Starting phenix.real_space_refine on Sat Aug 8 14:10:29 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8bmw_16126/08_2026/8bmw_16126.cif Found real_map, /net/cci-nas-00/data/ceres_data/8bmw_16126/08_2026/8bmw_16126.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8bmw_16126/08_2026/8bmw_16126.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8bmw_16126/08_2026/8bmw_16126.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/8bmw_16126/08_2026/8bmw_16126.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8bmw_16126/08_2026/8bmw_16126.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8bmw_16126/08_2026/8bmw_16126.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8bmw_16126/08_2026/8bmw_16126.map" } resolution = 3.5 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 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 47 5.49 5 S 107 5.16 5 C 18138 2.51 5 N 4786 2.21 5 O 5580 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 24 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 28658 Number of models: 1 Model: "" Number of chains: 15 Chain: "A" Number of atoms: 964 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 964 Classifications: {'peptide': 121} Link IDs: {'PTRANS': 4, 'TRANS': 116} Chain: "B" Number of atoms: 948 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 948 Classifications: {'peptide': 119} Link IDs: {'PTRANS': 4, 'TRANS': 114} Chain: "C" Number of atoms: 957 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 957 Classifications: {'peptide': 120} Link IDs: {'PTRANS': 4, 'TRANS': 115} Chain: "D" Number of atoms: 964 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 964 Classifications: {'peptide': 121} Link IDs: {'PTRANS': 4, 'TRANS': 116} Chain: "E" Number of atoms: 973 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 973 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 4, 'TRANS': 117} Chain: "J" Number of atoms: 2121 Number of conformers: 1 Conformer: "" Number of residues, atoms: 270, 2121 Classifications: {'peptide': 270} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 11, 'TRANS': 258} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 3 Chain: "L" Number of atoms: 1585 Number of conformers: 1 Conformer: "" Number of residues, atoms: 201, 1585 Classifications: {'peptide': 201} Link IDs: {'PTRANS': 9, 'TRANS': 191} Chain: "N" Number of atoms: 2029 Number of conformers: 1 Conformer: "" Number of residues, atoms: 251, 2029 Classifications: {'peptide': 251} Link IDs: {'PTRANS': 4, 'TRANS': 246} Chain: "R" Number of atoms: 971 Number of conformers: 1 Conformer: "" Number of residues, atoms: 48, 971 Classifications: {'RNAv2': 48} Modifications used: {'rna2p_pur': 5, 'rna2p_pyr': 26, 'rna3p_pur': 1, 'rna3p_pyr': 16} Link IDs: {'rna2p': 30, 'rna3p': 17} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "G" Number of atoms: 1877 Number of conformers: 1 Conformer: "" Number of residues, atoms: 238, 1877 Classifications: {'peptide': 238} Link IDs: {'PTRANS': 8, 'TRANS': 229} Chain breaks: 1 Chain: "F" Number of atoms: 1876 Number of conformers: 1 Conformer: "" Number of residues, atoms: 239, 1876 Classifications: {'peptide': 239} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 230} Chain breaks: 1 Chain: "H" Number of atoms: 2168 Number of conformers: 1 Conformer: "" Number of residues, atoms: 275, 2168 Classifications: {'peptide': 275} Link IDs: {'PTRANS': 9, 'TRANS': 265} Chain: "I" Number of atoms: 2164 Number of conformers: 1 Conformer: "" Number of residues, atoms: 275, 2164 Classifications: {'peptide': 275} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 265} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "K" Number of atoms: 6678 Number of conformers: 1 Conformer: "" Number of residues, atoms: 829, 6678 Classifications: {'peptide': 829} Link IDs: {'PCIS': 1, 'PTRANS': 20, 'TRANS': 807} Chain: "M" Number of atoms: 2383 Number of conformers: 1 Conformer: "" Number of residues, atoms: 294, 2383 Classifications: {'peptide': 294} Link IDs: {'PTRANS': 11, 'TRANS': 282} Chain breaks: 1 Time building chain proxies: 6.20, per 1000 atoms: 0.22 Number of scatterers: 28658 At special positions: 0 Unit cell: (126.566, 119.244, 242.672, 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 107 16.00 P 47 15.00 O 5580 8.00 N 4786 7.00 C 18138 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=15, symmetry=0 Simple disulfide: pdb=" SG CYS J 223 " - pdb=" SG CYS J 255 " distance=2.03 Simple disulfide: pdb=" SG CYS L 58 " - pdb=" SG CYS L 75 " distance=2.03 Simple disulfide: pdb=" SG CYS L 58 " - pdb=" SG CYS L 78 " distance=2.03 Simple disulfide: pdb=" SG CYS L 75 " - pdb=" SG CYS L 78 " distance=2.03 Simple disulfide: pdb=" SG CYS L 180 " - pdb=" SG CYS L 185 " distance=2.03 Simple disulfide: pdb=" SG CYS G 80 " - pdb=" SG CYS G 87 " distance=2.03 Simple disulfide: pdb=" SG CYS G 105 " - pdb=" SG CYS G 108 " distance=2.03 Simple disulfide: pdb=" SG CYS F 3 " - pdb=" SG CYS F 90 " distance=2.03 Simple disulfide: pdb=" SG CYS F 80 " - pdb=" SG CYS F 87 " distance=2.03 Simple disulfide: pdb=" SG CYS F 105 " - pdb=" SG CYS F 108 " distance=2.03 Simple disulfide: pdb=" SG CYS H 82 " - pdb=" SG CYS H 123 " distance=2.02 Simple disulfide: pdb=" SG CYS H 90 " - pdb=" SG CYS H 120 " distance=2.03 Simple disulfide: pdb=" SG CYS K 261 " - pdb=" SG CYS K 278 " distance=2.03 Simple disulfide: pdb=" SG CYS K 265 " - pdb=" SG CYS K 275 " distance=2.03 Simple disulfide: pdb=" SG CYS M 220 " - pdb=" SG CYS M 224 " distance=2.03 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: 2.34 Conformation dependent library (CDL) restraints added in 1.1 seconds 6882 Ramachandran restraints generated. 3441 Oldfield, 0 Emsley, 3441 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6496 Finding SS restraints... Secondary structure from input PDB file: 119 helices and 35 sheets defined 44.3% alpha, 12.9% beta 0 base pairs and 6 stacking pairs defined. Time for finding SS restraints: 3.17 Creating SS restraints... Processing helix chain 'A' and resid 19 through 31 removed outlier: 3.548A pdb=" N ILE A 23 " --> pdb=" O ASP A 19 " (cutoff:3.500A) Processing helix chain 'A' and resid 48 through 61 Processing helix chain 'A' and resid 63 through 76 Processing helix chain 'A' and resid 80 through 93 removed outlier: 4.634A pdb=" N ASP A 93 " --> pdb=" O ALA A 89 " (cutoff:3.500A) Processing helix chain 'A' and resid 95 through 117 Processing helix chain 'A' and resid 128 through 139 removed outlier: 3.651A pdb=" N VAL A 139 " --> pdb=" O ILE A 135 " (cutoff:3.500A) Processing helix chain 'B' and resid 20 through 32 Processing helix chain 'B' and resid 46 through 61 removed outlier: 3.649A pdb=" N ILE B 50 " --> pdb=" O ASP B 46 " (cutoff:3.500A) Processing helix chain 'B' and resid 62 through 76 Processing helix chain 'B' and resid 80 through 91 Processing helix chain 'B' and resid 95 through 117 Processing helix chain 'B' and resid 119 through 123 Processing helix chain 'B' and resid 128 through 136 Processing helix chain 'C' and resid 20 through 32 Processing helix chain 'C' and resid 46 through 61 Processing helix chain 'C' and resid 63 through 76 Processing helix chain 'C' and resid 80 through 91 Processing helix chain 'C' and resid 95 through 117 Processing helix chain 'C' and resid 119 through 123 Processing helix chain 'C' and resid 129 through 138 Processing helix chain 'D' and resid 20 through 32 Processing helix chain 'D' and resid 46 through 61 Processing helix chain 'D' and resid 62 through 76 removed outlier: 3.508A pdb=" N LEU D 66 " --> pdb=" O ASN D 62 " (cutoff:3.500A) Processing helix chain 'D' and resid 80 through 91 Processing helix chain 'D' and resid 95 through 117 Processing helix chain 'D' and resid 128 through 139 Processing helix chain 'E' and resid 19 through 32 Processing helix chain 'E' and resid 46 through 60 Processing helix chain 'E' and resid 62 through 76 Processing helix chain 'E' and resid 80 through 91 Processing helix chain 'E' and resid 92 through 94 No H-bonds generated for 'chain 'E' and resid 92 through 94' Processing helix chain 'E' and resid 96 through 117 Processing helix chain 'E' and resid 119 through 124 removed outlier: 3.613A pdb=" N VAL E 123 " --> pdb=" O ASN E 119 " (cutoff:3.500A) Processing helix chain 'E' and resid 128 through 139 Processing helix chain 'J' and resid 56 through 62 removed outlier: 3.714A pdb=" N LEU J 60 " --> pdb=" O VAL J 56 " (cutoff:3.500A) Processing helix chain 'J' and resid 69 through 74 removed outlier: 3.773A pdb=" N TYR J 74 " --> pdb=" O ASN J 70 " (cutoff:3.500A) Processing helix chain 'J' and resid 92 through 108 Processing helix chain 'J' and resid 123 through 130 Processing helix chain 'J' and resid 150 through 156 Processing helix chain 'J' and resid 206 through 217 Processing helix chain 'J' and resid 255 through 266 Processing helix chain 'L' and resid 35 through 50 removed outlier: 3.597A pdb=" N ILE L 39 " --> pdb=" O PRO L 35 " (cutoff:3.500A) Processing helix chain 'L' and resid 62 through 70 Processing helix chain 'L' and resid 75 through 82 Processing helix chain 'L' and resid 144 through 160 removed outlier: 3.697A pdb=" N ARG L 159 " --> pdb=" O ILE L 155 " (cutoff:3.500A) removed outlier: 4.060A pdb=" N TYR L 160 " --> pdb=" O LEU L 156 " (cutoff:3.500A) Processing helix chain 'L' and resid 176 through 183 removed outlier: 3.754A pdb=" N VAL L 183 " --> pdb=" O ILE L 179 " (cutoff:3.500A) Processing helix chain 'L' and resid 186 through 198 removed outlier: 3.989A pdb=" N ARG L 198 " --> pdb=" O ASN L 194 " (cutoff:3.500A) Processing helix chain 'N' and resid 42 through 59 Processing helix chain 'N' and resid 60 through 65 removed outlier: 3.594A pdb=" N GLU N 65 " --> pdb=" O GLU N 61 " (cutoff:3.500A) Processing helix chain 'N' and resid 73 through 84 Processing helix chain 'N' and resid 84 through 96 Processing helix chain 'N' and resid 111 through 126 Processing helix chain 'N' and resid 127 through 134 Processing helix chain 'N' and resid 195 through 208 removed outlier: 3.516A pdb=" N GLU N 207 " --> pdb=" O LYS N 203 " (cutoff:3.500A) Processing helix chain 'N' and resid 215 through 219 removed outlier: 3.571A pdb=" N GLY N 219 " --> pdb=" O LYS N 216 " (cutoff:3.500A) Processing helix chain 'N' and resid 247 through 252 Processing helix chain 'G' and resid 53 through 73 removed outlier: 3.655A pdb=" N ASN G 73 " --> pdb=" O THR G 69 " (cutoff:3.500A) Processing helix chain 'G' and resid 105 through 112 Processing helix chain 'G' and resid 185 through 199 Processing helix chain 'G' and resid 240 through 244 Processing helix chain 'F' and resid 53 through 73 removed outlier: 3.595A pdb=" N ASN F 73 " --> pdb=" O THR F 69 " (cutoff:3.500A) Processing helix chain 'F' and resid 105 through 112 Processing helix chain 'F' and resid 180 through 200 Processing helix chain 'F' and resid 240 through 245 Processing helix chain 'H' and resid 58 through 77 Processing helix chain 'H' and resid 89 through 94 Processing helix chain 'H' and resid 96 through 106 removed outlier: 3.613A pdb=" N LYS H 105 " --> pdb=" O ASN H 101 " (cutoff:3.500A) Processing helix chain 'H' and resid 107 through 118 removed outlier: 3.612A pdb=" N ALA H 111 " --> pdb=" O ASN H 107 " (cutoff:3.500A) Processing helix chain 'H' and resid 121 through 126 Processing helix chain 'H' and resid 189 through 205 Processing helix chain 'H' and resid 253 through 270 Proline residue: H 263 - end of helix Processing helix chain 'I' and resid 58 through 77 Processing helix chain 'I' and resid 97 through 106 removed outlier: 3.738A pdb=" N ASN I 101 " --> pdb=" O GLU I 97 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N LYS I 105 " --> pdb=" O ASN I 101 " (cutoff:3.500A) removed outlier: 4.057A pdb=" N GLU I 106 " --> pdb=" O SER I 102 " (cutoff:3.500A) Processing helix chain 'I' and resid 107 through 118 Processing helix chain 'I' and resid 120 through 127 Processing helix chain 'I' and resid 189 through 206 Processing helix chain 'I' and resid 253 through 261 Processing helix chain 'I' and resid 261 through 270 Processing helix chain 'K' and resid 17 through 44 removed outlier: 4.477A pdb=" N LYS K 26 " --> pdb=" O GLN K 22 " (cutoff:3.500A) removed outlier: 4.151A pdb=" N ASP K 27 " --> pdb=" O SER K 23 " (cutoff:3.500A) Processing helix chain 'K' and resid 47 through 63 removed outlier: 3.503A pdb=" N TYR K 62 " --> pdb=" O ILE K 58 " (cutoff:3.500A) Processing helix chain 'K' and resid 78 through 90 Processing helix chain 'K' and resid 101 through 112 Processing helix chain 'K' and resid 115 through 136 removed outlier: 3.781A pdb=" N TYR K 123 " --> pdb=" O GLU K 119 " (cutoff:3.500A) removed outlier: 4.513A pdb=" N ARG K 125 " --> pdb=" O LEU K 121 " (cutoff:3.500A) removed outlier: 5.713A pdb=" N THR K 126 " --> pdb=" O ASP K 122 " (cutoff:3.500A) Processing helix chain 'K' and resid 149 through 165 removed outlier: 3.710A pdb=" N HIS K 153 " --> pdb=" O SER K 149 " (cutoff:3.500A) Processing helix chain 'K' and resid 171 through 188 Processing helix chain 'K' and resid 191 through 207 Processing helix chain 'K' and resid 211 through 224 Processing helix chain 'K' and resid 230 through 245 Processing helix chain 'K' and resid 250 through 255 Processing helix chain 'K' and resid 271 through 283 Processing helix chain 'K' and resid 283 through 300 Processing helix chain 'K' and resid 323 through 329 Processing helix chain 'K' and resid 332 through 364 removed outlier: 3.982A pdb=" N TYR K 350 " --> pdb=" O VAL K 346 " (cutoff:3.500A) removed outlier: 4.432A pdb=" N SER K 351 " --> pdb=" O THR K 347 " (cutoff:3.500A) Processing helix chain 'K' and resid 370 through 374 removed outlier: 3.791A pdb=" N LEU K 374 " --> pdb=" O ALA K 371 " (cutoff:3.500A) Processing helix chain 'K' and resid 392 through 408 Processing helix chain 'K' and resid 430 through 441 Processing helix chain 'K' and resid 442 through 446 removed outlier: 4.096A pdb=" N TYR K 446 " --> pdb=" O SER K 442 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 442 through 446' Processing helix chain 'K' and resid 482 through 495 removed outlier: 4.512A pdb=" N ASN K 494 " --> pdb=" O ASP K 490 " (cutoff:3.500A) removed outlier: 4.040A pdb=" N ARG K 495 " --> pdb=" O LEU K 491 " (cutoff:3.500A) Processing helix chain 'K' and resid 496 through 502 Processing helix chain 'K' and resid 516 through 521 Processing helix chain 'K' and resid 534 through 541 Processing helix chain 'K' and resid 560 through 567 Processing helix chain 'K' and resid 570 through 598 Processing helix chain 'K' and resid 602 through 616 Processing helix chain 'K' and resid 633 through 643 Processing helix chain 'K' and resid 644 through 649 Processing helix chain 'K' and resid 665 through 680 Processing helix chain 'K' and resid 701 through 712 Processing helix chain 'K' and resid 726 through 736 Processing helix chain 'K' and resid 740 through 750 removed outlier: 3.638A pdb=" N ASN K 750 " --> pdb=" O GLU K 746 " (cutoff:3.500A) Processing helix chain 'K' and resid 750 through 775 removed outlier: 4.436A pdb=" N LYS K 756 " --> pdb=" O GLU K 752 " (cutoff:3.500A) removed outlier: 4.951A pdb=" N SER K 764 " --> pdb=" O ASP K 760 " (cutoff:3.500A) removed outlier: 5.164A pdb=" N LEU K 765 " --> pdb=" O LYS K 761 " (cutoff:3.500A) Processing helix chain 'K' and resid 776 through 790 Processing helix chain 'K' and resid 795 through 806 removed outlier: 3.872A pdb=" N ARG K 799 " --> pdb=" O SER K 795 " (cutoff:3.500A) Processing helix chain 'K' and resid 815 through 829 removed outlier: 3.783A pdb=" N ILE K 825 " --> pdb=" O ILE K 821 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N ILE K 829 " --> pdb=" O ILE K 825 " (cutoff:3.500A) Processing helix chain 'M' and resid 31 through 47 Processing helix chain 'M' and resid 86 through 91 Processing helix chain 'M' and resid 100 through 105 Processing helix chain 'M' and resid 179 through 185 removed outlier: 4.057A pdb=" N ASP M 183 " --> pdb=" O SER M 179 " (cutoff:3.500A) Processing helix chain 'M' and resid 295 through 300 removed outlier: 3.689A pdb=" N ILE M 299 " --> pdb=" O LEU M 296 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'J' and resid 90 through 91 removed outlier: 7.959A pdb=" N PHE J 170 " --> pdb=" O LYS J 199 " (cutoff:3.500A) removed outlier: 8.762A pdb=" N LYS J 199 " --> pdb=" O PHE J 170 " (cutoff:3.500A) removed outlier: 5.433A pdb=" N MET J 172 " --> pdb=" O ALA J 197 " (cutoff:3.500A) removed outlier: 6.537A pdb=" N ALA J 197 " --> pdb=" O MET J 172 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N SER J 174 " --> pdb=" O ILE J 195 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'J' and resid 90 through 91 removed outlier: 7.959A pdb=" N PHE J 170 " --> pdb=" O LYS J 199 " (cutoff:3.500A) removed outlier: 8.762A pdb=" N LYS J 199 " --> pdb=" O PHE J 170 " (cutoff:3.500A) removed outlier: 5.433A pdb=" N MET J 172 " --> pdb=" O ALA J 197 " (cutoff:3.500A) removed outlier: 6.537A pdb=" N ALA J 197 " --> pdb=" O MET J 172 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N SER J 174 " --> pdb=" O ILE J 195 " (cutoff:3.500A) removed outlier: 4.999A pdb=" N LEU J 19 " --> pdb=" O SER J 204 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'J' and resid 37 through 40 removed outlier: 4.693A pdb=" N LYS J 40 " --> pdb=" O LEU J 81 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'J' and resid 177 through 178 Processing sheet with id=AA5, first strand: chain 'L' and resid 91 through 95 Processing sheet with id=AA6, first strand: chain 'L' and resid 102 through 107 Processing sheet with id=AA7, first strand: chain 'N' and resid 142 through 144 Processing sheet with id=AA8, first strand: chain 'N' and resid 15 through 16 Processing sheet with id=AA9, first strand: chain 'N' and resid 15 through 16 Processing sheet with id=AB1, first strand: chain 'G' and resid 120 through 122 removed outlier: 4.479A pdb=" N ASP G 219 " --> pdb=" O LYS G 18 " (cutoff:3.500A) removed outlier: 6.566A pdb=" N ARG G 20 " --> pdb=" O LEU G 217 " (cutoff:3.500A) removed outlier: 5.233A pdb=" N LEU G 217 " --> pdb=" O ARG G 20 " (cutoff:3.500A) removed outlier: 5.662A pdb=" N GLU G 22 " --> pdb=" O ILE G 215 " (cutoff:3.500A) removed outlier: 7.558A pdb=" N ILE G 215 " --> pdb=" O GLU G 22 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N ILE G 236 " --> pdb=" O LEU G 224 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'G' and resid 51 through 52 Processing sheet with id=AB3, first strand: chain 'G' and resid 132 through 137 Processing sheet with id=AB4, first strand: chain 'F' and resid 120 through 122 removed outlier: 3.575A pdb=" N LYS F 18 " --> pdb=" O ASP F 219 " (cutoff:3.500A) removed outlier: 4.489A pdb=" N ASP F 219 " --> pdb=" O LYS F 18 " (cutoff:3.500A) removed outlier: 6.684A pdb=" N ARG F 20 " --> pdb=" O LEU F 217 " (cutoff:3.500A) removed outlier: 5.294A pdb=" N LEU F 217 " --> pdb=" O ARG F 20 " (cutoff:3.500A) removed outlier: 4.349A pdb=" N ILE F 236 " --> pdb=" O LEU F 224 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'F' and resid 51 through 52 Processing sheet with id=AB6, first strand: chain 'F' and resid 90 through 91 Processing sheet with id=AB7, first strand: chain 'F' and resid 132 through 137 removed outlier: 3.532A pdb=" N LEU F 155 " --> pdb=" O ARG F 135 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'H' and resid 135 through 137 Processing sheet with id=AB9, first strand: chain 'H' and resid 135 through 137 Processing sheet with id=AC1, first strand: chain 'H' and resid 127 through 128 Processing sheet with id=AC2, first strand: chain 'H' and resid 147 through 152 removed outlier: 3.671A pdb=" N VAL H 168 " --> pdb=" O MET H 152 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'I' and resid 135 through 137 removed outlier: 3.559A pdb=" N LEU I 141 " --> pdb=" O SER I 180 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'I' and resid 135 through 137 removed outlier: 4.307A pdb=" N LYS I 225 " --> pdb=" O ASP I 21 " (cutoff:3.500A) removed outlier: 6.502A pdb=" N GLU I 23 " --> pdb=" O PHE I 223 " (cutoff:3.500A) removed outlier: 5.168A pdb=" N PHE I 223 " --> pdb=" O GLU I 23 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'I' and resid 147 through 151 Processing sheet with id=AC6, first strand: chain 'K' and resid 4 through 7 Processing sheet with id=AC7, first strand: chain 'K' and resid 382 through 387 removed outlier: 6.692A pdb=" N ALA K 311 " --> pdb=" O TYR K 424 " (cutoff:3.500A) removed outlier: 6.447A pdb=" N TYR K 424 " --> pdb=" O ALA K 311 " (cutoff:3.500A) removed outlier: 6.929A pdb=" N GLY K 313 " --> pdb=" O PHE K 422 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ASP K 319 " --> pdb=" O ASP K 416 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'K' and resid 447 through 448 removed outlier: 4.090A pdb=" N ILE M 239 " --> pdb=" O ILE K 448 " (cutoff:3.500A) removed outlier: 5.662A pdb=" N PHE M 234 " --> pdb=" O PHE M 276 " (cutoff:3.500A) removed outlier: 6.873A pdb=" N PHE M 276 " --> pdb=" O PHE M 234 " (cutoff:3.500A) removed outlier: 7.942A pdb=" N ALA M 236 " --> pdb=" O GLU M 274 " (cutoff:3.500A) removed outlier: 6.609A pdb=" N GLU M 274 " --> pdb=" O ALA M 236 " (cutoff:3.500A) removed outlier: 4.101A pdb=" N TYR M 238 " --> pdb=" O TYR M 272 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N VAL M 271 " --> pdb=" O LEU M 218 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N VAL M 273 " --> pdb=" O GLY M 216 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'K' and resid 505 through 507 Processing sheet with id=AD1, first strand: chain 'K' and resid 625 through 627 removed outlier: 3.697A pdb=" N ASN K 724 " --> pdb=" O ILE K 690 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'K' and resid 717 through 718 Processing sheet with id=AD3, first strand: chain 'M' and resid 60 through 61 Processing sheet with id=AD4, first strand: chain 'M' and resid 10 through 12 removed outlier: 3.551A pdb=" N GLY M 10 " --> pdb=" O PHE M 169 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N MET M 160 " --> pdb=" O ALA M 148 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N ALA M 148 " --> pdb=" O MET M 160 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N LYS M 140 " --> pdb=" O GLU M 168 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'M' and resid 64 through 66 removed outlier: 6.378A pdb=" N LYS M 133 " --> pdb=" O GLU M 125 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'M' and resid 227 through 228 Processing sheet with id=AD7, first strand: chain 'M' and resid 243 through 244 Processing sheet with id=AD8, first strand: chain 'M' and resid 247 through 249 removed outlier: 6.196A pdb=" N GLY M 248 " --> pdb=" O LYS M 259 " (cutoff:3.500A) 1291 hydrogen bonds defined for protein. 