Starting phenix.real_space_refine on Mon Jul 6 20:12:07 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9cqc_45813/07_2026/9cqc_45813.cif Found real_map, /net/cci-nas-00/data/ceres_data/9cqc_45813/07_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_45813/07_2026/9cqc_45813.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9cqc_45813/07_2026/9cqc_45813.map" model { file = "/net/cci-nas-00/data/ceres_data/9cqc_45813/07_2026/9cqc_45813.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9cqc_45813/07_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): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 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: 7.90, per 1000 atoms: 0.20 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: 3.35 Conformation dependent library (CDL) restraints added in 1.7 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: 4.57 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: 11.09 Time building geometry restraints manager: 4.44 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: 12.870 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: 0.040 Extract box with map and model: 1.010 Check model and map are aligned: 0.130 Set scattering table: 0.080 Process input model: 40.460 Find NCS groups from input model: 0.580 Set up NCS constraints: 0.130 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:1.220 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 56.530 ------------------------------------------------------------------------------- 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 : 0.530 15.041 54945 Z= 0.342 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 0.52989 / 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 : 1.386 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: 0.8828 (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: 0.8494 (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: 0.6873 (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: 0.2244 time to fit residues: 163.2864 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 : 1.459 ------------------------------------------------------------------------------- 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: 10.0000 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 D 9 HIS b 432 GLN b 527 GLN c 168 GLN f 146 GLN f 848 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3605 r_free = 0.3605 target = 0.064627 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2960 r_free = 0.2960 target = 0.044026 restraints weight = 253438.405| |-----------------------------------------------------------------------------| r_work (start): 0.2893 rms_B_bonded: 4.94 r_work (final): 0.2893 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2894 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2894 r_free = 0.2894 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 = 0.2894 r_free = 0.2894 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: 0.2894 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8664 moved from start: 0.1310 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.066 40252 Z= 0.212 Angle : 0.600 10.237 54945 Z= 0.324 Chirality : 0.041 0.189 6097 Planarity : 0.004 0.055 6539 Dihedral : 16.449 91.360 6481 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 4.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer: Outliers : 1.64 % Allowed : 22.16 % Favored : 76.20 % 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: 1.73 (0.13), residues: 4457 helix: 2.81 (0.12), residues: 1762 sheet: 0.55 (0.19), residues: 740 loop : -0.15 (0.14), residues: 1955 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG e 153 TYR 0.017 0.001 TYR B 264 PHE 0.025 0.002 PHE b 183 TRP 0.018 0.001 TRP d 43 HIS 0.006 0.001 HIS F 745 Details of bonding type rmsd/Z covalent geometry : bond 0.00469 / 0.21 (40252) covalent geometry : angle 0.59970 / 0.32 (54945) hydrogen bonds : bond 0.03930 / 2.65 ( 1999) hydrogen bonds : angle 4.67129 / 3.22 ( 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 380 residues out of total 4027 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 314 time to evaluate : 1.284 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: symmetry clash revert: symmetry clash REVERT: A 134 MET cc_start: 0.9342 (ppp) cc_final: 0.9141 (ppp) REVERT: B 115 MET cc_start: 0.9500 (mpp) cc_final: 0.9133 (mpp) REVERT: C 159 MET cc_start: 0.8993 (mmp) cc_final: 0.8770 (mmm) REVERT: C 182 GLU cc_start: 0.8818 (mp0) cc_final: 0.8569 (mp0) REVERT: C 195 ILE cc_start: 0.9247 (tp) cc_final: 0.8833 (pt) REVERT: C 219 MET cc_start: 0.8772 (mmm) cc_final: 0.8505 (mmm) REVERT: D 61 MET cc_start: 0.8407 (ppp) cc_final: 0.7979 (ppp) REVERT: D 66 TYR cc_start: 0.8236 (t80) cc_final: 0.7919 (t80) REVERT: E 145 GLN cc_start: 0.9656 (tp-100) cc_final: 0.9358 (tm-30) REVERT: F 692 ASN cc_start: 0.9360 (OUTLIER) cc_final: 0.8568 (m-40) REVERT: F 746 MET cc_start: 0.8005 (mmt) cc_final: 0.7680 (mmt) REVERT: H 194 LYS cc_start: 0.8981 (ptpp) cc_final: 0.8754 (ttpp) REVERT: a 145 GLU cc_start: 0.8659 (mt-10) cc_final: 0.8366 (mt-10) REVERT: a 152 ASN cc_start: 0.9112 (m-40) cc_final: 0.8785 (m-40) REVERT: a 311 LEU cc_start: 0.9178 (OUTLIER) cc_final: 0.8737 (mt) REVERT: a 409 TYR cc_start: 0.8338 (OUTLIER) cc_final: 0.7700 (t80) REVERT: c 63 LYS cc_start: 0.8594 (tppt) cc_final: 0.8389 (mmtm) REVERT: c 85 LYS cc_start: 0.9047 (mtmm) cc_final: 0.8785 (mtmm) REVERT: d 1 MET cc_start: 0.8997 (OUTLIER) cc_final: 0.8784 (tpt) REVERT: d 61 MET cc_start: 0.3859 (OUTLIER) cc_final: 0.3471 (ppp) REVERT: e 54 GLN cc_start: 0.9711 (tp40) cc_final: 0.9119 (tp-100) REVERT: e 57 ASP cc_start: 0.8844 (m-30) cc_final: 0.8523 (p0) REVERT: e 172 LEU cc_start: 0.9506 (tt) cc_final: 0.9226 (mt) REVERT: f 95 GLU cc_start: 0.9338 (tp30) cc_final: 0.8864 (tm-30) REVERT: f 121 ASP cc_start: 0.6701 (p0) cc_final: 0.4501 (p0) REVERT: f 127 MET cc_start: 0.8848 (mpp) cc_final: 0.8380 (mtm) REVERT: f 249 MET cc_start: 0.7881 (mmm) cc_final: 0.7626 (mmm) REVERT: f 279 MET cc_start: 0.8713 (mmm) cc_final: 0.8468 (mmm) REVERT: f 329 ASP cc_start: 0.8692 (p0) cc_final: 0.8348 (p0) REVERT: f 368 ASP cc_start: 0.8832 (m-30) cc_final: 0.8376 (m-30) REVERT: f 374 ASN cc_start: 0.8995 (m-40) cc_final: 0.8737 (t0) REVERT: f 447 TRP cc_start: 0.8646 (m-10) cc_final: 0.8003 (m-10) REVERT: f 459 MET cc_start: 0.9208 (mmp) cc_final: 0.8913 (mmp) REVERT: f 743 MET cc_start: 0.9170 (pmm) cc_final: 0.8525 (pmm) REVERT: f 776 GLU cc_start: 0.9451 (mm-30) cc_final: 0.9163 (pt0) outliers start: 66 outliers final: 29 residues processed: 362 average time/residue: 0.2079 time to fit residues: 127.6257 Evaluate side-chains 316 residues out of total 4027 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 282 time to evaluate : 1.486 ------------------------------------------------------------------------------- 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 132 SER Chi-restraints excluded: chain c residue 164 ILE Chi-restraints excluded: chain c residue 174 LEU