Starting phenix.real_space_refine on Sat Jul 4 13:30:22 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9g9d_51148/07_2026/9g9d_51148.cif Found real_map, /net/cci-nas-00/data/ceres_data/9g9d_51148/07_2026/9g9d_51148.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9g9d_51148/07_2026/9g9d_51148.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9g9d_51148/07_2026/9g9d_51148.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9g9d_51148/07_2026/9g9d_51148.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9g9d_51148/07_2026/9g9d_51148.map" } resolution = 2.9 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.015 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 72 5.49 5 S 57 5.16 5 C 13322 2.51 5 N 3652 2.21 5 O 4230 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 11 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 21333 Number of models: 1 Model: "" Number of chains: 12 Chain: "C" Number of atoms: 1102 Number of conformers: 1 Conformer: "" Number of residues, atoms: 132, 1102 Classifications: {'peptide': 132} Link IDs: {'PTRANS': 1, 'TRANS': 130} Chain: "B" Number of atoms: 1065 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 1065 Classifications: {'peptide': 128} Link IDs: {'PTRANS': 1, 'TRANS': 126} Chain breaks: 1 Chain: "F" Number of atoms: 1620 Number of conformers: 1 Conformer: "" Number of residues, atoms: 210, 1620 Classifications: {'peptide': 210} Link IDs: {'PTRANS': 7, 'TRANS': 202} Chain: "E" Number of atoms: 1620 Number of conformers: 1 Conformer: "" Number of residues, atoms: 210, 1620 Classifications: {'peptide': 210} Link IDs: {'PTRANS': 7, 'TRANS': 202} Chain: "D" Number of atoms: 1548 Number of conformers: 1 Conformer: "" Number of residues, atoms: 200, 1548 Classifications: {'peptide': 200} Link IDs: {'PTRANS': 6, 'TRANS': 193} Chain breaks: 2 Chain: "G" Number of atoms: 2341 Number of conformers: 1 Conformer: "" Number of residues, atoms: 296, 2341 Classifications: {'peptide': 296} Link IDs: {'PTRANS': 7, 'TRANS': 288} Chain breaks: 1 Chain: "R" Number of atoms: 816 Number of conformers: 1 Conformer: "" Number of residues, atoms: 38, 816 Classifications: {'RNA': 38} Modifications used: {'5*END': 1, 'rna2p_pur': 10, 'rna2p_pyr': 8, 'rna3p_pur': 14, 'rna3p_pyr': 6} Link IDs: {'rna2p': 18, 'rna3p': 19} Chain: "T" Number of atoms: 740 Number of conformers: 1 Conformer: "" Number of residues, atoms: 35, 740 Classifications: {'RNA': 35} Modifications used: {'rna2p_pur': 3, 'rna2p_pyr': 1, 'rna3p_pur': 12, 'rna3p_pyr': 19} Link IDs: {'rna2p': 3, 'rna3p': 31} Chain: "I" Number of atoms: 1620 Number of conformers: 1 Conformer: "" Number of residues, atoms: 210, 1620 Classifications: {'peptide': 210} Link IDs: {'PTRANS': 7, 'TRANS': 202} Chain: "J" Number of atoms: 1124 Number of conformers: 1 Conformer: "" Number of residues, atoms: 135, 1124 Classifications: {'peptide': 135} Link IDs: {'PTRANS': 1, 'TRANS': 133} Chain: "H" Number of atoms: 2510 Number of conformers: 1 Conformer: "" Number of residues, atoms: 310, 2510 Classifications: {'peptide': 310} Link IDs: {'PCIS': 1, 'PTRANS': 14, 'TRANS': 294} Chain breaks: 4 Chain: "A" Number of atoms: 5227 Number of conformers: 1 Conformer: "" Number of residues, atoms: 653, 5227 Classifications: {'peptide': 653} Link IDs: {'PTRANS': 14, 'TRANS': 638} Chain breaks: 4 Time building chain proxies: 3.68, per 1000 atoms: 0.17 Number of scatterers: 21333 At special positions: 0 Unit cell: (102.7, 120.25, 195, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 57 16.00 P 72 15.00 O 4230 8.00 N 3652 7.00 C 13322 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.87 Conformation dependent library (CDL) restraints added in 734.0 milliseconds 4880 Ramachandran restraints generated. 2440 Oldfield, 0 Emsley, 2440 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4624 Finding SS restraints... Secondary structure from input PDB file: 100 helices and 28 sheets defined 49.4% alpha, 18.3% beta 23 base pairs and 35 stacking pairs defined. Time for finding SS restraints: 2.31 Creating SS restraints... Processing helix chain 'C' and resid 6 through 10 removed outlier: 3.646A pdb=" N GLU C 10 " --> pdb=" O LYS C 7 " (cutoff:3.500A) Processing helix chain 'C' and resid 13 through 25 Processing helix chain 'C' and resid 43 through 63 removed outlier: 3.646A pdb=" N LEU C 47 " --> pdb=" O THR C 43 " (cutoff:3.500A) Processing helix chain 'C' and resid 70 through 91 Processing helix chain 'C' and resid 91 through 102 Processing helix chain 'C' and resid 102 through 114 Processing helix chain 'C' and resid 115 through 137 Processing helix chain 'B' and resid 6 through 10 removed outlier: 3.627A pdb=" N GLU B 10 " --> pdb=" O LYS B 7 " (cutoff:3.500A) Processing helix chain 'B' and resid 13 through 25 Processing helix chain 'B' and resid 43 through 64 removed outlier: 3.510A pdb=" N SER B 64 " --> pdb=" O LYS B 60 " (cutoff:3.500A) Processing helix chain 'B' and resid 70 through 91 Processing helix chain 'B' and resid 91 through 102 Processing helix chain 'B' and resid 102 through 114 Processing helix chain 'B' and resid 115 through 136 Processing helix chain 'F' and resid 47 through 64 Processing helix chain 'F' and resid 71 through 75 removed outlier: 3.524A pdb=" N GLN F 74 " --> pdb=" O MET F 71 " (cutoff:3.500A) Processing helix chain 'F' and resid 76 through 84 Processing helix chain 'F' and resid 104 through 115 Processing helix chain 'F' and resid 161 through 178 Processing helix chain 'F' and resid 184 through 188 Processing helix chain 'E' and resid 47 through 64 Processing helix chain 'E' and resid 71 through 75 removed outlier: 3.627A pdb=" N ASP E 75 " --> pdb=" O HIS E 72 " (cutoff:3.500A) Processing helix chain 'E' and resid 76 through 84 Processing helix chain 'E' and resid 104 through 113 Processing helix chain 'E' and resid 114 through 116 No H-bonds generated for 'chain 'E' and resid 114 through 116' Processing helix chain 'E' and resid 158 through 160 No H-bonds generated for 'chain 'E' and resid 158 through 160' Processing helix chain 'E' and resid 161 through 179 Processing helix chain 'E' and resid 184 through 188 Processing helix chain 'D' and resid 47 through 64 Processing helix chain 'D' and resid 76 through 84 Processing helix chain 'D' and resid 104 through 113 Processing helix chain 'D' and resid 114 through 116 No H-bonds generated for 'chain 'D' and resid 114 through 116' Processing helix chain 'D' and resid 158 through 160 No H-bonds generated for 'chain 'D' and resid 158 through 160' Processing helix chain 'D' and resid 161 through 179 Processing helix chain 'D' and resid 184 through 188 Processing helix chain 'G' and resid 32 through 47 Processing helix chain 'G' and resid 51 through 58 removed outlier: 3.546A pdb=" N LEU G 58 " --> pdb=" O LEU G 54 " (cutoff:3.500A) Processing helix chain 'G' and resid 90 through 96 Processing helix chain 'G' and resid 101 through 110 removed outlier: 3.676A pdb=" N GLU G 106 " --> pdb=" O GLU G 102 " (cutoff:3.500A) Processing helix chain 'G' and resid 113 through 124 Processing helix chain 'G' and resid 137 through 142 removed outlier: 3.837A pdb=" N ASP G 141 " --> pdb=" O LEU G 137 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N HIS G 142 " --> pdb=" O GLN G 138 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 137 through 142' Processing helix chain 'G' and resid 169 through 187 removed outlier: 4.279A pdb=" N TYR G 185 " --> pdb=" O HIS G 181 " (cutoff:3.500A) Processing helix chain 'G' and resid 206 through 214 Processing helix chain 'G' and resid 229 through 237 removed outlier: 3.996A pdb=" N ASP G 235 " --> pdb=" O GLU G 231 " (cutoff:3.500A) Processing helix chain 'I' and resid 47 through 64 Processing helix chain 'I' and resid 76 through 84 Processing helix chain 'I' and resid 104 through 114 Processing helix chain 'I' and resid 158 through 160 No H-bonds generated for 'chain 'I' and resid 158 through 160' Processing helix chain 'I' and resid 161 through 179 Processing helix chain 'J' and resid 6 through 10 Processing helix chain 'J' and resid 13 through 24 Processing helix chain 'J' and resid 43 through 64 removed outlier: 3.588A pdb=" N LEU J 47 " --> pdb=" O THR J 43 " (cutoff:3.500A) removed outlier: 4.207A pdb=" N VAL J 57 " --> pdb=" O LEU J 53 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N SER J 64 " --> pdb=" O LYS J 60 " (cutoff:3.500A) Processing helix chain 'J' and resid 70 through 91 Processing helix chain 'J' and resid 91 through 102 Processing helix chain 'J' and resid 102 through 114 Processing helix chain 'J' and resid 115 through 137 Processing helix chain 'H' and resid 42 through 53 Processing helix chain 'H' and resid 55 through 66 removed outlier: 3.501A pdb=" N THR H 66 " --> pdb=" O TYR H 62 " (cutoff:3.500A) Processing helix chain 'H' and resid 71 through 80 Processing helix chain 'H' and resid 82 through 89 removed outlier: 3.928A pdb=" N PHE H 89 " --> pdb=" O ASP H 85 " (cutoff:3.500A) Processing helix chain 'H' and resid 140 through 153 Processing helix chain 'H' and resid 174 through 176 No H-bonds generated for 'chain 'H' and resid 174 through 176' Processing helix chain 'H' and resid 218 through 237 Processing helix chain 'H' and resid 237 through 243 Processing helix chain 'H' and resid 244 through 253 Processing helix chain 'H' and resid 282 through 287 removed outlier: 3.673A pdb=" N GLN H 286 " --> pdb=" O THR H 282 " (cutoff:3.500A) Processing helix chain 'H' and resid 288 through 304 Processing helix chain 'A' and resid 3 through 13 Processing helix chain 'A' and resid 15 through 23 removed outlier: 3.913A pdb=" N ILE A 19 " --> pdb=" O ASP A 15 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N VAL A 20 " --> pdb=" O ILE A 16 " (cutoff:3.500A) Processing helix chain 'A' and resid 33 through 44 removed outlier: 3.617A pdb=" N LYS A 43 " --> pdb=" O GLN A 39 " (cutoff:3.500A) removed outlier: 4.268A pdb=" N PHE A 44 " --> pdb=" O PHE A 40 " (cutoff:3.500A) Processing helix chain 'A' and resid 45 through 48 Processing helix chain 'A' and resid 49 through 61 removed outlier: 3.559A pdb=" N VAL A 56 " --> pdb=" O ILE A 52 " (cutoff:3.500A) removed outlier: 4.291A pdb=" N HIS A 60 " --> pdb=" O VAL A 56 " (cutoff:3.500A) removed outlier: 4.457A pdb=" N TYR A 61 " --> pdb=" O SER A 57 " (cutoff:3.500A) Processing helix chain 'A' and resid 76 through 85 Processing helix chain 'A' and resid 150 through 168 Processing helix chain 'A' and resid 175 through 188 removed outlier: 3.532A pdb=" N LEU A 186 " --> pdb=" O TRP A 182 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N SER A 188 " --> pdb=" O GLU A 184 " (cutoff:3.500A) Processing helix chain 'A' and resid 203 through 225 Processing helix chain 'A' and resid 242 through 247 removed outlier: 3.638A pdb=" N GLN A 246 " --> pdb=" O LYS A 242 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N GLU A 247 " --> pdb=" O GLN A 243 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 242 through 247' Processing helix chain 'A' and resid 259 through 265 removed outlier: 3.565A pdb=" N TYR A 265 " --> pdb=" O GLN A 261 " (cutoff:3.500A) Processing helix chain 'A' and resid 271 through 299 removed outlier: 3.561A pdb=" N ARG A 277 " --> pdb=" O LEU A 273 " (cutoff:3.500A) Processing helix chain 'A' and resid 301 through 303 No H-bonds generated for 'chain 'A' and resid 301 through 303' Processing helix chain 'A' and resid 320 through 342 Processing helix chain 'A' and resid 356 through 361 removed outlier: 3.517A pdb=" N LEU A 360 " --> pdb=" O THR A 356 " (cutoff:3.500A) Processing helix chain 'A' and resid 362 through 364 No H-bonds generated for 'chain 'A' and resid 362 through 364' Processing helix chain 'A' and resid 365 through 385 removed outlier: 3.994A pdb=" N ASP A 369 " --> pdb=" O GLY A 365 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N TRP A 371 " --> pdb=" O TYR A 367 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N GLN A 372 " --> pdb=" O SER A 368 " (cutoff:3.500A) Processing helix chain 'A' and resid 387 through 395 removed outlier: 3.524A pdb=" N ASN A 395 " --> pdb=" O ILE A 391 " (cutoff:3.500A) Processing helix chain 'A' and resid 421 through 437 removed outlier: 3.704A pdb=" N GLY A 426 " --> pdb=" O LYS A 422 " (cutoff:3.500A) removed outlier: 4.188A pdb=" N ASN A 432 " --> pdb=" O ILE A 428 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N ASP A 433 " --> pdb=" O ALA A 429 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N ARG A 435 " --> pdb=" O SER A 431 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N ASP A 436 " --> pdb=" O ASN A 432 " (cutoff:3.500A) Processing helix chain 'A' and resid 460 through 471 Processing helix chain 'A' and resid 499 through 502 Processing helix chain 'A' and resid 503 through 510 removed outlier: 3.642A pdb=" N GLN A 509 " --> pdb=" O GLU A 505 " (cutoff:3.500A) Processing helix chain 'A' and resid 511 through 516 removed outlier: 3.856A pdb=" N VAL A 515 " --> pdb=" O ILE A 511 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N ASN A 516 " --> pdb=" O ALA A 512 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 511 through 516' Processing helix chain 'A' and resid 533 through 541 removed outlier: 3.782A pdb=" N ILE A 539 " --> pdb=" O GLY A 535 " (cutoff:3.500A) Processing helix chain 'A' and resid 548 through 571 removed outlier: 3.511A pdb=" N ALA A 553 " --> pdb=" O ILE A 549 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N GLU A 566 " --> pdb=" O PHE A 562 " (cutoff:3.500A) removed outlier: 4.623A pdb=" N LEU A 567 " --> pdb=" O PHE A 563 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N SER A 568 " --> pdb=" O LYS A 564 " (cutoff:3.500A) removed outlier: 4.081A pdb=" N ASN A 569 " --> pdb=" O PHE A 565 " (cutoff:3.500A) Processing helix chain 'A' and resid 592 through 611 removed outlier: 3.513A pdb=" N ILE A 