3747 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 6 stacking parallelities Total time for adding SS restraints: 5.43 Time building geometry restraints manager: 3.01 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 4873 1.32 - 1.45: 7460 1.45 - 1.57: 16633 1.57 - 1.69: 94 1.69 - 1.81: 177 Bond restraints: 29237 Sorted by residual: bond pdb=" N ILE I 57 " pdb=" CA ILE I 57 " ideal model delta sigma weight residual 1.460 1.496 -0.036 7.50e-03 1.78e+04 2.34e+01 bond pdb=" CA SER J 163 " pdb=" CB SER J 163 " ideal model delta sigma weight residual 1.529 1.468 0.061 1.38e-02 5.25e+03 1.98e+01 bond pdb=" CA SER I 60 " pdb=" CB SER I 60 " ideal model delta sigma weight residual 1.528 1.476 0.052 1.56e-02 4.11e+03 1.11e+01 bond pdb=" CA SER H 83 " pdb=" CB SER H 83 " ideal model delta sigma weight residual 1.532 1.478 0.054 1.65e-02 3.67e+03 1.07e+01 bond pdb=" CA SER I 61 " pdb=" CB SER I 61 " ideal model delta sigma weight residual 1.528 1.478 0.050 1.56e-02 4.11e+03 1.04e+01 ... (remaining 29232 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.66: 38600 1.66 - 3.31: 761 3.31 - 4.97: 197 4.97 - 6.63: 27 6.63 - 8.28: 8 Bond angle restraints: 39593 Sorted by residual: angle pdb=" N SER L 24 " pdb=" CA SER L 24 " pdb=" C SER L 24 " ideal model delta sigma weight residual 114.62 106.54 8.08 1.14e+00 7.69e-01 5.02e+01 angle pdb=" N ARG J 164 " pdb=" CA ARG J 164 " pdb=" C ARG J 164 " ideal model delta sigma weight residual 113.19 104.91 8.28 1.19e+00 7.06e-01 4.84e+01 angle pdb=" C PRO H 189 " pdb=" CA PRO H 189 " pdb=" CB PRO H 189 " ideal model delta sigma weight residual 111.23 103.69 7.54 1.28e+00 6.10e-01 3.47e+01 angle pdb=" C3' G R 4 " pdb=" O3' G R 4 " pdb=" P A R 5 " ideal model delta sigma weight residual 119.70 125.60 -5.90 1.20e+00 6.94e-01 2.42e+01 angle pdb=" C TYR K 282 " pdb=" CA TYR K 282 " pdb=" CB TYR K 282 " ideal model delta sigma weight residual 109.07 117.25 -8.18 1.68e+00 3.54e-01 2.37e+01 ... (remaining 39588 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.71: 17491 35.71 - 71.42: 310 71.42 - 107.14: 25 107.14 - 142.85: 0 142.85 - 178.56: 1 Dihedral angle restraints: 17827 sinusoidal: 7710 harmonic: 10117 Sorted by residual: dihedral pdb=" C4' U R 35 " pdb=" C3' U R 35 " pdb=" C2' U R 35 " pdb=" C1' U R 35 " ideal model delta sinusoidal sigma weight residual 36.34 -37.12 73.46 1 3.10e+00 1.04e-01 7.15e+02 dihedral pdb=" C4' A R 5 " pdb=" C3' A R 5 " pdb=" C2' A R 5 " pdb=" C1' A R 5 " ideal model delta sinusoidal sigma weight residual 36.34 -36.84 73.18 1 3.10e+00 1.04e-01 7.10e+02 dihedral pdb=" C4' U R 25 " pdb=" C3' U R 25 " pdb=" C2' U R 25 " pdb=" C1' U R 25 " ideal model delta sinusoidal sigma weight residual 36.34 -36.66 73.01 1 3.10e+00 1.04e-01 7.07e+02 ... (remaining 17824 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.065: 3927 0.065 - 0.131: 454 0.131 - 0.196: 27 0.196 - 0.261: 79 0.261 - 0.327: 37 Chirality restraints: 4524 Sorted by residual: chirality pdb=" P A R 5 " pdb=" OP1 A R 5 " pdb=" OP2 A R 5 " pdb=" O5' A R 5 " both_signs ideal model delta sigma weight residual True 2.17 -2.50 -0.33 2.00e-01 2.50e+01 2.67e+00 chirality pdb=" C2' U R 35 " pdb=" C3' U R 35 " pdb=" O2' U R 35 " pdb=" C1' U R 35 " both_signs ideal model delta sigma weight residual False -2.79 -2.49 -0.30 2.00e-01 2.50e+01 2.29e+00 chirality pdb=" C2' G R 4 " pdb=" C3' G R 4 " pdb=" O2' G R 4 " pdb=" C1' G R 4 " both_signs ideal model delta sigma weight residual False -2.79 -2.50 -0.29 2.00e-01 2.50e+01 2.13e+00 ... (remaining 4521 not shown) Planarity restraints: 4852 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASP H 88 " 0.021 2.00e-02 2.50e+03 4.35e-02 1.89e+01 pdb=" C ASP H 88 " -0.075 2.00e-02 2.50e+03 pdb=" O ASP H 88 " 0.028 2.00e-02 2.50e+03 pdb=" N TYR H 89 " 0.026 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA CYS H 82 " -0.013 2.00e-02 2.50e+03 2.62e-02 6.88e+00 pdb=" C CYS H 82 " 0.045 2.00e-02 2.50e+03 pdb=" O CYS H 82 " -0.017 2.00e-02 2.50e+03 pdb=" N SER H 83 " -0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PHE I 115 " -0.010 2.00e-02 2.50e+03 2.04e-02 4.17e+00 pdb=" C PHE I 115 " 0.035 2.00e-02 2.50e+03 pdb=" O PHE I 115 " -0.013 2.00e-02 2.50e+03 pdb=" N TRP I 116 " -0.012 2.00e-02 2.50e+03 ... (remaining 4849 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 2440 2.74 - 3.28: 30904 3.28 - 3.82: 49718 3.82 - 4.36: 57607 4.36 - 4.90: 98284 Nonbonded interactions: 238953 Sorted by model distance: nonbonded pdb=" OG1 THR L 38 " pdb=" OP1 U R 9 " model vdw 2.196 3.040 nonbonded pdb=" OH TYR K 173 " pdb=" OD1 ASN K 213 " model vdw 2.198 3.040 nonbonded pdb=" O2' U R 23 " pdb=" O PHE G 113 " model vdw 2.200 3.040 nonbonded pdb=" OD1 ASP L 94 " pdb=" OG1 THR L 137 " model vdw 2.201 3.040 nonbonded pdb=" O LEU L 151 " pdb=" OG SER L 154 " model vdw 2.201 3.040 ... (remaining 238948 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 19 through 137) selection = chain 'B' selection = (chain 'C' and resid 19 through 137) selection = (chain 'D' and resid 19 through 137) selection = (chain 'E' and resid 19 through 137) } ncs_group { reference = (chain 'F' and resid 4 through 244) selection = (chain 'G' and (resid 4 through 94 or resid 101 through 244)) } ncs_group { reference = (chain 'H' and (resid 4 through 81 or (resid 82 and (name N or name CA or name C \ or name O or name CB )) or resid 83 through 89 or (resid 90 and (name N or name \ CA or name C or name O or name CB )) or resid 91 through 119 or (resid 120 and \ (name N or name CA or name C or name O or name CB )) or resid 121 through 122 or \ (resid 123 and (name N or name CA or name C or name O or name CB )) or resid 12 \ 4 through 278)) selection = chain 'I' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 1.820 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.040 Extract box with map and model: 0.520 Check model and map are aligned: 0.100 Set scattering table: 0.090 Process input model: 27.440 Find NCS groups from input model: 0.310 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.420 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.810 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8468 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 29252 Z= 0.188 Angle : 0.606 8.282 39623 Z= 0.344 Chirality : 0.056 0.327 4524 Planarity : 0.003 0.043 4852 Dihedral : 12.894 178.559 11286 Min Nonbonded Distance : 2.196 Molprobity Statistics. All-atom Clashscore : 11.98 Ramachandran Plot: Outliers : 0.12 % Allowed : 6.10 % Favored : 93.78 % Rotamer: Outliers : 0.49 % Allowed : 11.33 % Favored : 88.19 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 2.73 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.69 (0.15), residues: 3441 helix: 2.45 (0.14), residues: 1468 sheet: 0.20 (0.25), residues: 449 loop : -1.57 (0.15), residues: 1524 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG H 67 TYR 0.016 0.001 TYR H 195 PHE 0.014 0.001 PHE G 144 TRP 0.013 0.001 TRP M 249 HIS 0.004 0.001 HIS K 225 Details of bonding type rmsd/Z covalent geometry : bond 0.00325 / 0.19 (29237) covalent geometry : angle 0.60329 / 0.34 (39593) SS BOND : bond 0.00347 / 0.20 ( 15) SS BOND : angle 1.98010 / 1.12 ( 30) hydrogen bonds : bond 0.15673 / 10.27 ( 1274) hydrogen bonds : angle 6.62998 / 4.80 ( 3747) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6882 Ramachandran restraints generated. 3441 Oldfield, 0 Emsley, 3441 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6882 Ramachandran restraints generated. 3441 Oldfield, 0 Emsley, 3441 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 880 residues out of total 3097 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 865 time to evaluate : 0.990 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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 29 ILE cc_start: 0.9424 (tp) cc_final: 0.9158 (tt) REVERT: A 56 PHE cc_start: 0.8842 (t80) cc_final: 0.8597 (t80) REVERT: A 60 ARG cc_start: 0.9199 (mmp80) cc_final: 0.8853 (mmm160) REVERT: A 79 ILE cc_start: 0.8988 (mm) cc_final: 0.8661 (mp) REVERT: A 111 ASP cc_start: 0.8846 (t0) cc_final: 0.8514 (t0) REVERT: A 131 GLU cc_start: 0.9413 (mt-10) cc_final: 0.8954 (mt-10) REVERT: B 22 ASP cc_start: 0.8657 (m-30) cc_final: 0.8037 (m-30) REVERT: B 39 ASN cc_start: 0.8836 (p0) cc_final: 0.8418 (p0) REVERT: B 90 SER cc_start: 0.9627 (m) cc_final: 0.9219 (p) REVERT: B 98 ASP cc_start: 0.8796 (t70) cc_final: 0.8531 (t0) REVERT: B 103 LEU cc_start: 0.9725 (mt) cc_final: 0.9347 (mt) REVERT: B 107 LYS cc_start: 0.9731 (ttpt) cc_final: 0.9511 (pttt) REVERT: B 127 LYS cc_start: 0.8964 (mmtm) cc_final: 0.8507 (mmtt) REVERT: B 128 THR cc_start: 0.9064 (p) cc_final: 0.8629 (t) REVERT: B 129 PHE cc_start: 0.9154 (t80) cc_final: 0.8922 (t80) REVERT: B 134 ASN cc_start: 0.9070 (m110) cc_final: 0.8702 (m110) REVERT: C 22 ASP cc_start: 0.8708 (m-30) cc_final: 0.8411 (m-30) REVERT: C 44 TYR cc_start: 0.8762 (t80) cc_final: 0.8483 (t80) REVERT: C 58 GLN cc_start: 0.9647 (mm-40) cc_final: 0.9245 (mm-40) REVERT: C 71 MET cc_start: 0.9365 (mtm) cc_final: 0.9056 (mtm) REVERT: C 92 LYS cc_start: 0.9563 (ttmt) cc_final: 0.9182 (ttmm) REVERT: C 97 LYS cc_start: 0.9659 (ptpt) cc_final: 0.9424 (pptt) REVERT: C 101 ASN cc_start: 0.9526 (m-40) cc_final: 0.9325 (m-40) REVERT: C 114 THR cc_start: 0.9425 (m) cc_final: 0.9013 (p) REVERT: D 44 TYR cc_start: 0.9288 (t80) cc_final: 0.8748 (t80) REVERT: D 58 GLN cc_start: 0.9420 (mp10) cc_final: 0.9132 (mm-40) REVERT: D 90 SER cc_start: 0.9500 (m) cc_final: 0.9243 (p) REVERT: D 114 THR cc_start: 0.9520 (m) cc_final: 0.9174 (p) REVERT: D 127 LYS cc_start: 0.9168 (mtpp) cc_final: 0.8948 (mtpt) REVERT: D 131 GLU cc_start: 0.9097 (mt-10) cc_final: 0.8831 (mt-10) REVERT: E 55 SER cc_start: 0.9756 (m) cc_final: 0.9481 (p) REVERT: E 76 ARG cc_start: 0.9417 (mmm-85) cc_final: 0.8997 (mmm-85) REVERT: E 78 GLU cc_start: 0.8404 (mt-10) cc_final: 0.7944 (mt-10) REVERT: E 82 GLU cc_start: 0.9192 (tm-30) cc_final: 0.8945 (tm-30) REVERT: E 101 ASN cc_start: 0.9396 (m110) cc_final: 0.8799 (m110) REVERT: E 105 TYR cc_start: 0.9073 (m-10) cc_final: 0.8464 (m-80) REVERT: E 114 THR cc_start: 0.9441 (m) cc_final: 0.9175 (p) REVERT: E 131 GLU cc_start: 0.8986 (tp30) cc_final: 0.8650 (tm-30) REVERT: E 135 ILE cc_start: 0.9508 (mm) cc_final: 0.9151 (mm) REVERT: J 46 MET cc_start: 0.8427 (mtp) cc_final: 0.7621 (mtp) REVERT: J 81 LEU cc_start: 0.9348 (mt) cc_final: 0.9066 (mp) REVERT: J 146 PHE cc_start: 0.9023 (m-80) cc_final: 0.8750 (m-80) REVERT: J 166 SER cc_start: 0.8525 (m) cc_final: 0.8212 (t) REVERT: J 209 GLU cc_start: 0.9248 (mm-30) cc_final: 0.8605 (mp0) REVERT: J 229 MET cc_start: 0.8142 (mtp) cc_final: 0.7610 (ttm) REVERT: L 8 MET cc_start: 0.8810 (tmm) cc_final: 0.8345 (tmm) REVERT: L 40 LYS cc_start: 0.9236 (tttt) cc_final: 0.8900 (tttm) REVERT: L 62 GLU cc_start: 0.8949 (tp30) cc_final: 0.8593 (tp30) REVERT: L 64 GLU cc_start: 0.8739 (tm-30) cc_final: 0.8384 (tm-30) REVERT: L 79 LYS cc_start: 0.9289 (mtmt) cc_final: 0.8988 (mttp) REVERT: L 115 GLN cc_start: 0.8786 (mm110) cc_final: 0.8363 (mm-40) REVERT: L 118 LYS cc_start: 0.9531 (tppp) cc_final: 0.9071 (tppt) REVERT: L 126 GLN cc_start: 0.8242 (tt0) cc_final: 0.8037 (tt0) REVERT: L 178 GLU cc_start: 0.8656 (pt0) cc_final: 0.8322 (pt0) REVERT: N 30 ARG cc_start: 0.9015 (mmp-170) cc_final: 0.8663 (mmm-85) REVERT: N 49 MET cc_start: 0.9541 (tmm) cc_final: 0.9264 (tmm) REVERT: N 102 GLN cc_start: 0.9163 (tp40) cc_final: 0.8673 (tp40) REVERT: N 196 GLU cc_start: 0.8377 (tp30) cc_final: 0.7703 (tp30) REVERT: N 232 TYR cc_start: 0.9002 (p90) cc_final: 0.8576 (p90) REVERT: N 249 ARG cc_start: 0.9202 (mtp-110) cc_final: 0.8925 (ptm-80) REVERT: G 40 ASP cc_start: 0.9099 (m-30) cc_final: 0.8880 (p0) REVERT: G 52 ILE cc_start: 0.9686 (mt) cc_final: 0.9373 (tp) REVERT: G 66 GLU cc_start: 0.9233 (mt-10) cc_final: 0.8989 (mt-10) REVERT: G 137 MET cc_start: 0.8758 (mpp) cc_final: 0.8457 (mpp) REVERT: G 168 MET cc_start: 0.9030 (ttp) cc_final: 0.8604 (ttm) REVERT: G 169 MET cc_start: 0.8556 (mmm) cc_final: 0.8277 (mmm) REVERT: F 33 GLN cc_start: 0.9223 (mp10) cc_final: 0.8899 (mp10) REVERT: F 43 ILE cc_start: 0.8091 (pt) cc_final: 0.7409 (pt) REVERT: F 62 ARG cc_start: 0.9428 (ttt90) cc_final: 0.9124 (ttm-80) REVERT: F 73 ASN cc_start: 0.9403 (t0) cc_final: 0.9138 (t0) REVERT: F 121 TYR cc_start: 0.8643 (m-80) cc_final: 0.8402 (m-80) REVERT: F 135 ARG cc_start: 0.8785 (ttm170) cc_final: 0.8196 (ttm170) REVERT: F 157 TYR cc_start: 0.6195 (m-80) cc_final: 0.5358 (m-80) REVERT: F 174 ASN cc_start: 0.9104 (m-40) cc_final: 0.7265 (m-40) REVERT: F 239 LYS cc_start: 0.9639 (mmtm) cc_final: 0.8966 (mmmm) REVERT: H 56 ILE cc_start: 0.9394 (pt) cc_final: 0.9151 (mm) REVERT: H 145 TYR cc_start: 0.8610 (p90) cc_final: 0.7706 (p90) REVERT: H 174 ASP cc_start: 0.8597 (t0) cc_final: 0.7946 (t70) REVERT: H 238 ASP cc_start: 0.8961 (p0) cc_final: 0.8754 (p0) REVERT: H 255 ASP cc_start: 0.9039 (m-30) cc_final: 0.8602 (p0) REVERT: H 261 MET cc_start: 0.9572 (mmp) cc_final: 0.9299 (mmm) REVERT: H 265 MET cc_start: 0.9421 (mtp) cc_final: 0.9124 (mtt) REVERT: H 266 GLU cc_start: 0.9417 (mt-10) cc_final: 0.9204 (mt-10) REVERT: H 270 ASN cc_start: 0.9282 (m110) cc_final: 0.9070 (m110) REVERT: I 17 MET cc_start: 0.8692 (tpp) cc_final: 0.8193 (tpp) REVERT: I 99 ASP cc_start: 0.9488 (m-30) cc_final: 0.9252 (p0) REVERT: I 110 GLN cc_start: 0.9554 (tp40) cc_final: 0.9291 (tp-100) REVERT: I 118 TYR cc_start: 0.9097 (m-80) cc_final: 0.8837 (m-10) REVERT: I 261 MET cc_start: 0.9599 (mmm) cc_final: 0.9296 (mpp) REVERT: I 275 TYR cc_start: 0.8871 (p90) cc_final: 0.8376 (p90) REVERT: K 56 ASP cc_start: 0.9163 (m-30) cc_final: 0.8864 (m-30) REVERT: K 60 MET cc_start: 0.9403 (tmm) cc_final: 0.8868 (tmm) REVERT: K 61 ILE cc_start: 0.9285 (mt) cc_final: 0.8903 (mt) REVERT: K 81 GLU cc_start: 0.8941 (mt-10) cc_final: 0.8556 (mt-10) REVERT: K 128 ARG cc_start: 0.9504 (ttm110) cc_final: 0.9063 (ptp-110) REVERT: K 129 LYS cc_start: 0.9618 (mttt) cc_final: 0.9351 (mtmt) REVERT: K 156 LEU cc_start: 0.9004 (mt) cc_final: 0.8740 (mt) REVERT: K 201 ASP cc_start: 0.9284 (t0) cc_final: 0.8718 (t0) REVERT: K 202 GLU cc_start: 0.8651 (mt-10) cc_final: 0.8261 (pt0) REVERT: K 314 TYR cc_start: 0.8720 (m-80) cc_final: 0.8267 (m-80) REVERT: K 330 PHE cc_start: 0.9054 (m-80) cc_final: 0.8228 (m-80) REVERT: K 336 MET cc_start: 0.8793 (mmm) cc_final: 0.8422 (mmm) REVERT: K 369 ILE cc_start: 0.9443 (mt) cc_final: 0.9062 (mm) REVERT: K 406 SER cc_start: 0.9202 (m) cc_final: 0.8947 (p) REVERT: K 474 ARG cc_start: 0.3068 (mtt180) cc_final: 0.2602 (mtt180) REVERT: K 481 LEU cc_start: 0.8464 (tp) cc_final: 0.8169 (tp) REVERT: K 520 ASP cc_start: 0.7929 (m-30) cc_final: 0.7635 (m-30) REVERT: K 538 ILE cc_start: 0.9469 (mt) cc_final: 0.9215 (mt) REVERT: K 587 LYS cc_start: 0.9113 (mmtm) cc_final: 0.8441 (tppt) REVERT: K 597 MET cc_start: 0.9059 (mmt) cc_final: 0.8846 (mmm) REVERT: K 625 ILE cc_start: 0.9407 (mt) cc_final: 0.9091 (mm) REVERT: K 639 VAL cc_start: 0.9644 (t) cc_final: 0.9433 (p) REVERT: K 641 MET cc_start: 0.9271 (ttt) cc_final: 0.8968 (ttm) REVERT: K 677 MET cc_start: 0.9127 (ttp) cc_final: 0.8867 (ttp) REVERT: K 692 VAL cc_start: 0.9476 (t) cc_final: 0.9269 (p) REVERT: K 730 GLU cc_start: 0.8995 (tt0) cc_final: 0.8744 (tp30) REVERT: K 739 ASP cc_start: 0.8448 (p0) cc_final: 0.8248 (p0) REVERT: M 16 MET cc_start: 0.8711 (mmt) cc_final: 0.8352 (mmp) REVERT: M 28 ASN cc_start: 0.9056 (t0) cc_final: 0.8854 (t0) REVERT: M 62 ILE cc_start: 0.9627 (OUTLIER) cc_final: 0.9342 (mm) REVERT: M 69 TYR cc_start: 0.8126 (t80) cc_final: 0.7061 (t80) REVERT: M 82 ILE cc_start: 0.9314 (pt) cc_final: 0.8830 (mm) REVERT: M 144 GLN cc_start: 0.8607 (mm-40) cc_final: 0.8309 (mm110) REVERT: M 169 PHE cc_start: 0.9169 (m-80) cc_final: 0.8955 (m-10) REVERT: M 215 LYS cc_start: 0.9302 (mtmt) cc_final: 0.8968 (tttm) REVERT: M 231 LYS cc_start: 0.9093 (mmtt) cc_final: 0.8861 (mmtp) outliers start: 15 outliers final: 4 residues processed: 876 average time/residue: 0.1937 time to fit residues: 259.4878 Evaluate side-chains 554 residues out of total 3097 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 549 time to evaluate : 1.018 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 164 ARG Chi-restraints excluded: chain L residue 21 THR Chi-restraints excluded: chain L residue 22 ILE Chi-restraints excluded: chain M residue 30 ILE Chi-restraints excluded: chain M residue 62 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 346 random chunks: chunk 197 optimal weight: 0.9980 chunk 215 optimal weight: 0.9990 chunk 20 optimal weight: 7.9990 chunk 132 optimal weight: 9.9990 chunk 261 optimal weight: 7.9990 chunk 248 optimal weight: 7.9990 chunk 207 optimal weight: 0.9990 chunk 155 optimal weight: 9.9990 chunk 244 optimal weight: 3.9990 chunk 183 optimal weight: 6.9990 chunk 298 optimal weight: 0.0030 overall best weight: 1.3996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 134 ASN D 73 GLN E 39 ASN E 134 ASN J 148 GLN ** L 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 134 GLN G 141 ASN K 223 GLN M 46 GLN ** M 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3306 r_free = 0.3306 target = 0.053821 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3077 r_free = 0.3077 target = 0.045118 restraints weight = 143140.518| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3125 r_free = 0.3125 target = 0.046932 restraints weight = 74122.592| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3158 r_free = 0.3158 target = 0.048190 restraints weight = 46616.308| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3180 r_free = 0.3180 target = 0.049055 restraints weight = 32701.897| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3196 r_free = 0.3196 target = 0.049674 restraints weight = 24819.180| |-----------------------------------------------------------------------------| r_work (final): 0.3195 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8445 moved from start: 0.2413 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 29252 Z= 0.183 Angle : 1.010 24.016 39623 Z= 0.439 Chirality : 0.095 1.366 4524 Planarity : 0.004 0.053 4852 Dihedral : 10.391 167.870 4397 Min Nonbonded Distance : 2.150 Molprobity Statistics. All-atom Clashscore : 14.37 Ramachandran Plot: Outliers : 0.12 % Allowed : 5.20 % Favored : 94.68 % Rotamer: Outliers : 2.75 % Allowed : 18.19 % Favored : 79.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.73 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.31 (0.15), residues: 3441 helix: 2.03 (0.14), residues: 1466 sheet: 0.08 (0.25), residues: 433 loop : -1.65 (0.15), residues: 1542 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG K 786 TYR 0.022 0.002 TYR A 69 PHE 0.033 0.001 PHE K 245 TRP 0.013 0.001 TRP E 108 HIS 0.004 0.001 HIS M 113 Details of bonding type rmsd/Z covalent geometry : bond 0.00391 / 0.18 (29237) covalent geometry : angle 1.00858 / 0.44 (39593) SS BOND : bond 0.00335 / 0.21 ( 15) SS BOND : angle 1.93745 / 1.10 ( 30) hydrogen bonds : bond 0.04219 / 2.80 ( 1274) hydrogen bonds : angle 5.35105 / 3.85 ( 3747) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6882 Ramachandran restraints generated. 3441 Oldfield, 0 Emsley, 3441 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6882 Ramachandran restraints generated. 