Starting phenix.real_space_refine on Wed May 21 08:44:26 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9g9d_51148/05_2025/9g9d_51148.cif Found real_map, /net/cci-nas-00/data/ceres_data/9g9d_51148/05_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_51148/05_2025/9g9d_51148.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9g9d_51148/05_2025/9g9d_51148.map" model { file = "/net/cci-nas-00/data/ceres_data/9g9d_51148/05_2025/9g9d_51148.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9g9d_51148/05_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): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/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: 12.29, per 1000 atoms: 0.58 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: 4.88 Conformation dependent library (CDL) restraints added in 2.5 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: 7.04 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: 7.50 Time building geometry restraints manager: 5.73 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: 9.900 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.960 Check model and map are aligned: 0.150 Set scattering table: 0.180 Process input model: 49.850 Find NCS groups from input model: 0.510 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:10.240 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 71.900 ------------------------------------------------------------------------------- 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 : 2.178 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: 1.1789 time to fit residues: 699.8096 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 : 2.191 ------------------------------------------------------------------------------- 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 = 34)----------------| | r_work = 0.3748 r_free = 0.3748 target = 0.139728 restraints weight = 26231.188| |-----------------------------------------------------------------------------| r_work (start): 0.3698 rms_B_bonded: 2.02 r_work: 0.3543 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.3428 rms_B_bonded: 4.22 restraints_weight: 0.2500 r_work (final): 0.3428 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7590 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 : 2.323 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 43 THR cc_start: 0.8314 (p) cc_final: 0.8060 (t) REVERT: C 121 ASP cc_start: 0.8095 (OUTLIER) cc_final: 0.7380 (m-30) REVERT: C 127 GLU cc_start: 0.6660 (mt-10) cc_final: 0.6052 (mt-10) REVERT: B 11 MET cc_start: 0.5956 (tpp) cc_final: 0.5373 (tmm) REVERT: B 74 ARG cc_start: 0.7700 (mtp85) cc_final: 0.7279 (mtp-110) REVERT: F 28 ILE cc_start: 0.8672 (mt) cc_final: 0.8294 (mp) REVERT: E 28 ILE cc_start: 0.8148 (mt) cc_final: 0.7599 (mp) REVERT: E 167 GLU cc_start: 0.7921 (mm-30) cc_final: 0.7291 (tp30) REVERT: E 203 VAL cc_start: 0.7693 (t) cc_final: 0.7408 (t) REVERT: D 139 ILE cc_start: 0.8748 (pt) cc_final: 0.8543 (pt) REVERT: D 161 GLU cc_start: 0.7007 (OUTLIER) cc_final: 0.6772 (mp0) REVERT: G 159 GLU cc_start: 0.7177 (mm-30) cc_final: 0.6869 (mm-30) REVERT: G 259 GLN cc_start: 0.7569 (pt0) cc_final: 0.7216 (pm20) REVERT: G 277 GLN cc_start: 0.6951 (tp40) cc_final: 0.6639 (tp-100) REVERT: I 161 GLU cc_start: 0.6923 (OUTLIER) cc_final: 0.6598 (mt-10) REVERT: J 10 GLU cc_start: 0.5960 (tp30) cc_final: 0.5304 (pt0) REVERT: J 40 ASN cc_start: 0.7941 (m110) cc_final: 0.7711 (m110) REVERT: J 59 THR cc_start: 0.8006 (OUTLIER) cc_final: 0.7628 (m) REVERT: J 61 VAL cc_start: 0.6109 (t) cc_final: 0.5787 (t) REVERT: J 91 GLU cc_start: 0.7159 (tp30) cc_final: 0.6755 (tp30) REVERT: H 22 LYS cc_start: 0.7151 (tttt) cc_final: 0.6528 (mppt) REVERT: H 145 LYS cc_start: 0.7089 (OUTLIER) cc_final: 0.6671 (tptt) REVERT: H 168 SER cc_start: 0.7504 (p) cc_final: 0.6926 (p) REVERT: H 202 VAL cc_start: 0.8485 (m) cc_final: 0.8204 (t) REVERT: H 212 ILE cc_start: 0.6789 (OUTLIER) cc_final: 0.6365 (pp) REVERT: A 77 ILE cc_start: 0.6689 (mt) cc_final: 0.6317 (mt) REVERT: A 242 LYS cc_start: 0.7612 (mttt) cc_final: 0.7162 (mptt) REVERT: A 252 LEU cc_start: 0.6327 (tt) cc_final: 0.6094 (tp) REVERT: A 439 PHE cc_start: 0.7954 (m-80) cc_final: 0.7436 (m-10) REVERT: A 455 TYR cc_start: 0.7393 (m-80) cc_final: 0.7160 (m-10) REVERT: A 469 LYS cc_start: 0.7002 (mttm) cc_final: 0.6776 (mmtt) REVERT: A 569 ASN cc_start: 0.7138 (m110) cc_final: 0.6886 (m-40) REVERT: A 655 ASN cc_start: 0.7357 (OUTLIER) cc_final: 0.7150 (m-40) REVERT: A 671 LYS cc_start: 0.8071 (mttm) cc_final: 0.7809 (ptpt) REVERT: A 751 ILE cc_start: 0.7595 (tt) cc_final: 0.7299 (pt) outliers start: 94 outliers final: 30 residues processed: 419 average time/residue: 1.1262 time to fit residues: 546.0818 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 : 2.417 ------------------------------------------------------------------------------- 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: 1.9990 chunk 150 optimal weight: 0.7980 chunk 114 optimal weight: 8.9990 chunk 113 optimal weight: 0.9990 chunk 39 optimal weight: 3.9990 chunk 75 optimal weight: 4.9990 chunk 28 optimal weight: 0.6980 chunk 118 optimal weight: 3.9990 chunk 187 optimal weight: 8.9990 chunk 15 optimal weight: 5.9990 chunk 91 optimal weight: 0.6980 overall best weight: 1.0384 ------------------------------------------------------------------------------- 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 = 0.4139 r_free = 0.4139 target = 0.180297 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3732 r_free = 0.3732 target = 0.138211 restraints weight = 26177.893| |-----------------------------------------------------------------------------| r_work (start): 0.3675 rms_B_bonded: 2.02 r_work: 0.3518 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.3404 rms_B_bonded: 4.17 restraints_weight: 0.2500 r_work (final): 0.3404 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7600 moved from start: 0.2371 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 21865 Z= 0.149 Angle : 0.563 10.163 29807 Z= 0.299 Chirality : 0.042 0.351 3405 Planarity : 0.004 0.048 3514 Dihedral : 15.158 164.487 3851 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 10.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Rotamer: Outliers : 4.10 % Allowed : 17.88 % Favored : 78.02 % 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: 0.97 (0.16), residues: 2440 helix: 1.82 (0.15), residues: 1097 sheet: 0.17 (0.24), residues: 424 loop : -0.52 (0.19), residues: 919 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 592 HIS 0.004 0.001 HIS F 151 PHE 0.022 0.002 PHE D 150 TYR 0.022 0.001 TYR A 307 ARG 0.008 0.000 ARG A 466 Details of bonding type rmsd hydrogen bonds : bond 0.04604 ( 1075) hydrogen bonds : angle 4.78956 ( 3116) covalent geometry : bond 0.00322 (21865) covalent geometry : angle 0.56326 (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 407 residues out of total 2170 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 318 time to evaluate : 2.344 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 121 ASP cc_start: 0.8119 (OUTLIER) cc_final: 0.7376 (m-30) REVERT: C 127 GLU cc_start: 0.6729 (mt-10) cc_final: 0.6508 (mt-10) REVERT: B 11 MET cc_start: 0.6086 (tpp) cc_final: 0.5562 (tmm) REVERT: B 74 ARG cc_start: 0.7644 (mtp85) cc_final: 0.7261 (mtp-110) REVERT: F 42 ARG cc_start: 0.8635 (OUTLIER) cc_final: 0.8366 (mtm110) REVERT: E 28 ILE cc_start: 0.8035 (mt) cc_final: 0.7499 (mp) REVERT: E 42 ARG cc_start: 0.8097 (OUTLIER) cc_final: 0.6996 (mtm180) REVERT: E 167 GLU cc_start: 0.7877 (mm-30) cc_final: 0.7223 (tp30) REVERT: E 203 VAL cc_start: 0.7774 (t) cc_final: 0.7489 (t) REVERT: D 124 GLU cc_start: 0.8379 (OUTLIER) cc_final: 0.8030 (mt-10) REVERT: D 139 ILE cc_start: 