Starting phenix.real_space_refine on Sun Aug 9 21:58:47 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9cqc_45813/08_2026/9cqc_45813.cif Found real_map, /net/cci-nas-00/data/ceres_data/9cqc_45813/08_2026/9cqc_45813.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9cqc_45813/08_2026/9cqc_45813.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9cqc_45813/08_2026/9cqc_45813.map" model { file = "/net/cci-nas-00/data/ceres_data/9cqc_45813/08_2026/9cqc_45813.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9cqc_45813/08_2026/9cqc_45813.cif" } resolution = 3.4 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= 0.004 sd= 1.326 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 149 5.49 5 S 200 5.16 5 C 24475 2.51 5 N 6661 2.21 5 O 7664 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 23 residue(s): 0.04s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 39149 Number of models: 1 Model: "" Number of chains: 19 Chain: "A" Number of atoms: 4094 Number of conformers: 1 Conformer: "" Number of residues, atoms: 507, 4094 Classifications: {'peptide': 507} Link IDs: {'PTRANS': 28, 'TRANS': 478} Chain: "B" Number of atoms: 4223 Number of conformers: 1 Conformer: "" Number of residues, atoms: 528, 4223 Classifications: {'peptide': 528} Link IDs: {'PTRANS': 26, 'TRANS': 501} Chain breaks: 1 Chain: "C" Number of atoms: 1813 Number of conformers: 1 Conformer: "" Number of residues, atoms: 228, 1813 Classifications: {'peptide': 228} Link IDs: {'PTRANS': 11, 'TRANS': 216} Chain: "D" Number of atoms: 1628 Number of conformers: 1 Conformer: "" Number of residues, atoms: 201, 1628 Classifications: {'peptide': 201} Link IDs: {'PTRANS': 3, 'TRANS': 197} Chain: "E" Number of atoms: 1628 Number of conformers: 1 Conformer: "" Number of residues, atoms: 201, 1628 Classifications: {'peptide': 201} Link IDs: {'PTRANS': 3, 'TRANS': 197} Chain: "F" Number of atoms: 2069 Number of conformers: 1 Conformer: "" Number of residues, atoms: 255, 2069 Classifications: {'peptide': 255} Link IDs: {'PTRANS': 10, 'TRANS': 244} Chain: "G" Number of atoms: 165 Number of conformers: 1 Conformer: "" Number of residues, atoms: 23, 165 Classifications: {'peptide': 23} Link IDs: {'PTRANS': 3, 'TRANS': 19} Chain: "H" Number of atoms: 174 Number of conformers: 1 Conformer: "" Number of residues, atoms: 24, 174 Classifications: {'peptide': 24} Link IDs: {'PTRANS': 3, 'TRANS': 20} Chain: "I" Number of atoms: 771 Number of conformers: 1 Conformer: "" Number of residues, atoms: 38, 771 Classifications: {'DNA': 38} Link IDs: {'rna3p': 37} Chain: "J" Number of atoms: 818 Number of conformers: 1 Conformer: "" Number of residues, atoms: 40, 818 Classifications: {'DNA': 40} Link IDs: {'rna3p': 39} Chain: "K" Number of atoms: 702 Number of conformers: 1 Conformer: "" Number of residues, atoms: 34, 702 Classifications: {'DNA': 34} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 33} Chain: "L" Number of atoms: 720 Number of conformers: 1 Conformer: "" Number of residues, atoms: 35, 720 Classifications: {'DNA': 35} Modifications used: {'p5*END': 1} Link IDs: {'rna3p': 34} Chain: "a" Number of atoms: 4171 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 514, 4160 Classifications: {'peptide': 514} Link IDs: {'PTRANS': 28, 'TRANS': 485} Chain breaks: 1 Conformer: "B" Number of residues, atoms: 514, 4160 Classifications: {'peptide': 514} Link IDs: {'PTRANS': 28, 'TRANS': 485} Chain breaks: 1 bond proxies already assigned to first conformer: 4232 Chain: "b" Number of atoms: 4211 Number of conformers: 1 Conformer: "" Number of residues, atoms: 526, 4211 Classifications: {'peptide': 526} Link IDs: {'PTRANS': 26, 'TRANS': 499} Chain breaks: 1 Chain: "c" Number of atoms: 1831 Number of conformers: 1 Conformer: "" Number of residues, atoms: 231, 1831 Classifications: {'peptide': 231} Link IDs: {'PTRANS': 11, 'TRANS': 219} Chain: "d" Number of atoms: 1628 Number of conformers: 1 Conformer: "" Number of residues, atoms: 201, 1628 Classifications: {'peptide': 201} Link IDs: {'PTRANS': 3, 'TRANS': 197} Chain: "e" Number of atoms: 1628 Number of conformers: 1 Conformer: "" Number of residues, atoms: 201, 1628 Classifications: {'peptide': 201} Link IDs: {'PTRANS': 3, 'TRANS': 197} Chain: "f" Number of atoms: 6845 Number of conformers: 1 Conformer: "" Number of residues, atoms: 852, 6845 Classifications: {'peptide': 852} Link IDs: {'PTRANS': 37, 'TRANS': 814} Chain breaks: 2 Chain: "I" Number of atoms: 30 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 30 Unusual residues: {'DZ4': 1} Classifications: {'undetermined': 1} Residues with excluded nonbonded symmetry interactions: 1 residue: pdb=" N AARG a 444 " occ=0.49 ... (20 atoms not shown) pdb=" NH2BARG a 444 " occ=0.51 Time building chain proxies: 8.47, per 1000 atoms: 0.22 Number of scatterers: 39149 At special positions: 0 Unit cell: (202.419, 243.236, 179.928, 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 200 16.00 P 149 15.00 O 7664 8.00 N 6661 7.00 C 24475 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: 3.30 Conformation dependent library (CDL) restraints added in 1.8 seconds 8914 Ramachandran restraints generated. 4457 Oldfield, 0 Emsley, 4457 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8568 Finding SS restraints... Secondary structure from input PDB file: 152 helices and 43 sheets defined 44.4% alpha, 19.4% beta 73 base pairs and 125 stacking pairs defined. Time for finding SS restraints: 4.70 Creating SS restraints... Processing helix chain 'A' and resid 45 through 49 Processing helix chain 'A' and resid 58 through 78 removed outlier: 3.520A pdb=" N ILE A 76 " --> pdb=" O ILE A 72 " (cutoff:3.500A) Processing helix chain 'A' and resid 112 through 121 Processing helix chain 'A' and resid 124 through 136 Processing helix chain 'A' and resid 142 through 157 removed outlier: 3.633A pdb=" N VAL A 157 " --> pdb=" O LEU A 153 " (cutoff:3.500A) Processing helix chain 'A' and resid 179 through 197 removed outlier: 3.650A pdb=" N ALA A 183 " --> pdb=" O ASP A 179 " (cutoff:3.500A) Processing helix chain 'A' and resid 216 through 220 removed outlier: 4.201A pdb=" N ASP A 219 " --> pdb=" O PHE A 216 " (cutoff:3.500A) Processing helix chain 'A' and resid 226 through 229 removed outlier: 3.583A pdb=" N LEU A 229 " --> pdb=" O ASP A 226 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 226 through 229' Processing helix chain 'A' and resid 237 through 244 removed outlier: 3.823A pdb=" N ASP A 241 " --> pdb=" O SER A 237 " (cutoff:3.500A) Processing helix chain 'A' and resid 330 through 338 removed outlier: 3.895A pdb=" N LYS A 338 " --> pdb=" O THR A 334 " (cutoff:3.500A) Processing helix chain 'A' and resid 354 through 356 No H-bonds generated for 'chain 'A' and resid 354 through 356' Processing helix chain 'A' and resid 377 through 393 removed outlier: 3.583A pdb=" N LEU A 381 " --> pdb=" O GLY A 377 " (cutoff:3.500A) Processing helix chain 'A' and resid 455 through 469 Processing helix chain 'A' and resid 480 through 496 Processing helix chain 'A' and resid 510 through 519 removed outlier: 3.709A pdb=" N MET A 514 " --> pdb=" O LYS A 510 " (cutoff:3.500A) Processing helix chain 'A' and resid 520 through 530 Processing helix chain 'B' and resid 17 through 22 removed outlier: 3.834A pdb=" N SER B 21 " --> pdb=" O GLY B 17 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N ASN B 22 " --> pdb=" O PHE B 18 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 17 through 22' Processing helix chain 'B' and resid 29 through 48 Processing helix chain 'B' and resid 66 through 70 removed outlier: 4.211A pdb=" N GLY B 70 " --> pdb=" O PRO B 67 " (cutoff:3.500A) Processing helix chain 'B' and resid 87 through 96 removed outlier: 3.512A pdb=" N LEU B 91 " --> pdb=" O ASP B 87 " (cutoff:3.500A) Processing helix chain 'B' and resid 106 through 123 removed outlier: 3.611A pdb=" N ALA B 110 " --> pdb=" O ASP B 106 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N ILE B 123 " --> pdb=" O GLN B 119 " (cutoff:3.500A) Processing helix chain 'B' and resid 143 through 145 No H-bonds generated for 'chain 'B' and resid 143 through 145' Processing helix chain 'B' and resid 146 through 158 Processing helix chain 'B' and resid 198 through 216 Processing helix chain 'B' and resid 218 through 222 Processing helix chain 'B' and resid 227 through 231 Processing helix chain 'B' and resid 232 through 233 No H-bonds generated for 'chain 'B' and resid 232 through 233' Processing helix chain 'B' and resid 234 through 238 removed outlier: 3.533A pdb=" N PHE B 237 " --> pdb=" O LEU B 234 " (cutoff:3.500A) Processing helix chain 'B' and resid 324 through 332 Processing helix chain 'B' and resid 352 through 356 Processing helix chain 'B' and resid 370 through 388 Processing helix chain 'B' and resid 447 through 461 Processing helix chain 'B' and resid 478 through 482 Processing helix chain 'B' and resid 484 through 500 removed outlier: 3.928A pdb=" N GLN B 488 " --> pdb=" O ASN B 484 " (cutoff:3.500A) Processing helix chain 'B' and resid 509 through 516 Processing helix chain 'B' and resid 519 through 525 removed outlier: 3.519A pdb=" N THR B 523 " --> pdb=" O PRO B 519 " (cutoff:3.500A) Processing helix chain 'B' and resid 526 through 537 Processing helix chain 'C' and resid 1 through 10 Processing helix chain 'C' and resid 51 through 62 Processing helix chain 'C' and resid 68 through 86 Proline residue: C 82 - end of helix Processing helix chain 'C' and resid 127 through 170 removed outlier: 4.980A pdb=" N ARG C 137 " --> pdb=" O GLN C 133 " (cutoff:3.500A) Proline residue: C 138 - end of helix Processing helix chain 'C' and resid 176 through 180 removed outlier: 3.873A pdb=" N LEU C 179 " --> pdb=" O ARG C 176 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N LYS C 180 " --> pdb=" O ASP C 177 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 176 through 180' Processing helix chain 'C' and resid 185 through 197 Processing helix chain 'C' and resid 197 through 202 Processing helix chain 'C' and resid 207 through 214 Processing helix chain 'C' and resid 214 through 227 Processing helix chain 'D' and resid 27 through 31 removed outlier: 3.536A pdb=" N SER D 30 " --> pdb=" O THR D 27 " (cutoff:3.500A) Processing helix chain 'D' and resid 48 through 60 Processing helix chain 'D' and resid 62 through 75 Processing helix chain 'D' and resid 118 through 201 removed outlier: 4.542A pdb=" N VAL D 122 " --> pdb=" O ASN D 118 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N LEU D 199 " --> pdb=" O HIS D 195 " (cutoff:3.500A) removed outlier: 4.334A pdb=" N ASN D 200 " --> pdb=" O ASN D 196 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N ALA D 201 " --> pdb=" O LYS D 197 " (cutoff:3.500A) Processing helix chain 'E' and resid 48 through 60 Processing helix chain 'E' and resid 62 through 75 Processing helix chain 'E' and resid 118 through 201 removed outlier: 4.341A pdb=" N VAL E 122 " --> pdb=" O ASN E 118 " (cutoff:3.500A) removed outlier: 4.114A pdb=" N GLU E 170 " --> pdb=" O VAL E 166 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N ALA E 171 " --> pdb=" O SER E 167 " (cutoff:3.500A) Processing helix chain 'F' and resid 674 through 685 Processing helix chain 'F' and resid 706 through 715 Processing helix chain 'F' and resid 723 through 733 removed outlier: 3.614A pdb=" N LEU F 727 " --> pdb=" O PRO F 723 " (cutoff:3.500A) Processing helix chain 'F' and resid 747 through 758 removed outlier: 3.537A pdb=" N GLU F 757 " --> pdb=" O HIS F 753 " (cutoff:3.500A) Processing helix chain 'F' and resid 770 through 781 removed outlier: 3.644A pdb=" N ILE F 781 " --> pdb=" O VAL F 777 " (cutoff:3.500A) Processing helix chain 'F' and resid 788 through 804 Processing helix chain 'F' and resid 805 through 808 removed outlier: 3.553A pdb=" N SER F 808 " --> pdb=" O TRP F 805 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 805 through 808' Processing helix chain 'F' and resid 811 through 815 removed outlier: 3.696A pdb=" N ARG F 815 " --> pdb=" O MET F 812 " (cutoff:3.500A) Processing helix chain 'F' and resid 836 through 849 removed outlier: 3.965A pdb=" N ILE F 840 " --> pdb=" O THR F 836 " (cutoff:3.500A) Processing helix chain 'F' and resid 871 through 882 Processing helix chain 'F' and resid 891 through 901 removed outlier: 3.508A pdb=" N THR F 895 " --> pdb=" O GLU F 891 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N ASP F 899 " --> pdb=" O THR F 895 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N LYS F 900 " --> pdb=" O ASP F 896 " (cutoff:3.500A) Processing helix chain 'F' and resid 906 through 910 removed outlier: 3.647A pdb=" N LEU F 910 " --> pdb=" O ASN F 907 " (cutoff:3.500A) Processing helix chain 'a' and resid 45 through 49 Processing helix chain 'a' and resid 58 through 78 Processing helix chain 'a' and resid 112 through 120 Processing helix chain 'a' and resid 121 through 123 No H-bonds generated for 'chain 'a' and resid 121 through 123' Processing helix chain 'a' and resid 124 through 136 Processing helix chain 'a' and resid 142 through 157 removed outlier: 3.591A pdb=" N VAL a 146 " --> pdb=" O SER a 142 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N VAL a 157 " --> pdb=" O LEU a 153 " (cutoff:3.500A) Processing helix chain 'a' and resid 179 through 197 removed outlier: 4.023A pdb=" N ALA a 183 " --> pdb=" O ASP a 179 " (cutoff:3.500A) Processing helix chain 'a' and resid 216 through 220 removed outlier: 3.968A pdb=" N ASP a 219 " --> pdb=" O PHE a 216 " (cutoff:3.500A) Processing helix chain 'a' and resid 237 through 244 removed outlier: 3.752A pdb=" N ASP a 241 " --> pdb=" O SER a 237 " (cutoff:3.500A) Processing helix chain 'a' and resid 312 through 314 No H-bonds generated for 'chain 'a' and resid 312 through 314' Processing helix chain 'a' and resid 330 through 338 removed outlier: 4.033A pdb=" N LYS a 338 " --> pdb=" O THR a 334 " (cutoff:3.500A) Processing helix chain 'a' and resid 354 through 356 No H-bonds generated for 'chain 'a' and resid 354 through 356' Processing helix chain 'a' and resid 377 through 393 removed outlier: 3.925A pdb=" N LEU a 381 " --> pdb=" O GLY a 377 " (cutoff:3.500A) Processing helix chain 'a' and resid 455 through 469 Processing helix chain 'a' and resid 480 through 496 Processing helix chain 'a' and resid 510 through 518 removed outlier: 3.626A pdb=" N MET a 514 " --> pdb=" O LYS a 510 " (cutoff:3.500A) Processing helix chain 'a' and resid 520 through 530 Processing helix chain 'b' and resid 17 through 22 removed outlier: 3.597A pdb=" N SER b 21 " --> pdb=" O GLY b 17 " (cutoff:3.500A) Processing helix chain 'b' and resid 29 through 48 Processing helix chain 'b' and resid 87 through 96 Processing helix chain 'b' and resid 106 through 122 removed outlier: 4.029A pdb=" N ALA b 110 " --> pdb=" O ASP b 106 " (cutoff:3.500A) Processing helix chain 'b' and resid 146 through 158 Processing helix chain 'b' and resid 198 through 217 Processing helix chain 'b' and resid 218 through 222 Processing helix chain 'b' and resid 227 through 231 Processing helix chain 'b' and resid 237 through 241 removed outlier: 3.794A pdb=" N GLU b 241 " --> pdb=" O LYS b 238 " (cutoff:3.500A) Processing helix chain 'b' and resid 306 through 308 No H-bonds generated for 'chain 'b' and resid 306 through 308' Processing helix chain 'b' and resid 324 through 332 Processing helix chain 'b' and resid 349 through 351 No H-bonds generated for 'chain 'b' and resid 349 through 351' Processing helix chain 'b' and resid 352 through 356 Processing helix chain 'b' and resid 371 through 388 Processing helix chain 'b' and resid 441 through 445 Processing helix chain 'b' and resid 447 through 461 Processing helix chain 'b' and resid 478 through 482 Processing helix chain 'b' and