Starting phenix.real_space_refine on Sat Feb 7 13:10:41 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8gl8_40194/02_2026/8gl8_40194.cif Found real_map, /net/cci-nas-00/data/ceres_data/8gl8_40194/02_2026/8gl8_40194.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8gl8_40194/02_2026/8gl8_40194.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8gl8_40194/02_2026/8gl8_40194.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8gl8_40194/02_2026/8gl8_40194.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8gl8_40194/02_2026/8gl8_40194.map" } resolution = 2.2 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= 0.014 sd= 1.271 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: 4 Type Number sf(0) Gaussians S 79 5.16 5 C 20366 2.51 5 N 5395 2.21 5 O 7439 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 63 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 33279 Number of models: 1 Model: "" Number of chains: 18 Chain: "A" Number of atoms: 18190 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2290, 18190 Classifications: {'peptide': 2290} Link IDs: {'PCIS': 3, 'PTRANS': 105, 'TRANS': 2181} Chain breaks: 3 Chain: "B" Number of atoms: 990 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 990 Classifications: {'peptide': 128} Link IDs: {'PTRANS': 5, 'TRANS': 122} Chain breaks: 1 Chain: "F" Number of atoms: 2861 Number of conformers: 1 Conformer: "" Number of residues, atoms: 367, 2861 Classifications: {'peptide': 367} Link IDs: {'PTRANS': 17, 'TRANS': 349} Chain breaks: 1 Chain: "D" Number of atoms: 748 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 75, 602 Classifications: {'peptide': 75} Modifications used: {'COO': 1} Link IDs: {'TRANS': 74} Conformer: "B" Number of residues, atoms: 75, 602 Classifications: {'peptide': 75} Modifications used: {'COO': 1} Link IDs: {'TRANS': 74} bond proxies already assigned to first conformer: 459 Chain: "G" Number of atoms: 1435 Number of conformers: 1 Conformer: "" Number of residues, atoms: 173, 1435 Classifications: {'peptide': 173} Link IDs: {'PTRANS': 1, 'TRANS': 171} Chain: "C" Number of atoms: 1414 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 1414 Classifications: {'peptide': 172} Link IDs: {'PTRANS': 2, 'TRANS': 169} Chain breaks: 1 Chain: "E" Number of atoms: 1251 Number of conformers: 1 Conformer: "" Number of residues, atoms: 152, 1251 Classifications: {'peptide': 152} Link IDs: {'PTRANS': 1, 'TRANS': 150} Chain: "I" Number of atoms: 5168 Number of conformers: 1 Conformer: "" Number of residues, atoms: 624, 5168 Classifications: {'peptide': 624} Link IDs: {'CIS': 1, 'PTRANS': 17, 'TRANS': 605} Chain breaks: 2 Chain: "A" Number of atoms: 69 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 69 Unusual residues: {'LMN': 1} Classifications: {'undetermined': 1} Chain: "I" Number of atoms: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 66 Unusual residues: {'MAN': 6} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "A" Number of atoms: 767 Number of conformers: 1 Conformer: "" Number of residues, atoms: 767, 767 Classifications: {'water': 767} Link IDs: {None: 766} Chain: "B" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 42, 42 Classifications: {'water': 42} Link IDs: {None: 41} Chain: "F" Number of atoms: 103 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 103 Classifications: {'water': 103} Link IDs: {None: 102} Chain: "D" Number of atoms: 23 Number of conformers: 1 Conformer: "" Number of residues, atoms: 23, 23 Classifications: {'water': 23} Link IDs: {None: 22} Chain: "G" Number of atoms: 23 Number of conformers: 1 Conformer: "" Number of residues, atoms: 23, 23 Classifications: {'water': 23} Link IDs: {None: 22} Chain: "C" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 27, 27 Classifications: {'water': 27} Link IDs: {None: 26} Chain: "E" Number of atoms: 15 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 15 Classifications: {'water': 15} Link IDs: {None: 14} Chain: "I" Number of atoms: 87 Number of conformers: 1 Conformer: "" Number of residues, atoms: 87, 87 Classifications: {'water': 87} Link IDs: {None: 86} Residues with excluded nonbonded symmetry interactions: 18 residue: pdb=" N ALYS D1076 " occ=0.57 ... (16 atoms not shown) pdb=" NZ BLYS D1076 " occ=0.43 residue: pdb=" N ALYS D1077 " occ=0.57 ... (16 atoms not shown) pdb=" NZ BLYS D1077 " occ=0.43 residue: pdb=" N AVAL D1078 " occ=0.57 ... (12 atoms not shown) pdb=" CG2BVAL D1078 " occ=0.43 residue: pdb=" N AGLU D1079 " occ=0.57 ... (16 atoms not shown) pdb=" OE2BGLU D1079 " occ=0.43 residue: pdb=" N AASN D1080 " occ=0.57 ... (14 atoms not shown) pdb=" ND2BASN D1080 " occ=0.43 residue: pdb=" N ATHR D1081 " occ=0.57 ... (12 atoms not shown) pdb=" CG2BTHR D1081 " occ=0.43 residue: pdb=" N AGLU D1082 " occ=0.57 ... (16 atoms not shown) pdb=" OE2BGLU D1082 " occ=0.43 residue: pdb=" N APHE D1083 " occ=0.57 ... (20 atoms not shown) pdb=" CZ BPHE D1083 " occ=0.43 residue: pdb=" N AGLN D1084 " occ=0.57 ... (16 atoms not shown) pdb=" NE2BGLN D1084 " occ=0.43 residue: pdb=" N AVAL D1085 " occ=0.57 ... (12 atoms not shown) pdb=" CG2BVAL D1085 " occ=0.43 residue: pdb=" N ASER D1086 " occ=0.57 ... (10 atoms not shown) pdb=" OG BSER D1086 " occ=0.43 residue: pdb=" N AASN D1087 " occ=0.57 ... (14 atoms not shown) pdb=" ND2BASN D1087 " occ=0.43 ... (remaining 6 not shown) Time building chain proxies: 8.01, per 1000 atoms: 0.24 Number of scatterers: 33279 At special positions: 0 Unit cell: (292.032, 280.384, 295.36, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 79 16.00 O 7439 8.00 N 5395 7.00 C 20366 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 Links applied MAN-SER " MAN I 901 " - " SER I 249 " " MAN I 902 " - " SER I 212 " " MAN I 903 " - " SER I 371 " " MAN I 904 " - " SER I 408 " MAN-THR " MAN I 906 " - " THR I 288 " Time building additional restraints: 2.46 Conformation dependent library (CDL) restraints added in 1.4 seconds 7938 Ramachandran restraints generated. 3969 Oldfield, 0 Emsley, 3969 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7512 Finding SS restraints... Secondary structure from input PDB file: 114 helices and 25 sheets defined 33.4% alpha, 23.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.85 Creating SS restraints... Processing helix chain 'A' and resid 80 through 103 removed outlier: 3.723A pdb=" N LEU A 84 " --> pdb=" O GLU A 80 " (cutoff:3.500A) Processing helix chain 'A' and resid 107 through 112 removed outlier: 3.740A pdb=" N ALA A 111 " --> pdb=" O GLY A 107 " (cutoff:3.500A) Processing helix chain 'A' and resid 113 through 115 No H-bonds generated for 'chain 'A' and resid 113 through 115' Processing helix chain 'A' and resid 116 through 120 removed outlier: 3.611A pdb=" N TYR A 120 " --> pdb=" O PRO A 117 " (cutoff:3.500A) Processing helix chain 'A' and resid 160 through 164 Processing helix chain 'A' and resid 284 through 286 No H-bonds generated for 'chain 'A' and resid 284 through 286' Processing helix chain 'A' and resid 295 through 306 removed outlier: 4.667A pdb=" N ASP A 303 " --> pdb=" O ARG A 299 " (cutoff:3.500A) removed outlier: 5.009A pdb=" N VAL A 304 " --> pdb=" O ASN A 300 " (cutoff:3.500A) Processing helix chain 'A' and resid 359 through 363 Processing helix chain 'A' and resid 382 through 386 removed outlier: 4.208A pdb=" N ASN A 386 " --> pdb=" O ASN A 383 " (cutoff:3.500A) Processing helix chain 'A' and resid 389 through 393 removed outlier: 3.576A pdb=" N ILE A 393 " --> pdb=" O PRO A 390 " (cutoff:3.500A) Processing helix chain 'A' and resid 401 through 406 Processing helix chain 'A' and resid 410 through 414 Processing helix chain 'A' and resid 435 through 437 No H-bonds generated for 'chain 'A' and resid 435 through 437' Processing helix chain 'A' and resid 517 through 522 removed outlier: 3.968A pdb=" N ASN A 521 " --> pdb=" O ASN A 517 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N LEU A 522 " --> pdb=" O PRO A 518 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 517 through 522' Processing helix chain 'A' and resid 569 through 573 removed outlier: 4.058A pdb=" N LYS A 573 " --> pdb=" O PRO A 570 " (cutoff:3.500A) Processing helix chain 'A' and resid 578 through 583 Processing helix chain 'A' and resid 626 through 633 Processing helix chain 'A' and resid 643 through 647 removed outlier: 3.559A pdb=" N TYR A 647 " --> pdb=" O PRO A 644 " (cutoff:3.500A) Processing helix chain 'A' and resid 650 through 655 Processing helix chain 'A' and resid 657 through 662 Processing helix chain 'A' and resid 663 through 668 Processing helix chain 'A' and resid 669 through 674 removed outlier: 5.888A pdb=" N ASP A 672 " --> pdb=" O GLN A 669 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N LYS A 673 " --> pdb=" O ASP A 670 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N ASN A 674 " --> pdb=" O SER A 671 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 669 through 674' Processing helix chain 'A' and resid 730 through 735 removed outlier: 3.643A pdb=" N ALA A 735 " --> pdb=" O PRO A 731 " (cutoff:3.500A) Processing helix chain 'A' and resid 810 through 818 removed outlier: 3.871A pdb=" N THR A 814 " --> pdb=" O VAL A 810 " (cutoff:3.500A) Processing helix chain 'A' and resid 845 through 847 No H-bonds generated for 'chain 'A' and resid 845 through 847' Processing helix chain 'A' and resid 872 through 876 Processing helix chain 'A' and resid 898 through 903 Processing helix chain 'A' and resid 915 through 920 Processing helix chain 'A' and resid 940 through 944 Processing helix chain 'A' and resid 982 through 985 Processing helix chain 'A' and resid 998 through 1003 Processing helix chain 'A' and resid 1048 through 1052 Processing helix chain 'A' and resid 1081 through 1089 Processing helix chain 'A' and resid 1099 through 1104 removed outlier: 4.212A pdb=" N ILE A1103 " --> pdb=" O ARG A1099 " (cutoff:3.500A) Processing helix chain 'A' and resid 1105 through 1108 removed outlier: 3.508A pdb=" N ALA A1108 " --> pdb=" O THR A1105 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1105 through 1108' Processing helix chain 'A' and resid 1127 through 1132 Processing helix chain 'A' and resid 1412 through 1417 Processing helix chain 'A' and resid 1418 through 1422 Processing helix chain 'A' and resid 1427 through 1438 Processing helix chain 'A' and resid 1454 through 1458 Processing helix chain 'A' and resid 1573 through 1576 Processing helix chain 'A' and resid 1607 through 1614 Processing helix chain 'A' and resid 1617 through 1629 removed outlier: 3.605A pdb=" N ALA A1628 " --> pdb=" O ILE A1624 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N ILE A1629 " --> pdb=" O ARG A1625 " (cutoff:3.500A) Processing helix chain 'A' and resid 1656 through 1658 No H-bonds generated for 'chain 'A' and resid 1656 through 1658' Processing helix chain 'A' and resid 1830 through 1834 removed outlier: 3.701A pdb=" N LYS A1833 " --> pdb=" O PRO A1830 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N ILE A1834 " --> pdb=" O ILE A1831 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1830 through 1834' Processing helix chain 'A' and resid 1856 through 1861 Processing helix chain 'A' and resid 1941 through 1943 No H-bonds generated for 'chain 'A' and resid 1941 through 1943' Processing helix chain 'A' and resid 1976 through 1981 Processing helix chain 'A' and resid 1987 through 1995 Processing helix chain 'A' and resid 2071 through 2075 Processing helix chain 'A' and resid 2084 through 2106 removed outlier: 3.722A pdb=" N ARG A2094 " --> pdb=" O PHE A2090 " (cutoff:3.500A) removed outlier: 4.789A pdb=" N LEU A2095 " --> pdb=" O ARG A2091 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N ILE A2096 " --> pdb=" O SER A2092 " (cutoff:3.500A) Processing helix chain 'A' and resid 2129 through 2136 Processing helix chain 'A' and resid 2147 through 2161 Proline residue: A2153 - end of helix Processing helix chain 'A' and resid 2186 through 2190 removed outlier: 4.159A pdb=" N ARG A2189 " --> pdb=" O GLY A2186 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N TYR A2190 " --> pdb=" O LEU A2187 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 2186 through 2190' Processing helix chain 'B' and resid 27 through 42 Processing helix chain 'B' and resid 126 through 133 Processing helix chain 'B' and resid 134 through 136 No H-bonds generated for 'chain 'B' and resid 134 through 136' Processing helix chain 'F' and resid 30 through 35 Processing helix chain 'F' and resid 38 through 44 Processing helix chain 'F' and resid 61 through 68 removed outlier: 3.704A pdb=" N ALA F 66 " --> pdb=" O ALA F 63 " (cutoff:3.500A) Processing helix chain 'F' and resid 284 through 297 removed outlier: 3.956A pdb=" N ASP F 288 " --> pdb=" O GLN F 284 " (cutoff:3.500A) Processing helix chain 'F' and resid 299 through 308 removed outlier: 3.761A pdb=" N PHE F 305 " --> pdb=" O VAL F 301 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N PHE F 308 " --> pdb=" O ILE F 304 " (cutoff:3.500A) Processing helix chain 'F' and resid 314 through 319 Processing helix chain 'G' and resid 31 through 38 Processing helix chain 'G' and resid 39 through 77 removed outlier: 3.510A pdb=" N GLU G 77 " --> pdb=" O GLY G 73 " (cutoff:3.500A) Processing helix chain 'G' and resid 82 through 109 Processing helix chain 'G' and resid 112 through 120 Processing helix chain 'G' and resid 122 through 140 Processing helix chain 'G' and resid 159 through 162 Processing helix chain 'G' and resid 163 through 176 Processing helix chain 'G' and resid 181 through 193 Processing helix chain 'C' and resid 31 through 37 Processing helix chain 'C' and resid 39 through 76 removed outlier: 3.808A pdb=" N LYS C 43 " --> pdb=" O VAL C 39 " (cutoff:3.500A) Processing helix chain 'C' and resid 82 through 108 Processing helix chain 'C' and resid 114 through 141 Proline residue: C 124 - end of helix Processing helix chain 'C' and resid 163 through 173 Processing helix chain 'C' and resid 203 through 223 removed outlier: 3.764A pdb=" N ILE C 222 " --> pdb=" O ARG C 218 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N GLU C 223 " --> pdb=" O GLU C 219 " (cutoff:3.500A) Processing helix chain 'E' and resid 31 through 40 Processing helix chain 'E' and resid 41 through 77 removed outlier: 3.591A pdb=" N ALA E 45 " --> pdb=" O ASP E 41 " (cutoff:3.500A) Processing helix chain 'E' and resid 83 through 109 Processing helix chain 'E' and resid 114 through 141 Proline residue: E 124 - end of helix Processing helix chain 'E' and resid 164 through 174 removed outlier: 3.511A pdb=" N THR E 174 " --> pdb=" O ILE E 170 " (cutoff:3.500A) Processing helix chain 'I' and resid 27 through 40 Processing helix chain 'I' and resid 41 through 59 Processing helix chain 'I' and resid 88 through 103 removed outlier: 3.811A pdb=" N GLU I 92 " --> pdb=" O ASN I 88 " (cutoff:3.500A) Processing helix chain 'I' and resid 117 through 132 Processing helix chain 'I' and resid 134 through 149 Processing helix chain 'I' and resid 154 through 169 Processing helix chain 'I' and resid 171 through 185 removed outlier: 4.211A pdb=" N LYS I 185 " --> pdb=" O GLN I 181 " (cutoff:3.500A) Processing helix chain 'I' and resid 189 through 207 Processing helix chain 'I' and resid 209 through 224 Processing helix chain 'I' and resid 226 through 245 Processing helix chain 'I' and resid 246 through 259 Processing helix chain 'I' and resid 265 through 279 removed outlier: 4.008A pdb=" N MET I 269 " --> pdb=" O ASP I 265 " (cutoff:3.500A) Processing helix chain 'I' and resid 286 through 299 Processing helix chain 'I' and resid 300 through 305 removed outlier: 3.523A pdb=" N ASN I 303 " --> pdb=" O ASP I 300 " (cutoff:3.500A) Proline residue: I 305 - end of helix Processing helix chain 'I' and resid 306 through 321 Processing helix chain 'I' and resid 323 through 337 Processing helix chain 'I' and resid 341 through 359 Processing helix chain 'I' and resid 361 through 376 removed outlier: 3.621A pdb=" N THR I 374 " --> pdb=" O ASP I 370 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N LYS I 375 " --> pdb=" O SER I 371 " (cutoff:3.500A) Processing helix chain 