Starting phenix.real_space_refine on Sun Jul 5 14:48:55 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8bmw_16126/07_2026/8bmw_16126.cif Found real_map, /net/cci-nas-00/data/ceres_data/8bmw_16126/07_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 { restraint_files = "/net/cci-nas-00/data/ceres_data/8bmw_16126/07_2026/8bmw_16126.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8bmw_16126/07_2026/8bmw_16126.cif" model { file = "/net/cci-nas-00/data/ceres_data/8bmw_16126/07_2026/8bmw_16126.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8bmw_16126/07_2026/8bmw_16126.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8bmw_16126/07_2026/8bmw_16126.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8bmw_16126/07_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-dev-6108/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: {'RNA': 48} Modifications used: {'5*END': 1, 'rna2p_pur': 5, 'rna2p_pyr': 26, 'rna3p_pur': 1, 'rna3p_pyr': 16} Link IDs: {'rna2p': 30, 'rna3p': 17} 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: 6.14, per 1000 atoms: 0.21 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: 2.50 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: 3.38 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: 5.62 Time building geometry restraints manager: 3.31 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: 38868 1.66 - 3.31: 599 3.31 - 4.97: 96 4.97 - 6.63: 22 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=" 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 angle pdb=" N LEU I 112 " pdb=" CA LEU I 112 " pdb=" C LEU I 112 " ideal model delta sigma weight residual 111.07 105.90 5.17 1.07e+00 8.73e-01 2.33e+01 ... (remaining 39588 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.71: 17611 35.71 - 71.42: 196 71.42 - 107.14: 9 107.14 - 142.85: 0 142.85 - 178.56: 11 Dihedral angle restraints: 17827 sinusoidal: 7710 harmonic: 10117 Sorted by residual: dihedral pdb=" CB CYS H 90 " pdb=" SG CYS H 90 " pdb=" SG CYS H 120 " pdb=" CB CYS H 120 " ideal model delta sinusoidal sigma weight residual 93.00 178.30 -85.30 1 1.00e+01 1.00e-02 8.81e+01 dihedral pdb=" O4' U R 23 " pdb=" C1' U R 23 " pdb=" N1 U R 23 " pdb=" C2 U R 23 " ideal model delta sinusoidal sigma weight residual 200.00 28.17 171.83 1 1.50e+01 4.44e-03 8.49e+01 dihedral pdb=" CB CYS L 75 " pdb=" SG CYS L 75 " pdb=" SG CYS L 78 " pdb=" CB CYS L 78 " ideal model delta sinusoidal sigma weight residual 93.00 9.89 83.11 1 1.00e+01 1.00e-02 8.45e+01 ... (remaining 17824 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.050: 3706 0.050 - 0.099: 648 0.099 - 0.149: 146 0.149 - 0.198: 14 0.198 - 0.248: 10 Chirality restraints: 4524 Sorted by residual: chirality pdb=" CA ARG J 164 " pdb=" N ARG J 164 " pdb=" C ARG J 164 " pdb=" CB ARG J 164 " both_signs ideal model delta sigma weight residual False 2.51 2.76 -0.25 2.00e-01 2.50e+01 1.54e+00 chirality pdb=" CA PRO H 189 " pdb=" N PRO H 189 " pdb=" C PRO H 189 " pdb=" CB PRO H 189 " both_signs ideal model delta sigma weight residual False 2.72 2.96 -0.24 2.00e-01 2.50e+01 1.50e+00 chirality pdb=" CA ILE I 114 " pdb=" N ILE I 114 " pdb=" C ILE I 114 " pdb=" CB ILE I 114 " both_signs ideal model delta sigma weight residual False 2.43 2.68 -0.24 2.00e-01 2.50e+01 1.49e+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: 2.300 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 0.530 Check model and map are aligned: 0.080 Set scattering table: 0.080 Process input model: 28.250 Find NCS groups from input model: 0.380 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:1.290 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.010 ------------------------------------------------------------------------------- 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= 0.185 Angle : 0.539 8.282 39623 Z= 0.331 Chirality : 0.042 0.248 4524 Planarity : 0.003 0.043 4852 Dihedral : 12.144 178.559 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 0.00317 / 0.19 (29237) covalent geometry : angle 0.53678 / 0.33 (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 : 1.014 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: 0.2170 time to fit residues: 289.8062 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 : 1.184 ------------------------------------------------------------------------------- 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: 10.0000 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: 7.9990 chunk 298 optimal weight: 0.0030 overall best weight: 1.3996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 64 ASN ** B 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 134 ASN D 73 GLN E 39 ASN ** J 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 173 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 134 GLN G 141 ASN K 155 GLN K 223 GLN K 711 ASN M 46 GLN ** M 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.053420 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3063 r_free = 0.3063 target = 0.044715 restraints weight = 143444.336| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3112 r_free = 0.3112 target = 0.046509 restraints weight = 74715.723| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3145 r_free = 0.3145 target = 0.047764 restraints weight = 46948.183| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3168 r_free = 0.3168 target = 0.048640 restraints weight = 32955.939| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3184 r_free = 0.3184 target = 0.049244 restraints weight = 24938.609| |-----------------------------------------------------------------------------| r_work (final): 0.3183 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8448 moved from start: 0.2253 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 29252 Z= 0.158 Angle : 0.663 11.650 39623 Z= 0.346 Chirality : 0.044 0.208 4524 Planarity : 0.004 0.053 4852 Dihedral : 11.420 178.721 4397 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 14.26 Ramachandran Plot: Outliers : 0.12 % Allowed : 5.35 % Favored : 94.54 % Rotamer: Outliers : 2.62 % Allowed : 18.41 % Favored : 78.96 % 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: 0.36 (0.15), residues: 3441 helix: 2.07 (0.14), residues: 1466 sheet: 0.12 (0.25), residues: 431 loop : -1.64 (0.15), residues: 1544 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG K 786 TYR 0.021 0.002 TYR L 104 PHE 0.032 0.001 PHE K 245 TRP 0.010 0.001 TRP E 108 HIS 0.003 0.001 HIS M 113 Details of bonding type rmsd/Z covalent geometry : bond 0.00343 / 0.16 (29237) covalent geometry : angle 0.66115 / 0.35 (39593) SS BOND : bond 0.00415 / 0.28 ( 15) SS BOND : angle 1.88767 / 1.07 ( 30) hydrogen bonds : bond 0.04239 / 2.82 ( 1274) hydrogen bonds : angle 5.35779 / 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 723 residues out of total 3097 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 642 time to evaluate : 1.192 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: A 22 ASP cc_start: 0.8584 (m-30) cc_final: 0.8103 (t0) REVERT: A 29 ILE cc_start: 0.9370 (tp) cc_final: 0.9039 (tt) REVERT: A 42 GLU cc_start: 0.8137 (mm-30) cc_final: 0.7816 (mm-30) REVERT: A 56 PHE cc_start: 0.8971 (t80) cc_final: 0.8563 (t80) REVERT: A 60 ARG cc_start: 0.9270 (mmp80) cc_final: 0.8865 (mmm160) REVERT: A 79 ILE cc_start: 0.8891 (mm) cc_final: 0.8613 (mp) REVERT: A 110 TYR cc_start: 0.9052 (t80) cc_final: 0.8759 (t80) REVERT: A 111 ASP cc_start: 0.9008 (t0) cc_final: 0.8703 (t0) REVERT: A 131 GLU cc_start: 0.9437 (mt-10) cc_final: 0.9015 (mt-10) REVERT: B 22 ASP cc_start: 0.8843 (m-30) cc_final: 0.8500 (m-30) REVERT: B 44 TYR cc_start: 0.9374 (t80) cc_final: 0.9064 (t80) REVERT: B 69 TYR cc_start: 0.9136 (t80) cc_final: 0.8814 (t80) REVERT: B 73 GLN cc_start: 0.9322 (tp40) cc_final: 0.9035 (mp10) REVERT: B 78 GLU cc_start: 0.9140 (mm-30) cc_final: 0.8908 (tp30) REVERT: B 90 SER cc_start: 0.9602 (m) cc_final: 0.9190 (p) REVERT: B 103 LEU cc_start: 0.9781 (mt) cc_final: 0.9446 (tp) REVERT: B 128 THR cc_start: 0.9345 (p) cc_final: 0.8499 (p) REVERT: B 129 PHE cc_start: 0.9286 (t80) cc_final: 0.9049 (t80) REVERT: B 131 GLU cc_start: 0.8987 (mt-10) cc_final: 0.8711 (mt-10) REVERT: B 134 ASN cc_start: 0.9224 (m-40) cc_final: 0.8870 (m110) REVERT: C 22 ASP cc_start: 0.9097 (m-30) cc_final: 0.8680 (m-30) REVERT: C 45 VAL cc_start: 0.9338 (t) cc_final: 0.9016 (p) REVERT: C 71 MET cc_start: 0.9441 (mtm) cc_final: 0.9050 (mtm) REVERT: C 77 ASP cc_start: 0.9084 (t0) cc_final: 0.8876 (t0) REVERT: C 80 ASP cc_start: 0.8714 (t70) cc_final: 0.8485 (t70) REVERT: C 105 TYR cc_start: 0.9379 (m-80) cc_final: 0.9157 (m-80) REVERT: C 134 ASN cc_start: 0.9684 (m-40) cc_final: 0.9414 (m110) REVERT: D 26 ARG cc_start: 0.9539 (mtm-85) cc_final: 0.9183 (ptp90) REVERT: D 29 ILE cc_start: 0.8926 (OUTLIER) cc_final: 0.8724 (mm) REVERT: D 44 TYR cc_start: 0.9195 (t80) cc_final: 0.8766 (t80) REVERT: D 58 GLN cc_start: 0.9493 (mp10) cc_final: 0.9167 (mm-40) REVERT: D 90 SER cc_start: 0.9449 (m) cc_final: 0.9226 (p) REVERT: D 101 ASN cc_start: 0.9558 (m110) cc_final: 0.9329 (m110) REVERT: D 131 GLU cc_start: 0.9130 (mt-10) cc_final: 0.8873 (mt-10) REVERT: E 42 GLU cc_start: 0.8589 (pt0) cc_final: 0.8315 (pm20) REVERT: E 48 SER cc_start: 0.9774 (m) cc_final: 0.9557 (p) REVERT: E 55 SER cc_start: 0.9782 (m) cc_final: 0.9513 (p) REVERT: E 71 MET cc_start: 0.9316 (mtp) cc_final: 0.9057 (ptp) REVERT: E 76 ARG cc_start: 0.9494 (mmm-85) cc_final: 0.8754 (mmm-85) REVERT: E 78 GLU cc_start: 0.8400 (mt-10) cc_final: 0.8058 (mp0) REVERT: E 82 GLU cc_start: 0.9375 (tm-30) cc_final: 0.9014 (tm-30) REVERT: E 101 ASN cc_start: 0.9484 (m110) cc_final: 0.8985 (m110) REVERT: E 105 TYR cc_start: 0.9341 (m-10) cc_final: 0.8725 (m-80) REVERT: E 114 THR cc_start: 0.9485 (m) cc_final: 0.9225 (p) REVERT: E 130 LYS cc_start: 0.9546 (ptmt) cc_final: 0.9215 (ttpp) REVERT: E 131 GLU cc_start: 0.9084 (tp30) cc_final: 0.8615 (tm-30) REVERT: E 134 ASN cc_start: 0.9462 (m-40) cc_final: 0.8619 (m-40) REVERT: E 135 ILE cc_start: 0.9593 (mm) cc_final: 0.9227 (mm) REVERT: J 6 ILE cc_start: 0.8534 (OUTLIER) cc_final: 0.8184 (tp) REVERT: J 46 MET cc_start: 0.8325 (mtp) cc_final: 0.7695 (mtp) REVERT: J 56 VAL cc_start: 0.9462 (OUTLIER) cc_final: 0.8510 (m) REVERT: J 81 LEU cc_start: 0.9377 (mt) cc_final: 0.9152 (mp) REVERT: J 146 PHE cc_start: 0.9177 (m-80) cc_final: 0.8875 (m-80) REVERT: J 166 SER cc_start: 0.8999 (m) cc_final: 0.8576 (t) REVERT: J 209 GLU cc_start: 0.9234 (mm-30) cc_final: 0.8362 (mp0) REVERT: J 229 MET cc_start: 0.8601 (mtp) cc_final: 0.8260 (ttm) REVERT: L 62 GLU cc_start: 0.8897 (tp30) cc_final: 0.8148 (mp0) REVERT: L 113 LYS cc_start: 0.9404 (ttmm) cc_final: 0.9107 (tppt) REVERT: L 115 GLN cc_start: 0.8895 (mm110) cc_final: 0.8544 (mm-40) REVERT: L 118 LYS cc_start: 0.9407 (tppp) cc_final: 0.9200 (tppt) REVERT: L 178 GLU cc_start: 0.9096 (pt0) cc_final: 0.8807 (pm20) REVERT: N 49 MET cc_start: 0.9613 (tmm) cc_final: 0.9271 (tmm) REVERT: N 155 MET cc_start: 0.8825 (pmm) cc_final: 0.8620 (pmm) REVERT: N 161 THR cc_start: 0.9136 (OUTLIER) cc_final: 0.8877 (p) REVERT: N 196 GLU cc_start: 0.8376 (tp30) cc_final: 0.7668 (tp30) REVERT: N 229 GLU cc_start: 0.8238 (tp30) cc_final: 0.7871 (tp30) REVERT: N 249 ARG cc_start: 0.9317 (mtp-110) cc_final: 0.9100 (ptm-80) REVERT: G 40 ASP cc_start: 0.9142 (m-30) cc_final: 0.8892 (p0) REVERT: G 66 GLU cc_start: 0.9291 (mt-10) cc_final: 0.9050 (mt-10) REVERT: G 167 MET cc_start: 0.7731 (tpp) cc_final: 0.7412 (tpp) REVERT: G 168 MET cc_start: 0.8766 (ttp) cc_final: 0.8565 (ttm) REVERT: F 33 GLN cc_start: 0.9256 (mp10) cc_final: 0.8893 (mp10) REVERT: F 73 ASN cc_start: 0.9506 (t0) cc_final: 0.9228 (t0) REVERT: F 121 TYR cc_start: 0.8811 (m-80) cc_final: 0.8493 (m-80) REVERT: F 137 MET cc_start: 0.8295 (ptp) cc_final: 0.7988 (ptp) REVERT: F 169 MET cc_start: 0.8938 (mtp) cc_final: 0.8698 (mtp) REVERT: F 239 LYS cc_start: 0.9470 (mmtm) cc_final: 0.9244 (mmmm) REVERT: H 56 ILE cc_start: 0.9387 (pt) cc_final: 0.9060 (mm) REVERT: H 110 GLN cc_start: 0.9601 (tp40) cc_final: 0.9193 (mp10) REVERT: H 145 TYR cc_start: 0.8257 (p90) cc_final: 0.7774 (p90) REVERT: H 174 ASP cc_start: 0.8643 (t0) cc_final: 0.8205 (t70) REVERT: H 182 LYS cc_start: 0.9260 (ttmt) cc_final: 0.9031 (tttm) REVERT: H 193 ILE cc_start: 0.9330 (OUTLIER) cc_final: 0.9111 (pt) REVERT: H 200 MET cc_start: 0.9223 (tpp) cc_final: 0.8763 (tmm) REVERT: H 255 ASP cc_start: 0.9096 (m-30) cc_final: 0.8644 (p0) REVERT: H 261 MET cc_start: 0.9601 (mmp) cc_final: 0.9285 (mmm) REVERT: H 265 MET cc_start: 0.9545 (mtp) cc_final: 0.9227 (mtt) REVERT: H 266 GLU cc_start: 0.9510 (mt-10) cc_final: 0.9213 (mt-10) REVERT: I 80 GLU cc_start: 0.8960 (tt0) cc_final: 0.8621 (pt0) REVERT: I 99 ASP cc_start: 0.9487 (m-30) cc_final: 0.9204 (p0) REVERT: I 110 GLN cc_start: 0.9629 (tp40) cc_final: 0.9351 (tp40) REVERT: I 118 TYR cc_start: 0.9071 (m-80) cc_final: 0.8761 (m-10) REVERT: I 152 MET cc_start: 0.7606 (OUTLIER) cc_final: 0.7353 (mmm) REVERT: I 182 LYS cc_start: 0.8676 (OUTLIER) cc_final: 0.7928 (tptp) REVERT: K 56 ASP cc_start: 0.9099 (m-30) cc_final: 0.8797 (m-30) REVERT: K 60 MET cc_start: 0.9205 (tmm) cc_final: 0.8761 (tmm) REVERT: K 61 ILE cc_start: 0.9190 (mt) cc_final: 0.8760 (mt) REVERT: K 128 ARG cc_start: 0.9527 (ttm110) cc_final: 0.9214 (ptp-110) REVERT: K 160 LEU cc_start: 0.9428 (mm) cc_final: 0.9162 (mt) REVERT: K 202 GLU cc_start: 0.8634 (mt-10) cc_final: 0.8207 (mt-10) REVERT: K 270 VAL cc_start: 0.8499 (OUTLIER) cc_final: 0.8271 (t) REVERT: K 273 LYS cc_start: 0.9506 (tppt) cc_final: 0.8899 (mttm) REVERT: K 274 GLU cc_start: 0.8587 (mp0) cc_final: 0.8081 (mp0) REVERT: K 314 TYR cc_start: 0.8650 (m-80) cc_final: 0.8150 (m-80) REVERT: K 330 PHE cc_start: 0.9113 (m-80) cc_final: 0.8451 (m-80) REVERT: K 336 