Starting phenix.real_space_refine on Wed Jun 18 12:02:15 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9g9d_51148/06_2025/9g9d_51148.cif Found real_map, /net/cci-nas-00/data/ceres_data/9g9d_51148/06_2025/9g9d_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/9g9d_51148/06_2025/9g9d_51148.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9g9d_51148/06_2025/9g9d_51148.map" model { file = "/net/cci-nas-00/data/ceres_data/9g9d_51148/06_2025/9g9d_51148.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9g9d_51148/06_2025/9g9d_51148.cif" } resolution = 2.9 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 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): 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: 15.64, per 1000 atoms: 0.73 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: 6.51 Conformation dependent library (CDL) restraints added in 2.9 seconds 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: 8.11 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: 8.72 Time building geometry restraints manager: 7.59 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: 7.460 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: 1.080 Check model and map are aligned: 0.180 Set scattering table: 0.230 Process input model: 60.170 Find NCS groups from input model: 0.610 Set up NCS constraints: 0.100 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:13.840 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 83.690 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7570 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= 0.454 Angle : 0.992 9.021 29807 Z= 0.657 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.87 (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 TRP 0.005 0.001 TRP A 592 HIS 0.006 0.001 HIS I 18 PHE 0.023 0.001 PHE D 150 TYR 0.024 0.001 TYR A 307 ARG 0.007 0.001 ARG I 187 Details of bonding type rmsd hydrogen bonds : bond 0.18606 ( 1075) hydrogen bonds : angle 6.75726 ( 3116) covalent geometry : bond 0.00663 (21865) covalent geometry : angle 0.99217 (29807) *********************** 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 : 2.408 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: 0.4819 (t70) cc_final: 0.3098 (t70) REVERT: A 257 MET cc_start: 0.6709 (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: 1.2172 time to fit residues: 723.0989 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 : 2.565 ------------------------------------------------------------------------------- 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 212 optimal weight: 0.9990 chunk 191 optimal weight: 5.9990 chunk 105 optimal weight: 1.9990 chunk 65 optimal weight: 0.9990 chunk 128 optimal weight: 3.9990 chunk 102 optimal weight: 4.9990 chunk 197 optimal weight: 0.3980 chunk 76 optimal weight: 0.7980 chunk 120 optimal weight: 4.9990 chunk 147 optimal weight: 0.7980 chunk 228 optimal weight: 0.9980 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 18 HIS D 97 GLN ** D 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 155 ASN G 67 ASN G 252 GLN I 92 GLN I 178 ASN J 24 ASN J 49 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: 29 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4153 r_free = 0.4153 target = 0.181593 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3784 r_free = 0.3784 target = 0.143210 restraints weight = 26231.187| |-----------------------------------------------------------------------------| r_work (start): 0.3749 rms_B_bonded: 3.19 r_work: 0.3482 rms_B_bonded: 3.49 restraints_weight: 0.5000 r_work (final): 0.3482 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7544 moved from start: 0.2029 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 21865 Z= 0.143 Angle : 0.579 10.495 29807 Z= 0.309 Chirality : 0.043 0.330 3405 Planarity : 0.004 0.043 3514 Dihedral : 15.314 163.787 3860 Min Nonbonded Distance : 2.414 Molprobity Statistics. All-atom Clashscore : 10.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 4.33 % Allowed : 15.53 % Favored : 80.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.54 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.02 (0.16), residues: 2440 helix: 1.86 (0.15), residues: 1095 sheet: 0.18 (0.24), residues: 436 loop : -0.50 (0.19), residues: 909 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP H 237 HIS 0.004 0.001 HIS H 283 PHE 0.026 0.002 PHE D 150 TYR 0.025 0.001 TYR H 284 ARG 0.008 0.001 ARG A 466 Details of bonding type rmsd hydrogen bonds : bond 0.04861 ( 1075) hydrogen bonds : angle 4.95735 ( 3116) covalent geometry : bond 0.00303 (21865) covalent geometry : angle 0.57927 (29807) *********************** 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 447 residues out of total 2170 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 353 time to evaluate : 2.248 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 43 THR cc_start: 0.8276 (p) cc_final: 0.8028 (t) REVERT: C 121 ASP cc_start: 0.8100 (OUTLIER) cc_final: 0.7371 (m-30) REVERT: C 127 GLU cc_start: 0.6617 (mt-10) cc_final: 0.5996 (mt-10) REVERT: B 11 MET cc_start: 0.5965 (tpp) cc_final: 0.5386 (tmm) REVERT: B 74 ARG cc_start: 0.7690 (mtp85) cc_final: 0.7274 (mtp-110) REVERT: F 28 ILE cc_start: 0.8649 (mt) cc_final: 0.8266 (mp) REVERT: E 28 ILE cc_start: 0.8099 (mt) cc_final: 0.7558 (mp) REVERT: E 167 GLU cc_start: 0.7849 (mm-30) cc_final: 0.7230 (tp30) REVERT: E 203 VAL cc_start: 0.7687 (t) cc_final: 0.7407 (t) REVERT: D 139 ILE cc_start: 0.8694 (pt) cc_final: 0.8493 (pt) REVERT: D 161 GLU cc_start: 0.6990 (OUTLIER) cc_final: 0.6781 (mp0) REVERT: G 159 GLU cc_start: 0.7100 (mm-30) cc_final: 0.6792 (mm-30) REVERT: G 259 GLN cc_start: 0.7563 (pt0) cc_final: 0.7223 (pm20) REVERT: G 277 GLN cc_start: 0.6917 (tp40) cc_final: 0.6619 (tp-100) REVERT: I 161 GLU cc_start: 0.6848 (OUTLIER) cc_final: 0.6578 (mt-10) REVERT: J 10 GLU cc_start: 0.5951 (tp30) cc_final: 0.5301 (pt0) REVERT: J 40 ASN cc_start: 0.7916 (m110) cc_final: 0.7685 (m110) REVERT: J 59 THR cc_start: 0.7984 (OUTLIER) cc_final: 0.7604 (m) REVERT: J 61 VAL cc_start: 0.6065 (t) cc_final: 0.5751 (t) REVERT: J 91 GLU cc_start: 0.7146 (tp30) cc_final: 0.6742 (tp30) REVERT: H 22 LYS cc_start: 0.7126 (tttt) cc_final: 0.6499 (mppt) REVERT: H 145 LYS cc_start: 0.7019 (OUTLIER) cc_final: 0.6600 (tptt) REVERT: H 168 SER cc_start: 0.7496 (p) cc_final: 0.6919 (p) REVERT: H 202 VAL cc_start: 0.8483 (m) cc_final: 0.8204 (t) REVERT: H 212 ILE cc_start: 0.6801 (OUTLIER) cc_final: 0.6375 (pp) REVERT: A 77 ILE cc_start: 0.6674 (mt) cc_final: 0.6303 (mt) REVERT: A 242 LYS cc_start: 0.7612 (mttt) cc_final: 0.7164 (mptt) REVERT: A 252 LEU cc_start: 0.6296 (tt) cc_final: 0.6062 (tp) REVERT: A 439 PHE cc_start: 0.7946 (m-80) cc_final: 0.7419 (m-10) REVERT: A 455 TYR cc_start: 0.7360 (m-80) cc_final: 0.7130 (m-10) REVERT: A 469 LYS cc_start: 0.7007 (mttm) cc_final: 0.6778 (mmtt) REVERT: A 569 ASN cc_start: 0.7130 (m110) cc_final: 0.6881 (m-40) REVERT: A 655 ASN cc_start: 0.7308 (OUTLIER) cc_final: 0.7099 (m-40) REVERT: A 671 LYS cc_start: 0.8018 (mttm) cc_final: 0.7783 (ptpt) REVERT: A 751 ILE cc_start: 0.7564 (tt) cc_final: 0.7276 (pt) outliers start: 94 outliers final: 30 residues processed: 419 average time/residue: 1.2074 time to fit residues: 583.6843 Evaluate side-chains 335 residues out of total 2170 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 298 time to evaluate : 2.415 ------------------------------------------------------------------------------- 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 104 ASP Chi-restraints excluded: chain C residue 121 ASP Chi-restraints excluded: chain B residue 6 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 79 ILE Chi-restraints excluded: chain F