Starting phenix.real_space_refine on Mon Sep 14 04:26:32 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6gfw_4397/09_2026/6gfw_4397_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/6gfw_4397/09_2026/6gfw_4397.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/6gfw_4397/09_2026/6gfw_4397_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6gfw_4397/09_2026/6gfw_4397_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6gfw_4397/09_2026/6gfw_4397.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6gfw_4397/09_2026/6gfw_4397.map" } resolution = 3.7 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= 0.001 sd= 0.008 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 103 5.49 5 S 93 5.16 5 C 17192 2.51 5 N 4997 2.21 5 O 5620 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 66 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 28005 Number of models: 1 Model: "" Number of chains: 11 Chain: "A" Number of atoms: 1763 Number of conformers: 1 Conformer: "" Number of residues, atoms: 233, 1763 Classifications: {'peptide': 233} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PTRANS': 9, 'TRANS': 223} Unresolved non-hydrogen bonds: 46 Unresolved non-hydrogen angles: 57 Unresolved non-hydrogen dihedrals: 37 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 4, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 32 Chain: "B" Number of atoms: 1735 Number of conformers: 1 Conformer: "" Number of residues, atoms: 235, 1735 Classifications: {'peptide': 235} Incomplete info: {'truncation_to_alanine': 20} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 225} Unresolved non-hydrogen bonds: 93 Unresolved non-hydrogen angles: 115 Unresolved non-hydrogen dihedrals: 78 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 6, 'HIS:plan': 2, 'TYR:plan': 1, 'ASP:plan': 3, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 75 Chain: "C" Number of atoms: 9998 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1341, 9998 Classifications: {'peptide': 1341} Incomplete info: {'truncation_to_alanine': 135} Link IDs: {'PCIS': 1, 'PTRANS': 55, 'TRANS': 1284} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 596 Unresolved non-hydrogen angles: 728 Unresolved non-hydrogen dihedrals: 511 Unresolved non-hydrogen chiralities: 15 Planarities with less than four sites: {'TYR:plan': 7, 'GLN:plan1': 7, 'GLU:plan': 25, 'ARG:plan': 20, 'HIS:plan': 3, 'ASN:plan1': 4, 'ASP:plan': 16, 'PHE:plan': 6, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 397 Chain: "D" Number of atoms: 9722 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1345, 9722 Classifications: {'peptide': 1345} Incomplete info: {'truncation_to_alanine': 186} Link IDs: {'PCIS': 1, 'PTRANS': 52, 'TRANS': 1291} Chain breaks: 4 Unresolved non-hydrogen bonds: 766 Unresolved non-hydrogen angles: 934 Unresolved non-hydrogen dihedrals: 652 Unresolved non-hydrogen chiralities: 25 Planarities with less than four sites: {'GLN:plan1': 14, 'ARG:plan': 22, 'ASP:plan': 20, 'GLU:plan': 32, 'PHE:plan': 12, 'TYR:plan': 4, 'ASN:plan1': 5, 'HIS:plan': 2, 'TRP:plan': 2} Unresolved non-hydrogen planarities: 497 Chain: "E" Number of atoms: 546 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 546 Classifications: {'peptide': 74} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PTRANS': 2, 'TRANS': 71} Unresolved non-hydrogen bonds: 45 Unresolved non-hydrogen angles: 55 Unresolved non-hydrogen dihedrals: 35 Planarities with less than four sites: {'ARG:plan': 1, 'ASP:plan': 1, 'GLU:plan': 4, 'GLN:plan1': 4} Unresolved non-hydrogen planarities: 40 Chain: "F" Number of atoms: 1027 Number of conformers: 1 Conformer: "" Number of residues, atoms: 50, 1027 Classifications: {'DNA': 50} Link IDs: {'rna3p': 49} Chain: "G" Number of atoms: 1026 Number of conformers: 1 Conformer: "" Number of residues, atoms: 50, 1026 Classifications: {'DNA': 50} Link IDs: {'rna3p': 49} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen planarities: 1 Chain: "M" Number of atoms: 973 Number of conformers: 1 Conformer: "" Number of residues, atoms: 154, 973 Classifications: {'peptide': 154} Incomplete info: {'truncation_to_alanine': 67} Link IDs: {'PTRANS': 4, 'TRANS': 149} Unresolved non-hydrogen bonds: 276 Unresolved non-hydrogen angles: 350 Unresolved non-hydrogen dihedrals: 228 Unresolved non-hydrogen chiralities: 14 Planarities with less than four sites: {'TYR:plan': 3, 'GLN:plan1': 5, 'ASP:plan': 11, 'GLU:plan': 12, 'ARG:plan': 6, 'PHE:plan': 3, 'TRP:plan': 1, 'HIS:plan': 2, 'ASN:plan1': 2} Unresolved non-hydrogen planarities: 195 Chain: "M" Number of atoms: 748 Number of conformers: 1 Conformer: "" Number of residues, atoms: 137, 748 Classifications: {'peptide': 137} Incomplete info: {'truncation_to_alanine': 99} Link IDs: {'PTRANS': 3, 'TRANS': 133} Chain breaks: 1 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 322 Unresolved non-hydrogen angles: 420 Unresolved non-hydrogen dihedrals: 244 Unresolved non-hydrogen chiralities: 15 Planarities with less than four sites: {'UNK:plan-1': 33, 'ARG:plan': 8, 'ASN:plan1': 4, 'GLN:plan1': 9, 'TYR:plan': 2, 'ASP:plan': 4, 'PHE:plan': 3, 'GLU:plan': 7, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 202 Chain: "M" Number of atoms: 381 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 381 Classifications: {'peptide': 75} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 61} Link IDs: {'CIS': 1, 'PTRANS': 4, 'TRANS': 69} Chain breaks: 1 Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 180 Unresolved non-hydrogen angles: 230 Unresolved non-hydrogen dihedrals: 136 Unresolved non-hydrogen chiralities: 15 Planarities with less than four sites: {'UNK:plan-1': 16, 'ARG:plan': 5, 'GLU:plan': 3, 'ASN:plan1': 2, 'ASP:plan': 1, 'GLN:plan1': 2, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 77 Chain: "R" Number of atoms: 86 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 86 Classifications: {'RNA': 4} Modifications used: {'5*END': 1, 'rna3p_pur': 3, 'rna3p_pyr': 1} Link IDs: {'rna3p': 3} Residues with excluded nonbonded symmetry interactions: 4 residue: pdb=" N GLY M 166 " occ=0.20 ... (2 atoms not shown) pdb=" O GLY M 166 " occ=0.20 residue: pdb=" N ASP M 168 " occ=0.20 ... (3 atoms not shown) pdb=" CB ASP M 168 " occ=0.20 residue: pdb=" N GLU M 169 " occ=0.20 ... (3 atoms not shown) pdb=" CB GLU M 169 " occ=0.20 residue: pdb=" N GLY M 171 " occ=0.20 ... (2 atoms not shown) pdb=" O GLY M 171 " occ=0.20 Time building chain proxies: 5.53, per 1000 atoms: 0.20 Number of scatterers: 28005 At special positions: 0 Unit cell: (138.24, 171.72, 165.24, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 93 16.00 P 103 15.00 O 5620 8.00 N 4997 7.00 C 17192 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.32 Conformation dependent library (CDL) restraints added in 1.1 seconds 7042 Ramachandran restraints generated. 3521 Oldfield, 0 Emsley, 3521 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6674 Finding SS restraints... Warning! O2 atom is missing from residue DC G 5 Was trying to link: DC G 5 O2 with DG F -5 N2, Saenger class: 19 Warning! O2 atom is missing from residue DC G 5 Was trying to link: DC G 5 O2 with DG F -5 N1, Saenger class: 22 Warning! O2 atom is missing from residue DC G 5 Was trying to link: DC G 5 O2 with DG F -5 N2, Saenger class: 19 Warning! O2 atom is missing from residue DC G 5 Was trying to link: DC G 5 O2 with DG F -5 N1, Saenger class: 22 Warning! O2 atom is missing from residue DC G 5 Was trying to link: DC G 5 O2 with DG F -5 N2, Saenger class: 19 Warning! O2 atom is missing from residue DC G 5 Was trying to link: DC G 5 O2 with DG F -5 N1, Saenger class: 22 Secondary structure from input PDB file: 119 helices and 40 sheets defined 38.1% alpha, 11.6% beta 30 base pairs and 79 stacking pairs defined. Time for finding SS restraints: 3.26 Creating SS restraints... Processing helix chain 'A' and resid 34 through 50 removed outlier: 4.258A pdb=" N THR A 38 " --> pdb=" O GLY A 34 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N SER A 50 " --> pdb=" O ILE A 46 " (cutoff:3.500A) Processing helix chain 'A' and resid 77 through 87 removed outlier: 3.889A pdb=" N GLY A 87 " --> pdb=" O LEU A 83 " (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 154 through 158 removed outlier: 3.886A pdb=" N ARG A 158 " --> pdb=" O ALA A 155 " (cutoff:3.500A) Processing helix chain 'A' and resid 160 through 164 removed outlier: 3.845A pdb=" N ASP A 164 " --> pdb=" O SER A 161 " (cutoff:3.500A) Processing helix chain 'A' and resid 212 through 227 Processing helix chain 'A' and resid 228 through 231 Processing helix chain 'B' and resid 34 through 50 removed outlier: 3.985A pdb=" N THR B 38 " --> pdb=" O GLY B 34 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N SER B 50 " --> pdb=" O ILE B 46 " (cutoff:3.500A) Processing helix chain 'B' and resid 77 through 85 Processing helix chain 'B' and resid 111 through 115 removed outlier: 3.904A pdb=" N ASP B 114 " --> pdb=" O THR B 111 " (cutoff:3.500A) Processing helix chain 'B' and resid 166 through 171 Processing helix chain 'B' and resid 212 through 228 removed outlier: 4.037A pdb=" N LEU B 228 " --> pdb=" O LEU B 224 " (cutoff:3.500A) Processing helix chain 'B' and resid 230 through 235 removed outlier: 4.648A pdb=" N LEU B 234 " --> pdb=" O ALA B 230 " (cutoff:3.500A) removed outlier: 4.497A pdb=" N ARG B 235 " --> pdb=" O PHE B 231 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 230 through 235' Processing helix chain 'C' and resid 28 through 39 Processing helix chain 'C' and resid 48 through 57 removed outlier: 3.595A pdb=" N ALA C 52 " --> pdb=" O GLY C 48 " (cutoff:3.500A) Processing helix chain 'C' and resid 81 through 88 Processing helix chain 'C' and resid 206 through 212 removed outlier: 3.955A pdb=" N ALA C 212 " --> pdb=" O ILE C 208 " (cutoff:3.500A) Processing helix chain 'C' and resid 216 through 225 Processing helix chain 'C' and resid 270 through 280 removed outlier: 3.572A pdb=" N ILE C 274 " --> pdb=" O THR C 270 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N ASP C 280 " --> pdb=" O GLN C 276 " (cutoff:3.500A) Processing helix chain 'C' and resid 320 through 329 removed outlier: 4.165A pdb=" N LYS C 324 " --> pdb=" O ASP C 320 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N GLY C 329 " --> pdb=" O LEU C 325 " (cutoff:3.500A) Processing helix chain 'C' and resid 347 through 354 removed outlier: 3.761A pdb=" N ASP C 354 " --> pdb=" O THR C 350 " (cutoff:3.500A) Processing helix chain 'C' and resid 358 through 371 Processing helix chain 'C' and resid 378 through 389 removed outlier: 4.090A pdb=" N GLU C 382 " --> pdb=" O ARG C 378 " (cutoff:3.500A) Processing helix chain 'C' and resid 397 through 409 Processing helix chain 'C' and resid 421 through 437 removed outlier: 4.155A pdb=" N ILE C 425 " --> pdb=" O SER C 421 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N ILE C 426 " --> pdb=" O LYS C 422 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N ARG C 436 " --> pdb=" O LEU C 432 " (cutoff:3.500A) Processing helix chain 'C' and resid 447 through 449 No H-bonds generated for 'chain 'C' and resid 447 through 449' Processing helix chain 'C' and resid 455 through 479 removed outlier: 3.792A pdb=" N ALA C 474 " --> pdb=" O ARG C 470 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N LYS C 476 " --> pdb=" O GLU C 472 " (cutoff:3.500A) removed outlier: 4.200A pdb=" N GLU C 477 " --> pdb=" O ARG C 473 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N ARG C 478 " --> pdb=" O ALA C 474 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N LEU C 479 " --> pdb=" O VAL C 475 " (cutoff:3.500A) Processing helix chain 'C' and resid 495 through 508 Processing helix chain 'C' and resid 519 through 528 removed outlier: 3.739A pdb=" N GLU C 523 " --> pdb=" O ASN C 519 " (cutoff:3.500A) Processing helix chain 'C' and resid 551 through 555 removed outlier: 3.602A pdb=" N TYR C 555 " --> pdb=" O PRO C 552 " (cutoff:3.500A) Processing helix chain 'C' and resid 607 through 614 removed outlier: 3.868A pdb=" N ASN C 613 " --> pdb=" O ILE C 609 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N TYR C 614 " --> pdb=" O GLU C 610 " (cutoff:3.500A) Processing helix chain 'C' and resid 656 through 661 removed outlier: 4.087A pdb=" N GLN C 659 " --> pdb=" O SER C 656 " (cutoff:3.500A) removed outlier: 4.266A pdb=" N VAL C 660 " --> pdb=" O THR C 657 " (cutoff:3.500A) Processing helix chain 'C' and resid 664 through 668 removed outlier: 3.707A pdb=" N LEU C 667 " --> pdb=" O GLY C 664 " (cutoff:3.500A) Processing helix chain 'C' and resid 670 through 674 Processing helix chain 'C' and resid 675 through 686 Processing helix chain 'C' and resid 687 through 689 No H-bonds generated for 'chain 'C' and resid 687 through 689' Processing helix chain 'C' and resid 704 through 712 Processing helix chain 'C' and resid 820 through 825 Processing helix chain 'C' and resid 858 through 863 removed outlier: 3.506A pdb=" N LEU C 862 " --> pdb=" O GLY C 858 " (cutoff:3.500A) Processing helix chain 'C' and resid 896 through 906 removed outlier: 3.924A pdb=" N LYS C 900 " --> pdb=" O THR C 896 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N ILE C 905 " --> pdb=" O LEU C 901 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N PHE C 906 " --> pdb=" O LEU C 902 " (cutoff:3.500A) Processing helix chain 'C' and resid 944 through 982 removed outlier: 3.752A pdb=" N ILE C 948 " --> pdb=" O ARG C 944 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N GLU C 949 " --> pdb=" O ALA C 945 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N GLU C 962 " --> pdb=" O LYS C 958 " (cutoff:3.500A) removed outlier: 4.715A pdb=" N GLU C 963 " --> pdb=" O ASP C 959 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N LEU C 964 " --> pdb=" O LEU C 960 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N GLY C 982 " --> pdb=" O VAL C 978 " (cutoff:3.500A) Processing helix chain 'C' and resid 986 through 992 removed outlier: 3.572A pdb=" N ASP C 990 " --> pdb=" O ALA C 986 " (cutoff:3.500A) Processing helix chain 'C' and resid 992 through 1000 removed outlier: 3.612A pdb=" N ARG C 996 " --> pdb=" O LEU C 992 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N TRP C 997 " --> pdb=" O PRO C 993 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N LEU C 998 " --> pdb=" O ARG C 994 " (cutoff:3.500A) removed outlier: 4.040A pdb=" N LEU C1000 " --> pdb=" O ARG C 996 " (cutoff:3.500A) Processing helix chain 'C' and resid 1003 through 1009 Processing helix chain 'C' and resid 1009 through 1037 removed outlier: 3.589A pdb=" N THR C1037 " --> pdb=" O ARG C1033 " (cutoff:3.500A) Processing helix chain 'C' and resid 1081 through 1085 Processing helix chain 'C' and resid 1101 through 1107 removed outlier: 4.336A pdb=" N SER C1105 " --> pdb=" O LEU C1101 " (cutoff:3.500A) Processing helix chain 'C' and resid 1109 through 1134 removed outlier: 3.995A pdb=" N ILE C1124 " --> pdb=" O ALA C1120 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N GLY C1125 " --> pdb=" O ALA C1121 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N GLN C1134 " --> pdb=" O ALA C1130 " (cutoff:3.500A) Processing helix chain 'C' and resid 1137 through 1150 Processing helix chain 'C' and resid 1168 through 1177 Processing helix chain 'C' and resid 1191 through 1201 Processing helix chain 'C' and resid 1271 through 1282 removed outlier: 3.580A pdb=" N VAL C1275 " --> pdb=" O GLY C1271 " (cutoff:3.500A) Processing helix chain 'C' and resid 1283 through 1292 removed outlier: 4.003A pdb=" N LEU C1287 " --> pdb=" O ALA C1283 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N MET C1290 " --> pdb=" O THR C1286 " (cutoff:3.500A) Processing helix chain 'C' and resid 1297 through 1310 removed outlier: 3.558A