596 " --> pdb=" O TRP A 592 " (cutoff:3.500A) Processing helix chain 'A' and resid 628 through 646 Processing helix chain 'A' and resid 661 through 667 Processing helix chain 'A' and resid 673 through 684 removed outlier: 3.501A pdb=" N THR A 682 " --> pdb=" O GLN A 678 " (cutoff:3.500A) Processing helix chain 'A' and resid 688 through 699 Processing helix chain 'A' and resid 704 through 717 removed outlier: 3.644A pdb=" N ALA A 708 " --> pdb=" O GLN A 704 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N ARG A 716 " --> pdb=" O TYR A 712 " (cutoff:3.500A) Processing helix chain 'A' and resid 720 through 733 removed outlier: 3.646A pdb=" N ASN A 733 " --> pdb=" O ALA A 729 " (cutoff:3.500A) Processing helix chain 'A' and resid 733 through 752 removed outlier: 3.779A pdb=" N VAL A 738 " --> pdb=" O LYS A 734 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'F' and resid 96 through 98 removed outlier: 3.611A pdb=" N SER F 3 " --> pdb=" O VAL F 156 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N PHE F 102 " --> pdb=" O ASP F 149 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'F' and resid 96 through 98 removed outlier: 3.611A pdb=" N SER F 3 " --> pdb=" O VAL F 156 " (cutoff:3.500A) removed outlier: 6.399A pdb=" N LYS F 4 " --> pdb=" O VAL F 202 " (cutoff:3.500A) removed outlier: 6.549A pdb=" N LYS F 10 " --> pdb=" O ILE F 196 " (cutoff:3.500A) removed outlier: 5.239A pdb=" N ILE F 196 " --> pdb=" O LYS F 10 " (cutoff:3.500A) removed outlier: 6.956A pdb=" N ASP F 12 " --> pdb=" O PHE F 194 " (cutoff:3.500A) removed outlier: 5.760A pdb=" N PHE F 194 " --> pdb=" O ASP F 12 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'F' and resid 119 through 127 Processing sheet with id=AA4, first strand: chain 'E' and resid 45 through 46 removed outlier: 3.505A pdb=" N PHE E 102 " --> pdb=" O ASP E 149 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'E' and resid 45 through 46 removed outlier: 3.505A pdb=" N PHE E 102 " --> pdb=" O ASP E 149 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N SER E 3 " --> pdb=" O VAL E 156 " (cutoff:3.500A) removed outlier: 6.915A pdb=" N LYS E 4 " --> pdb=" O THR E 201 " (cutoff:3.500A) removed outlier: 4.801A pdb=" N THR E 201 " --> pdb=" O LYS E 4 " (cutoff:3.500A) removed outlier: 5.939A pdb=" N ARG E 6 " --> pdb=" O ILE E 199 " (cutoff:3.500A) removed outlier: 4.234A pdb=" N ILE E 199 " --> pdb=" O ARG E 6 " (cutoff:3.500A) removed outlier: 6.954A pdb=" N VAL E 8 " --> pdb=" O ASP E 197 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'E' and resid 119 through 124 Processing sheet with id=AA7, first strand: chain 'D' and resid 96 through 98 Processing sheet with id=AA8, first strand: chain 'D' and resid 96 through 98 removed outlier: 3.911A pdb=" N SER D 3 " --> pdb=" O VAL D 156 " (cutoff:3.500A) removed outlier: 6.707A pdb=" N LYS D 4 " --> pdb=" O THR D 201 " (cutoff:3.500A) removed outlier: 4.667A pdb=" N THR D 201 " --> pdb=" O LYS D 4 " (cutoff:3.500A) removed outlier: 6.772A pdb=" N ARG D 6 " --> pdb=" O ILE D 199 " (cutoff:3.500A) removed outlier: 4.617A pdb=" N ILE D 199 " --> pdb=" O ARG D 6 " (cutoff:3.500A) removed outlier: 6.739A pdb=" N VAL D 8 " --> pdb=" O ASP D 197 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'D' and resid 85 through 87 removed outlier: 4.072A pdb=" N GLN D 87 " --> pdb=" O ALA D 90 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 119 through 127 Processing sheet with id=AB2, first strand: chain 'G' and resid 59 through 60 Processing sheet with id=AB3, first strand: chain 'G' and resid 59 through 60 Processing sheet with id=AB4, first strand: chain 'G' and resid 72 through 74 Processing sheet with id=AB5, first strand: chain 'G' and resid 127 through 136 Processing sheet with id=AB6, first strand: chain 'G' and resid 240 through 241 Processing sheet with id=AB7, first strand: chain 'G' and resid 244 through 247 Processing sheet with id=AB8, first strand: chain 'G' and resid 284 through 285 Processing sheet with id=AB9, first strand: chain 'I' and resid 102 through 103 removed outlier: 3.646A pdb=" N PHE I 102 " --> pdb=" O ASP I 149 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'I' and resid 102 through 103 removed outlier: 3.646A pdb=" N PHE I 102 " --> pdb=" O ASP I 149 " (cutoff:3.500A) removed outlier: 6.487A pdb=" N LYS I 4 " --> pdb=" O VAL I 202 " (cutoff:3.500A) removed outlier: 6.243A pdb=" N LYS I 10 " --> pdb=" O ILE I 196 " (cutoff:3.500A) removed outlier: 5.305A pdb=" N ILE I 196 " --> pdb=" O LYS I 10 " (cutoff:3.500A) removed outlier: 7.219A pdb=" N ASP I 12 " --> pdb=" O PHE I 194 " (cutoff:3.500A) removed outlier: 5.600A pdb=" N PHE I 194 " --> pdb=" O ASP I 12 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'I' and resid 37 through 38 removed outlier: 3.636A pdb=" N LEU I 43 " --> pdb=" O ASP I 38 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'I' and resid 119 through 127 Processing sheet with id=AC4, first strand: chain 'J' and resid 25 through 26 Processing sheet with id=AC5, first strand: chain 'H' and resid 166 through 167 Processing sheet with id=AC6, first strand: chain 'H' and resid 166 through 167 Processing sheet with id=AC7, first strand: chain 'H' and resid 19 through 25 removed outlier: 5.500A pdb=" N LYS H 22 " --> pdb=" O LEU H 128 " (cutoff:3.500A) removed outlier: 5.881A pdb=" N ASP H 125 " --> pdb=" O TYR H 196 " (cutoff:3.500A) removed outlier: 7.545A pdb=" N GLU H 198 " --> pdb=" O ASP H 125 " (cutoff:3.500A) removed outlier: 7.069A pdb=" N HIS H 127 " --> pdb=" O GLU H 198 " (cutoff:3.500A) removed outlier: 9.169A pdb=" N VAL H 200 " --> pdb=" O HIS H 127 " (cutoff:3.500A) removed outlier: 11.376A pdb=" N PHE H 129 " --> pdb=" O VAL H 200 " (cutoff:3.500A) removed outlier: 7.328A pdb=" N MET H 193 " --> pdb=" O ASP H 185 " (cutoff:3.500A) removed outlier: 7.546A pdb=" N ASP H 185 " --> pdb=" O MET H 193 " (cutoff:3.500A) removed outlier: 5.006A pdb=" N LEU H 195 " --> pdb=" O LYS H 183 " (cutoff:3.500A) removed outlier: 13.523A pdb=" N LEU H 178 " --> pdb=" O LEU H 91 " (cutoff:3.500A) removed outlier: 8.719A pdb=" N THR H 93 " --> pdb=" O LEU H 178 " (cutoff:3.500A) removed outlier: 8.079A pdb=" N ILE H 180 " --> pdb=" O THR H 93 " (cutoff:3.500A) removed outlier: 6.266A pdb=" N ARG H 95 " --> pdb=" O ILE H 180 " (cutoff:3.500A) removed outlier: 8.225A pdb=" N GLN H 182 " --> pdb=" O ARG H 95 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'A' and resid 305 through 309 removed outlier: 5.411A pdb=" N LEU A 305 " --> pdb=" O LEU A 316 " (cutoff:3.500A) removed outlier: 6.575A pdb=" N LEU A 316 " --> pdb=" O LEU A 305 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'A' and resid 448 through 450 removed outlier: 3.531A pdb=" N PHE A 439 " --> pdb=" O GLU A 459 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N ARG A 475 " --> pdb=" O VAL A 442 " (cutoff:3.500A) removed outlier: 6.932A pdb=" N ILE A 476 " --> pdb=" O THR A 490 " (cutoff:3.500A) removed outlier: 7.343A pdb=" N LEU A 492 " --> pdb=" O ILE A 476 " (cutoff:3.500A) removed outlier: 5.914A pdb=" N SER A 478 " --> pdb=" O LEU A 492 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'A' and resid 576 through 580 removed outlier: 7.053A pdb=" N PHE A 587 " --> pdb=" O ILE A 579 " (cutoff:3.500A) 1044 hydrogen bonds defined for protein. 3000 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 58 hydrogen bonds 116 hydrogen bond angles 0 basepair planarities 23 basepair parallelities 35 stacking parallelities Total time for adding SS restraints: 4.06 Time building geometry restraints manager: 2.45 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 6621 1.34 - 1.46: 4048 1.46 - 1.58: 10954 1.58 - 1.69: 143 1.69 - 1.81: 99 Bond restraints: 21865 Sorted by residual: bond pdb=" C ARG C 90 " pdb=" N GLU C 91 " ideal model delta sigma weight residual 1.331 1.398 -0.067 1.36e-02 5.41e+03 2.41e+01 bond pdb=" C LEU D 175 " pdb=" N LEU D 176 " ideal model delta sigma weight residual 1.335 1.278 0.057 1.36e-02 5.41e+03 1.75e+01 bond pdb=" N ILE I 192 " pdb=" CA ILE I 192 " ideal model delta sigma weight residual 1.457 1.501 -0.044 1.11e-02 8.12e+03 1.59e+01 bond pdb=" N PHE H 277 " pdb=" CA PHE H 277 " ideal model delta sigma weight residual 1.462 1.495 -0.033 8.50e-03 1.38e+04 1.53e+01 bond pdb=" C LEU D 176 " pdb=" N GLU D 177 " ideal model delta sigma weight residual 1.334 1.378 -0.044 1.27e-02 6.20e+03 1.20e+01 ... (remaining 21860 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.80: 27553 1.80 - 3.61: 1823 3.61 - 5.41: 301 5.41 - 7.22: 120 7.22 - 9.02: 10 Bond angle restraints: 29807 Sorted by residual: angle pdb=" N THR I 186 " pdb=" CA THR I 186 " pdb=" C THR I 186 " ideal model delta sigma weight residual 111.28 104.71 6.57 1.09e+00 8.42e-01 3.63e+01 angle pdb=" N ASN A 266 " pdb=" CA ASN A 266 " pdb=" C ASN A 266 " ideal model delta sigma weight residual 112.88 105.28 7.60 1.29e+00 6.01e-01 3.47e+01 angle pdb=" N SER A 268 " pdb=" CA SER A 268 " pdb=" C SER A 268 " ideal model delta sigma weight residual 111.28 105.10 6.18 1.09e+00 8.42e-01 3.22e+01 angle pdb=" N PHE H 270 " pdb=" CA PHE H 270 " pdb=" CB PHE H 270 " ideal model delta sigma weight residual 110.58 102.78 7.80 1.44e+00 4.82e-01 2.94e+01 angle pdb=" CA PHE D 150 " pdb=" CB PHE D 150 " pdb=" CG PHE D 150 " ideal model delta sigma weight residual 113.80 119.17 -5.37 1.00e+00 1.00e+00 2.89e+01 ... (remaining 29802 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.97: 12882 33.97 - 67.93: 373 67.93 - 101.90: 38 101.90 - 135.86: 1 135.86 - 169.83: 2 Dihedral angle restraints: 13296 sinusoidal: 6097 harmonic: 7199 Sorted by residual: dihedral pdb=" C5' C R 23 " pdb=" C4' C R 23 " pdb=" C3' C R 23 " pdb=" O3' C R 23 " ideal model delta sinusoidal sigma weight residual 147.00 110.10 36.90 1 8.00e+00 1.56e-02 3.00e+01 dihedral pdb=" C5' C R 29 " pdb=" C4' C R 29 " pdb=" C3' C R 29 " pdb=" O3' C R 29 " ideal model delta sinusoidal sigma weight residual 147.00 111.83 35.17 1 8.00e+00 1.56e-02 2.74e+01 dihedral pdb=" C3' C R 23 " pdb=" C4' C R 23 " pdb=" O4' C R 23 " pdb=" C1' C R 23 " ideal model delta sinusoidal sigma weight residual -2.00 30.74 -32.74 1 8.00e+00 1.56e-02 2.38e+01 ... (remaining 13293 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.115: 3049 0.115 - 0.230: 260 0.230 - 0.346: 25 0.346 - 0.461: 50 0.461 - 0.576: 21 Chirality restraints: 3405 Sorted by residual: chirality pdb=" P C T 8 " pdb=" OP1 C T 8 " pdb=" OP2 C T 8 " pdb=" O5' C T 8 " both_signs ideal model delta sigma weight residual True 2.41 -2.99 -0.58 2.00e-01 2.50e+01 8.29e+00 chirality pdb=" P U R 2 " pdb=" OP1 U R 2 " pdb=" OP2 U R 2 " pdb=" O5' U R 2 " both_signs ideal model delta sigma weight residual True 2.41 -2.96 -0.55 2.00e-01 2.50e+01 7.53e+00 chirality pdb=" P G R 5 " pdb=" OP1 G R 5 " pdb=" OP2 G R 5 " pdb=" O5' G R 5 " both_signs ideal model delta sigma weight residual True 2.41 -2.95 -0.54 2.00e-01 2.50e+01 7.28e+00 ... (remaining 3402 not shown) Planarity restraints: 3514 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG F 144 " -0.568 9.50e-02 1.11e+02 2.54e-01 3.96e+01 pdb=" NE ARG F 144 " 0.032 2.00e-02 2.50e+03 pdb=" CZ ARG F 144 " 0.011 2.00e-02 2.50e+03 pdb=" NH1 ARG F 144 " 0.003 2.00e-02 2.50e+03 pdb=" NH2 ARG F 144 " -0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG I 193 " 0.526 9.50e-02 1.11e+02 2.36e-01 3.40e+01 pdb=" NE ARG I 193 " -0.033 2.00e-02 2.50e+03 pdb=" CZ ARG I 193 " -0.002 2.00e-02 2.50e+03 pdb=" NH1 ARG I 193 " -0.005 2.00e-02 2.50e+03 pdb=" NH2 ARG I 193 " 0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG D 187 " -0.346 9.50e-02 1.11e+02 1.55e-01 1.49e+01 pdb=" NE ARG D 187 " 0.023 2.00e-02 2.50e+03 pdb=" CZ ARG D 187 " -0.002 2.00e-02 2.50e+03 pdb=" NH1 ARG D 187 " 0.005 2.00e-02 2.50e+03 pdb=" NH2 ARG D 187 " -0.010 2.00e-02 2.50e+03 ... (remaining 3511 not shown) Histogram of nonbonded interaction distances: 2.12 - 2.68: 532 2.68 - 3.23: 20840 3.23 - 3.79: 35836 3.79 - 4.34: 50128 4.34 - 4.90: 79925 Nonbonded interactions: 187261 Sorted by model distance: nonbonded pdb=" OH TYR A 514 " pdb=" OG SER A 577 " model vdw 2.123 3.040 nonbonded pdb=" OH TYR H 62 " pdb=" OG1 THR H 74 " model vdw 2.184 3.040 nonbonded pdb=" O VAL C 61 " pdb=" OG SER C 64 " model vdw 2.229 3.040 nonbonded pdb=" OG SER B 70 " pdb=" OD1 ASP B 72 " model vdw 2.230 3.040 nonbonded pdb=" NZ LYS F 4 " pdb=" OD1 ASN F 155 " model vdw 2.260 3.120 ... (remaining 187256 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' and resid 6 through 137) selection = (chain 'C' and (resid 6 through 28 or resid 35 through 137)) selection = (chain 'J' and (resid 6 through 28 or resid 35 through 137)) } ncs_group { reference = (chain 'D' and resid 2 through 211) selection = (chain 'E' and (resid 2 through 21 or resid 26 through 64 or resid 74 through 21 \ 1)) selection = (chain 'F' and (resid 2 through 21 or resid 26 through 64 or resid 74 through 21 \ 1)) selection = (chain 'I' and (resid 2 through 21 or resid 26 through 64 or resid 74 through 21 \ 1)) } 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=1.00 max=1.00 mean=1.00 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: 8.100 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: 0.020 Extract box with map and model: 0.360 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 19.430 Find NCS groups from input model: 0.250 Set up NCS constraints: 0.040 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: 0.000 Load rotamer database and sin/cos tables:6.120 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.390 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7800 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 : 0.007 0.067 21865 Z= 0.460 Angle : 0.992 9.021 29807 Z= 0.667 Chirality : 0.090 0.576 3405 Planarity : 0.009 0.254 3514 Dihedral : 15.181 169.830 8672 Min Nonbonded Distance : 2.123 Molprobity Statistics. All-atom Clashscore : 10.