residue 178 ASN 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 G residue 95 LYS Chi-restraints excluded: chain G residue 140 VAL 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 41 VAL Chi-restraints excluded: chain H residue 145 LYS 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 260 ILE Chi-restraints excluded: chain A residue 281 PHE Chi-restraints excluded: chain A residue 289 SER 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 448 VAL Chi-restraints excluded: chain A residue 468 ILE Chi-restraints excluded: chain A residue 542 ILE Chi-restraints excluded: chain A residue 642 LEU Chi-restraints excluded: chain A residue 655 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 228 optimal weight: 2.9990 chunk 150 optimal weight: 0.7980 chunk 114 optimal weight: 9.9990 chunk 113 optimal weight: 1.9990 chunk 39 optimal weight: 3.9990 chunk 75 optimal weight: 4.9990 chunk 28 optimal weight: 0.7980 chunk 118 optimal weight: 3.9990 chunk 187 optimal weight: 7.9990 chunk 15 optimal weight: 4.9990 chunk 91 optimal weight: 0.6980 overall best weight: 1.4584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 56 HIS B 56 HIS ** D 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 184 GLN H 187 ASN ** A 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 159 ASN ** A 687 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 725 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4114 r_free = 0.4114 target = 0.177995 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3705 r_free = 0.3705 target = 0.135562 restraints weight = 26231.465| |-----------------------------------------------------------------------------| r_work (start): 0.3643 rms_B_bonded: 2.02 r_work: 0.3491 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.3378 rms_B_bonded: 4.07 restraints_weight: 0.2500 r_work (final): 0.3378 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7662 moved from start: 0.2388 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 21865 Z= 0.177 Angle : 0.589 10.340 29807 Z= 0.312 Chirality : 0.043 0.347 3405 Planarity : 0.004 0.048 3514 Dihedral : 15.176 165.949 3851 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 10.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer: Outliers : 4.56 % Allowed : 17.51 % Favored : 77.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.54 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.90 (0.16), residues: 2440 helix: 1.74 (0.15), residues: 1097 sheet: 0.21 (0.25), residues: 409 loop : -0.56 (0.18), residues: 934 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 592 HIS 0.004 0.001 HIS F 151 PHE 0.022 0.002 PHE C 119 TYR 0.025 0.002 TYR A 307 ARG 0.007 0.001 ARG A 466 Details of bonding type rmsd hydrogen bonds : bond 0.04829 ( 1075) hydrogen bonds : angle 4.85360 ( 3116) covalent geometry : bond 0.00392 (21865) covalent geometry : angle 0.58899 (29807) *********************** 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 415 residues out of total 2170 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 99 poor density : 316 time to evaluate : 2.239 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 121 ASP cc_start: 0.8112 (OUTLIER) cc_final: 0.7340 (m-30) REVERT: B 11 MET cc_start: 0.6116 (tpp) cc_final: 0.5629 (tmm) REVERT: B 25 LYS cc_start: 0.7988 (OUTLIER) cc_final: 0.7773 (tptp) REVERT: B 74 ARG cc_start: 0.7661 (mtp85) cc_final: 0.7271 (mtp-110) REVERT: F 28 ILE cc_start: 0.8731 (mt) cc_final: 0.8437 (mp) REVERT: F 42 ARG cc_start: 0.8678 (OUTLIER) cc_final: 0.8429 (mtm110) REVERT: E 28 ILE cc_start: 0.8054 (mt) cc_final: 0.7549 (mp) REVERT: E 42 ARG cc_start: 0.8101 (OUTLIER) cc_final: 0.7020 (mtm180) REVERT: E 120 GLU cc_start: 0.8632 (OUTLIER) cc_final: 0.8146 (pm20) REVERT: E 167 GLU cc_start: 0.7899 (mm-30) cc_final: 0.7221 (tp30) REVERT: E 203 VAL cc_start: 0.7795 (t) cc_final: 0.7518 (t) REVERT: D 124 GLU cc_start: 0.8450 (OUTLIER) cc_final: 0.8094 (mt-10) REVERT: D 139 ILE cc_start: 0.8800 (pt) cc_final: 0.8586 (pt) REVERT: D 161 GLU cc_start: 0.6886 (OUTLIER) cc_final: 0.6635 (mp0) REVERT: G 95 LYS cc_start: 0.7238 (OUTLIER) cc_final: 0.6561 (pptt) REVERT: G 159 GLU cc_start: 0.7180 (mm-30) cc_final: 0.6916 (mm-30) REVERT: G 213 LEU cc_start: 0.6980 (tt) cc_final: 0.6555 (mt) REVERT: G 277 GLN cc_start: 0.6952 (tp40) cc_final: 0.6645 (tp-100) REVERT: I 55 MET cc_start: 0.8142 (OUTLIER) cc_final: 0.7919 (mtp) REVERT: I 161 GLU cc_start: 0.6923 (OUTLIER) cc_final: 0.6633 (mt-10) REVERT: J 40 ASN cc_start: 0.8005 (m110) cc_final: 0.7791 (m110) REVERT: J 59 THR cc_start: 0.7933 (OUTLIER) cc_final: 0.7562 (m) REVERT: J 61 VAL cc_start: 0.6077 (t) cc_final: 0.5763 (t) REVERT: J 78 GLU cc_start: 0.8907 (mm-30) cc_final: 0.8600 (mm-30) REVERT: J 91 GLU cc_start: 0.7165 (tp30) cc_final: 0.6754 (tp30) REVERT: H 22 LYS cc_start: 0.7094 (tttt) cc_final: 0.6473 (mppt) REVERT: H 145 LYS cc_start: 0.7333 (OUTLIER) cc_final: 0.7044 (tptm) REVERT: H 193 MET cc_start: 0.7799 (ttm) cc_final: 0.7586 (ttm) REVERT: H 202 VAL cc_start: 0.8443 (m) cc_final: 0.8177 (t) REVERT: H 212 ILE cc_start: 0.6785 (OUTLIER) cc_final: 0.6383 (pp) REVERT: A 59 HIS cc_start: 0.4261 (OUTLIER) cc_final: 0.3387 (p-80) REVERT: A 200 MET cc_start: -0.0121 (ppp) cc_final: -0.0720 (pmt) REVERT: A 242 LYS cc_start: 0.7763 (mttt) cc_final: 0.7202 (mppt) REVERT: A 361 MET cc_start: 0.5215 (OUTLIER) cc_final: 0.4727 (ttt) REVERT: A 439 PHE cc_start: 0.7937 (m-80) cc_final: 0.7574 (m-10) REVERT: A 455 TYR cc_start: 0.7442 (m-80) cc_final: 0.7107 (m-10) REVERT: A 468 ILE cc_start: 0.7036 (OUTLIER) cc_final: 0.6742 (mm) REVERT: A 469 LYS cc_start: 0.7106 (mttm) cc_final: 0.6808 (mmtt) REVERT: A 569 ASN cc_start: 0.7086 (m110) cc_final: 0.6818 (t160) REVERT: A 608 ARG cc_start: 0.5842 (mtm110) cc_final: 0.5583 (ttm170) REVERT: A 671 LYS cc_start: 0.8071 (mttm) cc_final: 0.7779 (ptpt) outliers start: 99 outliers final: 38 residues processed: 383 average time/residue: 1.1437 time to fit residues: 506.8282 Evaluate side-chains 333 residues out of total 2170 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 279 time to evaluate : 2.227 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 25 LYS Chi-restraints excluded: chain B residue 44 THR Chi-restraints excluded: chain B residue 57 VAL 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 42 ARG Chi-restraints excluded: chain F residue 119 THR Chi-restraints excluded: chain F residue 120 GLU Chi-restraints excluded: chain F residue 126 THR Chi-restraints excluded: chain F residue 133 VAL 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 202 VAL Chi-restraints excluded: chain D residue 124 GLU 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 I residue 38 ASP Chi-restraints excluded: chain I residue 55 MET 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 98 ILE Chi-restraints excluded: chain H residue 41 VAL Chi-restraints excluded: chain H residue 145 LYS 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 59 HIS 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 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 448 VAL Chi-restraints excluded: chain A residue 468 ILE Chi-restraints excluded: chain A residue 622 MET Chi-restraints excluded: chain A residue 634 SER Chi-restraints excluded: chain A residue 687 HIS Chi-restraints excluded: chain A residue 695 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 58 optimal weight: 1.9990 chunk 79 optimal weight: 1.9990 chunk 121 optimal weight: 3.9990 chunk 160 optimal weight: 0.7980 chunk 152 optimal weight: 4.9990 chunk 68 optimal weight: 2.9990 chunk 211 optimal weight: 9.9990 chunk 243 optimal weight: 3.9990 chunk 146 optimal weight: 0.7980 chunk 177 optimal weight: 5.9990 chunk 164 optimal weight: 4.9990 overall best weight: 1.