pdb=" N ARG C1301 " --> pdb=" O ASP C1297 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N THR C1302 " --> pdb=" O VAL C1298 " (cutoff:3.500A) Processing helix chain 'C' and resid 1320 through 1333 removed outlier: 3.895A pdb=" N ASN C1324 " --> pdb=" O PRO C1320 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N LEU C1333 " --> pdb=" O GLU C1329 " (cutoff:3.500A) Processing helix chain 'D' and resid 26 through 34 Processing helix chain 'D' and resid 70 through 74 removed outlier: 3.681A pdb=" N GLY D 73 " --> pdb=" O CYS D 70 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N LYS D 74 " --> pdb=" O LEU D 71 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 70 through 74' Processing helix chain 'D' and resid 95 through 99 removed outlier: 3.773A pdb=" N ARG D 98 " --> pdb=" O THR D 95 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N ARG D 99 " --> pdb=" O LYS D 96 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 95 through 99' Processing helix chain 'D' and resid 131 through 139 Processing helix chain 'D' and resid 161 through 172 Processing helix chain 'D' and resid 182 through 191 removed outlier: 4.247A pdb=" N GLN D 186 " --> pdb=" O ALA D 182 " (cutoff:3.500A) Processing helix chain 'D' and resid 193 through 208 removed outlier: 3.570A pdb=" N GLU D 197 " --> pdb=" O ASP D 193 " (cutoff:3.500A) Processing helix chain 'D' and resid 212 through 231 removed outlier: 3.816A pdb=" N LYS D 216 " --> pdb=" O THR D 212 " (cutoff:3.500A) Processing helix chain 'D' and resid 233 through 238 removed outlier: 3.765A pdb=" N ILE D 238 " --> pdb=" O GLU D 235 " (cutoff:3.500A) Processing helix chain 'D' and resid 265 through 284 removed outlier: 4.183A pdb=" N TYR D 269 " --> pdb=" O LEU D 265 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N ARG D 270 " --> pdb=" O ASN D 266 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N ASP D 284 " --> pdb=" O LYS D 280 " (cutoff:3.500A) Processing helix chain 'D' and resid 288 through 308 removed outlier: 3.667A pdb=" N VAL D 292 " --> pdb=" O PRO D 288 " (cutoff:3.500A) Processing helix chain 'D' and resid 377 through 388 Processing helix chain 'D' and resid 393 through 403 Processing helix chain 'D' and resid 405 through 417 removed outlier: 3.625A pdb=" N TRP D 409 " --> pdb=" O GLU D 405 " (cutoff:3.500A) Processing helix chain 'D' and resid 430 through 432 No H-bonds generated for 'chain 'D' and resid 430 through 432' Processing helix chain 'D' and resid 450 through 458 removed outlier: 4.063A pdb=" N ALA D 455 " --> pdb=" O PRO D 451 " (cutoff:3.500A) removed outlier: 4.547A pdb=" N ALA D 456 " --> pdb=" O LEU D 452 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N TYR D 457 " --> pdb=" O VAL D 453 " (cutoff:3.500A) Processing helix chain 'D' and resid 474 through 482 Processing helix chain 'D' and resid 504 through 514 removed outlier: 3.583A pdb=" N LEU D 508 " --> pdb=" O GLN D 504 " (cutoff:3.500A) Processing helix chain 'D' and resid 573 through 580 Processing helix chain 'D' and resid 588 through 592 removed outlier: 3.699A pdb=" N ILE D 591 " --> pdb=" O PRO D 588 " (cutoff:3.500A) Processing helix chain 'D' and resid 598 through 613 Processing helix chain 'D' and resid 613 through 636 removed outlier: 3.834A pdb=" N THR D 617 " --> pdb=" O GLY D 613 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N GLY D 636 " --> pdb=" O ALA D 632 " (cutoff:3.500A) Processing helix chain 'D' and resid 649 through 670 removed outlier: 3.537A pdb=" N SER D 670 " --> pdb=" O GLU D 666 " (cutoff:3.500A) Processing helix chain 'D' and resid 674 through 704 removed outlier: 3.994A pdb=" N ILE D 683 " --> pdb=" O TYR D 679 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N ASP D 684 " --> pdb=" O ASN D 680 " (cutoff:3.500A) removed outlier: 4.383A pdb=" N THR D 703 " --> pdb=" O ASP D 699 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N GLU D 704 " --> pdb=" O ASN D 700 " (cutoff:3.500A) Processing helix chain 'D' and resid 720 through 729 Processing helix chain 'D' and resid 733 through 741 Processing helix chain 'D' and resid 768 through 787 removed outlier: 4.348A pdb=" N HIS D 777 " --> pdb=" O PHE D 773 " (cutoff:3.500A) removed outlier: 4.193A pdb=" N GLY D 778 " --> pdb=" O ILE D 774 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N LEU D 783 " --> pdb=" O ALA D 779 " (cutoff:3.500A) Processing helix chain 'D' and resid 788 through 804 removed outlier: 4.115A pdb=" N ASN D 792 " --> pdb=" O LEU D 788 " (cutoff:3.500A) Processing helix chain 'D' and resid 805 through 807 No H-bonds generated for 'chain 'D' and resid 805 through 807' Processing helix chain 'D' and resid 834 through 840 removed outlier: 4.164A pdb=" N ARG D 838 " --> pdb=" O PRO D 834 " (cutoff:3.500A) Processing helix chain 'D' and resid 865 through 874 Processing helix chain 'D' and resid 914 through 916 No H-bonds generated for 'chain 'D' and resid 914 through 916' Processing helix chain 'D' and resid 917 through 925 removed outlier: 5.465A pdb=" N ILE D 923 " --> pdb=" O ALA D 919 " (cutoff:3.500A) Processing helix chain 'D' and resid 1140 through 1146 Processing helix chain 'D' and resid 1216 through 1224 Processing helix chain 'D' and resid 1225 through 1242 removed outlier: 3.546A pdb=" N VAL D1229 " --> pdb=" O GLY D1225 " (cutoff:3.500A) Processing helix chain 'D' and resid 1249 through 1261 removed outlier: 4.383A pdb=" N ILE D1253 " --> pdb=" O ASN D1249 " (cutoff:3.500A) Processing helix chain 'D' and resid 1279 through 1293 Processing helix chain 'D' and resid 1312 through 1316 removed outlier: 3.552A pdb=" N THR D1316 " --> pdb=" O SER D1313 " (cutoff:3.500A) Processing helix chain 'D' and resid 1327 through 1339 removed outlier: 4.104A pdb=" N VAL D1331 " --> pdb=" O GLU D1327 " (cutoff:3.500A) Processing helix chain 'D' and resid 1346 through 1354 Processing helix chain 'D' and resid 1360 through 1374 removed outlier: 3.807A pdb=" N ALA D1364 " --> pdb=" O GLY D1360 " (cutoff:3.500A) removed outlier: 4.175A pdb=" N TYR D1365 " --> pdb=" O THR D1361 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N ARG D1372 " --> pdb=" O ASP D1368 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N ALA D1374 " --> pdb=" O MET D1370 " (cutoff:3.500A) Processing helix chain 'E' and resid 6 through 13 removed outlier: 4.136A pdb=" N ILE E 13 " --> pdb=" O ALA E 9 " (cutoff:3.500A) Processing helix chain 'E' and resid 17 through 33 removed outlier: 4.229A pdb=" N LEU E 21 " --> pdb=" O PHE E 17 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N GLY E 33 " --> pdb=" O GLN E 29 " (cutoff:3.500A) Processing helix chain 'E' and resid 45 through 57 removed outlier: 3.527A pdb=" N ILE E 49 " --> pdb=" O LYS E 45 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N GLY E 57 " --> pdb=" O GLU E 53 " (cutoff:3.500A) Processing helix chain 'E' and resid 60 through 75 Processing helix chain 'M' and resid 123 through 130 removed outlier: 3.691A pdb=" N LEU M 130 " --> pdb=" O TRP M 126 " (cutoff:3.500A) Processing helix chain 'M' and resid 135 through 147 removed outlier: 4.285A pdb=" N ALA M 139 " --> pdb=" O ASP M 135 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N ALA M 147 " --> pdb=" O SER M 143 " (cutoff:3.500A) Processing helix chain 'M' and resid 157 through 166 removed outlier: 4.335A pdb=" N GLY M 166 " --> pdb=" O VAL M 162 " (cutoff:3.500A) Processing helix chain 'M' and resid 171 through 186 removed outlier: 3.963A pdb=" N VAL M 175 " --> pdb=" O GLY M 171 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N ARG M 184 " --> pdb=" O LYS M 180 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N PHE M 185 " --> pdb=" O ARG M 181 " (cutoff:3.500A) Processing helix chain 'M' and resid 195 through 203 removed outlier: 4.530A pdb=" N LEU M 199 " --> pdb=" O LEU M 195 " (cutoff:3.500A) Processing helix chain 'M' and resid 213 through 223 removed outlier: 4.261A pdb=" N ILE M 219 " --> pdb=" O GLU M 215 " (cutoff:3.500A) Processing helix chain 'M' and resid 224 through 231 removed outlier: 4.352A pdb=" N HIS M 230 " --> pdb=" O LEU M 226 " (cutoff:3.500A) removed outlier: 4.561A pdb=" N ASP M 231 " --> pdb=" O LEU M 227 " (cutoff:3.500A) Processing helix chain 'M' and resid 234 through 239 Processing helix chain 'M' and resid 242 through 245 Processing helix chain 'M' and resid 246 through 255 removed outlier: 3.809A pdb=" N SER M 255 " --> pdb=" O ASN M 251 " (cutoff:3.500A) Processing helix chain 'M' and resid 296 through 310 removed outlier: 3.813A pdb=" N GLY M 307 " --> pdb=" O TYR M 303 " (cutoff:3.500A) removed outlier: 4.205A pdb=" N ALA M 310 " --> pdb=" O MET M 306 " (cutoff:3.500A) Processing helix chain 'M' and resid 321 through 355 removed outlier: 3.651A pdb=" N ALA M 326 " --> pdb=" O ASN M 322 " (cutoff:3.500A) Processing helix chain 'M' and resid 366 through 375 removed outlier: 3.657A pdb=" N ILE M 370 " --> pdb=" O VAL M 366 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N VAL M 374 " --> pdb=" O ILE M 370 " (cutoff:3.500A) Processing helix chain 'M' and resid 377 through 385 removed outlier: 3.609A pdb=" N ILE M 381 " --> pdb=" O HIS M 377 " (cutoff:3.500A) Processing helix chain 'M' and resid 400 through 404 removed outlier: 3.513A pdb=" N UNK M 403 " --> pdb=" O UNK M 400 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N UNK M 404 " --> pdb=" O UNK M 401 " (cutoff:3.500A) No H-bonds generated for 'chain 'M' and resid 400 through 404' Processing helix chain 'M' and resid 417 through 430 removed outlier: 4.125A pdb=" N ALA M 430 " --> pdb=" O LYS M 426 " (cutoff:3.500A) Processing helix chain 'M' and resid 439 through 448 Processing helix chain 'M' and resid 457 through 464 Processing sheet with id=AA1, first strand: chain 'A' and resid 14 through 17 removed outlier: 5.104A pdb=" N ASP A 15 " --> pdb=" O THR A 27 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N THR A 27 " --> pdb=" O ASP A 15 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 99 through 105 removed outlier: 6.587A pdb=" N ARG A 143 " --> pdb=" O VAL A 59 " (cutoff:3.500A) removed outlier: 4.451A pdb=" N VAL A 59 " --> pdb=" O ARG A 143 " (cutoff:3.500A) removed outlier: 6.955A pdb=" N LYS A 145 " --> pdb=" O THR A 57 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 110 through 111 removed outlier: 3.687A pdb=" N VAL A 110 " --> pdb=" O ILE A 130 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 15 through 19 removed outlier: 6.481A pdb=" N ASP B 199 " --> pdb=" O PRO B 30 " (cutoff:3.500A) removed outlier: 5.543A pdb=" N THR B 196 " --> pdb=" O VAL B 192 " (cutoff:3.500A) removed outlier: 6.345A pdb=" N VAL B 192 " --> pdb=" O THR B 196 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N ALA B 190 " --> pdb=" O LEU B 198 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 52 through 61 removed outlier: 4.835A pdb=" N CYS B 54 " --> pdb=" O GLY B 149 " (cutoff:3.500A) removed outlier: 6.577A pdb=" N GLY B 149 " --> pdb=" O CYS B 54 " (cutoff:3.500A) removed outlier: 5.417A pdb=" N VAL B 56 " --> pdb=" O GLN B 147 " (cutoff:3.500A) removed outlier: 6.387A pdb=" N GLN B 147 " --> pdb=" O VAL B 56 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 90 through 92 Processing sheet with id=AA7, first strand: chain 'B' and resid 152 through 153 Processing sheet with id=AA8, first strand: chain 'C' and resid 13 through 14 removed outlier: 5.713A pdb=" N LYS C 13 " --> pdb=" O ALA C1183 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 59 through 60 removed outlier: 3.741A pdb=" N ILE C 59 " --> pdb=" O LEU C 68 " (cutoff:3.500A) removed outlier: 6.946A pdb=" N SER C 66 " --> pdb=" O TYR C 105 " (cutoff:3.500A) removed outlier: 7.228A pdb=" N TYR C 105 " --> pdb=" O SER C 66 " (cutoff:3.500A) removed outlier: 5.539A pdb=" N LEU C 68 " --> pdb=" O VAL C 103 " (cutoff:3.500A) removed outlier: 7.225A pdb=" N VAL C 103 " --> pdb=" O LEU C 68 " (cutoff:3.500A) removed outlier: 5.652A pdb=" N TYR C 70 " --> pdb=" O ARG C 101 " (cutoff:3.500A) removed outlier: 6.882A pdb=" N ARG C 101 " --> pdb=" O TYR C 70 " (cutoff:3.500A) removed outlier: 5.232A pdb=" N SER C 72 " --> pdb=" O LYS C 99 " (cutoff:3.500A) removed outlier: 4.622A pdb=" N LYS C 99 " --> pdb=" O SER C 72 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N ILE C 104 " --> pdb=" O LYS C 115 " (cutoff:3.500A) removed outlier: 4.137A pdb=" N LYS C 115 " --> pdb=" O ILE C 104 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 59 through 60 removed outlier: 3.741A pdb=" N ILE C 59 " --> pdb=" O LEU C 68 " (cutoff:3.500A) removed outlier: 6.946A pdb=" N SER C 66 " --> pdb=" O TYR C 105 " (cutoff:3.500A) removed outlier: 7.228A pdb=" N TYR C 105 " --> pdb=" O SER C 66 " (cutoff:3.500A) removed outlier: 5.539A pdb=" N LEU C 68 " --> pdb=" O VAL C 103 " (cutoff:3.500A) removed outlier: 7.225A pdb=" N VAL C 103 " --> pdb=" O LEU C 68 " (cutoff:3.500A) removed outlier: 5.652A pdb=" N TYR C 70 " --> pdb=" O ARG C 101 " (cutoff:3.500A) removed outlier: 6.882A pdb=" N ARG C 101 " --> pdb=" O TYR C 70 " (cutoff:3.500A) removed outlier: 5.232A pdb=" N SER C 72 " --> pdb=" O LYS C 99 " (cutoff:3.500A) removed outlier: 4.622A pdb=" N LYS C 99 " --> pdb=" O SER C 72 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 144 through 145 removed outlier: 3.649A pdb=" N GLN C 513 " --> pdb=" O VAL C 144 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 451 through 454 removed outlier: 3.737A pdb=" N SER C 531 " --> pdb=" O SER C 147 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 154 through 158 Processing sheet with id=AB5, first strand: chain 'C' and resid 227 through 228 Processing sheet with id=AB6, first strand: chain 'C' and resid 230 through 231 removed outlier: 3.512A pdb=" N GLN C 238 " --> pdb=" O GLU C 231 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N ILE C 285 " --> pdb=" O MET C 239 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 255 through 257 removed outlier: 6.945A pdb=" N ILE C 255 " --> pdb=" O TYR C 262 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 580 through 581 removed outlier: 3.517A pdb=" N GLN C 580 " --> pdb=" O GLU C 588 " (cutoff:3.500A) removed outlier: 5.382A pdb=" N GLU C 602 " --> pdb=" O LYS C 593 " (cutoff:3.500A) removed outlier: 6.577A pdb=" N THR C 595 " --> pdb=" O THR C 600 " (cutoff:3.500A) removed outlier: 5.734A pdb=" N THR C 600 " --> pdb=" O THR C 595 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 580 through 581 removed outlier: 3.517A pdb=" N GLN C 580 " --> pdb=" O GLU C 588 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 616 through 617 Processing sheet with id=AC2, first strand: chain 'C' and resid 716 through 718 removed outlier: 6.649A pdb=" N ALA C 716 " --> pdb=" O LEU C 783 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N ASP C 781 " --> pdb=" O ALA C 718 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N ASP C 785 " --> pdb=" O MET C 768 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N MET C 768 " --> pdb=" O ASP C 785 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 722 through 727 removed outlier: 5.024A pdb=" N VAL C 724 " --> pdb=" O LYS C 735 " (cutoff:3.500A) removed outlier: 5.676A pdb=" N LYS C 735 " --> pdb=" O VAL C 724 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N TYR C 726 " --> pdb=" O VAL C 733 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'C' and resid 757 through 758 removed outlier: 3.807A pdb=" N THR C 757 " --> pdb=" O ILE C 765 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N ILE C 765 " --> pdb=" O THR C 757 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC4 Processing sheet with id=AC5, first strand: chain 'C' and resid 789 through 790 Processing sheet with id=AC6, first strand: chain 'C' and resid 1066 through 1067 removed outlier: 4.857A pdb=" N