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.89 % Favored : 98.11 % Rotamer: Outliers : 2.03 % Allowed : 7.65 % Favored : 90.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.54 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.87 (0.16), residues: 2440 helix: 1.71 (0.15), residues: 1062 sheet: 0.06 (0.25), residues: 423 loop : -0.41 (0.19), residues: 955 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG I 187 TYR 0.024 0.001 TYR A 307 PHE 0.023 0.001 PHE D 150 TRP 0.005 0.001 TRP A 592 HIS 0.006 0.001 HIS I 18 Details of bonding type rmsd/Z covalent geometry : bond 0.00663 / 0.46 (21865) covalent geometry : angle 0.99216 / 0.67 (29807) hydrogen bonds : bond 0.18606 / 12.27 ( 1075) hydrogen bonds : angle 6.75726 / 4.81 ( 3116) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4880 Ramachandran restraints generated. 2440 Oldfield, 0 Emsley, 2440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4880 Ramachandran restraints generated. 2440 Oldfield, 0 Emsley, 2440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 533 residues out of total 2170 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 489 time to evaluate : 0.532 Fit side-chains revert: symmetry clash REVERT: F 6 ARG cc_start: 0.7886 (ttp80) cc_final: 0.7646 (ttp80) REVERT: F 28 ILE cc_start: 0.8665 (mt) cc_final: 0.8295 (mp) REVERT: F 45 ILE cc_start: 0.8196 (OUTLIER) cc_final: 0.7867 (tt) REVERT: E 28 ILE cc_start: 0.8105 (mt) cc_final: 0.7625 (mp) REVERT: E 167 GLU cc_start: 0.7895 (mm-30) cc_final: 0.7245 (tp30) REVERT: D 10 LYS cc_start: 0.8204 (ttpp) cc_final: 0.7984 (ttmt) REVERT: D 139 ILE cc_start: 0.8586 (pt) cc_final: 0.8376 (pt) REVERT: G 159 GLU cc_start: 0.7166 (mm-30) cc_final: 0.6850 (mm-30) REVERT: G 259 GLN cc_start: 0.7688 (pt0) cc_final: 0.7267 (pm20) REVERT: I 124 GLU cc_start: 0.7830 (OUTLIER) cc_final: 0.7113 (mt-10) REVERT: I 161 GLU cc_start: 0.6818 (OUTLIER) cc_final: 0.6515 (mt-10) REVERT: J 40 ASN cc_start: 0.7911 (m110) cc_final: 0.7685 (m110) REVERT: J 61 VAL cc_start: 0.5960 (t) cc_final: 0.5611 (t) REVERT: J 78 GLU cc_start: 0.8834 (mm-30) cc_final: 0.8624 (mm-30) REVERT: J 96 THR cc_start: 0.8279 (m) cc_final: 0.8025 (t) REVERT: H 22 LYS cc_start: 0.6837 (tttt) cc_final: 0.6187 (tppt) REVERT: H 79 GLU cc_start: 0.7459 (tt0) cc_final: 0.6646 (mp0) REVERT: H 145 LYS cc_start: 0.7139 (OUTLIER) cc_final: 0.6654 (tptt) REVERT: H 202 VAL cc_start: 0.8565 (m) cc_final: 0.8272 (t) REVERT: H 248 LYS cc_start: 0.7004 (mmmt) cc_final: 0.6801 (mmmt) REVERT: A 77 ILE cc_start: 0.6851 (mt) cc_final: 0.6255 (mt) REVERT: A 218 ILE cc_start: 0.8716 (mt) cc_final: 0.8512 (pt) REVERT: A 242 LYS cc_start: 0.7518 (mttt) cc_final: 0.7064 (mptt) REVERT: A 256 ASP cc_start: 0.4820 (t70) cc_final: 0.3098 (t70) REVERT: A 257 MET cc_start: 0.6710 (mtt) cc_final: 0.6247 (tpp) REVERT: A 297 ASP cc_start: 0.7694 (m-30) cc_final: 0.7429 (m-30) REVERT: A 350 ILE cc_start: 0.8160 (mt) cc_final: 0.7670 (pp) REVERT: A 352 TYR cc_start: 0.7816 (p90) cc_final: 0.7528 (p90) REVERT: A 378 LEU cc_start: 0.7004 (tp) cc_final: 0.6647 (tp) REVERT: A 569 ASN cc_start: 0.7147 (m110) cc_final: 0.6738 (t160) REVERT: A 572 LYS cc_start: 0.7221 (ttpp) cc_final: 0.6481 (ttpp) REVERT: A 671 LYS cc_start: 0.8149 (mttm) cc_final: 0.7783 (ptpt) REVERT: A 751 ILE cc_start: 0.7690 (tt) cc_final: 0.7428 (pt) outliers start: 44 outliers final: 9 residues processed: 516 average time/residue: 0.5145 time to fit residues: 306.4774 Evaluate side-chains 332 residues out of total 2170 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 319 time to evaluate : 0.770 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 45 ILE Chi-restraints excluded: chain E residue 36 VAL Chi-restraints excluded: chain I residue 124 GLU Chi-restraints excluded: chain I residue 161 GLU Chi-restraints excluded: chain J residue 14 LEU Chi-restraints excluded: chain H residue 41 VAL Chi-restraints excluded: chain H residue 145 LYS Chi-restraints excluded: chain H residue 212 ILE Chi-restraints excluded: chain H residue 327 ASN Chi-restraints excluded: chain A residue 21 TYR Chi-restraints excluded: chain A residue 281 PHE Chi-restraints excluded: chain A residue 388 LEU Chi-restraints excluded: chain A residue 542 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 216 optimal weight: 8.9990 chunk 98 optimal weight: 4.9990 chunk 194 optimal weight: 6.9990 chunk 227 optimal weight: 5.9990 chunk 107 optimal weight: 10.0000 chunk 10 optimal weight: 0.8980 chunk 66 optimal weight: 0.8980 chunk 247 optimal weight: 1.9990 chunk 130 optimal weight: 0.9990 chunk 124 optimal weight: 0.0170 chunk 103 optimal weight: 6.9990 overall best weight: 0.9622 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 34 GLN C 49 ASN C 56 HIS B 15 ASN B 56 HIS F 178 ASN E 69 GLN E 97 GLN E 125 ASN E 158 ASN D 97 GLN D 125 ASN D 155 ASN G 67 ASN G 252 GLN I 92 GLN J 24 ASN H 78 GLN H 80 GLN H 187 ASN A 2 ASN ** A 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 246 GLN A 261 GLN A 312 HIS A 678 GLN ** A 687 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 701 ASN A 706 ASN Total number of N/Q/H flips: 27 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4145 r_free = 0.4145 target = 0.180718 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3737 r_free = 0.3737 target = 0.138549 restraints weight = 26257.415| |-----------------------------------------------------------------------------| r_work (start): 0.3681 rms_B_bonded: 2.04 r_work: 0.3525 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.3412 rms_B_bonded: 4.20 restraints_weight: 0.2500 r_work (final): 0.3412 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7830 moved from start: 0.1736 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.085 21865 Z= 0.166 Angle : 0.608 11.731 29807 Z= 0.332 Chirality : 0.045 0.334 3405 Planarity : 0.004 0.042 3514 Dihedral : 15.444 166.401 3860 Min Nonbonded Distance : 2.360 Molprobity Statistics. All-atom Clashscore : 11.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.21 % Favored : 97.79 % Rotamer: Outliers : 4.42 % Allowed : 15.25 % Favored : 80.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.54 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.88 (0.16), residues: 2440 helix: 1.73 (0.15), residues: 1103 sheet: 0.16 (0.24), residues: 434 loop : -0.58 (0.19), residues: 903 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 517 TYR 0.031 0.002 TYR H 284 PHE 0.025 0.002 PHE A 563 TRP 0.007 0.001 TRP H 234 HIS 0.004 0.001 HIS F 151 Details of bonding type rmsd/Z covalent geometry : bond 0.00349 / 0.17 (21865) covalent geometry : angle 0.60793 / 0.33 (29807) hydrogen bonds : bond 0.05947 / 3.89 ( 1075) hydrogen bonds : angle 5.21258 / 3.71 ( 3116) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4880 Ramachandran restraints generated. 2440 Oldfield, 0 Emsley, 2440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4880 Ramachandran restraints generated. 2440 Oldfield, 0 Emsley, 2440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 454 residues out of total 2170 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 358 time to evaluate : 0.775 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 121 ASP cc_start: 0.8136 (OUTLIER) cc_final: 0.7409 (m-30) REVERT: C 127 GLU cc_start: 0.6691 (mt-10) cc_final: 0.6070 (mt-10) REVERT: B 11 MET cc_start: 0.5876 (tpp) cc_final: 0.5248 (tmm) REVERT: B 74 ARG cc_start: 0.7643 (mtp85) cc_final: 0.7273 (mtp-110) REVERT: F 28 ILE cc_start: 0.8636 (mt) cc_final: 0.8234 (mp) REVERT: E 28 ILE cc_start: 0.8176 (mt) cc_final: 0.7678 (mp) REVERT: E 167 GLU cc_start: 0.7850 (mm-30) cc_final: 0.7223 (tp30) REVERT: D 139 ILE cc_start: 0.8736 (pt) cc_final: 0.8525 (pt) REVERT: D 161 GLU cc_start: 0.7102 (OUTLIER) cc_final: 0.6849 (mp0) REVERT: G 159 GLU cc_start: 0.7209 (mm-30) cc_final: 0.6922 (mm-30) REVERT: G 259 GLN cc_start: 0.7626 (pt0) cc_final: 0.7257 (pm20) REVERT: G 277 GLN cc_start: 0.6911 (tp40) cc_final: 0.6601 (tp-100) REVERT: I 161 GLU cc_start: 0.6920 (OUTLIER) cc_final: 0.6627 (mt-10) REVERT: J 10 GLU cc_start: 0.5898 (tp30) cc_final: 0.5304 (pt0) REVERT: J 40 ASN cc_start: 0.7972 (m110) cc_final: 0.7742 (m110) REVERT: J 61 VAL cc_start: 0.6048 (t) cc_final: 0.5737 (t) REVERT: J 78 GLU cc_start: 0.8878 (mm-30) cc_final: 0.8429 (mm-30) REVERT: J 91 GLU cc_start: 0.7217 (tp30) cc_final: 0.6818 (tp30) REVERT: H 22 LYS cc_start: 0.7137 (tttt) cc_final: 0.6470 (mppt) REVERT: H 168 SER cc_start: 0.7630 (OUTLIER) cc_final: 0.7111 (p) REVERT: H 202 VAL cc_start: 0.8494 (m) cc_final: 0.8214 (t) REVERT: H 212 ILE cc_start: 0.6756 (OUTLIER) cc_final: 0.6320 (pp) REVERT: A 77 ILE cc_start: 0.6720 (mt) cc_final: 0.6282 (mt) REVERT: A 242 LYS cc_start: 0.7469 (mttt) cc_final: 0.7032 (mptt) REVERT: A 252 LEU cc_start: 0.6279 (tt) cc_final: 0.5979 (tp) REVERT: A 321 GLU cc_start: 0.6848 (tp30) cc_final: 0.6144 (tm-30) REVERT: A 445 GLU cc_start: 0.7724 (mp0) cc_final: 0.7506 (mm-30) REVERT: A 455 TYR cc_start: 0.7390 (m-80) cc_final: 0.7174 (m-10) REVERT: A 469 LYS cc_start: 0.7085 (mttm) cc_final: 0.6878 (mmtt) REVERT: A 569 ASN cc_start: 0.7143 (m110) cc_final: 0.6906 (m-40) REVERT: A 655 ASN cc_start: 0.7368 (OUTLIER) cc_final: 0.7130 (m-40) REVERT: A 671 LYS cc_start: 0.8140 (mttm) cc_final: 0.7834 (ptpt) REVERT: A 722 GLU cc_start: 0.7452 (OUTLIER) cc_final: 0.7143 (pp20) REVERT: A 751 ILE cc_start: 0.7660 (tt) cc_final: 0.7391 (pt) outliers start: 96 outliers final: 34 residues processed: 422 average time/residue: 0.5151 time to fit residues: 251.9025 Evaluate side-chains 349 residues out of total 2170 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 308 time to evaluate : 0.700 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 12 ILE Chi-restraints excluded: chain C residue 67 THR Chi-restraints excluded: chain C residue 108 ASP Chi-restraints excluded: chain C residue 121 ASP Chi-restraints excluded: chain B residue 6 THR Chi-restraints excluded: chain B residue 44 THR Chi-restraints excluded: chain B residue 67 THR Chi-restraints excluded: chain B residue 68 THR Chi-restraints excluded: chain B residue 115 THR Chi-restraints excluded: chain F residue 26 SER Chi-restraints excluded: chain F residue 126 THR Chi-restraints excluded: chain E residue 36 VAL Chi-restraints excluded: chain E residue 202 VAL Chi-restraints excluded: chain D residue 125 ASN Chi-restraints excluded: chain D residue 161 GLU Chi-restraints excluded: chain G residue 95 LYS Chi-restraints excluded: chain G residue 140 VAL Chi-restraints excluded: chain I residue 38 ASP Chi-restraints excluded: chain I residue 78 GLU Chi-restraints excluded: chain I residue 161 GLU Chi-restraints excluded: chain J residue 14 LEU Chi-restraints excluded: chain J residue 28 LYS Chi-restraints excluded: chain J residue 59 THR Chi-restraints excluded: chain H residue 41 VAL Chi-restraints excluded: chain H residue 168 SER Chi-restraints excluded: chain H residue 209 THR Chi-restraints excluded: chain H residue 212 ILE Chi-restraints excluded: chain H residue 290 GLU Chi-restraints excluded: chain A residue 21 TYR Chi-restraints excluded: chain A residue 204 LEU Chi-restraints excluded: chain A residue 260 ILE Chi-restraints excluded: chain A residue 281 PHE Chi-restraints excluded: chain A residue 289 SER Chi-restraints excluded: chain A residue 316 LEU Chi-restraints excluded: chain A residue 374 VAL Chi-restraints excluded: chain A residue 388 LEU Chi-restraints excluded: chain A residue 458 VAL Chi-restraints excluded: chain A residue 519 VAL Chi-restraints excluded: chain A residue 542 ILE Chi-restraints excluded: chain A residue 655 ASN Chi-restraints excluded: chain A residue 722 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 73 optimal weight: 0.7980 chunk 246 optimal weight: 0.9980 chunk 182 optimal weight: 0.9980 chunk 181 optimal weight: 8.9990 chunk 204 optimal weight: 3.9990 chunk 95 optimal weight: 0.3980 chunk 118 optimal weight: 6.9990 chunk 214 optimal weight: 9.9990 chunk 163 optimal weight: 0.9980 chunk 29 optimal weight: 2.9990 chunk 184 optimal weight: 3.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 56 HIS B 56 HIS F 178 ASN ** D 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 184 GLN I 178 ASN J 49 ASN ** A 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 159 ASN ** A 687 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 704 GLN A 725 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4143 r_free = 0.4143 target = 0.180653 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3738 r_free = 0.3738 target = 0.138885 restraints weight = 26377.946| |-----------------------------------------------------------------------------| r_work (start): 0.3690 rms_B_bonded: 2.01 r_work: 0.3525 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.3410 rms_B_bonded: 4.25 restraints_weight: 0.2500 r_work (final): 0.3410 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7838 moved from start: 0.2126 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 21865 Z= 0.148 Angle : 0.567 11.574 29807 Z= 0.311 Chirality : 0.043 0.352 3405 Planarity : 0.004 0.040 3514 Dihedral : 15.269 164.535 3849 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 10.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Rotamer: Outliers : 4.06 % Allowed : 17.28 % Favored : 78.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.54 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.84 (0.16), residues: 2440 helix: 1.73 (0.15), residues: 1097 sheet: 0.07 (0.24), residues: 424 loop : -0.58 (0.18), residues: 919 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 466 TYR 0.023 0.001 TYR A 307 PHE 0.023 0.002 PHE D 150 TRP 0.006 0.001 TRP H 237 HIS 0.004 0.001 HIS H 283 Details of bonding type rmsd/Z covalent geometry : bond 0.00310 / 0.15 (21865) covalent geometry : angle 0.56721 / 0.31 (29807) hydrogen bonds : bond 0.05023 / 3.30 ( 1075) hydrogen bonds : angle 4.96182 / 3.51 ( 3116) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4880 Ramachandran restraints generated. 