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 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: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4102 r_free = 0.4102 target = 0.176796 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3687 r_free = 0.3687 target = 0.134538 restraints weight = 26501.003| |-----------------------------------------------------------------------------| r_work (start): 0.3632 rms_B_bonded: 2.07 r_work: 0.3460 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.3346 rms_B_bonded: 4.27 restraints_weight: 0.2500 r_work (final): 0.3346 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7684 moved from start: 0.2617 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 21865 Z= 0.194 Angle : 0.595 8.769 29807 Z= 0.316 Chirality : 0.044 0.368 3405 Planarity : 0.004 0.047 3514 Dihedral : 15.115 167.141 3849 Min Nonbonded Distance : 2.400 Molprobity Statistics. All-atom Clashscore : 10.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.79 % Favored : 97.21 % Rotamer: Outliers : 4.98 % Allowed : 18.39 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.71 (0.16), residues: 2440 helix: 1.58 (0.15), residues: 1102 sheet: 0.11 (0.25), residues: 409 loop : -0.66 (0.18), residues: 929 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 493 HIS 0.005 0.001 HIS F 151 PHE 0.027 0.002 PHE C 119 TYR 0.021 0.002 TYR A 307 ARG 0.009 0.001 ARG A 466 Details of bonding type rmsd hydrogen bonds : bond 0.04751 ( 1075) hydrogen bonds : angle 4.84642 ( 3116) covalent geometry : bond 0.00433 (21865) covalent geometry : angle 0.59548 (29807) *********************** 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 415 residues out of total 2170 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 108 poor density : 307 time to evaluate : 2.405 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 121 ASP cc_start: 0.8164 (OUTLIER) cc_final: 0.7419 (m-30) REVERT: C 127 GLU cc_start: 0.6793 (mt-10) cc_final: 0.6193 (mt-10) REVERT: B 11 MET cc_start: 0.6154 (tpp) cc_final: 0.5667 (tmm) REVERT: B 47 LEU cc_start: 0.8675 (OUTLIER) cc_final: 0.8261 (tt) REVERT: F 28 ILE cc_start: 0.8786 (mt) cc_final: 0.8415 (mp) REVERT: E 28 ILE cc_start: 0.8110 (mt) cc_final: 0.7605 (mp) REVERT: E 42 ARG cc_start: 0.8101 (OUTLIER) cc_final: 0.7020 (mtm180) REVERT: E 120 GLU cc_start: 0.8681 (OUTLIER) cc_final: 0.8196 (pm20) REVERT: E 161 GLU cc_start: 0.7076 (mt-10) cc_final: 0.6870 (mt-10) REVERT: E 167 GLU cc_start: 0.7903 (mm-30) cc_final: 0.7233 (tp30) REVERT: E 203 VAL cc_start: 0.7826 (t) cc_final: 0.7577 (t) REVERT: D 124 GLU cc_start: 0.8523 (OUTLIER) cc_final: 0.8156 (mt-10) REVERT: D 139 ILE cc_start: 0.8806 (pt) cc_final: 0.8605 (pt) REVERT: D 161 GLU cc_start: 0.6951 (OUTLIER) cc_final: 0.6652 (mp0) REVERT: G 95 LYS cc_start: 0.7275 (OUTLIER) cc_final: 0.6588 (pptt) REVERT: G 159 GLU cc_start: 0.7207 (mm-30) cc_final: 0.6935 (mm-30) REVERT: G 213 LEU cc_start: 0.6961 (tt) cc_final: 0.6522 (mt) REVERT: G 277 GLN cc_start: 0.7029 (tp40) cc_final: 0.6727 (tp-100) REVERT: I 161 GLU cc_start: 0.6962 (OUTLIER) cc_final: 0.6662 (mt-10) REVERT: J 40 ASN cc_start: 0.8016 (m110) cc_final: 0.7812 (m110) REVERT: J 59 THR cc_start: 0.7973 (OUTLIER) cc_final: 0.7603 (m) REVERT: J 61 VAL cc_start: 0.6174 (t) cc_final: 0.5862 (t) REVERT: J 78 GLU cc_start: 0.8894 (mm-30) cc_final: 0.8683 (mm-30) REVERT: J 91 GLU cc_start: 0.7194 (tp30) cc_final: 0.6742 (tp30) REVERT: H 22 LYS cc_start: 0.7096 (tttt) cc_final: 0.6478 (mppt) REVERT: H 145 LYS cc_start: 0.7416 (OUTLIER) cc_final: 0.7093 (ttmm) REVERT: H 202 VAL cc_start: 0.8453 (m) cc_final: 0.8186 (t) REVERT: H 212 ILE cc_start: 0.6894 (OUTLIER) cc_final: 0.6513 (pp) REVERT: A 59 HIS cc_start: 0.4248 (OUTLIER) cc_final: 0.3256 (p-80) REVERT: A 80 ILE cc_start: 0.7449 (OUTLIER) cc_final: 0.7168 (pp) REVERT: A 200 MET cc_start: 0.0251 (ppp) cc_final: -0.0561 (pmt) REVERT: A 242 LYS cc_start: 0.7878 (mttt) cc_final: 0.7254 (mppt) REVERT: A 281 PHE cc_start: 0.7233 (OUTLIER) cc_final: 0.6467 (p90) REVERT: A 361 MET cc_start: 0.5170 (OUTLIER) cc_final: 0.4788 (ttt) REVERT: A 439 PHE cc_start: 0.7985 (m-80) cc_final: 0.7592 (m-10) REVERT: A 468 ILE cc_start: 0.7103 (OUTLIER) cc_final: 0.6810 (mm) REVERT: A 469 LYS cc_start: 0.7169 (mttm) cc_final: 0.6863 (mmtt) REVERT: A 569 ASN cc_start: 0.7029 (m110) cc_final: 0.6765 (t160) REVERT: A 608 ARG cc_start: 0.5849 (mtm110) cc_final: 0.5591 (ttm170) REVERT: A 671 LYS cc_start: 0.8084 (mttm) cc_final: 0.7766 (ptpt) outliers start: 108 outliers final: 47 residues processed: 380 average time/residue: 1.2093 time to fit residues: 535.3425 Evaluate side-chains 346 residues out of total 2170 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 283 time to evaluate : 2.530 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 44 THR Chi-restraints excluded: chain B residue 47 LEU Chi-restraints excluded: chain B residue 57 VAL 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 119 THR Chi-restraints excluded: chain F residue 120 GLU 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 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 140 VAL Chi-restraints excluded: chain I residue 45 ILE 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 J residue 98 ILE Chi-restraints excluded: chain H residue 23 ILE Chi-restraints excluded: chain H residue 41 VAL Chi-restraints excluded: chain H residue 145 LYS 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 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 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 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 634 SER 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 173 optimal weight: 0.1980 chunk 13 optimal weight: 6.9990 chunk 62 optimal weight: 0.7980 chunk 28 optimal weight: 0.6980 chunk 86 optimal weight: 7.9990 chunk 197 optimal weight: 4.9990 chunk 209 optimal weight: 4.9990 chunk 10 optimal weight: 0.9990 chunk 51 optimal weight: 0.8980 chunk 136 optimal weight: 4.9990 chunk 172 optimal weight: 8.9990 overall best weight: 0.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 56 HIS B 56 HIS ** 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 159 ASN 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 = 0.4138 r_free = 0.4138 target = 0.180442 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3737 r_free = 0.3737 target = 0.138874 restraints weight = 26438.947| |-----------------------------------------------------------------------------| r_work (start): 0.3687 rms_B_bonded: 2.01 r_work: 0.3530 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.3416 rms_B_bonded: 4.19 restraints_weight: 0.2500 r_work (final): 0.3416 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7598 moved from start: 0.2852 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 21865 Z= 0.125 Angle : 0.540 12.616 29807 Z= 0.287 Chirality : 0.042 0.390 3405 Planarity : 0.004 0.050 3514 Dihedral : 14.990 163.285 3848 Min Nonbonded Distance : 2.387 Molprobity Statistics. All-atom Clashscore : 9.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer: Outliers : 4.65 % Allowed : 19.45 % Favored : 75.