0.8750 (pt) cc_final: 0.8538 (pt) REVERT: D 161 GLU cc_start: 0.6918 (OUTLIER) cc_final: 0.6667 (mp0) REVERT: G 95 LYS cc_start: 0.7207 (OUTLIER) cc_final: 0.6519 (pptt) REVERT: G 159 GLU cc_start: 0.7161 (mm-30) cc_final: 0.6878 (mm-30) REVERT: G 213 LEU cc_start: 0.6931 (tt) cc_final: 0.6484 (mt) REVERT: G 277 GLN cc_start: 0.6957 (tp40) cc_final: 0.6631 (tp-100) REVERT: I 161 GLU cc_start: 0.6902 (OUTLIER) cc_final: 0.6581 (mt-10) REVERT: J 40 ASN cc_start: 0.7976 (m110) cc_final: 0.7756 (m110) REVERT: J 59 THR cc_start: 0.7889 (OUTLIER) cc_final: 0.7528 (m) REVERT: J 61 VAL cc_start: 0.6048 (t) cc_final: 0.5723 (t) REVERT: J 78 GLU cc_start: 0.8898 (mm-30) cc_final: 0.8592 (mm-30) REVERT: J 91 GLU cc_start: 0.7136 (tp30) cc_final: 0.6696 (tp30) REVERT: H 22 LYS cc_start: 0.7062 (tttt) cc_final: 0.6432 (mppt) REVERT: H 168 SER cc_start: 0.7550 (p) cc_final: 0.6940 (p) REVERT: H 193 MET cc_start: 0.7799 (ttm) cc_final: 0.7403 (ttm) REVERT: H 202 VAL cc_start: 0.8416 (m) cc_final: 0.8146 (t) REVERT: H 212 ILE cc_start: 0.6750 (OUTLIER) cc_final: 0.6340 (pp) REVERT: A 200 MET cc_start: 0.0009 (ppp) cc_final: -0.0744 (pmt) REVERT: A 242 LYS cc_start: 0.7715 (mttt) cc_final: 0.7169 (mppt) REVERT: A 252 LEU cc_start: 0.6283 (tt) cc_final: 0.6066 (tp) REVERT: A 439 PHE cc_start: 0.7892 (m-80) cc_final: 0.7558 (m-10) REVERT: A 455 TYR cc_start: 0.7393 (m-80) cc_final: 0.7098 (m-10) REVERT: A 468 ILE cc_start: 0.7029 (OUTLIER) cc_final: 0.6732 (mm) REVERT: A 469 LYS cc_start: 0.7043 (mttm) cc_final: 0.6756 (mmtt) REVERT: A 569 ASN cc_start: 0.7079 (m110) cc_final: 0.6815 (t160) REVERT: A 608 ARG cc_start: 0.5865 (mtm110) cc_final: 0.5608 (ttm170) REVERT: A 671 LYS cc_start: 0.8050 (mttm) cc_final: 0.7762 (ptpt) REVERT: A 751 ILE cc_start: 0.7573 (tt) cc_final: 0.7244 (pt) outliers start: 89 outliers final: 35 residues processed: 378 average time/residue: 1.1226 time to fit residues: 491.7434 Evaluate side-chains 326 residues out of total 2170 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 281 time to evaluate : 2.313 ------------------------------------------------------------------------------- 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 44 THR Chi-restraints excluded: chain B residue 68 THR Chi-restraints excluded: chain B residue 103 VAL Chi-restraints excluded: chain B residue 115 THR Chi-restraints excluded: chain F residue 10 LYS Chi-restraints excluded: chain F residue 26 SER Chi-restraints excluded: chain F residue 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 42 ARG 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 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 153 GLU Chi-restraints excluded: chain H residue 209 THR Chi-restraints excluded: chain H residue 212 ILE 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 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 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: 0.7980 chunk 79 optimal weight: 2.9990 chunk 121 optimal weight: 3.9990 chunk 160 optimal weight: 0.6980 chunk 152 optimal weight: 0.0470 chunk 68 optimal weight: 3.9990 chunk 211 optimal weight: 8.9990 chunk 243 optimal weight: 6.9990 chunk 146 optimal weight: 4.9990 chunk 177 optimal weight: 6.9990 chunk 164 optimal weight: 2.9990 overall best weight: 1.5082 ------------------------------------------------------------------------------- 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 187 ASN ** A 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 516 ASN ** A 687 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4110 r_free = 0.4110 target = 0.177580 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3694 r_free = 0.3694 target = 0.134904 restraints weight = 26517.702| |-----------------------------------------------------------------------------| r_work (start): 0.3631 rms_B_bonded: 1.97 r_work: 0.3483 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.3372 rms_B_bonded: 4.03 restraints_weight: 0.2500 r_work (final): 0.3372 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7679 moved from start: 0.2613 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 21865 Z= 0.178 Angle : 0.584 8.651 29807 Z= 0.310 Chirality : 0.043 0.366 3405 Planarity : 0.004 0.044 3514 Dihedral : 15.072 166.422 3844 Min Nonbonded Distance : 2.399 Molprobity Statistics. All-atom Clashscore : 10.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer: Outliers : 4.75 % Allowed : 18.25 % Favored : 77.00 % 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: 0.81 (0.16), residues: 2440 helix: 1.69 (0.15), residues: 1092 sheet: 0.14 (0.25), residues: 409 loop : -0.61 (0.18), residues: 939 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 493 HIS 0.004 0.001 HIS F 151 PHE 0.024 0.002 PHE A 40 TYR 0.024 0.002 TYR C 122 ARG 0.008 0.001 ARG A 466 Details of bonding type rmsd hydrogen bonds : bond 0.04658 ( 1075) hydrogen bonds : angle 4.79742 ( 3116) covalent geometry : bond 0.00395 (21865) covalent geometry : angle 0.58404 (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 410 residues out of total 2170 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 103 poor density : 307 time to evaluate : 2.418 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 11 MET cc_start: 0.6116 (tpp) cc_final: 0.5667 (tmm) REVERT: B 35 GLU cc_start: 0.7310 (mp0) cc_final: 0.7108 (mm-30) REVERT: B 47 LEU cc_start: 0.8682 (OUTLIER) cc_final: 0.8258 (tt) REVERT: B 74 ARG cc_start: 0.7661 (mtp85) cc_final: 0.7305 (mtp-110) REVERT: F 28 ILE cc_start: 0.8779 (mt) cc_final: 0.8509 (mp) REVERT: F 42 ARG cc_start: 0.8677 (OUTLIER) cc_final: 0.8444 (mtm110) REVERT: E 28 ILE cc_start: 0.8098 (mt) cc_final: 0.7599 (mp) REVERT: E 42 ARG cc_start: 0.8081 (OUTLIER) cc_final: 0.7022 (mtm180) REVERT: E 120 GLU cc_start: 0.8661 (OUTLIER) cc_final: 0.7893 (pm20) REVERT: E 167 GLU cc_start: 0.7885 (mm-30) cc_final: 0.7209 (tp30) REVERT: E 203 VAL cc_start: 0.7826 (t) cc_final: 0.7567 (t) REVERT: D 124 GLU cc_start: 0.8474 (OUTLIER) cc_final: 0.8095 (mt-10) REVERT: D 139 ILE cc_start: 0.8779 (pt) cc_final: 0.8573 (pt) REVERT: D 161 GLU cc_start: 0.6923 (OUTLIER) cc_final: 0.6634 (mp0) REVERT: G 95 LYS cc_start: 0.7271 (OUTLIER) cc_final: 0.6599 (pptt) REVERT: G 159 GLU cc_start: 0.7185 (mm-30) cc_final: 0.6939 (mm-30) REVERT: G 213 LEU cc_start: 0.6995 (tt) cc_final: 0.6547 (mt) REVERT: G 259 GLN cc_start: 0.7595 (pt0) cc_final: 0.7222 (pm20) REVERT: G 277 GLN cc_start: 0.7017 (tp40) cc_final: 0.6728 (tp-100) REVERT: I 161 GLU cc_start: 0.6909 (OUTLIER) cc_final: 0.6643 (mt-10) REVERT: J 40 ASN cc_start: 0.7979 (m110) cc_final: 0.7773 (m110) REVERT: J 59 THR cc_start: 0.7976 (OUTLIER) cc_final: 0.7609 (m) REVERT: J 78 GLU cc_start: 0.8903 (mm-30) cc_final: 0.8614 (mm-30) REVERT: J 91 GLU cc_start: 0.7196 (tp30) cc_final: 0.6782 (tp30) REVERT: H 22 LYS cc_start: 0.7094 (tttt) cc_final: 0.6495 (tppt) REVERT: H 202 VAL cc_start: 0.8445 (m) cc_final: 0.8188 (t) REVERT: H 212 ILE cc_start: 0.6859 (OUTLIER) cc_final: 0.6476 (pp) REVERT: A 59 HIS cc_start: 0.4180 (OUTLIER) cc_final: 0.3150 (p-80) REVERT: A 80 ILE cc_start: 0.7437 (OUTLIER) cc_final: 0.7149 (pp) REVERT: A 200 MET cc_start: 0.0346 (ppp) cc_final: -0.0452 (pmt) REVERT: A 242 LYS cc_start: 0.7835 (mttt) cc_final: 0.7241 (mppt) REVERT: A 281 PHE cc_start: 0.7239 (OUTLIER) cc_final: 0.6655 (p90) REVERT: A 361 MET cc_start: 0.6177 (OUTLIER) cc_final: 0.4885 (tpt) REVERT: A 439 PHE cc_start: 0.7924 (m-80) cc_final: 0.7555 (m-10) REVERT: A 455 TYR cc_start: 0.7435 (m-80) cc_final: 0.7092 (m-10) REVERT: A 468 ILE cc_start: 0.7098 (OUTLIER) cc_final: 0.6805 (mm) REVERT: A 469 LYS cc_start: 0.7164 (mttm) cc_final: 0.6852 (mmtt) REVERT: A 569 ASN cc_start: 0.7035 (m110) cc_final: 0.6783 (t160) REVERT: A 671 LYS cc_start: 