+03 angle pdb=" O3' DT N 25 " pdb=" P DG N 26 " pdb=" OP2 DG N 26 " ideal model delta sigma weight residual 108.00 7.94 100.06 3.00e+00 1.11e-01 1.11e+03 angle pdb=" CA ASP I 588 " pdb=" C ASP I 588 " pdb=" N GLU I 589 " ideal model delta sigma weight residual 117.22 89.57 27.65 1.17e+00 7.31e-01 5.58e+02 ... (remaining 85689 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.35: 21271 34.35 - 68.71: 980 68.71 - 103.06: 67 103.06 - 137.42: 2 137.42 - 171.77: 4 Dihedral angle restraints: 22324 sinusoidal: 12739 harmonic: 9585 Sorted by residual: dihedral pdb=" O4' C L 45 " pdb=" C1' C L 45 " pdb=" N1 C L 45 " pdb=" C2 C L 45 " ideal model delta sinusoidal sigma weight residual 200.00 58.44 141.56 1 1.50e+01 4.44e-03 7.61e+01 dihedral pdb=" O4' U L 6 " pdb=" C1' U L 6 " pdb=" N1 U L 6 " pdb=" C2 U L 6 " ideal model delta sinusoidal sigma weight residual 232.00 60.23 171.77 1 1.70e+01 3.46e-03 6.61e+01 dihedral pdb=" C LYS B 72 " pdb=" N LYS B 72 " pdb=" CA LYS B 72 " pdb=" CB LYS B 72 " ideal model delta harmonic sigma weight residual -122.60 -141.50 18.90 0 2.50e+00 1.60e-01 5.71e+01 ... (remaining 22321 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.158: 2317 0.158 - 0.316: 93 0.316 - 0.474: 379 0.474 - 0.631: 757 0.631 - 0.789: 158 Chirality restraints: 3704 Sorted by residual: chirality pdb=" C4' A L 47 " pdb=" C5' A L 47 " pdb=" O4' A L 47 " pdb=" C3' A L 47 " both_signs ideal model delta sigma weight residual False -2.50 -1.71 -0.79 2.00e-01 2.50e+01 1.56e+01 chirality pdb=" CG LEU A 114 " pdb=" CB LEU A 114 " pdb=" CD1 LEU A 114 " pdb=" CD2 LEU A 114 " both_signs ideal model delta sigma weight residual False -2.59 -1.86 -0.73 2.00e-01 2.50e+01 1.34e+01 chirality pdb=" CG LEU A 115 " pdb=" CB LEU A 115 " pdb=" CD1 LEU A 115 " pdb=" CD2 LEU A 115 " both_signs ideal model delta sigma weight residual False -2.59 -1.86 -0.73 2.00e-01 2.50e+01 1.32e+01 ... (remaining 3701 not shown) Planarity restraints: 6865 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASP I 588 " -0.038 2.00e-02 2.50e+03 2.67e-01 7.15e+02 pdb=" N GLU I 589 " 0.447 2.00e-02 2.50e+03 pdb=" CA GLU I 589 " -0.181 2.00e-02 2.50e+03 pdb=" H GLU I 589 " -0.228 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASP K 100 " 0.032 2.00e-02 2.50e+03 2.64e-01 6.98e+02 pdb=" N GLU K 101 " -0.440 2.00e-02 2.50e+03 pdb=" CA GLU K 101 " 0.176 2.00e-02 2.50e+03 pdb=" H GLU K 101 " 0.232 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR G 68 " -0.270 2.00e-02 2.50e+03 1.12e-01 3.76e+02 pdb=" CG TYR G 68 " 0.074 2.00e-02 2.50e+03 pdb=" CD1 TYR G 68 " 0.092 2.00e-02 2.50e+03 pdb=" CD2 TYR G 68 " 0.102 2.00e-02 2.50e+03 pdb=" CE1 TYR G 68 " 0.077 2.00e-02 2.50e+03 pdb=" CE2 TYR G 68 " 0.052 2.00e-02 2.50e+03 pdb=" CZ TYR G 68 " 0.003 2.00e-02 2.50e+03 pdb=" OH TYR G 68 " -0.199 2.00e-02 2.50e+03 pdb=" HD1 TYR G 68 " 0.007 2.00e-02 2.50e+03 pdb=" HD2 TYR G 68 " 0.060 2.00e-02 2.50e+03 pdb=" HE1 TYR G 68 " 0.027 2.00e-02 2.50e+03 pdb=" HE2 TYR G 68 " -0.024 2.00e-02 2.50e+03 ... (remaining 6862 not shown) Histogram of nonbonded interaction distances: 1.44 - 2.07: 1280 2.07 - 2.70: 70120 2.70 - 3.34: 132852 3.34 - 3.97: 168520 3.97 - 4.60: 262439 Nonbonded interactions: 635211 Sorted by model distance: nonbonded pdb=" OD1 ASN I 221 " pdb="HH21 ARG I 363 " model vdw 1.439 2.450 nonbonded pdb=" C3' DT N 25 " pdb=" OP2 DG N 26 " model vdw 1.474 2.480 nonbonded pdb=" OD2 ASP I 580 " pdb="HH22 ARG J 7 " model vdw 1.494 2.450 nonbonded pdb=" H ASN H 66 " pdb=" O ASN H 112 " model vdw 1.499 2.450 nonbonded pdb="HH11 ARG F 64 " pdb=" O THR F 111 " model vdw 1.513 2.450 ... (remaining 635206 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'B' selection = (chain 'C' and (resid 1 through 84 or resid 101 through 290)) selection = (chain 'D' and (resid 1 through 84 or resid 101 through 290)) selection = (chain 'E' and (resid 1 through 84 or resid 101 through 290)) selection = (chain 'F' and (resid 1 through 84 or resid 101 through 290)) selection = (chain 'G' and (resid 1 through 84 or resid 101 through 290)) selection = (chain 'H' and (resid 1 through 84 or resid 101 through 290)) } ncs_group { reference = chain 'J' selection = chain 'K' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.00 max=1.00 mean=0.98 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: 2.280 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: 0.580 Extract box with map and model: 1.250 Check model and map are aligned: 0.240 Set scattering table: 0.320 Process input model: 85.980 Find NCS groups from input model: 1.000 Set up NCS constraints: 0.130 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:10.940 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 102.730 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6379 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 : 0.037 1.422 24407 Z= 2.507 Angle : 2.796 100.064 33297 Z= 1.849 Chirality : 0.318 0.789 3704 Planarity : 0.012 0.161 4139 Dihedral : 16.533 171.774 9528 Min Nonbonded Distance : 1.474 Molprobity Statistics. All-atom Clashscore : 3.88 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.33 % Favored : 94.64 % Rotamer: Outliers : 1.63 % Allowed : 9.41 % Favored : 88.96 % Cbeta Deviations : 12.04 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.30 (0.15), residues: 2798 helix: -0.83 (0.16), residues: 866 sheet: 0.50 (0.22), residues: 480 loop : -1.34 (0.15), residues: 1452 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.135 0.010 TRP G 108 HIS 0.022 0.002 HIS F 79 PHE 0.070 0.007 PHE I 287 TYR 0.250 0.014 TYR G 68 ARG 0.014 0.001 ARG G 226 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5596 Ramachandran restraints generated. 2798 Oldfield, 0 Emsley, 2798 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5596 Ramachandran restraints generated. 2798 Oldfield, 0 Emsley, 2798 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 180 is missing expected H atoms. Skipping. Evaluate side-chains 393 residues out of total 2393 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 354 time to evaluate : 2.706 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 11 ILE cc_start: 0.8160 (mt) cc_final: 0.7590 (pp) REVERT: A 35 ASP cc_start: 0.7189 (m-30) cc_final: 0.6573 (p0) REVERT: A 61 ARG cc_start: 0.7425 (mtt180) cc_final: 0.6825 (mtm-85) REVERT: A 129 THR cc_start: 0.7661 (OUTLIER) cc_final: 0.7425 (p) REVERT: B 123 MET cc_start: 0.7694 (mmm) cc_final: 0.7018 (mmt) REVERT: C 138 MET cc_start: 0.8311 (ptm) cc_final: 0.8043 (ptm) REVERT: C 175 MET cc_start: 0.7357 (mmm) cc_final: 0.6884 (mmm) REVERT: C 264 SER cc_start: 0.6680 (t) cc_final: 0.6300 (p) REVERT: D 157 MET cc_start: 0.6528 (mmp) cc_final: 0.6069 (mmp) REVERT: D 177 ARG cc_start: 0.7507 (mmm-85) cc_final: 0.6814 (ptp90) REVERT: D 289 MET cc_start: 0.5154 (pmm) cc_final: 0.4294 (tmm) REVERT: E 104 ARG cc_start: 0.5816 (mtm-85) cc_final: 0.5029 (tpm170) REVERT: E 109 MET cc_start: 0.4879 (mtt) cc_final: 0.4661 (mmt) REVERT: E 150 GLN cc_start: 0.6045 (mt0) cc_final: 0.5691 (mm-40) REVERT: E 156 ARG cc_start: 0.4582 (ttp80) cc_final: 0.4014 (ttt180) REVERT: F 30 MET cc_start: 0.6296 (mmt) cc_final: 0.6077 (mtm) REVERT: F 179 HIS cc_start: 0.7863 (OUTLIER) cc_final: 0.7658 (m90) REVERT: F 221 ASP cc_start: 0.7222 (t0) cc_final: 0.6905 (t0) REVERT: F 289 MET cc_start: 0.8333 (mmm) cc_final: 0.8008 (mtp) REVERT: G 123 MET cc_start: 0.4871 (pmm) cc_final: 0.3791 (pmm) REVERT: G 142 ARG cc_start: 0.7180 (ptt-90) cc_final: 0.6882 (ttp80) REVERT: G 157 MET cc_start: -0.0245 (OUTLIER) cc_final: -0.0647 (mpt) REVERT: H 47 LEU cc_start: 0.7239 (mt) cc_final: 0.7025 (mm) REVERT: H 87 ASP cc_start: 0.1902 (p0) cc_final: 0.1358 (t0) REVERT: H 112 ASN cc_start: 0.2422 (OUTLIER) cc_final: 0.1377 (p0) REVERT: H 123 MET cc_start: 0.2561 (tmt) cc_final: 0.2256 (tmt) REVERT: H 229 MET cc_start: 0.0169 (mpp) cc_final: -0.0057 (mtm) REVERT: H 289 MET cc_start: 0.5905 (pmm) cc_final: 0.5325 (tpt) REVERT: I 209 ARG cc_start: 0.6614 (ttm170) cc_final: 0.6181 (mtp-110) REVERT: I 231 GLU cc_start: 0.6548 (mt-10) cc_final: 0.6251 (pm20) REVERT: I 326 MET cc_start: 0.4520 (ptt) cc_final: 0.4235 (ptm) REVERT: I 338 ARG cc_start: 0.4444 (mtp85) cc_final: 0.3827 (mtp180) REVERT: I 343 MET cc_start: 0.3263 (mtp) cc_final: 0.2946 (mtp) REVERT: I 346 MET cc_start: 0.4017 (mtp) cc_final: 0.3692 (mtm) REVERT: I 377 MET cc_start: 0.6150 (tmm) cc_final: 0.5389 (tpt) REVERT: I 408 ARG cc_start: 0.5266 (ttm170) cc_final: 0.4929 (mtp180) REVERT: I 588 ASP cc_start: 0.6587 (m-30) cc_final: 0.6355 (m-30) REVERT: I 594 MET cc_start: 0.6028 (mmt) cc_final: 0.5522 (mmt) REVERT: J 26 GLU cc_start: 0.6486 (tp30) cc_final: 0.6050 (mt-10) REVERT: J 33 ASN cc_start: 0.4740 (m110) cc_final: 0.4160 (p0) REVERT: J 82 MET cc_start: 0.5775 (mtt) cc_final: 0.5540 (mtp) REVERT: K 87 ILE cc_start: 0.6907 (tp) cc_final: 0.6651 (mt) REVERT: K 97 MET cc_start: 0.6160 (mtm) cc_final: 0.5864 (mtm) outliers start: 39 outliers final: 14 residues processed: 375 average time/residue: 2.4952 time to fit residues: 1070.7840 Evaluate side-chains 210 residues out of total 2393 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 192 time to evaluate : 2.682 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 129 THR Chi-restraints excluded: chain C residue 83 TYR Chi-restraints excluded: chain C residue 87 ASP Chi-restraints excluded: chain C residue 129 CYS Chi-restraints excluded: chain C residue 191 PHE Chi-restraints excluded: chain D residue 229 MET Chi-restraints excluded: chain E residue 129 CYS Chi-restraints excluded: chain E residue 229 MET Chi-restraints excluded: chain F residue 83 TYR Chi-restraints excluded: chain F residue 122 VAL Chi-restraints excluded: chain F residue 179 HIS Chi-restraints excluded: chain G residue 105 VAL Chi-restraints excluded: chain G residue 157 MET Chi-restraints excluded: chain H residue 105 VAL Chi-restraints excluded: chain H residue 112 ASN Chi-restraints excluded: chain H residue 124 THR Chi-restraints excluded: chain I residue 287 PHE Chi-restraints excluded: chain I residue 402 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 285 random chunks: chunk 240 optimal weight: 0.9990 chunk 216 optimal weight: 5.9990 chunk 119 optimal weight: 0.9990 chunk 73 optimal weight: 0.7980 chunk 145 optimal weight: 5.9990 chunk 115 optimal weight: 0.9990 chunk 223 optimal weight: 0.8980 chunk 86 optimal weight: 2.9990 chunk 135 optimal weight: 0.8980 chunk 166 optimal weight: 0.9990 chunk 258 optimal weight: 0.9980 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 279 GLN D 216 ASN E 6 ASN E 29 ASN F 240 GLN ** G 79 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 6 ASN H 22 ASN ** H 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 79 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 260 GLN K 89 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6426 moved from start: 0.2339 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 24407 Z= 0.215 Angle : 0.702 27.358 33297 Z= 0.375 Chirality : 0.056 1.885 3704 Planarity : 0.005 0.067 4139 Dihedral : 15.213 172.699 4065 Min Nonbonded Distance : 2.261 Molprobity Statistics. All-atom Clashscore : 3.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.71 % Favored : 96.29 % Rotamer: Outliers : 2.17 % Allowed : 12.25 % Favored : 85.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.29 (0.15), residues: 2804 helix: 0.85 (0.17), residues: 906 sheet: 0.67 (0.23), residues: 476 loop : -1.21 (0.15), residues: 1422 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP I 369 HIS 0.011 0.002 HIS G 79 PHE 0.018 0.001 PHE J 105 TYR 0.024 0.002 TYR G 68 ARG 0.006 0.001 ARG F 64 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5608 Ramachandran restraints generated. 2804 Oldfield, 0 Emsley, 2804 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5608 Ramachandran restraints generated. 2804 Oldfield, 0 Emsley, 2804 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 180 is missing expected H atoms. Skipping. Evaluate side-chains 259 residues out of total 2393 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 207 time to evaluate : 2.714 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 11 ILE cc_start: 0.7542 (mt) cc_final: 0.7071 (pp) REVERT: A 30 GLU cc_start: 0.6547 (OUTLIER) cc_final: 0.5829 (mp0) REVERT: A 61 ARG cc_start: 0.7606 (mtt180) cc_final: 0.6969 (mtm-85) REVERT: A 114 LEU cc_start: 0.6443 (OUTLIER) cc_final: 0.5806 (pp) REVERT: A 126 PHE cc_start: 0.7351 (OUTLIER) cc_final: 0.5388 (t80) REVERT: C 64 ARG cc_start: 0.7018 (mtp-110) cc_final: 0.6765 (mtp85) REVERT: C 175 MET cc_start: 0.7385 (mmm) cc_final: 0.6858 (mmm) REVERT: C 177 ARG cc_start: 0.8047 (OUTLIER) cc_final: 0.6819 (ptp-110) REVERT: C 240 GLN cc_start: 0.8448 (tp40) cc_final: 0.8096 (tp40) REVERT: C 264 SER cc_start: 0.7066 (t) cc_final: 0.6615 (p) REVERT: D 157 MET cc_start: 0.6821 (mmp) cc_final: 0.6244 (mmp) REVERT: D 177 ARG cc_start: 0.7672 (mmm-85) cc_final: 0.6929 (ptp90) REVERT: D 253 ASP cc_start: 0.7057 (OUTLIER) cc_final: 0.6770 (p0) REVERT: D 289 MET cc_start: 0.4845 (pmm) cc_final: 0.4008 (tmm) REVERT: E 104 ARG cc_start: 0.5992 (mtm-85) cc_final: 0.5219 (tpm170) REVERT: E 150 GLN cc_start: 0.6096 (mt0) cc_final: 0.5657 (mm-40) REVERT: E 156 ARG cc_start: 0.5202 (ttp80) cc_final: 0.4367 (tpp80) REVERT: F 221 ASP cc_start: 0.7779 (t0) cc_final: 0.7102 (t0) REVERT: F 289 MET cc_start: 0.7952 (mmm) cc_final: 0.7607 (mtp) REVERT: G 175 MET cc_start: 0.2528 (OUTLIER) cc_final: 0.2198 (ptt) REVERT: H 87 ASP cc_start: 0.1432 (p0) cc_final: 0.1053 (t0) REVERT: I 189 GLU cc_start: 0.6450 (OUTLIER) cc_final: 0.5795 (mt-10) REVERT: I 246 TYR cc_start: 0.5527 (OUTLIER) cc_final: 0.4128 (t80) REVERT: I 286 MET cc_start: 0.3835 (mpt) cc_final: 0.3553 (pp-130) REVERT: I 338 ARG cc_start: 0.4287 (mtp85) cc_final: 0.3676 (mtp180) REVERT: I 343 MET cc_start: 0.3579 (mtp) cc_final: 0.3377 (mtp) REVERT: I 377 MET cc_start: 0.6116 (tmm) cc_final: 0.5578 (tpt) REVERT: I 408 ARG cc_start: 0.5301 (ttm170) cc_final: 0.4933 (mtp85) REVERT: I 594 MET cc_start: 0.6238 (mmt) cc_final: 0.5812 (mmt) REVERT: J 26 GLU cc_start: 0.6289 (tp30) cc_final: 0.5831 (mt-10) REVERT: J 33 ASN cc_start: 0.4781 (m110) cc_final: 0.4276 (m-40) REVERT: J 82 MET cc_start: 0.5768 (mtt) cc_final: 0.5545 (ttm) REVERT: J 113 ARG cc_start: 0.6461 (ttt90) cc_final: 0.5854 (ttm-80) REVERT: K 26 GLU cc_start: 0.5924 (tm-30) cc_final: 0.5563 (tp30) REVERT: K 81 ILE cc_start: 0.7045 (OUTLIER) cc_final: 0.6834 (mp) REVERT: K 88 ASP cc_start: 0.7215 (m-30) cc_final: 0.6984 (m-30) REVERT: K 97 MET cc_start: 0.6435 (mtm) cc_final: 0.6060 (mtm) outliers start: 52 outliers final: 14 residues processed: 244 average time/residue: 2.4257 time to fit residues: 680.3238 Evaluate side-chains 200 residues out of total 2393 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 177 time to evaluate : 2.709 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 ASP Chi-restraints excluded: chain A residue 30 GLU Chi-restraints excluded: chain A residue 114 LEU Chi-restraints excluded: chain A residue 126 PHE Chi-restraints excluded: chain A residue 185 LYS Chi-restraints excluded: chain B residue 148 VAL Chi-restraints excluded: chain C residue 83 TYR Chi-restraints excluded: chain C residue 177 ARG Chi-restraints excluded: chain C residue 191 PHE Chi-restraints excluded: chain D residue 160 THR Chi-restraints excluded: chain D residue 253 ASP Chi-restraints excluded: chain F residue 83 TYR Chi-restraints excluded: chain F residue 122 VAL Chi-restraints excluded: chain G residue 175 MET Chi-restraints excluded: chain H residue 30 MET Chi-restraints excluded: chain H residue 49 ARG Chi-restraints excluded: chain I residue 189 GLU Chi-restraints excluded: chain I residue 246 TYR Chi-restraints excluded: chain I residue 287 PHE Chi-restraints excluded: chain I residue 390 ILE Chi-restraints excluded: chain I residue 402 SER Chi-restraints excluded: chain J residue 2 SER Chi-restraints excluded: chain K residue 81 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 285 random chunks: chunk 143 optimal weight: 2.9990 chunk 80 optimal weight: 2.9990 chunk 215 optimal weight: 9.9990 chunk 176 optimal weight: 2.9990 chunk 71 optimal weight: 2.9990 chunk 259 optimal weight: 2.9990 chunk 280 optimal weight: 3.9990 chunk 230 optimal weight: 4.9990 chunk 257 optimal weight: 2.9990 chunk 88 optimal weight: 2.9990 chunk 208 optimal weight: 3.