resid 484 through 500 removed outlier: 3.963A pdb=" N GLN b 488 " --> pdb=" O ASN b 484 " (cutoff:3.500A) Processing helix chain 'b' and resid 509 through 517 removed outlier: 3.630A pdb=" N TRP b 513 " --> pdb=" O GLN b 509 " (cutoff:3.500A) Processing helix chain 'b' and resid 519 through 537 removed outlier: 3.794A pdb=" N THR b 523 " --> pdb=" O PRO b 519 " (cutoff:3.500A) removed outlier: 5.185A pdb=" N ILE b 528 " --> pdb=" O THR b 524 " (cutoff:3.500A) Proline residue: b 529 - end of helix Processing helix chain 'c' and resid 0 through 11 Processing helix chain 'c' and resid 51 through 63 Processing helix chain 'c' and resid 68 through 86 Proline residue: c 82 - end of helix Processing helix chain 'c' and resid 127 through 170 removed outlier: 4.910A pdb=" N ARG c 137 " --> pdb=" O GLN c 133 " (cutoff:3.500A) Proline residue: c 138 - end of helix Processing helix chain 'c' and resid 185 through 197 Processing helix chain 'c' and resid 197 through 202 Processing helix chain 'c' and resid 207 through 214 removed outlier: 3.674A pdb=" N VAL c 211 " --> pdb=" O GLY c 207 " (cutoff:3.500A) Processing helix chain 'c' and resid 215 through 229 Processing helix chain 'd' and resid 49 through 60 removed outlier: 3.823A pdb=" N MET d 59 " --> pdb=" O GLU d 55 " (cutoff:3.500A) Processing helix chain 'd' and resid 62 through 75 Processing helix chain 'd' and resid 119 through 201 removed outlier: 3.799A pdb=" N LYS d 197 " --> pdb=" O SER d 193 " (cutoff:3.500A) removed outlier: 4.133A pdb=" N LEU d 198 " --> pdb=" O LEU d 194 " (cutoff:3.500A) removed outlier: 4.235A pdb=" N LEU d 199 " --> pdb=" O HIS d 195 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N ASN d 200 " --> pdb=" O ASN d 196 " (cutoff:3.500A) Processing helix chain 'e' and resid 27 through 31 Processing helix chain 'e' and resid 48 through 60 Processing helix chain 'e' and resid 62 through 75 Processing helix chain 'e' and resid 118 through 201 removed outlier: 4.397A pdb=" N VAL e 122 " --> pdb=" O ASN e 118 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N GLU e 170 " --> pdb=" O VAL e 166 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N ALA e 171 " --> pdb=" O SER e 167 " (cutoff:3.500A) Processing helix chain 'f' and resid 9 through 14 Processing helix chain 'f' and resid 15 through 29 removed outlier: 3.914A pdb=" N LEU f 19 " --> pdb=" O PRO f 15 " (cutoff:3.500A) Processing helix chain 'f' and resid 31 through 54 Processing helix chain 'f' and resid 64 through 72 Processing helix chain 'f' and resid 73 through 76 Processing helix chain 'f' and resid 85 through 98 Processing helix chain 'f' and resid 103 through 111 Processing helix chain 'f' and resid 124 through 134 removed outlier: 3.633A pdb=" N ILE f 128 " --> pdb=" O ASP f 124 " (cutoff:3.500A) Processing helix chain 'f' and resid 144 through 161 Processing helix chain 'f' and resid 164 through 177 Processing helix chain 'f' and resid 179 through 192 Processing helix chain 'f' and resid 199 through 208 Processing helix chain 'f' and resid 210 through 219 removed outlier: 3.639A pdb=" N LEU f 214 " --> pdb=" O ASP f 210 " (cutoff:3.500A) Processing helix chain 'f' and resid 220 through 228 removed outlier: 3.559A pdb=" N VAL f 224 " --> pdb=" O ASP f 220 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N CYS f 225 " --> pdb=" O LEU f 221 " (cutoff:3.500A) Processing helix chain 'f' and resid 258 through 264 Processing helix chain 'f' and resid 298 through 303 Processing helix chain 'f' and resid 311 through 316 Processing helix chain 'f' and resid 381 through 391 Processing helix chain 'f' and resid 410 through 424 removed outlier: 3.507A pdb=" N VAL f 414 " --> pdb=" O THR f 410 " (cutoff:3.500A) Processing helix chain 'f' and resid 451 through 455 Processing helix chain 'f' and resid 473 through 477 Processing helix chain 'f' and resid 511 through 522 Processing helix chain 'f' and resid 589 through 593 Processing helix chain 'f' and resid 595 through 607 removed outlier: 4.008A pdb=" N ALA f 606 " --> pdb=" O LEU f 602 " (cutoff:3.500A) Processing helix chain 'f' and resid 674 through 685 Processing helix chain 'f' and resid 706 through 716 Processing helix chain 'f' and resid 722 through 733 removed outlier: 4.287A pdb=" N LEU f 726 " --> pdb=" O LYS f 722 " (cutoff:3.500A) Processing helix chain 'f' and resid 747 through 758 removed outlier: 3.708A pdb=" N ARG f 756 " --> pdb=" O GLU f 752 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N GLU f 757 " --> pdb=" O HIS f 753 " (cutoff:3.500A) Processing helix chain 'f' and resid 770 through 781 Processing helix chain 'f' and resid 788 through 804 Processing helix chain 'f' and resid 805 through 808 Processing helix chain 'f' and resid 836 through 848 removed outlier: 4.114A pdb=" N ILE f 840 " --> pdb=" O THR f 836 " (cutoff:3.500A) Processing helix chain 'f' and resid 871 through 882 Processing helix chain 'f' and resid 890 through 901 removed outlier: 3.737A pdb=" N VAL f 894 " --> pdb=" O LYS f 890 " (cutoff:3.500A) Processing helix chain 'f' and resid 905 through 910 removed outlier: 3.543A pdb=" N GLN f 908 " --> pdb=" O GLU f 905 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N LEU f 910 " --> pdb=" O ASN f 907 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 102 through 109 removed outlier: 6.458A pdb=" N VAL A 85 " --> pdb=" O LEU A 105 " (cutoff:3.500A) removed outlier: 5.563A pdb=" N GLU A 107 " --> pdb=" O LEU A 83 " (cutoff:3.500A) removed outlier: 5.718A pdb=" N LEU A 83 " --> pdb=" O GLU A 107 " (cutoff:3.500A) removed outlier: 6.129A pdb=" N ASP A 36 " --> pdb=" O LEU A 82 " (cutoff:3.500A) removed outlier: 7.869A pdb=" N ALA A 84 " --> pdb=" O ASP A 36 " (cutoff:3.500A) removed outlier: 6.460A pdb=" N LEU A 38 " --> pdb=" O ALA A 84 " (cutoff:3.500A) removed outlier: 7.682A pdb=" N VAL A 86 " --> pdb=" O LEU A 38 " (cutoff:3.500A) removed outlier: 5.777A pdb=" N PHE A 40 " --> pdb=" O VAL A 86 " (cutoff:3.500A) removed outlier: 7.053A pdb=" N TYR A 88 " --> pdb=" O PHE A 40 " (cutoff:3.500A) removed outlier: 6.350A pdb=" N VAL A 42 " --> pdb=" O TYR A 88 " (cutoff:3.500A) removed outlier: 6.749A pdb=" N ARG A 35 " --> pdb=" O HIS A 163 " (cutoff:3.500A) removed outlier: 8.243A pdb=" N ARG A 165 " --> pdb=" O ARG A 35 " (cutoff:3.500A) removed outlier: 6.353A pdb=" N SER A 37 " --> pdb=" O ARG A 165 " (cutoff:3.500A) removed outlier: 7.775A pdb=" N MET A 167 " --> pdb=" O SER A 37 " (cutoff:3.500A) removed outlier: 6.391A pdb=" N ILE A 39 " --> pdb=" O MET A 167 " (cutoff:3.500A) removed outlier: 7.462A pdb=" N PHE A 169 " --> pdb=" O ILE A 39 " (cutoff:3.500A) removed outlier: 6.890A pdb=" N LEU A 41 " --> pdb=" O PHE A 169 " (cutoff:3.500A) removed outlier: 8.833A pdb=" N PHE A 199 " --> pdb=" O SER A 162 " (cutoff:3.500A) removed outlier: 6.740A pdb=" N LYS A 164 " --> pdb=" O PHE A 199 " (cutoff:3.500A) removed outlier: 8.030A pdb=" N ASP A 201 " --> pdb=" O LYS A 164 " (cutoff:3.500A) removed outlier: 6.351A pdb=" N ILE A 166 " --> pdb=" O ASP A 201 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 211 through 212 Processing sheet with id=AA3, first strand: chain 'A' and resid 257 through 262 removed outlier: 3.582A pdb=" N SER A 257 " --> pdb=" O ILE A 273 " (cutoff:3.500A) removed outlier: 8.333A pdb=" N VAL A 394 " --> pdb=" O PRO A 415 " (cutoff:3.500A) removed outlier: 6.315A pdb=" N ALA A 395 " --> pdb=" O PHE A 350 " (cutoff:3.500A) removed outlier: 4.612A pdb=" N PHE A 350 " --> pdb=" O ALA A 395 " (cutoff:3.500A) removed outlier: 4.470A pdb=" N LEU A 397 " --> pdb=" O MET A 348 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 286 through 289 Processing sheet with id=AA5, first strand: chain 'A' and resid 296 through 304 removed outlier: 4.614A pdb=" N TYR B 295 " --> pdb=" O VAL B 305 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 325 through 329 removed outlier: 3.501A pdb=" N THR B 277 " --> pdb=" O SER A 319 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 375 through 376 removed outlier: 3.535A pdb=" N ILE B 540 " --> pdb=" O ILE A 376 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 419 through 421 removed outlier: 6.534A pdb=" N GLU A 419 " --> pdb=" O VAL A 427 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N ILE A 425 " --> pdb=" O ASP A 421 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 77 through 84 removed outlier: 6.403A pdb=" N LEU B 56 " --> pdb=" O HIS B 80 " (cutoff:3.500A) removed outlier: 5.624A pdb=" N HIS B 82 " --> pdb=" O ILE B 54 " (cutoff:3.500A) removed outlier: 5.530A pdb=" N ILE B 54 " --> pdb=" O HIS B 82 " (cutoff:3.500A) removed outlier: 6.577A pdb=" N MET B 84 " --> pdb=" O ASP B 52 " (cutoff:3.500A) removed outlier: 7.074A pdb=" N ASP B 52 " --> pdb=" O MET B 84 " (cutoff:3.500A) removed outlier: 6.483A pdb=" N ALA B 8 " --> pdb=" O GLU B 53 " (cutoff:3.500A) removed outlier: 8.042A pdb=" N ALA B 55 " --> pdb=" O ALA B 8 " (cutoff:3.500A) removed outlier: 6.488A pdb=" N VAL B 10 " --> pdb=" O ALA B 55 " (cutoff:3.500A) removed outlier: 7.745A pdb=" N VAL B 57 " --> pdb=" O VAL B 10 " (cutoff:3.500A) removed outlier: 5.755A pdb=" N LEU B 12 " --> pdb=" O VAL B 57 " (cutoff:3.500A) removed outlier: 7.127A pdb=" N PHE B 59 " --> pdb=" O LEU B 12 " (cutoff:3.500A) removed outlier: 6.215A pdb=" N MET B 14 " --> pdb=" O PHE B 59 " (cutoff:3.500A) removed outlier: 6.745A pdb=" N ARG B 130 " --> pdb=" O SER B 160 " (cutoff:3.500A) removed outlier: 8.257A pdb=" N GLN B 162 " --> pdb=" O ARG B 130 " (cutoff:3.500A) removed outlier: 6.487A pdb=" N ILE B 132 " --> pdb=" O GLN B 162 " (cutoff:3.500A) removed outlier: 7.959A pdb=" N PHE B 164 " --> pdb=" O ILE B 132 " (cutoff:3.500A) removed outlier: 6.450A pdb=" N ILE B 134 " --> pdb=" O PHE B 164 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 247 through 252 removed outlier: 6.741A pdb=" N VAL B 361 " --> pdb=" O SER B 266 " (cutoff:3.500A) removed outlier: 8.428A pdb=" N GLN B 360 " --> pdb=" O GLN B 423 " (cutoff:3.500A) removed outlier: 5.041A pdb=" N GLN B 423 " --> pdb=" O GLN B 360 " (cutoff:3.500A) removed outlier: 6.249A pdb=" N ALA B 366 " --> pdb=" O GLU B 417 " (cutoff:3.500A) removed outlier: 10.610A pdb=" N GLU B 417 " --> pdb=" O ALA B 366 " (cutoff:3.500A) removed outlier: 8.909A pdb=" N MET B 389 " --> pdb=" O PRO B 410 " (cutoff:3.500A) removed outlier: 6.525A pdb=" N VAL B 390 " --> pdb=" O PHE B 345 " (cutoff:3.500A) removed outlier: 4.514A pdb=" N PHE B 345 " --> pdb=" O VAL B 390 " (cutoff:3.500A) removed outlier: 6.656A pdb=" N ILE B 392 " --> pdb=" O LEU B 343 " (cutoff:3.500A) removed outlier: 8.109A pdb=" N PHE B 340 " --> pdb=" O PRO B 248 " (cutoff:3.500A) removed outlier: 5.397A pdb=" N ARG B 250 " --> pdb=" O PHE B 340 " (cutoff:3.500A) removed outlier: 7.020A pdb=" N VAL B 342 " --> pdb=" O ARG B 250 " (cutoff:3.500A) removed outlier: 7.079A pdb=" N THR B 252 " --> pdb=" O VAL B 342 " (cutoff:3.500A) removed outlier: 7.711A pdb=" N GLY B 344 " --> pdb=" O THR B 252 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 464 through 467 Processing sheet with id=AB3, first strand: chain 'C' and resid 14 through 18 removed outlier: 3.530A pdb=" N MET C 124 " --> pdb=" O HIS C 46 " (cutoff:3.500A) removed outlier: 6.365A pdb=" N GLN C 48 " --> pdb=" O HIS C 122 " (cutoff:3.500A) removed outlier: 8.672A pdb=" N HIS C 122 " --> pdb=" O GLN C 48 " (cutoff:3.500A) removed outlier: 10.683A pdb=" N ASP C 50 " --> pdb=" O ASN C 120 " (cutoff:3.500A) removed outlier: 12.183A pdb=" N ASN C 120 " --> pdb=" O ASP C 50 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 65 through 66 removed outlier: 6.737A pdb=" N PHE E 97 " --> pdb=" O LEU E 108 " (cutoff:3.500A) removed outlier: 4.597A pdb=" N SER E 110 " --> pdb=" O PHE E 95 " (cutoff:3.500A) removed outlier: 6.901A pdb=" N PHE E 95 " --> pdb=" O SER E 110 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 2 through 8 Processing sheet with id=AB6, first strand: chain 'D' and resid 83 through 89 removed outlier: 4.211A pdb=" N VAL D 83 " --> pdb=" O ASN D 100 " (cutoff:3.500A) removed outlier: 6.026A pdb=" N LYS D 99 " --> pdb=" O ARG D 107 " (cutoff:3.500A) removed outlier: 5.555A pdb=" N ARG D 107 " --> pdb=" O LYS D 99 " (cutoff:3.500A) removed outlier: 6.919A pdb=" N LEU D 101 " --> pdb=" O SER D 105 " (cutoff:3.500A) removed outlier: 4.787A pdb=" N SER D 105 " --> pdb=" O LEU D 101 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'E' and resid 2 through 8 Processing sheet with id=AB8, first strand: chain 'F' and resid 688 through 689 removed outlier: 8.385A pdb=" N ILE F 701 " --> pdb=" O GLU F 663 " (cutoff:3.500A) removed outlier: 6.369A pdb=" N CYS F 665 " --> pdb=" O ILE F 701 " (cutoff:3.500A) removed outlier: 6.917A pdb=" N VAL F 700 " --> pdb=" O VAL F 721 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'F' and resid 851 through 852 removed outlier: 6.133A pdb=" N THR F 817 " --> pdb=" O HIS F 862 " (cutoff:3.500A) removed outlier: 7.608A pdb=" N ILE F 864 " --> pdb=" O THR F 817 " (cutoff:3.500A) removed outlier: 6.718A pdb=" N TYR F 819 " --> pdb=" O ILE F 864 " (cutoff:3.500A) removed outlier: 5.872A pdb=" N VAL F 863 " --> pdb=" O LEU F 889 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'a' and resid 102 through 109 removed outlier: 6.467A pdb=" N VAL a 85 " --> pdb=" O LEU a 105 " (cutoff:3.500A) removed outlier: 5.463A pdb=" N GLU a 107 " --> pdb=" O LEU a 83 " (cutoff:3.500A) removed outlier: 5.612A pdb=" N LEU a 83 " --> pdb=" O GLU a 107 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N TYR a 88 " --> pdb=" O VAL a 42 " (cutoff:3.500A) removed outlier: 6.571A pdb=" N ARG a 35 " --> pdb=" O HIS a 163 " (cutoff:3.500A) removed outlier: 8.233A pdb=" N ARG a 165 " --> pdb=" O ARG a 35 " (cutoff:3.500A) removed outlier: 6.597A pdb=" N SER a 37 " --> pdb=" O ARG a 165 " (cutoff:3.500A) removed outlier: 7.768A pdb=" N MET a 167 " --> pdb=" O SER a 37 " (cutoff:3.500A) removed outlier: 6.253A pdb=" N ILE a 39 " --> pdb=" O MET a 167 " (cutoff:3.500A) removed outlier: 7.133A pdb=" N PHE a 169 " --> pdb=" O ILE a 39 " (cutoff:3.500A) removed outlier: 6.234A pdb=" N LEU a 41 " --> pdb=" O PHE a 169 " (cutoff:3.500A) removed outlier: 9.118A pdb=" N PHE a 199 " --> pdb=" O SER a 162 " (cutoff:3.500A) removed outlier: 6.584A pdb=" N LYS a 164 " --> pdb=" O PHE a 199 " (cutoff:3.500A) removed outlier: 7.890A pdb=" N ASP a 201 " --> pdb=" O LYS a 164 " (cutoff:3.500A) removed outlier: 6.260A pdb=" N ILE a 166 " --> pdb=" O ASP a 201 " (cutoff:3.500A) removed outlier: 7.438A pdb=" N MET a 203 " --> pdb=" O ILE a 166 " (cutoff:3.500A) removed outlier: 6.695A pdb=" N LEU a 168 " --> pdb=" O MET a 203 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'a' and resid 211 through 212 Processing sheet with id=AC3, first strand: chain 'a' and resid 257 through 262 removed outlier: 3.542A pdb=" N SER a 257 " --> pdb=" O ILE a 273 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N GLY a 431 " --> pdb=" O GLN a 416 " (cutoff:3.500A) removed outlier: 8.107A pdb=" N VAL a 394 " --> pdb=" O PRO a 415 " (cutoff:3.500A) removed outlier: 4.255A pdb=" N GLY a 349 " --> pdb=" O LEU a 397 " (cutoff:3.500A) removed outlier: 5.896A pdb=" N ARG a 399 " --> pdb=" O LEU a 347 " (cutoff:3.500A) removed outlier: 5.209A pdb=" N LEU a 347 " --> pdb=" O ARG a 399 " (cutoff:3.500A) removed outlier: 7.460A pdb=" N THR a 401 " --> pdb=" O LEU a 345 " (cutoff:3.500A) removed outlier: 5.574A pdb=" N LEU a 345 " --> pdb=" O THR a 401 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N LEU a 345 " --> pdb=" O LYS a 260 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'a' and resid 286 through 289 Processing sheet with id=AC5, first strand: chain 'a' and resid 297 through 302 Processing sheet with