0.8076 (mttm) cc_final: 0.7789 (ptpt) outliers start: 103 outliers final: 47 residues processed: 376 average time/residue: 1.1225 time to fit residues: 493.4552 Evaluate side-chains 341 residues out of total 2170 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 279 time to evaluate : 2.203 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 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 33 SER Chi-restraints excluded: chain E residue 36 VAL Chi-restraints excluded: chain E residue 42 ARG Chi-restraints excluded: chain E residue 91 ILE Chi-restraints excluded: chain E residue 120 GLU Chi-restraints excluded: chain E residue 143 THR Chi-restraints excluded: chain E residue 202 VAL Chi-restraints excluded: chain D residue 124 GLU Chi-restraints excluded: chain D residue 161 GLU Chi-restraints excluded: chain G residue 95 LYS Chi-restraints excluded: chain G residue 102 GLU Chi-restraints excluded: chain G residue 140 VAL Chi-restraints excluded: chain G residue 212 LEU 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 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 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 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 173 optimal weight: 10.0000 chunk 13 optimal weight: 7.9990 chunk 62 optimal weight: 1.9990 chunk 28 optimal weight: 0.5980 chunk 86 optimal weight: 0.6980 chunk 197 optimal weight: 4.9990 chunk 209 optimal weight: 10.0000 chunk 10 optimal weight: 0.9990 chunk 51 optimal weight: 0.7980 chunk 136 optimal weight: 5.9990 chunk 172 optimal weight: 8.9990 overall best weight: 1.0184 ------------------------------------------------------------------------------- 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** ** 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 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 = 0.4126 r_free = 0.4126 target = 0.179193 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3714 r_free = 0.3714 target = 0.136848 restraints weight = 26431.002| |-----------------------------------------------------------------------------| r_work (start): 0.3662 rms_B_bonded: 1.99 r_work: 0.3509 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.3396 rms_B_bonded: 4.13 restraints_weight: 0.2500 r_work (final): 0.3396 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7656 moved from start: 0.2774 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 21865 Z= 0.143 Angle : 0.555 12.128 29807 Z= 0.294 Chirality : 0.042 0.380 3405 Planarity : 0.004 0.053 3514 Dihedral : 15.002 164.673 3844 Min Nonbonded Distance : 2.358 Molprobity Statistics. All-atom Clashscore : 9.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Rotamer: Outliers : 4.29 % Allowed : 19.59 % Favored : 76.13 % 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: 0.86 (0.16), residues: 2440 helix: 1.74 (0.15), residues: 1094 sheet: 0.16 (0.25), residues: 409 loop : -0.61 (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 0.023 0.001 PHE A 660 TYR 0.023 0.001 TYR C 122 ARG 0.009 0.000 ARG A 466 Details of bonding type rmsd hydrogen bonds : bond 0.04344 ( 1075) hydrogen bonds : angle 4.67942 ( 3116) covalent geometry : bond 0.00309 (21865) covalent geometry : angle 0.55486 (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 401 residues out of total 2170 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 308 time to evaluate : 2.265 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 127 GLU cc_start: 0.6701 (mt-10) cc_final: 0.6120 (mt-10) REVERT: B 11 MET cc_start: 0.5948 (tpp) cc_final: 0.5583 (tmm) REVERT: B 74 ARG cc_start: 0.7666 (mtp85) cc_final: 0.7329 (mtp-110) REVERT: F 28 ILE cc_start: 0.8759 (mt) cc_final: 0.8456 (mp) REVERT: F 133 VAL cc_start: 0.8626 (OUTLIER) cc_final: 0.8403 (t) REVERT: E 28 ILE cc_start: 0.8100 (mt) cc_final: 0.7596 (mp) REVERT: E 42 ARG cc_start: 0.8101 (OUTLIER) cc_final: 0.7028 (mtm180) REVERT: E 120 GLU cc_start: 0.8642 (OUTLIER) cc_final: 0.7951 (pm20) REVERT: E 167 GLU cc_start: 0.7906 (mm-30) cc_final: 0.7251 (tp30) REVERT: E 203 VAL cc_start: 0.7807 (t) cc_final: 0.7544 (t) REVERT: D 124 GLU cc_start: 0.8479 (OUTLIER) cc_final: 0.8098 (mt-10) REVERT: D 139 ILE cc_start: 0.8754 (pt) cc_final: 0.8546 (pt) REVERT: D 161 GLU cc_start: 0.6941 (OUTLIER) cc_final: 0.6698 (mp0) REVERT: G 95 LYS cc_start: 0.7300 (OUTLIER) cc_final: 0.6582 (pptt) REVERT: G 159 GLU cc_start: 0.7202 (mm-30) cc_final: 0.6950 (mm-30) REVERT: G 213 LEU cc_start: 0.7009 (tt) cc_final: 0.6604 (mt) REVERT: G 259 GLN cc_start: 0.7604 (pt0) cc_final: 0.7209 (pm20) REVERT: G 277 GLN cc_start: 0.7002 (tp40) cc_final: 0.6726 (tp-100) REVERT: I 123 PHE cc_start: 0.7780 (OUTLIER) cc_final: 0.7366 (t80) REVERT: I 161 GLU cc_start: 0.6908 (OUTLIER) cc_final: 0.6640 (mt-10) REVERT: J 10 GLU cc_start: 0.5623 (tp30) cc_final: 0.5227 (pt0) REVERT: J 59 THR cc_start: 0.7996 (OUTLIER) cc_final: 0.7647 (m) REVERT: J 61 VAL cc_start: 0.6152 (t) cc_final: 0.5668 (t) REVERT: J 78 GLU cc_start: 0.8912 (mm-30) cc_final: 0.8627 (mm-30) REVERT: J 91 GLU cc_start: 0.7157 (tp30) cc_final: 0.6740 (tp30) REVERT: H 22 LYS cc_start: 0.7109 (tttt) cc_final: 0.6504 (tppt) REVERT: H 202 VAL cc_start: 0.8425 (m) cc_final: 0.8174 (t) REVERT: H 212 ILE cc_start: 0.6833 (OUTLIER) cc_final: 0.6457 (pp) REVERT: A 59 HIS cc_start: 0.4108 (OUTLIER) cc_final: 0.3145 (p-80) REVERT: A 80 ILE cc_start: 0.7430 (OUTLIER) cc_final: 0.7141 (pp) REVERT: A 200 MET cc_start: 0.0888 (ppp) cc_final: 0.0528 (pmt) REVERT: A 242 LYS cc_start: 0.7845 (mttt) cc_final: 0.7236 (mppt) REVERT: A 281 PHE cc_start: 0.7334 (OUTLIER) cc_final: 0.6563 (p90) REVERT: A 361 MET cc_start: 0.6041 (OUTLIER) cc_final: 0.4817 (tpt) REVERT: A 439 PHE cc_start: 0.7916 (m-80) cc_final: 0.7566 (m-10) REVERT: A 441 VAL cc_start: 0.7880 (t) cc_final: 0.7638 (m) REVERT: A 455 TYR cc_start: 0.7464 (m-80) cc_final: 0.7137 (m-10) REVERT: A 459 GLU cc_start: 0.6899 (mm-30) cc_final: 0.6320 (tp30) REVERT: A 468 ILE cc_start: 0.7103 (OUTLIER) cc_final: 0.6819 (mm) REVERT: A 469 LYS cc_start: 0.7084 (mttm) cc_final: 0.6757 (mmtt) REVERT: A 538 PHE cc_start: 0.6712 (OUTLIER) cc_final: 0.6156 (m-80) REVERT: A 569 ASN cc_start: 0.7023 (m110) cc_final: 0.6764 (t160) REVERT: A 671 LYS cc_start: 0.8079 (mttm) cc_final: 0.7778 (ptpt) outliers start: 93 outliers final: 47 residues processed: 365 average time/residue: 1.0841 time to fit residues: 460.7808 Evaluate side-chains 345 residues out of total 2170 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 282 time to evaluate : 2.222 ------------------------------------------------------------------------------- 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 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 88 LYS 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 36 VAL Chi-restraints excluded: chain E residue 42 ARG Chi-restraints excluded: chain E residue 120 GLU Chi-restraints excluded: chain E residue 143 THR Chi-restraints excluded: chain E residue 202 VAL Chi-restraints excluded: chain D residue 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 59 THR Chi-restraints excluded: chain J residue 98 ILE Chi-restraints excluded: chain J residue 106 LEU Chi-restraints excluded: chain H residue 23 ILE Chi-restraints excluded: chain H residue 41 VAL Chi-restraints excluded: chain H residue 153 GLU Chi-restraints excluded: chain H residue 209 THR Chi-restraints excluded: chain H residue 212 ILE Chi-restraints excluded: chain A residue 59 HIS Chi-restraints excluded: chain A residue 77 ILE Chi-restraints excluded: chain A residue 80 ILE Chi-restraints excluded: chain A residue 204 LEU Chi-restraints excluded: chain A residue 206 ASP Chi-restraints excluded: chain A residue 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 