3441 Oldfield, 0 Emsley, 3441 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 730 residues out of total 3097 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 645 time to evaluate : 1.052 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 22 ASP cc_start: 0.8614 (m-30) cc_final: 0.8135 (t0) REVERT: A 29 ILE cc_start: 0.9383 (tp) cc_final: 0.9043 (tt) REVERT: A 42 GLU cc_start: 0.8169 (mm-30) cc_final: 0.7823 (mm-30) REVERT: A 56 PHE cc_start: 0.8972 (t80) cc_final: 0.8575 (t80) REVERT: A 60 ARG cc_start: 0.9269 (mmp80) cc_final: 0.8865 (mmm160) REVERT: A 79 ILE cc_start: 0.8906 (mm) cc_final: 0.8627 (mp) REVERT: A 110 TYR cc_start: 0.9060 (t80) cc_final: 0.8748 (t80) REVERT: A 111 ASP cc_start: 0.8993 (t0) cc_final: 0.8696 (t0) REVERT: A 131 GLU cc_start: 0.9436 (mt-10) cc_final: 0.9014 (mt-10) REVERT: B 22 ASP cc_start: 0.8836 (m-30) cc_final: 0.7988 (m-30) REVERT: B 26 ARG cc_start: 0.9100 (ptp-110) cc_final: 0.8455 (ptp90) REVERT: B 42 GLU cc_start: 0.8539 (mm-30) cc_final: 0.8053 (mm-30) REVERT: B 44 TYR cc_start: 0.9389 (t80) cc_final: 0.9066 (t80) REVERT: B 69 TYR cc_start: 0.9137 (t80) cc_final: 0.8841 (t80) REVERT: B 73 GLN cc_start: 0.9315 (tp40) cc_final: 0.9090 (mm-40) REVERT: B 78 GLU cc_start: 0.9136 (mm-30) cc_final: 0.8861 (tp30) REVERT: B 90 SER cc_start: 0.9601 (m) cc_final: 0.9187 (p) REVERT: B 103 LEU cc_start: 0.9782 (mt) cc_final: 0.9452 (tp) REVERT: B 128 THR cc_start: 0.9345 (p) cc_final: 0.8447 (p) REVERT: B 129 PHE cc_start: 0.9274 (t80) cc_final: 0.9030 (t80) REVERT: B 131 GLU cc_start: 0.8991 (mt-10) cc_final: 0.8708 (mt-10) REVERT: B 134 ASN cc_start: 0.9219 (m-40) cc_final: 0.8863 (m110) REVERT: C 22 ASP cc_start: 0.9096 (m-30) cc_final: 0.8676 (m-30) REVERT: C 45 VAL cc_start: 0.9352 (t) cc_final: 0.9049 (p) REVERT: C 71 MET cc_start: 0.9429 (mtm) cc_final: 0.9039 (mtm) REVERT: C 105 TYR cc_start: 0.9374 (m-80) cc_final: 0.9153 (m-80) REVERT: C 134 ASN cc_start: 0.9683 (m-40) cc_final: 0.9416 (m110) REVERT: D 26 ARG cc_start: 0.9564 (mtm-85) cc_final: 0.9206 (ptp90) REVERT: D 44 TYR cc_start: 0.9176 (t80) cc_final: 0.8749 (t80) REVERT: D 58 GLN cc_start: 0.9479 (mp10) cc_final: 0.9170 (mm-40) REVERT: D 82 GLU cc_start: 0.9581 (tt0) cc_final: 0.9347 (tm-30) REVERT: D 83 THR cc_start: 0.9549 (m) cc_final: 0.9291 (p) REVERT: D 90 SER cc_start: 0.9446 (m) cc_final: 0.9227 (p) REVERT: D 101 ASN cc_start: 0.9559 (m110) cc_final: 0.9340 (m110) REVERT: D 131 GLU cc_start: 0.9118 (mt-10) cc_final: 0.8864 (mt-10) REVERT: E 42 GLU cc_start: 0.8588 (pt0) cc_final: 0.8314 (pm20) REVERT: E 48 SER cc_start: 0.9774 (m) cc_final: 0.9557 (p) REVERT: E 55 SER cc_start: 0.9781 (m) cc_final: 0.9510 (p) REVERT: E 71 MET cc_start: 0.9297 (mtp) cc_final: 0.9048 (ptp) REVERT: E 76 ARG cc_start: 0.9483 (mmm-85) cc_final: 0.8743 (mmm-85) REVERT: E 78 GLU cc_start: 0.8385 (mt-10) cc_final: 0.8054 (mp0) REVERT: E 82 GLU cc_start: 0.9367 (tm-30) cc_final: 0.9009 (tm-30) REVERT: E 101 ASN cc_start: 0.9477 (m110) cc_final: 0.8978 (m110) REVERT: E 105 TYR cc_start: 0.9333 (m-10) cc_final: 0.8717 (m-80) REVERT: E 114 THR cc_start: 0.9480 (m) cc_final: 0.9218 (p) REVERT: E 130 LYS cc_start: 0.9535 (ptmt) cc_final: 0.9231 (ttpp) REVERT: E 131 GLU cc_start: 0.9064 (tp30) cc_final: 0.8596 (tm-30) REVERT: E 134 ASN cc_start: 0.9448 (m110) cc_final: 0.8849 (m-40) REVERT: E 135 ILE cc_start: 0.9590 (mm) cc_final: 0.9222 (mm) REVERT: J 6 ILE cc_start: 0.8536 (OUTLIER) cc_final: 0.8191 (tp) REVERT: J 46 MET cc_start: 0.8319 (mtp) cc_final: 0.7695 (mtp) REVERT: J 56 VAL cc_start: 0.9460 (OUTLIER) cc_final: 0.8497 (m) REVERT: J 81 LEU cc_start: 0.9373 (mt) cc_final: 0.9154 (mp) REVERT: J 146 PHE cc_start: 0.9179 (m-80) cc_final: 0.8870 (m-80) REVERT: J 148 GLN cc_start: 0.9388 (OUTLIER) cc_final: 0.9156 (mm-40) REVERT: J 159 MET cc_start: 0.8881 (tpp) cc_final: 0.8645 (tpp) REVERT: J 166 SER cc_start: 0.9011 (m) cc_final: 0.8585 (t) REVERT: J 209 GLU cc_start: 0.9235 (mm-30) cc_final: 0.8369 (mp0) REVERT: J 229 MET cc_start: 0.8577 (mtp) cc_final: 0.8255 (ttm) REVERT: L 40 LYS cc_start: 0.9336 (tttt) cc_final: 0.9080 (tttp) REVERT: L 62 GLU cc_start: 0.8895 (tp30) cc_final: 0.8131 (mp0) REVERT: L 113 LYS cc_start: 0.9410 (ttmm) cc_final: 0.9115 (tppt) REVERT: L 115 GLN cc_start: 0.8936 (mm110) cc_final: 0.8645 (mm-40) REVERT: L 118 LYS cc_start: 0.9421 (tppp) cc_final: 0.9195 (tppt) REVERT: L 127 ILE cc_start: 0.9503 (pt) cc_final: 0.9027 (mm) REVERT: L 178 GLU cc_start: 0.9090 (pt0) cc_final: 0.8837 (pm20) REVERT: N 49 MET cc_start: 0.9615 (tmm) cc_final: 0.9276 (tmm) REVERT: N 155 MET cc_start: 0.8840 (pmm) cc_final: 0.8627 (pmm) REVERT: N 196 GLU cc_start: 0.8373 (tp30) cc_final: 0.7664 (tp30) REVERT: N 229 GLU cc_start: 0.8232 (tp30) cc_final: 0.7870 (tp30) REVERT: N 249 ARG cc_start: 0.9301 (mtp-110) cc_final: 0.9086 (ptm-80) REVERT: G 40 ASP cc_start: 0.9132 (m-30) cc_final: 0.8889 (p0) REVERT: G 66 GLU cc_start: 0.9283 (mt-10) cc_final: 0.9042 (mt-10) REVERT: G 167 MET cc_start: 0.7788 (tpp) cc_final: 0.7467 (tpp) REVERT: G 168 MET cc_start: 0.8783 (ttp) cc_final: 0.8581 (ttm) REVERT: F 33 GLN cc_start: 0.9255 (mp10) cc_final: 0.8895 (mp10) REVERT: F 73 ASN cc_start: 0.9497 (t0) cc_final: 0.9218 (t0) REVERT: F 121 TYR cc_start: 0.8805 (m-80) cc_final: 0.8473 (m-80) REVERT: F 137 MET cc_start: 0.8222 (ptp) cc_final: 0.7903 (ptp) REVERT: F 168 MET cc_start: 0.9012 (ttp) cc_final: 0.8803 (ttp) REVERT: F 169 MET cc_start: 0.8946 (mtp) cc_final: 0.8718 (mtp) REVERT: F 207 ARG cc_start: 0.7635 (OUTLIER) cc_final: 0.7395 (mtp85) REVERT: F 239 LYS cc_start: 0.9459 (mmtm) cc_final: 0.9252 (mmmm) REVERT: H 56 ILE cc_start: 0.9387 (pt) cc_final: 0.9064 (mm) REVERT: H 110 GLN cc_start: 0.9597 (tp40) cc_final: 0.9198 (mp10) REVERT: H 145 TYR cc_start: 0.8253 (p90) cc_final: 0.7777 (p90) REVERT: H 174 ASP cc_start: 0.8636 (t0) cc_final: 0.8165 (t70) REVERT: H 182 LYS cc_start: 0.9261 (ttmt) cc_final: 0.9037 (tttm) REVERT: H 193 ILE cc_start: 0.9330 (OUTLIER) cc_final: 0.9117 (pt) REVERT: H 200 MET cc_start: 0.9225 (tpp) cc_final: 0.8762 (tmm) REVERT: H 255 ASP cc_start: 0.9068 (m-30) cc_final: 0.8622 (p0) REVERT: H 261 MET cc_start: 0.9591 (mmp) cc_final: 0.9277 (mmm) REVERT: H 265 MET cc_start: 0.9539 (mtp) cc_final: 0.9222 (mtt) REVERT: H 266 GLU cc_start: 0.9498 (mt-10) cc_final: 0.9203 (mt-10) REVERT: I 80 GLU cc_start: 0.8933 (tt0) cc_final: 0.8615 (pt0) REVERT: I 99 ASP cc_start: 0.9479 (m-30) cc_final: 0.9200 (p0) REVERT: I 110 GLN cc_start: 0.9628 (tp40) cc_final: 0.9331 (tp40) REVERT: I 118 TYR cc_start: 0.9064 (m-80) cc_final: 0.8750 (m-10) REVERT: I 129 MET cc_start: 0.9263 (OUTLIER) cc_final: 0.9005 (mmm) REVERT: I 182 LYS cc_start: 0.8722 (OUTLIER) cc_final: 0.7962 (tptp) REVERT: K 56 ASP cc_start: 0.9091 (m-30) cc_final: 0.8785 (m-30) REVERT: K 60 MET cc_start: 0.9213 (tmm) cc_final: 0.8772 (tmm) REVERT: K 61 ILE cc_start: 0.9198 (mt) cc_final: 0.8795 (mt) REVERT: K 128 ARG cc_start: 0.9521 (ttm110) cc_final: 0.9199 (ptp-110) REVERT: K 160 LEU cc_start: 0.9458 (mm) cc_final: 0.9218 (mt) REVERT: K 201 ASP cc_start: 0.9161 (t0) cc_final: 0.8602 (t0) REVERT: K 202 GLU cc_start: 0.8634 (mt-10) cc_final: 0.8207 (mt-10) REVERT: K 205 GLU cc_start: 0.8361 (mm-30) cc_final: 0.8059 (mm-30) REVERT: K 270 VAL cc_start: 0.8512 (OUTLIER) cc_final: 0.8287 (t) REVERT: K 273 LYS cc_start: 0.9501 (tppt) cc_final: 0.8910 (mttm) REVERT: K 274 GLU cc_start: 0.8571 (mp0) cc_final: 0.8037 (mp0) REVERT: K 314 TYR cc_start: 0.8645 (m-80) cc_final: 0.8146 (m-80) REVERT: K 330 PHE cc_start: 0.9110 (m-80) cc_final: 0.8331 (m-80) REVERT: K 336 MET cc_start: 0.8870 (mmm) cc_final: 0.8458 (mmm) REVERT: K 369 ILE cc_start: 0.9367 (mt) cc_final: 0.8934 (mm) REVERT: K 386 VAL cc_start: 0.9100 (m) cc_final: 0.8857 (m) REVERT: K 406 SER cc_start: 0.9185 (m) cc_final: 0.8941 (p) REVERT: K 438 MET cc_start: 0.8750 (mmt) cc_final: 0.8226 (mmt) REVERT: K 439 MET cc_start: 0.8743 (mmt) cc_final: 0.8392 (mmp) REVERT: K 474 ARG cc_start: 0.2936 (mtt180) cc_final: 0.2282 (mtt180) REVERT: K 481 LEU cc_start: 0.8579 (tp) cc_final: 0.8266 (tp) REVERT: K 520 ASP cc_start: 0.7990 (m-30) cc_final: 0.7691 (m-30) REVERT: K 527 LYS cc_start: 0.8983 (mmmt) cc_final: 0.8744 (mmtt) REVERT: K 619 TYR cc_start: 0.8805 (p90) cc_final: 0.8551 (p90) REVERT: K 625 ILE cc_start: 0.9452 (mt) cc_final: 0.9131 (mm) REVERT: K 627 LEU cc_start: 0.9552 (mt) cc_final: 0.9341 (tp) REVERT: K 677 MET cc_start: 0.8928 (ttp) cc_final: 0.8544 (ttp) REVERT: M 5 LYS cc_start: 0.9585 (OUTLIER) cc_final: 0.9234 (tttp) REVERT: M 16 MET cc_start: 0.8685 (mmt) cc_final: 0.8247 (mmp) REVERT: M 40 LEU cc_start: 0.9497 (mm) cc_final: 0.9277 (mt) REVERT: M 144 GLN cc_start: 0.8704 (mm-40) cc_final: 0.8352 (mm110) REVERT: M 231 LYS cc_start: 0.9240 (mmtt) cc_final: 0.9040 (mmtp) outliers start: 85 outliers final: 26 residues processed: 703 average time/residue: 0.1689 time to fit residues: 191.6009 Evaluate side-chains 575 residues out of total 3097 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 540 time to evaluate : 1.090 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 VAL Chi-restraints excluded: chain A residue 102 LEU Chi-restraints excluded: chain B residue 21 LEU Chi-restraints excluded: chain B residue 54 LEU Chi-restraints excluded: chain C residue 37 LYS Chi-restraints excluded: chain E residue 46 ASP Chi-restraints excluded: chain J residue 6 ILE Chi-restraints excluded: chain J residue 43 VAL Chi-restraints excluded: chain J residue 56 VAL Chi-restraints excluded: chain J residue 148 GLN Chi-restraints excluded: chain L residue 21 THR Chi-restraints excluded: chain L residue 74 VAL Chi-restraints excluded: chain N residue 56 ILE Chi-restraints excluded: chain N residue 190 ILE Chi-restraints excluded: chain N residue 191 VAL Chi-restraints excluded: chain G residue 157 TYR Chi-restraints excluded: chain F residue 207 ARG Chi-restraints excluded: chain H residue 168 VAL Chi-restraints excluded: chain H residue 193 ILE Chi-restraints excluded: chain I residue 129 MET Chi-restraints excluded: chain I residue 182 LYS Chi-restraints excluded: chain I residue 210 VAL Chi-restraints excluded: chain K residue 14 VAL Chi-restraints excluded: chain K residue 270 VAL Chi-restraints excluded: chain K residue 378 TYR Chi-restraints excluded: chain K residue 385 ILE Chi-restraints excluded: chain K residue 532 THR Chi-restraints excluded: chain K residue 824 SER Chi-restraints excluded: chain M residue 5 LYS Chi-restraints excluded: chain M residue 30 ILE Chi-restraints excluded: chain M residue 62 ILE Chi-restraints excluded: chain M residue 75 GLU Chi-restraints excluded: chain M residue 157 TYR Chi-restraints excluded: chain M residue 200 VAL Chi-restraints excluded: chain M residue 218 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 346 random chunks: chunk 136 optimal weight: 7.9990 chunk 120 optimal weight: 6.9990 chunk 72 optimal weight: 20.0000 chunk 243 optimal weight: 9.9990 chunk 331 optimal weight: 2.9990 chunk 270 optimal weight: 8.9990 chunk 116 optimal weight: 5.9990 chunk 259 optimal weight: 0.6980 chunk 56 optimal weight: 1.9990 chunk 340 optimal weight: 10.0000 chunk 134 optimal weight: 10.0000 overall best weight: 3.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 101 ASN ** D 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 134 ASN N 59 ASN ** G 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 134 GLN F 147 GLN ** H 204 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 80 HIS K 100 ASN K 734 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3306 r_free = 0.3306 target = 0.052361 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3080 r_free = 0.3080 target = 0.043979 restraints weight = 144856.910| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3127 r_free = 0.3127 target = 0.045714 restraints weight = 74606.202| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3159 r_free = 0.3159 target = 0.046905 restraints weight = 46645.559| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3181 r_free = 0.3181 target = 0.047736 restraints weight = 32689.756| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3197 r_free = 0.3197 target = 0.048320 restraints weight = 24800.761| |-----------------------------------------------------------------------------| r_work (final): 0.3184 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8515 moved from start: 0.3032 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.072 29252 Z= 0.257 Angle : 0.858 20.815 39623 Z= 0.401 Chirality : 0.071 1.178 4524 Planarity : 0.004 0.051 4852 Dihedral : 11.093 155.473 4391 Min Nonbonded Distance : 2.316 Molprobity Statistics. All-atom Clashscore : 16.35 Ramachandran Plot: Outliers : 0.12 % Allowed : 6.36 % Favored : 93.52 % Rotamer: Outliers : 3.85 % Allowed : 18.22 % Favored : 77.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.73 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.05 (0.14), residues: 3441 helix: 1.78 (0.14), residues: 1468 sheet: -0.24 (0.23), residues: 466 loop : -1.72 (0.15), residues: 1507 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG G 47 TYR 0.030 0.002 TYR L 104 PHE 0.038 0.002 PHE E 56 TRP 0.010 0.001 TRP K 749 HIS 0.006 0.001 HIS M 146 Details of bonding type rmsd/Z covalent geometry : bond 0.00549 / 0.26 (29237) covalent geometry : angle 0.85655 / 0.40 (39593) SS BOND : bond 0.00528 / 0.34 ( 15) SS BOND : angle 1.84435 / 1.10 ( 30) hydrogen bonds : bond 0.04060 / 2.70 ( 1274) hydrogen bonds : angle 5.29969 / 3.80 ( 3747) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6882 Ramachandran restraints generated. 3441 Oldfield, 0 Emsley, 3441 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6882 Ramachandran restraints generated. 3441 Oldfield, 0 Emsley, 3441 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 662 residues out of total 3097 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 119 poor density : 543 time to evaluate : 0.871 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 22 ASP cc_start: 0.8726 (m-30) cc_final: 0.8251 (t0) REVERT: A 29 ILE cc_start: 0.9396 (tp) cc_final: 0.9066 (tt) REVERT: A 42 GLU cc_start: 0.8164 (mm-30) cc_final: 0.7861 (mm-30) REVERT: A 56 PHE cc_start: 0.9005 (t80) cc_final: 0.8596 (t80) REVERT: A 60 ARG cc_start: 0.9283 (mmp80) cc_final: 0.8882 (mmm160) REVERT: A 79 ILE cc_start: 0.8979 (mm) cc_final: 0.8696 (mp) REVERT: A 110 TYR cc_start: 0.9050 (t80) cc_final: 0.8790 (t80) REVERT: A 111 ASP cc_start: 0.8993 (t0) cc_final: 0.8670 (t0) REVERT: A 126 VAL cc_start: 0.9319 (t) cc_final: 0.9069 (p) REVERT: A 131 GLU cc_start: 0.9427 (mt-10) cc_final: 0.8900 (mt-10) REVERT: B 22 ASP cc_start: 0.8897 (m-30) cc_final: 0.8012 (m-30) REVERT: B 26 ARG cc_start: 0.9097 (ptp-110) cc_final: 0.8380 (ptp90) REVERT: B 78 GLU cc_start: 0.9168 (mm-30) cc_final: 0.8633 (mm-30) REVERT: B 90 SER cc_start: 0.9647 (m) cc_final: 0.9257 (p) REVERT: B 103 LEU cc_start: 0.9787 (mt) cc_final: 0.9472 (tp) REVERT: B 131 GLU cc_start: 0.9084 (mt-10) cc_final: 0.8753 (mt-10) REVERT: B 134 ASN cc_start: 0.9224 (m-40) cc_final: 0.8885 (m110) REVERT: C 22 ASP cc_start: 0.9096 (m-30) cc_final: 0.8767 (m-30) REVERT: C 45 VAL cc_start: 0.9579 (t) cc_final: 0.9336 (p) REVERT: C 134 ASN cc_start: 0.9710 (m-40) cc_final: 0.9419 (m110) REVERT: D 37 LYS cc_start: 0.9305 (tptt) cc_final: 0.9077 (tptp) REVERT: D 44 TYR cc_start: 0.9267 (t80) cc_final: 0.8813 (t80) REVERT: D 58 GLN cc_start: 0.9480 (mp10) cc_final: 0.9164 (mm-40) REVERT: D 82 GLU cc_start: 0.9582 (tt0) cc_final: 0.9313 (tm-30) REVERT: D 83 THR cc_start: 0.9568 (OUTLIER) cc_final: 0.9239 (p) REVERT: D 90 SER cc_start: 0.9468 (m) cc_final: 0.9256 (p) REVERT: D 95 GLU cc_start: 0.8470 (tp30) cc_final: 0.8219 (tm-30) REVERT: D 134 ASN cc_start: 0.9147 (m-40) cc_final: 0.8671 (m110) REVERT: E 42 GLU cc_start: 0.8594 (pt0) cc_final: 0.8301 (pm20) REVERT: E 48 SER cc_start: 0.9763 (m) cc_final: 0.9528 (p) REVERT: E 56 PHE cc_start: 0.9483 (t80) cc_final: 0.9261 (t80) REVERT: E 76 ARG cc_start: 0.9477 (mmm-85) cc_final: 0.9213 (mmm-85) REVERT: E 82 GLU cc_start: 0.9347 (tm-30) cc_final: 0.9002 (tm-30) REVERT: E 94 ARG cc_start: 0.8735 (mmm-85) cc_final: 0.8497 (mtt90) REVERT: E 101 ASN cc_start: 0.9503 (m110) cc_final: 0.9082 (m110) REVERT: E 105 TYR cc_start: 0.9317 (m-10) cc_final: 0.8751 (m-80) REVERT: E 114 THR cc_start: 0.9501 (m) cc_final: 0.9244 (p) REVERT: E 131 GLU cc_start: 0.9031 (tp30) cc_final: 0.8672 (tm-30) REVERT: E 135 ILE cc_start: 0.9610 (mm) cc_final: 0.9270 (mm) REVERT: J 57 GLU cc_start: 0.8249 (mp0) cc_final: 0.8042 (tm-30) REVERT: J 82 MET cc_start: 0.8814 (mmt) cc_final: 0.8586 (mmt) REVERT: J 146 PHE cc_start: 0.9158 (m-80) cc_final: 0.8810 (m-80) REVERT: J 159 MET cc_start: 0.9010 (tpp) cc_final: 0.8737 (tpp) REVERT: J 166 SER cc_start: 0.9086 (m) cc_final: 0.8625 (t) REVERT: J 209 GLU cc_start: 0.9337 (mm-30) cc_final: 0.8441 (mp0) REVERT: J 229 MET cc_start: 0.8557 (mtp) cc_final: 0.8256 (mtp) REVERT: L 40 LYS cc_start: 0.9453 (tttt) cc_final: 0.9167 (tttp) REVERT: L 113 LYS cc_start: 0.9455 (ttmm) cc_final: 0.9178 (tppt) REVERT: L 115 GLN cc_start: 0.9051 (mm110) cc_final: 0.8733 (mm110) REVERT: L 118 LYS cc_start: 0.9552 (tppp) cc_final: 0.9246 (tppt) REVERT: N 49 MET cc_start: 0.9648 (tmm) cc_final: 0.9287 (tmm) REVERT: N 137 TYR cc_start: 0.7867 (OUTLIER) cc_final: 0.7476 (p90) REVERT: N 249 ARG cc_start: 0.9266 (mtp-110) cc_final: 0.8997 (ptm-80) REVERT: G 40 ASP cc_start: 0.9041 (m-30) cc_final: 0.8815 (p0) REVERT: G 66 GLU cc_start: 0.9311 (mt-10) cc_final: 0.9003 (mt-10) REVERT: F 33 GLN cc_start: 0.9316 (mp10) cc_final: 0.8967 (mp10) REVERT: F 73 ASN cc_start: 0.9526 (t0) cc_final: 0.9270 (t0) REVERT: F 166 PHE cc_start: 0.9070 (t80) cc_final: 0.8817 (t80) REVERT: F 239 LYS cc_start: 0.9533 (mmtm) cc_final: 0.9332 (mmmm) REVERT: H 56 ILE cc_start: 0.9441 (pt) cc_final: 0.9065 (mm) REVERT: H 110 GLN cc_start: 0.9632 (tp40) cc_final: 0.9201 (mp10) REVERT: H 145 TYR cc_start: 0.8401 (p90) cc_final: 0.8005 (p90) REVERT: H 174 ASP cc_start: 0.8674 (t0) cc_final: 0.8240 (t70) REVERT: H 255 ASP cc_start: 0.9113 (m-30) cc_final: 0.8641 (p0) REVERT: H 265 MET cc_start: 0.9513 (mtp) cc_final: 0.9198 (mtt) REVERT: I 80 GLU cc_start: 0.8995 (tt0) cc_final: 0.8772 (tt0) REVERT: I 99 ASP cc_start: 0.9505 (m-30) cc_final: 0.9205 (p0) REVERT: I 110 GLN cc_start: 0.9619 (tp40) cc_final: 0.9322 (tp40) REVERT: I 118 TYR cc_start: 0.9090 (m-10) cc_final: 0.8258 (m-10) REVERT: I 129 MET cc_start: 0.9435 (OUTLIER) cc_final: 0.9136 (mmm) REVERT: I 265 MET cc_start: 0.9629 (mtm) cc_final: 0.9090 (mtm) REVERT: K 30 ASP cc_start: 0.8493 (m-30) cc_final: 0.8275 (m-30) REVERT: K 56 ASP cc_start: 0.9164 (m-30) cc_final: 0.8844 (m-30) REVERT: K 60 MET cc_start: 0.9270 (tmm) cc_final: 0.8826 (tmm) REVERT: K 61 ILE cc_start: 0.9216 (mt) cc_final: 0.8827 (mt) REVERT: K 81 GLU cc_start: 0.8922 (mt-10) cc_final: 0.8552 (mt-10) REVERT: K 111 GLU cc_start: 0.9454 (OUTLIER) cc_final: 0.8978 (pt0) REVERT: K 128 ARG cc_start: 0.9526 (ttm110) cc_final: 0.9091 (ptp-110) REVERT: K 160 LEU cc_start: 0.9441 (mm) cc_final: 0.9217 (mt) REVERT: K 201 ASP cc_start: 0.9232 (t0) cc_final: 0.8689 (t0) REVERT: K 202 GLU cc_start: 0.8591 (mt-10) cc_final: 0.8224 (mt-10) REVERT: K 205 GLU cc_start: 0.8473 (mm-30) cc_final: 0.8167 (mm-30) REVERT: K 220 LEU cc_start: 0.9388 (OUTLIER) cc_final: 0.9080 (pp) REVERT: K 238 LEU cc_start: 0.9047 (mt) cc_final: 0.8686 (pp) REVERT: K 273 LYS cc_start: 0.9435 (tppt) cc_final: 0.8888 (mttm) REVERT: K 274 GLU cc_start: 0.8784 (mp0) cc_final: 0.8154 (mp0) REVERT: K 330 PHE cc_start: 0.9111 (m-80) cc_final: 0.8338 (m-80) REVERT: K 336 MET cc_start: 0.8851 (mmm) cc_final: 0.8523 (mmm) REVERT: K 369 ILE cc_start: 0.9433 (mt) cc_final: 0.9004 (mm) REVERT: K 406 SER cc_start: 0.9214 (m) cc_final: 0.8956 (p) REVERT: K 438 MET cc_start: 0.8791 (mmt) cc_final: 0.8266 (mmt) REVERT: K 439 MET cc_start: 0.8849 (mmt) cc_final: 0.8553 (mmp) REVERT: K 474 ARG cc_start: 0.3002 (mtt180) cc_final: 0.2559 (mtt180) REVERT: K 481 LEU cc_start: 0.8607 (tp) cc_final: 0.8273 (tp) REVERT: K 502 LYS cc_start: 0.9409 (mtpt) cc_final: 0.9089 (mtmm) REVERT: K 520 ASP cc_start: 0.8187 (m-30) cc_final: 0.7829 (m-30) REVERT: K 527 LYS cc_start: 0.8891 (mmmt) cc_final: 0.8663 (mmtt) REVERT: K 538 ILE cc_start: 0.9335 (tp) cc_final: 0.9122 (tp) REVERT: K 588 MET cc_start: 0.9180 (mtm) cc_final: 0.8717 (mtp) REVERT: K 625 ILE cc_start: 0.9424 (mt) cc_final: 0.9075 (mm) REVERT: K 637 PHE cc_start: 0.9538 (t80) cc_final: 0.9325 (t80) REVERT: K 677 MET cc_start: 0.8944 (ttp) cc_final: 0.8465 (ttp) REVERT: K 730 GLU cc_start: 0.9031 (tt0) cc_final: 0.8583 (tp30) REVERT: K 734 ASN cc_start: 0.8938 (m110) cc_final: 0.8232 (m-40) REVERT: K 745 MET cc_start: 0.8992 (mpp) cc_final: 0.8706 (mpp) REVERT: M 16 MET cc_start: 0.8692 (mmt) cc_final: 0.8307 (mmp) REVERT: M 167 LYS cc_start: 0.9412 (mmmt) cc_final: 0.9197 (mmtp) REVERT: M 169 PHE cc_start: 0.9092 (m-10) cc_final: 0.8781 (m-80) REVERT: M 170 ASP cc_start: 0.9018 (t0) cc_final: 0.8667 (t0) REVERT: M 262 PHE cc_start: 0.5489 (m-80) cc_final: 0.5204 (m-80) REVERT: M 290 MET cc_start: 0.9127 (pmm) cc_final: 0.8744 (pmm) outliers start: 119 outliers final: 64 residues processed: 630 average time/residue: 0.1611 time to fit residues: 164.4021 Evaluate side-chains 567 residues out of total 3097 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 498 time to evaluate : 1.127 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 LEU Chi-restraints excluded: chain A residue 25 THR Chi-restraints excluded: chain A residue 63 VAL Chi-restraints excluded: chain A residue 102 LEU Chi-restraints excluded: chain A residue 122 ASN Chi-restraints excluded: chain B residue 21 LEU Chi-restraints excluded: chain B residue 54 LEU Chi-restraints excluded: chain B residue 77 ASP Chi-restraints excluded: chain B residue 118 VAL Chi-restraints excluded: chain C residue 37 LYS Chi-restraints excluded: chain C residue 98 ASP Chi-restraints excluded: chain C residue 118 VAL Chi-restraints excluded: chain C residue 128 THR Chi-restraints excluded: chain D residue 83 THR Chi-restraints excluded: chain E residue 39 ASN Chi-restraints excluded: chain E residue 46 ASP Chi-restraints excluded: chain E residue 100 VAL Chi-restraints excluded: chain E residue 126 VAL Chi-restraints excluded: chain J residue 43 VAL Chi-restraints excluded: chain J residue 90 VAL Chi-restraints excluded: chain J residue 177 VAL Chi-restraints excluded: chain J residue 200 VAL Chi-restraints excluded: chain J residue 239 LYS Chi-restraints excluded: chain J residue 274 GLU Chi-restraints excluded: chain L residue 21 THR Chi-restraints excluded: chain L residue 34 VAL Chi-restraints excluded: chain L residue 74 VAL Chi-restraints excluded: chain N residue 56 ILE Chi-restraints excluded: chain N residue 137 TYR Chi-restraints excluded: chain N residue 161 THR Chi-restraints excluded: chain N residue 190 ILE Chi-restraints excluded: chain N residue 191 VAL Chi-restraints excluded: chain G residue 157 TYR Chi-restraints excluded: chain F residue 140 ILE Chi-restraints excluded: chain F residue 232 VAL Chi-restraints excluded: chain H residue 16 THR Chi-restraints excluded: chain H residue 168 VAL Chi-restraints excluded: chain H residue 193 ILE Chi-restraints excluded: chain H residue 227 LYS Chi-restraints excluded: chain H residue 241 ILE Chi-restraints excluded: chain I residue 129 MET Chi-restraints excluded: chain I residue 162 VAL Chi-restraints excluded: chain I residue 182 LYS Chi-restraints excluded: chain I residue 183 MET Chi-restraints excluded: chain I residue 210 VAL Chi-restraints excluded: chain K residue 14 VAL Chi-restraints excluded: chain K residue 77 SER Chi-restraints excluded: chain K residue 111 GLU Chi-restraints excluded: chain K residue 156 LEU Chi-restraints excluded: chain K residue 173 TYR Chi-restraints excluded: chain K residue 220 LEU Chi-restraints excluded: chain K residue 230 THR Chi-restraints excluded: chain K residue 304 SER Chi-restraints excluded: chain K residue 378 TYR Chi-restraints excluded: chain K residue 385 ILE Chi-restraints excluded: chain K residue 460 HIS Chi-restraints excluded: chain K residue 532 THR Chi-restraints excluded: chain K residue 628 LEU Chi-restraints excluded: chain K residue 661 LYS Chi-restraints excluded: chain K residue 824 SER Chi-restraints excluded: chain M residue 30 ILE Chi-restraints excluded: chain M residue 62 ILE Chi-restraints excluded: chain M residue 82 ILE Chi-restraints excluded: chain M residue 118 ILE Chi-restraints excluded: chain M residue 157 TYR Chi-restraints excluded: chain M residue 182 ILE Chi-restraints excluded: chain M residue 200 VAL Chi-restraints excluded: chain M residue 218 LEU Chi-restraints excluded: chain M residue 291 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 346 random chunks: chunk 91 optimal weight: 0.5980 chunk 209 optimal weight: 9.9990 chunk 13 optimal weight: 10.0000 chunk 311 optimal weight: 2.9990 chunk 204 optimal weight: 5.9990 chunk 278 optimal weight: 0.9990 chunk 69 optimal weight: 7.9990 chunk 328 optimal weight: 0.8980 chunk 44 optimal weight: 3.9990 chunk 197 optimal weight: 9.9990 chunk 290 optimal weight: 2.9990 overall best weight: 1.