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 70 GLN B 241 ASN C 279 GLN D 216 ASN H 39 HIS ** H 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 79 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6509 moved from start: 0.3282 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.057 24407 Z= 0.403 Angle : 0.784 25.917 33297 Z= 0.426 Chirality : 0.060 1.914 3704 Planarity : 0.007 0.075 4139 Dihedral : 15.149 173.471 4044 Min Nonbonded Distance : 2.254 Molprobity Statistics. All-atom Clashscore : 3.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.99 % Favored : 95.01 % Rotamer: Outliers : 2.51 % Allowed : 12.58 % Favored : 84.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % 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: -0.61 (0.15), residues: 2804 helix: 0.70 (0.17), residues: 900 sheet: 0.66 (0.23), residues: 462 loop : -1.54 (0.15), residues: 1442 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP I 272 HIS 0.015 0.003 HIS H 220 PHE 0.018 0.002 PHE B 202 TYR 0.023 0.003 TYR G 68 ARG 0.008 0.001 ARG D 49 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5608 Ramachandran restraints generated. 2804 Oldfield, 0 Emsley, 2804 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5608 Ramachandran restraints generated. 2804 Oldfield, 0 Emsley, 2804 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 180 is missing expected H atoms. Skipping. Evaluate side-chains 243 residues out of total 2393 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 183 time to evaluate : 2.761 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 11 ILE cc_start: 0.7825 (mt) cc_final: 0.7218 (pp) REVERT: A 30 GLU cc_start: 0.7109 (OUTLIER) cc_final: 0.5942 (mp0) REVERT: A 61 ARG cc_start: 0.7645 (mtt180) cc_final: 0.7083 (mtm-85) REVERT: A 114 LEU cc_start: 0.6358 (OUTLIER) cc_final: 0.5756 (pp) REVERT: A 126 PHE cc_start: 0.7474 (OUTLIER) cc_final: 0.6006 (t80) REVERT: A 129 THR cc_start: 0.7825 (OUTLIER) cc_final: 0.7578 (p) REVERT: A 201 MET cc_start: 0.4629 (OUTLIER) cc_final: 0.3367 (mpt) REVERT: B 1 MET cc_start: 0.3334 (tmt) cc_final: 0.3095 (tmt) REVERT: B 109 MET cc_start: 0.7122 (ttm) cc_final: 0.6828 (ttp) REVERT: C 175 MET cc_start: 0.7438 (mmm) cc_final: 0.7075 (mmm) REVERT: C 264 SER cc_start: 0.6512 (t) cc_final: 0.6113 (p) REVERT: D 9 GLU cc_start: 0.8252 (OUTLIER) cc_final: 0.7976 (mp0) REVERT: D 157 MET cc_start: 0.6759 (mmp) cc_final: 0.6270 (mmp) REVERT: D 177 ARG cc_start: 0.7588 (mmm-85) cc_final: 0.6907 (ptp90) REVERT: D 253 ASP cc_start: 0.7175 (OUTLIER) cc_final: 0.6884 (p0) REVERT: D 289 MET cc_start: 0.5082 (pmm) cc_final: 0.4225 (tmm) REVERT: E 104 ARG cc_start: 0.5898 (mtm-85) cc_final: 0.5310 (tpm170) REVERT: E 150 GLN cc_start: 0.6134 (mt0) cc_final: 0.5786 (mm-40) REVERT: E 156 ARG cc_start: 0.5170 (ttp80) cc_final: 0.4417 (ttt180) REVERT: E 157 MET cc_start: 0.5444 (ttm) cc_final: 0.5227 (ptm) REVERT: F 30 MET cc_start: 0.6720 (mmt) cc_final: 0.6469 (mtt) REVERT: F 221 ASP cc_start: 0.8326 (t0) cc_final: 0.7371 (t70) REVERT: F 253 ASP cc_start: 0.8221 (OUTLIER) cc_final: 0.7882 (t0) REVERT: F 289 MET cc_start: 0.8056 (mmm) cc_final: 0.7816 (mtp) REVERT: H 87 ASP cc_start: 0.1711 (p0) cc_final: 0.1377 (t0) REVERT: I 209 ARG cc_start: 0.7016 (ttm-80) cc_final: 0.6670 (mtp-110) REVERT: I 246 TYR cc_start: 0.6097 (OUTLIER) cc_final: 0.4832 (t80) REVERT: I 346 MET cc_start: 0.5269 (OUTLIER) cc_final: 0.4962 (mtm) REVERT: I 377 MET cc_start: 0.5770 (tmm) cc_final: 0.5467 (tpt) REVERT: I 594 MET cc_start: 0.6300 (mmt) cc_final: 0.5984 (mmt) REVERT: J 26 GLU cc_start: 0.6494 (tp30) cc_final: 0.6158 (mt-10) REVERT: J 33 ASN cc_start: 0.4649 (m110) cc_final: 0.4109 (m110) REVERT: J 82 MET cc_start: 0.5729 (mtt) cc_final: 0.5511 (mtm) REVERT: J 113 ARG cc_start: 0.6455 (ttt90) cc_final: 0.5778 (ttm-80) REVERT: K 88 ASP cc_start: 0.7354 (m-30) cc_final: 0.7087 (m-30) outliers start: 60 outliers final: 21 residues processed: 225 average time/residue: 2.3393 time to fit residues: 607.9269 Evaluate side-chains 195 residues out of total 2393 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 164 time to evaluate : 2.678 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 ASP Chi-restraints excluded: chain A residue 30 GLU Chi-restraints excluded: chain A residue 114 LEU Chi-restraints excluded: chain A residue 126 PHE Chi-restraints excluded: chain A residue 129 THR Chi-restraints excluded: chain A residue 185 LYS Chi-restraints excluded: chain A residue 201 MET Chi-restraints excluded: chain B residue 33 ILE Chi-restraints excluded: chain B residue 148 VAL Chi-restraints excluded: chain B residue 160 THR Chi-restraints excluded: chain B residue 263 SER Chi-restraints excluded: chain C residue 83 TYR Chi-restraints excluded: chain C residue 177 ARG Chi-restraints excluded: chain D residue 9 GLU Chi-restraints excluded: chain D residue 253 ASP Chi-restraints excluded: chain E residue 26 ASP Chi-restraints excluded: chain F residue 83 TYR Chi-restraints excluded: chain F residue 122 VAL Chi-restraints excluded: chain F residue 253 ASP Chi-restraints excluded: chain G residue 138 MET Chi-restraints excluded: chain H residue 49 ARG Chi-restraints excluded: chain I residue 185 LEU Chi-restraints excluded: chain I residue 246 TYR Chi-restraints excluded: chain I residue 287 PHE Chi-restraints excluded: chain I residue 346 MET Chi-restraints excluded: chain I residue 402 SER Chi-restraints excluded: chain I residue 413 LEU Chi-restraints excluded: chain I residue 569 ILE Chi-restraints excluded: chain J residue 36 ILE Chi-restraints excluded: chain K residue 83 MET Chi-restraints excluded: chain K residue 92 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 285 random chunks: chunk 256 optimal weight: 2.9990 chunk 194 optimal weight: 10.0000 chunk 134 optimal weight: 0.9980 chunk 28 optimal weight: 2.9990 chunk 123 optimal weight: 0.9990 chunk 174 optimal weight: 2.9990 chunk 260 optimal weight: 0.7980 chunk 275 optimal weight: 8.9990 chunk 135 optimal weight: 1.9990 chunk 246 optimal weight: 3.9990 chunk 74 optimal weight: 2.9990 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 279 GLN D 216 ASN G 112 ASN H 18 ASN H 20 ASN ** H 79 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 409 GLN I 414 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6481 moved from start: 0.3584 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 24407 Z= 0.233 Angle : 0.653 24.871 33297 Z= 0.346 Chirality : 0.056 1.968 3704 Planarity : 0.005 0.080 4139 Dihedral : 15.112 174.659 4042 Min Nonbonded Distance : 2.342 Molprobity Statistics. All-atom Clashscore : 3.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.85 % Favored : 96.15 % Rotamer: Outliers : 2.26 % Allowed : 13.80 % Favored : 83.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % 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: -0.40 (0.15), residues: 2804 helix: 1.03 (0.17), residues: 893 sheet: 0.70 (0.23), residues: 472 loop : -1.51 (0.15), residues: 1439 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP I 369 HIS 0.009 0.002 HIS G 79 PHE 0.014 0.001 PHE B 202 TYR 0.014 0.002 TYR E 8 ARG 0.005 0.000 ARG I 338 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5608 Ramachandran restraints generated. 2804 Oldfield, 0 Emsley, 2804 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5608 Ramachandran restraints generated. 