Chi-restraints excluded: chain d residue 1 MET 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 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 250 LEU 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: 7.9990 chunk 376 optimal weight: 5.9990 chunk 195 optimal weight: 10.0000 chunk 50 optimal weight: 9.9990 chunk 241 optimal weight: 1.9990 chunk 265 optimal weight: 0.9980 chunk 302 optimal weight: 0.6980 chunk 156 optimal weight: 0.9990 chunk 207 optimal weight: 3.9990 chunk 298 optimal weight: 1.9990 chunk 326 optimal weight: 2.9990 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 458 GLN D 195 HIS ** e 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** f 316 HIS ** f 745 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** f 848 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3628 r_free = 0.3628 target = 0.065011 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.2992 r_free = 0.2992 target = 0.044496 restraints weight = 277086.126| |-----------------------------------------------------------------------------| r_work (start): 0.2919 rms_B_bonded: 4.98 r_work (final): 0.2919 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2920 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2920 r_free = 0.2920 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 = 0.2920 r_free = 0.2920 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: 0.2920 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8671 moved from start: 0.1541 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 40252 Z= 0.143 Angle : 0.534 9.268 54945 Z= 0.289 Chirality : 0.040 0.430 6097 Planarity : 0.003 0.054 6539 Dihedral : 16.550 77.783 6480 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 4.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 1.84 % Allowed : 21.72 % Favored : 76.45 % 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: 1.67 (0.13), residues: 4457 helix: 2.75 (0.12), residues: 1764 sheet: 0.66 (0.20), residues: 728 loop : -0.24 (0.14), residues: 1965 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG E 153 TYR 0.028 0.001 TYR D 129 PHE 0.023 0.001 PHE f 125 TRP 0.012 0.001 TRP C 119 HIS 0.004 0.001 HIS a 137 Details of bonding type rmsd/Z covalent geometry : bond 0.00310 / 0.14 (40252) covalent geometry : angle 0.53371 / 0.29 (54945) hydrogen bonds : bond 0.03470 / 2.32 ( 1999) hydrogen bonds : angle 4.43779 / 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 379 residues out of total 4027 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 305 time to evaluate : 1.504 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: symmetry clash REVERT: A 135 MET cc_start: 0.8580 (tpp) cc_final: 0.8271 (tpp) REVERT: B 133 GLU cc_start: 0.9072 (mt-10) cc_final: 0.8737 (mt-10) REVERT: C 165 GLN cc_start: 0.9524 (mt0) cc_final: 0.9295 (tm-30) REVERT: C 182 GLU cc_start: 0.8776 (mp0) cc_final: 0.8546 (mp0) REVERT: C 195 ILE cc_start: 0.9215 (tp) cc_final: 0.8808 (pt) REVERT: D 61 MET cc_start: 0.8452 (ppp) cc_final: 0.8153 (ppp) REVERT: D 66 TYR cc_start: 0.8101 (t80) cc_final: 0.7803 (t80) REVERT: E 145 GLN cc_start: 0.9609 (tp-100) cc_final: 0.9314 (tm-30) REVERT: F 692 ASN cc_start: 0.9324 (OUTLIER) cc_final: 0.8621 (m-40) REVERT: a 62 MET cc_start: 0.8415 (tpp) cc_final: 0.8103 (tpp) REVERT: a 99 PHE cc_start: 0.8610 (m-80) cc_final: 0.8284 (t80) REVERT: a 152 ASN cc_start: 0.9126 (m-40) cc_final: 0.8808 (m-40) REVERT: a 311 LEU cc_start: 0.9150 (OUTLIER) cc_final: 0.8754 (mt) REVERT: a 348 MET cc_start: 0.7734 (mtt) cc_final: 0.7475 (mtt) REVERT: a 409 TYR cc_start: 0.8429 (OUTLIER) cc_final: 0.7732 (t80) REVERT: b 84 MET cc_start: 0.8713 (pmm) cc_final: 0.8476 (pmm) REVERT: c 63 LYS cc_start: 0.8607 (tppt) cc_final: 0.8106 (mmtm) REVERT: d 1 MET cc_start: 0.8897 (OUTLIER) cc_final: 0.8488 (tpt) REVERT: d 61 MET cc_start: 0.3758 (tmm) cc_final: 0.3179 (ppp) REVERT: e 94 TYR cc_start: 0.9176 (t80) cc_final: 0.8815 (t80) REVERT: f 95 GLU cc_start: 0.9228 (tp30) cc_final: 0.8742 (tm-30) REVERT: f 127 MET cc_start: 0.8712 (mpp) cc_final: 0.8246 (mtm) REVERT: f 249 MET cc_start: 0.7885 (mmm) cc_final: 0.7635 (mmm) REVERT: f 329 ASP cc_start: 0.8630 (p0) cc_final: 0.8196 (p0) REVERT: f 332 MET cc_start: 0.9231 (mmm) cc_final: 0.8756 (mmm) REVERT: f 368 ASP cc_start: 0.8751 (m-30) cc_final: 0.8319 (m-30) REVERT: f 374 ASN cc_start: 0.8965 (m-40) cc_final: 0.8582 (t0) REVERT: f 447 TRP cc_start: 0.8532 (m-10) cc_final: 0.7893 (m-10) REVERT: f 459 MET cc_start: 0.9172 (mmp) cc_final: 0.8923 (mmp) REVERT: f 480 MET cc_start: 0.9241 (mmm) cc_final: 0.8849 (tpp) REVERT: f 743 MET cc_start: 0.9085 (pmm) cc_final: 0.8531 (pmm) REVERT: f 776 GLU cc_start: 0.9434 (mm-30) cc_final: 0.9129 (pt0) REVERT: f 782 LYS cc_start: 0.9343 (mtpt) cc_final: 0.9133 (tmmt) REVERT: f 792 MET cc_start: 0.9354 (tmm) cc_final: 0.9149 (tpt) REVERT: f 811 SER cc_start: 0.9549 (OUTLIER) cc_final: 0.9280 (t) REVERT: f 812 MET cc_start: 0.9274 (pmm) cc_final: 0.8598 (pmm) outliers start: 74 outliers final: 33 residues processed: 357 average time/residue: 0.2039 time to fit residues: 123.8948 Evaluate side-chains 318 residues out of total 4027 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 280 time to evaluate : 1.416 ------------------------------------------------------------------------------- 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 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 331 MET Chi-restraints excluded: chain b residue 533 ILE 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 c residue 181 THR 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 19 PHE 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 191 ILE Chi-restraints excluded: chain f residue 250 LEU Chi-restraints excluded: chain f residue 287 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 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: 1.9990 chunk 246 optimal weight: 3.9990 chunk 359 optimal weight: 8.9990 chunk 209 optimal weight: 4.9990 chunk 385 optimal weight: 7.9990 chunk 146 optimal weight: 0.0980 chunk 52 optimal weight: 7.9990 chunk 364 optimal weight: 2.9990 chunk 207 optimal weight: 4.9990 chunk 84 optimal weight: 3.9990 overall best weight: 2.6188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 152 HIS ** e 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 745 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 = 0.3605 r_free = 0.3605 target = 0.063962 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2943 r_free = 0.2943 target = 0.042994 restraints weight = 283453.642| |-----------------------------------------------------------------------------| r_work (start): 0.2870 rms_B_bonded: 4.97 r_work (final): 0.2870 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2871 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2871 r_free = 0.2871 target_work(ls_wunit_k1) = 0.041 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2871 r_free = 0.2871 target_work(ls_wunit_k1) = 0.041 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2871 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8727 moved from start: 0.1831 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.058 40252 Z= 0.219 Angle : 0.567 9.914 54945 Z= 0.303 Chirality : 0.039 0.290 6097 Planarity : 0.004 0.054 6539 Dihedral : 16.727 75.911 6480 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 5.