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** D 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 121 ASN ** L 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 9 ASN N 59 ASN G 134 GLN G 141 ASN G 147 GLN ** H 204 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 148 ASN ** M 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.053180 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3101 r_free = 0.3101 target = 0.044695 restraints weight = 142123.465| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3148 r_free = 0.3148 target = 0.046473 restraints weight = 72438.461| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3181 r_free = 0.3181 target = 0.047695 restraints weight = 45112.242| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3203 r_free = 0.3203 target = 0.048528 restraints weight = 31484.072| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.3220 r_free = 0.3220 target = 0.049137 restraints weight = 23889.931| |-----------------------------------------------------------------------------| r_work (final): 0.3213 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8481 moved from start: 0.3309 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 29252 Z= 0.155 Angle : 0.779 17.636 39623 Z= 0.362 Chirality : 0.063 0.889 4524 Planarity : 0.004 0.057 4852 Dihedral : 11.079 158.087 4391 Min Nonbonded Distance : 2.414 Molprobity Statistics. All-atom Clashscore : 14.09 Ramachandran Plot: Outliers : 0.12 % Allowed : 5.55 % Favored : 94.33 % Rotamer: Outliers : 3.33 % Allowed : 19.81 % Favored : 76.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.73 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.07 (0.15), residues: 3441 helix: 1.79 (0.14), residues: 1468 sheet: -0.26 (0.23), residues: 475 loop : -1.70 (0.15), residues: 1498 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG K 461 TYR 0.025 0.002 TYR N 222 PHE 0.027 0.001 PHE E 129 TRP 0.009 0.001 TRP M 173 HIS 0.004 0.001 HIS N 173 Details of bonding type rmsd/Z covalent geometry : bond 0.00337 / 0.15 (29237) covalent geometry : angle 0.77664 / 0.36 (39593) SS BOND : bond 0.00597 / 0.28 ( 15) SS BOND : angle 2.53193 / 1.99 ( 30) hydrogen bonds : bond 0.03752 / 2.51 ( 1274) hydrogen bonds : angle 5.06916 / 3.63 ( 3747) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6882 Ramachandran restraints generated. 3441 Oldfield, 0 Emsley, 3441 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6882 Ramachandran restraints generated. 3441 Oldfield, 0 Emsley, 3441 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 663 residues out of total 3097 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 103 poor density : 560 time to evaluate : 0.822 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 22 ASP cc_start: 0.8693 (m-30) cc_final: 0.8213 (t0) REVERT: A 29 ILE cc_start: 0.9388 (OUTLIER) cc_final: 0.9003 (tt) REVERT: A 42 GLU cc_start: 0.8197 (mm-30) cc_final: 0.7897 (mm-30) REVERT: A 56 PHE cc_start: 0.8960 (t80) cc_final: 0.8574 (t80) REVERT: A 60 ARG cc_start: 0.9290 (mmp80) cc_final: 0.8885 (mmm160) REVERT: A 69 TYR cc_start: 0.9190 (t80) cc_final: 0.8932 (t80) REVERT: A 79 ILE cc_start: 0.8972 (mm) cc_final: 0.8684 (mp) REVERT: A 110 TYR cc_start: 0.9054 (t80) cc_final: 0.8790 (t80) REVERT: A 111 ASP cc_start: 0.8950 (t0) cc_final: 0.8606 (t0) REVERT: A 121 ASN cc_start: 0.9317 (m-40) cc_final: 0.9035 (p0) REVERT: A 131 GLU cc_start: 0.9411 (mt-10) cc_final: 0.8977 (mt-10) REVERT: B 22 ASP cc_start: 0.8946 (m-30) cc_final: 0.8177 (m-30) REVERT: B 26 ARG cc_start: 0.9109 (ptp-110) cc_final: 0.8435 (ptp90) REVERT: B 73 GLN cc_start: 0.9239 (tp40) cc_final: 0.9019 (tp-100) REVERT: B 78 GLU cc_start: 0.9096 (mm-30) cc_final: 0.8543 (tp30) REVERT: B 90 SER cc_start: 0.9657 (m) cc_final: 0.9268 (p) REVERT: B 129 PHE cc_start: 0.9131 (t80) cc_final: 0.8734 (t80) REVERT: B 134 ASN cc_start: 0.9211 (m-40) cc_final: 0.8855 (m110) REVERT: C 22 ASP cc_start: 0.9094 (m-30) cc_final: 0.8703 (m-30) REVERT: C 45 VAL cc_start: 0.9572 (t) cc_final: 0.9328 (p) REVERT: C 71 MET cc_start: 0.9409 (mtm) cc_final: 0.9034 (mtm) REVERT: C 103 LEU cc_start: 0.9619 (OUTLIER) cc_final: 0.9352 (tp) REVERT: C 134 ASN cc_start: 0.9701 (m-40) cc_final: 0.9406 (m110) REVERT: D 44 TYR cc_start: 0.9181 (t80) cc_final: 0.8747 (t80) REVERT: D 58 GLN cc_start: 0.9475 (mp10) cc_final: 0.9157 (mm-40) REVERT: D 66 LEU cc_start: 0.9685 (tt) cc_final: 0.9331 (mm) REVERT: D 82 GLU cc_start: 0.9559 (tt0) cc_final: 0.9071 (tp30) REVERT: D 90 SER cc_start: 0.9437 (m) cc_final: 0.9232 (p) REVERT: D 101 ASN cc_start: 0.9590 (m110) cc_final: 0.9336 (m-40) REVERT: E 48 SER cc_start: 0.9762 (m) cc_final: 0.9541 (p) REVERT: E 55 SER cc_start: 0.9746 (m) cc_final: 0.9481 (p) REVERT: E 56 PHE cc_start: 0.9502 (t80) cc_final: 0.9259 (t80) REVERT: E 71 MET cc_start: 0.9364 (mtp) cc_final: 0.9140 (ptp) REVERT: E 82 GLU cc_start: 0.9319 (tm-30) cc_final: 0.8964 (tm-30) REVERT: E 94 ARG cc_start: 0.8708 (mmm-85) cc_final: 0.8476 (mtt90) REVERT: E 101 ASN cc_start: 0.9499 (m110) cc_final: 0.9050 (m110) REVERT: E 105 TYR cc_start: 0.9291 (m-10) cc_final: 0.8696 (m-80) REVERT: E 114 THR cc_start: 0.9477 (m) cc_final: 0.9213 (p) REVERT: E 131 GLU cc_start: 0.9000 (tp30) cc_final: 0.8646 (tm-30) REVERT: E 134 ASN cc_start: 0.9414 (m110) cc_final: 0.9173 (m-40) REVERT: E 135 ILE cc_start: 0.9583 (mm) cc_final: 0.9247 (mm) REVERT: J 82 MET cc_start: 0.8865 (mmt) cc_final: 0.8663 (mmt) REVERT: J 146 PHE cc_start: 0.9173 (m-80) cc_final: 0.8834 (m-80) REVERT: J 159 MET cc_start: 0.9028 (tpp) cc_final: 0.8767 (tpp) REVERT: J 166 SER cc_start: 0.9059 (m) cc_final: 0.8586 (t) REVERT: J 229 MET cc_start: 0.8558 (mtp) cc_final: 0.8271 (mtp) REVERT: L 40 LYS cc_start: 0.9453 (tttt) cc_final: 0.9195 (tttp) REVERT: L 83 TYR cc_start: 0.7931 (m-10) cc_final: 0.7707 (m-10) REVERT: L 113 LYS cc_start: 0.9449 (ttmm) cc_final: 0.9161 (tppt) REVERT: N 40 MET cc_start: 0.8666 (tmm) cc_final: 0.8395 (tmm) REVERT: N 49 MET cc_start: 0.9639 (tmm) cc_final: 0.9274 (tmm) REVERT: N 137 TYR cc_start: 0.7785 (OUTLIER) cc_final: 0.7378 (p90) REVERT: N 155 MET cc_start: 0.8902 (pmm) cc_final: 0.8643 (pmm) REVERT: N 249 ARG cc_start: 0.9259 (mtp-110) cc_final: 0.9033 (ptm-80) REVERT: G 40 ASP cc_start: 0.9040 (m-30) cc_final: 0.8825 (p0) REVERT: G 66 GLU cc_start: 0.9268 (mt-10) cc_final: 0.8959 (mt-10) REVERT: F 33 GLN cc_start: 0.9341 (mp10) cc_final: 0.9025 (mp10) REVERT: F 73 ASN cc_start: 0.9506 (t0) cc_final: 0.9246 (t0) REVERT: F 121 TYR cc_start: 0.8761 (m-80) cc_final: 0.8088 (m-80) REVERT: F 122 ILE cc_start: 0.9246 (mt) cc_final: 0.8987 (mm) REVERT: F 207 ARG cc_start: 0.7435 (OUTLIER) cc_final: 0.7216 (mtp85) REVERT: F 239 LYS cc_start: 0.9537 (mmtm) cc_final: 0.9287 (mmmm) REVERT: H 5 THR cc_start: 0.8952 (OUTLIER) cc_final: 0.8694 (m) REVERT: H 19 GLU cc_start: 0.8526 (tm-30) cc_final: 0.8156 (tm-30) REVERT: H 56 ILE cc_start: 0.9410 (pt) cc_final: 0.9038 (mm) REVERT: H 145 TYR cc_start: 0.8372 (p90) cc_final: 0.7964 (p90) REVERT: H 174 ASP cc_start: 0.8676 (t0) cc_final: 0.8249 (t70) REVERT: H 193 ILE cc_start: 0.9336 (OUTLIER) cc_final: 0.9132 (pt) REVERT: H 200 MET cc_start: 0.9322 (tpp) cc_final: 0.8946 (mmm) REVERT: H 255 ASP cc_start: 0.9117 (m-30) cc_final: 0.8603 (p0) REVERT: I 80 GLU cc_start: 0.8955 (tt0) cc_final: 0.8744 (tt0) REVERT: I 99 ASP cc_start: 0.9492 (m-30) cc_final: 0.9161 (p0) REVERT: I 110 GLN cc_start: 0.9613 (tp40) cc_final: 0.9298 (tp40) REVERT: I 129 MET cc_start: 0.9377 (OUTLIER) cc_final: 0.9129 (mmm) REVERT: I 200 MET cc_start: 0.9270 (OUTLIER) cc_final: 0.9058 (ttp) REVERT: I 265 MET cc_start: 0.9617 (mtm) cc_final: 0.8985 (mtm) REVERT: K 56 ASP cc_start: 0.9098 (m-30) cc_final: 0.8779 (m-30) REVERT: K 60 MET cc_start: 0.9251 (tmm) cc_final: 0.8797 (tmm) REVERT: K 61 ILE cc_start: 0.9202 (mt) cc_final: 0.8838 (mt) REVERT: K 128 ARG cc_start: 0.9524 (ttm110) cc_final: 0.9002 (ptp-110) REVERT: K 201 ASP cc_start: 0.9256 (t0) cc_final: 0.8597 (t0) REVERT: K 202 GLU cc_start: 0.8551 (mt-10) cc_final: 0.8137 (mt-10) REVERT: K 205 GLU cc_start: 0.8504 (mm-30) cc_final: 0.8151 (mm-30) REVERT: K 220 LEU cc_start: 0.9405 (OUTLIER) cc_final: 0.9137 (pp) REVERT: K 238 LEU cc_start: 0.9027 (mt) cc_final: 0.8690 (pp) REVERT: K 273 LYS cc_start: 0.9425 (tppt) cc_final: 0.8901 (mttm) REVERT: K 336 MET cc_start: 0.8861 (mmm) cc_final: 0.8501 (mmm) REVERT: K 369 ILE cc_start: 0.9405 (mt) cc_final: 0.8963 (mm) REVERT: K 406 SER cc_start: 0.9192 (m) cc_final: 0.8938 (p) REVERT: K 438 MET cc_start: 0.8886 (mmt) cc_final: 0.8491 (mmt) REVERT: K 447 LEU cc_start: 0.8377 (OUTLIER) cc_final: 0.7521 (mm) REVERT: K 454 VAL cc_start: 0.7558 (OUTLIER) cc_final: 0.6840 (m) REVERT: K 474 ARG cc_start: 0.2945 (mtt180) cc_final: 0.2490 (mtt180) REVERT: K 481 LEU cc_start: 0.8597 (tp) cc_final: 0.8275 (tp) REVERT: K 527 LYS cc_start: 0.8784 (mmmt) cc_final: 0.8497 (mmmt) REVERT: K 538 ILE cc_start: 0.9340 (tp) cc_final: 0.9088 (tp) REVERT: K 587 LYS cc_start: 0.9205 (mmtm) cc_final: 0.8668 (tppt) REVERT: K 588 MET cc_start: 0.9281 (mtm) cc_final: 0.8764 (mtp) REVERT: K 619 TYR cc_start: 0.8875 (p90) cc_final: 0.8562 (p90) REVERT: K 625 ILE cc_start: 0.9401 (mt) cc_final: 0.9107 (mm) REVERT: K 627 LEU cc_start: 0.9505 (mt) cc_final: 0.9246 (tp) REVERT: K 677 MET cc_start: 0.8906 (ttp) cc_final: 0.8647 (ttp) REVERT: K 727 ASP cc_start: 0.9467 (m-30) cc_final: 0.8762 (t0) REVERT: K 730 GLU cc_start: 0.8983 (tt0) cc_final: 0.8634 (tp30) REVERT: K 745 MET cc_start: 0.8956 (mpp) cc_final: 0.8686 (mtm) REVERT: M 5 LYS cc_start: 0.9490 (ttmm) cc_final: 0.9245 (ttpp) REVERT: M 15 GLN cc_start: 0.8004 (mm-40) cc_final: 0.7772 (tp40) REVERT: M 16 MET cc_start: 0.8721 (mmt) cc_final: 0.8318 (mmp) REVERT: M 40 LEU cc_start: 0.9505 (mm) cc_final: 0.9293 (mt) REVERT: M 167 LYS cc_start: 0.9399 (mmmt) cc_final: 0.9182 (mmtp) REVERT: M 169 PHE cc_start: 0.9063 (m-10) cc_final: 0.8734 (m-80) REVERT: M 290 MET cc_start: 0.8886 (pmm) cc_final: 0.8576 (pmm) outliers start: 103 outliers final: 51 residues processed: 632 average time/residue: 0.1601 time to fit residues: 165.1862 Evaluate side-chains 555 residues out of total 3097 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 493 time to evaluate : 0.838 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 LEU Chi-restraints excluded: chain A residue 25 THR Chi-restraints excluded: chain A residue 29 ILE Chi-restraints excluded: chain A residue 63 VAL Chi-restraints excluded: chain A residue 102 LEU Chi-restraints excluded: chain A residue 122 ASN Chi-restraints excluded: chain C residue 37 LYS Chi-restraints excluded: chain C residue 103 LEU Chi-restraints excluded: chain E residue 39 ASN Chi-restraints excluded: chain E residue 46 ASP Chi-restraints excluded: chain E residue 100 VAL Chi-restraints excluded: chain E residue 126 VAL Chi-restraints excluded: chain J residue 43 VAL Chi-restraints excluded: chain J residue 208 VAL Chi-restraints excluded: chain L residue 21 THR Chi-restraints excluded: chain L residue 34 VAL Chi-restraints excluded: chain L residue 74 VAL Chi-restraints excluded: chain L residue 152 LEU Chi-restraints excluded: chain N residue 56 ILE Chi-restraints excluded: chain N residue 137 TYR Chi-restraints excluded: chain N residue 190 ILE Chi-restraints excluded: chain N residue 191 VAL Chi-restraints excluded: chain G residue 101 GLU Chi-restraints excluded: chain F residue 140 ILE Chi-restraints excluded: chain F residue 157 TYR Chi-restraints excluded: chain F residue 207 ARG Chi-restraints excluded: chain F residue 232 VAL Chi-restraints excluded: chain F residue 236 ILE Chi-restraints excluded: chain H residue 5 THR Chi-restraints excluded: chain H residue 11 VAL Chi-restraints excluded: chain H residue 16 THR Chi-restraints excluded: chain H residue 90 CYS Chi-restraints excluded: chain H residue 123 CYS Chi-restraints excluded: chain H residue 193 ILE Chi-restraints excluded: chain I residue 129 MET Chi-restraints excluded: chain I residue 183 MET Chi-restraints excluded: chain I residue 200 MET Chi-restraints excluded: chain I residue 210 VAL Chi-restraints excluded: chain K residue 14 VAL Chi-restraints excluded: chain K residue 173 TYR Chi-restraints excluded: chain K residue 220 LEU Chi-restraints excluded: chain K residue 230 THR Chi-restraints excluded: chain K residue 310 ASN Chi-restraints excluded: chain K residue 378 TYR Chi-restraints excluded: chain K residue 385 ILE Chi-restraints excluded: chain K residue 447 LEU Chi-restraints excluded: chain K residue 454 VAL Chi-restraints excluded: chain K residue 460 HIS Chi-restraints excluded: chain K residue 532 THR Chi-restraints excluded: chain K residue 576 ASP Chi-restraints excluded: chain K residue 602 ASP Chi-restraints excluded: chain K residue 628 LEU Chi-restraints excluded: chain K residue 661 LYS Chi-restraints excluded: chain M residue 30 ILE Chi-restraints excluded: chain M residue 62 ILE Chi-restraints excluded: chain M residue 82 ILE Chi-restraints excluded: chain M residue 118 ILE Chi-restraints excluded: chain M residue 157 TYR Chi-restraints excluded: chain M residue 182 ILE Chi-restraints excluded: chain M residue 200 VAL Chi-restraints excluded: chain M residue 218 LEU Chi-restraints excluded: chain M residue 291 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 346 random chunks: chunk 186 optimal weight: 0.1980 chunk 159 optimal weight: 6.9990 chunk 143 optimal weight: 0.0970 chunk 319 optimal weight: 6.9990 chunk 227 optimal weight: 0.9990 chunk 125 optimal weight: 8.9990 chunk 25 optimal weight: 7.9990 chunk 148 optimal weight: 2.9990 chunk 10 optimal weight: 4.9990 chunk 74 optimal weight: 6.9990 chunk 126 optimal weight: 0.9990 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 73 GLN D 121 ASN D 134 ASN ** E 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 134 GLN F 134 GLN ** H 204 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 146 HIS ** M 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3350 r_free = 0.3350 target = 0.053922 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3128 r_free = 0.3128 target = 0.045467 restraints weight = 142254.278| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3174 r_free = 0.3174 target = 0.047251 restraints weight = 73025.569| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3207 r_free = 0.3207 target = 0.048462 restraints weight = 45660.379| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3228 r_free = 0.3228 target = 0.049289 restraints weight = 31991.223| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3244 r_free = 0.3244 target = 0.049902 restraints weight = 24373.428| |-----------------------------------------------------------------------------| r_work (final): 0.3231 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8466 moved from start: 0.3566 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.067 29252 Z= 0.142 Angle : 0.762 14.744 39623 Z= 0.357 Chirality : 0.060 0.759 4524 Planarity : 0.004 0.059 4852 Dihedral : 10.994 156.800 4391 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 13.65 Ramachandran Plot: Outliers : 0.12 % Allowed : 5.58 % Favored : 94.30 % Rotamer: Outliers : 3.37 % Allowed : 20.52 % Favored : 76.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.73 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.06 (0.14), residues: 3441 helix: 1.71 (0.14), residues: 1462 sheet: -0.16 (0.23), residues: 464 loop : -1.64 (0.15), residues: 1515 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG E 76 TYR 0.024 0.002 TYR K 62 PHE 0.032 0.001 PHE F 166 TRP 0.018 0.001 TRP G 182 HIS 0.005 0.001 HIS M 146 Details of bonding type rmsd/Z covalent geometry : bond 0.00315 / 0.14 (29237) covalent geometry : angle 0.76016 / 0.36 (39593) SS BOND : bond 0.00372 / 0.24 ( 15) SS BOND : angle 2.00046 / 1.41 ( 30) hydrogen bonds : bond 0.03669 / 2.47 ( 1274) hydrogen bonds : angle 4.96161 / 3.55 ( 3747) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6882 Ramachandran restraints generated. 3441 Oldfield, 0 Emsley, 3441 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6882 Ramachandran restraints generated. 