MET cc_start: 0.8872 (mmm) cc_final: 0.8416 (mmm) REVERT: K 369 ILE cc_start: 0.9363 (mt) cc_final: 0.8929 (mm) REVERT: K 386 VAL cc_start: 0.9101 (m) cc_final: 0.8857 (m) REVERT: K 406 SER cc_start: 0.9190 (m) cc_final: 0.8947 (p) REVERT: K 438 MET cc_start: 0.8764 (mmt) cc_final: 0.8391 (mmt) REVERT: K 474 ARG cc_start: 0.2912 (mtt180) cc_final: 0.2267 (mtt180) REVERT: K 481 LEU cc_start: 0.8585 (tp) cc_final: 0.8270 (tp) REVERT: K 520 ASP cc_start: 0.7993 (m-30) cc_final: 0.7692 (m-30) REVERT: K 527 LYS cc_start: 0.9022 (mmmt) cc_final: 0.8792 (mmtt) REVERT: K 619 TYR cc_start: 0.8813 (p90) cc_final: 0.8551 (p90) REVERT: K 625 ILE cc_start: 0.9444 (mt) cc_final: 0.9123 (mm) REVERT: K 627 LEU cc_start: 0.9555 (mt) cc_final: 0.9340 (tp) REVERT: K 667 GLN cc_start: 0.9127 (pm20) cc_final: 0.8796 (pm20) REVERT: K 677 MET cc_start: 0.8908 (ttp) cc_final: 0.8516 (ttp) REVERT: M 16 MET cc_start: 0.8650 (mmt) cc_final: 0.8239 (mmp) REVERT: M 40 LEU cc_start: 0.9499 (mm) cc_final: 0.9265 (mt) REVERT: M 144 GLN cc_start: 0.8700 (mm-40) cc_final: 0.8340 (mm110) REVERT: M 231 LYS cc_start: 0.9247 (mmtt) cc_final: 0.9044 (mmtp) REVERT: M 242 ASP cc_start: 0.8872 (t70) cc_final: 0.8659 (t0) outliers start: 81 outliers final: 27 residues processed: 696 average time/residue: 0.1899 time to fit residues: 212.3961 Evaluate side-chains 571 residues out of total 3097 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 536 time to evaluate : 1.122 ------------------------------------------------------------------------------- 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 D residue 29 ILE 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 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 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 H residue 168 VAL Chi-restraints excluded: chain H residue 193 ILE Chi-restraints excluded: chain I residue 152 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 173 TYR 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 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: 6.9990 chunk 120 optimal weight: 8.9990 chunk 72 optimal weight: 20.0000 chunk 243 optimal weight: 9.9990 chunk 331 optimal weight: 1.9990 chunk 270 optimal weight: 8.9990 chunk 116 optimal weight: 10.0000 chunk 259 optimal weight: 0.8980 chunk 56 optimal weight: 2.9990 chunk 340 optimal weight: 7.9990 chunk 134 optimal weight: 10.0000 overall best weight: 4.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 101 ASN ** D 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 134 ASN E 134 ASN ** J 10 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 9 ASN N 59 ASN ** H 204 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 80 HIS K 100 ASN K 155 GLN K 734 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3277 r_free = 0.3277 target = 0.051415 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3047 r_free = 0.3047 target = 0.043092 restraints weight = 146476.309| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3095 r_free = 0.3095 target = 0.044795 restraints weight = 75465.612| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3127 r_free = 0.3127 target = 0.045971 restraints weight = 47356.896| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3150 r_free = 0.3150 target = 0.046789 restraints weight = 33279.554| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.3166 r_free = 0.3166 target = 0.047371 restraints weight = 25289.769| |-----------------------------------------------------------------------------| r_work (final): 0.3154 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8535 moved from start: 0.2960 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.080 29252 Z= 0.274 Angle : 0.703 9.365 39623 Z= 0.369 Chirality : 0.045 0.230 4524 Planarity : 0.004 0.057 4852 Dihedral : 11.514 179.522 4391 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 17.54 Ramachandran Plot: Outliers : 0.12 % Allowed : 6.60 % Favored : 93.29 % Rotamer: Outliers : 4.05 % Allowed : 18.48 % Favored : 77.48 % 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: -0.01 (0.14), residues: 3441 helix: 1.68 (0.14), residues: 1474 sheet: -0.13 (0.24), residues: 454 loop : -1.74 (0.15), residues: 1513 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG J 47 TYR 0.030 0.002 TYR L 104 PHE 0.038 0.002 PHE E 56 TRP 0.012 0.001 TRP K 749 HIS 0.006 0.001 HIS L 70 Details of bonding type rmsd/Z covalent geometry : bond 0.00573 / 0.27 (29237) covalent geometry : angle 0.70130 / 0.37 (39593) SS BOND : bond 0.00530 / 0.34 ( 15) SS BOND : angle 1.93825 / 1.17 ( 30) hydrogen bonds : bond 0.04104 / 2.73 ( 1274) hydrogen bonds : angle 5.33958 / 3.82 ( 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 659 residues out of total 3097 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 125 poor density : 534 time to evaluate : 1.220 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: 0.8728 (m-30) cc_final: 0.8254 (t0) REVERT: A 29 ILE cc_start: 0.9399 (tp) cc_final: 0.9068 (tt) REVERT: A 42 GLU cc_start: 0.8196 (mm-30) cc_final: 0.7887 (mm-30) REVERT: A 56 PHE cc_start: 0.8995 (t80) cc_final: 0.8592 (t80) REVERT: A 60 ARG cc_start: 0.9279 (mmp80) cc_final: 0.8878 (mmm160) REVERT: A 79 ILE cc_start: 0.9002 (mm) cc_final: 0.8720 (mp) REVERT: A 110 TYR cc_start: 0.9046 (t80) cc_final: 0.8784 (t80) REVERT: A 111 ASP cc_start: 0.8980 (t0) cc_final: 0.8661 (t0) REVERT: A 126 VAL cc_start: 0.9335 (t) cc_final: 0.9112 (p) REVERT: A 131 GLU cc_start: 0.9428 (mt-10) cc_final: 0.8904 (mt-10) REVERT: B 22 ASP cc_start: 0.8897 (m-30) cc_final: 0.7912 (m-30) REVERT: B 26 ARG cc_start: 0.9099 (ptp-110) cc_final: 0.8354 (ptp90) REVERT: B 61 ARG cc_start: 0.9075 (mtp85) cc_final: 0.8872 (mtp85) REVERT: B 78 GLU cc_start: 0.9185 (mm-30) cc_final: 0.8666 (mm-30) REVERT: B 90 SER cc_start: 0.9633 (m) cc_final: 0.9237 (p) REVERT: B 131 GLU cc_start: 0.9099 (mt-10) cc_final: 0.8767 (mt-10) REVERT: B 134 ASN cc_start: 0.9231 (m-40) cc_final: 0.8901 (m110) REVERT: C 22 ASP cc_start: 0.9121 (m-30) cc_final: 0.8798 (m-30) REVERT: C 45 VAL cc_start: 0.9575 (t) cc_final: 0.9319 (p) REVERT: C 77 ASP cc_start: 0.9175 (t0) cc_final: 0.8889 (t0) REVERT: C 134 ASN cc_start: 0.9717 (m-40) cc_final: 0.9428 (m110) REVERT: D 37 LYS cc_start: 0.9309 (tptt) cc_final: 0.9083 (tptp) REVERT: D 44 TYR cc_start: 0.9274 (t80) cc_final: 0.8825 (t80) REVERT: D 58 GLN cc_start: 0.9486 (mp10) cc_final: 0.9168 (mm-40) REVERT: D 82 GLU cc_start: 0.9517 (tt0) cc_final: 0.9300 (tm-30) REVERT: D 90 SER cc_start: 0.9474 (m) cc_final: 0.9261 (p) REVERT: D 95 GLU cc_start: 0.8491 (tp30) cc_final: 0.8200 (tm-30) REVERT: D 134 ASN cc_start: 0.9154 (m-40) cc_final: 0.8679 (m110) REVERT: E 42 GLU cc_start: 0.8623 (pt0) cc_final: 0.8332 (pm20) REVERT: E 48 SER cc_start: 0.9768 (m) cc_final: 0.9538 (p) REVERT: E 56 PHE cc_start: 0.9504 (t80) cc_final: 0.9270 (t80) REVERT: E 76 ARG cc_start: 0.9470 (mmm-85) cc_final: 0.9186 (mmm-85) REVERT: E 82 GLU cc_start: 0.9334 (tm-30) cc_final: 0.8986 (tm-30) REVERT: E 101 ASN cc_start: 0.9514 (m110) cc_final: 0.9074 (m110) REVERT: E 105 TYR cc_start: 0.9316 (m-10) cc_final: 0.8775 (m-80) REVERT: E 114 THR cc_start: 0.9515 (m) cc_final: 0.9258 (p) REVERT: E 131 GLU cc_start: 0.9035 (tp30) cc_final: 0.8716 (tm-30) REVERT: E 135 ILE cc_start: 0.9601 (mm) cc_final: 0.9264 (mm) REVERT: J 146 PHE cc_start: 0.9183 (m-80) cc_final: 0.8838 (m-80) REVERT: J 159 MET cc_start: 0.8951 (tpp) cc_final: 0.8681 (tpp) REVERT: J 166 SER cc_start: 0.9112 (m) cc_final: 0.8607 (t) REVERT: J 229 MET cc_start: 0.8619 (mtp) cc_final: 0.8202 (mtp) REVERT: L 40 LYS cc_start: 0.9405 (tttt) cc_final: 0.9098 (tttp) REVERT: L 113 LYS cc_start: 0.9464 (ttmm) cc_final: 0.9258 (tppp) REVERT: L 115 GLN cc_start: 0.9094 (mm110) cc_final: 0.8670 (mm-40) REVERT: L 118 LYS cc_start: 0.9581 (tppp) cc_final: 0.9264 (tppt) REVERT: N 49 MET cc_start: 0.9620 (tmm) cc_final: 0.9282 (tmm) REVERT: N 137 TYR cc_start: 0.7923 (OUTLIER) cc_final: 0.7538 (p90) REVERT: N 249 ARG cc_start: 0.9273 (mtp-110) cc_final: 0.8966 (ptm-80) REVERT: G 40 ASP cc_start: 0.9049 (m-30) cc_final: 0.8810 (p0) REVERT: G 66 GLU cc_start: 0.9291 (mt-10) cc_final: 0.8960 (mt-10) REVERT: G 168 MET cc_start: 0.8841 (ttp) cc_final: 0.8639 (ttm) REVERT: F 33 GLN cc_start: 0.9283 (mp10) cc_final: 0.8915 (mp10) REVERT: F 73 ASN cc_start: 0.9526 (t0) cc_final: 0.9274 (t0) REVERT: F 137 MET cc_start: 0.8524 (ptp) cc_final: 0.8167 (ptp) REVERT: F 166 PHE cc_start: 0.9072 (t80) cc_final: 0.8833 (t80) REVERT: F 207 ARG cc_start: 0.7666 (OUTLIER) cc_final: 0.7346 (mtp85) REVERT: F 212 TYR cc_start: 0.7479 (m-10) cc_final: 0.7255 (m-10) REVERT: H 145 TYR cc_start: 0.8461 (p90) cc_final: 0.8030 (p90) REVERT: H 174 ASP cc_start: 0.8700 (t0) cc_final: 0.8287 (t70) REVERT: H 255 ASP cc_start: 0.9149 (m-30) cc_final: 0.8671 (p0) REVERT: H 265 MET cc_start: 0.9520 (mtp) cc_final: 0.9200 (mtt) REVERT: I 17 MET cc_start: 0.8603 (tpp) cc_final: 0.8239 (tpp) REVERT: I 80 GLU cc_start: 0.8993 (tt0) cc_final: 0.8788 (tt0) REVERT: I 99 ASP cc_start: 0.9516 (m-30) cc_final: 0.9208 (p0) REVERT: I 110 GLN cc_start: 0.9623 (tp40) cc_final: 0.9289 (tp-100) REVERT: I 118 TYR cc_start: 0.9082 (m-10) cc_final: 0.8274 (m-10) REVERT: I 129 MET cc_start: 0.9377 (mmp) cc_final: 0.9155 (mmm) REVERT: I 182 LYS cc_start: 0.8931 (OUTLIER) cc_final: 0.8075 (tptp) REVERT: I 265 MET cc_start: 0.9634 (mtm) cc_final: 0.9038 (mtm) REVERT: K 30 ASP cc_start: 0.8494 (m-30) cc_final: 0.8274 (m-30) REVERT: K 56 ASP cc_start: 0.9190 (m-30) cc_final: 0.8866 (m-30) REVERT: K 60 MET cc_start: 0.9279 (tmm) cc_final: 0.8834 (tmm) REVERT: K 61 ILE cc_start: 0.9216 (mt) cc_final: 0.8826 (mt) REVERT: K 81 GLU cc_start: 0.8909 (mt-10) cc_final: 0.8557 (mt-10) REVERT: K 111 GLU cc_start: 0.9442 (OUTLIER) cc_final: 0.8974 (pt0) REVERT: K 160 LEU cc_start: 0.9446 (mm) cc_final: 0.9232 (mt) REVERT: K 201 ASP cc_start: 0.9195 (t0) cc_final: 0.8655 (t0) REVERT: K 202 GLU cc_start: 0.8578 (mt-10) cc_final: 0.8247 (mt-10) REVERT: K 205 GLU cc_start: 0.8473 (mm-30) cc_final: 0.8243 (mm-30) REVERT: K 220 LEU cc_start: 0.9384 (OUTLIER) cc_final: 0.9095 (pp) REVERT: K 238 LEU cc_start: 0.9056 (mt) cc_final: 0.8647 (pp) REVERT: K 273 LYS cc_start: 0.9444 (tppt) cc_final: 0.8897 (mttm) REVERT: K 274 GLU cc_start: 0.8777 (mp0) cc_final: 0.8138 (mp0) REVERT: K 336 MET cc_start: 0.8864 (mmm) cc_final: 0.8604 (mmm) REVERT: K 369 ILE cc_start: 0.9466 (mt) cc_final: 0.9047 (mm) REVERT: K 406 SER cc_start: 0.9230 (m) cc_final: 0.8975 (p) REVERT: K 438 MET cc_start: 0.8776 (mmt) cc_final: 0.8407 (mmt) REVERT: K 447 LEU cc_start: 0.8404 (OUTLIER) cc_final: 0.7591 (mm) REVERT: K 461 ARG cc_start: 0.5473 (OUTLIER) cc_final: 0.4917 (mmm160) REVERT: K 474 ARG cc_start: 0.2989 (mtt180) cc_final: 0.2555 (mtt180) REVERT: K 481 LEU cc_start: 0.8627 (tp) cc_final: 0.8285 (tp) REVERT: K 502 LYS cc_start: 0.9425 (mtpt) cc_final: 0.9106 (mtmm) REVERT: K 520 ASP cc_start: 0.8142 (m-30) cc_final: 0.7833 (m-30) REVERT: K 527 LYS cc_start: 0.8958 (mmmt) cc_final: 0.8737 (mmtt) REVERT: K 538 ILE cc_start: 0.9337 (tp) cc_final: 0.9118 (tp) REVERT: K 588 MET cc_start: 0.9210 (mtm) cc_final: 0.8762 (mtp) REVERT: K 625 ILE cc_start: 0.9420 (mt) cc_final: 0.9075 (mm) REVERT: K 677 MET cc_start: 0.8919 (ttp) cc_final: 0.8461 (ttp) REVERT: K 745 MET cc_start: 0.8985 (mpp) cc_final: 0.8752 (mpp) REVERT: M 5 LYS cc_start: 0.9474 (ttmm) cc_final: 0.9152 (ptmm) REVERT: M 16 MET cc_start: 0.8667 (mmt) cc_final: 0.8322 (mmp) REVERT: M 62 ILE cc_start: 0.9640 (OUTLIER) cc_final: 0.9351 (mm) REVERT: M 167 LYS cc_start: 0.9412 (mmmt) cc_final: 0.9211 (mmtp) REVERT: M 169 PHE cc_start: 0.9114 (m-10) cc_final: 0.8816 (m-80) REVERT: M 170 ASP cc_start: 0.9037 (t0) cc_final: 0.8679 (t0) REVERT: M 262 PHE cc_start: 0.5499 (m-80) cc_final: 0.5259 (m-80) REVERT: M 290 MET cc_start: 0.9094 (pmm) cc_final: 0.8801 (pmm) outliers start: 125 outliers final: 64 residues processed: 629 average time/residue: 0.1825 time to fit residues: 185.0108 Evaluate side-chains 558 residues out of total 3097 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 486 time to evaluate : 1.073 ------------------------------------------------------------------------------- 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 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 29 ILE 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 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 27 ASN Chi-restraints excluded: chain N residue 56 ILE Chi-restraints excluded: chain N residue 137 TYR Chi-restraints excluded: chain N residue 187 VAL 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 157 TYR Chi-restraints excluded: chain F residue 207 ARG Chi-restraints excluded: chain F residue 232 VAL Chi-restraints excluded: chain H residue 16 THR Chi-restraints excluded: chain H residue 123 CYS 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 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 20 GLU 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 447 LEU Chi-restraints excluded: chain K residue 460 HIS Chi-restraints excluded: chain K residue 461 ARG 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 794 ASN 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: 1.9990 chunk 209 optimal weight: 9.9990 chunk 13 optimal weight: 5.9990 chunk 311 optimal weight: 1.9990 chunk 204 optimal weight: 7.9990 chunk 278 optimal weight: 0.8980 chunk 69 optimal weight: 8.9990 chunk 328 optimal weight: 10.0000 chunk 44 optimal weight: 1.9990 chunk 197 optimal weight: 6.9990 chunk 290 optimal weight: 2.9990 overall best weight: 1.