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 2.13 % Allowed : 22.41 % 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: 1.55 (0.13), residues: 4457 helix: 2.63 (0.12), residues: 1771 sheet: 0.54 (0.19), residues: 743 loop : -0.28 (0.14), residues: 1943 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG D 3 TYR 0.030 0.001 TYR D 129 PHE 0.022 0.001 PHE f 125 TRP 0.015 0.001 TRP f 46 HIS 0.006 0.001 HIS F 745 Details of bonding type rmsd/Z covalent geometry : bond 0.00486 / 0.22 (40252) covalent geometry : angle 0.56731 / 0.30 (54945) hydrogen bonds : bond 0.03621 / 2.43 ( 1999) hydrogen bonds : angle 4.42941 / 3.07 ( 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 367 residues out of total 4027 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 281 time to evaluate : 1.492 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: 0.9417 (OUTLIER) cc_final: 0.9008 (mpp) REVERT: C 165 GLN cc_start: 0.9543 (mt0) cc_final: 0.9325 (tm-30) REVERT: C 182 GLU cc_start: 0.8840 (mp0) cc_final: 0.8608 (mp0) REVERT: C 195 ILE cc_start: 0.9239 (tp) cc_final: 0.8845 (pt) REVERT: D 61 MET cc_start: 0.8561 (ppp) cc_final: 0.8218 (ppp) REVERT: D 66 TYR cc_start: 0.8206 (t80) cc_final: 0.7902 (t80) REVERT: D 152 LEU cc_start: 0.9720 (OUTLIER) cc_final: 0.9490 (mt) REVERT: E 21 GLN cc_start: 0.8984 (pp30) cc_final: 0.8600 (pp30) REVERT: E 145 GLN cc_start: 0.9619 (tp-100) cc_final: 0.9326 (tm-30) REVERT: E 184 LEU cc_start: 0.9639 (OUTLIER) cc_final: 0.9428 (mm) REVERT: a 62 MET cc_start: 0.8445 (tpp) cc_final: 0.8155 (tpp) REVERT: a 152 ASN cc_start: 0.9160 (m-40) cc_final: 0.8843 (m-40) REVERT: a 311 LEU cc_start: 0.9196 (OUTLIER) cc_final: 0.8740 (mt) REVERT: a 348 MET cc_start: 0.7806 (mtt) cc_final: 0.7482 (mtt) REVERT: a 409 TYR cc_start: 0.8591 (OUTLIER) cc_final: 0.7816 (t80) REVERT: b 20 MET cc_start: 0.8561 (ttt) cc_final: 0.8324 (ttt) REVERT: b 84 MET cc_start: 0.8713 (pmm) cc_final: 0.8440 (pmm) REVERT: c 81 ARG cc_start: 0.8749 (tpp-160) cc_final: 0.8495 (tpp80) REVERT: c 85 LYS cc_start: 0.9129 (mtmm) cc_final: 0.8816 (mtmm) REVERT: c 156 LEU cc_start: 0.9068 (OUTLIER) cc_final: 0.8781 (tt) REVERT: d 1 MET cc_start: 0.8982 (OUTLIER) cc_final: 0.8592 (tpt) REVERT: d 61 MET cc_start: 0.4007 (tmm) cc_final: 0.3309 (ppp) REVERT: e 57 ASP cc_start: 0.8910 (OUTLIER) cc_final: 0.8591 (p0) REVERT: f 95 GLU cc_start: 0.9261 (tp30) cc_final: 0.8737 (tm-30) REVERT: f 127 MET cc_start: 0.8743 (mpp) cc_final: 0.8232 (mtm) REVERT: f 249 MET cc_start: 0.8043 (mmm) cc_final: 0.7810 (mmm) REVERT: f 279 MET cc_start: 0.8828 (mmm) cc_final: 0.8430 (mmm) REVERT: f 329 ASP cc_start: 0.8586 (p0) cc_final: 0.8139 (p0) REVERT: f 368 ASP cc_start: 0.8810 (m-30) cc_final: 0.8404 (m-30) REVERT: f 371 MET cc_start: 0.8572 (tmm) cc_final: 0.8310 (tmm) REVERT: f 374 ASN cc_start: 0.9022 (m-40) cc_final: 0.8603 (t0) REVERT: f 459 MET cc_start: 0.9227 (mmp) cc_final: 0.9008 (mmp) REVERT: f 480 MET cc_start: 0.9307 (mmm) cc_final: 0.8997 (tpp) REVERT: f 743 MET cc_start: 0.9064 (pmm) cc_final: 0.8647 (pmm) REVERT: f 776 GLU cc_start: 0.9468 (mm-30) cc_final: 0.9188 (pt0) REVERT: f 782 LYS cc_start: 0.9381 (mtpt) cc_final: 0.9159 (tmmt) REVERT: f 792 MET cc_start: 0.9357 (tmm) cc_final: 0.9146 (tpt) REVERT: f 812 MET cc_start: 0.9280 (pmm) cc_final: 0.8561 (pmm) outliers start: 86 outliers final: 47 residues processed: 348 average time/residue: 0.2150 time to fit residues: 126.4120 Evaluate side-chains 324 residues out of total 4027 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 269 time to evaluate : 1.481 ------------------------------------------------------------------------------- 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 108 VAL Chi-restraints excluded: chain C residue 123 CYS Chi-restraints excluded: chain D residue 94 TYR Chi-restraints excluded: chain D residue 143 HIS Chi-restraints excluded: chain D residue 152 LEU Chi-restraints excluded: chain E residue 108 LEU Chi-restraints excluded: chain E residue 165 CYS Chi-restraints excluded: chain E residue 184 LEU 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 40 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 b residue 533 ILE 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 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 1 MET 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 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 191 ILE Chi-restraints excluded: chain f residue 250 LEU Chi-restraints excluded: chain f residue 287 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 Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 457 random chunks: chunk 361 optimal weight: 4.9990 chunk 73 optimal weight: 3.9990 chunk 6 optimal weight: 5.9990 chunk 424 optimal weight: 9.9990 chunk 430 optimal weight: 10.0000 chunk 63 optimal weight: 1.9990 chunk 197 optimal weight: 10.0000 chunk 366 optimal weight: 10.0000 chunk 207 optimal weight: 2.9990 chunk 99 optimal weight: 2.9990 chunk 90 optimal weight: 0.8980 overall best weight: 2.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 43 GLN ** e 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** f 745 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3594 r_free = 0.3594 target = 0.063499 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.2923 r_free = 0.2923 target = 0.042348 restraints weight = 307358.395| |-----------------------------------------------------------------------------| r_work (start): 0.2852 rms_B_bonded: 5.16 r_work (final): 0.2852 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2852 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2852 r_free = 0.2852 target_work(ls_wunit_k1) = 0.040 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2852 r_free = 0.2852 target_work(ls_wunit_k1) = 0.040 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2852 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8743 moved from start: 0.2027 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 40252 Z= 0.213 Angle : 0.570 11.512 54945 Z= 0.302 Chirality : 0.039 0.191 6097 Planarity : 0.004 0.118 6539 Dihedral : 16.845 77.526 6480 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 6.