'I' and resid 380 through 392 Processing helix chain 'I' and resid 393 through 415 removed outlier: 4.030A pdb=" N MET I 415 " --> pdb=" O LYS I 411 " (cutoff:3.500A) Processing helix chain 'I' and resid 417 through 443 removed outlier: 3.536A pdb=" N LYS I 421 " --> pdb=" O ASP I 417 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N GLU I 443 " --> pdb=" O ARG I 439 " (cutoff:3.500A) Processing helix chain 'I' and resid 552 through 563 Processing helix chain 'I' and resid 569 through 593 Processing helix chain 'I' and resid 598 through 610 Processing helix chain 'I' and resid 616 through 631 Processing helix chain 'I' and resid 632 through 646 removed outlier: 3.781A pdb=" N ALA I 636 " --> pdb=" O ASP I 632 " (cutoff:3.500A) Processing helix chain 'I' and resid 651 through 657 removed outlier: 3.617A pdb=" N ASN I 657 " --> pdb=" O ALA I 653 " (cutoff:3.500A) Processing helix chain 'I' and resid 673 through 680 Processing helix chain 'I' and resid 684 through 697 removed outlier: 4.157A pdb=" N ASP I 688 " --> pdb=" O ASP I 684 " (cutoff:3.500A) removed outlier: 4.608A pdb=" N ASN I 695 " --> pdb=" O ASP I 691 " (cutoff:3.500A) Processing helix chain 'I' and resid 701 through 718 removed outlier: 3.993A pdb=" N LYS I 705 " --> pdb=" O GLU I 701 " (cutoff:3.500A) Processing helix chain 'I' and resid 719 through 734 Processing helix chain 'I' and resid 737 through 756 removed outlier: 3.592A pdb=" N GLU I 748 " --> pdb=" O ARG I 744 " (cutoff:3.500A) Proline residue: I 752 - end of helix Processing sheet with id=AA1, first strand: chain 'A' and resid 47 through 53 Processing sheet with id=AA2, first strand: chain 'A' and resid 138 through 154 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 166 through 173 current: chain 'A' and resid 187 through 194 removed outlier: 6.394A pdb=" N PHE A 205 " --> pdb=" O ASN A 224 " (cutoff:3.500A) removed outlier: 6.757A pdb=" N ILE A 217 " --> pdb=" O LEU A 247 " (cutoff:3.500A) removed outlier: 6.695A pdb=" N LEU A 247 " --> pdb=" O ILE A 217 " (cutoff:3.500A) removed outlier: 6.627A pdb=" N LYS A 219 " --> pdb=" O THR A 245 " (cutoff:3.500A) removed outlier: 4.350A pdb=" N THR A 245 " --> pdb=" O LYS A 219 " (cutoff:3.500A) removed outlier: 6.619A pdb=" N GLU A 221 " --> pdb=" O VAL A 243 " (cutoff:3.500A) removed outlier: 4.298A pdb=" N VAL A 243 " --> pdb=" O GLU A 221 " (cutoff:3.500A) removed outlier: 6.330A pdb=" N GLY A 223 " --> pdb=" O PHE A 241 " (cutoff:3.500A) removed outlier: 4.126A pdb=" N PHE A 241 " --> pdb=" O GLY A 223 " (cutoff:3.500A) removed outlier: 6.985A pdb=" N VAL A 225 " --> pdb=" O SER A 239 " (cutoff:3.500A) removed outlier: 4.623A pdb=" N SER A 239 " --> pdb=" O VAL A 225 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N THR A 253 " --> pdb=" O GLU A 763 " (cutoff:3.500A) removed outlier: 4.567A pdb=" N ARG A 755 " --> pdb=" O GLN A 261 " (cutoff:3.500A) removed outlier: 6.553A pdb=" N PHE A 770 " --> pdb=" O ILE A 766 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 770 through 773 current: chain 'A' and resid 796 through 809 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 1559 through 1571 current: chain 'A' and resid 1630 through 1644 removed outlier: 5.444A pdb=" N THR A1632 " --> pdb=" O HIS A1672 " (cutoff:3.500A) removed outlier: 7.467A pdb=" N HIS A1672 " --> pdb=" O THR A1632 " (cutoff:3.500A) removed outlier: 5.490A pdb=" N ARG A1634 " --> pdb=" O GLU A1670 " (cutoff:3.500A) removed outlier: 7.281A pdb=" N GLU A1670 " --> pdb=" O ARG A1634 " (cutoff:3.500A) removed outlier: 5.453A pdb=" N SER A1636 " --> pdb=" O GLN A1668 " (cutoff:3.500A) removed outlier: 7.477A pdb=" N GLN A1668 " --> pdb=" O SER A1636 " (cutoff:3.500A) removed outlier: 5.278A pdb=" N ASN A1638 " --> pdb=" O TYR A1666 " (cutoff:3.500A) removed outlier: 7.345A pdb=" N TYR A1666 " --> pdb=" O ASN A1638 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N ILE A1640 " --> pdb=" O GLN A1664 " (cutoff:3.500A) removed outlier: 6.411A pdb=" N GLN A1664 " --> pdb=" O ILE A1640 " (cutoff:3.500A) removed outlier: 4.767A pdb=" N LYS A1644 " --> pdb=" O PHE A1660 " (cutoff:3.500A) removed outlier: 6.464A pdb=" N PHE A1660 " --> pdb=" O LYS A1644 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 1757 through 1760 current: chain 'A' and resid 1779 through 1789 removed outlier: 5.525A pdb=" N ILE A1789 " --> pdb=" O PRO A1816 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N THR A1847 " --> pdb=" O SER A1881 " (cutoff:3.500A) removed outlier: 6.427A pdb=" N ILE A1876 " --> pdb=" O PRO A1961 " (cutoff:3.500A) removed outlier: 7.407A pdb=" N ASN A1878 " --> pdb=" O VAL A1959 " (cutoff:3.500A) removed outlier: 5.433A pdb=" N VAL A1959 " --> pdb=" O ASN A1878 " (cutoff:3.500A) removed outlier: 7.209A pdb=" N ASN A1880 " --> pdb=" O GLY A1957 " (cutoff:3.500A) removed outlier: 5.579A pdb=" N GLY A1957 " --> pdb=" O ASN A1880 " (cutoff:3.500A) removed outlier: 6.848A pdb=" N ASN A1882 " --> pdb=" O ASN A1955 " (cutoff:3.500A) removed outlier: 4.921A pdb=" N ASN A1955 " --> pdb=" O ASN A1882 " (cutoff:3.500A) removed outlier: 7.208A pdb=" N LEU A1884 " --> pdb=" O THR A1953 " (cutoff:3.500A) removed outlier: 5.328A pdb=" N THR A1953 " --> pdb=" O LEU A1884 " (cutoff:3.500A) removed outlier: 7.440A pdb=" N THR A1886 " --> pdb=" O ASN A1951 " (cutoff:3.500A) removed outlier: 5.363A pdb=" N ASN A1951 " --> pdb=" O THR A1886 " (cutoff:3.500A) removed outlier: 6.614A pdb=" N ILE A1945 " --> pdb=" O ASP A2022 " (cutoff:3.500A) removed outlier: 6.539A pdb=" N ASP A2022 " --> pdb=" O ILE A1945 " (cutoff:3.500A) removed outlier: 4.145A pdb=" N ASN A1947 " --> pdb=" O ASN A2020 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N ASN A1951 " --> pdb=" O LYS A2016 " (cutoff:3.500A) removed outlier: 4.077A pdb=" N LEU A2023 " --> pdb=" O LEU A2027 " (cutoff:3.500A) removed outlier: 6.936A pdb=" N LEU A2027 " --> pdb=" O LEU A2023 " (cutoff:3.500A) removed outlier: 9.499A pdb=" N SER A2032 " --> pdb=" O THR A2069 " (cutoff:3.500A) removed outlier: 7.105A pdb=" N THR A2069 " --> pdb=" O SER A2032 " (cutoff:3.500A) removed outlier: 6.753A pdb=" N ASP A2034 " --> pdb=" O ILE A2067 " (cutoff:3.500A) removed outlier: 4.536A pdb=" N ILE A2067 " --> pdb=" O ASP A2034 " (cutoff:3.500A) removed outlier: 6.668A pdb=" N SER A2036 " --> pdb=" O PHE A2065 " (cutoff:3.500A) removed outlier: 4.458A pdb=" N PHE A2065 " --> pdb=" O SER A2036 " (cutoff:3.500A) removed outlier: 6.561A pdb=" N SER A2038 " --> pdb=" O GLY A2063 " (cutoff:3.500A) removed outlier: 4.269A pdb=" N GLY A2063 " --> pdb=" O SER A2038 " (cutoff:3.500A) removed outlier: 6.715A pdb=" N ASN A2040 " --> pdb=" O THR A2061 " (cutoff:3.500A) removed outlier: 4.356A pdb=" N THR A2061 " --> pdb=" O ASN A2040 " (cutoff:3.500A) removed outlier: 6.726A pdb=" N SER A2042 " --> pdb=" O PRO A2059 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 2054 through 2069 current: chain 'A' and resid 2197 through 2217 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 2238 through 2240 current: chain 'A' and resid 2264 through 2278 removed outlier: 3.822A pdb=" N VAL A2287 " --> pdb=" O ALA A2274 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N ASP A2302 " --> pdb=" O SER A2319 " (cutoff:3.500A) removed outlier: 5.558A pdb=" N SER A2319 " --> pdb=" O ASP A2302 " (cutoff:3.500A) removed outlier: 7.707A pdb=" N ASP A2320 " --> pdb=" O TYR A2361 " (cutoff:3.500A) removed outlier: 4.635A pdb=" N TYR A2361 " --> pdb=" O ASP A2320 " (cutoff:3.500A) removed outlier: 6.287A pdb=" N ASN A2322 " --> pdb=" O ALA A2359 " (cutoff:3.500A) removed outlier: 4.086A pdb=" N ALA A2359 " --> pdb=" O ASN A2322 " (cutoff:3.500A) removed outlier: 6.725A pdb=" N LYS A2324 " --> pdb=" O LEU A2357 " (cutoff:3.500A) removed outlier: 4.366A pdb=" N LEU A2357 " --> pdb=" O LYS A2324 " (cutoff:3.500A) removed outlier: 6.421A pdb=" N ASP A2326 " --> pdb=" O LEU A2355 " (cutoff:3.500A) removed outlier: 4.079A pdb=" N LEU A2355 " --> pdb=" O ASP A2326 " (cutoff:3.500A) removed outlier: 6.596A pdb=" N SER A2328 " --> pdb=" O TRP A2353 " (cutoff:3.500A) removed outlier: 4.372A pdb=" N TRP A2353 " --> pdb=" O SER A2328 " (cutoff:3.500A) removed outlier: 6.423A pdb=" N ARG A2330 " --> pdb=" O ASN A2351 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N ASN A2351 " --> pdb=" O ARG A2330 " (cutoff:3.500A) removed outlier: 6.361A pdb=" N ASN A2332 " --> pdb=" O GLY A2349 " (cutoff:3.500A) removed outlier: 4.308A pdb=" N GLY A2349 " --> pdb=" O ASN A2332 " (cutoff:3.500A) removed outlier: 6.599A pdb=" N THR A2334 " --> pdb=" O ALA A2347 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N ASN A2351 " --> pdb=" O LYS A2379 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 264 through 270 Processing sheet with id=AA4, first strand: chain 'A' and resid 275 through 282 Processing sheet with id=AA5, first strand: chain 'A' and resid 291 through 293 removed outlier: 3.855A pdb=" N TYR A 447 " --> pdb=" O ASN A 442 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 471 through 474 removed outlier: 6.311A pdb=" N LEU A 460 " --> pdb=" O LEU A 508 " (cutoff:3.500A) removed outlier: 7.965A pdb=" N PHE A 464 " --> pdb=" O VAL A 504 " (cutoff:3.500A) removed outlier: 11.868A pdb=" N VAL A 504 " --> pdb=" O PHE A 464 " (cutoff:3.500A) removed outlier: 8.851A pdb=" N LEU A 503 " --> pdb=" O LEU A 341 " (cutoff:3.500A) removed outlier: 6.918A pdb=" N ASN A 343 " --> pdb=" O LEU A 503 " (cutoff:3.500A) removed outlier: 7.627A pdb=" N LEU A 505 " --> pdb=" O ASN A 343 " (cutoff:3.500A) removed outlier: 6.471A pdb=" N ILE A 345 " --> pdb=" O LEU A 505 " (cutoff:3.500A) removed outlier: 6.611A pdb=" N MET A 507 " --> pdb=" O ILE A 345 " (cutoff:3.500A) removed outlier: 6.383A pdb=" N LEU A 347 " --> pdb=" O MET A 507 " (cutoff:3.500A) removed outlier: 8.291A pdb=" N LYS A 509 " --> pdb=" O LEU A 347 " (cutoff:3.500A) removed outlier: 5.194A pdb=" N ARG A 342 " --> pdb=" O ASN A 430 " (cutoff:3.500A) removed outlier: 4.123A pdb=" N ASN A 430 " --> pdb=" O ARG A 342 " (cutoff:3.500A) removed outlier: 5.342A pdb=" N ILE A 318 " --> pdb=" O THR A 467 " (cutoff:3.500A) removed outlier: 6.535A pdb=" N THR A 467 " --> pdb=" O ILE A 318 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 486 through 489 Processing sheet with id=AA8, first strand: chain 'A' and resid 527 through 529 Processing sheet with id=AA9, first strand: chain 'A' and resid 690 through 691 Processing sheet with id=AB1, first strand: chain 'A' and resid 849 through 850 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 853 through 859 current: chain 'A' and resid 1326 through 1337 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 1326 through 1337 current: chain 'A' and resid 1423 through 1426 Processing sheet with id=AB2, first strand: chain 'A' and resid 866 through 869 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 866 through 869 current: chain 'A' and resid 960 through 969 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 960 through 969 current: chain 'A' and resid 1208 through 1219 No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'A' and resid 877 through 878 Processing sheet with id=AB4, first strand: chain 'A' and resid 938 through 939 removed outlier: 4.443A pdb=" N ILE A 938 " --> pdb=" O VAL A 957 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 1265 through 1266 removed outlier: 7.000A pdb=" N ARG A1343 " --> pdb=" O LYS A1491 " (cutoff:3.500A) removed outlier: 5.334A pdb=" N LYS A1491 " --> pdb=" O ARG A1343 " (cutoff:3.500A) removed outlier: 7.112A pdb=" N VAL A1345 " --> pdb=" O GLY A1489 " (cutoff:3.500A) removed outlier: 5.117A pdb=" N GLY A1489 " --> pdb=" O VAL A1345 " (cutoff:3.500A) removed outlier: 7.330A pdb=" N LYS A1347 " --> pdb=" O MET A1487 " (cutoff:3.500A) removed outlier: 5.390A pdb=" N MET A1487 " --> pdb=" O LYS A1347 " (cutoff:3.500A) removed outlier: 6.485A pdb=" N VAL A1349 " --> pdb=" O ASN A1485 " (cutoff:3.500A) removed outlier: 4.760A pdb=" N ASN A1485 " --> pdb=" O VAL A1349 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 1313 through 1315 Processing sheet with id=AB7, first strand: chain 'A' and resid 1862 through 1863 Processing sheet with id=AB8, first strand: chain 'B' and resid 47 through 48 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 54 through 59 current: chain 'B' and resid 110 through 113 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 110 through 113 current: chain 'B' and resid 166 through 174 Processing sheet with id=AB9, first strand: chain 'F' and resid 193 through 194 removed outlier: 4.045A pdb=" N ILE F 240 " --> pdb=" O ASN F 199 " (cutoff:3.500A) removed outlier: 6.409A pdb=" N LEU F 387 " --> pdb=" O PRO F 80 " (cutoff:3.500A) removed outlier: 6.662A pdb=" N ASP F 397 " --> pdb=" O ASP F 70 " (cutoff:3.500A) removed outlier: 4.740A pdb=" N ASP F 70 " --> pdb=" O ASP F 397 " (cutoff:3.500A) removed outlier: 5.764A pdb=" N VAL F 182 " --> pdb=" O ASN F 210 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'F' and resid 118 through 120 removed outlier: 3.955A pdb=" N ARG F 131 " --> pdb=" O LEU F 120 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'F' and resid 215 through 220 removed outlier: 4.431A pdb=" N TYR F 217 " --> pdb=" O SER F 223 " (cutoff:3.500A) removed outlier: 9.536A pdb=" N SER F 223 " --> pdb=" O TYR F 217 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'D' and resid 1041 through 1045 removed outlier: 6.665A pdb=" N ILE D1050 " --> pdb=" O BPHE D1083 " (cutoff:3.500A) removed outlier: 6.672A pdb=" N BPHE D1083 " --> pdb=" O ILE D1050 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'D' and resid 1071 through 1075 removed outlier: 6.537A pdb=" N LEU D1071 " --> pdb=" O ASP D1066 " (cutoff:3.500A) removed outlier: 6.393A pdb=" N ASP D1066 " --> pdb=" O LEU D1071 " (cutoff:3.500A) removed outlier: 6.597A pdb=" N THR D1100 " --> pdb=" O ARG D1060 " (cutoff:3.500A) removed outlier: 4.394A pdb=" N VAL D1062 " --> pdb=" O LYS D1098 " (cutoff:3.500A) removed outlier: 6.721A pdb=" N LYS D1098 " --> pdb=" O VAL D1062 " (cutoff:3.500A) removed outlier: 4.242A pdb=" N ILE D1064 " --> pdb=" O ILE D1096 " (cutoff:3.500A) removed outlier: 6.406A pdb=" N ILE D1096 " --> pdb=" O ILE D1064 " (cutoff:3.500A) removed outlier: 5.586A pdb=" N ASP D1066 " --> pdb=" O VAL D1094 " (cutoff:3.500A) removed outlier: 8.348A pdb=" N VAL D1094 " --> pdb=" O ASP D1066 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'G' and resid 27 through 30 removed outlier: 6.318A pdb=" N ILE G 145 " --> pdb=" O LEU C 155 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'G' and resid 154 through 157 removed outlier: 5.723A pdb=" N MET G 154 " --> pdb=" O ASP E 147 " (cutoff:3.500A) removed outlier: 6.312A pdb=" N ASP E 147 " --> pdb=" O MET G 154 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'C' and resid 27 through 29 removed outlier: 6.643A pdb=" N GLY C 28 " --> pdb=" O PHE C 146 " (cutoff:3.500A) 1391 hydrogen bonds defined for protein. 