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 73 GLN ** D 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 51 ASN ** E 134 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 10 ASN ** L 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 59 ASN G 134 GLN G 141 ASN ** H 204 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 223 GLN ** 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 = 0.3312 r_free = 0.3312 target = 0.052492 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3086 r_free = 0.3086 target = 0.044113 restraints weight = 143040.411| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3133 r_free = 0.3133 target = 0.045843 restraints weight = 72981.802| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3166 r_free = 0.3166 target = 0.047042 restraints weight = 45543.228| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3189 r_free = 0.3189 target = 0.047885 restraints weight = 31843.297| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3205 r_free = 0.3205 target = 0.048473 restraints weight = 24035.290| |-----------------------------------------------------------------------------| r_work (final): 0.3186 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8499 moved from start: 0.3182 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 29252 Z= 0.163 Angle : 0.647 10.720 39623 Z= 0.334 Chirality : 0.044 0.291 4524 Planarity : 0.004 0.058 4852 Dihedral : 11.507 179.975 4391 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 14.40 Ramachandran Plot: Outliers : 0.12 % Allowed : 5.73 % Favored : 94.16 % Rotamer: Outliers : 3.20 % Allowed : 20.03 % Favored : 76.76 % 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: 0.08 (0.15), residues: 3441 helix: 1.78 (0.14), residues: 1466 sheet: -0.19 (0.23), residues: 468 loop : -1.69 (0.15), residues: 1507 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG H 98 TYR 0.023 0.002 TYR N 222 PHE 0.027 0.001 PHE E 56 TRP 0.009 0.001 TRP K 749 HIS 0.004 0.001 HIS M 146 Details of bonding type rmsd/Z covalent geometry : bond 0.00355 / 0.16 (29237) covalent geometry : angle 0.64380 / 0.33 (39593) SS BOND : bond 0.00411 / 0.24 ( 15) SS BOND : angle 2.46422 / 1.90 ( 30) hydrogen bonds : bond 0.03801 / 2.54 ( 1274) hydrogen bonds : angle 5.11018 / 3.65 ( 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 636 residues out of total 3097 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 99 poor density : 537 time to evaluate : 1.208 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: A 22 ASP cc_start: 0.8679 (m-30) cc_final: 0.8202 (t0) REVERT: A 29 ILE cc_start: 0.9382 (OUTLIER) cc_final: 0.9000 (tt) REVERT: A 42 GLU cc_start: 0.8189 (mm-30) cc_final: 0.7874 (mm-30) REVERT: A 56 PHE cc_start: 0.8958 (t80) cc_final: 0.8558 (t80) REVERT: A 60 ARG cc_start: 0.9287 (mmp80) cc_final: 0.8881 (mmm160) REVERT: A 69 TYR cc_start: 0.9193 (t80) cc_final: 0.8945 (t80) REVERT: A 79 ILE cc_start: 0.8994 (mm) cc_final: 0.8703 (mp) REVERT: A 110 TYR cc_start: 0.9062 (t80) cc_final: 0.8791 (t80) REVERT: A 111 ASP cc_start: 0.8962 (t0) cc_final: 0.8617 (t0) REVERT: A 121 ASN cc_start: 0.9344 (m-40) cc_final: 0.9069 (p0) REVERT: A 126 VAL cc_start: 0.9279 (t) cc_final: 0.9056 (p) REVERT: A 131 GLU cc_start: 0.9418 (mt-10) cc_final: 0.8878 (mt-10) REVERT: B 22 ASP cc_start: 0.8952 (m-30) cc_final: 0.8104 (m-30) REVERT: B 26 ARG cc_start: 0.9083 (ptp-110) cc_final: 0.8378 (ptp90) REVERT: B 73 GLN cc_start: 0.9259 (tp40) cc_final: 0.9040 (tp-100) REVERT: B 78 GLU cc_start: 0.9136 (mm-30) cc_final: 0.8591 (tp30) REVERT: B 90 SER cc_start: 0.9622 (m) cc_final: 0.9231 (p) REVERT: B 129 PHE cc_start: 0.9152 (t80) cc_final: 0.8798 (t80) REVERT: B 134 ASN cc_start: 0.9217 (m-40) cc_final: 0.8871 (m110) REVERT: C 22 ASP cc_start: 0.9099 (m-30) cc_final: 0.8694 (m-30) REVERT: C 45 VAL cc_start: 0.9556 (t) cc_final: 0.9299 (p) REVERT: C 71 MET cc_start: 0.9421 (mtm) cc_final: 0.9091 (mtm) REVERT: C 77 ASP cc_start: 0.9172 (t0) cc_final: 0.8856 (t0) REVERT: C 103 LEU cc_start: 0.9633 (OUTLIER) cc_final: 0.9356 (tp) REVERT: C 134 ASN cc_start: 0.9703 (m-40) cc_final: 0.9413 (m110) REVERT: D 32 ILE cc_start: 0.9069 (tp) cc_final: 0.8859 (tp) REVERT: D 44 TYR cc_start: 0.9195 (t80) cc_final: 0.8768 (t80) REVERT: D 58 GLN cc_start: 0.9482 (mp10) cc_final: 0.9163 (mm-40) REVERT: D 66 LEU cc_start: 0.9687 (tt) cc_final: 0.9333 (mm) REVERT: D 82 GLU cc_start: 0.9482 (tt0) cc_final: 0.9039 (tp30) REVERT: D 90 SER cc_start: 0.9502 (m) cc_final: 0.9290 (p) REVERT: D 101 ASN cc_start: 0.9578 (m110) cc_final: 0.9338 (m-40) REVERT: E 42 GLU cc_start: 0.8641 (pt0) cc_final: 0.8380 (pm20) REVERT: E 48 SER cc_start: 0.9765 (m) cc_final: 0.9553 (p) REVERT: E 55 SER cc_start: 0.9763 (m) cc_final: 0.9506 (p) REVERT: E 56 PHE cc_start: 0.9496 (t80) cc_final: 0.9245 (t80) REVERT: E 71 MET cc_start: 0.9362 (mtp) cc_final: 0.9142 (ptp) REVERT: E 82 GLU cc_start: 0.9343 (tm-30) cc_final: 0.8981 (tm-30) REVERT: E 101 ASN cc_start: 0.9531 (m110) cc_final: 0.9068 (m110) REVERT: E 105 TYR cc_start: 0.9298 (m-10) cc_final: 0.8708 (m-80) REVERT: E 114 THR cc_start: 0.9491 (m) cc_final: 0.9226 (p) REVERT: E 131 GLU cc_start: 0.8991 (tp30) cc_final: 0.8600 (tm-30) REVERT: E 135 ILE cc_start: 0.9595 (mm) cc_final: 0.9223 (mm) REVERT: J 146 PHE cc_start: 0.9200 (m-80) cc_final: 0.8867 (m-80) REVERT: J 159 MET cc_start: 0.8874 (tpp) cc_final: 0.8584 (tpp) REVERT: J 209 GLU cc_start: 0.9385 (mm-30) cc_final: 0.8448 (mp0) REVERT: J 229 MET cc_start: 0.8630 (mtp) cc_final: 0.8194 (mtp) REVERT: L 83 TYR cc_start: 0.7831 (m-80) cc_final: 0.7587 (m-10) REVERT: L 113 LYS cc_start: 0.9456 (ttmm) cc_final: 0.9174 (tppt) REVERT: L 115 GLN cc_start: 0.9043 (mm110) cc_final: 0.8758 (mm110) REVERT: L 118 LYS cc_start: 0.9590 (tppp) cc_final: 0.9257 (tppt) REVERT: N 49 MET cc_start: 0.9604 (tmm) cc_final: 0.9287 (tmm) REVERT: N 137 TYR cc_start: 0.7784 (OUTLIER) cc_final: 0.7281 (p90) REVERT: N 155 MET cc_start: 0.8856 (pmm) cc_final: 0.8597 (pmm) REVERT: N 249 ARG cc_start: 0.9280 (mtp-110) cc_final: 0.8995 (ptm-80) REVERT: G 40 ASP cc_start: 0.9032 (m-30) cc_final: 0.8815 (p0) REVERT: G 66 GLU cc_start: 0.9258 (mt-10) cc_final: 0.8936 (mt-10) REVERT: G 188 GLU cc_start: 0.9318 (mm-30) cc_final: 0.8811 (mp0) REVERT: F 33 GLN cc_start: 0.9321 (mp10) cc_final: 0.8992 (mp10) REVERT: F 73 ASN cc_start: 0.9516 (t0) cc_final: 0.9269 (t0) REVERT: F 137 MET cc_start: 0.8416 (ptp) cc_final: 0.8064 (ptp) REVERT: F 167 MET cc_start: 0.8928 (tpp) cc_final: 0.8696 (tpp) REVERT: F 207 ARG cc_start: 0.7597 (OUTLIER) cc_final: 0.7268 (mtp85) REVERT: F 239 LYS cc_start: 0.9524 (mmtm) cc_final: 0.9279 (mmmm) REVERT: H 19 GLU cc_start: 0.8536 (tm-30) cc_final: 0.8169 (tm-30) REVERT: H 145 TYR cc_start: 0.8444 (p90) cc_final: 0.7979 (p90) REVERT: H 174 ASP cc_start: 0.8709 (t0) cc_final: 0.8285 (t70) REVERT: H 193 ILE cc_start: 0.9336 (OUTLIER) cc_final: 0.9113 (pt) REVERT: H 200 MET cc_start: 0.9335 (tpp) cc_final: 0.8964 (mmm) REVERT: H 255 ASP cc_start: 0.9146 (m-30) cc_final: 0.8680 (p0) REVERT: I 99 ASP cc_start: 0.9501 (m-30) cc_final: 0.9166 (p0) REVERT: I 110 GLN cc_start: 0.9620 (tp40) cc_final: 0.9325 (tp40) REVERT: I 129 MET cc_start: 0.9333 (mmp) cc_final: 0.9098 (mmm) REVERT: I 200 MET cc_start: 0.9178 (ttm) cc_final: 0.8938 (ttp) REVERT: I 265 MET cc_start: 0.9623 (mtm) cc_final: 0.8995 (mtm) REVERT: K 56 ASP cc_start: 0.9132 (m-30) cc_final: 0.8811 (m-30) REVERT: K 60 MET cc_start: 0.9281 (tmm) cc_final: 0.8835 (tmm) REVERT: K 61 ILE cc_start: 0.9201 (mt) cc_final: 0.8837 (mt) REVERT: K 81 GLU cc_start: 0.8963 (mt-10) cc_final: 0.8570 (mt-10) REVERT: K 148 THR cc_start: 0.9212 (OUTLIER) cc_final: 0.8750 (t) REVERT: K 201 ASP cc_start: 0.9189 (t0) cc_final: 0.8632 (t0) REVERT: K 202 GLU cc_start: 0.8560 (mt-10) cc_final: 0.8170 (mt-10) REVERT: K 205 GLU cc_start: 0.8482 (mm-30) cc_final: 0.8224 (mm-30) REVERT: K 220 LEU cc_start: 0.9474 (OUTLIER) cc_final: 0.9227 (pp) REVERT: K 238 LEU cc_start: 0.9029 (mt) cc_final: 0.8735 (pp) REVERT: K 273 LYS cc_start: 0.9436 (tppt) cc_final: 0.8882 (mttm) REVERT: K 293 ARG cc_start: 0.8548 (OUTLIER) cc_final: 0.8346 (tmm-80) REVERT: K 336 MET cc_start: 0.8878 (mmm) cc_final: 0.8520 (mmm) REVERT: K 369 ILE cc_start: 0.9423 (mt) cc_final: 0.8978 (mm) REVERT: K 406 SER cc_start: 0.9225 (m) cc_final: 0.8975 (p) REVERT: K 438 MET cc_start: 0.8851 (mmt) cc_final: 0.8428 (mmt) REVERT: K 474 ARG cc_start: 0.2930 (mtt180) cc_final: 0.2294 (mtt180) REVERT: K 481 LEU cc_start: 0.8691 (tp) cc_final: 0.8362 (tp) REVERT: K 502 LYS cc_start: 0.9361 (mtpt) cc_final: 0.9049 (mtmm) REVERT: K 527 LYS cc_start: 0.8960 (mmmt) cc_final: 0.8749 (mmtt) REVERT: K 538 ILE cc_start: 0.9324 (tp) cc_final: 0.9071 (tp) REVERT: K 587 LYS cc_start: 0.9215 (mmtm) cc_final: 0.8718 (tppt) REVERT: K 588 MET cc_start: 0.9290 (mtm) cc_final: 0.8772 (mtp) REVERT: K 619 TYR cc_start: 0.8925 (p90) cc_final: 0.8615 (p90) REVERT: K 625 ILE cc_start: 0.9398 (mt) cc_final: 0.9131 (mm) REVERT: K 627 LEU cc_start: 0.9529 (mt) cc_final: 0.9310 (mm) REVERT: K 677 MET cc_start: 0.8933 (ttp) cc_final: 0.8664 (ttp) REVERT: K 727 ASP cc_start: 0.9476 (m-30) cc_final: 0.8838 (t0) REVERT: K 745 MET cc_start: 0.8991 (mpp) cc_final: 0.8703 (mtm) REVERT: M 5 LYS cc_start: 0.9490 (ttmm) cc_final: 0.9283 (ttpp) REVERT: M 16 MET cc_start: 0.8709 (mmt) cc_final: 0.8334 (mmp) REVERT: M 40 LEU cc_start: 0.9526 (mm) cc_final: 0.9312 (mt) REVERT: M 62 ILE cc_start: 0.9645 (OUTLIER) cc_final: 0.9382 (mm) REVERT: M 167 LYS cc_start: 0.9389 (mmmt) cc_final: 0.9175 (mmtp) REVERT: M 169 PHE cc_start: 0.9106 (m-10) cc_final: 0.8757 (m-80) REVERT: M 242 ASP cc_start: 0.8762 (t70) cc_final: 0.8531 (t70) REVERT: M 282 LEU cc_start: 0.9534 (mm) cc_final: 0.9237 (tt) REVERT: M 290 MET cc_start: 0.8948 (pmm) cc_final: 0.8692 (pmm) outliers start: 99 outliers final: 56 residues processed: 607 average time/residue: 0.1797 time to fit residues: 177.3797 Evaluate side-chains 550 residues out of total 3097 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 485 time to evaluate : 1.098 ------------------------------------------------------------------------------- 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 122 ASN Chi-restraints excluded: chain C residue 37 LYS Chi-restraints excluded: chain C residue 103 LEU Chi-restraints excluded: chain D residue 29 ILE 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 208 VAL Chi-restraints excluded: chain J residue 239 LYS 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 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 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 11 VAL Chi-restraints excluded: chain H residue 16 THR Chi-restraints excluded: chain H residue 90 CYS Chi-restraints excluded: chain H residue 193 ILE Chi-restraints excluded: chain I residue 152 MET Chi-restraints excluded: chain I residue 175 VAL Chi-restraints excluded: chain I residue 182 LYS 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 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 173 TYR Chi-restraints excluded: chain K residue 177 SER Chi-restraints excluded: chain K residue 220 LEU Chi-restraints excluded: chain K residue 230 THR Chi-restraints excluded: chain K residue 293 ARG 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 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: 6.9990 chunk 159 optimal weight: 5.9990 chunk 143 optimal weight: 0.9990 chunk 319 optimal weight: 0.0870 chunk 227 optimal weight: 0.8980 chunk 125 optimal weight: 6.9990 chunk 25 optimal weight: 8.9990 chunk 148 optimal weight: 10.0000 chunk 10 optimal weight: 0.5980 chunk 74 optimal weight: 9.9990 chunk 126 optimal weight: 2.9990 overall best weight: 1.1162 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** D 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 134 ASN ** E 134 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 134 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: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.053270 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3105 r_free = 0.3105 target = 0.044862 restraints weight = 142783.724| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3153 r_free = 0.3153 target = 0.046624 restraints weight = 73287.230| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3185 r_free = 0.3185 target = 0.047833 restraints weight = 45719.880| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3206 r_free = 0.3206 target = 0.048653 restraints weight = 31955.069| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3223 r_free = 0.3223 target = 0.049269 restraints weight = 24281.016| |-----------------------------------------------------------------------------| r_work (final): 0.3205 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8479 moved from start: 0.3405 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= 0.133 Angle : 0.627 9.919 39623 Z= 0.324 Chirality : 0.043 0.201 4524 Planarity : 0.004 0.059 4852 Dihedral : 11.514 179.750 4391 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 13.62 Ramachandran Plot: Outliers : 0.12 % Allowed : 5.73 % Favored : 94.16 % Rotamer: Outliers : 3.17 % Allowed : 21.00 % Favored : 75.83 % 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 (0.14), residues: 3441 helix: 1.70 (0.14), residues: 1462 sheet: -0.05 (0.23), residues: 463 loop : -1.65 (0.15), residues: 1516 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG E 76 TYR 0.024 0.001 TYR K 62 PHE 0.030 0.001 PHE F 166 TRP 0.009 0.001 TRP M 173 HIS 0.002 0.001 HIS L 70 Details of bonding type rmsd/Z covalent geometry : bond 0.00295 / 0.13 (29237) covalent geometry : angle 0.62518 / 0.32 (39593) SS BOND : bond 0.00465 / 0.32 ( 15) SS BOND : angle 1.94908 / 1.35 ( 30) hydrogen bonds : bond 0.03650 / 2.45 ( 1274) hydrogen bonds : angle 4.94604 / 3.53 ( 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 627 residues out of total 3097 