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.87 % Favored : 97.13 % Rotamer: Outliers : 2.26 % Allowed : 22.78 % Favored : 74.96 % 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: 2.56 (0.12), residues: 1764 sheet: 0.50 (0.19), residues: 737 loop : -0.36 (0.14), residues: 1956 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.000 ARG C 178 TYR 0.027 0.001 TYR D 129 PHE 0.023 0.001 PHE f 125 TRP 0.015 0.001 TRP C 119 HIS 0.007 0.001 HIS f 745 Details of bonding type rmsd/Z covalent geometry : bond 0.00470 / 0.21 (40252) covalent geometry : angle 0.57047 / 0.30 (54945) hydrogen bonds : bond 0.03542 / 2.37 ( 1999) hydrogen bonds : angle 4.40381 / 3.05 ( 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 368 residues out of total 4027 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 277 time to evaluate : 1.373 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: 0.9392 (OUTLIER) cc_final: 0.9021 (mpp) REVERT: C 165 GLN cc_start: 0.9541 (mt0) cc_final: 0.9302 (tm-30) REVERT: C 182 GLU cc_start: 0.8858 (mp0) cc_final: 0.8612 (mp0) REVERT: C 195 ILE cc_start: 0.9219 (tp) cc_final: 0.8824 (pt) REVERT: D 61 MET cc_start: 0.8594 (ppp) cc_final: 0.8223 (ppp) REVERT: D 66 TYR cc_start: 0.8197 (t80) cc_final: 0.7883 (t80) REVERT: D 152 LEU cc_start: 0.9725 (OUTLIER) cc_final: 0.9500 (mt) REVERT: E 21 GLN cc_start: 0.9049 (pp30) cc_final: 0.8417 (pp30) REVERT: E 36 LEU cc_start: 0.9464 (tp) cc_final: 0.9202 (pt) REVERT: E 85 THR cc_start: 0.9185 (OUTLIER) cc_final: 0.8639 (p) REVERT: E 145 GLN cc_start: 0.9615 (tp-100) cc_final: 0.9337 (tm-30) REVERT: E 184 LEU cc_start: 0.9641 (OUTLIER) cc_final: 0.9426 (mm) REVERT: a 62 MET cc_start: 0.8479 (tpp) cc_final: 0.8210 (tpp) REVERT: a 152 ASN cc_start: 0.9164 (m-40) cc_final: 0.8850 (m-40) REVERT: a 311 LEU cc_start: 0.9194 (OUTLIER) cc_final: 0.8736 (mt) REVERT: a 348 MET cc_start: 0.7781 (mtt) cc_final: 0.7452 (mtt) REVERT: a 409 TYR cc_start: 0.8606 (OUTLIER) cc_final: 0.7831 (t80) REVERT: b 84 MET cc_start: 0.8705 (pmm) cc_final: 0.8404 (pmm) REVERT: c 81 ARG cc_start: 0.8772 (tpp-160) cc_final: 0.8564 (tpp80) REVERT: e 57 ASP cc_start: 0.8950 (m-30) cc_final: 0.8636 (p0) REVERT: e 108 LEU cc_start: 0.9540 (tp) cc_final: 0.9298 (tp) REVERT: f 95 GLU cc_start: 0.9272 (tp30) cc_final: 0.9059 (tp30) REVERT: f 127 MET cc_start: 0.8729 (OUTLIER) cc_final: 0.8453 (mtm) REVERT: f 249 MET cc_start: 0.8181 (mmm) cc_final: 0.7970 (mmm) REVERT: f 329 ASP cc_start: 0.8695 (p0) cc_final: 0.8199 (p0) REVERT: f 368 ASP cc_start: 0.8796 (m-30) cc_final: 0.8425 (m-30) REVERT: f 374 ASN cc_start: 0.9019 (m-40) cc_final: 0.8618 (t0) REVERT: f 593 CYS cc_start: 0.7397 (t) cc_final: 0.6831 (t) REVERT: f 743 MET cc_start: 0.9080 (pmm) cc_final: 0.8677 (pmm) REVERT: f 776 GLU cc_start: 0.9496 (mm-30) cc_final: 0.9210 (mt-10) REVERT: f 782 LYS cc_start: 0.9392 (mtpt) cc_final: 0.9010 (tmmt) REVERT: f 812 MET cc_start: 0.9293 (pmm) cc_final: 0.8409 (pmm) outliers start: 91 outliers final: 49 residues processed: 348 average time/residue: 0.2084 time to fit residues: 123.5167 Evaluate side-chains 326 residues out of total 4027 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 270 time to evaluate : 1.362 ------------------------------------------------------------------------------- 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 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 C residue 176 ARG Chi-restraints excluded: chain C residue 204 ILE 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 152 LEU Chi-restraints excluded: chain E residue 33 VAL Chi-restraints excluded: chain E residue 85 THR Chi-restraints excluded: chain E residue 92 SER 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 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 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 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 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 127 MET Chi-restraints excluded: chain f residue 191 ILE Chi-restraints excluded: chain f residue 194 LEU Chi-restraints excluded: chain f residue 224 VAL 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 Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 457 random chunks: chunk 131 optimal weight: 10.0000 chunk 206 optimal weight: 0.0170 chunk 30 optimal weight: 4.9990 chunk 3 optimal weight: 2.9990 chunk 425 optimal weight: 0.8980 chunk 288 optimal weight: 1.9990 chunk 215 optimal weight: 3.9990 chunk 418 optimal weight: 10.0000 chunk 199 optimal weight: 20.0000 chunk 136 optimal weight: 0.8980 chunk 291 optimal weight: 0.5980 overall best weight: 0.8820 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... d 195 HIS ** e 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 558 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** f 673 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3614 r_free = 0.3614 target = 0.064346 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.2954 r_free = 0.2954 target = 0.043293 restraints weight = 301082.978| |-----------------------------------------------------------------------------| r_work (start): 0.2885 rms_B_bonded: 5.16 r_work (final): 0.2885 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2884 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2884 r_free = 0.2884 target_work(ls_wunit_k1) = 0.041 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2884 r_free = 0.2884 target_work(ls_wunit_k1) = 0.041 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2884 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8711 moved from start: 0.2100 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 40252 Z= 0.124 Angle : 0.555 11.317 54945 Z= 0.292 Chirality : 0.039 0.169 6097 Planarity : 0.004 0.104 6539 Dihedral : 16.826 76.693 6480 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 6.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer: Outliers : 1.99 % Allowed : 23.01 % Favored : 75.01 % 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: 1.47 (0.13), residues: 4457 helix: 2.56 (0.12), residues: 1771 sheet: 0.56 (0.19), residues: 758 loop : -0.35 (0.14), residues: 1928 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.000 ARG f 585 TYR 0.025 0.001 TYR D 129 PHE 0.024 0.001 PHE f 125 TRP 0.015 0.001 TRP C 119 HIS 0.006 0.001 HIS f 745 Details of bonding type rmsd/Z covalent geometry : bond 0.00264 / 0.12 (40252) covalent geometry : angle 0.55547 / 0.29 (54945) hydrogen bonds : bond 0.03259 / 2.18 ( 1999) hydrogen bonds : angle 4.27355 / 2.96 ( 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 372 residues out of total 4027 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 292 time to evaluate : 1.508 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 111 LEU cc_start: 0.9677 (OUTLIER) cc_final: 0.9417 (mp) REVERT: B 115 MET cc_start: 0.9426 (OUTLIER) cc_final: 0.9016 (mpp) REVERT: C 165 GLN cc_start: 0.9524 (mt0) cc_final: 0.9289 (tm-30) REVERT: C 182 GLU cc_start: 0.8857 (mp0) cc_final: 0.8615 (mp0) REVERT: C 195 ILE cc_start: 0.9205 (tp) cc_final: 0.8818 (pt) REVERT: D 61 MET cc_start: 0.8651 (ppp) cc_final: 0.8201 (ppp) REVERT: D 66 TYR cc_start: 0.8117 (t80) cc_final: 0.7799 (t80) REVERT: E 21 GLN cc_start: 0.9095 (pp30) cc_final: 0.8701 (pp30) REVERT: E 36 LEU cc_start: 0.9474 (tp) cc_final: 0.9234 (pt) REVERT: E 145 GLN cc_start: 0.9605 (tp-100) cc_final: 0.9319 (tm-30) REVERT: a 62 MET cc_start: 0.8473 (tpp) cc_final: 0.8187 (tpp) REVERT: a 152 ASN cc_start: 0.9144 (m-40) cc_final: 0.8830 (m-40) REVERT: a 311 