2440 Oldfield, 0 Emsley, 2440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4880 Ramachandran restraints generated. 2440 Oldfield, 0 Emsley, 2440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 413 residues out of total 2170 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 325 time to evaluate : 0.960 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 11 MET cc_start: 0.5896 (tpp) cc_final: 0.5476 (tmm) REVERT: B 25 LYS cc_start: 0.7948 (OUTLIER) cc_final: 0.7744 (tptp) REVERT: B 74 ARG cc_start: 0.7631 (mtp85) cc_final: 0.7265 (mtp-110) REVERT: F 28 ILE cc_start: 0.8669 (mt) cc_final: 0.8395 (mp) REVERT: F 45 ILE cc_start: 0.8215 (OUTLIER) cc_final: 0.7896 (tt) REVERT: F 105 LYS cc_start: 0.8414 (OUTLIER) cc_final: 0.8193 (ttmm) REVERT: E 28 ILE cc_start: 0.8125 (mt) cc_final: 0.7618 (mp) REVERT: E 167 GLU cc_start: 0.7886 (mm-30) cc_final: 0.7255 (tp30) REVERT: D 161 GLU cc_start: 0.7055 (OUTLIER) cc_final: 0.6817 (mp0) REVERT: G 159 GLU cc_start: 0.7188 (mm-30) cc_final: 0.6898 (mm-30) REVERT: G 213 LEU cc_start: 0.6973 (tt) cc_final: 0.6468 (mt) REVERT: G 277 GLN cc_start: 0.6976 (tp40) cc_final: 0.6650 (tp-100) REVERT: G 303 LEU cc_start: 0.7335 (OUTLIER) cc_final: 0.7120 (mp) REVERT: I 161 GLU cc_start: 0.6939 (OUTLIER) cc_final: 0.6606 (mt-10) REVERT: J 10 GLU cc_start: 0.5865 (tp30) cc_final: 0.5266 (pt0) REVERT: J 40 ASN cc_start: 0.7990 (m110) cc_final: 0.7770 (m110) REVERT: J 59 THR cc_start: 0.8032 (OUTLIER) cc_final: 0.7648 (m) REVERT: J 61 VAL cc_start: 0.6108 (t) cc_final: 0.5789 (t) REVERT: J 78 GLU cc_start: 0.8894 (mm-30) cc_final: 0.8576 (mm-30) REVERT: J 91 GLU cc_start: 0.7227 (tp30) cc_final: 0.6833 (tp30) REVERT: H 22 LYS cc_start: 0.7105 (tttt) cc_final: 0.6464 (mppt) REVERT: H 94 GLU cc_start: 0.7269 (mt-10) cc_final: 0.6989 (mt-10) REVERT: H 168 SER cc_start: 0.7516 (p) cc_final: 0.6952 (p) REVERT: H 202 VAL cc_start: 0.8476 (m) cc_final: 0.8213 (t) REVERT: H 212 ILE cc_start: 0.6779 (OUTLIER) cc_final: 0.6352 (pp) REVERT: A 206 ASP cc_start: 0.7288 (t0) cc_final: 0.7044 (t0) REVERT: A 242 LYS cc_start: 0.7551 (mttt) cc_final: 0.7116 (mptt) REVERT: A 288 GLU cc_start: 0.6795 (mm-30) cc_final: 0.6503 (tt0) REVERT: A 321 GLU cc_start: 0.6857 (tp30) cc_final: 0.6173 (tm-30) REVERT: A 361 MET cc_start: 0.5420 (OUTLIER) cc_final: 0.5053 (ttt) REVERT: A 439 PHE cc_start: 0.8007 (m-80) cc_final: 0.7515 (m-10) REVERT: A 469 LYS cc_start: 0.7047 (mttm) cc_final: 0.6842 (mmtt) REVERT: A 569 ASN cc_start: 0.7078 (m110) cc_final: 0.6815 (t0) REVERT: A 642 LEU cc_start: 0.6025 (OUTLIER) cc_final: 0.5792 (mp) REVERT: A 655 ASN cc_start: 0.7432 (OUTLIER) cc_final: 0.7199 (m-40) REVERT: A 671 LYS cc_start: 0.8109 (mttm) cc_final: 0.7820 (ptpt) REVERT: A 722 GLU cc_start: 0.7523 (OUTLIER) cc_final: 0.7154 (pp20) REVERT: A 751 ILE cc_start: 0.7643 (tt) cc_final: 0.7376 (pt) outliers start: 88 outliers final: 35 residues processed: 381 average time/residue: 0.5087 time to fit residues: 226.1953 Evaluate side-chains 328 residues out of total 2170 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 281 time to evaluate : 0.606 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 13 ASP Chi-restraints excluded: chain C residue 42 LEU Chi-restraints excluded: chain C residue 67 THR Chi-restraints excluded: chain C residue 103 VAL Chi-restraints excluded: chain C residue 104 ASP Chi-restraints excluded: chain B residue 6 THR Chi-restraints excluded: chain B residue 25 LYS Chi-restraints excluded: chain B residue 68 THR Chi-restraints excluded: chain B residue 103 VAL Chi-restraints excluded: chain B residue 115 THR Chi-restraints excluded: chain F residue 26 SER Chi-restraints excluded: chain F residue 45 ILE Chi-restraints excluded: chain F residue 105 LYS Chi-restraints excluded: chain F residue 126 THR Chi-restraints excluded: chain F residue 133 VAL Chi-restraints excluded: chain F residue 186 THR Chi-restraints excluded: chain E residue 36 VAL Chi-restraints excluded: chain E residue 202 VAL Chi-restraints excluded: chain D residue 161 GLU Chi-restraints excluded: chain D residue 211 LEU Chi-restraints excluded: chain G residue 95 LYS Chi-restraints excluded: chain G residue 140 VAL Chi-restraints excluded: chain G residue 212 LEU Chi-restraints excluded: chain G residue 303 LEU Chi-restraints excluded: chain I residue 78 GLU Chi-restraints excluded: chain I residue 161 GLU Chi-restraints excluded: chain J residue 14 LEU Chi-restraints excluded: chain J residue 59 THR Chi-restraints excluded: chain H residue 23 ILE Chi-restraints excluded: chain H residue 41 VAL Chi-restraints excluded: chain H residue 142 SER Chi-restraints excluded: chain H residue 153 GLU Chi-restraints excluded: chain H residue 209 THR Chi-restraints excluded: chain H residue 212 ILE Chi-restraints excluded: chain A residue 260 ILE Chi-restraints excluded: chain A residue 281 PHE Chi-restraints excluded: chain A residue 289 SER Chi-restraints excluded: chain A residue 315 LEU Chi-restraints excluded: chain A residue 361 MET Chi-restraints excluded: chain A residue 374 VAL Chi-restraints excluded: chain A residue 388 LEU Chi-restraints excluded: chain A residue 542 ILE Chi-restraints excluded: chain A residue 642 LEU Chi-restraints excluded: chain A residue 655 ASN Chi-restraints excluded: chain A residue 687 HIS Chi-restraints excluded: chain A residue 695 MET Chi-restraints excluded: chain A residue 722 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 81 optimal weight: 1.9990 chunk 22 optimal weight: 0.9990 chunk 55 optimal weight: 0.0970 chunk 140 optimal weight: 3.9990 chunk 204 optimal weight: 0.8980 chunk 202 optimal weight: 5.9990 chunk 177 optimal weight: 0.9990 chunk 7 optimal weight: 0.9980 chunk 125 optimal weight: 0.6980 chunk 27 optimal weight: 6.9990 chunk 61 optimal weight: 0.8980 overall best weight: 0.7178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 56 HIS B 56 HIS F 178 ASN ** D 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 187 ASN ** A 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 59 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 687 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4149 r_free = 0.4149 target = 0.181232 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3750 r_free = 0.3750 target = 0.140021 restraints weight = 26433.610| |-----------------------------------------------------------------------------| r_work (start): 0.3702 rms_B_bonded: 2.05 r_work: 0.3532 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.3416 rms_B_bonded: 4.29 restraints_weight: 0.2500 r_work (final): 0.3416 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7810 moved from start: 0.2370 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 21865 Z= 0.131 Angle : 0.544 9.643 29807 Z= 0.297 Chirality : 0.042 0.367 3405 Planarity : 0.004 0.048 3514 Dihedral : 15.195 163.951 3847 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 10.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer: Outliers : 4.29 % Allowed : 18.53 % Favored : 77.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.54 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.88 (0.16), residues: 2440 helix: 1.74 (0.15), residues: 1097 sheet: 0.18 (0.25), residues: 409 loop : -0.58 (0.18), residues: 934 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A 466 TYR 0.026 0.001 TYR A 219 PHE 0.029 0.002 PHE E 150 TRP 0.006 0.001 TRP A 187 HIS 0.004 0.001 HIS E 151 Details of bonding type rmsd/Z covalent geometry : bond 0.00275 / 0.13 (21865) covalent geometry : angle 0.54442 / 0.30 (29807) hydrogen bonds : bond 0.04670 / 3.07 ( 1075) hydrogen bonds : angle 4.81923 / 3.40 ( 3116) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4880 Ramachandran restraints generated. 2440 Oldfield, 0 Emsley, 2440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4880 Ramachandran restraints generated. 2440 Oldfield, 0 Emsley, 2440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 401 residues out of total 2170 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 308 time to evaluate : 0.677 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 121 ASP cc_start: 0.8052 (OUTLIER) cc_final: 0.7362 (m-30) REVERT: C 127 GLU cc_start: 0.6742 (mt-10) cc_final: 0.6177 (mt-10) REVERT: B 11 MET cc_start: 0.5852 (tpp) cc_final: 0.5493 (tmm) REVERT: B 25 LYS cc_start: 0.7902 (OUTLIER) cc_final: 0.7689 (tptp) REVERT: B 35 GLU cc_start: 0.7415 (mp0) cc_final: 0.7069 (mm-30) REVERT: B 74 ARG cc_start: 0.7624 (mtp85) cc_final: 0.7294 (mtp-110) REVERT: F 28 ILE cc_start: 0.8657 (mt) cc_final: 0.8372 (mp) REVERT: F 45 ILE cc_start: 0.8177 (OUTLIER) cc_final: 0.7858 (tt) REVERT: F 105 LYS cc_start: 0.8408 (OUTLIER) cc_final: 0.8178 (ttmm) REVERT: E 28 ILE cc_start: 0.8109 (mt) cc_final: 0.7586 (mp) REVERT: E 167 GLU cc_start: 0.7872 (mm-30) cc_final: 0.7226 (tp30) REVERT: D 124 GLU cc_start: 0.8446 (OUTLIER) cc_final: 0.8183 (mt-10) REVERT: D 161 GLU cc_start: 0.6944 (OUTLIER) cc_final: 0.6687 (mp0) REVERT: G 95 LYS cc_start: 0.7196 (OUTLIER) cc_final: 0.6500 (pptt) REVERT: G 159 GLU cc_start: 0.7135 (mm-30) cc_final: 0.6854 (mm-30) REVERT: G 213 LEU cc_start: 0.6993 (tt) cc_final: 0.6525 (mt) REVERT: G 277 GLN cc_start: 0.6980 (tp40) cc_final: 0.6658 (tp-100) REVERT: G 303 LEU cc_start: 0.7341 (OUTLIER) cc_final: 0.7112 (mp) REVERT: I 161 GLU cc_start: 0.6926 (OUTLIER) cc_final: 0.6607 (mt-10) REVERT: J 40 ASN cc_start: 0.7946 (m110) cc_final: 0.7726 (m110) REVERT: J 59 THR cc_start: 0.7942 (OUTLIER) cc_final: 0.7572 (m) REVERT: J 61 VAL cc_start: 0.6141 (t) cc_final: 0.5809 (t) REVERT: H 22 LYS cc_start: 0.7133 (tttt) cc_final: 0.6502 (tppt) REVERT: H 168 SER cc_start: 0.7496 (p) cc_final: 0.6868 (p) REVERT: H 202 VAL cc_start: 0.8430 (m) cc_final: 0.8156 (t) REVERT: H 212 ILE cc_start: 0.6772 (OUTLIER) cc_final: 0.6351 (pp) REVERT: A 59 HIS cc_start: 0.4436 (OUTLIER) cc_final: 0.4069 (p-80) REVERT: A 80 ILE cc_start: 0.7496 (OUTLIER) cc_final: 0.7210 (pp) REVERT: A 242 LYS cc_start: 0.7642 (mttt) cc_final: 0.7173 (mptt) REVERT: A 439 PHE cc_start: 0.7926 (m-80) cc_final: 0.7511 (m-10) REVERT: A 469 LYS cc_start: 0.7055 (mttm) cc_final: 0.6834 (mmtt) REVERT: A 563 PHE cc_start: 0.5483 (OUTLIER) cc_final: 0.5137 (t80) REVERT: A 566 GLU cc_start: 0.7589 (tp30) cc_final: 0.7368 (tp30) REVERT: A 569 ASN cc_start: 0.7029 (m110) cc_final: 0.6747 (t0) REVERT: A 608 ARG cc_start: 0.5965 (mtm110) cc_final: 0.5606 (ttm170) REVERT: A 642 LEU cc_start: 0.5944 (OUTLIER) cc_final: 0.5699 (mp) REVERT: A 655 ASN cc_start: 0.7498 (OUTLIER) cc_final: 0.7291 (m-40) REVERT: A 671 LYS cc_start: 0.8100 (mttm) cc_final: 0.7817 (ptpt) REVERT: A 751 ILE cc_start: 0.7623 (tt) cc_final: 0.7364 (pt) outliers start: 93 outliers final: 38 residues processed: 377 average time/residue: 0.5298 time to fit residues: 232.8634 Evaluate side-chains 324 residues out of total 2170 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 270 time to evaluate : 0.911 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 12 ILE Chi-restraints excluded: chain C residue 67 THR Chi-restraints excluded: chain C residue 103 VAL Chi-restraints excluded: chain C residue 121 ASP Chi-restraints excluded: chain B residue 6 THR Chi-restraints excluded: chain B residue 14 LEU Chi-restraints excluded: chain B residue 25 LYS Chi-restraints excluded: chain B residue 44 THR Chi-restraints excluded: chain B residue 68 THR Chi-restraints excluded: chain B residue 103 VAL Chi-restraints excluded: chain B residue 115 THR Chi-restraints excluded: chain F residue 10 LYS Chi-restraints excluded: chain F residue 26 SER Chi-restraints excluded: chain F residue 45 ILE Chi-restraints excluded: chain F residue 79 ILE Chi-restraints excluded: chain F residue 105 LYS Chi-restraints excluded: chain F residue 119 THR Chi-restraints excluded: chain F residue 126 THR Chi-restraints excluded: chain F residue 133 VAL Chi-restraints excluded: chain E residue 33 SER Chi-restraints excluded: chain E residue 202 VAL Chi-restraints excluded: chain D residue 124 GLU Chi-restraints excluded: chain D residue 161 GLU Chi-restraints excluded: chain G residue 95 LYS Chi-restraints excluded: chain G residue 140 VAL Chi-restraints excluded: chain G residue 212 LEU Chi-restraints excluded: chain G residue 303 LEU Chi-restraints excluded: chain I residue 78 GLU Chi-restraints excluded: chain I residue 161 GLU Chi-restraints excluded: chain J residue 14 LEU Chi-restraints excluded: chain J residue 28 LYS Chi-restraints excluded: chain J residue 59 THR Chi-restraints excluded: chain H residue 41 VAL Chi-restraints excluded: chain H residue 153 GLU Chi-restraints excluded: chain H residue 209 THR Chi-restraints excluded: chain H residue 212 ILE Chi-restraints excluded: chain H residue 341 LEU Chi-restraints excluded: chain A residue 59 HIS Chi-restraints excluded: chain A residue 77 ILE Chi-restraints excluded: chain A residue 80 ILE Chi-restraints excluded: chain A residue 204 LEU Chi-restraints excluded: chain A residue 225 MET Chi-restraints excluded: chain A residue 260 ILE Chi-restraints excluded: chain A residue 281 PHE Chi-restraints excluded: chain A residue 315 LEU Chi-restraints excluded: chain A residue 374 VAL Chi-restraints excluded: chain A residue 388 LEU Chi-restraints excluded: chain A residue 408 CYS Chi-restraints excluded: chain A residue 549 ILE Chi-restraints excluded: chain A residue 563 PHE Chi-restraints excluded: chain A residue 642 LEU Chi-restraints excluded: chain A residue 655 ASN Chi-restraints excluded: chain A residue 687 HIS Chi-restraints excluded: chain A residue 695 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 11 optimal weight: 0.9990 chunk 146 optimal weight: 8.9990 chunk 79 optimal weight: 3.9990 chunk 224 optimal weight: 5.9990 chunk 137 optimal weight: 0.9980 chunk 197 optimal weight: 7.9990 chunk 219 optimal weight: 0.7980 chunk 140 optimal weight: 4.9990 chunk 123 optimal weight: 2.9990 chunk 33 optimal weight: 4.9990 chunk 129 optimal weight: 4.9990 overall best weight: 1.