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.54 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.88 (0.16), residues: 2440 helix: 1.77 (0.15), residues: 1094 sheet: 0.16 (0.25), residues: 409 loop : -0.60 (0.18), residues: 937 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 493 HIS 0.004 0.001 HIS B 56 PHE 0.024 0.001 PHE A 660 TYR 0.020 0.001 TYR C 58 ARG 0.010 0.000 ARG A 466 Details of bonding type rmsd hydrogen bonds : bond 0.04183 ( 1075) hydrogen bonds : angle 4.61156 ( 3116) covalent geometry : bond 0.00265 (21865) covalent geometry : angle 0.54030 (29807) *********************** 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 418 residues out of total 2170 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 101 poor density : 317 time to evaluate : 3.597 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 121 ASP cc_start: 0.8119 (OUTLIER) cc_final: 0.7386 (m-30) REVERT: C 127 GLU cc_start: 0.6711 (mt-10) cc_final: 0.6166 (mt-10) REVERT: B 11 MET cc_start: 0.5976 (tpp) cc_final: 0.5555 (tmm) REVERT: B 74 ARG cc_start: 0.7700 (mtp85) cc_final: 0.7233 (mtp-110) REVERT: F 28 ILE cc_start: 0.8742 (mt) cc_final: 0.8415 (mp) REVERT: F 45 ILE cc_start: 0.8143 (OUTLIER) cc_final: 0.7753 (tt) REVERT: F 133 VAL cc_start: 0.8591 (OUTLIER) cc_final: 0.8370 (t) REVERT: E 28 ILE cc_start: 0.8086 (mt) cc_final: 0.7566 (mp) REVERT: E 42 ARG cc_start: 0.8112 (OUTLIER) cc_final: 0.7027 (mtm180) REVERT: E 167 GLU cc_start: 0.7848 (mm-30) cc_final: 0.7181 (tp30) REVERT: E 203 VAL cc_start: 0.7766 (t) cc_final: 0.7508 (t) REVERT: D 124 GLU cc_start: 0.8433 (OUTLIER) cc_final: 0.8050 (mt-10) REVERT: D 139 ILE cc_start: 0.8733 (pt) cc_final: 0.8525 (pt) REVERT: D 161 GLU cc_start: 0.6969 (OUTLIER) cc_final: 0.6686 (mp0) REVERT: G 54 LEU cc_start: 0.7208 (tt) cc_final: 0.6938 (pp) REVERT: G 95 LYS cc_start: 0.7259 (OUTLIER) cc_final: 0.6562 (pptt) REVERT: G 159 GLU cc_start: 0.7202 (mm-30) cc_final: 0.6922 (mm-30) REVERT: G 213 LEU cc_start: 0.6986 (tt) cc_final: 0.6633 (mt) REVERT: G 277 GLN cc_start: 0.7055 (tp40) cc_final: 0.6767 (tp-100) REVERT: I 123 PHE cc_start: 0.7736 (OUTLIER) cc_final: 0.7383 (t80) REVERT: I 161 GLU cc_start: 0.6901 (OUTLIER) cc_final: 0.6571 (mt-10) REVERT: J 10 GLU cc_start: 0.5630 (tp30) cc_final: 0.5214 (pt0) REVERT: J 59 THR cc_start: 0.7893 (t) cc_final: 0.7550 (m) REVERT: J 61 VAL cc_start: 0.6113 (t) cc_final: 0.5771 (t) REVERT: J 78 GLU cc_start: 0.8900 (mm-30) cc_final: 0.8608 (mm-30) REVERT: J 91 GLU cc_start: 0.7121 (tp30) cc_final: 0.6700 (tp30) REVERT: H 22 LYS cc_start: 0.7095 (tttt) cc_final: 0.6453 (tppt) REVERT: H 145 LYS cc_start: 0.7318 (OUTLIER) cc_final: 0.7047 (ttmm) REVERT: H 202 VAL cc_start: 0.8424 (m) cc_final: 0.8159 (t) REVERT: H 212 ILE cc_start: 0.6834 (OUTLIER) cc_final: 0.6472 (pp) REVERT: A 22 ARG cc_start: 0.6879 (mtt90) cc_final: 0.6659 (mtt90) REVERT: A 59 HIS cc_start: 0.4159 (OUTLIER) cc_final: 0.3162 (p-80) REVERT: A 80 ILE cc_start: 0.7456 (OUTLIER) cc_final: 0.7164 (pp) REVERT: A 200 MET cc_start: 0.1131 (ppp) cc_final: 0.0842 (pmt) REVERT: A 242 LYS cc_start: 0.7844 (mttt) cc_final: 0.7204 (mppt) REVERT: A 281 PHE cc_start: 0.7265 (OUTLIER) cc_final: 0.6421 (p90) REVERT: A 361 MET cc_start: 0.5061 (OUTLIER) cc_final: 0.4825 (ttt) REVERT: A 439 PHE cc_start: 0.7880 (m-80) cc_final: 0.7539 (m-10) REVERT: A 441 VAL cc_start: 0.7876 (t) cc_final: 0.7633 (m) REVERT: A 459 GLU cc_start: 0.6817 (mm-30) cc_final: 0.6282 (tp30) REVERT: A 468 ILE cc_start: 0.7096 (OUTLIER) cc_final: 0.6827 (mm) REVERT: A 469 LYS cc_start: 0.7055 (mttm) cc_final: 0.6714 (mmtt) REVERT: A 538 PHE cc_start: 0.6670 (OUTLIER) cc_final: 0.6073 (m-80) REVERT: A 569 ASN cc_start: 0.7023 (m110) cc_final: 0.6759 (t160) REVERT: A 671 LYS cc_start: 0.8069 (mttm) cc_final: 0.7771 (ptpt) outliers start: 101 outliers final: 48 residues processed: 380 average time/residue: 1.2823 time to fit residues: 571.4688 Evaluate side-chains 356 residues out of total 2170 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 291 time to evaluate : 2.509 ------------------------------------------------------------------------------- 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 12 ILE Chi-restraints excluded: chain B residue 14 LEU Chi-restraints excluded: chain B residue 44 THR Chi-restraints excluded: chain B residue 57 VAL 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 119 THR Chi-restraints excluded: chain F residue 120 GLU Chi-restraints excluded: chain F residue 126 THR Chi-restraints excluded: chain F residue 133 VAL Chi-restraints excluded: chain E residue 36 VAL Chi-restraints excluded: chain E residue 42 ARG 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 52 GLU 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 145 LYS 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 80 ILE Chi-restraints excluded: chain A residue 157 LEU 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 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 538 PHE 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 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 55 optimal weight: 4.9990 chunk 80 optimal weight: 4.9990 chunk 236 optimal weight: 5.9990 chunk 205 optimal weight: 7.9990 chunk 170 optimal weight: 0.9990 chunk 0 optimal weight: 9.9990 chunk 103 optimal weight: 6.9990 chunk 20 optimal weight: 4.9990 chunk 146 optimal weight: 3.9990 chunk 155 optimal weight: 5.9990 chunk 131 optimal weight: 3.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 56 HIS B 56 HIS F 92 GLN ** D 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 57 ASN ** G 198 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 168 ASN ** J 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 187 ASN ** A 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 261 GLN A 649 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 = 0.4052 r_free = 0.4052 target = 0.171609 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3622 r_free = 0.3622 target = 0.129087 restraints weight = 26350.244| |-----------------------------------------------------------------------------| r_work (start): 0.3560 rms_B_bonded: 2.05 r_work: 0.3390 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.3278 rms_B_bonded: 4.11 restraints_weight: 0.2500 r_work (final): 0.3278 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7785 moved from start: 0.3058 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.083 21865 Z= 0.355 Angle : 0.753 11.019 29807 Z= 0.395 Chirality : 0.051 0.367 3405 Planarity : 0.005 0.054 3514 Dihedral : 15.237 175.058 3848 Min Nonbonded Distance : 2.328 Molprobity Statistics. All-atom Clashscore : 11.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.52 % Favored : 96.48 % Rotamer: Outliers : 5.71 % Allowed : 19.49 % Favored : 74.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.54 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.25 (0.16), residues: 2440 helix: 1.11 (0.15), residues: 1092 sheet: -0.09 (0.25), residues: 407 loop : -0.76 (0.18), residues: 941 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A 592 HIS 0.008 0.002 HIS F 151 PHE 0.038 0.003 PHE C 119 TYR 0.031 0.003 TYR G 66 ARG 0.007 0.001 ARG A 466 Details of bonding type rmsd hydrogen bonds : bond 0.05624 ( 1075) hydrogen bonds : angle 5.18227 ( 3116) covalent geometry : bond 0.00813 (21865) covalent geometry : angle 0.75289 (29807) *********************** 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 436 residues out of total 2170 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 124 poor density : 312 time to evaluate : 2.503 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 121 ASP cc_start: 0.8124 (OUTLIER) cc_final: 0.7292 (m-30) REVERT: B 11 MET cc_start: 0.5726 (tpp) cc_final: 0.5458 (tmm) REVERT: B 18 ARG cc_start: 0.7914 (ttp80) cc_final: 0.7566 (ttp80) REVERT: B 47 LEU cc_start: 0.8675 (OUTLIER) cc_final: 0.8222 (tt) REVERT: F 28 ILE cc_start: 0.8871 (mt) cc_final: 0.8589 (mp) REVERT: F 42 ARG cc_start: 0.8794 (mtp180) cc_final: 0.8549 (mtm110) REVERT: F 45 ILE cc_start: 0.8367 (OUTLIER) cc_final: 0.8038 (tt) REVERT: F 170 LYS cc_start: 0.7653 (tttt) cc_final: 0.6194 (tptp) REVERT: E 28 ILE cc_start: 0.8141 (mt) cc_final: 0.7664 (mp) REVERT: E 42 ARG cc_start: 