LEU cc_start: 0.9167 (OUTLIER) cc_final: 0.8755 (mt) REVERT: a 409 TYR cc_start: 0.8552 (OUTLIER) cc_final: 0.7797 (t80) REVERT: b 84 MET cc_start: 0.8742 (pmm) cc_final: 0.8434 (pmm) REVERT: b 115 MET cc_start: 0.9570 (mmt) cc_final: 0.9019 (mmm) REVERT: b 230 SER cc_start: 0.9205 (OUTLIER) cc_final: 0.8976 (p) REVERT: c 63 LYS cc_start: 0.8571 (tppt) cc_final: 0.8071 (mmmt) REVERT: c 85 LYS cc_start: 0.9004 (mtmm) cc_final: 0.8776 (mtmm) REVERT: e 57 ASP cc_start: 0.8937 (m-30) cc_final: 0.8629 (p0) REVERT: e 108 LEU cc_start: 0.9540 (tp) cc_final: 0.9284 (tp) REVERT: f 95 GLU cc_start: 0.9225 (tp30) cc_final: 0.9006 (tp30) REVERT: f 127 MET cc_start: 0.8648 (OUTLIER) cc_final: 0.8380 (mtm) REVERT: f 249 MET cc_start: 0.8261 (mmm) cc_final: 0.8024 (mmm) REVERT: f 279 MET cc_start: 0.8855 (mmm) cc_final: 0.8217 (mmm) REVERT: f 329 ASP cc_start: 0.8617 (p0) cc_final: 0.8078 (p0) REVERT: f 368 ASP cc_start: 0.8792 (m-30) cc_final: 0.8344 (m-30) REVERT: f 374 ASN cc_start: 0.8964 (m-40) cc_final: 0.8673 (t0) REVERT: f 447 TRP cc_start: 0.8690 (m-10) cc_final: 0.8125 (m-10) REVERT: f 513 LYS cc_start: 0.9622 (mppt) cc_final: 0.9139 (mppt) REVERT: f 593 CYS cc_start: 0.7485 (t) cc_final: 0.6996 (t) REVERT: f 743 MET cc_start: 0.9068 (pmm) cc_final: 0.8694 (pmm) REVERT: f 776 GLU cc_start: 0.9483 (mm-30) cc_final: 0.9194 (mt-10) REVERT: f 812 MET cc_start: 0.9297 (pmm) cc_final: 0.8418 (pmm) outliers start: 80 outliers final: 43 residues processed: 352 average time/residue: 0.2165 time to fit residues: 129.8101 Evaluate side-chains 320 residues out of total 4027 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 271 time to evaluate : 1.547 ------------------------------------------------------------------------------- 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 409 TYR 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 123 CYS Chi-restraints excluded: chain C residue 176 ARG 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 108 LEU Chi-restraints excluded: chain E residue 165 CYS 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 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 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 162 LEU Chi-restraints excluded: chain c residue 174 LEU Chi-restraints excluded: chain c residue 181 THR Chi-restraints excluded: chain d residue 1 MET Chi-restraints excluded: chain d residue 127 ILE Chi-restraints excluded: chain e residue 122 VAL Chi-restraints excluded: chain f residue 94 ILE Chi-restraints excluded: chain f residue 127 MET Chi-restraints excluded: chain f residue 191 ILE 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 Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 457 random chunks: chunk 85 optimal weight: 3.9990 chunk 389 optimal weight: 2.9990 chunk 158 optimal weight: 0.9990 chunk 227 optimal weight: 10.0000 chunk 411 optimal weight: 3.9990 chunk 182 optimal weight: 6.9990 chunk 130 optimal weight: 0.0770 chunk 333 optimal weight: 0.0040 chunk 393 optimal weight: 7.9990 chunk 245 optimal weight: 0.9990 chunk 206 optimal weight: 6.9990 overall best weight: 1.0156 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 213 ASN ** e 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** e 100 ASN ** f 558 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3615 r_free = 0.3615 target = 0.064328 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.2964 r_free = 0.2964 target = 0.043563 restraints weight = 252503.569| |-----------------------------------------------------------------------------| r_work (start): 0.2894 rms_B_bonded: 4.72 r_work (final): 0.2894 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2895 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2895 r_free = 0.2895 target_work(ls_wunit_k1) = 0.041 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2895 r_free = 0.2895 target_work(ls_wunit_k1) = 0.041 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2895 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8704 moved from start: 0.2187 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 40252 Z= 0.128 Angle : 0.570 15.023 54945 Z= 0.296 Chirality : 0.039 0.246 6097 Planarity : 0.003 0.087 6539 Dihedral : 16.829 77.431 6480 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 6.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer: Outliers : 1.96 % Allowed : 23.18 % Favored : 74.86 % 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: 1.46 (0.13), residues: 4457 helix: 2.58 (0.12), residues: 1766 sheet: 0.51 (0.19), residues: 764 loop : -0.36 (0.14), residues: 1927 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG a 218 TYR 0.026 0.001 TYR D 129 PHE 0.024 0.001 PHE f 125 TRP 0.019 0.001 TRP f 46 HIS 0.007 0.001 HIS f 745 Details of bonding type rmsd/Z covalent geometry : bond 0.00275 / 0.13 (40252) covalent geometry : angle 0.57042 / 0.30 (54945) hydrogen bonds : bond 0.03199 / 2.15 ( 1999) hydrogen bonds : angle 4.21720 / 2.92 ( 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 363 residues out of total 4027 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 284 time to evaluate : 1.346 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: 0.8934 (ptp) cc_final: 0.8691 (pmm) REVERT: B 111 LEU cc_start: 0.9674 (OUTLIER) cc_final: 0.9416 (mp) REVERT: B 115 MET cc_start: 0.9450 (OUTLIER) cc_final: 0.9081 (mpp) REVERT: C 165 GLN cc_start: 0.9518 (mt0) cc_final: 0.9300 (tm-30) REVERT: C 182 GLU cc_start: 0.8839 (mp0) cc_final: 0.8603 (mp0) REVERT: C 195 ILE cc_start: 0.9216 (tp) cc_final: 0.8821 (pt) REVERT: C 212 MET cc_start: 0.8547 (ptm) cc_final: 0.8342 (ptp) REVERT: D 61 MET cc_start: 0.8720 (ppp) cc_final: 0.8237 (ppp) REVERT: D 66 TYR cc_start: 0.8107 (t80) cc_final: 0.7783 (t80) REVERT: E 21 GLN cc_start: 0.9123 (pp30) cc_final: 0.8728 (pp30) REVERT: E 85 THR cc_start: 0.9163 (OUTLIER) cc_final: 0.8611 (p) REVERT: E 145 GLN cc_start: 0.9597 (tp-100) cc_final: 0.9318 (tm-30) REVERT: F 692 ASN cc_start: 0.9255 (OUTLIER) cc_final: 0.8583 (m-40) REVERT: a 62 MET cc_start: 0.8498 (tpp) cc_final: 0.8211 (tpp) REVERT: a 152 ASN cc_start: 0.9126 (m-40) cc_final: 0.8807 (m-40) REVERT: a 311 LEU cc_start: 0.9153 (OUTLIER) cc_final: 0.8762 (mt) REVERT: a 348 MET cc_start: 0.7624 (mtt) cc_final: 0.7296 (mtt) REVERT: a 409 TYR cc_start: 0.8543 (OUTLIER) cc_final: 0.7778 (t80) REVERT: b 20 MET cc_start: 0.8621 (ttt) cc_final: 0.8395 (ttt) REVERT: b 84 MET cc_start: 0.8748 (pmm) cc_final: 0.8427 (pmm) REVERT: b 115 MET cc_start: 0.9568 (mmt) cc_final: 0.9094 (mmm) REVERT: b 230 SER cc_start: 0.9202 (OUTLIER) cc_final: 0.8980 (p) REVERT: c 63 LYS cc_start: 0.8569 (tppt) cc_final: 0.8057 (mmmt) REVERT: d 36 LEU cc_start: 0.9218 (OUTLIER) cc_final: 0.8949 (pt) REVERT: e 57 ASP cc_start: 0.8919 (m-30) cc_final: 0.8646 (p0) REVERT: e 108 LEU cc_start: 0.9537 (tp) cc_final: 0.9269 (tp) REVERT: f 95 GLU cc_start: 0.9223 (tp30) cc_final: 0.8995 (tp30) REVERT: f 127 MET cc_start: 0.8628 (OUTLIER) cc_final: 0.8353 (mtm) REVERT: f 249 MET cc_start: 0.8293 (mmm) cc_final: 0.8070 (mmm) REVERT: f 263 MET cc_start: 0.8871 (mmm) cc_final: 0.8499 (mmm) REVERT: f 279 MET cc_start: 0.8895 (mmm) cc_final: 0.8343 (mmm) REVERT: f 281 MET cc_start: 0.8250 (ptp) cc_final: 0.7656 (pmm) REVERT: f 311 LEU cc_start: 0.9304 (tt) cc_final: 0.8934 (tt) REVERT: f 368 ASP cc_start: 0.8639 (m-30) cc_final: 0.8268 (m-30) REVERT: f 374 ASN cc_start: 0.8949 (m-40) cc_final: 0.8525 (t0) REVERT: f 447 TRP cc_start: 0.8667 (m-10) cc_final: 0.8099 (m-10) REVERT: f 593 CYS cc_start: 0.7368 (t) cc_final: 0.6823 (t) REVERT: f 776 GLU cc_start: 0.9450 (mm-30) cc_final: 0.9164 (mt-10) REVERT: f 812 MET cc_start: 0.9276 (pmm) cc_final: 0.8364 (pmm) outliers start: 79 outliers final: 51 residues processed: 347 average time/residue: 0.2076 time to fit residues: 123.5269 Evaluate side-chains 332 residues out of total 4027 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 272 time to evaluate : 1.472 ------------------------------------------------------------------------------- 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 409 TYR 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 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 162 LEU 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 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 165 CYS Chi-restraints excluded: chain E residue 172 LEU Chi-restraints excluded: chain E residue 184 LEU Chi-restraints excluded: chain F residue 692 ASN Chi-restraints excluded: chain F residue 769 THR 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 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 125 LEU Chi-restraints excluded: chain c residue 132 SER Chi-restraints excluded: chain c residue 153 LEU 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 36 LEU Chi-restraints excluded: chain d residue 127 ILE 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 127 MET Chi-restraints excluded: chain f residue 224 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 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: 10.0000 chunk 211 optimal weight: 5.9990 chunk 56 optimal weight: 3.9990 chunk 277 optimal weight: 3.9990 chunk 0 optimal weight: 6.9990 chunk 146 optimal weight: 0.0570 chunk 319 optimal weight: 6.9990 chunk 129 optimal weight: 3.9990 chunk 206 optimal weight: 6.9990 overall best weight: 3.0106 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 95 ASN A 152 ASN A 485 GLN A 489 ASN C 78 ASN b 243 HIS c 122 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** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3586 r_free = 0.3586 target = 0.062943 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2919 r_free = 0.2919 target = 0.042002 restraints weight = 261701.503| |-----------------------------------------------------------------------------| r_work (start): 0.2844 rms_B_bonded: 4.73 r_work (final): 0.2844 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2843 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2843 r_free = 0.2843 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 = 0.2843 r_free = 0.2843 target_work(ls_wunit_k1) = 0.040 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2843 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8759 moved from start: 0.2429 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.085 40252 Z= 0.251 Angle : 0.639 11.561 54945 Z= 0.329 Chirality : 0.040 0.346 6097 Planarity : 0.004 0.065 6539 Dihedral : 16.976 79.895 6480 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 7.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.46 % Favored : 96.54 % Rotamer: Outliers : 1.96 % Allowed : 23.43 % Favored : 74.61 % 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: 1.31 (0.13), residues: 4457 helix: 2.45 (0.12), residues: 1780 sheet: 0.35 (0.19), residues: 756 loop : -0.41 (0.14), residues: 1921 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 178 TYR 0.025 0.001 TYR D 129 PHE 0.026 0.002 PHE a 131 TRP 0.023 0.001 TRP f 46 HIS 0.007 0.001 HIS f 745 Details of bonding type rmsd/Z covalent geometry : bond 0.00553 / 0.25 (40252) covalent geometry : angle 0.63914 / 0.33 (54945) hydrogen bonds : bond 0.03721 / 2.49 ( 1999) hydrogen bonds : angle 4.39263 / 3.04 ( 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 345 residues out of total 4027 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 266 time to evaluate : 1.459 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 111 LEU cc_start: 0.9683 (OUTLIER) cc_final: 0.9425 (mp) REVERT: B 115 MET cc_start: 0.9454 (OUTLIER) cc_final: 0.9044 (mpp) REVERT: C 85 LYS cc_start: 0.9652 (ttpt) cc_final: 0.9368 (ptpp) REVERT: C 182 GLU cc_start: 0.8876 (mp0) cc_final: 0.8622 (mp0) REVERT: C 195 ILE cc_start: 0.9214 (tp) cc_final: 0.8823 (pt) REVERT: D 61 MET cc_start: 0.8714 (ppp) cc_final: 0.8261 (ppp) REVERT: D 66 TYR cc_start: 0.8161 (t80) cc_final: 0.7824 (t80) REVERT: E 85 THR cc_start: 0.9209 (OUTLIER) cc_final: 0.8694 (p) REVERT: E 145 GLN cc_start: 0.9612 (tp-100) cc_final: 0.9342 (tm-30) REVERT: E 184 LEU cc_start: 0.9644 (OUTLIER) cc_final: 0.9424 (mm) REVERT: a 62 MET cc_start: 0.8509 (tpp) cc_final: 0.8220 (tpp) REVERT: a 152 ASN cc_start: 0.9153 (m-40) cc_final: 0.8826 (m-40) REVERT: a 311 LEU cc_start: 0.9178 (OUTLIER) cc_final: 0.8718 (mt) REVERT: a 348 MET cc_start: 0.7767 (mtt) cc_final: 0.7420 (mtt) REVERT: a 409 TYR cc_start: 0.8639 (OUTLIER) cc_final: 0.7848 (t80) REVERT: b 84 MET cc_start: 0.8703 (pmm) cc_final: 0.8397 (pmm) REVERT: b 115 MET cc_start: 0.9573 (mmt) cc_final: 0.9218 (mmm) REVERT: b 230 SER cc_start: 0.9269 (OUTLIER) cc_final: 0.9011 (p) REVERT: d 132 ASP cc_start: 0.8987 (m-30) cc_final: 0.8698 (p0) REVERT: d 144 LEU cc_start: 0.9847 (OUTLIER) cc_final: 0.9495 (tp) REVERT: e 57 ASP cc_start: 0.8884 (m-30) cc_final: 0.8617 (p0) REVERT: e 108 LEU cc_start: 0.9551 (tp) cc_final: 0.9273 (tp) REVERT: f 95 GLU cc_start: 0.9281 (tp30) cc_final: 0.9047 (tp30) REVERT: f 279 MET cc_start: 0.8891 (mmm) cc_final: 0.8398 (mmm) REVERT: f 374 ASN cc_start: 0.9026 (m-40) cc_final: 0.8607 (t0) REVERT: f 743 MET cc_start: 0.9090 (pmm) cc_final: 0.8590 (pmm) REVERT: f 776 GLU cc_start: 0.9477 (mm-30) cc_final: 0.9205 (mt-10) REVERT: f 812 MET cc_start: 0.9305 (pmm) cc_final: 0.8400 (pmm) outliers start: 79 outliers final: 57 residues processed: 333 average time/residue: 0.1998 time to fit residues: 114.3386 Evaluate side-chains 321 residues out of total 4027 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 256 time to evaluate : 1.362 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 SER Chi-restraints excluded: chain A residue 95 ASN 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 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 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 36 LEU 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 E residue 184 LEU Chi-restraints excluded: chain F residue 751 LYS Chi-restraints excluded: chain F residue 769 THR 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 d residue 1 MET