2804 Oldfield, 0 Emsley, 2804 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 180 is missing expected H atoms. Skipping. Evaluate side-chains 225 residues out of total 2393 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 171 time to evaluate : 2.718 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 11 ILE cc_start: 0.7815 (mt) cc_final: 0.7301 (pp) REVERT: A 30 GLU cc_start: 0.6872 (OUTLIER) cc_final: 0.5740 (mp0) REVERT: A 61 ARG cc_start: 0.7605 (mtt180) cc_final: 0.7009 (mtm-85) REVERT: A 114 LEU cc_start: 0.6300 (OUTLIER) cc_final: 0.5713 (pp) REVERT: A 126 PHE cc_start: 0.7435 (OUTLIER) cc_final: 0.5896 (t80) REVERT: A 129 THR cc_start: 0.7861 (OUTLIER) cc_final: 0.7649 (p) REVERT: A 131 LYS cc_start: 0.8327 (ttmt) cc_final: 0.7984 (ttpp) REVERT: B 1 MET cc_start: 0.2939 (tmt) cc_final: 0.2652 (tmt) REVERT: B 109 MET cc_start: 0.7092 (ttm) cc_final: 0.6781 (ttp) REVERT: C 175 MET cc_start: 0.7550 (mmm) cc_final: 0.7200 (mmm) REVERT: D 157 MET cc_start: 0.6363 (mmp) cc_final: 0.5711 (mmp) REVERT: D 177 ARG cc_start: 0.7595 (mmm-85) cc_final: 0.6922 (ptp90) REVERT: D 253 ASP cc_start: 0.7135 (OUTLIER) cc_final: 0.6895 (p0) REVERT: D 289 MET cc_start: 0.5035 (pmm) cc_final: 0.4179 (tmm) REVERT: E 104 ARG cc_start: 0.6068 (mtm-85) cc_final: 0.5445 (tpm170) REVERT: E 150 GLN cc_start: 0.6086 (mt0) cc_final: 0.5777 (mm-40) REVERT: E 156 ARG cc_start: 0.5020 (ttp80) cc_final: 0.4295 (tpp80) REVERT: E 157 MET cc_start: 0.5629 (ttm) cc_final: 0.5360 (ptm) REVERT: F 30 MET cc_start: 0.6780 (mmt) cc_final: 0.6426 (mtt) REVERT: F 112 ASN cc_start: 0.7425 (OUTLIER) cc_final: 0.7116 (m-40) REVERT: F 289 MET cc_start: 0.7896 (mmm) cc_final: 0.7582 (mtp) REVERT: G 30 MET cc_start: 0.7368 (OUTLIER) cc_final: 0.6733 (mpp) REVERT: H 49 ARG cc_start: 0.5934 (OUTLIER) cc_final: 0.5392 (tmm-80) REVERT: H 87 ASP cc_start: 0.1369 (p0) cc_final: 0.1001 (t0) REVERT: I 4 GLN cc_start: 0.6851 (mp10) cc_final: 0.6152 (mt0) REVERT: I 209 ARG cc_start: 0.7000 (ttm-80) cc_final: 0.6631 (mtp180) REVERT: I 246 TYR cc_start: 0.6038 (OUTLIER) cc_final: 0.4794 (t80) REVERT: I 377 MET cc_start: 0.5640 (tmm) cc_final: 0.5426 (tpt) REVERT: I 594 MET cc_start: 0.6260 (mmt) cc_final: 0.5942 (mmt) REVERT: J 26 GLU cc_start: 0.6428 (tp30) cc_final: 0.6006 (mt-10) REVERT: J 33 ASN cc_start: 0.4718 (m110) cc_final: 0.4141 (m110) REVERT: J 82 MET cc_start: 0.5721 (mtt) cc_final: 0.5493 (mtm) REVERT: J 113 ARG cc_start: 0.6458 (ttt90) cc_final: 0.5780 (ttm-80) REVERT: K 26 GLU cc_start: 0.5822 (tm-30) cc_final: 0.5532 (tp30) REVERT: K 88 ASP cc_start: 0.7382 (m-30) cc_final: 0.7095 (m-30) outliers start: 54 outliers final: 19 residues processed: 209 average time/residue: 2.3404 time to fit residues: 566.4843 Evaluate side-chains 191 residues out of total 2393 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 163 time to evaluate : 2.687 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 ASP Chi-restraints excluded: chain A residue 30 GLU Chi-restraints excluded: chain A residue 114 LEU Chi-restraints excluded: chain A residue 122 ILE Chi-restraints excluded: chain A residue 126 PHE Chi-restraints excluded: chain A residue 129 THR Chi-restraints excluded: chain B residue 33 ILE Chi-restraints excluded: chain B residue 160 THR Chi-restraints excluded: chain C residue 83 TYR Chi-restraints excluded: chain C residue 123 MET Chi-restraints excluded: chain C residue 177 ARG Chi-restraints excluded: chain D residue 160 THR Chi-restraints excluded: chain D residue 253 ASP Chi-restraints excluded: chain E residue 9 GLU Chi-restraints excluded: chain E residue 26 ASP Chi-restraints excluded: chain F residue 83 TYR Chi-restraints excluded: chain F residue 112 ASN Chi-restraints excluded: chain G residue 30 MET Chi-restraints excluded: chain G residue 79 HIS Chi-restraints excluded: chain H residue 49 ARG Chi-restraints excluded: chain I residue 185 LEU Chi-restraints excluded: chain I residue 246 TYR Chi-restraints excluded: chain I residue 287 PHE Chi-restraints excluded: chain I residue 390 ILE Chi-restraints excluded: chain I residue 487 VAL Chi-restraints excluded: chain I residue 569 ILE Chi-restraints excluded: chain J residue 36 ILE Chi-restraints excluded: chain K residue 92 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 285 random chunks: chunk 229 optimal weight: 1.9990 chunk 156 optimal weight: 2.9990 chunk 4 optimal weight: 2.9990 chunk 205 optimal weight: 6.9990 chunk 113 optimal weight: 5.9990 chunk 235 optimal weight: 0.9980 chunk 190 optimal weight: 6.9990 chunk 0 optimal weight: 2.9990 chunk 140 optimal weight: 10.0000 chunk 247 optimal weight: 2.9990 chunk 69 optimal weight: 1.9990 overall best weight: 2.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 279 GLN D 216 ASN ** F 79 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 22 ASN ** H 79 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 599 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6504 moved from start: 0.3859 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 24407 Z= 0.306 Angle : 0.686 24.817 33297 Z= 0.367 Chirality : 0.057 1.978 3704 Planarity : 0.006 0.066 4139 Dihedral : 15.073 178.476 4040 Min Nonbonded Distance : 2.338 Molprobity Statistics. All-atom Clashscore : 2.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.92 % Favored : 95.08 % Rotamer: Outliers : 2.34 % Allowed : 14.21 % Favored : 83.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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: 2804 helix: 0.96 (0.17), residues: 891 sheet: 0.74 (0.23), residues: 464 loop : -1.60 (0.15), residues: 1449 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 16 HIS 0.008 0.002 HIS G 189 PHE 0.016 0.002 PHE B 202 TYR 0.018 0.002 TYR E 8 ARG 0.007 0.001 ARG J 7 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5608 Ramachandran restraints generated. 2804 Oldfield, 0 Emsley, 2804 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5608 Ramachandran restraints generated. 2804 Oldfield, 0 Emsley, 2804 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 180 is missing expected H atoms. Skipping. Evaluate side-chains 223 residues out of total 2393 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 167 time to evaluate : 2.775 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 11 ILE cc_start: 0.7855 (mt) cc_final: 0.7339 (pp) REVERT: A 30 GLU cc_start: 0.7105 (OUTLIER) cc_final: 0.5866 (mp0) REVERT: A 61 ARG cc_start: 0.7649 (mtt180) cc_final: 0.7052 (mtm-85) REVERT: A 114 LEU cc_start: 0.6319 (OUTLIER) cc_final: 0.5711 (pp) REVERT: A 126 PHE cc_start: 0.7527 (OUTLIER) cc_final: 0.5925 (t80) REVERT: A 129 THR cc_start: 0.7871 (OUTLIER) cc_final: 0.7659 (p) REVERT: A 131 LYS cc_start: 0.8326 (ttmt) cc_final: 0.7980 (ttpp) REVERT: B 1 MET cc_start: 0.3319 (tmt) cc_final: 0.2966 (tmt) REVERT: B 67 ILE cc_start: 0.7792 (OUTLIER) cc_final: 0.7565 (mm) REVERT: B 109 MET cc_start: 0.7013 (ttm) cc_final: 0.6737 (ttp) REVERT: C 104 ARG cc_start: 0.4947 (mtm180) cc_final: 0.4446 (mmm160) REVERT: C 175 MET cc_start: 0.7491 (mmm) cc_final: 0.7250 (mmm) REVERT: D 9 GLU cc_start: 0.8206 (OUTLIER) cc_final: 0.7883 (mp0) REVERT: D 157 MET cc_start: 0.6764 (mmp) cc_final: 0.6307 (mmp) REVERT: D 177 ARG cc_start: 0.7528 (mmm-85) cc_final: 0.6936 (ptp90) REVERT: D 253 ASP cc_start: 0.7174 (OUTLIER) cc_final: 0.6907 (p0) REVERT: E 104 ARG cc_start: 0.6027 (mtm-85) cc_final: 0.5396 (tpm170) REVERT: E 150 GLN cc_start: 0.6229 (mt0) cc_final: 0.5939 (mm-40) REVERT: E 156 ARG cc_start: 0.4813 (ttp80) cc_final: 0.3915 (ttt180) REVERT: F 30 MET cc_start: 0.6760 (mmt) cc_final: 0.6346 (mtt) REVERT: F 112 ASN cc_start: 0.7426 (OUTLIER) cc_final: 0.7095 (m-40) REVERT: F 289 MET cc_start: 0.7945 (mmm) cc_final: 0.7717 (mtp) REVERT: G 30 MET cc_start: 0.7385 (OUTLIER) cc_final: 0.6762 (mpp) REVERT: H 87 ASP cc_start: 0.1545 (p0) cc_final: 0.1295 (t0) REVERT: I 209 ARG cc_start: 0.7047 (ttm-80) cc_final: 0.6645 (mtp180) REVERT: I 246 TYR cc_start: 0.6247 (OUTLIER) cc_final: 0.4757 (t80) REVERT: I 594 MET cc_start: 0.6196 (mmt) cc_final: 0.5933 (mmt) REVERT: J 26 GLU cc_start: 0.6376 (tp30) cc_final: 0.5982 (mt-10) REVERT: J 33 ASN cc_start: 0.4619 (m110) cc_final: 0.3965 (m110) REVERT: J 82 MET cc_start: 0.5977 (mtt) cc_final: 0.5718 (mtm) REVERT: J 113 ARG cc_start: 0.6543 (ttt90) cc_final: 0.5853 (ttm-80) REVERT: K 88 ASP cc_start: 0.7387 (m-30) cc_final: 0.7101 (m-30) outliers start: 56 outliers final: 24 residues processed: 207 average time/residue: 2.4613 time to fit residues: 593.4596 Evaluate side-chains 200 residues out of total 2393 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 166 time to evaluate : 2.711 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 