id=AC6, first strand: chain 'a' and resid 326 through 329 Processing sheet with id=AC7, first strand: chain 'a' and resid 375 through 376 Processing sheet with id=AC8, first strand: chain 'a' and resid 419 through 420 removed outlier: 6.590A pdb=" N GLU a 419 " --> pdb=" O VAL a 427 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'b' and resid 77 through 84 removed outlier: 6.446A pdb=" N LEU b 56 " --> pdb=" O HIS b 80 " (cutoff:3.500A) removed outlier: 5.478A pdb=" N HIS b 82 " --> pdb=" O ILE b 54 " (cutoff:3.500A) removed outlier: 5.311A pdb=" N ILE b 54 " --> pdb=" O HIS b 82 " (cutoff:3.500A) removed outlier: 6.021A pdb=" N ALA b 8 " --> pdb=" O GLU b 53 " (cutoff:3.500A) removed outlier: 7.714A pdb=" N ALA b 55 " --> pdb=" O ALA b 8 " (cutoff:3.500A) removed outlier: 6.457A pdb=" N VAL b 10 " --> pdb=" O ALA b 55 " (cutoff:3.500A) removed outlier: 7.578A pdb=" N VAL b 57 " --> pdb=" O VAL b 10 " (cutoff:3.500A) removed outlier: 6.100A pdb=" N LEU b 12 " --> pdb=" O VAL b 57 " (cutoff:3.500A) removed outlier: 7.682A pdb=" N PHE b 59 " --> pdb=" O LEU b 12 " (cutoff:3.500A) removed outlier: 6.321A pdb=" N MET b 14 " --> pdb=" O PHE b 59 " (cutoff:3.500A) removed outlier: 6.723A pdb=" N ARG b 130 " --> pdb=" O SER b 160 " (cutoff:3.500A) removed outlier: 8.202A pdb=" N GLN b 162 " --> pdb=" O ARG b 130 " (cutoff:3.500A) removed outlier: 6.518A pdb=" N ILE b 132 " --> pdb=" O GLN b 162 " (cutoff:3.500A) removed outlier: 8.060A pdb=" N PHE b 164 " --> pdb=" O ILE b 132 " (cutoff:3.500A) removed outlier: 6.552A pdb=" N ILE b 134 " --> pdb=" O PHE b 164 " (cutoff:3.500A) removed outlier: 8.646A pdb=" N TYR b 225 " --> pdb=" O LEU b 161 " (cutoff:3.500A) removed outlier: 6.444A pdb=" N PHE b 163 " --> pdb=" O TYR b 225 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'b' and resid 247 through 252 removed outlier: 6.826A pdb=" N VAL b 361 " --> pdb=" O SER b 266 " (cutoff:3.500A) removed outlier: 8.264A pdb=" N GLN b 360 " --> pdb=" O GLN b 423 " (cutoff:3.500A) removed outlier: 4.917A pdb=" N GLN b 423 " --> pdb=" O GLN b 360 " (cutoff:3.500A) removed outlier: 6.205A pdb=" N ALA b 366 " --> pdb=" O GLU b 417 " (cutoff:3.500A) removed outlier: 10.379A pdb=" N GLU b 417 " --> pdb=" O ALA b 366 " (cutoff:3.500A) removed outlier: 9.008A pdb=" N MET b 389 " --> pdb=" O PRO b 410 " (cutoff:3.500A) removed outlier: 6.254A pdb=" N VAL b 390 " --> pdb=" O PHE b 345 " (cutoff:3.500A) removed outlier: 4.592A pdb=" N PHE b 345 " --> pdb=" O VAL b 390 " (cutoff:3.500A) removed outlier: 6.677A pdb=" N ILE b 392 " --> pdb=" O LEU b 343 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N CYS b 339 " --> pdb=" O ALA b 396 " (cutoff:3.500A) removed outlier: 8.149A pdb=" N PHE b 340 " --> pdb=" O PRO b 248 " (cutoff:3.500A) removed outlier: 5.452A pdb=" N ARG b 250 " --> pdb=" O PHE b 340 " (cutoff:3.500A) removed outlier: 7.054A pdb=" N VAL b 342 " --> pdb=" O ARG b 250 " (cutoff:3.500A) removed outlier: 7.029A pdb=" N THR b 252 " --> pdb=" O VAL b 342 " (cutoff:3.500A) removed outlier: 7.922A pdb=" N GLY b 344 " --> pdb=" O THR b 252 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'b' and resid 464 through 466 Processing sheet with id=AD3, first strand: chain 'c' and resid 14 through 17 removed outlier: 6.923A pdb=" N GLN c 48 " --> pdb=" O HIS c 122 " (cutoff:3.500A) removed outlier: 8.815A pdb=" N HIS c 122 " --> pdb=" O GLN c 48 " (cutoff:3.500A) removed outlier: 10.563A pdb=" N ASP c 50 " --> pdb=" O ASN c 120 " (cutoff:3.500A) removed outlier: 11.897A pdb=" N ASN c 120 " --> pdb=" O ASP c 50 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'c' and resid 65 through 66 removed outlier: 5.428A pdb=" N SER e 105 " --> pdb=" O LEU e 101 " (cutoff:3.500A) removed outlier: 7.743A pdb=" N LEU e 101 " --> pdb=" O SER e 105 " (cutoff:3.500A) removed outlier: 5.984A pdb=" N ARG e 107 " --> pdb=" O LYS e 99 " (cutoff:3.500A) removed outlier: 6.700A pdb=" N LYS e 99 " --> pdb=" O ARG e 107 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'd' and resid 2 through 8 Processing sheet with id=AD6, first strand: chain 'd' and resid 85 through 89 Processing sheet with id=AD7, first strand: chain 'd' and resid 85 through 89 Processing sheet with id=AD8, first strand: chain 'e' and resid 2 through 8 Processing sheet with id=AD9, first strand: chain 'f' and resid 250 through 253 removed outlier: 8.252A pdb=" N LEU f 250 " --> pdb=" O GLY f 444 " (cutoff:3.500A) removed outlier: 7.000A pdb=" N GLY f 446 " --> pdb=" O LEU f 250 " (cutoff:3.500A) removed outlier: 8.345A pdb=" N ALA f 252 " --> pdb=" O GLY f 446 " (cutoff:3.500A) removed outlier: 5.414A pdb=" N LEU f 448 " --> pdb=" O ALA f 252 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'f' and resid 287 through 292 removed outlier: 7.458A pdb=" N ILE f 325 " --> pdb=" O MET f 371 " (cutoff:3.500A) removed outlier: 7.336A pdb=" N MET f 371 " --> pdb=" O ILE f 325 " (cutoff:3.500A) removed outlier: 7.753A pdb=" N ILE f 327 " --> pdb=" O VAL f 369 " (cutoff:3.500A) removed outlier: 5.192A pdb=" N VAL f 369 " --> pdb=" O ILE f 327 " (cutoff:3.500A) removed outlier: 7.353A pdb=" N ASP f 329 " --> pdb=" O PHE f 367 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N VAL f 372 " --> pdb=" O LYS f 375 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'f' and resid 341 through 343 removed outlier: 3.773A pdb=" N ALA f 334 " --> pdb=" O MET f 343 " (cutoff:3.500A) removed outlier: 7.458A pdb=" N ILE f 325 " --> pdb=" O MET f 371 " (cutoff:3.500A) removed outlier: 7.336A pdb=" N MET f 371 " --> pdb=" O ILE f 325 " (cutoff:3.500A) removed outlier: 7.753A pdb=" N ILE f 327 " --> pdb=" O VAL f 369 " (cutoff:3.500A) removed outlier: 5.192A pdb=" N VAL f 369 " --> pdb=" O ILE f 327 " (cutoff:3.500A) removed outlier: 7.353A pdb=" N ASP f 329 " --> pdb=" O PHE f 367 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'f' and resid 527 through 528 removed outlier: 3.612A pdb=" N LEU f 484 " --> pdb=" O GLY f 468 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N HIS f 482 " --> pdb=" O TYR f 470 " (cutoff:3.500A) removed outlier: 7.041A pdb=" N PHE f 483 " --> pdb=" O ARG f 505 " (cutoff:3.500A) removed outlier: 5.014A pdb=" N ARG f 505 " --> pdb=" O PHE f 483 " (cutoff:3.500A) removed outlier: 7.199A pdb=" N CYS f 485 " --> pdb=" O LEU f 503 " (cutoff:3.500A) removed outlier: 6.025A pdb=" N PHE f 500 " --> pdb=" O LEU f 539 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'f' and resid 527 through 528 removed outlier: 3.612A pdb=" N LEU f 484 " --> pdb=" O GLY f 468 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N HIS f 482 " --> pdb=" O TYR f 470 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N LEU f 465 " --> pdb=" O ALA f 486 " (cutoff:3.500A) removed outlier: 7.359A pdb=" N ALA f 488 " --> pdb=" O ASP f 463 " (cutoff:3.500A) removed outlier: 11.294A pdb=" N ASP f 463 " --> pdb=" O ALA f 488 " (cutoff:3.500A) removed outlier: 4.153A pdb=" N ILE f 556 " --> pdb=" O ARG f 585 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N LYS f 583 " --> pdb=" O GLN f 558 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'f' and resid 563 through 566 removed outlier: 4.220A pdb=" N GLU f 563 " --> pdb=" O ARG f 577 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'f' and resid 688 through 689 removed outlier: 6.901A pdb=" N GLU f 663 " --> pdb=" O CYS f 699 " (cutoff:3.500A) removed outlier: 8.023A pdb=" N ILE f 701 " --> pdb=" O GLU f 663 " (cutoff:3.500A) removed outlier: 6.441A pdb=" N CYS f 665 " --> pdb=" O ILE f 701 " (cutoff:3.500A) removed outlier: 6.372A pdb=" N VAL f 700 " --> pdb=" O VAL f 721 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N HIS f 745 " --> pdb=" O VAL f 720 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'f' and resid 851 through 853 removed outlier: 4.423A pdb=" N LEU f 820 " --> pdb=" O VAL f 853 " (cutoff:3.500A) removed outlier: 6.313A pdb=" N VAL f 863 " --> pdb=" O LEU f 889 " (cutoff:3.500A) 1842 hydrogen bonds defined for protein. 5178 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 176 hydrogen bonds 352 hydrogen bond angles 0 basepair planarities 73 basepair parallelities 125 stacking parallelities Total time for adding SS restraints: 9.56 Time building geometry restraints manager: 4.30 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: 12195 1.34 - 1.46: 7474 1.46 - 1.58: 19972 1.58 - 1.70: 293 1.70 - 1.82: 318 Bond restraints: 40252 Sorted by residual: bond pdb=" C2' DZ4 I 101 " pdb=" C3' DZ4 I 101 " ideal model delta sigma weight residual 1.526 1.315 0.211 2.00e-02 2.50e+03 1.11e+02 bond pdb=" C1' DZ4 I 101 " pdb=" O4' DZ4 I 101 " ideal model delta sigma weight residual 1.396 1.565 -0.169 2.00e-02 2.50e+03 7.15e+01 bond pdb=" C4' DZ4 I 101 " pdb=" O4' DZ4 I 101 " ideal model delta sigma weight residual 1.431 1.293 0.138 2.00e-02 2.50e+03 4.78e+01 bond pdb=" C6 DZ4 I 101 " pdb=" N6 DZ4 I 101 " ideal model delta sigma weight residual 1.336 1.464 -0.128 2.00e-02 2.50e+03 4.07e+01 bond pdb=" C1' DZ4 I 101 " pdb=" N9 DZ4 I 101 " ideal model delta sigma weight residual 1.466 1.349 0.117 2.00e-02 2.50e+03 3.42e+01 ... (remaining 40247 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.01: 54659 3.01 - 6.02: 263 6.02 - 9.02: 20 9.02 - 12.03: 1 12.03 - 15.04: 2 Bond angle restraints: 54945 Sorted by residual: angle pdb=" PA DZ4 I 101 " pdb=" N3A DZ4 I 101 " pdb=" PB DZ4 I 101 " ideal model delta sigma weight residual 135.12 120.08 15.04 3.00e+00 1.11e-01 2.51e+01 angle pdb=" N3 DT I 35 " pdb=" C4 DT I 35 " pdb=" O4 DT I 35 " ideal model delta sigma weight residual 119.90 122.54 -2.64 6.00e-01 2.78e+00 1.94e+01 angle pdb=" N3 DT J 46 " pdb=" C4 DT J 46 " pdb=" O4 DT J 46 " ideal model delta sigma weight residual 119.90 122.45 -2.55 6.00e-01 2.78e+00 1.81e+01 angle pdb=" N3 DT I 46 " pdb=" C4 DT I 46 " pdb=" O4 DT I 46 " ideal model delta sigma weight residual 119.90 122.45 -2.55 6.00e-01 2.78e+00 1.80e+01 angle pdb=" N3 DT I 52 " pdb=" C4 DT I 52 " pdb=" O4 DT I 52 " ideal model delta sigma weight residual 119.90 122.44 -2.54 6.00e-01 2.78e+00 1.79e+01 ... (remaining 54940 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.17: 21072 22.17 - 44.35: 2477 44.35 - 66.52: 619 66.52 - 88.70: 67 88.70 - 110.87: 5 Dihedral angle restraints: 24240 sinusoidal: 11070 harmonic: 13170 Sorted by residual: dihedral pdb=" O2B DZ4 I 101 " pdb=" O3B DZ4 I 101 " pdb=" PB DZ4 I 101 " pdb=" PG DZ4 I 101 " ideal model delta sinusoidal sigma weight residual 167.68 56.81 110.87 1 3.00e+01 1.11e-03 1.45e+01 dihedral pdb=" N3A DZ4 I 101 " pdb=" O3B DZ4 I 101 " pdb=" PB DZ4 I 101 " pdb=" PG DZ4 I 101 " ideal model delta sinusoidal sigma weight residual 278.09 176.67 101.42 1 3.00e+01 1.11e-03 1.28e+01 dihedral pdb=" O1B DZ4 I 101 " pdb=" O3B DZ4 I 101 " pdb=" PB DZ4 I 101 " pdb=" PG DZ4 I 101 " ideal model delta sinusoidal sigma weight residual 38.56 -62.78 101.34 1 3.00e+01 1.11e-03 1.28e+01 ... (remaining 24237 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.034: 4451 0.034 - 0.067: 1003 0.067 - 0.101: 286 0.101 - 0.134: 255 0.134 - 0.168: 102 Chirality restraints: 6097 Sorted by residual: chirality pdb=" CB THR a 10 " pdb=" CA THR a 10 " pdb=" OG1 THR a 10 " pdb=" CG2 THR a 10 " both_signs ideal model delta sigma weight residual False 2.55 2.72 -0.17 2.00e-01 2.50e+01 7.05e-01 chirality pdb=" C3' DG J 61 " pdb=" C4' DG J 61 " pdb=" O3' DG J 61 " pdb=" C2' DG J 61 " both_signs ideal model delta sigma weight residual False -2.73 -2.57 -0.16 2.00e-01 2.50e+01 6.43e-01 chirality pdb=" C3' DG I 65 " pdb=" C4' DG I 65 " pdb=" O3' DG I 65 " pdb=" C2' DG I 65 " both_signs ideal model delta sigma weight residual False -2.73 -2.57 -0.16 2.00e-01 2.50e+01 6.42e-01 ... (remaining 6094 not shown) Planarity restraints: 6539 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C HIS C 89 " -0.025 5.00e-02 4.00e+02 3.83e-02 2.35e+00 pdb=" N PRO C 90 " 0.066 5.00e-02 4.00e+02 pdb=" CA PRO C 90 " -0.020 5.00e-02 4.00e+02 pdb=" CD PRO C 90 " -0.021 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLN f 673 " 0.024 5.00e-02 4.00e+02 3.73e-02 2.22e+00 pdb=" N PRO f 674 " -0.064 5.00e-02 4.00e+02 pdb=" CA PRO f 674 " 0.019 5.00e-02 4.00e+02 pdb=" CD PRO f 674 " 0.021 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA LEU f 795 " 0.007 2.00e-02 2.50e+03 1.46e-02 2.13e+00 pdb=" C LEU f 795 " -0.025 2.00e-02 2.50e+03 pdb=" O LEU f 795 " 0.009 2.00e-02 2.50e+03 pdb=" N ILE f 796 " 0.008 2.00e-02 2.50e+03 ... (remaining 6536 not shown) Histogram of nonbonded interaction distances: 2.28 - 2.81: 10018 2.81 - 3.33: 37809 3.33 - 3.85: 65774 3.85 - 4.38: 73380 4.38 - 4.90: 124625 Nonbonded interactions: 311606 Sorted by model distance: nonbonded pdb=" OG1 THR A 305 " pdb=" O GLU B 287 " model vdw 2.284 3.040 nonbonded pdb=" O LYS a 331 " pdb=" OG1 THR a 334 " model vdw 2.303 3.040 nonbonded pdb=" O ASP A 228 " pdb=" OD1 ASP A 228 " model vdw 2.330 3.040 nonbonded pdb=" O ILE B 118 " pdb=" OG1 THR B 122 " model vdw 2.340 3.040 nonbonded pdb=" O LYS d 72 " pdb=" OG SER d 76 " model vdw 2.344 3.040 ... (remaining 311601 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 'A' and (resid 32 through 443 or resid 445 through 536)) selection = (chain 'a' and (resid 32 through 443 or resid 445 through 536)) } ncs_group { reference = (chain 'B' and (resid 6 through 169 or resid 181 through 542)) selection = chain 'b' } ncs_group { reference = chain 'C' selection = (chain 'c' and resid 0 through 227) } ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'd' selection = chain 'e' } ncs_group { reference = chain 'G' selection = (chain 'H' and resid 180 through 202) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.49 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: 9.960 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: 0.030 Extract box with map and model: 0.910 Check model and map are aligned: 0.120 Set scattering table: 0.090 Process input model: 38.990 Find NCS groups from input model: 0.730 Set up NCS constraints: 0.120 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.320 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 52.280 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8096 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 : 0.003 0.211 40252 Z= 0.238 Angle : 0.531 15.041 54945 Z= 0.343 Chirality : 0.042 0.168 6097 Planarity : 0.002 0.038 6539 Dihedral : 18.890 110.870 15672 Min Nonbonded Distance : 2.284 Molprobity Statistics. All-atom Clashscore : 2.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.31 % Favored : 97.69 % Rotamer: Outliers : 0.10 % Allowed : 20.80 % Favored : 79.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.17 (0.13), residues: 4457 helix: 3.35 (0.13), residues: 1754 sheet: 0.76 (0.20), residues: 753 loop : -0.07 (0.14), residues: 1950 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 242 TYR 0.014 0.001 TYR d 177 PHE 0.016 0.001 PHE b 18 TRP 0.007 0.000 TRP a 148 HIS 0.002 0.000 HIS f 848 Details of bonding type rmsd/Z covalent geometry : bond 0.00342 / 0.24 (40252) covalent geometry : angle 0.53077 / 0.34 (54945) hydrogen bonds : bond 0.11331 / 7.70 ( 1999) hydrogen bonds : angle 5.13661 / 3.51 ( 5530) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8914 Ramachandran restraints generated. 4457 Oldfield, 0 Emsley, 4457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8914 Ramachandran restraints generated. 