THR C1226 " --> pdb=" O PHE C 804 " (cutoff:3.500A) removed outlier: 8.171A pdb=" N ILE C1096 " --> pdb=" O ASN C 799 " (cutoff:3.500A) removed outlier: 5.624A pdb=" N ARG C 801 " --> pdb=" O ILE C1096 " (cutoff:3.500A) removed outlier: 7.180A pdb=" N LEU C1098 " --> pdb=" O ARG C 801 " (cutoff:3.500A) removed outlier: 6.165A pdb=" N ALA C 803 " --> pdb=" O LEU C1098 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N VAL C1097 " --> pdb=" O LEU C 817 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N LEU C 817 " --> pdb=" O VAL C1097 " (cutoff:3.500A) removed outlier: 8.267A pdb=" N ILE C 816 " --> pdb=" O SER C1077 " (cutoff:3.500A) removed outlier: 7.104A pdb=" N ILE C1079 " --> pdb=" O ILE C 816 " (cutoff:3.500A) removed outlier: 7.018A pdb=" N VAL C 818 " --> pdb=" O ILE C1079 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'C' and resid 1066 through 1067 removed outlier: 3.715A pdb=" N VAL C1225 " --> pdb=" O ILE C1210 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'C' and resid 829 through 841 removed outlier: 6.830A pdb=" N LYS C1051 " --> pdb=" O VAL C 931 " (cutoff:3.500A) removed outlier: 4.718A pdb=" N VAL C 931 " --> pdb=" O LYS C1051 " (cutoff:3.500A) removed outlier: 6.436A pdb=" N TYR C1053 " --> pdb=" O ILE C 929 " (cutoff:3.500A) removed outlier: 5.653A pdb=" N LYS C1057 " --> pdb=" O SER C 925 " (cutoff:3.500A) removed outlier: 8.580A pdb=" N SER C 925 " --> pdb=" O LYS C1057 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N GLY C 926 " --> pdb=" O VAL C 877 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'C' and resid 865 through 866 Processing sheet with id=AD1, first strand: chain 'C' and resid 888 through 889 removed outlier: 3.980A pdb=" N THR C 888 " --> pdb=" O LYS C 914 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'C' and resid 1335 through 1338 removed outlier: 3.620A pdb=" N LYS D 21 " --> pdb=" O GLU C1338 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'D' and resid 104 through 106 Processing sheet with id=AD4, first strand: chain 'D' and resid 146 through 147 removed outlier: 4.136A pdb=" N ASP D 177 " --> pdb=" O ILE D 147 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'D' and resid 353 through 356 removed outlier: 5.870A pdb=" N CYS D 366 " --> pdb=" O VAL D 440 " (cutoff:3.500A) removed outlier: 6.526A pdb=" N ILE D 442 " --> pdb=" O CYS D 366 " (cutoff:3.500A) removed outlier: 5.503A pdb=" N LEU D 368 " --> pdb=" O ILE D 442 " (cutoff:3.500A) removed outlier: 4.092A pdb=" N SER D 353 " --> pdb=" O MET D 466 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'D' and resid 526 through 528 removed outlier: 4.091A pdb=" N LEU D 527 " --> pdb=" O LYS D 549 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N ARG D 551 " --> pdb=" O LEU D 527 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'D' and resid 820 through 822 removed outlier: 4.285A pdb=" N VAL D 843 " --> pdb=" O ARG D 883 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'D' and resid 959 through 961 Processing sheet with id=AD9, first strand: chain 'D' and resid 966 through 967 removed outlier: 3.554A pdb=" N VAL D 966 " --> pdb=" O VAL D 974 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'D' and resid 1002 through 1003 Processing sheet with id=AE2, first strand: chain 'D' and resid 1059 through 1060 Processing sheet with id=AE3, first strand: chain 'D' and resid 1174 through 1177 removed outlier: 5.210A pdb=" N LEU D1175 " --> pdb=" O ILE D1190 " (cutoff:3.500A) removed outlier: 4.757A pdb=" N ILE D1190 " --> pdb=" O LEU D1175 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'D' and resid 1264 through 1266 974 hydrogen bonds defined for protein. 2778 hydrogen bond angles defined for protein. NA hbond rejected because one of the atoms is absent Restraints generated for nucleic acids: 75 hydrogen bonds 150 hydrogen bond angles 0 basepair planarities 30 basepair parallelities 79 stacking parallelities Total time for adding SS restraints: 7.54 Time building geometry restraints manager: 2.92 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: 9111 1.34 - 1.46: 3770 1.46 - 1.57: 15358 1.57 - 1.69: 199 1.69 - 1.81: 162 Bond restraints: 28600 Sorted by residual: bond pdb=" O3' DG F -5 " pdb=" P DC F -4 " ideal model delta sigma weight residual 1.607 1.469 0.138 1.20e-02 6.94e+03 1.32e+02 bond pdb=" O3' DG G 16 " pdb=" P DC G 17 " ideal model delta sigma weight residual 1.607 1.471 0.136 1.20e-02 6.94e+03 1.29e+02 bond pdb=" C ALA D 426 " pdb=" N PRO D 427 " ideal model delta sigma weight residual 1.334 1.592 -0.258 2.34e-02 1.83e+03 1.21e+02 bond pdb=" O3' DT F 6 " pdb=" P DG F 7 " ideal model delta sigma weight residual 1.607 1.502 0.105 1.20e-02 6.94e+03 7.61e+01 bond pdb=" O3' DC F -2 " pdb=" P DC F -1 " ideal model delta sigma weight residual 1.607 1.689 -0.082 1.20e-02 6.94e+03 4.66e+01 ... (remaining 28595 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.69: 39149 4.69 - 9.38: 166 9.38 - 14.07: 25 14.07 - 18.76: 6 18.76 - 23.45: 3 Bond angle restraints: 39349 Sorted by residual: angle pdb=" O5' DG F -5 " pdb=" C5' DG F -5 " pdb=" C4' DG F -5 " ideal model delta sigma weight residual 109.40 127.85 -18.45 8.00e-01 1.56e+00 5.32e+02 angle pdb=" C5' DG F -5 " pdb=" C4' DG F -5 " pdb=" C3' DG F -5 " ideal model delta sigma weight residual 114.10 93.59 20.51 1.80e+00 3.09e-01 1.30e+02 angle pdb=" C2' DG F -5 " pdb=" C1' DG F -5 " pdb=" N9 DG F -5 " ideal model delta sigma weight residual 114.30 100.95 13.35 1.40e+00 5.10e-01 9.09e+01 angle pdb=" C4' DG F -5 " pdb=" C3' DG F -5 " pdb=" O3' DG F -5 " ideal model delta sigma weight residual 109.70 133.15 -23.45 2.50e+00 1.60e-01 8.80e+01 angle pdb=" O4' DG F -5 " pdb=" C1' DG F -5 " pdb=" N9 DG F -5 " ideal model delta sigma weight residual 108.00 114.13 -6.13 7.00e-01 2.04e+00 7.67e+01 ... (remaining 39344 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.52: 16483 35.52 - 71.05: 611 71.05 - 106.57: 19 106.57 - 142.09: 2 142.09 - 177.62: 7 Dihedral angle restraints: 17122 sinusoidal: 6793 harmonic: 10329 Sorted by residual: dihedral pdb=" CA ALA C1263 " pdb=" C ALA C1263 " pdb=" N GLN C1264 " pdb=" CA GLN C1264 " ideal model delta harmonic sigma weight residual -180.00 -139.47 -40.53 0 5.00e+00 4.00e-02 6.57e+01 dihedral pdb=" CA LEU D1138 " pdb=" C LEU D1138 " pdb=" N PRO D1139 " pdb=" CA PRO D1139 " ideal model delta harmonic sigma weight residual 180.00 142.29 37.71 0 5.00e+00 4.00e-02 5.69e+01 dihedral pdb=" CA LYS D 118 " pdb=" C LYS D 118 " pdb=" N SER D 119 " pdb=" CA SER D 119 " ideal model delta harmonic sigma weight residual 180.00 144.02 35.98 0 5.00e+00 4.00e-02 5.18e+01 ... (remaining 17119 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.171: 4674 0.171 - 0.343: 51 0.343 - 0.514: 3 0.514 - 0.685: 4 0.685 - 0.857: 2 Chirality restraints: 4734 Sorted by residual: chirality pdb=" C3' DG F -5 " pdb=" C4' DG F -5 " pdb=" O3' DG F -5 " pdb=" C2' DG F -5 " both_signs ideal model delta sigma weight residual False -2.73 -1.87 -0.86 2.00e-01 2.50e+01 1.83e+01 chirality pdb=" P DC G 17 " pdb=" OP1 DC G 17 " pdb=" OP2 DC G 17 " pdb=" O5' DC G 17 " both_signs ideal model delta sigma weight residual True 2.34 -1.65 0.69 2.00e-01 2.50e+01 1.18e+01 chirality pdb=" C3' DG F -7 " pdb=" C4' DG F -7 " pdb=" O3' DG F -7 " pdb=" C2' DG F -7 " both_signs ideal model delta sigma weight residual False -2.73 -2.09 -0.64 2.00e-01 2.50e+01 1.03e+01 ... (remaining 4731 not shown) Planarity restraints: 4806 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' DC F 0 " 0.227 2.00e-02 2.50e+03 1.05e-01 2.50e+02 pdb=" N1 DC F 0 " -0.079 2.00e-02 2.50e+03 pdb=" C2 DC F 0 " -0.041 2.00e-02 2.50e+03 pdb=" O2 DC F 0 " -0.103 2.00e-02 2.50e+03 pdb=" N3 DC F 0 " 0.038 2.00e-02 2.50e+03 pdb=" C4 DC F 0 " 0.052 2.00e-02 2.50e+03 pdb=" N4 DC F 0 " 0.088 2.00e-02 2.50e+03 pdb=" C5 DC F 0 " -0.064 2.00e-02 2.50e+03 pdb=" C6 DC F 0 " -0.119 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DC F -4 " -0.132 2.00e-02 2.50e+03 6.44e-02 9.34e+01 pdb=" N1 DC F -4 " 0.104 2.00e-02 2.50e+03 pdb=" C2 DC F -4 " 0.038 2.00e-02 2.50e+03 pdb=" O2 DC F -4 " 0.005 2.00e-02 2.50e+03 pdb=" N3 DC F -4 " 0.005 2.00e-02 2.50e+03 pdb=" C4 DC F -4 " 0.008 2.00e-02 2.50e+03 pdb=" N4 DC F -4 " -0.079 2.00e-02 2.50e+03 pdb=" C5 DC F -4 " 0.024 2.00e-02 2.50e+03 pdb=" C6 DC F -4 " 0.026 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DG F -5 " -0.099 2.00e-02 2.50e+03 4.96e-02 7.38e+01 pdb=" N9 DG F -5 " 0.116 2.00e-02 2.50e+03 pdb=" C8 DG F -5 " -0.011 2.00e-02 2.50e+03 pdb=" N7 DG F -5 " -0.032 2.00e-02 2.50e+03 pdb=" C5 DG F -5 " 0.036 2.00e-02 2.50e+03 pdb=" C6 DG F -5 " -0.007 2.00e-02 2.50e+03 pdb=" O6 DG F -5 " -0.030 2.00e-02 2.50e+03 pdb=" N1 DG F -5 " 0.003 2.00e-02 2.50e+03 pdb=" C2 DG F -5 " -0.028 2.00e-02 2.50e+03 pdb=" N2 DG F -5 " 0.002 2.00e-02 2.50e+03 pdb=" N3 DG F -5 " 0.003 2.00e-02 2.50e+03 pdb=" C4 DG F -5 " 0.047 2.00e-02 2.50e+03 ... (remaining 4803 not shown) Histogram of nonbonded interaction distances: 1.88 - 2.48: 130 2.48 - 3.09: 19936 3.09 - 3.69: 39892 3.69 - 4.30: 55793 4.30 - 4.90: 90407 Nonbonded interactions: 206158 Sorted by model distance: nonbonded pdb=" N GLU D1327 " pdb=" OE1 GLU D1327 " model vdw 1.878 3.120 nonbonded pdb=" OE2 GLU A 165 " pdb=" N ARG A 166 " model vdw 2.022 3.120 nonbonded pdb=" O3' DG G -8 " pdb=" O4' DA G -7 " model vdw 2.067 3.040 nonbonded pdb=" C2' DT G -17 " pdb=" C7 DT G -16 " model vdw 2.194 3.860 nonbonded pdb=" O ILE D 937 " pdb=" N GLY D 939 " model vdw 2.197 3.120 ... (remaining 206153 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 5 through 57 or (resid 58 and (name N or name CA or name C \ or name O or name CB )) or resid 59 through 65 or (resid 66 through 68 and (nam \ e N or name CA or name C or name O or name CB )) or resid 69 through 70 or (resi \ d 71 through 72 and (name N or name CA or name C or name O or name CB )) or resi \ d 73 through 79 or (resid 80 and (name N or name CA or name C or name O or name \ CB )) or resid 81 through 134 or (resid 135 through 136 and (name N or name CA o \ r name C or name O or name CB )) or resid 137 through 141 or (resid 142 and (nam \ e N or name CA or name C or name O or name CB )) or resid 143 through 157 or (re \ sid 158 through 160 and (name N or name CA or name C or name O or name CB )) or \ resid 161 through 162 or (resid 163 through 166 and (name N or name CA or name C \ or name O or name CB )) or resid 167 through 169 or (resid 170 and (name N or n \ ame CA or name C or name O or name CB )) or resid 171 through 232 or (resid 233 \ and (name N or name CA or name C or name O or name CB )) or resid 234 or (resid \ 235 and (name N or name CA or name C or name O or name CB )) or resid 236 throug \ h 237)) selection = (chain 'B' and ((resid 5 and (name N or name CA or name C or name O or name CB ) \ ) or resid 6 through 7 or (resid 8 and (name N or name CA or name C or name O or \ name CB )) or resid 9 through 71 or (resid 72 and (name N or name CA or name C \ or name O or name CB )) or resid 73 through 94 or (resid 95 and (name N or name \ CA or name C or name O or name CB )) or resid 96 through 135 or (resid 136 and ( \ name N or name CA or name C or name O or name CB )) or resid 137 through 190 or \ (resid 191 and (name N or name CA or name C or name O or name CB )) or resid 192 \ or (resid 193 and (name N or name CA or name C or name O or name CB )) or resid \ 194 or (resid 195 and (name N or name CA or name C or name O or name CB )) or r \ esid 196 through 216 or (resid 217 and (name N or name CA or name C or name O or \ name CB )) or resid 218 through 236 or (resid 237 and (name N or name CA or nam \ e C or name O or name CB )))) } 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=0.20 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue 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: 1.670 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 0.440 Check model and map are aligned: 0.090 Set scattering table: 0.070 Process input model: 28.610 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: 0.000 Load rotamer database and sin/cos tables:1.240 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.460 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7913 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 : 0.005 0.258 28600 Z= 0.311 Angle : 0.904 23.450 39349 Z= 0.554 Chirality : 0.059 0.857 4734 Planarity : 0.005 0.157 4806 Dihedral : 15.248 177.618 10448 Min Nonbonded Distance : 1.878 Molprobity Statistics. All-atom Clashscore : 16.46 Ramachandran Plot: Outliers : 0.60 % Allowed : 9.29 % Favored : 90.12 % Rotamer: Outliers : 0.72 % Allowed : 1.57 % Favored : 97.71 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 2.14 % Cis-general : 0.03 % Twisted Proline : 0.71 % Twisted General : 0.09 % 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: -3.47 (0.11), residues: 3521 helix: -2.58 (0.12), residues: 1130 sheet: -1.31 (0.24), residues: 314 loop : -2.37 (0.11), residues: 2077 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 425 TYR 0.020 0.001 TYR C1231 PHE 0.016 0.001 PHE D 620 TRP 0.009 0.001 TRP D 33 HIS 0.004 0.000 HIS D 450 Details of bonding type rmsd/Z covalent geometry : bond 0.00465 / 0.31 (28600) covalent geometry : angle 0.90392 / 0.55 (39349) hydrogen bonds : bond 0.18137 / 13.21 ( 1043) hydrogen bonds : angle 10.47691 / 7.36 ( 2928) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7042 Ramachandran restraints generated. 3521 Oldfield, 0 Emsley, 3521 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7042 Ramachandran restraints generated. 