ASP Chi-restraints excluded: chain A residue 30 GLU Chi-restraints excluded: chain A residue 114 LEU Chi-restraints excluded: chain A residue 122 ILE Chi-restraints excluded: chain A residue 126 PHE Chi-restraints excluded: chain A residue 129 THR Chi-restraints excluded: chain B residue 33 ILE Chi-restraints excluded: chain B residue 67 ILE Chi-restraints excluded: chain B residue 160 THR Chi-restraints excluded: chain B residue 263 SER Chi-restraints excluded: chain C residue 15 ASP Chi-restraints excluded: chain C residue 83 TYR Chi-restraints excluded: chain C residue 123 MET Chi-restraints excluded: chain C residue 177 ARG Chi-restraints excluded: chain D residue 9 GLU Chi-restraints excluded: chain D residue 152 VAL Chi-restraints excluded: chain D residue 160 THR Chi-restraints excluded: chain D residue 253 ASP Chi-restraints excluded: chain E residue 9 GLU Chi-restraints excluded: chain E residue 26 ASP Chi-restraints excluded: chain E residue 160 THR Chi-restraints excluded: chain F residue 83 TYR Chi-restraints excluded: chain F residue 112 ASN Chi-restraints excluded: chain G residue 30 MET Chi-restraints excluded: chain G residue 79 HIS Chi-restraints excluded: chain H residue 49 ARG Chi-restraints excluded: chain I residue 246 TYR Chi-restraints excluded: chain I residue 287 PHE Chi-restraints excluded: chain I residue 390 ILE Chi-restraints excluded: chain I residue 487 VAL Chi-restraints excluded: chain I residue 569 ILE Chi-restraints excluded: chain J residue 36 ILE Chi-restraints excluded: chain K residue 83 MET Chi-restraints excluded: chain K residue 92 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 285 random chunks: chunk 92 optimal weight: 1.9990 chunk 248 optimal weight: 2.9990 chunk 54 optimal weight: 1.9990 chunk 161 optimal weight: 4.9990 chunk 68 optimal weight: 0.0970 chunk 275 optimal weight: 4.9990 chunk 228 optimal weight: 3.9990 chunk 127 optimal weight: 2.9990 chunk 22 optimal weight: 2.9990 chunk 91 optimal weight: 0.7980 chunk 144 optimal weight: 0.9990 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 279 GLN D 216 ASN E 216 ASN ** F 79 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 22 ASN ** H 79 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 414 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6476 moved from start: 0.4008 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 24407 Z= 0.195 Angle : 0.614 25.040 33297 Z= 0.323 Chirality : 0.055 1.978 3704 Planarity : 0.005 0.061 4139 Dihedral : 15.039 174.912 4040 Min Nonbonded Distance : 2.341 Molprobity Statistics. All-atom Clashscore : 2.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.92 % Favored : 96.08 % Rotamer: Outliers : 1.92 % Allowed : 14.67 % Favored : 83.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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: -0.30 (0.16), residues: 2804 helix: 1.23 (0.18), residues: 891 sheet: 0.84 (0.24), residues: 467 loop : -1.55 (0.15), residues: 1446 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP I 369 HIS 0.007 0.001 HIS G 79 PHE 0.014 0.001 PHE B 202 TYR 0.012 0.001 TYR E 8 ARG 0.005 0.000 ARG I 338 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5608 Ramachandran restraints generated. 2804 Oldfield, 0 Emsley, 2804 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5608 Ramachandran restraints generated. 2804 Oldfield, 0 Emsley, 2804 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 180 is missing expected H atoms. Skipping. Evaluate side-chains 214 residues out of total 2393 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 168 time to evaluate : 2.743 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 11 ILE cc_start: 0.7772 (mt) cc_final: 0.7307 (pp) REVERT: A 61 ARG cc_start: 0.7608 (mtt180) cc_final: 0.7017 (mtm-85) REVERT: A 126 PHE cc_start: 0.7508 (OUTLIER) cc_final: 0.5904 (t80) REVERT: A 131 LYS cc_start: 0.8288 (ttmt) cc_final: 0.7893 (ttpp) REVERT: B 1 MET cc_start: 0.3322 (tmt) cc_final: 0.2977 (tmt) REVERT: B 109 MET cc_start: 0.6951 (ttm) cc_final: 0.6679 (ttp) REVERT: C 70 GLN cc_start: 0.5909 (OUTLIER) cc_final: 0.5341 (tp40) REVERT: C 104 ARG cc_start: 0.4937 (mtm180) cc_final: 0.4472 (mmm160) REVERT: C 175 MET cc_start: 0.7584 (mmm) cc_final: 0.7175 (mmm) REVERT: D 157 MET cc_start: 0.6486 (mmp) cc_final: 0.5877 (mmp) REVERT: D 177 ARG cc_start: 0.7535 (mmm-85) cc_final: 0.6980 (ptp90) REVERT: D 253 ASP cc_start: 0.7136 (OUTLIER) cc_final: 0.6905 (p0) REVERT: E 104 ARG cc_start: 0.6066 (mtm-85) cc_final: 0.5417 (tpm170) REVERT: E 106 THR cc_start: 0.6529 (m) cc_final: 0.6263 (p) REVERT: E 150 GLN cc_start: 0.6173 (mt0) cc_final: 0.5898 (mm-40) REVERT: E 156 ARG cc_start: 0.4897 (ttp80) cc_final: 0.4010 (tpp80) REVERT: E 157 MET cc_start: 0.5550 (ttm) cc_final: 0.3765 (ptm) REVERT: F 30 MET cc_start: 0.6711 (mmt) cc_final: 0.6283 (mtt) REVERT: F 112 ASN cc_start: 0.7527 (OUTLIER) cc_final: 0.7167 (m-40) REVERT: F 289 MET cc_start: 0.7854 (mmm) cc_final: 0.7538 (mtp) REVERT: G 30 MET cc_start: 0.7371 (OUTLIER) cc_final: 0.6793 (mpp) REVERT: G 175 MET cc_start: 0.2211 (pmm) cc_final: 0.1610 (ptm) REVERT: H 87 ASP cc_start: 0.1267 (p0) cc_final: 0.0959 (t0) REVERT: I 209 ARG cc_start: 0.6918 (ttm-80) cc_final: 0.6545 (mtp180) REVERT: I 246 TYR cc_start: 0.6190 (OUTLIER) cc_final: 0.4817 (t80) REVERT: I 338 ARG cc_start: 0.4392 (mtp85) cc_final: 0.3801 (mtp180) REVERT: J 26 GLU cc_start: 0.6339 (tp30) cc_final: 0.5884 (mt-10) REVERT: J 33 ASN cc_start: 0.4724 (m110) cc_final: 0.4052 (m-40) REVERT: J 82 MET cc_start: 0.5941 (mtt) cc_final: 0.5703 (mtm) REVERT: J 113 ARG cc_start: 0.6484 (ttt90) cc_final: 0.5772 (ttm-80) REVERT: K 26 GLU cc_start: 0.5841 (tm-30) cc_final: 0.5538 (tp30) REVERT: K 88 ASP cc_start: 0.7492 (m-30) cc_final: 0.7141 (m-30) outliers start: 46 outliers final: 19 residues processed: 201 average time/residue: 2.4677 time to fit residues: 570.1422 Evaluate side-chains 188 residues out of total 2393 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 163 time to evaluate : 2.722 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 ASP Chi-restraints excluded: chain A residue 126 PHE Chi-restraints excluded: chain B residue 33 ILE Chi-restraints excluded: chain B residue 160 THR Chi-restraints excluded: chain C residue 70 GLN Chi-restraints excluded: chain C residue 83 TYR Chi-restraints excluded: chain C residue 177 ARG Chi-restraints excluded: chain D residue 152 VAL Chi-restraints excluded: chain D residue 160 THR Chi-restraints excluded: chain D residue 253 ASP Chi-restraints excluded: chain E residue 26 ASP Chi-restraints excluded: chain F residue 83 TYR Chi-restraints excluded: chain F residue 112 ASN Chi-restraints excluded: chain G residue 30 MET Chi-restraints excluded: chain G residue 79 HIS Chi-restraints excluded: chain H residue 30 MET Chi-restraints excluded: chain H residue 49 ARG Chi-restraints excluded: chain H residue 68 TYR Chi-restraints excluded: chain I residue 246 TYR Chi-restraints excluded: chain I residue 287 PHE Chi-restraints excluded: chain I residue 390 ILE Chi-restraints excluded: chain I residue 487 VAL Chi-restraints excluded: chain I residue 569 ILE Chi-restraints excluded: chain K residue 83 MET Chi-restraints excluded: chain K residue 92 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 285 random chunks: chunk 265 optimal weight: 3.9990 chunk 31 optimal weight: 3.9990 chunk 157 optimal weight: 0.5980 chunk 201 optimal weight: 3.9990 chunk 156 optimal weight: 2.9990 chunk 232 optimal weight: 0.1980 chunk 153 optimal weight: 1.9990 chunk 274 optimal weight: 3.9990 chunk 171 optimal weight: 7.9990 chunk 167 optimal weight: 9.9990 chunk 126 optimal weight: 2.9990 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 279 GLN ** F 79 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 414 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6494 moved from start: 0.4171 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 24407 Z= 0.254 Angle : 0.643 24.800 33297 Z= 0.342 Chirality : 0.056 1.985 3704 Planarity : 0.005 0.063 4139 Dihedral : 14.967 174.159 4040 Min Nonbonded Distance : 2.348 Molprobity Statistics. All-atom Clashscore : 2.