549 ILE Chi-restraints excluded: chain A residue 563 PHE 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 55 optimal weight: 0.9980 chunk 80 optimal weight: 3.9990 chunk 236 optimal weight: 0.1980 chunk 205 optimal weight: 5.9990 chunk 170 optimal weight: 1.9990 chunk 0 optimal weight: 9.9990 chunk 103 optimal weight: 0.7980 chunk 20 optimal weight: 1.9990 chunk 146 optimal weight: 0.9990 chunk 155 optimal weight: 4.9990 chunk 131 optimal weight: 0.8980 overall best weight: 0.7782 ------------------------------------------------------------------------------- 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** ** G 198 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 27 GLN H 187 ASN ** A 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 516 ASN ** A 649 ASN ** 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 = 0.4138 r_free = 0.4138 target = 0.180325 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3733 r_free = 0.3733 target = 0.138536 restraints weight = 26286.526| |-----------------------------------------------------------------------------| r_work (start): 0.3680 rms_B_bonded: 2.01 r_work: 0.3522 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.3408 rms_B_bonded: 4.20 restraints_weight: 0.2500 r_work (final): 0.3408 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7607 moved from start: 0.2927 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 21865 Z= 0.130 Angle : 0.544 10.377 29807 Z= 0.288 Chirality : 0.042 0.381 3405 Planarity : 0.004 0.053 3514 Dihedral : 14.957 164.038 3844 Min Nonbonded Distance : 2.339 Molprobity Statistics. All-atom Clashscore : 9.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer: Outliers : 4.06 % Allowed : 20.55 % Favored : 75.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.54 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.78 (0.15), residues: 1093 sheet: 0.15 (0.25), residues: 415 loop : -0.58 (0.18), residues: 932 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 493 HIS 0.004 0.001 HIS B 56 PHE 0.026 0.001 PHE A 40 TYR 0.026 0.001 TYR A 205 ARG 0.010 0.000 ARG A 466 Details of bonding type rmsd hydrogen bonds : bond 0.04177 ( 1075) hydrogen bonds : angle 4.63717 ( 3116) covalent geometry : bond 0.00278 (21865) covalent geometry : angle 0.54431 (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 396 residues out of total 2170 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 308 time to evaluate : 2.204 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 127 GLU cc_start: 0.6701 (mt-10) cc_final: 0.6074 (mt-10) REVERT: B 11 MET cc_start: 0.5806 (tpp) cc_final: 0.5485 (tmm) REVERT: B 74 ARG cc_start: 0.7605 (mtp85) cc_final: 0.7289 (mtp-110) REVERT: F 28 ILE cc_start: 0.8704 (mt) cc_final: 0.8420 (mp) REVERT: F 133 VAL cc_start: 0.8603 (OUTLIER) cc_final: 0.8386 (t) REVERT: E 28 ILE cc_start: 0.8084 (mt) cc_final: 0.7559 (mp) REVERT: E 42 ARG cc_start: 0.8089 (OUTLIER) cc_final: 0.7014 (mtm180) REVERT: E 120 GLU cc_start: 0.8645 (OUTLIER) cc_final: 0.7943 (pm20) REVERT: E 167 GLU cc_start: 0.7866 (mm-30) cc_final: 0.7201 (tp30) REVERT: E 203 VAL cc_start: 0.7763 (t) cc_final: 0.7495 (t) REVERT: D 124 GLU cc_start: 0.8443 (OUTLIER) cc_final: 0.8041 (mt-10) REVERT: D 139 ILE cc_start: 0.8737 (pt) cc_final: 0.8528 (pt) REVERT: D 161 GLU cc_start: 0.6961 (OUTLIER) cc_final: 0.6707 (mp0) REVERT: G 54 LEU cc_start: 0.7265 (tt) cc_final: 0.6934 (pp) REVERT: G 95 LYS cc_start: 0.7263 (OUTLIER) cc_final: 0.6556 (pptt) REVERT: G 159 GLU cc_start: 0.7170 (mm-30) cc_final: 0.6902 (mm-30) REVERT: G 213 LEU cc_start: 0.7007 (tt) cc_final: 0.6582 (mt) REVERT: G 259 GLN cc_start: 0.7600 (pt0) cc_final: 0.7185 (pm20) REVERT: G 277 GLN cc_start: 0.7049 (tp40) cc_final: 0.6742 (tp-100) REVERT: I 123 PHE cc_start: 0.7736 (OUTLIER) cc_final: 0.7339 (t80) REVERT: I 161 GLU cc_start: 0.6892 (OUTLIER) cc_final: 0.6598 (mt-10) REVERT: J 10 GLU cc_start: 0.5681 (tp30) cc_final: 0.5252 (pt0) REVERT: J 59 THR cc_start: 0.7889 (OUTLIER) cc_final: 0.7540 (m) REVERT: J 61 VAL cc_start: 0.6096 (t) cc_final: 0.5622 (t) REVERT: J 78 GLU cc_start: 0.8896 (mm-30) cc_final: 0.8620 (mm-30) REVERT: J 91 GLU cc_start: 0.7104 (tp30) cc_final: 0.6695 (tp30) REVERT: H 22 LYS cc_start: 0.7107 (tttt) cc_final: 0.6467 (tppt) REVERT: H 200 VAL cc_start: 0.7967 (OUTLIER) cc_final: 0.7706 (p) REVERT: H 202 VAL cc_start: 0.8411 (m) cc_final: 0.8150 (t) REVERT: H 212 ILE cc_start: 0.6769 (OUTLIER) cc_final: 0.6407 (pp) REVERT: A 59 HIS cc_start: 0.4108 (OUTLIER) cc_final: 0.3131 (p-80) REVERT: A 80 ILE cc_start: 0.7436 (OUTLIER) cc_final: 0.7147 (pp) REVERT: A 200 MET cc_start: 0.1341 (ppp) cc_final: 0.0754 (pmt) REVERT: A 242 LYS cc_start: 0.7834 (mttt) cc_final: 0.7213 (mppt) REVERT: A 281 PHE cc_start: 0.7300 (OUTLIER) cc_final: 0.6470 (p90) REVERT: A 361 MET cc_start: 0.6099 (OUTLIER) cc_final: 0.4862 (tpt) REVERT: A 439 PHE cc_start: 0.7853 (m-80) cc_final: 0.7545 (m-10) REVERT: A 441 VAL cc_start: 0.7886 (t) cc_final: 0.7640 (m) REVERT: A 455 TYR cc_start: 0.7440 (m-80) cc_final: 0.7111 (m-10) REVERT: A 459 GLU cc_start: 0.6900 (mm-30) cc_final: 0.6348 (tp30) REVERT: A 468 ILE cc_start: 0.7117 (OUTLIER) cc_final: 0.6840 (mm) REVERT: A 469 LYS cc_start: 0.7065 (mttm) cc_final: 0.6745 (mmtt) REVERT: A 538 PHE cc_start: 0.6607 (OUTLIER) cc_final: 0.6040 (m-80) REVERT: A 569 ASN cc_start: 0.6983 (m110) cc_final: 0.6739 (t160) REVERT: A 671 LYS cc_start: 0.8068 (mttm) cc_final: 0.7768 (ptpt) outliers start: 88 outliers final: 42 residues processed: 365 average time/residue: 1.0523 time to fit residues: 448.5835 Evaluate side-chains 352 residues out of total 2170 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 293 time to evaluate : 2.233 ------------------------------------------------------------------------------- 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 68 THR Chi-restraints excluded: chain B residue 103 VAL Chi-restraints excluded: chain B residue 115 THR Chi-restraints excluded: chain F residue 26 SER Chi-restraints excluded: chain F residue 119 THR Chi-restraints excluded: chain F residue 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 36 VAL Chi-restraints excluded: chain E residue 42 ARG Chi-restraints excluded: chain E residue 120 GLU Chi-restraints excluded: chain E residue 143 THR Chi-restraints excluded: chain E residue 202 VAL Chi-restraints excluded: chain D residue 79 ILE Chi-restraints excluded: chain D residue 124 GLU Chi-restraints excluded: chain D residue 161 GLU Chi-restraints excluded: chain G residue 95 LYS Chi-restraints excluded: chain G residue 140 VAL Chi-restraints excluded: chain I residue 45 ILE Chi-restraints excluded: chain I residue 78 GLU Chi-restraints excluded: chain I residue 123 PHE Chi-restraints excluded: chain I residue 161 GLU Chi-restraints excluded: chain J residue 14 LEU Chi-restraints excluded: chain J residue 59 THR Chi-restraints excluded: chain J residue 98 ILE Chi-restraints excluded: chain J residue 106 LEU Chi-restraints excluded: chain H residue 23 ILE Chi-restraints excluded: chain H residue 41 VAL Chi-restraints excluded: chain H residue 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 290 GLU Chi-restraints excluded: chain A residue 59 HIS Chi-restraints excluded: chain A residue 80 ILE Chi-restraints excluded: chain A residue 260 ILE Chi-restraints excluded: chain A residue 281 PHE Chi-restraints excluded: chain A residue 315 LEU Chi-restraints excluded: chain A residue 361 MET Chi-restraints excluded: chain A residue 374 VAL Chi-restraints excluded: chain A residue 408 CYS Chi-restraints excluded: chain A residue 434 LEU Chi-restraints excluded: chain A residue 448 VAL Chi-restraints excluded: chain A residue 468 ILE Chi-restraints excluded: chain A residue 538 PHE Chi-restraints excluded: chain A residue 549 ILE Chi-restraints excluded: chain A residue 563 PHE Chi-restraints excluded: chain A residue 607 THR Chi-restraints excluded: chain A residue 622 MET Chi-restraints excluded: chain A residue 634 SER Chi-restraints excluded: chain A residue 687 HIS Chi-restraints excluded: chain A residue 695 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 2 optimal weight: 2.9990 chunk 63 optimal weight: 1.9990 chunk 154 optimal weight: 0.4980 chunk 0 optimal weight: 10.0000 chunk 165 optimal weight: 10.0000 chunk 241 optimal weight: 10.0000 chunk 33 optimal weight: 1.9990 chunk 134 optimal weight: 8.9990 chunk 207 optimal weight: 9.9990 chunk 163 optimal weight: 0.0770 chunk 80 optimal weight: 4.9990 overall best weight: 1.5144 ------------------------------------------------------------------------------- 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** ** G 198 GLN ** 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 516 ASN ** A 649 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.4108 r_free = 0.4108 target = 0.177227 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3694 r_free = 0.3694 target = 0.135218 restraints weight = 26118.594| |-----------------------------------------------------------------------------| r_work (start): 0.3646 rms_B_bonded: 2.00 r_work: 0.3472 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.3358 rms_B_bonded: 4.20 restraints_weight: 0.2500 r_work (final): 0.3358 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7673 moved from start: 0.3006 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 21865 Z= 0.177 Angle : 0.590 11.618 29807 Z= 0.311 Chirality : 0.044 0.378 3405 Planarity : 0.004 0.053 3514 Dihedral : 14.967 166.599 3842 Min Nonbonded Distance : 2.307 Molprobity Statistics. All-atom Clashscore : 10.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer: Outliers : 4.19 % Allowed : 21.20 % Favored : 74.61 % 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: 0.78 (0.16), residues: 2440 helix: 1.67 (0.15), residues: 1098 sheet: 0.05 (0.25), residues: 415 loop : -0.61 (0.19), residues: 927 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 493 HIS 0.005 0.001 HIS A 312 PHE 0.032 0.002 PHE A 250 TYR 0.023 0.002 TYR C 122 ARG 0.010 0.000 ARG A 466 Details of bonding type rmsd hydrogen bonds : bond 0.04490 ( 1075) hydrogen bonds : angle 4.74777 ( 3116) covalent geometry : bond 0.00394 (21865) covalent geometry : angle 0.58972 (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 388 residues out of total 2170 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 297 time to evaluate : 2.371 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 43 THR cc_start: 0.8310 (OUTLIER) cc_final: 0.8106 (t) REVERT: C 127 GLU cc_start: 0.6787 (mt-10) cc_final: 0.6239 (mt-10) REVERT: B 11 MET cc_start: 0.5787 (tpp) cc_final: 0.5497 (tmm) REVERT: F 28 ILE cc_start: 0.8756 (mt) cc_final: 0.8444 (mp) REVERT: E 28 ILE cc_start: 0.8116 (mt) cc_final: 0.7609 (mp) REVERT: E 120 GLU cc_start: 0.8668 (OUTLIER) cc_final: 0.7965 (pm20) REVERT: E 167 GLU cc_start: 0.7870 (mm-30) cc_final: 0.7182 (tp30) REVERT: E 203 VAL cc_start: 0.7771 (t) cc_final: 0.7505 (t) REVERT: D 124 GLU cc_start: 0.8524 (OUTLIER) cc_final: 0.8154 (mt-10) REVERT: D 139 ILE cc_start: 0.8794 (pt) cc_final: 0.8593 (pt) REVERT: D 161 GLU cc_start: 0.6985 (OUTLIER) cc_final: 0.6767 (mp0) REVERT: G 54 LEU cc_start: 0.7254 (tt) cc_final: 0.6916 (pp) REVERT: G 95 LYS cc_start: 0.7269 (OUTLIER) cc_final: 0.6552 (pptt) REVERT: G 159 GLU cc_start: 0.7191 (mm-30) cc_final: 0.6911 (mm-30) REVERT: G 213 LEU cc_start: 0.7120 (tt) cc_final: 0.6646 (mt) REVERT: G 259 GLN cc_start: 0.7601 (pt0) cc_final: 0.7195 (pm20) REVERT: G 277 GLN cc_start: 0.7050 (tp40) cc_final: 0.6768 (tp-100) REVERT: I 123 PHE cc_start: 0.7807 (OUTLIER) cc_final: 0.7390 (t80) REVERT: I 161 GLU cc_start: 0.6955 (OUTLIER) cc_final: 0.6658 (mt-10) REVERT: J 10 GLU cc_start: 0.5643 (tp30) cc_final: 0.5263 (pt0) REVERT: J 59 THR cc_start: 0.7954 (OUTLIER) cc_final: 0.7597 (m) REVERT: J 78 GLU cc_start: 0.8909 (mm-30) cc_final: 0.8540 (mm-30) REVERT: J 91 GLU cc_start: 0.7067 (tp30) cc_final: 0.6733 (tp30) REVERT: H 22 LYS cc_start: 0.7118 (tttt) cc_final: 0.6472 (tppt) REVERT: H 200 VAL cc_start: 0.7991 (OUTLIER) cc_final: 0.7721 (p) REVERT: H 202 VAL cc_start: 0.8399 (m) cc_final: 0.8126 (t) REVERT: H 212 ILE cc_start: 0.6830 (OUTLIER) cc_final: 0.6467 (pp) REVERT: H 225 GLN cc_start: 0.6865 (OUTLIER) cc_final: 0.6525 (tt0) REVERT: A 59 HIS cc_start: 0.4005 (OUTLIER) cc_final: 0.3032 (p-80) REVERT: A 80 ILE cc_start: 0.7433 (OUTLIER) cc_final: 0.7146 (pp) REVERT: A 200 MET cc_start: 0.1930 (ppp) cc_final: 0.1381 (pmt) REVERT: A 242 LYS cc_start: 0.7920 (mttt) cc_final: 0.7263 (mppt) REVERT: A 281 PHE cc_start: 0.7283 (OUTLIER) cc_final: 0.6610 (p90) REVERT: A 361 MET cc_start: 0.6077 (OUTLIER) cc_final: 0.4943 (tpt) REVERT: A 439 PHE cc_start: 0.7927 (m-80) cc_final: 0.7615 (m-10) REVERT: A 441 VAL cc_start: 0.7915 (t) cc_final: 0.7674 (m) REVERT: A 459 GLU cc_start: 0.6900 (mm-30) cc_final: 0.6345 (tp30) REVERT: A 468 ILE cc_start: 0.7142 (OUTLIER) cc_final: 0.6882 (mm) REVERT: A 469 LYS cc_start: 0.7038 (mttm) cc_final: 0.6723 (mmtt) REVERT: A 538 PHE cc_start: 0.6701 (OUTLIER) cc_final: 0.6014 (m-80) REVERT: A 569 ASN cc_start: 0.6994 (m110) cc_final: 0.6752 (t160) REVERT: A 572 LYS cc_start: 0.6887 (tttp) cc_final: 0.6258 (tmmt) REVERT: A 671 LYS cc_start: 0.8082 (mttm) cc_final: 0.7651 (ttpt) outliers start: 91 outliers final: 50 residues processed: 358 average time/residue: 1.1498 time to fit residues: 482.0955 Evaluate side-chains 341 residues out of total 2170 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 274 time to evaluate : 2.277 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 12 ILE Chi-restraints excluded: chain C residue 43 THR 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 68 THR Chi-restraints excluded: chain B residue 103 VAL Chi-restraints excluded: chain B residue 115 THR Chi-restraints excluded: chain F residue 26 SER Chi-restraints excluded: chain F residue 119 THR Chi-restraints excluded: chain F residue 126 THR Chi-restraints excluded: chain F residue 133 VAL Chi-restraints excluded: chain E residue 33 SER Chi-restraints excluded: chain E residue 36 VAL 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 140 VAL Chi-restraints excluded: chain G residue 212 LEU Chi-restraints excluded: chain I residue 38 ASP Chi-restraints excluded: chain I residue 45 ILE Chi-restraints excluded: chain I residue 78 GLU Chi-restraints excluded: chain I residue 123 PHE Chi-restraints excluded: chain I residue 161 GLU Chi-restraints excluded: chain J residue 14 LEU Chi-restraints excluded: chain J residue 52 GLU Chi-restraints excluded: chain J residue 59 THR Chi-restraints excluded: chain 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 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 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 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 549 ILE Chi-restraints excluded: chain A residue 563 PHE Chi-restraints excluded: chain A residue 607 THR Chi-restraints excluded: chain A residue 622 MET Chi-restraints excluded: chain A residue 634 SER Chi-restraints excluded: chain A residue 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: 0.7980 chunk 131 optimal weight: 0.9990 chunk 159 optimal weight: 8.9990 chunk 184 optimal weight: 6.9990 chunk 20 optimal weight: 3.9990 chunk 88 optimal weight: 1.9990 chunk 147 optimal weight: 2.9990 chunk 129 optimal weight: 0.1980 chunk 9 optimal weight: 2.9990 chunk 112 optimal weight: 0.9980 overall best weight: 0.9984 ------------------------------------------------------------------------------- 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** ** G 198 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 187 ASN ** A 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 649 ASN ** A 687 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4127 r_free = 0.4127 target = 0.179253 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3721 r_free = 0.3721 target = 0.137528 restraints weight = 26339.515| |-----------------------------------------------------------------------------| r_work (start): 0.3673 rms_B_bonded: 2.04 r_work: 0.3504 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.3389 rms_B_bonded: 4.27 restraints_weight: 0.2500 r_work (final): 0.3389 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7635 moved from start: 0.3134 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 21865 Z= 0.143 Angle : 0.569 12.117 29807 Z= 0.299 Chirality : 0.042 0.388 3405 Planarity : 0.004 0.055 3514 Dihedral : 14.925 164.406 3842 Min Nonbonded Distance : 2.294 Molprobity Statistics. All-atom Clashscore : 10.