3521 Oldfield, 0 Emsley, 3521 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 809 residues out of total 3027 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 791 time to evaluate : 1.017 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 15 ASP cc_start: 0.9132 (t0) cc_final: 0.8862 (m-30) REVERT: A 31 LEU cc_start: 0.8305 (mt) cc_final: 0.8077 (mt) REVERT: A 77 ASP cc_start: 0.8566 (m-30) cc_final: 0.8350 (m-30) REVERT: A 96 ASP cc_start: 0.6428 (p0) cc_final: 0.6029 (p0) REVERT: A 97 GLU cc_start: 0.7637 (mm-30) cc_final: 0.7139 (pt0) REVERT: A 173 VAL cc_start: 0.8967 (m) cc_final: 0.8117 (p) REVERT: A 181 GLU cc_start: 0.9219 (tp30) cc_final: 0.8923 (mm-30) REVERT: A 215 GLU cc_start: 0.9475 (mt-10) cc_final: 0.9164 (tp30) REVERT: B 46 ILE cc_start: 0.8828 (mt) cc_final: 0.8572 (mt) REVERT: B 96 ASP cc_start: 0.8723 (p0) cc_final: 0.8273 (m-30) REVERT: B 114 ASP cc_start: 0.9469 (m-30) cc_final: 0.9248 (p0) REVERT: B 118 ASP cc_start: 0.8744 (m-30) cc_final: 0.7957 (t70) REVERT: B 186 ASN cc_start: 0.8560 (t0) cc_final: 0.8125 (t0) REVERT: B 198 LEU cc_start: 0.8227 (mt) cc_final: 0.7801 (mp) REVERT: B 212 ASP cc_start: 0.8076 (t0) cc_final: 0.7668 (t0) REVERT: C 5 TYR cc_start: 0.8029 (t80) cc_final: 0.7583 (m-80) REVERT: C 23 ASP cc_start: 0.8974 (m-30) cc_final: 0.8675 (p0) REVERT: C 130 MET cc_start: 0.9309 (ttt) cc_final: 0.8749 (ttm) REVERT: C 195 PHE cc_start: 0.6892 (m-80) cc_final: 0.6415 (m-80) REVERT: C 419 ILE cc_start: 0.7940 (pt) cc_final: 0.7664 (pt) REVERT: C 469 VAL cc_start: 0.8854 (t) cc_final: 0.8630 (p) REVERT: C 473 ARG cc_start: 0.9105 (tpt90) cc_final: 0.8434 (tmm160) REVERT: C 526 HIS cc_start: 0.9074 (t70) cc_final: 0.8851 (t-90) REVERT: C 580 GLN cc_start: 0.8485 (pt0) cc_final: 0.7918 (pt0) REVERT: C 603 ILE cc_start: 0.9356 (pt) cc_final: 0.8830 (mp) REVERT: C 734 ILE cc_start: 0.9431 (mt) cc_final: 0.9120 (pt) REVERT: C 766 ASN cc_start: 0.8298 (t0) cc_final: 0.7723 (p0) REVERT: C 775 GLU cc_start: 0.9133 (tt0) cc_final: 0.8872 (pm20) REVERT: C 843 THR cc_start: 0.9623 (p) cc_final: 0.9331 (t) REVERT: C 857 VAL cc_start: 0.8707 (t) cc_final: 0.8401 (m) REVERT: C 946 LEU cc_start: 0.9158 (mp) cc_final: 0.8791 (pt) REVERT: C 974 ARG cc_start: 0.9474 (ttt90) cc_final: 0.9232 (ptp-170) REVERT: C 1019 ASP cc_start: 0.9622 (m-30) cc_final: 0.9312 (p0) REVERT: C 1040 ASP cc_start: 0.8267 (m-30) cc_final: 0.7814 (t0) REVERT: C 1140 LYS cc_start: 0.9390 (mmtp) cc_final: 0.9183 (mtmm) REVERT: C 1210 ILE cc_start: 0.8750 (tt) cc_final: 0.8463 (pt) REVERT: D 34 SER cc_start: 0.8099 (m) cc_final: 0.7866 (p) REVERT: D 60 ARG cc_start: 0.7862 (ttp-170) cc_final: 0.7488 (mtm110) REVERT: D 88 CYS cc_start: 0.8181 (m) cc_final: 0.7960 (m) REVERT: D 105 ILE cc_start: 0.9377 (tp) cc_final: 0.9096 (mt) REVERT: D 196 GLN cc_start: 0.9616 (mm-40) cc_final: 0.9371 (tm-30) REVERT: D 303 VAL cc_start: 0.9118 (t) cc_final: 0.8722 (p) REVERT: D 306 LEU cc_start: 0.8524 (tt) cc_final: 0.8106 (tp) REVERT: D 330 MET cc_start: 0.8116 (ttt) cc_final: 0.7851 (ttt) REVERT: D 339 ARG cc_start: 0.8480 (mmt180) cc_final: 0.8102 (mtt180) REVERT: D 414 GLU cc_start: 0.9017 (tt0) cc_final: 0.8703 (tm-30) REVERT: D 437 PHE cc_start: 0.8599 (m-10) cc_final: 0.8050 (m-10) REVERT: D 442 ILE cc_start: 0.8760 (tp) cc_final: 0.8489 (tp) REVERT: D 591 ILE cc_start: 0.8261 (tp) cc_final: 0.7966 (pt) REVERT: D 809 VAL cc_start: 0.7634 (t) cc_final: 0.7344 (p) REVERT: D 810 THR cc_start: 0.8829 (t) cc_final: 0.8601 (p) REVERT: D 820 ILE cc_start: 0.8821 (mt) cc_final: 0.8489 (tt) REVERT: D 832 LYS cc_start: 0.7308 (mmmt) cc_final: 0.7046 (mmmt) REVERT: D 835 LEU cc_start: 0.8497 (tp) cc_final: 0.8222 (tt) REVERT: D 1146 GLU cc_start: 0.9192 (mm-30) cc_final: 0.8789 (mt-10) REVERT: D 1149 ARG cc_start: 0.9317 (mtt180) cc_final: 0.8864 (mtm180) REVERT: D 1320 ILE cc_start: 0.9002 (mt) cc_final: 0.8720 (tp) REVERT: D 1328 THR cc_start: 0.8865 (p) cc_final: 0.8629 (m) REVERT: D 1357 ILE cc_start: 0.9128 (mt) cc_final: 0.8550 (pt) REVERT: E 5 THR cc_start: 0.8242 (m) cc_final: 0.7054 (p) REVERT: E 21 LEU cc_start: 0.8471 (mp) cc_final: 0.8264 (mt) REVERT: E 67 ARG cc_start: 0.8757 (mmt90) cc_final: 0.8549 (mmm160) REVERT: M 127 GLN cc_start: 0.9214 (tp40) cc_final: 0.8964 (tt0) REVERT: M 205 GLN cc_start: 0.8965 (pt0) cc_final: 0.8595 (pm20) REVERT: M 221 SER cc_start: 0.9071 (t) cc_final: 0.8849 (p) outliers start: 18 outliers final: 9 residues processed: 806 average time/residue: 0.2016 time to fit residues: 246.9572 Evaluate side-chains 430 residues out of total 3027 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 421 time to evaluate : 1.053 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 159 ILE Chi-restraints excluded: chain A residue 161 SER Chi-restraints excluded: chain C residue 540 ARG Chi-restraints excluded: chain C residue 542 ARG Chi-restraints excluded: chain C residue 545 PHE Chi-restraints excluded: chain C residue 905 ILE Chi-restraints excluded: chain D residue 109 SER Chi-restraints excluded: chain D residue 547 ARG Chi-restraints excluded: chain D residue 934 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 346 random chunks: chunk 197 optimal weight: 50.0000 chunk 215 optimal weight: 0.0270 chunk 20 optimal weight: 8.9990 chunk 132 optimal weight: 9.9990 chunk 261 optimal weight: 8.9990 chunk 248 optimal weight: 7.9990 chunk 207 optimal weight: 10.0000 chunk 155 optimal weight: 0.9990 chunk 244 optimal weight: 9.9990 chunk 183 optimal weight: 10.0000 chunk 298 optimal weight: 1.9990 overall best weight: 4.0046 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 75 GLN A 160 HIS B 23 HIS C 510 GLN C 526 HIS C 832 HIS C1061 GLN C1072 ASN ** C1244 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 309 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 419 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 430 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 477 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 861 ASN D 897 HIS D1218 HIS ** D1244 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4031 r_free = 0.4031 target = 0.150073 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3557 r_free = 0.3557 target = 0.115278 restraints weight = 54870.374| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3493 r_free = 0.3493 target = 0.112530 restraints weight = 77795.150| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3509 r_free = 0.3509 target = 0.113972 restraints weight = 58659.791| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3510 r_free = 0.3510 target = 0.114103 restraints weight = 35791.369| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3547 r_free = 0.3547 target = 0.117664 restraints weight = 33845.841| |-----------------------------------------------------------------------------| r_work (final): 0.3532 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3530 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3530 r_free = 0.3530 target_work(ls_wunit_k1) = 0.114 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3526 r_free = 0.3526 target_work(ls_wunit_k1) = 0.114 | | occupancies: max = 1.00 min = 0.61 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 6 (11 function evaluations) r_final: 0.3526 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7865 moved from start: 0.3250 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.083 28600 Z= 0.296 Angle : 0.895 12.879 39349 Z= 0.464 Chirality : 0.055 0.477 4734 Planarity : 0.006 0.081 4806 Dihedral : 18.724 179.806 4998 Min Nonbonded Distance : 2.351 Molprobity Statistics. All-atom Clashscore : 9.14 Ramachandran Plot: Outliers : 0.65 % Allowed : 6.79 % Favored : 92.56 % Rotamer: Outliers : 3.54 % Allowed : 10.82 % Favored : 85.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.14 % Cis-general : 0.03 % Twisted Proline : 0.71 % Twisted General : 0.15 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.29 (0.12), residues: 3521 helix: -0.67 (0.14), residues: 1172 sheet: -0.86 (0.26), residues: 332 loop : -2.25 (0.12), residues: 2017 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG D 133 TYR 0.028 0.003 TYR D 537 PHE 0.033 0.002 PHE D 629 TRP 0.015 0.002 TRP D 409 HIS 0.010 0.002 HIS C1237 Details of bonding type rmsd/Z covalent geometry : bond 0.00673 / 0.30 (28600) covalent geometry : angle 0.89458 / 0.46 (39349) hydrogen bonds : bond 0.06205 / 4.28 ( 1043) hydrogen bonds : angle 5.73353 / 3.97 ( 2928) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7042 Ramachandran restraints generated. 3521 Oldfield, 0 Emsley, 3521 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7042 Ramachandran restraints generated. 3521 Oldfield, 0 Emsley, 3521 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 512 residues out of total 3027 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 424 time to evaluate : 1.065 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 147 GLN cc_start: 0.8170 (pt0) cc_final: 0.7948 (pt0) REVERT: C 473 ARG cc_start: 0.8331 (tpt90) cc_final: 0.7986 (tmm160) REVERT: C 576 SER cc_start: 0.8891 (t) cc_final: 0.8610 (m) REVERT: C 653 MET cc_start: 0.8176 (tpp) cc_final: 0.7773 (ttt) REVERT: C 766 ASN cc_start: 0.8361 (t0) cc_final: 0.8092 (t0) REVERT: C 1304 MET cc_start: 0.8968 (tpp) cc_final: 0.8211 (tpp) REVERT: C 1329 GLU cc_start: 0.7696 (mt-10) cc_final: 0.7335 (mt-10) REVERT: D 159 ILE cc_start: 0.8706 (mt) cc_final: 0.8464 (mp) REVERT: D 330 MET cc_start: 0.6961 (ttt) cc_final: 0.6431 (ttp) REVERT: D 665 GLN cc_start: 0.8576 (tm-30) cc_final: 0.8343 (pp30) REVERT: D 719 PHE cc_start: 0.8654 (OUTLIER) cc_final: 0.7863 (t80) REVERT: D 1040 MET cc_start: -0.0124 (ttt) cc_final: -0.1982 (tpt) REVERT: E 5 THR cc_start: 0.7986 (m) cc_final: 0.7668 (p) REVERT: E 30 MET cc_start: 0.8279 (mtt) cc_final: 0.8059 (mtt) REVERT: M 181 ARG cc_start: 0.8355 (ttt180) cc_final: 0.8110 (ttt180) outliers start: 88 outliers final: 49 residues processed: 482 average time/residue: 0.1828 time to fit residues: 141.0297 Evaluate side-chains 351 residues out of total 3027 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 301 time to evaluate : 0.862 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 GLN Chi-restraints excluded: chain A residue 146 VAL Chi-restraints excluded: chain A residue 161 SER Chi-restraints excluded: chain B residue 14 VAL Chi-restraints excluded: chain B residue 26 VAL Chi-restraints excluded: chain B residue 132 HIS Chi-restraints excluded: chain B residue 153 VAL Chi-restraints excluded: chain C residue 104 ILE Chi-restraints excluded: chain C residue 144 VAL Chi-restraints excluded: chain C residue 146 VAL Chi-restraints excluded: chain C residue 395 TYR Chi-restraints excluded: chain C residue 428 VAL Chi-restraints excluded: chain C residue 471 VAL Chi-restraints excluded: chain C residue 475 VAL Chi-restraints excluded: chain C residue 542 ARG Chi-restraints excluded: chain C residue 545 PHE Chi-restraints excluded: chain C residue 685 MET Chi-restraints excluded: chain C residue 710 VAL Chi-restraints excluded: chain C residue 740 GLU Chi-restraints excluded: chain C residue 1036 ILE Chi-restraints excluded: chain C residue 1052 VAL Chi-restraints excluded: chain C residue 1207 SER Chi-restraints excluded: chain C residue 1327 LEU Chi-restraints excluded: chain D residue 8 LEU Chi-restraints excluded: chain D residue 70 CYS Chi-restraints excluded: chain D residue 109 SER Chi-restraints excluded: chain D residue 117 LEU Chi-restraints excluded: chain D residue 290 ILE Chi-restraints excluded: chain D residue 316 ILE Chi-restraints excluded: chain D residue 317 THR Chi-restraints excluded: chain D residue 440 VAL Chi-restraints excluded: chain D residue 454 CYS Chi-restraints excluded: chain D residue 470 VAL Chi-restraints excluded: chain D residue 487 THR Chi-restraints excluded: chain D residue 518 VAL Chi-restraints excluded: chain D residue 592 VAL Chi-restraints excluded: chain D residue 612 LEU Chi-restraints excluded: chain D residue 645 VAL Chi-restraints excluded: chain D residue 660 GLU Chi-restraints excluded: chain D residue 719 PHE Chi-restraints excluded: chain D residue 801 VAL Chi-restraints excluded: chain D residue 803 VAL Chi-restraints excluded: chain D residue 823 THR Chi-restraints excluded: chain D residue 915 ILE Chi-restraints excluded: chain D residue 1144 LEU Chi-restraints excluded: chain D residue 1266 ILE Chi-restraints excluded: chain D residue 1267 VAL Chi-restraints excluded: chain E residue 39 VAL Chi-restraints excluded: chain M residue 143 SER Chi-restraints excluded: chain M residue 255 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 346 random chunks: chunk 190 optimal weight: 10.0000 chunk 50 optimal weight: 8.9990 chunk 157 optimal weight: 1.9990 chunk 210 optimal weight: 6.9990 chunk 43 optimal weight: 9.9990 chunk 329 optimal weight: 40.0000 chunk 158 optimal weight: 0.9990 chunk 16 optimal weight: 5.9990 chunk 295 optimal weight: 20.0000 chunk 345 optimal weight: 30.0000 chunk 101 optimal weight: 0.8980 overall best weight: 3.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 160 HIS C1220 GLN ** C1244 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C1313 HIS D 309 ASN D 340 GLN ** D 430 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 504 GLN ** D 716 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1244 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 127 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3974 r_free = 0.3974 target = 0.145803 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 117)---------------| | r_work = 0.3212 r_free = 0.3212 target = 0.094807 restraints weight = 54397.964| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3168 r_free = 0.3168 target = 0.093762 restraints weight = 39205.487| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3163 r_free = 0.3163 target = 0.093656 restraints weight = 33988.068| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3170 r_free = 0.3170 target = 0.094024 restraints weight = 36781.548| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3172 r_free = 0.3172 target = 0.094122 restraints weight = 32117.721| |-----------------------------------------------------------------------------| r_work (final): 0.3125 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3124 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3124 r_free = 0.3124 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.61 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3124 r_free = 0.3124 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.59 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3124 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8426 moved from start: 0.4296 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.073 28600 Z= 0.233 Angle : 0.777 13.490 39349 Z= 0.405 Chirality : 0.050 0.340 4734 Planarity : 0.005 0.093 4806 Dihedral : 18.595 178.454 4985 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 8.58 Ramachandran Plot: Outliers : 0.60 % Allowed : 8.21 % Favored : 91.20 % Rotamer: Outliers : 4.06 % Allowed : 13.96 % Favored : 81.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.14 % Cis-general : 0.03 % Twisted Proline : 0.71 % Twisted General : 0.12 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.79 (0.13), residues: 3521 helix: 0.13 (0.14), residues: 1189 sheet: -0.56 (0.27), residues: 322 loop : -2.23 (0.12), residues: 2010 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG D1345 TYR 0.023 0.002 TYR D 537 PHE 0.025 0.002 PHE D 629 TRP 0.009 0.002 TRP D 686 HIS 0.007 0.002 HIS C1237 Details of bonding type rmsd/Z covalent geometry : bond 0.00536 / 0.23 (28600) covalent geometry : angle 0.77713 / 0.41 (39349) hydrogen bonds : bond 0.05426 / 3.77 ( 1043) hydrogen bonds : angle 5.05603 / 3.54 ( 2928) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7042 Ramachandran restraints generated. 3521 Oldfield, 0 Emsley, 3521 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7042 Ramachandran restraints generated. 