4457 Oldfield, 0 Emsley, 4457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 444 residues out of total 4027 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 440 time to evaluate : 1.175 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 180 LYS cc_start: 0.9359 (tttp) cc_final: 0.9158 (tptp) REVERT: C 195 ILE cc_start: 0.9219 (tp) cc_final: 0.8997 (pt) REVERT: D 35 THR cc_start: 0.9097 (m) cc_final: 0.8827 (m) REVERT: E 145 GLN cc_start: 0.9508 (tp-100) cc_final: 0.9194 (tm-30) REVERT: F 746 MET cc_start: 0.7435 (mmt) cc_final: 0.7024 (mmt) REVERT: a 152 ASN cc_start: 0.8813 (m-40) cc_final: 0.8495 (t0) REVERT: a 409 TYR cc_start: 0.8033 (OUTLIER) cc_final: 0.7493 (t80) REVERT: b 222 ASP cc_start: 0.8069 (m-30) cc_final: 0.7812 (p0) REVERT: b 533 ILE cc_start: 0.9228 (mt) cc_final: 0.8959 (mt) REVERT: e 54 GLN cc_start: 0.9790 (tp40) cc_final: 0.9534 (tp-100) REVERT: e 94 TYR cc_start: 0.9179 (t80) cc_final: 0.8849 (t80) REVERT: e 172 LEU cc_start: 0.9547 (tt) cc_final: 0.9297 (mt) REVERT: e 181 ILE cc_start: 0.9044 (tp) cc_final: 0.8783 (tp) REVERT: f 14 VAL cc_start: 0.9020 (t) cc_final: 0.8502 (p) REVERT: f 95 GLU cc_start: 0.8646 (tp30) cc_final: 0.8441 (tm-30) REVERT: f 374 ASN cc_start: 0.8447 (m-40) cc_final: 0.8089 (t0) REVERT: f 412 ASN cc_start: 0.8816 (m110) cc_final: 0.8416 (t0) REVERT: f 500 PHE cc_start: 0.8090 (m-80) cc_final: 0.7685 (m-80) REVERT: f 511 THR cc_start: 0.8878 (OUTLIER) cc_final: 0.8482 (t) REVERT: f 557 VAL cc_start: 0.9408 (t) cc_final: 0.9190 (p) REVERT: f 743 MET cc_start: 0.7626 (pmm) cc_final: 0.6941 (pmm) outliers start: 4 outliers final: 0 residues processed: 444 average time/residue: 0.2258 time to fit residues: 164.3912 Evaluate side-chains 306 residues out of total 4027 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 304 time to evaluate : 1.650 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 409 TYR Chi-restraints excluded: chain f residue 511 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 457 random chunks: chunk 432 optimal weight: 9.9990 chunk 197 optimal weight: 9.9990 chunk 388 optimal weight: 0.6980 chunk 455 optimal weight: 20.0000 chunk 215 optimal weight: 6.9990 chunk 20 optimal weight: 8.9990 chunk 132 optimal weight: 10.0000 chunk 261 optimal weight: 4.9990 chunk 248 optimal weight: 0.2980 chunk 207 optimal weight: 0.8980 chunk 401 optimal weight: 4.9990 overall best weight: 2.3784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 485 GLN b 432 GLN b 527 GLN c 168 GLN f 146 GLN f 848 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3607 r_free = 0.3607 target = 0.064722 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.2963 r_free = 0.2963 target = 0.044105 restraints weight = 252682.433| |-----------------------------------------------------------------------------| r_work (start): 0.2896 rms_B_bonded: 4.92 r_work (final): 0.2896 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2896 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2896 r_free = 0.2896 target_work(ls_wunit_k1) = 0.042 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2896 r_free = 0.2896 target_work(ls_wunit_k1) = 0.042 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 5 (7 function evaluations) r_final: 0.2896 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8661 moved from start: 0.1252 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 40252 Z= 0.211 Angle : 0.598 10.187 54945 Z= 0.322 Chirality : 0.040 0.164 6097 Planarity : 0.004 0.054 6539 Dihedral : 16.393 92.638 6481 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 4.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Rotamer: Outliers : 1.64 % Allowed : 22.26 % Favored : 76.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.76 (0.13), residues: 4457 helix: 2.84 (0.12), residues: 1763 sheet: 0.57 (0.19), residues: 756 loop : -0.14 (0.14), residues: 1938 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG D 124 TYR 0.019 0.001 TYR B 264 PHE 0.021 0.001 PHE f 125 TRP 0.017 0.001 TRP f 447 HIS 0.006 0.001 HIS F 745 Details of bonding type rmsd/Z covalent geometry : bond 0.00468 / 0.21 (40252) covalent geometry : angle 0.59777 / 0.32 (54945) hydrogen bonds : bond 0.03927 / 2.65 ( 1999) hydrogen bonds : angle 4.69284 / 3.24 ( 5530) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8914 Ramachandran restraints generated. 4457 Oldfield, 0 Emsley, 4457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8914 Ramachandran restraints generated. 4457 Oldfield, 0 Emsley, 4457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 381 residues out of total 4027 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 315 time to evaluate : 1.972 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 115 MET cc_start: 0.9501 (mpp) cc_final: 0.9140 (mpp) REVERT: C 159 MET cc_start: 0.9009 (mmp) cc_final: 0.8808 (mmm) REVERT: C 165 GLN cc_start: 0.9550 (mt0) cc_final: 0.9321 (tm-30) REVERT: C 182 GLU cc_start: 0.8805 (mp0) cc_final: 0.8554 (mp0) REVERT: C 195 ILE cc_start: 0.9254 (tp) cc_final: 0.8838 (pt) REVERT: D 61 MET cc_start: 0.8462 (ppp) cc_final: 0.8031 (ppp) REVERT: D 66 TYR cc_start: 0.8190 (t80) cc_final: 0.7872 (t80) REVERT: E 145 GLN cc_start: 0.9652 (tp-100) cc_final: 0.9353 (tm-30) REVERT: F 692 ASN cc_start: 0.9363 (OUTLIER) cc_final: 0.8592 (m-40) REVERT: F 746 MET cc_start: 0.7968 (mmt) cc_final: 0.7639 (mmt) REVERT: H 194 LYS cc_start: 0.8983 (ptpp) cc_final: 0.8760 (ttpp) REVERT: a 99 PHE cc_start: 0.8594 (m-80) cc_final: 0.8272 (t80) REVERT: a 145 GLU cc_start: 0.8679 (mt-10) cc_final: 0.8349 (mt-10) REVERT: a 152 ASN cc_start: 0.9109 (m-40) cc_final: 0.8783 (m-40) REVERT: a 311 LEU cc_start: 0.9169 (OUTLIER) cc_final: 0.8739 (mt) REVERT: a 409 TYR cc_start: 0.8299 (OUTLIER) cc_final: 0.7601 (t80) REVERT: c 63 LYS cc_start: 0.8572 (tppt) cc_final: 0.8304 (mmtm) REVERT: c 85 LYS cc_start: 0.9042 (mtmm) cc_final: 0.8783 (mtmm) REVERT: d 61 MET cc_start: 0.3861 (OUTLIER) cc_final: 0.3428 (ppp) REVERT: e 54 GLN cc_start: 0.9709 (tp40) cc_final: 0.9121 (tp-100) REVERT: e 57 ASP cc_start: 0.8838 (m-30) cc_final: 0.8524 (p0) REVERT: e 94 TYR cc_start: 0.9251 (t80) cc_final: 0.8926 (t80) REVERT: e 172 LEU cc_start: 0.9499 (tt) cc_final: 0.9218 (mt) REVERT: f 95 GLU cc_start: 0.9334 (tp30) cc_final: 0.8857 (tm-30) REVERT: f 121 ASP cc_start: 0.6676 (p0) cc_final: 0.4649 (p0) REVERT: f 127 MET cc_start: 0.8790 (mpp) cc_final: 0.8202 (mtm) REVERT: f 279 MET cc_start: 0.8682 (mmm) cc_final: 0.8456 (mmm) REVERT: f 329 ASP cc_start: 0.8691 (p0) cc_final: 0.8326 (p0) REVERT: f 332 MET cc_start: 0.9229 (mmm) cc_final: 0.8876 (mmm) REVERT: f 368 ASP cc_start: 0.8840 (m-30) cc_final: 0.8373 (m-30) REVERT: f 374 ASN cc_start: 0.9010 (m-40) cc_final: 0.8698 (t0) REVERT: f 447 TRP cc_start: 0.8636 (m-10) cc_final: 0.7994 (m-10) REVERT: f 459 MET cc_start: 0.9179 (mmp) cc_final: 0.8893 (mmp) REVERT: f 743 MET cc_start: 0.9172 (pmm) cc_final: 0.8519 (pmm) REVERT: f 776 GLU cc_start: 0.9449 (mm-30) cc_final: 0.9159 (pt0) outliers start: 66 outliers final: 29 residues processed: 363 average time/residue: 0.2208 time to fit residues: 136.4965 Evaluate side-chains 316 residues out of total 4027 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 283 time to evaluate : 1.533 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 251 THR Chi-restraints excluded: chain A residue 409 TYR Chi-restraints excluded: chain A residue 495 LEU Chi-restraints excluded: chain A residue 524 GLU Chi-restraints excluded: chain B residue 10 VAL Chi-restraints excluded: chain C residue 41 LEU Chi-restraints excluded: chain C residue 80 LEU Chi-restraints excluded: chain C residue 99 CYS Chi-restraints excluded: chain C residue 123 CYS Chi-restraints excluded: chain C residue 204 ILE Chi-restraints excluded: chain D residue 94 TYR Chi-restraints excluded: chain D residue 102 LYS Chi-restraints excluded: chain E residue 108 LEU Chi-restraints excluded: chain E residue 184 LEU Chi-restraints excluded: chain F residue 692 ASN Chi-restraints excluded: chain a residue 311 LEU Chi-restraints excluded: chain a residue 409 TYR Chi-restraints excluded: chain b residue 331 MET Chi-restraints excluded: chain c residue 16 LEU Chi-restraints excluded: chain c residue 54 VAL Chi-restraints excluded: chain c residue 164 ILE Chi-restraints excluded: chain c residue 174 LEU Chi-restraints excluded: chain d residue 18 HIS Chi-restraints excluded: chain d residue 61 MET Chi-restraints excluded: chain d residue 143 HIS Chi-restraints excluded: chain e residue 19 PHE Chi-restraints excluded: chain e residue 122 VAL Chi-restraints excluded: chain f residue 94 ILE Chi-restraints excluded: chain f residue 250 LEU Chi-restraints excluded: chain f residue 315 ILE Chi-restraints excluded: chain f residue 409 HIS Chi-restraints excluded: chain f residue 483 PHE Chi-restraints excluded: chain f residue 498 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 457 random chunks: chunk 413 optimal weight: 6.9990 chunk 376 optimal weight: 5.9990 chunk 195 optimal weight: 10.0000 chunk 50 optimal weight: 9.9990 chunk 241 optimal weight: 0.9990 chunk 265 optimal weight: 0.3980 chunk 302 optimal weight: 5.9990 chunk 156 optimal weight: 0.9990 chunk 207 optimal weight: 2.9990 chunk 298 optimal weight: 3.9990 chunk 326 optimal weight: 0.9980 overall best weight: 1.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 458 GLN D 9 HIS D 195 HIS ** e 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** f 316 HIS ** f 745 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3633 r_free = 0.3633 target = 0.065247 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.2990 r_free = 0.2990 target = 0.044454 restraints weight = 278345.769| |-----------------------------------------------------------------------------| r_work (start): 0.2917 rms_B_bonded: 4.96 r_work (final): 0.2917 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2916 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2916 r_free = 0.2916 target_work(ls_wunit_k1) = 0.042 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2916 r_free = 0.2916 target_work(ls_wunit_k1) = 0.042 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (7 function evaluations) r_final: 0.2916 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8674 moved from start: 0.1525 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 40252 Z= 0.140 Angle : 0.534 8.788 54945 Z= 0.289 Chirality : 0.040 0.420 6097 Planarity : 0.003 0.054 6539 Dihedral : 16.516 77.828 6480 Min Nonbonded Distance : 2.415 Molprobity Statistics. All-atom Clashscore : 4.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer: Outliers : 1.71 % Allowed : 21.87 % Favored : 76.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.66 (0.13), residues: 4457 helix: 2.72 (0.12), residues: 1765 sheet: 0.65 (0.20), residues: 736 loop : -0.23 (0.14), residues: 1956 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG E 150 TYR 0.027 0.001 TYR D 129 PHE 0.020 0.001 PHE f 125 TRP 0.011 0.001 TRP C 119 HIS 0.004 0.001 HIS a 137 Details of bonding type rmsd/Z covalent geometry : bond 0.00304 / 0.14 (40252) covalent geometry : angle 0.53408 / 0.29 (54945) hydrogen bonds : bond 0.03456 / 2.31 ( 1999) hydrogen bonds : angle 4.43714 / 3.07 ( 5530) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8914 Ramachandran restraints generated. 4457 Oldfield, 0 Emsley, 4457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8914 Ramachandran restraints generated. 4457 Oldfield, 0 Emsley, 4457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 371 residues out of total 4027 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 302 time to evaluate : 1.512 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 133 GLU cc_start: 0.9057 (mt-10) cc_final: 0.8727 (mt-10) REVERT: C 165 GLN cc_start: 0.9525 (mt0) cc_final: 0.9290 (tm-30) REVERT: C 182 GLU cc_start: 0.8783 (mp0) cc_final: 0.8547 (mp0) REVERT: C 195 ILE cc_start: 0.9220 (tp) cc_final: 0.8814 (pt) REVERT: D 61 MET cc_start: 0.8449 (ppp) cc_final: 0.8154 (ppp) REVERT: D 66 TYR cc_start: 0.8103 (t80) cc_final: 0.7809 (t80) REVERT: E 145 GLN cc_start: 0.9620 (tp-100) cc_final: 0.9319 (tm-30) REVERT: F 692 ASN cc_start: 0.9329 (OUTLIER) cc_final: 0.8627 (m-40) REVERT: a 62 MET cc_start: 0.8409 (tpp) cc_final: 0.8102 (tpp) REVERT: a 135 MET cc_start: 0.8309 (mmt) cc_final: 0.8065 (mmt) REVERT: a 145 GLU cc_start: 0.8650 (mt-10) cc_final: 0.8351 (mt-10) REVERT: a 152 ASN cc_start: 0.9129 (m-40) cc_final: 0.8813 (m-40) REVERT: a 311 LEU cc_start: 0.9153 (OUTLIER) cc_final: 0.8757 (mt) REVERT: a 348 MET cc_start: 0.7704 (mtt) cc_final: 0.7439 (mtt) REVERT: a 409 TYR cc_start: 0.8420 (OUTLIER) cc_final: 0.7725 (t80) REVERT: b 84 MET cc_start: 0.8705 (pmm) cc_final: 0.8457 (pmm) REVERT: c 156 LEU cc_start: 0.9075 (OUTLIER) cc_final: 0.8779 (tt) REVERT: d 61 MET cc_start: 0.3995 (tmm) cc_final: 0.3380 (ppp) REVERT: e 94 TYR cc_start: 0.9164 (t80) cc_final: 0.8801 (t80) REVERT: f 95 GLU cc_start: 0.9205 (tp30) cc_final: 0.8731 (tm-30) REVERT: f 127 MET cc_start: 0.8636 (mpp) cc_final: 0.8128 (mtm) REVERT: f 329 ASP cc_start: 0.8597 (p0) cc_final: 0.8202 (p0) REVERT: f 332 MET cc_start: 0.9238 (mmm) cc_final: 0.8864 (mmm) REVERT: f 368 ASP cc_start: 0.8722 (m-30) cc_final: 0.8307 (m-30) REVERT: f 374 ASN cc_start: 0.8971 (m-40) cc_final: 0.8680 (t0) REVERT: f 447 TRP cc_start: 0.8529 (m-10) cc_final: 0.8000 (m-10) REVERT: f 459 MET cc_start: 0.9154 (mmp) cc_final: 0.8911 (mmp) REVERT: f 480 MET cc_start: 0.9248 (mmm) cc_final: 0.8881 (tpp) REVERT: f 743 MET cc_start: 0.9067 (pmm) cc_final: 0.8490 (pmm) REVERT: f 776 GLU cc_start: 0.9430 (mm-30) cc_final: 0.9151 (pt0) REVERT: f 782 LYS cc_start: 0.9357 (mtpt) cc_final: 0.9146 (tmmt) REVERT: f 811 SER cc_start: 0.9563 (OUTLIER) cc_final: 0.9295 (t) REVERT: f 812 MET cc_start: 0.9266 (pmm) cc_final: 0.8536 (pmm) outliers start: 69 outliers final: 31 residues processed: 350 average time/residue: 0.2146 time to fit residues: 128.4317 Evaluate side-chains 319 residues out of total 4027 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 283 time to evaluate : 1.470 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 302 THR Chi-restraints excluded: chain A residue 409 TYR Chi-restraints excluded: chain A residue 495 LEU Chi-restraints excluded: chain A residue 524 GLU Chi-restraints excluded: chain B residue 10 VAL Chi-restraints excluded: chain B residue 515 MET Chi-restraints excluded: chain C residue 80 LEU Chi-restraints excluded: chain C residue 123 CYS Chi-restraints excluded: chain D residue 94 TYR Chi-restraints excluded: chain E residue 92 SER Chi-restraints excluded: chain E residue 108 LEU Chi-restraints excluded: chain E residue 184 LEU Chi-restraints excluded: chain E residue 189 THR Chi-restraints excluded: chain F residue 692 ASN Chi-restraints excluded: chain a residue 311 LEU Chi-restraints excluded: chain a residue 409 TYR Chi-restraints excluded: chain b residue 78 THR Chi-restraints excluded: chain b residue 131 HIS Chi-restraints excluded: chain b residue 331 MET Chi-restraints excluded: chain c residue 16 LEU Chi-restraints excluded: chain c residue 54 VAL Chi-restraints excluded: chain c residue 132 SER Chi-restraints excluded: chain c residue 156 LEU Chi-restraints excluded: chain c residue 164 ILE Chi-restraints excluded: chain c residue 174 LEU Chi-restraints excluded: chain c residue 181 THR Chi-restraints excluded: chain d residue 127 ILE Chi-restraints excluded: chain e residue 19 PHE Chi-restraints excluded: chain e residue 122 VAL Chi-restraints excluded: chain f residue 94 ILE Chi-restraints excluded: chain f residue 250 LEU Chi-restraints excluded: chain f residue 406 THR Chi-restraints excluded: chain f residue 409 HIS Chi-restraints excluded: chain f residue 412 ASN Chi-restraints excluded: chain f residue 498 SER Chi-restraints excluded: chain f residue 811 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 457 random chunks: chunk 264 optimal weight: 7.9990 chunk 322 optimal weight: 3.9990 chunk 246 optimal weight: 0.0870 chunk 359 optimal weight: 9.9990 chunk 209 optimal weight: 4.9990 chunk 385 optimal weight: 7.9990 chunk 146 optimal weight: 4.9990 chunk 52 optimal weight: 8.9990 chunk 364 optimal weight: 2.9990 chunk 207 optimal weight: 4.9990 chunk 84 optimal weight: 3.9990 overall best weight: 3.2166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 43 GLN B 152 HIS c 122 HIS ** e 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 745 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 848 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 = 0.3594 r_free = 0.3594 target = 0.063471 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.2926 r_free = 0.2926 target = 0.042370 restraints weight = 284905.932| |-----------------------------------------------------------------------------| r_work (start): 0.2849 rms_B_bonded: 4.97 r_work (final): 0.2849 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2850 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2850 r_free = 0.2850 target_work(ls_wunit_k1) = 0.040 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2850 r_free = 0.2850 target_work(ls_wunit_k1) = 0.040 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2850 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8748 moved from start: 0.1932 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.080 40252 Z= 0.260 Angle : 0.605 9.264 54945 Z= 0.320 Chirality : 0.040 0.196 6097 Planarity : 0.004 0.053 6539 Dihedral : 16.795 77.302 6480 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 6.