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.92 % Favored : 95.08 % Rotamer: Outliers : 2.17 % Allowed : 14.26 % Favored : 83.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.36 (0.16), residues: 2804 helix: 1.18 (0.18), residues: 892 sheet: 0.86 (0.23), residues: 467 loop : -1.62 (0.15), residues: 1445 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 211 HIS 0.007 0.002 HIS G 79 PHE 0.015 0.002 PHE B 202 TYR 0.073 0.002 TYR H 68 ARG 0.004 0.000 ARG I 338 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5608 Ramachandran restraints generated. 2804 Oldfield, 0 Emsley, 2804 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5608 Ramachandran restraints generated. 2804 Oldfield, 0 Emsley, 2804 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 180 is missing expected H atoms. Skipping. Evaluate side-chains 219 residues out of total 2393 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 167 time to evaluate : 2.721 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 11 ILE cc_start: 0.7812 (mt) cc_final: 0.7334 (pp) REVERT: A 61 ARG cc_start: 0.7608 (mtt180) cc_final: 0.7039 (mtm-85) REVERT: A 114 LEU cc_start: 0.6235 (OUTLIER) cc_final: 0.5614 (pp) REVERT: A 126 PHE cc_start: 0.7544 (OUTLIER) cc_final: 0.5927 (t80) REVERT: A 131 LYS cc_start: 0.8299 (ttmt) cc_final: 0.8037 (ttpp) REVERT: B 1 MET cc_start: 0.3427 (tmt) cc_final: 0.3043 (tmt) REVERT: B 109 MET cc_start: 0.6985 (ttm) cc_final: 0.6773 (ttp) REVERT: C 104 ARG cc_start: 0.4517 (mtm180) cc_final: 0.4135 (mmm160) REVERT: D 157 MET cc_start: 0.6605 (mmp) cc_final: 0.6047 (mmp) REVERT: D 177 ARG cc_start: 0.7535 (mmm-85) cc_final: 0.7019 (ptp90) REVERT: D 253 ASP cc_start: 0.7167 (OUTLIER) cc_final: 0.6916 (p0) REVERT: E 104 ARG cc_start: 0.6103 (mtm-85) cc_final: 0.5470 (tpm170) REVERT: E 150 GLN cc_start: 0.6207 (mt0) cc_final: 0.5925 (mm-40) REVERT: E 156 ARG cc_start: 0.4942 (ttp80) cc_final: 0.4301 (ttm-80) REVERT: E 157 MET cc_start: 0.5496 (ttm) cc_final: 0.3893 (ptm) REVERT: F 30 MET cc_start: 0.6688 (mmt) cc_final: 0.6300 (mtt) REVERT: F 112 ASN cc_start: 0.7455 (OUTLIER) cc_final: 0.7021 (m110) REVERT: F 289 MET cc_start: 0.7900 (mmm) cc_final: 0.7601 (mtp) REVERT: G 30 MET cc_start: 0.7370 (OUTLIER) cc_final: 0.6799 (mpp) REVERT: G 175 MET cc_start: 0.2370 (pmm) cc_final: 0.1664 (ptm) REVERT: H 87 ASP cc_start: 0.1239 (p0) cc_final: 0.0963 (t70) REVERT: I 209 ARG cc_start: 0.6900 (ttm-80) cc_final: 0.6481 (mtp180) REVERT: I 246 TYR cc_start: 0.6338 (OUTLIER) cc_final: 0.4896 (t80) REVERT: I 338 ARG cc_start: 0.4474 (mtp85) cc_final: 0.3905 (mtp180) REVERT: J 26 GLU cc_start: 0.6327 (tp30) cc_final: 0.5870 (mt-10) REVERT: J 33 ASN cc_start: 0.4887 (m110) cc_final: 0.4378 (m110) REVERT: J 82 MET cc_start: 0.5985 (mtt) cc_final: 0.5761 (mtm) REVERT: J 100 ASP cc_start: 0.6319 (p0) cc_final: 0.5427 (m-30) REVERT: J 113 ARG cc_start: 0.6495 (ttt90) cc_final: 0.5781 (ttm-80) REVERT: K 58 ASN cc_start: 0.7480 (m-40) cc_final: 0.6358 (t0) REVERT: K 88 ASP cc_start: 0.7486 (m-30) cc_final: 0.7149 (m-30) outliers start: 52 outliers final: 21 residues processed: 199 average time/residue: 2.3858 time to fit residues: 547.3380 Evaluate side-chains 188 residues out of total 2393 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 161 time to evaluate : 2.658 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 ASP Chi-restraints excluded: chain A residue 114 LEU Chi-restraints excluded: chain A residue 126 PHE Chi-restraints excluded: chain B residue 33 ILE Chi-restraints excluded: chain B residue 160 THR Chi-restraints excluded: chain C residue 83 TYR Chi-restraints excluded: chain C residue 123 MET Chi-restraints excluded: chain C residue 177 ARG Chi-restraints excluded: chain D residue 152 VAL Chi-restraints excluded: chain D residue 160 THR Chi-restraints excluded: chain D residue 253 ASP Chi-restraints excluded: chain E residue 9 GLU Chi-restraints excluded: chain E residue 26 ASP Chi-restraints excluded: chain F residue 83 TYR Chi-restraints excluded: chain F residue 112 ASN Chi-restraints excluded: chain G residue 30 MET Chi-restraints excluded: chain G residue 79 HIS Chi-restraints excluded: chain H residue 30 MET Chi-restraints excluded: chain H residue 49 ARG Chi-restraints excluded: chain I residue 246 TYR Chi-restraints excluded: chain I residue 287 PHE Chi-restraints excluded: chain I residue 390 ILE Chi-restraints excluded: chain I residue 487 VAL Chi-restraints excluded: chain I residue 569 ILE Chi-restraints excluded: chain K residue 77 ILE Chi-restraints excluded: chain K residue 83 MET Chi-restraints excluded: chain K residue 92 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 285 random chunks: chunk 169 optimal weight: 9.9990 chunk 109 optimal weight: 1.9990 chunk 164 optimal weight: 2.9990 chunk 82 optimal weight: 1.9990 chunk 53 optimal weight: 1.9990 chunk 174 optimal weight: 3.9990 chunk 187 optimal weight: 7.9990 chunk 135 optimal weight: 1.9990 chunk 25 optimal weight: 0.9990 chunk 215 optimal weight: 0.6980 chunk 249 optimal weight: 4.9990 overall best weight: 1.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 179 HIS C 279 GLN D 216 ASN ** F 79 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 414 ASN I 538 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6487 moved from start: 0.4310 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 24407 Z= 0.226 Angle : 0.623 24.853 33297 Z= 0.328 Chirality : 0.055 1.987 3704 Planarity : 0.005 0.061 4139 Dihedral : 14.943 174.594 4040 Min Nonbonded Distance : 2.239 Molprobity Statistics. All-atom Clashscore : 2.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.24 % Favored : 95.76 % Rotamer: Outliers : 1.84 % Allowed : 15.38 % Favored : 82.78 % 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: -0.30 (0.16), residues: 2804 helix: 1.28 (0.18), residues: 891 sheet: 0.82 (0.23), residues: 480 loop : -1.60 (0.16), residues: 1433 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP I 369 HIS 0.006 0.001 HIS G 79 PHE 0.018 0.001 PHE E 191 TYR 0.013 0.002 TYR E 8 ARG 0.004 0.000 ARG I 338 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5608 Ramachandran restraints generated. 2804 Oldfield, 0 Emsley, 2804 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5608 Ramachandran restraints generated. 2804 Oldfield, 0 Emsley, 2804 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 180 is missing expected H atoms. Skipping. Evaluate side-chains 211 residues out of total 2393 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 167 time to evaluate : 2.755 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 11 ILE cc_start: 0.7802 (mt) cc_final: 0.7341 (pp) REVERT: A 61 ARG cc_start: 0.7595 (mtt180) cc_final: 0.7044 (mtm-85) REVERT: A 114 LEU cc_start: 0.6230 (OUTLIER) cc_final: 0.5599 (pp) REVERT: A 126 PHE cc_start: 0.7527 (OUTLIER) cc_final: 0.5920 (t80) REVERT: A 131 LYS cc_start: 0.8323 (ttmt) cc_final: 0.7971 (ttpp) REVERT: B 1 MET cc_start: 0.3340 (tmt) cc_final: 0.2926 (tmt) REVERT: B 109 MET cc_start: 0.7009 (ttm) cc_final: 0.6757 (ttp) REVERT: C 104 ARG cc_start: 0.4434 (mtm180) cc_final: 0.4067 (mmm160) REVERT: D 157 MET cc_start: 0.6586 (mmp) cc_final: 0.6021 (mmp) REVERT: D 177 ARG cc_start: 0.7523 (mmm-85) cc_final: 0.6897 (ptp90) REVERT: D 253 ASP cc_start: 0.7148 (OUTLIER) cc_final: 0.6911 (p0) REVERT: E 104 ARG cc_start: 0.6194 (mtm-85) cc_final: 0.5497 (tpm170) REVERT: E 150 GLN cc_start: 0.6181 (mt0) cc_final: 0.5916 (mm-40) REVERT: E 156 ARG cc_start: 0.4830 (ttp80) cc_final: 0.4373 (ttm-80) REVERT: E 157 MET cc_start: 0.5408 (ttm) cc_final: 0.3881 (ptm) REVERT: F 30 MET cc_start: 0.6663 (mmt) cc_final: 0.6257 (mtt) REVERT: F 112 ASN cc_start: 0.7591 (OUTLIER) cc_final: 0.7265 (m-40) REVERT: F 289 MET cc_start: 0.7871 (mmm) cc_final: 0.7548 (mtp) REVERT: G 30 MET cc_start: 0.7389 (OUTLIER) cc_final: 0.6812 (mpp) REVERT: G 175 MET cc_start: 0.2343 (pmm) cc_final: 0.1664 (ptm) REVERT: H 87 ASP cc_start: 0.1343 (p0) cc_final: 0.1087 (t70) REVERT: I 209 ARG cc_start: 0.6896 (ttm-80) cc_final: 0.6481 (mtp180) REVERT: I 246 TYR cc_start: 0.6319 (OUTLIER) cc_final: 0.4881 (t80) REVERT: I 338 ARG cc_start: 0.4444 (mtp85) cc_final: 0.3864 (mtp180) REVERT: J 26 GLU cc_start: 0.6272 (tp30) cc_final: 0.5806 (mt-10) REVERT: J 33 ASN cc_start: 0.4940 (m110) cc_final: 0.4115 (m-40) REVERT: J 40 TYR cc_start: 0.6876 (m-80) cc_final: 0.6597 (m-80) REVERT: J 82 MET cc_start: 0.5969 (mtt) cc_final: 0.5760 (mtm) REVERT: J 92 ASP cc_start: 0.7011 (OUTLIER) cc_final: 0.6773 (m-30) REVERT: J 100 ASP cc_start: 0.6214 (p0) cc_final: 0.5382 (m-30) REVERT: J 113 ARG cc_start: 0.6490 (ttt90) cc_final: 0.5793 (ttm-80) REVERT: K 26 GLU cc_start: 0.6062 (tm-30) cc_final: 0.5709 (tp30) REVERT: K 58 ASN cc_start: 0.7469 (m-40) cc_final: 0.6334 (t0) REVERT: K 88 ASP cc_start: 0.7509 (m-30) cc_final: 0.7146 (m-30) outliers start: 44 outliers final: 21 residues processed: 197 average time/residue: 2.4239 time to fit residues: 554.9982 Evaluate side-chains 191 residues out of total 2393 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 163 time to evaluate : 2.688 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 ASP Chi-restraints excluded: chain A residue 114 LEU Chi-restraints excluded: chain A residue 126 PHE Chi-restraints excluded: chain A residue 172 LEU Chi-restraints excluded: chain B residue 33 ILE Chi-restraints excluded: chain B residue 160 THR Chi-restraints excluded: chain C residue 83 TYR Chi-restraints excluded: chain C residue 123 MET Chi-restraints excluded: chain C residue 290 LEU Chi-restraints excluded: chain D residue 152 VAL Chi-restraints excluded: chain D residue 160 THR Chi-restraints excluded: chain D residue 253 ASP Chi-restraints excluded: chain E residue 26 ASP Chi-restraints excluded: chain E residue 160 THR Chi-restraints excluded: chain F residue 83 TYR Chi-restraints excluded: chain F residue 112 ASN Chi-restraints excluded: chain G residue 30 MET Chi-restraints excluded: chain G residue 79 HIS Chi-restraints excluded: chain H residue 30 MET Chi-restraints excluded: chain H residue 49 ARG Chi-restraints excluded: chain I residue 214 VAL Chi-restraints excluded: chain I residue 246 TYR Chi-restraints excluded: chain I residue 287 PHE Chi-restraints excluded: chain I residue 487 VAL Chi-restraints excluded: chain I residue 569 ILE Chi-restraints excluded: chain J residue 92 ASP Chi-restraints excluded: chain K residue 83 MET Chi-restraints excluded: chain K residue 92 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 285 random chunks: chunk 263 optimal weight: 2.9990 chunk 240 optimal weight: 1.9990 chunk 255 optimal weight: 2.9990 chunk 154 optimal weight: 2.9990 chunk 111 optimal weight: 3.9990 chunk 201 optimal weight: 1.9990 chunk 78 optimal weight: 2.9990 chunk 231 optimal weight: 5.9990 chunk 242 optimal weight: 0.1980 chunk 168 optimal weight: 9.9990 chunk 270 optimal weight: 2.9990 overall best weight: 2.0388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 279 GLN D 216 ASN E 29 ASN H 39 HIS H 240 GLN I 414 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6504 moved from start: 0.4438 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 24407 Z= 0.280 Angle : 0.656 24.754 33297 Z= 0.348 Chirality : 0.056 1.994 3704 Planarity : 0.005 0.063 4139 Dihedral : 14.934 174.037 4040 Min Nonbonded Distance : 2.223 Molprobity Statistics. All-atom Clashscore : 3.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.03 % Favored : 94.97 % Rotamer: Outliers : 1.84 % Allowed : 15.51 % Favored : 82.65 % 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: -0.41 (0.16), residues: 2804 helix: 1.17 (0.18), residues: 891 sheet: 0.88 (0.24), residues: 458 loop : -1.67 (0.15), residues: 1455 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP G 108 HIS 0.007 0.002 HIS G 79 PHE 0.020 0.002 PHE E 191 TYR 0.017 0.002 TYR E 8 ARG 0.004 0.001 ARG I 338 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5608 Ramachandran restraints generated. 2804 Oldfield, 0 Emsley, 2804 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5608 Ramachandran restraints generated. 2804 Oldfield, 0 Emsley, 2804 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 180 is missing expected H atoms. Skipping. Evaluate side-chains 210 residues out of total 2393 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 166 time to evaluate : 2.771 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 11 ILE cc_start: 0.7834 (mt) cc_final: 0.7369 (pp) REVERT: A 61 ARG cc_start: 0.7621 (mtt180) cc_final: 0.7074 (mtm-85) REVERT: A 114 LEU cc_start: 0.6250 (OUTLIER) cc_final: 0.5638 (pp) REVERT: A 131 LYS cc_start: 0.8338 (ttmt) cc_final: 0.7998 (ttpp) REVERT: B 1 MET cc_start: 0.3363 (tmt) cc_final: 0.2932 (tmt) REVERT: C 104 ARG cc_start: 0.4405 (mtm180) cc_final: 0.4094 (mmm160) REVERT: D 157 MET cc_start: 0.6742 (mmp) cc_final: 0.6247 (mmp) REVERT: D 177 ARG cc_start: 0.7461 (mmm-85) cc_final: 0.6950 (ptp90) REVERT: D 253 ASP cc_start: 0.7171 (OUTLIER) cc_final: 0.6911 (p0) REVERT: E 104 ARG cc_start: 0.6134 (mtm-85) cc_final: 0.5456 (tpm170) REVERT: E 150 GLN cc_start: 0.6208 (mt0) cc_final: 0.5941 (mm-40) REVERT: E 156 ARG cc_start: 0.4887 (ttp80) cc_final: 0.4568 (ttm-80) REVERT: E 157 MET cc_start: 0.5467 (ttm) cc_final: 0.3735 (ptm) REVERT: E 282 GLU cc_start: 0.6421 (pm20) cc_final: 0.6060 (tt0) REVERT: F 30 MET cc_start: 0.6708 (mmt) cc_final: 0.6322 (mtt) REVERT: F 83 TYR cc_start: -0.0300 (OUTLIER) cc_final: -0.1525 (t80) REVERT: F 112 ASN cc_start: 0.7364 (OUTLIER) cc_final: 0.7049 (m-40) REVERT: F 289 MET cc_start: 0.7921 (mmm) cc_final: 0.7655 (mtp) REVERT: G 30 MET cc_start: 0.7444 (OUTLIER) cc_final: 0.6902 (mpp) REVERT: G 175 MET cc_start: 0.2652 (pmm) cc_final: 0.1921 (ptm) REVERT: G 229 MET cc_start: 0.8569 (OUTLIER) cc_final: 0.8107 (mtt) REVERT: H 87 ASP cc_start: 0.1366 (p0) cc_final: 0.1041 (t0) REVERT: H 289 MET cc_start: 0.5637 (pmm) cc_final: 0.4491 (mpp) REVERT: I 209 ARG cc_start: 0.6909 (ttm-80) cc_final: 0.6487 (mtp180) REVERT: I 246 TYR cc_start: 0.6405 (OUTLIER) cc_final: 0.4858 (t80) REVERT: I 338 ARG cc_start: 0.4412 (mtp85) cc_final: 0.3832 (mtp180) REVERT: J 26 GLU cc_start: 0.6359 (tp30) cc_final: 0.5934 (tt0) REVERT: J 33 ASN cc_start: 0.4688 (m110) cc_final: 0.3977 (m-40) REVERT: J 40 TYR cc_start: 0.6924 (m-80) cc_final: 0.6684 (m-80) REVERT: J 82 MET cc_start: 0.6085 (mtt) cc_final: 0.5849 (mtm) REVERT: J 92 ASP cc_start: 0.7053 (OUTLIER) cc_final: 0.6817 (m-30) REVERT: J 100 ASP cc_start: 0.6158 (p0) cc_final: 0.5396 (m-30) REVERT: J 113 ARG cc_start: 0.6509 (ttt90) cc_final: 0.5812 (ttm-80) REVERT: K 58 ASN cc_start: 0.6983 (m-40) cc_final: 0.5940 (t0) REVERT: K 88 ASP cc_start: 0.7494 (m-30) cc_final: 0.7139 (m-30) outliers start: 44 outliers final: 25 residues processed: 194 average time/residue: 2.4244 time to fit residues: 540.8931 Evaluate side-chains 195 residues out of total 2393 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 162 time to evaluate : 2.689 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 ASP Chi-restraints excluded: chain A residue 114 LEU Chi-restraints excluded: chain A residue 122 ILE Chi-restraints excluded: chain A residue 126 PHE Chi-restraints excluded: chain A residue 172 LEU Chi-restraints excluded: chain B residue 33 ILE Chi-restraints excluded: chain B residue 160 THR Chi-restraints excluded: chain C residue 83 TYR Chi-restraints excluded: chain C residue 123 MET Chi-restraints excluded: chain C residue 177 ARG Chi-restraints excluded: chain C residue 290 LEU Chi-restraints excluded: chain D residue 69 ILE Chi-restraints excluded: chain D residue 152 VAL Chi-restraints excluded: chain D residue 160 THR Chi-restraints excluded: chain D residue 253 ASP Chi-restraints excluded: chain E residue 26 ASP Chi-restraints excluded: chain E residue 106 THR Chi-restraints excluded: chain E residue 160 THR Chi-restraints excluded: chain F residue 83 TYR Chi-restraints excluded: chain F residue 112 ASN Chi-restraints excluded: chain G residue 30 MET Chi-restraints excluded: chain G residue 79 HIS Chi-restraints excluded: chain G residue 157 MET Chi-restraints excluded: chain G residue 229 MET Chi-restraints