Starting phenix.real_space_refine on Thu Sep 18 23:36:08 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9g9d_51148/09_2025/9g9d_51148.cif Found real_map, /net/cci-nas-00/data/ceres_data/9g9d_51148/09_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_51148/09_2025/9g9d_51148.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9g9d_51148/09_2025/9g9d_51148.map" model { file = "/net/cci-nas-00/data/ceres_data/9g9d_51148/09_2025/9g9d_51148.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9g9d_51148/09_2025/9g9d_51148.cif" } resolution = 2.9 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.015 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 72 5.49 5 S 57 5.16 5 C 13322 2.51 5 N 3652 2.21 5 O 4230 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 11 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 21333 Number of models: 1 Model: "" Number of chains: 12 Chain: "C" Number of atoms: 1102 Number of conformers: 1 Conformer: "" Number of residues, atoms: 132, 1102 Classifications: {'peptide': 132} Link IDs: {'PTRANS': 1, 'TRANS': 130} Chain: "B" Number of atoms: 1065 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 1065 Classifications: {'peptide': 128} Link IDs: {'PTRANS': 1, 'TRANS': 126} Chain breaks: 1 Chain: "F" Number of atoms: 1620 Number of conformers: 1 Conformer: "" Number of residues, atoms: 210, 1620 Classifications: {'peptide': 210} Link IDs: {'PTRANS': 7, 'TRANS': 202} Chain: "E" Number of atoms: 1620 Number of conformers: 1 Conformer: "" Number of residues, atoms: 210, 1620 Classifications: {'peptide': 210} Link IDs: {'PTRANS': 7, 'TRANS': 202} Chain: "D" Number of atoms: 1548 Number of conformers: 1 Conformer: "" Number of residues, atoms: 200, 1548 Classifications: {'peptide': 200} Link IDs: {'PTRANS': 6, 'TRANS': 193} Chain breaks: 2 Chain: "G" Number of atoms: 2341 Number of conformers: 1 Conformer: "" Number of residues, atoms: 296, 2341 Classifications: {'peptide': 296} Link IDs: {'PTRANS': 7, 'TRANS': 288} Chain breaks: 1 Chain: "R" Number of atoms: 816 Number of conformers: 1 Conformer: "" Number of residues, atoms: 38, 816 Classifications: {'RNA': 38} Modifications used: {'5*END': 1, 'rna2p_pur': 10, 'rna2p_pyr': 8, 'rna3p_pur': 14, 'rna3p_pyr': 6} Link IDs: {'rna2p': 18, 'rna3p': 19} Chain: "T" Number of atoms: 740 Number of conformers: 1 Conformer: "" Number of residues, atoms: 35, 740 Classifications: {'RNA': 35} Modifications used: {'rna2p_pur': 3, 'rna2p_pyr': 1, 'rna3p_pur': 12, 'rna3p_pyr': 19} Link IDs: {'rna2p': 3, 'rna3p': 31} Chain: "I" Number of atoms: 1620 Number of conformers: 1 Conformer: "" Number of residues, atoms: 210, 1620 Classifications: {'peptide': 210} Link IDs: {'PTRANS': 7, 'TRANS': 202} Chain: "J" Number of atoms: 1124 Number of conformers: 1 Conformer: "" Number of residues, atoms: 135, 1124 Classifications: {'peptide': 135} Link IDs: {'PTRANS': 1, 'TRANS': 133} Chain: "H" Number of atoms: 2510 Number of conformers: 1 Conformer: "" Number of residues, atoms: 310, 2510 Classifications: {'peptide': 310} Link IDs: {'PCIS': 1, 'PTRANS': 14, 'TRANS': 294} Chain breaks: 4 Chain: "A" Number of atoms: 5227 Number of conformers: 1 Conformer: "" Number of residues, atoms: 653, 5227 Classifications: {'peptide': 653} Link IDs: {'PTRANS': 14, 'TRANS': 638} Chain breaks: 4 Time building chain proxies: 3.84, per 1000 atoms: 0.18 Number of scatterers: 21333 At special positions: 0 Unit cell: (102.7, 120.25, 195, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 57 16.00 P 72 15.00 O 4230 8.00 N 3652 7.00 C 13322 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.90 Conformation dependent library (CDL) restraints added in 735.6 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 4880 Ramachandran restraints generated. 2440 Oldfield, 0 Emsley, 2440 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4624 Finding SS restraints... Secondary structure from input PDB file: 100 helices and 28 sheets defined 49.4% alpha, 18.3% beta 23 base pairs and 35 stacking pairs defined. Time for finding SS restraints: 2.36 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: 3.12 Time building geometry restraints manager: 2.40 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: 9.910 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.480 Check model and map are aligned: 0.070 Set scattering table: 0.050 Process input model: 18.400 Find NCS groups from input model: 0.250 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:8.500 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 37.710 ------------------------------------------------------------------------------- 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.87 (0.16), residues: 2440 helix: 1.71 (0.15), residues: 1062 sheet: 0.06 (0.25), residues: 423 loop : -0.41 (0.19), residues: 955 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG I 187 TYR 0.024 0.001 TYR A 307 PHE 0.023 0.001 PHE D 150 TRP 0.005 0.001 TRP A 592 HIS 0.006 0.001 HIS I 18 Details of bonding type rmsd covalent geometry : bond 0.00663 (21865) covalent geometry : angle 0.99217 (29807) hydrogen bonds : bond 0.18606 ( 1075) hydrogen bonds : angle 6.75726 ( 3116) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4880 Ramachandran restraints generated. 2440 Oldfield, 0 Emsley, 2440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4880 Ramachandran restraints generated. 2440 Oldfield, 0 Emsley, 2440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 533 residues out of total 2170 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 489 time to evaluate : 0.730 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: 0.5705 time to fit residues: 338.7626 Evaluate side-chains 332 residues out of total 2170 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 319 time to evaluate : 0.901 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 45 ILE Chi-restraints excluded: chain E residue 36 VAL Chi-restraints excluded: chain I residue 124 GLU Chi-restraints excluded: chain I residue 161 GLU Chi-restraints excluded: chain J residue 14 LEU Chi-restraints excluded: chain H residue 41 VAL Chi-restraints excluded: chain H residue 145 LYS Chi-restraints excluded: chain H residue 212 ILE Chi-restraints excluded: chain H residue 327 ASN Chi-restraints excluded: chain A residue 21 TYR Chi-restraints excluded: chain A residue 281 PHE Chi-restraints excluded: chain A residue 388 LEU Chi-restraints excluded: chain A residue 542 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 216 optimal weight: 8.9990 chunk 98 optimal weight: 4.9990 chunk 194 optimal weight: 6.9990 chunk 227 optimal weight: 5.9990 chunk 107 optimal weight: 10.0000 chunk 10 optimal weight: 0.8980 chunk 66 optimal weight: 0.8980 chunk 247 optimal weight: 1.9990 chunk 130 optimal weight: 0.9990 chunk 124 optimal weight: 0.0170 chunk 103 optimal weight: 6.9990 overall best weight: 0.9622 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 = 0.4145 r_free = 0.4145 target = 0.180735 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3737 r_free = 0.3737 target = 0.138818 restraints weight = 26289.971| |-----------------------------------------------------------------------------| r_work (start): 0.3685 rms_B_bonded: 2.02 r_work: 0.3522 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.3408 rms_B_bonded: 4.25 restraints_weight: 0.2500 r_work (final): 0.3408 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7615 moved from start: 0.1987 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 21865 Z= 0.155 Angle : 0.586 10.562 29807 Z= 0.313 Chirality : 0.043 0.336 3405 Planarity : 0.004 0.041 3514 Dihedral : 15.317 164.547 3860 Min Nonbonded Distance : 2.407 Molprobity Statistics. All-atom Clashscore : 10.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.21 % Favored : 97.79 % Rotamer: Outliers : 4.61 % Allowed : 15.35 % Favored : 80.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.54 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.01 (0.16), residues: 2440 helix: 1.86 (0.15), residues: 1095 sheet: 0.17 (0.24), residues: 440 loop : -0.50 (0.19), residues: 905 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 466 TYR 0.026 0.001 TYR A 307 PHE 0.025 0.002 PHE D 150 TRP 0.007 0.001 TRP H 237 HIS 0.004 0.001 HIS H 283 Details of bonding type rmsd covalent geometry : bond 0.00335 (21865) covalent geometry : angle 0.58619 (29807) hydrogen bonds : bond 0.04918 ( 1075) hydrogen bonds : angle 4.98921 ( 3116) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4880 Ramachandran restraints generated. 2440 Oldfield, 0 Emsley, 2440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4880 Ramachandran restraints generated. 