0.8179 (OUTLIER) cc_final: 0.7085 (mtm180) REVERT: E 120 GLU cc_start: 0.8669 (OUTLIER) cc_final: 0.7937 (pm20) REVERT: E 167 GLU cc_start: 0.7957 (mm-30) cc_final: 0.7260 (tp30) REVERT: E 203 VAL cc_start: 0.7856 (t) cc_final: 0.7626 (t) REVERT: D 124 GLU cc_start: 0.8651 (OUTLIER) cc_final: 0.8304 (mt-10) REVERT: D 161 GLU cc_start: 0.7025 (OUTLIER) cc_final: 0.6704 (mp0) REVERT: G 62 ASP cc_start: 0.8168 (m-30) cc_final: 0.7788 (t70) REVERT: G 95 LYS cc_start: 0.7268 (OUTLIER) cc_final: 0.6564 (pptt) REVERT: G 159 GLU cc_start: 0.7156 (mm-30) cc_final: 0.6886 (mm-30) REVERT: G 213 LEU cc_start: 0.7144 (tt) cc_final: 0.6615 (mp) REVERT: G 277 GLN cc_start: 0.7126 (tp40) cc_final: 0.6818 (tp-100) REVERT: I 75 ASP cc_start: 0.8938 (OUTLIER) cc_final: 0.8702 (m-30) REVERT: I 123 PHE cc_start: 0.7849 (OUTLIER) cc_final: 0.7476 (t80) REVERT: I 161 GLU cc_start: 0.7062 (OUTLIER) cc_final: 0.6738 (mt-10) REVERT: J 10 GLU cc_start: 0.5636 (tp30) cc_final: 0.5214 (pt0) REVERT: J 78 GLU cc_start: 0.8890 (mm-30) cc_final: 0.8521 (mm-30) REVERT: J 91 GLU cc_start: 0.7223 (tp30) cc_final: 0.6808 (tp30) REVERT: H 22 LYS cc_start: 0.7203 (tttt) cc_final: 0.6578 (mppt) REVERT: H 145 LYS cc_start: 0.7728 (OUTLIER) cc_final: 0.7155 (ttmm) REVERT: H 200 VAL cc_start: 0.8055 (OUTLIER) cc_final: 0.7811 (p) REVERT: H 202 VAL cc_start: 0.8542 (m) cc_final: 0.8274 (t) REVERT: H 212 ILE cc_start: 0.7044 (OUTLIER) cc_final: 0.6709 (pp) REVERT: H 225 GLN cc_start: 0.6865 (OUTLIER) cc_final: 0.6617 (tt0) REVERT: A 59 HIS cc_start: 0.4152 (OUTLIER) cc_final: 0.3254 (p-80) REVERT: A 80 ILE cc_start: 0.7477 (OUTLIER) cc_final: 0.7213 (pp) REVERT: A 200 MET cc_start: 0.1113 (ppp) cc_final: 0.0523 (pmt) REVERT: A 242 LYS cc_start: 0.8050 (mttt) cc_final: 0.7362 (mppt) REVERT: A 436 ASP cc_start: 0.7936 (m-30) cc_final: 0.7713 (m-30) REVERT: A 439 PHE cc_start: 0.8136 (m-80) cc_final: 0.7800 (m-10) REVERT: A 459 GLU cc_start: 0.6867 (mm-30) cc_final: 0.6310 (tp30) REVERT: A 468 ILE cc_start: 0.7235 (OUTLIER) cc_final: 0.6945 (mm) REVERT: A 469 LYS cc_start: 0.7137 (mttm) cc_final: 0.6798 (mmtt) REVERT: A 538 PHE cc_start: 0.6772 (OUTLIER) cc_final: 0.6036 (m-80) REVERT: A 572 LYS cc_start: 0.7096 (tttp) cc_final: 0.6500 (tmmt) REVERT: A 671 LYS cc_start: 0.8123 (mttm) cc_final: 0.7662 (ttpt) outliers start: 124 outliers final: 57 residues processed: 395 average time/residue: 1.2186 time to fit residues: 555.2838 Evaluate side-chains 367 residues out of total 2170 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 291 time to evaluate : 2.429 ------------------------------------------------------------------------------- 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 73 VAL 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 44 THR Chi-restraints excluded: chain B residue 47 LEU Chi-restraints excluded: chain B residue 57 VAL 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 119 THR Chi-restraints excluded: chain F residue 126 THR Chi-restraints excluded: chain F residue 133 VAL Chi-restraints excluded: chain F residue 195 VAL Chi-restraints excluded: chain E residue 31 ILE Chi-restraints excluded: chain E residue 33 SER 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 D residue 203 VAL Chi-restraints excluded: chain G residue 95 LYS Chi-restraints excluded: chain G residue 99 ILE Chi-restraints excluded: chain G residue 102 GLU Chi-restraints excluded: chain G residue 212 LEU Chi-restraints excluded: chain I residue 75 ASP 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 J residue 98 ILE Chi-restraints excluded: chain H residue 23 ILE Chi-restraints excluded: chain H residue 41 VAL Chi-restraints excluded: chain H residue 145 LYS Chi-restraints excluded: chain H residue 151 VAL 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 225 GLN 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 180 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 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 458 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 607 THR Chi-restraints excluded: chain A residue 634 SER Chi-restraints excluded: chain A residue 686 GLU 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 2 optimal weight: 0.5980 chunk 63 optimal weight: 0.9990 chunk 154 optimal weight: 4.9990 chunk 0 optimal weight: 10.0000 chunk 165 optimal weight: 4.9990 chunk 241 optimal weight: 6.9990 chunk 33 optimal weight: 0.9980 chunk 134 optimal weight: 1.9990 chunk 207 optimal weight: 0.0870 chunk 163 optimal weight: 1.9990 chunk 80 optimal weight: 0.8980 overall best weight: 0.7160 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 56 HIS B 56 HIS ** D 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 198 GLN H 187 ASN ** A 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 159 ASN A 516 ASN A 569 ASN ** A 687 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4120 r_free = 0.4120 target = 0.178672 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3715 r_free = 0.3715 target = 0.137077 restraints weight = 26254.614| |-----------------------------------------------------------------------------| r_work (start): 0.3665 rms_B_bonded: 2.03 r_work: 0.3498 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.3383 rms_B_bonded: 4.26 restraints_weight: 0.2500 r_work (final): 0.3383 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7644 moved from start: 0.3146 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 21865 Z= 0.133 Angle : 0.565 10.051 29807 Z= 0.300 Chirality : 0.043 0.401 3405 Planarity : 0.004 0.056 3514 Dihedral : 14.952 163.518 3848 Min Nonbonded Distance : 2.338 Molprobity Statistics. All-atom Clashscore : 10.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer: Outliers : 4.19 % Allowed : 21.52 % Favored : 74.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.54 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.59 (0.16), residues: 2440 helix: 1.51 (0.15), residues: 1098 sheet: -0.04 (0.25), residues: 414 loop : -0.69 (0.19), residues: 928 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 493 HIS 0.005 0.001 HIS B 56 PHE 0.035 0.002 PHE E 150 TYR 0.032 0.001 TYR C 122 ARG 0.011 0.000 ARG A 466 Details of bonding type rmsd hydrogen bonds : bond 0.04294 ( 1075) hydrogen bonds : angle 4.74752 ( 3116) covalent geometry : bond 0.00284 (21865) covalent geometry : angle 0.56522 (29807) *********************** 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 389 residues out of total 2170 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 298 time to evaluate : 2.259 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 127 GLU cc_start: 0.6691 (mt-10) cc_final: 0.6169 (mt-10) REVERT: B 11 MET cc_start: 0.5399 (tpp) cc_final: 0.4993 (tmm) REVERT: B 60 LYS cc_start: 0.7603 (mppt) cc_final: 0.7401 (mtmm) REVERT: B 76 GLU cc_start: 0.7521 (OUTLIER) cc_final: 0.6666 (mm-30) REVERT: F 28 ILE cc_start: 0.8756 (mt) cc_final: 0.8444 (mp) REVERT: F 42 ARG cc_start: 0.8701 (mtp180) cc_final: 0.8405 (mtm180) REVERT: F 133 VAL cc_start: 0.8585 (OUTLIER) cc_final: 0.8346 (t) REVERT: E 28 ILE cc_start: 0.8160 (mt) cc_final: 0.7651 (mp) REVERT: E 42 ARG cc_start: 0.8083 (OUTLIER) cc_final: 0.6993 (mtm180) REVERT: E 120 GLU cc_start: 0.8666 (OUTLIER) cc_final: 0.8026 (pm20) REVERT: E 167 GLU cc_start: 0.7838 (mm-30) cc_final: 0.7171 (tp30) REVERT: E 203 VAL cc_start: 0.7751 (t) cc_final: 0.7528 (t) REVERT: D 124 GLU cc_start: 0.8519 (OUTLIER) cc_final: 0.8178 (mt-10) REVERT: D 161 GLU cc_start: 0.6949 (OUTLIER) cc_final: 0.6724 (mp0) REVERT: G 54 LEU cc_start: 0.7196 (tt) cc_final: 0.6941 (pp) REVERT: G 95 LYS cc_start: 0.7307 (OUTLIER) cc_final: 0.6601 (pptt) REVERT: G 147 GLU cc_start: 0.8224 (OUTLIER) cc_final: 0.7847 (pp20) REVERT: G 