3906 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 10.50 Time building geometry restraints manager: 3.35 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: 10610 1.34 - 1.46: 7273 1.46 - 1.58: 14791 1.58 - 1.70: 4 1.70 - 1.82: 155 Bond restraints: 32833 Sorted by residual: bond pdb=" C1 LMN A2501 " pdb=" O5 LMN A2501 " ideal model delta sigma weight residual 1.403 1.552 -0.149 2.00e-02 2.50e+03 5.58e+01 bond pdb=" CCS LMN A2501 " pdb=" OBZ LMN A2501 " ideal model delta sigma weight residual 1.394 1.480 -0.086 2.00e-02 2.50e+03 1.86e+01 bond pdb=" CCR LMN A2501 " pdb=" OBY LMN A2501 " ideal model delta sigma weight residual 1.393 1.476 -0.083 2.00e-02 2.50e+03 1.70e+01 bond pdb=" C4 LMN A2501 " pdb=" O4 LMN A2501 " ideal model delta sigma weight residual 1.409 1.482 -0.073 2.00e-02 2.50e+03 1.33e+01 bond pdb=" C1 LMN A2501 " pdb=" O1 LMN A2501 " ideal model delta sigma weight residual 1.374 1.305 0.069 2.00e-02 2.50e+03 1.18e+01 ... (remaining 32828 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.13: 43809 2.13 - 4.25: 505 4.25 - 6.38: 72 6.38 - 8.50: 10 8.50 - 10.63: 4 Bond angle restraints: 44400 Sorted by residual: angle pdb=" CA LYS A 79 " pdb=" CB LYS A 79 " pdb=" CG LYS A 79 " ideal model delta sigma weight residual 114.10 122.82 -8.72 2.00e+00 2.50e-01 1.90e+01 angle pdb=" CA LYS I 725 " pdb=" CB LYS I 725 " pdb=" CG LYS I 725 " ideal model delta sigma weight residual 114.10 121.95 -7.85 2.00e+00 2.50e-01 1.54e+01 angle pdb=" CB LYS C 83 " pdb=" CG LYS C 83 " pdb=" CD LYS C 83 " ideal model delta sigma weight residual 111.30 120.28 -8.98 2.30e+00 1.89e-01 1.52e+01 angle pdb=" N PHE A 199 " pdb=" CA PHE A 199 " pdb=" C PHE A 199 " ideal model delta sigma weight residual 110.80 119.04 -8.24 2.13e+00 2.20e-01 1.49e+01 angle pdb=" N VAL A1987 " pdb=" CA VAL A1987 " pdb=" C VAL A1987 " ideal model delta sigma weight residual 113.20 109.70 3.50 9.60e-01 1.09e+00 1.33e+01 ... (remaining 44395 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 27.93: 18358 27.93 - 55.86: 1395 55.86 - 83.80: 196 83.80 - 111.73: 39 111.73 - 139.66: 5 Dihedral angle restraints: 19993 sinusoidal: 8272 harmonic: 11721 Sorted by residual: dihedral pdb=" CA ARG F 121 " pdb=" C ARG F 121 " pdb=" N GLN F 122 " pdb=" CA GLN F 122 " ideal model delta harmonic sigma weight residual 180.00 155.40 24.60 0 5.00e+00 4.00e-02 2.42e+01 dihedral pdb=" CA MET I 260 " pdb=" C MET I 260 " pdb=" N ASN I 261 " pdb=" CA ASN I 261 " ideal model delta harmonic sigma weight residual -180.00 -156.41 -23.59 0 5.00e+00 4.00e-02 2.23e+01 dihedral pdb=" CAB LMN A2501 " pdb=" CAX LMN A2501 " pdb=" CAZ LMN A2501 " pdb=" CBB LMN A2501 " ideal model delta sinusoidal sigma weight residual -179.97 -40.31 -139.66 1 3.00e+01 1.11e-03 1.88e+01 ... (remaining 19990 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.052: 3867 0.052 - 0.103: 777 0.103 - 0.155: 171 0.155 - 0.206: 5 0.206 - 0.258: 1 Chirality restraints: 4821 Sorted by residual: chirality pdb=" CA PHE A 199 " pdb=" N PHE A 199 " pdb=" C PHE A 199 " pdb=" CB PHE A 199 " both_signs ideal model delta sigma weight residual False 2.51 2.25 0.26 2.00e-01 2.50e+01 1.66e+00 chirality pdb=" CCQ LMN A2501 " pdb=" CCF LMN A2501 " pdb=" CCH LMN A2501 " pdb=" OCB LMN A2501 " both_signs ideal model delta sigma weight residual False -2.61 -2.42 -0.19 2.00e-01 2.50e+01 8.91e-01 chirality pdb=" CCV LMN A2501 " pdb=" CCR LMN A2501 " pdb=" CCT LMN A2501 " pdb=" OAU LMN A2501 " both_signs ideal model delta sigma weight residual False 2.28 2.47 -0.19 2.00e-01 2.50e+01 8.68e-01 ... (remaining 4818 not shown) Planarity restraints: 5825 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA PHE A1639 " -0.012 2.00e-02 2.50e+03 2.43e-02 5.91e+00 pdb=" C PHE A1639 " 0.042 2.00e-02 2.50e+03 pdb=" O PHE A1639 " -0.016 2.00e-02 2.50e+03 pdb=" N ILE A1640 " -0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA SER A 176 " 0.012 2.00e-02 2.50e+03 2.37e-02 5.63e+00 pdb=" C SER A 176 " -0.041 2.00e-02 2.50e+03 pdb=" O SER A 176 " 0.016 2.00e-02 2.50e+03 pdb=" N MET A 177 " 0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASN A2351 " -0.011 2.00e-02 2.50e+03 2.18e-02 4.75e+00 pdb=" C ASN A2351 " 0.038 2.00e-02 2.50e+03 pdb=" O ASN A2351 " -0.014 2.00e-02 2.50e+03 pdb=" N ILE A2352 " -0.012 2.00e-02 2.50e+03 ... (remaining 5822 not shown) Histogram of nonbonded interaction distances: 2.06 - 2.62: 494 2.62 - 3.19: 27881 3.19 - 3.76: 53738 3.76 - 4.33: 78249 4.33 - 4.90: 123521 Nonbonded interactions: 283883 Sorted by model distance: nonbonded pdb=" O LEU I 182 " pdb=" OG1 THR I 186 " model vdw 2.055 3.040 nonbonded pdb=" ND2 ASN A1392 " pdb=" O GLY A1476 " model vdw 2.152 3.120 nonbonded pdb=" OD1 ASP A1165 " pdb=" O HOH A2601 " model vdw 2.153 3.040 nonbonded pdb=" OE1 GLN A 753 " pdb=" OG SER A 794 " model vdw 2.157 3.040 nonbonded pdb=" OD1 ASN A1163 " pdb=" O HOH A2601 " model vdw 2.160 3.040 ... (remaining 283878 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 'C' and resid 24 through 173) selection = (chain 'E' and resid 24 through 173) selection = (chain 'G' and resid 24 through 173) } 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=0.43 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: 6.130 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: 1.680 Check model and map are aligned: 0.100 Set scattering table: 0.140 Process input model: 35.200 Find NCS groups from input model: 0.250 Set up NCS constraints: 0.060 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:7.080 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 50.690 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8063 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 0.149 32838 Z= 0.165 Angle : 0.569 10.627 44410 Z= 0.300 Chirality : 0.043 0.258 4821 Planarity : 0.003 0.052 5825 Dihedral : 19.298 139.662 12481 Min Nonbonded Distance : 2.055 Molprobity Statistics. All-atom Clashscore : 7.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.51 % Favored : 95.49 % Rotamer: Outliers : 3.70 % Allowed : 23.00 % Favored : 73.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.00 % Cis-general : 0.03 % 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: 0.64 (0.14), residues: 3969 helix: 1.78 (0.16), residues: 1171 sheet: 0.52 (0.15), residues: 1105 loop : -0.57 (0.15), residues: 1693 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.000 ARG E 116 TYR 0.015 0.001 TYR I 294 PHE 0.023 0.001 PHE A1009 TRP 0.015 0.001 TRP I 674 HIS 0.004 0.001 HIS I 271 Details of bonding type rmsd covalent geometry : bond 0.00346 (32833) covalent geometry : angle 0.56926 (44400) hydrogen bonds : bond 0.11161 ( 1391) hydrogen bonds : angle 5.17224 ( 3906) link_MAN-SER : bond 0.00119 ( 4) link_MAN-SER : angle 0.67886 ( 8) link_MAN-THR : bond 0.00070 ( 1) link_MAN-THR : angle 0.59745 ( 2) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7938 Ramachandran restraints generated. 3969 Oldfield, 0 Emsley, 3969 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7938 Ramachandran restraints generated. 3969 Oldfield, 0 Emsley, 3969 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 540 residues out of total 3475 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 125 poor density : 415 time to evaluate : 1.385 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 246 GLN cc_start: 0.8178 (OUTLIER) cc_final: 0.7737 (tt0) REVERT: A 2207 ARG cc_start: 0.7149 (OUTLIER) cc_final: 0.6726 (ttp-110) REVERT: I 674 TRP cc_start: 0.7481 (m-90) cc_final: 0.6976 (m-90) outliers start: 125 outliers final: 110 residues processed: 529 average time/residue: 0.6874 time to fit residues: 439.5578 Evaluate side-chains 520 residues out of total 3475 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 112 poor density : 408 time to evaluate : 1.468 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 GLU Chi-restraints excluded: chain A residue 69 SER Chi-restraints excluded: chain A residue 75 VAL Chi-restraints excluded: chain A residue 76 LEU Chi-restraints excluded: chain A residue 121 ILE Chi-restraints excluded: chain A residue 124 SER Chi-restraints excluded: chain A residue 176 SER Chi-restraints excluded: chain A residue 239 SER Chi-restraints excluded: chain A residue 246 GLN Chi-restraints excluded: chain A residue 365 VAL Chi-restraints excluded: chain A residue 374 ASN Chi-restraints excluded: chain A residue 407 ILE Chi-restraints excluded: chain A residue 417 THR Chi-restraints excluded: chain A residue 486 THR Chi-restraints excluded: chain A residue 556 ILE Chi-restraints excluded: chain A residue 610 VAL Chi-restraints excluded: chain A residue 671 SER Chi-restraints excluded: chain A residue 743 SER Chi-restraints excluded: chain A residue 827 VAL Chi-restraints excluded: chain A residue 884 ILE Chi-restraints excluded: chain A residue 931 SER Chi-restraints excluded: chain A residue 996 SER Chi-restraints excluded: chain A residue 1071 SER Chi-restraints excluded: chain A residue 1122 LEU Chi-restraints excluded: chain A residue 1162 ILE Chi-restraints excluded: chain A residue 1167 THR Chi-restraints excluded: chain A residue 1179 ILE Chi-restraints excluded: chain A residue 1189 GLU Chi-restraints excluded: chain A residue 1290 VAL Chi-restraints excluded: chain A residue 1665 SER Chi-restraints excluded: chain A residue 1730 SER Chi-restraints excluded: chain A residue 1736 LEU Chi-restraints excluded: chain A residue 1739 SER Chi-restraints excluded: chain A residue 1783 SER Chi-restraints excluded: chain A residue 1809 ASP Chi-restraints excluded: chain A residue 1856 SER Chi-restraints excluded: chain A residue 1881 SER Chi-restraints excluded: chain A residue 1943 THR Chi-restraints excluded: chain A residue 1944 SER Chi-restraints excluded: chain A residue 1945 ILE Chi-restraints excluded: chain A residue 1956 SER Chi-restraints excluded: chain A residue 2011 SER Chi-restraints excluded: chain A residue 2016 LYS Chi-restraints excluded: chain A residue 2092 SER Chi-restraints excluded: chain A residue 2132 VAL Chi-restraints excluded: chain A residue 2136 ASN Chi-restraints excluded: chain A residue 2141 ILE Chi-restraints excluded: chain A residue 2207 ARG Chi-restraints excluded: chain A residue 2273 ARG Chi-restraints excluded: chain A residue 2319 SER Chi-restraints excluded: chain A residue 2382 ILE Chi-restraints excluded: chain A residue 2396 THR Chi-restraints excluded: chain B residue 58 THR Chi-restraints excluded: chain B residue 106 THR Chi-restraints excluded: chain B residue 115 THR Chi-restraints excluded: chain B residue 138 SER Chi-restraints excluded: chain B residue 173 VAL Chi-restraints excluded: chain F residue 83 THR Chi-restraints excluded: chain F residue 241 PHE Chi-restraints excluded: chain F residue 254 THR Chi-restraints excluded: chain F residue 302 SER Chi-restraints excluded: chain F residue 349 LYS Chi-restraints excluded: chain F residue 390 SER Chi-restraints excluded: chain F residue 392 THR Chi-restraints excluded: chain G residue 65 LEU Chi-restraints excluded: chain G residue 69 SER Chi-restraints excluded: chain G residue 82 THR Chi-restraints excluded: chain G residue 96 GLN Chi-restraints excluded: chain G residue 114 LEU Chi-restraints excluded: chain G residue 140 LYS Chi-restraints excluded: chain G residue 150 SER Chi-restraints excluded: chain G residue 174 THR Chi-restraints excluded: chain C residue 43 LYS Chi-restraints excluded: chain C residue 60 ILE Chi-restraints excluded: chain C residue 67 ILE Chi-restraints excluded: chain C residue 69 SER Chi-restraints excluded: chain C residue 70 LEU Chi-restraints excluded: chain C residue 80 LEU Chi-restraints excluded: chain C residue 81 LEU Chi-restraints excluded: chain C residue 148 LYS Chi-restraints excluded: chain E residue 69 SER Chi-restraints excluded: chain E residue 96 GLN Chi-restraints excluded: chain E residue 101 LEU Chi-restraints excluded: chain E residue 125 ILE Chi-restraints excluded: chain I residue 29 VAL Chi-restraints excluded: chain I residue 33 SER Chi-restraints excluded: chain I residue 54 LEU Chi-restraints excluded: chain I residue 58 LYS Chi-restraints excluded: chain I residue 67 LYS Chi-restraints excluded: chain I residue 188 LEU Chi-restraints excluded: chain I residue 192 THR Chi-restraints excluded: chain I residue 194 SER Chi-restraints excluded: chain I residue 244 VAL Chi-restraints excluded: chain I residue 298 VAL Chi-restraints excluded: chain I residue 309 VAL Chi-restraints excluded: chain I residue 340 LYS Chi-restraints excluded: chain I residue 371 SER Chi-restraints excluded: chain I residue 372 THR Chi-restraints excluded: chain I residue 376 LEU Chi-restraints excluded: chain I residue 408 SER Chi-restraints excluded: chain I residue 426 SER Chi-restraints excluded: chain I residue 438 LYS Chi-restraints excluded: chain I residue 568 THR Chi-restraints excluded: chain I residue 616 LEU Chi-restraints excluded: chain I residue 631 THR Chi-restraints excluded: chain I residue 639 ILE Chi-restraints excluded: chain I residue 641 SER Chi-restraints excluded: chain I residue 650 SER Chi-restraints excluded: chain I residue 666 SER Chi-restraints excluded: chain I residue 690 ILE Chi-restraints excluded: chain I residue 698 SER Chi-restraints excluded: chain I residue 713 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 395 random chunks: chunk 197 optimal weight: 3.9990 chunk 388 optimal weight: 10.0000 chunk 215 optimal weight: 5.9990 chunk 20 optimal weight: 0.0270 chunk 132 optimal weight: 0.7980 chunk 261 optimal weight: 1.9990 chunk 248 optimal weight: 0.6980 chunk 207 optimal weight: 0.0570 chunk 155 optimal weight: 2.9990 chunk 244 optimal weight: 6.9990 chunk 183 optimal weight: 0.0050 overall best weight: 0.3170 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 491 ASN A 581 ASN A 727 GLN A1247 ASN A1293 GLN A1528 ASN A1664 GLN A2020 ASN A2350 GLN A2400 ASN F 385 ASN ** D1053 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D1074 ASN D1075 ASN D1105 ASN G 58 GLN I 30 ASN I 261 ASN I 679 GLN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4037 r_free = 0.4037 target = 0.158770 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3663 r_free = 0.3663 target = 0.122268 restraints weight = 56790.610| |-----------------------------------------------------------------------------| r_work (start): 0.3584 rms_B_bonded: 2.32 r_work: 0.3471 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.3370 rms_B_bonded: 4.31 restraints_weight: 0.2500 r_work (final): 0.3370 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3343 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3343 r_free = 0.3343 target_work(ls_wunit_k1) = 0.101 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3343 r_free = 0.3343 target_work(ls_wunit_k1) = 0.101 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3343 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8057 moved from start: 0.0610 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 32838 Z= 0.104 Angle : 0.509 7.275 44410 Z= 0.271 Chirality : 0.043 0.254 4821 Planarity : 0.003 0.042 5825 Dihedral : 9.994 100.337 4808 Min Nonbonded Distance : 2.412 Molprobity Statistics. All-atom Clashscore : 5.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.56 % Favored : 95.44 % Rotamer: Outliers : 3.93 % Allowed : 21.43 % Favored : 74.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.00 % Cis-general : 0.03 % 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: 0.73 (0.14), residues: 3969 helix: 1.92 (0.16), residues: 1184 sheet: 0.55 (0.16), residues: 1105 loop : -0.56 (0.15), residues: 1680 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG E 116 TYR 0.017 0.001 TYR I 294 PHE 0.017 0.001 PHE I 28 TRP 0.011 0.001 TRP A1996 HIS 0.003 0.001 HIS A1672 Details of bonding type rmsd covalent geometry : bond 0.00219 (32833) covalent geometry : angle 0.50860 (44400) hydrogen bonds : bond 0.03429 ( 1391) hydrogen bonds : angle 4.53202 ( 3906) link_MAN-SER : bond 0.00212 ( 4) link_MAN-SER : angle 0.86174 ( 8) link_MAN-THR : bond 0.00061 ( 1) link_MAN-THR : angle 0.17149 ( 2) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7938 Ramachandran restraints generated. 3969 Oldfield, 0 Emsley, 3969 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7938 Ramachandran restraints generated. 