3441 Oldfield, 0 Emsley, 3441 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 630 residues out of total 3097 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 104 poor density : 526 time to evaluate : 1.326 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 22 ASP cc_start: 0.8694 (m-30) cc_final: 0.8214 (t0) REVERT: A 42 GLU cc_start: 0.8296 (mm-30) cc_final: 0.8048 (mm-30) REVERT: A 56 PHE cc_start: 0.8954 (t80) cc_final: 0.8553 (t80) REVERT: A 60 ARG cc_start: 0.9283 (mmp80) cc_final: 0.8907 (mmm160) REVERT: A 79 ILE cc_start: 0.8969 (mm) cc_final: 0.8672 (mp) REVERT: A 110 TYR cc_start: 0.9040 (t80) cc_final: 0.8793 (t80) REVERT: A 111 ASP cc_start: 0.8968 (t0) cc_final: 0.8623 (t0) REVERT: A 131 GLU cc_start: 0.9436 (mt-10) cc_final: 0.8789 (mt-10) REVERT: A 134 ASN cc_start: 0.9548 (m110) cc_final: 0.9332 (p0) REVERT: B 22 ASP cc_start: 0.8915 (m-30) cc_final: 0.8177 (m-30) REVERT: B 26 ARG cc_start: 0.9105 (ptp-110) cc_final: 0.8425 (ptp90) REVERT: B 44 TYR cc_start: 0.9317 (t80) cc_final: 0.8906 (t80) REVERT: B 73 GLN cc_start: 0.9284 (tp40) cc_final: 0.9008 (tp-100) REVERT: B 78 GLU cc_start: 0.9066 (mm-30) cc_final: 0.8508 (tp30) REVERT: B 90 SER cc_start: 0.9655 (m) cc_final: 0.9271 (p) REVERT: B 129 PHE cc_start: 0.9003 (t80) cc_final: 0.8641 (t80) REVERT: B 134 ASN cc_start: 0.9207 (m-40) cc_final: 0.8827 (m110) REVERT: C 22 ASP cc_start: 0.9097 (m-30) cc_final: 0.8729 (m-30) REVERT: C 45 VAL cc_start: 0.9530 (t) cc_final: 0.9245 (p) REVERT: C 71 MET cc_start: 0.9397 (mtm) cc_final: 0.9095 (mtm) REVERT: C 77 ASP cc_start: 0.9061 (t0) cc_final: 0.8726 (t0) REVERT: C 103 LEU cc_start: 0.9614 (OUTLIER) cc_final: 0.9340 (tp) REVERT: C 105 TYR cc_start: 0.9346 (m-80) cc_final: 0.9136 (m-80) REVERT: C 134 ASN cc_start: 0.9699 (m-40) cc_final: 0.9391 (m110) REVERT: D 26 ARG cc_start: 0.9535 (mtm-85) cc_final: 0.9250 (ptp90) REVERT: D 44 TYR cc_start: 0.9219 (t80) cc_final: 0.8679 (t80) REVERT: D 58 GLN cc_start: 0.9490 (mp10) cc_final: 0.9156 (mm-40) REVERT: D 66 LEU cc_start: 0.9696 (tt) cc_final: 0.9370 (mm) REVERT: D 82 GLU cc_start: 0.9489 (tt0) cc_final: 0.9115 (tm-30) REVERT: D 90 SER cc_start: 0.9434 (m) cc_final: 0.9210 (p) REVERT: D 101 ASN cc_start: 0.9584 (m110) cc_final: 0.9352 (m110) REVERT: D 134 ASN cc_start: 0.9100 (m-40) cc_final: 0.8553 (m110) REVERT: E 44 TYR cc_start: 0.8925 (t80) cc_final: 0.8630 (t80) REVERT: E 48 SER cc_start: 0.9756 (m) cc_final: 0.9533 (p) REVERT: E 51 ASN cc_start: 0.9523 (m-40) cc_final: 0.9299 (m110) REVERT: E 55 SER cc_start: 0.9737 (m) cc_final: 0.9466 (p) REVERT: E 56 PHE cc_start: 0.9508 (t80) cc_final: 0.9274 (t80) REVERT: E 71 MET cc_start: 0.9355 (mtp) cc_final: 0.9139 (ptp) REVERT: E 76 ARG cc_start: 0.9563 (mmm-85) cc_final: 0.9293 (mtp85) REVERT: E 82 GLU cc_start: 0.9353 (tm-30) cc_final: 0.9012 (tm-30) REVERT: E 101 ASN cc_start: 0.9507 (m110) cc_final: 0.9084 (m110) REVERT: E 105 TYR cc_start: 0.9282 (m-10) cc_final: 0.8718 (m-80) REVERT: E 114 THR cc_start: 0.9453 (m) cc_final: 0.9197 (p) REVERT: E 131 GLU cc_start: 0.8989 (tp30) cc_final: 0.8505 (tm-30) REVERT: E 135 ILE cc_start: 0.9578 (mm) cc_final: 0.9246 (mm) REVERT: J 57 GLU cc_start: 0.8173 (mp0) cc_final: 0.7829 (tm-30) REVERT: J 99 MET cc_start: 0.9511 (ttp) cc_final: 0.9198 (ppp) REVERT: J 146 PHE cc_start: 0.9169 (m-80) cc_final: 0.8842 (m-80) REVERT: J 159 MET cc_start: 0.9054 (tpp) cc_final: 0.8787 (tpp) REVERT: J 209 GLU cc_start: 0.9350 (mm-30) cc_final: 0.8464 (mp0) REVERT: J 229 MET cc_start: 0.8529 (mtp) cc_final: 0.8246 (mtp) REVERT: L 40 LYS cc_start: 0.9446 (tttt) cc_final: 0.9163 (tttp) REVERT: L 113 LYS cc_start: 0.9459 (ttmm) cc_final: 0.9172 (tppt) REVERT: L 118 LYS cc_start: 0.9517 (ttmm) cc_final: 0.8965 (tppt) REVERT: L 127 ILE cc_start: 0.9441 (pt) cc_final: 0.9231 (mm) REVERT: N 49 MET cc_start: 0.9635 (tmm) cc_final: 0.9351 (tmm) REVERT: N 137 TYR cc_start: 0.7741 (OUTLIER) cc_final: 0.7336 (p90) REVERT: N 249 ARG cc_start: 0.9254 (mtp-110) cc_final: 0.9048 (ptm-80) REVERT: G 40 ASP cc_start: 0.9033 (m-30) cc_final: 0.8812 (p0) REVERT: G 66 GLU cc_start: 0.9283 (mt-10) cc_final: 0.8964 (mt-10) REVERT: F 33 GLN cc_start: 0.9357 (mp10) cc_final: 0.9051 (mp10) REVERT: F 73 ASN cc_start: 0.9491 (t0) cc_final: 0.9224 (t0) REVERT: F 121 TYR cc_start: 0.8801 (m-80) cc_final: 0.8353 (m-80) REVERT: F 134 GLN cc_start: 0.8546 (tm130) cc_final: 0.7960 (tm-30) REVERT: F 239 LYS cc_start: 0.9558 (mmtm) cc_final: 0.9310 (mmmm) REVERT: H 5 THR cc_start: 0.8934 (OUTLIER) cc_final: 0.8663 (m) REVERT: H 19 GLU cc_start: 0.8546 (tm-30) cc_final: 0.8154 (tm-30) REVERT: H 145 TYR cc_start: 0.8402 (p90) cc_final: 0.8116 (p90) REVERT: H 174 ASP cc_start: 0.8652 (t0) cc_final: 0.8198 (t70) REVERT: H 200 MET cc_start: 0.9319 (tpp) cc_final: 0.8948 (mmm) REVERT: H 255 ASP cc_start: 0.9110 (m-30) cc_final: 0.8622 (p0) REVERT: H 265 MET cc_start: 0.9516 (mtp) cc_final: 0.9217 (mtt) REVERT: I 80 GLU cc_start: 0.8930 (tt0) cc_final: 0.8703 (tt0) REVERT: I 99 ASP cc_start: 0.9493 (m-30) cc_final: 0.9178 (p0) REVERT: I 110 GLN cc_start: 0.9621 (tp40) cc_final: 0.9310 (tp40) REVERT: I 118 TYR cc_start: 0.9070 (m-10) cc_final: 0.8796 (m-10) REVERT: I 129 MET cc_start: 0.9347 (OUTLIER) cc_final: 0.9109 (mmm) REVERT: I 200 MET cc_start: 0.9243 (OUTLIER) cc_final: 0.8991 (ttp) REVERT: I 265 MET cc_start: 0.9605 (mtm) cc_final: 0.9379 (mtm) REVERT: K 56 ASP cc_start: 0.9075 (m-30) cc_final: 0.8753 (m-30) REVERT: K 60 MET cc_start: 0.9159 (tmm) cc_final: 0.8766 (tmm) REVERT: K 61 ILE cc_start: 0.9140 (mt) cc_final: 0.8666 (mt) REVERT: K 148 THR cc_start: 0.9229 (OUTLIER) cc_final: 0.8927 (t) REVERT: K 201 ASP cc_start: 0.9252 (t0) cc_final: 0.8605 (t0) REVERT: K 202 GLU cc_start: 0.8505 (mt-10) cc_final: 0.8234 (pt0) REVERT: K 205 GLU cc_start: 0.8508 (mm-30) cc_final: 0.8162 (mm-30) REVERT: K 220 LEU cc_start: 0.9398 (OUTLIER) cc_final: 0.9138 (pp) REVERT: K 238 LEU cc_start: 0.9016 (mt) cc_final: 0.8766 (pp) REVERT: K 273 LYS cc_start: 0.9410 (tppt) cc_final: 0.8900 (mttm) REVERT: K 330 PHE cc_start: 0.9092 (m-80) cc_final: 0.8236 (m-80) REVERT: K 336 MET cc_start: 0.8872 (mmm) cc_final: 0.8471 (mmm) REVERT: K 369 ILE cc_start: 0.9416 (mt) cc_final: 0.8986 (mm) REVERT: K 406 SER cc_start: 0.9192 (m) cc_final: 0.8943 (p) REVERT: K 438 MET cc_start: 0.8883 (mmt) cc_final: 0.8460 (mmt) REVERT: K 447 LEU cc_start: 0.8358 (OUTLIER) cc_final: 0.7433 (mm) REVERT: K 454 VAL cc_start: 0.7473 (OUTLIER) cc_final: 0.6694 (m) REVERT: K 474 ARG cc_start: 0.2868 (mtt180) cc_final: 0.2400 (mtt180) REVERT: K 481 LEU cc_start: 0.8621 (tp) cc_final: 0.8282 (tp) REVERT: K 527 LYS cc_start: 0.8814 (mmmt) cc_final: 0.8541 (mmmt) REVERT: K 538 ILE cc_start: 0.9338 (OUTLIER) cc_final: 0.9086 (tp) REVERT: K 587 LYS cc_start: 0.9206 (mmtm) cc_final: 0.8677 (tppt) REVERT: K 588 MET cc_start: 0.9289 (mtm) cc_final: 0.8676 (mtp) REVERT: K 619 TYR cc_start: 0.8860 (p90) cc_final: 0.8582 (p90) REVERT: K 625 ILE cc_start: 0.9401 (mt) cc_final: 0.9121 (mm) REVERT: K 677 MET cc_start: 0.8909 (ttp) cc_final: 0.8429 (ttp) REVERT: K 727 ASP cc_start: 0.9462 (m-30) cc_final: 0.8787 (t0) REVERT: K 730 GLU cc_start: 0.8971 (tt0) cc_final: 0.8644 (tp30) REVERT: K 745 MET cc_start: 0.9051 (mpp) cc_final: 0.8732 (mtm) REVERT: M 16 MET cc_start: 0.8744 (mmt) cc_final: 0.8317 (mmp) REVERT: M 144 GLN cc_start: 0.8404 (tt0) cc_final: 0.7945 (pp30) REVERT: M 167 LYS cc_start: 0.9392 (mmmt) cc_final: 0.9171 (mmtp) REVERT: M 169 PHE cc_start: 0.9046 (m-10) cc_final: 0.8727 (m-80) REVERT: M 290 MET cc_start: 0.8854 (pmm) cc_final: 0.8549 (pmm) outliers start: 104 outliers final: 65 residues processed: 597 average time/residue: 0.1621 time to fit residues: 157.6569 Evaluate side-chains 570 residues out of total 3097 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 495 time to evaluate : 1.002 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 LEU Chi-restraints excluded: chain A residue 63 VAL Chi-restraints excluded: chain A residue 102 LEU Chi-restraints excluded: chain A residue 121 ASN Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain C residue 37 LYS Chi-restraints excluded: chain C residue 98 ASP Chi-restraints excluded: chain C residue 103 LEU Chi-restraints excluded: chain C residue 128 THR Chi-restraints excluded: chain D residue 40 LYS Chi-restraints excluded: chain E residue 39 ASN Chi-restraints excluded: chain E residue 46 ASP Chi-restraints excluded: chain E residue 100 VAL Chi-restraints excluded: chain E residue 126 VAL Chi-restraints excluded: chain J residue 43 VAL Chi-restraints excluded: chain J residue 120 THR Chi-restraints excluded: chain J residue 177 VAL Chi-restraints excluded: chain J residue 212 MET Chi-restraints excluded: chain L residue 34 VAL Chi-restraints excluded: chain L residue 74 VAL Chi-restraints excluded: chain L residue 137 THR Chi-restraints excluded: chain L residue 152 LEU Chi-restraints excluded: chain N residue 56 ILE Chi-restraints excluded: chain N residue 95 VAL Chi-restraints excluded: chain N residue 137 TYR Chi-restraints excluded: chain N residue 190 ILE Chi-restraints excluded: chain N residue 191 VAL Chi-restraints excluded: chain G residue 32 THR Chi-restraints excluded: chain G residue 101 GLU Chi-restraints excluded: chain F residue 140 ILE Chi-restraints excluded: chain F residue 157 TYR Chi-restraints excluded: chain F residue 232 VAL Chi-restraints excluded: chain F residue 236 ILE Chi-restraints excluded: chain H residue 5 THR Chi-restraints excluded: chain H residue 11 VAL Chi-restraints excluded: chain H residue 16 THR Chi-restraints excluded: chain H residue 90 CYS Chi-restraints excluded: chain H residue 123 CYS Chi-restraints excluded: chain H residue 168 VAL Chi-restraints excluded: chain I residue 129 MET Chi-restraints excluded: chain I residue 183 MET Chi-restraints excluded: chain I residue 193 ILE Chi-restraints excluded: chain I residue 200 MET Chi-restraints excluded: chain I residue 209 GLN Chi-restraints excluded: chain I residue 210 VAL Chi-restraints excluded: chain K residue 148 THR Chi-restraints excluded: chain K residue 154 LEU Chi-restraints excluded: chain K residue 156 LEU Chi-restraints excluded: chain K residue 173 TYR Chi-restraints excluded: chain K residue 174 LEU Chi-restraints excluded: chain K residue 220 LEU Chi-restraints excluded: chain K residue 230 THR Chi-restraints excluded: chain K residue 304 SER Chi-restraints excluded: chain K residue 310 ASN Chi-restraints excluded: chain K residue 342 LEU Chi-restraints excluded: chain K residue 378 TYR Chi-restraints excluded: chain K residue 385 ILE Chi-restraints excluded: chain K residue 447 LEU Chi-restraints excluded: chain K residue 454 VAL Chi-restraints excluded: chain K residue 460 HIS Chi-restraints excluded: chain K residue 532 THR Chi-restraints excluded: chain K residue 538 ILE Chi-restraints excluded: chain K residue 576 ASP Chi-restraints excluded: chain K residue 602 ASP Chi-restraints excluded: chain K residue 661 LYS Chi-restraints excluded: chain M residue 30 ILE Chi-restraints excluded: chain M residue 62 ILE Chi-restraints excluded: chain M residue 82 ILE Chi-restraints excluded: chain M residue 118 ILE Chi-restraints excluded: chain M residue 157 TYR Chi-restraints excluded: chain M residue 182 ILE Chi-restraints excluded: chain M residue 200 VAL Chi-restraints excluded: chain M residue 218 LEU Chi-restraints excluded: chain M residue 220 CYS Chi-restraints excluded: chain M residue 291 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 346 random chunks: chunk 222 optimal weight: 7.9990 chunk 285 optimal weight: 2.9990 chunk 282 optimal weight: 5.9990 chunk 98 optimal weight: 0.8980 chunk 160 optimal weight: 3.9990 chunk 263 optimal weight: 10.0000 chunk 26 optimal weight: 2.9990 chunk 223 optimal weight: 0.4980 chunk 156 optimal weight: 10.0000 chunk 317 optimal weight: 9.9990 chunk 28 optimal weight: 0.9990 overall best weight: 1.6786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 121 ASN ** L 175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 33 GLN ** H 204 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 195 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3342 r_free = 0.3342 target = 0.053520 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3120 r_free = 0.3120 target = 0.045172 restraints weight = 143214.691| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3167 r_free = 0.3167 target = 0.046920 restraints weight = 73653.881| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3199 r_free = 0.3199 target = 0.048123 restraints weight = 46023.630| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3222 r_free = 0.3222 target = 0.048959 restraints weight = 32157.360| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 42)----------------| | r_work = 0.3238 r_free = 0.3238 target = 0.049558 restraints weight = 24342.145| |-----------------------------------------------------------------------------| r_work (final): 0.3218 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8478 moved from start: 0.3741 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 29252 Z= 0.152 Angle : 0.744 15.934 39623 Z= 0.351 Chirality : 0.058 0.664 4524 Planarity : 0.004 0.050 4852 Dihedral : 11.033 153.238 4390 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 14.03 Ramachandran Plot: Outliers : 0.12 % Allowed : 5.64 % Favored : 94.25 % Rotamer: Outliers : 3.20 % Allowed : 21.49 % Favored : 75.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.73 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.06 (0.14), residues: 3441 helix: 1.66 (0.14), residues: 1468 sheet: -0.11 (0.23), residues: 459 loop : -1.61 (0.15), residues: 1514 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 76 TYR 0.046 0.001 TYR K 62 PHE 0.040 0.001 PHE K 245 TRP 0.018 0.001 TRP G 182 HIS 0.005 0.001 HIS K 153 Details of bonding type rmsd/Z covalent geometry : bond 0.00336 / 0.15 (29237) covalent geometry : angle 0.74219 / 0.35 (39593) SS BOND : bond 0.00512 / 0.34 ( 15) SS BOND : angle 1.93953 / 1.31 ( 30) hydrogen bonds : bond 0.03603 / 2.42 ( 1274) hydrogen bonds : angle 4.88710 / 3.49 ( 3747) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6882 Ramachandran restraints generated. 3441 Oldfield, 0 Emsley, 3441 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6882 Ramachandran restraints generated. 3441 Oldfield, 0 Emsley, 3441 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 613 residues out of total 3097 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 99 poor density : 514 time to evaluate : 1.084 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 22 ASP cc_start: 0.8705 (m-30) cc_final: 0.8216 (t0) REVERT: A 42 GLU cc_start: 0.8319 (mm-30) cc_final: 0.8080 (mm-30) REVERT: A 56 PHE cc_start: 0.8920 (t80) cc_final: 0.8462 (t80) REVERT: A 60 ARG cc_start: 0.9275 (mmp80) cc_final: 0.8868 (mmm-85) REVERT: A 69 TYR cc_start: 0.9206 (t80) cc_final: 0.8913 (t80) REVERT: A 79 ILE cc_start: 0.8996 (mm) cc_final: 0.8701 (mp) REVERT: A 110 TYR cc_start: 0.9063 (t80) cc_final: 0.8854 (t80) REVERT: A 111 ASP cc_start: 0.8968 (t0) cc_final: 0.8609 (t0) REVERT: A 131 GLU cc_start: 0.9434 (mt-10) cc_final: 0.8924 (mt-10) REVERT: B 22 ASP cc_start: 0.8817 (m-30) cc_final: 0.8165 (m-30) REVERT: B 26 ARG cc_start: 0.9135 (ptp-110) cc_final: 0.8470 (ptp90) REVERT: B 69 TYR cc_start: 0.8911 (t80) cc_final: 0.8563 (t80) REVERT: B 73 GLN cc_start: 0.9303 (tp40) cc_final: 0.9015 (tp-100) REVERT: B 78 GLU cc_start: 0.9030 (mm-30) cc_final: 0.8330 (tp30) REVERT: B 90 SER cc_start: 0.9659 (m) cc_final: 0.9278 (p) REVERT: B 129 PHE cc_start: 0.8942 (t80) cc_final: 0.8648 (t80) REVERT: B 131 GLU cc_start: 0.9189 (mp0) cc_final: 0.8757 (pm20) REVERT: B 134 ASN cc_start: 0.9187 (m-40) cc_final: 0.8785 (m110) REVERT: C 22 ASP cc_start: 0.9091 (m-30) cc_final: 0.8712 (m-30) REVERT: C 45 VAL cc_start: 0.9540 (t) cc_final: 0.9252 (p) REVERT: C 71 MET cc_start: 0.9375 (mtm) cc_final: 0.9050 (mtm) REVERT: C 77 ASP cc_start: 0.9081 (t0) cc_final: 0.8750 (t0) REVERT: C 103 LEU cc_start: 0.9608 (OUTLIER) cc_final: 0.9308 (tp) REVERT: C 105 TYR cc_start: 0.9384 (m-80) cc_final: 0.9138 (m-80) REVERT: C 134 ASN cc_start: 0.9695 (m-40) cc_final: 0.9380 (m110) REVERT: D 26 ARG cc_start: 0.9533 (mtm-85) cc_final: 0.9261 (ptp90) REVERT: D 32 ILE cc_start: 0.9048 (tp) cc_final: 0.8847 (tp) REVERT: D 44 TYR cc_start: 0.9134 (t80) cc_final: 0.8735 (t80) REVERT: D 58 GLN cc_start: 0.9469 (mp10) cc_final: 0.9195 (mm-40) REVERT: D 66 LEU cc_start: 0.9689 (tt) cc_final: 0.9372 (mm) REVERT: D 82 GLU cc_start: 0.9454 (tt0) cc_final: 0.9023 (tp30) REVERT: D 101 ASN cc_start: 0.9567 (m110) cc_final: 0.9331 (m110) REVERT: D 134 ASN cc_start: 0.9192 (m-40) cc_final: 0.8626 (m110) REVERT: E 44 TYR cc_start: 0.8932 (t80) cc_final: 0.8612 (t80) REVERT: E 55 SER cc_start: 0.9753 (m) cc_final: 0.9486 (p) REVERT: E 56 PHE cc_start: 0.9514 (t80) cc_final: 0.9282 (t80) REVERT: E 76 ARG cc_start: 0.9563 (mmm-85) cc_final: 0.8671 (mtp85) REVERT: E 78 GLU cc_start: 0.8610 (mt-10) cc_final: 0.8213 (mp0) REVERT: E 82 GLU cc_start: 0.9341 (tm-30) cc_final: 0.9013 (tm-30) REVERT: E 101 ASN cc_start: 0.9506 (m110) cc_final: 0.9062 (m110) REVERT: E 105 TYR cc_start: 0.9290 (m-10) cc_final: 0.8737 (m-80) REVERT: E 114 THR cc_start: 0.9419 (m) cc_final: 0.9103 (p) REVERT: E 131 GLU cc_start: 0.9004 (tp30) cc_final: 0.8600 (tm-30) REVERT: E 135 ILE cc_start: 0.9575 (mm) cc_final: 0.9243 (mm) REVERT: J 99 MET cc_start: 0.9513 (ttp) cc_final: 0.9186 (ppp) REVERT: J 146 PHE cc_start: 0.9161 (m-80) cc_final: 0.8830 (m-80) REVERT: J 159 MET cc_start: 0.9097 (tpp) cc_final: 0.8832 (tpp) REVERT: J 209 GLU cc_start: 0.9355 (mm-30) cc_final: 0.8494 (mp0) REVERT: J 229 MET cc_start: 0.8530 (mtp) cc_final: 0.8227 (mtp) REVERT: L 40 LYS cc_start: 0.9444 (tttt) cc_final: 0.9146 (tttp) REVERT: L 83 TYR cc_start: 0.7994 (m-80) cc_final: 0.7764 (m-80) REVERT: L 113 LYS cc_start: 0.9468 (ttmm) cc_final: 0.9180 (tppt) REVERT: L 118 LYS cc_start: 0.9527 (ttmm) cc_final: 0.8998 (tppt) REVERT: N 49 MET cc_start: 0.9632 (tmm) cc_final: 0.9337 (tmm) REVERT: N 146 ASP cc_start: 0.8513 (m-30) cc_final: 0.7847 (m-30) REVERT: N 155 MET cc_start: 0.8979 (pmm) cc_final: 0.8775 (pmm) REVERT: N 249 ARG cc_start: 0.9267 (mtp-110) cc_final: 0.8982 (ptm-80) REVERT: G 40 ASP cc_start: 0.9032 (m-30) cc_final: 0.8824 (p0) REVERT: G 66 GLU cc_start: 0.9284 (mt-10) cc_final: 0.8973 (mt-10) REVERT: F 33 GLN cc_start: 0.9355 (mp10) cc_final: 0.9033 (mp10) REVERT: F 73 ASN cc_start: 0.9500 (t0) cc_final: 0.9230 (t0) REVERT: F 121 TYR cc_start: 0.8779 (m-80) cc_final: 0.8338 (m-80) REVERT: F 134 GLN cc_start: 0.8533 (tm130) cc_final: 0.7992 (tm-30) REVERT: F 167 MET cc_start: 0.9074 (tpp) cc_final: 0.8833 (tpp) REVERT: F 177 GLU cc_start: 0.9208 (pt0) cc_final: 0.8927 (pp20) REVERT: F 239 LYS cc_start: 0.9551 (mmtm) cc_final: 0.9283 (mmmm) REVERT: H 5 THR cc_start: 0.8970 (OUTLIER) cc_final: 0.8701 (m) REVERT: H 19 GLU cc_start: 0.8558 (tm-30) cc_final: 0.8144 (tm-30) REVERT: H 145 TYR cc_start: 0.8639 (p90) cc_final: 0.8202 (p90) REVERT: H 174 ASP cc_start: 0.8656 (t0) cc_final: 0.8213 (t70) REVERT: H 200 MET cc_start: 0.9327 (tpp) cc_final: 0.8953 (mmm) REVERT: H 255 ASP cc_start: 0.9104 (m-30) cc_final: 0.8620 (p0) REVERT: H 265 MET cc_start: 0.9476 (mtp) cc_final: 0.9172 (mtt) REVERT: I 110 GLN cc_start: 0.9615 (tp40) cc_final: 0.9306 (tp40) REVERT: I 118 TYR cc_start: 0.9081 (m-10) cc_final: 0.8784 (m-10) REVERT: I 129 MET cc_start: 0.9369 (OUTLIER) cc_final: 0.9134 (mmm) REVERT: I 200 MET cc_start: 0.9247 (OUTLIER) cc_final: 0.9015 (ttp) REVERT: K 56 ASP cc_start: 0.9079 (m-30) cc_final: 0.8743 (m-30) REVERT: K 60 MET cc_start: 0.9058 (tmm) cc_final: 0.8695 (tmm) REVERT: K 61 ILE cc_start: 0.9055 (mt) cc_final: 0.8591 (mt) REVERT: K 134 LEU cc_start: 0.9673 (OUTLIER) cc_final: 0.9460 (mm) REVERT: K 148 THR cc_start: 0.9229 (OUTLIER) cc_final: 0.8936 (t) REVERT: K 153 HIS cc_start: 0.9058 (OUTLIER) cc_final: 0.8779 (t70) REVERT: K 201 ASP cc_start: 0.9265 (t0) cc_final: 0.8643 (t0) REVERT: K 202 GLU cc_start: 0.8477 (mt-10) cc_final: 0.8222 (pt0) REVERT: K 205 GLU cc_start: 0.8636 (mm-30) cc_final: 0.8244 (mm-30) REVERT: K 238 LEU cc_start: 0.9024 (mt) cc_final: 0.8732 (pp) REVERT: K 273 LYS cc_start: 0.9407 (tppt) cc_final: 0.8888 (mttm) REVERT: K 330 PHE cc_start: 0.9099 (m-80) cc_final: 0.8266 (m-80) REVERT: K 336 MET cc_start: 0.8865 (mmm) cc_final: 0.8470 (mmm) REVERT: K 369 ILE cc_start: 0.9452 (mt) cc_final: 0.9050 (mm) REVERT: K 406 SER cc_start: 0.9197 (m) cc_final: 0.8958 (p) REVERT: K 438 MET cc_start: 0.8883 (mmt) cc_final: 0.8402 (mmt) REVERT: K 439 MET cc_start: 0.8843 (mmt) cc_final: 0.8578 (mmm) REVERT: K 447 LEU cc_start: 0.8339 (OUTLIER) cc_final: 0.7406 (mm) REVERT: K 454 VAL cc_start: 0.7494 (OUTLIER) cc_final: 0.6700 (m) REVERT: K 474 ARG cc_start: 0.3018 (mtt180) cc_final: 0.2535 (mtt180) REVERT: K 481 LEU cc_start: 0.8607 (tp) cc_final: 0.8270 (tp) REVERT: K 502 LYS cc_start: 0.9346 (mtpt) cc_final: 0.9031 (mtmm) REVERT: K 527 LYS cc_start: 0.8845 (mmmt) cc_final: 0.8562 (mmmt) REVERT: K 538 ILE cc_start: 0.9343 (OUTLIER) cc_final: 0.9014 (tp) REVERT: K 587 LYS cc_start: 0.9253 (mmtm) cc_final: 0.8747 (tppt) REVERT: K 588 MET cc_start: 0.9314 (mtm) cc_final: 0.8707 (mtp) REVERT: K 619 TYR cc_start: 0.8855 (p90) cc_final: 0.8538 (p90) REVERT: K 625 ILE cc_start: 0.9388 (mt) cc_final: 0.9083 (mm) REVERT: K 677 MET cc_start: 0.8927 (ttp) cc_final: 0.8646 (ttp) REVERT: K 727 ASP cc_start: 0.9463 (m-30) cc_final: 0.8799 (t0) REVERT: K 730 GLU cc_start: 0.8955 (tt0) cc_final: 0.8653 (tp30) REVERT: K 745 MET cc_start: 0.9066 (mpp) cc_final: 0.8820 (mpp) REVERT: M 15 GLN cc_start: 0.7994 (tp40) cc_final: 0.7712 (tp40) REVERT: M 16 MET cc_start: 0.8772 (mmt) cc_final: 0.8293 (mmp) REVERT: M 62 ILE cc_start: 0.9625 (OUTLIER) cc_final: 0.9337 (mm) REVERT: M 144 GLN cc_start: 0.8379 (tt0) cc_final: 0.8099 (tt0) REVERT: M 167 LYS cc_start: 0.9416 (mmmt) cc_final: 0.9180 (mmtp) REVERT: M 169 PHE cc_start: 0.9036 (m-10) cc_final: 0.8719 (m-80) REVERT: M 290 MET cc_start: 0.8836 (pmm) cc_final: 0.8525 (pmm) outliers start: 99 outliers final: 70 residues processed: 582 average time/residue: 0.1620 time to fit residues: 154.6767 Evaluate side-chains 568 residues out of total 3097 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 487 time to evaluate : 1.129 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 LEU Chi-restraints excluded: chain A residue 29 ILE Chi-restraints excluded: chain A residue 63 VAL Chi-restraints excluded: chain A residue 102 LEU Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain B residue 65 GLU Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain C residue 37 LYS Chi-restraints excluded: chain C residue 98 ASP Chi-restraints excluded: chain C residue 103 LEU Chi-restraints excluded: chain C residue 128 THR Chi-restraints excluded: chain E residue 39 ASN Chi-restraints excluded: chain E residue 46 ASP Chi-restraints excluded: chain E residue 121 ASN Chi-restraints excluded: chain E residue 126 VAL Chi-restraints excluded: chain J residue 36 VAL Chi-restraints excluded: chain J residue 43 VAL Chi-restraints excluded: chain J residue 120 THR Chi-restraints excluded: chain J residue 166 SER Chi-restraints excluded: chain J residue 177 VAL Chi-restraints excluded: chain J residue 208 VAL Chi-restraints excluded: chain J residue 261 ASP Chi-restraints excluded: chain L residue 34 VAL Chi-restraints excluded: chain L residue 74 VAL Chi-restraints excluded: chain L residue 137 THR Chi-restraints excluded: chain L residue 152 LEU Chi-restraints excluded: chain N residue 56 ILE Chi-restraints excluded: chain N residue 95 VAL Chi-restraints excluded: chain N residue 149 ILE Chi-restraints excluded: chain N residue 190 ILE Chi-restraints excluded: chain N residue 191 VAL Chi-restraints excluded: chain G residue 101 GLU Chi-restraints excluded: chain F residue 140 ILE Chi-restraints excluded: chain F residue 157 TYR Chi-restraints excluded: chain F residue 232 VAL Chi-restraints excluded: chain H residue 5 THR Chi-restraints excluded: chain H residue 11 VAL Chi-restraints excluded: chain H residue 16 THR Chi-restraints excluded: chain H residue 90 CYS Chi-restraints excluded: chain H residue 123 CYS Chi-restraints excluded: chain H residue 168 VAL Chi-restraints excluded: chain H residue 227 LYS Chi-restraints excluded: chain I residue 129 MET Chi-restraints excluded: chain I residue 183 MET Chi-restraints excluded: chain I residue 200 MET Chi-restraints excluded: chain I residue 209 GLN Chi-restraints excluded: chain I residue 210 VAL Chi-restraints excluded: chain K residue 14 VAL Chi-restraints excluded: chain K residue 77 SER Chi-restraints excluded: chain K residue 134 LEU Chi-restraints excluded: chain K residue 148 THR Chi-restraints excluded: chain K residue 153 HIS Chi-restraints excluded: chain K residue 156 LEU Chi-restraints excluded: chain K residue 173 TYR Chi-restraints excluded: chain K residue 174 LEU Chi-restraints excluded: chain K residue 230 THR Chi-restraints excluded: chain K residue 304 SER Chi-restraints excluded: chain K residue 310 ASN Chi-restraints excluded: chain K residue 342 LEU Chi-restraints excluded: chain K residue 378 TYR Chi-restraints excluded: chain K residue 385 ILE Chi-restraints excluded: chain K residue 447 LEU Chi-restraints excluded: chain K residue 454 VAL Chi-restraints excluded: chain K residue 460 HIS Chi-restraints excluded: chain K residue 532 THR Chi-restraints excluded: chain K residue 538 ILE Chi-restraints excluded: chain K residue 576 ASP Chi-restraints excluded: chain K residue 602 ASP Chi-restraints excluded: chain K residue 624 ASP Chi-restraints excluded: chain K residue 661 LYS Chi-restraints excluded: chain K residue 666 VAL Chi-restraints excluded: chain M residue 30 ILE Chi-restraints excluded: chain M residue 62 ILE Chi-restraints excluded: chain M residue 82 ILE Chi-restraints excluded: chain M residue 118 ILE Chi-restraints excluded: chain M residue 157 TYR Chi-restraints excluded: chain M residue 182 ILE Chi-restraints excluded: chain M residue 200 VAL Chi-restraints excluded: chain M residue 211 LEU Chi-restraints excluded: chain M residue 218 LEU Chi-restraints excluded: chain M residue 291 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 346 random chunks: chunk 302 optimal weight: 2.9990 chunk 100 optimal weight: 9.9990 chunk 313 optimal weight: 4.9990 chunk 159 optimal weight: 6.9990 chunk 91 optimal weight: 6.9990 chunk 15 optimal weight: 0.8980 chunk 0 optimal weight: 10.0000 chunk 70 optimal weight: 20.0000 chunk 299 optimal weight: 10.0000 chunk 49 optimal weight: 9.9990 chunk 62 optimal weight: 10.0000 overall best weight: 4.