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Rotamer: Outliers : 2.33 % Allowed : 22.21 % Favored : 75.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.44 (0.13), residues: 4457 helix: 2.52 (0.12), residues: 1772 sheet: 0.44 (0.19), residues: 745 loop : -0.30 (0.14), residues: 1940 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG D 3 TYR 0.037 0.001 TYR D 129 PHE 0.027 0.002 PHE a 131 TRP 0.017 0.001 TRP f 46 HIS 0.007 0.001 HIS F 745 Details of bonding type rmsd/Z covalent geometry : bond 0.00575 / 0.26 (40252) covalent geometry : angle 0.60488 / 0.32 (54945) hydrogen bonds : bond 0.03909 / 2.63 ( 1999) hydrogen bonds : angle 4.48415 / 3.11 ( 5530) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8914 Ramachandran restraints generated. 4457 Oldfield, 0 Emsley, 4457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8914 Ramachandran restraints generated. 4457 Oldfield, 0 Emsley, 4457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 370 residues out of total 4027 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 276 time to evaluate : 1.742 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 115 MET cc_start: 0.9416 (OUTLIER) cc_final: 0.9007 (mpp) REVERT: C 182 GLU cc_start: 0.8862 (mp0) cc_final: 0.8628 (mp0) REVERT: C 195 ILE cc_start: 0.9230 (tp) cc_final: 0.8823 (pt) REVERT: D 61 MET cc_start: 0.8541 (ppp) cc_final: 0.8251 (ppp) REVERT: D 66 TYR cc_start: 0.8263 (t80) cc_final: 0.7966 (t80) REVERT: E 145 GLN cc_start: 0.9626 (tp-100) cc_final: 0.9339 (tm-30) REVERT: E 184 LEU cc_start: 0.9645 (OUTLIER) cc_final: 0.9423 (mm) REVERT: E 185 ASN cc_start: 0.9453 (OUTLIER) cc_final: 0.9058 (p0) REVERT: a 62 MET cc_start: 0.8459 (tpp) cc_final: 0.8187 (tpp) REVERT: a 99 PHE cc_start: 0.8716 (m-80) cc_final: 0.8511 (t80) REVERT: a 135 MET cc_start: 0.8452 (mmt) cc_final: 0.8097 (mmt) REVERT: a 145 GLU cc_start: 0.8751 (mt-10) cc_final: 0.8507 (mt-10) REVERT: a 152 ASN cc_start: 0.9189 (m-40) cc_final: 0.8868 (m-40) REVERT: a 311 LEU cc_start: 0.9205 (OUTLIER) cc_final: 0.8727 (mt) REVERT: a 409 TYR cc_start: 0.8624 (OUTLIER) cc_final: 0.7843 (t80) REVERT: b 20 MET cc_start: 0.8581 (OUTLIER) cc_final: 0.8327 (ttt) REVERT: b 84 MET cc_start: 0.8697 (pmm) cc_final: 0.8434 (pmm) REVERT: c 63 LYS cc_start: 0.8623 (tppt) cc_final: 0.8279 (mmtm) REVERT: c 81 ARG cc_start: 0.8763 (tpp-160) cc_final: 0.8472 (tpp80) REVERT: c 85 LYS cc_start: 0.9140 (mtmm) cc_final: 0.8926 (mttp) REVERT: d 61 MET cc_start: 0.4048 (tmm) cc_final: 0.3306 (ppp) REVERT: d 132 ASP cc_start: 0.8992 (OUTLIER) cc_final: 0.8691 (p0) REVERT: d 175 ASP cc_start: 0.9454 (t0) cc_final: 0.8920 (m-30) REVERT: e 57 ASP cc_start: 0.8935 (OUTLIER) cc_final: 0.8607 (p0) REVERT: f 95 GLU cc_start: 0.9286 (tp30) cc_final: 0.8768 (tm-30) REVERT: f 127 MET cc_start: 0.8714 (mpp) cc_final: 0.8157 (mtm) REVERT: f 249 MET cc_start: 0.7959 (mmm) cc_final: 0.7631 (mmm) REVERT: f 279 MET cc_start: 0.8823 (mmm) cc_final: 0.8456 (mmm) REVERT: f 329 ASP cc_start: 0.8668 (p0) cc_final: 0.8219 (p0) REVERT: f 368 ASP cc_start: 0.8849 (m-30) cc_final: 0.8457 (m-30) REVERT: f 371 MET cc_start: 0.8545 (tmm) cc_final: 0.8333 (tmm) REVERT: f 374 ASN cc_start: 0.9086 (m-40) cc_final: 0.8734 (t0) REVERT: f 459 MET cc_start: 0.9241 (mmp) cc_final: 0.9019 (mmp) REVERT: f 480 MET cc_start: 0.9459 (mmm) cc_final: 0.9090 (tpp) REVERT: f 593 CYS cc_start: 0.7353 (t) cc_final: 0.6780 (t) REVERT: f 743 MET cc_start: 0.9087 (pmm) cc_final: 0.8650 (pmm) REVERT: f 776 GLU cc_start: 0.9478 (mm-30) cc_final: 0.9201 (mt-10) REVERT: f 782 LYS cc_start: 0.9406 (mtpt) cc_final: 0.9188 (tmmt) REVERT: f 812 MET cc_start: 0.9324 (pmm) cc_final: 0.8581 (pmm) outliers start: 94 outliers final: 52 residues processed: 351 average time/residue: 0.2319 time to fit residues: 138.7062 Evaluate side-chains 326 residues out of total 4027 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 266 time to evaluate : 1.525 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 SER Chi-restraints excluded: chain A residue 231 VAL Chi-restraints excluded: chain A residue 237 SER Chi-restraints excluded: chain A residue 251 THR Chi-restraints excluded: chain A residue 302 THR Chi-restraints excluded: chain A residue 495 LEU Chi-restraints excluded: chain A residue 524 GLU Chi-restraints excluded: chain B residue 10 VAL Chi-restraints excluded: chain B residue 115 MET Chi-restraints excluded: chain B residue 258 SER Chi-restraints excluded: chain B residue 515 MET Chi-restraints excluded: chain C residue 41 LEU Chi-restraints excluded: chain C residue 80 LEU Chi-restraints excluded: chain C residue 99 CYS Chi-restraints excluded: chain C residue 108 VAL Chi-restraints excluded: chain C residue 123 CYS Chi-restraints excluded: chain D residue 52 ILE Chi-restraints excluded: chain D residue 94 TYR Chi-restraints excluded: chain D residue 143 HIS Chi-restraints excluded: chain D residue 153 ARG Chi-restraints excluded: chain E residue 33 VAL Chi-restraints excluded: chain E residue 92 SER Chi-restraints excluded: chain E residue 165 CYS Chi-restraints excluded: chain E residue 184 LEU Chi-restraints excluded: chain E residue 185 ASN Chi-restraints excluded: chain F residue 659 PHE Chi-restraints excluded: chain a residue 311 LEU Chi-restraints excluded: chain a residue 409 TYR Chi-restraints excluded: chain b residue 10 VAL Chi-restraints excluded: chain b residue 20 MET Chi-restraints excluded: chain b residue 78 THR Chi-restraints excluded: chain b residue 131 HIS Chi-restraints excluded: chain b residue 331 MET Chi-restraints excluded: chain c residue 10 MET Chi-restraints excluded: chain c residue 16 LEU Chi-restraints excluded: chain c residue 49 VAL Chi-restraints excluded: chain c residue 54 VAL Chi-restraints excluded: chain c residue 125 LEU Chi-restraints excluded: chain c residue 132 SER Chi-restraints excluded: chain c residue 162 LEU Chi-restraints excluded: chain c residue 164 ILE Chi-restraints excluded: chain c residue 174 LEU Chi-restraints excluded: chain c residue 181 THR Chi-restraints excluded: chain d residue 127 ILE Chi-restraints excluded: chain d residue 132 ASP Chi-restraints excluded: chain d residue 143 HIS Chi-restraints excluded: chain d residue 163 GLU Chi-restraints excluded: chain e residue 19 PHE Chi-restraints excluded: chain e residue 57 ASP Chi-restraints excluded: chain e residue 122 VAL Chi-restraints excluded: chain f residue 94 ILE Chi-restraints excluded: chain f residue 109 LEU Chi-restraints excluded: chain f residue 250 LEU Chi-restraints excluded: chain f residue 287 VAL Chi-restraints excluded: chain f residue 326 CYS Chi-restraints excluded: chain f residue 406 THR Chi-restraints excluded: chain f residue 409 HIS Chi-restraints excluded: chain f residue 412 ASN Chi-restraints excluded: chain f residue 483 PHE Chi-restraints excluded: chain f residue 498 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 457 random chunks: chunk 361 optimal weight: 3.9990 chunk 73 optimal weight: 2.9990 chunk 6 optimal weight: 0.0040 chunk 424 optimal weight: 4.9990 chunk 430 optimal weight: 10.0000 chunk 63 optimal weight: 0.0060 chunk 197 optimal weight: 10.0000 chunk 366 optimal weight: 1.9990 chunk 207 optimal weight: 1.9990 chunk 99 optimal weight: 0.8980 chunk 90 optimal weight: 1.9990 overall best weight: 0.9812 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... a 125 GLN ** e 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 558 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 745 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 848 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3618 r_free = 0.3618 target = 0.064435 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.2961 r_free = 0.2961 target = 0.043388 restraints weight = 304545.103| |-----------------------------------------------------------------------------| r_work (start): 0.2886 rms_B_bonded: 5.18 r_work (final): 0.2886 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2885 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2885 r_free = 0.2885 target_work(ls_wunit_k1) = 0.041 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2885 r_free = 0.2885 target_work(ls_wunit_k1) = 0.041 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (7 function evaluations) r_final: 0.2885 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8709 moved from start: 0.1978 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 40252 Z= 0.124 Angle : 0.543 12.131 54945 Z= 0.288 Chirality : 0.039 0.192 6097 Planarity : 0.003 0.054 6539 Dihedral : 16.778 76.115 6480 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 5.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 2.11 % Allowed : 22.24 % Favored : 75.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.45 (0.13), residues: 4457 helix: 2.55 (0.12), residues: 1765 sheet: 0.52 (0.19), residues: 748 loop : -0.33 (0.14), residues: 1944 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG D 3 TYR 0.027 0.001 TYR D 129 PHE 0.020 0.001 PHE f 125 TRP 0.014 0.001 TRP C 119 HIS 0.004 0.001 HIS f 501 Details of bonding type rmsd/Z covalent geometry : bond 0.00265 / 0.12 (40252) covalent geometry : angle 0.54305 / 0.29 (54945) hydrogen bonds : bond 0.03276 / 2.19 ( 1999) hydrogen bonds : angle 4.32500 / 3.00 ( 5530) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8914 Ramachandran restraints generated. 4457 Oldfield, 0 Emsley, 4457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8914 Ramachandran restraints generated. 4457 Oldfield, 0 Emsley, 4457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 375 residues out of total 4027 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 290 time to evaluate : 1.598 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 115 MET cc_start: 0.9387 (OUTLIER) cc_final: 0.9010 (mpp) REVERT: C 165 GLN cc_start: 0.9531 (mt0) cc_final: 0.9300 (tm-30) REVERT: C 182 GLU cc_start: 0.8853 (mp0) cc_final: 0.8621 (mp0) REVERT: C 195 ILE cc_start: 0.9205 (tp) cc_final: 0.8800 (pt) REVERT: C 197 LYS cc_start: 0.9438 (mtmm) cc_final: 0.8386 (mtmm) REVERT: D 61 MET cc_start: 0.8595 (ppp) cc_final: 0.8200 (ppp) REVERT: D 66 TYR cc_start: 0.8116 (t80) cc_final: 0.7799 (t80) REVERT: E 85 THR cc_start: 0.9163 (OUTLIER) cc_final: 0.8615 (p) REVERT: E 145 GLN cc_start: 0.9616 (tp-100) cc_final: 0.9328 (tm-30) REVERT: a 62 MET cc_start: 0.8475 (tpp) cc_final: 0.8190 (tpp) REVERT: a 99 PHE cc_start: 0.8667 (m-80) cc_final: 0.8416 (t80) REVERT: a 135 MET cc_start: 0.8473 (mmt) cc_final: 0.8229 (mmt) REVERT: a 145 GLU cc_start: 0.8759 (mt-10) cc_final: 0.8486 (mt-10) REVERT: a 152 ASN cc_start: 0.9163 (m-40) cc_final: 0.8852 (m-40) REVERT: a 311 LEU cc_start: 0.9173 (OUTLIER) cc_final: 0.8760 (mt) REVERT: a 409 TYR cc_start: 0.8547 (OUTLIER) cc_final: 0.7872 (t80) REVERT: b 84 MET cc_start: 0.8738 (pmm) cc_final: 0.8433 (pmm) REVERT: b 215 LEU cc_start: 0.9432 (tp) cc_final: 0.9007 (mt) REVERT: c 63 LYS cc_start: 0.8584 (tppt) cc_final: 0.8191 (mmtt) REVERT: c 81 ARG cc_start: 0.8739 (tpp-160) cc_final: 0.8439 (tpp80) REVERT: c 85 LYS cc_start: 0.9044 (mtmm) cc_final: 0.8770 (mtmt) REVERT: c 156 LEU cc_start: 0.9040 (OUTLIER) cc_final: 0.8749 (tt) REVERT: d 61 MET cc_start: 0.4105 (tmm) cc_final: 0.3375 (ppp) REVERT: d 144 LEU cc_start: 0.9840 (OUTLIER) cc_final: 0.9459 (tp) REVERT: d 175 ASP cc_start: 0.9421 (t0) cc_final: 0.9196 (t0) REVERT: e 57 ASP cc_start: 0.8949 (m-30) cc_final: 0.8646 (p0) REVERT: e 108 LEU cc_start: 0.9527 (tp) cc_final: 0.9283 (tp) REVERT: f 78 GLU cc_start: 0.9189 (tp30) cc_final: 0.8900 (tm-30) REVERT: f 95 GLU cc_start: 0.9233 (tp30) cc_final: 0.9021 (tp30) REVERT: f 127 MET cc_start: 0.8638 (mpp) cc_final: 0.8381 (mtm) REVERT: f 249 MET cc_start: 0.7955 (mmm) cc_final: 0.7731 (mmt) REVERT: f 329 ASP cc_start: 0.8641 (p0) cc_final: 0.8136 (p0) REVERT: f 368 ASP cc_start: 0.8780 (m-30) cc_final: 0.8402 (m-30) REVERT: f 374 ASN cc_start: 0.9031 (m-40) cc_final: 0.8581 (t0) REVERT: f 447 TRP cc_start: 0.8672 (m-10) cc_final: 0.8204 (m-10) REVERT: f 480 MET cc_start: 0.9331 (mmm) cc_final: 0.9018 (tpp) REVERT: f 593 CYS cc_start: 0.7430 (t) cc_final: 0.6954 (t) REVERT: f 743 MET cc_start: 0.9103 (pmm) cc_final: 0.8639 (pmm) REVERT: f 776 GLU cc_start: 0.9491 (mm-30) cc_final: 0.9198 (mt-10) REVERT: f 782 LYS cc_start: 0.9373 (mtpt) cc_final: 0.9126 (tmmt) REVERT: f 812 MET cc_start: 0.9309 (pmm) cc_final: 0.8662 (pmm) outliers start: 85 outliers final: 44 residues processed: 353 average time/residue: 0.2185 time to fit residues: 131.8831 Evaluate side-chains 326 residues out of total 4027 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 276 time to evaluate : 1.510 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 SER Chi-restraints excluded: chain A residue 251 THR Chi-restraints excluded: chain A residue 302 THR Chi-restraints excluded: chain A residue 409 TYR Chi-restraints excluded: chain A residue 524 GLU Chi-restraints excluded: chain B residue 10 VAL Chi-restraints excluded: chain B residue 115 MET Chi-restraints excluded: chain B residue 258 SER Chi-restraints excluded: chain B residue 515 MET Chi-restraints excluded: chain C residue 41 LEU Chi-restraints excluded: chain C residue 66 THR Chi-restraints excluded: chain C residue 80 LEU Chi-restraints excluded: chain C residue 123 CYS Chi-restraints excluded: chain C residue 176 ARG Chi-restraints excluded: chain D residue 94 TYR Chi-restraints excluded: chain D residue 143 HIS Chi-restraints excluded: chain E residue 85 THR Chi-restraints excluded: chain E residue 108 LEU Chi-restraints excluded: chain E residue 172 LEU Chi-restraints excluded: chain E residue 184 LEU Chi-restraints excluded: chain F residue 825 VAL Chi-restraints excluded: chain H residue 193 LYS Chi-restraints excluded: chain a residue 311 LEU Chi-restraints excluded: chain a residue 409 TYR Chi-restraints excluded: chain b residue 78 THR Chi-restraints excluded: chain b residue 331 MET Chi-restraints excluded: chain b residue 533 ILE Chi-restraints excluded: chain c residue 16 LEU Chi-restraints excluded: chain c residue 39 SER Chi-restraints excluded: chain c residue 49 VAL Chi-restraints excluded: chain c residue 54 VAL Chi-restraints excluded: chain c residue 125 LEU Chi-restraints excluded: chain c residue 132 SER Chi-restraints excluded: chain c residue 156 LEU Chi-restraints excluded: chain c residue 162 LEU Chi-restraints excluded: chain c residue 164 ILE Chi-restraints excluded: chain c residue 174 LEU Chi-restraints excluded: chain c residue 181 THR Chi-restraints excluded: chain d residue 127 ILE Chi-restraints excluded: chain d residue 144 LEU Chi-restraints excluded: chain d residue 163 GLU Chi-restraints excluded: chain e residue 122 VAL Chi-restraints excluded: chain f residue 94 ILE Chi-restraints excluded: chain f residue 224 VAL Chi-restraints excluded: chain f residue 250 LEU Chi-restraints excluded: chain f residue 315 ILE Chi-restraints excluded: chain f residue 326 CYS Chi-restraints excluded: chain f residue 409 HIS Chi-restraints excluded: chain f residue 412 ASN Chi-restraints excluded: chain f residue 498 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 457 random chunks: chunk 131 optimal weight: 9.9990 chunk 206 optimal weight: 0.7980 chunk 30 optimal weight: 5.9990 chunk 3 optimal weight: 4.9990 chunk 425 optimal weight: 6.9990 chunk 288 optimal weight: 3.9990 chunk 215 optimal weight: 4.9990 chunk 418 optimal weight: 2.9990 chunk 199 optimal weight: 20.0000 chunk 136 optimal weight: 3.9990 chunk 291 optimal weight: 2.9990 overall best weight: 2.