3969 Oldfield, 0 Emsley, 3969 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 560 residues out of total 3475 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 133 poor density : 427 time to evaluate : 1.324 Fit side-chains revert: symmetry clash REVERT: A 79 LYS cc_start: 0.7063 (tppp) cc_final: 0.6767 (tppp) REVERT: A 221 GLU cc_start: 0.8509 (OUTLIER) cc_final: 0.8238 (mt-10) REVERT: A 266 LYS cc_start: 0.7991 (tttt) cc_final: 0.7733 (tttt) REVERT: A 374 ASN cc_start: 0.8133 (OUTLIER) cc_final: 0.7811 (p0) REVERT: A 407 ILE cc_start: 0.8128 (OUTLIER) cc_final: 0.7369 (mp) REVERT: A 1448 ASP cc_start: 0.6557 (m-30) cc_final: 0.6292 (m-30) REVERT: A 1565 ASN cc_start: 0.7919 (t0) cc_final: 0.7008 (p0) REVERT: A 1680 GLU cc_start: 0.8556 (OUTLIER) cc_final: 0.7069 (tm-30) REVERT: A 1841 LYS cc_start: 0.7446 (OUTLIER) cc_final: 0.7179 (ttmt) REVERT: A 1949 GLN cc_start: 0.7409 (OUTLIER) cc_final: 0.7108 (tp-100) REVERT: A 2379 LYS cc_start: 0.7554 (ttmt) cc_final: 0.6937 (ttpt) REVERT: B 93 LEU cc_start: 0.7282 (OUTLIER) cc_final: 0.6731 (tm) REVERT: F 348 MET cc_start: 0.6375 (mmm) cc_final: 0.5756 (mmp) REVERT: D 1061 GLU cc_start: 0.6919 (tt0) cc_final: 0.6704 (tt0) REVERT: C 56 TRP cc_start: 0.8032 (m100) cc_final: 0.7472 (m-10) REVERT: C 148 LYS cc_start: 0.8949 (OUTLIER) cc_final: 0.8737 (tttt) REVERT: E 26 ARG cc_start: 0.8069 (OUTLIER) cc_final: 0.7856 (ttt180) REVERT: I 67 LYS cc_start: 0.9080 (OUTLIER) cc_final: 0.8812 (ptpp) REVERT: I 284 LYS cc_start: 0.9103 (mmtt) cc_final: 0.8727 (mtpt) REVERT: I 321 LYS cc_start: 0.8702 (OUTLIER) cc_final: 0.8497 (mmmt) REVERT: I 564 GLN cc_start: 0.7846 (mm110) cc_final: 0.7396 (tp-100) REVERT: I 654 GLN cc_start: 0.8312 (OUTLIER) cc_final: 0.8078 (pt0) outliers start: 133 outliers final: 53 residues processed: 523 average time/residue: 0.7315 time to fit residues: 457.8608 Evaluate side-chains 472 residues out of total 3475 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 407 time to evaluate : 1.387 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 GLU Chi-restraints excluded: chain A residue 75 VAL Chi-restraints excluded: chain A residue 76 LEU Chi-restraints excluded: chain A residue 121 ILE Chi-restraints excluded: chain A residue 221 GLU Chi-restraints excluded: chain A residue 277 GLN Chi-restraints excluded: chain A residue 365 VAL Chi-restraints excluded: chain A residue 374 ASN Chi-restraints excluded: chain A residue 407 ILE Chi-restraints excluded: chain A residue 480 SER Chi-restraints excluded: chain A residue 486 THR Chi-restraints excluded: chain A residue 743 SER Chi-restraints excluded: chain A residue 827 VAL Chi-restraints excluded: chain A residue 1122 LEU Chi-restraints excluded: chain A residue 1189 GLU Chi-restraints excluded: chain A residue 1290 VAL Chi-restraints excluded: chain A residue 1680 GLU Chi-restraints excluded: chain A residue 1722 PHE Chi-restraints excluded: chain A residue 1730 SER Chi-restraints excluded: chain A residue 1841 LYS Chi-restraints excluded: chain A residue 1949 GLN Chi-restraints excluded: chain A residue 2016 LYS Chi-restraints excluded: chain A residue 2028 LYS Chi-restraints excluded: chain A residue 2071 MET Chi-restraints excluded: chain A residue 2083 GLN Chi-restraints excluded: chain A residue 2136 ASN Chi-restraints excluded: chain A residue 2357 LEU Chi-restraints excluded: chain A residue 2360 ASP Chi-restraints excluded: chain A residue 2382 ILE Chi-restraints excluded: chain A residue 2396 THR Chi-restraints excluded: chain B residue 93 LEU Chi-restraints excluded: chain B residue 106 THR Chi-restraints excluded: chain B residue 173 VAL Chi-restraints excluded: chain F residue 83 THR Chi-restraints excluded: chain F residue 101 ASN Chi-restraints excluded: chain F residue 130 THR Chi-restraints excluded: chain F residue 241 PHE Chi-restraints excluded: chain F residue 254 THR Chi-restraints excluded: chain F residue 302 SER Chi-restraints excluded: chain F residue 392 THR Chi-restraints excluded: chain D residue 1058 VAL Chi-restraints excluded: chain G residue 96 GLN Chi-restraints excluded: chain G residue 114 LEU Chi-restraints excluded: chain C residue 60 ILE Chi-restraints excluded: chain C residue 69 SER Chi-restraints excluded: chain C residue 81 LEU Chi-restraints excluded: chain C residue 148 LYS Chi-restraints excluded: chain C residue 154 MET Chi-restraints excluded: chain C residue 173 ARG Chi-restraints excluded: chain E residue 26 ARG Chi-restraints excluded: chain I residue 29 VAL Chi-restraints excluded: chain I residue 33 SER Chi-restraints excluded: chain I residue 54 LEU Chi-restraints excluded: chain I residue 67 LYS Chi-restraints excluded: chain I residue 244 VAL Chi-restraints excluded: chain I residue 298 VAL Chi-restraints excluded: chain I residue 321 LYS Chi-restraints excluded: chain I residue 340 LYS Chi-restraints excluded: chain I residue 371 SER Chi-restraints excluded: chain I residue 376 LEU Chi-restraints excluded: chain I residue 382 GLU Chi-restraints excluded: chain I residue 568 THR Chi-restraints excluded: chain I residue 639 ILE Chi-restraints excluded: chain I residue 654 GLN Chi-restraints excluded: chain I residue 709 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 395 random chunks: chunk 216 optimal weight: 3.9990 chunk 202 optimal weight: 0.2980 chunk 274 optimal weight: 6.9990 chunk 130 optimal weight: 3.9990 chunk 25 optimal weight: 4.9990 chunk 367 optimal weight: 1.9990 chunk 208 optimal weight: 7.9990 chunk 315 optimal weight: 0.3980 chunk 278 optimal weight: 9.9990 chunk 163 optimal weight: 6.9990 chunk 320 optimal weight: 4.9990 overall best weight: 2.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 32 GLN A 196 GLN A 246 GLN A 437 ASN A 613 GLN A 982 ASN A1247 ASN A1293 GLN A1392 ASN A1528 ASN A1792 ASN A2350 GLN A2400 ASN F 385 ASN D1074 ASN D1075 ASN D1105 ASN G 58 GLN I 261 ASN I 611 ASN Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3980 r_free = 0.3980 target = 0.153960 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3565 r_free = 0.3565 target = 0.116864 restraints weight = 59291.339| |-----------------------------------------------------------------------------| r_work (start): 0.3502 rms_B_bonded: 2.48 r_work: 0.3356 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.3252 rms_B_bonded: 4.41 restraints_weight: 0.2500 r_work (final): 0.3252 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3244 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3244 r_free = 0.3244 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3244 r_free = 0.3244 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3244 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8230 moved from start: 0.0832 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.063 32838 Z= 0.255 Angle : 0.629 9.510 44410 Z= 0.336 Chirality : 0.048 0.424 4821 Planarity : 0.004 0.050 5825 Dihedral : 8.584 89.364 4696 Min Nonbonded Distance : 2.241 Molprobity Statistics. All-atom Clashscore : 5.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.09 % Favored : 94.91 % Rotamer: Outliers : 4.53 % Allowed : 20.92 % Favored : 74.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.00 % Cis-general : 0.03 % 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: 0.59 (0.14), residues: 3969 helix: 1.65 (0.15), residues: 1193 sheet: 0.59 (0.16), residues: 1112 loop : -0.65 (0.15), residues: 1664 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG I 609 TYR 0.023 0.002 TYR I 294 PHE 0.025 0.002 PHE A1480 TRP 0.023 0.002 TRP A1580 HIS 0.007 0.002 HIS I 271 Details of bonding type rmsd covalent geometry : bond 0.00588 (32833) covalent geometry : angle 0.62883 (44400) hydrogen bonds : bond 0.04421 ( 1391) hydrogen bonds : angle 4.71566 ( 3906) link_MAN-SER : bond 0.00314 ( 4) link_MAN-SER : angle 1.16759 ( 8) link_MAN-THR : bond 0.00070 ( 1) link_MAN-THR : angle 0.62035 ( 2) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7938 Ramachandran restraints generated. 3969 Oldfield, 0 Emsley, 3969 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7938 Ramachandran restraints generated. 3969 Oldfield, 0 Emsley, 3969 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 553 residues out of total 3475 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 154 poor density : 399 time to evaluate : 1.304 Fit side-chains revert: symmetry clash REVERT: A 79 LYS cc_start: 0.7316 (tppp) cc_final: 0.7110 (tppp) REVERT: A 221 GLU cc_start: 0.8628 (OUTLIER) cc_final: 0.8396 (mt-10) REVERT: A 344 ILE cc_start: 0.8345 (OUTLIER) cc_final: 0.7537 (mp) REVERT: A 407 ILE cc_start: 0.8307 (OUTLIER) cc_final: 0.7635 (mp) REVERT: A 1645 ASP cc_start: 0.7565 (OUTLIER) cc_final: 0.7341 (t0) REVERT: A 1680 GLU cc_start: 0.8948 (OUTLIER) cc_final: 0.7629 (tm-30) REVERT: A 1732 ASN cc_start: 0.8112 (p0) cc_final: 0.7886 (p0) REVERT: A 2053 GLU cc_start: 0.7961 (OUTLIER) cc_final: 0.7028 (tm-30) REVERT: A 2188 MET cc_start: 0.6501 (OUTLIER) cc_final: 0.6252 (mmp) REVERT: A 2326 ASP cc_start: 0.7758 (OUTLIER) cc_final: 0.7485 (m-30) REVERT: B 93 LEU cc_start: 0.7330 (OUTLIER) cc_final: 0.6833 (tm) REVERT: D 1051 LYS cc_start: 0.7158 (tptt) cc_final: 0.6821 (tptp) REVERT: E 26 ARG cc_start: 0.8142 (OUTLIER) cc_final: 0.7890 (ttt180) REVERT: I 92 GLU cc_start: 0.8709 (OUTLIER) cc_final: 0.7848 (mp0) REVERT: I 284 LYS cc_start: 0.9111 (mmtt) cc_final: 0.8771 (mtpt) REVERT: I 564 GLN cc_start: 0.7800 (mm110) cc_final: 0.7343 (tp-100) REVERT: I 654 GLN cc_start: 0.8342 (OUTLIER) cc_final: 0.7864 (pt0) outliers start: 154 outliers final: 78 residues processed: 499 average time/residue: 0.6671 time to fit residues: 397.9762 Evaluate side-chains 480 residues out of total 3475 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 390 time to evaluate : 1.021 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 GLU Chi-restraints excluded: chain A residue 75 VAL Chi-restraints excluded: chain A residue 76 LEU Chi-restraints excluded: chain A residue 199 PHE Chi-restraints excluded: chain A residue 221 GLU Chi-restraints excluded: chain A residue 277 GLN Chi-restraints excluded: chain A residue 344 ILE Chi-restraints excluded: chain A residue 365 VAL Chi-restraints excluded: chain A residue 374 ASN Chi-restraints excluded: chain A residue 407 ILE Chi-restraints excluded: chain A residue 416 ASN Chi-restraints excluded: chain A residue 486 THR Chi-restraints excluded: chain A residue 743 SER Chi-restraints excluded: chain A residue 816 LEU Chi-restraints excluded: chain A residue 827 VAL Chi-restraints excluded: chain A residue 931 SER Chi-restraints excluded: chain A residue 1122 LEU Chi-restraints excluded: chain A residue 1162 ILE Chi-restraints excluded: chain A residue 1189 GLU Chi-restraints excluded: chain A residue 1373 THR Chi-restraints excluded: chain A residue 1645 ASP Chi-restraints excluded: chain A residue 1680 GLU Chi-restraints excluded: chain A residue 1730 SER Chi-restraints excluded: chain A residue 1809 ASP Chi-restraints excluded: chain A residue 1857 THR Chi-restraints excluded: chain A residue 1879 SER Chi-restraints excluded: chain A residue 1977 LEU Chi-restraints excluded: chain A residue 2008 THR Chi-restraints excluded: chain A residue 2016 LYS Chi-restraints excluded: chain A residue 2018 THR Chi-restraints excluded: chain A residue 2028 LYS Chi-restraints excluded: chain A residue 2053 GLU Chi-restraints excluded: chain A residue 2066 SER Chi-restraints excluded: chain A residue 2071 MET Chi-restraints excluded: chain A residue 2083 GLN Chi-restraints excluded: chain A residue 2136 ASN Chi-restraints excluded: chain A residue 2188 MET Chi-restraints excluded: chain A residue 2198 LYS Chi-restraints excluded: chain A residue 2272 ASP Chi-restraints excluded: chain A residue 2326 ASP Chi-restraints excluded: chain A residue 2360 ASP Chi-restraints excluded: chain A residue 2382 ILE Chi-restraints excluded: chain A residue 2396 THR Chi-restraints excluded: chain B residue 93 LEU Chi-restraints excluded: chain B residue 106 THR Chi-restraints excluded: chain B residue 173 VAL Chi-restraints excluded: chain F residue 83 THR Chi-restraints excluded: chain F residue 101 ASN Chi-restraints excluded: chain F residue 123 THR Chi-restraints excluded: chain F residue 130 THR Chi-restraints excluded: chain F residue 241 PHE Chi-restraints excluded: chain F residue 250 SER Chi-restraints excluded: chain F residue 254 THR Chi-restraints excluded: chain F residue 266 THR Chi-restraints excluded: chain F residue 302 SER Chi-restraints excluded: chain F residue 365 MET Chi-restraints excluded: chain F residue 392 THR Chi-restraints excluded: chain D residue 1058 VAL Chi-restraints excluded: chain D residue 1066 ASP Chi-restraints excluded: chain G residue 40 SER Chi-restraints excluded: chain G residue 96 GLN Chi-restraints excluded: chain G residue 113 ASN Chi-restraints excluded: chain G residue 114 LEU Chi-restraints excluded: chain G residue 140 LYS Chi-restraints excluded: chain C residue 30 ILE Chi-restraints excluded: chain C residue 43 LYS Chi-restraints excluded: chain C residue 60 ILE Chi-restraints excluded: chain C residue 67 ILE Chi-restraints excluded: chain C residue 70 LEU Chi-restraints excluded: chain C residue 76 THR Chi-restraints excluded: chain C residue 81 LEU Chi-restraints excluded: chain C residue 173 ARG Chi-restraints excluded: chain E residue 26 ARG Chi-restraints excluded: chain E residue 157 SER Chi-restraints excluded: chain I residue 29 VAL Chi-restraints excluded: chain I residue 33 SER Chi-restraints excluded: chain I residue 54 LEU Chi-restraints excluded: chain I residue 67 LYS Chi-restraints excluded: chain I residue 92 GLU Chi-restraints excluded: chain I residue 188 LEU Chi-restraints excluded: chain I residue 244 VAL Chi-restraints excluded: chain I residue 298 VAL Chi-restraints excluded: chain I residue 371 SER Chi-restraints excluded: chain I residue 376 LEU Chi-restraints excluded: chain I residue 382 GLU Chi-restraints excluded: chain I residue 407 ASP Chi-restraints excluded: chain I residue 568 THR Chi-restraints excluded: chain I residue 639 ILE Chi-restraints excluded: chain I residue 654 GLN Chi-restraints excluded: chain I residue 666 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 395 random chunks: chunk 364 optimal weight: 1.9990 chunk 290 optimal weight: 4.9990 chunk 202 optimal weight: 2.9990 chunk 51 optimal weight: 3.9990 chunk 222 optimal weight: 4.9990 chunk 331 optimal weight: 0.8980 chunk 320 optimal weight: 3.9990 chunk 14 optimal weight: 0.8980 chunk 215 optimal weight: 0.9980 chunk 391 optimal weight: 1.9990 chunk 321 optimal weight: 0.9980 overall best weight: 1.1582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 246 GLN A 437 ASN A 491 ASN A 613 GLN A 727 GLN A1247 ASN A1528 ASN A1565 ASN A1792 ASN A2020 ASN A2350 GLN A2400 ASN F 385 ASN D1074 ASN D1075 ASN D1105 ASN G 58 GLN I 611 ASN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4000 r_free = 0.4000 target = 0.155565 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3597 r_free = 0.3597 target = 0.118808 restraints weight = 60729.203| |-----------------------------------------------------------------------------| r_work (start): 0.3530 rms_B_bonded: 2.51 r_work: 0.3383 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.3281 rms_B_bonded: 4.49 restraints_weight: 0.2500 r_work (final): 0.3281 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3272 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3272 r_free = 0.3272 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3272 r_free = 0.3272 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3272 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8198 moved from start: 0.0840 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 32838 Z= 0.159 Angle : 0.550 8.048 44410 Z= 0.295 Chirality : 0.044 0.365 4821 Planarity : 0.004 0.045 5825 Dihedral : 7.604 89.748 4684 Min Nonbonded Distance : 2.405 Molprobity Statistics. All-atom Clashscore : 5.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.58 % Favored : 95.42 % Rotamer: Outliers : 4.08 % Allowed : 21.46 % Favored : 74.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.00 % Cis-general : 0.03 % 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: 0.61 (0.14), residues: 3969 helix: 1.73 (0.15), residues: 1193 sheet: 0.54 (0.16), residues: 1116 loop : -0.64 (0.15), residues: 1660 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG I 609 TYR 0.019 0.001 TYR I 294 PHE 0.017 0.001 PHE A1009 TRP 0.021 0.002 TRP A1580 HIS 0.004 0.001 HIS I 271 Details of bonding type rmsd covalent geometry : bond 0.00359 (32833) covalent geometry : angle 0.54972 (44400) hydrogen bonds : bond 0.03718 ( 1391) hydrogen bonds : angle 4.58776 ( 3906) link_MAN-SER : bond 0.00185 ( 4) link_MAN-SER : angle 0.77538 ( 8) link_MAN-THR : bond 0.00025 ( 1) link_MAN-THR : angle 0.35166 ( 2) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7938 Ramachandran restraints generated. 3969 Oldfield, 0 Emsley, 3969 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7938 Ramachandran restraints generated. 