Chi-restraints excluded: chain d residue 127 ILE Chi-restraints excluded: chain d residue 143 HIS 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 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 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 Chi-restraints excluded: chain f residue 555 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 457 random chunks: chunk 246 optimal weight: 0.0170 chunk 210 optimal weight: 0.8980 chunk 397 optimal weight: 0.0060 chunk 283 optimal weight: 0.9990 chunk 53 optimal weight: 0.9980 chunk 23 optimal weight: 1.9990 chunk 381 optimal weight: 0.0670 chunk 50 optimal weight: 10.0000 chunk 421 optimal weight: 0.9990 chunk 47 optimal weight: 4.9990 chunk 358 optimal weight: 5.9990 overall best weight: 0.3972 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 137 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** b 243 HIS ** 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** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3613 r_free = 0.3613 target = 0.064183 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2963 r_free = 0.2963 target = 0.043436 restraints weight = 251576.557| |-----------------------------------------------------------------------------| r_work (start): 0.2896 rms_B_bonded: 4.68 r_work: 0.2713 rms_B_bonded: 4.98 restraints_weight: 0.5000 r_work (final): 0.2713 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2712 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2712 r_free = 0.2712 target_work(ls_wunit_k1) = 0.037 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2712 r_free = 0.2712 target_work(ls_wunit_k1) = 0.037 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2712 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8815 moved from start: 0.2418 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.065 40252 Z= 0.117 Angle : 0.609 13.949 54945 Z= 0.312 Chirality : 0.040 0.302 6097 Planarity : 0.003 0.063 6539 Dihedral : 16.925 77.490 6480 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 6.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.31 % Favored : 97.69 % Rotamer: Outliers : 1.34 % Allowed : 24.45 % Favored : 74.21 % 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: 1.39 (0.13), residues: 4457 helix: 2.47 (0.12), residues: 1773 sheet: 0.54 (0.19), residues: 752 loop : -0.39 (0.14), residues: 1932 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.021 0.000 ARG D 153 TYR 0.027 0.001 TYR D 129 PHE 0.028 0.001 PHE b 183 TRP 0.019 0.001 TRP f 46 HIS 0.006 0.001 HIS f 745 Details of bonding type rmsd/Z covalent geometry : bond 0.00244 / 0.12 (40252) covalent geometry : angle 0.60911 / 0.31 (54945) hydrogen bonds : bond 0.03236 / 2.17 ( 1999) hydrogen bonds : angle 4.24400 / 2.93 ( 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 333 residues out of total 4027 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 279 time to evaluate : 1.109 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: 0.9069 (ptp) cc_final: 0.8719 (pmm) REVERT: B 111 LEU cc_start: 0.9676 (OUTLIER) cc_final: 0.9429 (mp) REVERT: B 115 MET cc_start: 0.9468 (OUTLIER) cc_final: 0.9096 (mpp) REVERT: C 85 LYS cc_start: 0.9636 (ttpt) cc_final: 0.9352 (ptpp) REVERT: C 182 GLU cc_start: 0.9232 (mp0) cc_final: 0.8979 (mp0) REVERT: C 195 ILE cc_start: 0.9310 (tp) cc_final: 0.8913 (pt) REVERT: D 61 MET cc_start: 0.8823 (ppp) cc_final: 0.8207 (ppp) REVERT: D 66 TYR cc_start: 0.8333 (t80) cc_final: 0.7936 (t80) REVERT: E 85 THR cc_start: 0.9257 (OUTLIER) cc_final: 0.8743 (p) REVERT: E 145 GLN cc_start: 0.9619 (tp-100) cc_final: 0.9342 (tm-30) REVERT: F 743 MET cc_start: 0.8305 (ptm) cc_final: 0.7359 (tmm) REVERT: a 62 MET cc_start: 0.8953 (tpp) cc_final: 0.8657 (tpp) REVERT: a 152 ASN cc_start: 0.9134 (m-40) cc_final: 0.8831 (m-40) REVERT: a 297 LYS cc_start: 0.9294 (OUTLIER) cc_final: 0.8971 (mmmm) REVERT: a 311 LEU cc_start: 0.9144 (OUTLIER) cc_final: 0.8739 (mt) REVERT: a 409 TYR cc_start: 0.9074 (OUTLIER) cc_final: 0.8400 (t80) REVERT: b 84 MET cc_start: 0.8755 (pmm) cc_final: 0.8418 (pmm) REVERT: b 230 SER cc_start: 0.9320 (OUTLIER) cc_final: 0.9110 (p) REVERT: c 63 LYS cc_start: 0.8768 (tppt) cc_final: 0.8254 (mmmt) REVERT: c 219 MET cc_start: 0.9329 (mmm) cc_final: 0.9116 (mmt) REVERT: d 144 LEU cc_start: 0.9823 (OUTLIER) cc_final: 0.9447 (tp) REVERT: e 57 ASP cc_start: 0.9013 (m-30) cc_final: 0.8657 (p0) REVERT: e 108 LEU cc_start: 0.9572 (tp) cc_final: 0.9303 (tp) REVERT: f 78 GLU cc_start: 0.9490 (tp30) cc_final: 0.9236 (tm-30) REVERT: f 95 GLU cc_start: 0.9507 (tp30) cc_final: 0.9297 (tp30) REVERT: f 127 MET cc_start: 0.9531 (mmm) cc_final: 0.9109 (mpp) REVERT: f 281 MET cc_start: 0.8805 (ptp) cc_final: 0.8096 (pmm) REVERT: f 368 ASP cc_start: 0.8934 (m-30) cc_final: 0.8560 (m-30) REVERT: f 374 ASN cc_start: 0.9076 (m-40) cc_final: 0.8629 (t0) REVERT: f 430 MET cc_start: 0.8093 (tpp) cc_final: 0.7868 (tpp) REVERT: f 447 TRP cc_start: 0.8735 (m-10) cc_final: 0.8084 (m-10) REVERT: f 508 SER cc_start: 0.9342 (p) cc_final: 0.9116 (p) REVERT: f 743 MET cc_start: 0.9288 (pmm) cc_final: 0.8704 (pmm) REVERT: f 776 GLU cc_start: 0.9416 (mm-30) cc_final: 0.9117 (mt-10) REVERT: f 812 MET cc_start: 0.9303 (pmm) cc_final: 0.8374 (pmm) outliers start: 54 outliers final: 42 residues processed: 321 average time/residue: 0.2091 time to fit residues: 114.7191 Evaluate side-chains 318 residues out of total 4027 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 268 time to evaluate : 1.484 ------------------------------------------------------------------------------- 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 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 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 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 769 THR 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 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 d residue 1 MET 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 326 CYS Chi-restraints excluded: chain f residue 409 HIS Chi-restraints excluded: chain f residue 412 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 457 random chunks: chunk 441 optimal weight: 3.9990 chunk 456 optimal weight: 8.9990 chunk 143 optimal weight: 2.9990 chunk 89 optimal weight: 0.6980 chunk 420 optimal weight: 9.9990 chunk 409 optimal weight: 2.9990 chunk 415 optimal weight: 0.0980 chunk 301 optimal weight: 4.9990 chunk 343 optimal weight: 0.8980 chunk 337 optimal weight: 6.9990 chunk 222 optimal weight: 6.9990 overall best weight: 1.5384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 137 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** b 243 HIS ** b 382 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3606 r_free = 0.3606 target = 0.063726 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.2951 r_free = 0.2951 target = 0.042895 restraints weight = 253565.087| |-----------------------------------------------------------------------------| r_work (start): 0.2876 rms_B_bonded: 4.75 r_work (final): 0.2876 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2876 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2876 r_free = 0.2876 target_work(ls_wunit_k1) = 0.041 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2876 r_free = 0.2876 target_work(ls_wunit_k1) = 0.041 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2876 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8728 moved from start: 0.2489 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 40252 Z= 0.155 Angle : 0.613 13.872 54945 Z= 0.313 Chirality : 0.039 0.253 6097 Planarity : 0.003 0.060 6539 Dihedral : 16.933 79.208 6480 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 6.