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 121 ASN ** D 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 10 ASN N 59 ASN N 193 ASN ** H 204 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3226 r_free = 0.3226 target = 0.050250 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2990 r_free = 0.2990 target = 0.041958 restraints weight = 147893.013| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3039 r_free = 0.3039 target = 0.043654 restraints weight = 76027.984| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3073 r_free = 0.3073 target = 0.044834 restraints weight = 47730.061| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3097 r_free = 0.3097 target = 0.045662 restraints weight = 33534.328| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3113 r_free = 0.3113 target = 0.046238 restraints weight = 25444.142| |-----------------------------------------------------------------------------| r_work (final): 0.3107 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8549 moved from start: 0.3970 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.069 29252 Z= 0.296 Angle : 0.832 14.588 39623 Z= 0.403 Chirality : 0.059 0.653 4524 Planarity : 0.004 0.052 4852 Dihedral : 11.400 163.620 4390 Min Nonbonded Distance : 2.314 Molprobity Statistics. All-atom Clashscore : 18.51 Ramachandran Plot: Outliers : 0.12 % Allowed : 6.89 % Favored : 93.00 % Rotamer: Outliers : 3.88 % Allowed : 21.42 % Favored : 74.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.73 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.14 (0.14), residues: 3441 helix: 1.45 (0.14), residues: 1473 sheet: -0.27 (0.23), residues: 462 loop : -1.65 (0.15), residues: 1506 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG K 125 TYR 0.026 0.002 TYR K 457 PHE 0.029 0.002 PHE E 129 TRP 0.019 0.002 TRP G 182 HIS 0.007 0.001 HIS G 230 Details of bonding type rmsd/Z covalent geometry : bond 0.00624 / 0.30 (29237) covalent geometry : angle 0.83035 / 0.40 (39593) SS BOND : bond 0.00465 / 0.29 ( 15) SS BOND : angle 1.94700 / 1.30 ( 30) hydrogen bonds : bond 0.03987 / 2.64 ( 1274) hydrogen bonds : angle 5.18776 / 3.71 ( 3747) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6882 Ramachandran restraints generated. 3441 Oldfield, 0 Emsley, 3441 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6882 Ramachandran restraints generated. 3441 Oldfield, 0 Emsley, 3441 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 597 residues out of total 3097 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 120 poor density : 477 time to evaluate : 0.961 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 22 ASP cc_start: 0.8703 (m-30) cc_final: 0.8224 (t0) REVERT: A 42 GLU cc_start: 0.8369 (mm-30) cc_final: 0.8044 (mm-30) REVERT: A 56 PHE cc_start: 0.8982 (t80) cc_final: 0.8516 (t80) REVERT: A 60 ARG cc_start: 0.9288 (mmp80) cc_final: 0.8908 (mmm-85) REVERT: A 69 TYR cc_start: 0.9261 (t80) cc_final: 0.8982 (t80) REVERT: A 79 ILE cc_start: 0.9069 (mm) cc_final: 0.8791 (mp) REVERT: A 110 TYR cc_start: 0.9046 (t80) cc_final: 0.8818 (t80) REVERT: A 111 ASP cc_start: 0.9004 (t0) cc_final: 0.8629 (t0) REVERT: A 131 GLU cc_start: 0.9482 (mt-10) cc_final: 0.9029 (mt-10) REVERT: B 22 ASP cc_start: 0.8860 (m-30) cc_final: 0.8153 (m-30) REVERT: B 26 ARG cc_start: 0.9153 (ptp-110) cc_final: 0.8430 (ptp90) REVERT: B 73 GLN cc_start: 0.9318 (tp40) cc_final: 0.9052 (tp-100) REVERT: B 78 GLU cc_start: 0.9141 (mm-30) cc_final: 0.8616 (tp30) REVERT: B 90 SER cc_start: 0.9648 (m) cc_final: 0.9262 (p) REVERT: B 129 PHE cc_start: 0.8925 (t80) cc_final: 0.8612 (t80) REVERT: B 131 GLU cc_start: 0.9228 (mp0) cc_final: 0.8949 (mp0) REVERT: B 134 ASN cc_start: 0.9157 (m-40) cc_final: 0.8730 (m110) REVERT: C 22 ASP cc_start: 0.9158 (m-30) cc_final: 0.8759 (m-30) REVERT: C 44 TYR cc_start: 0.9097 (t80) cc_final: 0.8688 (t80) REVERT: C 71 MET cc_start: 0.9433 (mtm) cc_final: 0.9103 (mtm) REVERT: C 77 ASP cc_start: 0.9172 (t0) cc_final: 0.8919 (t0) REVERT: C 103 LEU cc_start: 0.9651 (OUTLIER) cc_final: 0.9411 (tp) REVERT: C 105 TYR cc_start: 0.9392 (m-80) cc_final: 0.9134 (m-80) REVERT: C 134 ASN cc_start: 0.9727 (m-40) cc_final: 0.9422 (m110) REVERT: D 26 ARG cc_start: 0.9572 (mtm-85) cc_final: 0.9146 (ptp-110) REVERT: D 32 ILE cc_start: 0.9102 (tp) cc_final: 0.8886 (tp) REVERT: D 44 TYR cc_start: 0.9190 (t80) cc_final: 0.8745 (t80) REVERT: D 58 GLN cc_start: 0.9495 (mp10) cc_final: 0.9255 (mm-40) REVERT: D 82 GLU cc_start: 0.9490 (tt0) cc_final: 0.9166 (tp30) REVERT: D 101 ASN cc_start: 0.9514 (m110) cc_final: 0.9051 (m-40) REVERT: D 133 VAL cc_start: 0.9791 (t) cc_final: 0.9583 (p) REVERT: D 134 ASN cc_start: 0.9232 (m-40) cc_final: 0.8617 (m110) REVERT: E 44 TYR cc_start: 0.9090 (t80) cc_final: 0.8853 (t80) REVERT: E 78 GLU cc_start: 0.8538 (mt-10) cc_final: 0.8127 (mt-10) REVERT: E 82 GLU cc_start: 0.9346 (tm-30) cc_final: 0.9027 (tm-30) REVERT: E 101 ASN cc_start: 0.9567 (m110) cc_final: 0.9115 (m110) REVERT: E 105 TYR cc_start: 0.9339 (m-10) cc_final: 0.8843 (m-80) REVERT: E 131 GLU cc_start: 0.9069 (tp30) cc_final: 0.8690 (tm-30) REVERT: E 135 ILE cc_start: 0.9595 (mm) cc_final: 0.9268 (mm) REVERT: J 57 GLU cc_start: 0.8366 (mp0) cc_final: 0.7867 (tm-30) REVERT: J 146 PHE cc_start: 0.9222 (m-80) cc_final: 0.8862 (m-80) REVERT: J 159 MET cc_start: 0.9093 (tpp) cc_final: 0.8788 (tpp) REVERT: J 166 SER cc_start: 0.9176 (OUTLIER) cc_final: 0.8691 (t) REVERT: J 209 GLU cc_start: 0.9420 (mm-30) cc_final: 0.8612 (mp0) REVERT: J 229 MET cc_start: 0.8671 (mtp) cc_final: 0.8232 (mtp) REVERT: L 40 LYS cc_start: 0.9471 (tttt) cc_final: 0.9175 (tttp) REVERT: L 43 MET cc_start: 0.8953 (ttp) cc_final: 0.8677 (tpp) REVERT: L 113 LYS cc_start: 0.9508 (ttmm) cc_final: 0.9220 (tppt) REVERT: N 49 MET cc_start: 0.9642 (tmm) cc_final: 0.9256 (tmm) REVERT: N 137 TYR cc_start: 0.8020 (OUTLIER) cc_final: 0.7544 (p90) REVERT: N 146 ASP cc_start: 0.8500 (m-30) cc_final: 0.7880 (m-30) REVERT: N 155 MET cc_start: 0.8705 (pmm) cc_final: 0.8436 (pmm) REVERT: N 249 ARG cc_start: 0.9287 (mtp-110) cc_final: 0.8993 (ptm-80) REVERT: G 40 ASP cc_start: 0.9108 (m-30) cc_final: 0.8861 (p0) REVERT: G 66 GLU cc_start: 0.9316 (mt-10) cc_final: 0.8986 (mt-10) REVERT: F 33 GLN cc_start: 0.9393 (mp10) cc_final: 0.8997 (mp10) REVERT: F 73 ASN cc_start: 0.9566 (t0) cc_final: 0.9334 (t0) REVERT: F 167 MET cc_start: 0.9035 (tpp) cc_final: 0.8758 (tpp) REVERT: F 177 GLU cc_start: 0.9278 (pt0) cc_final: 0.9012 (pp20) REVERT: F 207 ARG cc_start: 0.7493 (OUTLIER) cc_final: 0.7259 (mtp85) REVERT: F 239 LYS cc_start: 0.9507 (mmtm) cc_final: 0.9236 (mmmm) REVERT: H 129 MET cc_start: 0.9477 (mmm) cc_final: 0.9229 (mmm) REVERT: H 145 TYR cc_start: 0.8834 (p90) cc_final: 0.8327 (p90) REVERT: H 174 ASP cc_start: 0.8808 (t0) cc_final: 0.8353 (t70) REVERT: H 200 MET cc_start: 0.9369 (tpp) cc_final: 0.9123 (tpp) REVERT: H 255 ASP cc_start: 0.9168 (m-30) cc_final: 0.8716 (p0) REVERT: I 110 GLN cc_start: 0.9645 (tp40) cc_final: 0.9350 (tp40) REVERT: I 118 TYR cc_start: 0.9171 (m-10) cc_final: 0.8850 (m-10) REVERT: I 129 MET cc_start: 0.9514 (OUTLIER) cc_final: 0.9226 (mmm) REVERT: I 265 MET cc_start: 0.9666 (mtm) cc_final: 0.8986 (mtm) REVERT: K 56 ASP cc_start: 0.9164 (m-30) cc_final: 0.8821 (m-30) REVERT: K 60 MET cc_start: 0.9146 (tmm) cc_final: 0.8753 (tmm) REVERT: K 61 ILE cc_start: 0.9097 (mt) cc_final: 0.8518 (mt) REVERT: K 81 GLU cc_start: 0.8903 (mt-10) cc_final: 0.8573 (mt-10) REVERT: K 148 THR cc_start: 0.9187 (OUTLIER) cc_final: 0.8899 (t) REVERT: K 201 ASP cc_start: 0.9269 (t0) cc_final: 0.8641 (t0) REVERT: K 202 GLU cc_start: 0.8538 (mt-10) cc_final: 0.8218 (mt-10) REVERT: K 205 GLU cc_start: 0.8716 (mm-30) cc_final: 0.8354 (mm-30) REVERT: K 336 MET cc_start: 0.8902 (mmm) cc_final: 0.8637 (mmm) REVERT: K 369 ILE cc_start: 0.9525 (mt) cc_final: 0.9196 (mt) REVERT: K 406 SER cc_start: 0.9292 (m) cc_final: 0.9050 (p) REVERT: K 438 MET cc_start: 0.8881 (mmt) cc_final: 0.8552 (mmt) REVERT: K 474 ARG cc_start: 0.2888 (mtt180) cc_final: 0.2269 (mtt180) REVERT: K 481 LEU cc_start: 0.8666 (tp) cc_final: 0.8356 (tp) REVERT: K 502 LYS cc_start: 0.9424 (mtpt) cc_final: 0.9108 (mtmm) REVERT: K 527 LYS cc_start: 0.8810 (mmmt) cc_final: 0.8548 (mmmt) REVERT: K 538 ILE cc_start: 0.9413 (tp) cc_final: 0.9093 (tp) REVERT: K 587 LYS cc_start: 0.9260 (mmtm) cc_final: 0.8830 (tppt) REVERT: K 588 MET cc_start: 0.9359 (mtm) cc_final: 0.8868 (mtp) REVERT: K 619 TYR cc_start: 0.8971 (p90) cc_final: 0.8622 (p90) REVERT: K 625 ILE cc_start: 0.9374 (mt) cc_final: 0.9066 (mm) REVERT: K 677 MET cc_start: 0.8970 (ttp) cc_final: 0.8679 (ttp) REVERT: K 727 ASP cc_start: 0.9477 (m-30) cc_final: 0.8836 (t0) REVERT: K 730 GLU cc_start: 0.9016 (tt0) cc_final: 0.8744 (tp30) REVERT: K 745 MET cc_start: 0.8945 (mpp) cc_final: 0.8531 (mtm) REVERT: M 16 MET cc_start: 0.8701 (mmt) cc_final: 0.8325 (mmp) REVERT: M 62 ILE cc_start: 0.9659 (OUTLIER) cc_final: 0.9391 (mm) REVERT: M 144 GLN cc_start: 0.8290 (tt0) cc_final: 0.8044 (tt0) REVERT: M 160 MET cc_start: 0.7388 (pmm) cc_final: 0.7119 (pmm) REVERT: M 169 PHE cc_start: 0.9091 (m-10) cc_final: 0.8837 (m-80) REVERT: M 170 ASP cc_start: 0.9080 (t0) cc_final: 0.8805 (t0) REVERT: M 267 GLU cc_start: 0.8514 (OUTLIER) cc_final: 0.8286 (mm-30) REVERT: M 290 MET cc_start: 0.8919 (pmm) cc_final: 0.8572 (pmm) outliers start: 120 outliers final: 88 residues processed: 562 average time/residue: 0.1584 time to fit residues: 146.2919 Evaluate side-chains 545 residues out of total 3097 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 449 time to evaluate : 1.079 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 LEU Chi-restraints excluded: chain A residue 25 THR Chi-restraints excluded: chain A residue 29 ILE Chi-restraints excluded: chain A residue 63 VAL Chi-restraints excluded: chain A residue 102 LEU Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain B residue 21 LEU Chi-restraints excluded: chain B residue 65 GLU Chi-restraints excluded: chain B residue 98 ASP Chi-restraints excluded: chain B residue 118 VAL Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain C residue 37 LYS Chi-restraints excluded: chain C residue 98 ASP Chi-restraints excluded: chain C residue 103 LEU Chi-restraints excluded: chain C residue 118 VAL Chi-restraints excluded: chain C residue 128 THR Chi-restraints excluded: chain D residue 40 LYS Chi-restraints excluded: chain E residue 39 ASN Chi-restraints excluded: chain E residue 46 ASP Chi-restraints excluded: chain E residue 50 ILE Chi-restraints excluded: chain E residue 77 ASP Chi-restraints excluded: chain E residue 121 ASN Chi-restraints excluded: chain E residue 126 VAL Chi-restraints excluded: chain J residue 23 ILE Chi-restraints excluded: chain J residue 43 VAL Chi-restraints excluded: chain J residue 120 THR Chi-restraints excluded: chain J residue 166 SER Chi-restraints excluded: chain J residue 208 VAL Chi-restraints excluded: chain J residue 239 LYS Chi-restraints excluded: chain J residue 261 ASP Chi-restraints excluded: chain L residue 21 THR Chi-restraints excluded: chain L residue 34 VAL Chi-restraints excluded: chain L residue 74 VAL Chi-restraints excluded: chain L residue 137 THR Chi-restraints excluded: chain L residue 152 LEU Chi-restraints excluded: chain N residue 95 VAL Chi-restraints excluded: chain N residue 103 ASN Chi-restraints excluded: chain N residue 117 ASP Chi-restraints excluded: chain N residue 137 TYR Chi-restraints excluded: chain N residue 149 ILE Chi-restraints excluded: chain N residue 190 ILE Chi-restraints excluded: chain G residue 32 THR Chi-restraints excluded: chain G residue 101 GLU Chi-restraints excluded: chain G residue 138 VAL Chi-restraints excluded: chain G residue 156 ASP Chi-restraints excluded: chain G residue 188 GLU Chi-restraints excluded: chain F residue 39 THR Chi-restraints excluded: chain F residue 140 ILE Chi-restraints excluded: chain F residue 157 TYR Chi-restraints excluded: chain F residue 207 ARG Chi-restraints excluded: chain H residue 11 VAL Chi-restraints excluded: chain H residue 16 THR Chi-restraints excluded: chain H residue 90 CYS Chi-restraints excluded: chain H residue 123 CYS Chi-restraints excluded: chain H residue 168 VAL Chi-restraints excluded: chain H residue 227 LYS Chi-restraints excluded: chain I residue 129 MET Chi-restraints excluded: chain I residue 175 VAL Chi-restraints excluded: chain I residue 183 MET Chi-restraints excluded: chain I residue 193 ILE Chi-restraints excluded: chain I residue 209 GLN Chi-restraints excluded: chain I residue 210 VAL Chi-restraints excluded: chain I residue 230 ASP Chi-restraints excluded: chain K residue 14 VAL Chi-restraints excluded: chain K residue 29 VAL Chi-restraints excluded: chain K residue 77 SER Chi-restraints excluded: chain K residue 148 THR Chi-restraints excluded: chain K residue 156 LEU Chi-restraints excluded: chain K residue 173 TYR Chi-restraints excluded: chain K residue 174 LEU Chi-restraints excluded: chain K residue 230 THR Chi-restraints excluded: chain K residue 304 SER Chi-restraints excluded: chain K residue 342 LEU Chi-restraints excluded: chain K residue 378 TYR Chi-restraints excluded: chain K residue 385 ILE Chi-restraints excluded: chain K residue 460 HIS Chi-restraints excluded: chain K residue 532 THR Chi-restraints excluded: chain K residue 576 ASP Chi-restraints excluded: chain K residue 624 ASP Chi-restraints excluded: chain K residue 628 LEU Chi-restraints excluded: chain K residue 661 LYS Chi-restraints excluded: chain K residue 666 VAL Chi-restraints excluded: chain M residue 30 ILE Chi-restraints excluded: chain M residue 62 ILE Chi-restraints excluded: chain M residue 82 ILE Chi-restraints excluded: chain M residue 118 ILE Chi-restraints excluded: chain M residue 157 TYR Chi-restraints excluded: chain M residue 182 ILE Chi-restraints excluded: chain M residue 200 VAL Chi-restraints excluded: chain M residue 211 LEU Chi-restraints excluded: chain M residue 218 LEU Chi-restraints excluded: chain M residue 220 CYS Chi-restraints excluded: chain M residue 240 ILE Chi-restraints excluded: chain M residue 267 GLU Chi-restraints excluded: chain M residue 282 LEU Chi-restraints excluded: chain M residue 291 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 346 random chunks: chunk 63 optimal weight: 10.0000 chunk 108 optimal weight: 7.9990 chunk 68 optimal weight: 2.9990 chunk 154 optimal weight: 1.9990 chunk 273 optimal weight: 1.9990 chunk 235 optimal weight: 1.9990 chunk 303 optimal weight: 5.9990 chunk 148 optimal weight: 1.9990 chunk 240 optimal weight: 2.9990 chunk 314 optimal weight: 4.9990 chunk 96 optimal weight: 2.9990 overall best weight: 2.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 51 ASN ** D 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 174 ASN ** L 175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 59 ASN F 147 GLN ** H 204 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3300 r_free = 0.3300 target = 0.051973 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3078 r_free = 0.3078 target = 0.043746 restraints weight = 144667.053| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3125 r_free = 0.3125 target = 0.045486 restraints weight = 73355.399| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3157 r_free = 0.3157 target = 0.046658 restraints weight = 45533.969| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3180 r_free = 0.3180 target = 0.047493 restraints weight = 31820.178| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3196 r_free = 0.3196 target = 0.048077 restraints weight = 23985.429| |-----------------------------------------------------------------------------| r_work (final): 0.3179 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8509 moved from start: 0.4096 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 29252 Z= 0.176 Angle : 0.781 14.754 39623 Z= 0.373 Chirality : 0.056 0.556 4524 Planarity : 0.004 0.052 4852 Dihedral : 11.436 161.120 4390 Min Nonbonded Distance : 2.345 Molprobity Statistics. All-atom Clashscore : 15.97 Ramachandran Plot: Outliers : 0.12 % Allowed : 6.25 % Favored : 93.64 % Rotamer: Outliers : 3.66 % Allowed : 22.69 % Favored : 73.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.73 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.06 (0.14), residues: 3441 helix: 1.54 (0.14), residues: 1475 sheet: -0.26 (0.23), residues: 466 loop : -1.64 (0.15), residues: 1500 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG K 268 TYR 0.027 0.002 TYR K 62 PHE 0.039 0.001 PHE E 56 TRP 0.018 0.001 TRP G 182 HIS 0.003 0.001 HIS K 153 Details of bonding type rmsd/Z covalent geometry : bond 0.00385 / 0.18 (29237) covalent geometry : angle 0.77939 / 0.37 (39593) SS BOND : bond 0.00394 / 0.26 ( 15) SS BOND : angle 1.80645 / 1.24 ( 30) hydrogen bonds : bond 0.03748 / 2.49 ( 1274) hydrogen bonds : angle 5.03696 / 3.59 ( 3747) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6882 Ramachandran restraints generated. 3441 Oldfield, 0 Emsley, 3441 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6882 Ramachandran restraints generated. 