3521 Oldfield, 0 Emsley, 3521 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 420 residues out of total 3027 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 101 poor density : 319 time to evaluate : 0.996 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 75 GLN cc_start: 0.9084 (OUTLIER) cc_final: 0.8294 (tm-30) REVERT: C 225 PHE cc_start: 0.7990 (OUTLIER) cc_final: 0.7371 (t80) REVERT: C 370 MET cc_start: 0.8687 (tmm) cc_final: 0.8425 (tmm) REVERT: C 473 ARG cc_start: 0.8572 (tpt90) cc_final: 0.8147 (tmm160) REVERT: C 653 MET cc_start: 0.8308 (tpp) cc_final: 0.8079 (ttt) REVERT: C 758 ARG cc_start: 0.9335 (OUTLIER) cc_final: 0.9074 (ttp80) REVERT: C 964 LEU cc_start: 0.9038 (tp) cc_final: 0.8489 (mm) REVERT: C 974 ARG cc_start: 0.8702 (ttm110) cc_final: 0.8302 (ptp-110) REVERT: C 1288 GLN cc_start: 0.9430 (OUTLIER) cc_final: 0.8900 (tt0) REVERT: C 1304 MET cc_start: 0.9082 (tpp) cc_final: 0.8212 (tpp) REVERT: D 454 CYS cc_start: 0.8533 (OUTLIER) cc_final: 0.8169 (m) REVERT: D 691 ASP cc_start: 0.8146 (m-30) cc_final: 0.7886 (m-30) REVERT: D 1040 MET cc_start: -0.0281 (ttt) cc_final: -0.1599 (tpt) outliers start: 101 outliers final: 59 residues processed: 392 average time/residue: 0.1635 time to fit residues: 105.1708 Evaluate side-chains 338 residues out of total 3027 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 274 time to evaluate : 0.990 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 GLN Chi-restraints excluded: chain A residue 77 ASP Chi-restraints excluded: chain A residue 146 VAL Chi-restraints excluded: chain A residue 198 LEU Chi-restraints excluded: chain B residue 14 VAL Chi-restraints excluded: chain B residue 26 VAL Chi-restraints excluded: chain B residue 46 ILE Chi-restraints excluded: chain B residue 96 ASP Chi-restraints excluded: chain C residue 104 ILE Chi-restraints excluded: chain C residue 117 ILE Chi-restraints excluded: chain C residue 144 VAL Chi-restraints excluded: chain C residue 146 VAL Chi-restraints excluded: chain C residue 225 PHE Chi-restraints excluded: chain C residue 246 LEU Chi-restraints excluded: chain C residue 365 GLU Chi-restraints excluded: chain C residue 395 TYR Chi-restraints excluded: chain C residue 400 VAL Chi-restraints excluded: chain C residue 428 VAL Chi-restraints excluded: chain C residue 469 VAL Chi-restraints excluded: chain C residue 471 VAL Chi-restraints excluded: chain C residue 475 VAL Chi-restraints excluded: chain C residue 479 LEU Chi-restraints excluded: chain C residue 545 PHE Chi-restraints excluded: chain C residue 630 VAL Chi-restraints excluded: chain C residue 710 VAL Chi-restraints excluded: chain C residue 740 GLU Chi-restraints excluded: chain C residue 758 ARG Chi-restraints excluded: chain C residue 785 ASP Chi-restraints excluded: chain C residue 814 ASP Chi-restraints excluded: chain C residue 1021 LEU Chi-restraints excluded: chain C residue 1052 VAL Chi-restraints excluded: chain C residue 1101 LEU Chi-restraints excluded: chain C residue 1207 SER Chi-restraints excluded: chain C residue 1288 GLN Chi-restraints excluded: chain C residue 1297 ASP Chi-restraints excluded: chain D residue 8 LEU Chi-restraints excluded: chain D residue 29 MET Chi-restraints excluded: chain D residue 70 CYS Chi-restraints excluded: chain D residue 109 SER Chi-restraints excluded: chain D residue 255 LEU Chi-restraints excluded: chain D residue 290 ILE Chi-restraints excluded: chain D residue 303 VAL Chi-restraints excluded: chain D residue 317 THR Chi-restraints excluded: chain D residue 440 VAL Chi-restraints excluded: chain D residue 454 CYS Chi-restraints excluded: chain D residue 470 VAL Chi-restraints excluded: chain D residue 487 THR Chi-restraints excluded: chain D residue 499 ILE Chi-restraints excluded: chain D residue 532 GLU Chi-restraints excluded: chain D residue 569 LEU Chi-restraints excluded: chain D residue 612 LEU Chi-restraints excluded: chain D residue 645 VAL Chi-restraints excluded: chain D residue 661 VAL Chi-restraints excluded: chain D residue 705 THR Chi-restraints excluded: chain D residue 756 GLU Chi-restraints excluded: chain D residue 801 VAL Chi-restraints excluded: chain D residue 803 VAL Chi-restraints excluded: chain D residue 823 THR Chi-restraints excluded: chain D residue 825 VAL Chi-restraints excluded: chain D residue 1209 VAL Chi-restraints excluded: chain D residue 1267 VAL Chi-restraints excluded: chain E residue 39 VAL Chi-restraints excluded: chain M residue 137 ASP Chi-restraints excluded: chain M residue 309 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 346 random chunks: chunk 256 optimal weight: 0.0170 chunk 228 optimal weight: 2.9990 chunk 22 optimal weight: 1.9990 chunk 325 optimal weight: 50.0000 chunk 183 optimal weight: 9.9990 chunk 176 optimal weight: 1.9990 chunk 39 optimal weight: 20.0000 chunk 26 optimal weight: 3.9990 chunk 333 optimal weight: 0.8980 chunk 37 optimal weight: 6.9990 chunk 147 optimal weight: 6.9990 overall best weight: 1.5824 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1244 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 430 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 861 ASN D1366 HIS E 43 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3979 r_free = 0.3979 target = 0.146152 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 92)----------------| | r_work = 0.3182 r_free = 0.3182 target = 0.094217 restraints weight = 53658.044| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3198 r_free = 0.3198 target = 0.094931 restraints weight = 36154.177| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3190 r_free = 0.3190 target = 0.094584 restraints weight = 27725.481| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3193 r_free = 0.3193 target = 0.094760 restraints weight = 30636.190| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3194 r_free = 0.3194 target = 0.094786 restraints weight = 27632.506| |-----------------------------------------------------------------------------| r_work (final): 0.3152 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3152 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3152 r_free = 0.3152 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.59 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3152 r_free = 0.3152 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.57 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3152 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8392 moved from start: 0.4534 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 28600 Z= 0.154 Angle : 0.700 10.981 39349 Z= 0.363 Chirality : 0.046 0.338 4734 Planarity : 0.005 0.086 4806 Dihedral : 18.460 177.446 4980 Min Nonbonded Distance : 2.183 Molprobity Statistics. All-atom Clashscore : 7.91 Ramachandran Plot: Outliers : 0.60 % Allowed : 7.75 % Favored : 91.65 % Rotamer: Outliers : 3.54 % Allowed : 15.57 % Favored : 80.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.14 % Cis-general : 0.03 % Twisted Proline : 0.71 % Twisted General : 0.12 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.52 (0.13), residues: 3521 helix: 0.52 (0.15), residues: 1189 sheet: -0.61 (0.28), residues: 315 loop : -2.14 (0.12), residues: 2017 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.000 ARG D 339 TYR 0.017 0.002 TYR A 185 PHE 0.014 0.001 PHE D 620 TRP 0.009 0.001 TRP D 580 HIS 0.007 0.001 HIS D 651 Details of bonding type rmsd/Z covalent geometry : bond 0.00333 / 0.15 (28600) covalent geometry : angle 0.70031 / 0.36 (39349) hydrogen bonds : bond 0.04577 / 3.19 ( 1043) hydrogen bonds : angle 4.76216 / 3.34 ( 2928) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7042 Ramachandran restraints generated. 3521 Oldfield, 0 Emsley, 3521 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7042 Ramachandran restraints generated. 3521 Oldfield, 0 Emsley, 3521 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 379 residues out of total 3027 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 291 time to evaluate : 1.055 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 473 ARG cc_start: 0.8591 (tpt90) cc_final: 0.8054 (tmm160) REVERT: C 653 MET cc_start: 0.8286 (tpp) cc_final: 0.8042 (ttt) REVERT: C 758 ARG cc_start: 0.9303 (OUTLIER) cc_final: 0.7883 (ttm170) REVERT: C 766 ASN cc_start: 0.8429 (t0) cc_final: 0.8188 (t0) REVERT: D 454 CYS cc_start: 0.8566 (OUTLIER) cc_final: 0.8209 (m) REVERT: D 552 ILE cc_start: 0.8984 (mt) cc_final: 0.8713 (pt) REVERT: D 1040 MET cc_start: -0.0262 (OUTLIER) cc_final: -0.1726 (tpt) REVERT: M 181 ARG cc_start: 0.8644 (ttt180) cc_final: 0.7981 (ttt180) outliers start: 88 outliers final: 60 residues processed: 358 average time/residue: 0.1575 time to fit residues: 93.3637 Evaluate side-chains 329 residues out of total 3027 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 266 time to evaluate : 0.974 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 77 ASP Chi-restraints excluded: chain A residue 102 LEU Chi-restraints excluded: chain A residue 146 VAL Chi-restraints excluded: chain A residue 183 ILE Chi-restraints excluded: chain A residue 198 LEU Chi-restraints excluded: chain B residue 14 VAL Chi-restraints excluded: chain B residue 26 VAL Chi-restraints excluded: chain B residue 46 ILE Chi-restraints excluded: chain B residue 96 ASP Chi-restraints excluded: chain B residue 153 VAL Chi-restraints excluded: chain B residue 180 VAL Chi-restraints excluded: chain C residue 104 ILE Chi-restraints excluded: chain C residue 144 VAL Chi-restraints excluded: chain C residue 146 VAL Chi-restraints excluded: chain C residue 246 LEU Chi-restraints excluded: chain C residue 365 GLU Chi-restraints excluded: chain C residue 395 TYR Chi-restraints excluded: chain C residue 428 VAL Chi-restraints excluded: chain C residue 469 VAL Chi-restraints excluded: chain C residue 471 VAL Chi-restraints excluded: chain C residue 475 VAL Chi-restraints excluded: chain C residue 481 LEU Chi-restraints excluded: chain C residue 545 PHE Chi-restraints excluded: chain C residue 558 VAL Chi-restraints excluded: chain C residue 663 VAL Chi-restraints excluded: chain C residue 710 VAL Chi-restraints excluded: chain C residue 740 GLU Chi-restraints excluded: chain C residue 758 ARG Chi-restraints excluded: chain C residue 785 ASP Chi-restraints excluded: chain C residue 796 LEU Chi-restraints excluded: chain C residue 878 THR Chi-restraints excluded: chain C residue 1052 VAL Chi-restraints excluded: chain C residue 1207 SER Chi-restraints excluded: chain C residue 1322 SER Chi-restraints excluded: chain C residue 1327 LEU Chi-restraints excluded: chain D residue 8 LEU Chi-restraints excluded: chain D residue 70 CYS Chi-restraints excluded: chain D residue 109 SER Chi-restraints excluded: chain D residue 117 LEU Chi-restraints excluded: chain D residue 290 ILE Chi-restraints excluded: chain D residue 303 VAL Chi-restraints excluded: chain D residue 316 ILE Chi-restraints excluded: chain D residue 317 THR Chi-restraints excluded: chain D residue 440 VAL Chi-restraints excluded: chain D residue 454 CYS Chi-restraints excluded: chain D residue 470 VAL Chi-restraints excluded: chain D residue 487 THR Chi-restraints excluded: chain D residue 499 ILE Chi-restraints excluded: chain D residue 612 LEU Chi-restraints excluded: chain D residue 645 VAL Chi-restraints excluded: chain D residue 661 VAL Chi-restraints excluded: chain D residue 705 THR Chi-restraints excluded: chain D residue 756 GLU Chi-restraints excluded: chain D residue 803 VAL Chi-restraints excluded: chain D residue 823 THR Chi-restraints excluded: chain D residue 825 VAL Chi-restraints excluded: chain D residue 1040 MET Chi-restraints excluded: chain D residue 1175 LEU Chi-restraints excluded: chain D residue 1209 VAL Chi-restraints excluded: chain D residue 1266 ILE Chi-restraints excluded: chain D residue 1267 VAL Chi-restraints excluded: chain E residue 39 VAL Chi-restraints excluded: chain M residue 137 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 346 random chunks: chunk 114 optimal weight: 5.9990 chunk 317 optimal weight: 0.0570 chunk 210 optimal weight: 9.9990 chunk 132 optimal weight: 10.0000 chunk 38 optimal weight: 20.0000 chunk 123 optimal weight: 5.9990 chunk 305 optimal weight: 7.9990 chunk 96 optimal weight: 3.9990 chunk 155 optimal weight: 3.9990 chunk 95 optimal weight: 1.9990 chunk 87 optimal weight: 0.5980 overall best weight: 2.1304 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1244 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 430 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 504 GLN D 817 HIS D 861 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3966 r_free = 0.3966 target = 0.145081 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 85)----------------| | r_work = 0.3163 r_free = 0.3163 target = 0.093306 restraints weight = 53501.705| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3182 r_free = 0.3182 target = 0.094082 restraints weight = 35834.144| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3172 r_free = 0.3172 target = 0.093560 restraints weight = 28652.773| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3176 r_free = 0.3176 target = 0.093805 restraints weight = 30982.013| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3174 r_free = 0.3174 target = 0.093679 restraints weight = 28914.307| |-----------------------------------------------------------------------------| r_work (final): 0.3127 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3127 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3127 r_free = 0.3127 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.57 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3127 r_free = 0.3127 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.54 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3127 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8416 moved from start: 0.4846 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 28600 Z= 0.168 Angle : 0.693 11.290 39349 Z= 0.359 Chirality : 0.046 0.335 4734 Planarity : 0.005 0.083 4806 Dihedral : 18.368 177.234 4980 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 7.64 Ramachandran Plot: Outliers : 0.60 % Allowed : 8.52 % Favored : 90.88 % Rotamer: Outliers : 4.10 % Allowed : 15.53 % Favored : 80.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.14 % Cis-general : 0.03 % Twisted Proline : 0.71 % Twisted General : 0.12 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.32 (0.14), residues: 3521 helix: 0.82 (0.15), residues: 1191 sheet: -0.51 (0.28), residues: 316 loop : -2.11 (0.13), residues: 2014 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 974 TYR 0.028 0.002 TYR A 185 PHE 0.015 0.001 PHE D 620 TRP 0.037 0.002 TRP C 183 HIS 0.005 0.001 HIS C1237 Details of bonding type rmsd/Z covalent geometry : bond 0.00373 / 0.17 (28600) covalent geometry : angle 0.69263 / 0.36 (39349) hydrogen bonds : bond 0.04411 / 3.07 ( 1043) hydrogen bonds : angle 4.57884 / 3.22 ( 2928) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7042 Ramachandran restraints generated. 3521 Oldfield, 0 Emsley, 3521 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7042 Ramachandran restraints generated. 3521 Oldfield, 0 Emsley, 3521 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 392 residues out of total 3027 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 102 poor density : 290 time to evaluate : 0.942 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 97 GLU cc_start: 0.8333 (mm-30) cc_final: 0.7988 (tp30) REVERT: B 49 SER cc_start: 0.8705 (t) cc_final: 0.8081 (m) REVERT: C 653 MET cc_start: 0.8319 (tpp) cc_final: 0.8082 (ttt) REVERT: C 758 ARG cc_start: 0.9299 (OUTLIER) cc_final: 0.7891 (ttm170) REVERT: C 964 LEU cc_start: 0.9090 (tp) cc_final: 0.8575 (mm) REVERT: C 1288 GLN cc_start: 0.9443 (OUTLIER) cc_final: 0.8973 (tt0) REVERT: D 93 THR cc_start: 0.7995 (m) cc_final: 0.7539 (p) REVERT: D 332 LYS cc_start: 0.5456 (OUTLIER) cc_final: 0.4834 (mmmt) REVERT: D 454 CYS cc_start: 0.8562 (OUTLIER) cc_final: 0.8200 (m) REVERT: D 552 ILE cc_start: 0.9037 (mt) cc_final: 0.8792 (pt) REVERT: D 691 ASP cc_start: 0.8225 (m-30) cc_final: 0.7961 (m-30) REVERT: D 1040 MET cc_start: -0.0182 (OUTLIER) cc_final: -0.1729 (tpt) outliers start: 102 outliers final: 73 residues processed: 370 average time/residue: 0.1605 time to fit residues: 98.5029 Evaluate side-chains 352 residues out of total 3027 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 274 time to evaluate : 0.898 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 LEU Chi-restraints excluded: chain A residue 77 ASP Chi-restraints excluded: chain A residue 102 LEU Chi-restraints excluded: chain A residue 146 VAL Chi-restraints excluded: chain A residue 180 VAL Chi-restraints excluded: chain A residue 183 ILE Chi-restraints excluded: chain A residue 198 LEU Chi-restraints excluded: chain A residue 205 MET Chi-restraints excluded: chain B residue 14 VAL Chi-restraints excluded: chain B residue 26 VAL Chi-restraints excluded: chain B residue 46 ILE Chi-restraints excluded: chain B residue 96 ASP Chi-restraints excluded: chain B residue 153 VAL Chi-restraints excluded: chain B residue 180 VAL Chi-restraints excluded: chain C residue 104 ILE Chi-restraints excluded: chain C residue 144 VAL Chi-restraints excluded: chain C residue 146 VAL Chi-restraints excluded: chain C residue 158 ASP Chi-restraints excluded: chain C residue 176 ILE Chi-restraints excluded: chain C residue 182 SER Chi-restraints excluded: chain C residue 246 LEU Chi-restraints excluded: chain C residue 365 GLU Chi-restraints excluded: chain C residue 395 TYR Chi-restraints excluded: chain C residue 469 VAL Chi-restraints excluded: chain C residue 471 VAL Chi-restraints excluded: chain C residue 475 VAL Chi-restraints excluded: chain C residue 481 LEU Chi-restraints excluded: chain C residue 487 LEU Chi-restraints excluded: chain C residue 545 PHE Chi-restraints excluded: chain C residue 558 VAL Chi-restraints excluded: chain C residue 630 VAL Chi-restraints excluded: chain C residue 663 VAL Chi-restraints excluded: chain C residue 710 VAL Chi-restraints excluded: chain C residue 740 GLU Chi-restraints excluded: chain C residue 758 ARG Chi-restraints excluded: chain C residue 785 ASP Chi-restraints excluded: chain C residue 796 LEU Chi-restraints excluded: chain C residue 878 THR Chi-restraints excluded: chain C residue 1052 VAL Chi-restraints excluded: chain C residue 1207 SER Chi-restraints excluded: chain C residue 1275 VAL Chi-restraints excluded: chain C residue 1288 GLN Chi-restraints excluded: chain C residue 1297 ASP Chi-restraints excluded: chain C residue 1322 SER Chi-restraints excluded: chain C residue 1327 LEU Chi-restraints excluded: chain D residue 8 LEU Chi-restraints excluded: chain D residue 70 CYS Chi-restraints excluded: chain D residue 117 LEU Chi-restraints excluded: chain D residue 130 MET Chi-restraints excluded: chain D residue 290 ILE Chi-restraints excluded: chain D residue 303 VAL Chi-restraints excluded: chain D residue 316 ILE Chi-restraints excluded: chain D residue 317 THR Chi-restraints excluded: chain D residue 332 LYS Chi-restraints excluded: chain D residue 353 SER Chi-restraints excluded: chain D residue 421 VAL Chi-restraints excluded: chain D residue 440 VAL Chi-restraints excluded: chain D residue 454 CYS Chi-restraints excluded: chain D residue 470 VAL Chi-restraints excluded: chain D residue 487 THR Chi-restraints excluded: chain D residue 499 ILE Chi-restraints excluded: chain D residue 518 VAL Chi-restraints excluded: chain D residue 548 VAL Chi-restraints excluded: chain D residue 612 LEU Chi-restraints excluded: chain D residue 645 VAL Chi-restraints excluded: chain D residue 661 VAL Chi-restraints excluded: chain D residue 705 THR Chi-restraints excluded: chain D residue 801 VAL Chi-restraints excluded: chain D residue 803 VAL Chi-restraints excluded: chain D residue 823 THR Chi-restraints excluded: chain D residue 825 VAL Chi-restraints excluded: chain D residue 1040 MET Chi-restraints excluded: chain D residue 1175 LEU Chi-restraints excluded: chain D residue 1209 VAL Chi-restraints excluded: chain D residue 1267 VAL Chi-restraints excluded: chain E residue 39 VAL Chi-restraints excluded: chain M residue 137 ASP Chi-restraints excluded: chain M residue 219 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 346 random chunks: chunk 98 optimal weight: 1.9990 chunk 265 optimal weight: 1.9990 chunk 184 optimal weight: 4.9990 chunk 29 optimal weight: 30.0000 chunk 194 optimal weight: 4.9990 chunk 27 optimal weight: 0.0270 chunk 249 optimal weight: 10.0000 chunk 99 optimal weight: 2.9990 chunk 153 optimal weight: 0.3980 chunk 19 optimal weight: 0.9990 chunk 341 optimal weight: 10.0000 overall best weight: 1.0844 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 75 GLN ** B 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 519 ASN ** C1244 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 113 HIS D 504 GLN D 861 ASN M 157 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3982 r_free = 0.3982 target = 0.146300 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3381 r_free = 0.3381 target = 0.103465 restraints weight = 53543.961| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3315 r_free = 0.3315 target = 0.102251 restraints weight = 50263.852| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3273 r_free = 0.3273 target = 0.098324 restraints weight = 30573.843| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3259 r_free = 0.3259 target = 0.097627 restraints weight = 29414.856| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3261 r_free = 0.3261 target = 0.097798 restraints weight = 30980.867| |-----------------------------------------------------------------------------| r_work (final): 0.3235 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3234 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3234 r_free = 0.3234 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.54 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3234 r_free = 0.3234 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.51 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3234 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8263 moved from start: 0.4967 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 28600 Z= 0.128 Angle : 0.662 14.577 39349 Z= 0.341 Chirality : 0.045 0.328 4734 Planarity : 0.004 0.080 4806 Dihedral : 18.237 178.108 4979 Min Nonbonded Distance : 2.381 Molprobity Statistics. All-atom Clashscore : 7.27 Ramachandran Plot: Outliers : 0.57 % Allowed : 8.04 % Favored : 91.39 % Rotamer: Outliers : 3.46 % Allowed : 16.18 % Favored : 80.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.14 % Cis-general : 0.03 % Twisted Proline : 0.71 % Twisted General : 0.09 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.14 (0.14), residues: 3521 helix: 1.04 (0.15), residues: 1197 sheet: -0.43 (0.29), residues: 311 loop : -2.06 (0.13), residues: 2013 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 473 TYR 0.021 0.001 TYR A 185 PHE 0.011 0.001 PHE D 620 TRP 0.050 0.002 TRP C 183 HIS 0.005 0.001 HIS C 554 Details of bonding type rmsd/Z covalent geometry : bond 0.00260 / 0.13 (28600) covalent geometry : angle 0.66177 / 0.34 (39349) hydrogen bonds : bond 0.03858 / 2.68 ( 1043) hydrogen bonds : angle 4.40084 / 3.08 ( 2928) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7042 Ramachandran restraints generated. 3521 Oldfield, 0 Emsley, 3521 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7042 Ramachandran restraints generated. 3521 Oldfield, 0 Emsley, 3521 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 376 residues out of total 3027 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 290 time to evaluate : 1.058 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 97 GLU cc_start: 0.8324 (mm-30) cc_final: 0.7984 (tp30) REVERT: B 49 SER cc_start: 0.8713 (t) cc_final: 0.8061 (m) REVERT: C 473 ARG cc_start: 0.8258 (ttp80) cc_final: 0.8034 (tpt90) REVERT: C 758 ARG cc_start: 0.9279 (OUTLIER) cc_final: 0.7854 (ttm170) REVERT: C 766 ASN cc_start: 0.8379 (t0) cc_final: 0.8123 (t0) REVERT: D 93 THR cc_start: 0.8035 (OUTLIER) cc_final: 0.7646 (p) REVERT: D 332 LYS cc_start: 0.5569 (OUTLIER) cc_final: 0.4967 (mmmt) REVERT: D 552 ILE cc_start: 0.9018 (mt) cc_final: 0.8772 (pt) REVERT: D 1040 MET cc_start: -0.0266 (OUTLIER) cc_final: -0.1925 (tpt) outliers start: 86 outliers final: 64 residues processed: 359 average time/residue: 0.1614 time to fit residues: 95.3328 Evaluate side-chains 342 residues out of total 3027 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 274 time to evaluate : 0.993 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 77 ASP Chi-restraints excluded: chain A residue 102 LEU Chi-restraints excluded: chain A residue 146 VAL Chi-restraints excluded: chain A residue 160 HIS Chi-restraints excluded: chain A residue 180 VAL Chi-restraints excluded: chain A residue 183 ILE Chi-restraints excluded: chain A residue 187 VAL Chi-restraints excluded: chain A residue 198 LEU Chi-restraints excluded: chain B residue 14 VAL Chi-restraints excluded: chain B residue 26 VAL Chi-restraints excluded: chain B residue 46 ILE Chi-restraints excluded: chain B residue 74 VAL Chi-restraints excluded: chain B residue 117 HIS Chi-restraints excluded: chain B residue 153 VAL Chi-restraints excluded: chain B residue 180 VAL Chi-restraints excluded: chain C residue 144 VAL Chi-restraints excluded: chain C residue 146 VAL Chi-restraints excluded: chain C residue 176 ILE Chi-restraints excluded: chain C residue 182 SER Chi-restraints excluded: chain C residue 338 THR Chi-restraints excluded: chain C residue 365 GLU Chi-restraints excluded: chain C residue 395 TYR Chi-restraints excluded: chain C residue 420 LEU Chi-restraints excluded: chain C residue 469 VAL Chi-restraints excluded: chain C residue 471 VAL Chi-restraints excluded: chain C residue 479 LEU Chi-restraints excluded: chain C residue 481 LEU Chi-restraints excluded: chain C residue 545 PHE Chi-restraints excluded: chain C residue 630 VAL Chi-restraints excluded: chain C residue 740 GLU Chi-restraints excluded: chain C residue 758 ARG Chi-restraints excluded: chain C residue 759 SER Chi-restraints excluded: chain C residue 796 LEU Chi-restraints excluded: chain C residue 839 VAL Chi-restraints excluded: chain C residue 878 THR Chi-restraints excluded: chain C residue 1037 THR Chi-restraints excluded: chain C residue 1052 VAL Chi-restraints excluded: chain C residue 1101 LEU Chi-restraints excluded: chain C residue 1207 SER Chi-restraints excluded: chain C residue 1322 SER Chi-restraints excluded: chain C residue 1327 LEU Chi-restraints excluded: chain D residue 70 CYS Chi-restraints excluded: chain D residue 93 THR Chi-restraints excluded: chain D residue 117 LEU Chi-restraints excluded: chain D residue 255 LEU Chi-restraints excluded: chain D residue 290 ILE Chi-restraints excluded: chain D residue 317 THR Chi-restraints excluded: chain D residue 332 LYS Chi-restraints excluded: chain D residue 353 SER Chi-restraints excluded: chain D residue 440 VAL Chi-restraints excluded: chain D residue 454 CYS Chi-restraints excluded: chain D residue 470 VAL Chi-restraints excluded: chain D residue 499 ILE Chi-restraints excluded: chain D residue 518 VAL Chi-restraints excluded: chain D residue 548 VAL Chi-restraints excluded: chain D residue 612 LEU Chi-restraints excluded: chain D residue 645 VAL Chi-restraints excluded: chain D residue 661 VAL Chi-restraints excluded: chain D residue 756 GLU Chi-restraints excluded: chain D residue 803 VAL Chi-restraints excluded: chain D residue 823 THR Chi-restraints excluded: chain D residue 825 VAL Chi-restraints excluded: chain D residue 1040 MET Chi-restraints excluded: chain D residue 1175 LEU Chi-restraints excluded: chain D residue 1266 ILE Chi-restraints excluded: chain D residue 1267 VAL Chi-restraints excluded: chain D residue 1310 THR Chi-restraints excluded: chain E residue 39 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 346 random chunks: chunk 269 optimal weight: 0.8980 chunk 102 optimal weight: 1.9990 chunk 68 optimal weight: 20.0000 chunk 65 optimal weight: 9.9990 chunk 223 optimal weight: 4.9990 chunk 280 optimal weight: 40.0000 chunk 211 optimal weight: 6.9990 chunk 6 optimal weight: 4.9990 chunk 109 optimal weight: 5.9990 chunk 82 optimal weight: 6.9990 chunk 258 optimal weight: 3.9990 overall best weight: 3.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 519 ASN C1017 GLN ** D 430 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 477 GLN D 504 GLN D 861 ASN M 157 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3932 r_free = 0.3932 target = 0.142420 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 98)----------------| | r_work = 0.3153 r_free = 0.3153 target = 0.090981 restraints weight = 53541.068| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3096 r_free = 0.3096 target = 0.089516 restraints weight = 40254.723| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3094 r_free = 0.3094 target = 0.089543 restraints weight = 34432.411| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3099 r_free = 0.3099 target = 0.089840 restraints weight = 34514.843| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3099 r_free = 0.3099 target = 0.089866 restraints weight = 32299.676| |-----------------------------------------------------------------------------| r_work (final): 0.3046 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3045 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3045 r_free = 0.3045 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.51 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3045 r_free = 0.3045 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.51 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3045 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8518 moved from start: 0.5367 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 28600 Z= 0.233 Angle : 0.739 12.351 39349 Z= 0.386 Chirality : 0.048 0.562 4734 Planarity : 0.005 0.082 4806 Dihedral : 18.238 179.353 4979 Min Nonbonded Distance : 2.368 Molprobity Statistics. All-atom Clashscore : 7.87 Ramachandran Plot: Outliers : 0.57 % Allowed : 9.37 % Favored : 90.06 % Rotamer: Outliers : 4.23 % Allowed : 15.57 % Favored : 80.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.14 % Cis-general : 0.03 % Twisted Proline : 0.71 % Twisted General : 0.09 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.20 (0.14), residues: 3521 helix: 1.03 (0.15), residues: 1191 sheet: -0.23 (0.30), residues: 297 loop : -2.15 (0.13), residues: 2033 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 10 TYR 0.024 0.002 TYR M 123 PHE 0.019 0.002 PHE D 380 TRP 0.016 0.002 TRP C 183 HIS 0.006 0.001 HIS C1237 Details of bonding type rmsd/Z covalent geometry : bond 0.00548 / 0.23 (28600) covalent geometry : angle 0.73897 / 0.39 (39349) hydrogen bonds : bond 0.04895 / 3.39 ( 1043) hydrogen bonds : angle 4.50684 / 3.15 ( 2928) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7042 Ramachandran restraints generated. 3521 Oldfield, 0 Emsley, 3521 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7042 Ramachandran restraints generated. 