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 1.29 % Allowed : 24.65 % Favored : 74.06 % 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: 2.44 (0.12), residues: 1781 sheet: 0.47 (0.19), residues: 762 loop : -0.38 (0.14), residues: 1914 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.000 ARG D 153 TYR 0.026 0.001 TYR D 129 PHE 0.022 0.001 PHE f 125 TRP 0.023 0.001 TRP f 46 HIS 0.004 0.001 HIS f 745 Details of bonding type rmsd/Z covalent geometry : bond 0.00341 / 0.15 (40252) covalent geometry : angle 0.61288 / 0.31 (54945) hydrogen bonds : bond 0.03335 / 2.24 ( 1999) hydrogen bonds : angle 4.27224 / 2.95 ( 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 320 residues out of total 4027 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 268 time to evaluate : 1.286 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: B 84 MET cc_start: 0.8968 (ptp) cc_final: 0.8741 (pmm) REVERT: B 111 LEU cc_start: 0.9690 (OUTLIER) cc_final: 0.9429 (mp) REVERT: B 115 MET cc_start: 0.9448 (OUTLIER) cc_final: 0.9088 (mpp) REVERT: B 210 MET cc_start: 0.9428 (tmm) cc_final: 0.9112 (ppp) REVERT: C 85 LYS cc_start: 0.9652 (ttpt) cc_final: 0.9385 (ptpp) REVERT: C 165 GLN cc_start: 0.9510 (mt0) cc_final: 0.9293 (tm-30) REVERT: C 182 GLU cc_start: 0.8817 (mp0) cc_final: 0.8573 (mp0) REVERT: C 195 ILE cc_start: 0.9196 (tp) cc_final: 0.8809 (pt) REVERT: D 61 MET cc_start: 0.8833 (ppp) cc_final: 0.8352 (ppp) REVERT: D 66 TYR cc_start: 0.8069 (t80) cc_final: 0.7741 (t80) REVERT: E 85 THR cc_start: 0.9164 (OUTLIER) cc_final: 0.8641 (p) REVERT: E 145 GLN cc_start: 0.9598 (tp-100) cc_final: 0.9327 (tm-30) REVERT: a 62 MET cc_start: 0.8518 (tpp) cc_final: 0.8221 (tpp) REVERT: a 152 ASN cc_start: 0.9137 (m-40) cc_final: 0.8822 (m-40) REVERT: a 297 LYS cc_start: 0.9209 (OUTLIER) cc_final: 0.8841 (mmmm) REVERT: a 311 LEU cc_start: 0.9150 (OUTLIER) cc_final: 0.8748 (mt) REVERT: a 348 MET cc_start: 0.7653 (mtt) cc_final: 0.7308 (mtt) REVERT: a 409 TYR cc_start: 0.8592 (OUTLIER) cc_final: 0.7831 (t80) REVERT: b 20 MET cc_start: 0.8614 (ttt) cc_final: 0.8280 (ttt) REVERT: b 84 MET cc_start: 0.8735 (pmm) cc_final: 0.8413 (pmm) REVERT: b 115 MET cc_start: 0.9396 (mmm) cc_final: 0.9144 (mmm) REVERT: b 230 SER cc_start: 0.9251 (OUTLIER) cc_final: 0.9007 (p) REVERT: c 63 LYS cc_start: 0.8593 (tppt) cc_final: 0.8095 (mmmt) REVERT: d 132 ASP cc_start: 0.9007 (m-30) cc_final: 0.8714 (p0) REVERT: e 57 ASP cc_start: 0.8887 (m-30) cc_final: 0.8552 (p0) REVERT: e 108 LEU cc_start: 0.9541 (tp) cc_final: 0.9250 (tp) REVERT: f 95 GLU cc_start: 0.9237 (tp30) cc_final: 0.8997 (tp30) REVERT: f 279 MET cc_start: 0.8759 (mmm) cc_final: 0.8110 (mmm) REVERT: f 281 MET cc_start: 0.8328 (ptp) cc_final: 0.7779 (pmm) REVERT: f 368 ASP cc_start: 0.8664 (m-30) cc_final: 0.8263 (m-30) REVERT: f 374 ASN cc_start: 0.8964 (m-40) cc_final: 0.8552 (t0) REVERT: f 743 MET cc_start: 0.9088 (pmm) cc_final: 0.8573 (pmm) REVERT: f 776 GLU cc_start: 0.9454 (mm-30) cc_final: 0.9178 (mt-10) REVERT: f 812 MET cc_start: 0.9284 (pmm) cc_final: 0.8346 (pmm) outliers start: 52 outliers final: 43 residues processed: 312 average time/residue: 0.2020 time to fit residues: 108.2709 Evaluate side-chains 316 residues out of total 4027 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 266 time to evaluate : 1.394 ------------------------------------------------------------------------------- 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 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 176 ARG 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 85 THR 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 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 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 f residue 94 ILE Chi-restraints excluded: chain f residue 224 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 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: 4.9990 chunk 300 optimal weight: 4.9990 chunk 119 optimal weight: 10.0000 chunk 162 optimal weight: 3.9990 chunk 273 optimal weight: 3.9990 chunk 345 optimal weight: 3.9990 chunk 307 optimal weight: 0.8980 chunk 81 optimal weight: 4.9990 chunk 378 optimal weight: 3.9990 overall best weight: 3.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 137 HIS b 243 HIS b 312 GLN ** d 137 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** f 294 ASN f 336 ASN ** f 558 GLN ** 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 = 0.3576 r_free = 0.3576 target = 0.062421 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.2911 r_free = 0.2911 target = 0.041697 restraints weight = 242836.338| |-----------------------------------------------------------------------------| r_work (start): 0.2838 rms_B_bonded: 4.53 r_work: 0.2655 rms_B_bonded: 4.86 restraints_weight: 0.5000 r_work (final): 0.2655 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2652 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2652 r_free = 0.2652 target_work(ls_wunit_k1) = 0.035 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2652 r_free = 0.2652 target_work(ls_wunit_k1) = 0.035 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2652 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8875 moved from start: 0.2688 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.068 40252 Z= 0.267 Angle : 0.675 16.462 54945 Z= 0.343 Chirality : 0.040 0.233 6097 Planarity : 0.004 0.057 6539 Dihedral : 17.083 81.715 6480 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 8.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer: Outliers : 1.49 % Allowed : 24.42 % Favored : 74.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % 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: 1.22 (0.13), residues: 4457 helix: 2.32 (0.12), residues: 1783 sheet: 0.34 (0.19), residues: 742 loop : -0.42 (0.14), residues: 1932 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG D 153 TYR 0.030 0.001 TYR D 129 PHE 0.028 0.002 PHE a 131 TRP 0.020 0.002 TRP f 46 HIS 0.008 0.001 HIS c 134 Details of bonding type rmsd/Z covalent geometry : bond 0.00590 / 0.27 (40252) covalent geometry : angle 0.67455 / 0.34 (54945) hydrogen bonds : bond 0.03835 / 2.58 ( 1999) hydrogen bonds : angle 4.44467 / 3.07 ( 5530) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10616.58 seconds wall clock time: 182 minutes 42.59 seconds (10962.59 seconds total)