3969 Oldfield, 0 Emsley, 3969 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 550 residues out of total 3475 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 138 poor density : 412 time to evaluate : 1.385 Fit side-chains revert: symmetry clash REVERT: A 74 LEU cc_start: 0.8318 (tp) cc_final: 0.8085 (tp) REVERT: A 144 GLU cc_start: 0.8435 (OUTLIER) cc_final: 0.8179 (mt-10) REVERT: A 196 GLN cc_start: 0.7433 (mm110) cc_final: 0.6949 (mp-120) REVERT: A 221 GLU cc_start: 0.8622 (OUTLIER) cc_final: 0.8384 (mt-10) REVERT: A 344 ILE cc_start: 0.8293 (OUTLIER) cc_final: 0.7526 (mp) REVERT: A 407 ILE cc_start: 0.8236 (OUTLIER) cc_final: 0.7681 (mp) REVERT: A 1189 GLU cc_start: 0.8271 (OUTLIER) cc_final: 0.7155 (pp20) REVERT: A 1580 TRP cc_start: 0.6776 (OUTLIER) cc_final: 0.3403 (p-90) REVERT: A 1645 ASP cc_start: 0.7490 (OUTLIER) cc_final: 0.7275 (t0) REVERT: A 1680 GLU cc_start: 0.8814 (OUTLIER) cc_final: 0.7477 (tm-30) REVERT: A 1841 LYS cc_start: 0.7552 (OUTLIER) cc_final: 0.7337 (ttmt) REVERT: A 2053 GLU cc_start: 0.7961 (OUTLIER) cc_final: 0.7010 (tm-30) REVERT: A 2188 MET cc_start: 0.6337 (mmp) cc_final: 0.5949 (mmp) REVERT: B 93 LEU cc_start: 0.7345 (OUTLIER) cc_final: 0.6816 (tm) REVERT: D 1051 LYS cc_start: 0.7179 (tptt) cc_final: 0.6800 (tptp) REVERT: I 58 LYS cc_start: 0.8658 (OUTLIER) cc_final: 0.8384 (mppt) REVERT: I 284 LYS cc_start: 0.9107 (mmtt) cc_final: 0.8763 (mtpt) REVERT: I 564 GLN cc_start: 0.7759 (mm110) cc_final: 0.7337 (tp-100) REVERT: I 654 GLN cc_start: 0.8354 (OUTLIER) cc_final: 0.7960 (pt0) outliers start: 138 outliers final: 76 residues processed: 507 average time/residue: 0.7330 time to fit residues: 445.3035 Evaluate side-chains 488 residues out of total 3475 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 399 time to evaluate : 1.271 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 GLU Chi-restraints excluded: chain A residue 75 VAL Chi-restraints excluded: chain A residue 76 LEU Chi-restraints excluded: chain A residue 121 ILE Chi-restraints excluded: chain A residue 144 GLU Chi-restraints excluded: chain A residue 221 GLU Chi-restraints excluded: chain A residue 277 GLN Chi-restraints excluded: chain A residue 344 ILE Chi-restraints excluded: chain A residue 365 VAL Chi-restraints excluded: chain A residue 374 ASN Chi-restraints excluded: chain A residue 407 ILE Chi-restraints excluded: chain A residue 416 ASN Chi-restraints excluded: chain A residue 486 THR Chi-restraints excluded: chain A residue 537 LYS Chi-restraints excluded: chain A residue 743 SER Chi-restraints excluded: chain A residue 816 LEU Chi-restraints excluded: chain A residue 827 VAL Chi-restraints excluded: chain A residue 931 SER Chi-restraints excluded: chain A residue 1122 LEU Chi-restraints excluded: chain A residue 1162 ILE Chi-restraints excluded: chain A residue 1179 ILE Chi-restraints excluded: chain A residue 1189 GLU Chi-restraints excluded: chain A residue 1290 VAL Chi-restraints excluded: chain A residue 1519 MET Chi-restraints excluded: chain A residue 1580 TRP Chi-restraints excluded: chain A residue 1645 ASP Chi-restraints excluded: chain A residue 1661 THR Chi-restraints excluded: chain A residue 1680 GLU Chi-restraints excluded: chain A residue 1722 PHE Chi-restraints excluded: chain A residue 1736 LEU Chi-restraints excluded: chain A residue 1809 ASP Chi-restraints excluded: chain A residue 1841 LYS Chi-restraints excluded: chain A residue 1857 THR Chi-restraints excluded: chain A residue 1977 LEU Chi-restraints excluded: chain A residue 2008 THR Chi-restraints excluded: chain A residue 2012 ASN Chi-restraints excluded: chain A residue 2016 LYS Chi-restraints excluded: chain A residue 2018 THR Chi-restraints excluded: chain A residue 2053 GLU Chi-restraints excluded: chain A residue 2066 SER Chi-restraints excluded: chain A residue 2071 MET Chi-restraints excluded: chain A residue 2083 GLN Chi-restraints excluded: chain A residue 2136 ASN Chi-restraints excluded: chain A residue 2141 ILE Chi-restraints excluded: chain A residue 2198 LYS Chi-restraints excluded: chain A residue 2272 ASP Chi-restraints excluded: chain A residue 2350 GLN Chi-restraints excluded: chain A residue 2357 LEU Chi-restraints excluded: chain A residue 2360 ASP Chi-restraints excluded: chain A residue 2382 ILE Chi-restraints excluded: chain A residue 2396 THR Chi-restraints excluded: chain B residue 93 LEU Chi-restraints excluded: chain B residue 173 VAL Chi-restraints excluded: chain F residue 70 ASP Chi-restraints excluded: chain F residue 83 THR Chi-restraints excluded: chain F residue 101 ASN Chi-restraints excluded: chain F residue 123 THR Chi-restraints excluded: chain F residue 130 THR Chi-restraints excluded: chain F residue 241 PHE Chi-restraints excluded: chain F residue 254 THR Chi-restraints excluded: chain F residue 266 THR Chi-restraints excluded: chain F residue 302 SER Chi-restraints excluded: chain F residue 349 LYS Chi-restraints excluded: chain F residue 392 THR Chi-restraints excluded: chain D residue 1058 VAL Chi-restraints excluded: chain D residue 1059 MET Chi-restraints excluded: chain D residue 1066 ASP Chi-restraints excluded: chain G residue 96 GLN Chi-restraints excluded: chain G residue 113 ASN Chi-restraints excluded: chain G residue 114 LEU Chi-restraints excluded: chain G residue 140 LYS Chi-restraints excluded: chain C residue 30 ILE Chi-restraints excluded: chain C residue 43 LYS Chi-restraints excluded: chain C residue 70 LEU Chi-restraints excluded: chain C residue 81 LEU Chi-restraints excluded: chain C residue 173 ARG Chi-restraints excluded: chain I residue 54 LEU Chi-restraints excluded: chain I residue 58 LYS Chi-restraints excluded: chain I residue 67 LYS Chi-restraints excluded: chain I residue 244 VAL Chi-restraints excluded: chain I residue 298 VAL Chi-restraints excluded: chain I residue 371 SER Chi-restraints excluded: chain I residue 376 LEU Chi-restraints excluded: chain I residue 382 GLU Chi-restraints excluded: chain I residue 568 THR Chi-restraints excluded: chain I residue 639 ILE Chi-restraints excluded: chain I residue 654 GLN Chi-restraints excluded: chain I residue 666 SER Chi-restraints excluded: chain I residue 709 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 395 random chunks: chunk 95 optimal weight: 7.9990 chunk 206 optimal weight: 3.9990 chunk 248 optimal weight: 5.9990 chunk 194 optimal weight: 1.9990 chunk 220 optimal weight: 0.4980 chunk 21 optimal weight: 6.9990 chunk 107 optimal weight: 1.9990 chunk 204 optimal weight: 0.5980 chunk 105 optimal weight: 0.7980 chunk 388 optimal weight: 3.9990 chunk 112 optimal weight: 0.9980 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 246 GLN A 437 ASN A 491 ASN A 613 GLN A 727 GLN A1247 ASN A1528 ASN A1792 ASN A2020 ASN A2400 ASN F 385 ASN D1074 ASN D1075 ASN D1105 ASN G 58 GLN I 261 ASN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4004 r_free = 0.4004 target = 0.155903 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3609 r_free = 0.3609 target = 0.118662 restraints weight = 53222.163| |-----------------------------------------------------------------------------| r_work (start): 0.3532 rms_B_bonded: 2.31 r_work: 0.3410 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.3309 rms_B_bonded: 4.10 restraints_weight: 0.2500 r_work (final): 0.3309 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3301 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3301 r_free = 0.3301 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3301 r_free = 0.3301 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3301 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8167 moved from start: 0.0877 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 32838 Z= 0.145 Angle : 0.541 9.011 44410 Z= 0.290 Chirality : 0.044 0.328 4821 Planarity : 0.004 0.044 5825 Dihedral : 7.208 88.014 4678 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 5.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.74 % Favored : 95.26 % Rotamer: Outliers : 3.85 % Allowed : 21.80 % Favored : 74.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.00 % Cis-general : 0.03 % 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: 0.63 (0.14), residues: 3969 helix: 1.75 (0.15), residues: 1198 sheet: 0.57 (0.16), residues: 1110 loop : -0.65 (0.15), residues: 1661 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG I 609 TYR 0.018 0.001 TYR I 294 PHE 0.024 0.001 PHE I 28 TRP 0.020 0.002 TRP A1580 HIS 0.004 0.001 HIS I 271 Details of bonding type rmsd covalent geometry : bond 0.00326 (32833) covalent geometry : angle 0.54107 (44400) hydrogen bonds : bond 0.03589 ( 1391) hydrogen bonds : angle 4.53464 ( 3906) link_MAN-SER : bond 0.00126 ( 4) link_MAN-SER : angle 0.71727 ( 8) link_MAN-THR : bond 0.00062 ( 1) link_MAN-THR : angle 0.47457 ( 2) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7938 Ramachandran restraints generated. 3969 Oldfield, 0 Emsley, 3969 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7938 Ramachandran restraints generated. 3969 Oldfield, 0 Emsley, 3969 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 532 residues out of total 3475 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 130 poor density : 402 time to evaluate : 1.420 Fit side-chains revert: symmetry clash REVERT: A 144 GLU cc_start: 0.8409 (OUTLIER) cc_final: 0.8032 (mt-10) REVERT: A 221 GLU cc_start: 0.8581 (OUTLIER) cc_final: 0.8332 (mt-10) REVERT: A 344 ILE cc_start: 0.8262 (OUTLIER) cc_final: 0.7497 (mp) REVERT: A 407 ILE cc_start: 0.8232 (OUTLIER) cc_final: 0.7704 (mp) REVERT: A 554 ASN cc_start: 0.7939 (OUTLIER) cc_final: 0.7733 (m110) REVERT: A 1122 LEU cc_start: 0.8989 (OUTLIER) cc_final: 0.8331 (mp) REVERT: A 1189 GLU cc_start: 0.8223 (OUTLIER) cc_final: 0.7104 (pp20) REVERT: A 1580 TRP cc_start: 0.6771 (OUTLIER) cc_final: 0.3435 (p-90) REVERT: A 1645 ASP cc_start: 0.7485 (OUTLIER) cc_final: 0.7265 (t0) REVERT: A 1680 GLU cc_start: 0.8770 (OUTLIER) cc_final: 0.7403 (tm-30) REVERT: A 1732 ASN cc_start: 0.8227 (p0) cc_final: 0.7922 (p0) REVERT: A 2053 GLU cc_start: 0.7928 (OUTLIER) cc_final: 0.6967 (tm-30) REVERT: A 2188 MET cc_start: 0.6411 (mmp) cc_final: 0.6003 (mmp) REVERT: B 93 LEU cc_start: 0.7287 (OUTLIER) cc_final: 0.6731 (tm) REVERT: F 171 GLU cc_start: 0.6067 (OUTLIER) cc_final: 0.5551 (pm20) REVERT: F 293 LYS cc_start: 0.6533 (OUTLIER) cc_final: 0.5659 (tptp) REVERT: I 58 LYS cc_start: 0.8641 (OUTLIER) cc_final: 0.8370 (mppt) REVERT: I 284 LYS cc_start: 0.9100 (mmtt) cc_final: 0.8751 (mtpt) REVERT: I 382 GLU cc_start: 0.8848 (OUTLIER) cc_final: 0.8483 (tt0) REVERT: I 564 GLN cc_start: 0.7711 (mm110) cc_final: 0.7298 (tp-100) REVERT: I 654 GLN cc_start: 0.8463 (OUTLIER) cc_final: 0.7951 (pt0) outliers start: 130 outliers final: 63 residues processed: 488 average time/residue: 0.7333 time to fit residues: 427.0114 Evaluate side-chains 474 residues out of total 3475 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 394 time to evaluate : 1.383 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 GLU Chi-restraints excluded: chain A residue 75 VAL Chi-restraints excluded: chain A residue 76 LEU Chi-restraints excluded: chain A residue 144 GLU Chi-restraints excluded: chain A residue 221 GLU Chi-restraints excluded: chain A residue 277 GLN Chi-restraints excluded: chain A residue 344 ILE Chi-restraints excluded: chain A residue 365 VAL Chi-restraints excluded: chain A residue 407 ILE Chi-restraints excluded: chain A residue 416 ASN Chi-restraints excluded: chain A residue 486 THR Chi-restraints excluded: chain A residue 554 ASN Chi-restraints excluded: chain A residue 743 SER Chi-restraints excluded: chain A residue 816 LEU Chi-restraints excluded: chain A residue 827 VAL Chi-restraints excluded: chain A residue 1122 LEU Chi-restraints excluded: chain A residue 1162 ILE Chi-restraints excluded: chain A residue 1179 ILE Chi-restraints excluded: chain A residue 1189 GLU Chi-restraints excluded: chain A residue 1290 VAL Chi-restraints excluded: chain A residue 1580 TRP Chi-restraints excluded: chain A residue 1645 ASP Chi-restraints excluded: chain A residue 1680 GLU Chi-restraints excluded: chain A residue 1722 PHE Chi-restraints excluded: chain A residue 1736 LEU Chi-restraints excluded: chain A residue 1809 ASP Chi-restraints excluded: chain A residue 1857 THR Chi-restraints excluded: chain A residue 2008 THR Chi-restraints excluded: chain A residue 2016 LYS Chi-restraints excluded: chain A residue 2018 THR Chi-restraints excluded: chain A residue 2053 GLU Chi-restraints excluded: chain A residue 2066 SER Chi-restraints excluded: chain A residue 2071 MET Chi-restraints excluded: chain A residue 2083 GLN Chi-restraints excluded: chain A residue 2136 ASN Chi-restraints excluded: chain A residue 2141 ILE Chi-restraints excluded: chain A residue 2198 LYS Chi-restraints excluded: chain A residue 2272 ASP Chi-restraints excluded: chain A residue 2357 LEU Chi-restraints excluded: chain A residue 2360 ASP Chi-restraints excluded: chain A residue 2382 ILE Chi-restraints excluded: chain A residue 2396 THR Chi-restraints excluded: chain B residue 93 LEU Chi-restraints excluded: chain B residue 173 VAL Chi-restraints excluded: chain F residue 70 ASP Chi-restraints excluded: chain F residue 83 THR Chi-restraints excluded: chain F residue 88 ASP Chi-restraints excluded: chain F residue 101 ASN Chi-restraints excluded: chain F residue 123 THR Chi-restraints excluded: chain F residue 130 THR Chi-restraints excluded: chain F residue 171 GLU Chi-restraints excluded: chain F residue 241 PHE Chi-restraints excluded: chain F residue 266 THR Chi-restraints excluded: chain F residue 293 LYS Chi-restraints excluded: chain F residue 392 THR Chi-restraints excluded: chain D residue 1047 ASP Chi-restraints excluded: chain D residue 1058 VAL Chi-restraints excluded: chain D residue 1059 MET Chi-restraints excluded: chain G residue 40 SER Chi-restraints excluded: chain G residue 96 GLN Chi-restraints excluded: chain G residue 113 ASN Chi-restraints excluded: chain G residue 114 LEU Chi-restraints excluded: chain G residue 140 LYS Chi-restraints excluded: chain C residue 30 ILE Chi-restraints excluded: chain C residue 43 LYS Chi-restraints excluded: chain C residue 70 LEU Chi-restraints excluded: chain C residue 81 LEU Chi-restraints excluded: chain C residue 154 MET Chi-restraints excluded: chain C residue 173 ARG Chi-restraints excluded: chain E residue 101 LEU Chi-restraints excluded: chain I residue 54 LEU Chi-restraints excluded: chain I residue 58 LYS Chi-restraints excluded: chain I residue 67 LYS Chi-restraints excluded: chain I residue 298 VAL Chi-restraints excluded: chain I residue 371 SER Chi-restraints excluded: chain I residue 382 GLU Chi-restraints excluded: chain I residue 568 THR Chi-restraints excluded: chain I residue 639 ILE Chi-restraints excluded: chain I residue 654 GLN Chi-restraints excluded: chain I residue 666 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 395 random chunks: chunk 188 optimal weight: 3.9990 chunk 318 optimal weight: 0.7980 chunk 249 optimal weight: 5.9990 chunk 59 optimal weight: 0.9980 chunk 202 optimal weight: 2.9990 chunk 316 optimal weight: 9.9990 chunk 106 optimal weight: 5.9990 chunk 309 optimal weight: 1.9990 chunk 78 optimal weight: 0.6980 chunk 305 optimal weight: 2.9990 chunk 238 optimal weight: 6.9990 overall best weight: 1.4984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 246 GLN A 437 ASN A 613 GLN A 727 GLN A1247 ASN A1326 GLN A1528 ASN A1781 ASN A1792 ASN A2350 GLN A2400 ASN F 385 ASN D1074 ASN D1075 ASN D1105 ASN G 58 GLN I 261 ASN I 611 ASN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3990 r_free = 0.3990 target = 0.154796 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3585 r_free = 0.3585 target = 0.117742 restraints weight = 59733.557| |-----------------------------------------------------------------------------| r_work (start): 0.3515 rms_B_bonded: 2.42 r_work: 0.3374 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.3272 rms_B_bonded: 4.37 restraints_weight: 0.2500 r_work (final): 0.3272 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3261 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3261 r_free = 0.3261 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3261 r_free = 0.3261 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3261 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8206 moved from start: 0.0948 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 32838 Z= 0.191 Angle : 0.576 8.370 44410 Z= 0.310 Chirality : 0.045 0.286 4821 Planarity : 0.004 0.048 5825 Dihedral : 7.116 83.657 4671 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 5.