2440 Oldfield, 0 Emsley, 2440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 450 residues out of total 2170 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 100 poor density : 350 time to evaluate : 0.923 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 121 ASP cc_start: 0.8089 (OUTLIER) cc_final: 0.7345 (m-30) REVERT: C 127 GLU cc_start: 0.6686 (mt-10) cc_final: 0.6086 (mt-10) REVERT: B 11 MET cc_start: 0.5971 (tpp) cc_final: 0.5298 (tmm) REVERT: B 74 ARG cc_start: 0.7691 (mtp85) cc_final: 0.7267 (mtp-110) REVERT: F 28 ILE cc_start: 0.8675 (mt) cc_final: 0.8275 (mp) REVERT: E 28 ILE cc_start: 0.8164 (mt) cc_final: 0.7645 (mp) REVERT: E 167 GLU cc_start: 0.7892 (mm-30) cc_final: 0.7262 (tp30) REVERT: E 203 VAL cc_start: 0.7706 (t) cc_final: 0.7499 (t) REVERT: D 124 GLU cc_start: 0.8407 (OUTLIER) cc_final: 0.8096 (mt-10) REVERT: D 139 ILE cc_start: 0.8762 (pt) cc_final: 0.8552 (pt) REVERT: D 161 GLU cc_start: 0.7026 (OUTLIER) cc_final: 0.6793 (mp0) REVERT: G 159 GLU cc_start: 0.7210 (mm-30) cc_final: 0.6903 (mm-30) REVERT: G 259 GLN cc_start: 0.7591 (pt0) cc_final: 0.7241 (pm20) REVERT: G 277 GLN cc_start: 0.6963 (tp40) cc_final: 0.6643 (tp-100) REVERT: I 161 GLU cc_start: 0.6930 (OUTLIER) cc_final: 0.6645 (mt-10) REVERT: J 10 GLU cc_start: 0.5968 (tp30) cc_final: 0.5339 (pt0) REVERT: J 40 ASN cc_start: 0.7956 (m110) cc_final: 0.7723 (m110) REVERT: J 59 THR cc_start: 0.7961 (OUTLIER) cc_final: 0.7584 (m) REVERT: J 61 VAL cc_start: 0.6079 (t) cc_final: 0.5754 (t) REVERT: J 91 GLU cc_start: 0.7148 (tp30) cc_final: 0.6745 (tp30) REVERT: H 22 LYS cc_start: 0.7153 (tttt) cc_final: 0.6551 (mppt) REVERT: H 168 SER cc_start: 0.7499 (p) cc_final: 0.6924 (p) REVERT: H 202 VAL cc_start: 0.8473 (m) cc_final: 0.8206 (t) REVERT: H 212 ILE cc_start: 0.6799 (OUTLIER) cc_final: 0.6373 (pp) REVERT: A 77 ILE cc_start: 0.6707 (mt) cc_final: 0.6330 (mt) REVERT: A 242 LYS cc_start: 0.7631 (mttt) cc_final: 0.7176 (mptt) REVERT: A 252 LEU cc_start: 0.6363 (tt) cc_final: 0.6121 (tp) REVERT: A 439 PHE cc_start: 0.7976 (m-80) cc_final: 0.7437 (m-10) REVERT: A 455 TYR cc_start: 0.7410 (m-80) cc_final: 0.7156 (m-10) REVERT: A 469 LYS cc_start: 0.7071 (mttm) cc_final: 0.6845 (mmtt) REVERT: A 569 ASN cc_start: 0.7137 (m110) cc_final: 0.6878 (m-40) REVERT: A 655 ASN cc_start: 0.7393 (OUTLIER) cc_final: 0.7177 (m-40) REVERT: A 671 LYS cc_start: 0.8083 (mttm) cc_final: 0.7811 (ptpt) REVERT: A 751 ILE cc_start: 0.7627 (tt) cc_final: 0.7317 (pt) outliers start: 100 outliers final: 30 residues processed: 418 average time/residue: 0.5900 time to fit residues: 285.5288 Evaluate side-chains 332 residues out of total 2170 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 295 time to evaluate : 0.880 ------------------------------------------------------------------------------- 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 44 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 178 ASN Chi-restraints excluded: chain E residue 36 VAL Chi-restraints excluded: chain E residue 202 VAL Chi-restraints excluded: chain D residue 124 GLU Chi-restraints excluded: chain D residue 161 GLU Chi-restraints excluded: chain G residue 95 LYS Chi-restraints excluded: chain G residue 140 VAL Chi-restraints excluded: chain 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 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 73 optimal weight: 0.9990 chunk 246 optimal weight: 0.9980 chunk 182 optimal weight: 0.9980 chunk 181 optimal weight: 5.9990 chunk 204 optimal weight: 2.9990 chunk 95 optimal weight: 6.9990 chunk 118 optimal weight: 3.9990 chunk 214 optimal weight: 10.0000 chunk 163 optimal weight: 0.8980 chunk 29 optimal weight: 0.5980 chunk 184 optimal weight: 6.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- 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 = 0.4143 r_free = 0.4143 target = 0.180699 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3739 r_free = 0.3739 target = 0.138892 restraints weight = 26414.222| |-----------------------------------------------------------------------------| r_work (start): 0.3686 rms_B_bonded: 2.02 r_work: 0.3526 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.3413 rms_B_bonded: 4.20 restraints_weight: 0.2500 r_work (final): 0.3413 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7590 moved from start: 0.2367 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 21865 Z= 0.140 Angle : 0.557 10.158 29807 Z= 0.296 Chirality : 0.042 0.351 3405 Planarity : 0.004 0.047 3514 Dihedral : 15.152 164.036 3847 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 10.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer: Outliers : 4.33 % Allowed : 17.47 % Favored : 78.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.54 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.97 (0.16), residues: 2440 helix: 1.83 (0.15), residues: 1097 sheet: 0.13 (0.24), residues: 432 loop : -0.52 (0.19), residues: 911 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 466 TYR 0.021 0.001 TYR A 307 PHE 0.023 0.002 PHE A 40 TRP 0.006 0.001 TRP A 592 HIS 0.003 0.001 HIS F 151 Details of bonding type rmsd covalent geometry : bond 0.00302 (21865) covalent geometry : angle 0.55734 (29807) hydrogen bonds : bond 0.04571 ( 1075) hydrogen bonds : angle 4.77975 ( 3116) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4880 Ramachandran restraints generated. 2440 Oldfield, 0 Emsley, 2440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4880 Ramachandran restraints generated. 2440 Oldfield, 0 Emsley, 2440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 408 residues out of total 2170 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 314 time to evaluate : 0.884 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 121 ASP cc_start: 0.8115 (OUTLIER) cc_final: 0.7372 (m-30) REVERT: B 11 MET cc_start: 0.5885 (tpp) cc_final: 0.5424 (tmm) REVERT: B 74 ARG cc_start: 0.7639 (mtp85) cc_final: 0.7251 (mtp-110) REVERT: F 28 ILE cc_start: 0.8684 (mt) cc_final: 0.8363 (mp) REVERT: F 42 ARG cc_start: 0.8633 (OUTLIER) cc_final: 0.8363 (mtm110) REVERT: E 28 ILE cc_start: 0.8029 (mt) cc_final: 0.7496 (mp) REVERT: E 42 ARG cc_start: 0.8084 (OUTLIER) cc_final: 0.6967 (mtm180) REVERT: E 167 GLU cc_start: 0.7901 (mm-30) cc_final: 0.7251 (tp30) REVERT: E 203 VAL cc_start: 0.7757 (t) cc_final: 0.7478 (t) REVERT: D 139 ILE cc_start: 0.8757 (pt) cc_final: 0.8537 (pt) REVERT: D 161 GLU cc_start: 0.6862 (OUTLIER) cc_final: 0.6619 (mp0) REVERT: G 95 LYS cc_start: 0.7222 (OUTLIER) cc_final: 0.6534 (pptt) REVERT: G 159 GLU cc_start: 0.7166 (mm-30) cc_final: 0.6883 (mm-30) REVERT: G 213 LEU cc_start: 0.6968 (tt) cc_final: 0.6531 (mt) REVERT: G 277 GLN cc_start: 0.6950 (tp40) cc_final: 0.6629 (tp-100) REVERT: I 161 GLU cc_start: 0.6899 (OUTLIER) cc_final: 0.6579 (mt-10) REVERT: J 40 ASN cc_start: 0.7977 (m110) cc_final: 0.7758 (m110) REVERT: J 59 THR cc_start: 0.7893 (OUTLIER) cc_final: 0.7528 (m) REVERT: J 61 VAL cc_start: 0.6069 (t) cc_final: 0.5745 (t) REVERT: J 91 GLU cc_start: 0.7113 (tp30) cc_final: 0.6681 (tp30) REVERT: H 22 LYS cc_start: 0.7071 (tttt) cc_final: 0.6450 (mppt) REVERT: H 168 SER cc_start: 0.7537 (p) cc_final: 0.6919 (p) REVERT: H 193 MET cc_start: 0.7808 (ttm) cc_final: 0.7374 (ttm) REVERT: H 202 VAL cc_start: 0.8416 (m) cc_final: 0.8146 (t) REVERT: H 212 ILE cc_start: 0.6736 (OUTLIER) cc_final: 0.6340 (pp) REVERT: A 80 ILE cc_start: 0.7442 (OUTLIER) cc_final: 0.7167 (pp) REVERT: A 200 MET cc_start: 0.0044 (ppp) cc_final: -0.0631 (pmt) REVERT: A 242 LYS cc_start: 0.7721 (mttt) cc_final: 0.7174 (mppt) REVERT: A 252 LEU cc_start: 0.6282 (tt) cc_final: 0.6079 (tp) REVERT: A 288 GLU cc_start: 0.6698 (mm-30) cc_final: 0.6494 (mt-10) REVERT: A 314 TYR cc_start: 0.7127 (m-80) cc_final: 0.6922 (m-80) REVERT: A 361 MET cc_start: 0.5349 (OUTLIER) cc_final: 0.4799 (ttt) REVERT: A 439 PHE cc_start: 0.7889 (m-80) cc_final: 0.7542 (m-10) REVERT: A 455 TYR cc_start: 0.7370 (m-80) cc_final: 0.7086 (m-10) REVERT: A 468 ILE cc_start: 0.7037 (OUTLIER) cc_final: 0.6742 (mm) REVERT: A 469 LYS cc_start: 0.7073 (mttm) cc_final: 0.6784 (mmtt) REVERT: A 569 ASN cc_start: 0.7075 (m110) cc_final: 0.6818 (t160) REVERT: A 671 LYS cc_start: 0.8052 (mttm) cc_final: 0.7755 (ptpt) REVERT: A 751 ILE cc_start: 0.7568 (tt) cc_final: 0.7243 (pt) outliers start: 94 outliers final: 37 residues processed: 375 average time/residue: 0.5454 time to fit residues: 236.9941 Evaluate side-chains 321 residues out of total 2170 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 273 time to evaluate : 0.759 ------------------------------------------------------------------------------- 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 12 ILE 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 79 ILE Chi-restraints excluded: chain F residue 119 THR Chi-restraints excluded: chain F residue 120 GLU Chi-restraints excluded: chain F residue 126 THR Chi-restraints excluded: chain F residue 133 VAL Chi-restraints excluded: chain E residue 42 ARG Chi-restraints excluded: chain E residue 202 VAL Chi-restraints excluded: chain D residue 161 GLU Chi-restraints excluded: chain D residue 211 LEU Chi-restraints excluded: chain G residue 95 LYS Chi-restraints excluded: chain G residue 140 VAL Chi-restraints excluded: chain G residue 212 LEU Chi-restraints excluded: chain 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 80 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 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 563 PHE 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 81 optimal weight: 2.9990 chunk 22 optimal weight: 0.6980 chunk 55 optimal weight: 4.9990 chunk 140 optimal weight: 1.9990 chunk 204 optimal weight: 4.9990 chunk 202 optimal weight: 9.9990 chunk 177 optimal weight: 6.9990 chunk 7 optimal weight: 1.9990 chunk 125 optimal weight: 0.8980 chunk 27 optimal weight: 0.5980 chunk 61 optimal weight: 1.9990 overall best weight: 1.2384 ------------------------------------------------------------------------------- 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 687 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4125 r_free = 0.4125 target = 0.179008 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3716 r_free = 0.3716 target = 0.137014 restraints weight = 26444.549| |-----------------------------------------------------------------------------| r_work (start): 0.3662 rms_B_bonded: 2.06 r_work: 0.3495 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.3380 rms_B_bonded: 4.25 restraints_weight: 0.2500 r_work (final): 0.3380 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7668 moved from start: 0.2599 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= 0.158 Angle : 0.564 8.683 29807 Z= 0.299 Chirality : 0.043 0.368 3405 Planarity : 0.004 0.045 3514 Dihedral : 15.062 165.533 3844 Min Nonbonded Distance : 2.411 Molprobity Statistics. All-atom Clashscore : 10.