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer: Outliers : 3.69 % Allowed : 22.17 % Favored : 74.15 % 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: 0.83 (0.16), residues: 2440 helix: 1.72 (0.15), residues: 1097 sheet: 0.06 (0.25), residues: 415 loop : -0.59 (0.19), residues: 928 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 493 HIS 0.005 0.001 HIS B 56 PHE 0.038 0.002 PHE A 250 TYR 0.021 0.001 TYR J 86 ARG 0.013 0.000 ARG A 466 Details of bonding type rmsd hydrogen bonds : bond 0.04223 ( 1075) hydrogen bonds : angle 4.68107 ( 3116) covalent geometry : bond 0.00312 (21865) covalent geometry : angle 0.56909 (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 379 residues out of total 2170 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 299 time to evaluate : 2.279 Fit side-chains revert: symmetry clash REVERT: C 43 THR cc_start: 0.8244 (OUTLIER) cc_final: 0.8037 (t) REVERT: C 127 GLU cc_start: 0.6631 (mt-10) cc_final: 0.6424 (mt-10) REVERT: B 11 MET cc_start: 0.5683 (tpp) cc_final: 0.5400 (tmm) REVERT: F 28 ILE cc_start: 0.8816 (mt) cc_final: 0.8581 (mt) REVERT: F 133 VAL cc_start: 0.8592 (OUTLIER) cc_final: 0.8372 (t) REVERT: E 28 ILE cc_start: 0.8102 (mt) cc_final: 0.7583 (mp) REVERT: E 42 ARG cc_start: 0.8093 (OUTLIER) cc_final: 0.7033 (mtm180) REVERT: E 120 GLU cc_start: 0.8667 (OUTLIER) cc_final: 0.8027 (pm20) REVERT: E 144 ARG cc_start: 0.7655 (ttp80) cc_final: 0.7342 (mtm180) REVERT: E 167 GLU cc_start: 0.7892 (mm-30) cc_final: 0.7225 (tp30) REVERT: E 203 VAL cc_start: 0.7759 (t) cc_final: 0.7489 (t) REVERT: D 124 GLU cc_start: 0.8522 (OUTLIER) cc_final: 0.8156 (mt-10) REVERT: D 139 ILE cc_start: 0.8765 (pt) cc_final: 0.8564 (pt) REVERT: G 54 LEU cc_start: 0.7206 (tt) cc_final: 0.6970 (pp) REVERT: G 95 LYS cc_start: 0.7274 (OUTLIER) cc_final: 0.6575 (pptt) REVERT: G 159 GLU cc_start: 0.7164 (mm-30) cc_final: 0.6889 (mm-30) REVERT: G 213 LEU cc_start: 0.7071 (tt) cc_final: 0.6619 (mt) REVERT: G 259 GLN cc_start: 0.7563 (pt0) cc_final: 0.7159 (pm20) REVERT: G 277 GLN cc_start: 0.7042 (tp40) cc_final: 0.6767 (tp-100) REVERT: I 123 PHE cc_start: 0.7784 (OUTLIER) cc_final: 0.7442 (t80) REVERT: I 161 GLU cc_start: 0.6939 (OUTLIER) cc_final: 0.6624 (mt-10) REVERT: J 10 GLU cc_start: 0.5614 (tp30) cc_final: 0.5226 (pt0) REVERT: J 59 THR cc_start: 0.7919 (OUTLIER) cc_final: 0.7569 (m) REVERT: J 61 VAL cc_start: 0.6193 (t) cc_final: 0.5697 (t) REVERT: J 78 GLU cc_start: 0.8896 (mm-30) cc_final: 0.8538 (mm-30) REVERT: J 91 GLU cc_start: 0.7069 (tp30) cc_final: 0.6749 (tp30) REVERT: H 22 LYS cc_start: 0.7122 (tttt) cc_final: 0.6484 (tppt) REVERT: H 200 VAL cc_start: 0.7983 (OUTLIER) cc_final: 0.7722 (p) REVERT: H 202 VAL cc_start: 0.8393 (m) cc_final: 0.8121 (t) REVERT: H 212 ILE cc_start: 0.6810 (OUTLIER) cc_final: 0.6489 (pp) REVERT: H 225 GLN cc_start: 0.6846 (OUTLIER) cc_final: 0.6513 (tt0) REVERT: H 248 LYS cc_start: 0.6592 (mmmt) cc_final: 0.5746 (mmpt) REVERT: A 59 HIS cc_start: 0.3970 (OUTLIER) cc_final: 0.3092 (p-80) REVERT: A 80 ILE cc_start: 0.7434 (OUTLIER) cc_final: 0.7144 (pp) REVERT: A 200 MET cc_start: 0.2197 (ppp) cc_final: 0.1758 (pmt) REVERT: A 242 LYS cc_start: 0.7912 (mttt) cc_final: 0.7250 (mppt) REVERT: A 281 PHE cc_start: 0.7288 (OUTLIER) cc_final: 0.6597 (p90) REVERT: A 361 MET cc_start: 0.6050 (OUTLIER) cc_final: 0.4936 (tpt) REVERT: A 439 PHE cc_start: 0.7862 (m-80) cc_final: 0.7577 (m-10) REVERT: A 441 VAL cc_start: 0.7930 (t) cc_final: 0.7705 (m) REVERT: A 459 GLU cc_start: 0.6924 (mm-30) cc_final: 0.6345 (tp30) REVERT: A 468 ILE cc_start: 0.7223 (OUTLIER) cc_final: 0.6951 (mm) REVERT: A 469 LYS cc_start: 0.7054 (mttm) cc_final: 0.6746 (mmtt) REVERT: A 538 PHE cc_start: 0.6686 (OUTLIER) cc_final: 0.5919 (m-80) REVERT: A 671 LYS cc_start: 0.8081 (mttm) cc_final: 0.7636 (ttpt) outliers start: 80 outliers final: 45 residues processed: 353 average time/residue: 1.0806 time to fit residues: 445.1555 Evaluate side-chains 345 residues out of total 2170 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 282 time to evaluate : 2.187 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 12 ILE Chi-restraints excluded: chain C residue 43 THR 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 68 THR Chi-restraints excluded: chain B residue 103 VAL Chi-restraints excluded: chain B residue 115 THR Chi-restraints excluded: chain F residue 26 SER Chi-restraints excluded: chain F residue 119 THR Chi-restraints excluded: chain F residue 126 THR Chi-restraints excluded: chain F residue 133 VAL Chi-restraints excluded: chain E residue 33 SER Chi-restraints excluded: chain E residue 36 VAL Chi-restraints excluded: chain E residue 42 ARG Chi-restraints excluded: chain E residue 91 ILE Chi-restraints excluded: chain E residue 120 GLU Chi-restraints excluded: chain E residue 143 THR Chi-restraints excluded: chain E residue 202 VAL Chi-restraints excluded: chain D residue 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 140 VAL Chi-restraints excluded: chain I residue 38 ASP Chi-restraints excluded: chain I residue 45 ILE Chi-restraints excluded: chain I residue 78 GLU Chi-restraints excluded: chain I residue 123 PHE Chi-restraints excluded: chain I residue 161 GLU Chi-restraints excluded: chain J residue 14 LEU Chi-restraints excluded: chain J residue 52 GLU Chi-restraints excluded: chain J residue 59 THR Chi-restraints excluded: chain 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 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 A residue 59 HIS Chi-restraints excluded: chain A residue 80 ILE 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 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 563 PHE Chi-restraints excluded: chain A residue 607 THR Chi-restraints excluded: chain A residue 622 MET Chi-restraints excluded: chain A residue 634 SER Chi-restraints excluded: chain A residue 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: 1.9990 chunk 74 optimal weight: 0.9980 chunk 10 optimal weight: 0.9990 chunk 111 optimal weight: 2.9990 chunk 77 optimal weight: 3.9990 chunk 113 optimal weight: 3.9990 chunk 5 optimal weight: 3.9990 chunk 146 optimal weight: 0.0870 chunk 186 optimal weight: 4.9990 chunk 131 optimal weight: 1.9990 chunk 58 optimal weight: 0.4980 overall best weight: 0.9162 ------------------------------------------------------------------------------- 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** ** G 198 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 189 ASN H 39 HIS H 187 ASN ** A 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 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 = 0.4133 r_free = 0.4133 target = 0.179815 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3728 r_free = 0.3728 target = 0.138171 restraints weight = 26210.710| |-----------------------------------------------------------------------------| r_work (start): 0.3678 rms_B_bonded: 2.02 r_work: 0.3511 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.3397 rms_B_bonded: 4.24 restraints_weight: 0.2500 r_work (final): 0.3397 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7625 moved from start: 0.3205 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 21865 Z= 0.139 Angle : 0.572 12.353 29807 Z= 0.300 Chirality : 0.042 0.388 3405 Planarity : 0.004 0.058 3514 Dihedral : 14.896 164.271 3842 Min Nonbonded Distance : 2.273 Molprobity Statistics. All-atom Clashscore : 10.