159 GLU cc_start: 0.7300 (mm-30) cc_final: 0.6992 (mm-30) REVERT: G 213 LEU cc_start: 0.7075 (tt) cc_final: 0.6666 (mt) REVERT: G 277 GLN cc_start: 0.7041 (tp40) cc_final: 0.6790 (tp-100) REVERT: I 161 GLU cc_start: 0.6997 (OUTLIER) cc_final: 0.6645 (mt-10) REVERT: J 59 THR cc_start: 0.7921 (OUTLIER) cc_final: 0.7585 (m) REVERT: J 79 TYR cc_start: 0.7279 (t80) cc_final: 0.7007 (t80) REVERT: J 91 GLU cc_start: 0.7096 (tp30) cc_final: 0.6720 (tp30) REVERT: H 22 LYS cc_start: 0.7173 (tttt) cc_final: 0.6552 (tppt) REVERT: H 145 LYS cc_start: 0.7430 (OUTLIER) cc_final: 0.6856 (tttt) REVERT: H 200 VAL cc_start: 0.7958 (OUTLIER) cc_final: 0.7741 (p) REVERT: H 202 VAL cc_start: 0.8441 (m) cc_final: 0.8166 (t) REVERT: H 212 ILE cc_start: 0.6940 (OUTLIER) cc_final: 0.6600 (pp) REVERT: H 225 GLN cc_start: 0.6849 (OUTLIER) cc_final: 0.6489 (tt0) REVERT: A 59 HIS cc_start: 0.3999 (OUTLIER) cc_final: 0.3009 (p-80) REVERT: A 80 ILE cc_start: 0.7460 (OUTLIER) cc_final: 0.7181 (pp) REVERT: A 200 MET cc_start: 0.2012 (ppp) cc_final: 0.1629 (pmt) REVERT: A 242 LYS cc_start: 0.8037 (mttt) cc_final: 0.7365 (mppt) REVERT: A 436 ASP cc_start: 0.7958 (m-30) cc_final: 0.7756 (m-30) REVERT: A 439 PHE cc_start: 0.7991 (m-80) cc_final: 0.7657 (m-10) REVERT: A 441 VAL cc_start: 0.7893 (t) cc_final: 0.7628 (m) REVERT: A 459 GLU cc_start: 0.6870 (mm-30) cc_final: 0.6304 (tp30) REVERT: A 468 ILE cc_start: 0.7200 (OUTLIER) cc_final: 0.6946 (mm) REVERT: A 469 LYS cc_start: 0.7030 (mttm) cc_final: 0.6715 (mmtt) REVERT: A 538 PHE cc_start: 0.6686 (OUTLIER) cc_final: 0.5863 (m-80) REVERT: A 671 LYS cc_start: 0.8060 (mttm) cc_final: 0.7611 (ttpt) outliers start: 91 outliers final: 47 residues processed: 361 average time/residue: 1.0873 time to fit residues: 458.0771 Evaluate side-chains 349 residues out of total 2170 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 284 time to evaluate : 2.343 ------------------------------------------------------------------------------- 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 14 LEU 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 76 GLU 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 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 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 102 GLU Chi-restraints excluded: chain G residue 113 ASP Chi-restraints excluded: chain G residue 147 GLU 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 J residue 98 ILE Chi-restraints excluded: chain H residue 23 ILE Chi-restraints excluded: chain H residue 41 VAL Chi-restraints excluded: chain H residue 145 LYS 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 225 GLN Chi-restraints excluded: chain H residue 327 ASN Chi-restraints excluded: chain H residue 338 VAL 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 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 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 132 optimal weight: 1.9990 chunk 104 optimal weight: 1.9990 chunk 131 optimal weight: 3.9990 chunk 159 optimal weight: 9.9990 chunk 184 optimal weight: 3.9990 chunk 20 optimal weight: 0.7980 chunk 88 optimal weight: 0.9990 chunk 147 optimal weight: 0.9980 chunk 129 optimal weight: 0.0770 chunk 9 optimal weight: 3.9990 chunk 112 optimal weight: 0.8980 overall best weight: 0.7540 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 56 HIS B 56 HIS F 178 ASN ** D 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 189 ASN H 187 ASN H 335 GLN ** 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: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4132 r_free = 0.4132 target = 0.179789 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3724 r_free = 0.3724 target = 0.137810 restraints weight = 26386.830| |-----------------------------------------------------------------------------| r_work (start): 0.3667 rms_B_bonded: 1.98 r_work: 0.3519 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.3406 rms_B_bonded: 4.11 restraints_weight: 0.2500 r_work (final): 0.3406 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7623 moved from start: 0.3273 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 21865 Z= 0.132 Angle : 0.563 11.551 29807 Z= 0.297 Chirality : 0.042 0.389 3405 Planarity : 0.004 0.057 3514 Dihedral : 14.860 164.841 3846 Min Nonbonded Distance : 2.302 Molprobity Statistics. All-atom Clashscore : 9.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Rotamer: Outliers : 3.64 % Allowed : 22.67 % Favored : 73.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.54 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.74 (0.16), residues: 2440 helix: 1.65 (0.15), residues: 1099 sheet: 0.06 (0.25), residues: 407 loop : -0.65 (0.19), residues: 934 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 493 HIS 0.005 0.001 HIS B 56 PHE 0.037 0.002 PHE A 250 TYR 0.031 0.001 TYR C 122 ARG 0.013 0.000 ARG A 466 Details of bonding type rmsd hydrogen bonds : bond 0.04167 ( 1075) hydrogen bonds : angle 4.65365 ( 3116) covalent geometry : bond 0.00285 (21865) covalent geometry : angle 0.56319 (29807) *********************** 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 383 residues out of total 2170 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 304 time to evaluate : 2.410 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 127 GLU cc_start: 0.6522 (mt-10) cc_final: 0.6176 (mt-10) REVERT: B 11 MET cc_start: 0.5225 (tpp) cc_final: 0.4952 (tmm) REVERT: B 25 LYS cc_start: 0.7905 (OUTLIER) cc_final: 0.6705 (tttp) REVERT: F 28 ILE cc_start: 0.8741 (mt) cc_final: 0.8387 (mp) REVERT: F 133 VAL cc_start: 0.8597 (OUTLIER) cc_final: 0.8385 (t) REVERT: E 28 ILE cc_start: 0.8156 (mt) cc_final: 0.7640 (mp) REVERT: E 42 ARG cc_start: 0.8116 (OUTLIER) cc_final: 0.7039 (mtm180) REVERT: E 120 GLU cc_start: 0.8665 (OUTLIER) cc_final: 0.8034 (pm20) REVERT: E 167 GLU cc_start: 0.7852 (mm-30) cc_final: 0.7186 (tp30) REVERT: E 203 VAL cc_start: 0.7778 (t) cc_final: 0.7538 (t) REVERT: D 124 GLU cc_start: 0.8461 (OUTLIER) cc_final: 0.8087 (mt-10) REVERT: G 54 LEU cc_start: 0.7189 (tt) cc_final: 0.6982 (pp) REVERT: G 95 LYS cc_start: 0.7258 (OUTLIER) cc_final: 0.6570 (pptt) REVERT: G 159 GLU cc_start: 0.7201 (mm-30) cc_final: 0.6854 (mm-30) REVERT: G 213 LEU cc_start: 0.7083 (tt) cc_final: 0.6669 (mt) REVERT: I 161 GLU cc_start: 0.6922 (OUTLIER) cc_final: 0.6565 (mt-10) REVERT: J 59 THR cc_start: 0.7894 (OUTLIER) cc_final: 0.7556 (m) REVERT: J 61 VAL cc_start: 0.6198 (t) cc_final: 0.5710 (t) REVERT: J 91 GLU cc_start: 0.7066 (tp30) cc_final: 0.6695 (tp30) REVERT: H 22 LYS cc_start: 0.7164 (tttt) cc_final: 0.6503 (tppt) REVERT: H 200 VAL cc_start: 0.7937 (OUTLIER) cc_final: 0.7727 (p) REVERT: H 202 VAL cc_start: 0.8391 (m) cc_final: 0.8107 (t) REVERT: A 22 ARG cc_start: 0.6717 (mtt90) cc_final: 0.6512 (mtt90) REVERT: A 59 HIS cc_start: 0.3988 (OUTLIER) cc_final: 0.3070 (p-80) REVERT: A 80 ILE cc_start: 0.7458 (OUTLIER) cc_final: 0.7204 (pp) REVERT: A 200 MET cc_start: 0.2483 (ppp) cc_final: 0.2149 (pmt) REVERT: A 242 LYS cc_start: 0.8040 (mttt) cc_final: 0.7361 (mppt) REVERT: A 249 VAL cc_start: 0.7160 (t) cc_final: 0.6918 (t) REVERT: A 436 ASP cc_start: 0.7996 (m-30) cc_final: 0.7788 (m-30) REVERT: A 439 PHE cc_start: 0.7910 (m-80) cc_final: 0.7654 (m-10) REVERT: A 441 VAL cc_start: 0.7933 (t) cc_final: 0.7724 (m) REVERT: A 459 GLU cc_start: 0.6887 (mm-30) cc_final: 0.6309 (tp30) REVERT: A 468 ILE cc_start: 0.7227 (OUTLIER) cc_final: 0.6970 (mm) REVERT: A 469 LYS cc_start: 0.7060 (mttm) cc_final: 0.6738 (mmtt) REVERT: A 538 PHE cc_start: 0.6628 (OUTLIER) cc_final: 0.5812 (m-80) REVERT: A 563 PHE cc_start: 0.4908 (OUTLIER) cc_final: 0.4565 (t80) REVERT: A 671 LYS cc_start: 0.8027 (mttm) cc_final: 0.7629 (ttpt) outliers start: 