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer: Outliers : 4.70 % Allowed : 18.29 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.89 (0.16), residues: 2440 helix: 1.75 (0.15), residues: 1093 sheet: 0.18 (0.25), residues: 409 loop : -0.56 (0.18), residues: 938 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 466 TYR 0.025 0.001 TYR C 122 PHE 0.034 0.002 PHE E 150 TRP 0.007 0.001 TRP A 592 HIS 0.004 0.001 HIS F 151 Details of bonding type rmsd covalent geometry : bond 0.00348 (21865) covalent geometry : angle 0.56381 (29807) hydrogen bonds : bond 0.04493 ( 1075) hydrogen bonds : angle 4.73373 ( 3116) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4880 Ramachandran restraints generated. 2440 Oldfield, 0 Emsley, 2440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4880 Ramachandran restraints generated. 2440 Oldfield, 0 Emsley, 2440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 413 residues out of total 2170 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 102 poor density : 311 time to evaluate : 0.863 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 127 GLU cc_start: 0.6688 (mt-10) cc_final: 0.6162 (mt-10) REVERT: B 11 MET cc_start: 0.5947 (tpp) cc_final: 0.5527 (tmm) REVERT: B 74 ARG cc_start: 0.7640 (mtp85) cc_final: 0.7279 (mtp-110) REVERT: F 28 ILE cc_start: 0.8727 (mt) cc_final: 0.8422 (mp) REVERT: E 28 ILE cc_start: 0.8123 (mt) cc_final: 0.7611 (mp) REVERT: E 42 ARG cc_start: 0.8098 (OUTLIER) cc_final: 0.7023 (mtm180) REVERT: E 120 GLU cc_start: 0.8675 (OUTLIER) cc_final: 0.7930 (pm20) REVERT: E 167 GLU cc_start: 0.7886 (mm-30) cc_final: 0.7210 (tp30) REVERT: E 203 VAL cc_start: 0.7802 (t) cc_final: 0.7546 (t) REVERT: D 124 GLU cc_start: 0.8470 (OUTLIER) cc_final: 0.8094 (mt-10) REVERT: D 139 ILE cc_start: 0.8774 (pt) cc_final: 0.8554 (pt) REVERT: D 161 GLU cc_start: 0.6921 (OUTLIER) cc_final: 0.6629 (mp0) REVERT: G 95 LYS cc_start: 0.7270 (OUTLIER) cc_final: 0.6590 (pptt) REVERT: G 159 GLU cc_start: 0.7206 (mm-30) cc_final: 0.6958 (mm-30) REVERT: G 213 LEU cc_start: 0.6980 (tt) cc_final: 0.6532 (mt) REVERT: G 259 GLN cc_start: 0.7582 (pt0) cc_final: 0.7211 (pm20) REVERT: G 277 GLN cc_start: 0.7029 (tp40) cc_final: 0.6734 (tp-100) REVERT: I 161 GLU cc_start: 0.6924 (OUTLIER) cc_final: 0.6657 (mt-10) REVERT: J 40 ASN cc_start: 0.7969 (m110) cc_final: 0.7762 (m110) REVERT: J 59 THR cc_start: 0.7978 (OUTLIER) cc_final: 0.7600 (m) REVERT: J 61 VAL cc_start: 0.6163 (t) cc_final: 0.5840 (t) REVERT: J 91 GLU cc_start: 0.7153 (tp30) cc_final: 0.6740 (tp30) REVERT: H 22 LYS cc_start: 0.7104 (tttt) cc_final: 0.6502 (tppt) REVERT: H 202 VAL cc_start: 0.8454 (m) cc_final: 0.8199 (t) REVERT: H 212 ILE cc_start: 0.6843 (OUTLIER) cc_final: 0.6458 (pp) REVERT: A 59 HIS cc_start: 0.4197 (OUTLIER) cc_final: 0.3175 (p-80) REVERT: A 80 ILE cc_start: 0.7465 (OUTLIER) cc_final: 0.7206 (pp) REVERT: A 200 MET cc_start: 0.0434 (ppp) cc_final: -0.0353 (pmt) REVERT: A 242 LYS cc_start: 0.7813 (mttt) cc_final: 0.7229 (mppt) REVERT: A 281 PHE cc_start: 0.7197 (OUTLIER) cc_final: 0.6547 (p90) REVERT: A 288 GLU cc_start: 0.6818 (mm-30) cc_final: 0.6351 (mt-10) REVERT: A 361 MET cc_start: 0.5275 (OUTLIER) cc_final: 0.4797 (ttm) REVERT: A 439 PHE cc_start: 0.7910 (m-80) cc_final: 0.7562 (m-10) REVERT: A 455 TYR cc_start: 0.7414 (m-80) cc_final: 0.7095 (m-10) REVERT: A 468 ILE cc_start: 0.7064 (OUTLIER) cc_final: 0.6765 (mm) REVERT: A 469 LYS cc_start: 0.7149 (mttm) cc_final: 0.6845 (mmtt) REVERT: A 569 ASN cc_start: 0.7008 (m110) cc_final: 0.6761 (t160) REVERT: A 671 LYS cc_start: 0.8086 (mttm) cc_final: 0.7804 (ptpt) outliers start: 102 outliers final: 46 residues processed: 380 average time/residue: 0.5479 time to fit residues: 241.5106 Evaluate side-chains 329 residues out of total 2170 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 270 time to evaluate : 0.773 ------------------------------------------------------------------------------- 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 12 ILE Chi-restraints excluded: chain B residue 44 THR Chi-restraints excluded: chain B residue 57 VAL Chi-restraints excluded: chain B residue 68 THR Chi-restraints excluded: chain B residue 103 VAL Chi-restraints excluded: chain B residue 115 THR Chi-restraints excluded: chain F residue 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 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 204 LEU Chi-restraints excluded: chain A residue 225 MET Chi-restraints excluded: chain A residue 260 ILE Chi-restraints excluded: chain A residue 281 PHE Chi-restraints excluded: chain A residue 289 SER Chi-restraints excluded: chain A residue 315 LEU Chi-restraints excluded: chain A residue 361 MET Chi-restraints excluded: chain A residue 374 VAL Chi-restraints excluded: chain A residue 388 LEU Chi-restraints excluded: chain A residue 408 CYS Chi-restraints excluded: chain A residue 434 LEU Chi-restraints excluded: chain A residue 448 VAL Chi-restraints excluded: chain A residue 468 ILE Chi-restraints excluded: chain A residue 542 ILE Chi-restraints excluded: chain A residue 563 PHE 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 11 optimal weight: 0.9990 chunk 146 optimal weight: 1.9990 chunk 79 optimal weight: 3.9990 chunk 224 optimal weight: 10.0000 chunk 137 optimal weight: 3.9990 chunk 197 optimal weight: 0.0980 chunk 219 optimal weight: 4.9990 chunk 140 optimal weight: 3.9990 chunk 123 optimal weight: 0.5980 chunk 33 optimal weight: 0.7980 chunk 129 optimal weight: 0.8980 overall best weight: 0.6782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 56 HIS B 56 HIS ** D 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 198 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 158 ASN H 187 ASN ** A 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 159 ASN ** A 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 = 0.4151 r_free = 0.4151 target = 0.181655 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3750 r_free = 0.3750 target = 0.139957 restraints weight = 26340.627| |-----------------------------------------------------------------------------| r_work (start): 0.3696 rms_B_bonded: 1.99 r_work: 0.3546 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.3433 rms_B_bonded: 4.16 restraints_weight: 0.2500 r_work (final): 0.3433 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7605 moved from start: 0.2846 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 21865 Z= 0.122 Angle : 0.536 12.126 29807 Z= 0.284 Chirality : 0.041 0.383 3405 Planarity : 0.004 0.053 3514 Dihedral : 14.965 163.211 3844 Min Nonbonded Distance : 2.358 Molprobity Statistics. All-atom Clashscore : 9.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer: Outliers : 3.82 % Allowed : 20.05 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.01 (0.16), residues: 2440 helix: 1.87 (0.15), residues: 1094 sheet: 0.25 (0.25), residues: 409 loop : -0.53 (0.18), residues: 937 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG I 193 TYR 0.024 0.001 TYR C 122 PHE 0.027 0.001 PHE E 150 TRP 0.008 0.001 TRP H 237 HIS 0.004 0.001 HIS B 56 Details of bonding type rmsd covalent geometry : bond 0.00257 (21865) covalent geometry : angle 0.53577 (29807) hydrogen bonds : bond 0.04111 ( 1075) hydrogen bonds : angle 4.55831 ( 3116) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4880 Ramachandran restraints generated. 2440 Oldfield, 0 Emsley, 2440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4880 Ramachandran restraints generated. 