3521 Oldfield, 0 Emsley, 3521 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 386 residues out of total 3027 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 105 poor density : 281 time to evaluate : 0.759 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 33 ARG cc_start: 0.7572 (mmm160) cc_final: 0.7191 (tpt90) REVERT: B 49 SER cc_start: 0.8755 (t) cc_final: 0.8180 (m) REVERT: C 370 MET cc_start: 0.8689 (tmm) cc_final: 0.8458 (tmm) REVERT: C 1288 GLN cc_start: 0.9474 (OUTLIER) cc_final: 0.8893 (tt0) REVERT: D 93 THR cc_start: 0.8441 (OUTLIER) cc_final: 0.8017 (p) REVERT: D 186 GLN cc_start: 0.9174 (tt0) cc_final: 0.8776 (tm-30) REVERT: D 332 LYS cc_start: 0.5826 (OUTLIER) cc_final: 0.5276 (mmtt) REVERT: D 454 CYS cc_start: 0.8513 (OUTLIER) cc_final: 0.8253 (m) REVERT: D 552 ILE cc_start: 0.9045 (mt) cc_final: 0.8812 (pt) REVERT: D 691 ASP cc_start: 0.8216 (m-30) cc_final: 0.8009 (m-30) REVERT: D 1040 MET cc_start: 0.0126 (OUTLIER) cc_final: -0.1408 (tpt) REVERT: E 69 ARG cc_start: 0.8031 (mtm110) cc_final: 0.7827 (mtm110) REVERT: M 121 GLN cc_start: 0.5560 (tm-30) cc_final: 0.5287 (tm-30) REVERT: M 181 ARG cc_start: 0.8692 (ttt180) cc_final: 0.7980 (ttt180) outliers start: 105 outliers final: 80 residues processed: 360 average time/residue: 0.1614 time to fit residues: 95.9931 Evaluate side-chains 351 residues out of total 3027 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 266 time to evaluate : 1.023 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 LEU Chi-restraints excluded: chain A residue 15 ASP Chi-restraints excluded: chain A residue 77 ASP Chi-restraints excluded: chain A residue 146 VAL Chi-restraints excluded: chain A residue 157 THR Chi-restraints excluded: chain A residue 160 HIS Chi-restraints excluded: chain A residue 180 VAL Chi-restraints excluded: chain A residue 183 ILE Chi-restraints excluded: chain A residue 187 VAL Chi-restraints excluded: chain A residue 198 LEU Chi-restraints excluded: chain A residue 205 MET Chi-restraints excluded: chain B residue 14 VAL Chi-restraints excluded: chain B residue 26 VAL Chi-restraints excluded: chain B residue 46 ILE Chi-restraints excluded: chain B residue 74 VAL Chi-restraints excluded: chain B residue 153 VAL Chi-restraints excluded: chain B residue 180 VAL Chi-restraints excluded: chain C residue 104 ILE Chi-restraints excluded: chain C residue 144 VAL Chi-restraints excluded: chain C residue 146 VAL Chi-restraints excluded: chain C residue 158 ASP Chi-restraints excluded: chain C residue 176 ILE Chi-restraints excluded: chain C residue 182 SER Chi-restraints excluded: chain C residue 246 LEU Chi-restraints excluded: chain C residue 338 THR Chi-restraints excluded: chain C residue 365 GLU Chi-restraints excluded: chain C residue 395 TYR Chi-restraints excluded: chain C residue 420 LEU Chi-restraints excluded: chain C residue 426 ILE Chi-restraints excluded: chain C residue 428 VAL Chi-restraints excluded: chain C residue 469 VAL Chi-restraints excluded: chain C residue 471 VAL Chi-restraints excluded: chain C residue 475 VAL Chi-restraints excluded: chain C residue 479 LEU Chi-restraints excluded: chain C residue 481 LEU Chi-restraints excluded: chain C residue 545 PHE Chi-restraints excluded: chain C residue 558 VAL Chi-restraints excluded: chain C residue 630 VAL Chi-restraints excluded: chain C residue 663 VAL Chi-restraints excluded: chain C residue 710 VAL Chi-restraints excluded: chain C residue 740 GLU Chi-restraints excluded: chain C residue 759 SER Chi-restraints excluded: chain C residue 785 ASP Chi-restraints excluded: chain C residue 796 LEU Chi-restraints excluded: chain C residue 878 THR Chi-restraints excluded: chain C residue 1037 THR Chi-restraints excluded: chain C residue 1052 VAL Chi-restraints excluded: chain C residue 1207 SER Chi-restraints excluded: chain C residue 1275 VAL Chi-restraints excluded: chain C residue 1288 GLN Chi-restraints excluded: chain C residue 1297 ASP Chi-restraints excluded: chain C residue 1322 SER Chi-restraints excluded: chain D residue 8 LEU Chi-restraints excluded: chain D residue 29 MET Chi-restraints excluded: chain D residue 70 CYS Chi-restraints excluded: chain D residue 93 THR Chi-restraints excluded: chain D residue 105 ILE Chi-restraints excluded: chain D residue 117 LEU Chi-restraints excluded: chain D residue 290 ILE Chi-restraints excluded: chain D residue 303 VAL Chi-restraints excluded: chain D residue 316 ILE Chi-restraints excluded: chain D residue 317 THR Chi-restraints excluded: chain D residue 332 LYS Chi-restraints excluded: chain D residue 353 SER Chi-restraints excluded: chain D residue 421 VAL Chi-restraints excluded: chain D residue 440 VAL Chi-restraints excluded: chain D residue 454 CYS Chi-restraints excluded: chain D residue 470 VAL Chi-restraints excluded: chain D residue 499 ILE Chi-restraints excluded: chain D residue 518 VAL Chi-restraints excluded: chain D residue 548 VAL Chi-restraints excluded: chain D residue 612 LEU Chi-restraints excluded: chain D residue 645 VAL Chi-restraints excluded: chain D residue 661 VAL Chi-restraints excluded: chain D residue 712 GLN Chi-restraints excluded: chain D residue 801 VAL Chi-restraints excluded: chain D residue 803 VAL Chi-restraints excluded: chain D residue 823 THR Chi-restraints excluded: chain D residue 825 VAL Chi-restraints excluded: chain D residue 1040 MET Chi-restraints excluded: chain D residue 1175 LEU Chi-restraints excluded: chain D residue 1209 VAL Chi-restraints excluded: chain D residue 1267 VAL Chi-restraints excluded: chain D residue 1351 VAL Chi-restraints excluded: chain E residue 39 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 346 random chunks: chunk 302 optimal weight: 0.9980 chunk 65 optimal weight: 20.0000 chunk 179 optimal weight: 2.9990 chunk 67 optimal weight: 8.9990 chunk 52 optimal weight: 10.0000 chunk 178 optimal weight: 0.7980 chunk 234 optimal weight: 7.9990 chunk 335 optimal weight: 0.0060 chunk 187 optimal weight: 9.9990 chunk 123 optimal weight: 0.8980 chunk 176 optimal weight: 4.9990 overall best weight: 1.1398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 430 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 504 GLN D 861 ASN D 929 GLN E 15 ASN E 43 ASN M 157 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3964 r_free = 0.3964 target = 0.144844 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 90)----------------| | r_work = 0.3138 r_free = 0.3138 target = 0.092119 restraints weight = 53683.322| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3167 r_free = 0.3167 target = 0.093453 restraints weight = 35379.932| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3148 r_free = 0.3148 target = 0.092645 restraints weight = 26348.976| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3156 r_free = 0.3156 target = 0.093062 restraints weight = 28721.232| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3156 r_free = 0.3156 target = 0.093114 restraints weight = 25284.729| |-----------------------------------------------------------------------------| r_work (final): 0.3095 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3095 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3095 r_free = 0.3095 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.51 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3095 r_free = 0.3095 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3095 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8477 moved from start: 0.5406 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 28600 Z= 0.130 Angle : 0.666 11.493 39349 Z= 0.346 Chirality : 0.045 0.357 4734 Planarity : 0.004 0.079 4806 Dihedral : 18.105 178.500 4979 Min Nonbonded Distance : 2.201 Molprobity Statistics. All-atom Clashscore : 7.33 Ramachandran Plot: Outliers : 0.62 % Allowed : 7.95 % Favored : 91.42 % Rotamer: Outliers : 3.30 % Allowed : 16.82 % Favored : 79.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.14 % Cis-general : 0.03 % Twisted Proline : 0.71 % Twisted General : 0.09 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.02 (0.14), residues: 3521 helix: 1.26 (0.15), residues: 1191 sheet: -0.29 (0.30), residues: 301 loop : -2.06 (0.13), residues: 2029 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 473 TYR 0.028 0.001 TYR A 185 PHE 0.010 0.001 PHE D 62 TRP 0.015 0.001 TRP C 183 HIS 0.005 0.001 HIS C 554 Details of bonding type rmsd/Z covalent geometry : bond 0.00266 / 0.13 (28600) covalent geometry : angle 0.66593 / 0.35 (39349) hydrogen bonds : bond 0.03899 / 2.71 ( 1043) hydrogen bonds : angle 4.30095 / 3.00 ( 2928) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7042 Ramachandran restraints generated. 3521 Oldfield, 0 Emsley, 3521 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7042 Ramachandran restraints generated. 3521 Oldfield, 0 Emsley, 3521 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 356 residues out of total 3027 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 274 time to evaluate : 0.993 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 33 ARG cc_start: 0.7518 (mmm160) cc_final: 0.7208 (tpt90) REVERT: B 49 SER cc_start: 0.8652 (t) cc_final: 0.8066 (m) REVERT: C 473 ARG cc_start: 0.8400 (ttp80) cc_final: 0.7765 (tmm160) REVERT: C 1288 GLN cc_start: 0.9451 (OUTLIER) cc_final: 0.8948 (tt0) REVERT: D 93 THR cc_start: 0.8299 (OUTLIER) cc_final: 0.7889 (p) REVERT: D 186 GLN cc_start: 0.9216 (tt0) cc_final: 0.8791 (tm-30) REVERT: D 322 ARG cc_start: 0.7614 (mmt-90) cc_final: 0.7391 (mmt-90) REVERT: D 332 LYS cc_start: 0.5625 (OUTLIER) cc_final: 0.5043 (mmtt) REVERT: D 454 CYS cc_start: 0.8446 (OUTLIER) cc_final: 0.8075 (m) REVERT: D 552 ILE cc_start: 0.9025 (mt) cc_final: 0.8792 (pt) REVERT: D 691 ASP cc_start: 0.8160 (m-30) cc_final: 0.7924 (m-30) REVERT: D 1040 MET cc_start: 0.0204 (OUTLIER) cc_final: -0.1268 (tpt) REVERT: D 1155 ILE cc_start: 0.8290 (OUTLIER) cc_final: 0.8046 (tp) REVERT: M 146 ASP cc_start: 0.8612 (p0) cc_final: 0.8314 (p0) outliers start: 82 outliers final: 64 residues processed: 339 average time/residue: 0.1647 time to fit residues: 91.8830 Evaluate side-chains 331 residues out of total 3027 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 261 time to evaluate : 0.722 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 77 ASP Chi-restraints excluded: chain A residue 102 LEU Chi-restraints excluded: chain A residue 146 VAL Chi-restraints excluded: chain A residue 160 HIS Chi-restraints excluded: chain A residue 180 VAL Chi-restraints excluded: chain A residue 183 ILE Chi-restraints excluded: chain A residue 187 VAL Chi-restraints excluded: chain A residue 198 LEU Chi-restraints excluded: chain B residue 14 VAL Chi-restraints excluded: chain B residue 26 VAL Chi-restraints excluded: chain B residue 46 ILE Chi-restraints excluded: chain B residue 74 VAL Chi-restraints excluded: chain B residue 153 VAL Chi-restraints excluded: chain B residue 180 VAL Chi-restraints excluded: chain C residue 144 VAL Chi-restraints excluded: chain C residue 146 VAL Chi-restraints excluded: chain C residue 176 ILE Chi-restraints excluded: chain C residue 182 SER Chi-restraints excluded: chain C residue 338 THR Chi-restraints excluded: chain C residue 365 GLU Chi-restraints excluded: chain C residue 395 TYR Chi-restraints excluded: chain C residue 420 LEU Chi-restraints excluded: chain C residue 426 ILE Chi-restraints excluded: chain C residue 469 VAL Chi-restraints excluded: chain C residue 471 VAL Chi-restraints excluded: chain C residue 479 LEU Chi-restraints excluded: chain C residue 481 LEU Chi-restraints excluded: chain C residue 541 GLU Chi-restraints excluded: chain C residue 545 PHE Chi-restraints excluded: chain C residue 630 VAL Chi-restraints excluded: chain C residue 740 GLU Chi-restraints excluded: chain C residue 759 SER Chi-restraints excluded: chain C residue 773 LEU Chi-restraints excluded: chain C residue 796 LEU Chi-restraints excluded: chain C residue 878 THR Chi-restraints excluded: chain C residue 1037 THR Chi-restraints excluded: chain C residue 1052 VAL Chi-restraints excluded: chain C residue 1275 VAL Chi-restraints excluded: chain C residue 1288 GLN Chi-restraints excluded: chain C residue 1322 SER Chi-restraints excluded: chain C residue 1327 LEU Chi-restraints excluded: chain D residue 29 MET Chi-restraints excluded: chain D residue 70 CYS Chi-restraints excluded: chain D residue 88 CYS Chi-restraints excluded: chain D residue 93 THR Chi-restraints excluded: chain D residue 117 LEU Chi-restraints excluded: chain D residue 130 MET Chi-restraints excluded: chain D residue 290 ILE Chi-restraints excluded: chain D residue 317 THR Chi-restraints excluded: chain D residue 332 LYS Chi-restraints excluded: chain D residue 353 SER Chi-restraints excluded: chain D residue 440 VAL Chi-restraints excluded: chain D residue 454 CYS Chi-restraints excluded: chain D residue 470 VAL Chi-restraints excluded: chain D residue 499 ILE Chi-restraints excluded: chain D residue 518 VAL Chi-restraints excluded: chain D residue 548 VAL Chi-restraints excluded: chain D residue 612 LEU Chi-restraints excluded: chain D residue 645 VAL Chi-restraints excluded: chain D residue 661 VAL Chi-restraints excluded: chain D residue 803 VAL Chi-restraints excluded: chain D residue 823 THR Chi-restraints excluded: chain D residue 825 VAL Chi-restraints excluded: chain D residue 1040 MET Chi-restraints excluded: chain D residue 1155 ILE Chi-restraints excluded: chain D residue 1175 LEU Chi-restraints excluded: chain D residue 1209 VAL Chi-restraints excluded: chain D residue 1267 VAL Chi-restraints excluded: chain D residue 1351 VAL Chi-restraints excluded: chain E residue 39 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 346 random chunks: chunk 324 optimal weight: 50.0000 chunk 329 optimal weight: 30.0000 chunk 13 optimal weight: 9.9990 chunk 131 optimal weight: 10.0000 chunk 311 optimal weight: 3.9990 chunk 9 optimal weight: 0.9980 chunk 20 optimal weight: 10.0000 chunk 255 optimal weight: 6.9990 chunk 111 optimal weight: 5.9990 chunk 213 optimal weight: 0.0980 chunk 269 optimal weight: 6.9990 overall best weight: 3.6186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 430 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 504 GLN D 861 ASN ** E 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 43 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3926 r_free = 0.3926 target = 0.141993 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 104)---------------| | r_work = 0.3149 r_free = 0.3149 target = 0.090793 restraints weight = 53754.049| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3092 r_free = 0.3092 target = 0.089251 restraints weight = 39394.549| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3092 r_free = 0.3092 target = 0.089404 restraints weight = 34630.427| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3098 r_free = 0.3098 target = 0.089772 restraints weight = 33531.871| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3097 r_free = 0.3097 target = 0.089650 restraints weight = 31858.989| |-----------------------------------------------------------------------------| r_work (final): 0.3047 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3048 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3048 r_free = 0.3048 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3047 r_free = 0.3047 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3047 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8512 moved from start: 0.5634 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.059 28600 Z= 0.236 Angle : 0.720 11.444 39349 Z= 0.376 Chirality : 0.047 0.403 4734 Planarity : 0.005 0.081 4806 Dihedral : 18.088 179.264 4979 Min Nonbonded Distance : 2.168 Molprobity Statistics. All-atom Clashscore : 7.81 Ramachandran Plot: Outliers : 0.62 % Allowed : 9.74 % Favored : 89.63 % Rotamer: Outliers : 3.50 % Allowed : 16.74 % Favored : 79.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.14 % Cis-general : 0.03 % Twisted Proline : 0.71 % Twisted General : 0.09 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.09 (0.14), residues: 3521 helix: 1.19 (0.15), residues: 1200 sheet: -0.33 (0.29), residues: 309 loop : -2.13 (0.13), residues: 2012 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG D 744 TYR 0.020 0.002 TYR A 185 PHE 0.015 0.001 PHE D 380 TRP 0.015 0.002 TRP C 183 HIS 0.004 0.001 HIS C1237 Details of bonding type rmsd/Z covalent geometry : bond 0.00564 / 0.24 (28600) covalent geometry : angle 0.72014 / 0.38 (39349) hydrogen bonds : bond 0.04695 / 3.25 ( 1043) hydrogen bonds : angle 4.39100 / 3.06 ( 2928) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7042 Ramachandran restraints generated. 3521 Oldfield, 0 Emsley, 3521 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7042 Ramachandran restraints generated. 