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.84 % Favored : 95.16 % Rotamer: Outliers : 4.19 % Allowed : 21.57 % Favored : 74.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.00 % Cis-general : 0.03 % 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: 0.59 (0.13), residues: 3969 helix: 1.70 (0.15), residues: 1194 sheet: 0.59 (0.16), residues: 1110 loop : -0.67 (0.15), residues: 1665 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG I 609 TYR 0.021 0.002 TYR I 294 PHE 0.021 0.002 PHE A1480 TRP 0.024 0.002 TRP A1580 HIS 0.005 0.001 HIS I 271 Details of bonding type rmsd covalent geometry : bond 0.00437 (32833) covalent geometry : angle 0.57572 (44400) hydrogen bonds : bond 0.03914 ( 1391) hydrogen bonds : angle 4.60518 ( 3906) link_MAN-SER : bond 0.00209 ( 4) link_MAN-SER : angle 0.92049 ( 8) link_MAN-THR : bond 0.00070 ( 1) link_MAN-THR : angle 0.64419 ( 2) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7938 Ramachandran restraints generated. 3969 Oldfield, 0 Emsley, 3969 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7938 Ramachandran restraints generated. 3969 Oldfield, 0 Emsley, 3969 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 549 residues out of total 3475 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 142 poor density : 407 time to evaluate : 1.275 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 74 LEU cc_start: 0.8333 (tp) cc_final: 0.8082 (tp) REVERT: A 125 LEU cc_start: 0.7274 (OUTLIER) cc_final: 0.5937 (pp) REVERT: A 190 ASN cc_start: 0.8628 (m-40) cc_final: 0.8401 (m-40) REVERT: A 221 GLU cc_start: 0.8632 (OUTLIER) cc_final: 0.8390 (mt-10) REVERT: A 344 ILE cc_start: 0.8310 (OUTLIER) cc_final: 0.7544 (mp) REVERT: A 407 ILE cc_start: 0.8283 (OUTLIER) cc_final: 0.7726 (mp) REVERT: A 554 ASN cc_start: 0.8052 (OUTLIER) cc_final: 0.7753 (m110) REVERT: A 1189 GLU cc_start: 0.8241 (OUTLIER) cc_final: 0.7146 (pp20) REVERT: A 1202 ASP cc_start: 0.8588 (m-30) cc_final: 0.8379 (m-30) REVERT: A 1580 TRP cc_start: 0.6852 (OUTLIER) cc_final: 0.3553 (p-90) REVERT: A 1680 GLU cc_start: 0.8827 (OUTLIER) cc_final: 0.7585 (tm-30) REVERT: A 1745 ARG cc_start: 0.8742 (OUTLIER) cc_final: 0.7930 (ptp-110) REVERT: A 1949 GLN cc_start: 0.7486 (OUTLIER) cc_final: 0.6586 (tp-100) REVERT: A 2053 GLU cc_start: 0.7953 (OUTLIER) cc_final: 0.6996 (tm-30) REVERT: A 2188 MET cc_start: 0.6333 (mmp) cc_final: 0.6006 (mmp) REVERT: A 2326 ASP cc_start: 0.7741 (OUTLIER) cc_final: 0.7457 (m-30) REVERT: B 93 LEU cc_start: 0.7306 (OUTLIER) cc_final: 0.6655 (tm) REVERT: F 171 GLU cc_start: 0.6090 (OUTLIER) cc_final: 0.5587 (pm20) REVERT: D 1051 LYS cc_start: 0.7108 (tptt) cc_final: 0.6900 (tptp) REVERT: I 58 LYS cc_start: 0.8685 (OUTLIER) cc_final: 0.8375 (mppt) REVERT: I 284 LYS cc_start: 0.9099 (mmtt) cc_final: 0.8758 (mtpt) REVERT: I 564 GLN cc_start: 0.7737 (mm110) cc_final: 0.7276 (tp-100) REVERT: I 654 GLN cc_start: 0.8466 (OUTLIER) cc_final: 0.7972 (pt0) REVERT: I 674 TRP cc_start: 0.8513 (m-90) cc_final: 0.7994 (m-90) REVERT: I 676 LYS cc_start: 0.8958 (OUTLIER) cc_final: 0.8758 (mptm) outliers start: 142 outliers final: 73 residues processed: 503 average time/residue: 0.7008 time to fit residues: 420.8475 Evaluate side-chains 480 residues out of total 3475 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 390 time to evaluate : 1.284 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 GLU Chi-restraints excluded: chain A residue 75 VAL Chi-restraints excluded: chain A residue 76 LEU Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 221 GLU Chi-restraints excluded: chain A residue 277 GLN Chi-restraints excluded: chain A residue 344 ILE Chi-restraints excluded: chain A residue 365 VAL Chi-restraints excluded: chain A residue 407 ILE Chi-restraints excluded: chain A residue 416 ASN Chi-restraints excluded: chain A residue 486 THR Chi-restraints excluded: chain A residue 554 ASN Chi-restraints excluded: chain A residue 816 LEU Chi-restraints excluded: chain A residue 827 VAL Chi-restraints excluded: chain A residue 931 SER Chi-restraints excluded: chain A residue 1122 LEU Chi-restraints excluded: chain A residue 1162 ILE Chi-restraints excluded: chain A residue 1167 THR Chi-restraints excluded: chain A residue 1179 ILE Chi-restraints excluded: chain A residue 1189 GLU Chi-restraints excluded: chain A residue 1290 VAL Chi-restraints excluded: chain A residue 1519 MET Chi-restraints excluded: chain A residue 1580 TRP Chi-restraints excluded: chain A residue 1661 THR Chi-restraints excluded: chain A residue 1680 GLU Chi-restraints excluded: chain A residue 1722 PHE Chi-restraints excluded: chain A residue 1736 LEU Chi-restraints excluded: chain A residue 1745 ARG Chi-restraints excluded: chain A residue 1809 ASP Chi-restraints excluded: chain A residue 1857 THR Chi-restraints excluded: chain A residue 1879 SER Chi-restraints excluded: chain A residue 1949 GLN Chi-restraints excluded: chain A residue 1977 LEU Chi-restraints excluded: chain A residue 2008 THR Chi-restraints excluded: chain A residue 2018 THR Chi-restraints excluded: chain A residue 2053 GLU Chi-restraints excluded: chain A residue 2066 SER Chi-restraints excluded: chain A residue 2071 MET Chi-restraints excluded: chain A residue 2083 GLN Chi-restraints excluded: chain A residue 2136 ASN Chi-restraints excluded: chain A residue 2141 ILE Chi-restraints excluded: chain A residue 2198 LYS Chi-restraints excluded: chain A residue 2272 ASP Chi-restraints excluded: chain A residue 2326 ASP Chi-restraints excluded: chain A residue 2350 GLN Chi-restraints excluded: chain A residue 2357 LEU Chi-restraints excluded: chain A residue 2382 ILE Chi-restraints excluded: chain A residue 2396 THR Chi-restraints excluded: chain B residue 93 LEU Chi-restraints excluded: chain B residue 173 VAL Chi-restraints excluded: chain F residue 88 ASP Chi-restraints excluded: chain F residue 101 ASN Chi-restraints excluded: chain F residue 123 THR Chi-restraints excluded: chain F residue 130 THR Chi-restraints excluded: chain F residue 171 GLU Chi-restraints excluded: chain F residue 241 PHE Chi-restraints excluded: chain F residue 266 THR Chi-restraints excluded: chain F residue 293 LYS Chi-restraints excluded: chain F residue 392 THR Chi-restraints excluded: chain D residue 1047 ASP Chi-restraints excluded: chain D residue 1058 VAL Chi-restraints excluded: chain D residue 1059 MET Chi-restraints excluded: chain D residue 1066 ASP Chi-restraints excluded: chain G residue 40 SER Chi-restraints excluded: chain G residue 65 LEU Chi-restraints excluded: chain G residue 96 GLN Chi-restraints excluded: chain G residue 113 ASN Chi-restraints excluded: chain G residue 114 LEU Chi-restraints excluded: chain G residue 140 LYS Chi-restraints excluded: chain C residue 30 ILE Chi-restraints excluded: chain C residue 43 LYS Chi-restraints excluded: chain C residue 69 SER Chi-restraints excluded: chain C residue 70 LEU Chi-restraints excluded: chain C residue 76 THR Chi-restraints excluded: chain C residue 81 LEU Chi-restraints excluded: chain C residue 85 LEU Chi-restraints excluded: chain C residue 173 ARG Chi-restraints excluded: chain E residue 101 LEU Chi-restraints excluded: chain E residue 157 SER Chi-restraints excluded: chain I residue 54 LEU Chi-restraints excluded: chain I residue 58 LYS Chi-restraints excluded: chain I residue 67 LYS Chi-restraints excluded: chain I residue 192 THR Chi-restraints excluded: chain I residue 298 VAL Chi-restraints excluded: chain I residue 371 SER Chi-restraints excluded: chain I residue 382 GLU Chi-restraints excluded: chain I residue 568 THR Chi-restraints excluded: chain I residue 654 GLN Chi-restraints excluded: chain I residue 666 SER Chi-restraints excluded: chain I residue 676 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 395 random chunks: chunk 80 optimal weight: 4.9990 chunk 308 optimal weight: 4.9990 chunk 151 optimal weight: 0.7980 chunk 4 optimal weight: 0.4980 chunk 63 optimal weight: 3.9990 chunk 90 optimal weight: 1.9990 chunk 392 optimal weight: 6.9990 chunk 89 optimal weight: 3.9990 chunk 73 optimal weight: 1.9990 chunk 93 optimal weight: 0.7980 chunk 355 optimal weight: 0.4980 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 246 GLN A 437 ASN A 491 ASN A 727 GLN A 752 GLN A1247 ASN A1291 ASN A1316 ASN A1528 ASN A1781 ASN A1792 ASN A2020 ASN A2400 ASN B 143 GLN F 385 ASN D1074 ASN D1075 ASN D1105 ASN G 58 GLN I 261 ASN I 611 ASN Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4004 r_free = 0.4004 target = 0.155888 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3607 r_free = 0.3607 target = 0.119084 restraints weight = 64730.014| |-----------------------------------------------------------------------------| r_work (start): 0.3535 rms_B_bonded: 2.52 r_work: 0.3386 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.3284 rms_B_bonded: 4.57 restraints_weight: 0.2500 r_work (final): 0.3284 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3275 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3275 r_free = 0.3275 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3275 r_free = 0.3275 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3275 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8190 moved from start: 0.0949 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 32838 Z= 0.141 Angle : 0.542 7.200 44410 Z= 0.292 Chirality : 0.044 0.257 4821 Planarity : 0.004 0.044 5825 Dihedral : 6.804 84.341 4663 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 5.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.58 % Favored : 95.42 % Rotamer: Outliers : 3.68 % Allowed : 22.31 % Favored : 74.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.00 % Cis-general : 0.03 % 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: 0.62 (0.14), residues: 3969 helix: 1.77 (0.15), residues: 1194 sheet: 0.57 (0.16), residues: 1110 loop : -0.66 (0.15), residues: 1665 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG I 609 TYR 0.018 0.001 TYR I 294 PHE 0.025 0.001 PHE I 28 TRP 0.021 0.002 TRP A1580 HIS 0.004 0.001 HIS I 271 Details of bonding type rmsd covalent geometry : bond 0.00318 (32833) covalent geometry : angle 0.54230 (44400) hydrogen bonds : bond 0.03556 ( 1391) hydrogen bonds : angle 4.52977 ( 3906) link_MAN-SER : bond 0.00136 ( 4) link_MAN-SER : angle 0.71180 ( 8) link_MAN-THR : bond 0.00061 ( 1) link_MAN-THR : angle 0.50629 ( 2) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7938 Ramachandran restraints generated. 3969 Oldfield, 0 Emsley, 3969 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7938 Ramachandran restraints generated. 3969 Oldfield, 0 Emsley, 3969 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 522 residues out of total 3475 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 124 poor density : 398 time to evaluate : 1.333 Fit side-chains revert: symmetry clash REVERT: A 79 LYS cc_start: 0.7208 (tppp) cc_final: 0.7007 (tppp) REVERT: A 144 GLU cc_start: 0.8435 (OUTLIER) cc_final: 0.8138 (mt-10) REVERT: A 190 ASN cc_start: 0.8651 (m-40) cc_final: 0.8394 (m-40) REVERT: A 221 GLU cc_start: 0.8642 (OUTLIER) cc_final: 0.8402 (mt-10) REVERT: A 246 GLN cc_start: 0.8190 (OUTLIER) cc_final: 0.7896 (tt0) REVERT: A 344 ILE cc_start: 0.8272 (OUTLIER) cc_final: 0.7504 (mp) REVERT: A 407 ILE cc_start: 0.8230 (OUTLIER) cc_final: 0.7735 (mp) REVERT: A 554 ASN cc_start: 0.8015 (OUTLIER) cc_final: 0.7749 (m110) REVERT: A 884 ILE cc_start: 0.7048 (OUTLIER) cc_final: 0.6320 (tp) REVERT: A 1122 LEU cc_start: 0.8998 (OUTLIER) cc_final: 0.8377 (mp) REVERT: A 1189 GLU cc_start: 0.8197 (OUTLIER) cc_final: 0.7123 (pp20) REVERT: A 1202 ASP cc_start: 0.8587 (m-30) cc_final: 0.8373 (m-30) REVERT: A 1580 TRP cc_start: 0.6799 (OUTLIER) cc_final: 0.3488 (p-90) REVERT: A 1680 GLU cc_start: 0.8832 (OUTLIER) cc_final: 0.7517 (tm-30) REVERT: A 1745 ARG cc_start: 0.8719 (OUTLIER) cc_final: 0.7974 (ptp-110) REVERT: A 1949 GLN cc_start: 0.7475 (OUTLIER) cc_final: 0.6588 (tp-100) REVERT: A 2053 GLU cc_start: 0.7956 (OUTLIER) cc_final: 0.6994 (tm-30) REVERT: A 2188 MET cc_start: 0.6283 (mmp) cc_final: 0.5902 (mmp) REVERT: B 93 LEU cc_start: 0.7237 (OUTLIER) cc_final: 0.6711 (tm) REVERT: F 171 GLU cc_start: 0.6057 (OUTLIER) cc_final: 0.5561 (pm20) REVERT: F 183 ASP cc_start: 0.8202 (m-30) cc_final: 0.7669 (m-30) REVERT: D 1051 LYS cc_start: 0.7109 (tptt) cc_final: 0.6895 (tptp) REVERT: I 58 LYS cc_start: 0.8675 (OUTLIER) cc_final: 0.8407 (mppt) REVERT: I 284 LYS cc_start: 0.9105 (mmtt) cc_final: 0.8748 (mtpt) REVERT: I 564 GLN cc_start: 0.7720 (mm110) cc_final: 0.7277 (tp-100) REVERT: I 654 GLN cc_start: 0.8500 (OUTLIER) cc_final: 0.8007 (pt0) REVERT: I 674 TRP cc_start: 0.8491 (m-90) cc_final: 0.7998 (m-90) REVERT: I 733 ASN cc_start: 0.8714 (m-40) cc_final: 0.8308 (m110) outliers start: 124 outliers final: 62 residues processed: 481 average time/residue: 0.7176 time to fit residues: 411.5353 Evaluate side-chains 473 residues out of total 3475 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 393 time to evaluate : 1.108 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 GLU Chi-restraints excluded: chain A residue 75 VAL Chi-restraints excluded: chain A residue 144 GLU Chi-restraints excluded: chain A residue 199 PHE Chi-restraints excluded: chain A residue 221 GLU Chi-restraints excluded: chain A residue 246 GLN Chi-restraints excluded: chain A residue 277 GLN Chi-restraints excluded: chain A residue 344 ILE Chi-restraints excluded: chain A residue 365 VAL Chi-restraints excluded: chain A residue 407 ILE Chi-restraints excluded: chain A residue 416 ASN Chi-restraints excluded: chain A residue 486 THR Chi-restraints excluded: chain A residue 554 ASN Chi-restraints excluded: chain A residue 827 VAL Chi-restraints excluded: chain A residue 884 ILE Chi-restraints excluded: chain A residue 1028 LYS Chi-restraints excluded: chain A residue 1122 LEU Chi-restraints excluded: chain A residue 1162 ILE Chi-restraints excluded: chain A residue 1189 GLU Chi-restraints excluded: chain A residue 1290 VAL Chi-restraints excluded: chain A residue 1519 MET Chi-restraints excluded: chain A residue 1580 TRP Chi-restraints excluded: chain A residue 1680 GLU Chi-restraints excluded: chain A residue 1736 LEU Chi-restraints excluded: chain A residue 1745 ARG Chi-restraints excluded: chain A residue 1809 ASP Chi-restraints excluded: chain A residue 1857 THR Chi-restraints excluded: chain A residue 1949 GLN Chi-restraints excluded: chain A residue 1977 LEU Chi-restraints excluded: chain A residue 2008 THR Chi-restraints excluded: chain A residue 2018 THR Chi-restraints excluded: chain A residue 2053 GLU Chi-restraints excluded: chain A residue 2066 SER Chi-restraints excluded: chain A residue 2071 MET Chi-restraints excluded: chain A residue 2083 GLN Chi-restraints excluded: chain A residue 2136 ASN Chi-restraints excluded: chain A residue 2141 ILE Chi-restraints excluded: chain A residue 2198 LYS Chi-restraints excluded: chain A residue 2272 ASP Chi-restraints excluded: chain A residue 2357 LEU Chi-restraints excluded: chain A residue 2360 ASP Chi-restraints excluded: chain A residue 2382 ILE Chi-restraints excluded: chain A residue 2396 THR Chi-restraints excluded: chain B residue 93 LEU Chi-restraints excluded: chain B residue 173 VAL Chi-restraints excluded: chain F residue 101 ASN Chi-restraints excluded: chain F residue 130 THR Chi-restraints excluded: chain F residue 171 GLU Chi-restraints excluded: chain F residue 241 PHE Chi-restraints excluded: chain F residue 254 THR Chi-restraints excluded: chain F residue 266 THR Chi-restraints excluded: chain F residue 392 THR Chi-restraints excluded: chain D residue 1047 ASP Chi-restraints excluded: chain D residue 1058 VAL Chi-restraints excluded: chain D residue 1059 MET Chi-restraints excluded: chain G residue 40 SER Chi-restraints excluded: chain G residue 96 GLN Chi-restraints excluded: chain G residue 113 ASN Chi-restraints excluded: chain G residue 114 LEU Chi-restraints excluded: chain G residue 140 LYS Chi-restraints excluded: chain C residue 43 LYS Chi-restraints excluded: chain C residue 69 SER Chi-restraints excluded: chain C residue 70 LEU Chi-restraints excluded: chain C residue 81 LEU Chi-restraints excluded: chain C residue 154 MET Chi-restraints excluded: chain C residue 173 ARG Chi-restraints excluded: chain E residue 101 LEU Chi-restraints excluded: chain E residue 157 SER Chi-restraints excluded: chain I residue 31 ARG Chi-restraints excluded: chain I residue 58 LYS Chi-restraints excluded: chain I residue 67 LYS Chi-restraints excluded: chain I residue 188 LEU Chi-restraints excluded: chain I residue 298 VAL Chi-restraints excluded: chain I residue 340 LYS Chi-restraints excluded: chain I residue 371 SER Chi-restraints excluded: chain I residue 382 GLU Chi-restraints excluded: chain I residue 568 THR Chi-restraints excluded: chain I residue 639 ILE Chi-restraints excluded: chain I residue 654 GLN Chi-restraints excluded: chain I residue 666 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 395 random chunks: chunk 377 optimal weight: 5.9990 chunk 220 optimal weight: 0.7980 chunk 314 optimal weight: 0.9980 chunk 11 optimal weight: 6.9990 chunk 231 optimal weight: 9.9990 chunk 35 optimal weight: 0.9980 chunk 30 optimal weight: 2.9990 chunk 114 optimal weight: 0.9990 chunk 318 optimal weight: 0.8980 chunk 359 optimal weight: 0.5980 chunk 207 optimal weight: 4.