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 529 time to evaluate : 1.086 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: 0.8691 (m-30) cc_final: 0.8216 (t0) REVERT: A 29 ILE cc_start: 0.9333 (OUTLIER) cc_final: 0.8910 (tt) REVERT: A 42 GLU cc_start: 0.8304 (mm-30) cc_final: 0.8072 (mm-30) REVERT: A 56 PHE cc_start: 0.8940 (t80) cc_final: 0.8569 (t80) REVERT: A 60 ARG cc_start: 0.9279 (mmp80) cc_final: 0.8876 (mmm160) REVERT: A 69 TYR cc_start: 0.9178 (t80) cc_final: 0.8974 (t80) REVERT: A 79 ILE cc_start: 0.8970 (mm) cc_final: 0.8675 (mp) REVERT: A 110 TYR cc_start: 0.9052 (t80) cc_final: 0.8787 (t80) REVERT: A 111 ASP cc_start: 0.8968 (t0) cc_final: 0.8629 (t0) REVERT: A 131 GLU cc_start: 0.9388 (mt-10) cc_final: 0.8936 (mt-10) REVERT: B 22 ASP cc_start: 0.8926 (m-30) cc_final: 0.8137 (m-30) REVERT: B 26 ARG cc_start: 0.9099 (ptp-110) cc_final: 0.8392 (ptp90) REVERT: B 44 TYR cc_start: 0.9274 (t80) cc_final: 0.8870 (t80) REVERT: B 78 GLU cc_start: 0.9043 (mm-30) cc_final: 0.8510 (mm-30) REVERT: B 90 SER cc_start: 0.9652 (m) cc_final: 0.9264 (p) REVERT: B 129 PHE cc_start: 0.8988 (t80) cc_final: 0.8633 (t80) REVERT: B 134 ASN cc_start: 0.9205 (m-40) cc_final: 0.8827 (m110) REVERT: C 22 ASP cc_start: 0.9080 (m-30) cc_final: 0.8672 (m-30) REVERT: C 45 VAL cc_start: 0.9527 (t) cc_final: 0.9278 (p) REVERT: C 71 MET cc_start: 0.9404 (mtm) cc_final: 0.9100 (mtm) REVERT: C 77 ASP cc_start: 0.9220 (t0) cc_final: 0.8927 (t0) REVERT: C 134 ASN cc_start: 0.9701 (m-40) cc_final: 0.9392 (m110) REVERT: D 22 ASP cc_start: 0.8926 (m-30) cc_final: 0.8370 (t0) REVERT: D 26 ARG cc_start: 0.9534 (mtm-85) cc_final: 0.9248 (ptp90) REVERT: D 29 ILE cc_start: 0.8907 (OUTLIER) cc_final: 0.8547 (tp) REVERT: D 32 ILE cc_start: 0.9108 (tp) cc_final: 0.8869 (tp) REVERT: D 44 TYR cc_start: 0.9190 (t80) cc_final: 0.8737 (t80) REVERT: D 58 GLN cc_start: 0.9491 (mp10) cc_final: 0.9150 (mm-40) REVERT: D 66 LEU cc_start: 0.9700 (tt) cc_final: 0.9376 (mm) REVERT: D 82 GLU cc_start: 0.9478 (tt0) cc_final: 0.9024 (tp30) REVERT: D 101 ASN cc_start: 0.9572 (m110) cc_final: 0.9312 (m-40) REVERT: D 134 ASN cc_start: 0.9106 (m-40) cc_final: 0.8560 (m110) REVERT: E 48 SER cc_start: 0.9751 (m) cc_final: 0.9527 (p) REVERT: E 55 SER cc_start: 0.9754 (m) cc_final: 0.9493 (p) REVERT: E 56 PHE cc_start: 0.9501 (t80) cc_final: 0.9267 (t80) REVERT: E 71 MET cc_start: 0.9356 (mtp) cc_final: 0.9116 (ptp) REVERT: E 76 ARG cc_start: 0.9548 (mmm-85) cc_final: 0.9224 (mtp85) REVERT: E 82 GLU cc_start: 0.9340 (tm-30) cc_final: 0.9009 (tm-30) REVERT: E 101 ASN cc_start: 0.9528 (m110) cc_final: 0.9064 (m110) REVERT: E 105 TYR cc_start: 0.9284 (m-10) cc_final: 0.8707 (m-80) REVERT: E 114 THR cc_start: 0.9456 (m) cc_final: 0.9199 (p) REVERT: E 131 GLU cc_start: 0.8989 (tp30) cc_final: 0.8588 (tm-30) REVERT: E 135 ILE cc_start: 0.9580 (mm) cc_final: 0.9208 (mm) REVERT: J 99 MET cc_start: 0.9443 (ttp) cc_final: 0.9187 (ppp) REVERT: J 146 PHE cc_start: 0.9186 (m-80) cc_final: 0.8860 (m-80) REVERT: J 159 MET cc_start: 0.8895 (tpp) cc_final: 0.8600 (tpp) REVERT: J 166 SER cc_start: 0.8979 (OUTLIER) cc_final: 0.8632 (t) REVERT: J 200 VAL cc_start: 0.8733 (OUTLIER) cc_final: 0.8522 (p) REVERT: J 209 GLU cc_start: 0.9389 (mm-30) cc_final: 0.8476 (mp0) REVERT: J 229 MET cc_start: 0.8553 (mtp) cc_final: 0.8202 (mtp) REVERT: L 83 TYR cc_start: 0.7802 (m-80) cc_final: 0.7579 (m-10) REVERT: L 113 LYS cc_start: 0.9432 (ttmm) cc_final: 0.9143 (tppt) REVERT: L 115 GLN cc_start: 0.9006 (mm110) cc_final: 0.8723 (mm-40) REVERT: N 49 MET cc_start: 0.9597 (tmm) cc_final: 0.9281 (tmm) REVERT: N 137 TYR cc_start: 0.7757 (OUTLIER) cc_final: 0.7261 (p90) REVERT: N 249 ARG cc_start: 0.9276 (mtp-110) cc_final: 0.9013 (ptm-80) REVERT: G 40 ASP cc_start: 0.9038 (m-30) cc_final: 0.8810 (p0) REVERT: G 66 GLU cc_start: 0.9264 (mt-10) cc_final: 0.8952 (mt-10) REVERT: F 33 GLN cc_start: 0.9330 (mp10) cc_final: 0.8958 (mp10) REVERT: F 73 ASN cc_start: 0.9506 (t0) cc_final: 0.9241 (t0) REVERT: F 121 TYR cc_start: 0.8780 (m-80) cc_final: 0.8220 (m-80) REVERT: F 137 MET cc_start: 0.8411 (ptp) cc_final: 0.8043 (ptp) REVERT: F 239 LYS cc_start: 0.9519 (mmtm) cc_final: 0.9274 (mmmm) REVERT: H 5 THR cc_start: 0.8913 (OUTLIER) cc_final: 0.8634 (m) REVERT: H 19 GLU cc_start: 0.8530 (tm-30) cc_final: 0.8120 (tm-30) REVERT: H 129 MET cc_start: 0.9289 (tpt) cc_final: 0.9066 (tpp) REVERT: H 145 TYR cc_start: 0.8419 (p90) cc_final: 0.7969 (p90) REVERT: H 174 ASP cc_start: 0.8677 (t0) cc_final: 0.8222 (t70) REVERT: H 200 MET cc_start: 0.9334 (tpp) cc_final: 0.8962 (mmm) REVERT: H 255 ASP cc_start: 0.9120 (m-30) cc_final: 0.8623 (p0) REVERT: H 265 MET cc_start: 0.9514 (mtp) cc_final: 0.9215 (mtt) REVERT: I 99 ASP cc_start: 0.9494 (m-30) cc_final: 0.9165 (p0) REVERT: I 110 GLN cc_start: 0.9620 (tp40) cc_final: 0.9318 (tp40) REVERT: I 129 MET cc_start: 0.9286 (mmp) cc_final: 0.9022 (mmm) REVERT: I 200 MET cc_start: 0.9151 (ttm) cc_final: 0.8901 (ttp) REVERT: I 265 MET cc_start: 0.9603 (mtm) cc_final: 0.9384 (mtm) REVERT: K 56 ASP cc_start: 0.9081 (m-30) cc_final: 0.8761 (m-30) REVERT: K 60 MET cc_start: 0.9180 (tmm) cc_final: 0.8762 (tmm) REVERT: K 61 ILE cc_start: 0.9137 (mt) cc_final: 0.8674 (mt) REVERT: K 148 THR cc_start: 0.9234 (OUTLIER) cc_final: 0.8949 (t) REVERT: K 201 ASP cc_start: 0.9238 (t0) cc_final: 0.8714 (t0) REVERT: K 202 GLU cc_start: 0.8453 (mt-10) cc_final: 0.8198 (pt0) REVERT: K 205 GLU cc_start: 0.8577 (mm-30) cc_final: 0.8267 (mm-30) REVERT: K 220 LEU cc_start: 0.9407 (OUTLIER) cc_final: 0.9154 (pp) REVERT: K 238 LEU cc_start: 0.9030 (mt) cc_final: 0.8740 (pp) REVERT: K 273 LYS cc_start: 0.9408 (tppt) cc_final: 0.8897 (mttm) REVERT: K 330 PHE cc_start: 0.9093 (m-80) cc_final: 0.8385 (m-80) REVERT: K 336 MET cc_start: 0.8884 (mmm) cc_final: 0.8462 (mmm) REVERT: K 369 ILE cc_start: 0.9423 (mt) cc_final: 0.9009 (mm) REVERT: K 406 SER cc_start: 0.9201 (m) cc_final: 0.8960 (p) REVERT: K 438 MET cc_start: 0.8893 (mmt) cc_final: 0.8449 (mmt) REVERT: K 447 LEU cc_start: 0.8461 (OUTLIER) cc_final: 0.7949 (mt) REVERT: K 474 ARG cc_start: 0.2880 (mtt180) cc_final: 0.2205 (mtt180) REVERT: K 481 LEU cc_start: 0.8633 (tp) cc_final: 0.8291 (tp) REVERT: K 527 LYS cc_start: 0.8943 (mmmt) cc_final: 0.8718 (mmtt) REVERT: K 538 ILE cc_start: 0.9315 (OUTLIER) cc_final: 0.9060 (tp) REVERT: K 587 LYS cc_start: 0.9248 (mmtm) cc_final: 0.8736 (tppt) REVERT: K 588 MET cc_start: 0.9309 (mtm) cc_final: 0.8820 (mtp) REVERT: K 619 TYR cc_start: 0.8890 (p90) cc_final: 0.8616 (p90) REVERT: K 625 ILE cc_start: 0.9390 (mt) cc_final: 0.9104 (mm) REVERT: K 667 GLN cc_start: 0.9154 (pm20) cc_final: 0.8822 (pm20) REVERT: K 677 MET cc_start: 0.8929 (ttp) cc_final: 0.8459 (ttp) REVERT: K 727 ASP cc_start: 0.9478 (m-30) cc_final: 0.8852 (t0) REVERT: K 745 MET cc_start: 0.9042 (mpp) cc_final: 0.8740 (mtm) REVERT: M 16 MET cc_start: 0.8718 (mmt) cc_final: 0.8335 (mmp) REVERT: M 62 ILE cc_start: 0.9629 (OUTLIER) cc_final: 0.9374 (mm) REVERT: M 167 LYS cc_start: 0.9395 (mmmt) cc_final: 0.9161 (mmtp) REVERT: M 169 PHE cc_start: 0.9053 (m-10) cc_final: 0.8720 (m-80) REVERT: M 282 LEU cc_start: 0.9514 (mm) cc_final: 0.9233 (tt) REVERT: M 290 MET cc_start: 0.8791 (pmm) cc_final: 0.8470 (pmm) outliers start: 98 outliers final: 59 residues processed: 594 average time/residue: 0.1826 time to fit residues: 176.4952 Evaluate side-chains 564 residues out of total 3097 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 494 time to evaluate : 1.459 ------------------------------------------------------------------------------- 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 122 ASN Chi-restraints excluded: chain C residue 37 LYS Chi-restraints excluded: chain C residue 128 THR Chi-restraints excluded: chain D residue 29 ILE Chi-restraints excluded: chain E residue 39 ASN Chi-restraints excluded: chain E residue 46 ASP 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 166 SER Chi-restraints excluded: chain J residue 177 VAL Chi-restraints excluded: chain J residue 200 VAL Chi-restraints excluded: chain J residue 208 VAL Chi-restraints excluded: chain J residue 212 MET 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 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 32 THR Chi-restraints excluded: chain G residue 101 GLU 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 H residue 227 LYS 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 K residue 14 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 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 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: 10.0000 chunk 285 optimal weight: 7.9990 chunk 282 optimal weight: 0.1980 chunk 98 optimal weight: 2.9990 chunk 160 optimal weight: 0.9990 chunk 263 optimal weight: 10.0000 chunk 26 optimal weight: 1.9990 chunk 223 optimal weight: 9.9990 chunk 156 optimal weight: 10.0000 chunk 317 optimal weight: 0.9980 chunk 28 optimal weight: 0.9990 overall best weight: 1.0386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** E 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 134 ASN ** L 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 193 ASN G 134 GLN ** H 204 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.053610 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3114 r_free = 0.3114 target = 0.045177 restraints weight = 142444.709| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3161 r_free = 0.3161 target = 0.046930 restraints weight = 73304.193| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3194 r_free = 0.3194 target = 0.048142 restraints weight = 45900.034| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3216 r_free = 0.3216 target = 0.048976 restraints weight = 32091.274| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3232 r_free = 0.3232 target = 0.049582 restraints weight = 24333.429| |-----------------------------------------------------------------------------| r_work (final): 0.3214 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8472 moved from start: 0.3571 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 29252 Z= 0.130 Angle : 0.636 14.936 39623 Z= 0.325 Chirality : 0.043 0.252 4524 Planarity : 0.004 0.051 4852 Dihedral : 11.496 178.571 4390 Min Nonbonded Distance : 2.355 Molprobity Statistics. All-atom Clashscore : 13.13 Ramachandran Plot: Outliers : 0.12 % Allowed : 5.84 % Favored : 94.04 % Rotamer: Outliers : 3.37 % Allowed : 21.42 % Favored : 75.21 % 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: 1.67 (0.14), residues: 1468 sheet: 0.03 (0.23), residues: 468 loop : -1.60 (0.15), residues: 1505 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG E 60 TYR 0.043 0.001 TYR K 62 PHE 0.032 0.001 PHE E 129 TRP 0.011 0.001 TRP M 173 HIS 0.006 0.001 HIS K 153 Details of bonding type rmsd/Z covalent geometry : bond 0.00291 / 0.13 (29237) covalent geometry : angle 0.63426 / 0.32 (39593) SS BOND : bond 0.00485 / 0.33 ( 15) SS BOND : angle 1.85120 / 1.22 ( 30) hydrogen bonds : bond 0.03547 / 2.38 ( 1274) hydrogen bonds : angle 4.86698 / 3.47 ( 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 633 residues out of total 3097 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 104 poor density : 529 time to evaluate : 1.069 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: 0.8690 (m-30) cc_final: 0.8206 (t0) REVERT: A 42 GLU cc_start: 0.8293 (mm-30) cc_final: 0.8057 (mm-30) REVERT: A 56 PHE cc_start: 0.8949 (t80) cc_final: 0.8565 (t80) REVERT: A 60 ARG cc_start: 0.9277 (mmp80) cc_final: 0.8875 (mmm160) REVERT: A 69 TYR cc_start: 0.9190 (t80) cc_final: 0.8968 (t80) REVERT: A 79 ILE cc_start: 0.8961 (mm) cc_final: 0.8659 (mp) REVERT: A 110 TYR cc_start: 0.9061 (t80) cc_final: 0.8852 (t80) REVERT: A 111 ASP cc_start: 0.8965 (t0) cc_final: 0.8604 (t0) REVERT: A 131 GLU cc_start: 0.9435 (mt-10) cc_final: 0.8729 (mt-10) REVERT: B 22 ASP cc_start: 0.8866 (m-30) cc_final: 0.8114 (m-30) REVERT: B 26 ARG cc_start: 0.9114 (ptp-110) cc_final: 0.8424 (ptp90) REVERT: B 44 TYR cc_start: 0.9222 (t80) cc_final: 0.8815 (t80) REVERT: B 73 GLN cc_start: 0.9298 (tp40) cc_final: 0.9070 (tp-100) REVERT: B 78 GLU cc_start: 0.9050 (mm-30) cc_final: 0.8520 (tp30) REVERT: B 90 SER cc_start: 0.9645 (m) cc_final: 0.9263 (p) REVERT: B 129 PHE cc_start: 0.8913 (t80) cc_final: 0.8611 (t80) REVERT: B 131 GLU cc_start: 0.9195 (mp0) cc_final: 0.8758 (pm20) REVERT: B 134 ASN cc_start: 0.9183 (m-40) cc_final: 0.8779 (m110) REVERT: C 22 ASP cc_start: 0.9128 (m-30) cc_final: 0.8784 (m-30) REVERT: C 45 VAL cc_start: 0.9546 (t) cc_final: 0.9280 (p) REVERT: C 71 MET cc_start: 0.9368 (mtm) cc_final: 0.9055 (mtm) REVERT: C 77 ASP cc_start: 0.9235 (t0) cc_final: 0.8956 (t0) REVERT: C 103 LEU cc_start: 0.9582 (OUTLIER) cc_final: 0.9282 (tp) REVERT: C 134 ASN cc_start: 0.9703 (m-40) cc_final: 0.9394 (m110) REVERT: D 26 ARG cc_start: 0.9522 (mtm-85) cc_final: 0.9240 (ptp-110) REVERT: D 29 ILE cc_start: 0.8884 (OUTLIER) cc_final: 0.8510 (tp) REVERT: D 32 ILE cc_start: 0.9146 (tp) cc_final: 0.8930 (tp) REVERT: D 44 TYR cc_start: 0.9177 (t80) cc_final: 0.8813 (t80) REVERT: D 58 GLN cc_start: 0.9460 (mp10) cc_final: 0.9179 (mm-40) REVERT: D 66 LEU cc_start: 0.9695 (tt) cc_final: 0.9385 (mm) REVERT: D 82 GLU cc_start: 0.9482 (tt0) cc_final: 0.9061 (tp30) REVERT: D 101 ASN cc_start: 0.9542 (m110) cc_final: 0.9316 (m110) REVERT: D 134 ASN cc_start: 0.9218 (m-40) cc_final: 0.8662 (m110) REVERT: E 48 SER cc_start: 0.9748 (m) cc_final: 0.9525 (p) REVERT: E 55 SER cc_start: 0.9752 (m) cc_final: 0.9484 (p) REVERT: E 56 PHE cc_start: 0.9534 (t80) cc_final: 0.9299 (t80) REVERT: E 76 ARG cc_start: 0.9579 (mmm-85) cc_final: 0.8714 (mtp85) REVERT: E 78 GLU cc_start: 0.8614 (mt-10) cc_final: 0.8159 (mp0) REVERT: E 82 GLU cc_start: 0.9328 (tm-30) cc_final: 0.9000 (tm-30) REVERT: E 101 ASN cc_start: 0.9523 (m110) cc_final: 0.9063 (m110) REVERT: E 105 TYR cc_start: 0.9291 (m-10) cc_final: 0.8718 (m-80) REVERT: E 114 THR cc_start: 0.9446 (m) cc_final: 0.9172 (p) REVERT: E 131 GLU cc_start: 0.8997 (tp30) cc_final: 0.8590 (tm-30) REVERT: E 135 ILE cc_start: 0.9573 (mm) cc_final: 0.9204 (mm) REVERT: J 99 MET cc_start: 0.9451 (ttp) cc_final: 0.9211 (ppp) REVERT: J 146 PHE cc_start: 0.9182 (m-80) cc_final: 0.8852 (m-80) REVERT: J 159 MET cc_start: 0.8919 (tpp) cc_final: 0.8624 (tpp) REVERT: J 166 SER cc_start: 0.9108 (m) cc_final: 0.8680 (t) REVERT: J 209 GLU cc_start: 0.9369 (mm-30) cc_final: 0.8504 (mp0) REVERT: J 229 MET cc_start: 0.8542 (mtp) cc_final: 0.8174 (mtp) REVERT: L 43 MET cc_start: 0.8873 (ttp) cc_final: 0.8606 (tpp) REVERT: L 113 LYS cc_start: 0.9430 (ttmm) cc_final: 0.9142 (tppt) REVERT: L 115 GLN cc_start: 0.9003 (mm110) cc_final: 0.8731 (mm110) REVERT: L 118 LYS cc_start: 0.9561 (ttmm) cc_final: 0.9105 (ttmm) REVERT: N 49 MET cc_start: 0.9597 (tmm) cc_final: 0.9277 (tmm) REVERT: N 249 ARG cc_start: 0.9288 (mtp-110) cc_final: 0.8983 (ptm-80) REVERT: G 40 ASP cc_start: 0.9023 (m-30) cc_final: 0.8801 (p0) REVERT: G 66 GLU cc_start: 0.9273 (mt-10) cc_final: 0.8954 (mt-10) REVERT: F 33 GLN cc_start: 0.9371 (mp10) cc_final: 0.8991 (mp10) REVERT: F 73 ASN cc_start: 0.9492 (t0) cc_final: 0.9216 (t0) REVERT: F 134 GLN cc_start: 0.9154 (tt0) cc_final: 0.8888 (tt0) REVERT: F 137 MET cc_start: 0.8421 (ptp) cc_final: 0.8140 (mpp) REVERT: F 168 MET cc_start: 0.9070 (ttp) cc_final: 0.8672 (ttm) REVERT: F 207 ARG cc_start: 0.7399 (OUTLIER) cc_final: 0.6729 (mtp85) REVERT: F 239 LYS cc_start: 0.9551 (mmtm) cc_final: 0.9285 (mmmm) REVERT: H 5 THR cc_start: 0.8923 (OUTLIER) cc_final: 0.8643 (m) REVERT: H 19 GLU cc_start: 0.8542 (tm-30) cc_final: 0.8129 (tm-30) REVERT: H 98 ARG cc_start: 0.9110 (mmp80) cc_final: 0.8743 (mmp80) REVERT: H 145 TYR cc_start: 0.8376 (p90) cc_final: 0.7952 (p90) REVERT: H 174 ASP cc_start: 0.8691 (t0) cc_final: 0.8223 (t70) REVERT: H 200 MET cc_start: 0.9332 (tpp) cc_final: 0.8957 (mmm) REVERT: H 255 ASP cc_start: 0.9098 (m-30) cc_final: 0.8603 (p0) REVERT: H 265 MET cc_start: 0.9466 (mtp) cc_final: 0.9171 (mtt) REVERT: I 99 ASP cc_start: 0.9473 (m-30) cc_final: 0.9160 (p0) REVERT: I 110 GLN cc_start: 0.9618 (tp40) cc_final: 0.9302 (tp40) REVERT: I 129 MET cc_start: 0.9276 (mmp) cc_final: 0.9002 (mmm) REVERT: I 183 MET cc_start: 0.8790 (OUTLIER) cc_final: 0.8394 (tmm) REVERT: I 184 MET cc_start: 0.9024 (mtm) cc_final: 0.8664 (mtm) REVERT: I 200 MET cc_start: 0.9186 (ttm) cc_final: 0.8984 (ttp) REVERT: I 209 GLN cc_start: 0.8025 (OUTLIER) cc_final: 0.7131 (pt0) REVERT: I 265 MET cc_start: 0.9606 (mtm) cc_final: 0.9331 (mtm) REVERT: K 56 ASP cc_start: 0.9076 (m-30) cc_final: 0.8742 (m-30) REVERT: K 60 MET cc_start: 0.9023 (tmm) cc_final: 0.8656 (tmm) REVERT: K 61 ILE cc_start: 0.9005 (mt) cc_final: 0.8546 (mt) REVERT: K 148 THR cc_start: 0.9245 (OUTLIER) cc_final: 0.8964 (t) REVERT: K 153 HIS cc_start: 0.8987 (OUTLIER) cc_final: 0.8734 (t70) REVERT: K 202 GLU cc_start: 0.8460 (mt-10) cc_final: 0.8258 (pt0) REVERT: K 205 GLU cc_start: 0.8587 (mm-30) cc_final: 0.8275 (mm-30) REVERT: K 220 LEU cc_start: 0.9402 (OUTLIER) cc_final: 0.9140 (pp) REVERT: K 238 LEU cc_start: 0.9023 (mt) cc_final: 0.8748 (pp) REVERT: K 273 LYS cc_start: 0.9399 (tppt) cc_final: 0.8930 (mttm) REVERT: K 330 PHE cc_start: 0.9113 (m-80) cc_final: 0.8403 (m-80) REVERT: K 336 MET cc_start: 0.8887 (mmm) cc_final: 0.8463 (mmm) REVERT: K 369 ILE cc_start: 0.9432 (mt) cc_final: 0.9056 (mt) REVERT: K 406 SER cc_start: 0.9215 (m) cc_final: 0.8982 (p) REVERT: K 438 MET cc_start: 0.8891 (mmt) cc_final: 0.8379 (mmt) REVERT: K 447 LEU cc_start: 0.8319 (OUTLIER) cc_final: 0.7752 (mt) REVERT: K 474 ARG cc_start: 0.2999 (mtt180) cc_final: 0.2524 (mtt180) REVERT: K 481 LEU cc_start: 0.8619 (tp) cc_final: 0.8276 (tp) REVERT: K 527 LYS cc_start: 0.8962 (mmmt) cc_final: 0.8736 (mmtt) REVERT: K 538 ILE cc_start: 0.9305 (tp) cc_final: 0.9044 (tp) REVERT: K 587 LYS cc_start: 0.9252 (mmtm) cc_final: 0.8753 (tppt) REVERT: K 588 MET cc_start: 0.9317 (mtm) cc_final: 0.8842 (mtp) REVERT: K 619 TYR cc_start: 0.8859 (p90) cc_final: 0.8525 (p90) REVERT: K 625 ILE cc_start: 0.9395 (mt) cc_final: 0.9115 (mm) REVERT: K 667 GLN cc_start: 0.9140 (pm20) cc_final: 0.8802 (pm20) REVERT: K 677 MET cc_start: 0.8928 (ttp) cc_final: 0.8644 (ttp) REVERT: K 727 ASP cc_start: 0.9479 (m-30) cc_final: 0.8855 (t0) REVERT: K 745 MET cc_start: 0.9060 (mpp) cc_final: 0.8818 (mpp) REVERT: M 16 MET cc_start: 0.8700 (mmt) cc_final: 0.8327 (mmp) REVERT: M 62 ILE cc_start: 0.9618 (OUTLIER) cc_final: 0.9367 (mm) REVERT: M 69 TYR cc_start: 0.8164 (t80) cc_final: 0.7780 (t80) REVERT: M 105 MET cc_start: 0.7672 (ptt) cc_final: 0.7464 (ptt) REVERT: M 167 LYS cc_start: 0.9395 (mmmt) cc_final: 0.9156 (mmtp) REVERT: M 169 PHE cc_start: 0.9003 (m-10) cc_final: 0.8676 (m-80) REVERT: M 206 VAL cc_start: 0.9425 (OUTLIER) cc_final: 0.9168 (m) REVERT: M 240 ILE cc_start: 0.9294 (OUTLIER) cc_final: 0.8457 (tp) REVERT: M 290 MET cc_start: 0.8809 (pmm) cc_final: 0.8474 (pmm) outliers start: 104 outliers final: 65 residues processed: 597 average time/residue: 0.1778 time to fit residues: 173.2280 Evaluate side-chains 569 residues out of total 3097 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 491 time to evaluate : 0.970 ------------------------------------------------------------------------------- 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 121 ASN 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 37 LYS Chi-restraints excluded: chain C residue 68 LEU Chi-restraints excluded: chain C residue 103 LEU Chi-restraints excluded: chain C residue 128 THR Chi-restraints excluded: chain D residue 29 ILE Chi-restraints excluded: chain E residue 39 ASN Chi-restraints excluded: chain E residue 46 ASP 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 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 190 ILE Chi-restraints excluded: chain N residue 191 VAL Chi-restraints excluded: chain N residue 239 SER Chi-restraints excluded: chain G residue 32 THR Chi-restraints excluded: chain G residue 101 GLU Chi-restraints excluded: chain G residue 156 ASP Chi-restraints excluded: chain G residue 188 GLU 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 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 183 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 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 177 SER 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 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 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 624 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 206 VAL 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 346 random chunks: chunk 302 optimal weight: 5.9990 chunk 100 optimal weight: 10.0000 chunk 313 optimal weight: 0.8980 chunk 159 optimal weight: 2.9990 chunk 91 optimal weight: 7.9990 chunk 15 optimal weight: 3.9990 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: 4.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** D 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 64 ASN N 59 ASN G 134 GLN ** H 204 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3214 r_free = 0.3214 target = 0.049828 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2977 r_free = 0.2977 target = 0.041584 restraints weight = 148556.541| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3027 r_free = 0.3027 target = 0.043265 restraints weight = 76728.584| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3060 r_free = 0.3060 target = 0.044433 restraints weight = 48112.654| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3083 r_free = 0.3083 target = 0.045233 restraints weight = 33788.313| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 42)----------------| | r_work = 0.3100 r_free = 0.3100 target = 0.045822 restraints weight = 25791.754| |-----------------------------------------------------------------------------| r_work (final): 0.3099 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8554 moved from start: 0.3818 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.063 29252 Z= 0.282 Angle : 0.731 14.618 39623 Z= 0.379 Chirality : 0.045 0.245 4524 Planarity : 0.004 0.051 4852 Dihedral : 11.693 179.642 4390 Min Nonbonded Distance : 2.386 Molprobity Statistics. All-atom Clashscore : 18.29 Ramachandran Plot: Outliers : 0.15 % Allowed : 6.77 % Favored : 93.08 % Rotamer: Outliers : 4.27 % Allowed : 21.75 % Favored : 73.98 % 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: -0.08 (0.14), residues: 3441 helix: 1.43 (0.14), residues: 1474 sheet: -0.11 (0.23), residues: 459 loop : -1.60 (0.15), residues: 1508 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG E 60 TYR 0.026 0.002 TYR I 195 PHE 0.036 0.002 PHE K 245 TRP 0.012 0.002 TRP K 749 HIS 0.008 0.001 HIS M 146 Details of bonding type rmsd/Z covalent geometry : bond 0.00596 / 0.28 (29237) covalent geometry : angle 0.72949 / 0.38 (39593) SS BOND : bond 0.00466 / 0.28 ( 15) SS BOND : angle 1.90219 / 1.29 ( 30) hydrogen bonds : bond 0.03978 / 2.62 ( 1274) hydrogen bonds : angle 5.18238 / 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 616 residues out of total 3097 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 132 poor density : 484 time to evaluate : 1.173 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: A 22 ASP cc_start: 0.8691 (m-30) cc_final: 0.8218 (t0) REVERT: A 42 GLU cc_start: 0.8370 (mm-30) cc_final: 0.8048 (mm-30) REVERT: A 56 PHE cc_start: 0.8999 (t80) cc_final: 0.8597 (t80) REVERT: A 60 ARG cc_start: 0.9287 (mmp80) cc_final: 0.8884 (mmm160) REVERT: A 79 ILE cc_start: 0.9047 (mm) cc_final: 0.8764 (mp) REVERT: A 110 TYR cc_start: 0.9049 (t80) cc_final: 0.8817 (t80) REVERT: A 111 ASP cc_start: 0.8997 (t0) cc_final: 0.8647 (t0) REVERT: A 131 GLU cc_start: 0.9385 (mt-10) cc_final: 0.8995 (mt-10) REVERT: B 22 ASP cc_start: 0.8827 (m-30) cc_final: 0.8092 (m-30) REVERT: B 26 ARG cc_start: 0.9131 (ptp-110) cc_final: 0.8391 (ptp90) REVERT: B 73 GLN cc_start: 0.9336 (tp40) cc_final: 0.9052 (tp-100) REVERT: B 78 GLU cc_start: 0.9140 (mm-30) cc_final: 0.8613 (tp30) REVERT: B 90 SER cc_start: 0.9650 (m) cc_final: 0.9269 (p) REVERT: B 129 PHE cc_start: 0.8900 (t80) cc_final: 0.8594 (t80) REVERT: B 131 GLU cc_start: 0.9230 (mp0) cc_final: 0.8960 (mp0) REVERT: B 134 ASN cc_start: 0.9149 (m-40) cc_final: 0.8718 (m110) REVERT: C 22 ASP cc_start: 0.9172 (m-30) cc_final: 0.8818 (m-30) REVERT: C 71 MET cc_start: 0.9425 (mtm) cc_final: 0.9100 (mtm) REVERT: C 77 ASP cc_start: 0.9303 (t0) cc_final: 0.9061 (t0) REVERT: C 103 LEU cc_start: 0.9638 (OUTLIER) cc_final: 0.9394 (tp) REVERT: C 134 ASN cc_start: 0.9721 (m-40) cc_final: 0.9418 (m110) REVERT: D 26 ARG cc_start: 0.9569 (mtm-85) cc_final: 0.9171 (ptp90) REVERT: D 32 ILE cc_start: 0.9144 (tp) cc_final: 0.8898 (tp) REVERT: D 58 GLN cc_start: 0.9478 (mp10) cc_final: 0.9231 (mm-40) REVERT: D 82 GLU cc_start: 0.9505 (tt0) cc_final: 0.9123 (tp30) REVERT: D 101 ASN cc_start: 0.9493 (m110) cc_final: 0.9055 (m110) REVERT: D 134 ASN cc_start: 0.9232 (m-40) cc_final: 0.8645 (m110) REVERT: E 44 TYR cc_start: 0.8843 (t80) cc_final: 0.8533 (t80) REVERT: E 55 SER cc_start: 0.9812 (m) cc_final: 0.9553 (p) REVERT: E 78 GLU cc_start: 0.8549 (mt-10) cc_final: 0.8221 (mt-10) REVERT: E 82 GLU cc_start: 0.9342 (tm-30) cc_final: 0.9016 (tm-30) REVERT: E 101 ASN cc_start: 0.9558 (m110) cc_final: 0.9171 (m110) REVERT: E 105 TYR cc_start: 0.9329 (m-10) cc_final: 0.8932 (m-80) REVERT: E 131 GLU cc_start: 0.9049 (tp30) cc_final: 0.8652 (tm-30) REVERT: E 135 ILE cc_start: 0.9626 (mm) cc_final: 0.9269 (mm) REVERT: J 44 GLU cc_start: 0.8800 (pp20) cc_final: 0.7412 (pp20) REVERT: J 46 MET cc_start: 0.8443 (mtt) cc_final: 0.7949 (mmm) REVERT: J 146 PHE cc_start: 0.9228 (m-80) cc_final: 0.8876 (m-80) REVERT: J 159 MET cc_start: 0.9021 (tpp) cc_final: 0.8698 (tpp) REVERT: J 166 SER cc_start: 0.9148 (OUTLIER) cc_final: 0.8638 (t) REVERT: J 209 GLU cc_start: 0.9427 (mm-30) cc_final: 0.8576 (mp0) REVERT: J 229 MET cc_start: 0.8692 (mtp) cc_final: 0.8194 (mtp) REVERT: L 43 MET cc_start: 0.8908 (ttp) cc_final: 0.8638 (tpp) REVERT: L 79 LYS cc_start: 0.9275 (ttmm) cc_final: 0.8888 (mtmm) REVERT: L 113 LYS cc_start: 0.9491 (ttmm) cc_final: 0.9211 (tppt) REVERT: L 115 GLN cc_start: 0.9219 (mm110) cc_final: 0.8979 (tp40) REVERT: L 118 LYS cc_start: 0.9637 (ttmm) cc_final: 0.9197 (ttmm) REVERT: L 168 MET cc_start: 0.8868 (pmm) cc_final: 0.8608 (pmm) REVERT: N 49 MET cc_start: 0.9607 (tmm) cc_final: 0.9279 (tmm) REVERT: N 137 TYR cc_start: 0.8001 (OUTLIER) cc_final: 0.7427 (p90) REVERT: N 155 MET cc_start: 0.8910 (pmm) cc_final: 0.8665 (pmm) REVERT: N 249 ARG cc_start: 0.9309 (mtp-110) cc_final: 0.9037 (ptm-80) REVERT: G 40 ASP cc_start: 0.9107 (m-30) cc_final: 0.8841 (p0) REVERT: G 66 GLU cc_start: 0.9305 (mt-10) cc_final: 0.8975 (mt-10) REVERT: F 33 GLN cc_start: 0.9370 (mp10) cc_final: 0.8955 (mp10) REVERT: F 73 ASN cc_start: 0.9566 (t0) cc_final: 0.9330 (t0) REVERT: F 134 GLN cc_start: 0.9253 (tt0) cc_final: 0.8991 (tt0) REVERT: F 137 MET cc_start: 0.8682 (ptp) cc_final: 0.8315 (mpp) REVERT: F 167 MET cc_start: 0.8897 (tpp) cc_final: 0.8619 (tpp) REVERT: F 239 LYS cc_start: 0.9512 (mmtm) cc_final: 0.9260 (mmmm) REVERT: H 5 THR cc_start: 0.8999 (OUTLIER) cc_final: 0.8780 (m) REVERT: H 129 MET cc_start: 0.9300 (tpt) cc_final: 0.9081 (mmm) REVERT: H 145 TYR cc_start: 0.8672 (p90) cc_final: 0.8141 (p90) REVERT: H 174 ASP cc_start: 0.8831 (t0) cc_final: 0.8390 (t70) REVERT: H 200 MET cc_start: 0.9366 (tpp) cc_final: 0.9119 (tpp) REVERT: H 255 ASP cc_start: 0.9180 (m-30) cc_final: 0.8724 (p0) REVERT: I 110 GLN cc_start: 