3441 Oldfield, 0 Emsley, 3441 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 595 residues out of total 3097 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 113 poor density : 482 time to evaluate : 0.809 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 22 ASP cc_start: 0.8668 (m-30) cc_final: 0.8186 (t0) REVERT: A 42 GLU cc_start: 0.8329 (mm-30) cc_final: 0.8032 (mm-30) REVERT: A 56 PHE cc_start: 0.8921 (t80) cc_final: 0.8490 (t80) REVERT: A 60 ARG cc_start: 0.9282 (mmp80) cc_final: 0.8932 (mmm-85) REVERT: A 61 ARG cc_start: 0.9238 (mmm160) cc_final: 0.9019 (mmm160) REVERT: A 69 TYR cc_start: 0.9226 (t80) cc_final: 0.8850 (t80) REVERT: A 71 MET cc_start: 0.9005 (mmm) cc_final: 0.8733 (mmt) REVERT: A 79 ILE cc_start: 0.9043 (mm) cc_final: 0.8739 (mp) REVERT: A 110 TYR cc_start: 0.9031 (t80) cc_final: 0.8765 (t80) REVERT: A 111 ASP cc_start: 0.8976 (t0) cc_final: 0.8630 (t0) REVERT: A 131 GLU cc_start: 0.9477 (mt-10) cc_final: 0.8809 (mt-10) REVERT: B 22 ASP cc_start: 0.8861 (m-30) cc_final: 0.8188 (m-30) REVERT: B 26 ARG cc_start: 0.9152 (ptp-110) cc_final: 0.8476 (ptp90) REVERT: B 73 GLN cc_start: 0.9321 (tp40) cc_final: 0.9055 (tp-100) REVERT: B 78 GLU cc_start: 0.9080 (mm-30) cc_final: 0.8566 (tp30) REVERT: B 90 SER cc_start: 0.9649 (m) cc_final: 0.9269 (p) REVERT: B 129 PHE cc_start: 0.8817 (t80) cc_final: 0.8480 (t80) REVERT: B 131 GLU cc_start: 0.9231 (mp0) cc_final: 0.8938 (mp0) REVERT: B 134 ASN cc_start: 0.9156 (m-40) cc_final: 0.8712 (m110) REVERT: C 22 ASP cc_start: 0.9107 (m-30) cc_final: 0.8716 (m-30) REVERT: C 71 MET cc_start: 0.9369 (mtm) cc_final: 0.9034 (mtm) REVERT: C 77 ASP cc_start: 0.9214 (t0) cc_final: 0.8961 (t0) REVERT: C 81 GLU cc_start: 0.8681 (pm20) cc_final: 0.8476 (pm20) REVERT: C 105 TYR cc_start: 0.9342 (m-80) cc_final: 0.9081 (m-80) REVERT: C 134 ASN cc_start: 0.9710 (m-40) cc_final: 0.9408 (m110) REVERT: D 26 ARG cc_start: 0.9562 (mtm-85) cc_final: 0.9297 (ptp-110) REVERT: D 32 ILE cc_start: 0.9119 (tp) cc_final: 0.8877 (tp) REVERT: D 44 TYR cc_start: 0.9159 (t80) cc_final: 0.8723 (t80) REVERT: D 58 GLN cc_start: 0.9473 (mp10) cc_final: 0.9261 (mm-40) REVERT: D 61 ARG cc_start: 0.9186 (mmm-85) cc_final: 0.8954 (mmm-85) REVERT: D 82 GLU cc_start: 0.9471 (tt0) cc_final: 0.9099 (tp30) REVERT: D 101 ASN cc_start: 0.9437 (m110) cc_final: 0.9119 (m-40) REVERT: D 131 GLU cc_start: 0.9263 (mt-10) cc_final: 0.9046 (pt0) REVERT: D 133 VAL cc_start: 0.9744 (t) cc_final: 0.9536 (p) REVERT: D 134 ASN cc_start: 0.9234 (m-40) cc_final: 0.9012 (m110) REVERT: E 19 ASP cc_start: 0.9162 (p0) cc_final: 0.8955 (p0) REVERT: E 44 TYR cc_start: 0.9006 (t80) cc_final: 0.8752 (t80) REVERT: E 55 SER cc_start: 0.9799 (m) cc_final: 0.9524 (p) REVERT: E 78 GLU cc_start: 0.8595 (mt-10) cc_final: 0.8153 (mt-10) REVERT: E 82 GLU cc_start: 0.9348 (tm-30) cc_final: 0.9031 (tm-30) REVERT: E 101 ASN cc_start: 0.9541 (m110) cc_final: 0.9062 (m110) REVERT: E 105 TYR cc_start: 0.9320 (m-10) cc_final: 0.8796 (m-80) REVERT: E 131 GLU cc_start: 0.8998 (tp30) cc_final: 0.8650 (tm-30) REVERT: E 135 ILE cc_start: 0.9578 (mm) cc_final: 0.9296 (mm) REVERT: J 44 GLU cc_start: 0.8769 (pp20) cc_final: 0.7224 (pp20) REVERT: J 46 MET cc_start: 0.8323 (mtt) cc_final: 0.7853 (mmm) REVERT: J 146 PHE cc_start: 0.9198 (m-80) cc_final: 0.8857 (m-80) REVERT: J 159 MET cc_start: 0.9037 (tpp) cc_final: 0.8776 (tpp) REVERT: J 166 SER cc_start: 0.9161 (OUTLIER) cc_final: 0.8639 (t) REVERT: J 209 GLU cc_start: 0.9372 (mm-30) cc_final: 0.8545 (mp0) REVERT: J 229 MET cc_start: 0.8585 (mtp) cc_final: 0.7992 (mtp) REVERT: L 113 LYS cc_start: 0.9502 (ttmm) cc_final: 0.9208 (tppt) REVERT: N 49 MET cc_start: 0.9644 (tmm) cc_final: 0.9360 (tmm) REVERT: N 137 TYR cc_start: 0.7890 (OUTLIER) cc_final: 0.7313 (p90) REVERT: N 155 MET cc_start: 0.8795 (pmm) cc_final: 0.8510 (pmm) REVERT: N 249 ARG cc_start: 0.9290 (mtp-110) cc_final: 0.8997 (ptm-80) REVERT: G 40 ASP cc_start: 0.9066 (m-30) cc_final: 0.8821 (p0) REVERT: G 66 GLU cc_start: 0.9270 (mt-10) cc_final: 0.8935 (mt-10) REVERT: F 33 GLN cc_start: 0.9391 (mp10) cc_final: 0.9013 (mp10) REVERT: F 73 ASN cc_start: 0.9539 (t0) cc_final: 0.9279 (t0) REVERT: F 167 MET cc_start: 0.8997 (tpp) cc_final: 0.8695 (tpp) REVERT: F 177 GLU cc_start: 0.9262 (pt0) cc_final: 0.8966 (pp20) REVERT: F 207 ARG cc_start: 0.7384 (OUTLIER) cc_final: 0.6943 (mtp85) REVERT: F 239 LYS cc_start: 0.9521 (mmtm) cc_final: 0.9291 (mmmm) REVERT: H 5 THR cc_start: 0.8929 (OUTLIER) cc_final: 0.8670 (m) REVERT: H 19 GLU cc_start: 0.8570 (tm-30) cc_final: 0.8045 (tm-30) REVERT: H 129 MET cc_start: 0.9433 (mmm) cc_final: 0.9186 (mmm) REVERT: H 145 TYR cc_start: 0.8702 (p90) cc_final: 0.8038 (p90) REVERT: H 174 ASP cc_start: 0.8761 (t0) cc_final: 0.8315 (t70) REVERT: H 200 MET cc_start: 0.9365 (tpp) cc_final: 0.9117 (tpp) REVERT: H 255 ASP cc_start: 0.9158 (m-30) cc_final: 0.8710 (p0) REVERT: I 110 GLN cc_start: 0.9632 (tp40) cc_final: 0.9323 (tp40) REVERT: I 118 TYR cc_start: 0.9181 (m-10) cc_final: 0.8883 (m-10) REVERT: I 129 MET cc_start: 0.9433 (OUTLIER) cc_final: 0.9132 (mmm) REVERT: I 200 MET cc_start: 0.9272 (ttp) cc_final: 0.9007 (ttp) REVERT: K 56 ASP cc_start: 0.9110 (m-30) cc_final: 0.8754 (m-30) REVERT: K 60 MET cc_start: 0.9091 (tmm) cc_final: 0.8653 (tmm) REVERT: K 61 ILE cc_start: 0.8934 (mt) cc_final: 0.8356 (mt) REVERT: K 148 THR cc_start: 0.9201 (OUTLIER) cc_final: 0.8908 (t) REVERT: K 153 HIS cc_start: 0.8804 (OUTLIER) cc_final: 0.8584 (t70) REVERT: K 201 ASP cc_start: 0.9261 (t0) cc_final: 0.8609 (t0) REVERT: K 202 GLU cc_start: 0.8512 (mt-10) cc_final: 0.8193 (mt-10) REVERT: K 205 GLU cc_start: 0.8693 (mm-30) cc_final: 0.8315 (mm-30) REVERT: K 273 LYS cc_start: 0.9432 (tppt) cc_final: 0.8951 (mttm) REVERT: K 336 MET cc_start: 0.8880 (mmm) cc_final: 0.8521 (mmm) REVERT: K 369 ILE cc_start: 0.9498 (mt) cc_final: 0.9164 (mt) REVERT: K 406 SER cc_start: 0.9268 (m) cc_final: 0.9035 (p) REVERT: K 438 MET cc_start: 0.8948 (mmt) cc_final: 0.8453 (mmt) REVERT: K 439 MET cc_start: 0.8913 (mmt) cc_final: 0.8608 (mmm) REVERT: K 474 ARG cc_start: 0.3022 (mtt180) cc_final: 0.2489 (mtt180) REVERT: K 481 LEU cc_start: 0.8621 (tp) cc_final: 0.8297 (tp) REVERT: K 502 LYS cc_start: 0.9375 (mtpt) cc_final: 0.9067 (mtmm) REVERT: K 538 ILE cc_start: 0.9369 (OUTLIER) cc_final: 0.9029 (tp) REVERT: K 587 LYS cc_start: 0.9275 (OUTLIER) cc_final: 0.8839 (tppt) REVERT: K 588 MET cc_start: 0.9380 (mtm) cc_final: 0.8781 (mtp) REVERT: K 619 TYR cc_start: 0.8932 (p90) cc_final: 0.8550 (p90) REVERT: K 625 ILE cc_start: 0.9403 (mt) cc_final: 0.9121 (mm) REVERT: K 727 ASP cc_start: 0.9452 (m-30) cc_final: 0.8853 (t0) REVERT: K 730 GLU cc_start: 0.9009 (tt0) cc_final: 0.8689 (tp30) REVERT: K 745 MET cc_start: 0.9063 (mpp) cc_final: 0.8686 (mtm) REVERT: K 781 LEU cc_start: 0.9408 (OUTLIER) cc_final: 0.9194 (mm) REVERT: M 16 MET cc_start: 0.8752 (mmt) cc_final: 0.8361 (mmp) REVERT: M 62 ILE cc_start: 0.9655 (OUTLIER) cc_final: 0.9417 (mm) REVERT: M 144 GLN cc_start: 0.8481 (tt0) cc_final: 0.8219 (tt0) REVERT: M 160 MET cc_start: 0.7144 (pmm) cc_final: 0.6848 (pmm) REVERT: M 169 PHE cc_start: 0.9076 (m-10) cc_final: 0.8755 (m-80) REVERT: M 290 MET cc_start: 0.8841 (pmm) cc_final: 0.8417 (pmm) outliers start: 113 outliers final: 88 residues processed: 562 average time/residue: 0.1603 time to fit residues: 147.0084 Evaluate side-chains 559 residues out of total 3097 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 99 poor density : 460 time to evaluate : 0.869 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 LEU Chi-restraints excluded: chain A residue 29 ILE Chi-restraints excluded: chain A residue 63 VAL Chi-restraints excluded: chain A residue 102 LEU Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain B residue 65 GLU Chi-restraints excluded: chain B residue 66 LEU Chi-restraints excluded: chain B residue 118 VAL Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain C residue 23 ILE Chi-restraints excluded: chain C residue 37 LYS Chi-restraints excluded: chain C residue 98 ASP Chi-restraints excluded: chain C residue 128 THR Chi-restraints excluded: chain D residue 39 ASN Chi-restraints excluded: chain D residue 40 LYS Chi-restraints excluded: chain E residue 39 ASN Chi-restraints excluded: chain E residue 50 ILE Chi-restraints excluded: chain E residue 77 ASP Chi-restraints excluded: chain E residue 126 VAL Chi-restraints excluded: chain J residue 43 VAL Chi-restraints excluded: chain J residue 90 VAL Chi-restraints excluded: chain J residue 115 VAL Chi-restraints excluded: chain J residue 120 THR Chi-restraints excluded: chain J residue 165 VAL Chi-restraints excluded: chain J residue 166 SER Chi-restraints excluded: chain J residue 208 VAL Chi-restraints excluded: chain J residue 261 ASP Chi-restraints excluded: chain J residue 274 GLU Chi-restraints excluded: chain L residue 21 THR Chi-restraints excluded: chain L residue 34 VAL Chi-restraints excluded: chain L residue 74 VAL Chi-restraints excluded: chain L residue 137 THR Chi-restraints excluded: chain L residue 152 LEU Chi-restraints excluded: chain N residue 56 ILE Chi-restraints excluded: chain N residue 95 VAL Chi-restraints excluded: chain N residue 137 TYR Chi-restraints excluded: chain N residue 149 ILE Chi-restraints excluded: chain N residue 173 HIS Chi-restraints excluded: chain N residue 190 ILE Chi-restraints excluded: chain G residue 101 GLU Chi-restraints excluded: chain G residue 138 VAL Chi-restraints excluded: chain G residue 156 ASP Chi-restraints excluded: chain G residue 157 TYR Chi-restraints excluded: chain G residue 188 GLU Chi-restraints excluded: chain F residue 140 ILE Chi-restraints excluded: chain F residue 157 TYR Chi-restraints excluded: chain F residue 207 ARG Chi-restraints excluded: chain H residue 5 THR Chi-restraints excluded: chain H residue 11 VAL Chi-restraints excluded: chain H residue 16 THR Chi-restraints excluded: chain H residue 90 CYS Chi-restraints excluded: chain H residue 123 CYS Chi-restraints excluded: chain H residue 168 VAL Chi-restraints excluded: chain H residue 210 VAL Chi-restraints excluded: chain H residue 227 LYS Chi-restraints excluded: chain I residue 7 ILE Chi-restraints excluded: chain I residue 129 MET Chi-restraints excluded: chain I residue 152 MET Chi-restraints excluded: chain I residue 175 VAL Chi-restraints excluded: chain I residue 183 MET Chi-restraints excluded: chain I residue 209 GLN Chi-restraints excluded: chain I residue 210 VAL Chi-restraints excluded: chain I residue 230 ASP Chi-restraints excluded: chain K residue 14 VAL Chi-restraints excluded: chain K residue 77 SER Chi-restraints excluded: chain K residue 148 THR Chi-restraints excluded: chain K residue 153 HIS Chi-restraints excluded: chain K residue 156 LEU Chi-restraints excluded: chain K residue 173 TYR Chi-restraints excluded: chain K residue 174 LEU Chi-restraints excluded: chain K residue 214 LEU Chi-restraints excluded: chain K residue 230 THR Chi-restraints excluded: chain K residue 287 TYR Chi-restraints excluded: chain K residue 304 SER Chi-restraints excluded: chain K residue 342 LEU Chi-restraints excluded: chain K residue 378 TYR Chi-restraints excluded: chain K residue 385 ILE Chi-restraints excluded: chain K residue 460 HIS Chi-restraints excluded: chain K residue 532 THR Chi-restraints excluded: chain K residue 538 ILE Chi-restraints excluded: chain K residue 576 ASP Chi-restraints excluded: chain K residue 587 LYS Chi-restraints excluded: chain K residue 602 ASP Chi-restraints excluded: chain K residue 624 ASP Chi-restraints excluded: chain K residue 628 LEU Chi-restraints excluded: chain K residue 661 LYS Chi-restraints excluded: chain K residue 666 VAL Chi-restraints excluded: chain K residue 781 LEU Chi-restraints excluded: chain M residue 30 ILE Chi-restraints excluded: chain M residue 62 ILE Chi-restraints excluded: chain M residue 82 ILE Chi-restraints excluded: chain M residue 118 ILE Chi-restraints excluded: chain M residue 157 TYR Chi-restraints excluded: chain M residue 182 ILE Chi-restraints excluded: chain M residue 200 VAL Chi-restraints excluded: chain M residue 211 LEU Chi-restraints excluded: chain M residue 218 LEU Chi-restraints excluded: chain M residue 220 CYS Chi-restraints excluded: chain M residue 291 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 346 random chunks: chunk 156 optimal weight: 9.9990 chunk 9 optimal weight: 0.8980 chunk 175 optimal weight: 5.9990 chunk 190 optimal weight: 3.9990 chunk 319 optimal weight: 7.9990 chunk 90 optimal weight: 10.0000 chunk 298 optimal weight: 0.6980 chunk 8 optimal weight: 1.9990 chunk 118 optimal weight: 5.9990 chunk 143 optimal weight: 6.9990 chunk 236 optimal weight: 5.9990 overall best weight: 2.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** D 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 21 ASN ** H 204 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3248 r_free = 0.3248 target = 0.051012 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3015 r_free = 0.3015 target = 0.042691 restraints weight = 145456.796| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3063 r_free = 0.3063 target = 0.044435 restraints weight = 74576.849| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3097 r_free = 0.3097 target = 0.045624 restraints weight = 46694.999| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3121 r_free = 0.3121 target = 0.046457 restraints weight = 32752.660| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 42)----------------| | r_work = 0.3137 r_free = 0.3137 target = 0.047047 restraints weight = 24834.567| |-----------------------------------------------------------------------------| r_work (final): 0.3134 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8520 moved from start: 0.4208 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 29252 Z= 0.201 Angle : 0.780 14.729 39623 Z= 0.377 Chirality : 0.056 0.485 4524 Planarity : 0.004 0.049 4852 Dihedral : 11.590 164.999 4390 Min Nonbonded Distance : 2.369 Molprobity Statistics. All-atom Clashscore : 16.77 Ramachandran Plot: Outliers : 0.12 % Allowed : 6.54 % Favored : 93.34 % Rotamer: Outliers : 3.62 % Allowed : 22.85 % Favored : 73.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.73 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.11 (0.14), residues: 3441 helix: 1.46 (0.14), residues: 1474 sheet: -0.14 (0.23), residues: 467 loop : -1.66 (0.15), residues: 1500 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG K 612 TYR 0.023 0.002 TYR B 105 PHE 0.034 0.002 PHE E 56 TRP 0.021 0.001 TRP G 182 HIS 0.004 0.001 HIS G 230 Details of bonding type rmsd/Z covalent geometry : bond 0.00435 / 0.20 (29237) covalent geometry : angle 0.77848 / 0.38 (39593) SS BOND : bond 0.00379 / 0.24 ( 15) SS BOND : angle 1.86988 / 1.29 ( 30) hydrogen bonds : bond 0.03792 / 2.50 ( 1274) hydrogen bonds : angle 5.05566 / 3.62 ( 3747) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6882 Ramachandran restraints generated. 3441 Oldfield, 0 Emsley, 3441 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6882 Ramachandran restraints generated. 3441 Oldfield, 0 Emsley, 3441 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 582 residues out of total 3097 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 112 poor density : 470 time to evaluate : 0.948 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 22 ASP cc_start: 0.8691 (m-30) cc_final: 0.8217 (t0) REVERT: A 42 GLU cc_start: 0.8338 (mm-30) cc_final: 0.8023 (mm-30) REVERT: A 56 PHE cc_start: 0.8930 (t80) cc_final: 0.8487 (t80) REVERT: A 60 ARG cc_start: 0.9287 (mmp80) cc_final: 0.8936 (mmm-85) REVERT: A 61 ARG cc_start: 0.9241 (mmm160) cc_final: 0.9035 (mmm160) REVERT: A 69 TYR cc_start: 0.9260 (t80) cc_final: 0.8959 (t80) REVERT: A 71 MET cc_start: 0.9076 (mmm) cc_final: 0.8837 (mmt) REVERT: A 79 ILE cc_start: 0.9027 (mm) cc_final: 0.8719 (mp) REVERT: A 110 TYR cc_start: 0.9093 (t80) cc_final: 0.8866 (t80) REVERT: A 111 ASP cc_start: 0.8987 (t0) cc_final: 0.8629 (t0) REVERT: A 131 GLU cc_start: 0.9417 (mt-10) cc_final: 0.8963 (mt-10) REVERT: B 22 ASP cc_start: 0.8839 (m-30) cc_final: 0.8139 (m-30) REVERT: B 26 ARG cc_start: 0.9138 (ptp-110) cc_final: 0.8448 (ptp90) REVERT: B 73 GLN cc_start: 0.9333 (tp40) cc_final: 0.9041 (tp-100) REVERT: B 78 GLU cc_start: 0.9091 (mm-30) cc_final: 0.8541 (tp30) REVERT: B 90 SER cc_start: 0.9660 (m) cc_final: 0.9280 (p) REVERT: B 129 PHE cc_start: 0.8787 (t80) cc_final: 0.8475 (t80) REVERT: B 131 GLU cc_start: 0.9231 (mp0) cc_final: 0.8896 (pm20) REVERT: B 134 ASN cc_start: 0.9147 (m-40) cc_final: 0.8697 (m110) REVERT: C 22 ASP cc_start: 0.9151 (m-30) cc_final: 0.8775 (m-30) REVERT: C 71 MET cc_start: 0.9397 (mtm) cc_final: 0.9070 (mtm) REVERT: C 77 ASP cc_start: 0.9238 (t0) cc_final: 0.8976 (t0) REVERT: C 105 TYR cc_start: 0.9357 (m-80) cc_final: 0.9087 (m-80) REVERT: C 134 ASN cc_start: 0.9720 (m-40) cc_final: 0.9419 (m110) REVERT: D 26 ARG cc_start: 0.9583 (mtm-85) cc_final: 0.9292 (ptp-110) REVERT: D 32 ILE cc_start: 0.9132 (tp) cc_final: 0.8912 (tp) REVERT: D 44 TYR cc_start: 0.9102 (t80) cc_final: 0.8738 (t80) REVERT: D 58 GLN cc_start: 0.9483 (mp10) cc_final: 0.9274 (mm-40) REVERT: D 61 ARG cc_start: 0.9203 (mmm-85) cc_final: 0.8970 (mmm-85) REVERT: D 82 GLU cc_start: 0.9490 (tt0) cc_final: 0.9129 (tp30) REVERT: D 95 GLU cc_start: 0.8666 (tp30) cc_final: 0.8067 (tm-30) REVERT: D 101 ASN cc_start: 0.9439 (m110) cc_final: 0.9141 (m110) REVERT: D 131 GLU cc_start: 0.9269 (mt-10) cc_final: 0.9058 (pt0) REVERT: D 133 VAL cc_start: 0.9764 (t) cc_final: 0.9560 (p) REVERT: D 134 ASN cc_start: 0.9240 (m-40) cc_final: 0.9013 (m110) REVERT: E 19 ASP cc_start: 0.9186 (p0) cc_final: 0.8974 (p0) REVERT: E 44 TYR cc_start: 0.9015 (t80) cc_final: 0.8723 (t80) REVERT: E 55 SER cc_start: 0.9793 (m) cc_final: 0.9515 (p) REVERT: E 78 GLU cc_start: 0.8638 (mt-10) cc_final: 0.8187 (mt-10) REVERT: E 82 GLU cc_start: 0.9361 (tm-30) cc_final: 0.9047 (tm-30) REVERT: E 101 ASN cc_start: 0.9553 (m110) cc_final: 0.9092 (m110) REVERT: E 105 TYR cc_start: 0.9322 (m-10) cc_final: 0.8842 (m-80) REVERT: E 131 GLU cc_start: 0.9027 (tp30) cc_final: 0.8655 (tm-30) REVERT: E 135 ILE cc_start: 0.9584 (mm) cc_final: 0.9261 (mm) REVERT: J 44 GLU cc_start: 0.8780 (pp20) cc_final: 0.7280 (pp20) REVERT: J 46 MET cc_start: 0.8358 (mtt) cc_final: 0.7914 (mmm) REVERT: J 146 PHE cc_start: 0.9232 (m-80) cc_final: 0.8901 (m-80) REVERT: J 159 MET cc_start: 0.9066 (tpp) cc_final: 0.8786 (tpp) REVERT: J 166 SER cc_start: 0.9167 (OUTLIER) cc_final: 0.8646 (t) REVERT: J 209 GLU cc_start: 0.9393 (mm-30) cc_final: 0.8586 (mp0) REVERT: J 229 MET cc_start: 0.8449 (mtp) cc_final: 0.8185 (mtm) REVERT: L 40 LYS cc_start: 0.9454 (tttt) cc_final: 0.9134 (tttp) REVERT: L 43 MET cc_start: 0.8952 (ttp) cc_final: 0.8680 (tpp) REVERT: L 98 THR cc_start: 0.7921 (OUTLIER) cc_final: 0.7677 (p) REVERT: L 113 LYS cc_start: 0.9491 (ttmm) cc_final: 0.9256 (tppp) REVERT: L 168 MET cc_start: 0.8841 (pmm) cc_final: 0.8638 (pmm) REVERT: N 49 MET cc_start: 0.9653 (tmm) cc_final: 0.9241 (tmm) REVERT: N 137 TYR cc_start: 0.7911 (OUTLIER) cc_final: 0.7331 (p90) REVERT: N 249 ARG cc_start: 0.9294 (mtp-110) cc_final: 0.8979 (ptm-80) REVERT: G 40 ASP cc_start: 0.9106 (m-30) cc_final: 0.8836 (p0) REVERT: G 66 GLU cc_start: 0.9281 (mt-10) cc_final: 0.8951 (mt-10) REVERT: G 167 MET cc_start: 0.8899 (tpt) cc_final: 0.8685 (tpp) REVERT: F 33 GLN cc_start: 0.9378 (mp10) cc_final: 0.9006 (mp10) REVERT: F 73 ASN cc_start: 0.9556 (t0) cc_final: 0.9317 (t0) REVERT: F 167 MET cc_start: 0.8980 (tpp) cc_final: 0.8666 (tpp) REVERT: F 177 GLU cc_start: 0.9289 (pt0) cc_final: 0.8982 (pp20) REVERT: F 207 ARG cc_start: 0.7383 (OUTLIER) cc_final: 0.7148 (mtp85) REVERT: F 239 LYS cc_start: 0.9522 (mmtm) cc_final: 0.9294 (mmmm) REVERT: H 5 THR cc_start: 0.8947 (OUTLIER) cc_final: 0.8700 (m) REVERT: H 19 GLU cc_start: 0.8590 (tm-30) cc_final: 0.8081 (tm-30) REVERT: H 129 MET cc_start: 0.9414 (mmm) cc_final: 0.9169 (mmm) REVERT: H 145 TYR cc_start: 0.8705 (p90) cc_final: 0.7988 (p90) REVERT: H 174 ASP cc_start: 0.8846 (t0) cc_final: 0.8392 (t70) REVERT: H 200 MET cc_start: 0.9363 (tpp) cc_final: 0.9098 (tpp) REVERT: H 255 ASP cc_start: 0.9176 (m-30) cc_final: 0.8715 (p0) REVERT: I 99 ASP cc_start: 0.9550 (m-30) cc_final: 0.9182 (p0) REVERT: I 110 GLN cc_start: 0.9626 (tp40) cc_final: 0.9317 (tp40) REVERT: I 118 TYR cc_start: 0.9198 (m-10) cc_final: 0.8896 (m-10) REVERT: I 129 MET cc_start: 0.9481 (OUTLIER) cc_final: 0.9196 (mmm) REVERT: I 200 MET cc_start: 0.9286 (ttp) cc_final: 0.9036 (ttp) REVERT: K 56 ASP cc_start: 0.9102 (m-30) cc_final: 0.8751 (m-30) REVERT: K 60 MET cc_start: 0.9073 (tmm) cc_final: 0.8647 (tmm) REVERT: K 61 ILE cc_start: 0.8915 (mt) cc_final: 0.8469 (mt) REVERT: K 148 THR cc_start: 0.9216 (OUTLIER) cc_final: 0.8939 (t) REVERT: K 201 ASP cc_start: 0.9271 (t0) cc_final: 0.8637 (t0) REVERT: K 202 GLU cc_start: 0.8571 (mt-10) cc_final: 0.8247 (mt-10) REVERT: K 205 GLU cc_start: 0.8701 (mm-30) cc_final: 0.8351 (mm-30) REVERT: K 273 LYS cc_start: 0.9445 (tppt) cc_final: 0.8942 (mttm) REVERT: K 330 PHE cc_start: 0.9102 (m-80) cc_final: 0.8195 (m-80) REVERT: K 336 MET cc_start: 0.8904 (mmm) cc_final: 0.8471 (mmm) REVERT: K 369 ILE cc_start: 0.9504 (mt) cc_final: 0.9173 (mt) REVERT: K 385 ILE cc_start: 0.9242 (OUTLIER) cc_final: 0.8709 (tp) REVERT: K 406 SER cc_start: 0.9292 (m) cc_final: 0.9059 (p) REVERT: K 438 MET cc_start: 0.8933 (mmt) cc_final: 0.8431 (mmt) REVERT: K 439 MET cc_start: 0.8908 (mmt) cc_final: 0.8609 (mmm) REVERT: K 474 ARG cc_start: 0.2977 (mtt180) cc_final: 0.2268 (mtt180) REVERT: K 481 LEU cc_start: 0.8632 (tp) cc_final: 0.8307 (tp) REVERT: K 502 LYS cc_start: 0.9404 (mtpt) cc_final: 0.9088 (mtmm) REVERT: K 538 ILE cc_start: 0.9382 (tp) cc_final: 0.9039 (tp) REVERT: K 587 LYS cc_start: 0.9291 (OUTLIER) cc_final: 0.8855 (tppt) REVERT: K 588 MET cc_start: 0.9386 (mtm) cc_final: 0.8793 (mtp) REVERT: K 619 TYR cc_start: 0.8927 (p90) cc_final: 0.8557 (p90) REVERT: K 625 ILE cc_start: 0.9421 (mt) cc_final: 0.9100 (mm) REVERT: K 626 MET cc_start: 0.9537 (tpp) cc_final: 0.9094 (tpp) REVERT: K 677 MET cc_start: 0.8922 (ttp) cc_final: 0.8531 (ttp) REVERT: K 727 ASP cc_start: 0.9455 (m-30) cc_final: 0.8870 (t0) REVERT: K 730 GLU cc_start: 0.9011 (tt0) cc_final: 0.8705 (tp30) REVERT: K 745 MET cc_start: 0.9073 (mpp) cc_final: 0.8674 (mtm) REVERT: M 15 GLN cc_start: 0.8180 (tp40) cc_final: 0.7969 (tp-100) REVERT: M 16 MET cc_start: 0.8742 (mmt) cc_final: 0.8337 (mmp) REVERT: M 62 ILE cc_start: 0.9648 (OUTLIER) cc_final: 0.9412 (mm) REVERT: M 144 GLN cc_start: 0.8485 (tt0) cc_final: 0.8228 (tt0) REVERT: M 169 PHE cc_start: 0.9083 (m-10) cc_final: 0.8766 (m-80) REVERT: M 290 MET cc_start: 0.8863 (pmm) cc_final: 0.8457 (pmm) outliers start: 112 outliers final: 87 residues processed: 552 average time/residue: 0.1582 time to fit residues: 142.5274 Evaluate side-chains 550 residues out of total 3097 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 97 poor density : 453 time to evaluate : 0.705 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 LEU Chi-restraints excluded: chain A residue 29 ILE Chi-restraints excluded: chain A residue 63 VAL Chi-restraints excluded: chain A residue 88 LEU Chi-restraints excluded: chain A residue 102 LEU Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain B residue 65 GLU Chi-restraints excluded: chain B residue 118 VAL Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain C residue 23 ILE Chi-restraints excluded: chain C residue 37 LYS Chi-restraints excluded: chain C residue 98 ASP Chi-restraints excluded: chain C residue 128 THR Chi-restraints excluded: chain E residue 39 ASN Chi-restraints excluded: chain E residue 50 ILE Chi-restraints excluded: chain E residue 77 ASP Chi-restraints excluded: chain E residue 126 VAL Chi-restraints excluded: chain J residue 23 ILE Chi-restraints excluded: chain J residue 43 VAL Chi-restraints excluded: chain J residue 90 VAL Chi-restraints excluded: chain J residue 115 VAL Chi-restraints excluded: chain J residue 120 THR Chi-restraints excluded: chain J residue 165 VAL Chi-restraints excluded: chain J residue 166 SER Chi-restraints excluded: chain