2440 Oldfield, 0 Emsley, 2440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 394 residues out of total 2170 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 311 time to evaluate : 0.894 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 127 GLU cc_start: 0.6687 (mt-10) cc_final: 0.6181 (mt-10) REVERT: B 11 MET cc_start: 0.5738 (tpp) cc_final: 0.5373 (tmm) REVERT: B 74 ARG cc_start: 0.7626 (mtp85) cc_final: 0.7297 (mtp-110) REVERT: B 76 GLU cc_start: 0.7556 (OUTLIER) cc_final: 0.6804 (mm-30) REVERT: F 28 ILE cc_start: 0.8623 (mt) cc_final: 0.8366 (mp) REVERT: F 133 VAL cc_start: 0.8605 (OUTLIER) cc_final: 0.8381 (t) REVERT: E 28 ILE cc_start: 0.8069 (mt) cc_final: 0.7536 (mp) REVERT: E 42 ARG cc_start: 0.8094 (OUTLIER) cc_final: 0.7040 (mtm180) REVERT: E 120 GLU cc_start: 0.8649 (OUTLIER) cc_final: 0.7938 (pm20) REVERT: E 167 GLU cc_start: 0.7867 (mm-30) cc_final: 0.7194 (tp30) REVERT: E 203 VAL cc_start: 0.7818 (t) cc_final: 0.7551 (t) REVERT: D 124 GLU cc_start: 0.8443 (OUTLIER) cc_final: 0.8059 (mt-10) REVERT: D 139 ILE cc_start: 0.8713 (pt) cc_final: 0.8499 (pt) REVERT: D 161 GLU cc_start: 0.6937 (OUTLIER) cc_final: 0.6688 (mp0) REVERT: G 54 LEU cc_start: 0.7196 (tt) cc_final: 0.6889 (pp) REVERT: G 95 LYS cc_start: 0.7289 (mptm) cc_final: 0.6574 (pptt) REVERT: G 159 GLU cc_start: 0.7130 (mm-30) cc_final: 0.6872 (mm-30) REVERT: G 213 LEU cc_start: 0.7007 (tt) cc_final: 0.6679 (mt) REVERT: G 259 GLN cc_start: 0.7555 (pt0) cc_final: 0.7183 (pm20) REVERT: G 277 GLN cc_start: 0.7045 (tp40) cc_final: 0.6768 (tp-100) REVERT: I 123 PHE cc_start: 0.7762 (OUTLIER) cc_final: 0.7358 (t80) REVERT: I 161 GLU cc_start: 0.6920 (OUTLIER) cc_final: 0.6606 (mt-10) REVERT: J 59 THR cc_start: 0.7930 (t) cc_final: 0.7581 (m) REVERT: J 61 VAL cc_start: 0.6136 (t) cc_final: 0.5827 (t) REVERT: J 78 GLU cc_start: 0.8897 (mm-30) cc_final: 0.8630 (mm-30) REVERT: J 91 GLU cc_start: 0.7081 (tp30) cc_final: 0.6677 (tp30) REVERT: H 22 LYS cc_start: 0.7104 (tttt) cc_final: 0.6489 (tppt) REVERT: H 202 VAL cc_start: 0.8400 (m) cc_final: 0.8144 (t) REVERT: H 212 ILE cc_start: 0.6811 (OUTLIER) cc_final: 0.6447 (pp) REVERT: A 22 ARG cc_start: 0.6885 (mtt90) cc_final: 0.6666 (mtt90) REVERT: A 59 HIS cc_start: 0.4220 (OUTLIER) cc_final: 0.3244 (p-80) REVERT: A 77 ILE cc_start: 0.6591 (OUTLIER) cc_final: 0.6250 (tt) REVERT: A 80 ILE cc_start: 0.7482 (OUTLIER) cc_final: 0.7191 (pp) REVERT: A 83 ASN cc_start: 0.6879 (m110) cc_final: 0.6653 (m-40) REVERT: A 200 MET cc_start: 0.1222 (ppp) cc_final: 0.0959 (pmt) REVERT: A 242 LYS cc_start: 0.7822 (mttt) cc_final: 0.7196 (mppt) REVERT: A 252 LEU cc_start: 0.6360 (tt) cc_final: 0.6110 (tp) REVERT: A 288 GLU cc_start: 0.6785 (mm-30) cc_final: 0.6481 (mt-10) REVERT: A 361 MET cc_start: 0.5261 (OUTLIER) cc_final: 0.4939 (ttt) REVERT: A 439 PHE cc_start: 0.7837 (m-80) cc_final: 0.7546 (m-10) REVERT: A 441 VAL cc_start: 0.7919 (t) cc_final: 0.7678 (m) REVERT: A 455 TYR cc_start: 0.7415 (m-80) cc_final: 0.7138 (m-10) REVERT: A 459 GLU cc_start: 0.6866 (mm-30) cc_final: 0.6297 (tp30) REVERT: A 468 ILE cc_start: 0.7113 (OUTLIER) cc_final: 0.6820 (mm) REVERT: A 469 LYS cc_start: 0.7152 (mttm) cc_final: 0.6832 (mmtt) REVERT: A 538 PHE cc_start: 0.6723 (OUTLIER) cc_final: 0.6184 (m-80) REVERT: A 569 ASN cc_start: 0.7027 (m110) cc_final: 0.6781 (t160) REVERT: A 671 LYS cc_start: 0.8097 (mttm) cc_final: 0.7828 (ptpt) outliers start: 83 outliers final: 42 residues processed: 359 average time/residue: 0.5856 time to fit residues: 244.7616 Evaluate side-chains 347 residues out of total 2170 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 290 time to evaluate : 0.865 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 12 ILE Chi-restraints excluded: chain C residue 67 THR Chi-restraints excluded: chain C residue 103 VAL Chi-restraints excluded: chain B residue 6 THR Chi-restraints excluded: chain B residue 44 THR Chi-restraints excluded: chain B residue 57 VAL Chi-restraints excluded: chain B residue 68 THR Chi-restraints excluded: chain B residue 76 GLU Chi-restraints excluded: chain B residue 103 VAL Chi-restraints excluded: chain B residue 115 THR Chi-restraints excluded: chain F residue 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 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 113 ASP Chi-restraints excluded: chain G residue 140 VAL Chi-restraints excluded: chain I residue 75 ASP Chi-restraints excluded: chain I residue 78 GLU Chi-restraints excluded: chain I residue 123 PHE Chi-restraints excluded: chain I residue 161 GLU Chi-restraints excluded: chain J residue 14 LEU Chi-restraints excluded: chain H residue 23 ILE Chi-restraints excluded: chain H residue 41 VAL Chi-restraints excluded: chain H residue 209 THR Chi-restraints excluded: chain H residue 212 ILE Chi-restraints excluded: chain A residue 59 HIS Chi-restraints excluded: chain A residue 77 ILE Chi-restraints excluded: chain A residue 80 ILE Chi-restraints excluded: chain A residue 157 LEU Chi-restraints excluded: chain A residue 204 LEU Chi-restraints excluded: chain A residue 206 ASP Chi-restraints excluded: chain A residue 225 MET Chi-restraints excluded: chain A residue 260 ILE Chi-restraints excluded: chain A residue 281 PHE Chi-restraints excluded: chain A residue 315 LEU Chi-restraints excluded: chain A residue 361 MET Chi-restraints excluded: chain A residue 374 VAL Chi-restraints excluded: chain A residue 388 LEU Chi-restraints excluded: chain A residue 408 CYS Chi-restraints excluded: chain A residue 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 622 MET Chi-restraints excluded: chain A residue 687 HIS Chi-restraints excluded: chain A residue 695 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 72 optimal weight: 2.9990 chunk 100 optimal weight: 0.6980 chunk 13 optimal weight: 8.9990 chunk 86 optimal weight: 0.2980 chunk 127 optimal weight: 1.9990 chunk 97 optimal weight: 10.0000 chunk 185 optimal weight: 4.9990 chunk 40 optimal weight: 0.6980 chunk 107 optimal weight: 9.9990 chunk 1 optimal weight: 0.9980 chunk 152 optimal weight: 0.8980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 56 HIS B 56 HIS ** D 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 198 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 189 ASN H 27 GLN 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: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4150 r_free = 0.4150 target = 0.181585 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3750 r_free = 0.3750 target = 0.140137 restraints weight = 26298.528| |-----------------------------------------------------------------------------| r_work (start): 0.3699 rms_B_bonded: 2.02 r_work: 0.3538 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.3423 rms_B_bonded: 4.25 restraints_weight: 0.2500 r_work (final): 0.3423 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7590 moved from start: 0.2965 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 21865 Z= 0.124 Angle : 0.532 10.399 29807 Z= 0.281 Chirality : 0.041 0.378 3405 Planarity : 0.004 0.056 3514 Dihedral : 14.917 163.920 3844 Min Nonbonded Distance : 2.333 Molprobity Statistics. All-atom Clashscore : 9.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer: Outliers : 4.33 % Allowed : 20.41 % Favored : 75.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.54 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.02 (0.16), residues: 2440 helix: 1.90 (0.15), residues: 1094 sheet: 0.20 (0.25), residues: 415 loop : -0.54 (0.19), residues: 931 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A 466 TYR 0.024 0.001 TYR C 122 PHE 0.024 0.001 PHE E 150 TRP 0.006 0.001 TRP H 237 HIS 0.005 0.001 HIS B 56 Details of bonding type rmsd covalent geometry : bond 0.00263 (21865) covalent geometry : angle 0.53157 (29807) hydrogen bonds : bond 0.04056 ( 1075) hydrogen bonds : angle 4.53183 ( 3116) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4880 Ramachandran restraints generated. 2440 Oldfield, 0 Emsley, 2440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4880 Ramachandran restraints generated. 2440 Oldfield, 0 Emsley, 2440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 399 residues out of total 2170 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 305 time to evaluate : 0.822 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 127 GLU cc_start: 0.6508 (mt-10) cc_final: 0.6202 (mt-10) REVERT: B 11 MET cc_start: 0.5587 (tpp) cc_final: 0.5252 (tmm) REVERT: B 74 ARG cc_start: 0.7618 (mtp85) cc_final: 0.7308 (mtp-110) REVERT: F 28 ILE cc_start: 0.8716 (mt) cc_final: 0.8408 (mp) REVERT: F 133 VAL cc_start: 0.8600 (OUTLIER) cc_final: 0.8378 (t) REVERT: E 28 ILE cc_start: 0.8059 (mt) cc_final: 0.7533 (mp) REVERT: E 42 ARG cc_start: 0.8083 (OUTLIER) cc_final: 0.7015 (mtm180) REVERT: E 120 GLU cc_start: 0.8666 (OUTLIER) cc_final: 0.7944 (pm20) REVERT: E 144 ARG cc_start: 0.7676 (ttp80) cc_final: 0.7323 (mtm180) REVERT: E 167 GLU cc_start: 0.7856 (mm-30) cc_final: 0.7169 (tp30) REVERT: E 203 VAL cc_start: 0.7799 (t) cc_final: 0.7528 (t) REVERT: D 124 GLU cc_start: 0.8450 (OUTLIER) cc_final: 0.8047 (mt-10) REVERT: D 139 ILE cc_start: 0.8712 (pt) cc_final: 0.8502 (pt) REVERT: D 161 GLU cc_start: 0.6919 (OUTLIER) cc_final: 0.6660 (mp0) REVERT: G 54 LEU cc_start: 0.7181 (tt) cc_final: 0.6909 (pp) REVERT: G 95 LYS cc_start: 0.7269 (OUTLIER) cc_final: 0.6570 (pptt) REVERT: G 159 GLU cc_start: 0.7142 (mm-30) cc_final: 0.6872 (mm-30) REVERT: G 213 LEU cc_start: 0.7016 (tt) cc_final: 0.6678 (mt) REVERT: G 259 GLN cc_start: 0.7580 (pt0) cc_final: 0.7168 (pm20) REVERT: G 277 GLN cc_start: 0.7059 (tp40) cc_final: 0.6784 (tp-100) REVERT: I 123 PHE cc_start: 0.7741 (OUTLIER) cc_final: 0.7355 (t80) REVERT: I 161 GLU cc_start: 0.6887 (OUTLIER) cc_final: 0.6564 (mt-10) REVERT: J 10 GLU cc_start: 0.5620 (tp30) cc_final: 0.5208 (pt0) REVERT: J 59 THR cc_start: 0.7864 (OUTLIER) cc_final: 0.7507 (m) REVERT: J 61 VAL cc_start: 0.6121 (t) cc_final: 0.5795 (t) REVERT: J 78 GLU