0.9631 (tp40) cc_final: 0.9335 (tp40) REVERT: I 129 MET cc_start: 0.9443 (mmp) cc_final: 0.9139 (mmm) REVERT: I 265 MET cc_start: 0.9668 (mtm) cc_final: 0.8973 (mtm) REVERT: K 56 ASP cc_start: 0.9170 (m-30) cc_final: 0.8826 (m-30) REVERT: K 60 MET cc_start: 0.9106 (tmm) cc_final: 0.8728 (tmm) REVERT: K 61 ILE cc_start: 0.9062 (mt) cc_final: 0.8501 (mt) REVERT: K 81 GLU cc_start: 0.8910 (mt-10) cc_final: 0.8561 (mt-10) REVERT: K 148 THR cc_start: 0.9202 (OUTLIER) cc_final: 0.8916 (t) REVERT: K 153 HIS cc_start: 0.8908 (OUTLIER) cc_final: 0.8691 (t70) REVERT: K 202 GLU cc_start: 0.8523 (mt-10) cc_final: 0.8260 (mt-10) REVERT: K 205 GLU cc_start: 0.8647 (mm-30) cc_final: 0.8376 (mm-30) REVERT: K 233 ASN cc_start: 0.8801 (m110) cc_final: 0.8515 (m110) REVERT: K 336 MET cc_start: 0.8928 (mmm) cc_final: 0.8662 (mmm) REVERT: K 369 ILE cc_start: 0.9522 (mt) cc_final: 0.9105 (mm) REVERT: K 406 SER cc_start: 0.9303 (m) cc_final: 0.9062 (p) REVERT: K 438 MET cc_start: 0.8870 (mmt) cc_final: 0.8535 (mmt) REVERT: K 474 ARG cc_start: 0.2904 (mtt180) cc_final: 0.2281 (mtt180) REVERT: K 481 LEU cc_start: 0.8655 (tp) cc_final: 0.8342 (tp) REVERT: K 502 LYS cc_start: 0.9417 (mtpt) cc_final: 0.9103 (mtmm) REVERT: K 538 ILE cc_start: 0.9381 (OUTLIER) cc_final: 0.9075 (tp) REVERT: K 587 LYS cc_start: 0.9259 (OUTLIER) cc_final: 0.8823 (tppt) REVERT: K 588 MET cc_start: 0.9355 (mtm) cc_final: 0.8868 (mtp) REVERT: K 619 TYR cc_start: 0.8956 (p90) cc_final: 0.8607 (p90) REVERT: K 625 ILE cc_start: 0.9379 (mt) cc_final: 0.9090 (mm) REVERT: K 677 MET cc_start: 0.8996 (ttp) cc_final: 0.8696 (ttp) REVERT: K 727 ASP cc_start: 0.9515 (m-30) cc_final: 0.8911 (t0) REVERT: K 745 MET cc_start: 0.9021 (mpp) cc_final: 0.8655 (mtm) REVERT: M 16 MET cc_start: 0.8720 (mmt) cc_final: 0.8377 (mmp) REVERT: M 62 ILE cc_start: 0.9662 (OUTLIER) cc_final: 0.9403 (mm) REVERT: M 160 MET cc_start: 0.7347 (pmm) cc_final: 0.7130 (pmm) REVERT: M 169 PHE cc_start: 0.9092 (m-10) cc_final: 0.8852 (m-80) REVERT: M 170 ASP cc_start: 0.9076 (t0) cc_final: 0.8801 (t0) REVERT: M 290 MET cc_start: 0.8854 (pmm) cc_final: 0.8452 (pmm) outliers start: 132 outliers final: 92 residues processed: 581 average time/residue: 0.1684 time to fit residues: 159.0791 Evaluate side-chains 554 residues out of total 3097 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 101 poor density : 453 time to evaluate : 1.036 ------------------------------------------------------------------------------- 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 118 VAL Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain C residue 37 LYS Chi-restraints excluded: chain C residue 90 SER 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 29 ILE 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 46 ASP Chi-restraints excluded: chain E residue 77 ASP Chi-restraints excluded: chain E residue 103 LEU 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 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 137 TYR Chi-restraints excluded: chain N residue 149 ILE Chi-restraints excluded: chain N residue 190 ILE Chi-restraints excluded: chain N residue 239 SER Chi-restraints excluded: chain G residue 32 THR Chi-restraints excluded: chain G residue 101 GLU Chi-restraints excluded: chain G residue 144 PHE Chi-restraints excluded: chain G residue 188 GLU 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 56 ILE 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 7 ILE Chi-restraints excluded: chain I residue 56 ILE Chi-restraints excluded: chain I residue 152 MET Chi-restraints excluded: chain I residue 162 VAL Chi-restraints excluded: chain I residue 175 VAL 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 29 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 177 SER 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 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 103 GLU 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 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: 20.0000 chunk 108 optimal weight: 5.9990 chunk 68 optimal weight: 0.9980 chunk 154 optimal weight: 4.9990 chunk 273 optimal weight: 5.9990 chunk 235 optimal weight: 3.9990 chunk 303 optimal weight: 5.9990 chunk 148 optimal weight: 8.9990 chunk 240 optimal weight: 2.9990 chunk 314 optimal weight: 4.9990 chunk 96 optimal weight: 5.9990 overall best weight: 3.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 121 ASN ** D 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 64 ASN ** L 175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 204 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3265 r_free = 0.3265 target = 0.050780 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3043 r_free = 0.3043 target = 0.042666 restraints weight = 145033.705| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3092 r_free = 0.3092 target = 0.044369 restraints weight = 72989.332| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3124 r_free = 0.3124 target = 0.045530 restraints weight = 45060.869| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3147 r_free = 0.3147 target = 0.046330 restraints weight = 31363.040| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.3163 r_free = 0.3163 target = 0.046901 restraints weight = 23691.265| |-----------------------------------------------------------------------------| r_work (final): 0.3137 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8540 moved from start: 0.4004 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.060 29252 Z= 0.236 Angle : 0.720 14.641 39623 Z= 0.372 Chirality : 0.045 0.286 4524 Planarity : 0.004 0.050 4852 Dihedral : 11.730 179.081 4390 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 17.43 Ramachandran Plot: Outliers : 0.12 % Allowed : 6.60 % Favored : 93.29 % Rotamer: Outliers : 4.14 % Allowed : 22.88 % Favored : 72.98 % 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: 1.41 (0.14), residues: 1471 sheet: -0.14 (0.23), residues: 463 loop : -1.59 (0.15), residues: 1507 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG G 142 TYR 0.040 0.002 TYR K 62 PHE 0.040 0.002 PHE E 56 TRP 0.009 0.001 TRP K 749 HIS 0.006 0.001 HIS M 146 Details of bonding type rmsd/Z covalent geometry : bond 0.00504 / 0.24 (29237) covalent geometry : angle 0.71828 / 0.37 (39593) SS BOND : bond 0.00343 / 0.19 ( 15) SS BOND : angle 1.95356 / 1.33 ( 30) hydrogen bonds : bond 0.03914 / 2.59 ( 1274) hydrogen bonds : angle 5.18106 / 3.70 ( 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 592 residues out of total 3097 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 128 poor density : 464 time to evaluate : 1.078 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: A 22 ASP cc_start: 0.8725 (m-30) cc_final: 0.8255 (t0) REVERT: A 42 GLU cc_start: 0.8338 (mm-30) cc_final: 0.8030 (mm-30) REVERT: A 56 PHE cc_start: 0.8966 (t80) cc_final: 0.8573 (t80) REVERT: A 60 ARG cc_start: 0.9272 (mmp80) cc_final: 0.8884 (mmm160) REVERT: A 79 ILE cc_start: 0.9052 (mm) cc_final: 0.8748 (mp) REVERT: A 110 TYR cc_start: 0.9041 (t80) cc_final: 0.8810 (t80) REVERT: A 111 ASP cc_start: 0.8995 (t0) cc_final: 0.8647 (t0) REVERT: A 131 GLU cc_start: 0.9450 (mt-10) cc_final: 0.8992 (mt-10) REVERT: B 22 ASP cc_start: 0.8862 (m-30) cc_final: 0.8163 (m-30) REVERT: B 26 ARG cc_start: 0.9140 (ptp-110) cc_final: 0.8415 (ptp90) REVERT: B 73 GLN cc_start: 0.9302 (tp40) cc_final: 0.9089 (tp-100) REVERT: B 78 GLU cc_start: 0.9121 (mm-30) cc_final: 0.8568 (tp30) REVERT: B 90 SER cc_start: 0.9649 (m) cc_final: 0.9261 (p) REVERT: B 129 PHE cc_start: 0.8874 (t80) cc_final: 0.8561 (t80) REVERT: B 131 GLU cc_start: 0.9241 (mp0) cc_final: 0.8969 (mp0) REVERT: B 134 ASN cc_start: 0.9140 (m-40) cc_final: 0.8695 (m110) REVERT: C 22 ASP cc_start: 0.9162 (m-30) cc_final: 0.8803 (m-30) REVERT: C 71 MET cc_start: 0.9412 (mtm) cc_final: 0.9088 (mtm) REVERT: C 77 ASP cc_start: 0.9317 (t0) cc_final: 0.9104 (t0) REVERT: C 103 LEU cc_start: 0.9623 (OUTLIER) cc_final: 0.9373 (tp) REVERT: C 134 ASN cc_start: 0.9715 (m-40) cc_final: 0.9424 (m110) REVERT: D 26 ARG cc_start: 0.9568 (mtm-85) cc_final: 0.9201 (ptp90) REVERT: D 29 ILE cc_start: 0.9025 (OUTLIER) cc_final: 0.8673 (tp) REVERT: D 32 ILE cc_start: 0.9183 (tp) cc_final: 0.8924 (tp) REVERT: D 44 TYR cc_start: 0.9037 (t80) cc_final: 0.8659 (t80) REVERT: D 58 GLN cc_start: 0.9482 (mp10) cc_final: 0.9209 (mm-40) REVERT: D 61 ARG cc_start: 0.9226 (mmm-85) cc_final: 0.8990 (mmm-85) REVERT: D 66 LEU cc_start: 0.9715 (tt) cc_final: 0.9376 (mm) REVERT: D 82 GLU cc_start: 0.9511 (tt0) cc_final: 0.9104 (tp30) REVERT: D 95 GLU cc_start: 0.8661 (tp30) cc_final: 0.8030 (tm-30) REVERT: D 101 ASN cc_start: 0.9428 (m110) cc_final: 0.9092 (m-40) REVERT: D 133 VAL cc_start: 0.9768 (t) cc_final: 0.9563 (p) REVERT: D 134 ASN cc_start: 0.9238 (m-40) cc_final: 0.9004 (m110) REVERT: E 19 ASP cc_start: 0.9179 (p0) cc_final: 0.8967 (p0) REVERT: E 44 TYR cc_start: 0.8792 (t80) cc_final: 0.8583 (t80) REVERT: E 55 SER cc_start: 0.9811 (m) cc_final: 0.9541 (p) REVERT: E 78 GLU cc_start: 0.8596 (mt-10) cc_final: 0.8194 (mt-10) REVERT: E 82 GLU cc_start: 0.9330 (tm-30) cc_final: 0.9023 (tm-30) REVERT: E 101 ASN cc_start: 0.9539 (m110) cc_final: 0.9130 (m110) REVERT: E 105 TYR cc_start: 0.9324 (m-10) cc_final: 0.8877 (m-80) REVERT: E 131 GLU cc_start: 0.8984 (tp30) cc_final: 0.8612 (tm-30) REVERT: E 135 ILE cc_start: 0.9622 (mm) cc_final: 0.9269 (mm) REVERT: J 44 GLU cc_start: 0.8795 (pp20) cc_final: 0.7390 (pp20) REVERT: J 46 MET cc_start: 0.8427 (mtt) cc_final: 0.7993 (mmm) REVERT: J 146 PHE cc_start: 0.9215 (m-80) cc_final: 0.8883 (m-80) REVERT: J 159 MET cc_start: 0.8964 (tpp) cc_final: 0.8713 (tpp) REVERT: J 166 SER cc_start: 0.9215 (OUTLIER) cc_final: 0.8700 (t) REVERT: J 229 MET cc_start: 0.8660 (mtp) cc_final: 0.8211 (mtp) REVERT: L 113 LYS cc_start: 0.9485 (ttmm) cc_final: 0.9203 (tppt) REVERT: L 115 GLN cc_start: 0.9209 (mm110) cc_final: 0.8960 (tp40) REVERT: L 118 LYS cc_start: 0.9639 (ttmm) cc_final: 0.9193 (ttmm) REVERT: N 49 MET cc_start: 0.9607 (tmm) cc_final: 0.9281 (tmm) REVERT: N 137 TYR cc_start: 0.7908 (OUTLIER) cc_final: 0.7223 (p90) REVERT: N 155 MET cc_start: 0.8903 (pmm) cc_final: 0.8641 (pmm) REVERT: N 249 ARG cc_start: 0.9306 (mtp-110) cc_final: 0.9019 (ptm-80) REVERT: G 40 ASP cc_start: 0.9096 (m-30) cc_final: 0.8825 (p0) REVERT: G 66 GLU cc_start: 0.9260 (mt-10) cc_final: 0.8917 (mt-10) REVERT: G 147 GLN cc_start: 0.8362 (pm20) cc_final: 0.7890 (pm20) REVERT: F 33 GLN cc_start: 0.9372 (mp10) cc_final: 0.8923 (mp10) REVERT: F 49 ARG cc_start: 0.9037 (OUTLIER) cc_final: 0.8636 (mmm-85) REVERT: F 73 ASN cc_start: 0.9557 (t0) cc_final: 0.9304 (t0) REVERT: F 134 GLN cc_start: 0.9293 (tt0) cc_final: 0.9038 (tt0) REVERT: F 137 MET cc_start: 0.8647 (ptp) cc_final: 0.8334 (mpp) REVERT: F 207 ARG cc_start: 0.7775 (OUTLIER) cc_final: 0.6968 (mtp85) REVERT: F 239 LYS cc_start: 0.9510 (mmtm) cc_final: 0.9236 (mmmm) REVERT: H 5 THR cc_start: 0.8937 (OUTLIER) cc_final: 0.8702 (m) REVERT: H 145 TYR cc_start: 0.8771 (p90) cc_final: 0.8255 (p90) REVERT: H 174 ASP cc_start: 0.8810 (t0) cc_final: 0.8353 (t70) REVERT: H 200 MET cc_start: 0.9373 (tpp) cc_final: 0.9124 (tpp) REVERT: H 255 ASP cc_start: 0.9152 (m-30) cc_final: 0.8684 (p0) REVERT: I 99 ASP cc_start: 0.9555 (m-30) cc_final: 0.9185 (p0) REVERT: I 110 GLN cc_start: 0.9629 (tp40) cc_final: 0.9322 (tp40) REVERT: I 129 MET cc_start: 0.9440 (mmp) cc_final: 0.9092 (mmm) REVERT: I 265 MET cc_start: 0.9665 (mtm) cc_final: 0.8962 (mtm) REVERT: K 56 ASP cc_start: 0.9162 (m-30) cc_final: 0.8803 (m-30) REVERT: K 60 MET cc_start: 0.9112 (tmm) cc_final: 0.8682 (tmm) REVERT: K 61 ILE cc_start: 0.8961 (mt) cc_final: 0.8433 (mt) REVERT: K 81 GLU cc_start: 0.8907 (mt-10) cc_final: 0.8565 (mt-10) REVERT: K 148 THR cc_start: 0.9215 (OUTLIER) cc_final: 0.8916 (t) REVERT: K 202 GLU cc_start: 0.8536 (mt-10) cc_final: 0.8273 (mt-10) REVERT: K 205 GLU cc_start: 0.8691 (mm-30) cc_final: 0.8454 (mm-30) REVERT: K 233 ASN cc_start: 0.8771 (m110) cc_final: 0.8501 (m110) REVERT: K 273 LYS cc_start: 0.9436 (tppt) cc_final: 0.8957 (mttm) REVERT: K 336 MET cc_start: 0.8924 (mmm) cc_final: 0.8573 (mmm) REVERT: K 369 ILE cc_start: 0.9521 (mt) cc_final: 0.9195 (mt) REVERT: K 406 SER cc_start: 0.9296 (m) cc_final: 0.9060 (p) REVERT: K 438 MET cc_start: 0.8952 (mmt) cc_final: 0.8479 (mmt) REVERT: K 447 LEU cc_start: 0.8889 (OUTLIER) cc_final: 0.8631 (tp) REVERT: K 474 ARG cc_start: 0.2935 (mtt180) cc_final: 0.2708 (mtt180) REVERT: K 481 LEU cc_start: 0.8627 (tp) cc_final: 0.8286 (tp) REVERT: K 502 LYS cc_start: 0.9394 (mtpt) cc_final: 0.9079 (mtmm) REVERT: K 538 ILE cc_start: 0.9380 (OUTLIER) cc_final: 0.9071 (tp) REVERT: K 587 LYS cc_start: 0.9284 (OUTLIER) cc_final: 0.8844 (tppt) REVERT: K 588 MET cc_start: 0.9393 (mtm) cc_final: 0.8910 (mtp) REVERT: K 619 TYR cc_start: 0.8982 (p90) cc_final: 0.8606 (p90) REVERT: K 625 ILE cc_start: 0.9394 (mt) cc_final: 0.9102 (mm) REVERT: K 727 ASP cc_start: 0.9481 (m-30) cc_final: 0.8901 (t0) REVERT: K 745 MET cc_start: 0.8996 (mpp) cc_final: 0.8634 (mtm) REVERT: M 16 MET cc_start: 0.8722 (mmt) cc_final: 0.8374 (mmp) REVERT: M 62 ILE cc_start: 0.9661 (OUTLIER) cc_final: 0.9409 (mm) REVERT: M 160 MET cc_start: 0.7034 (pmm) cc_final: 0.6746 (pmm) REVERT: M 169 PHE cc_start: 0.9113 (m-10) cc_final: 0.8771 (m-80) REVERT: M 170 ASP cc_start: 0.9071 (t0) cc_final: 0.8786 (t0) REVERT: M 290 MET cc_start: 0.8882 (pmm) cc_final: 0.8514 (pmm) outliers start: 128 outliers final: 91 residues processed: 558 average time/residue: 0.1672 time to fit residues: 152.3490 Evaluate side-chains 550 residues out of total 3097 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 103 poor density : 447 time to evaluate : 1.149 ------------------------------------------------------------------------------- 