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 32 GLN A 437 ASN A 576 GLN A 727 GLN A 752 GLN A1247 ASN A1528 ASN A1781 ASN A1792 ASN A2350 GLN A2400 ASN B 143 GLN F 385 ASN D1074 ASN D1075 ASN D1105 ASN G 58 GLN I 261 ASN I 611 ASN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4009 r_free = 0.4009 target = 0.156168 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3618 r_free = 0.3618 target = 0.119897 restraints weight = 62492.203| |-----------------------------------------------------------------------------| r_work (start): 0.3542 rms_B_bonded: 2.49 r_work: 0.3393 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.3291 rms_B_bonded: 4.53 restraints_weight: 0.2500 r_work (final): 0.3291 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3282 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3282 r_free = 0.3282 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3282 r_free = 0.3282 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3282 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8192 moved from start: 0.0973 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 32838 Z= 0.135 Angle : 0.534 6.995 44410 Z= 0.288 Chirality : 0.043 0.230 4821 Planarity : 0.004 0.044 5825 Dihedral : 6.606 83.827 4659 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 5.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.71 % Favored : 95.29 % Rotamer: Outliers : 3.39 % Allowed : 22.71 % Favored : 73.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.00 % Cis-general : 0.03 % 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: 0.65 (0.14), residues: 3969 helix: 1.81 (0.15), residues: 1193 sheet: 0.57 (0.16), residues: 1110 loop : -0.66 (0.15), residues: 1666 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG I 609 TYR 0.017 0.001 TYR I 294 PHE 0.024 0.001 PHE I 28 TRP 0.019 0.002 TRP A1580 HIS 0.004 0.001 HIS I 271 Details of bonding type rmsd covalent geometry : bond 0.00304 (32833) covalent geometry : angle 0.53415 (44400) hydrogen bonds : bond 0.03478 ( 1391) hydrogen bonds : angle 4.49117 ( 3906) link_MAN-SER : bond 0.00119 ( 4) link_MAN-SER : angle 0.68243 ( 8) link_MAN-THR : bond 0.00062 ( 1) link_MAN-THR : angle 0.51715 ( 2) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7938 Ramachandran restraints generated. 3969 Oldfield, 0 Emsley, 3969 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7938 Ramachandran restraints generated. 3969 Oldfield, 0 Emsley, 3969 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 510 residues out of total 3475 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 113 poor density : 397 time to evaluate : 1.336 Fit side-chains revert: symmetry clash REVERT: A 125 LEU cc_start: 0.7271 (OUTLIER) cc_final: 0.5964 (pp) REVERT: A 144 GLU cc_start: 0.8429 (OUTLIER) cc_final: 0.8150 (mt-10) REVERT: A 190 ASN cc_start: 0.8648 (m-40) cc_final: 0.8378 (m-40) REVERT: A 221 GLU cc_start: 0.8631 (OUTLIER) cc_final: 0.8385 (mt-10) REVERT: A 344 ILE cc_start: 0.8284 (OUTLIER) cc_final: 0.7511 (mp) REVERT: A 407 ILE cc_start: 0.8242 (OUTLIER) cc_final: 0.7752 (mp) REVERT: A 554 ASN cc_start: 0.8012 (OUTLIER) cc_final: 0.7777 (m110) REVERT: A 884 ILE cc_start: 0.7016 (OUTLIER) cc_final: 0.6298 (tp) REVERT: A 1189 GLU cc_start: 0.8200 (OUTLIER) cc_final: 0.7149 (pp20) REVERT: A 1202 ASP cc_start: 0.8580 (m-30) cc_final: 0.8358 (m-30) REVERT: A 1580 TRP cc_start: 0.6787 (OUTLIER) cc_final: 0.3490 (p-90) REVERT: A 1680 GLU cc_start: 0.8820 (OUTLIER) cc_final: 0.7538 (tm-30) REVERT: A 1745 ARG cc_start: 0.8715 (OUTLIER) cc_final: 0.7971 (ptp-110) REVERT: A 1949 GLN cc_start: 0.7480 (OUTLIER) cc_final: 0.7148 (tp40) REVERT: A 2053 GLU cc_start: 0.7965 (OUTLIER) cc_final: 0.7000 (tm-30) REVERT: A 2188 MET cc_start: 0.6301 (mmp) cc_final: 0.5931 (mmp) REVERT: B 93 LEU cc_start: 0.7255 (OUTLIER) cc_final: 0.6496 (tm) REVERT: B 123 ARG cc_start: 0.7899 (ptp90) cc_final: 0.7571 (ptm160) REVERT: F 171 GLU cc_start: 0.5953 (OUTLIER) cc_final: 0.5480 (pm20) REVERT: F 183 ASP cc_start: 0.8148 (m-30) cc_final: 0.7603 (m-30) REVERT: D 1051 LYS cc_start: 0.7093 (tptt) cc_final: 0.6747 (tptp) REVERT: I 284 LYS cc_start: 0.9101 (mmtt) cc_final: 0.8747 (mtpt) REVERT: I 382 GLU cc_start: 0.8878 (OUTLIER) cc_final: 0.8490 (tt0) REVERT: I 564 GLN cc_start: 0.7690 (mm110) cc_final: 0.7254 (tp-100) REVERT: I 651 ARG cc_start: 0.7346 (mmm160) cc_final: 0.7005 (mtp-110) REVERT: I 654 GLN cc_start: 0.8494 (OUTLIER) cc_final: 0.7968 (pt0) REVERT: I 674 TRP cc_start: 0.8475 (m-90) cc_final: 0.7993 (m-90) REVERT: I 733 ASN cc_start: 0.8709 (m-40) cc_final: 0.8291 (m110) outliers start: 113 outliers final: 64 residues processed: 479 average time/residue: 0.7557 time to fit residues: 431.0904 Evaluate side-chains 469 residues out of total 3475 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 388 time to evaluate : 1.381 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 GLU Chi-restraints excluded: chain A residue 75 VAL Chi-restraints excluded: chain A residue 121 ILE Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 144 GLU Chi-restraints excluded: chain A residue 199 PHE Chi-restraints excluded: chain A residue 221 GLU Chi-restraints excluded: chain A residue 277 GLN Chi-restraints excluded: chain A residue 329 GLN Chi-restraints excluded: chain A residue 344 ILE Chi-restraints excluded: chain A residue 365 VAL Chi-restraints excluded: chain A residue 407 ILE Chi-restraints excluded: chain A residue 416 ASN Chi-restraints excluded: chain A residue 486 THR Chi-restraints excluded: chain A residue 554 ASN Chi-restraints excluded: chain A residue 827 VAL Chi-restraints excluded: chain A residue 884 ILE Chi-restraints excluded: chain A residue 931 SER Chi-restraints excluded: chain A residue 1189 GLU Chi-restraints excluded: chain A residue 1243 MET Chi-restraints excluded: chain A residue 1290 VAL Chi-restraints excluded: chain A residue 1580 TRP Chi-restraints excluded: chain A residue 1680 GLU Chi-restraints excluded: chain A residue 1722 PHE Chi-restraints excluded: chain A residue 1736 LEU Chi-restraints excluded: chain A residue 1745 ARG Chi-restraints excluded: chain A residue 1809 ASP Chi-restraints excluded: chain A residue 1857 THR Chi-restraints excluded: chain A residue 1949 GLN Chi-restraints excluded: chain A residue 1977 LEU Chi-restraints excluded: chain A residue 2008 THR Chi-restraints excluded: chain A residue 2018 THR Chi-restraints excluded: chain A residue 2053 GLU Chi-restraints excluded: chain A residue 2066 SER Chi-restraints excluded: chain A residue 2071 MET Chi-restraints excluded: chain A residue 2083 GLN Chi-restraints excluded: chain A residue 2136 ASN Chi-restraints excluded: chain A residue 2141 ILE Chi-restraints excluded: chain A residue 2198 LYS Chi-restraints excluded: chain A residue 2272 ASP Chi-restraints excluded: chain A residue 2357 LEU Chi-restraints excluded: chain A residue 2360 ASP Chi-restraints excluded: chain A residue 2382 ILE Chi-restraints excluded: chain A residue 2396 THR Chi-restraints excluded: chain B residue 93 LEU Chi-restraints excluded: chain B residue 173 VAL Chi-restraints excluded: chain F residue 21 ASP Chi-restraints excluded: chain F residue 101 ASN Chi-restraints excluded: chain F residue 130 THR Chi-restraints excluded: chain F residue 171 GLU Chi-restraints excluded: chain F residue 241 PHE Chi-restraints excluded: chain F residue 254 THR Chi-restraints excluded: chain F residue 392 THR Chi-restraints excluded: chain D residue 1047 ASP Chi-restraints excluded: chain D residue 1058 VAL Chi-restraints excluded: chain D residue 1059 MET Chi-restraints excluded: chain G residue 40 SER Chi-restraints excluded: chain G residue 96 GLN Chi-restraints excluded: chain G residue 113 ASN Chi-restraints excluded: chain G residue 114 LEU Chi-restraints excluded: chain G residue 140 LYS Chi-restraints excluded: chain C residue 30 ILE Chi-restraints excluded: chain C residue 69 SER Chi-restraints excluded: chain C residue 70 LEU Chi-restraints excluded: chain C residue 76 THR Chi-restraints excluded: chain C residue 81 LEU Chi-restraints excluded: chain C residue 154 MET Chi-restraints excluded: chain C residue 173 ARG Chi-restraints excluded: chain E residue 101 LEU Chi-restraints excluded: chain E residue 157 SER Chi-restraints excluded: chain I residue 31 ARG Chi-restraints excluded: chain I residue 67 LYS Chi-restraints excluded: chain I residue 188 LEU Chi-restraints excluded: chain I residue 298 VAL Chi-restraints excluded: chain I residue 340 LYS Chi-restraints excluded: chain I residue 371 SER Chi-restraints excluded: chain I residue 382 GLU Chi-restraints excluded: chain I residue 568 THR Chi-restraints excluded: chain I residue 639 ILE Chi-restraints excluded: chain I residue 654 GLN Chi-restraints excluded: chain I residue 666 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 395 random chunks: chunk 156 optimal weight: 3.9990 chunk 360 optimal weight: 0.8980 chunk 153 optimal weight: 0.8980 chunk 115 optimal weight: 1.9990 chunk 386 optimal weight: 4.9990 chunk 384 optimal weight: 1.9990 chunk 171 optimal weight: 0.8980 chunk 86 optimal weight: 4.9990 chunk 329 optimal weight: 0.3980 chunk 191 optimal weight: 5.9990 chunk 164 optimal weight: 5.9990 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 246 GLN A 437 ASN A 613 GLN A 727 GLN A 752 GLN A1247 ASN A1528 ASN A1781 ASN A1792 ASN A2350 GLN A2400 ASN B 143 GLN F 385 ASN D1074 ASN D1075 ASN D1105 ASN G 58 GLN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4005 r_free = 0.4005 target = 0.155985 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3606 r_free = 0.3606 target = 0.118709 restraints weight = 51955.062| |-----------------------------------------------------------------------------| r_work (start): 0.3531 rms_B_bonded: 2.33 r_work: 0.3409 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.3307 rms_B_bonded: 4.13 restraints_weight: 0.2500 r_work (final): 0.3307 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3300 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3300 r_free = 0.3300 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3300 r_free = 0.3300 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3300 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8167 moved from start: 0.0997 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 32838 Z= 0.148 Angle : 0.543 7.296 44410 Z= 0.292 Chirality : 0.044 0.189 4821 Planarity : 0.004 0.044 5825 Dihedral : 6.481 81.786 4657 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 5.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.71 % Favored : 95.29 % Rotamer: Outliers : 3.31 % Allowed : 22.94 % Favored : 73.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.00 % Cis-general : 0.03 % 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: 0.65 (0.14), residues: 3969 helix: 1.82 (0.15), residues: 1190 sheet: 0.57 (0.16), residues: 1115 loop : -0.66 (0.15), residues: 1664 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG E 169 TYR 0.019 0.001 TYR I 294 PHE 0.023 0.001 PHE I 28 TRP 0.020 0.002 TRP A1580 HIS 0.004 0.001 HIS I 271 Details of bonding type rmsd covalent geometry : bond 0.00334 (32833) covalent geometry : angle 0.54343 (44400) hydrogen bonds : bond 0.03555 ( 1391) hydrogen bonds : angle 4.48763 ( 3906) link_MAN-SER : bond 0.00135 ( 4) link_MAN-SER : angle 0.72328 ( 8) link_MAN-THR : bond 0.00063 ( 1) link_MAN-THR : angle 0.56194 ( 2) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7938 Ramachandran restraints generated. 3969 Oldfield, 0 Emsley, 3969 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7938 Ramachandran restraints generated. 3969 Oldfield, 0 Emsley, 3969 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 507 residues out of total 3475 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 110 poor density : 397 time to evaluate : 1.366 Fit side-chains revert: symmetry clash REVERT: A 125 LEU cc_start: 0.7233 (OUTLIER) cc_final: 0.5904 (pp) REVERT: A 144 GLU cc_start: 0.8446 (OUTLIER) cc_final: 0.8151 (mt-10) REVERT: A 188 GLU cc_start: 0.8011 (OUTLIER) cc_final: 0.6469 (tm-30) REVERT: A 190 ASN cc_start: 0.8616 (m-40) cc_final: 0.8167 (m-40) REVERT: A 221 GLU cc_start: 0.8585 (OUTLIER) cc_final: 0.8329 (mt-10) REVERT: A 246 GLN cc_start: 0.8184 (OUTLIER) cc_final: 0.7863 (tt0) REVERT: A 344 ILE cc_start: 0.8271 (OUTLIER) cc_final: 0.7506 (mp) REVERT: A 407 ILE cc_start: 0.8232 (OUTLIER) cc_final: 0.7766 (mp) REVERT: A 554 ASN cc_start: 0.7976 (OUTLIER) cc_final: 0.7764 (m110) REVERT: A 752 GLN cc_start: 0.7990 (OUTLIER) cc_final: 0.7765 (mm-40) REVERT: A 884 ILE cc_start: 0.6990 (OUTLIER) cc_final: 0.6281 (tp) REVERT: A 1189 GLU cc_start: 0.8194 (OUTLIER) cc_final: 0.7119 (pp20) REVERT: A 1580 TRP cc_start: 0.6781 (OUTLIER) cc_final: 0.3496 (p-90) REVERT: A 1680 GLU cc_start: 0.8809 (OUTLIER) cc_final: 0.7526 (tm-30) REVERT: A 1745 ARG cc_start: 0.8678 (OUTLIER) cc_final: 0.7946 (ptp-110) REVERT: A 1949 GLN cc_start: 0.7475 (OUTLIER) cc_final: 0.7130 (tp40) REVERT: A 2053 GLU cc_start: 0.7931 (OUTLIER) cc_final: 0.6958 (tm-30) REVERT: A 2188 MET cc_start: 0.6288 (mmp) cc_final: 0.5951 (mmp) REVERT: B 93 LEU cc_start: 0.7247 (OUTLIER) cc_final: 0.6621 (tm) REVERT: F 171 GLU cc_start: 0.5869 (OUTLIER) cc_final: 0.5415 (pm20) REVERT: F 183 ASP cc_start: 0.8141 (m-30) cc_final: 0.7586 (m-30) REVERT: D 1051 LYS cc_start: 0.7084 (tptt) cc_final: 0.6725 (tptp) REVERT: I 284 LYS cc_start: 0.9084 (mmtt) cc_final: 0.8735 (mtpt) REVERT: I 382 GLU cc_start: 0.8854 (OUTLIER) cc_final: 0.8329 (tt0) REVERT: I 564 GLN cc_start: 0.7682 (mm110) cc_final: 0.7245 (tp-100) REVERT: I 651 ARG cc_start: 0.7342 (mmm160) cc_final: 0.7012 (mtp-110) REVERT: I 654 GLN cc_start: 0.8504 (OUTLIER) cc_final: 0.7979 (pt0) REVERT: I 674 TRP cc_start: 0.8502 (m-90) cc_final: 0.8048 (m-90) REVERT: I 733 ASN cc_start: 0.8706 (m-40) cc_final: 0.8316 (m110) outliers start: 110 outliers final: 69 residues processed: 470 average time/residue: 0.7188 time to fit residues: 403.5629 Evaluate side-chains 478 residues out of total 3475 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 389 time to evaluate : 1.379 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 GLU Chi-restraints excluded: chain A residue 75 VAL Chi-restraints excluded: chain A residue 