79 outliers final: 47 residues processed: 355 average time/residue: 1.2033 time to fit residues: 497.2608 Evaluate side-chains 344 residues out of total 2170 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 283 time to evaluate : 2.260 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 67 THR Chi-restraints excluded: chain C residue 99 GLU Chi-restraints excluded: chain C residue 103 VAL 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 104 ASP 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 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 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 G residue 95 LYS Chi-restraints excluded: chain G residue 140 VAL 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 98 ILE Chi-restraints excluded: chain H residue 23 ILE Chi-restraints excluded: chain H residue 41 VAL Chi-restraints excluded: chain H residue 125 ASP 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 H residue 338 VAL Chi-restraints excluded: chain A residue 5 LEU Chi-restraints excluded: chain A residue 59 HIS Chi-restraints excluded: chain A residue 80 ILE Chi-restraints excluded: chain A residue 204 LEU Chi-restraints excluded: chain A residue 214 ILE 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 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 615 THR 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 215 optimal weight: 7.9990 chunk 74 optimal weight: 3.9990 chunk 10 optimal weight: 0.9990 chunk 111 optimal weight: 3.9990 chunk 77 optimal weight: 4.9990 chunk 113 optimal weight: 7.9990 chunk 5 optimal weight: 2.9990 chunk 146 optimal weight: 2.9990 chunk 186 optimal weight: 4.9990 chunk 131 optimal weight: 3.9990 chunk 58 optimal weight: 3.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 56 HIS B 56 HIS F 178 ASN ** D 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 189 ASN ** J 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 39 HIS H 187 ASN ** H 327 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 14 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 = 0.4068 r_free = 0.4068 target = 0.173307 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3642 r_free = 0.3642 target = 0.130869 restraints weight = 26284.144| |-----------------------------------------------------------------------------| r_work (start): 0.3581 rms_B_bonded: 2.05 r_work: 0.3410 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.3297 rms_B_bonded: 4.16 restraints_weight: 0.2500 r_work (final): 0.3297 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7760 moved from start: 0.3323 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.066 21865 Z= 0.294 Angle : 0.710 11.296 29807 Z= 0.372 Chirality : 0.049 0.373 3405 Planarity : 0.005 0.053 3514 Dihedral : 15.030 171.645 3842 Min Nonbonded Distance : 2.250 Molprobity Statistics. All-atom Clashscore : 11.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.48 % Favored : 96.52 % Rotamer: Outliers : 4.24 % Allowed : 22.26 % Favored : 73.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.54 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.33 (0.16), residues: 2440 helix: 1.23 (0.15), residues: 1095 sheet: -0.17 (0.25), residues: 414 loop : -0.75 (0.19), residues: 931 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP A 493 HIS 0.007 0.001 HIS F 151 PHE 0.033 0.002 PHE C 119 TYR 0.028 0.002 TYR C 122 ARG 0.014 0.001 ARG A 466 Details of bonding type rmsd hydrogen bonds : bond 0.05180 ( 1075) hydrogen bonds : angle 5.02735 ( 3116) covalent geometry : bond 0.00672 (21865) covalent geometry : angle 0.70990 (29807) *********************** 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 381 residues out of total 2170 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 289 time to evaluate : 2.979 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 11 MET cc_start: 0.5319 (tpp) cc_final: 0.4999 (tmm) REVERT: B 25 LYS cc_start: 0.8057 (OUTLIER) cc_final: 0.6857 (tttp) REVERT: B 95 ARG cc_start: 0.6231 (ttm-80) cc_final: 0.5835 (ttm-80) REVERT: E 28 ILE cc_start: 0.8176 (mt) cc_final: 0.7708 (mp) REVERT: E 120 GLU cc_start: 0.8672 (OUTLIER) cc_final: 0.7931 (pm20) REVERT: E 167 GLU cc_start: 0.7934 (mm-30) cc_final: 0.7249 (tp30) REVERT: E 203 VAL cc_start: 0.7823 (t) cc_final: 0.7598 (t) REVERT: D 124 GLU cc_start: 0.8631 (OUTLIER) cc_final: 0.8277 (mt-10) REVERT: G 95 LYS cc_start: 0.7273 (OUTLIER) cc_final: 0.6552 (pptt) REVERT: G 159 GLU cc_start: 0.7219 (mm-30) cc_final: 0.6937 (mm-30) REVERT: G 213 LEU cc_start: 0.7217 (tt) cc_final: 0.6724 (mt) REVERT: I 161 GLU cc_start: 0.7040 (OUTLIER) cc_final: 0.6716 (mt-10) REVERT: J 10 GLU cc_start: 0.5747 (tp30) cc_final: 0.5170 (pt0) REVERT: J 59 THR cc_start: 0.7980 (OUTLIER) cc_final: 0.7610 (m) REVERT: J 91 GLU cc_start: 0.7139 (tp30) cc_final: 0.6743 (tp30) REVERT: H 22 LYS cc_start: 0.7198 (tttt) cc_final: 0.6536 (mppt) REVERT: H 200 VAL cc_start: 0.7991 (OUTLIER) cc_final: 0.7772 (p) REVERT: H 202 VAL cc_start: 0.8501 (m) cc_final: 0.8223 (t) REVERT: H 225 GLN cc_start: 0.6843 (OUTLIER) cc_final: 0.6609 (tt0) REVERT: A 59 HIS cc_start: 0.3914 (OUTLIER) cc_final: 0.3089 (p-80) REVERT: A 80 ILE cc_start: 0.7369 (OUTLIER) cc_final: 0.7125 (pp) REVERT: A 200 MET cc_start: 0.2438 (ppp) cc_final: 0.2134 (pmt) REVERT: A 242 LYS cc_start: 0.8113 (mttt) cc_final: 0.7417 (mppt) REVERT: A 377 LYS cc_start: 0.7750 (ttmt) cc_final: 0.7272 (tmtt) REVERT: A 435 ARG cc_start: 0.6795 (ptt180) cc_final: 0.6518 (ttp-110) REVERT: A 436 ASP cc_start: 0.8099 (m-30) cc_final: 0.7790 (m-30) REVERT: A 439 PHE cc_start: 0.8106 (m-80) cc_final: 0.7809 (m-10) REVERT: A 459 GLU cc_start: 0.6944 (mm-30) cc_final: 0.6349 (tp30) REVERT: A 468 ILE cc_start: 0.7243 (OUTLIER) cc_final: 0.6982 (mm) REVERT: A 538 PHE cc_start: 0.6662 (OUTLIER) cc_final: 0.5820 (m-80) REVERT: A 671 LYS cc_start: 0.8055 (mttm) cc_final: 0.7674 (ttpt) outliers start: 92 outliers final: 51 residues processed: 346 average time/residue: 1.3858 time to fit residues: 556.1120 Evaluate side-chains 336 residues out of total 2170 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 273 time to evaluate : 2.257 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 67 THR Chi-restraints excluded: chain C residue 99 GLU Chi-restraints excluded: chain C residue 103 VAL 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 104 ASP 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 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 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 G residue 95 LYS Chi-restraints excluded: chain G residue 102 GLU Chi-restraints excluded: chain G residue 113 ASP 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 161 GLU Chi-restraints excluded: chain J residue 14 LEU Chi-restraints excluded: chain J residue 59 THR Chi-restraints excluded: chain J residue 98 ILE Chi-restraints excluded: chain H residue 23 ILE Chi-restraints excluded: chain H residue 41 VAL Chi-restraints excluded: chain H residue 125 ASP 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 225 GLN Chi-restraints excluded: chain H residue 285 LEU Chi-restraints excluded: chain A residue 59 HIS Chi-restraints excluded: chain A residue 80 ILE Chi-restraints excluded: chain A residue 180 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 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 615 THR 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 143 optimal weight: 4.9990 chunk 149 optimal weight: 0.1980 chunk 65 optimal weight: 0.8980 chunk 163 optimal weight: 0.7980 chunk 105 optimal weight: 0.5980 chunk 69 optimal weight: 0.0980 chunk 123 optimal weight: 1.9990 chunk 207 optimal weight: 0.9990 chunk 0 optimal weight: 10.0000 chunk 73 optimal weight: 0.0980 chunk 240 optimal weight: 1.9990 overall best weight: 0.3580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 56 HIS B 56 HIS F 178 ASN ** J 30 ASN ** 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: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4140 r_free = 0.4140 target = 0.180645 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3736 r_free = 0.3736 target = 0.138945 restraints weight = 26493.164| |-----------------------------------------------------------------------------| r_work (start): 0.3685 rms_B_bonded: 2.02 r_work: 0.3527 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.3413 rms_B_bonded: 4.25 restraints_weight: 0.2500 r_work (final): 0.3413 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7609 moved from start: 0.3424 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 21865 Z= 0.124 Angle : 0.591 11.670 29807 Z= 0.311 Chirality : 0.043 0.400 3405 Planarity : 0.004 0.059 3514 Dihedral : 14.906 161.602 3842 Min Nonbonded Distance : 2.261 Molprobity Statistics. All-atom Clashscore : 10.