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 37 LYS 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 29 ILE 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 77 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 90 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 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 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 N residue 239 SER Chi-restraints excluded: chain G residue 32 THR Chi-restraints excluded: chain G residue 101 GLU Chi-restraints excluded: chain G residue 144 PHE Chi-restraints excluded: chain G residue 156 ASP Chi-restraints excluded: chain F residue 49 ARG Chi-restraints excluded: chain F residue 157 TYR Chi-restraints excluded: chain F residue 207 ARG 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 56 ILE 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 152 MET Chi-restraints excluded: chain I residue 162 VAL 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 177 SER Chi-restraints excluded: chain K residue 214 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 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 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 748 TYR 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 218 LEU Chi-restraints excluded: chain M residue 220 CYS Chi-restraints excluded: chain M residue 240 ILE Chi-restraints excluded: chain M residue 282 LEU 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: 3.9990 chunk 175 optimal weight: 4.9990 chunk 190 optimal weight: 0.9990 chunk 319 optimal weight: 0.3980 chunk 90 optimal weight: 3.9990 chunk 298 optimal weight: 0.0570 chunk 8 optimal weight: 2.9990 chunk 118 optimal weight: 5.9990 chunk 143 optimal weight: 0.0270 chunk 236 optimal weight: 8.9990 overall best weight: 0.8960 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 51 ASN ** D 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 59 ASN ** H 204 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 110 GLN ** K 165 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3321 r_free = 0.3321 target = 0.052747 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3102 r_free = 0.3102 target = 0.044466 restraints weight = 142069.484| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3150 r_free = 0.3150 target = 0.046216 restraints weight = 71783.703| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3182 r_free = 0.3182 target = 0.047414 restraints weight = 44518.411| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 46)----------------| | r_work = 0.3205 r_free = 0.3205 target = 0.048246 restraints weight = 30956.315| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3221 r_free = 0.3221 target = 0.048838 restraints weight = 23342.682| |-----------------------------------------------------------------------------| r_work (final): 0.3193 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8487 moved from start: 0.4070 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 29252 Z= 0.137 Angle : 0.691 15.542 39623 Z= 0.351 Chirality : 0.044 0.269 4524 Planarity : 0.004 0.050 4852 Dihedral : 11.675 177.568 4390 Min Nonbonded Distance : 2.415 Molprobity Statistics. All-atom Clashscore : 14.85 Ramachandran Plot: Outliers : 0.12 % Allowed : 6.04 % Favored : 93.84 % Rotamer: Outliers : 3.27 % Allowed : 23.43 % Favored : 73.30 % 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: -0.01 (0.15), residues: 3441 helix: 1.48 (0.14), residues: 1470 sheet: 0.03 (0.24), residues: 445 loop : -1.55 (0.15), residues: 1526 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG G 142 TYR 0.035 0.002 TYR K 62 PHE 0.034 0.001 PHE K 245 TRP 0.010 0.001 TRP M 249 HIS 0.006 0.001 HIS K 153 Details of bonding type rmsd/Z covalent geometry : bond 0.00306 / 0.14 (29237) covalent geometry : angle 0.68947 / 0.35 (39593) SS BOND : bond 0.00321 / 0.21 ( 15) SS BOND : angle 1.72896 / 1.20 ( 30) hydrogen bonds : bond 0.03728 / 2.47 ( 1274) hydrogen bonds : angle 4.97653 / 3.55 ( 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 593 residues out of total 3097 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 101 poor density : 492 time to evaluate : 0.965 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: 0.8667 (m-30) cc_final: 0.8179 (t0) REVERT: A 42 GLU cc_start: 0.8351 (mm-30) cc_final: 0.8082 (mm-30) REVERT: A 56 PHE cc_start: 0.8947 (t80) cc_final: 0.8498 (t80) REVERT: A 60 ARG cc_start: 0.9268 (mmp80) cc_final: 0.8923 (mmm-85) REVERT: A 79 ILE cc_start: 0.9007 (mm) cc_final: 0.8689 (mp) REVERT: A 110 TYR cc_start: 0.9069 (t80) cc_final: 0.8812 (t80) REVERT: A 111 ASP cc_start: 0.8976 (t0) cc_final: 0.8635 (t0) REVERT: A 131 GLU cc_start: 0.9426 (mt-10) cc_final: 0.8972 (mt-10) REVERT: B 22 ASP cc_start: 0.8845 (m-30) cc_final: 0.8039 (m-30) REVERT: B 26 ARG cc_start: 0.9128 (ptp-110) cc_final: 0.8410 (ptp90) REVERT: B 73 GLN cc_start: 0.9305 (tp40) cc_final: 0.9007 (tp-100) REVERT: B 78 GLU cc_start: 0.9046 (mm-30) cc_final: 0.8472 (tp30) REVERT: B 90 SER cc_start: 0.9641 (m) cc_final: 0.9253 (p) REVERT: B 103 LEU cc_start: 0.9760 (mm) cc_final: 0.9514 (tp) REVERT: B 129 PHE cc_start: 0.8754 (t80) cc_final: 0.8425 (t80) REVERT: B 131 GLU cc_start: 0.9223 (mp0) cc_final: 0.8934 (mp0) REVERT: B 134 ASN cc_start: 0.9135 (m-40) cc_final: 0.8668 (m110) REVERT: C 22 ASP cc_start: 0.9195 (m-30) cc_final: 0.8838 (m-30) REVERT: C 71 MET cc_start: 0.9346 (mtm) cc_final: 0.9029 (mtm) REVERT: C 77 ASP cc_start: 0.9296 (t0) cc_final: 0.9060 (t0) REVERT: C 103 LEU cc_start: 0.9593 (OUTLIER) cc_final: 0.9382 (tp) REVERT: C 116 LEU cc_start: 0.9607 (mm) cc_final: 0.9315 (mt) REVERT: C 134 ASN cc_start: 0.9693 (m-40) cc_final: 0.9418 (m110) REVERT: D 22 ASP cc_start: 0.8913 (m-30) cc_final: 0.8376 (t0) REVERT: D 26 ARG cc_start: 0.9495 (mtm-85) cc_final: 0.9116 (ptp90) REVERT: D 29 ILE cc_start: 0.8980 (OUTLIER) cc_final: 0.8533 (tp) REVERT: D 32 ILE cc_start: 0.9167 (tp) cc_final: 0.8910 (tp) REVERT: D 44 TYR cc_start: 0.8898 (t80) cc_final: 0.8480 (t80) REVERT: D 58 GLN cc_start: 0.9480 (mp10) cc_final: 0.9168 (mm-40) REVERT: D 61 ARG cc_start: 0.9184 (mmm-85) cc_final: 0.8942 (mmm-85) REVERT: D 66 LEU cc_start: 0.9703 (tt) cc_final: 0.9366 (mm) REVERT: D 82 GLU cc_start: 0.9505 (tt0) cc_final: 0.9082 (tp30) REVERT: D 95 GLU cc_start: 0.8658 (tp30) cc_final: 0.8066 (tm-30) REVERT: D 101 ASN cc_start: 0.9408 (m110) cc_final: 0.9130 (m110) REVERT: D 134 ASN cc_start: 0.9232 (m-40) cc_final: 0.9025 (m110) REVERT: E 44 TYR cc_start: 0.8724 (t80) cc_final: 0.8465 (t80) REVERT: E 48 SER cc_start: 0.9749 (m) cc_final: 0.9528 (p) REVERT: E 55 SER cc_start: 0.9770 (m) cc_final: 0.9479 (p) REVERT: E 78 GLU cc_start: 0.8696 (mt-10) cc_final: 0.8339 (mt-10) REVERT: E 82 GLU cc_start: 0.9313 (tm-30) cc_final: 0.9008 (tm-30) REVERT: E 101 ASN cc_start: 0.9510 (m110) cc_final: 0.9097 (m110) REVERT: E 105 TYR cc_start: 0.9277 (m-10) cc_final: 0.8824 (m-80) REVERT: E 114 THR cc_start: 0.9399 (m) cc_final: 0.9141 (p) REVERT: E 131 GLU cc_start: 0.8977 (tp30) cc_final: 0.8563 (tm-30) REVERT: E 135 ILE cc_start: 0.9607 (mm) cc_final: 0.9260 (mm) REVERT: J 44 GLU cc_start: 0.8752 (pp20) cc_final: 0.7360 (pp20) REVERT: J 46 MET cc_start: 0.8283 (mtt) cc_final: 0.7903 (mmm) REVERT: J 146 PHE cc_start: 0.9253 (m-80) cc_final: 0.8918 (m-80) REVERT: J 159 MET cc_start: 0.8928 (tpp) cc_final: 0.8660 (tpp) REVERT: J 166 SER cc_start: 0.9065 (m) cc_final: 0.8582 (t) REVERT: J 209 GLU cc_start: 0.9348 (mm-30) cc_final: 0.8521 (mp0) REVERT: J 229 MET cc_start: 0.8635 (mtp) cc_final: 0.8212 (mtp) REVERT: L 98 THR cc_start: 0.7840 (OUTLIER) cc_final: 0.7633 (p) REVERT: L 113 LYS cc_start: 0.9474 (ttmm) cc_final: 0.9246 (tppp) REVERT: L 115 GLN cc_start: 0.9077 (mm110) cc_final: 0.8848 (tp40) REVERT: L 118 LYS cc_start: 0.9623 (ttmm) cc_final: 0.9137 (ttmm) REVERT: N 137 TYR cc_start: 0.7774 (OUTLIER) cc_final: 0.7155 (p90) REVERT: N 155 MET cc_start: 0.9005 (pmm) cc_final: 0.8731 (pmm) REVERT: N 249 ARG cc_start: 0.9292 (mtp-110) cc_final: 0.8966 (ptm-80) REVERT: G 40 ASP cc_start: 0.9062 (m-30) cc_final: 0.8785 (p0) REVERT: G 167 MET cc_start: 0.8708 (tpt) cc_final: 0.8427 (tpp) REVERT: F 33 GLN cc_start: 0.9383 (mp10) cc_final: 0.8935 (mp10) REVERT: F 49 ARG cc_start: 0.9027 (OUTLIER) cc_final: 0.8630 (mmm-85) REVERT: F 73 ASN cc_start: 0.9529 (t0) cc_final: 0.9269 (t0) REVERT: F 82 LEU cc_start: 0.8786 (OUTLIER) cc_final: 0.8555 (tp) REVERT: F 130 TYR cc_start: 0.8737 (p90) cc_final: 0.8409 (p90) REVERT: F 137 MET cc_start: 0.8506 (ptp) cc_final: 0.8219 (mpp) REVERT: F 207 ARG cc_start: 0.7496 (OUTLIER) cc_final: 0.7008 (mtp85) REVERT: F 239 LYS cc_start: 0.9526 (mmtm) cc_final: 0.9276 (mmmm) REVERT: H 5 THR cc_start: 0.8866 (OUTLIER) cc_final: 0.8586 (m) REVERT: H 19 GLU cc_start: 0.8583 (tm-30) cc_final: 0.8074 (tm-30) REVERT: H 98 ARG cc_start: 0.9152 (mmp80) cc_final: 0.8867 (mmp80) REVERT: H 145 TYR cc_start: 0.8716 (p90) cc_final: 0.8194 (p90) REVERT: H 174 ASP cc_start: 0.8783 (t0) cc_final: 0.8268 (t70) REVERT: H 200 MET cc_start: 0.9345 (tpp) cc_final: 0.9090 (tpp) REVERT: H 255 ASP cc_start: 0.9146 (m-30) cc_final: 0.8726 (p0) REVERT: I 110 GLN cc_start: 0.9609 (tp-100) cc_final: 0.9301 (tp40) REVERT: I 118 TYR cc_start: 0.9179 (m-10) cc_final: 0.8975 (m-10) REVERT: I 129 MET cc_start: 0.9348 (mmp) cc_final: 0.8985 (mmm) REVERT: I 200 MET cc_start: 0.9171 (ttm) cc_final: 0.8858 (ttp) REVERT: I 275 TYR cc_start: 0.8997 (p90) cc_final: 0.8217 (p90) REVERT: K 56 ASP cc_start: 0.9093 (m-30) cc_final: 0.8719 (m-30) REVERT: K 60 MET cc_start: 0.9043 (tmm) cc_final: 0.8617 (tmm) REVERT: K 61 ILE cc_start: 0.8772 (mt) cc_final: 0.8239 (mt) REVERT: K 148 THR cc_start: 0.9256 (OUTLIER) cc_final: 0.8948 (t) REVERT: K 202 GLU cc_start: 0.8543 (mt-10) cc_final: 0.8280 (mt-10) REVERT: K 205 GLU cc_start: 0.8621 (mm-30) cc_final: 0.8340 (mm-30) REVERT: K 220 LEU cc_start: 0.9404 (OUTLIER) cc_final: 0.9145 (pp) REVERT: K 233 ASN cc_start: 0.8822 (m110) cc_final: 0.8526 (m110) REVERT: K 244 ARG cc_start: 0.8852 (mmp80) cc_final: 0.8611 (mmp80) REVERT: K 273 LYS cc_start: 0.9411 (tppt) cc_final: 0.8914 (mttm) REVERT: K 330 PHE cc_start: 0.9080 (m-80) cc_final: 0.8208 (m-80) REVERT: K 336 MET cc_start: 0.8895 (mmm) cc_final: 0.8501 (mmm) REVERT: K 369 ILE cc_start: 0.9467 (mt) cc_final: 0.9135 (mt) REVERT: K 385 ILE cc_start: 0.9233 (OUTLIER) cc_final: 0.8724 (tp) REVERT: K 406 SER cc_start: 0.9276 (m) cc_final: 0.9055 (p) REVERT: K 438 MET cc_start: 0.8957 (mmt) cc_final: 0.8476 (mmt) REVERT: K 474 ARG cc_start: 0.2956 (mtt180) cc_final: 0.2640 (mtt180) REVERT: K 481 LEU cc_start: 0.8604 (tp) cc_final: 0.8269 (tp) REVERT: K 502 LYS cc_start: 0.9357 (mtpt) cc_final: 0.9025 (mtmm) REVERT: K 538 ILE cc_start: 0.9340 (OUTLIER) cc_final: 0.9018 (tp) REVERT: K 587 LYS cc_start: 0.9296 (OUTLIER) cc_final: 0.8829 (tppt) REVERT: K 588 MET cc_start: 0.9403 (mtm) cc_final: 0.8823 (mtp) REVERT: K 619 TYR cc_start: 0.8876 (p90) cc_final: 0.8473 (p90) REVERT: K 625 ILE cc_start: 0.9424 (mt) cc_final: 0.9106 (mm) REVERT: K 626 MET cc_start: 0.9521 (tpp) cc_final: 0.9110 (tpp) REVERT: K 677 MET cc_start: 0.8901 (ttp) cc_final: 0.8496 (ttp) REVERT: K 727 ASP cc_start: 0.9494 (m-30) cc_final: 0.8882 (t0) REVERT: K 745 MET cc_start: 0.9071 (mpp) cc_final: 0.8663 (mtm) REVERT: M 16 MET cc_start: 0.8729 (mmt) cc_final: 0.8339 (mmp) REVERT: M 62 ILE cc_start: 0.9632 (OUTLIER) cc_final: 0.9403 (mm) REVERT: M 144 GLN cc_start: 0.8477 (tt0) cc_final: 0.8185 (pp30) REVERT: M 160 MET cc_start: 0.6687 (pmm) cc_final: 0.6439 (pmm) REVERT: M 169 PHE cc_start: 0.9061 (m-10) cc_final: 0.8731 (m-80) REVERT: M 215 LYS cc_start: 0.9464 (mtmt) cc_final: 0.8906 (tttm) REVERT: M 275 SER cc_start: 0.8718 (p) cc_final: 0.8505 (m) REVERT: M 290 MET cc_start: 0.8840 (pmm) cc_final: 0.8398 (pmm) outliers start: 101 outliers final: 77 residues processed: 565 average time/residue: 0.1683 time to fit residues: 154.0967 Evaluate side-chains 567 residues out of total 3097 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 476 time to evaluate : 1.035 ------------------------------------------------------------------------------- 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 37 LYS Chi-restraints excluded: chain C residue 103 LEU Chi-restraints excluded: chain C residue 128 THR Chi-restraints excluded: chain D residue 29 ILE Chi-restraints excluded: chain E residue 39 ASN Chi-restraints excluded: chain E residue 126 VAL Chi-restraints excluded: chain J residue 23 ILE Chi-restraints excluded: chain J residue 36 VAL Chi-restraints excluded: chain J residue 43 VAL Chi-restraints excluded: chain J residue 82 MET 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 107 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 N residue 239 SER Chi-restraints excluded: chain G residue 32 THR Chi-restraints excluded: chain G residue 101 GLU Chi-restraints excluded: chain G residue 144 PHE Chi-restraints excluded: chain G residue 156 ASP Chi-restraints excluded: chain G residue 157 TYR Chi-restraints excluded: chain F residue 49 ARG Chi-restraints excluded: chain F residue 82 LEU 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 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 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 214 LEU Chi-restraints excluded: chain K residue 220 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 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: 9.9990 chunk 205 optimal weight: 6.9990 chunk 181 optimal weight: 6.9990 chunk 174 optimal weight: 1.9990 chunk 281 optimal weight: 3.9990 chunk 223 optimal weight: 0.0570 chunk 171 optimal weight: 3.9990 chunk 134 optimal weight: 9.9990 chunk 163 optimal weight: 9.9990 chunk 340 optimal weight: 3.9990 chunk 148 optimal weight: 10.0000 overall best weight: 2.8106 ------------------------------------------------------------------------------- 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** ** H 204 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 165 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3292 r_free = 0.3292 target = 0.051597 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3072 r_free = 0.3072 target = 0.043441 restraints weight = 143560.116| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3120 r_free = 0.3120 target = 0.045159 restraints weight = 72035.346| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3152 r_free = 0.3152 target = 0.046326 restraints weight = 44649.930| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3173 r_free = 0.3173 target = 0.047118 restraints weight = 31050.884| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3189 r_free = 0.3189 target = 0.047701 restraints weight = 23541.823| |-----------------------------------------------------------------------------| r_work (final): 0.3170 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8518 moved from start: 0.4136 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 29252 Z= 0.200 Angle : 0.713 14.789 39623 Z= 0.363 Chirality : 0.044 0.272 4524 Planarity : 0.004 0.051 4852 Dihedral : 11.735 178.998 4390 Min Nonbonded Distance : 2.402 Molprobity Statistics. All-atom Clashscore : 16.58 Ramachandran Plot: Outliers : 0.12 % Allowed : 6.28 % Favored : 93.61 % Rotamer: Outliers : 3.17 % Allowed : 23.79 % Favored : 73.