cc_start: 0.8885 (mm-30) cc_final: 0.8625 (mm-30) REVERT: J 91 GLU cc_start: 0.7080 (tp30) cc_final: 0.6672 (tp30) REVERT: H 22 LYS cc_start: 0.7119 (tttt) cc_final: 0.6474 (tppt) REVERT: H 200 VAL cc_start: 0.7973 (OUTLIER) cc_final: 0.7704 (p) REVERT: H 202 VAL cc_start: 0.8395 (m) cc_final: 0.8139 (t) REVERT: H 212 ILE cc_start: 0.6727 (OUTLIER) cc_final: 0.6346 (pp) REVERT: A 22 ARG cc_start: 0.6855 (mtt90) cc_final: 0.6655 (mtt90) REVERT: A 59 HIS cc_start: 0.4164 (OUTLIER) cc_final: 0.3188 (p-80) REVERT: A 80 ILE cc_start: 0.7458 (OUTLIER) cc_final: 0.7164 (pp) REVERT: A 200 MET cc_start: 0.1494 (ppp) cc_final: 0.0955 (pmt) REVERT: A 242 LYS cc_start: 0.7838 (mttt) cc_final: 0.7207 (mppt) REVERT: A 288 GLU cc_start: 0.6768 (mm-30) cc_final: 0.6463 (mt-10) REVERT: A 361 MET cc_start: 0.5222 (OUTLIER) cc_final: 0.4834 (ttt) REVERT: A 439 PHE cc_start: 0.7811 (m-80) cc_final: 0.7526 (m-10) REVERT: A 441 VAL cc_start: 0.7901 (t) cc_final: 0.7666 (m) REVERT: A 459 GLU cc_start: 0.6856 (mm-30) cc_final: 0.6308 (tp30) REVERT: A 469 LYS cc_start: 0.7055 (mttm) cc_final: 0.6767 (mmtt) REVERT: A 538 PHE cc_start: 0.6705 (OUTLIER) cc_final: 0.6120 (m-80) REVERT: A 569 ASN cc_start: 0.6984 (m110) cc_final: 0.6756 (t160) REVERT: A 671 LYS cc_start: 0.8115 (mttm) cc_final: 0.7824 (ptpt) REVERT: A 674 MET cc_start: 0.7370 (OUTLIER) cc_final: 0.6510 (tmm) outliers start: 94 outliers final: 45 residues processed: 366 average time/residue: 0.5739 time to fit residues: 243.6776 Evaluate side-chains 350 residues out of total 2170 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 289 time to evaluate : 0.706 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 12 ILE Chi-restraints excluded: chain C residue 67 THR Chi-restraints excluded: chain C residue 103 VAL Chi-restraints excluded: chain B residue 6 THR Chi-restraints excluded: chain B residue 44 THR Chi-restraints excluded: chain B residue 68 THR Chi-restraints excluded: chain B residue 103 VAL Chi-restraints excluded: chain B residue 115 THR Chi-restraints excluded: chain F residue 26 SER Chi-restraints excluded: chain F residue 119 THR Chi-restraints excluded: chain F residue 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 102 GLU 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 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 290 GLU Chi-restraints excluded: chain A residue 59 HIS Chi-restraints excluded: chain A residue 80 ILE Chi-restraints excluded: chain A residue 157 LEU Chi-restraints excluded: chain A residue 204 LEU Chi-restraints excluded: chain A residue 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 326 VAL 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 532 ASP Chi-restraints excluded: chain A residue 538 PHE Chi-restraints excluded: chain A residue 542 ILE Chi-restraints excluded: chain A residue 563 PHE Chi-restraints excluded: chain A residue 622 MET Chi-restraints excluded: chain A residue 674 MET Chi-restraints excluded: chain A residue 687 HIS Chi-restraints excluded: chain A residue 695 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 139 optimal weight: 2.9990 chunk 146 optimal weight: 3.9990 chunk 248 optimal weight: 4.9990 chunk 177 optimal weight: 9.9990 chunk 118 optimal weight: 3.9990 chunk 75 optimal weight: 1.9990 chunk 237 optimal weight: 1.9990 chunk 111 optimal weight: 1.9990 chunk 131 optimal weight: 2.9990 chunk 13 optimal weight: 5.9990 chunk 137 optimal weight: 1.9990 overall best weight: 2.1990 ------------------------------------------------------------------------------- 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 57 ASN ** G 198 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 39 HIS H 187 ASN H 335 GLN ** A 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 159 ASN A 649 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4089 r_free = 0.4089 target = 0.175346 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3668 r_free = 0.3668 target = 0.133052 restraints weight = 26337.896| |-----------------------------------------------------------------------------| r_work (start): 0.3620 rms_B_bonded: 2.01 r_work: 0.3445 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.3332 rms_B_bonded: 4.17 restraints_weight: 0.2500 r_work (final): 0.3332 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7713 moved from start: 0.2994 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.060 21865 Z= 0.230 Angle : 0.635 11.693 29807 Z= 0.334 Chirality : 0.046 0.371 3405 Planarity : 0.004 0.054 3514 Dihedral : 15.017 168.371 3842 Min Nonbonded Distance : 2.313 Molprobity Statistics. All-atom Clashscore : 11.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Rotamer: Outliers : 4.70 % Allowed : 20.74 % Favored : 74.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.54 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.70 (0.16), residues: 2440 helix: 1.59 (0.15), residues: 1098 sheet: -0.02 (0.25), residues: 417 loop : -0.61 (0.19), residues: 925 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG A 466 TYR 0.021 0.002 TYR A 307 PHE 0.030 0.002 PHE C 119 TRP 0.007 0.001 TRP A 493 HIS 0.006 0.001 HIS F 151 Details of bonding type rmsd covalent geometry : bond 0.00524 (21865) covalent geometry : angle 0.63462 (29807) hydrogen bonds : bond 0.04778 ( 1075) hydrogen bonds : angle 4.82920 ( 3116) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4880 Ramachandran restraints generated. 2440 Oldfield, 0 Emsley, 2440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4880 Ramachandran restraints generated. 2440 Oldfield, 0 Emsley, 2440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 405 residues out of total 2170 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 102 poor density : 303 time to evaluate : 0.730 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 11 MET cc_start: 0.5492 (tpp) cc_final: 0.5246 (tmm) REVERT: E 28 ILE cc_start: 0.8089 (mt) cc_final: 0.7597 (mp) REVERT: E 88 LYS cc_start: 0.8140 (OUTLIER) cc_final: 0.7935 (tttm) REVERT: E 120 GLU cc_start: 0.8658 (OUTLIER) cc_final: 0.7870 (pm20) REVERT: E 167 GLU cc_start: 0.7895 (mm-30) cc_final: 0.7225 (tp30) REVERT: E 203 VAL cc_start: 0.7855 (t) cc_final: 0.7590 (t) REVERT: D 124 GLU cc_start: 0.8560 (OUTLIER) cc_final: 0.8228 (mt-10) REVERT: D 161 GLU cc_start: 0.6954 (OUTLIER) cc_final: 0.6710 (mp0) REVERT: G 95 LYS cc_start: 0.7274 (OUTLIER) cc_final: 0.6571 (pptt) REVERT: G 159 GLU cc_start: 0.7224 (mm-30) cc_final: 0.6949 (mm-30) REVERT: G 213 LEU cc_start: 0.7129 (tt) cc_final: 0.6658 (mt) REVERT: G 259 GLN cc_start: 0.7600 (pt0) cc_final: 0.7195 (pm20) REVERT: G 277 GLN cc_start: 0.7064 (tp40) cc_final: 0.6775 (tp-100) REVERT: I 123 PHE cc_start: 0.7831 (OUTLIER) cc_final: 0.7476 (t80) REVERT: I 161 GLU cc_start: 0.6984 (OUTLIER) cc_final: 0.6688 (mt-10) REVERT: J 10 GLU cc_start: 0.5775 (tp30) cc_final: 0.5240 (pt0) REVERT: J 59 THR cc_start: 0.8005 (OUTLIER) cc_final: 0.7636 (m) REVERT: J 61 VAL cc_start: 0.6292 (t) cc_final: 0.5984 (t) REVERT: J 78 GLU cc_start: 0.8910 (mm-30) cc_final: 0.8580 (mm-30) REVERT: J 91 GLU cc_start: 0.7172 (tp30) cc_final: 0.6761 (tp30) REVERT: H 22 LYS cc_start: 0.7143 (tttt) cc_final: 0.6512 (tppt) REVERT: H 200 VAL cc_start: 0.8017 (OUTLIER) cc_final: 0.7750 (p) REVERT: H 202 VAL cc_start: 0.8403 (m) cc_final: 0.8142 (t) REVERT: H 212 ILE cc_start: 0.6858 (OUTLIER) cc_final: 0.6499 (pp) REVERT: A 59 HIS cc_start: 0.4065 (OUTLIER) cc_final: 0.3097 (p-80) REVERT: A 80 ILE cc_start: 0.7412 (OUTLIER) cc_final: 0.7148 (pp) REVERT: A 200 MET cc_start: 0.1943 (ppp) cc_final: 0.1439 (pmt) REVERT: A 242 LYS cc_start: 0.7941 (mttt) cc_final: 0.7267 (mppt) REVERT: A 288 GLU cc_start: 0.6835 (mm-30) cc_final: 0.6492 (mt-10) REVERT: A 361 MET cc_start: 0.5152 (OUTLIER) cc_final: 0.4249 (tpt) REVERT: A 439 PHE cc_start: 0.7983 (m-80) cc_final: 0.7647 (m-10) REVERT: A 459 GLU cc_start: 0.6884 (mm-30) cc_final: 0.6275 (tp30) REVERT: A 468 ILE cc_start: 0.7217 (OUTLIER) cc_final: 0.6911 (mm) REVERT: A 469 LYS cc_start: 0.7153 (mttm) cc_final: 0.6815 (mmtt) REVERT: A 538 PHE cc_start: 0.6764 (OUTLIER) cc_final: 0.6033 (m-80) REVERT: A 569 ASN cc_start: 0.6995 (m110) cc_final: 0.6756 (t160) REVERT: A 671 LYS cc_start: 0.8093 (mttm) cc_final: 0.7666 (ttpt) REVERT: A 674 MET cc_start: 0.7490 (OUTLIER) cc_final: 0.6594 (tmm) outliers start: 102 outliers final: 55 residues processed: 369 average time/residue: 0.5647 time to fit residues: 241.4159 Evaluate side-chains 356 residues out of total 2170 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 285 time to evaluate : 0.850 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 12 ILE Chi-restraints excluded: chain C residue 67 THR Chi-restraints excluded: chain C residue 103 VAL Chi-restraints excluded: chain B residue 6 THR Chi-restraints excluded: chain B residue 44 THR Chi-restraints excluded: chain B residue 68 THR Chi-restraints excluded: chain B residue 103 VAL Chi-restraints excluded: chain B residue 115 THR Chi-restraints excluded: chain F residue 10 LYS Chi-restraints excluded: chain F residue 26 SER Chi-restraints excluded: chain F residue 119 THR Chi-restraints excluded: chain F residue 126 THR Chi-restraints excluded: chain F residue 133 VAL Chi-restraints excluded: chain E residue 