J residue 208 VAL Chi-restraints excluded: chain J residue 261 ASP Chi-restraints excluded: chain J residue 274 GLU Chi-restraints excluded: chain L residue 21 THR Chi-restraints excluded: chain L residue 34 VAL Chi-restraints excluded: chain L residue 74 VAL Chi-restraints excluded: chain L residue 98 THR Chi-restraints excluded: chain L residue 137 THR Chi-restraints excluded: chain L residue 152 LEU Chi-restraints excluded: chain N residue 56 ILE Chi-restraints excluded: chain N residue 95 VAL Chi-restraints excluded: chain N residue 137 TYR Chi-restraints excluded: chain N residue 149 ILE Chi-restraints excluded: chain N residue 190 ILE Chi-restraints excluded: chain N residue 191 VAL Chi-restraints excluded: chain G residue 101 GLU Chi-restraints excluded: chain G residue 138 VAL Chi-restraints excluded: chain G residue 156 ASP Chi-restraints excluded: chain G residue 157 TYR Chi-restraints excluded: chain G residue 188 GLU Chi-restraints excluded: chain F residue 140 ILE Chi-restraints excluded: chain F residue 157 TYR Chi-restraints excluded: chain F residue 207 ARG Chi-restraints excluded: chain H residue 5 THR Chi-restraints excluded: chain H residue 11 VAL Chi-restraints excluded: chain H residue 16 THR Chi-restraints excluded: chain H residue 90 CYS Chi-restraints excluded: chain H residue 123 CYS Chi-restraints excluded: chain H residue 168 VAL Chi-restraints excluded: chain H residue 227 LYS Chi-restraints excluded: chain H residue 241 ILE Chi-restraints excluded: chain I residue 7 ILE Chi-restraints excluded: chain I residue 129 MET Chi-restraints excluded: chain I residue 175 VAL Chi-restraints excluded: chain I residue 183 MET Chi-restraints excluded: chain I residue 209 GLN Chi-restraints excluded: chain I residue 210 VAL Chi-restraints excluded: chain I residue 230 ASP Chi-restraints excluded: chain K residue 14 VAL Chi-restraints excluded: chain K residue 77 SER Chi-restraints excluded: chain K residue 148 THR Chi-restraints excluded: chain K residue 156 LEU Chi-restraints excluded: chain K residue 173 TYR Chi-restraints excluded: chain K residue 174 LEU Chi-restraints excluded: chain K residue 214 LEU Chi-restraints excluded: chain K residue 230 THR Chi-restraints excluded: chain K residue 264 LEU Chi-restraints excluded: chain K residue 287 TYR Chi-restraints excluded: chain K residue 304 SER Chi-restraints excluded: chain K residue 310 ASN Chi-restraints excluded: chain K residue 342 LEU Chi-restraints excluded: chain K residue 378 TYR Chi-restraints excluded: chain K residue 385 ILE Chi-restraints excluded: chain K residue 460 HIS Chi-restraints excluded: chain K residue 532 THR Chi-restraints excluded: chain K residue 576 ASP Chi-restraints excluded: chain K residue 587 LYS Chi-restraints excluded: chain K residue 602 ASP Chi-restraints excluded: chain K residue 624 ASP Chi-restraints excluded: chain K residue 628 LEU Chi-restraints excluded: chain K residue 661 LYS Chi-restraints excluded: chain K residue 666 VAL Chi-restraints excluded: chain M residue 30 ILE Chi-restraints excluded: chain M residue 62 ILE Chi-restraints excluded: chain M residue 82 ILE Chi-restraints excluded: chain M residue 118 ILE Chi-restraints excluded: chain M residue 157 TYR Chi-restraints excluded: chain M residue 182 ILE Chi-restraints excluded: chain M residue 200 VAL Chi-restraints excluded: chain M residue 211 LEU Chi-restraints excluded: chain M residue 218 LEU Chi-restraints excluded: chain M residue 220 CYS Chi-restraints excluded: chain M residue 291 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 346 random chunks: chunk 259 optimal weight: 0.9990 chunk 205 optimal weight: 1.9990 chunk 181 optimal weight: 4.9990 chunk 174 optimal weight: 9.9990 chunk 281 optimal weight: 1.9990 chunk 223 optimal weight: 5.9990 chunk 171 optimal weight: 10.0000 chunk 134 optimal weight: 10.0000 chunk 163 optimal weight: 7.9990 chunk 340 optimal weight: 1.9990 chunk 148 optimal weight: 2.9990 overall best weight: 1.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** D 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 21 ASN ** H 204 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 110 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3262 r_free = 0.3262 target = 0.051553 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3028 r_free = 0.3028 target = 0.043177 restraints weight = 144106.663| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3077 r_free = 0.3077 target = 0.044906 restraints weight = 74433.614| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3110 r_free = 0.3110 target = 0.046102 restraints weight = 46706.302| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3134 r_free = 0.3134 target = 0.046956 restraints weight = 32868.618| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 45)----------------| | r_work = 0.3150 r_free = 0.3150 target = 0.047547 restraints weight = 24911.972| |-----------------------------------------------------------------------------| r_work (final): 0.3145 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8504 moved from start: 0.4298 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 29252 Z= 0.171 Angle : 0.791 14.886 39623 Z= 0.380 Chirality : 0.056 0.456 4524 Planarity : 0.004 0.060 4852 Dihedral : 11.594 165.647 4390 Min Nonbonded Distance : 2.382 Molprobity Statistics. All-atom Clashscore : 15.83 Ramachandran Plot: Outliers : 0.15 % Allowed : 6.28 % Favored : 93.58 % Rotamer: Outliers : 3.30 % Allowed : 23.04 % Favored : 73.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.73 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.09 (0.14), residues: 3441 helix: 1.45 (0.14), residues: 1473 sheet: -0.11 (0.23), residues: 462 loop : -1.63 (0.15), residues: 1506 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG K 244 TYR 0.031 0.002 TYR K 62 PHE 0.047 0.002 PHE K 245 TRP 0.021 0.001 TRP G 182 HIS 0.003 0.001 HIS K 153 Details of bonding type rmsd/Z covalent geometry : bond 0.00376 / 0.17 (29237) covalent geometry : angle 0.78946 / 0.38 (39593) SS BOND : bond 0.00366 / 0.23 ( 15) SS BOND : angle 1.79338 / 1.23 ( 30) hydrogen bonds : bond 0.03766 / 2.49 ( 1274) hydrogen bonds : angle 5.01727 / 3.58 ( 3747) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6882 Ramachandran restraints generated. 3441 Oldfield, 0 Emsley, 3441 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6882 Ramachandran restraints generated. 3441 Oldfield, 0 Emsley, 3441 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 571 residues out of total 3097 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 102 poor density : 469 time to evaluate : 0.912 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 22 ASP cc_start: 0.8666 (m-30) cc_final: 0.8185 (t0) REVERT: A 42 GLU cc_start: 0.8359 (mm-30) cc_final: 0.8083 (mm-30) REVERT: A 56 PHE cc_start: 0.8921 (t80) cc_final: 0.8487 (t80) REVERT: A 60 ARG cc_start: 0.9285 (mmp80) cc_final: 0.8938 (mmm-85) REVERT: A 61 ARG cc_start: 0.9238 (mmm160) cc_final: 0.9034 (mmm160) REVERT: A 69 TYR cc_start: 0.9184 (t80) cc_final: 0.8872 (t80) REVERT: A 71 MET cc_start: 0.9066 (mmm) cc_final: 0.8820 (mmt) REVERT: A 79 ILE cc_start: 0.9021 (mm) cc_final: 0.8709 (mp) REVERT: A 110 TYR cc_start: 0.9078 (t80) cc_final: 0.8857 (t80) REVERT: A 111 ASP cc_start: 0.8983 (t0) cc_final: 0.8628 (t0) REVERT: A 131 GLU cc_start: 0.9397 (mt-10) cc_final: 0.8887 (mt-10) REVERT: B 22 ASP cc_start: 0.8807 (m-30) cc_final: 0.8138 (m-30) REVERT: B 26 ARG cc_start: 0.9147 (ptp-110) cc_final: 0.8480 (ptp90) REVERT: B 73 GLN cc_start: 0.9336 (tp40) cc_final: 0.9046 (tp-100) REVERT: B 78 GLU cc_start: 0.9066 (mm-30) cc_final: 0.8505 (tp30) REVERT: B 90 SER cc_start: 0.9658 (m) cc_final: 0.9235 (p) REVERT: B 131 GLU cc_start: 0.9228 (mp0) cc_final: 0.8890 (pm20) REVERT: B 134 ASN cc_start: 0.9155 (m-40) cc_final: 0.8703 (m110) REVERT: C 22 ASP cc_start: 0.9148 (m-30) cc_final: 0.8768 (m-30) REVERT: C 45 VAL cc_start: 0.9601 (OUTLIER) cc_final: 0.9237 (p) REVERT: C 71 MET cc_start: 0.9385 (mtm) cc_final: 0.9064 (mtm) REVERT: C 77 ASP cc_start: 0.9256 (t0) cc_final: 0.9000 (t0) REVERT: C 134 ASN cc_start: 0.9716 (m-40) cc_final: 0.9416 (m110) REVERT: D 22 ASP cc_start: 0.8928 (m-30) cc_final: 0.8303 (t0) REVERT: D 26 ARG cc_start: 0.9590 (mtm-85) cc_final: 0.9202 (ptp90) REVERT: D 32 ILE cc_start: 0.9125 (tp) cc_final: 0.8902 (tp) REVERT: D 44 TYR cc_start: 0.9042 (t80) cc_final: 0.8733 (t80) REVERT: D 58 GLN cc_start: 0.9474 (mp10) cc_final: 0.9163 (mm-40) REVERT: D 61 ARG cc_start: 0.9200 (mmm-85) cc_final: 0.8970 (mmm-85) REVERT: D 82 GLU cc_start: 0.9484 (tt0) cc_final: 0.9102 (tp30) REVERT: D 95 GLU cc_start: 0.8688 (tp30) cc_final: 0.8220 (tm-30) REVERT: D 101 ASN cc_start: 0.9432 (m110) cc_final: 0.9124 (m110) REVERT: D 131 GLU cc_start: 0.9274 (mt-10) cc_final: 0.9058 (pt0) REVERT: D 133 VAL cc_start: 0.9757 (t) cc_final: 0.9550 (p) REVERT: D 134 ASN cc_start: 0.9235 (m-40) cc_final: 0.9003 (m110) REVERT: E 19 ASP cc_start: 0.9173 (p0) cc_final: 0.8956 (p0) REVERT: E 44 TYR cc_start: 0.9005 (t80) cc_final: 0.8709 (t80) REVERT: E 55 SER cc_start: 0.9783 (m) cc_final: 0.9496 (p) REVERT: E 78 GLU cc_start: 0.8692 (mt-10) cc_final: 0.8209 (mt-10) REVERT: E 82 GLU cc_start: 0.9357 (tm-30) cc_final: 0.9036 (tm-30) REVERT: E 101 ASN cc_start: 0.9549 (m110) cc_final: 0.9089 (m110) REVERT: E 105 TYR cc_start: 0.9312 (m-10) cc_final: 0.8817 (m-80) REVERT: E 131 GLU cc_start: 0.9016 (tp30) cc_final: 0.8656 (tm-30) REVERT: E 135 ILE cc_start: 0.9577 (mm) cc_final: 0.9297 (mm) REVERT: J 44 GLU cc_start: 0.8763 (pp20) cc_final: 0.7286 (pp20) REVERT: J 46 MET cc_start: 0.8317 (mtt) cc_final: 0.7910 (mmm) REVERT: J 146 PHE cc_start: 0.9232 (m-80) cc_final: 0.8906 (m-80) REVERT: J 159 MET cc_start: 0.9076 (tpp) cc_final: 0.8790 (tpp) REVERT: J 166 SER cc_start: 0.9166 (OUTLIER) cc_final: 0.8639 (t) REVERT: J 209 GLU cc_start: 0.9379 (mm-30) cc_final: 0.8571 (mp0) REVERT: L 40 LYS cc_start: 0.9449 (tttt) cc_final: 0.9142 (tttp) REVERT: L 43 MET cc_start: 0.8946 (ttp) cc_final: 0.8669 (tpp) REVERT: L 98 THR cc_start: 0.7897 (OUTLIER) cc_final: 0.7674 (p) REVERT: L 113 LYS cc_start: 0.9482 (ttmm) cc_final: 0.9241 (tppp) REVERT: N 49 MET cc_start: 0.9646 (tmm) cc_final: 0.9353 (tmm) REVERT: N 137 TYR cc_start: 0.7852 (OUTLIER) cc_final: 0.7166 (p90) REVERT: N 249 ARG cc_start: 0.9291 (mtp-110) cc_final: 0.8966 (ptm-80) REVERT: G 40 ASP cc_start: 0.9105 (m-30) cc_final: 0.8833 (p0) REVERT: G 66 GLU cc_start: 0.9283 (mt-10) cc_final: 0.8967 (mt-10) REVERT: G 167 MET cc_start: 0.8904 (tpt) cc_final: 0.8696 (tpp) REVERT: F 33 GLN cc_start: 0.9379 (mp10) cc_final: 0.9008 (mp10) REVERT: F 73 ASN cc_start: 0.9554 (t0) cc_final: 0.9310 (t0) REVERT: F 137 MET cc_start: 0.8291 (mpp) cc_final: 0.7422 (mpp) REVERT: F 167 MET cc_start: 0.8975 (tpp) cc_final: 0.8652 (tpp) REVERT: F 177 GLU cc_start: 0.9288 (pt0) cc_final: 0.8979 (pp20) REVERT: F 207 ARG cc_start: 0.7402 (OUTLIER) cc_final: 0.6961 (mtp85) REVERT: F 239 LYS cc_start: 0.9527 (mmtm) cc_final: 0.9281 (mmmm) REVERT: H 5 THR cc_start: 0.8934 (OUTLIER) cc_final: 0.8682 (m) REVERT: H 19 GLU cc_start: 0.8587 (tm-30) cc_final: 0.8064 (tm-30) REVERT: H 129 MET cc_start: 0.9416 (mmm) cc_final: 0.9172 (mmm) REVERT: H 145 TYR cc_start: 0.8702 (p90) cc_final: 0.7994 (p90) REVERT: H 174 ASP cc_start: 0.8829 (t0) cc_final: 0.8368 (t70) REVERT: H 200 MET cc_start: 0.9352 (tpp) cc_final: 0.9096 (tpp) REVERT: H 255 ASP cc_start: 0.9186 (m-30) cc_final: 0.8730 (p0) REVERT: H 261 MET cc_start: 0.8882 (mmm) cc_final: 0.8618 (mmm) REVERT: I 110 GLN cc_start: 0.9611 (tp-100) cc_final: 0.9320 (tp40) REVERT: I 118 TYR cc_start: 0.9169 (m-10) cc_final: 0.8875 (m-10) REVERT: I 129 MET cc_start: 0.9418 (OUTLIER) cc_final: 0.9105 (mmm) REVERT: I 164 ARG cc_start: 0.7531 (mtm180) cc_final: 0.7178 (ttp80) REVERT: I 200 MET cc_start: 0.9274 (ttp) cc_final: 0.8699 (ttp) REVERT: K 56 ASP cc_start: 0.9095 (m-30) cc_final: 0.8721 (m-30) REVERT: K 60 MET cc_start: 0.8984 (tmm) cc_final: 0.8588 (tmm) REVERT: K 61 ILE cc_start: 0.8877 (mt) cc_final: 0.8301 (mt) REVERT: K 148 THR cc_start: 0.9231 (OUTLIER) cc_final: 0.8941 (t) REVERT: K 201 ASP cc_start: 0.9271 (t0) cc_final: 0.8651 (t0) REVERT: K 202 GLU cc_start: 0.8591 (mt-10) cc_final: 0.8256 (mt-10) REVERT: K 205 GLU cc_start: 0.8699 (mm-30) cc_final: 0.8344 (mm-30) REVERT: K 273 LYS cc_start: 0.9421 (tppt) cc_final: 0.8953 (mttm) REVERT: K 336 MET cc_start: 0.8910 (mmm) cc_final: 0.8575 (mmm) REVERT: K 369 ILE cc_start: 0.9496 (mt) cc_final: 0.9161 (mt) REVERT: K 385 ILE cc_start: 0.9260 (OUTLIER) cc_final: 0.8731 (tp) REVERT: K 406 SER cc_start: 0.9285 (m) cc_final: 0.9052 (p) REVERT: K 438 MET cc_start: 0.8957 (mmt) cc_final: 0.8440 (mmt) REVERT: K 439 MET cc_start: 0.8887 (mmt) cc_final: 0.8591 (mmm) REVERT: K 474 ARG cc_start: 0.2994 (mtt180) cc_final: 0.2621 (mtt180) REVERT: K 481 LEU cc_start: 0.8607 (tp) cc_final: 0.8279 (tp) REVERT: K 502 LYS cc_start: 0.9390 (mtpt) cc_final: 0.9069 (mtmm) REVERT: K 538 ILE cc_start: 0.9375 (OUTLIER) cc_final: 0.9031 (tp) REVERT: K 587 LYS cc_start: 0.9285 (OUTLIER) cc_final: 0.8841 (tppt) REVERT: K 588 MET cc_start: 0.9396 (mtm) cc_final: 0.8800 (mtp) REVERT: K 619 TYR cc_start: 0.8899 (p90) cc_final: 0.8530 (p90) REVERT: K 625 ILE cc_start: 0.9423 (mt) cc_final: 0.9088 (mm) REVERT: K 626 MET cc_start: 0.9534 (tpp) cc_final: 0.9069 (tpp) REVERT: K 677 MET cc_start: 0.8964 (ttp) cc_final: 0.8576 (ttp) REVERT: K 727 ASP cc_start: 0.9456 (m-30) cc_final: 0.8867 (t0) REVERT: K 730 GLU cc_start: 0.9021 (tt0) cc_final: 0.8695 (tp30) REVERT: K 745 MET cc_start: 0.9077 (mpp) cc_final: 0.8673 (mtm) REVERT: M 15 GLN cc_start: 0.8161 (tp40) cc_final: 0.7954 (tp-100) REVERT: M 16 MET cc_start: 0.8719 (mmt) cc_final: 0.8300 (mmp) REVERT: M 62 ILE cc_start: 0.9648 (OUTLIER) cc_final: 0.9410 (mm) REVERT: M 144 GLN cc_start: 0.8500 (tt0) cc_final: 0.8265 (tt0) REVERT: M 169 PHE cc_start: 0.9055 (m-10) cc_final: 0.8740 (m-80) REVERT: M 290 MET cc_start: 0.8820 (pmm) cc_final: 0.8384 (pmm) outliers start: 102 outliers final: 84 residues processed: 541 average time/residue: 0.1549 time to fit residues: 136.5602 Evaluate side-chains 558 residues out of total 3097 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 462 time to evaluate : 0.818 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 LEU Chi-restraints excluded: chain A residue 29 ILE Chi-restraints excluded: chain A residue 63 VAL Chi-restraints excluded: chain A residue 102 LEU Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain B residue 118 VAL Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain C residue 23 ILE Chi-restraints excluded: chain C residue 37 LYS Chi-restraints excluded: chain C residue 45 VAL Chi-restraints excluded: chain C residue 98 ASP Chi-restraints excluded: chain C residue 128 THR Chi-restraints excluded: chain D residue 49 THR Chi-restraints excluded: chain E residue 39 ASN Chi-restraints excluded: chain E residue 50 ILE Chi-restraints excluded: chain E residue 77 ASP Chi-restraints excluded: chain E residue 126 VAL Chi-restraints excluded: chain J residue 43 VAL Chi-restraints excluded: chain J residue 115 VAL Chi-restraints excluded: chain J residue 120 THR Chi-restraints excluded: chain J residue 165 VAL Chi-restraints excluded: chain J residue 166 SER Chi-restraints excluded: chain J residue 261 ASP Chi-restraints excluded: chain J residue 274 GLU Chi-restraints excluded: chain L residue 21 THR Chi-restraints excluded: chain L residue 34 VAL Chi-restraints excluded: chain L residue 74 VAL Chi-restraints excluded: chain L residue 98 THR Chi-restraints excluded: chain L residue 137 THR Chi-restraints excluded: chain L residue 152 LEU Chi-restraints excluded: chain N residue 56 ILE Chi-restraints excluded: chain N residue 95 VAL Chi-restraints excluded: chain N residue 103 ASN Chi-restraints excluded: chain N residue 137 TYR Chi-restraints excluded: chain N residue 149 ILE Chi-restraints excluded: chain N residue 190 ILE Chi-restraints excluded: chain N residue 191 VAL Chi-restraints excluded: chain G residue 101 GLU Chi-restraints excluded: chain G residue 138 VAL Chi-restraints excluded: chain G residue 156 ASP Chi-restraints excluded: chain G residue 157 TYR Chi-restraints excluded: chain G residue 188 GLU Chi-restraints excluded: chain F residue 140 ILE Chi-restraints excluded: chain F residue 157 TYR Chi-restraints excluded: chain F residue 207 ARG Chi-restraints excluded: chain H residue 5 THR Chi-restraints excluded: chain H residue 11 VAL Chi-restraints excluded: chain H residue 16 THR Chi-restraints excluded: chain H residue 90 CYS Chi-restraints excluded: chain H residue 123 CYS Chi-restraints excluded: chain H residue 168 VAL Chi-restraints excluded: chain H residue 210 VAL Chi-restraints excluded: chain H residue 227 LYS Chi-restraints excluded: chain I residue 7 ILE Chi-restraints excluded: chain I residue 129 MET Chi-restraints excluded: chain I residue 175 VAL Chi-restraints excluded: chain I residue 183 MET Chi-restraints excluded: chain I residue 209 GLN Chi-restraints excluded: chain I residue 210 VAL Chi-restraints excluded: chain I residue 230 ASP Chi-restraints excluded: chain K residue 14 VAL Chi-restraints excluded: chain K residue 77 SER Chi-restraints excluded: chain K residue 148 THR Chi-restraints excluded: chain K residue 156 LEU Chi-restraints excluded: chain K residue 173 TYR Chi-restraints excluded: chain K residue 174 LEU Chi-restraints excluded: chain K residue 214 LEU Chi-restraints excluded: chain K residue 230 THR Chi-restraints excluded: chain K residue 287 TYR Chi-restraints excluded: chain K residue 304 SER Chi-restraints excluded: chain K residue 310 ASN Chi-restraints excluded: chain K residue 342 LEU Chi-restraints excluded: chain K residue 378 TYR Chi-restraints excluded: chain K residue 385 ILE Chi-restraints excluded: chain K residue 460 HIS Chi-restraints excluded: chain K residue 532 THR Chi-restraints excluded: chain K residue 538 ILE Chi-restraints excluded: chain K residue 576 ASP Chi-restraints excluded: chain K residue 587 LYS Chi-restraints excluded: chain K residue 602 ASP Chi-restraints excluded: chain K residue 624 ASP Chi-restraints excluded: chain K residue 628 LEU Chi-restraints excluded: chain K residue 661 LYS Chi-restraints excluded: chain K residue 666 VAL Chi-restraints excluded: chain M residue 30 ILE Chi-restraints excluded: chain M residue 62 ILE Chi-restraints excluded: chain M residue 82 ILE Chi-restraints excluded: chain M residue 118 ILE Chi-restraints excluded: chain M residue 157 TYR Chi-restraints excluded: chain M residue 182 ILE Chi-restraints excluded: chain M residue 200 VAL Chi-restraints excluded: chain M residue 211 LEU Chi-restraints excluded: chain M residue 218 LEU Chi-restraints excluded: chain M residue 220 CYS Chi-restraints excluded: chain M residue 240 ILE Chi-restraints excluded: chain M residue 291 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 346 random chunks: chunk 240 optimal weight: 6.9990 chunk 308 optimal weight: 4.9990 chunk 11 optimal weight: 0.9990 chunk 108 optimal weight: 9.9990 chunk 2 optimal weight: 5.9990 chunk 339 optimal weight: 7.9990 chunk 336 optimal weight: 6.9990 chunk 261 optimal weight: 6.9990 chunk 42 optimal weight: 0.0470 chunk 68 optimal weight: 0.9990 chunk 210 optimal weight: 1.9990 overall best weight: 1.8086 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** D 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 21 ASN ** H 204 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3272 r_free = 0.3272 target = 0.052187 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3037 r_free = 0.3037 target = 0.043642 restraints weight = 144427.062| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3086 r_free = 0.3086 target = 0.045417 restraints weight = 74191.240| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3120 r_free = 0.3120 target = 0.046644 restraints weight = 46527.293| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3143 r_free = 0.3143 target = 0.047491 restraints weight = 32618.330| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3159 r_free = 0.3159 target = 0.048100 restraints weight = 24762.465| |-----------------------------------------------------------------------------| r_work (final): 0.3154 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8499 moved from start: 0.4389 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 29252 Z= 0.162 Angle : 0.770 14.614 39623 Z= 0.372 Chirality : 0.055 0.438 4524 Planarity : 0.004 0.064 4852 Dihedral : 11.568 167.092 4390 Min Nonbonded Distance : 2.391 Molprobity Statistics. All-atom Clashscore : 15.50 Ramachandran Plot: Outliers : 0.12 % Allowed : 6.34 % Favored : 93.55 % Rotamer: Outliers : 3.43 % Allowed : 23.24 % Favored : 73.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.73 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.07 (0.15), residues: 3441 helix: 1.46 (0.14), residues: 1473 sheet: -0.07 (0.23), residues: 455 loop : -1.62 (0.15), residues: 1513 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG K 244 TYR 0.032 0.002 TYR B 105 PHE 0.034 0.002 PHE K 589 TRP 0.024 0.001 TRP G 182 HIS 0.003 0.001 HIS K 153 Details of bonding type rmsd/Z covalent geometry : bond 0.00362 / 0.16 (29237) covalent geometry : angle 0.76864 / 0.37 (39593) SS BOND : bond 0.00358 / 0.23 ( 15) SS BOND : angle 1.81826 / 1.25 ( 30) hydrogen bonds : bond 0.03694 / 2.45 ( 1274) hydrogen bonds : angle 4.96439 / 3.55 ( 3747) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5128.07 seconds wall clock time: 89 minutes 45.05 seconds (5385.05 seconds total)