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.73 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: 1.41 (0.14), residues: 1472 sheet: 0.01 (0.24), residues: 465 loop : -1.57 (0.15), residues: 1504 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG K 244 TYR 0.028 0.002 TYR I 195 PHE 0.032 0.001 PHE E 56 TRP 0.020 0.001 TRP M 173 HIS 0.005 0.001 HIS M 146 Details of bonding type rmsd/Z covalent geometry : bond 0.00436 / 0.20 (29237) covalent geometry : angle 0.71119 / 0.36 (39593) SS BOND : bond 0.00345 / 0.20 ( 15) SS BOND : angle 1.86017 / 1.30 ( 30) hydrogen bonds : bond 0.03803 / 2.52 ( 1274) hydrogen bonds : angle 5.03811 / 3.60 ( 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 581 residues out of total 3097 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 483 time to evaluate : 0.853 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: A 22 ASP cc_start: 0.8688 (m-30) cc_final: 0.8213 (t0) REVERT: A 42 GLU cc_start: 0.8364 (mm-30) cc_final: 0.8094 (mm-30) REVERT: A 56 PHE cc_start: 0.8966 (t80) cc_final: 0.8495 (t80) REVERT: A 60 ARG cc_start: 0.9298 (mmp80) cc_final: 0.8900 (mmm-85) REVERT: A 79 ILE cc_start: 0.9068 (mm) cc_final: 0.8760 (mp) REVERT: A 110 TYR cc_start: 0.9092 (t80) cc_final: 0.8866 (t80) REVERT: A 111 ASP cc_start: 0.8994 (t0) cc_final: 0.8622 (t0) REVERT: A 131 GLU cc_start: 0.9441 (mt-10) cc_final: 0.9009 (mt-10) REVERT: B 22 ASP cc_start: 0.8855 (m-30) cc_final: 0.8154 (m-30) REVERT: B 26 ARG cc_start: 0.9131 (ptp-110) cc_final: 0.8416 (ptp90) REVERT: B 73 GLN cc_start: 0.9317 (tp40) cc_final: 0.9095 (tp-100) REVERT: B 78 GLU cc_start: 0.9083 (mm-30) cc_final: 0.8523 (tp30) REVERT: B 90 SER cc_start: 0.9653 (m) cc_final: 0.9229 (p) REVERT: B 129 PHE cc_start: 0.8752 (t80) cc_final: 0.8446 (t80) REVERT: B 131 GLU cc_start: 0.9234 (mp0) cc_final: 0.8905 (pm20) REVERT: B 134 ASN cc_start: 0.9145 (m-40) cc_final: 0.8688 (m110) REVERT: C 22 ASP cc_start: 0.9196 (m-30) cc_final: 0.8838 (m-30) REVERT: C 71 MET cc_start: 0.9398 (mtm) cc_final: 0.9065 (mtm) REVERT: C 77 ASP cc_start: 0.9305 (t0) cc_final: 0.9081 (t0) REVERT: C 103 LEU cc_start: 0.9615 (OUTLIER) cc_final: 0.9393 (tp) REVERT: C 134 ASN cc_start: 0.9711 (m-40) cc_final: 0.9431 (m110) REVERT: D 22 ASP cc_start: 0.8919 (m-30) cc_final: 0.8324 (t0) REVERT: D 26 ARG cc_start: 0.9562 (mtm-85) cc_final: 0.9144 (ptp90) REVERT: D 29 ILE cc_start: 0.9018 (OUTLIER) cc_final: 0.8541 (tp) REVERT: D 32 ILE cc_start: 0.9170 (tp) cc_final: 0.8908 (tp) REVERT: D 44 TYR cc_start: 0.8950 (t80) cc_final: 0.8533 (t80) REVERT: D 58 GLN cc_start: 0.9496 (mp10) cc_final: 0.9219 (mm-40) REVERT: D 61 ARG cc_start: 0.9201 (mmm-85) cc_final: 0.8939 (mmm-85) REVERT: D 66 LEU cc_start: 0.9712 (tt) cc_final: 0.9381 (mm) REVERT: D 82 GLU cc_start: 0.9525 (tt0) cc_final: 0.9084 (tp30) REVERT: D 95 GLU cc_start: 0.8675 (tp30) cc_final: 0.8120 (tm-30) REVERT: D 101 ASN cc_start: 0.9440 (m110) cc_final: 0.9139 (m110) REVERT: D 134 ASN cc_start: 0.9240 (m-40) cc_final: 0.8733 (m110) REVERT: E 44 TYR cc_start: 0.8781 (t80) cc_final: 0.8483 (t80) REVERT: E 48 SER cc_start: 0.9745 (m) cc_final: 0.9511 (p) REVERT: E 55 SER cc_start: 0.9773 (m) cc_final: 0.9485 (p) REVERT: E 78 GLU cc_start: 0.8672 (mt-10) cc_final: 0.8230 (mt-10) REVERT: E 82 GLU cc_start: 0.9335 (tm-30) cc_final: 0.9044 (tm-30) REVERT: E 101 ASN cc_start: 0.9509 (m110) cc_final: 0.9081 (m110) REVERT: E 105 TYR cc_start: 0.9292 (m-10) cc_final: 0.8820 (m-80) REVERT: E 131 GLU cc_start: 0.9009 (tp30) cc_final: 0.8607 (tm-30) REVERT: E 135 ILE cc_start: 0.9623 (mm) cc_final: 0.9271 (mm) REVERT: J 44 GLU cc_start: 0.8758 (pp20) cc_final: 0.7410 (pp20) REVERT: J 46 MET cc_start: 0.8379 (mtt) cc_final: 0.7997 (mmm) REVERT: J 99 MET cc_start: 0.9462 (ttp) cc_final: 0.9173 (ppp) REVERT: J 146 PHE cc_start: 0.9217 (m-80) cc_final: 0.8881 (m-80) REVERT: J 159 MET cc_start: 0.9020 (tpp) cc_final: 0.8752 (tpp) REVERT: J 166 SER cc_start: 0.9155 (m) cc_final: 0.8589 (t) REVERT: J 209 GLU cc_start: 0.9400 (mm-30) cc_final: 0.8584 (mp0) REVERT: J 229 MET cc_start: 0.8671 (mtp) cc_final: 0.8154 (mtm) REVERT: L 62 GLU cc_start: 0.8807 (tp30) cc_final: 0.8395 (mp0) REVERT: L 64 GLU cc_start: 0.9150 (mp0) cc_final: 0.8808 (mp0) REVERT: L 98 THR cc_start: 0.7903 (OUTLIER) cc_final: 0.7668 (p) REVERT: L 113 LYS cc_start: 0.9484 (ttmm) cc_final: 0.9262 (tppp) REVERT: L 115 GLN cc_start: 0.9199 (mm110) cc_final: 0.8951 (tp40) REVERT: L 118 LYS cc_start: 0.9637 (ttmm) cc_final: 0.9181 (ttmm) REVERT: N 137 TYR cc_start: 0.7891 (OUTLIER) cc_final: 0.7226 (p90) REVERT: N 249 ARG cc_start: 0.9303 (mtp-110) cc_final: 0.8979 (ptm-80) REVERT: G 7 ASP cc_start: 0.9294 (OUTLIER) cc_final: 0.9072 (p0) REVERT: G 40 ASP cc_start: 0.9091 (m-30) cc_final: 0.8812 (p0) REVERT: G 66 GLU cc_start: 0.9275 (mt-10) cc_final: 0.9033 (mt-10) REVERT: G 167 MET cc_start: 0.8689 (tpt) cc_final: 0.8428 (tpp) REVERT: F 33 GLN cc_start: 0.9395 (mp10) cc_final: 0.8952 (mp10) REVERT: F 49 ARG cc_start: 0.9046 (OUTLIER) cc_final: 0.8651 (mmm-85) REVERT: F 73 ASN cc_start: 0.9542 (t0) cc_final: 0.9306 (t0) REVERT: F 130 TYR cc_start: 0.8743 (p90) cc_final: 0.8434 (p90) REVERT: F 134 GLN cc_start: 0.9207 (tt0) cc_final: 0.8995 (tt0) REVERT: F 137 MET cc_start: 0.8599 (ptp) cc_final: 0.8263 (mpp) REVERT: F 207 ARG cc_start: 0.7625 (OUTLIER) cc_final: 0.6925 (mtp85) REVERT: F 239 LYS cc_start: 0.9525 (mmtm) cc_final: 0.9276 (mmmm) REVERT: H 5 THR cc_start: 0.8931 (OUTLIER) cc_final: 0.8680 (m) REVERT: H 19 GLU cc_start: 0.8585 (tm-30) cc_final: 0.8045 (tm-30) REVERT: H 98 ARG cc_start: 0.9158 (mmp80) cc_final: 0.8876 (mmp80) REVERT: H 145 TYR cc_start: 0.8827 (p90) cc_final: 0.8262 (p90) REVERT: H 174 ASP cc_start: 0.8797 (t0) cc_final: 0.8338 (t70) REVERT: H 200 MET cc_start: 0.9381 (tpp) cc_final: 0.9115 (tpp) REVERT: H 255 ASP cc_start: 0.9180 (m-30) cc_final: 0.8708 (p0) REVERT: H 261 MET cc_start: 0.8907 (mmm) cc_final: 0.8658 (mmm) REVERT: I 110 GLN cc_start: 0.9611 (tp-100) cc_final: 0.9318 (tp40) REVERT: I 129 MET cc_start: 0.9425 (mmp) cc_final: 0.9097 (mmm) REVERT: K 56 ASP cc_start: 0.9122 (m-30) cc_final: 0.8770 (m-30) REVERT: K 60 MET cc_start: 0.9050 (tmm) cc_final: 0.8654 (tmm) REVERT: K 61 ILE cc_start: 0.8692 (mt) cc_final: 0.8197 (mt) REVERT: K 81 GLU cc_start: 0.8945 (mt-10) cc_final: 0.8570 (mt-10) REVERT: K 148 THR cc_start: 0.9259 (OUTLIER) cc_final: 0.8964 (t) REVERT: K 202 GLU cc_start: 0.8571 (mt-10) cc_final: 0.8304 (mt-10) REVERT: K 205 GLU cc_start: 0.8641 (mm-30) cc_final: 0.8378 (mm-30) REVERT: K 273 LYS cc_start: 0.9433 (tppt) cc_final: 0.8956 (mttm) REVERT: K 336 MET cc_start: 0.8921 (mmm) cc_final: 0.8566 (mmm) REVERT: K 369 ILE cc_start: 0.9503 (mt) cc_final: 0.9178 (mt) REVERT: K 385 ILE cc_start: 0.9283 (OUTLIER) cc_final: 0.8748 (tp) REVERT: K 406 SER cc_start: 0.9300 (m) cc_final: 0.9074 (p) REVERT: K 438 MET cc_start: 0.8965 (mmt) cc_final: 0.8470 (mmt) REVERT: K 474 ARG cc_start: 0.3076 (mtt180) cc_final: 0.2821 (mtt180) REVERT: K 481 LEU cc_start: 0.8636 (tp) cc_final: 0.8316 (tp) REVERT: K 502 LYS cc_start: 0.9398 (mtpt) cc_final: 0.9072 (mtmm) REVERT: K 538 ILE cc_start: 0.9371 (tp) cc_final: 0.9064 (tp) REVERT: K 587 LYS cc_start: 0.9280 (mmtm) cc_final: 0.8818 (tppt) REVERT: K 588 MET cc_start: 0.9404 (mtm) cc_final: 0.8819 (mtp) REVERT: K 619 TYR cc_start: 0.8935 (p90) cc_final: 0.8555 (p90) REVERT: K 625 ILE cc_start: 0.9413 (mt) cc_final: 0.9090 (mm) REVERT: K 626 MET cc_start: 0.9543 (tpp) cc_final: 0.9067 (tpp) REVERT: K 677 MET cc_start: 0.8924 (ttp) cc_final: 0.8526 (ttp) REVERT: K 727 ASP cc_start: 0.9491 (m-30) cc_final: 0.8912 (t0) REVERT: K 745 MET cc_start: 0.9075 (mpp) cc_final: 0.8661 (mtm) REVERT: M 16 MET cc_start: 0.8735 (mmt) cc_final: 0.8359 (mmp) REVERT: M 62 ILE cc_start: 0.9638 (OUTLIER) cc_final: 0.9401 (mm) REVERT: M 160 MET cc_start: 0.6802 (pmm) cc_final: 0.6518 (pmm) REVERT: M 169 PHE cc_start: 0.9096 (m-10) cc_final: 0.8775 (m-80) REVERT: M 290 MET cc_start: 0.8891 (pmm) cc_final: 0.8496 (pmm) outliers start: 98 outliers final: 81 residues processed: 556 average time/residue: 0.1720 time to fit residues: 154.6865 Evaluate side-chains 560 residues out of total 3097 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 468 time to evaluate : 1.144 ------------------------------------------------------------------------------- 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 65 GLU 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 103 LEU Chi-restraints excluded: chain C residue 128 THR Chi-restraints excluded: chain D residue 29 ILE Chi-restraints excluded: chain E residue 39 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 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 103 ASN Chi-restraints excluded: chain N residue 107 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 N residue 239 SER Chi-restraints excluded: chain G residue 7 ASP Chi-restraints excluded: chain G residue 32 THR Chi-restraints excluded: chain G residue 101 GLU Chi-restraints excluded: chain G residue 144 PHE Chi-restraints excluded: chain G residue 156 ASP Chi-restraints excluded: chain G residue 157 TYR Chi-restraints excluded: chain G residue 180 LYS Chi-restraints excluded: chain F residue 49 ARG 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 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 220 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 576 ASP 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 240 optimal weight: 3.9990 chunk 308 optimal weight: 3.9990 chunk 11 optimal weight: 2.9990 chunk 108 optimal weight: 1.9990 chunk 2 optimal weight: 0.9990 chunk 339 optimal weight: 4.9990 chunk 336 optimal weight: 7.9990 chunk 261 optimal weight: 6.9990 chunk 42 optimal weight: 0.9980 chunk 68 optimal weight: 5.9990 chunk 210 optimal weight: 6.9990 overall best weight: 2.1988 ------------------------------------------------------------------------------- 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 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 204 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 165 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3255 r_free = 0.3255 target = 0.051330 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3023 r_free = 0.3023 target = 0.042951 restraints weight = 145000.620| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3072 r_free = 0.3072 target = 0.044689 restraints weight = 74465.885| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3106 r_free = 0.3106 target = 0.045886 restraints weight = 46562.114| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3129 r_free = 0.3129 target = 0.046731 restraints weight = 32661.963| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.3145 r_free = 0.3145 target = 0.047320 restraints weight = 24725.998| |-----------------------------------------------------------------------------| r_work (final): 0.3133 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8517 moved from start: 0.4226 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= 0.175 Angle : 0.719 18.333 39623 Z= 0.365 Chirality : 0.045 0.279 4524 Planarity : 0.004 0.050 4852 Dihedral : 11.749 178.707 4390 Min Nonbonded Distance : 2.403 Molprobity Statistics. All-atom Clashscore : 16.00 Ramachandran Plot: Outliers : 0.12 % Allowed : 6.54 % Favored : 93.34 % Rotamer: Outliers : 3.30 % Allowed : 23.98 % Favored : 72.72 % 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: -0.04 (0.14), residues: 3441 helix: 1.40 (0.14), residues: 1470 sheet: 0.14 (0.24), residues: 437 loop : -1.56 (0.15), residues: 1534 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG G 142 TYR 0.030 0.002 TYR B 105 PHE 0.028 0.001 PHE E 56 TRP 0.018 0.001 TRP M 173 HIS 0.004 0.001 HIS M 146 Details of bonding type rmsd/Z covalent geometry : bond 0.00386 / 0.17 (29237) covalent geometry : angle 0.71710 / 0.36 (39593) SS BOND : bond 0.00374 / 0.23 ( 15) SS BOND : angle 1.80282 / 1.25 ( 30) hydrogen bonds : bond 0.03774 / 2.50 ( 1274) hydrogen bonds : angle 5.00686 / 3.58 ( 3747) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5378.64 seconds wall clock time: 94 minutes 8.34 seconds (5648.34 seconds total)