31 ILE Chi-restraints excluded: chain E residue 33 SER Chi-restraints excluded: chain E residue 36 VAL 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 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 179 LEU 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 J residue 110 VAL 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 285 LEU Chi-restraints excluded: chain A residue 59 HIS Chi-restraints excluded: chain A residue 77 ILE Chi-restraints excluded: chain A residue 80 ILE Chi-restraints excluded: chain A residue 157 LEU Chi-restraints excluded: chain A residue 204 LEU Chi-restraints excluded: chain A residue 214 ILE Chi-restraints excluded: chain A residue 260 ILE Chi-restraints excluded: chain A residue 281 PHE Chi-restraints excluded: chain A residue 289 SER Chi-restraints excluded: chain A residue 315 LEU Chi-restraints excluded: chain A residue 361 MET Chi-restraints excluded: chain A residue 374 VAL Chi-restraints excluded: chain A residue 388 LEU Chi-restraints excluded: chain A residue 408 CYS Chi-restraints excluded: chain A residue 434 LEU Chi-restraints excluded: chain A residue 448 VAL Chi-restraints excluded: chain A residue 468 ILE Chi-restraints excluded: chain A residue 532 ASP Chi-restraints excluded: chain A residue 538 PHE Chi-restraints excluded: chain A residue 542 ILE Chi-restraints excluded: chain A residue 549 ILE Chi-restraints excluded: chain A residue 607 THR Chi-restraints excluded: chain A residue 634 SER Chi-restraints excluded: chain A residue 674 MET Chi-restraints excluded: chain A residue 687 HIS Chi-restraints excluded: chain A residue 695 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 93 optimal weight: 0.7980 chunk 56 optimal weight: 2.9990 chunk 130 optimal weight: 1.9990 chunk 158 optimal weight: 1.9990 chunk 189 optimal weight: 20.0000 chunk 48 optimal weight: 10.0000 chunk 243 optimal weight: 2.9990 chunk 36 optimal weight: 1.9990 chunk 141 optimal weight: 5.9990 chunk 10 optimal weight: 1.9990 chunk 170 optimal weight: 0.8980 overall best weight: 1.5386 ------------------------------------------------------------------------------- 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 516 ASN ** A 687 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4103 r_free = 0.4103 target = 0.176724 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3690 r_free = 0.3690 target = 0.134951 restraints weight = 26170.794| |-----------------------------------------------------------------------------| r_work (start): 0.3645 rms_B_bonded: 2.01 r_work: 0.3466 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.3352 rms_B_bonded: 4.22 restraints_weight: 0.2500 r_work (final): 0.3352 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7683 moved from start: 0.3083 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 21865 Z= 0.180 Angle : 0.601 11.116 29807 Z= 0.317 Chirality : 0.044 0.385 3405 Planarity : 0.004 0.058 3514 Dihedral : 14.979 166.311 3842 Min Nonbonded Distance : 2.308 Molprobity Statistics. All-atom Clashscore : 10.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer: Outliers : 3.73 % Allowed : 22.30 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.66 (0.16), residues: 2440 helix: 1.56 (0.15), residues: 1098 sheet: 0.01 (0.25), residues: 410 loop : -0.66 (0.19), residues: 932 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG A 466 TYR 0.021 0.002 TYR A 307 PHE 0.033 0.002 PHE A 250 TRP 0.008 0.001 TRP A 493 HIS 0.005 0.001 HIS B 56 Details of bonding type rmsd covalent geometry : bond 0.00404 (21865) covalent geometry : angle 0.60146 (29807) hydrogen bonds : bond 0.04500 ( 1075) hydrogen bonds : angle 4.77858 ( 3116) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4880 Ramachandran restraints generated. 2440 Oldfield, 0 Emsley, 2440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4880 Ramachandran restraints generated. 2440 Oldfield, 0 Emsley, 2440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 374 residues out of total 2170 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 293 time to evaluate : 0.918 Fit side-chains revert: symmetry clash REVERT: B 11 MET cc_start: 0.5464 (tpp) cc_final: 0.5163 (tmm) REVERT: E 28 ILE cc_start: 0.8112 (mt) cc_final: 0.7606 (mp) REVERT: E 88 LYS cc_start: 0.8109 (OUTLIER) cc_final: 0.7897 (tttm) REVERT: E 120 GLU cc_start: 0.8659 (OUTLIER) cc_final: 0.7942 (pm20) REVERT: E 167 GLU cc_start: 0.7883 (mm-30) cc_final: 0.7215 (tp30) REVERT: E 203 VAL cc_start: 0.7810 (t) cc_final: 0.7563 (t) REVERT: D 124 GLU cc_start: 0.8549 (OUTLIER) cc_final: 0.8210 (mt-10) REVERT: D 161 GLU cc_start: 0.6940 (OUTLIER) cc_final: 0.6709 (mp0) REVERT: G 95 LYS cc_start: 0.7261 (OUTLIER) cc_final: 0.6549 (pptt) REVERT: G 159 GLU cc_start: 0.7233 (mm-30) cc_final: 0.6951 (mm-30) REVERT: G 213 LEU cc_start: 0.7143 (tt) cc_final: 0.6677 (mt) REVERT: G 259 GLN cc_start: 0.7625 (pt0) cc_final: 0.7214 (pm20) REVERT: G 277 GLN cc_start: 0.7058 (tp40) cc_final: 0.6784 (tp-100) REVERT: I 123 PHE cc_start: 0.7808 (OUTLIER) cc_final: 0.7456 (t80) REVERT: I 161 GLU cc_start: 0.6994 (OUTLIER) cc_final: 0.6672 (mt-10) REVERT: J 59 THR cc_start: 0.7977 (OUTLIER) cc_final: 0.7625 (m) REVERT: J 61 VAL cc_start: 0.6268 (t) cc_final: 0.5947 (t) REVERT: J 78 GLU cc_start: 0.8908 (mm-30) cc_final: 0.8583 (mm-30) REVERT: H 22 LYS cc_start: 0.7168 (tttt) cc_final: 0.6517 (tppt) REVERT: H 200 VAL cc_start: 0.7979 (OUTLIER) cc_final: 0.7747 (p) REVERT: H 202 VAL cc_start: 0.8416 (m) cc_final: 0.8143 (t) REVERT: H 212 ILE cc_start: 0.6840 (OUTLIER) cc_final: 0.6504 (pp) REVERT: H 225 GLN cc_start: 0.6853 (OUTLIER) cc_final: 0.6489 (tt0) REVERT: H 248 LYS cc_start: 0.6649 (mmmt) cc_final: 0.5803 (mmpt) REVERT: A 22 ARG cc_start: 0.6723 (mtt90) cc_final: 0.6489 (mtt90) REVERT: A 59 HIS cc_start: 0.3941 (OUTLIER) cc_final: 0.2972 (p-80) REVERT: A 80 ILE cc_start: 0.7402 (OUTLIER) cc_final: 0.7136 (pp) REVERT: A 200 MET cc_start: 0.2521 (ppp) cc_final: 0.2050 (pmt) REVERT: A 242 LYS cc_start: 0.7978 (mttt) cc_final: 0.7305 (mppt) REVERT: A 281 PHE cc_start: 0.7332 (OUTLIER) cc_final: 0.6569 (p90) REVERT: A 288 GLU cc_start: 0.6906 (mm-30) cc_final: 0.6585 (mt-10) REVERT: A 361 MET cc_start: 0.5210 (OUTLIER) cc_final: 0.4311 (tpt) REVERT: A 377 LYS cc_start: 0.7687 (ttmt) cc_final: 0.7312 (tmtt) REVERT: A 439 PHE cc_start: 0.7959 (m-80) cc_final: 0.7660 (m-10) REVERT: A 459 GLU cc_start: 0.6872 (mm-30) cc_final: 0.6268 (tp30) REVERT: A 468 ILE cc_start: 0.7208 (OUTLIER) cc_final: 0.6930 (mm) REVERT: A 469 LYS cc_start: 0.7078 (mttm) cc_final: 0.6758 (mmtt) REVERT: A 538 PHE cc_start: 0.6641 (OUTLIER) cc_final: 0.5881 (m-80) REVERT: A 671 LYS cc_start: 0.8070 (mttm) cc_final: 0.7657 (ttpt) REVERT: A 674 MET cc_start: 0.7490 (OUTLIER) cc_final: 0.6554 (tmm) outliers start: 81 outliers final: 54 residues processed: 344 average time/residue: 0.5700 time to fit residues: 227.7526 Evaluate side-chains 348 residues out of total 2170 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 276 time to evaluate : 1.082 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 12 ILE Chi-restraints excluded: chain C residue 67 THR Chi-restraints excluded: chain C residue 73 VAL Chi-restraints excluded: chain C residue 103 VAL Chi-restraints excluded: chain B residue 6 THR Chi-restraints excluded: chain B residue 44 THR Chi-restraints excluded: chain B residue 67 THR Chi-restraints excluded: chain B residue 68 THR Chi-restraints excluded: chain B residue 103 VAL Chi-restraints excluded: chain B residue 115 THR Chi-restraints excluded: chain F residue 10 LYS Chi-restraints excluded: chain F residue 26 SER Chi-restraints excluded: chain F residue 119 THR Chi-restraints excluded: chain F residue 126 THR Chi-restraints excluded: chain F residue 133 VAL Chi-restraints excluded: chain E residue 33 SER Chi-restraints excluded: chain E residue 36 VAL 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 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 179 LEU Chi-restraints excluded: chain G residue 212 LEU Chi-restraints excluded: chain I residue 38 ASP Chi-restraints excluded: chain I residue 78 GLU Chi-restraints excluded: chain I residue 123 PHE Chi-restraints excluded: chain I residue 161 GLU Chi-restraints excluded: chain J residue 14 LEU Chi-restraints excluded: chain J residue 52 GLU Chi-restraints excluded: chain J residue 59 THR Chi-restraints excluded: chain J residue 98 ILE Chi-restraints excluded: chain J residue 110 VAL 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 285 LEU Chi-restraints excluded: chain H residue 327 ASN Chi-restraints excluded: chain A residue 59 HIS Chi-restraints excluded: chain A residue 77 ILE Chi-restraints excluded: chain A residue 80 ILE Chi-restraints excluded: chain A residue 157 LEU Chi-restraints excluded: chain A residue 204 LEU Chi-restraints excluded: chain A residue 214 ILE Chi-restraints excluded: chain A residue 225 MET Chi-restraints excluded: chain A residue 260 ILE Chi-restraints excluded: chain A residue 281 PHE Chi-restraints excluded: chain A residue 289 SER Chi-restraints excluded: chain A residue 315 LEU Chi-restraints excluded: chain A residue 361 MET Chi-restraints excluded: chain A residue 374 VAL Chi-restraints excluded: chain A