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer: Outliers : 3.36 % Allowed : 22.44 % Favored : 74.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.54 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.84 (0.16), residues: 2440 helix: 1.73 (0.15), residues: 1098 sheet: 0.10 (0.25), residues: 410 loop : -0.60 (0.19), residues: 932 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 0.001 PHE A 40 TYR 0.038 0.001 TYR A 219 ARG 0.010 0.000 ARG B 74 Details of bonding type rmsd hydrogen bonds : bond 0.04172 ( 1075) hydrogen bonds : angle 4.67277 ( 3116) covalent geometry : bond 0.00302 (21865) covalent geometry : angle 0.57163 (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 362 residues out of total 2170 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 289 time to evaluate : 2.551 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 43 THR cc_start: 0.8231 (OUTLIER) cc_final: 0.8013 (t) REVERT: B 11 MET cc_start: 0.5716 (tpp) cc_final: 0.5377 (tmm) REVERT: F 133 VAL cc_start: 0.8609 (OUTLIER) cc_final: 0.8387 (t) REVERT: E 28 ILE cc_start: 0.8115 (mt) cc_final: 0.7607 (mp) REVERT: E 42 ARG cc_start: 0.8107 (OUTLIER) cc_final: 0.7054 (mtm180) REVERT: E 88 LYS cc_start: 0.8051 (OUTLIER) cc_final: 0.7834 (tttm) REVERT: E 120 GLU cc_start: 0.8662 (OUTLIER) cc_final: 0.8037 (pm20) REVERT: E 144 ARG cc_start: 0.7641 (ttp80) cc_final: 0.7337 (mtm180) REVERT: E 167 GLU cc_start: 0.7875 (mm-30) cc_final: 0.7207 (tp30) REVERT: E 203 VAL cc_start: 0.7735 (t) cc_final: 0.7470 (t) REVERT: D 124 GLU cc_start: 0.8496 (OUTLIER) cc_final: 0.8111 (mt-10) REVERT: D 139 ILE cc_start: 0.8753 (pt) cc_final: 0.8542 (pt) REVERT: G 8 LEU cc_start: 0.7791 (OUTLIER) cc_final: 0.7454 (tp) REVERT: G 54 LEU cc_start: 0.7209 (tt) cc_final: 0.7007 (pp) REVERT: G 95 LYS cc_start: 0.7257 (OUTLIER) cc_final: 0.6589 (pptt) REVERT: G 159 GLU cc_start: 0.7091 (mm-30) cc_final: 0.6832 (mm-30) REVERT: G 213 LEU cc_start: 0.7055 (tt) cc_final: 0.6631 (mt) REVERT: G 259 GLN cc_start: 0.7544 (pt0) cc_final: 0.7149 (pm20) REVERT: G 277 GLN cc_start: 0.7071 (tp40) cc_final: 0.6799 (tp-100) REVERT: I 123 PHE cc_start: 0.7781 (OUTLIER) cc_final: 0.7329 (t80) REVERT: I 161 GLU cc_start: 0.6922 (OUTLIER) cc_final: 0.6603 (mt-10) REVERT: J 10 GLU cc_start: 0.5599 (tp30) cc_final: 0.5218 (pt0) REVERT: J 59 THR cc_start: 0.7899 (OUTLIER) cc_final: 0.7554 (m) REVERT: J 61 VAL cc_start: 0.6181 (t) cc_final: 0.5680 (t) REVERT: J 78 GLU cc_start: 0.8896 (mm-30) cc_final: 0.8592 (mm-30) REVERT: J 91 GLU cc_start: 0.7066 (tp30) cc_final: 0.6741 (tp30) REVERT: H 22 LYS cc_start: 0.7121 (tttt) cc_final: 0.6482 (tppt) REVERT: H 200 VAL cc_start: 0.7968 (OUTLIER) cc_final: 0.7717 (p) REVERT: H 202 VAL cc_start: 0.8380 (m) cc_final: 0.8113 (t) REVERT: H 212 ILE cc_start: 0.6849 (OUTLIER) cc_final: 0.6508 (pp) REVERT: H 248 LYS cc_start: 0.6643 (mmmt) cc_final: 0.5791 (mmpt) REVERT: A 59 HIS cc_start: 0.4120 (OUTLIER) cc_final: 0.3323 (p-80) REVERT: A 80 ILE cc_start: 0.7426 (OUTLIER) cc_final: 0.7170 (pp) REVERT: A 200 MET cc_start: 0.2603 (ppp) cc_final: 0.2138 (pmt) REVERT: A 242 LYS cc_start: 0.7970 (mttt) cc_final: 0.7300 (mppt) REVERT: A 361 MET cc_start: 0.6017 (OUTLIER) cc_final: 0.4912 (tpt) REVERT: A 439 PHE cc_start: 0.7853 (m-80) cc_final: 0.7600 (m-10) REVERT: A 441 VAL cc_start: 0.7910 (t) cc_final: 0.7685 (m) REVERT: A 459 GLU cc_start: 0.6938 (mm-30) cc_final: 0.6347 (tp30) REVERT: A 468 ILE cc_start: 0.7191 (OUTLIER) cc_final: 0.6928 (mm) REVERT: A 469 LYS cc_start: 0.7053 (mttm) cc_final: 0.6704 (mmtt) REVERT: A 538 PHE cc_start: 0.6619 (OUTLIER) cc_final: 0.5829 (m-80) REVERT: A 563 PHE cc_start: 0.5009 (OUTLIER) cc_final: 0.4675 (t80) REVERT: A 671 LYS cc_start: 0.8015 (mttm) cc_final: 0.7627 (ttpt) outliers start: 73 outliers final: 43 residues processed: 339 average time/residue: 1.1551 time to fit residues: 455.7583 Evaluate side-chains 341 residues out of total 2170 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 279 time to evaluate : 2.217 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 43 THR 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 68 THR Chi-restraints excluded: chain B residue 103 VAL Chi-restraints excluded: chain B residue 115 THR 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 36 VAL Chi-restraints excluded: chain E residue 42 ARG Chi-restraints excluded: chain E residue 88 LYS 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 8 LEU 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 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 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 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 5 LEU Chi-restraints excluded: chain A residue 59 HIS Chi-restraints excluded: chain A residue 80 ILE Chi-restraints excluded: chain A residue 214 ILE Chi-restraints excluded: chain A residue 260 ILE Chi-restraints excluded: chain A residue 281 PHE Chi-restraints excluded: chain A residue 315 LEU Chi-restraints excluded: chain A residue 361 MET Chi-restraints excluded: chain A residue 374 VAL Chi-restraints excluded: chain A residue 388 LEU Chi-restraints excluded: chain A residue 408 CYS Chi-restraints excluded: chain A residue 434 LEU Chi-restraints excluded: chain A residue 448 VAL Chi-restraints excluded: chain A residue 468 ILE Chi-restraints excluded: chain A residue 538 PHE Chi-restraints excluded: chain A residue 561 MET Chi-restraints excluded: chain A residue 563 PHE Chi-restraints excluded: chain A residue 607 THR Chi-restraints excluded: chain A residue 622 MET Chi-restraints excluded: chain A residue 634 SER Chi-restraints excluded: chain A residue 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: 3.9990 chunk 149 optimal weight: 7.9990 chunk 65 optimal weight: 0.9980 chunk 163 optimal weight: 0.9990 chunk 105 optimal weight: 2.9990 chunk 69 optimal weight: 0.5980 chunk 123 optimal weight: 0.9980 chunk 207 optimal weight: 2.9990 chunk 0 optimal weight: 9.9990 chunk 73 optimal weight: 0.8980 chunk 240 optimal weight: 0.7980 overall best weight: 0.8580 ------------------------------------------------------------------------------- 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** ** G 198 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 189 ASN H 187 ASN ** A 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 687 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4140 r_free = 0.4140 target = 0.180535 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3733 r_free = 0.3733 target = 0.138517 restraints weight = 26471.462| |-----------------------------------------------------------------------------| r_work (start): 0.3683 rms_B_bonded: 2.00 r_work: 0.3527 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.3413 rms_B_bonded: 4.16 restraints_weight: 0.2500 r_work (final): 0.3413 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7615 moved from start: 0.3298 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 21865 Z= 0.135 Angle : 0.569 12.362 29807 Z= 0.299 Chirality : 0.042 0.387 3405 Planarity : 0.004 0.057 3514 Dihedral : 14.873 164.120 3842 Min Nonbonded Distance : 2.249 Molprobity Statistics. All-atom Clashscore : 10.