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 56 HIS B 56 HIS F 178 ASN D 18 HIS D 125 ASN D 174 HIS G 57 ASN ** G 198 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 189 ASN ** H 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 187 ASN ** A 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 687 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4103 r_free = 0.4103 target = 0.176683 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3692 r_free = 0.3692 target = 0.134891 restraints weight = 26279.512| |-----------------------------------------------------------------------------| r_work (start): 0.3643 rms_B_bonded: 2.00 r_work: 0.3468 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.3354 rms_B_bonded: 4.18 restraints_weight: 0.2500 r_work (final): 0.3354 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7921 moved from start: 0.2499 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.062 21865 Z= 0.206 Angle : 0.612 13.161 29807 Z= 0.329 Chirality : 0.045 0.380 3405 Planarity : 0.004 0.046 3514 Dihedral : 15.191 168.212 3844 Min Nonbonded Distance : 2.409 Molprobity Statistics. All-atom Clashscore : 11.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Rotamer: Outliers : 5.07 % Allowed : 18.29 % Favored : 76.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.54 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.67 (0.16), residues: 2440 helix: 1.55 (0.15), residues: 1097 sheet: 0.06 (0.25), residues: 409 loop : -0.65 (0.18), residues: 934 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 466 TYR 0.028 0.002 TYR A 219 PHE 0.030 0.002 PHE C 16 TRP 0.011 0.001 TRP A 493 HIS 0.006 0.001 HIS F 151 Details of bonding type rmsd/Z covalent geometry : bond 0.00464 / 0.21 (21865) covalent geometry : angle 0.61198 / 0.33 (29807) hydrogen bonds : bond 0.04989 / 3.28 ( 1075) hydrogen bonds : angle 4.90550 / 3.47 ( 3116) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4880 Ramachandran restraints generated. 2440 Oldfield, 0 Emsley, 2440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4880 Ramachandran restraints generated. 2440 Oldfield, 0 Emsley, 2440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 399 residues out of total 2170 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 110 poor density : 289 time to evaluate : 1.044 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 121 ASP cc_start: 0.8105 (OUTLIER) cc_final: 0.7383 (m-30) REVERT: B 11 MET cc_start: 0.5892 (tpp) cc_final: 0.5559 (tmm) REVERT: B 35 GLU cc_start: 0.7432 (mp0) cc_final: 0.7177 (mm-30) REVERT: B 47 LEU cc_start: 0.8696 (OUTLIER) cc_final: 0.8271 (tt) REVERT: F 28 ILE cc_start: 0.8768 (mt) cc_final: 0.8512 (mp) REVERT: F 45 ILE cc_start: 0.8293 (OUTLIER) cc_final: 0.7967 (tt) REVERT: F 105 LYS cc_start: 0.8456 (OUTLIER) cc_final: 0.8232 (ttmm) REVERT: E 28 ILE cc_start: 0.8156 (mt) cc_final: 0.7680 (mp) REVERT: E 42 ARG cc_start: 0.8103 (OUTLIER) cc_final: 0.7026 (mtm180) REVERT: E 120 GLU cc_start: 0.8666 (OUTLIER) cc_final: 0.7851 (pm20) REVERT: E 167 GLU cc_start: 0.7893 (mm-30) cc_final: 0.7255 (tp30) REVERT: D 124 GLU cc_start: 0.8567 (OUTLIER) cc_final: 0.8265 (mt-10) REVERT: D 161 GLU cc_start: 0.6991 (OUTLIER) cc_final: 0.6730 (mp0) REVERT: G 95 LYS cc_start: 0.7233 (OUTLIER) cc_final: 0.6540 (pptt) REVERT: G 111 GLU cc_start: 0.7649 (OUTLIER) cc_final: 0.7428 (mp0) REVERT: G 159 GLU cc_start: 0.7172 (mm-30) cc_final: 0.6912 (mm-30) REVERT: G 213 LEU cc_start: 0.7114 (tt) cc_final: 0.6558 (mp) REVERT: G 259 GLN cc_start: 0.7602 (pt0) cc_final: 0.7229 (pm20) REVERT: G 277 GLN cc_start: 0.7002 (tp40) cc_final: 0.6711 (tp-100) REVERT: I 55 MET cc_start: 0.8223 (OUTLIER) cc_final: 0.7949 (mtp) REVERT: I 161 GLU cc_start: 0.6974 (OUTLIER) cc_final: 0.6714 (mt-10) REVERT: J 40 ASN cc_start: 0.8002 (m110) cc_final: 0.7795 (m110) REVERT: J 59 THR cc_start: 0.7976 (OUTLIER) cc_final: 0.7592 (m) REVERT: J 78 GLU cc_start: 0.8903 (mm-30) cc_final: 0.8603 (mm-30) REVERT: J 91 GLU cc_start: 0.7235 (tp30) cc_final: 0.6779 (tp30) REVERT: H 22 LYS cc_start: 0.7162 (tttt) cc_final: 0.6533 (tppt) REVERT: H 200 VAL cc_start: 0.8002 (OUTLIER) cc_final: 0.7768 (p) REVERT: H 202 VAL cc_start: 0.8442 (m) cc_final: 0.8174 (t) REVERT: H 212 ILE cc_start: 0.6902 (OUTLIER) cc_final: 0.6502 (pp) REVERT: A 80 ILE cc_start: 0.7479 (OUTLIER) cc_final: 0.7226 (pp) REVERT: A 242 LYS cc_start: 0.7813 (mttt) cc_final: 0.7234 (mppt) REVERT: A 281 PHE cc_start: 0.7212 (OUTLIER) cc_final: 0.6487 (p90) REVERT: A 361 MET cc_start: 0.6370 (OUTLIER) cc_final: 0.5339 (tpt) REVERT: A 439 PHE cc_start: 0.7992 (m-80) cc_final: 0.7588 (m-10) REVERT: A 469 LYS cc_start: 0.7188 (mttm) cc_final: 0.6901 (mmtt) REVERT: A 563 PHE cc_start: 0.5534 (OUTLIER) cc_final: 0.5101 (t80) REVERT: A 569 ASN cc_start: 0.7073 (m110) cc_final: 0.6751 (t160) REVERT: A 608 ARG cc_start: 0.5912 (mtm110) cc_final: 0.5686 (ttm170) REVERT: A 671 LYS cc_start: 0.8152 (mttm) cc_final: 0.7825 (ptpt) REVERT: A 674 MET cc_start: 0.7478 (OUTLIER) cc_final: 0.6621 (tmm) REVERT: A 751 ILE cc_start: 0.7567 (tt) cc_final: 0.7237 (pt) outliers start: 110 outliers final: 53 residues processed: 367 average time/residue: 0.5428 time to fit residues: 231.7264 Evaluate side-chains 343 residues out of total 2170 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 270 time to evaluate : 0.817 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 12 ILE Chi-restraints excluded: chain C residue 67 THR Chi-restraints excluded: chain C residue 103 VAL Chi-restraints excluded: chain C residue 115 THR Chi-restraints excluded: chain C residue 121 ASP Chi-restraints excluded: chain B residue 6 THR Chi-restraints excluded: chain B residue 14 LEU Chi-restraints excluded: chain B residue 44 THR Chi-restraints excluded: chain B residue 47 LEU Chi-restraints excluded: chain B residue 68 THR Chi-restraints excluded: chain B residue 103 VAL Chi-restraints excluded: chain B residue 115 THR Chi-restraints excluded: chain F residue 10 LYS Chi-restraints excluded: chain F residue 26 SER Chi-restraints excluded: chain F residue 45 ILE Chi-restraints excluded: chain F residue 105 LYS Chi-restraints excluded: chain F residue 119 THR Chi-restraints excluded: chain F residue 126 THR Chi-restraints excluded: chain F residue 133 VAL Chi-restraints excluded: chain E residue 31 ILE Chi-restraints excluded: chain E residue 33 SER Chi-restraints excluded: chain E residue 36 VAL Chi-restraints excluded: chain E residue 42 ARG Chi-restraints excluded: chain E residue 91 ILE Chi-restraints excluded: chain E residue 120 GLU Chi-restraints excluded: chain E residue 143 THR Chi-restraints excluded: chain E residue 202 VAL Chi-restraints excluded: chain D residue 124 GLU Chi-restraints excluded: chain D residue 161 GLU Chi-restraints excluded: chain G residue 95 LYS Chi-restraints excluded: chain G residue 102 GLU Chi-restraints excluded: chain G residue 111 GLU Chi-restraints excluded: chain G residue 140 VAL Chi-restraints excluded: chain G residue 212 LEU Chi-restraints excluded: chain I residue 15 THR Chi-restraints excluded: chain I residue 55 MET Chi-restraints excluded: chain I residue 78 GLU Chi-restraints excluded: chain I residue 161 GLU Chi-restraints excluded: chain J residue 14 LEU Chi-restraints excluded: chain J residue 52 GLU Chi-restraints excluded: chain J residue 59 THR Chi-restraints excluded: chain H residue 23 ILE Chi-restraints excluded: chain H residue 41 VAL Chi-restraints excluded: chain H residue 153 GLU Chi-restraints excluded: chain H residue 200 VAL Chi-restraints excluded: chain H residue 209 THR Chi-restraints excluded: chain H residue 212 ILE Chi-restraints excluded: chain H residue 326 VAL Chi-restraints excluded: chain H residue 338 VAL Chi-restraints excluded: chain A residue 77 ILE Chi-restraints excluded: chain A residue 80 ILE Chi-restraints excluded: chain A residue 157 LEU Chi-restraints excluded: chain A residue 225 MET Chi-restraints excluded: chain A residue 260 ILE Chi-restraints excluded: chain A residue 281 PHE Chi-restraints excluded: chain A residue 289 SER Chi-restraints excluded: chain A residue 315 LEU Chi-restraints excluded: chain A residue 316 LEU Chi-restraints excluded: chain A residue 361 MET Chi-restraints excluded: chain A residue 374 VAL Chi-restraints excluded: chain A residue 388 LEU Chi-restraints excluded: chain A residue 408 CYS Chi-restraints excluded: chain A residue 434 LEU Chi-restraints excluded: chain A residue 448 VAL Chi-restraints excluded: chain A residue 542 ILE Chi-restraints excluded: chain A residue 563 PHE Chi-restraints excluded: chain A residue 607 THR Chi-restraints excluded: chain A residue 634 SER Chi-restraints excluded: chain A residue 655 ASN Chi-restraints excluded: chain A residue 674 MET Chi-restraints excluded: chain A residue 686 GLU Chi-restraints excluded: chain A residue 687 HIS Chi-restraints excluded: chain A residue 695 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 72 optimal weight: 3.9990 chunk 100 optimal weight: 0.0970 chunk 13 optimal weight: 2.9990 chunk 86 optimal weight: 6.9990 chunk 127 optimal weight: 0.8980 chunk 97 optimal weight: 4.9990 chunk 185 optimal weight: 5.9990 chunk 40 optimal weight: 0.8980 chunk 107 optimal weight: 9.9990 chunk 1 optimal weight: 0.4980 chunk 152 optimal weight: 0.9980 overall best weight: 0.6778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 56 HIS B 56 HIS F 178 ASN ** D 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 198 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 158 ASN H 187 ASN ** A 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 59 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 516 ASN ** A 687 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4139 r_free = 0.4139 target = 0.180465 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3772 r_free = 0.3772 target = 0.142318 restraints weight = 26298.693| |-----------------------------------------------------------------------------| r_work (start): 0.3733 rms_B_bonded: 3.07 r_work: 0.3468 rms_B_bonded: 3.38 restraints_weight: 0.5000 r_work (final): 0.3468 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7796 moved from start: 0.2665 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 21865 Z= 0.128 Angle : 0.544 10.159 29807 Z= 0.295 Chirality : 0.042 0.388 3405 Planarity : 0.004 0.050 3514 Dihedral : 15.139 162.340 3844 Min Nonbonded Distance : 2.401 Molprobity Statistics. All-atom Clashscore : 10.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer: Outliers : 3.87 % Allowed : 20.74 % Favored : 75.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.54 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.79 (0.16), residues: 2440 helix: 1.72 (0.15), residues: 1095 sheet: 0.03 (0.25), residues: 415 loop : -0.65 (0.18), residues: 930 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG A 466 TYR 0.028 0.001 TYR C 122 PHE 0.031 0.001 PHE E 150 TRP 0.010 0.001 TRP A 493 HIS 0.004 0.001 HIS B 56 Details of bonding type rmsd/Z covalent geometry : bond 0.00271 / 0.13 (21865) covalent geometry : angle 0.54369 / 0.29 (29807) hydrogen bonds : bond 0.04420 / 2.92 ( 1075) hydrogen bonds : angle 4.75424 / 3.35 ( 3116) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4880 Ramachandran restraints generated. 2440 Oldfield, 0 Emsley, 2440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4880 Ramachandran restraints generated. 