3521 Oldfield, 0 Emsley, 3521 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 352 residues out of total 3027 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 265 time to evaluate : 0.911 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 33 ARG cc_start: 0.7621 (mmm160) cc_final: 0.7243 (tpt90) REVERT: B 49 SER cc_start: 0.8709 (t) cc_final: 0.8135 (m) REVERT: C 974 ARG cc_start: 0.8589 (ptp-170) cc_final: 0.8221 (ptp-170) REVERT: C 1288 GLN cc_start: 0.9478 (OUTLIER) cc_final: 0.8896 (tt0) REVERT: D 93 THR cc_start: 0.8431 (OUTLIER) cc_final: 0.8009 (p) REVERT: D 186 GLN cc_start: 0.9141 (tt0) cc_final: 0.8778 (tm-30) REVERT: D 332 LYS cc_start: 0.5829 (OUTLIER) cc_final: 0.5181 (mmtt) REVERT: D 552 ILE cc_start: 0.9080 (mt) cc_final: 0.8838 (pt) REVERT: D 691 ASP cc_start: 0.8180 (m-30) cc_final: 0.7936 (m-30) REVERT: D 839 VAL cc_start: 0.8842 (t) cc_final: 0.8592 (t) REVERT: D 1040 MET cc_start: 0.0242 (OUTLIER) cc_final: -0.1304 (tpt) REVERT: D 1155 ILE cc_start: 0.8391 (OUTLIER) cc_final: 0.8077 (tp) REVERT: M 121 GLN cc_start: 0.5605 (tm-30) cc_final: 0.5302 (tm-30) REVERT: M 146 ASP cc_start: 0.8610 (p0) cc_final: 0.8162 (p0) outliers start: 87 outliers final: 75 residues processed: 332 average time/residue: 0.1627 time to fit residues: 89.4826 Evaluate side-chains 339 residues out of total 3027 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 259 time to evaluate : 0.998 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 ASP Chi-restraints excluded: chain A residue 77 ASP Chi-restraints excluded: chain A residue 102 LEU Chi-restraints excluded: chain A residue 146 VAL Chi-restraints excluded: chain A residue 160 HIS Chi-restraints excluded: chain A residue 180 VAL Chi-restraints excluded: chain A residue 183 ILE Chi-restraints excluded: chain A residue 187 VAL Chi-restraints excluded: chain A residue 198 LEU Chi-restraints excluded: chain A residue 205 MET Chi-restraints excluded: chain B residue 14 VAL Chi-restraints excluded: chain B residue 26 VAL Chi-restraints excluded: chain B residue 46 ILE Chi-restraints excluded: chain B residue 74 VAL Chi-restraints excluded: chain B residue 153 VAL Chi-restraints excluded: chain B residue 180 VAL Chi-restraints excluded: chain C residue 144 VAL Chi-restraints excluded: chain C residue 146 VAL Chi-restraints excluded: chain C residue 151 ARG Chi-restraints excluded: chain C residue 182 SER Chi-restraints excluded: chain C residue 338 THR Chi-restraints excluded: chain C residue 365 GLU Chi-restraints excluded: chain C residue 395 TYR Chi-restraints excluded: chain C residue 420 LEU Chi-restraints excluded: chain C residue 426 ILE Chi-restraints excluded: chain C residue 469 VAL Chi-restraints excluded: chain C residue 471 VAL Chi-restraints excluded: chain C residue 479 LEU Chi-restraints excluded: chain C residue 481 LEU Chi-restraints excluded: chain C residue 541 GLU Chi-restraints excluded: chain C residue 545 PHE Chi-restraints excluded: chain C residue 558 VAL Chi-restraints excluded: chain C residue 630 VAL Chi-restraints excluded: chain C residue 663 VAL Chi-restraints excluded: chain C residue 710 VAL Chi-restraints excluded: chain C residue 740 GLU Chi-restraints excluded: chain C residue 759 SER Chi-restraints excluded: chain C residue 773 LEU Chi-restraints excluded: chain C residue 785 ASP Chi-restraints excluded: chain C residue 796 LEU Chi-restraints excluded: chain C residue 878 THR Chi-restraints excluded: chain C residue 1037 THR Chi-restraints excluded: chain C residue 1052 VAL Chi-restraints excluded: chain C residue 1275 VAL Chi-restraints excluded: chain C residue 1288 GLN Chi-restraints excluded: chain C residue 1297 ASP Chi-restraints excluded: chain C residue 1322 SER Chi-restraints excluded: chain C residue 1327 LEU Chi-restraints excluded: chain D residue 29 MET Chi-restraints excluded: chain D residue 70 CYS Chi-restraints excluded: chain D residue 88 CYS Chi-restraints excluded: chain D residue 93 THR Chi-restraints excluded: chain D residue 117 LEU Chi-restraints excluded: chain D residue 130 MET Chi-restraints excluded: chain D residue 290 ILE Chi-restraints excluded: chain D residue 317 THR Chi-restraints excluded: chain D residue 332 LYS Chi-restraints excluded: chain D residue 353 SER Chi-restraints excluded: chain D residue 421 VAL Chi-restraints excluded: chain D residue 440 VAL Chi-restraints excluded: chain D residue 470 VAL Chi-restraints excluded: chain D residue 499 ILE Chi-restraints excluded: chain D residue 518 VAL Chi-restraints excluded: chain D residue 548 VAL Chi-restraints excluded: chain D residue 612 LEU Chi-restraints excluded: chain D residue 645 VAL Chi-restraints excluded: chain D residue 661 VAL Chi-restraints excluded: chain D residue 801 VAL Chi-restraints excluded: chain D residue 803 VAL Chi-restraints excluded: chain D residue 823 THR Chi-restraints excluded: chain D residue 825 VAL Chi-restraints excluded: chain D residue 1040 MET Chi-restraints excluded: chain D residue 1155 ILE Chi-restraints excluded: chain D residue 1175 LEU Chi-restraints excluded: chain D residue 1209 VAL Chi-restraints excluded: chain D residue 1267 VAL Chi-restraints excluded: chain D residue 1351 VAL Chi-restraints excluded: chain E residue 39 VAL Chi-restraints excluded: chain M residue 210 THR Chi-restraints excluded: chain M residue 418 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 346 random chunks: chunk 148 optimal weight: 0.9990 chunk 134 optimal weight: 3.9990 chunk 28 optimal weight: 5.9990 chunk 52 optimal weight: 9.9990 chunk 135 optimal weight: 10.0000 chunk 301 optimal weight: 4.9990 chunk 43 optimal weight: 4.9990 chunk 222 optimal weight: 0.9990 chunk 152 optimal weight: 0.9980 chunk 162 optimal weight: 4.9990 chunk 61 optimal weight: 2.9990 overall best weight: 1.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 430 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 504 GLN E 7 GLN ** E 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 43 ASN M 157 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3942 r_free = 0.3942 target = 0.143168 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 84)----------------| | r_work = 0.3175 r_free = 0.3175 target = 0.092086 restraints weight = 53627.885| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3120 r_free = 0.3120 target = 0.090397 restraints weight = 39139.082| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3126 r_free = 0.3126 target = 0.090943 restraints weight = 34083.757| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3129 r_free = 0.3129 target = 0.091054 restraints weight = 33602.612| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3129 r_free = 0.3129 target = 0.091076 restraints weight = 29377.345| |-----------------------------------------------------------------------------| r_work (final): 0.3085 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3083 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3083 r_free = 0.3083 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3083 r_free = 0.3083 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3083 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8467 moved from start: 0.5699 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 28600 Z= 0.159 Angle : 0.682 11.840 39349 Z= 0.355 Chirality : 0.045 0.369 4734 Planarity : 0.004 0.080 4806 Dihedral : 17.980 176.375 4979 Min Nonbonded Distance : 2.171 Molprobity Statistics. All-atom Clashscore : 7.46 Ramachandran Plot: Outliers : 0.62 % Allowed : 8.66 % Favored : 90.71 % Rotamer: Outliers : 3.22 % Allowed : 17.18 % Favored : 79.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.14 % Cis-general : 0.03 % Twisted Proline : 0.71 % Twisted General : 0.09 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.03 (0.14), residues: 3521 helix: 1.23 (0.15), residues: 1211 sheet: -0.38 (0.29), residues: 328 loop : -2.10 (0.13), residues: 1982 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 744 TYR 0.023 0.001 TYR A 185 PHE 0.011 0.001 PHE D 620 TRP 0.013 0.001 TRP C 183 HIS 0.004 0.001 HIS C 554 Details of bonding type rmsd/Z covalent geometry : bond 0.00355 / 0.16 (28600) covalent geometry : angle 0.68220 / 0.35 (39349) hydrogen bonds : bond 0.04153 / 2.89 ( 1043) hydrogen bonds : angle 4.28682 / 2.98 ( 2928) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7042 Ramachandran restraints generated. 3521 Oldfield, 0 Emsley, 3521 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7042 Ramachandran restraints generated. 3521 Oldfield, 0 Emsley, 3521 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 350 residues out of total 3027 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 270 time to evaluate : 1.038 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 33 ARG cc_start: 0.7596 (mmm160) cc_final: 0.7234 (tpt90) REVERT: B 49 SER cc_start: 0.8667 (t) cc_final: 0.8109 (m) REVERT: C 309 LEU cc_start: 0.5047 (OUTLIER) cc_final: 0.4662 (tp) REVERT: C 473 ARG cc_start: 0.8418 (ttp80) cc_final: 0.8103 (ttp80) REVERT: C 974 ARG cc_start: 0.8658 (ptp-170) cc_final: 0.8250 (ptp-170) REVERT: C 1288 GLN cc_start: 0.9491 (OUTLIER) cc_final: 0.8953 (tt0) REVERT: D 93 THR cc_start: 0.8418 (OUTLIER) cc_final: 0.7975 (p) REVERT: D 186 GLN cc_start: 0.9108 (tt0) cc_final: 0.8769 (tm-30) REVERT: D 332 LYS cc_start: 0.5745 (OUTLIER) cc_final: 0.5193 (mmtt) REVERT: D 552 ILE cc_start: 0.9055 (mt) cc_final: 0.8816 (pt) REVERT: D 691 ASP cc_start: 0.8171 (m-30) cc_final: 0.7955 (m-30) REVERT: D 1040 MET cc_start: 0.0247 (OUTLIER) cc_final: -0.1285 (tpt) REVERT: D 1155 ILE cc_start: 0.8308 (OUTLIER) cc_final: 0.8019 (tp) REVERT: M 121 GLN cc_start: 0.5604 (tm-30) cc_final: 0.5353 (tm-30) REVERT: M 146 ASP cc_start: 0.8563 (p0) cc_final: 0.8275 (p0) REVERT: M 181 ARG cc_start: 0.8598 (ttt180) cc_final: 0.7859 (ttt180) outliers start: 80 outliers final: 68 residues processed: 333 average time/residue: 0.1614 time to fit residues: 88.2565 Evaluate side-chains 331 residues out of total 3027 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 257 time to evaluate : 1.095 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 77 ASP Chi-restraints excluded: chain A residue 102 LEU Chi-restraints excluded: chain A residue 146 VAL Chi-restraints excluded: chain A residue 160 HIS Chi-restraints excluded: chain A residue 180 VAL Chi-restraints excluded: chain A residue 183 ILE Chi-restraints excluded: chain A residue 187 VAL Chi-restraints excluded: chain A residue 198 LEU Chi-restraints excluded: chain B residue 14 VAL Chi-restraints excluded: chain B residue 26 VAL Chi-restraints excluded: chain B residue 46 ILE Chi-restraints excluded: chain B residue 74 VAL Chi-restraints excluded: chain B residue 153 VAL Chi-restraints excluded: chain B residue 180 VAL Chi-restraints excluded: chain C residue 144 VAL Chi-restraints excluded: chain C residue 146 VAL Chi-restraints excluded: chain C residue 151 ARG Chi-restraints excluded: chain C residue 309 LEU Chi-restraints excluded: chain C residue 338 THR Chi-restraints excluded: chain C residue 365 GLU Chi-restraints excluded: chain C residue 395 TYR Chi-restraints excluded: chain C residue 420 LEU Chi-restraints excluded: chain C residue 426 ILE Chi-restraints excluded: chain C residue 469 VAL Chi-restraints excluded: chain C residue 471 VAL Chi-restraints excluded: chain C residue 479 LEU Chi-restraints excluded: chain C residue 481 LEU Chi-restraints excluded: chain C residue 541 GLU Chi-restraints excluded: chain C residue 545 PHE Chi-restraints excluded: chain C residue 558 VAL Chi-restraints excluded: chain C residue 630 VAL Chi-restraints excluded: chain C residue 663 VAL Chi-restraints excluded: chain C residue 740 GLU Chi-restraints excluded: chain C residue 759 SER Chi-restraints excluded: chain C residue 773 LEU Chi-restraints excluded: chain C residue 785 ASP Chi-restraints excluded: chain C residue 796 LEU Chi-restraints excluded: chain C residue 878 THR Chi-restraints excluded: chain C residue 1052 VAL Chi-restraints excluded: chain C residue 1275 VAL Chi-restraints excluded: chain C residue 1288 GLN Chi-restraints excluded: chain C residue 1322 SER Chi-restraints excluded: chain C residue 1327 LEU Chi-restraints excluded: chain D residue 29 MET Chi-restraints excluded: chain D residue 70 CYS Chi-restraints excluded: chain D residue 93 THR Chi-restraints excluded: chain D residue 117 LEU Chi-restraints excluded: chain D residue 130 MET Chi-restraints excluded: chain D residue 290 ILE Chi-restraints excluded: chain D residue 317 THR Chi-restraints excluded: chain D residue 332 LYS Chi-restraints excluded: chain D residue 353 SER Chi-restraints excluded: chain D residue 440 VAL Chi-restraints excluded: chain D residue 470 VAL Chi-restraints excluded: chain D residue 499 ILE Chi-restraints excluded: chain D residue 501 VAL Chi-restraints excluded: chain D residue 518 VAL Chi-restraints excluded: chain D residue 548 VAL Chi-restraints excluded: chain D residue 612 LEU Chi-restraints excluded: chain D residue 645 VAL Chi-restraints excluded: chain D residue 661 VAL Chi-restraints excluded: chain D residue 801 VAL Chi-restraints excluded: chain D residue 803 VAL Chi-restraints excluded: chain D residue 823 THR Chi-restraints excluded: chain D residue 825 VAL Chi-restraints excluded: chain D residue 1040 MET Chi-restraints excluded: chain D residue 1155 ILE Chi-restraints excluded: chain D residue 1175 LEU Chi-restraints excluded: chain D residue 1209 VAL Chi-restraints excluded: chain D residue 1267 VAL Chi-restraints excluded: chain D residue 1351 VAL Chi-restraints excluded: chain E residue 39 VAL Chi-restraints excluded: chain M residue 210 THR Chi-restraints excluded: chain M residue 418 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 346 random chunks: chunk 157 optimal weight: 1.9990 chunk 82 optimal weight: 20.0000 chunk 238 optimal weight: 0.0050 chunk 2 optimal weight: 9.9990 chunk 74 optimal weight: 0.0570 chunk 270 optimal weight: 1.9990 chunk 29 optimal weight: 4.9990 chunk 262 optimal weight: 0.5980 chunk 205 optimal weight: 0.7980 chunk 320 optimal weight: 9.9990 chunk 305 optimal weight: 10.0000 overall best weight: 0.6914 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 519 ASN ** D 430 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 504 GLN ** D 716 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 15 ASN E 43 ASN ** M 157 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3966 r_free = 0.3966 target = 0.144976 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 85)----------------| | r_work = 0.3223 r_free = 0.3223 target = 0.094631 restraints weight = 53731.466| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3178 r_free = 0.3178 target = 0.093545 restraints weight = 38844.838| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3174 r_free = 0.3174 target = 0.093550 restraints weight = 33020.712| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3180 r_free = 0.3180 target = 0.093949 restraints weight = 31120.113| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3180 r_free = 0.3180 target = 0.093952 restraints weight = 29551.445| |-----------------------------------------------------------------------------| r_work (final): 0.3135 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3133 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3133 r_free = 0.3133 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3133 r_free = 0.3133 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3133 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8417 moved from start: 0.5710 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 28600 Z= 0.121 Angle : 0.661 11.898 39349 Z= 0.341 Chirality : 0.044 0.361 4734 Planarity : 0.004 0.078 4806 Dihedral : 17.820 173.864 4979 Min Nonbonded Distance : 2.174 Molprobity Statistics. All-atom Clashscore : 7.14 Ramachandran Plot: Outliers : 0.57 % Allowed : 8.78 % Favored : 90.66 % Rotamer: Outliers : 2.98 % Allowed : 17.67 % Favored : 79.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.14 % Cis-general : 0.03 % Twisted Proline : 0.71 % Twisted General : 0.09 % 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: -0.95 (0.14), residues: 3521 helix: 1.32 (0.15), residues: 1211 sheet: -0.37 (0.28), residues: 347 loop : -2.07 (0.13), residues: 1963 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG D 322 TYR 0.025 0.001 TYR A 185 PHE 0.012 0.001 PHE C 390 TRP 0.014 0.001 TRP D 580 HIS 0.003 0.001 HIS C 554 Details of bonding type rmsd/Z covalent geometry : bond 0.00244 / 0.12 (28600) covalent geometry : angle 0.66128 / 0.34 (39349) hydrogen bonds : bond 0.03603 / 2.50 ( 1043) hydrogen bonds : angle 4.18822 / 2.91 ( 2928) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5075.52 seconds wall clock time: 87 minutes 52.72 seconds (5272.72 seconds total)