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer: Outliers : 3.27 % Allowed : 22.76 % Favored : 73.96 % 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: 0.85 (0.16), residues: 2440 helix: 1.74 (0.15), residues: 1098 sheet: 0.05 (0.25), residues: 415 loop : -0.56 (0.19), residues: 927 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 493 HIS 0.005 0.001 HIS B 56 PHE 0.038 0.002 PHE B 16 TYR 0.023 0.001 TYR H 59 ARG 0.014 0.000 ARG A 466 Details of bonding type rmsd hydrogen bonds : bond 0.04126 ( 1075) hydrogen bonds : angle 4.66409 ( 3116) covalent geometry : bond 0.00294 (21865) covalent geometry : angle 0.56887 (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 359 residues out of total 2170 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 288 time to evaluate : 2.550 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 43 THR cc_start: 0.8227 (OUTLIER) cc_final: 0.8007 (t) REVERT: B 11 MET cc_start: 0.5696 (tpp) cc_final: 0.5371 (tmm) REVERT: F 133 VAL cc_start: 0.8608 (OUTLIER) cc_final: 0.8391 (t) REVERT: E 28 ILE cc_start: 0.8111 (mt) cc_final: 0.7600 (mp) REVERT: E 42 ARG cc_start: 0.8100 (OUTLIER) cc_final: 0.7049 (mtm180) REVERT: E 88 LYS cc_start: 0.8067 (OUTLIER) cc_final: 0.7852 (tttm) REVERT: E 120 GLU cc_start: 0.8648 (OUTLIER) cc_final: 0.8045 (pm20) REVERT: E 144 ARG cc_start: 0.7630 (ttp80) cc_final: 0.7353 (mtm180) REVERT: E 167 GLU cc_start: 0.7874 (mm-30) cc_final: 0.7211 (tp30) REVERT: E 203 VAL cc_start: 0.7735 (t) cc_final: 0.7476 (t) REVERT: D 124 GLU cc_start: 0.8468 (OUTLIER) cc_final: 0.8079 (mt-10) REVERT: D 139 ILE cc_start: 0.8743 (pt) cc_final: 0.8532 (pt) REVERT: G 8 LEU cc_start: 0.7767 (OUTLIER) cc_final: 0.7440 (tp) REVERT: G 54 LEU cc_start: 0.7204 (tt) cc_final: 0.6998 (pp) REVERT: G 95 LYS cc_start: 0.7302 (OUTLIER) cc_final: 0.6607 (pptt) REVERT: G 147 GLU cc_start: 0.8152 (OUTLIER) cc_final: 0.7908 (pp20) REVERT: G 159 GLU cc_start: 0.7053 (mm-30) cc_final: 0.6800 (mm-30) REVERT: G 213 LEU cc_start: 0.7028 (tt) cc_final: 0.6613 (mt) REVERT: G 259 GLN cc_start: 0.7555 (pt0) cc_final: 0.7168 (pm20) REVERT: G 277 GLN cc_start: 0.7048 (tp40) cc_final: 0.6802 (tp-100) REVERT: I 123 PHE cc_start: 0.7758 (OUTLIER) cc_final: 0.7309 (t80) REVERT: I 161 GLU cc_start: 0.6908 (OUTLIER) cc_final: 0.6601 (mt-10) REVERT: J 10 GLU cc_start: 0.5530 (tp30) cc_final: 0.5170 (pt0) REVERT: J 59 THR cc_start: 0.7880 (OUTLIER) cc_final: 0.7546 (m) REVERT: J 78 GLU cc_start: 0.8905 (mm-30) cc_final: 0.8558 (mm-30) REVERT: J 91 GLU cc_start: 0.7077 (tp30) cc_final: 0.6740 (tp30) REVERT: H 22 LYS cc_start: 0.7115 (tttt) cc_final: 0.6494 (tppt) REVERT: H 200 VAL cc_start: 0.7975 (OUTLIER) cc_final: 0.7719 (p) REVERT: H 202 VAL cc_start: 0.8396 (m) cc_final: 0.8131 (t) REVERT: H 248 LYS cc_start: 0.6570 (mmmt) cc_final: 0.5700 (mmpt) REVERT: A 59 HIS cc_start: 0.4033 (OUTLIER) cc_final: 0.3234 (p-80) REVERT: A 80 ILE cc_start: 0.7355 (OUTLIER) cc_final: 0.7100 (pp) REVERT: A 200 MET cc_start: 0.2577 (ppp) cc_final: 0.2183 (pmt) REVERT: A 242 LYS cc_start: 0.7975 (mttt) cc_final: 0.7303 (mppt) REVERT: A 361 MET cc_start: 0.6017 (OUTLIER) cc_final: 0.4902 (tpt) REVERT: A 377 LYS cc_start: 0.7728 (ttmt) cc_final: 0.7256 (tmtt) REVERT: A 439 PHE cc_start: 0.7831 (m-80) cc_final: 0.7612 (m-10) REVERT: A 441 VAL cc_start: 0.7924 (t) cc_final: 0.7708 (m) REVERT: A 459 GLU cc_start: 0.6936 (mm-30) cc_final: 0.6346 (tp30) REVERT: A 468 ILE cc_start: 0.7167 (OUTLIER) cc_final: 0.6910 (mm) REVERT: A 469 LYS cc_start: 0.7035 (mttm) cc_final: 0.6701 (mmtt) REVERT: A 538 PHE cc_start: 0.6586 (OUTLIER) cc_final: 0.5807 (m-80) REVERT: A 563 PHE cc_start: 0.4981 (OUTLIER) cc_final: 0.4644 (t80) REVERT: A 671 LYS cc_start: 0.8033 (mttm) cc_final: 0.7659 (ttpt) outliers start: 71 outliers final: 46 residues processed: 337 average time/residue: 1.2035 time to fit residues: 478.5053 Evaluate side-chains 341 residues out of total 2170 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 276 time to evaluate : 2.205 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 43 THR 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 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 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 36 VAL Chi-restraints excluded: chain E residue 42 ARG Chi-restraints excluded: chain E residue 88 LYS 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 8 LEU 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 140 VAL Chi-restraints excluded: chain G residue 147 GLU 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 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 A residue 59 HIS Chi-restraints excluded: chain A residue 80 ILE Chi-restraints excluded: chain A residue 214 ILE Chi-restraints excluded: chain A residue 260 ILE Chi-restraints excluded: chain A residue 281 PHE Chi-restraints excluded: chain A residue 315 LEU Chi-restraints excluded: chain A residue 361 MET Chi-restraints excluded: chain A residue 374 VAL Chi-restraints excluded: chain A residue 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 549 ILE Chi-restraints excluded: chain A residue 561 MET Chi-restraints excluded: chain A residue 563 PHE Chi-restraints excluded: chain A residue 607 THR Chi-restraints excluded: chain A residue 622 MET Chi-restraints excluded: chain A residue 634 SER Chi-restraints excluded: chain A residue 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: 0.9980 chunk 14 optimal weight: 0.8980 chunk 188 optimal weight: 6.9990 chunk 88 optimal weight: 0.4980 chunk 182 optimal weight: 0.9990 chunk 240 optimal weight: 0.6980 chunk 189 optimal weight: 5.9990 chunk 27 optimal weight: 1.9990 chunk 56 optimal weight: 3.9990 chunk 223 optimal weight: 6.9990 chunk 204 optimal weight: 3.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- 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** ** G 198 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: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4144 r_free = 0.4144 target = 0.180937 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3739 r_free = 0.3739 target = 0.139038 restraints weight = 26276.540| |-----------------------------------------------------------------------------| r_work (start): 0.3685 rms_B_bonded: 2.01 r_work: 0.3526 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.3411 rms_B_bonded: 4.22 restraints_weight: 0.2500 r_work (final): 0.3411 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7613 moved from start: 0.3347 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.067 21865 Z= 0.134 Angle : 0.576 12.466 29807 Z= 0.301 Chirality : 0.042 0.386 3405 Planarity : 0.004 0.072 3514 Dihedral : 14.863 164.104 3842 Min Nonbonded Distance : 2.230 Molprobity Statistics. All-atom Clashscore : 10.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer: Outliers : 3.13 % Allowed : 23.32 % Favored : 73.55 % 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: 0.85 (0.16), residues: 2440 helix: 1.75 (0.15), residues: 1098 sheet: 0.05 (0.25), residues: 413 loop : -0.58 (0.19), residues: 929 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 493 HIS 0.005 0.001 HIS B 56 PHE 0.029 0.001 PHE A 40 TYR 0.050 0.001 TYR A 219 ARG 0.015 0.000 ARG G 79 Details of bonding type rmsd hydrogen bonds : bond 0.04095 ( 1075) hydrogen bonds : angle 4.66629 ( 3116) covalent geometry : bond 0.00294 (21865) covalent geometry : angle 0.57556 (29807) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 17603.01 seconds wall clock time: 303 minutes 38.20 seconds (18218.20 seconds total)