2440 Oldfield, 0 Emsley, 2440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 377 residues out of total 2170 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 293 time to evaluate : 0.640 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 112 LYS cc_start: 0.7326 (pptt) cc_final: 0.6945 (ptmm) REVERT: C 127 GLU cc_start: 0.6682 (mt-10) cc_final: 0.6041 (mt-10) REVERT: B 11 MET cc_start: 0.5910 (tpp) cc_final: 0.5602 (tmm) REVERT: B 74 ARG cc_start: 0.7632 (mtp85) cc_final: 0.7242 (mtp-110) REVERT: F 28 ILE cc_start: 0.8654 (mt) cc_final: 0.8365 (mp) REVERT: F 45 ILE cc_start: 0.8132 (OUTLIER) cc_final: 0.7742 (tt) REVERT: E 28 ILE cc_start: 0.8064 (mt) cc_final: 0.7572 (mp) REVERT: E 42 ARG cc_start: 0.8030 (OUTLIER) cc_final: 0.6951 (mtm180) REVERT: E 120 GLU cc_start: 0.8537 (OUTLIER) cc_final: 0.7862 (pm20) REVERT: E 167 GLU cc_start: 0.7781 (mm-30) cc_final: 0.7156 (tp30) REVERT: D 124 GLU cc_start: 0.8346 (OUTLIER) cc_final: 0.8038 (mt-10) REVERT: D 161 GLU cc_start: 0.6859 (OUTLIER) cc_final: 0.6631 (mp0) REVERT: G 95 LYS cc_start: 0.7241 (OUTLIER) cc_final: 0.6551 (pptt) REVERT: G 159 GLU cc_start: 0.7062 (mm-30) cc_final: 0.6804 (mm-30) REVERT: G 213 LEU cc_start: 0.7038 (tt) cc_final: 0.6544 (mt) REVERT: G 277 GLN cc_start: 0.6936 (tp40) cc_final: 0.6660 (tp-100) REVERT: I 161 GLU cc_start: 0.6846 (OUTLIER) cc_final: 0.6601 (mt-10) REVERT: J 40 ASN cc_start: 0.7977 (m110) cc_final: 0.7768 (m110) REVERT: J 59 THR cc_start: 0.7888 (OUTLIER) cc_final: 0.7537 (m) REVERT: J 61 VAL cc_start: 0.6092 (t) cc_final: 0.5618 (t) REVERT: J 91 GLU cc_start: 0.7117 (tp30) cc_final: 0.6714 (tp30) REVERT: H 22 LYS cc_start: 0.7121 (tttt) cc_final: 0.6501 (tppt) REVERT: H 202 VAL cc_start: 0.8422 (m) cc_final: 0.8152 (t) REVERT: H 212 ILE cc_start: 0.6812 (OUTLIER) cc_final: 0.6428 (pp) REVERT: A 80 ILE cc_start: 0.7465 (OUTLIER) cc_final: 0.7198 (pp) REVERT: A 242 LYS cc_start: 0.7822 (mttt) cc_final: 0.7206 (mppt) REVERT: A 281 PHE cc_start: 0.7158 (OUTLIER) cc_final: 0.6422 (p90) REVERT: A 361 MET cc_start: 0.6287 (OUTLIER) cc_final: 0.5271 (tpt) REVERT: A 439 PHE cc_start: 0.7932 (m-80) cc_final: 0.7562 (m-10) REVERT: A 441 VAL cc_start: 0.7816 (t) cc_final: 0.7566 (m) REVERT: A 459 GLU cc_start: 0.6932 (mm-30) cc_final: 0.6357 (tp30) REVERT: A 468 ILE cc_start: 0.7055 (OUTLIER) cc_final: 0.6779 (mm) REVERT: A 469 LYS cc_start: 0.7173 (mttm) cc_final: 0.6886 (mmtt) REVERT: A 532 ASP cc_start: 0.4284 (OUTLIER) cc_final: 0.3456 (t0) REVERT: A 563 PHE cc_start: 0.5380 (OUTLIER) cc_final: 0.5005 (t80) REVERT: A 569 ASN cc_start: 0.6938 (m110) cc_final: 0.6696 (t160) REVERT: A 671 LYS cc_start: 0.8027 (mttm) cc_final: 0.7678 (ttpt) REVERT: A 674 MET cc_start: 0.7436 (OUTLIER) cc_final: 0.6562 (tmm) REVERT: A 751 ILE cc_start: 0.7515 (tt) cc_final: 0.7232 (pt) outliers start: 84 outliers final: 41 residues processed: 346 average time/residue: 0.5380 time to fit residues: 216.5414 Evaluate side-chains 337 residues out of total 2170 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 280 time to evaluate : 0.830 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 12 ILE Chi-restraints excluded: chain C residue 67 THR Chi-restraints excluded: chain C residue 103 VAL Chi-restraints excluded: chain C residue 115 THR Chi-restraints excluded: chain B residue 6 THR Chi-restraints excluded: chain B residue 44 THR Chi-restraints excluded: chain B residue 68 THR Chi-restraints excluded: chain B residue 115 THR Chi-restraints excluded: chain F residue 10 LYS Chi-restraints excluded: chain F residue 26 SER Chi-restraints excluded: chain F residue 45 ILE Chi-restraints excluded: chain F residue 88 LYS Chi-restraints excluded: chain F residue 119 THR Chi-restraints excluded: chain F residue 126 THR Chi-restraints excluded: chain F residue 178 ASN Chi-restraints excluded: chain E residue 42 ARG Chi-restraints excluded: chain E residue 120 GLU Chi-restraints excluded: chain E residue 143 THR Chi-restraints excluded: chain E residue 202 VAL Chi-restraints excluded: chain D residue 124 GLU Chi-restraints excluded: chain D residue 161 GLU Chi-restraints excluded: chain G residue 95 LYS Chi-restraints excluded: chain G residue 140 VAL Chi-restraints excluded: chain G residue 212 LEU Chi-restraints excluded: chain I residue 78 GLU Chi-restraints excluded: chain I residue 161 GLU Chi-restraints excluded: chain J residue 14 LEU Chi-restraints excluded: chain J residue 59 THR Chi-restraints excluded: chain J residue 106 LEU Chi-restraints excluded: chain H residue 23 ILE Chi-restraints excluded: chain H residue 41 VAL Chi-restraints excluded: chain H residue 153 GLU Chi-restraints excluded: chain H residue 209 THR Chi-restraints excluded: chain H residue 212 ILE Chi-restraints excluded: chain A residue 80 ILE Chi-restraints excluded: chain A residue 204 LEU Chi-restraints excluded: chain A residue 225 MET Chi-restraints excluded: chain A residue 260 ILE Chi-restraints excluded: chain A residue 281 PHE Chi-restraints excluded: chain A residue 315 LEU Chi-restraints excluded: chain A residue 361 MET Chi-restraints excluded: chain A residue 374 VAL Chi-restraints excluded: chain A residue 408 CYS Chi-restraints excluded: chain A residue 434 LEU Chi-restraints excluded: chain A residue 448 VAL Chi-restraints excluded: chain A residue 468 ILE Chi-restraints excluded: chain A residue 532 ASP Chi-restraints excluded: chain A residue 542 ILE Chi-restraints excluded: chain A residue 563 PHE Chi-restraints excluded: chain A residue 607 THR Chi-restraints excluded: chain A residue 622 MET Chi-restraints excluded: chain A residue 634 SER Chi-restraints excluded: chain A residue 655 ASN Chi-restraints excluded: chain A residue 674 MET Chi-restraints excluded: chain A residue 686 GLU Chi-restraints excluded: chain A residue 687 HIS Chi-restraints excluded: chain A residue 695 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 139 optimal weight: 0.7980 chunk 146 optimal weight: 4.9990 chunk 248 optimal weight: 2.9990 chunk 177 optimal weight: 4.9990 chunk 118 optimal weight: 6.9990 chunk 75 optimal weight: 4.9990 chunk 237 optimal weight: 0.9990 chunk 111 optimal weight: 4.9990 chunk 131 optimal weight: 3.9990 chunk 13 optimal weight: 3.9990 chunk 137 optimal weight: 0.8980 overall best weight: 1.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 56 HIS B 56 HIS D 125 ASN ** G 198 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 187 ASN ** A 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 59 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 516 ASN ** A 687 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4103 r_free = 0.4103 target = 0.176798 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3689 r_free = 0.3689 target = 0.134635 restraints weight = 26325.498| |-----------------------------------------------------------------------------| r_work (start): 0.3637 rms_B_bonded: 2.06 r_work: 0.3468 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.3354 rms_B_bonded: 4.20 restraints_weight: 0.2500 r_work (final): 0.3354 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7892 moved from start: 0.2721 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 21865 Z= 0.201 Angle : 0.598 10.055 29807 Z= 0.322 Chirality : 0.044 0.388 3405 Planarity : 0.004 0.054 3514 Dihedral : 15.098 167.538 3842 Min Nonbonded Distance : 2.346 Molprobity Statistics. All-atom Clashscore : 10.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.79 % Favored : 97.21 % Rotamer: Outliers : 4.15 % Allowed : 21.29 % Favored : 74.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.54 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.65 (0.16), residues: 2440 helix: 1.57 (0.15), residues: 1093 sheet: 0.03 (0.25), residues: 409 loop : -0.69 (0.18), residues: 938 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG A 466 TYR 0.030 0.002 TYR H 59 PHE 0.030 0.002 PHE C 16 TRP 0.009 0.001 TRP A 493 HIS 0.005 0.001 HIS F 151 Details of bonding type rmsd/Z covalent geometry : bond 0.00454 / 0.20 (21865) covalent geometry : angle 0.59769 / 0.32 (29807) hydrogen bonds : bond 0.04764 / 3.15 ( 1075) hydrogen bonds : angle 4.83015 / 3.42 ( 3116) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4880 Ramachandran restraints generated. 2440 Oldfield, 0 Emsley, 2440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4880 Ramachandran restraints generated. 2440 Oldfield, 0 Emsley, 2440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 371 residues out of total 2170 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 281 time to evaluate : 0.789 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 127 GLU cc_start: 0.6759 (mt-10) cc_final: 0.6120 (mt-10) REVERT: B 11 MET cc_start: 0.5835 (tpp) cc_final: 0.5554 (tmm) REVERT: B 74 ARG cc_start: 0.7680 (mtp85) cc_final: 0.7242 (mtp-110) REVERT: F 28 ILE cc_start: 0.8729 (mt) cc_final: 0.8436 (mp) REVERT: F 42 ARG cc_start: 0.8724 (OUTLIER) cc_final: 0.8485 (mtp180) REVERT: F 45 ILE cc_start: 0.8232 (OUTLIER) cc_final: 0.7908 (tt) REVERT: E 28 ILE cc_start: 0.8136 (mt) cc_final: 0.7641 (mp) REVERT: E 42 ARG cc_start: 0.8098 (OUTLIER) cc_final: 0.7023 (mtm180) REVERT: E 120 GLU cc_start: 0.8664 (OUTLIER) cc_final: 0.7895 (pm20) REVERT: E 167 GLU cc_start: 0.7875 (mm-30) cc_final: 0.7222 (tp30) REVERT: D 124 GLU cc_start: 0.8549 (OUTLIER) cc_final: 0.8196 (mt-10) REVERT: D 161 GLU cc_start: 0.6932 (OUTLIER) cc_final: 0.6658 (mp0) REVERT: G 95 LYS cc_start: 0.7254 (OUTLIER) cc_final: 0.6573 (pptt) REVERT: G 147 GLU cc_start: 0.8229 (OUTLIER) cc_final: 0.7922 (pp20) REVERT: G 159 GLU cc_start: 0.7153 (mm-30) cc_final: 0.6906 (mm-30) REVERT: G 213 LEU cc_start: 0.7073 (tt) cc_final: 0.6525 (mp) REVERT: G 259 GLN cc_start: 0.7626 (pt0) cc_final: 0.7231 (pm20) REVERT: G 277 GLN cc_start: 0.7012 (tp40) cc_final: 0.6734 (tp-100) REVERT: I 123 PHE cc_start: 0.7769 (OUTLIER) cc_final: 0.7392 (t80) REVERT: I 161 GLU cc_start: 0.6974 (OUTLIER) cc_final: 0.6662 (mt-10) REVERT: J 40 ASN cc_start: 0.8001 (m110) cc_final: 0.7792 (m110) REVERT: J 59 THR cc_start: 0.7968 (OUTLIER) cc_final: 0.7598 (m) REVERT: J 91 GLU cc_start: 0.7183 (tp30) cc_final: 0.6765 (tp30) REVERT: H 22 LYS cc_start: 0.7151 (tttt) cc_final: 0.6499 (tppt) REVERT: H 195 LEU cc_start: 0.6685 (OUTLIER) cc_final: 0.6373 (mp) REVERT: H 200 VAL cc_start: 0.7992 (OUTLIER) cc_final: 0.7732 (p) REVERT: H 202 VAL cc_start: 0.8447 (m) cc_final: 0.8183 (t) REVERT: H 212 ILE cc_start: 0.6887 (OUTLIER) cc_final: 0.6505 (pp) REVERT: A 80 ILE cc_start: 0.7398 (OUTLIER) cc_final: 0.7143 (pp) REVERT: A 242 LYS cc_start: 0.7863 (mttt) cc_final: 0.7223 (mppt) REVERT: A 281 PHE cc_start: 0.7230 (OUTLIER) cc_final: 0.6551 (p90) REVERT: A 307 TYR cc_start: 0.5885 (OUTLIER) cc_final: 0.4818 (p90) REVERT: A 361 MET cc_start: 0.6297 (OUTLIER) cc_final: 0.5321 (tpt) REVERT: A 439 PHE cc_start: 0.8006 (m-80) cc_final: 0.7615 (m-10) REVERT: A 459 GLU cc_start: 0.6855 (mm-30) cc_final: 0.6239 (tp30) REVERT: A 468 ILE cc_start: 0.7131 (OUTLIER) cc_final: 0.6838 (mm) REVERT: A 469 LYS cc_start: 0.7188 (mttm) cc_final: 0.6873 (mmtt) REVERT: A 563 PHE cc_start: 0.5470 (OUTLIER) cc_final: 0.5073 (t80) REVERT: A 569 ASN cc_start: 0.6930 (m110) cc_final: 0.6686 (t160) REVERT: A 671 LYS cc_start: 0.8101 (mttm) cc_final: 0.7779 (ptpt) REVERT: A 674 MET cc_start: 0.7443 (OUTLIER) cc_final: 0.6565 (tmm) outliers start: 90 outliers final: 44 residues processed: 338 average time/residue: 0.5028 time to fit residues: 199.3087 Evaluate side-chains 330 residues out of total 2170 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 265 time to evaluate : 0.715 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 12 ILE Chi-restraints excluded: chain C residue 67 THR Chi-restraints excluded: chain C residue 103 VAL Chi-restraints excluded: chain C residue 115 THR Chi-restraints excluded: chain B residue 6 THR Chi-restraints excluded: chain B residue 44 THR Chi-restraints excluded: chain B residue 68 THR Chi-restraints excluded: chain B residue 103 VAL Chi-restraints excluded: chain B residue 115 THR Chi-restraints excluded: chain F residue 26 SER Chi-restraints excluded: chain F residue 42 ARG Chi-restraints excluded: chain F residue 45 ILE Chi-restraints excluded: chain F residue 119 THR Chi-restraints excluded: chain F residue 126 THR Chi-restraints excluded: chain F residue 133 VAL Chi-restraints excluded: chain E residue 31 ILE Chi-restraints excluded: chain E residue 33 SER Chi-restraints excluded: chain E residue 36 VAL Chi-restraints excluded: chain E residue 42 ARG Chi-restraints excluded: chain E residue 120 GLU Chi-restraints excluded: chain E residue 143 THR Chi-restraints excluded: chain E residue 202 VAL Chi-restraints excluded: chain D residue 79 ILE Chi-restraints excluded: chain D residue 124 GLU Chi-restraints excluded: chain D residue 161 GLU Chi-restraints excluded: chain G residue 95 LYS Chi-restraints excluded: chain G residue 140 VAL Chi-restraints excluded: chain G residue 147 GLU Chi-restraints excluded: chain I residue 45 ILE Chi-restraints excluded: chain I residue 78 GLU Chi-restraints excluded: chain I residue 123 PHE Chi-restraints excluded: chain I residue 161 GLU Chi-restraints excluded: chain J residue 14 LEU Chi-restraints excluded: chain J residue 52 GLU Chi-restraints excluded: chain J residue 59 THR Chi-restraints excluded: chain H residue 23 ILE Chi-restraints excluded: chain H residue 41 VAL Chi-restraints excluded: chain H residue 153 GLU Chi-restraints excluded: chain H residue 195 LEU Chi-restraints excluded: chain H residue 200 VAL Chi-restraints excluded: chain H residue 209 THR Chi-restraints excluded: chain H residue 212 ILE Chi-restraints excluded: chain A residue 77 ILE Chi-restraints excluded: chain A residue 80 ILE Chi-restraints excluded: chain A residue 260 ILE Chi-restraints excluded: chain A residue 281 PHE Chi-restraints excluded: chain A residue 307 TYR Chi-restraints excluded: chain A residue 315 LEU Chi-restraints excluded: chain A residue 316 LEU Chi-restraints excluded: chain A residue 361 MET Chi-restraints excluded: chain A residue 374 VAL Chi-restraints excluded: chain A residue 388 LEU Chi-restraints excluded: chain A residue 408 CYS Chi-restraints excluded: chain A residue 434 LEU Chi-restraints excluded: chain A residue 448 VAL Chi-restraints excluded: chain A residue 468 ILE Chi-restraints excluded: chain A residue 542 ILE Chi-restraints excluded: chain A residue 563 PHE Chi-restraints excluded: chain A residue 607 THR Chi-restraints excluded: chain A residue 634 SER Chi-restraints excluded: chain A residue 655 ASN Chi-restraints excluded: chain A residue 674 MET Chi-restraints excluded: chain A residue 686 GLU Chi-restraints excluded: chain A residue 687 HIS Chi-restraints excluded: chain A residue 695 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 93 optimal weight: 0.6980 chunk 56 optimal weight: 0.9990 chunk 130 optimal weight: 0.3980 chunk 158 optimal weight: 4.9990 chunk 189 optimal weight: 20.0000 chunk 48 optimal weight: 3.9990 chunk 243 optimal weight: 5.9990 chunk 36 optimal weight: 0.6980 chunk 141 optimal weight: 2.9990 chunk 10 optimal weight: 4.9990 chunk 170 optimal weight: 1.9990 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 56 HIS B 56 HIS F 178 ASN ** D 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 198 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 187 ASN ** A 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 516 ASN ** A 687 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4126 r_free = 0.4126 target = 0.178977 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3717 r_free = 0.3717 target = 0.137054 restraints weight = 26259.560| |-----------------------------------------------------------------------------| r_work (start): 0.3665 rms_B_bonded: 2.01 r_work: 0.3508 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.3394 rms_B_bonded: 4.18 restraints_weight: 0.2500 r_work (final): 0.3394 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7870 moved from start: 0.2825 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 21865 Z= 0.141 Angle : 0.560 10.068 29807 Z= 0.303 Chirality : 0.043 0.400 3405 Planarity : 0.004 0.054 3514 Dihedral : 15.053 163.609 3842 Min Nonbonded Distance : 2.328 Molprobity Statistics. All-atom Clashscore : 10.