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 95 ASN A 485 GLN A 489 ASN C 213 ASN E 21 GLN b 243 HIS d 195 HIS ** e 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 558 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 745 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 848 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3588 r_free = 0.3588 target = 0.063089 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2916 r_free = 0.2916 target = 0.041884 restraints weight = 302725.558| |-----------------------------------------------------------------------------| r_work (start): 0.2837 rms_B_bonded: 5.13 r_work (final): 0.2837 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2836 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2836 r_free = 0.2836 target_work(ls_wunit_k1) = 0.040 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2836 r_free = 0.2836 target_work(ls_wunit_k1) = 0.040 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2836 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8762 moved from start: 0.2237 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.061 40252 Z= 0.240 Angle : 0.597 12.677 54945 Z= 0.312 Chirality : 0.040 0.180 6097 Planarity : 0.004 0.052 6539 Dihedral : 16.908 78.801 6480 Min Nonbonded Distance : 2.397 Molprobity Statistics. All-atom Clashscore : 7.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.35 % Favored : 96.65 % Rotamer: Outliers : 2.56 % Allowed : 22.31 % Favored : 75.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.36 (0.13), residues: 4457 helix: 2.48 (0.12), residues: 1773 sheet: 0.40 (0.19), residues: 753 loop : -0.37 (0.14), residues: 1931 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG D 3 TYR 0.022 0.001 TYR D 129 PHE 0.025 0.001 PHE a 131 TRP 0.022 0.001 TRP f 46 HIS 0.005 0.001 HIS a 204 Details of bonding type rmsd/Z covalent geometry : bond 0.00530 / 0.24 (40252) covalent geometry : angle 0.59744 / 0.31 (54945) hydrogen bonds : bond 0.03690 / 2.48 ( 1999) hydrogen bonds : angle 4.38739 / 3.05 ( 5530) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8914 Ramachandran restraints generated. 4457 Oldfield, 0 Emsley, 4457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8914 Ramachandran restraints generated. 4457 Oldfield, 0 Emsley, 4457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 374 residues out of total 4027 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 103 poor density : 271 time to evaluate : 1.489 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 111 LEU cc_start: 0.9683 (OUTLIER) cc_final: 0.9433 (mp) REVERT: B 115 MET cc_start: 0.9455 (OUTLIER) cc_final: 0.9052 (mpp) REVERT: C 182 GLU cc_start: 0.8886 (mp0) cc_final: 0.8630 (mp0) REVERT: C 195 ILE cc_start: 0.9224 (tp) cc_final: 0.8823 (pt) REVERT: D 61 MET cc_start: 0.8681 (ppp) cc_final: 0.8279 (ppp) REVERT: D 66 TYR cc_start: 0.8194 (t80) cc_final: 0.7873 (t80) REVERT: E 85 THR cc_start: 0.9221 (OUTLIER) cc_final: 0.8686 (p) REVERT: E 145 GLN cc_start: 0.9633 (tp-100) cc_final: 0.9345 (tm-30) REVERT: E 184 LEU cc_start: 0.9637 (OUTLIER) cc_final: 0.9415 (mm) REVERT: a 62 MET cc_start: 0.8480 (tpp) cc_final: 0.8212 (tpp) REVERT: a 99 PHE cc_start: 0.8710 (m-80) cc_final: 0.8431 (t80) REVERT: a 135 MET cc_start: 0.8635 (mmt) cc_final: 0.8343 (mmt) REVERT: a 145 GLU cc_start: 0.8806 (mt-10) cc_final: 0.8461 (mt-10) REVERT: a 152 ASN cc_start: 0.9161 (m-40) cc_final: 0.8837 (m-40) REVERT: a 311 LEU cc_start: 0.9179 (OUTLIER) cc_final: 0.8719 (mt) REVERT: a 409 TYR cc_start: 0.8626 (OUTLIER) cc_final: 0.7848 (t80) REVERT: b 84 MET cc_start: 0.8700 (pmm) cc_final: 0.8411 (pmm) REVERT: b 115 MET cc_start: 0.9571 (mmt) cc_final: 0.9082 (mmm) REVERT: b 215 LEU cc_start: 0.9470 (tp) cc_final: 0.9057 (mt) REVERT: b 230 SER cc_start: 0.9267 (OUTLIER) cc_final: 0.8999 (p) REVERT: c 85 LYS cc_start: 0.9001 (mtmm) cc_final: 0.8727 (mtmm) REVERT: d 36 LEU cc_start: 0.9241 (OUTLIER) cc_final: 0.9003 (pt) REVERT: d 61 MET cc_start: 0.4209 (tmm) cc_final: 0.3752 (ppp) REVERT: e 57 ASP cc_start: 0.8936 (m-30) cc_final: 0.8610 (p0) REVERT: e 108 LEU cc_start: 0.9545 (tp) cc_final: 0.9287 (tp) REVERT: f 78 GLU cc_start: 0.9231 (tp30) cc_final: 0.8924 (tm-30) REVERT: f 95 GLU cc_start: 0.9293 (tp30) cc_final: 0.9064 (tp30) REVERT: f 249 MET cc_start: 0.8147 (mmm) cc_final: 0.7762 (mmm) REVERT: f 279 MET cc_start: 0.8794 (mmm) cc_final: 0.8355 (mmm) REVERT: f 329 ASP cc_start: 0.8744 (p0) cc_final: 0.8250 (p0) REVERT: f 368 ASP cc_start: 0.8889 (m-30) cc_final: 0.8488 (m-30) REVERT: f 374 ASN cc_start: 0.9031 (m-40) cc_final: 0.8619 (t0) REVERT: f 743 MET cc_start: 0.9146 (pmm) cc_final: 0.8764 (pmm) REVERT: f 746 MET cc_start: 0.8167 (ppp) cc_final: 0.7965 (ppp) REVERT: f 776 GLU cc_start: 0.9508 (mm-30) cc_final: 0.9230 (mt-10) REVERT: f 812 MET cc_start: 0.9312 (pmm) cc_final: 0.8637 (pmm) outliers start: 103 outliers final: 56 residues processed: 357 average time/residue: 0.2216 time to fit residues: 135.1653 Evaluate side-chains 321 residues out of total 4027 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 257 time to evaluate : 1.434 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 SER Chi-restraints excluded: chain A residue 231 VAL Chi-restraints excluded: chain A residue 251 THR Chi-restraints excluded: chain A residue 302 THR Chi-restraints excluded: chain A residue 373 SER Chi-restraints excluded: chain A residue 495 LEU Chi-restraints excluded: chain A residue 524 GLU Chi-restraints excluded: chain B residue 10 VAL Chi-restraints excluded: chain B residue 111 LEU Chi-restraints excluded: chain B residue 115 MET Chi-restraints excluded: chain B residue 258 SER Chi-restraints excluded: chain B residue 515 MET Chi-restraints excluded: chain C residue 41 LEU Chi-restraints excluded: chain C residue 80 LEU Chi-restraints excluded: chain C residue 108 VAL Chi-restraints excluded: chain C residue 123 CYS Chi-restraints excluded: chain C residue 140 MET Chi-restraints excluded: chain C residue 176 ARG Chi-restraints excluded: chain D residue 94 TYR Chi-restraints excluded: chain D residue 143 HIS Chi-restraints excluded: chain E residue 33 VAL Chi-restraints excluded: chain E residue 46 THR Chi-restraints excluded: chain E residue 85 THR Chi-restraints excluded: chain E residue 172 LEU Chi-restraints excluded: chain E residue 184 LEU Chi-restraints excluded: chain F residue 659 PHE Chi-restraints excluded: chain F residue 787 GLN Chi-restraints excluded: chain F residue 825 VAL Chi-restraints excluded: chain a residue 311 LEU Chi-restraints excluded: chain a residue 409 TYR Chi-restraints excluded: chain b residue 10 VAL Chi-restraints excluded: chain b residue 78 THR Chi-restraints excluded: chain b residue 230 SER Chi-restraints excluded: chain b residue 320 ILE Chi-restraints excluded: chain b residue 533 ILE Chi-restraints excluded: chain c residue 16 LEU Chi-restraints excluded: chain c residue 39 SER Chi-restraints excluded: chain c residue 49 VAL Chi-restraints excluded: chain c residue 54 VAL Chi-restraints excluded: chain c residue 97 CYS Chi-restraints excluded: chain c residue 125 LEU Chi-restraints excluded: chain c residue 132 SER Chi-restraints excluded: chain c residue 162 LEU Chi-restraints excluded: chain c residue 174 LEU Chi-restraints excluded: chain c residue 176 ARG Chi-restraints excluded: chain c residue 181 THR Chi-restraints excluded: chain d residue 36 LEU Chi-restraints excluded: chain d residue 69 GLU Chi-restraints excluded: chain d residue 127 ILE Chi-restraints excluded: chain d residue 143 HIS Chi-restraints excluded: chain d residue 163 GLU Chi-restraints excluded: chain e residue 122 VAL Chi-restraints excluded: chain e residue 162 PHE Chi-restraints excluded: chain f residue 94 ILE Chi-restraints excluded: chain f residue 109 LEU Chi-restraints excluded: chain f residue 194 LEU Chi-restraints excluded: chain f residue 224 VAL Chi-restraints excluded: chain f residue 235 LEU Chi-restraints excluded: chain f residue 287 VAL Chi-restraints excluded: chain f residue 326 CYS Chi-restraints excluded: chain f residue 406 THR Chi-restraints excluded: chain f residue 409 HIS Chi-restraints excluded: chain f residue 412 ASN Chi-restraints excluded: chain f residue 498 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 457 random chunks: chunk 85 optimal weight: 5.9990 chunk 389 optimal weight: 0.9990 chunk 158 optimal weight: 0.8980 chunk 227 optimal weight: 8.9990 chunk 411 optimal weight: 0.4980 chunk 182 optimal weight: 7.9990 chunk 130 optimal weight: 10.0000 chunk 333 optimal weight: 9.9990 chunk 393 optimal weight: 4.9990 chunk 245 optimal weight: 0.7980 chunk 206 optimal weight: 4.9990 overall best weight: 1.6384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 21 GLN b 243 HIS b 382 HIS ** e 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 558 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** f 673 GLN ** f 848 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3597 r_free = 0.3597 target = 0.063426 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.2938 r_free = 0.2938 target = 0.042591 restraints weight = 251722.160| |-----------------------------------------------------------------------------| r_work (start): 0.2868 rms_B_bonded: 4.66 r_work: 0.2685 rms_B_bonded: 4.94 restraints_weight: 0.5000 r_work (final): 0.2685 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2685 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2685 r_free = 0.2685 target_work(ls_wunit_k1) = 0.036 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2685 r_free = 0.2685 target_work(ls_wunit_k1) = 0.036 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2685 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8842 moved from start: 0.2316 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 40252 Z= 0.160 Angle : 0.576 11.432 54945 Z= 0.301 Chirality : 0.040 0.393 6097 Planarity : 0.004 0.130 6539 Dihedral : 16.911 77.481 6480 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 7.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.72 % Favored : 97.28 % Rotamer: Outliers : 2.06 % Allowed : 23.31 % Favored : 74.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.38 (0.13), residues: 4457 helix: 2.47 (0.12), residues: 1781 sheet: 0.46 (0.19), residues: 758 loop : -0.38 (0.14), residues: 1918 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG C 178 TYR 0.028 0.001 TYR D 129 PHE 0.019 0.001 PHE a 131 TRP 0.016 0.001 TRP f 46 HIS 0.004 0.001 HIS f 501 Details of bonding type rmsd/Z covalent geometry : bond 0.00351 / 0.16 (40252) covalent geometry : angle 0.57648 / 0.30 (54945) hydrogen bonds : bond 0.03384 / 2.27 ( 1999) hydrogen bonds : angle 4.31134 / 2.99 ( 5530) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8914 Ramachandran restraints generated. 4457 Oldfield, 0 Emsley, 4457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8914 Ramachandran restraints generated. 4457 Oldfield, 0 Emsley, 4457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 353 residues out of total 4027 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 270 time to evaluate : 1.450 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 115 MET cc_start: 0.9470 (OUTLIER) cc_final: 0.9051 (mpp) REVERT: C 85 LYS cc_start: 0.9634 (ttpt) cc_final: 0.9371 (ptpp) REVERT: C 165 GLN cc_start: 0.9567 (mt0) cc_final: 0.9328 (tm-30) REVERT: C 182 GLU cc_start: 0.9239 (mp0) cc_final: 0.8991 (mp0) REVERT: C 195 ILE cc_start: 0.9325 (tp) cc_final: 0.8932 (pt) REVERT: D 61 MET cc_start: 0.8685 (ppp) cc_final: 0.8278 (ppp) REVERT: D 66 TYR cc_start: 0.8397 (t80) cc_final: 0.8062 (t80) REVERT: E 85 THR cc_start: 0.9276 (OUTLIER) cc_final: 0.8750 (p) REVERT: E 145 GLN cc_start: 0.9650 (tp-100) cc_final: 0.9364 (tm-30) REVERT: a 62 MET cc_start: 0.8948 (tpp) cc_final: 0.8703 (tpp) REVERT: a 99 PHE cc_start: 0.8825 (m-80) cc_final: 0.8582 (t80) REVERT: a 135 MET cc_start: 0.8655 (mmt) cc_final: 0.8388 (mmt) REVERT: a 145 GLU cc_start: 0.8920 (mt-10) cc_final: 0.8596 (mt-10) REVERT: a 152 ASN cc_start: 0.9150 (m-40) cc_final: 0.8848 (m-40) REVERT: a 311 LEU cc_start: 0.9162 (OUTLIER) cc_final: 0.8732 (mt) REVERT: a 409 TYR cc_start: 0.9101 (OUTLIER) cc_final: 0.8417 (t80) REVERT: a 453 MET cc_start: 0.8889 (mmm) cc_final: 0.8554 (mmm) REVERT: b 84 MET cc_start: 0.8745 (pmm) cc_final: 0.8421 (pmm) REVERT: b 115 MET cc_start: 0.9639 (mmt) cc_final: 0.9216 (mmm) REVERT: b 215 LEU cc_start: 0.9432 (tp) cc_final: 0.9030 (mt) REVERT: b 230 SER cc_start: 0.9321 (OUTLIER) cc_final: 0.9086 (p) REVERT: c 85 LYS cc_start: 0.8893 (mtmm) cc_final: 0.8639 (mtmm) REVERT: d 1 MET cc_start: 0.8996 (OUTLIER) cc_final: 0.8380 (tpt) REVERT: d 36 LEU cc_start: 0.9274 (OUTLIER) cc_final: 0.9034 (pt) REVERT: d 132 ASP cc_start: 0.9092 (m-30) cc_final: 0.8848 (p0) REVERT: d 154 ASP cc_start: 0.9660 (m-30) cc_final: 0.9262 (t0) REVERT: e 57 ASP cc_start: 0.9034 (m-30) cc_final: 0.8671 (p0) REVERT: e 108 LEU cc_start: 0.9580 (tp) cc_final: 0.9323 (tp) REVERT: f 78 GLU cc_start: 0.9543 (tp30) cc_final: 0.9226 (tm-30) REVERT: f 95 GLU cc_start: 0.9549 (tp30) cc_final: 0.9343 (tp30) REVERT: f 127 MET cc_start: 0.9536 (mmm) cc_final: 0.9221 (mpp) REVERT: f 249 MET cc_start: 0.8332 (mmm) cc_final: 0.7919 (mmm) REVERT: f 263 MET cc_start: 0.8938 (mmm) cc_final: 0.8643 (mmm) REVERT: f 279 MET cc_start: 0.9125 (mmm) cc_final: 0.8667 (mmm) REVERT: f 329 ASP cc_start: 0.8717 (p0) cc_final: 0.8214 (p0) REVERT: f 368 ASP cc_start: 0.9077 (m-30) cc_final: 0.8633 (m-30) REVERT: f 374 ASN cc_start: 0.9138 (m-40) cc_final: 0.8637 (t0) REVERT: f 513 LYS cc_start: 0.9800 (mttt) cc_final: 0.9548 (tppt) REVERT: f 673 GLN cc_start: 0.9267 (OUTLIER) cc_final: 0.9046 (pm20) REVERT: f 776 GLU cc_start: 0.9450 (mm-30) cc_final: 0.9165 (mt-10) REVERT: f 812 MET cc_start: 0.9340 (pmm) cc_final: 0.8369 (pmm) outliers start: 83 outliers final: 53 residues processed: 335 average time/residue: 0.2116 time to fit residues: 122.1567 Evaluate side-chains 324 residues out of total 4027 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 263 time to evaluate : 1.582 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 SER Chi-restraints excluded: chain A residue 231 VAL Chi-restraints excluded: chain A residue 251 THR Chi-restraints excluded: chain A residue 302 THR Chi-restraints excluded: chain A residue 524 GLU Chi-restraints excluded: chain B residue 10 VAL Chi-restraints excluded: chain B residue 20 MET Chi-restraints excluded: chain B