121 ILE Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 144 GLU Chi-restraints excluded: chain A residue 188 GLU Chi-restraints excluded: chain A residue 221 GLU Chi-restraints excluded: chain A residue 246 GLN Chi-restraints excluded: chain A residue 277 GLN Chi-restraints excluded: chain A residue 344 ILE Chi-restraints excluded: chain A residue 365 VAL Chi-restraints excluded: chain A residue 407 ILE Chi-restraints excluded: chain A residue 416 ASN Chi-restraints excluded: chain A residue 554 ASN Chi-restraints excluded: chain A residue 752 GLN Chi-restraints excluded: chain A residue 816 LEU Chi-restraints excluded: chain A residue 827 VAL Chi-restraints excluded: chain A residue 884 ILE Chi-restraints excluded: chain A residue 931 SER Chi-restraints excluded: chain A residue 1028 LYS Chi-restraints excluded: chain A residue 1162 ILE Chi-restraints excluded: chain A residue 1189 GLU Chi-restraints excluded: chain A residue 1290 VAL Chi-restraints excluded: chain A residue 1580 TRP Chi-restraints excluded: chain A residue 1680 GLU Chi-restraints excluded: chain A residue 1722 PHE Chi-restraints excluded: chain A residue 1736 LEU Chi-restraints excluded: chain A residue 1745 ARG Chi-restraints excluded: chain A residue 1809 ASP Chi-restraints excluded: chain A residue 1857 THR Chi-restraints excluded: chain A residue 1879 SER Chi-restraints excluded: chain A residue 1949 GLN Chi-restraints excluded: chain A residue 1977 LEU Chi-restraints excluded: chain A residue 2008 THR Chi-restraints excluded: chain A residue 2018 THR Chi-restraints excluded: chain A residue 2028 LYS Chi-restraints excluded: chain A residue 2053 GLU Chi-restraints excluded: chain A residue 2066 SER Chi-restraints excluded: chain A residue 2071 MET Chi-restraints excluded: chain A residue 2083 GLN Chi-restraints excluded: chain A residue 2136 ASN Chi-restraints excluded: chain A residue 2141 ILE Chi-restraints excluded: chain A residue 2198 LYS Chi-restraints excluded: chain A residue 2272 ASP Chi-restraints excluded: chain A residue 2350 GLN Chi-restraints excluded: chain A residue 2357 LEU Chi-restraints excluded: chain A residue 2360 ASP Chi-restraints excluded: chain A residue 2382 ILE Chi-restraints excluded: chain A residue 2396 THR Chi-restraints excluded: chain B residue 93 LEU Chi-restraints excluded: chain B residue 173 VAL Chi-restraints excluded: chain F residue 21 ASP Chi-restraints excluded: chain F residue 88 ASP Chi-restraints excluded: chain F residue 101 ASN Chi-restraints excluded: chain F residue 130 THR Chi-restraints excluded: chain F residue 171 GLU Chi-restraints excluded: chain F residue 241 PHE Chi-restraints excluded: chain F residue 254 THR Chi-restraints excluded: chain F residue 392 THR Chi-restraints excluded: chain D residue 1047 ASP Chi-restraints excluded: chain D residue 1058 VAL Chi-restraints excluded: chain D residue 1059 MET Chi-restraints excluded: chain G residue 40 SER Chi-restraints excluded: chain G residue 96 GLN Chi-restraints excluded: chain G residue 113 ASN Chi-restraints excluded: chain G residue 114 LEU Chi-restraints excluded: chain G residue 140 LYS Chi-restraints excluded: chain C residue 30 ILE Chi-restraints excluded: chain C residue 43 LYS Chi-restraints excluded: chain C residue 69 SER Chi-restraints excluded: chain C residue 70 LEU Chi-restraints excluded: chain C residue 76 THR Chi-restraints excluded: chain C residue 81 LEU Chi-restraints excluded: chain C residue 154 MET Chi-restraints excluded: chain C residue 173 ARG Chi-restraints excluded: chain E residue 101 LEU Chi-restraints excluded: chain E residue 157 SER Chi-restraints excluded: chain I residue 67 LYS Chi-restraints excluded: chain I residue 188 LEU Chi-restraints excluded: chain I residue 298 VAL Chi-restraints excluded: chain I residue 340 LYS Chi-restraints excluded: chain I residue 371 SER Chi-restraints excluded: chain I residue 382 GLU Chi-restraints excluded: chain I residue 568 THR Chi-restraints excluded: chain I residue 616 LEU Chi-restraints excluded: chain I residue 630 ILE Chi-restraints excluded: chain I residue 639 ILE Chi-restraints excluded: chain I residue 654 GLN Chi-restraints excluded: chain I residue 666 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 395 random chunks: chunk 124 optimal weight: 0.8980 chunk 3 optimal weight: 6.9990 chunk 46 optimal weight: 0.9990 chunk 57 optimal weight: 2.9990 chunk 193 optimal weight: 3.9990 chunk 221 optimal weight: 7.9990 chunk 336 optimal weight: 0.6980 chunk 75 optimal weight: 0.8980 chunk 30 optimal weight: 7.9990 chunk 136 optimal weight: 1.9990 chunk 123 optimal weight: 0.9980 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 246 GLN A 437 ASN A 613 GLN A 727 GLN A 752 GLN A1247 ASN A1302 ASN A1528 ASN A1792 ASN A2400 ASN B 143 GLN F 385 ASN D1074 ASN D1075 ASN D1105 ASN G 58 GLN I 261 ASN I 611 ASN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4009 r_free = 0.4009 target = 0.156287 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3624 r_free = 0.3624 target = 0.119653 restraints weight = 55790.913| |-----------------------------------------------------------------------------| r_work (start): 0.3545 rms_B_bonded: 2.32 r_work: 0.3407 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.3306 rms_B_bonded: 4.30 restraints_weight: 0.2500 r_work (final): 0.3306 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3296 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3296 r_free = 0.3296 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3296 r_free = 0.3296 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3296 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8166 moved from start: 0.1011 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 32838 Z= 0.138 Angle : 0.538 7.995 44410 Z= 0.290 Chirality : 0.043 0.177 4821 Planarity : 0.004 0.044 5825 Dihedral : 6.415 81.653 4656 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 5.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.74 % Favored : 95.26 % Rotamer: Outliers : 2.99 % Allowed : 23.34 % Favored : 73.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.00 % Cis-general : 0.03 % 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: 0.65 (0.14), residues: 3969 helix: 1.84 (0.15), residues: 1189 sheet: 0.55 (0.16), residues: 1115 loop : -0.66 (0.15), residues: 1665 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG E 169 TYR 0.018 0.001 TYR I 294 PHE 0.022 0.001 PHE I 28 TRP 0.019 0.002 TRP A1580 HIS 0.004 0.001 HIS I 271 Details of bonding type rmsd covalent geometry : bond 0.00311 (32833) covalent geometry : angle 0.53776 (44400) hydrogen bonds : bond 0.03473 ( 1391) hydrogen bonds : angle 4.47365 ( 3906) link_MAN-SER : bond 0.00129 ( 4) link_MAN-SER : angle 0.67408 ( 8) link_MAN-THR : bond 0.00069 ( 1) link_MAN-THR : angle 0.57065 ( 2) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7938 Ramachandran restraints generated. 3969 Oldfield, 0 Emsley, 3969 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7938 Ramachandran restraints generated. 3969 Oldfield, 0 Emsley, 3969 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 494 residues out of total 3475 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 99 poor density : 395 time to evaluate : 1.446 Fit side-chains revert: symmetry clash REVERT: A 125 LEU cc_start: 0.7234 (OUTLIER) cc_final: 0.5901 (pp) REVERT: A 144 GLU cc_start: 0.8435 (OUTLIER) cc_final: 0.8136 (mt-10) REVERT: A 188 GLU cc_start: 0.8026 (OUTLIER) cc_final: 0.6487 (tm-30) REVERT: A 190 ASN cc_start: 0.8615 (m-40) cc_final: 0.8161 (m-40) REVERT: A 221 GLU cc_start: 0.8596 (OUTLIER) cc_final: 0.8339 (mt-10) REVERT: A 344 ILE cc_start: 0.8259 (OUTLIER) cc_final: 0.7489 (mp) REVERT: A 407 ILE cc_start: 0.8220 (OUTLIER) cc_final: 0.7754 (mp) REVERT: A 554 ASN cc_start: 0.7979 (OUTLIER) cc_final: 0.7763 (m110) REVERT: A 884 ILE cc_start: 0.6922 (OUTLIER) cc_final: 0.6242 (tp) REVERT: A 1189 GLU cc_start: 0.8178 (OUTLIER) cc_final: 0.7109 (pp20) REVERT: A 1580 TRP cc_start: 0.6765 (OUTLIER) cc_final: 0.3479 (p-90) REVERT: A 1680 GLU cc_start: 0.8814 (OUTLIER) cc_final: 0.7538 (tm-30) REVERT: A 1745 ARG cc_start: 0.8680 (OUTLIER) cc_final: 0.7900 (ptp-110) REVERT: A 1949 GLN cc_start: 0.7453 (OUTLIER) cc_final: 0.7104 (tp40) REVERT: A 2053 GLU cc_start: 0.7936 (OUTLIER) cc_final: 0.6964 (tm-30) REVERT: A 2188 MET cc_start: 0.6269 (mmp) cc_final: 0.5934 (mmp) REVERT: A 2326 ASP cc_start: 0.7704 (m-30) cc_final: 0.7195 (m-30) REVERT: B 93 LEU cc_start: 0.7184 (OUTLIER) cc_final: 0.6621 (tm) REVERT: F 171 GLU cc_start: 0.5853 (OUTLIER) cc_final: 0.5542 (pp20) REVERT: F 183 ASP cc_start: 0.8145 (m-30) cc_final: 0.7589 (m-30) REVERT: I 284 LYS cc_start: 0.9087 (mmtt) cc_final: 0.8732 (mtpt) REVERT: I 564 GLN cc_start: 0.7679 (mm110) cc_final: 0.7207 (tp-100) REVERT: I 651 ARG cc_start: 0.7342 (mmm160) cc_final: 0.7010 (mtp-110) REVERT: I 654 GLN cc_start: 0.8511 (OUTLIER) cc_final: 0.7984 (pt0) REVERT: I 674 TRP cc_start: 0.8503 (m-90) cc_final: 0.8029 (m-90) REVERT: I 733 ASN cc_start: 0.8692 (m-40) cc_final: 0.8291 (m110) outliers start: 99 outliers final: 65 residues processed: 462 average time/residue: 0.7702 time to fit residues: 423.0442 Evaluate side-chains 468 residues out of total 3475 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 386 time to evaluate : 1.418 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 GLU Chi-restraints excluded: chain A residue 75 VAL Chi-restraints excluded: chain A residue 121 ILE Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 144 GLU Chi-restraints excluded: chain A residue 188 GLU Chi-restraints excluded: chain A residue 199 PHE Chi-restraints excluded: chain A residue 221 GLU Chi-restraints excluded: chain A residue 277 GLN Chi-restraints excluded: chain A residue 344 ILE Chi-restraints excluded: chain A residue 365 VAL Chi-restraints excluded: chain A residue 407 ILE Chi-restraints excluded: chain A residue 416 ASN Chi-restraints excluded: chain A residue 486 THR Chi-restraints excluded: chain A residue 554 ASN Chi-restraints excluded: chain A residue 816 LEU Chi-restraints excluded: chain A residue 827 VAL Chi-restraints excluded: chain A residue 884 ILE Chi-restraints excluded: chain A residue 931 SER Chi-restraints excluded: chain A residue 1028 LYS Chi-restraints excluded: chain A residue 1189 GLU Chi-restraints excluded: chain A residue 1290 VAL Chi-restraints excluded: chain A residue 1580 TRP Chi-restraints excluded: chain A residue 1680 GLU Chi-restraints excluded: chain A residue 1722 PHE Chi-restraints excluded: chain A residue 1736 LEU Chi-restraints excluded: chain A residue 1745 ARG Chi-restraints excluded: chain A residue 1809 ASP Chi-restraints excluded: chain A residue 1857 THR Chi-restraints excluded: chain A residue 1949 GLN Chi-restraints excluded: chain A residue 1977 LEU Chi-restraints excluded: chain A residue 2008 THR Chi-restraints excluded: chain A residue 2018 THR Chi-restraints excluded: chain A residue 2028 LYS Chi-restraints excluded: chain A residue 2053 GLU Chi-restraints excluded: chain A residue 2066 SER Chi-restraints excluded: chain A residue 2071 MET Chi-restraints excluded: chain A residue 2083 GLN Chi-restraints excluded: chain A residue 2136 ASN Chi-restraints excluded: chain A residue 2141 ILE Chi-restraints excluded: chain A residue 2198 LYS Chi-restraints excluded: chain A residue 2272 ASP Chi-restraints excluded: chain A residue 2357 LEU Chi-restraints excluded: chain A residue 2360 ASP Chi-restraints excluded: chain A residue 2382 ILE Chi-restraints excluded: chain A residue 2396 THR Chi-restraints excluded: chain B residue 93 LEU Chi-restraints excluded: chain B residue 173 VAL Chi-restraints excluded: chain F residue 21 ASP Chi-restraints excluded: chain F residue 101 ASN Chi-restraints excluded: chain F residue 130 THR Chi-restraints excluded: chain F residue 171 GLU Chi-restraints excluded: chain F residue 241 PHE Chi-restraints excluded: chain F residue 254 THR Chi-restraints excluded: chain F residue 392 THR Chi-restraints excluded: chain D residue 1047 ASP Chi-restraints excluded: chain D residue 1058 VAL Chi-restraints excluded: chain G residue 40 SER Chi-restraints excluded: chain G residue 96 GLN Chi-restraints excluded: chain G residue 113 ASN Chi-restraints excluded: chain G residue 114 LEU Chi-restraints excluded: chain G residue 140 LYS Chi-restraints excluded: chain C residue 30 ILE Chi-restraints excluded: chain C residue 43 LYS Chi-restraints excluded: chain C residue 69 SER Chi-restraints excluded: chain C residue 70 LEU Chi-restraints excluded: chain C residue 76 THR Chi-restraints excluded: chain C residue 81 LEU Chi-restraints excluded: chain C residue 154 MET Chi-restraints excluded: chain C residue 173 ARG Chi-restraints excluded: chain E residue 101 LEU Chi-restraints excluded: chain I residue 67 LYS Chi-restraints excluded: chain I residue 188 LEU Chi-restraints excluded: chain I residue 298 VAL Chi-restraints excluded: chain I residue 340 LYS Chi-restraints excluded: chain I residue 371 SER Chi-restraints excluded: chain I residue 382 GLU Chi-restraints excluded: chain I residue 568 THR Chi-restraints excluded: chain I residue 616 LEU Chi-restraints excluded: chain I residue 639 ILE Chi-restraints excluded: chain I residue 654 GLN Chi-restraints excluded: chain I residue 666 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 395 random chunks: chunk 166 optimal weight: 6.9990 chunk 215 optimal weight: 0.8980 chunk 132 optimal weight: 0.7980 chunk 67 optimal weight: 5.9990 chunk 265 optimal weight: 5.9990 chunk 260 optimal weight: 0.8980 chunk 323 optimal weight: 6.9990 chunk 302 optimal weight: 1.9990 chunk 138 optimal weight: 2.9990 chunk 279 optimal weight: 0.0000 chunk 131 optimal weight: 0.8980 overall best weight: 0.6984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 437 ASN A 613 GLN A 727 GLN A1247 ASN A1528 ASN A1792 ASN A2244 ASN A2350 GLN A2400 ASN B 31 ASN B 143 GLN F 385 ASN D1074 ASN D1075 ASN D1105 ASN G 58 GLN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4019 r_free = 0.4019 target = 0.157078 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3632 r_free = 0.3632 target = 0.120525 restraints weight = 66995.156| |-----------------------------------------------------------------------------| r_work (start): 0.3553 rms_B_bonded: 2.60 r_work: 0.3408 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.3306 rms_B_bonded: 4.60 restraints_weight: 0.2500 r_work (final): 0.3306 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3296 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3296 r_free = 0.3296 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3296 r_free = 0.3296 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3296 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8161 moved from start: 0.1050 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 32838 Z= 0.121 Angle : 0.522 8.153 44410 Z= 0.280 Chirality : 0.043 0.175 4821 Planarity : 0.003 0.044 5825 Dihedral : 6.215 82.322 4656 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 5.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.61 % Favored : 95.39 % Rotamer: Outliers : 2.71 % Allowed : 23.65 % Favored : 73.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.00 % Cis-general : 0.03 % 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: 0.71 (0.14), residues: 3969 helix: 1.96 (0.15), residues: 1172 sheet: 0.54 (0.16), residues: 1120 loop : -0.61 (0.15), residues: 1677 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG E 169 TYR 0.016 0.001 TYR I 294 PHE 0.022 0.001 PHE I 28 TRP 0.017 0.001 TRP A1580 HIS 0.004 0.001 HIS I 271 Details of bonding type rmsd covalent geometry : bond 0.00271 (32833) covalent geometry : angle 0.52153 (44400) hydrogen bonds : bond 0.03283 ( 1391) hydrogen bonds : angle 4.40239 ( 3906) link_MAN-SER : bond 0.00098 ( 4) link_MAN-SER : angle 0.59150 ( 8) link_MAN-THR : bond 0.00058 ( 1) link_MAN-THR : angle 0.58259 ( 2) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 64538.42 seconds wall clock time: 1085 minutes 47.79 seconds (65147.79 seconds total)