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 3.96 % Allowed : 21.84 % Favored : 74.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.54 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.71 (0.16), residues: 2440 helix: 1.65 (0.15), residues: 1091 sheet: 0.01 (0.25), residues: 415 loop : -0.69 (0.18), residues: 934 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG A 466 TYR 0.030 0.001 TYR C 122 PHE 0.028 0.002 PHE E 150 TRP 0.008 0.001 TRP A 493 HIS 0.005 0.001 HIS B 56 Details of bonding type rmsd/Z covalent geometry : bond 0.00304 / 0.14 (21865) covalent geometry : angle 0.55957 / 0.30 (29807) hydrogen bonds : bond 0.04451 / 2.95 ( 1075) hydrogen bonds : angle 4.76380 / 3.37 ( 3116) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4880 Ramachandran restraints generated. 2440 Oldfield, 0 Emsley, 2440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4880 Ramachandran restraints generated. 2440 Oldfield, 0 Emsley, 2440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 372 residues out of total 2170 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 286 time to evaluate : 0.682 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 127 GLU cc_start: 0.6688 (mt-10) cc_final: 0.6073 (mt-10) REVERT: B 11 MET cc_start: 0.5784 (tpp) cc_final: 0.5527 (tmm) REVERT: B 47 LEU cc_start: 0.8678 (OUTLIER) cc_final: 0.8270 (tt) REVERT: B 74 ARG cc_start: 0.7671 (mtp85) cc_final: 0.7274 (mtp-110) REVERT: F 27 MET cc_start: 0.7415 (OUTLIER) cc_final: 0.7101 (ttp) REVERT: F 28 ILE cc_start: 0.8708 (mt) cc_final: 0.8427 (mp) REVERT: F 45 ILE cc_start: 0.8165 (OUTLIER) cc_final: 0.7837 (tt) REVERT: E 28 ILE cc_start: 0.8140 (mt) cc_final: 0.7661 (mp) REVERT: E 42 ARG cc_start: 0.8090 (OUTLIER) cc_final: 0.7003 (mtm180) REVERT: E 120 GLU cc_start: 0.8635 (OUTLIER) cc_final: 0.7985 (pm20) REVERT: E 167 GLU cc_start: 0.7862 (mm-30) cc_final: 0.7217 (tp30) REVERT: D 124 GLU cc_start: 0.8520 (OUTLIER) cc_final: 0.8207 (mt-10) REVERT: D 161 GLU cc_start: 0.6931 (OUTLIER) cc_final: 0.6702 (mp0) REVERT: G 95 LYS cc_start: 0.7277 (OUTLIER) cc_final: 0.6588 (pptt) REVERT: G 159 GLU cc_start: 0.7139 (mm-30) cc_final: 0.6910 (mm-30) REVERT: G 213 LEU cc_start: 0.7082 (tt) cc_final: 0.6582 (mt) REVERT: G 259 GLN cc_start: 0.7606 (pt0) cc_final: 0.7231 (pm20) REVERT: G 277 GLN cc_start: 0.6987 (tp40) cc_final: 0.6742 (tp-100) REVERT: I 123 PHE cc_start: 0.7769 (OUTLIER) cc_final: 0.7342 (t80) REVERT: I 161 GLU cc_start: 0.6944 (OUTLIER) cc_final: 0.6647 (mt-10) REVERT: J 59 THR cc_start: 0.7965 (OUTLIER) cc_final: 0.7614 (m) REVERT: J 61 VAL cc_start: 0.6159 (t) cc_final: 0.5667 (t) REVERT: J 91 GLU cc_start: 0.7179 (tp30) cc_final: 0.6761 (tp30) REVERT: H 22 LYS cc_start: 0.7127 (tttt) cc_final: 0.6513 (tppt) REVERT: H 200 VAL cc_start: 0.7996 (OUTLIER) cc_final: 0.7759 (p) REVERT: H 202 VAL cc_start: 0.8419 (m) cc_final: 0.8158 (t) REVERT: H 212 ILE cc_start: 0.6826 (OUTLIER) cc_final: 0.6441 (pp) REVERT: A 59 HIS cc_start: 0.4122 (OUTLIER) cc_final: 0.3243 (p-80) REVERT: A 80 ILE cc_start: 0.7457 (OUTLIER) cc_final: 0.7188 (pp) REVERT: A 242 LYS cc_start: 0.7848 (mttt) cc_final: 0.7203 (mppt) REVERT: A 281 PHE cc_start: 0.7233 (OUTLIER) cc_final: 0.6649 (p90) REVERT: A 361 MET cc_start: 0.6301 (OUTLIER) cc_final: 0.5374 (tpt) REVERT: A 439 PHE cc_start: 0.7964 (m-80) cc_final: 0.7598 (m-10) REVERT: A 441 VAL cc_start: 0.7907 (t) cc_final: 0.7670 (m) REVERT: A 459 GLU cc_start: 0.6893 (mm-30) cc_final: 0.6287 (tp30) REVERT: A 468 ILE cc_start: 0.7120 (OUTLIER) cc_final: 0.6839 (mm) REVERT: A 469 LYS cc_start: 0.7164 (mttm) cc_final: 0.6839 (mmtt) REVERT: A 538 PHE cc_start: 0.6693 (OUTLIER) cc_final: 0.6185 (m-80) REVERT: A 563 PHE cc_start: 0.5424 (OUTLIER) cc_final: 0.5122 (t80) REVERT: A 569 ASN cc_start: 0.6959 (m110) cc_final: 0.6719 (t160) REVERT: A 671 LYS cc_start: 0.8105 (mttm) cc_final: 0.7826 (ptpt) REVERT: A 674 MET cc_start: 0.7470 (OUTLIER) cc_final: 0.6564 (tmm) outliers start: 86 outliers final: 51 residues processed: 343 average time/residue: 0.5185 time to fit residues: 206.9512 Evaluate side-chains 342 residues out of total 2170 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 270 time to evaluate : 0.616 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 12 ILE Chi-restraints excluded: chain C residue 67 THR Chi-restraints excluded: chain C residue 103 VAL Chi-restraints excluded: chain C residue 115 THR Chi-restraints excluded: chain B residue 6 THR Chi-restraints excluded: chain B residue 44 THR Chi-restraints excluded: chain B residue 47 LEU Chi-restraints excluded: chain B residue 68 THR Chi-restraints excluded: chain B residue 103 VAL Chi-restraints excluded: chain B residue 115 THR Chi-restraints excluded: chain F residue 26 SER Chi-restraints excluded: chain F residue 27 MET Chi-restraints excluded: chain F residue 45 ILE Chi-restraints excluded: chain F residue 79 ILE Chi-restraints excluded: chain F residue 88 LYS Chi-restraints excluded: chain F residue 119 THR Chi-restraints excluded: chain F residue 126 THR Chi-restraints excluded: chain E residue 36 VAL Chi-restraints excluded: chain E residue 42 ARG Chi-restraints excluded: chain E residue 91 ILE Chi-restraints excluded: chain E residue 120 GLU Chi-restraints excluded: chain E residue 143 THR Chi-restraints excluded: chain E residue 202 VAL Chi-restraints excluded: chain D residue 79 ILE Chi-restraints excluded: chain D residue 124 GLU Chi-restraints excluded: chain D residue 161 GLU Chi-restraints excluded: chain G residue 95 LYS Chi-restraints excluded: chain G residue 113 ASP Chi-restraints excluded: chain G residue 140 VAL Chi-restraints excluded: chain G residue 212 LEU Chi-restraints excluded: chain I residue 78 GLU Chi-restraints excluded: chain I residue 123 PHE Chi-restraints excluded: chain I residue 161 GLU Chi-restraints excluded: chain J residue 14 LEU Chi-restraints excluded: chain J residue 28 LYS Chi-restraints excluded: chain J residue 52 GLU Chi-restraints excluded: chain J residue 59 THR Chi-restraints excluded: chain J residue 98 ILE Chi-restraints excluded: chain J residue 106 LEU Chi-restraints excluded: chain H residue 23 ILE Chi-restraints excluded: chain H residue 41 VAL Chi-restraints excluded: chain H residue 153 GLU Chi-restraints excluded: chain H residue 200 VAL Chi-restraints excluded: chain H residue 209 THR Chi-restraints excluded: chain H residue 212 ILE Chi-restraints excluded: chain A residue 59 HIS Chi-restraints excluded: chain A residue 77 ILE Chi-restraints excluded: chain A residue 80 ILE Chi-restraints excluded: chain A residue 204 LEU Chi-restraints excluded: chain A residue 206 ASP Chi-restraints excluded: chain A residue 225 MET Chi-restraints excluded: chain A residue 260 ILE Chi-restraints excluded: chain A residue 281 PHE Chi-restraints excluded: chain A residue 289 SER Chi-restraints excluded: chain A residue 315 LEU Chi-restraints excluded: chain A residue 361 MET Chi-restraints excluded: chain A residue 374 VAL Chi-restraints excluded: chain A residue 408 CYS Chi-restraints excluded: chain A residue 434 LEU Chi-restraints excluded: chain A residue 448 VAL Chi-restraints excluded: chain A residue 468 ILE Chi-restraints excluded: chain A residue 538 PHE Chi-restraints excluded: chain A residue 542 ILE Chi-restraints excluded: chain A residue 549 ILE Chi-restraints excluded: chain A residue 563 PHE Chi-restraints excluded: chain A residue 607 THR Chi-restraints excluded: chain A residue 634 SER Chi-restraints excluded: chain A residue 655 ASN Chi-restraints excluded: chain A residue 674 MET Chi-restraints excluded: chain A residue 686 GLU Chi-restraints excluded: chain A residue 687 HIS Chi-restraints excluded: chain A residue 695 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 141 optimal weight: 4.9990 chunk 218 optimal weight: 0.2980 chunk 31 optimal weight: 2.9990 chunk 7 optimal weight: 0.9990 chunk 1 optimal weight: 0.9980 chunk 235 optimal weight: 3.9990 chunk 54 optimal weight: 2.9990 chunk 198 optimal weight: 0.9980 chunk 139 optimal weight: 0.7980 chunk 89 optimal weight: 2.9990 chunk 145 optimal weight: 9.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 56 HIS B 56 HIS ** D 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 198 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 187 ASN H 335 GLN ** A 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 516 ASN A 649 ASN ** A 687 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4131 r_free = 0.4131 target = 0.179441 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3723 r_free = 0.3723 target = 0.137632 restraints weight = 26268.533| |-----------------------------------------------------------------------------| r_work (start): 0.3671 rms_B_bonded: 2.02 r_work: 0.3510 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.3395 rms_B_bonded: 4.24 restraints_weight: 0.2500 r_work (final): 0.3395 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7867 moved from start: 0.2889 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 21865 Z= 0.135 Angle : 0.564 13.415 29807 Z= 0.302 Chirality : 0.043 0.407 3405 Planarity : 0.004 0.060 3514 Dihedral : 15.018 163.982 3842 Min Nonbonded Distance : 2.293 Molprobity Statistics. All-atom Clashscore : 10.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer: Outliers : 3.36 % Allowed : 22.44 % Favored : 74.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.54 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.73 (0.16), residues: 2440 helix: 1.66 (0.15), residues: 1093 sheet: 0.03 (0.25), residues: 415 loop : -0.67 (0.18), residues: 932 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG A 466 TYR 0.027 0.001 TYR C 122 PHE 0.027 0.001 PHE E 150 TRP 0.008 0.001 TRP A 493 HIS 0.004 0.001 HIS B 56 Details of bonding type rmsd/Z covalent geometry : bond 0.00293 / 0.14 (21865) covalent geometry : angle 0.56424 / 0.30 (29807) hydrogen bonds : bond 0.04370 / 2.89 ( 1075) hydrogen bonds : angle 4.73431 / 3.35 ( 3116) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4880 Ramachandran restraints generated. 2440 Oldfield, 0 Emsley, 2440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4880 Ramachandran restraints generated. 2440 Oldfield, 0 Emsley, 2440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 353 residues out of total 2170 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 280 time to evaluate : 0.583 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 11 MET cc_start: 0.5756 (tpp) cc_final: 0.5518 (tmm) REVERT: B 74 ARG cc_start: 0.7677 (mtp85) cc_final: 0.7281 (mtp-110) REVERT: F 27 MET cc_start: 0.7363 (OUTLIER) cc_final: 0.7125 (ttp) REVERT: F 28 ILE cc_start: 0.8699 (mt) cc_final: 0.8439 (mp) REVERT: E 28 ILE cc_start: 0.8121 (mt) cc_final: 0.7630 (mp) REVERT: E 42 ARG cc_start: 0.8088 (OUTLIER) cc_final: 0.7007 (mtm180) REVERT: E 120 GLU cc_start: 0.8650 (OUTLIER) cc_final: 0.8018 (pm20) REVERT: E 167 GLU cc_start: 0.7894 (mm-30) cc_final: 0.7256 (tp30) REVERT: D 124 GLU cc_start: 0.8523 (OUTLIER) cc_final: 0.8199 (mt-10) REVERT: D 161 GLU cc_start: 0.6932 (OUTLIER) cc_final: 0.6700 (mp0) REVERT: G 95 LYS cc_start: 0.7281 (OUTLIER) cc_final: 0.6592 (pptt) REVERT: G 147 GLU cc_start: 0.8159 (OUTLIER) cc_final: 0.7894 (pp20) REVERT: G 159 GLU cc_start: 0.7139 (mm-30) cc_final: 0.6889 (mm-30) REVERT: G 213 LEU cc_start: 0.7072 (tt) cc_final: 0.6575 (mt) REVERT: G 259 GLN cc_start: 0.7608 (pt0) cc_final: 0.7228 (pm20) REVERT: G 277 GLN cc_start: 0.6991 (tp40) cc_final: 0.6751 (tp-100) REVERT: I 123 PHE cc_start: 0.7772 (OUTLIER) cc_final: 0.7357 (t80) REVERT: I 161 GLU cc_start: 0.6928 (OUTLIER) cc_final: 0.6637 (mt-10) REVERT: J 59 THR cc_start: 0.7981 (OUTLIER) cc_final: 0.7634 (m) REVERT: J 61 VAL cc_start: 0.6221 (t) cc_final: 0.5727 (t) REVERT: J 91 GLU cc_start: 0.7170 (tp30) cc_final: 0.6751 (tp30) REVERT: H 22 LYS cc_start: 0.7145 (tttt) cc_final: 0.6532 (tppt) REVERT: H 200 VAL cc_start: 0.8001 (OUTLIER) cc_final: 0.7765 (p) REVERT: H 202 VAL cc_start: 0.8417 (m) cc_final: 0.8158 (t) REVERT: H 212 ILE cc_start: 0.6842 (OUTLIER) cc_final: 0.6473 (pp) REVERT: A 59 HIS cc_start: 0.4183 (OUTLIER) cc_final: 0.3291 (p-80) REVERT: A 80 ILE cc_start: 0.7451 (OUTLIER) cc_final: 0.7197 (pp) REVERT: A 242 LYS cc_start: 0.7852 (mttt) cc_final: 0.7202 (mppt) REVERT: A 281 PHE cc_start: 0.7407 (OUTLIER) cc_final: 0.6614 (p90) REVERT: A 361 MET cc_start: 0.6285 (OUTLIER) cc_final: 0.5350 (tpt) REVERT: A 439 PHE cc_start: 0.7947 (m-80) cc_final: 0.7594 (m-10) REVERT: A 441 VAL cc_start: 0.7921 (t) cc_final: 0.7681 (m) REVERT: A 459 GLU cc_start: 0.6881 (mm-30) cc_final: 0.6281 (tp30) REVERT: A 468 ILE cc_start: 0.7197 (OUTLIER) cc_final: 0.6914 (mm) REVERT: A 469 LYS cc_start: 0.7181 (mttm) cc_final: 0.6882 (mmtt) REVERT: A 538 PHE cc_start: 0.6693 (OUTLIER) cc_final: 0.6130 (m-80) REVERT: A 563 PHE cc_start: 0.5425 (OUTLIER) cc_final: 0.5131 (t80) REVERT: A 569 ASN cc_start: 0.6956 (m110) cc_final: 0.6748 (t160) REVERT: A 671 LYS cc_start: 0.8097 (mttm) cc_final: 0.7820 (ptpt) REVERT: A 674 MET cc_start: 0.7474 (OUTLIER) cc_final: 0.6624 (tmm) outliers start: 73 outliers final: 41 residues processed: 325 average time/residue: 0.4914 time to fit residues: 185.5826 Evaluate side-chains 329 residues out of total 2170 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 268 time to evaluate : 0.726 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 12 ILE Chi-restraints excluded: chain C residue 67 