residue 388 LEU Chi-restraints excluded: chain A residue 408 CYS Chi-restraints excluded: chain A residue 434 LEU Chi-restraints excluded: chain A residue 448 VAL Chi-restraints excluded: chain A residue 468 ILE Chi-restraints excluded: chain A residue 532 ASP Chi-restraints excluded: chain A residue 538 PHE Chi-restraints excluded: chain A residue 549 ILE Chi-restraints excluded: chain A residue 607 THR Chi-restraints excluded: chain A residue 674 MET Chi-restraints excluded: chain A residue 687 HIS Chi-restraints excluded: chain A residue 695 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 141 optimal weight: 0.9980 chunk 218 optimal weight: 3.9990 chunk 31 optimal weight: 1.9990 chunk 7 optimal weight: 0.9990 chunk 1 optimal weight: 0.0010 chunk 235 optimal weight: 0.9990 chunk 54 optimal weight: 4.9990 chunk 198 optimal weight: 7.9990 chunk 139 optimal weight: 0.6980 chunk 89 optimal weight: 2.9990 chunk 145 optimal weight: 20.0000 overall best weight: 0.7390 ------------------------------------------------------------------------------- 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 516 ASN A 569 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 = 0.4141 r_free = 0.4141 target = 0.180536 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3740 r_free = 0.3740 target = 0.139186 restraints weight = 26239.281| |-----------------------------------------------------------------------------| r_work (start): 0.3692 rms_B_bonded: 2.02 r_work: 0.3525 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.3410 rms_B_bonded: 4.27 restraints_weight: 0.2500 r_work (final): 0.3410 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7616 moved from start: 0.3233 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 21865 Z= 0.128 Angle : 0.561 11.466 29807 Z= 0.296 Chirality : 0.042 0.395 3405 Planarity : 0.004 0.058 3514 Dihedral : 14.914 163.282 3842 Min Nonbonded Distance : 2.280 Molprobity Statistics. All-atom Clashscore : 10.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer: Outliers : 3.55 % Allowed : 22.63 % Favored : 73.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.54 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.81 (0.16), residues: 2440 helix: 1.70 (0.15), residues: 1099 sheet: 0.01 (0.25), residues: 410 loop : -0.57 (0.19), residues: 931 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG A 466 TYR 0.040 0.001 TYR A 219 PHE 0.031 0.002 PHE B 16 TRP 0.008 0.001 TRP A 493 HIS 0.006 0.001 HIS B 56 Details of bonding type rmsd covalent geometry : bond 0.00274 (21865) covalent geometry : angle 0.56089 (29807) hydrogen bonds : bond 0.04114 ( 1075) hydrogen bonds : angle 4.63709 ( 3116) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4880 Ramachandran restraints generated. 2440 Oldfield, 0 Emsley, 2440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4880 Ramachandran restraints generated. 2440 Oldfield, 0 Emsley, 2440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 366 residues out of total 2170 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 289 time to evaluate : 0.844 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 11 MET cc_start: 0.5455 (tpp) cc_final: 0.5175 (tmm) REVERT: F 27 MET cc_start: 0.7639 (mtp) cc_final: 0.7435 (mtp) REVERT: F 133 VAL cc_start: 0.8575 (OUTLIER) cc_final: 0.8358 (t) REVERT: E 28 ILE cc_start: 0.8122 (mt) cc_final: 0.7595 (mp) REVERT: E 42 ARG cc_start: 0.8089 (OUTLIER) cc_final: 0.7033 (mtm180) REVERT: E 88 LYS cc_start: 0.8060 (OUTLIER) cc_final: 0.7832 (tttm) REVERT: E 120 GLU cc_start: 0.8656 (OUTLIER) cc_final: 0.8017 (pm20) REVERT: E 144 ARG cc_start: 0.7611 (ttp80) cc_final: 0.7314 (mtm180) REVERT: E 167 GLU cc_start: 0.7884 (mm-30) cc_final: 0.7181 (tp30) REVERT: E 203 VAL cc_start: 0.7785 (t) cc_final: 0.7537 (t) REVERT: D 124 GLU cc_start: 0.8505 (OUTLIER) cc_final: 0.8131 (mt-10) REVERT: G 95 LYS cc_start: 0.7282 (OUTLIER) cc_final: 0.6591 (pptt) REVERT: G 159 GLU cc_start: 0.7179 (mm-30) cc_final: 0.6847 (mm-30) REVERT: G 213 LEU cc_start: 0.7001 (tt) cc_final: 0.6586 (mt) REVERT: G 259 GLN cc_start: 0.7589 (pt0) cc_final: 0.7202 (pm20) REVERT: G 277 GLN cc_start: 0.7046 (tp40) cc_final: 0.6805 (tp-100) REVERT: I 123 PHE cc_start: 0.7755 (OUTLIER) cc_final: 0.7368 (t80) REVERT: I 161 GLU cc_start: 0.6962 (OUTLIER) cc_final: 0.6616 (mt-10) REVERT: J 11 MET cc_start: 0.6593 (ppp) cc_final: 0.6198 (pmm) REVERT: J 59 THR cc_start: 0.7877 (OUTLIER) cc_final: 0.7542 (m) REVERT: J 61 VAL cc_start: 0.6233 (t) cc_final: 0.5912 (t) REVERT: J 78 GLU cc_start: 0.8890 (mm-30) cc_final: 0.8584 (mm-30) REVERT: H 22 LYS cc_start: 0.7166 (tttt) cc_final: 0.6531 (tppt) REVERT: H 200 VAL cc_start: 0.7952 (OUTLIER) cc_final: 0.7720 (p) REVERT: H 202 VAL cc_start: 0.8384 (m) cc_final: 0.8106 (t) REVERT: H 212 ILE cc_start: 0.6812 (OUTLIER) cc_final: 0.6478 (pp) REVERT: H 248 LYS cc_start: 0.6623 (mmmt) cc_final: 0.5805 (mmpt) REVERT: A 59 HIS cc_start: 0.3903 (OUTLIER) cc_final: 0.3122 (p-80) REVERT: A 80 ILE cc_start: 0.7408 (OUTLIER) cc_final: 0.7179 (pp) REVERT: A 200 MET cc_start: 0.2605 (ppp) cc_final: 0.2215 (pmt) REVERT: A 242 LYS cc_start: 0.7982 (mttt) cc_final: 0.7305 (mppt) REVERT: A 249 VAL cc_start: 0.7131 (t) cc_final: 0.6925 (t) REVERT: A 288 GLU cc_start: 0.6870 (mm-30) cc_final: 0.6578 (mt-10) REVERT: A 361 MET cc_start: 0.5177 (OUTLIER) cc_final: 0.4227 (tpt) REVERT: A 377 LYS cc_start: 0.7690 (ttmt) cc_final: 0.7319 (tmtt) REVERT: A 439 PHE cc_start: 0.7866 (m-80) cc_final: 0.7592 (m-10) REVERT: A 441 VAL cc_start: 0.7926 (t) cc_final: 0.7684 (m) REVERT: A 459 GLU cc_start: 0.6888 (mm-30) cc_final: 0.6319 (tp30) REVERT: A 469 LYS cc_start: 0.7008 (mttm) cc_final: 0.6675 (mmtt) REVERT: A 538 PHE cc_start: 0.6617 (OUTLIER) cc_final: 0.5778 (m-80) REVERT: A 563 PHE cc_start: 0.5389 (OUTLIER) cc_final: 0.5106 (t80) REVERT: A 671 LYS cc_start: 0.8063 (mttm) cc_final: 0.7674 (ttpt) REVERT: A 674 MET cc_start: 0.7455 (OUTLIER) cc_final: 0.6585 (tmm) outliers start: 77 outliers final: 44 residues processed: 342 average time/residue: 0.5785 time to fit residues: 229.4459 Evaluate side-chains 335 residues out of total 2170 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 274 time to evaluate : 0.950 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 12 ILE Chi-restraints excluded: chain C residue 67 THR Chi-restraints excluded: chain C residue 103 VAL Chi-restraints excluded: chain B residue 6 THR Chi-restraints excluded: chain B residue 44 THR Chi-restraints excluded: chain B residue 68 THR Chi-restraints excluded: chain B residue 103 VAL Chi-restraints excluded: chain B residue 104 ASP Chi-restraints excluded: chain B residue 115 THR Chi-restraints excluded: chain F residue 79 ILE Chi-restraints excluded: chain F residue 119 THR Chi-restraints excluded: chain F residue 126 THR Chi-restraints excluded: chain F residue 133 VAL Chi-restraints excluded: chain E residue 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 120 GLU Chi-restraints excluded: chain E residue 143 THR Chi-restraints excluded: chain E residue 202 VAL Chi-restraints excluded: chain D residue 79 ILE Chi-restraints excluded: chain D residue 124 GLU Chi-restraints excluded: chain G residue 95 LYS Chi-restraints excluded: chain G residue 102 GLU Chi-restraints excluded: chain G residue 113 ASP Chi-restraints excluded: chain G residue 179 LEU Chi-restraints excluded: chain I residue 38 ASP Chi-restraints excluded: chain I residue 78 GLU Chi-restraints excluded: chain I residue 123 PHE Chi-restraints excluded: chain I residue 161 GLU Chi-restraints excluded: chain J residue 14 LEU Chi-restraints excluded: chain J residue 52 GLU Chi-restraints excluded: chain J residue 59 THR Chi-restraints excluded: chain J residue 98 ILE Chi-restraints excluded: chain H residue 41 VAL Chi-restraints excluded: chain H residue 200 VAL Chi-restraints excluded: chain H residue 209 THR Chi-restraints excluded: chain H residue 212 ILE Chi-restraints excluded: chain H residue 327 ASN Chi-restraints excluded: chain A residue 59 HIS Chi-restraints excluded: chain A residue 80 ILE Chi-restraints excluded: chain A residue 157 LEU Chi-restraints excluded: chain A residue 204 LEU Chi-restraints excluded: chain A residue 214 ILE Chi-restraints excluded: chain A residue 260 ILE Chi-restraints excluded: chain A residue 281 PHE Chi-restraints excluded: chain A residue 289 SER Chi-restraints excluded: chain A residue 315 LEU Chi-restraints excluded: chain A residue 361 MET Chi-restraints excluded: chain A residue 374 VAL Chi-restraints excluded: chain A residue 408 CYS Chi-restraints excluded: chain A residue 434 LEU Chi-restraints excluded: chain A residue 448 VAL Chi-restraints excluded: chain A residue 532 ASP 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 674 MET Chi-restraints excluded: chain A residue 687 HIS Chi-restraints excluded: chain A residue 695 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 232 optimal weight: 5.9990 chunk 62 optimal weight: 0.8980 chunk 138 optimal weight: 0.8980 chunk 14 optimal weight: 0.8980 chunk 177 optimal weight: 4.9990 chunk 22 optimal weight: 0.7980 chunk 77 optimal weight: 1.9990 chunk 135 optimal weight: 0.9990 chunk 53 optimal weight: 2.9990 chunk 194 optimal weight: 9.9990 chunk 100 optimal weight: 4.