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer: Outliers : 2.58 % Allowed : 24.38 % Favored : 73.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.54 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.64 (0.16), residues: 2440 helix: 1.56 (0.15), residues: 1098 sheet: -0.13 (0.25), residues: 408 loop : -0.63 (0.19), residues: 934 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 493 HIS 0.006 0.001 HIS B 56 PHE 0.037 0.002 PHE B 16 TYR 0.032 0.001 TYR H 59 ARG 0.013 0.001 ARG A 466 Details of bonding type rmsd hydrogen bonds : bond 0.04175 ( 1075) hydrogen bonds : angle 4.72824 ( 3116) covalent geometry : bond 0.00261 (21865) covalent geometry : angle 0.59132 (29807) ********************** 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 337 residues out of total 2170 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 281 time to evaluate : 2.544 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 11 MET cc_start: 0.5160 (tpp) cc_final: 0.4852 (tmm) REVERT: B 25 LYS cc_start: 0.7932 (OUTLIER) cc_final: 0.6750 (tttp) REVERT: B 76 GLU cc_start: 0.7396 (OUTLIER) cc_final: 0.6509 (mt-10) REVERT: E 28 ILE cc_start: 0.8156 (mt) cc_final: 0.7641 (mp) REVERT: E 120 GLU cc_start: 0.8681 (OUTLIER) cc_final: 0.8143 (pm20) REVERT: E 144 ARG cc_start: 0.7392 (OUTLIER) cc_final: 0.7018 (mtm110) REVERT: E 167 GLU cc_start: 0.7851 (mm-30) cc_final: 0.7190 (tp30) REVERT: D 124 GLU cc_start: 0.8469 (OUTLIER) cc_final: 0.8116 (mt-10) REVERT: G 50 GLU cc_start: 0.6635 (pm20) cc_final: 0.6411 (pm20) REVERT: G 95 LYS cc_start: 0.7205 (mptm) cc_final: 0.6531 (pptt) REVERT: G 159 GLU cc_start: 0.7140 (mm-30) cc_final: 0.6917 (mm-30) REVERT: G 213 LEU cc_start: 0.7053 (tt) cc_final: 0.6652 (mt) REVERT: I 161 GLU cc_start: 0.6979 (OUTLIER) cc_final: 0.6622 (mt-10) REVERT: J 59 THR cc_start: 0.7872 (OUTLIER) cc_final: 0.7548 (m) REVERT: H 22 LYS cc_start: 0.7160 (tttt) cc_final: 0.6489 (tppt) REVERT: H 200 VAL cc_start: 0.7932 (OUTLIER) cc_final: 0.7721 (p) REVERT: H 202 VAL cc_start: 0.8410 (m) cc_final: 0.8125 (t) REVERT: A 59 HIS cc_start: 0.3882 (OUTLIER) cc_final: 0.3145 (p-80) REVERT: A 200 MET cc_start: 0.2778 (ppp) cc_final: 0.2529 (pmt) REVERT: A 242 LYS cc_start: 0.8089 (mttt) cc_final: 0.7399 (mppt) REVERT: A 249 VAL cc_start: 0.6967 (t) cc_final: 0.6696 (t) REVERT: A 281 PHE cc_start: 0.7357 (OUTLIER) cc_final: 0.6577 (p90) REVERT: A 377 LYS cc_start: 0.7719 (ttmt) cc_final: 0.7252 (tmtt) REVERT: A 436 ASP cc_start: 0.8078 (m-30) cc_final: 0.7866 (m-30) REVERT: A 439 PHE cc_start: 0.7969 (m-80) cc_final: 0.7721 (m-10) REVERT: A 441 VAL cc_start: 0.7922 (t) cc_final: 0.7699 (m) REVERT: A 459 GLU cc_start: 0.6900 (mm-30) cc_final: 0.6291 (tp30) REVERT: A 468 ILE cc_start: 0.7246 (OUTLIER) cc_final: 0.7019 (mm) REVERT: A 538 PHE cc_start: 0.6551 (OUTLIER) cc_final: 0.5650 (m-80) REVERT: A 563 PHE cc_start: 0.4994 (OUTLIER) cc_final: 0.4570 (t80) REVERT: A 671 LYS cc_start: 0.8029 (mttm) cc_final: 0.7643 (ttpt) outliers start: 56 outliers final: 37 residues processed: 320 average time/residue: 1.1842 time to fit residues: 445.1646 Evaluate side-chains 318 residues out of total 2170 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 268 time to evaluate : 2.166 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 67 THR Chi-restraints excluded: chain C residue 99 GLU Chi-restraints excluded: chain C residue 103 VAL 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 76 GLU Chi-restraints excluded: chain B residue 103 VAL Chi-restraints excluded: chain B residue 104 ASP Chi-restraints excluded: chain B residue 115 THR Chi-restraints excluded: chain F residue 10 LYS Chi-restraints excluded: chain F residue 119 THR Chi-restraints excluded: chain F residue 126 THR Chi-restraints excluded: chain E residue 120 GLU Chi-restraints excluded: chain E residue 143 THR Chi-restraints excluded: chain E residue 144 ARG 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 G residue 113 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 52 GLU Chi-restraints excluded: chain J residue 59 THR Chi-restraints excluded: chain H residue 41 VAL 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 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 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 563 PHE Chi-restraints excluded: chain A residue 607 THR Chi-restraints excluded: chain A residue 615 THR 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 137 optimal weight: 2.9990 chunk 14 optimal weight: 5.9990 chunk 188 optimal weight: 5.9990 chunk 88 optimal weight: 3.9990 chunk 182 optimal weight: 5.9990 chunk 240 optimal weight: 0.7980 chunk 189 optimal weight: 6.9990 chunk 27 optimal weight: 0.0670 chunk 56 optimal weight: 3.9990 chunk 223 optimal weight: 0.9990 chunk 204 optimal weight: 4.9990 overall best weight: 1.7724 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 56 HIS B 56 HIS F 178 ASN ** D 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 327 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4103 r_free = 0.4103 target = 0.176673 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3687 r_free = 0.3687 target = 0.134817 restraints weight = 26198.884| |-----------------------------------------------------------------------------| r_work (start): 0.3635 rms_B_bonded: 2.01 r_work: 0.3460 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.3347 rms_B_bonded: 4.21 restraints_weight: 0.2500 r_work (final): 0.3347 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7699 moved from start: 0.3422 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 21865 Z= 0.199 Angle : 0.633 11.467 29807 Z= 0.332 Chirality : 0.045 0.390 3405 Planarity : 0.004 0.056 3514 Dihedral : 14.923 167.609 3842 Min Nonbonded Distance : 2.410 Molprobity Statistics. All-atom Clashscore : 10.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.20 % Favored : 96.80 % Rotamer: Outliers : 2.95 % Allowed : 24.33 % Favored : 72.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.54 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.54 (0.16), residues: 2440 helix: 1.47 (0.15), residues: 1099 sheet: -0.12 (0.25), residues: 414 loop : -0.69 (0.19), residues: 927 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 493 HIS 0.005 0.001 HIS B 56 PHE 0.029 0.002 PHE A 250 TYR 0.045 0.002 TYR A 219 ARG 0.014 0.001 ARG A 466 Details of bonding type rmsd hydrogen bonds : bond 0.04558 ( 1075) hydrogen bonds : angle 4.83819 ( 3116) covalent geometry : bond 0.00450 (21865) covalent geometry : angle 0.63314 (29807) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 18356.27 seconds wall clock time: 318 minutes 6.56 seconds (19086.56 seconds total)