THR Chi-restraints excluded: chain C residue 103 VAL Chi-restraints excluded: chain B residue 6 THR Chi-restraints excluded: chain B residue 44 THR Chi-restraints excluded: chain B residue 68 THR Chi-restraints excluded: chain B residue 103 VAL Chi-restraints excluded: chain B residue 115 THR Chi-restraints excluded: chain F residue 26 SER Chi-restraints excluded: chain F residue 27 MET Chi-restraints excluded: chain F residue 119 THR Chi-restraints excluded: chain F residue 126 THR Chi-restraints excluded: chain E residue 36 VAL Chi-restraints excluded: chain E residue 42 ARG Chi-restraints excluded: chain E residue 120 GLU Chi-restraints excluded: chain E residue 143 THR Chi-restraints excluded: chain E residue 202 VAL Chi-restraints excluded: chain D residue 79 ILE Chi-restraints excluded: chain D residue 124 GLU Chi-restraints excluded: chain D residue 161 GLU Chi-restraints excluded: chain G residue 95 LYS Chi-restraints excluded: chain G residue 113 ASP Chi-restraints excluded: chain G residue 140 VAL Chi-restraints excluded: chain G residue 147 GLU Chi-restraints excluded: chain I residue 78 GLU Chi-restraints excluded: chain I residue 123 PHE Chi-restraints excluded: chain I residue 161 GLU Chi-restraints excluded: chain J residue 14 LEU Chi-restraints excluded: chain J residue 28 LYS Chi-restraints excluded: chain J residue 59 THR Chi-restraints excluded: chain J residue 98 ILE Chi-restraints excluded: chain J residue 106 LEU Chi-restraints excluded: chain H residue 41 VAL Chi-restraints excluded: chain H residue 153 GLU Chi-restraints excluded: chain H residue 200 VAL Chi-restraints excluded: chain H residue 209 THR Chi-restraints excluded: chain H residue 212 ILE Chi-restraints excluded: chain A residue 59 HIS Chi-restraints excluded: chain A residue 77 ILE Chi-restraints excluded: chain A residue 80 ILE Chi-restraints excluded: chain A residue 157 LEU Chi-restraints excluded: chain A residue 204 LEU Chi-restraints excluded: chain A residue 260 ILE Chi-restraints excluded: chain A residue 281 PHE Chi-restraints excluded: chain A residue 315 LEU Chi-restraints excluded: chain A residue 361 MET Chi-restraints excluded: chain A residue 374 VAL Chi-restraints excluded: chain A residue 408 CYS Chi-restraints excluded: chain A residue 434 LEU Chi-restraints excluded: chain A residue 448 VAL Chi-restraints excluded: chain A residue 468 ILE Chi-restraints excluded: chain A residue 538 PHE Chi-restraints excluded: chain A residue 542 ILE Chi-restraints excluded: chain A residue 549 ILE Chi-restraints excluded: chain A residue 563 PHE Chi-restraints excluded: chain A residue 607 THR Chi-restraints excluded: chain A residue 634 SER Chi-restraints excluded: chain A residue 674 MET Chi-restraints excluded: chain A residue 686 GLU Chi-restraints excluded: chain A residue 687 HIS Chi-restraints excluded: chain A residue 695 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 232 optimal weight: 7.9990 chunk 62 optimal weight: 0.7980 chunk 138 optimal weight: 3.9990 chunk 14 optimal weight: 0.9980 chunk 177 optimal weight: 10.0000 chunk 22 optimal weight: 0.9980 chunk 77 optimal weight: 0.8980 chunk 135 optimal weight: 0.8980 chunk 53 optimal weight: 2.9990 chunk 194 optimal weight: 6.9990 chunk 100 optimal weight: 3.9990 overall best weight: 0.9180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 56 HIS B 56 HIS D 125 ASN ** G 198 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 187 ASN ** A 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 516 ASN ** A 687 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4131 r_free = 0.4131 target = 0.179499 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3724 r_free = 0.3724 target = 0.137639 restraints weight = 26417.070| |-----------------------------------------------------------------------------| r_work (start): 0.3668 rms_B_bonded: 2.02 r_work: 0.3509 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.3394 rms_B_bonded: 4.21 restraints_weight: 0.2500 r_work (final): 0.3394 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7843 moved from start: 0.2940 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 21865 Z= 0.141 Angle : 0.570 16.263 29807 Z= 0.305 Chirality : 0.043 0.410 3405 Planarity : 0.004 0.063 3514 Dihedral : 14.990 164.401 3842 Min Nonbonded Distance : 2.298 Molprobity Statistics. All-atom Clashscore : 10.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 3.09 % Allowed : 23.13 % Favored : 73.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.54 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.73 (0.16), residues: 2440 helix: 1.68 (0.15), residues: 1093 sheet: -0.02 (0.24), residues: 421 loop : -0.67 (0.19), residues: 926 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG A 466 TYR 0.028 0.001 TYR C 122 PHE 0.027 0.002 PHE E 150 TRP 0.009 0.001 TRP A 493 HIS 0.006 0.001 HIS B 56 Details of bonding type rmsd/Z covalent geometry : bond 0.00310 / 0.14 (21865) covalent geometry : angle 0.57025 / 0.30 (29807) hydrogen bonds : bond 0.04366 / 2.90 ( 1075) hydrogen bonds : angle 4.73462 / 3.35 ( 3116) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4880 Ramachandran restraints generated. 2440 Oldfield, 0 Emsley, 2440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4880 Ramachandran restraints generated. 2440 Oldfield, 0 Emsley, 2440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 349 residues out of total 2170 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 282 time to evaluate : 0.808 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 127 GLU cc_start: 0.6590 (mt-10) cc_final: 0.6092 (mt-10) REVERT: B 11 MET cc_start: 0.5691 (tpp) cc_final: 0.5480 (tmm) REVERT: B 74 ARG cc_start: 0.7664 (mtp85) cc_final: 0.7252 (mtp-110) REVERT: F 28 ILE cc_start: 0.8649 (mt) cc_final: 0.8428 (mp) REVERT: E 28 ILE cc_start: 0.8091 (mt) cc_final: 0.7596 (mp) REVERT: E 42 ARG cc_start: 0.8092 (OUTLIER) cc_final: 0.6995 (mtm180) REVERT: E 120 GLU cc_start: 0.8656 (OUTLIER) cc_final: 0.7988 (pm20) REVERT: E 167 GLU cc_start: 0.7871 (mm-30) cc_final: 0.7219 (tp30) REVERT: D 124 GLU cc_start: 0.8498 (OUTLIER) cc_final: 0.8161 (mt-10) REVERT: D 161 GLU cc_start: 0.6990 (OUTLIER) cc_final: 0.6742 (mp0) REVERT: G 95 LYS cc_start: 0.7264 (OUTLIER) cc_final: 0.6570 (pptt) REVERT: G 147 GLU cc_start: 0.8156 (OUTLIER) cc_final: 0.7880 (pp20) REVERT: G 159 GLU cc_start: 0.7138 (mm-30) cc_final: 0.6878 (mm-30) REVERT: G 213 LEU cc_start: 0.7054 (tt) cc_final: 0.6571 (mt) REVERT: G 259 GLN cc_start: 0.7608 (pt0) cc_final: 0.7213 (pm20) REVERT: G 277 GLN cc_start: 0.6986 (tp40) cc_final: 0.6743 (tp-100) REVERT: I 123 PHE cc_start: 0.7754 (OUTLIER) cc_final: 0.7340 (t80) REVERT: I 161 GLU cc_start: 0.6916 (OUTLIER) cc_final: 0.6610 (mt-10) REVERT: J 59 THR cc_start: 0.7924 (OUTLIER) cc_final: 0.7579 (m) REVERT: J 61 VAL cc_start: 0.6140 (t) cc_final: 0.5648 (t) REVERT: J 91 GLU cc_start: 0.7121 (tp30) cc_final: 0.6709 (tp30) REVERT: H 22 LYS cc_start: 0.7123 (tttt) cc_final: 0.6501 (tppt) REVERT: H 200 VAL cc_start: 0.7945 (OUTLIER) cc_final: 0.7703 (p) REVERT: H 202 VAL cc_start: 0.8396 (m) cc_final: 0.8129 (t) REVERT: H 212 ILE cc_start: 0.6799 (OUTLIER) cc_final: 0.6430 (pp) REVERT: H 248 LYS cc_start: 0.6847 (mmmt) cc_final: 0.6186 (mmmt) REVERT: A 59 HIS cc_start: 0.4143 (OUTLIER) cc_final: 0.3239 (p-80) REVERT: A 80 ILE cc_start: 0.7412 (OUTLIER) cc_final: 0.7148 (pp) REVERT: A 242 LYS cc_start: 0.7862 (mttt) cc_final: 0.7212 (mppt) REVERT: A 281 PHE cc_start: 0.7370 (OUTLIER) cc_final: 0.6592 (p90) REVERT: A 361 MET cc_start: 0.6281 (OUTLIER) cc_final: 0.5382 (tpt) REVERT: A 439 PHE cc_start: 0.7916 (m-80) cc_final: 0.7573 (m-10) REVERT: A 441 VAL cc_start: 0.7902 (t) cc_final: 0.7659 (m) REVERT: A 459 GLU cc_start: 0.6868 (mm-30) cc_final: 0.6272 (tp30) REVERT: A 468 ILE cc_start: 0.7145 (OUTLIER) cc_final: 0.6870 (mm) REVERT: A 469 LYS cc_start: 0.7131 (mttm) cc_final: 0.6823 (mmtt) REVERT: A 563 PHE cc_start: 0.5414 (OUTLIER) cc_final: 0.5103 (t80) REVERT: A 569 ASN cc_start: 0.6948 (m110) cc_final: 0.6729 (t160) REVERT: A 671 LYS cc_start: 0.8089 (mttm) cc_final: 0.7652 (ttpt) REVERT: A 674 MET cc_start: 0.7430 (OUTLIER) cc_final: 0.6568 (tmm) outliers start: 67 outliers final: 44 residues processed: 322 average time/residue: 0.5304 time to fit residues: 198.8933 Evaluate side-chains 333 residues out of total 2170 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 271 time to evaluate : 0.665 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 12 ILE Chi-restraints excluded: chain C residue 67 THR Chi-restraints excluded: chain C residue 103 VAL Chi-restraints excluded: chain B residue 6 THR Chi-restraints excluded: chain B residue 44 THR Chi-restraints excluded: chain B residue 68 THR Chi-restraints excluded: chain B residue 103 VAL Chi-restraints excluded: chain B residue 115 THR Chi-restraints excluded: chain F residue 26 SER Chi-restraints excluded: chain F residue 119 THR Chi-restraints excluded: chain F residue 126 THR Chi-restraints excluded: chain E residue 36 VAL Chi-restraints excluded: chain E residue 42 ARG Chi-restraints excluded: chain E residue 120 GLU Chi-restraints excluded: chain E residue 143 THR Chi-restraints excluded: chain E residue 202 VAL Chi-restraints excluded: chain D residue 79 ILE Chi-restraints excluded: chain D residue 124 GLU Chi-restraints excluded: chain D residue 161 GLU Chi-restraints excluded: chain G residue 95 LYS Chi-restraints excluded: chain G residue 140 VAL Chi-restraints excluded: chain G residue 147 GLU Chi-restraints excluded: chain I residue 78 GLU Chi-restraints excluded: chain I residue 123 PHE Chi-restraints excluded: chain I residue 161 GLU Chi-restraints excluded: chain J residue 14 LEU Chi-restraints excluded: chain J residue 28 LYS Chi-restraints excluded: chain J residue 59 THR Chi-restraints excluded: chain J residue 98 ILE Chi-restraints excluded: chain J residue 106 LEU Chi-restraints excluded: chain H residue 23 ILE Chi-restraints excluded: chain H residue 41 VAL Chi-restraints excluded: chain H residue 153 GLU Chi-restraints excluded: chain H residue 200 VAL Chi-restraints excluded: chain H residue 209 THR Chi-restraints excluded: chain H residue 212 ILE Chi-restraints excluded: chain H residue 327 ASN Chi-restraints excluded: chain A residue 59 HIS Chi-restraints excluded: chain A residue 77 ILE Chi-restraints excluded: chain A residue 80 ILE Chi-restraints excluded: chain A residue 157 LEU Chi-restraints excluded: chain A residue 204 LEU Chi-restraints excluded: chain A residue 214 ILE Chi-restraints excluded: chain A residue 260 ILE Chi-restraints excluded: chain A residue 281 PHE Chi-restraints excluded: chain A residue 315 LEU Chi-restraints excluded: chain A residue 361 MET Chi-restraints excluded: chain A residue 374 VAL Chi-restraints excluded: chain A residue 388 LEU Chi-restraints excluded: chain A residue 408 CYS Chi-restraints excluded: chain A residue 434 LEU Chi-restraints excluded: chain A residue 448 VAL Chi-restraints excluded: chain A residue 468 ILE Chi-restraints excluded: chain A residue 542 ILE Chi-restraints excluded: chain A residue 549 ILE Chi-restraints excluded: chain A residue 563 PHE Chi-restraints excluded: chain A residue 607 THR Chi-restraints excluded: chain A residue 634 SER Chi-restraints excluded: chain A residue 674 MET Chi-restraints excluded: chain A residue 686 GLU Chi-restraints excluded: chain A residue 687 HIS Chi-restraints excluded: chain A residue 695 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 190 optimal weight: 3.9990 chunk 59 optimal weight: 4.9990 chunk 116 optimal weight: 8.9990 chunk 236 optimal weight: 5.9990 chunk 177 optimal weight: 0.9990 chunk 217 optimal weight: 0.7980 chunk 28 optimal weight: 0.8980 chunk 176 optimal weight: 3.9990 chunk 141 optimal weight: 1.9990 chunk 203 optimal weight: 0.7980 chunk 99 optimal weight: 0.7980 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 56 HIS B 56 HIS D 125 ASN D 174 HIS D 178 ASN ** G 198 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 189 ASN H 187 ASN ** A 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 516 ASN ** A 687 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4136 r_free = 0.4136 target = 0.179964 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3732 r_free = 0.3732 target = 0.138600 restraints weight = 26328.447| |-----------------------------------------------------------------------------| r_work (start): 0.3685 rms_B_bonded: 2.02 r_work: 0.3520 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.3405 rms_B_bonded: 4.23 restraints_weight: 0.2500 r_work (final): 0.3405 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7834 moved from start: 0.3037 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 21865 Z= 0.135 Angle : 0.560 13.309 29807 Z= 0.302 Chirality : 0.043 0.412 3405 Planarity : 0.004 0.068 3514 Dihedral : 14.953 164.162 3842 Min Nonbonded Distance : 2.289 Molprobity Statistics. All-atom Clashscore : 10.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer: Outliers : 3.13 % Allowed : 23.09 % Favored : 73.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.54 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.75 (0.16), residues: 2440 helix: 1.69 (0.15), residues: 1093 sheet: -0.04 (0.24), residues: 415 loop : -0.63 (0.19), residues: 932 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG A 466 TYR 0.028 0.001 TYR C 122 PHE 0.036 0.002 PHE A 250 TRP 0.010 0.001 TRP H 237 HIS 0.006 0.001 HIS B 56 Details of bonding type rmsd/Z covalent geometry : bond 0.00292 / 0.13 (21865) covalent geometry : angle 0.56032 / 0.30 (29807) hydrogen bonds : bond 0.04290 / 2.85 ( 1075) hydrogen bonds : angle 4.70649 / 3.33 ( 3116) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8135.62 seconds wall clock time: 139 minutes 35.91 seconds (8375.91 seconds total)