excluded: chain H residue 39 HIS Chi-restraints excluded: chain I residue 214 VAL Chi-restraints excluded: chain I residue 246 TYR Chi-restraints excluded: chain I residue 287 PHE Chi-restraints excluded: chain I residue 487 VAL Chi-restraints excluded: chain I residue 569 ILE Chi-restraints excluded: chain J residue 92 ASP Chi-restraints excluded: chain K residue 83 MET Chi-restraints excluded: chain K residue 92 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 285 random chunks: chunk 165 optimal weight: 1.9990 chunk 128 optimal weight: 1.9990 chunk 188 optimal weight: 7.9990 chunk 283 optimal weight: 4.9990 chunk 261 optimal weight: 3.9990 chunk 226 optimal weight: 0.7980 chunk 23 optimal weight: 2.9990 chunk 174 optimal weight: 0.9980 chunk 138 optimal weight: 2.9990 chunk 179 optimal weight: 0.6980 chunk 240 optimal weight: 0.9980 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 240 GLN I 414 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6482 moved from start: 0.4480 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 24407 Z= 0.188 Angle : 0.610 25.042 33297 Z= 0.320 Chirality : 0.055 1.989 3704 Planarity : 0.005 0.061 4139 Dihedral : 14.922 174.771 4040 Min Nonbonded Distance : 2.278 Molprobity Statistics. All-atom Clashscore : 3.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.42 % Favored : 95.58 % Rotamer: Outliers : 1.17 % Allowed : 16.26 % Favored : 82.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.28 (0.16), residues: 2804 helix: 1.36 (0.18), residues: 889 sheet: 0.80 (0.23), residues: 480 loop : -1.63 (0.16), residues: 1435 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP I 369 HIS 0.006 0.001 HIS G 79 PHE 0.017 0.001 PHE E 191 TYR 0.012 0.001 TYR E 8 ARG 0.004 0.000 ARG I 338 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5608 Ramachandran restraints generated. 2804 Oldfield, 0 Emsley, 2804 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5608 Ramachandran restraints generated. 2804 Oldfield, 0 Emsley, 2804 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 180 is missing expected H atoms. Skipping. Evaluate side-chains 194 residues out of total 2393 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 166 time to evaluate : 2.786 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 11 ILE cc_start: 0.7783 (mt) cc_final: 0.7336 (pp) REVERT: A 61 ARG cc_start: 0.7590 (mtt180) cc_final: 0.7040 (mtm-85) REVERT: A 114 LEU cc_start: 0.6216 (OUTLIER) cc_final: 0.5600 (pp) REVERT: A 131 LYS cc_start: 0.8333 (ttmt) cc_final: 0.7995 (ttpp) REVERT: B 1 MET cc_start: 0.3329 (tmt) cc_final: 0.2901 (tmt) REVERT: C 104 ARG cc_start: 0.4386 (mtm180) cc_final: 0.4105 (mmm160) REVERT: C 289 MET cc_start: 0.8395 (mmm) cc_final: 0.8158 (mtp) REVERT: D 157 MET cc_start: 0.6543 (mmp) cc_final: 0.5981 (mmp) REVERT: D 177 ARG cc_start: 0.7440 (mmm-85) cc_final: 0.6947 (ptp90) REVERT: D 253 ASP cc_start: 0.7139 (OUTLIER) cc_final: 0.6910 (p0) REVERT: E 104 ARG cc_start: 0.6196 (mtm-85) cc_final: 0.5498 (tpm170) REVERT: E 150 GLN cc_start: 0.6167 (mt0) cc_final: 0.5906 (mm-40) REVERT: E 156 ARG cc_start: 0.4872 (ttp80) cc_final: 0.4556 (ttm-80) REVERT: E 157 MET cc_start: 0.5475 (ttm) cc_final: 0.3858 (ptm) REVERT: E 282 GLU cc_start: 0.6393 (pm20) cc_final: 0.6046 (tt0) REVERT: F 30 MET cc_start: 0.6652 (mmt) cc_final: 0.6264 (mtt) REVERT: F 83 TYR cc_start: -0.0166 (OUTLIER) cc_final: -0.1480 (t80) REVERT: F 289 MET cc_start: 0.7859 (mmm) cc_final: 0.7546 (mtp) REVERT: G 30 MET cc_start: 0.7442 (OUTLIER) cc_final: 0.6888 (mpp) REVERT: G 175 MET cc_start: 0.2835 (pmm) cc_final: 0.2031 (ptm) REVERT: H 87 ASP cc_start: 0.1449 (p0) cc_final: 0.1071 (t0) REVERT: H 289 MET cc_start: 0.5610 (pmm) cc_final: 0.4433 (mpp) REVERT: I 209 ARG cc_start: 0.6893 (ttm-80) cc_final: 0.6513 (mtp180) REVERT: I 246 TYR cc_start: 0.6356 (OUTLIER) cc_final: 0.4933 (t80) REVERT: I 338 ARG cc_start: 0.4150 (mtp85) cc_final: 0.3555 (mtp180) REVERT: J 26 GLU cc_start: 0.6265 (tp30) cc_final: 0.5805 (mt-10) REVERT: J 33 ASN cc_start: 0.4627 (m110) cc_final: 0.3917 (m-40) REVERT: J 40 TYR cc_start: 0.6905 (m-80) cc_final: 0.6623 (m-80) REVERT: J 92 ASP cc_start: 0.7024 (OUTLIER) cc_final: 0.6795 (m-30) REVERT: J 100 ASP cc_start: 0.6149 (p0) cc_final: 0.5391 (m-30) REVERT: J 113 ARG cc_start: 0.6492 (ttt90) cc_final: 0.5796 (ttm-80) REVERT: K 26 GLU cc_start: 0.5982 (tm-30) cc_final: 0.5631 (tp30) REVERT: K 58 ASN cc_start: 0.7099 (m-40) cc_final: 0.6043 (t0) REVERT: K 88 ASP cc_start: 0.7494 (m-30) cc_final: 0.7133 (m-30) outliers start: 28 outliers final: 22 residues processed: 185 average time/residue: 2.4620 time to fit residues: 523.0440 Evaluate side-chains 192 residues out of total 2393 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 164 time to evaluate : 2.684 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 ASP Chi-restraints excluded: chain A residue 114 LEU Chi-restraints excluded: chain A residue 126 PHE Chi-restraints excluded: chain A residue 172 LEU Chi-restraints excluded: chain B residue 33 ILE Chi-restraints excluded: chain B residue 160 THR Chi-restraints excluded: chain C residue 83 TYR Chi-restraints excluded: chain C residue 123 MET Chi-restraints excluded: chain C residue 177 ARG Chi-restraints excluded: chain C residue 290 LEU Chi-restraints excluded: chain D residue 1 MET Chi-restraints excluded: chain D residue 152 VAL Chi-restraints excluded: chain D residue 160 THR Chi-restraints excluded: chain D residue 253 ASP Chi-restraints excluded: chain E residue 26 ASP Chi-restraints excluded: chain E residue 160 THR Chi-restraints excluded: chain F residue 83 TYR Chi-restraints excluded: chain G residue 30 MET Chi-restraints excluded: chain G residue 79 HIS Chi-restraints excluded: chain G residue 157 MET Chi-restraints excluded: chain I residue 214 VAL Chi-restraints excluded: chain I residue 246 TYR Chi-restraints excluded: chain I residue 287 PHE Chi-restraints excluded: chain I residue 487 VAL Chi-restraints excluded: chain I residue 569 ILE Chi-restraints excluded: chain J residue 92 ASP Chi-restraints excluded: chain K residue 83 MET Chi-restraints excluded: chain K residue 92 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 285 random chunks: chunk 69 optimal weight: 1.9990 chunk 208 optimal weight: 8.9990 chunk 33 optimal weight: 3.9990 chunk 62 optimal weight: 0.4980 chunk 226 optimal weight: 1.9990 chunk 94 optimal weight: 1.9990 chunk 232 optimal weight: 6.9990 chunk 28 optimal weight: 3.9990 chunk 41 optimal weight: 1.9990 chunk 198 optimal weight: 7.9990 chunk 12 optimal weight: 4.9990 overall best weight: 1.6988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 279 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4043 r_free = 0.4043 target = 0.138339 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3582 r_free = 0.3582 target = 0.103592 restraints weight = 109653.807| |-----------------------------------------------------------------------------| r_work (start): 0.3525 rms_B_bonded: 2.28 r_work: 0.3322 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.3211 rms_B_bonded: 4.24 restraints_weight: 0.2500 r_work (final): 0.3211 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8238 moved from start: 0.4546 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 24407 Z= 0.248 Angle : 0.634 24.906 33297 Z= 0.335 Chirality : 0.056 1.997 3704 Planarity : 0.005 0.062 4139 Dihedral : 14.902 174.304 4040 Min Nonbonded Distance : 2.274 Molprobity Statistics. All-atom Clashscore : 3.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.14 % Favored : 94.86 % Rotamer: Outliers : 1.42 % Allowed : 16.05 % Favored : 82.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.37 (0.16), residues: 2804 helix: 1.27 (0.18), residues: 889 sheet: 0.77 (0.23), residues: 475 loop : -1.67 (0.15), residues: 1440 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP G 108 HIS 0.006 0.001 HIS G 79 PHE 0.018 0.001 PHE E 191 TYR 0.015 0.002 TYR E 8 ARG 0.004 0.000 ARG I 338 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10998.82 seconds wall clock time: 189 minutes 21.23 seconds (11361.23 seconds total)