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4137 r_free = 0.4137 target = 0.180179 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3733 r_free = 0.3733 target = 0.138514 restraints weight = 26360.453| |-----------------------------------------------------------------------------| r_work (start): 0.3678 rms_B_bonded: 2.04 r_work: 0.3512 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.3396 rms_B_bonded: 4.27 restraints_weight: 0.2500 r_work (final): 0.3396 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7625 moved from start: 0.3294 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 21865 Z= 0.138 Angle : 0.566 10.361 29807 Z= 0.299 Chirality : 0.042 0.388 3405 Planarity : 0.004 0.066 3514 Dihedral : 14.895 164.359 3842 Min Nonbonded Distance : 2.237 Molprobity Statistics. All-atom Clashscore : 10.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer: Outliers : 3.09 % Allowed : 23.41 % Favored : 73.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.54 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.80 (0.16), residues: 2440 helix: 1.71 (0.15), residues: 1098 sheet: -0.00 (0.25), residues: 408 loop : -0.60 (0.19), residues: 934 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG G 79 TYR 0.024 0.001 TYR A 21 PHE 0.028 0.002 PHE A 40 TRP 0.010 0.001 TRP A 493 HIS 0.004 0.001 HIS B 56 Details of bonding type rmsd covalent geometry : bond 0.00301 (21865) covalent geometry : angle 0.56627 (29807) hydrogen bonds : bond 0.04137 ( 1075) hydrogen bonds : angle 4.64124 ( 3116) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4880 Ramachandran restraints generated. 2440 Oldfield, 0 Emsley, 2440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4880 Ramachandran restraints generated. 2440 Oldfield, 0 Emsley, 2440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 343 residues out of total 2170 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 276 time to evaluate : 0.880 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 11 MET cc_start: 0.5513 (tpp) cc_final: 0.5216 (tmm) REVERT: B 74 ARG cc_start: 0.7560 (mtp85) cc_final: 0.7249 (mtp-110) REVERT: F 27 MET cc_start: 0.7661 (mtp) cc_final: 0.7406 (mtp) REVERT: F 133 VAL cc_start: 0.8585 (OUTLIER) cc_final: 0.8365 (t) REVERT: E 28 ILE cc_start: 0.8150 (mt) cc_final: 0.7631 (mp) REVERT: E 42 ARG cc_start: 0.8102 (OUTLIER) cc_final: 0.7055 (mtm180) REVERT: E 88 LYS cc_start: 0.8067 (OUTLIER) cc_final: 0.7841 (tttm) REVERT: E 120 GLU cc_start: 0.8673 (OUTLIER) cc_final: 0.8055 (pm20) REVERT: E 144 ARG cc_start: 0.7628 (ttp80) cc_final: 0.7354 (mtm180) REVERT: E 167 GLU cc_start: 0.7877 (mm-30) cc_final: 0.7200 (tp30) REVERT: E 203 VAL cc_start: 0.7791 (t) cc_final: 0.7548 (t) REVERT: D 124 GLU cc_start: 0.8509 (OUTLIER) cc_final: 0.8132 (mt-10) REVERT: G 95 LYS cc_start: 0.7292 (OUTLIER) cc_final: 0.6607 (pptt) REVERT: G 159 GLU cc_start: 0.7133 (mm-30) cc_final: 0.6759 (mm-30) REVERT: G 213 LEU cc_start: 0.6963 (tt) cc_final: 0.6557 (mt) REVERT: G 259 GLN cc_start: 0.7608 (pt0) cc_final: 0.7207 (pm20) REVERT: I 123 PHE cc_start: 0.7761 (OUTLIER) cc_final: 0.7373 (t80) REVERT: I 161 GLU cc_start: 0.6921 (OUTLIER) cc_final: 0.6568 (mt-10) REVERT: J 11 MET cc_start: 0.6491 (ppp) cc_final: 0.6089 (pmm) REVERT: J 59 THR cc_start: 0.7885 (OUTLIER) cc_final: 0.7550 (m) REVERT: J 61 VAL cc_start: 0.6193 (t) cc_final: 0.5884 (t) REVERT: J 78 GLU cc_start: 0.8891 (mm-30) cc_final: 0.8581 (mm-30) REVERT: H 22 LYS cc_start: 0.7157 (tttt) cc_final: 0.6526 (tppt) REVERT: H 200 VAL cc_start: 0.7969 (OUTLIER) cc_final: 0.7730 (p) REVERT: H 202 VAL cc_start: 0.8389 (m) cc_final: 0.8119 (t) REVERT: H 225 GLN cc_start: 0.6864 (OUTLIER) cc_final: 0.6516 (tt0) REVERT: H 248 LYS cc_start: 0.6614 (mmmt) cc_final: 0.5789 (mmpt) REVERT: A 59 HIS cc_start: 0.3964 (OUTLIER) cc_final: 0.3169 (p-80) REVERT: A 80 ILE cc_start: 0.7394 (OUTLIER) cc_final: 0.7135 (pp) REVERT: A 200 MET cc_start: 0.2649 (ppp) cc_final: 0.2291 (pmt) REVERT: A 242 LYS cc_start: 0.8000 (mttt) cc_final: 0.7310 (mppt) REVERT: A 288 GLU cc_start: 0.6910 (mm-30) cc_final: 0.6617 (mt-10) REVERT: A 361 MET cc_start: 0.5248 (OUTLIER) cc_final: 0.4283 (tpt) REVERT: A 377 LYS cc_start: 0.7677 (ttmt) cc_final: 0.7282 (tmtt) REVERT: A 439 PHE cc_start: 0.7833 (m-80) cc_final: 0.7584 (m-10) REVERT: A 441 VAL cc_start: 0.7937 (t) cc_final: 0.7705 (m) REVERT: A 459 GLU cc_start: 0.6942 (mm-30) cc_final: 0.6345 (tp30) REVERT: A 469 LYS cc_start: 0.7014 (mttm) cc_final: 0.6673 (mmtt) REVERT: A 538 PHE cc_start: 0.6621 (OUTLIER) cc_final: 0.5819 (m-80) REVERT: A 563 PHE cc_start: 0.5412 (OUTLIER) cc_final: 0.4951 (t80) REVERT: A 671 LYS cc_start: 0.8047 (mttm) cc_final: 0.7670 (ttpt) REVERT: A 674 MET cc_start: 0.7458 (OUTLIER) cc_final: 0.6576 (tmm) outliers start: 67 outliers final: 48 residues processed: 322 average time/residue: 0.5873 time to fit residues: 219.7709 Evaluate side-chains 330 residues out of total 2170 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 265 time to evaluate : 0.836 ------------------------------------------------------------------------------- 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 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 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 120 GLU Chi-restraints excluded: chain E residue 143 THR Chi-restraints excluded: chain E residue 202 VAL Chi-restraints excluded: chain D residue 79 ILE Chi-restraints excluded: chain D residue 124 GLU Chi-restraints excluded: chain G residue 95 LYS Chi-restraints excluded: chain G residue 102 GLU Chi-restraints excluded: chain G residue 113 ASP Chi-restraints excluded: chain G residue 179 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 41 VAL Chi-restraints excluded: chain H residue 125 ASP Chi-restraints excluded: chain H residue 200 VAL Chi-restraints excluded: chain H residue 209 THR Chi-restraints excluded: chain H residue 212 ILE Chi-restraints excluded: chain H residue 225 GLN Chi-restraints excluded: chain H residue 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 157 LEU Chi-restraints excluded: chain A residue 204 LEU Chi-restraints excluded: chain A residue 214 ILE Chi-restraints excluded: chain A residue 260 ILE Chi-restraints excluded: chain A residue 281 PHE Chi-restraints excluded: chain A residue 289 SER Chi-restraints excluded: chain A residue 315 LEU Chi-restraints excluded: chain A residue 361 MET Chi-restraints excluded: chain A residue 374 VAL Chi-restraints excluded: chain A residue 388 LEU Chi-restraints excluded: chain A residue 408 CYS Chi-restraints excluded: chain A residue 434 LEU Chi-restraints excluded: chain A residue 448 VAL Chi-restraints excluded: chain A residue 502 LEU Chi-restraints excluded: chain A residue 532 ASP 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 634 SER Chi-restraints excluded: chain A residue 674 MET Chi-restraints excluded: chain A residue 687 HIS Chi-restraints excluded: chain A residue 695 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 190 optimal weight: 4.9990 chunk 59 optimal weight: 4.9990 chunk 116 optimal weight: 5.9990 chunk 236 optimal weight: 0.9980 chunk 177 optimal weight: 10.0000 chunk 217 optimal weight: 6.9990 chunk 28 optimal weight: 0.6980 chunk 176 optimal weight: 6.9990 chunk 141 optimal weight: 5.9990 chunk 203 optimal weight: 0.9990 chunk 99 optimal weight: 0.4980 overall best weight: 1.6384 ------------------------------------------------------------------------------- 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 ** G 198 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 187 ASN ** A 14 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 = 0.4106 r_free = 0.4106 target = 0.177026 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3742 r_free = 0.3742 target = 0.139271 restraints weight = 26293.175| |-----------------------------------------------------------------------------| r_work (start): 0.3697 rms_B_bonded: 2.96 r_work: 0.3422 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work (final): 0.3422 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7641 moved from start: 0.3312 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 21865 Z= 0.189 Angle : 0.614 10.059 29807 Z= 0.324 Chirality : 0.044 0.380 3405 Planarity : 0.004 0.064 3514 Dihedral : 14.938 166.777 3842 Min Nonbonded Distance : 2.222 Molprobity Statistics. All-atom Clashscore : 10.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer: Outliers : 3.64 % Allowed : 23.18 % Favored : 73.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.54 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.64 (0.16), residues: 2440 helix: 1.56 (0.15), residues: 1098 sheet: -0.06 (0.24), residues: 417 loop : -0.67 (0.19), residues: 925 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG G 79 TYR 0.049 0.002 TYR A 219 PHE 0.061 0.002 PHE B 119 TRP 0.012 0.001 TRP A 493 HIS 0.006 0.001 HIS B 56 Details of bonding type rmsd covalent geometry : bond 0.00425 (21865) covalent geometry : angle 0.61385 (29807) hydrogen bonds : bond 0.04479 ( 1075) hydrogen bonds : angle 4.76684 ( 3116) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9218.00 seconds wall clock time: 158 minutes 1.68 seconds (9481.68 seconds total)