residue 115 MET Chi-restraints excluded: chain B residue 258 SER Chi-restraints excluded: chain B residue 354 ARG Chi-restraints excluded: chain B residue 515 MET Chi-restraints excluded: chain C residue 41 LEU Chi-restraints excluded: chain C residue 80 LEU Chi-restraints excluded: chain C residue 108 VAL Chi-restraints excluded: chain C residue 123 CYS Chi-restraints excluded: chain C residue 176 ARG Chi-restraints excluded: chain D residue 94 TYR Chi-restraints excluded: chain D residue 143 HIS Chi-restraints excluded: chain E residue 33 VAL Chi-restraints excluded: chain E residue 46 THR Chi-restraints excluded: chain E residue 85 THR Chi-restraints excluded: chain E residue 108 LEU Chi-restraints excluded: chain E residue 172 LEU Chi-restraints excluded: chain E residue 184 LEU Chi-restraints excluded: chain F residue 769 THR Chi-restraints excluded: chain F residue 787 GLN Chi-restraints excluded: chain F residue 825 VAL Chi-restraints excluded: chain a residue 311 LEU Chi-restraints excluded: chain a residue 409 TYR Chi-restraints excluded: chain b residue 10 VAL Chi-restraints excluded: chain b residue 78 THR Chi-restraints excluded: chain b residue 230 SER Chi-restraints excluded: chain b residue 320 ILE Chi-restraints excluded: chain b residue 533 ILE Chi-restraints excluded: chain c residue 16 LEU Chi-restraints excluded: chain c residue 39 SER Chi-restraints excluded: chain c residue 49 VAL Chi-restraints excluded: chain c residue 54 VAL Chi-restraints excluded: chain c residue 125 LEU Chi-restraints excluded: chain c residue 132 SER Chi-restraints excluded: chain c residue 162 LEU Chi-restraints excluded: chain c residue 174 LEU Chi-restraints excluded: chain c residue 176 ARG Chi-restraints excluded: chain c residue 181 THR Chi-restraints excluded: chain d residue 1 MET Chi-restraints excluded: chain d residue 36 LEU Chi-restraints excluded: chain d residue 85 THR Chi-restraints excluded: chain d residue 127 ILE Chi-restraints excluded: chain d residue 143 HIS Chi-restraints excluded: chain d residue 145 GLN Chi-restraints excluded: chain d residue 163 GLU Chi-restraints excluded: chain e residue 122 VAL Chi-restraints excluded: chain e residue 162 PHE Chi-restraints excluded: chain f residue 94 ILE Chi-restraints excluded: chain f residue 224 VAL Chi-restraints excluded: chain f residue 250 LEU Chi-restraints excluded: chain f residue 409 HIS Chi-restraints excluded: chain f residue 412 ASN Chi-restraints excluded: chain f residue 498 SER Chi-restraints excluded: chain f residue 673 GLN Chi-restraints excluded: chain f residue 783 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 457 random chunks: chunk 180 optimal weight: 30.0000 chunk 150 optimal weight: 2.9990 chunk 347 optimal weight: 7.9990 chunk 211 optimal weight: 2.9990 chunk 56 optimal weight: 0.5980 chunk 277 optimal weight: 1.9990 chunk 0 optimal weight: 5.9990 chunk 146 optimal weight: 2.9990 chunk 319 optimal weight: 5.9990 chunk 129 optimal weight: 3.9990 chunk 206 optimal weight: 6.9990 overall best weight: 2.3188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 21 GLN b 243 HIS d 143 HIS e 18 HIS ** e 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** f 433 GLN ** f 558 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 848 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 = 0.3591 r_free = 0.3591 target = 0.063148 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2932 r_free = 0.2932 target = 0.042338 restraints weight = 259937.877| |-----------------------------------------------------------------------------| r_work (start): 0.2857 rms_B_bonded: 4.67 r_work: 0.2671 rms_B_bonded: 4.98 restraints_weight: 0.5000 r_work (final): 0.2671 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2670 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2670 r_free = 0.2670 target_work(ls_wunit_k1) = 0.036 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2670 r_free = 0.2670 target_work(ls_wunit_k1) = 0.036 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2670 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8857 moved from start: 0.2425 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 40252 Z= 0.198 Angle : 0.594 11.109 54945 Z= 0.308 Chirality : 0.040 0.313 6097 Planarity : 0.004 0.110 6539 Dihedral : 16.941 78.017 6480 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 7.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.19 % Favored : 96.81 % Rotamer: Outliers : 2.01 % Allowed : 23.43 % Favored : 74.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.34 (0.13), residues: 4457 helix: 2.44 (0.12), residues: 1780 sheet: 0.41 (0.19), residues: 759 loop : -0.39 (0.14), residues: 1918 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 178 TYR 0.025 0.001 TYR D 129 PHE 0.021 0.001 PHE a 131 TRP 0.022 0.001 TRP f 46 HIS 0.005 0.001 HIS d 143 Details of bonding type rmsd/Z covalent geometry : bond 0.00437 / 0.20 (40252) covalent geometry : angle 0.59397 / 0.31 (54945) hydrogen bonds : bond 0.03472 / 2.33 ( 1999) hydrogen bonds : angle 4.33841 / 3.01 ( 5530) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8914 Ramachandran restraints generated. 4457 Oldfield, 0 Emsley, 4457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8914 Ramachandran restraints generated. 4457 Oldfield, 0 Emsley, 4457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 344 residues out of total 4027 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 263 time to evaluate : 1.635 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 135 MET cc_start: 0.8779 (tpp) cc_final: 0.8219 (mmt) REVERT: B 84 MET cc_start: 0.9019 (ptp) cc_final: 0.8781 (pmm) REVERT: B 111 LEU cc_start: 0.9681 (OUTLIER) cc_final: 0.9441 (mp) REVERT: B 115 MET cc_start: 0.9478 (OUTLIER) cc_final: 0.9067 (mpp) REVERT: C 85 LYS cc_start: 0.9630 (ttpt) cc_final: 0.9335 (ptpp) REVERT: C 165 GLN cc_start: 0.9572 (mt0) cc_final: 0.9332 (tm-30) REVERT: C 182 GLU cc_start: 0.9243 (mp0) cc_final: 0.8987 (mp0) REVERT: C 195 ILE cc_start: 0.9333 (tp) cc_final: 0.8939 (pt) REVERT: D 61 MET cc_start: 0.8691 (ppp) cc_final: 0.8267 (ppp) REVERT: D 66 TYR cc_start: 0.8402 (t80) cc_final: 0.8064 (t80) REVERT: E 85 THR cc_start: 0.9274 (OUTLIER) cc_final: 0.8775 (p) REVERT: E 145 GLN cc_start: 0.9655 (tp-100) cc_final: 0.9366 (tm-30) REVERT: a 62 MET cc_start: 0.8967 (tpp) cc_final: 0.8671 (tpp) REVERT: a 99 PHE cc_start: 0.8842 (m-80) cc_final: 0.8590 (t80) REVERT: a 135 MET cc_start: 0.8611 (mmt) cc_final: 0.8388 (mmt) REVERT: a 145 GLU cc_start: 0.8937 (mt-10) cc_final: 0.8603 (mt-10) REVERT: a 152 ASN cc_start: 0.9156 (m-40) cc_final: 0.8857 (m-40) REVERT: a 311 LEU cc_start: 0.9171 (OUTLIER) cc_final: 0.8730 (mt) REVERT: a 409 TYR cc_start: 0.9135 (OUTLIER) cc_final: 0.8448 (t80) REVERT: a 453 MET cc_start: 0.8894 (mmm) cc_final: 0.8590 (mmm) REVERT: b 84 MET cc_start: 0.8733 (pmm) cc_final: 0.8410 (pmm) REVERT: b 115 MET cc_start: 0.9624 (mmt) cc_final: 0.9368 (mmm) REVERT: b 215 LEU cc_start: 0.9450 (tp) cc_final: 0.9020 (mt) REVERT: b 230 SER cc_start: 0.9322 (OUTLIER) cc_final: 0.9094 (p) REVERT: c 85 LYS cc_start: 0.8881 (mtmm) cc_final: 0.8664 (mtmm) REVERT: d 1 MET cc_start: 0.8956 (OUTLIER) cc_final: 0.8323 (tpt) REVERT: d 61 MET cc_start: 0.4554 (tmm) cc_final: 0.3603 (ppp) REVERT: d 154 ASP cc_start: 0.9661 (m-30) cc_final: 0.9268 (t0) REVERT: e 57 ASP cc_start: 0.8992 (m-30) cc_final: 0.8623 (p0) REVERT: e 108 LEU cc_start: 0.9580 (tp) cc_final: 0.9318 (tp) REVERT: f 78 GLU cc_start: 0.9548 (tp30) cc_final: 0.9231 (tm-30) REVERT: f 95 GLU cc_start: 0.9549 (tp30) cc_final: 0.9342 (tp30) REVERT: f 279 MET cc_start: 0.9024 (mmm) cc_final: 0.8676 (mmm) REVERT: f 329 ASP cc_start: 0.8754 (p0) cc_final: 0.8254 (p0) REVERT: f 368 ASP cc_start: 0.9041 (m-30) cc_final: 0.8597 (m-30) REVERT: f 374 ASN cc_start: 0.9147 (m-40) cc_final: 0.8643 (t0) REVERT: f 673 GLN cc_start: 0.9398 (OUTLIER) cc_final: 0.9165 (pm20) REVERT: f 743 MET cc_start: 0.9365 (pmm) cc_final: 0.8802 (pmm) REVERT: f 776 GLU cc_start: 0.9467 (mm-30) cc_final: 0.9190 (mt-10) REVERT: f 812 MET cc_start: 0.9352 (pmm) cc_final: 0.8376 (pmm) outliers start: 81 outliers final: 59 residues processed: 329 average time/residue: 0.2127 time to fit residues: 121.7922 Evaluate side-chains 329 residues out of total 4027 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 262 time to evaluate : 1.503 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 SER Chi-restraints excluded: chain A residue 231 VAL Chi-restraints excluded: chain A residue 251 THR Chi-restraints excluded: chain A residue 277 VAL Chi-restraints excluded: chain A residue 302 THR Chi-restraints excluded: chain A residue 524 GLU Chi-restraints excluded: chain B residue 10 VAL Chi-restraints excluded: chain B residue 20 MET Chi-restraints excluded: chain B residue 111 LEU Chi-restraints excluded: chain B residue 115 MET Chi-restraints excluded: chain B residue 258 SER Chi-restraints excluded: chain B residue 354 ARG Chi-restraints excluded: chain B residue 515 MET Chi-restraints excluded: chain C residue 41 LEU Chi-restraints excluded: chain C residue 80 LEU Chi-restraints excluded: chain C residue 108 VAL Chi-restraints excluded: chain C residue 123 CYS Chi-restraints excluded: chain C residue 176 ARG Chi-restraints excluded: chain C residue 204 ILE Chi-restraints excluded: chain D residue 94 TYR Chi-restraints excluded: chain D residue 143 HIS Chi-restraints excluded: chain E residue 33 VAL Chi-restraints excluded: chain E residue 46 THR Chi-restraints excluded: chain E residue 85 THR Chi-restraints excluded: chain E residue 165 CYS Chi-restraints excluded: chain E residue 172 LEU Chi-restraints excluded: chain F residue 659 PHE Chi-restraints excluded: chain F residue 698 TYR Chi-restraints excluded: chain F residue 769 THR Chi-restraints excluded: chain F residue 787 GLN Chi-restraints excluded: chain F residue 825 VAL Chi-restraints excluded: chain a residue 311 LEU Chi-restraints excluded: chain a residue 409 TYR Chi-restraints excluded: chain b residue 10 VAL Chi-restraints excluded: chain b residue 78 THR Chi-restraints excluded: chain b residue 230 SER Chi-restraints excluded: chain b residue 320 ILE Chi-restraints excluded: chain b residue 331 MET Chi-restraints excluded: chain b residue 533 ILE Chi-restraints excluded: chain c residue 16 LEU Chi-restraints excluded: chain c residue 39 SER Chi-restraints excluded: chain c residue 49 VAL Chi-restraints excluded: chain c residue 54 VAL Chi-restraints excluded: chain c residue 97 CYS Chi-restraints excluded: chain c residue 125 LEU Chi-restraints excluded: chain c residue 132 SER Chi-restraints excluded: chain c residue 162 LEU Chi-restraints excluded: chain c residue 174 LEU Chi-restraints excluded: chain c residue 176 ARG Chi-restraints excluded: chain c residue 181 THR Chi-restraints excluded: chain d residue 1 MET Chi-restraints excluded: chain d residue 85 THR Chi-restraints excluded: chain d residue 127 ILE Chi-restraints excluded: chain d residue 143 HIS Chi-restraints excluded: chain d residue 163 GLU Chi-restraints excluded: chain e residue 122 VAL Chi-restraints excluded: chain e residue 123 ILE Chi-restraints excluded: chain e residue 162 PHE Chi-restraints excluded: chain f residue 94 ILE Chi-restraints excluded: chain f residue 194 LEU Chi-restraints excluded: chain f residue 224 VAL Chi-restraints excluded: chain f residue 406 THR Chi-restraints excluded: chain f residue 409 HIS Chi-restraints excluded: chain f residue 412 ASN Chi-restraints excluded: chain f residue 498 SER Chi-restraints excluded: chain f residue 673 GLN Chi-restraints excluded: chain f residue 783 ASN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 457 random chunks: chunk 246 optimal weight: 6.9990 chunk 210 optimal weight: 0.9980 chunk 397 optimal weight: 0.5980 chunk 283 optimal weight: 0.7980 chunk 53 optimal weight: 1.9990 chunk 23 optimal weight: 0.9990 chunk 381 optimal weight: 0.7980 chunk 50 optimal weight: 9.9990 chunk 421 optimal weight: 7.9990 chunk 47 optimal weight: 0.7980 chunk 358 optimal weight: 3.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 21 GLN b 243 HIS c 62 ASN ** e 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 558 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 848 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 = 0.3605 r_free = 0.3605 target = 0.063819 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.2952 r_free = 0.2952 target = 0.043070 restraints weight = 251651.921| |-----------------------------------------------------------------------------| r_work (start): 0.2886 rms_B_bonded: 4.66 r_work: 0.2705 rms_B_bonded: 4.95 restraints_weight: 0.5000 r_work (final): 0.2705 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2703 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2703 r_free = 0.2703 target_work(ls_wunit_k1) = 0.037 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2703 r_free = 0.2703 target_work(ls_wunit_k1) = 0.037 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2703 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8825 moved from start: 0.2438 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.068 40252 Z= 0.122 Angle : 0.588 12.777 54945 Z= 0.302 Chirality : 0.040 0.322 6097 Planarity : 0.004 0.090 6539 Dihedral : 16.908 77.232 6480 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 6.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer: Outliers : 1.69 % Allowed : 23.98 % Favored : 74.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.40 (0.13), residues: 4457 helix: 2.48 (0.12), residues: 1771 sheet: 0.54 (0.19), residues: 749 loop : -0.37 (0.14), residues: 1937 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 3 TYR 0.029 0.001 TYR D 129 PHE 0.017 0.001 PHE a 131 TRP 0.021 0.001 TRP f 46 HIS 0.016 0.001 HIS d 143 Details of bonding type rmsd/Z covalent geometry : bond 0.00261 / 0.12 (40252) covalent geometry : angle 0.58841 / 0.30 (54945) hydrogen bonds : bond 0.03242 / 2.17 ( 1999) hydrogen bonds : angle 4.24643 / 2.94 ( 5530) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8914 Ramachandran restraints generated. 4457 Oldfield, 0 Emsley, 4457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8914 Ramachandran restraints generated. 4457 Oldfield, 0 Emsley, 4457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 349 residues out of total 4027 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 281 time to evaluate : 1.394 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 84 MET cc_start: 0.9036 (ptp) cc_final: 0.8834 (pmm) REVERT: B 115 MET cc_start: 0.9472 (OUTLIER) cc_final: 0.9090 (mpp) REVERT: C 85 LYS cc_start: 0.9636 (ttpt) cc_final: 0.9347 (ptpp) REVERT: C 165 GLN cc_start: 0.9558 (mt0) cc_final: 0.9311 (tm-30) REVERT: C 182 GLU cc_start: 0.9230 (mp0) cc_final: 0.8979 (mp0) REVERT: C 195 ILE cc_start: 0.9324 (tp) cc_final: 0.8927 (pt) REVERT: D 61 MET cc_start: 0.8800 (ppp) cc_final: 0.8172 (ppp) REVERT: D 66 TYR cc_start: 0.8345 (t80) cc_final: 0.7951 (t80) REVERT: E 85 THR cc_start: 0.9251 (OUTLIER) cc_final: 0.8740 (p) REVERT: E 145 GLN cc_start: 0.9632 (tp-100) cc_final: 0.9354 (tm-30) REVERT: a 62 MET cc_start: 0.8950 (tpp) cc_final: 0.8658 (tpp) REVERT: a 99 PHE cc_start: 0.8806 (m-80) cc_final: 0.8579 (t80) REVERT: a 135 MET cc_start: 0.8561 (mmt) cc_final: 0.8287 (mmt) REVERT: a 145 GLU cc_start: 0.8922 (mt-10) cc_final: 0.8593 (mt-10) REVERT: a 152 ASN cc_start: 0.9124 (m-40) cc_final: 0.8847 (m-40) REVERT: a 297 LYS cc_start: 0.9295 (OUTLIER) cc_final: 0.8977 (mmmm) REVERT: a 311 LEU cc_start: 0.9151 (OUTLIER) cc_final: 0.8741 (mt) REVERT: a 409 TYR cc_start: 0.9085 (OUTLIER) cc_final: 0.8421 (t80) REVERT: a 453 MET cc_start: 0.8894 (mmm) cc_final: 0.8622 (mmm) REVERT: b 84 MET cc_start: 0.8750 (pmm) cc_final: 0.8417 (pmm) REVERT: b 115 MET cc_start: 0.9613 (mmt) cc_final: 0.9399 (mmm) REVERT: b 215 LEU cc_start: 0.9423 (tp) cc_final: 0.9039 (mt) REVERT: b 230 SER cc_start: 0.9313 (OUTLIER) cc_final: 0.9093 (p) REVERT: b 331 MET cc_start: 0.8724 (OUTLIER) cc_final: 0.8425 (mtp) REVERT: c 219 MET cc_start: 0.9333 (mmm) cc_final: 0.9109 (mmt) REVERT: d 1 MET cc_start: 0.8912 (tpt) cc_final: 0.8282 (tpt) REVERT: d 61 MET cc_start: 0.4402 (tmm) cc_final: 0.4072 (ppp) REVERT: d 132 ASP cc_start: 0.9070 (m-30) cc_final: 0.8753 (p0) REVERT: d 154 ASP cc_start: 0.9651 (m-30) cc_final: 0.9267 (t0) REVERT: e 57 ASP cc_start: 0.8999 (m-30) cc_final: 0.8686 (p0) REVERT: e 108 LEU cc_start: 0.9577 (tp) cc_final: 0.9313 (tp) REVERT: f 78 GLU cc_start: 0.9542 (tp30) cc_final: 0.9230 (tm-30) REVERT: f 95 GLU cc_start: 0.9512 (tp30) cc_final: 0.9302 (tp30) REVERT: f 127 MET cc_start: 0.9534 (mmm) cc_final: 0.9135 (mtm) REVERT: f 279 MET cc_start: 0.9011 (mmm) cc_final: 0.8653 (mmm) REVERT: f 368 ASP cc_start: 0.8954 (m-30) cc_final: 0.8525 (m-30) REVERT: f 374 ASN cc_start: 0.9128 (m-40) cc_final: 0.8690 (t0) REVERT: f 743 MET cc_start: 0.9317 (pmm) cc_final: 0.8774 (pmm) REVERT: f 776 GLU cc_start: 0.9448 (mm-30) cc_final: 0.9164 (mt-10) REVERT: f 812 MET cc_start: 0.9335 (pmm) cc_final: 0.8376 (pmm) outliers start: 68 outliers final: 51 residues processed: 335 average time/residue: 0.2273 time to fit residues: 130.8508 Evaluate side-chains 323 residues out of total 4027 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 265 time to evaluate : 1.628 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 SER Chi-restraints excluded: chain A residue 231 VAL Chi-restraints excluded: chain A residue 251 THR Chi-restraints excluded: chain A residue 277 VAL Chi-restraints excluded: chain A residue 302 THR Chi-restraints excluded: chain A residue 524 GLU Chi-restraints excluded: chain B residue 10 VAL Chi-restraints excluded: chain B residue 20 MET Chi-restraints excluded: chain B residue 115 MET Chi-restraints excluded: chain B residue 258 SER Chi-restraints excluded: chain B residue 354 ARG Chi-restraints excluded: chain B residue 515 MET Chi-restraints excluded: chain C residue 41 LEU Chi-restraints excluded: chain C residue 80 LEU Chi-restraints excluded: chain C residue 123 CYS Chi-restraints excluded: chain C residue 176 ARG Chi-restraints excluded: chain C residue 198 LEU Chi-restraints excluded: chain C residue 204 ILE Chi-restraints excluded: chain D residue 94 TYR Chi-restraints excluded: chain E residue 33 VAL Chi-restraints excluded: chain E residue 85 THR Chi-restraints excluded: chain E residue 172 LEU Chi-restraints excluded: chain F residue 769 THR Chi-restraints excluded: chain F residue 787 GLN Chi-restraints excluded: chain F residue 825 VAL Chi-restraints excluded: chain a residue 297 LYS Chi-restraints excluded: chain a residue 311 LEU Chi-restraints excluded: chain a residue 409 TYR Chi-restraints excluded: chain b residue 10 VAL Chi-restraints excluded: chain b residue 20 MET Chi-restraints excluded: chain b residue 78 THR Chi-restraints excluded: chain b residue 230 SER Chi-restraints excluded: chain b residue 320 ILE Chi-restraints excluded: chain b residue 331 MET Chi-restraints excluded: chain b residue 533 ILE Chi-restraints excluded: chain c residue 10 MET Chi-restraints excluded: chain c residue 16 LEU Chi-restraints excluded: chain c residue 39 SER Chi-restraints excluded: chain c residue 49 VAL Chi-restraints excluded: chain c residue 54 VAL Chi-restraints excluded: chain c residue 125 LEU Chi-restraints excluded: chain c residue 132 SER Chi-restraints excluded: chain c residue 162 LEU Chi-restraints excluded: chain c residue 174 LEU Chi-restraints excluded: chain c residue 176 ARG Chi-restraints excluded: chain d residue 127 ILE Chi-restraints excluded: chain d residue 163 GLU Chi-restraints excluded: chain e residue 122 VAL Chi-restraints excluded: chain e residue 162 PHE Chi-restraints excluded: chain f residue 94 ILE Chi-restraints excluded: chain f residue 224 VAL Chi-restraints excluded: chain f residue 235 LEU Chi-restraints excluded: chain f residue 250 LEU Chi-restraints excluded: chain f residue 287 VAL Chi-restraints excluded: chain f residue 326 CYS Chi-restraints excluded: chain f residue 409 HIS Chi-restraints excluded: chain f residue 412 ASN Chi-restraints excluded: chain f residue 498 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 457 random chunks: chunk 441 optimal weight: 4.9990 chunk 456 optimal weight: 0.9990 chunk 143 optimal weight: 3.9990 chunk 89 optimal weight: 3.9990 chunk 420 optimal weight: 9.9990 chunk 409 optimal weight: 1.9990 chunk 415 optimal weight: 0.0020 chunk 301 optimal weight: 4.9990 chunk 343 optimal weight: 9.9990 chunk 337 optimal weight: 6.9990 chunk 222 optimal weight: 1.9990 overall best weight: 1.7996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 137 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 78 ASN ** D 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 21 GLN b 243 HIS c 62 ASN ** d 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 558 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 848 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3594 r_free = 0.3594 target = 0.063287 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2936 r_free = 0.2936 target = 0.042526 restraints weight = 254555.023| |-----------------------------------------------------------------------------| r_work (start): 0.2868 rms_B_bonded: 4.65 r_work: 0.2687 rms_B_bonded: 4.99 restraints_weight: 0.5000 r_work (final): 0.2687 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2685 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2685 r_free = 0.2685 target_work(ls_wunit_k1) = 0.036 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2685 r_free = 0.2685 target_work(ls_wunit_k1) = 0.036 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2685 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8842 moved from start: 0.2523 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 40252 Z= 0.168 Angle : 0.609 12.638 54945 Z= 0.313 Chirality : 0.040 0.294 6097 Planarity : 0.004 0.075 6539 Dihedral : 16.932 78.910 6480 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 7.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer: Outliers : 1.54 % Allowed : 24.10 % Favored : 74.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.36 (0.13), residues: 4457 helix: 2.43 (0.12), residues: 1779 sheet: 0.46 (0.19), residues: 760 loop : -0.37 (0.14), residues: 1918 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 178 TYR 0.026 0.001 TYR D 129 PHE 0.018 0.001 PHE a 131 TRP 0.025 0.001 TRP f 46 HIS 0.003 0.001 HIS c 134 Details of bonding type rmsd/Z covalent geometry : bond 0.00372 / 0.17 (40252) covalent geometry : angle 0.60949 / 0.31 (54945) hydrogen bonds : bond 0.03372 / 2.26 ( 1999) hydrogen bonds : angle 4.28083 / 2.97 ( 5530) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8914 Ramachandran restraints generated. 4457 Oldfield, 0 Emsley, 4457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8914 Ramachandran restraints generated. 4457 Oldfield, 0 Emsley, 4457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 330 residues out of total 4027 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 268 time to evaluate : 1.530 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 115 MET cc_start: 0.9478 (OUTLIER) cc_final: 0.9086 (mpp) REVERT: C 85 LYS cc_start: 0.9635 (ttpt) cc_final: 0.9341 (ptpp) REVERT: C 165 GLN cc_start: 0.9565 (mt0) cc_final: 0.9321 (tm-30) REVERT: C 182 GLU cc_start: 0.9248 (mp0) cc_final: 0.8995 (mp0) REVERT: C 195 ILE cc_start: 0.9316 (tp) cc_final: 0.8926 (pt) REVERT: D 61 MET cc_start: 0.8807 (ppp) cc_final: 0.8362 (ppp) REVERT: D 66 TYR cc_start: 0.8368 (t80) cc_final: 0.8043 (t80) REVERT: E 145 GLN cc_start: 0.9632 (tp-100) cc_final: 0.9347 (tm-30) REVERT: a 62 MET cc_start: 0.8964 (tpp) cc_final: 0.8631 (tpp) REVERT: a 99 PHE cc_start: 0.8825 (m-80) cc_final: 0.8594 (t80) REVERT: a 135 MET cc_start: 0.8691 (mmt) cc_final: 0.8353 (mmt) REVERT: a 145 GLU cc_start: 0.8941 (mt-10) cc_final: 0.8620 (mt-10) REVERT: a 152 ASN cc_start: 0.9143 (m-40) cc_final: 0.8841 (m-40) REVERT: a 297 LYS cc_start: 0.9308 (OUTLIER) cc_final: 0.9001 (mmmm) REVERT: a 311 LEU cc_start: 0.9150 (OUTLIER) cc_final: 0.8734 (mt) REVERT: a 348 MET cc_start: 0.8171 (mtt) cc_final: 0.7805 (mtt) REVERT: a 409 TYR cc_start: 0.9113 (OUTLIER) cc_final: 0.8426 (t80) REVERT: a 453 MET cc_start: 0.8909 (mmm) cc_final: 0.8647 (mmm) REVERT: b 84 MET cc_start: 0.8722 (pmm) cc_final: 0.8400 (pmm) REVERT: b 215 LEU cc_start: 0.9425 (tp) cc_final: 0.9036 (mt) REVERT: b 230 SER cc_start: 0.9320 (OUTLIER) cc_final: 0.9097 (p) REVERT: c 85 LYS cc_start: 0.8946 (mtmm) cc_final: 0.8744 (mtmm) REVERT: d 1 MET cc_start: 0.8866 (OUTLIER) cc_final: 0.8224 (tpt) REVERT: d 61 MET cc_start: 0.4310 (tmm) cc_final: 0.3991 (ppp) REVERT: d 132 ASP cc_start: 0.9082 (m-30) cc_final: 0.8777 (p0) REVERT: d 150 ARG cc_start: 0.9682 (tmm-80) cc_final: 0.9456 (ttp80) REVERT: d 154 ASP cc_start: 0.9652 (m-30) cc_final: 0.9235 (t0) REVERT: e 57 ASP cc_start: 0.8990 (m-30) cc_final: 0.8699 (p0) REVERT: e 108 LEU cc_start: 0.9570 (tp) cc_final: 0.9294 (tp) REVERT: f 78 GLU cc_start: 0.9557 (tp30) cc_final: 0.9241 (tm-30) REVERT: f 95 GLU cc_start: 0.9548 (tp30) cc_final: 0.9334 (tp30) REVERT: f 127 MET cc_start: 0.9558 (mmm) cc_final: 0.9151 (mtm) REVERT: f 249 MET cc_start: 0.8008 (mmt) cc_final: 0.7680 (mmt) REVERT: f 329 ASP cc_start: 0.8788 (p0) cc_final: 0.8564 (p0) REVERT: f 368 ASP cc_start: 0.8982 (m-30) cc_final: 0.8559 (m-30) REVERT: f 374 ASN cc_start: 0.9179 (m-40) cc_final: 0.8622 (t0) REVERT: f 743 MET cc_start: 0.9334 (pmm) cc_final: 0.8831 (pmm) REVERT: f 776 GLU cc_start: 0.9457 (mm-30) cc_final: 0.9181 (mt-10) REVERT: f 812 MET cc_start: 0.9339 (pmm) cc_final: 0.8357 (pmm) outliers start: 62 outliers final: 53 residues processed: 320 average time/residue: 0.2175 time to fit residues: 119.8849 Evaluate side-chains 319 residues out of total 4027 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 260 time to evaluate : 1.423 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 SER Chi-restraints excluded: chain A residue 231 VAL Chi-restraints excluded: chain A residue 251 THR Chi-restraints excluded: chain A residue 277 VAL Chi-restraints excluded: chain A residue 302 THR Chi-restraints excluded: chain A residue 524 GLU Chi-restraints excluded: chain B residue 10 VAL Chi-restraints excluded: chain B residue 20 MET Chi-restraints excluded: chain B residue 115 MET Chi-restraints excluded: chain B residue 244 SER Chi-restraints excluded: chain B residue 258 SER Chi-restraints excluded: chain B residue 354 ARG Chi-restraints excluded: chain B residue 515 MET Chi-restraints excluded: chain C residue 41 LEU Chi-restraints excluded: chain C residue 80 LEU Chi-restraints excluded: chain C residue 108 VAL Chi-restraints excluded: chain C residue 123 CYS Chi-restraints excluded: chain C residue 176 ARG Chi-restraints excluded: chain C residue 198 LEU Chi-restraints excluded: chain C residue 204 ILE Chi-restraints excluded: chain D residue 94 TYR Chi-restraints excluded: chain E residue 33 VAL Chi-restraints excluded: chain E residue 46 THR Chi-restraints excluded: chain E residue 165 CYS Chi-restraints excluded: chain E residue 172 LEU Chi-restraints excluded: chain F residue 769 THR Chi-restraints excluded: chain F residue 787 GLN Chi-restraints excluded: chain F residue 825 VAL Chi-restraints excluded: chain a residue 297 LYS Chi-restraints excluded: chain a residue 311 LEU Chi-restraints excluded: chain a residue 409 TYR Chi-restraints excluded: chain b residue 10 VAL Chi-restraints excluded: chain b residue 78 THR Chi-restraints excluded: chain b residue 230 SER Chi-restraints excluded: chain b residue 320 ILE Chi-restraints excluded: chain b residue 533 ILE Chi-restraints excluded: chain c residue 16 LEU Chi-restraints excluded: chain c residue 39 SER Chi-restraints excluded: chain c residue 49 VAL Chi-restraints excluded: chain c residue 54 VAL Chi-restraints excluded: chain c residue 97 CYS Chi-restraints excluded: chain c residue 125 LEU Chi-restraints excluded: chain c residue 132 SER Chi-restraints excluded: chain c residue 162 LEU Chi-restraints excluded: chain c residue 174 LEU Chi-restraints excluded: chain d residue 1 MET Chi-restraints excluded: chain d residue 127 ILE Chi-restraints excluded: chain d residue 163 GLU Chi-restraints excluded: chain e residue 122 VAL Chi-restraints excluded: chain e residue 162 PHE Chi-restraints excluded: chain f residue 94 ILE Chi-restraints excluded: chain f residue 224 VAL Chi-restraints excluded: chain f residue 235 LEU Chi-restraints excluded: chain f residue 250 LEU Chi-restraints excluded: chain f residue 287 VAL Chi-restraints excluded: chain f residue 326 CYS Chi-restraints excluded: chain f residue 409 HIS Chi-restraints excluded: chain f residue 412 ASN Chi-restraints excluded: chain f residue 498 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 457 random chunks: chunk 200 optimal weight: 20.0000 chunk 149 optimal weight: 3.9990 chunk 381 optimal weight: 3.9990 chunk 300 optimal weight: 3.9990 chunk 119 optimal weight: 10.0000 chunk 162 optimal weight: 2.9990 chunk 273 optimal weight: 2.9990 chunk 345 optimal weight: 0.0270 chunk 307 optimal weight: 0.4980 chunk 81 optimal weight: 3.9990 chunk 378 optimal weight: 0.4980 overall best weight: 1.4042 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 137 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 243 HIS c 62 ASN d 145 GLN ** e 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 558 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 848 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 = 0.3599 r_free = 0.3599 target = 0.063460 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.2945 r_free = 0.2945 target = 0.042812 restraints weight = 240293.506| |-----------------------------------------------------------------------------| r_work (start): 0.2877 rms_B_bonded: 4.55 r_work: 0.2699 rms_B_bonded: 4.90 restraints_weight: 0.5000 r_work (final): 0.2699 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2697 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2697 r_free = 0.2697 target_work(ls_wunit_k1) = 0.036 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2697 r_free = 0.2697 target_work(ls_wunit_k1) = 0.036 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2697 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8833 moved from start: 0.2569 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 40252 Z= 0.144 Angle : 0.604 15.222 54945 Z= 0.310 Chirality : 0.040 0.295 6097 Planarity : 0.003 0.061 6539 Dihedral : 16.938 79.343 6480 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 6.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer: Outliers : 1.54 % Allowed : 24.17 % Favored : 74.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.34 (0.13), residues: 4457 helix: 2.38 (0.12), residues: 1780 sheet: 0.53 (0.20), residues: 752 loop : -0.37 (0.14), residues: 1925 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 3 TYR 0.028 0.001 TYR D 129 PHE 0.018 0.001 PHE a 131 TRP 0.025 0.001 TRP f 46 HIS 0.003 0.001 HIS f 745 Details of bonding type rmsd/Z covalent geometry : bond 0.00315 / 0.14 (40252) covalent geometry : angle 0.60446 / 0.31 (54945) hydrogen bonds : bond 0.03282 / 2.20 ( 1999) hydrogen bonds : angle 4.26495 / 2.96 ( 5530) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 11809.46 seconds wall clock time: 202 minutes 37.85 seconds (12157.85 seconds total)